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Evolutionary Relationships Among Bacteria Radhey S. Gupta McMaster University Canada McMaster Origins Conference, May 27,2005

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  • Evolutionary Relationships Among

    Bacteria

    Radhey S. GuptaMcMaster University

    Canada

    McMaster Origins Conference, May 27,2005

  • First and sole Inhabitants of this planet for the first 2 billion yrs.

    Hold key to understanding:• Nature and origin of the first cell• Origin of Metabolism and Photosynthesis• Origin of Information transfer processes• Origin of eukaryotic cells including all animal and plant life.

    From: Campbell, N.A. (1996) Biology, Benjamin/Cumming

    Importance of Understanding Prokaryotic Phylogeny

    Chronology: Main Events in the Evolutionary History of Life

  • ProkaryotesArchaea

    Bacteria

    Bacteria comprise >98% of the known prokaryotes

    Photosynthetic capability is only found in Bacteria

    Central role in the origin of Mitochondria, Plastids as well as the eukaryotic cells

    Origin of the first cell and relationship to Archaea

    Importance of Understanding Bacterial Phylogeny

    (First cell)

  • Current View of Bacterial Phylogeny

    • No defined criteria for identifying the main groups within Bacteria.• Interrelationships of different groups to each other is not known.• Lateral gene transfer is indicated to be rampant among bacteria. Critical assessment of its impact on bacterial phylogeny.

    16S rRNA TreeBergey’s Manual (2001)

    Thermophilic organisms lie at the base of this tree: Hot Origin of Life? Photosynthesis is distributed in a number of different unrelated groups

    Unresolved Issues

  • What is Minimally Needed to Understand Bacterial Phylogeny?

    Development of well-defined and objective Criteria for Identifying the Main Groups Within Bacteria.

    To understand how different main groups are relatedto each other and in what order they have branched off from a common ancestor.

    New approach based on Rare Genomic ChangesSee also www.bacterialphylogeny.com

  • Use of Rare Genomic Changes to Understand Bacterial Phylogeny

    1. Conserved inserts or deletions unique to particular groups of Species2. Whole proteins that are uniquely present in particular groups.

    Two Types of Rare Genomic Changes

    Group-specific or Subgroup-Specific Signatures

    Provides mean for identifying different groups/subgroups of bacteria in clear molecular terms

  • Main-Line Signature

    Helpful in understanding the branching order or interrelationships among different groups

    Source: www.bacterialphylogeny.com

    Examples of Group-Specific and Main-Line Signatures

  • Signature Sequences for Cyanobacteria/Plastids

    Proteobacteria and other Gram –ve Bacteria

    Gram +vebacteria

    Plants/Plastids

    Cyanobacteria

    Gupta et al. IJSEM (2003) 53:1833-42

    EF-Tu

    UvrDSecAPolIFtsHFerrochelataseRib. S1 prot.IMP Dehydro.Sigma factorPhytoene Syn.ADP-Glu-PPase

    Exceptions 0/450

  • Firmicutes (Low G+C Gram+ve) SignatureRib. S12 protein

    Proteobacteria

    Firmicutes(Low G+C)

    Actinobacteria (High G+C)

    Chlorobi-CFBG-Aquifex, SpirochetesCyanobacteria

    Gupta, R.S. et al. (1999) Mol. Microbiol. 32: 893-906

    Exceptions 3/227

  • Signature Sequences for Deinococcus-Thermus

    Proteobacteria

    Chlamydiae-CFBG-Chlorobi

    Other Gram -ve

    Deinococcus-Thermus

    Gram +vebacteria

    Griffiths and Gupta, J. Bacteriol (2004) 186:3097-107

    Thr-RS

    RpoBSigma 70Ffh/SR54SerRSRib. Prot. L1UvrA

    Exceptions 0/

  • 326 368 E. coli LSFIVWLHHFFTMG AG ANVNAFFGITTMIIAIPTGVKIFNWLF Bord. parapertussis ---L--A--M--T- IP VVGQL--MYA--L-S----------VA V. vulnificus ---V--A--M--T- MP VFAEL--MYC--M--V---------VA Burk. fungorum ---M--A--M-AT- MP VTGQL--MYA--L--V-----V---VA Geo. sulfurreducens AGSL--G--M--S- MS DTAVLV-SFLSF-V---SAI-V---IS Yer. pseudotuberculosis -------------- S- ---------A----S------------ Ca. crescentus --Y----------- S- -S------------S----A------- A. tumefaciens --YL---------- S- --------------S----A------- Pse. aeruginosa -G-T---------- S- GD--G---VA--L-S------L----- Prochlor. marinus -GLV--A--MF-S- TP PWMRL--T-A-SF--V---I-F----A Glo. violaceus -GFL--A--M--S- TP DWLRM--MV-SFL--V---I-V-S--G Lep. interrogans V--L--G--M-VS- QS EFAGVL-SF---LVGV--AI-L---I Nostoc punctiforme -GLI--A--M--S- IP GWLRM--M-------V---I---S--A The. thermophilus -GTM--A--M--V- ES TLFQIA-AFF-AL--V-----L--IIG D. radiodurans V-C------M-AV- IP EAWQIA-M-S-L-V-V--------LIG Cfx. aurantiacus -G-L--G--M-VSS QS VYAGLI-SFI--LV---SAI-V---TA Cyt. hutchinsonii ------A--M-VT- MN PFLGSI-MFL-L---V-SA--A--YIA Aqu. aeolicus V--FL-I--M-VS- VP NWTRVL-SY--LL--V---I-----M Symbio. thermophilum MG-T--S--M--V- M- PV--SI-SL---A--V----------S Sta. aureus ---L--V------- N- -LI-S--S-S--L-G------L----L Lis. innocua ---L--V------- S- -L--S--S----M------I------ Geobac. kaustophilus ------V------- -- PA--SA-S----A-------------- Oceano. iheyensis ---V--V------- Q- -LT-SI-S----A--V---I------L Exiguobacterium sp -GFM--V--M--V- L- PVA--I-AVA--A--V----------- Bac. cereus ---V---------- -- PA--S--S-S--A-S----------- Cor. efficiens --MAV-A--MFVT- -VLLP--SFM-FL-SV-----F---VG Gord. westfalica --VA--A--MYVT- -VLLP--SFMTFL--V-----F---IG Myc. leprae --VA--A--M-AT- -VLLP--SFM-YL--V-----F---VG Tri. caesia --VV--A--M-AT- -VLLP--SVLSFL--V-----F---AG Cellu. fimi --VT--A-RMYVT- SVLLP--AFM--L--V-----F---IG Koc. rhizophila --VT--A--MYVT- -VALG--SFM--M--V-----F---IG Gord. rubripertincta --VA--A--MYVT- -VLLP--SFM-FL--V-----F---IG Microt. niveoalba --MT--A--M-AT- -ALLP--SMLSFL------I-F---TG Art. nicotinovorans --VT--A--MYVT- SVLLP--AFM--L--V-----F---IG Streptos. roseum --IT--A--M-PT- QVLLP--SFM-FL--V-----F---IG Pseud. halophobica --AA--A--MYAT- -VLL---SF--LL------I-FV--IG Tsu. paurometabola --VA--A--MYAT- -VLLP--SFM-FL--V-----F---I- N. corynebacterioides --IA--A--MYAT- -VLLP--SFM-FL--V-----F---IG Sac. erythraea --VV--A--MYAT- -VLLP--AF--FL--V---M-F---IG Micro. oxydans --VA--A--MHVT- SVLLP--ALM--L--V---------IG Krib. sandramycini --VA--A--I-VT- -MNLP--SFM-FL--V-----F---IG Wil. murale --VA--A--MYAT- -VLLP--SFM-F---V-----F---IG Oer. turbata --V---A--MYVT- -VLLP--AFM--L--V-----F---IG Strept. glaucoflavus --IT--A--M-VT- QVLLP--SFM-FL--V-----F---VG

    Gram-veBacteria

    Firmicutes

    Actinobacteria

    Signature Sequence for Actinobacteria

    Cox1

    All Available Sequences

    44 Actino homologs2-aa gap : 44/44

    224 Non-Actino homologs2-aa gap : 0/224

    Exceptions- none

    Beile Gao and Gupta (2005) Unpublished data

    CTP SynthGluRS

  • Chlamydiae-Specific Signatures

    Proteobacteria

    Chlamydiae

    Other Gram negatives

    Gram-positives

    Gyrase B

    MurAEF-PMgtETrmDCtproteaseGlmURpoATgtLysRSEF-Tu

    Griffiths and Gupta, Microbiology 148 (2002) 2541 and Microbiology (in press)

    41 114E. coli YP_026241 GRGIPTGIHPEEG VSAAEVIMTVLHAGGKFV. cholerae AAF93193 ------EM----K -----------------Pas. multocida NP_246415 -----VD------ -----------------X. fastidiosa NP_297298 -----VD--K--- -------L---------Ral. eutropha ZP_00167346 -----PLVKFDDK R----IA--E-------Bord. parapertussis NP_886525 ------D--KDDE R----IV--E-------Nei. gonorrhoeae A49794 ---M------K-- R----------------C. crescentus NP_418979 -----VDM-EG-- ---------Q-------R. prowazekii CAA15027 -----VE--E--- I--------Q-------A. tumefaciens NP_353052 ------D--SS-- ---------Q-------Geo. metallireducens ZP_00080460 ------EM--T-- KP----AL---------Des. desulfuricans ZP_00128492 -----VD---K-- RP-V--V----------Camp. jejuni NP_281225 -----VDM--T-N MPTLT-VL---------Hel. pylori NP_223171 -----VD---T-K IP-CT-VL-I-------Chl. trachomatis ACC67782 -----IQ--EK-S AKQGRE I--L--VL---------Chl. muridarum AAF39313 -----VQ--EK-S AKQGRE I--L--VL---------Chlam. caviae AAP05250 -----IQ--EK-S KKQGRD ---L--VL---------Chlam. pneumoniae AAP98215 -----IEV-ER-S AKQGRE ---L--VL---------Para. sp. UWE25 CAF23799 -----VER-EN-S RKQGRE ---I--V--I-------Wad. chondrophila AY845403 -----IQK-EK-S QKQGRE ---L--V--T-------Sim. negevensis AY845410 -----IQK-EN-S RKQGRE ---I--V--I-------Neo. hartmanellae AY845413 -----VEK-EN-S RKQGRE ---I--V--I-------Aqu. aeolicus NP_213700 -----VD----T- KP-V-MVF-M-G-----Cb. tepidum NP_663136 -----VD---VKK K--L-LV---IG-----Por. gingivalis AAQ66713 -----VDY-EK-- K--L--VL---------Bor. burgdorferi NP_212570 ------D--E--- I--L-LVL-K--S----Lep. interrogans AAN64015 -----VD---DKK I-TI--V--I-------Pro. marinus NP_876187 ------DV--KT- K--L-TVL---------Syn. sp. NP_896190 ------DV--RT- K--L-TVL---------Cf. aurantiacus ZP_00357283 -S---V----K-- I-TLTLV--R-------D. radiodurans NP_294630 -----VD-MKSK- RP-I---FSE-------The. thermophilus YP_144852 -----VDLM---- KP-V---Y-T--S----T. maritima AAC44498 -----VD------ R--L--VF---------Cor. diphtheriae CAE48516 -----VEM--SGA PTVQ-V--Q-------Myc. tuberculosis CAA55486 -----VAT-ASGI PTVD-V--Q-------Bac. subtilis NP_387887 -----V---EKM- RP-V-------------Clo. thermocellum ZP_00059734 -----V----KL- I-TV--VH-I-------

  • Group-Specific and Subgroup Specific Signatures for α-Proteobacteria

    Gupta, R.S. (2005) Cri. Rev. Microbiol. (in press);Kainth, P. and Gupta, R.S. (2005)BMC Genomics (In press)

  • Group-specific signatures have been identified for all main groups within Bacteria.

    Identification of different groups in precise molecular terms.

    How are these Groups Related to Each Other?

    Proteobacteria SpirochetesCyanobacteriaDeinococcus-ThermusChlamydiaeCFB-ChlorobiAquificalesFirmicutesActinobacteria

  • Proteobacteria

    Aquificales

    Chlamydiae-CFBG group

    CyanobacteriaSpirochetes

    Deino-Thermus

    Gram-positive bacteria

    Archaea

    Thermotoga Archaea

    ProteobacteriaChlamydiae-CFBGSpirochetesCyanobacteriaAquificalesDeino-Thermus

    Gram-positivesThermotoga

    Main Line Signature in Hsp70 Protein

    Gupta, Microbiol. Mol. Biol. Rev. 62(1998) 1435; Griffiths and Gupta, (2004) Int. Microbiol ,7; 41-52

    (334/335)

    (4/139)

  • Main Line Signature in RNA Polymerase ’

    Proteobacteria

    Aquificales

    Chlamydiae-CFBG groupSpirochetes

    Gram-positive bacteria

    Archaea

    Thermotoga

    CyanobacteriaDeino-Thermus

    Archaea

    ProteobacteriaChlamydiae-CFBGSpirochetesCyanobacteriaAquificales

    Deino-ThermusGram-positivesThermotoga

    Griffiths and Gupta, (2004) Int. Microbiol ,7; 41-52

    (0/108)

    (176/176)

  • Main Line Signature in RNA Polymerase

    Proteobacteria

    Aquificales

    Chlamydiae-CFBG groupSpirochetes

    Archaea

    Deino-ThermusThermotoga

    Cyanobacteria

    Gram-positive bacteria

    Archaea

    ProteobacteriaChlamydiae-CFBGAquificales

    SpirochetesCyanobacteriaDeino-ThermusGram-positivesThermotoga

    Griffiths and Gupta, (2004) Int. Microbiol ,7; 41-52

    (0/256)

    (209/209)

  • Main Line Signature in Alanyl-tRNA Synthetase

    Proteobacteria

    Aquificales

    Chlamydiae-CFBG groupSpirochetes

    Archaea

    Deino-ThermusThermotoga

    Cyanobacteria

    Gram-positive bacteria

    Archaea

    ProteobacteriaChlamydiae-CFBGAquificales

    SpirochetesCyanobacteriaDeino-ThermusGram-positivesThermotoga

    Gupta, MMBR 62(1998) 1435;Griffiths and Gupta, (2004) Int. Microbiol. 7: 41-52

    (157/157)

    (0/113)

  • Proteobacteria

    Aquificales

    Chlamydiae-CFBG group

    Spirochetes

    Deino, GNSCyanobacteria

    High G+C Gram-positive

    Archaea

    Proteobacteria

    AquificalesChlamydiae-CFBGSpirochetesCyanobacteriaDeino-ThermusGram-positivesThermotoga

    Low G+C Gram-positive

    Main Line Signature in CTP Synthase

    Griffiths and Gupta, (2004) Int. Microbiol ,7; 41-52

    (102/102)

    (115/115)

  • Branching Order of Bacteria Based on Signature Sequences

    The groups are arranged in the order in which they have branched off from a common ancestor.

    All main phyla are distinguished from each other based on both group-specific and main-line signatures.

    Cells bounded by one membrane are indicated to be phylogenetically distinct from those containing both inner and outer cell membranes. Of these Monoderms are indicated to be ancestral.

    How Reliable is this Branch Order?

    Is the observed pattern affected by Lateral Gene Transfer?

  • Test of the Model Using Genome Sequence Data

    The model makes specific predictions which indels should be present or absent in different groups.

    If the genes containing these indels were subject of frequent LGTs, then their presence or absence will not follow any predicted pattern.

    Compare the observed vs. predicted distribution of these indels in various completed bacterial genomes.

    The observed distribution of these indels in different genomes (> 200) is found to be almost exactly as predicted by the model. In > 10000 observations,

  • Implications Regarding Origin of Thermophyly

    Aquificales, which constitute one of the extreme thermophilic phylum is indicated to be a late branching lineage’

    The deep branching of Aquificales in 16S rRNA tree is likely a consequence of very high G+C content (>65%) of their rRNAs, which is similar to other thermophilic organisms (viz. Archaea). Genomic G+C content of Aquificales is only 40-42%. LGT?

    Thermophyly appears to be an adapative characteristic rather than an ancestral trait.

    Griffiths and Gupta, (2004) Int. Microbiol ,7; 41-52

  • Implications for Photosynthesis

    Heliobacterium , which contain RC-1, and comprise the only photosynthetic group bounded by a single membrane, is indicated to be the earliest branching lineage. The ancestral nature of this RC is also supported by other observations.

    The organisms containing either RC-1 or RC-2 evolved prior to the evolution of Cyanobacteria, which contains both RCs to carry out oxygenic photosynthesis.

    The presence of photosynthetic ability in the earliest branching bacterial phylum indicates that photosynthesis evolved very early in evolution and it is possible that the earliest prokaryotic organisms were photosynthetic.

    Gupta, R.S.(2003) Photosynth. Res.(2003) 76: 173-183.

  • Bhag SinghPinay KainthMany part-time students

    Research Support: NSERC, Canada

    Emma Griffiths

    Beile Gao

  • Proteins Specific to Alpha Proteobacteria

    Kainth, P. and Gupta, R. S. (2005) BMC Genomics (in press); Gupta, R.S. (2005) Crit. Rev. Microbiol. (in press);

  • CFB-Chlorobi Signatures

    Proteobacteria

    CFB-Chlorobi

    Other Gram negatives

    Gram-positives

    RpoB

    Gyrase BFtsKATPaseUvrBRpoCSHMT

    Gupta (2004) Crit. Rev. Microbiol. 30:123-143

    Exceptions 0/460

  • Main Line Signature in Inorganic Pyrophosphatase

    Proteobacteria

    Aquificales

    Chlamydiae-CFBG groupSpirochetes

    Thermus, GNSCyanobacteria

    Gram-positive bacteria

    Archaea

    ProteobacteriaAquificales

    Chlamydiae-CFBGSpirochetesCyanobacteriaDeino-ThermusGram-positivesThermotoga

    CTP Synthase

    Griffiths and Gupta, (2004) Int. Microbiol ,7; 41-52

    (150/157)

    (0/61)

  • Predicted vs ObservedDistribution of Various

    Indels in 100 CompletedBacterial Genomes

    The observed distribution of these indels in different genomes is found to be almost exactly as predicted by the model. In >4000 observations,

  • Signature Sequence Specific for Spirochetes

    Spirochetes

    Other Gram -ve Bacteria

    Gram +veBacteria

    Archaea

    Eukaryotes

    PRS

  • Main Line Signature in Inorganic Pyrophosphatase

    Proteobacteria

    Aquificales

    Chlamydiae-CFBG groupSpirochetes

    Thermus, GNSCyanobacteria

    Gram-positive bacteria

    Archaea

    ProteobacteriaAquificales

    Chlamydiae-CFBGSpirochetesCyanobacteriaDeino-ThermusGram-positivesThermotoga

    CTP Synthase

  • Archaea

    Proteobacteria

    Proteobacteria AquificalesChlamydiae-CFBGSpirochetesCyanobacteriaDeino-ThermusGram-positivesThermotoga

    Main Line Signature Distinctive of - ProteobacteriaValyl-tRNA Synthetase

    Proteobacteria

    Gram-positive bacteria

    Other Gram- negatives

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