evolutionary relationships among bacteria€¦ · evolutionary relationships among bacteria radhey...

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

Prokaryotes

Archaea

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) Signature

Rib. 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/<250

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

Cyanobacteria

Spirochetes

Deino-Thermus

Gram-positive bacteria

Archaea

ThermotogaArchaea

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


Spirochetes


Archaea

Thermotoga

Cyanobacteria

Deino-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


Spirochetes

Archaea

Deino-ThermusThermotoga

Cyanobacteria


Archaea

ProteobacteriaChlamydiae-CFBGAquificales

SpirochetesCyanobacteriaDeino-ThermusGram-positivesThermotoga


(0/256)

(209/209)

Main Line Signature in Alanyl-tRNA Synthetase

Proteobacteria

Aquificales


Spirochetes

Archaea

Deino-Thermus

Thermotoga

Cyanobacteria


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


Spirochetes

Deino, GNS

Cyanobacteria

High G+C Gram-positive

Archaea

Proteobacteria

AquificalesChlamydiae-CFBGSpirochetesCyanobacteriaDeino-ThermusGram-positivesThermotoga

Low G+C Gram-positive

Main Line Signature in CTP Synthase


(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, <150 exceptions are observed.

Gupta, R.S.(2002) Theor.Pop.Biol. 61:423-434.Photosynth. Res.(2003) 76: 173-183.

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.


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, GNS

Cyanobacteria


Archaea

ProteobacteriaAquificales

Chlamydiae-CFBGSpirochetesCyanobacteriaDeino-ThermusGram-positivesThermotoga

CTP Synthase


(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, <50 exceptions are observed.

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, GNS

Cyanobacteria


Archaea

ProteobacteriaAquificales

Chlamydiae-CFBGSpirochetesCyanobacteriaDeino-ThermusGram-positivesThermotoga

CTP Synthase

Archaea

Proteobacteria

Proteobacteria AquificalesChlamydiae-CFBGSpirochetesCyanobacteriaDeino-ThermusGram-positivesThermotoga

Main Line Signature Distinctive of - Proteobacteria

Valyl-tRNA Synthetase

Proteobacteria


Other Gram- negatives

evolutionary relationships among bacteria€¦ · evolutionary relationships among bacteria radhey...

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