GENE AND GENOME OF PLANT

Presented by:

LA ODE B. ABIDIN 10/306997/PMU/6710

SUDARMONO A.T. 11/322094/PMU/6977

Introduction of plant gene and genome

Differences of Nuclear and Organelle genomes

Mechanism involved in dna quantitiy variation

What is GENE?

• Region of DNA or RNA that encode for a polypeptide or for an RNA chain that has a function in the organism

• A modern definition : "a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regions“

Tree of plant genomes • Nuclear

genome• Mitochondrial

Genomes • Chloroplast

Genomes

What is GENOME?

• GENOME is all of a living thing's genetic material, includes both the genes and the non-coding sequences encoded either in DNA or RNA

Endosymbiotic evolution

Mitochondria arose from α-proteobacteria and chloroplasts arose from cyanobacteria

Nuclear vs Organelle genomes

Nuclear genome structureA chromosome is the visible state of genetic material during a phase of the division of the cell (prometafase/metaphase)

DNA in metaphase chromosomes must be shortened 10,000-fold by very efficient packing.

The DNA molecule is twisted onto itself, and the supercoiled molecule is wrapped around proteins which maintain its shape.

These proteins are histone proteins.

The complex DNA protein is called chromatin, while the structure formed by two turns of DNA around one histone is called a nucleosome.

Chromosome nuclear structure

Overview ofthe many ordersof DNAcondensationinto chromatin

Euchromatine & Heterochromatin• DNA containing genes

is called euchromatin• Non-genic DNA is called

heterochromatin.• Heterochromatin and

euchromatin stain differently.

• This difference causes the bands we see in a karyotype.

Genome composition

• Euchromatin (genes) usually contains a higher proportion of GC.

• Euchromatin has more unique DNA sequences.

• Heterochromatin (non-coding) usually contains a higher proportion of AT.

• Heterochromatin contains more repetitive sequence.s

Differences of organelle and nuclear genomes

No. Differences

Organelle genomes Nuclear genomes

1 DNA Structure Circular DNA Linear DNA2 Packing with histone

proteine No Yes

3 Intron in DNA sequence

No Yes

4 Inheritance Maternal Result of recombination from male and female

5 DNA polymerase DNA polymerase I, low proofreading activity

DNA polymerase 1, 2, 3 and ε with intrinsic proofreading activity

Nuclear genome size in different species

Sizes and coding content of some organelle and prokaryote genomes

Countinued……

Sizes and coding content of some organelle and prokaryote genomes

MECHANISM INVOLVED IN DNA QUANTITIY VARIATION

• Polyploidization• Revetitive

sequence

- rRNA gene

- centromers

- telomeres

- transposons

Ribosomal RNA genes

CENTROMERE

- The telomeres of most organisms' chromosomes consist of short sequence-asymmetric repeated sequences.

- Lengths are typically greater than 50 repeats in holotrichous ciliates, less than 350 repeats in Arabidopsis and 300 to 500 bp in Saccharomyces.

• A Drosophila chromosome, an exception, has a transposable element at the end of one of its chromosomes.

• Examples:

telomere Sentromere Knob

TELOMERES

Transposable Elements (TEs)

50-80% of plant genomes are

TEs

Discovered by Barbara

McClintock by studying unstable

corn kernel phenotypes

Fragments of DNA that can

insert into new chromosomal

locations

Often duplicate themselves

during the process of moving

around

Class 1 TEs use RNA intermediates to move around and undergo duplicative

transposition

Class 2 TEs are excised during transposition and may undergo “cut and paste”

transposition with no duplication or “gap repair” where the gap is filled with a

copy of the transposon

Autonomous elements contain necessary genes for transposition

Non-autonomous elements rely on products of other elements for transposition

• Move by a "cut andpaste" process: thetransposon is cut out ofits location andinserted into a newlocation• Requires atransposase to cut andinsert DNA fragment.• Transposon hasterminal invertedrepeats• Excision generatesdirect repeats (~ targetinsertion sites)

Class II Transposons

CONCLUSION

- The genomes are very dynamic- Genome of plant is located in

nuclues, mitochondria and chloroplast

- Genetic element is changed at different scales:• Gene• Chromosome segments• Genome

Literature1. Jenik, P.D. Jurkuta, R.E. and Barton, M.K. 2005.

Interactions between the cell cycle and embryonic patterning in Arabidopsis uncovered by a mutation in DNA polymerase epsilon. Plant Cell 17: 3362–3377

2. Parent, J. Lepage, E. and Brisson, N. 2011. Divergent Roles for the Two PolI-Like Organelle DNA Polymerases of Arabidopsis. Plant Physiology 156 (1): 254-262

3. Pearson, H. 2006. Genetics: what is a gene?. Nature 441: 398-401

4. Quiroz, H.C.2002. Plant genomics: an overview. Biological Research 35: 3-4 

5. Ridley, M. 2006. Genome. New York, NY: Harper Perennial.

6. Timmis, J.T. Ayliffe, M.A. Huang, C.Y. and Martin, W. 2004. Endosymbiotic gene transfer: Organelle genomes forge eukaryotic chromosomes. Nature 5: 123-135.

7. Casacuberta and Santiago, 2003, Plant LTR-retransposons and MITEs: control of transcription and impact on the evolution of plants genes and genomes. Elsevier Gene 311 (2003) 1-11.

Terima kasih…..

Coordination between the nucleus and organelle genomes

Anterogade signaling

Anterogade signaling

Retrogade signaling

Retrogade signaling

Polyploidy (here, autopolyploidy)

Structure of the different types of plant transposable elements