references - shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 ·...

55
References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant Ara- bidopsis thaliana. Nature, vol. 408, pages 796-815, 2000. vi, 3, 7, 8, 41, 141 [Aitken & Kirsch 2005] S. M. Aitken and J. F. Kirsch. The enzymology of cys- tathionine biosynthesis: strategies for the control of substrate and reaction Arch Biochem Biophys, vol. 433, pages 166-175, 2005. 40 [Akashi et al. 2004] K. Akashi, N. Nishimura, Y. Ishida and A. Yokota. Potent hydro.ryl radical-scavenging activity of drought-induced type-2 metalloth- ionein in wild watermelon. Biochem Biophys Res Com, vol. 323, pages 72-78, 2004. 74 [Albin et al. 1986] R. Albin, R. Weber and P. M. Silverman. The Cpx proteins of Escherichia coli K12. Immunologic detection of the chromosomal cpxA gene product. J Biol Chern, vol. 261, pages 4698-705, 1986. 109 [Allen & Tresini 2000] R. G. Allen and M. Tresini. Oxidative stress and gene regulation. Free Radic Biol Med, vol. 28, pages 463-499, 2000. 67 [Altschul et al. 1990] S. F. Altschul, W. Gish, W. Miller, E. W. Myers and D. J. Lipman. Basic local alignment search tool. J Mol Biol, vol. 3, page 403410, 1990. 12, 27, 43, 91 [Altschul et al. 1997] S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller and D. J. Lipman. Gapped BLAST and PSI-BLAST: 232

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Page 1: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

References

[AGI 2000] AGI. Analysis of the genome sequence of the flowering plant Ara­

bidopsis thaliana. Nature, vol. 408, pages 796-815, 2000. vi, 3, 7, 8, 41,

141

[Aitken & Kirsch 2005] S. M. Aitken and J. F. Kirsch. The enzymology of cys­

tathionine biosynthesis: strategies for the control of substrate and reaction

spec~ficity. Arch Biochem Biophys, vol. 433, pages 166-175, 2005. 40

[Akashi et al. 2004] K. Akashi, N. Nishimura, Y. Ishida and A. Yokota. Potent

hydro.ryl radical-scavenging activity of drought-induced type-2 metalloth­

ionein in wild watermelon. Biochem Biophys Res Com, vol. 323, pages

72-78, 2004. 74

[Albin et al. 1986] R. Albin, R. Weber and P. M. Silverman. The Cpx proteins

of Escherichia coli K12. Immunologic detection of the chromosomal cpxA

gene product. J Biol Chern, vol. 261, pages 4698-705, 1986. 109

[Allen & Tresini 2000] R. G. Allen and M. Tresini. Oxidative stress and gene

regulation. Free Radic Biol Med, vol. 28, pages 463-499, 2000. 67

[Altschul et al. 1990] S. F. Altschul, W. Gish, W. Miller, E. W. Myers and D. J.

Lipman. Basic local alignment search tool. J Mol Biol, vol. 3, page 403410,

1990. 12, 27, 43, 91

[Altschul et al. 1997] S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang,

Z. Zhang, W. Miller and D. J. Lipman. Gapped BLAST and PSI-BLAST:

232

Page 2: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

a new generation of protein database search programs. Nucleic Acids Res,

vol. 25, pages 389-402, 1997. 12, 75

[Anantharaman & Aravind 2001] V. Anantharaman and L. Aravind. The

CHASE domain: a predicted ligand-binding module in plant cytokinin re­

ceptors and other eukaryotic and bacterial receptors. Trends Biochem Sci,

vol. 26, pages 579-582, 2001. 115

[Appleby et al. 1996] J. L. Appleby, J. S. Parkinson and R. B. Bourret. Signal

transduction via the multi-step phosphorelay: not necessarily a road less

traveled. Cell, vol. 86, pages 845-848, 1996. 110

[Arad et al. 2002] M. Arad, D. W. Benson, A. R. P. Atayde, W. J. McKenna,

E. A. Sparks, R. J. Kanter, K. McGarry, J. G. Seidman and C. E. Seidman.

Constitutively active AMP kinase mutations cause glycogen storage disease

mimicking hypertrophic cardiomyopathy. J Clin Invest, vol. 109, pages

357-362, 2002. 41

[Aravind et al. 2002] L. Aravind, R. Mazumder, S. Vasudevan and E. V. Koonin.

Trends in protein evolution inferred from sequence and structure analysis.

Curr Opin Struct Biol, vol. 12, pages 392-329, 2002. 115

[Ashby & Houmard 2006] M. K. Ashby and J. Houmard. Cyanobacterial two­

component proteins: structure, diversity, distribution, and evolution. Mi­

crobial Mol Biol Rev, vol. 70, pages 472-509, 2006. 107

[Ausubel 2002] F. M. Ausubel. Summaries of National Science Foundation­

Sponsored Arabidopsis 2010 Projects and National Science Foundation­

Sponsored Plant Genome Projects That Are Generating Arabidopsis Re­

sources for the Community. Plant Physiol, vol. 129, pages 394-437, 2002.

3

[Babu et al. 2004] R. C. Babu, J. Zhang, A. Blume, T. D. H. Hod, R. \i\Tu and

H. T. Nguyen. HVA1, a LEA gene from barley confers dehydration tol­

erance in transgenic rice (Oryza sativa L.) via cell membrane protection.

Plant Sci, vol. 166, pages 855-862, 2004. 37

233

Page 3: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Baikalov et al. 1998] I. Baikalov, I. Schroder, M. Kaczor-Grzeskowiak, D. Cas­

cio, R. P. Gunsalus and R. E. Dickerson. NarL dimerization? Suggestive

evidence from a new crystal form. Biochemistry, vol. 37, pages 3665~3676,

1998. 129

[Barkan et al. 1994] A. Barkan, M. Walker, M. Nolasco and D. Johnson. A nu­

clear mutation in maize blocks the processing and translation of several

chloroplast mRNAs and provides evidence for the differential translation

of alternative mRNA forms. EMBO J, vol. 13, pages 3170~3181, 1994 .. SO

[Barkla et al. 1999] B. J. Barkla, R. Vera-Estrella and 0. Pantoja. Towards the

production of salt-tolerant crops. Adv Exp Med Biol, vol. 464, pages 77~89,

1999. 3

[Bartels & Sunkar 2005] D. Bartels and R. Sunkar. Drought and salt tolerance in

plants. Crit Rev Plant Sci, vol. 24, pages 23~58, 2005. 10

[Bateman 1997] A. Bateman. The structure of a domain common to archaebac­

teria and homocystinuria disease proteins. Trends Biochem Sci, vol. 22,

pages 12~ 13, 1997. 40

[Bateman 1999] A. Bateman. The SIS domain: a phosphosugar-binding domain.

Trends Biochem Sci, vol. 24, pages 94~95, 1999. 50, 54

[Batra et al. 2007] G. Batra, V. S. Chauhan, A. Singh, N. K. Sarkar and

A. Grover. Complexity of rice Hspl 00 gene family: lessons from rice

genome sequence data. J. Biosci., vol. 32, pages 611~619, 2007. 20

[Bausher et al. 2003] M. Bausher, R. Shatters, J. Chaparro, P. Dang, W. Hunter

and R. Niedz. An expressed sequence tag (EST) set from Citrus sinensis

L. Osbeck whole seedlings and the implications of further perennial source

investigations. Plant Sci, vol. 165, pages 415~422, 2003. 74

[Bent et al. 2004] C. J. Bent, N. W. Isaac, T. J. Mitchell and A. R. Tunnicliffe.

Crystal structure of the response regulator 02 receiver domain, the es­

sential YycF two-component system of Streptococcus pneumonia in both

234

Page 4: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

complexed and native states. J Bacteriology, vol. 186, pages 2872-2879,

2004. 128

[Bhatnagar-Mathur et al. 2008] P. Bhatnagar-Mathur, V. Vadez and K. K.

Sharma. !Transgenic approaches for abiotic stress tolerance in plants:

retrospect and prospects. Plant Cell Rep, vol. 27, pages 411-24, 2008. 3

[Bhumbla & Abrol 1978] D. Bhumbla and I. Abrol. Saline and sadie soil. In 'Soils

and Rice', pages 719-738. IRRI, Manila Philippines, 1978. 8

[Bilwes et al. 2003] A. M. Bilwes, S. Y. Park, C. M. Quezada, M. I. Simon and

B. R. Crane. Structure and function of chea, the'histidine kinase central to

bacterial chemotaxis. Histidine kinases in signal transduction. Academic

Press, San Diego, Calif, 2003. 109, 120

[Blanc et al. 2000] G. Blanc, A. Barakat, R. Guyot, R. Cooke and M. Delseny.

Extensive duplication and reshuffling in the A rabidopsis genome. Plant

Cell, vol. 12, pages 1093-1101, 2000. 57

[Blanc et al. 2003] G. Blanc, K. Hokamp and K. H. Wolfe. A recent polyploidy

superimposed on older large-scale duplications in the A rabidopsis genome.

Genome Res, vol. 13, pages 137-144, 2003 .. 57

[Blumwald & Grover 2006] E. Blumwald and A. Grover. Salt tolerance. Plant

biotechnology: current and future uses of genetically modified crops. John

\iViley and Sons Ltd., UK, 2006. 10

[Bohnert & Sheveleva 1998] H. J. Bohnert and E. Sheveleva. Plant stress

adaptations-making metabolism move. Curr Opin Plant Biol., vol. 1, pages

267-74, 1998. 1

[Bohnert et al. 2001] H. J. Bohnert, P. Ayoubid, C. Borcherta, R. A. Bressanc,

R. L. Burnapd, J. C. Cushmane, M.A. Cushmane, M. Deyholosb, R. Fis­

chera, D. W. Galbraithb, P. M. Hasegawac, M. Jenksc, S. Kawasaki,

H. Koiwac, S. Kore-edae, B. Leeb, C. B. Michalowskia, E. Misawad,

N. Ozturka M. Nomurae, R. Praded B. Postierd, C-P. Song, Y. Tanakab,

235

Page 5: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

H. Wangb and J-K. Zhub. A genomics approach towards salt stress toler­

ance. Plant Physiol Biochem, vol. 39, pages 295-311, 2001. 3, 145

[Bohnert et al. 2006] H. J. Bohnert, Q. Gong, P. Li and S. Ma. Unravelling

abiotic stress tolerance mechanisms-getting genomic going. Curr Opin

Plant Biol, vol. 9, pages 180-188, 2006. vii, 24

[Bonilla et al. 2002] P. Bonilla, J. Dvorak, D. Mackill, K. Deal and G. Gregorio.

RFLP and SSLP mapping of salinity tolerance genes in chromosome 1 of

rice (Oryza sativa L.) using recombinant inbred lines. Philipp J Agric Sci,

vol. 85, pages 68-76, 2002. 37

[Borevitz & Ecker 2004] J. 0. Borevitz and J. R. Ecker. Plant genomics: The

third wave. Annu Rev Genomics Hum Genet, vol. 5, page 443477, 2004. 8

[Boutrot et al. 2008] F. Boutrot, N. Chantret and M. F. Gautier. Genome­

wide analysis of the rice and arabidopsis non-specific lipid transfer protein

(nsLtp) gene families and ident~fication of wheat nsLtp genes by EST data

mining. BMC Genomics, vol. 9, page 86, 2008. 22

[Bowers et al. 2003] J. E. Bowers, B. A. Chapman, J. Rong and A. H. Pater­

son. Unravelling angiosperm genome evolution by phylogenetic analysis of

chromosomal duplication events. Nature, vol. 422, pages 433-438, 2003.

58, 90

[Bowne et al. 2002] S. J. Bowne, L. S. Sullivan, S. H. Blanton, C. L. Cepko,

S. Blackshaw, D. G. Birch, D. H. Wheaton, J. R. Heckenlively and S. P.

Daiger. Mutations in the inosine monophosphate dehydrogenase 1 gene

(IMPDH1) cause the RP10 form of a'utosomal dominant retinitis pigmen­

tosa. Hum Mol Genet, vol. 11, pages 559-568, 2002. 41, 50

[Boyer 1982] J. S. Boyer. Plant productivity and environment. Science, vol. 218,

pages 443-448, 1982. 3

[Bray et al. 2000] E. A. Bray, J. Baily-Serres and E. Weretilnyk. Responses to

abiotic stresses. Biochemistry and Molecular Biology of Plants. American

Society of Plant Physiologists, Rockville, 2000. 2

236

Page 6: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Brenner et al. 2000] S. Brenner, M. Johnson, J. Bridgham, G. Golda, D. H.

Lloyd, D. Johnson, S. Luo, S. McCurdy, M. Foy, M. Ewan and et al. Gene

expression analysis by massively parallel signature sequencing (MPSS) on

microbead arrays. Nat Biotechnol, vol. 18, pages 630-634, 2000. 63

[Bressan et al. 2009] R. Bressan, H. Bohnert and J. K. Zhu. Abiotic stress toler­

ance: from gene discovery in model organisms to crop improvement. Mol

Plant, vol. 2, pages 1-2, 2009. 3

[Bryson et al. 2005] K. Bryson, L. J. McGuffin, R. L. Marsden, J. J. Ward, .J. S.

Sodhi and D. T. Jones. Protein structure prediction servers at University

College London. Nucl Acids Res, vol. 33, pages \i\136-38, 2005. 76, 92, 112

[Buchanan-\iVollastion 1994] V. Buchanan-\iVollastion. Isolations of eDNA clones

for genes that are e.1;pressed during leaf senescence in Brassica napus. Iden­

t~fication of a gene encoding a senescence-specific metallothionein-like pro­

tein. Plant Physiol, vol. 105, pages 839-846, 1994. 73

[Bucher & Bairoch 1994] P. Bucher and A. Bairoch. A generalized profile syntax

for biomolecular sequence motifs and its function in automatic sequence

interpretation, pages 53-61. ISMB-94, Menlo park, CA, 1994. 15

[Bujnicki 2003] J. M. Bujnicki. Crystallographic and bioinformatic studies on

restriction endonucleases: inference of evolutionary relationships in the

"midnight zone" of homology. Curr Protein Pept Sci, vol. 4, pages 327-

337, 2003. 98

[Burr 2002] B. Burr. Mapping and Sequencing the Rice Genome. Plant Cell,

vol. 14, pages 521-523, 2002. 3

[Campbell et al. 2006] M.A. Campbell, B . .J. Haas, J.P. Hamilton, S.M. Mount

and C. R. Buell. Comprehensive analysis of alternative splicing in rice

and comparative analyses with Arabidopsis. BMC Genomics, vol. 7, page

327, 2006. 52

[Cantrell & Reeves 2002] R. P. Cantrell and T. G. Reeves. The cereal of the

worlds poor takes center stage. Science, vol. 296, pages 53-56, 2002. 8

237

Page 7: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Canutescu et al. 2003] A. A. Canutescu, A. A. Shelenkov and R. L. Dunbrack. A

graph theory algorithm for protein side-chain prediction. Protein science,

vol. 12, pages 2001-2014, 2003. 76, 93, 113

[Carbajosa et al. 1997] J. V. Carbajosa, S. P. Moose, R. L. Parsons and R. J.

Schmidt. A maize zinc-finger protein binds the prolamin box in zein gene

promoters and interacts with the basic leucine zipper transcriptional ac­

tivator Opaque2. Proc Natl Acad Sci, vol. 94, pages 7685-7690, 1997.

21

[Carling 2004] D. Carling. The AMP-activated protein kinase cascade: a unifying

system for energy control. Trends Biochem. Sci., vol. 29, pages 18-24,

2004. 94

[Chan et al. 1998] R. L. Chan, G. M. Gago, C. M. Palena and D. H. Gonzalez.

Homeoboxes in plant development. Biochim Biophys Acta, vol. 1442, pages

1-19, 1998. 22

[Chang et al. 1993] C. Chang, S. F. Kwok, A. B. Bleecker and E. M. Meyerowitz.

Arabidopsis ethylene-response gene ETRl: similarity of product to two­

component regulators. Science, vol. 262, pages 539-44, 1993. 107, 109

[Chao et al. 2005] D. Y. Chao, Y. H. Luo, M. Shi, D. Luo and H. X. Lin. Salt

responsive genes in rice revealed by eDNA microarray analysis. Cell Res,

vol. 15, pages 796-810, 2005. 25

[Chatterjee et al. 2006] A. D. Chatterjee, L. Goswami, S. Maitra, K. G. Dastidar,

S. Ray and A. L. Majumder. Introgression of a novel salt-tolerant Lmyo­

inositol 1-phosphate synthase from Porteresia coarctata (Roxb.) Tateoka

(PciNOl) confers salt tolerance to evolutionary diverse organisms. FEBS

Letter, vol. 580, pages 3980-3988, 2006. 25

[Chaw et al. 2004] S. M. Chaw, C. C. Chang, H. L. Chen and W. H. Li. Dating

the monocot-dicot divergence and the origin of core eudicots using whole

chloroplast genomes. J Mol Evol, vol. 58, pages 424-441, 2004. 10

238

Page 8: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Chen et al. 1997] M. Chen, P. Sanmiguel, A. C. de Oliveira, S. S. Woo, H. Zhang,

R. A. Wing and J. L. Bennetzen. Microcollinearity in sh2-homologous

regions of the maize, rice, and sorghum genomes. Proc Natl Acad Sci,

vol. 94, pages 3431-3435, 1997. 8

[Chen et al. 2006] F. Chen, Q. Li, L. Sun and Z. He. The rice 14-3-3 gene family

and its involvement in responses to biotic and abiotic stress. DNA Res,

vol. 13, pages 53-63, 2006. 37

[Chen et al. 2007] A. P. Chen, G. L. Wang, Z. L. Qu, C. X. Lu, N. Liu, F. Wang

and G. X. Xia. Ectopic expression of ThCYP 1, a stress-responsive cy­

clophilin gene from Thellungiella halophila, confers salt tolerance in fis­

sion yeast and tobacco cells. Plant Cell Rep, vol. 26, pages 237-245, 2007.

37

[Chinnusamy et al. 2005] V. Chinnusamy, A. Jagendorf and J. K. Zlm. Under­

standing and improving salt tolerance in plants. Crop Sci, vol. 45, pages

437-448, 2005. 10, 24

[Cho et al. 2006] U. S. Cho, M. W. Bader, M. F. Amaya, M. E. Daley, R. E.

Klevit, S. I. Miller and W. Xu. Metal bridges between the PhoQ sensor

domain and the membrane regulate transmembrane signaling. J Mol Biol,

vol. 356, pages 1193-1206, 2006. 114

[Clamp et al. 2004] M. Clamp, J. Cuff, S. M. Searle and G. J. Barton. The

Jalview Java Alignment Editor. Bioinformatics, vol. 20, pages 426-427,

2004. 43

[Cleiren et al. 2001] E. Cleiren, 0. Benichou, E. V. Hul, J. Gram, J. Bollerslev,

F. R. Singer, K. Beaverson, A. Aledo, M. P. Whyte, T. Yoneyama, M. C.

de Vernejoul and W. V. Hul. Albers-Schonberg disease (autosomal domi­

nant osteopetrosis, type II) results from mutations in the ClCN7 chloride

channel gene. Hum Mol Genet, vol. 10, pages 2861-2867, 2001. 41

[Clemens 2001] S. Clemens. Molecular mechanisms of plant metal tolerance and

homeostasis. Planta, vol. 212, pages 475-486, 2001. 73

239

Page 9: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Cobbett & Goldsbrough 2002] C. Cobbett and P. Goldsbrough. Phytochelatins

and metallothioneins: roles in heavy metal detoxification and homeostasis.

Annu Rev Plant Biol, vol. 53, pages 159-182, 2002. 73, 74, 77, 88

[Cole et al. 2008] C. Cole, J. D. Barber and G. J. Barton. The Jpred3 secondary

structure prediction server. Nucleic Acids Res, vol. 36, pages W197-W201,

2008. 76, 92, 112

[Coupe et al. 1995] S. A. Coupe, J. E. Taylor and J. A. Roberts. Characteriza­

tion of an mRNA encoding a metallothionein-like protein that accumulates

during ethylene-promoted abscission of Sambucus nigra L. leaflets. Planta,

vol. 97, pages 442-447, 1995. 74

[Cuff & Barton 1999] J. A. Cuff and G. J. Barton. Application of enhanced mul­

tiple sequence alignment profiles to improve protein secondary structure

prediction. Proteins, vol. 40, pages 502-511, 1999. 76, 92, 112

[Cuff et al. 2009] A. L. Cuff, I. Sillitoe, T. Lewis, 0. C. Redfern, R. Gar­

ratt, J. Thornton and C. A. Omega. The CATH classification revisited­

architectures reviewed and new ways to characterize structural divergence

in superfamilies. Nucl Acids Res, vol. 37, pages D310-D314, 2009. 76, 92,

112

[Cushman & Bohnert 2000] J. C. Cushman and H. J. Bohnert. Genomic ap­

proaches to plant stress tolerance. Curr Opin Plant Biol, vol. 3, pages

117-124, 2000. 4

[Cyert & Thorner 1992] M. S. Cyert and J. Thorner. Regulatory subunit (CNB1

gene product) of yeast Ca2+/calmodulin dependent phosphoprotein phos­

phatase is required for adaptation to pheromone. Mol Cell Biol, vol. 12,

pages 3460-3469, 1992. 100

[Czelusniak et al. 1990] J. Czelusniak, M. Goodman, N. D. Moncrief and S. M.

Kehoe. Maximum parsimony approach to construction of evolutionary

tTees from aligned homologous sequences. Methods Enzymol, vol. 183,

page 601615, 1990. 19

240

Page 10: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Czernic et al. 1999] P. Czernic, B. Visser, W. Sun, A. Savoure and L. Deslandes.

Characterization of an Arabidopsis thaliana receptor-like protein kinase

gene activated by oxidative stress and pathogen attack. Plant J, vol. 18,

pages 321-327, 1999. 37

[da Silva et al. 1974] J. Vieira da Silva, A. W. Naylor and J. Kramer. Some

ultrastructural and enzymatic effects of water stress in cotton (Gossypium

L.) leaves. Proc Natl Acad Sci, vol. 71, pages 3243-3247, 1974. 67

[Dat et al. 1998] J. F. Dat, H. Lopez-Delgado, C. H. Foyer and I. M. Scott. Par­

allel changes in H202 and catalase during thermotolerance induced by

salicylic acid or heat acclimation in mustard seedlings. Plant Physiol,

vol. 116, pages 1351-1357, 1998. 67

[Dayhoff et al. 1978] M. 0. Dayhoff, R. Schwartz and B. C. Orcutt. A model of

Evolutionary Change in Proteins. Atlas of protein sequence and structure,

vol. 5, pages 345-358, 1978. 11

[de Paula et al. 1990] F. Monteiro de Paula, A. T. Pham Thi, J. Vieira da Silva,

A. M. Justin, C. Demandre and P. Mazliak. Effects of water stress on the

molecular species composition of polar lipids from Vigna unguiculata L.

leaves. Plant Sci, vol. 66, pages 185-193, 1990. 67

[Desper & Gascuel 2006] R. Desper and 0. Gascuel. Getting a tree fast: Neigh­

bor joining, fastme, and distance-based methods. Curr Protoc Bioinfo,

Chapter 6, 2006. 18

[Dhedhiou & Golldack 2006] C. J. Dhedhiou and D. Golldack. Salt-dependent

regulation of chloride channel transcripts in rice. Plant Science, vol. 170,

pages 793-800, 2006. 54

[Djordjevic et al. 1998] S. Djordjevic, P. N. Goudreau, Q. Xu, A. M. Stock and

A. H. West. Structural basis for methylesterase CheB regulation by a

phosphorylation-activated domain. Proc N atl A cad Sci, vol. 95, pages

1381-1386, 1998. 129

241

Page 11: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Du & Chen 2000] L. Du and Z. Chen. Identification of genes encoding receptor­

like kinases as possible targets of pathogen-and salicylic acid-induced

WRKY DNA-binding proteins in Arabidopsis. Plant J, vol. 24, pages

837-847, 2000. 37

[Durbin et al. 2002] R. Durbin, S. Eddy, A. Krogh and G. Mitchison. Biological

sequence analysis. Cambridge University Press, 2002. 18

[Dutta & Inouye 2000] R. Dutta and M. Inouye. GHKL, an emergent AT­

Pasejkinase superfamily. Thends Biochem Sci, vol. 25, pages 24-28, 2000.

120

[Ecker et al. 1989] D. J. Ecker, T. R. Butt and S. T. Crooke. Yeast metalloth­

ionein: gene function and regulation by metal ions. Metal ions biol sys,

vol. 25, page 147:169, 1989. 73

[Eddy et al. 1995] S. R. Eddy, G. Mitchison and R. Durbin. Maximum discrim­

ination hidden Markov models of sequence consensus. J Comput Biol,

vol. 2, pages 9-23, 1995. 15

[Eddy 1998] S. R. Eddy. Profile hidden Markov models. Bioinformatics, vol. 14,

page 755763, 1998. 15

[Edgar 2004] R. C. Edgar. MUSCLE: multiple sequence alignment with high ac­

curacy and high throughput. Nucl Acids Res, vol. 32, pages 1792-1797,

2004. 16, 17, 43, 75, 91

[English & Vanderbilt 1995] J. M. English and C. A. Vanderbilt. Isolation of

MEK5 and differential expression of alternatively spliced forms. J Biol

Chem, vol. 270, pages 28897-28902, 1995. 50

[Epstein et al. 1980] E. Epstein, J. D. Norlyn, D. W. Rush, R. W. Kingsbury,

D. B. Kelley, G. A. Cunningham and A. F. Wrona. Saline Culture of

Crops: A Genetic Approach. Science, vol. 210, pages 399-404, 1980. 89

[Ermolaeva et al. 2003] M. D. Ermolaeva, M. M. \iVu, J. A. Eisen and S. L.

Salzberg. The age of the Arabidopsis thaliana genome duplication. Plant

Mol Biol, vol. 51, pages 859-866, 2003. 58

242

Page 12: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Estevez et al. 2004] R. Estevez, M. Pusch, C. Ferrer-Costa, M. Orozco and T. J.

Jentsch. Functional and structural characteristic conservation of BCS

domains from CLC chloride channels. J Physiol, vol. 557, pages 363-378,

2004. 54

[Eswar et al. 2000] N. Eswar, M. A. Marti-Renom, B. Webb, M. A. Madhusu­

dan, D. Eramian, M. Sherr, U. Pieper and A. Sali. Comparative protein

structure modeling with MODELLER. Cur Prot Bioinfo, vol. 15, pages

5.6.1-5.6.3, 2000. 76, 93, 112

[Fabret et al. 1999] C. Fabret, V. A. Feher and J. A. Hoch. Two-component

signal transduction in Bacillus subtilis: how one organism sees its world.

J Bacteriol, vol. 181, pages 1975-1983, 1999. 107

[Felsenstein 1981] J. Felsenstein. Evolutionary tree from DNA sequence: A ma.r­

imum likelihood approach. J Biol Evol, vol. 17, pages 368-382, 1981. 20

[Felsenstein 1984] J. Felsenstein. Distance methods for inferring phylogenies: A

justification. Evolution, vol. 38, page 1624, 1984. 18

[Felsenstein 1989] J. Felsenstein. PHYLIP - Phylogeny Inference Package.

Cladistics, vol. 5, pages 164-166, 1989. 43, 75, 92

[Feng & Doolittle 1987] D. F. Feng and R. F. Doolittle. Progressive sequence

alignment as a prerequisite to correct phylogenetic trees. J Mol Evol,

vol. 25, page 351360, 1987. 19

[Ferrari-Iliou et al. 1994] R. Ferrari-Iliou, A. d'Arcy Lameta, A. T. Pham-Thi,

Y. Zuily-Fodil and P. Mazliak. Effect of drought on photodynamic perox­

idation of leaf total lipophilic extracts. Phytochem, vol. 37, pages 1237-

1243, 1994. 67

[Finkel & Holbrook 2000] T. Finkel and N. J. Holbrook. Oxidants, oxidative

stress and the biology of ageing. Nature, vol. 408, pages 239-247, 2000. 67

[Finn et al. 1995] B. E. Finn, J. Evenas, T. Drakenberg, J.P. Waltho, E. Thulin

and S. Forsen. Calcium-induced structural changes and domain autonomy

in calmodulin. Nature Struct Biol, vol. 2, pages 777-783, 1995. 100

243

Page 13: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Finn et al. 2006] R. D. Finn, J. Mistry, B. S. Bockler, S. Griffiths-Janes, V. Hol­

lich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S. R.

Eddy, E. L. Sonnhammer and A. Bateman. Pfam: clans, web tools and

services. Nucl Acids Res, vol. 34, pages 247-251, 2006. 42, 112

[Fisher et al. 2000] A. Fisher, R. K. Do and A. Sali. Modelling of loops inprotein

structures. Protein Science, vol. 9, pages 1753-1773, 2000. 76, 93, 112

[Floris et al. 2009] M. Floris, H. Mahgoub, E. Lanet and B. Menand. Post­

Translational regulation of Gene experssion in plants during abiotic stress.

Int J Mol Sci, vol. 10, pages 3168-85, 2009. 3

[Flowers & Yeo 1995] T. J. Flowers and A. R. Yeo. Breeding for salinity resis­

tance in crop plants: where next? Aust .J Plant Physiol, vol. 22, pages

875-884, 1995. 10

[Fox & Guerinot 1998] T. C. Fox and M. L. Guerinot. Molecular biology of cation

transport in plants. Annu Rev Plant Physiol Plant Mol Biol, vol. 49, pages

669-696, 1998. 37

[Frishman & Argos 1995] D. Frishman and P. Argos. Knowledge-based secondary

structure assignment. Proteins, vol. 23, pages 566-579, 1995. 76, 92, 112

[Frishman & Argos 1996] D. Frishman and P. Argos. Incorporation of long­

distance interactions into a secondary prediction algorithm. Protein En­

gineering, vol. 9, pages 133-142, 1996. 76, 92, 112

[Frishman & Argos 1997] D. Frishman and P. Argos. 75% accuracy in protein

secondary structure prediction. Proteins, vol. 27, pages 329-335, 1997. 76,

92, 112

[Gale & Devos 2001] M. D. Gale and K. M. Devos. Comparative genetics and

cereal evolution. Israel J Plant Sci, vol. 49, pages S19-S23, 2001. 8

[Galperin et al. 2001] M. Y. Galperin, A. N. Nikolskaya and E. V. Koonin. Novel

domains of the prokaryotic two-component signal transduction systems.

FEMS Microbial Lett, vol. 203, pages 11-21, 2001. 114

244

Page 14: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Gao et al. 2007] JP. Gao, DY. Chao and HX. Lin. Understanding abiotic stress

tolerance mechanisms: Recent studies on stress response in Rice. J Int

Plant Biol, vol. 49, pages 742-750, 2007. 2

[Garcia-Hernandez et al. 1998] M. Garcia-Hernandez, A. Murphy and L. Taiz.

M etallothioneins 1 and 2 have distinct but overlapping expression patterns

in Arabidopsis. Plant Physiol, vol. 118, pages 387-397, 1998. 74

[Garcia et al. 1997] A. B. Garcia, J. E. de Almeida, S. Iyer, T. Gerats, M. Van

Montagu and A. B. Caplan. Effects of osmoprotectants upon NaCl stress

in rice. Plant Physiol, vol. 115, pages 159-169, 1997. 9

[Geelen et al. 2000] D. Geelen, C. Lurin, D. Bouchez, J. M. Frachisse, F. Lelievre,

B. Courtial, H. B. Brygoo and C. Maurel. Disruption of putative anion

channel gene AtCLC-a in Arabidopsis suggests a role in the regulation of

nitrate content. Plant J, vol. 21, pages 259-267, 2000. 41

[Gibson et al. 1991] M. M. Gibson, D. A. Bagga, C. G. Miller and M. E. Maguire.

Magnesium transport in Salmonella typhimurium: the influence of new

mutations conferring Co2+ resistance on the CorA Mg2+ transport sys­

tem. Mol Microbial, vol. 5, pages 2753-2762, 1991. 50

[Gisela et al. 2004] M. Gisela, D. Jordi, H. Gemma, W. J. Guo, P. Goldsbroug,

S. Atrian and M. Molinas. A plant type 2 metallothionein (MT) from cork

tissue responds to oxidative stress. J Exp Bot, vol. 55, pages 2483-2493,

2004. 74

[Godzik 2003] A. Godzik. Fold recognition methods. Methods Biochem Anal,

vol. 44, pages 525-546, 2003. 98

[Goff et al. 2002] S. A. Goff, D. Ricke, T. H. Lan, G. Presting, R. Wang, M. Dunn

and et al. A draft sequence of the rice genome (Oryza sativa L. ssp.

japonica). Science, vol. 296, pages 92-100, 2002. vi, 8, 29, 30, 141

[Goff et al. 2003] Stephen A. Goff, Darrell Ricke, Tien-Hung Lan, Gernot Prest­

ing, Ronglin \iVang, Molly Dunn, .Jane Glazebrook, Allen Sessions, Paul

245

Page 15: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

Oeller and et al. A draft sequence of the rice genome (Oryza sativa L. ssp.

Japonica). Science, vol. 296, pages 92-100, 2003. 3, 7

[Gollery et al. 2006] M. Gollery, J. Harper, J. Cushman, T. Mittler, T. Girke,

J. K. Zhu, J. B. Serres and R. Mittler. What makes species unique? The

contributions of proteins with obscure feature. Genome Biol, vol. 7, page

757, 2006. 39, 40

[Gollery et al. 2007] M. Gollery, J. Harper, J. Cushman, T. Mittler and R. Mit­

tler. POFs: what we dont know can hurt us. Trends Plant Sci, vol. 12,

pages 492-496, 2007. 40

[Gollob et al. 2001a] M. H. Gollob, M. S. Green, A. S. Tang, T. Gollob,

A. Karibe, A. S. A. Hassan, F. Ahmad, R. Lozado, G. Shah, L. Fanana­

pazir and et al. Identification of a gene responsible for familial Wo~ff­

Parkinson- White syndrome. N Engl J Med, vol. 344, pages 1823-1831,

2001. 41

[Gollob et al. 2001b] M. H. Gollob, J. J. Seger, T. N. Gollob, T. Tapscott,

0. Gonzales, L. Bachinski and R. Roberts. Novel PRKAG2 mutation

responsible for the genetic syndrome of ventricular preexcitation and con­

duction system disease with childhood onset and absence of cardiac hyper­

trophy. Circulation, vol. 104, pages 3030-3033, 2001. 41

[Gong et al. 2004] D. Gong, Y. Guo, K. S. Schumaker and J. K. Zhu. The SOS3

family of calcium sensor and SOS2 family of protein kinase in Arabidopsis.

Plant Physiol, vol. 134, pages 919-926, 2004. 90

[Gouet et al. 1999] P. Gouet, B. Fabry, V. Guillet, C. Birck, L. Mourey, D. Kahn

and J. P. Samama. Structural transitions in the Fix] receiver domain.

Structure, vol. 7, pages 1517-1526, 1999. 129

[Grebe & Stock 1999] T. Vv. Grebe and J. B. Stock. The histidine protein kinase

superfamily. Adv Microb Physiol, vol. 41, pages 139-227, 1999. 109

246

Page 16: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Grefen & Harter 2004] C. Grefen and K. Harter. Plant two-component systems:

principles, functions, complexity and cross talk. Planta, vol. 219, pages

733-742, 2004. 109

[Guo et al. 2001] Y. Guo, U. Halfter, M. Ishitani and J. K. Zhu. Molecular char­

acterization of functional domains in the protein kinase SOS2 that is re­

quired for plant salt tolerance. Plant Cell, vol. 13, pages 1383-1400, 2001.

90, 94, 102, 143

[Guo et al. 2003] W. J. Guo, W. Bundithya and P. B. Goldsbrough. Charac­

terization of the Arabidopsis metallothionein gene family: tissue-specific

expression and induction during senescence and in response to copper.

New Phytol, vol. 159, pages 369-381, 2003. 74

[Guo et al. 2008] W. J. Guo, M. Meetam and P.B. Goldsbrough. Examining the

specific contributions of individual Arabidopsis metallothioneins to copper

distribution and metal tolerance. Plant Physiol, vol. 146, pages 1697-1706,

2008. 74

[Guyot et al. 2004] R. Guyot, B. Keller and et al. Ancestral genome duplication

in rice. Genome, vol. 47, pages 610-614, 2004. 29

[Halfter et al. 2000] U. Halfter, M. Ishitani and J. K. Zlm. The Arabidopsis SOS2

protein kinase physically interacts with and is activated by the calcium­

binding protein SOS3. Proc Natl Acad Sci, vol. 97, pages 3735-3740,

2000. 90

[Hall 2002] J. L. Hall. Cellular mechanisms for heavy metal detoxification and

tolerance. J Exp Bot, vol. 53, pages 1-11, 2002. 73

[Hanks & Hunter 1995] S. K. Hanks and T. Hunter. Protein kinases 6: the eu­

karyotic protein kinase superfamily: kinase (catalytic) domain structure

and classification. FASEB J., vol. 9, pages 576-596, 1995. 94

[Hardie & Hawley 2001] D. G. Hardie and S. A. Hawley. AMP-activated protein

kinase: the energy change hypothesis revisited. Bioassay, vol. 23, pages

1112-1119, 2001. 53

247

Page 17: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Hardie et al. 1998] D. G. Hardie, D. Carling and M. Carlson. The AMP­

activated/SNF1 protein kinase subfamily: metabolic sensors of the eu­

karyotic cell? Annu Rev Biochem, vol. 67, pages 821-855, 1998. 94

[Hasegawa et al. 2000] P.M. Hasegawa, R. A. Bressan, J. K. Zhu and H. J. Bohn­

ert. Plant cellular and molecular responses to high salinity. Annu Rev

Plant Physiol Plant Mol Biol, vol. 51, pages 463-499, 2000. 3, 104

[Haug et al. 2003] K. Haug, M. Warnstedt, A. K. Alekov, T. Sander, A. Ramirez,

B. Poser, S. Maljevic, S. Hebeisen, C. Kubisch, J. Rebstock and et al. Mu­

tations in CLCN2 encoding a voltage-gated chloride channel are associated

with idiopathic generalized epilepsies. Nat Genet, vol. 33, pages 527-532,

2003. 41

[Hazen et al. 2003] S. P. Hazen, Y. Wu and J. A. Kreps. Gene Expression pro­

filing of plant responses to abiotic stress. Funct Integr Genomics, vol. 3,

pages 105-11, 2003. 3

[He & Zhang 2005] X. He and J. Zhang. Rapid subfunctionalization accompa­

nied by prolonged and substantial neofunctionalization in duplicate gene

evolution. Genetics, vol. 269, pages 1157-1164, 2005. 91

[Hechenberger et al. 1996] M. Hechenberger, B. Schwappach, W. N. Fischer,

Vv. B. Frommer, T. J. Jentsch and K. Steinmeyer. A family of puta­

tive chloride channels from A rabidopsis and functional complementation

of a yeast strain with a CLC gene disruption. J Biol Chem, vol. 271, pages

33632-33638, 1996. 41

[Reish et al. 1995] H. M. Reish, Vv. K. Liu and P. C. Huang. A novel stress­

inducible metallothionein-like gene from rice. Plant Mol Biol, vol. 28,

pages 381-389, 1995. 74

[Reish et al. 1996] H. M. Reish, Vv. K. Liu, A. Chang and P. C. Huang. RNA

expression patterns of a type 2 metallothionein-like gene from rice. Plant

Mol Biol, vol. 32, pages 525-529, 1996. 74

248

Page 18: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Henikoff & Henikoff 1992] S. Henikoff and J. G. Henikoff. Amino Acid Substi­

tution MatTices fTOm PTOtein Blocks. Proc Natl Acad Sci, vol. 89, page

1091510919, 1992. 11

[Heribert & Shinozaki 2004] H. Heribert and K. Shinozaki. Plant responses to

abiotic stress., volume 4 of Topics in CuTTent Genetics. Springer, 2004.

66

[Hirosawa et al. 1995] M. Hirosawa, Y. Totoki, M. Hoshida and M. Ishikawa.

CompTehensive study on itemtive algoTithms of multiple sequence align­

ment. Comput Appl Biosci, vol. 11, page 1318, 1995. 17

[Hsieh et al. 1995] H.M. Hsieh, W. K. Liu and P. C. Huang. A novel stTess­

inducible metallothionein-like gene from rice. Plant Mol Biol, vol. 28,

pages 381-389, 1995. 88

[Hua et al. 1995] J. Hua, C. Chang, Q. Sun and E. M. Meyerowitz. Ethylene

insensitivity conferred by Ambidopsis ERS gene. Science, vol. 269, pages

1712-1714, 1995. 109

[Hua et al. 1998] J. Hua, H. Sakai, S. Nourizadeh, Q. G. Chen, A. B. Bleecker,

J. R. Ecker and E. M. Meyerowitz. EIN4 and ERS2 are members of the

putative ethylene receptor gene family in Ambidopsis. Plant Cell, vol. 10,

pages 1321-1332, 1998. 109

[Hughey & Krogh 1996] R. Hughey and A. Krogh. Hidden markov models for

sequence analysis: extension and analysis of the basic method. Comput

Appl Biosci, vol. 12, pages 95-107, 1996. 15

[Hulko et al. 2006] M. Hulko, F. Berndt, M. Gruber, J. U. Linder, V. Truffault,

A. Schultz, J. Martin, J. E. Schultz, A. N. Lupa.s and M. Coles. The HAM?

domain structure implies helix rotation in tmnsmembmne signaling. Cell,

vol. 126, pages 929-940, 2006. 114

[Humphrey et al. 1996] W. Humphrey, A. Dalke and K. Schulten. VMD- Visual

Molecular Dynamics. J Molec Graphics, vol. 14, pages 33-38, 1996. 77,

93, 113

249

Page 19: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Huner et al. 1998] N. P. A. Huner, G. Oquist and F. Sarhan. Energy balance

and acclimation to light and cold. Trends Plant Sci, vol. 3, pages 224-230,

1998. 36

[Hutchings et al. 2004] M. I. Hutchings, P. A. Hoskisson, G. Chandra and M. J.

Buttner. Sensing and responding to diverse extracellular signals? Analysis

of the sensor kinases and response regulators of Streptomyces coelicolor

A3(2). Microbiology, vol. 150, page 27952806, 2004. 107

[Hwang & Sheen 2001] I. Hwang and J. Sheen. Two-component circuitry in Ara­

bidopsis cytokinin signal transduction. Nature, vol. 413, pages 383-389,

2001. 109

[Ignoul & Eggermont 2005] S. Ignoul and J. Eggermont. CBS domains: struc­

ture, function, and pathology in human proteins. Am J Physiol Cell Phys­

iol, vol. 289, pages C1369-C1378, 2005. 40, 56

[Imamura et al. 1999] A. Imamura, N. Hanaki, A. Nakamura, T. Suzuki,

M. Taniguchi, T. Kiba, C. Ueguchi, T. Sugiyama and T. Mizuno. Com­

pilation and characterization of Arabidopsis thaliana response regulators

implicated in His-Asp phosphorelay signal transduction. Plant Cell Phys­

iol, vol. 40, pages 733-742, 1999. 110, 111

[IRGSP 2005] IRGSP. The map-based sequence of the Rice genome. Nature,

vol. 436, pages 793-800, 2005. 8

[Ishige et al. 1994] K. Ishige, S. Nagasawa, S. Tokishita and T. Mizuno. A novel

device of bacterial signal transducers. EMBO J, vol. 13, pages 5195-5202,

1994. 131

[Ishitani et al. 2000] M. Ishitani, J. Liu, U. Halfter, C. S. Kim, W. Shi and J. K.

Zlm. SOS3 function in plant salt tolerance requires N-myristoylation and

calcium binding. Plant Cell, vol. 12, pages 1667-1677, 2000. 90, 97

[Ishitani et al. 2004] M. Ishitani, I. Rao, P. Wenzl, S. Beebe and J. Tohme. Inte­

gration of genomics approach with traditional breeding towards improving

250

Page 20: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

abiotic stress adaptation: drought and aluminum toxicity as case studies.

Field Crop Res, vol. 90, pages 35-45, 2004. vi

[Itoh et al. 2007] T. Itoh, T. Tanaka, R. A. Barrera and et al. Curated genome

annotation of Oryza sativa ssp. japonica and comparative genome analysis

with Arabidopsis thaliana. Genome Res, vol. 17, pages 175-183, 2007. 10

[Iuchi et al. 1990] S. Iuchi, Z. Matsuda, T. Fujiwara and E. C. C. Lin. The arcB

gene of Escherichia coli encodes a sensor-regulator protein for anaerobic

repression of the arc modulon. Mol Microbial, vol. 4, pages 715-727, 1990.

131

[Iuchi 1993] S. Iuchi. Phosphorylation/dephosphorylation of the receiver module

at the conserved aspartate residue controls transphosphorylation activity of

histidine kinase in sensor protein ArcB of Escherichia coli. J Biol Chern,

vol. 268, pages 23972-23980, 1993. 131

[Jain et al. 2008] M. Jain, A. K. Tyagi and J. P. Khurana. Genome-wide identi­

fication, classification, evolutionary expansion, and expression analyses of

homeobox genes in rice. FEES Journal, vol. 275, pages 2845-2861, 2008.

22

[Janiak-Spens et al. 1999] F. Janiak-Spens, J. M. Sparling, M. Gurfinkel and

A. H. West. D~fferential stabilities of phosphorylated response regulator

do- mains reflect functional roles of the yeast osmoregulatory SLN1 and

SSK1 proteins. J Bacterial, vol. 181, page 411417, 1999. 136

[Jeong et al. 2008] B. C. Jeong, K. S. Yoo, K. W. Jung, J. S. Shin and H. K. Song.

Purification, crystallization and preliminary X-ray diffraction analysis of

a cystathionine j3-synthase domain-containing protein, CDCP2, from Ara­

bidopsis thaliana. Acta Crystallographica, vol. F64, pages 825-827, 2008.

53

[Jin et al. 2006] S. Jin, Y. Cheng, Q. Guan, D. Liu and S. Liu T. Takano. A

metallothionein-like protein of rice ( rgMT) functions in E. coli and its

gene expression is induced by abiotic stresses. Biotech Lett, vol. 28, pages

1749-1753, 2006. 88

251

Page 21: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Johnson & Thomas 2007] D. A. Johnson and M. A. Thomas. The monosac­

charide transporter gene family in Arabidopsis and rice: a history of du­

plications, adaptive evolution, and functional divergence. Mol Biol Evol,

vol. 24, pages 2412-2423, 2007. 20, 22

[.Johnson et al. 1996] L. N. Johnson, M. E. M. Noble and D. J. Owen. Active

and inactive protein kinases: structural basis for·regulation. Cell, vol. 85,

pages 149-158, 1996. 94

[Johnston et al. 2005] J. S. Johnston, A. E. Pepper, A. E. Hall, Z. J. Chen,

G. Hodnett, J. Drabek, R. Lopez and H. J. Price. Evolution of genome

size of Brassicacae. Ann Bot, vol. 95, pages 229-235, 2005. 91

[Jones 1999] D. T. Jones. GenTHREADER: an efficient and reliable protein fold

recognition method for genomic sequences. J Mol Biol, vol. 287, pages

797-815, 1999. 92, 112

[Kabsch & Sander 1983] W. Kabsch and C. Sander. Dictionary of protein sec­

ondary structure: pattern recognition of hydrogen-bonded and geometrical

features. Bioploymers, vol. 22, pages 2577-2637, 1983. 76, 92, 112

[Kakimoto 1996] T. Kakimoto. CKIJ, a histidine kinase homolog implicated in

cytokinin signal transduction. Science, vol. 274, pages 982-985, 1996. 109

[Kamalay & Goldberg 1980] J. C. Kamalay and R. B. Goldberg. Regulation of

structural gene expression in tobacco. Cell, vol. 19, pages 935-946, 1980.

3

[Kamalay & Goldberg 1984] J. C. Kamalay and R. B. Goldberg. Organ-specific

nuclear RNAs in tobacco. Proc Natl Acad Sci, vol. 81, pages 2801-2805,

1984. 3

[Kapoor et al. 2008] M. Kapoor, R. Arora, T. Lama, A. Nijhawan, J.P. Khurana,

A. K. Tyagi and S. Kapoor. Genome-wide identification, organization and

phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA

Polymerase gene families and their expression analysis during reproductive

252

Page 22: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

development and stress in rice. BMC Genomics, vol. 9, page 451, 2008.

22, 23

[Karlin & Altschul 1990] S. Karlin and S. F. Altschul. Methods for assessing

the statistical sign~ficance of molecular sequence features by using general

scoring schemes. Proc Natl Acad Sci, vol. 87, pages 2264~2268, 1990. 12

[Karlin et al. 1990] S. Karlin, A. Dembo and T. Kawabata. Statistical Composi­

tion of High-Scoring Segments from Molecular Sequences. The Annals of

Statistics, vol. 18, pages 571 ~581, 1990. 12

[Kato et al. 1997] M. Kato, T. Mizuno, T. Shimizu and T. Hakoshima. Insights

into multistep phosphorelay from the crystal structure of the C-terminal

HPt domain of ArcB. Cell, vol. 88, pages 717~723, 1997. 132, 134, 136

[Kawasaki et al. 2001] S. Kawasaki, C. Borchert, M. Deyholos, H. Wang,

S. Brazille, K. Kawai, D. Galbraith and H. J. Bohnert. Gene expression

profiles during the ·initial phase of salt stress in rice. Plant Cell, vol. 13,

pages 889~905, 2001. 25, 30

[Kawashima et al. 1992] A. I. Kawashima, T. D. Kennedy, M. Chino and B. G.

Lane. Wheat Ec metallothionein genes. Eur J Biochem, vol. 209, pages

971-976, 1992. 73

[Keller & Feuillet 2000] B. Keller and C. Feuillet. Collinearity and gene density

in grass genomes. Trends Plant Sci, vol. 5, pages 246~251, 2000. 4

[Kelley et al. 2000] L. A. Kelley, R M. MacCallum and M. J. Sternberg. En­

hanced genome annotation using structural pro.files in the program 3D­

PSSM. J Mol Biol, vol. 299, pages 499~520, 2000. 76, 92, 112

[Khan et al. 1997] M. S. A. Khan, A. Hamid and M. A. Karim. Effect of sodium

chloride on germination and seedling characters of different types of rice

(Oryza sativa L.). J Agron Crop Sci, vol. 179, pages 163-169, 1997. 9

[Khush & Virk 2005] G. S. Khush and P. S. Virk. Selection criteria, volume 15

of IR varieties and their impact. International Rice Research Institute,

Los Borras, 2005. 27

253

Page 23: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Khush 1997] G. S. Khush. Origin, dispersal, cultivation and variation of rice.

Plant Mol Biol, vol. 35, pages 25-34, 1997. 8

[Kilian et al. 2007] J. Kilian, D. \iVhitehead, J. Horak, D. Wanke, S. Weinl,

0. Batistic, E. B. D'Angelo, J. Kudla and K. Harter. The AtGenEx­

press global stress expression data set: protocols, evaluation and model

data analysis of UV-B light, drought and cold stress responses. Plant J,

vol. 50, pages 347-363, 2007. 45

[Kimura et al. 2001] M. Kimura, T. Yoshizumi, K. Manabe, Y. Y. Yamamoto and

M. Matsui. Arabidopsis transcriptional regulation by light stress via hydro­

gen peroxide-dependent and -independent pathways. Genes Cells, vol. 6,

pages 607-617, 2001. 66

[Kishimoto et al. 1994] N. Kishimoto, H. Higo, K. Abe, S. Arai, A. Saito and

K. Higo. Identification of the duplicated segments in rice chromosomes 1

and 5 by linkage analysis of eDNA markers of known functions. Theor

Appl Genet, vol. 88, pages 722-726, 1994. 29

[Klaassen et al. 1999] C. D. Klaassen, J. Liu and S. Choudhari. Metallothionein:

an intracellular protein to protect against cadmium toxicity. Annu Rev

Pharmacal Toxicol, vol. 39, pages 267-294, 1999. 74

[Knight et al. 1997] H. Knight, A. J. Trewavas and M. R. Knight. Calcium sig­

nalling in Arabidopsis thaliana responding to drought and salinity. Plant

J, vol. 12, pages 1067-1078,1997.67

[Kocan et al. 2006] M. Kocan, S. Schaffer, T. Ishige, U. Sorger-Herrmann, V. F.

Wendisch and M. Bott. Two-component systems of Corynebacterium glu­

tamicum: deletion analysis and involvement of the PhoS-PhoR system in

the phosphate starvation response. J Bacterial, vol. 188, pages 724-732,

2006. 107

[Kofoid & Parkinson 1988] E. C. Kofoid and J. S. Parkinson. Transmitter andre­

ceiver modules in bacterial signaling proteins. Proc Natl Acad Sci, vol. 85,

pages 4981-4985, 1988. llO

254

Page 24: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Kolukisaoglu et al. 2004] U. Kolukisaoglu, S. Weinl, D. Blazevic, 0. Batistic and

J. Kudla. Calcium sensors and their interacting protein kinases: genomics

of the Arabidopsis and rice CBL-CIPK signaling networks. Plant Physiol,

vol. 134, pages 43-58, 2004. 90

[Konrad et al. 2000] M. Konrad, M. Vollmer, H. H. Lemmink, L. P. Heuvel,

N. Jeck, R. V. Pousson, A. Lakings, R. Ruf, G. Deschenes, C. Antignac

and et al. Mutations in the chloride channel gene CLCNKB as a cause of

classic Bartter syndrome. J Am Soc Nephrol, vol. 11, pages 1449-1459,

2000. 41

[Koretke et al. 2000] K. K. Koretke, A. N. Lupas, P. V. Warren, M. Rosenberg

and J. R. Brown. Evolution of two component signal transduction. Mol

Biol Evol, vol. 17, pages 1956-1970, 2000. 109

[Kornak et al. 2001] U. Kornak, D. Kasper, M. R. Bosl, E. Kaiser, M. Schweizer,

A. Schulz, W. Friedrich, G. Delling and T. J. Jentsch. Loss of the ClC-7

chloride channel leads to osteopetrosis in mice and man. Cell, vol. 104,

pages 205-215, 2001. 41

[Kowalski et al. 1994] S. D. Kowalski, T. H. Lan, K. A. Feldmann and A. H.

Paterson. Comparative mapping of Arabidopsis thaliana and Brassica ol­

ereracea chromosomes reveals islands of conserved organization. Genetics,

vol. 138, pages 499-510, 1994. 90

[Kozian & Kirschbaum 1999] D. H. Kozian and B. J. Kirschbaum. Comparative

gene expression analysis. Trends Biotechnol, vol. 17, pages 73-78, 1999.

vii, 10

[Krogh et al. 1994] A. Krogh, M. Brown, I. S. Mian, K. Sjolander and D. Haus­

sler. Hidden Markov models in computational biology. Applications to

protein modeling. J Mol Biol, vol. 235, page 15011531, 1994. 15

[Ku et al. 2000] H. M. Ku, T. Vision, J. Liu and S. D. Tanksley. Comparing

sequenced segments of the tomato and Arabidopsis genomics: Large-scale

duplication followed by selective gene loss creates a network of synteny.

Proc Natl Acad Sci, vol. 97, pages 9121-9126, 2000. 8

255

Page 25: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Kuboniwa et al. 1995] H. Kuboniwa, N. Tjandra, S. Grzesiek, H. Ren, C. B.

Klee and A. Bax. Solution structure of calcium free calmodulin. Nature

Struct Biol, vol. 2, pages 758-776, 1995. 100

[Kumar et al. 2008] G. Kumar, R. S. Purty, M. P. Sharma, S. L. Singla-Pareek

and A. Pareek. Physiological response among Brassica species under

salinity stress show strong correlation with transcript abundance for SOS

pathway-related genes. J plant physio, vol. 166, pages 507-20, 2008. 91,

104, 144

[Kumari et al. 2009] S. Kumari, V. P. Sabharwal, H. R. Kushwaha, S. K. Sopory,

S. L. Singla-Pareek and A. Pareek. Transcriptome map for seedling stage

specific salinity stress response indicates a specific set of genes as candi­

date for saline tolerance in Oryza sativa L. Functional and Integrative

Genomics, vol. 9, pages 109-123, 2009. 26, 38, 40, 72

[Kurata et al. 1994] N. Kurata, G. Moore, Y. Nagamura, T. Foote, M. Yano,

Y. Minobe and M. Gale. Conservation of genome structure between rice

and wheat. BioTechnology, vol. 12, pages 276-278, 1994. 29

[Kurtz et al. 2004] S. Kurtz, A. Phillippy, A. L. Deicher, M. Smoot, M. Shumway,

C. Antonescu and S. L. Salzberg. Versatile an open software for comparing

large genomes. Genome Biology, vol. 5, page R12, 2004. 75, 80

[Kushwaha et al. 2009] H. R. Kushwaha, A. K. Singh, S. K. Sopory, S. L. Singla­

Pareek and A. Pareek. Genome wide expression analysis of CBS domain

containing proteins in Arabidopsis thaliana (L.) Heynh and Oryza sativa

L. reveals their developmental and stress regulation. BMC Genomics,

vol. 10, page 200, 2009. 10, 20, 23

[Lafitte et al. 2004] H. R. Lafitte, A. Ismail and J. Bennett. Abiotic stress toler­

ance in rice for Asia: progress and the future. New Directions for a diverse

plant. Proceedings of the 4th International Crop Science Congress, 2004.

8, 10

256

Page 26: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Lagercrantz et al. 1996] U. Lagercrantz, J. Putterill and G. Couplandand D.

Lydiate. Comparative mapping in Arabidopsis and Brassica, fine scale

genome colinearity and congruence of genes controlling flowering time.

Plant J, vol. 9, pages 13-20, 1996. 90

[Lane et al. 1987] B. Lane, R. Kajioka and T. Kennedy. The wheat-germ Ec

protein is a zinc-containing metallothionein. Biochem Cell Biol, vol. 65,

pages 1001-1005, 1987. 74

[Larkin et al. 2007] M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna,

P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm,

R. Lopez, J. D. Thompson, T. J. Gibson and D. G. Higgins. Clustal W

and Clustal X version 2.0. Bioinformatics, vol. 23, pages 2947-2948, 2007.

93, 112

[Lashbrook et al. 1998] C. C. Lashbrook, D. M. Tieman and H. J. Klee. Differ­

ential regulation of the tomato ETR gene family throughout plant devel­

opment. Plant J, vol. 15, pages 243-252, 1998. 109

[Laskowski et al. 1993] R. A. Laskowski, M. W. MacArthur, D. S. Moss and J. M.

Thornton. PROCHECK: a program to check the stereochemical quality of

protein structures. J Appl Cryst, vol. 26, pages 283-291, 1993. 76, 93, 112

[Ledger & Gardner 1994] S. E. Ledger and R. C. Gardner. Cloning and char­

acterization of five cDNAs for genes differentially expressed during fruit

development of kiwifruit ( Actinidia deliciosa var. deliciosa). Plant Mol

Biol, vol. 25, pages 877-886, 1994. 74

[Leroux et al. 1987] B. Leroux, M. F. Yanofsky, S. C. Winans, J. E. Ward, S. F.

Ziegler and E. W. Nester. Characterization of the vir A locus of Agrobac­

terium tumefaciens: a transcriptional regulator and host range determi­

nant. EMBO J, vol. 6, pages 849-56, 1987. 109

[Levitt 1980] J. Levitt. Responses of plant to environmental stress chilling, freez­

ing, and high temperature stresses. 2nd ed. Academic Press, 1980. 3

257

Page 27: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Lewis et al. 1999] R. J. Lewis, J. A. Brannigan, K. Muchova, I. Barak and A. J.

Wilkinson. Phosphorylated aspartate in the structure of a response regu­

lator protein. J Mol Biol, vol. 294, pages 9-15, 1999. 129

[Lewitt-Bently & Rety 2000] A. Lewitt-Bently and S. Rety. Ef-hand calcium

binding proteins. Curr Opin Struct Biol, vol. 10, pages 637-643, 2000.

102

[Lijavetzky et al. 2003] D. Lijavetzky, P. Carbonero and J. Vicente-Carbajosa.

Genome-wide comparative phylogenetic analysis of the rice and Arabidop­

sis Dof gene families. BMC Evol Biol, vol. 3, pages 17-21, 2003. 20,

21

[Liu & Zhu 1980] J. Liu and J. K. Zhu. A calcium sensor homolog required for

plant salt tolerance. Science, vol. 280, pages 1943-1945, 1980. 89, 143

[Liu et al. 2000] J. Liu, M. Ishitani, U. Halfter, C. S. Kim and J. K. Zlm. The

Arabidopsis thaliana SOS2 gene encodes a protein kinase that is required

for salt tolerance. Proc Natl Acad Sci, vol. 97, pages 3730-3734, 2000. 89,

90, 143

[Liu 1998] B. H. Liu. Statistical genomics: linkage, mapping, and qtl analysis.

CRC Press, 1998. 4, 22

[Lloyd et al. 1997] S. E. Lloyd, W. Gunther, S. H. Pearce, A. Thomson, M. L.

Bianchi, M. Bosio, I. W. Craig, S. E. Fisher, S. J. Scheinman, 0. Wrong,

T. J. Jentsch and R. V. Thakker. Characterisation of renal chloride chan­

nel, CLCNS, mutations in hypercalciuric nephrolithiasis (kidney stones)

disorders. Hum Mol Genet, vol. 6, pages 1233-1239, 1997. 41

[Lu et al. 2004] J. Lu, B. Merriman, S. Nelson and G. Riggins. A comparison

of gene expression profiles produced by SAGE, long SAGE, and oligonu­

cleotide chips. Genomics, vol. 84, pages 631-6, 2004. vii, 10

[Luhua et al. 2008] S. Luhua, S. C. Yilmaz, J. Harper, J. Cushman and R. Mit­

tler. Enhanced tolerance to oxidative stress in transgenic A rabidopsis

258

Page 28: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

plants expressing proteins of unknown function. Plant Physiol, vol. 148,

pages 280-92, 2008. 39

[Lukens et al. 2003] L. Lukens, F. Zou, D. Lydiate, I. Parkin and T. Osborn.

Comparison of a Brassica oleracea genetic map with the genome of Ara­

bidopsis thaliana. Genetics, vol. 164, pages 359-372, 2003. 90, 143

[Lurin et al. 2000] C. Lurin, J. Guclu, C. Cheniclet, J. P. Carde, H. B. Brygoo

and C. Maurel. CLC-Ntl, a putative chloride channel protein of tobacco,

co-localizes with mitochondrial membrane markers. Biochem J, vol. 348,

pages 291-295, 2000. 41

[Lurin et al. 2004] C. Lurin, C. Andres, S. Aubourg, M. Bellaoui, F. Bit­

ton, C. Bruyere, M. Caboche, C. Debast, J. Gualberto, B. Hoffmann,

A. Lecharny, M. Le Ret, M. L. Martin-Magniette, H. Mireau, N. Peeters,

J.P. Renou, B. Szurek, L. Taconnat and I. Small. Genome-wide analysis

of Arabidopsis pentatricopeptide repeat proteins reveals their essential role

in organelle biogenesis. Plant Cell, vol. 16, pages 2089-2103, 2004. 55

[Lutts et al. 1995] S. Lutts, J. M. Kinet and J. Bouharmont. Changes in plant

response to NaCl during development of rice (Oryza sativa L.) varieties

differing in salinity resistance. J Exp Bot, vol. 46, pages 1843-1852, 1995.

8, 9, 24

[Lynch & Conery 2000] M. Lynch and J. S. Conery. The evolutionary fate and

consequences of duplicate genes. Science, vol. 290, pages 1151-1155, 2000.

10

[Lynch & Force 2000] M. Lynch and A. Force. The probability of duplicate gene

preservation by subfunctionalization. Genetics, vol. 154, pages 459-473,

2000. 91

[Lynch & Lin 1996] A. S. Lynch and E. C. C. Lin. Responses to molecular oxygen

in escherichia coli and salmonella: Cellular and molecular biology. ASM

Press, 'i\Tashington, DC, 1996. 131

259

Page 29: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Ma & Bohnert 2007] S. Ma and H. J. Bohnert. Integration of Arabidopsis

thaliana stress related transcript profiles, promoter structures, and cell­

specific expression. Genome Biol, vol. 8, page R49, 2007. 36

[Ma et al. 2005] X. Ma, Q. Qian and D. Zhu. Expression of a calcineurin gene

improves salt stress tolerance in transgenic rice. Plant Mol Biol, vol. 58,

pages 483-495, 2005. 24

[Maarouf et al. 1999] H. El Maarouf, Y. Zuily-Fodil, M. Gareil, A. d'Arcy Lameta

and A. T. Pham-Thi. Enzymatic activity and gene expression under water

stress of phospholipase D in two cultivars of Vigna unguiculata (L.). Plant

Mol Biol, vol. 39, pages 1257-1265, 1999. 67

[Maeda et al. 1994] T. Maeda, S. M. Wurgler-Murphy and H. Saito. A two­

component system that regulates an osmosensing MAP kinase cascade in

yeast. Nature, vol. 369, pages 242-245, 1994. 107

[Mahalakshmi et al. 2006] S. Mahalakshmi, G. S. Christopher, T. P. Reddy,

K. V. Rao and V. D. Reddy. Isolation of a eDNA clone (PcSrp) en­

coding serine-richprotein from Porteresia coarctata T. and its e.rpression

in yeast and finger millet (Eleusine coracana L.) affording salt tolerance.

Planta, vol. 224, pages 347-359, 2006. 25

[Mahmood et al. 2006] N. A. B. N. Mahmood, E. B. Oldehinkel, J. S. Patzlaff,

G. K. S. Wolters and B. Poolman. Ion specificity and ionic strength de­

pendence of the osmoregulatory ABC transporter OpuA. J Biol Chern,

vol. 281, pages 29830-29839, 2006. 41

[Manthey & McEwen 1995] G. M. Manthey and J. E. McEwen. The prod1tct

of the nuclear gene PET309 is required for translation of mature mRNA

and stability or production of intron-containing RNAs derived from the

mitochondrial COX1 locus of Saccharomyces cerevisiae. EMBO J, vol. 14,

pages 4031-4043, 1995. 50

[Marchler-Bauer et al. 2009] A. Marchler-Bauer, J. B. Anderson, F. Chitsaz,

M. K. Derbyshire, C. DeWeese-Scott, J. H. Fong, L. Y. Geer, R. C. Geer,

260

Page 30: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

N. R. Gonzales, M. Gwadz, S. He, D. I. Hurwitz, J. D. Jackson, Z. Ke,

C. J. Lanczycki, C. A. Liebert, C. Liu, F. Lu, S. Lu, G. H. Marchler,

M. Mullokandov, J. S. Song, A. Tasneem, N. Thanki, R. A. Yamashita,

D. Zhang, N. Zhang and S. H. Bryant. CDD: specific functional annota­

tion with the Conserved Domain Database. Nucleic Acids Res., vol. 37,

pages D205-10, 2009. 98, 112

[Margoshes & Valee 1957] M. Margoshes and B. L. Valee. A cadmium protein

from equine kidney cortex. J Am Chem Soc, vol. 79, pages 4813-4814,

1957. 73

[Marina et al. 2001] A. Marina, C. Mott, A. Auyzenber, W. A. Hendrickson and

C. D. \¥aldburger. Structural and mutational analysis of PhoQ histidine

kinase catalytic domain. J Biol Chem, vol. 276, pages 41182-41190, 2001.

120

[Marina et al. 2005] A. Marina, C. D. Waldburger and W. A. Hendrickson. Struc­

ture of the entire cytoplasmic portion of a sensor histidine-kinase protein.

EMBO J, vol. 24, pages 4247-4259, 2005. 120

[Marmagne et al. 2007] A. Marmagne, M. V. Douard, D. Monachella, A. F.

Longevialle, C. Charon, M. Allot, F. Rappaport, F. A. Wollman, H. B.

Brygoo and G. Ephritikhine. Two members of the Arabidopsis CLC ( chlo­

ride channel) family, AtCLCe and AtCLCf, are associated with thylakoid

and Golgi membranes, respectively. J Exp Bot, vol. 58, pages 3385-3393,

2007. 41

[Marti-Renom et al. 2000] M. A. Marti-Renom, A. Stuart, A. Fiser, R. Sanchez,

K. Melo and A. Sali. Comparative protein structure modeling of genes and

genomes. Annu Rev Biophys Biomol Struct, vol. 29, pages 291-325, 2000.

76, 93, 112

[Mascher et al. 2006] T. Mascher, J. D. Heimann and G. Unden. Stimulus per­

ception in bacterial signal-transducing histidine kinase. Micro Mol Biol

Rev, vol. 70, pages 910-938, 2006. 107, 110

261

Page 31: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Matos et al. 2001] A. R. Matos, A. d'Arcy Lameta, M. Franca, S. Petres,

L. Edelman, J. Kader, Y. Zuily-Fodil and A. T. Pham-Thi. A novel

patatin-like gene stimulated by drought stress encodes a galactolipid acyl

hydrolase. FEES Lett, vol. 491, pages 188-192, 2001. 67

[Matsouka 2005] M. Matsouka. New Directions of Post-rice genome sequencing.

Plant Cell Physiol, vol. 46, pages 1-2, 2005. 141

[Matsumura et al. 1999] H. Matsumura, S. Nirasawa and R. Terauchi. Transcript

profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene

expression (SAGE). Plant J, vol. 20, pages 719-726, 1999. 74

[McGuffiin & Jones 2003] L. McGuffiin and D. T. Jones. Improvement of the

GenTHREADER method for genomic fold recognition. Bioinformatics,

vol. 19, pages 874-881, 2003. 76, 92, 112

[Mehta et al. 2005] P. A. Mehta, K. Sivaprakash, M. Par ani, G. Venkataraman

and A. K. Parida. Generation and analysis of crpressed sequence tags

from the salt-tolerant mangrove species Avicennia marina (Forsk) Vierh.

Theor Appl Genet, vol. 110, pages 416-424, 2005. 30

[Mena et al. 1998] M. Mena, J. V. Carbajosa, R. J. Schmidt and P. Carbonero.

An endosperm-specific DOF protein from barley, highly conserved in

wheat, binds to and activates transcription fr-om the prolamin-box of a

native B-hordein promoter in barley endosperm. Plant J, vol. 16, pages

53-62, 1998. 21

[Miller et al. 2004] W. Miller, K. D. Makova, A. Nekrutenko and R. C. Hardison.

Comparative genomics. Annu Rev Genomics Hum Genet, vol. 5, pages 15-

56, 2004. 9

[Mindell & Maduke 2001] J. A. Mindell and M. Maduke. ClC chloride channels.

Genome Biol, vol. 2, pages 3003.1-3003.6, 2001. 50

[Mittler 2002] R. Mittler. Oxidative stress, antioxidants and stress tolerance.

Trends in Plant .Science, vol. 7, pages 405-410, 2002. 3

262

Page 32: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Miyata et al. 1998] S. Miyata, T. Urao, K. Yamaguchi-Shinozaki and K. Shi­

nozaki. Characterization of genes for two-component phosphorelay me­

diators with a single HPt domain in Arabidopsis thaliana. FEBS Lett,

vol. 437, pages 11~14, 1998. 111

[Mizuno et al. 1982] T. Mizuno, E. T. Wurtzel and M. Inouye. Osmoregulation of

gene expression. II. DNA sequence of the envZ gene of the ompB operon

of Escherichia coli and characterization of its gene product. J Biol Chern,

vol. 257, pages 13692~8, 1982. 109

[Mizuno 1997] T. Mizuno. Compilation of all genes encoding two-component

phosphotransfer signal transducers in the genome of Escherichia coli. DNA

Res, vol. 4, pages 161 ~ 168, 1997. 107, 110

[Morris et al. 1992] A. L. Morris, M. vV. MacArthur, E. G. Hutchinson and J. M.

Thornton. Stereochemical quality of protein structure coordinates. Pro­

teins, vol. 12, pages 345~364, 1992. 76, 93, 112

[Moscat et al. 2006] J. Moscat, M. T. Diaz-Meco, A. Albert and S. Campuzano.

Cell signaling and function organized by PEl domain interactions. Mol

Cell, vol. 23, pages 631 ~640, 2006. 56

[Mount 2004] D. Mount. Bioinformatics: Sequence and genome analysis. Cold

Spring Harbor Laboratory Press, New York, 2004. 16, 18, 19

[Moyle et al. 2005] R. Moyle, D. J. Fairbairn, J. Ripi, M. Crowe and J. R. Botella.

Developing pineapple fruit has a small trancriptome dominated by metal­

lothionein. J Exp Bot, vol. 56, pages 101 ~ 112, 2005. 7 4

[Mukhopadhyay et al. 2004] A. Mukhopadhyay, S. Vij and A. K. Tyagi. Overex­

pression of a zinc-finger protein gene from rice confers tolerance to cold,

dehydration, and salt stress in transgenic tobacco. Proc Natl Acad Sci,

vol. 101, pages 6309~6314, 2004. 3, 24

[Muller-Dieckmann et al. 1999] H. J. Muller-Dieckmann, A. A. Grantz and S. H.

Kim. The strncture of the signal receiver domain of the Arabidopsis

263

Page 33: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

thaliana ethylene receptor ETR1. Structure Fold Des, vol. 7, pages 154 7-

1556, 1999. 129

[Munns 2005] R. Munns. Genes and salt tolerance: bringing them together. New

Phytol, vol. 167, pages 645--663, 2005. 31

[Murphy & Taiz 1995] A. Murphy and L. Taiz. Comparison of metallothionein

gene-expression and nonprotein thiols in 10 Arabidopsis ecotypes - corre­

lation with copper tolerance. Plant physiol, vol. 109, pages 945-954, 1995.

74

[Murzin et al. 1995] A. G. Murzin, S. E. Brenner, T. Hubbard and C. Chothia.

SCOP: a structural classification of proteins database for the investigation

of sequences and structures. J Mol Biol, vol. 247, pages 536-540, 1995.

76, 92, 112

[Nagae et al. 2003] M. Nagae, A. Nozawa, N. Koizumi, H. Sarro, H. Hashimoto,

M. Sato and T. Shimizu. The crystal structure of the novel calcium-binding

protein AtCBL2 from Arabidops1;s thaliana. J Biol Chem, vol. 278, pages

42240-42246, 2003. 100

[Naga.mura et al. 1995] Y. Nagamura, T. Inoue, B. Antonio, T. Shimano, H. Ka­

jiya and et al. Conservation of duplicated segments between rice chromo­

somes 11 and 12. Breeding Sci, vol. 45, pages 373-376, 1995. 29

[Nakamura et al. 2006] A. Nakamura, A. Fukuda, S. Sakai andY. Tanaka. Molec­

ular cloning, functional expression and subcellular localization of two pu­

tative vacuolar voltage-gated chloride channels in Rice ( Oryza sativa L.).

Plant Cell Physiol, vol. 4 7, pages 32-42, 2006. 41

[Nakano et al. 2006] T. Nakano, K. Suzuki, T. Fujimura and H. Shinshi.

Genomewide analysis of the ERF gene family in Arabidopsis and rice.

Plant Physiology, vol. 140, pages 411-432, 2006. 20, 22

264

Page 34: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Navabpour et al. 2003] S. Navabpour, K. Morris, R. Allen, E. Harrison) S. A­

H-Mackerness and V. Buchanan-Wollaston. Expression of senescence­

enhanced genes in response to oxidative stress. J Exp Bot, vol. 54, pages

2285-2292, 2003. 74

[Neiditch et al. 2005] M. B. Neiditch, M. J. Federle, A. J. Pompeani, S. T. Miller,

D. L. Swem, P. D. Jeffrey, B. L. Bassler and F. M. Hughson. Regulation of

LuxPQ receptor activity by the quorum-sensing signal autoinducer-2. Mol

Cell, vol. 18, pages 507-518, 2005. 114

[Neiditch et al. 2006] M. B. Neiditch, M. J. Federle, A. J. Pompeani) R. C. Kelly,

D. L. Swem) P. D. Jeffrey, B. L. Bassler and F. M. Hughson. Ligand­

induced asymmetry in histidine sensor kinase complex regulates quorum

sensing. Cell, vol. 126, pages 1095-1108, 2006. 114

[Nelson et al. 2004] D. R. Nelson, M. A. Schuler, S. M. Paquette, D. Werck­

Reichhart and S. Bak. Comparative Genomics of Rice and Arabidopsis.

Analysis of 727 Cytochrome P450 Genes and Pseudogenes from a Monocot

and a Dicot. Plant Physiol, vol. 135) page 756772, 2004. 21

[Nielsen 2001] R. Nielsen. Statistical tests of selective neutrality in the age of

genomics. Heredity, vol. 86, pages 641-64 7, 2001. 9

[Nijhawan et al. 2008] A. Nijhawan, M. Jain, A. K. Tyagi and J. P. Khurana.

Genomic survey and gene expression analysis of the basic leucine zipper

transcription factor family in rice. Plant Physiol, vol. 146, pages 333-350,

2008. 57

[Niu et al. 1995] X. Niu, R. A. Bressan, P. M. Hasegawa and J. M. Pardo. Ion

homeostasis in NaCl stress environments. Plant Physiol, vol. 109, pages

735-742, 1995. 89

[Nixon et al. 1986] B. T. Nixon, C. W. Ronson and F. W. Ausubel. Two­

component regulatory systems responsive to environmental stimuli share

strongly conserved domains with the nitrogen assimilation regulatory genes

ntrB and ntrC. Proc N atl Acad Sci, vol. 83, pages 7850-4, 1986. 109

265

Page 35: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Ohtake et al. 2000] Y. Ohtake, T. Takahashi and Y. Komeda. Salicylic acid

induces the expression of a number of receptor-like kinase genes in Ara­

bidopsis thaliana. Plant Cell Physiol, vol. 41, pages 1038~1044, 2000. 37

[Okumura et al. 1991] N. Okumura, N. K. Nishizawa, Y. Umehara and S. Mori.

An iron deficiency-specific eDNA from barley roots having two homologous

cysteine-rich MT domains. Plant Mol Biol, vol. 17, pages 531~533, 1991.

73

[ONeill & Bancroft 2000] C. M. ONeill and I. Bancroft. Comparative physical

mapping of the segments of the genome of Brassica oleracea var. alboglabra

that are homologous to sequenced regions of chromosomes 4 and 5 of Ara­

bidopsis thaliana. Plant J, vol. 23, pages 233~ 243, 2000. 91

[Orengo et al. 1997] C. A. Orengo, A. D. Michie, D. T. Jones, M. B. Swindells

and J. M. Thornton. CATH: A hierarchic classification of protein domain

stmctures. Structure, vol. 5, pages 1093~1108, 1997. 76, 92, 112

[Ouyang & Isaacson 2008] Z. Ouyang and R. Isaacson. Identification of a novel

regulator for the Escherichia coli fit iron transport system. Open Microbio

J, vol. 2, pages 94~99, 2008. 54

[Ouyang et al. 2007] S. Ouyang, Vv. Zhu, J. Hamilton, H. Lin, M. Campbell,

K. Childs, F. T. Nissen, R. L. Malek, Y. Lee, L. Zheng, J. Orvis, B. Haas,

J. vVortman and C. R. Buell. The TIGR Rice genome annotation resource:

Improvements and new features. Nucleic Acids Res, vol. 35, pages D883~

D887, 2007. 27

[Ozturk et al. 2002] Z. N. Ozturk, V. Talame, M. Deyholos, C. B. Michalowski,

D. W. Galbraith, N. Gozukirmizi, R. Thberosa and H. J. Bohnert. Mon­

itoring large-scale changes in transcript abundance in drought- and salt­

stressed barley. Plant Mol Biol, vol. 48, pages 551 ~573, 2002. 26, 37

[Palmiter 1998] R. D. Palmiter. The elusive function of metallothioneins. Proc

Natl Acad Sci, vol. 95, pages 8428~8430, 1998. 73

266

Page 36: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Pappalardo et al. 2003] L. Pappalardo, I. G. Janausch, V. Vijayan, E. Zientz,

J. Junker, W. Peti, M. Zweckstetter, G. Unden and C. Griesinger. The

NMR structure of the sensory domain of the membranous two-component

fumarate sensor (histidine protein kinase) DeuS of Escherichia coli. J Biol

Chern, vol. 278, pages 39185-39188, 2003. 114

[Pareek et al. 1997] A. Pareek, S. L. Singla and A. Grover. Salt responsive pro­

teins/genes in crop plants. Strategies for improving salt tolerance in higher

plants. Science Publishers, USA, 1997. 9

[Pareek et al. 2006] A. Pareek, A. Singh, M. Kumar, H. R. Kushwaha, A. M.

Lynn and S. L. Singla-Pareek. Whole genome analysis of Oryza sativa

L. reveals similar architecture of two-component-signaling machinery with

Arabidopsis. Plant Physiology, vol. 142, pages 380-397, 2006. 10, 21, 45,

109

[Parkinson 1993] J. S. Parkinson. Signal transduction schemes of bacteria. Cell,

vol. 73, pages 857-871, 1993. 107

[Pas et al. 2004] J. Pas, W. Grotthuss, L. S. Wyrwicz, L. Rychlewski and

J. Barciszewski. Structure prediction, evolution and ligand interaction

of CHASE domain. FEBS Letter, vol. 576, pages 287-290, 2004. 114

[Paterson et al. 2004] A. H. Paterson, J. E. Bowers and B. A. Chapman. Ancient

polyploidization predating divergence of the cereals, and its consequences

for comparative genomics. Proc Natl Acad Sci, vol. 101, pages 9903-9908,

2004. 29

[Payton et al. 1996] S. Payton, R. G. Fray, S. Brown and D. Grierson. Ethylene

receptor expression is regulated during fruit ripening, flower senescence

and abscission. Plant Mol Biol, vol. 31, pages 1227-1231, 1996. 109

[Pevsner 2009] J. Pevsner. Bioinformatics and functional genomics. Wiley­

Blackwell, New York, 2009. 16

267

Page 37: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Pham-Thi et al. 1987] A. T. Pham-Thi, C. Borrel-Flood, J. Vieira da Silva,

A. M. Justin and P. Mazliak. Effects of drought on [1-14C}-oleic and

[1-14C)-linoleic acid desaturation in cotton leaves. Physiol Plant, vol. 69,

pages 147-150, 1987. 67

[Phillips et al. 2007] J. R. Phillips, T. Dalmay and D. Bartels. The role of small

RNAs in abiotic stress. FEES Lett., vol. 581, pages 3592-7, 2007. 3

[Ponting 1996] C. P. Ponting. Novel domains in NADPH oxidase subunits, sort­

ing nexins, and Ptdlns 3-kinases: binding partners of SH3 domains? Pro­

tein Sci, vol. 5, pages 2353-2357, 1996. 50

[Posas et al. 1996] F. Posas, S. M. Wurgler-Murphy, T. Maeda, E. A. Witten,

T. C. Thai and H. Saito. Yeast HOGl MAP kinase cascade is regulated

by a multistep phosphorelay mechanism in the SLNl- YPD1-SSK1 "two­

component" osmosensor. Cell, vol. 86, pages 865-875, 1996. 131

[Pruitt et al. 2003] K. D. Pruitt, T. Tatusova and D. R. Maglott. NCB! Reference

Sequence project: update and current status. Nucl Acids Res, vol. 31, pages

34-37, 2003. 75

[Qiu et al. 2002] Q. Qiu, Y. Guo, M. A. Dietrich, K. S. Schumaker and J. K.

Zhu. Regulation of SOSJ, a plasma membrane N+/H+ exchanger in Ara­

bidopsis thaliana, by SOS2 and SOS3. Proc Natl Acad Sci, vol. 99, pages

8436-8441, 2002. 90, 94

[Quan et al. 2007] R. Quan, H. Lin, I. Mendoza, Y. Zhang, W. Cao, Y. Yang,

M. Shang, S. Chen, J. M. Pardo and Y. Guo. SCABP8/CBL10, a pu­

tative calcium sensor, interacts with the protein kinase SOS2 to protect

Arabidopsis shoots from salt stress. Plant Cell, vol. 19, pages 1415-31,

2007. 89

[Quintero et al. 2002] F. J. Quintero, M. Ohta, H. Shi, J. K. Zhu and J. M.

Pardo. Reconstitution of the SOS signaling pathway for Na+ homeostasis

in plants. Proc Natl Acad Sci, vol. 99, pages 9061-9066, 2002. 90

268

Page 38: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Ramamoorthy et al. 2008] R. Ramamoorthy, S. Y. Jiang, N. Kumar, P. N.

Venkatesh and S. Ramachandran. A Comprehensive Transcriptional pro­

filing of the WRKY Gene Family in Rice under various abiotic and Phy­

tohormone treatments. Plant Cell Physiol, vol. 49, pages 865~879, 2008.

22

[Rana et al. 2004] D. Rana, T. van den Boogaart, C. M. ONeill, L. Hynes,

E. Bent, L. Macpherson, Park J. Y, Y. P. Lim and I. Bancroft. Conserva­

tion of the microstructure of genome segments in Brassica napus and its

diploid relatives. Plant J, vol. 40, pages 725~733, 2004. 91

[Rauser 1999] W. E. Rauser. Structure and function of metal chelators produced

by plant: the case for organic acids, amino acids, phytins, and metalloth­

ioneins. Cell Biochem Biophys, vol. 31, pages 19~48, 1999. 73

[Reinelt et al. 2003] S. Reinelt, E. Hofmann, T. Gerharz, M. Bott and D. R.

Madden. The structure of the periplasmic ligand-binding domain of the

sensor kinase CitA reveals the first extracellular PAS domain. J Biol

Chem, vol. 278, pages 39189~39196, 2003. 114

[Ren et al. 2005] Z. H. Ren, J. P. Gao, L. G. Li, X. L. Cai, W. Huang, D. Y.

Chao, M. Z. Zlm, Z. Y. Wang, S. Luan and H. X. Lin. A rice quantitative

trait locus for salt tolerance encodes a sodium transporter. Nat Genet,

vol. 37, pages 1141~1146, 2005. 37

[Reymond et al. 2000] P. Reymond, H. Weber, M. Damond and E. E. Farmer.

Differential gene expression in response to mechanical wounding and insect

feeding in Arabidopsis. Plant Cell, vol. 12, pages 707~719, 2000. 66

[Ribaut et al. 1996] J. M. Ribaut, D. A. Hosington, J. A. Deitsch, C. Jiang and

D. Gonzalez de Leon. Identification of quantitative trait loci under drought

conditions in tropical maize. 1. Flowering parameters and the anthesis­

silking interval. Theor Appl Genet, vol. 92, pages 905~914, 1996. 3

[Rice et al. 2000] P. Rice, I. Longden and A. Bleasby. EMBOSS: The European

Molecular Biology Open Software Suite. Trends in Genetics, vol. 16, pages

276~277, 2000. 75, 76, 80

269

Page 39: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Robinson et al. 2000] V. L. Robinson, D. R. Buckler and A. M. Stock. A tale of

two components: a novel kinase and a regulatory switch. Nature Structural

Biology, vol. 7, pages 626-633: 2000. 129, 130

[Rodrigue et al. 2000] A. Rodrigue, Y. Quentin, A. Lazdunski, V. Mejean and

M. Foglino. Two-component systems in Pseudomonas aeruginosa: why so

many? Trends Microbiol, vol. 8, pages 498-504, 2000. 107

[Ronald & Leung 2002] P. Ronald and H. Leung. THE RICE GENOME: The

Most Precious Things Are Not Jade and Pearls ... Science, vol. 296, pages

58-59, 2002. 3

[Ronson et al. 1987] C. W. Ronson, B. T. Nixon and F. M. Ausubel. Conserved

domains in bacterial regulatory proteins that respond to environmental

stimuli. Cell, vol. 49, pages 579-81, 1987. 109

[Roth et al. 2007] C. Roth, S. Rastogi, L. Arvestad, K. Dittmar, S. Light, D. Ek­

man and D. A. Liberles. Evolution after gene duplication: models, mech­

anisms, sequences, systems and organisms. J Exp Zool, vol. 306B, pages

58-73, 2007. 91

[Ruepp et al. 2004] A. Ruepp, A. Zollner, M. Dieter, K. Albermann, .J. Hani,

M. Mokrejs, I. Tetko, U. Guldener, G. Mannhaupt, M. Munssterkotter

and et al. The FunCat, a functional annotation scheme for systematic

classification of proteins from whole genomes. Nucleic Acids Res, vol. 32,

pages 5539-5545, 2004. 30

[Russell & Barton 1992] R. B. Russell and G . .J. Barton. Multiple sequence aligne­

ment from tertiary structure comparison: assignment of global and residue

confidence levels. Proteins: Struct Funct Genet, vol. 14, pages 309-323,

1992. 76, 92, 112

[Sachez-Barrena et al. 2005] M. J. Sachez-Barrena, M. M. Ripoll, J. K. Zhu and

A. Albert. The structure of the Arabidopsis thaliana SOS3: molecular

mechanism of sensing calcium for salt stress response. J Mol Biol, vol. 345,

pages 1253-1264, 2005. 100, 101, 102, 103

270

Page 40: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Sadowski & Quiros 1998] J. Sadowski and C. F. Quiros. Organization of an

Arabidopsis thaliana gene cluster on chromosome 4 including the RPS2

gene in the Brassica nigra genome. Theor Appl Genet, vol. 96, pages

468-474, 1998. 8

[Sagerstrom et al. 1997] C. G. Sagerstrom, B. I. Sun and H. L. Sive. Subtractive

cloning: Past, present q,nd future. Ann Rev Biochem, vol. 66, pages 751-

783, 1997. 26

[Saha et al. 2007] D. Saha, A. M. Prasad and R. Srinivasan. Pentatricopeptide

repeat proteins and their emerging roles in plants. Plant Physiol Biochem,

vol. 45, pages 521-534, 2007. 55

[Sahi et al. 2003] C. Sahi, M. Agarwal, M. K. Reddy, S. K. Sopory and A. Grover.

Isolation and expression analysis of salt stress-associated ESTs from con­

trasting rice cultivars using a PCR-based subtraction method. Theor Appl

Genet, vol. 106, pages 620-628, 2003. 26

[Sahi et al. 2006] C. Sahi, A. Singh, K. Kumar, E. Blumwald and A. Grover.

Salt stress response in rice: genetics, molecular biology, and comparative

genomics. Funct Integr Genomics, vol. 6, pages 263-284, 2006. 10, 24, 36

[Sahsah et al. 1998] Y. Sahsah, P. Campos, M. Gareil, Y. Zuily-Fodil and A. T.

Pham-Thi. Enzymatic degradation of polar lipids in Vigna unguiculata

leaves and influence of drought stress. Physiol Plant, vol. 104, pages 577-

586, 1998. 67

[Saitou & Nei 1987] N. Saitou and M Nei. The neighbour-joining method: A new

method for reconstructing phylogeneic trees. Mol Biol Evol, vol. 4, pages

406-425, 1987. 19

[Sakakibara et al. 1998] H. Sakakibara, M. Suzuki, K. Takei, A. Deji,

M. Taniguchi and T. Sugiyama. A response-regulator homolog possibly

involved in nitrogen signal transduction mediated by cytokinin in maize.

Plant J, vol. 14, pages 337-344, 1998. 109

271

Page 41: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Sakakibara et al. 1999] H. Sakakibara, A. Hayakawa ad A. Deji, S. Gawronski

and T. Sugiyama. His-Asp phosphotransfer possibly involved in a nitrogen

signal transduction mediated by cytokinin in maize: molecular cloning of

cDNAs for two-component regulatory factors and demonstration of phos­

photransfer activity in vitro. Plant Mol Biol, vol. 41, pages 563-573, 1999.

109, 134

[Sali & Blundell 1993] A. Sali and T. L. Blundell. Comparative protein modeling

by satisfaction of spatial restraints. J Mol Biol, vol. 234, pages 779-815,

1993. 76, 93, 112

[Sampedro et al. 2006] J. Sampedro, R. E. Carey and D. J. Cosgrove. Genome

histories clarify evolution of the expansin superfamily: new insights from

the poplar genome and pine ESTs. J Plant Res, vol. 119, pages 11-21,

2006. 21

[Sanchez & Singh 2002] L. 0. Sanchez and K. B. Singh. Identification of Ara­

bidopsis ethylene-responsive element binding factors with distinct induc­

tion kinetics after pathogen infection. Plant Physiology, vol. 128, pages

1313-1322, 2002. 22

[Sanchez-Barrena et al. 2007] M. J. Sanchez-Barrena, H. Fujii, I. Angulo,

M. Martinez-Ripoll, J. K. Zhu and A. Albert. The structure of the C­

terminal domain of the protein kinase AtSOS2 bound to the calcium sensor

AtSOS3. Mol Cell, vol. 26, pages 427-35, 2007. 94

[Sasaki & Sederoff 2003] T. Sasaki and R. R. Sederoff. Genome studies and

molecular genetics The rice genome and comparative genomics of higher

plants. Cur Opi Plant Biol, vol. 6, pages 97-100, 2003. 9

[Sasaki 2006] T. Sasaki. The complete Rice genome sequence: A gold mine for

innovation in rice research. Sci tech Trade Peace Pros, IRRI, vol. 94,

pages 103-110, 2006. 8

[Schaad et al. 1996] N. C. Schaad, E. De Castro, S. Nef, S. Hegi, R. Hinrichsen,

M. E. Martone, M. H. Ellisman, R. Sikkink, F. Rusnak, J. Sygush and

272

Page 42: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

P. Nef. Direct modulation of calmodulin targets by the neuronal calcium

sensor NCSJ. Proc Natl Acad Sci, vol. 93, pages 9253-9258, 1996. 100

[Schell et al. 1994] M. A. Schell, T. P. Denny and J. Huang. VsrA, a sec­

ond two component sensor regulating virulence genes of Pseudomonas

solanacearum. Mol Microbial, vol. 1L pages 489-500, 1994. 114

[Schena et al. 1995] M. Schena, D. Shalon, R. W. Davis and P. 0. Brown. Quanti­

tative monitoring of gene expression patterns with a complementary DNA

microarray. Science, vol. 270, pages 467-470, 1995. 7

[Schmidt et al. 2001] R. Schmidt, A. Acarkan and K. Boivin. Comparative struc­

tural genomics in the Brassicaceae family. Plant Phys Biochem, vol. 39,

pages 253-262, 200L 90

[Schneider-poetsch et al. 1991] H. A. Schneider-poetsch, B. Braun B, S. Marx

and A. Schaumburg. Phytochromes and bacterial sensor proteins are re­

lated by structural and functional homologies. Hypotheses on phytochrome­

mediated signal-transduction. FEES Lett., vol. 281, pages 245-249, 199L

109

[Schroeder et al. 2001] .J. I. Schroeder, J. M. Kwak and G . .J. Allen. Guard cell

abscisic acid signalling and engineering drought hardiness in plants. Na­

ture, vol. 410, pages 327-330, 2001. 3

[Schwappach et al. 1998] B. Schwappach, S. Stobrawa, M. Hechenberger,

K. Steinmeyer and T. J. Jentsch. Golgi localization and functionally im­

portant domain in the NH2 and GOGH terminus of the yeast CLC putative

chloride channels Geflp. J Biol Chem, vol. 273, pages 1511G-15118, 1998.

54

[Scott et al. 2004] .J. W. Scott, S. A. Hawley, K. A. Green, M. Anis, G. Stewart,

G. A. Scullion, D. G. Norman and D. G. Hardie. CBS domains form

energy-sensing modules whose binding of adenosine ligands is disrupted

by disease mutations . .J Clin Invest, vol. 113, pages 274-284, 2004. 55

273

Page 43: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Seki et al. 2002] M. Seki, M. Narusaka, J. Ishida, T. Nanjo, M. Fujita, Y. Oono,

A. Kamiya, M. Nakajima, A. Enju, T. Sakurai and et al. Monitoring

the expression profiles of 'l, 000 Arabidopsis genes under drought, cold and

high-salinity stresses using a full-length eDNA microarray. Plant J, vol. 31,

pages 279~292, 2002. 26

[Senadheera et al. 2009] P. Senadheera, R. K. Singh and F. J. M. Maathuis. Dif­

ferentially expressed membrane transporters in rice roots may contribute

to cultivar dependent salt tolerance. J Exp Bot, vol. 60, pages 2553~2563,

2009. 24, 25

[Serrano et al. 1999] R. Serrano, J. Mulet, G. Rios, J. Marquez, I. de Larrinoa,

M. Leube, I. Mendizabal, A. Pascual-Ahuir, M. Proft, R. Ros and C. Mon­

tesinos. A glimpse of the mechanisms of ion homeostasis during salt stress.

J Exp Bot, vol. 50, pages 1023~ 1036, 1999. 3

[Shaulsky et al. 1996] G. Shaulsky, R. Escalante and W. F. Loomis. Developmen­

tal signal transduction pathways uncovered by genetic suppressors. Proc

Natl Acad Sci, vol. 93, pages 15260-15265, 1996. 107

[Shaulsky et al. 1998] G. Shaulsky, D. Fuller and W. F. Loomis. A cAMP­

phosphodiesterase controls P KA -dependent differentiation. Development,

vol. 125, pages 691-699, 1998. 107

[Shi et al. 2000] H. Shi, M. Ishitani, C. Kim and J. K. Zhu. The Arabidopsis

thaliana salt tolerance gene SOSJ encodes a putative Na+/H+ antiporter.

Proc Natl Acad Sci, vol. 97, pages 6896~6901, 2000. 89, 90, 143

[Shi et al. 2001] J. Shi, T. L. Blundell and K. Mizuguchi. FUGUE:sequence­

structure homology recognition using environment-specific substitution ta­

bles and structure-dependent gap penalties. J Mol Biol, vol. 310, pages

243-257, 2001. 76, 92, 112

[Shi et al. 2002] H. Shi, F. J. Quintero, J. M. Pardo and J. K. Zhu. The putative

plasma membrane Na( + )/H( +) antiporter SOSJ controls long-distance

Na( +) transport in plants. Plant Cell, vol. 14, pages 465~4 77, 2002. 90

274

Page 44: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Shieh et al. 1997] J. C. Shieh, M. G. Wilkinson, V. Buck, B. A. Morgan,

K. Makino and J. B. Millar. The Mcs4 response regulator coordinately

controls the stress-activated Wakl- Wis1-Sty1 MAP kinase pathway and

fission yeast cell cycle. Genes Dev, vol. 11, pages 1008-1022, 1997. 107

[Simillion et al. 2002] C. Simillion, K. Vandepoele, M. C. Van Montagu,

M. Zabeau and Y. Van de Peer. The hidden duplication past of Ara­

bidopsis thaliana. Proc Natl Acad Sci, vol. 99, pages 13627-13632, 2002.

57

[Simillion et al. 2004] C. Simillion, K. Vandepoele, Y. Saeys and Y. VandePeer.

Building genomic profiles for uncovering segmental homology in the twi­

light zone. Genome Res, vol. 14, pages 1095-1106, 2004. 29

[Singh et al. 2008] A. Singh, H. R. Kushwaha and P. Sharma. Molecular mod­

elling and comparative structural account of aspartyl beta-semialdehyde de­

hydrogenase of Mycobacterium tuberculosis (H37Rv). J mol model, vol. 14,

pages 249-63, 2008. 113

[Sintchak et al. 1996] M. D. Sintchak, M. A. Fleming, 0. Futer, S. A. Raybuck,

S. P. Chambers, P. R. Caron and et al. Structure and mechanism of

inosine monophosphate dehydrogenase in complex with the immunosup­

pressent mycophenolic acid. Cell, vol. 85, pages 921-930, 1996. 53

[Sippi 1993] M. J. Sippi. Recognition of errors in three-dimensional structures of

proteins. Proteins, vol. 17, pages 355-362, 1993. 77, 93, 113

[Sivakumar et al. 1998] P. Sivakumar, P. Sharmila and P. P. Saradhi. Proline

suppresses Rubisco activity in higher plants. Biochem Biophys Res Com­

mun, vol. 252, pages 428-432, 1998. 9

[Small & Peeters 2000] I. D. Small and I. Peeters. The PPR motif - a TPR­

related motif prevalent in plant organellar proteins. Trends Biochem Sci,

vol. 25, pages 45-47, 2000. 50

[Smirnoff 1998] N Smirnoff. Plant resistance to environmental stress. Curr Opin

Plant Biol, vol. 9, pages 214-219, 1998. 3

275

Page 45: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Song et al. 1998] H. K. Song, J. Y. Lee, L. G. Lee, J. Moon, K. Min, J. K.

Yang and S. W. Suh. Insights into eukaryotic multistep phosphorelay

signal transduction revealed by the crystal structure of Ypdlp from Sac­

charomyces cerevisiae. J Mol Biol, vol. 293, pages 753~ 761, 1998. 132,

134

[Song et al. 2004] Y. Song, D. Peisach, A. A. Pioszak, Z. Xu and A. J. Ninfa.

Crystal structure of the C-terminal domain of the two-component system

transmitter protein nitrogen regulator II (NRII; NtrB), regulator of nitro­

gen assimilation in Escherichia coli. Biochemistry, vol. 43, pages 6670~

6678, 2004. 120

[Sottosanto et al. 2004] J. B. Sottosanto, A. Gelli and E. Blumwald. DNA array

analyses of Arabidopsis thaliana lacking a vacuolar Na+/H+ antiporter:

impact of AtNHX1 on gene expression. Plant J, vol. 40, pages 752~771,

2004. 30

[Sreenivasulu et al. 2007] N. Sreenivasulu, S. K. Sopory and P. B. Kavikishor.

Deciphering the regulatory mechanisms of abiotic stress tolerance in plants

by genomic approaches. Gene, vol. 388, pages 1 ~ 13, 2007. vii, 3, 24

[Stock et al. 1988] A. Stock, T. Chen, D. Welsh and J. Stock. CheA protein, a

central regulator of bacterial chemotaxis, belongs to a family of proteins

that control gene expression in response to changing environmental condi­

tions. Proc Natl Acad Sci, vol. 85, pages 1403~1407, 1988. 109, 110

[Stock et al. 1989] C. E. Stock, J. M. Mottonen, J. B. Stock and C. E. Schutt.

Three-dimensional structure of Che Y, the response regulator of bacterial

chemotaxis. Nature, vol. 337, pages 745~749, 1989. 110

[Stock et al. 1995] J. B. Stock, M. G. Surette, M. Levitt and P. Park. Two­

component signal transduction systems: structure-function relationships

and mechanism of catalysis. Two-component signal transduction. ASM

Press, \iVashington D.C, 1995. 107, 110

276

Page 46: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Stock et al. 2000] A. M. Stock, V. L. Robinson and P. N. Goudreau. Two­

component signal transduction. Annu Rev Biochem, vol. 69, pages 183-

215, 2000. 106, 107, 135

[Sumimoto et al. 2007] H. Sumimoto, S. Kamakura and T. Ito. Structure and

function of the P B 1 domain, a protein interaction module conserved in

animals, fungi, amoebas, and plants. Science, vol. 401, page re6, 2007. 56

[Suzuki et al. 1998] T. Suzuki, A. Imamura, C. Ueguchi and T. Mizuno.

Histidine-containing phosphotransfer (HPt) signal transducers implicated

in His-to-Asp phosphorelay in Arabidopsis. Plant Cell Physiol, vol. 39,

pages 1258-1268, 1998. 111

[Taji et al. 2004] T. Taji, M. Seki, M. Satou, T. Sakurai, M. Kobayashi,

K. Ishiyama, Y. Narusaka, M. Narusaka, J. K. Zhu and K. Shi­

nozaki. Comparative genomics in salt tolerance between Arabidopsis

and Arabidopsis-related halophyte salt cress using Arabidopsis microarray.

Plant Physiol, vol. 135, page 16971709, 2004. 25

[Tarchini et al. 2004] R. Tarchini, P. Biddle, R. Wineland, S. Tingey and

A. Rafalski. The complete sequence of 340 kb of DNA around the rice

Adh1Adh2 region reveals interrupted collinearity with maize chromosome

4. Proc 4th Int Crop Sci Cong, 2004. 8

[Teplyakov et al. 1998] A. Teplyakov, G. Obmolova, M. A. Badet-Denisot,

B. Badet and I. Polikarpov. Involvement of the C terminus in intramolec­

ular nitrogen channeling in glucosamine 6-phosphate synthase: evidence

from a 1. 6 A crystal structure of the isomerase domain. Structure, vol. 6,

pages 1047-1055, 1998. 50

[ter Huurne et al. 1994] A. A. ter Huurne, S. Muir, M. van Houten, B. A. van der

Zeijst, W. Gaastra and J. G. Kusters. Characterization of three putative

Serpulina hyodysenteriae hemolysins. Micro Patho, vol. 16, pages 269-282,

1994. 50

277

Page 47: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Thomason & Kay 2000] P. Thomason and R. Kay. Eukaryotic signal transduc­

tion via histidine-aspartate phosphorelay. J Cell Sci, vol. 113, pages 3141-

3150, 2000. 109

[Thomason et al. 1998] P. A. Thomason, D. Traynor, G. Cavet, Vv. T. Chang,

A. J. Harwood and R. R. Kay. An intersection of the cAMP /PKA and

two-component signal transduction systems in Dictyostelium. EMBO J,

vol. 17, pages 2838-45, 1998. 107

[Tommassen et al. 1982] J. Tommassen, P. de Geus, B. Lugtenberg, J. Hackett

and P. Reeves. Regulation of the pho regulon of Escherichia coli K-12.

Cloning of the regulatory genes phoB and phoR and identification of their

gene products. J Mol Biol, vol. 157, pages 265-274, 1982. 109

[Tomomori1 et al. 1999] C. Tomomori1, T. Toshiyuki, R. Dutta, H. Park, S. K.

Saha, Y. Zhu, R. Ishima, D. Liu, K. I. Tong, H. Kurokawa, H. Qian, M. In­

ouye and M. Ikura. Solution structure of the homodimeric core domain of

Escherichia coli histidine kinase EnvZ. Nature Struct Biol, vol. 6, pages

729-734, 1999. 109, 120

[Towler et al. 1988] D. A. Towler, S. P. Adams, S. R. Eubanks, D. S. Towery,

E. Jackson-Machelski, L. Glaser and J. I. Gordon. MyristoylCoA:protein

N-myristoylation activities from rat liver and yeast possess overlapping

yet distinct peptide substrate specificities. J Biol Chern, vol. 263, pages

1784-1790, 1988. 96

[Tramontano 1998] A. Tramontano. Homology modeling with low sequence iden­

tity. Methods, vol. 14, pages 293-300, 1998. 84, 98

[Tsuzuki et al. 1995] M. Tsuzuki, K. Ishige and T. Mizuno. Phosphotransfer cir­

cuitry of the putative multi-signal transducer, ArcB, of Escherichia coli:

in vitro studies with mutants. Mol Microbial, vol. 18, pages 953-962, 1995.

131

278

Page 48: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Tyagi et al. 1999] A. K. Tyagi, A. Mohanty, S. Bajaj, A. Choudhary and S. C.

Maheshwari. Transgenic rice: A valuable monocot system for crop im­

provement and gene research. Crit Rev Biotechnol, vol. 19, pages 41-70,

1999. 8

[Ueda et al. 2006] A. Ueda, A. Kathiresan, J. Bennet and T. Takabe. Compar­

ative transcriptome analyses of barley and rice under salt stress. Theor

Appl Genet, vol. 112, pages 1286-1294, 2006. 25

[Urao et al. 1999] T. Urao, B. Yakubov, R. Satoh, K. Yamaguchi-Shinozaki,

M. Seki, T. Hirayama and K. Shinozaki. A transmembrane hybrid-type

histidine kinase in Arabidopsis functions as an osmosensor. Plant Cell,

vol. 11, page 17431754, 1999. viii, 109, 111, 144

[van Hoof et al. 2001] N. A. van Hoof, V. H. Hassinen, H. W. Hakvoort, K. F.

Ballintijn, H. Schat, J. A. Verkleij, W. H. Ernst, S. 0. Karenlampi and

A. I. Tervahauta. Enhanced copper tolerance in Silene vulgaris (Moench)

Garcke populations from copper mines is associated with increased tran­

script levels of a 2b-type metallothionein gene. Plant Physiol, vol. 126,

pages 1519-1526, 2001. 73, 79

[Vandepoele et al. 2003] K. Vandepoele, C. Simillion and Y. VandePeer. Evi­

dence that rice and other cereals are ancient aneuploids. Plant Cell, vol. 15,

pages 2192-2202, 2003. 29, 30, 142

[Varshney & Tuberosa 2007] R. K. Varshney and R. Tuberosa, editeurs.

Genomics-assisted crop improvement, volume 1 of Genome approaches

and platforms. Springer-Verlag, New York, 2007. 141

[Varughese et al. 1998] K. I. Varughese, Madhusudan, X. Z. Zhou, J. M. White­

ley and J. A. Hoch. Formation of a Novel Four-Helix Bundle and Molec­

ular Recognition Sites by Dimerization of a Response Regulator Phospho­

transferase. Mol Cell, vol. 2, pages 485-93, 1998. 132

[Verdino et al. 2002] P. Verdino, K. Westritschnig, R. Valenta and VI. Keller.

The cross-reactive calcium-binding pollen allergen, Phl p 7, reveals a novel

dimer assembly. EMBO, vol. 21, pages 5007-5016, 2002. 100

279

Page 49: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Vij & Tyagi 2007] S. Vij and A. K. Tyagi. Emerging trends in functional ge­

nomics of abiotic response in crop plants. Plant Biotech J, vol. 5, pages

361-380, 2007. 24

[Vinocur & Altman 2005] B. Vinocur and A. Altman. Recent advances in en­

gineering plant tolerance to abiotic stress: achievements and limitations.

Curr Opin Biotechnol, vol. 16, pages 123-32, 2005. 3

[Vision et al. 2000] T. Vision, D. G. Brown and S. D. Tanksley. The origins of

genomic duplications in Arabidopsis. Science, vol. 290, pages 2114-2116,

2000. 8, 57

[Volkman et al. 1995] B. F. Volkman, M . .J. Nohaile, N. K. Amy, S. Kustu and

D. E. Wemmer. Three dimensional solution structure of the N-terminal

receiver domain of NtrC. Biochemistry, vol. 34, pages 1413-1424, 1995.

129

[Volz 1993] K. Volz. Structural conservation in the Che Y superfamily. Biochem­

istry, vol. 32, pages 11741-11753, 1993. 109

[Vriezen et al. 1997] W. H. Vriezen, C. P. E. Rijn, L. A. C. J. Voesenek and

C. Mariani. A homolog of the Arabidopsis thaliana ERS gene is actively

regulated 1;n Rumex palustris upon flooding. Plant J, vol. 11, pages 1265-

1271, 1997. 109

[Walia et al. 2005] H. Walia, C. Wilson, P. Condamine, X. Liu, A. M. Ismail,

L. Zeng, S. I. Wanamaker, J. Mandal, J. Xu, X. Cui and T. J. Close. Com­

parative transcriptional profiling of two contrasting rice genotypes under

salinity stress during the vegetative growth stage. Plant physiol, vol. 139,

pages 822-835, 2005. vii, 24, 25

[Wang et al. 2000] P. \iVang, K. D. Liu and Q. F. Zhang. Segmental duplications

are common in rice genome. Acta Bot Sin, vol. 42, pages 1150-1155, 2000.

29

280

Page 50: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[\iVang et al. 2003] W. Wang, B. Vinocur and A. Altman. Plant responses to

drought, salinity and extreme temperatures: towards genetic engineering

for stress tolerance. Planta, vol. 218, pages 1 ~ 14, 2003. 3

[\iVang et al. 2005] X. Wang, X. Shi, B. Hao, S. Ge and J. Luo. Duplication and

DNA segmental loss in the rice genome: implications for diploidization.

New Phytol, vol. 165, pages 937~946, 2005. 29, 58, 59

[Waterhouse et al. 2009] A. M. Waterhouse, J. B. Procter, D. M. A. Martin,

M. Clamp and G. J. Barton. Jalview version 2-multiple sequence alignment

editor and analysis workbench. Bioinformatics, vol. 25, pages 1189-1191,

2009. 76, 92

[Wei et al. 2009] W. Wei, J. Huang, H-F Zou Y-J Hao, H-W \iVang, J-Y Zhao,

X-Y Liu, W-K Zhang, B. Ma, J-S Zhang and S-Y Chen. Soybean GmPHD­

Type Transcription regulators improve stress tolerance in transgenic A ra­

bidopsis plants. PLoS ONE, vol. 4, page e7209, 2009. 3

[Weiderstaein & Sippl 2007] M. Weiderstaein and M. J. Sippl. ?roSA-web: inter­

active web service for the recognition of errors in three-dimensional struc­

tures of proteins. Nucl Acids Res, vol. 35, pages W407-W410, 2007. 77,

93, 113

[vVise & Pring 2002] R. P. \iVise and D. R. Pring. Nuclear-mediated mitochondrial

gene regulation and male fertility in higher plants: Light at the end of the

tunnel? Proc Natl Acad Sci, vol. 99, pages 10240-10242, 2002. 5.5

[Wolanin et al. 2002] P. M. Wolanin, P. A. Thomason and J. B. Stock. Histi­

dine protein kinases: key signal transducers outside the animal kingdom.

Genome Biol, vol. 3, page 301, 2002. 108

[Wong et al. 2004] H. L. Wong, T. Sakamoto, T. Kawasaki, K. Umemura and

K. Shimamoto. Down-regnlation of metallothionein, a reactive oxygen

scavenger, by the small GTPase OsRacl in rice. Plant Physiol, vol. 135,

pages 1447-1456, 2004. 74

281

Page 51: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Wong et al. 2006] C. E. Wong, Y. Li, A. Labbe, D. Guevara, P. Nuin, B. Whitty,

C. Diaz, G. B. Golding, G. R. Gray, E. A. Weretilnyk and et al. Transcrip­

tional profiling implicates novel interactions between abiotic stress and hor­

monal responses in Thellungiella, a close relative of Arabidopsis. Plant

Physiol, vol. 140, pages 1437-1450, 2006. 36

[Wu et al. 1996] S. J. Wu, L. Diong and J. K. Zhu. SOS1, a genetic locus essential

for salt tolerance and potassium acquisition. Plant Cell, vol. 8, pages 617-

627, 1996. 90

[Wu et al. 1998] J. Wu, N. Kurata, H. Tanoue, T. Shimokawa, Y. Umehara,

M. Yano and T. Sasaki. Physical mapping of duplicated genomic regions of

two chromosome ends in rice. Genetics, vol. 150, pages 1595-1603, 1998.

29

[Xie et al. 2000] J. H. Xie, F. J. Zapata-Arias, M. Sherr and R. Afza. Salinity tol­

erant performance and genetic diversity of four rice varieties. Euphytica,

vol. 116, pages 105-110, 2000. 24

[Xiong et al. 2002] L. Xiong, H. Lee, M. Ishitani and J. K. Zhu. Regulation of

Osmotic Stress-responsive Gene Expression by the LOS6/ ABA1 Locus in

Arabidopsis . .J Biol Chern, vol. 277, pages 8588-8596, 2002. 67

[Xu & West 1999] Q. Xu and A. H. West. Conservation of structure and function

among histidine-containing phosphotransfer (HPt) domains as revealed by

the crystal structure of YP D 1. .J Mol Biol, vol. 292, pages 1039-1050,

1999. 132, 133, 134, 135, 136

[Xu et al. 1996] D. Xu, X. Duan, B. Wang, B. Hong, T. H. D. Ho and R. Wu.

Rrpression of a late embryogenesis abundant protein gene, HVA1, from

',, barley confers tolerance to water deficit and salt stress in transgenic rice.

Plant Physiol, vol. 110, pages 249-257, 1996. 24

[Yamaguchi & Blumwald 2005] T. Yamaguchi and E. Blumwald. Developing salt­

tolerant crop plants: challenges and opportunities. Trends Plant Sci,

vol. 10, pages 615-20, 2005. 3

282

Page 52: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Yamaguchi-Shinozaki & Shinozaki 2006] K. Yamaguchi-Shinozaki and K. Shi­

nozaki. Transcriptional regulatory networks in cellular responses and tol­

erance to dehydration and cold stresses. Annu Rev Plant Biol, vol. 57,

pages 781-803, 2006. 3

[Yang &.Inouye 1993] Y. Yang and M. Inouye. Requirement of both kinase and

phosphatase activities of an Escherichia coli receptor (Tazl) for ligand­

dependent signal transduction. J Mol Biol, vol. 231, pages 335-342, 1993.

124

[Yang et al. 2008] Z. Yang, X. \i\Tang, S. Gu, Z. Hu, H. Xu and C. Xu. Compara­

tive study of SBP-box gene family in Arabidopsis and rice. Gene, vol. 407,

pages 1-11, 2008. 20

[Yeh & Lagarias 1998] K. C. Yeh and J. C. Lagarias. Eukaryotic phytochromes:

light-regulated serine/threonine protein kinases with histidine kinase an­

cestry. Proc Natl Acad Sci, vol. 95, pages 13976-13981, 1998. 109

[Yen et al. 1995] H. C. Yen, S. Lee, S. D. Tanksley, M. B. Lanahan, H. J. Klee

and J. J. Giovannoni. The tomato Never-ripe locus regulates ethylene­

inducible gene expression and is linked to a homolog of the Arabidopsis

ETRJ gene. Plant Physiol, vol. 107, pages 1343-53, 1995. 110

[Yeo et al. 1985] A. R. Yeo, S. J. M. Caporn and T. J. Flowers. The efj'ect of

salinity upon photosynthesis in rice (Oryza sativa L.): gas exchange by

individual leaves in relation to their salt content. J Exp Bot, vol. 36,

pages 1240-1248: 1985. 8, 9

[Yokoi et al. 2002] S. Yokoi, R. A. Bressan and P. M. Hasegawa. Stress Tolerance

of Plants. JIRCAS \i\Torking Report, pages 25-33, 2002. 10

[Yu et al. 2002] Jun Yu, Songnian Hu, Jun Wang, Cane Ka-Shu Wong, Songgang

Li, Bin Liu, Yajun Deng, Li Dai, Yan Zhou, Xiuqing Zhang, Mengliang

Cao, Jing Liu, Jiandong Sun, Jiabin Tang and et al. A draft sequence of

the rice genome (Oryza sativa L. ssp. indica). Science, vol. 296, pages

79-92, 2002. vi, 3, 10

283

Page 53: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Yuan et al. 2005] Q. Yuan, S. Ouyang, A. Wang, W. Zhu, R. Maiti, H. Lin,

J. Hamilton, B. Haas, R. Sultana, F. Cheung, J. Wortman and C. R.

Buell. The Institute of genomic research Osal rice genome annotation

database. Plant physiology, vol. 138, pages 18-26, 2005. 27

[Yuan et al. 2007] J. S. Yuan, X. Yang, J. Lai, H. Lin, Z-M. Cheng, H. Nonogaki

and F. Chen. The Endo-;3-Mannanase gene families in Arabidopsis, rice,

and poplar. Funct Integr Genomics, vol. 7, pages 1-16, 2007. 22

[Yuan et al. 2008] J. Yuan, D. Chen, Y. Ren, X. Zhang and J. Zhao. Char­

acteristic and Expression Analysis of a Metallothionein Gene, OsMT2b,

Down-Regulated by Cytokinin Suggests Functions in Root Development

and Seed Embryo Germination of Rice. Plant Physiol, vol. 146, pages

1637-50, 2008. 74

[Zhang et al. 1995] M. Zhang, T. Tanaka and M. Ikura. Calcium induced confor­

mational transition revealed by the solution structure of apo calmodulin.

Nature Struct Biol, vol. 2, pages 758-767, 1995. 100, 103

[Zhang et al. 1996] J. Zhang, A. L. George, R. C. Griggs, G. T. Fouad,

J. Roberts, H. Kwiecinski, A. M. Connolly and L . .J. Ptacek. Mutations

in the human skeletal muscle chloride channel gene (CLCNJ) associated

with dominant and recessive myotonia congenita. Neurology, vol. 4 7, pages

993-998, 1996. 50

[Zhang et al. 2001] H. Zhang, N. Sreenivasulu, W. Weschke, N. Stein, S. Rudd,

V. Radchuk, E. Potokina, U. Scholz, P. Schweizer, U. Zierold, P. Lan­

gridge, R. K. Varshney, U. Wobus and A. Graner. Large-scale analysis of

the barley transcriptome based on expressed sequence tags. Plant .J, vol. 40,

pages 276-290, 2001. 141

[Zhang et al. 2002] L. Zhang, T . .J. Vision and B.S. Gaut. Patterns of nucleotide

substitution among simultaneously duplicated gene pairs in Arabidopsis

thaliana. Mol Biol Evol, vol. 19, pages 1464-1473, 2002. 58

284

Page 54: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Zhou & Dalquihst 1997] H. Zhou and F. W. Dalquihst. Phosphotransfer site of

the chemotaxis-specific protein kinase CheA as revealed by NMR. Bio­

chemistry, vol. 36, pages 699-710, 1997. 109

[Zhou & Goldsbrough 1994] J. Zhou and P. B. Goldsbrough. Functional ho­

mologs of animal and fungal metallothionein genes from Arabidopsis.

Plant Cell, vol. 6, pages 875-884, 1994. 73, 74

[Zhou & Goldsbrough 1995] J. Zhou and P. B. Goldsbrough. Structure, organz­

zation and expression of metallothionein gene family in Arabidopsis. Mol

Gen Genet, vol. 248, pages 318-328, 1995. 73, 74

[Zhou et al. 1995a] G. Zhou, Z. Q. Bao and J. E. Dixon. Components of a new

human protein kinase signal transduction pathway. J Biol Chem, vol. 270,

pages 12665-12669, 1995. 50

[Zhou et al. 1995b] H. Zhou, D. F. Lowry, R. V. Swanson, M. I. Simon and F. W.

Dahlquist. Phosphotransfer and Che Y-Binding Domains of the Histidine

Autokinase CheA Are Joined by a Flexible Linker. Biochemistry, vol. 34,

pages 13858-70, 1995. 132

[Zhou et al. 2005] G. K. Zhou, Y. F. Xu and J. Y. Liu. Characterization of a rice

class II metallothionein gene: tissue expression patterns and induction in

response to abiotic factors. J Plant Physiol, vol. 162, pages 686-696, 2005.

74

[Zhou et al. 2006] G. Zhou, Y. Xu, J. Li, L. Yang and J. Y. Liu. Molecular

analyses of the metallothionein gene family in rice (Oryza sativa L.). J

Biochem Mol Biol, vol. 39, pages 595-606, 2006. 75

[Zhou et al. 2007] J. Zhou, X. Wang, Y. Jiao, Y. Qin, X. Liu, K. He, C. Chen,

L. Ma and J. Wang. Global genome expression analysis of rice in response

to drought and high-salinity stresses in shoot, flag leaf and panicle. Plant

Mol Biol, vol. 63, pages 591-608, 2007. 25

285

Page 55: References - Shodhgangashodhganga.inflibnet.ac.in/.../19493/17/16_references.pdf · 2018-07-09 · References [AGI 2000] AGI. Analysis of the genome sequence of the flowering plant

REFERENCES

[Zhu et al. 1998] J. K. Zhu, J. Liu and L. Xiong. Genetic analysis of salt tolerance

in arabidopsis. Evidence for a critical role of potassium nutrition. Plant

Cell, vol. 10, pages 1181-1191, 1998. 90

[Zhu et al. 2007] J. Zhu, X. Fu, Y. D. Koo, J. K. Zhu, F. E. Jenney Jr, M. Vv.

Adams, Y. Zhu, H. Shi, D. J. Yun, P. M. Hasegawa and R. A. Bressan.

An enhancer mutant of Arabidopsis salt overly sensitive 3 mediates both

ion homeostasis and the oxidative stress response. Mol Cell Biol, vol. 27,

pages 5214-5124, 2007. 90

[Zhu 2001a] J. K. Zhu. Cell signaling under salt, water and cold stresses. Curr

Opin Plant Biol, vol. 4, pages 401-406, 2001. 3

[Zhu 2001b] J. K. Zhu. Plant salt tolerance. Trends Plant Sci, vol. 6, pages 66-71,

2001. 3

[Zhu 2003] J. K. Zhu. Regulation of ion homeostasis under salt stress. Curr Opin

Plant Biol, vol. 6, pages 441-445, 2003. 36, 104

[Zhulin et al. 2003] I. B. Zhulin, A. N. Nikolskaya and M. Y. Galperin. Common

extracellular sensory domains in transmembrane receptors for diverse sig­

nal transduction pathways in bacteria and archaea. J Bacterial, vol. 185,

pages 285-294, 2003. 114

[Zimeri et al. 2005] A. M. Zimeri, 0. P. Dhankher, B. McCaig and R. Meagher.

The plant MTJ metallothioneins are stabilized by binding cadmium and

are required for cadmium tolerance and accnmulation. Plant Mol Biol,

vol. 58, pages 839-855, 2005. xxiii, 77, 78, 80

[Ziolkowski et al. 2003] P. A. Ziolkowski, G. Blanc and J. Sadowski. Structnral

divergence of chromosomal segments that arose from successive duplication

events in the Arabidopsis genome. Nucleic Acids Res, vol. 31, pages 1339-

1350, 2003. 59

286