Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups (original) (raw)

• Akiva E, Itzhaki Z, Margalit H (2008) Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. Proc Natl Acad Sci USA 105:13292–13297
  Article CAS PubMed Google Scholar
• Blankenship RE (1992) Origin and early evolution of photosynthesis. Photosynth Res 33:91–111
  Article CAS PubMed Google Scholar
• Blankenship RE, Hartman H (1998) The origin and evolution of oxygenic photosynthesis. Trends Biochem Sci 23:94–97
  Article CAS PubMed Google Scholar
• Blankenship RE, Olson JM, Miller M (1995) Antenna complexes from green photosynthetic bacteria. In: Blankenship RE, Madigan MT, Bauer CE (eds) Anoxygenic photosynthetic bacteria. Kluwer, Dordrecht, pp 399–435
  Google Scholar
• Boone DR, Castenholz RW, Garrity GM (2001) Bergey’s manual of systematic bacteriology. Springer, New York, pp 1–721
  Google Scholar
• Bryant DA, Frigaard NU (2006) Prokaryotic photosynthesis and phototrophy illuminated. Trends Microbiol 14:488–496
  Article CAS PubMed Google Scholar
• Bryant DA, Costas AM, Maresca JA, Chew AG, Klatt CG, Bateson MM, Tallon LJ, Hostetler J, Nelson WC, Heidelberg JF, Ward DM (2007) Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium. Science 317:523–526
  Article CAS PubMed Google Scholar
• Castenholz RW (2001) Phylum BX. Cyanobacteria: oxygenic photosynthetic bacteria. In: Boone DR, Castenholz RW (eds) Bergey’s manual of systematic bacteriology. Springer, New York, pp 474–487
  Google Scholar
• Chabriere E, Vernede X, Guigliarelli B, Charon MH, Hatchikian EC, Fontecilla-Camps JC (2001) Crystal structure of the free radical intermediate of pyruvate: ferredoxin oxidoreductase. Science 294:2559–2563
  Article CAS PubMed Google Scholar
• Charon MH, Volbeda A, Chabriere E, Pieulle L, Fontecilla-Camps JC (1999) Structure and electron transfer mechanism of pyruvate: ferredoxin oxidoreductase. Curr Opin Struct Biol 9:663–669
  Article CAS PubMed Google Scholar
• Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287
  Article CAS PubMed Google Scholar
• Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145
  Article CAS PubMed Google Scholar
• Delwiche CF, Kuhsel M, Palmer JD (1995) Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids. Mol Phylogenet Evol 4:110–128
  Article CAS PubMed Google Scholar
• Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, Barbe V, Duprat S, Galperin MY, Koonin EV, Le Gall F, Makarova KS, Ostrowski M, Oztas S, Robert C, Rogozin IB, Scanlan DJ, De Marsac NT, Weissenbach J, Wincker P, Wolf YI, Hess WR (2003) Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci USA 100:10020–10025
  Article CAS PubMed Google Scholar
• Dutilh BE, Snel B, Ettema TJ, Huynen MA (2008) Signature genes as a phylogenomic tool. Mol Biol Evol 25:1659–1667
  Article CAS PubMed Google Scholar
• Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, DeBoy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, Fraser CM (2002) The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci USA 99:9509–9514
  Article CAS PubMed Google Scholar
• Fang G, Rocha EP, Danchin A (2008) Persistence drives gene clustering in bacterial genomes. BMC Genomics 9:4
  Article PubMed Google Scholar
• Frigaard NU, Chew AG, Li H, Maresca JA, Bryant DA (2003) Chlorobium tepidum: insights into the structure, physiology, and metabolism of a green sulfur bacterium derived from the complete genome sequence. Photosynth Res 78:93–117
  Article CAS PubMed Google Scholar
• Gao B, Mohan R, Gupta RS (2009) Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria. Int J Syst Evol Microbiol 59:234–247
  Article CAS PubMed Google Scholar
• Gest H, Blankenship RE (2004) Time line of discoveries: anoxygenic bacterial photosynthesis. Photosynth Res 80:59–70
  Article CAS PubMed Google Scholar
• Gest H, Favinger J (1983) Heliobacterium chlorum, an anoxygenic brownish-green photosynthetic bacterium containing a “new” form of bacteriochlorophyll. Arch Microbiol 136:11–16
  Article CAS Google Scholar
• Golbeck JH (1993) Shared thematic elements in photochemical reaction centers. Proc Natl Acad Sci USA 90:1642–1646
  Article CAS PubMed Google Scholar
• Griffiths E, Gupta RS (2001) The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the _Cytophaga_-_Flavobacterium_-Bacteroides division. Microbiology 147:2611–2622
  CAS PubMed Google Scholar
• Griffiths E, Gupta RS (2004) Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales. Int Microbiol 7:41–52
  CAS PubMed Google Scholar
• Griffiths E, Gupta RS (2006) Lateral transfers of serine hydroxymethyl transferase (glyA) and UDP-_N_-acetylglucosamine enolpyruvyl transferase (murA) genes from free-living Actinobacteria to the parasitic chlamydiae. J Mol Evol 63:283–296
  Article CAS PubMed Google Scholar
• Griffiths E, Gupta RS (2007) Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae. Microbiology 153:2648–2654
  Article CAS PubMed Google Scholar
• Gupta RS (1998) Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and Eukaryotes. Microbiol Mol Biol Rev 62:1435–1491
  CAS PubMed Google Scholar
• Gupta RS (2000) The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24:367–402
  Article CAS PubMed Google Scholar
• Gupta RS (2001) The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Int Microbiol 4:187–202
  Article CAS PubMed Google Scholar
• Gupta RS (2003) Evolutionary relationships among photosynthetic bacteria. Photosynth Res 76:173–183
  Article CAS PubMed Google Scholar
• Gupta RS (2004) The Phylogeny and Signature Sequences characteristics of Fibrobacters, Chlorobi and Bacteroidetes. Crit Rev Microbiol 30:123–143
  Article CAS PubMed Google Scholar
• Gupta RS (2005a) Molecular sequences and the early history of life. In: Sapp J (ed) Microbial phylogeny and evolution: concepts and controversies. Oxford University Press, New York, pp 160–183
  Google Scholar
• Gupta RS (2005b) Protein signatures distinctive of Alpha proteobacteria and its subgroups and a model for Alpha proteobacterial evolution. Crit Rev Microbiol 31:101–135
  Article CAS PubMed Google Scholar
• Gupta RS (2006) Molecular signatures (unique proteins and conserved indels) that are specific for the epsilon Proteobacteria (Campylobacterales). BMC Genomics 7:167
  Article PubMed Google Scholar
• Gupta RS (2009) Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades. Int J Syst Evol Microbiol 59:2510–2526
  Article CAS PubMed Google Scholar
• Gupta RS, Griffiths E (2002) Critical issues in bacterial phylogenies. Theor Popul Biol 61:423–434
  Article PubMed Google Scholar
• Gupta RS, Johari V (1998) Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the _Deinococcus_-Thermus group and Cyanobacteria. J Mol Evol 46:716–720
  Article CAS PubMed Google Scholar
• Gupta RS, Lorenzini E (2007) Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species. BMC Evol Biol 7:71
  Article PubMed Google Scholar
• Gupta RS, Mathews DW (2010) Signature proteins for the major clades of Cyanobacteria. BMC Evol Biol 10:24
  Article PubMed Google Scholar
• Gupta RS, Mok A (2007) Phylogenomics and signature proteins for the alpha proteobacteria and its main groups. BMC Microbiol 7:106
  Article PubMed Google Scholar
• Gupta RS, Sneath PHA (2007) Application of the character compatibility approach to generalized molecular sequence data: branching order of the proteobacterial subdivisions. J Mol Evol 64:90–100
  Article CAS PubMed Google Scholar
• Gupta RS, Pereira M, Chandrasekera C, Johari V (2003) Molecular signatures in protein sequences that are characteristic of Cyanobacteria and plastid homologues. Int J Syst Evol Microbiol 53:1833–1842
  Article CAS PubMed Google Scholar
• Handa S, Pierson BK (2006) The family Chloroflexiae. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria. Springer, New York, pp 815–842
  Google Scholar
• Heinnickel M, Golbeck JH (2007) Heliobacterial photosynthesis. Photosynth Res 92:35–53
  Article CAS PubMed Google Scholar
• Helman Y, Tchernov D, Reinhold L, Shibata M, Ogawa T, Schwarz R, Ohad I, Kaplan A (2003) Genes encoding A-type flavoproteins are essential for photoreduction of O2 in Cyanobacteria. Curr Biol 13:230–235
  Article CAS PubMed Google Scholar
• Heyes DJ, Scrutton NS (2009) Conformational changes in the catalytic cycle of protochlorophyllide oxidoreductase: what lessons can be learnt from dihydrofolate reductase? Biochem Soc Trans 37:354–357
  Article CAS PubMed Google Scholar
• Hoffmann L, Komarek J, kastovsky J (2005) System of Cyanoprokaryotes (Cyanobacteria)—state in 2004. Algol Stud 117:95–115
  Google Scholar
• Hormozdiari F, Salari R, Hsing M, Schonhuth A, Chan SK, Sahinalp SC, Cherkasov A (2009) The effect of insertions and deletions on wirings in protein-protein interaction networks: a large-scale study. J Comput Biol 16:159–167
  Article CAS PubMed Google Scholar
• Imhoff JF (2001) The anoxygenic phototrophic purple bacteria. In: Boone DR, Castenholz RW (eds) Bergey’s manual of systematic bacteriology. Springer-Verlag, Berlin, pp 631–637
  Google Scholar
• Imhoff JF (2003) Phylogenetic taxonomy of the family Chlorobiaceae on the basis of 16S rRNA and fmo (Fenna-Matthews-Olson protein) gene sequences. Int J Syst Evol Microbiol 53:941–951
  Article CAS PubMed Google Scholar
• Kainth P, Gupta RS (2005) Signature proteins that are distinctive of alpha proteobacteria. BMC Genomics 6:94
  Article PubMed Google Scholar
• Kersters K, Devos P, Gillis M, Swings J, Vandamme P, Stackebrandt E (2006) Introduction to the Proteobacteria. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria. Springer, New York, pp 3–37
  Google Scholar
• Kirzhner V, Nevo E, Korol A, Bolshoy A (2003) A large-scale comparison of genomic sequences: one promising approach. Acta Biotheor 51:73–89
  Article PubMed Google Scholar
• Koonin EV, Aravind L, Kondrashov AS (2000) The impact of comparative genomics on our understanding of evolution. Cell 101:573–576
  Article CAS PubMed Google Scholar
• Kuo CH, Ochman H (2009) The fate of new bacterial genes. FEMS Microbiol Rev 33:38–43
  Article CAS PubMed Google Scholar
• Lang AS, Beatty JT (2007) Importance of widespread gene transfer agent genes in alpha Proteobacteria. Trends Microbiol 15:54–62
  Article CAS PubMed Google Scholar
• Lerat E, Daubin V, Ochman H, Moran NA (2005) Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 3:e130
  Article PubMed Google Scholar
• Ludwig W, Klenk H-P (2005) Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology. Springer-Verlag, Berlin, pp 49–65
  Chapter Google Scholar
• Madigan MT (2006) The family Heliobacteriaceae. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria. Springer, New York, pp 951–964
  Google Scholar
• Moore LR, Rocap G, Chisholm SW (1998) Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393:464–467
  Article CAS PubMed Google Scholar
• Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI, Dufresne A, Partensky F, Burd H, Kaznadzey D, Haselkorn R, Galperin MY (2006) The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci USA 103:13126–13131
  Article CAS PubMed Google Scholar
• Narra HP, Cordes MH, Ochman H (2008) Structural features and the persistence of acquired proteins. Proteomics 8:4772–4781
  Article CAS PubMed Google Scholar
• Nobrega MA, Pennacchio LA (2004) Comparative genomic analysis as a tool for biological discovery. J Physiol 554:31–39
  Article CAS PubMed Google Scholar
• Olsen GJ, Woese CR, Overbeek R (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1–6
  CAS PubMed Google Scholar
• Olson JM, Pierson BK (1987) Evolution of reaction centers in photosynthetic prokaryotes. Int Rev Cytol 108:209–248
  Article CAS PubMed Google Scholar
• Oren A, Stackebrandt E (2002) Prokaryote taxonomy online: challenges ahead. Nature 419:15
  Article CAS PubMed Google Scholar
• Overmann J (2003) The family Chlorobiaceae. In Dworkin M et al (eds) The Prokaryotes: an evolving electronic resource for the microbiological community. Springer-Verlag, New York
• Overmann J, Garcia-Pichel F (2000) The phototrophic way of life. In: Dworkin M et al (eds) The prokaryotes: an evolving electronic resource for the microbiological community. Springer-Verlag, New York
  Google Scholar
• Partensky F, Hess WR, Vaulot D (1999) Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol Mol Biol Rev 63:106–127
  CAS PubMed Google Scholar
• Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE (2002) Whole-genome analysis of photosynthetic prokaryotes. Science 298:1616–1620
  Article CAS PubMed Google Scholar
• Rippka R, Deruelles J, Waterbury JB, Herdman M, Stanier RY (1979) Generic assignments, strain histories and properties of pure cultures of Cyanobacteria. J Gen Microbiol 111:1–61
  Google Scholar
• Rivera MC, Lake JA (1992) Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257:74–76
  Article CAS PubMed Google Scholar
• Rocap G, Distel DL, Waterbury JB, Chisholm SW (2002) Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S–23S ribosomal DNA internal transcribed spacer sequences. Appl Environ Microbiol 68:1180–1191
  Article CAS PubMed Google Scholar
• Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042–1047
  Article CAS PubMed Google Scholar
• Rokas A, Holland PW (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15:454–459
  Article PubMed Google Scholar
• Sanchez-Baracaldo P, Hayes PK, Blank CE (2005) Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach. Geobiology 3:145–165
  Article CAS Google Scholar
• Sattley WM, Madigan MT, Swingley WD, Cheung PC, Clocksin KM, Conrad AL, Dejesa LC, Honchak BM, Jung DO, Karbach LE, Kurdoglu A, Lahiri S, Mastrian SD, Page LE, Taylor HL, Wang ZT, Raymond J, Chen M, Blankenship RE, Touchman JW (2008) The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus. J Bacteriol 190:4687–4696
  Article CAS PubMed Google Scholar
• Shi T, Falkowski PG (2008) Genome evolution in Cyanobacteria: the stable core and the variable shell. Proc Natl Acad Sci USA 105:2510–2515
  Article CAS PubMed Google Scholar
• Silaghi-Dumitrescu R, Kurtz D M Jr, Ljungdahl LG, Lanzilotta WN (2005) X-ray crystal structures of Moorella thermoacetica FprA. Novel diiron site structure and mechanistic insights into a scavenging nitric oxide reductase. Biochemistry 44:6492–6501
  Article CAS PubMed Google Scholar
• Singh B, Gupta RS (2009) Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth. Mol Genet Genomics 281:361–373
  Article CAS PubMed Google Scholar
• Sugishima M, Migita CT, Zhang X, Yoshida T, Fukuyama K (2004) Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme. Eur J Biochem 271:4517–4525
  Article CAS PubMed Google Scholar
• Sugishima M, Hagiwara Y, Zhang X, Yoshida T, Migita CT, Fukuyama K (2005) Crystal structure of dimeric heme oxygenase-2 from Synechocystis sp. PCC 6803 in complex with heme. Biochemistry 44:4257–4266
  Article CAS PubMed Google Scholar
• Swingley WD, Sadekar S, Mastrian SD, Matthies HJ, Hao J, Ramos H, Acharya CR, Conrad AL, Taylor HL, Dejesa LC, Shah MK, O’huallachain ME, Lince MT, Blankenship RE, Beatty JT, Touchman JW (2007) The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. J Bacteriol 189:683–690
  Article CAS PubMed Google Scholar
• Swingley WD, Blankenship RE, Raymond J (2008a) Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families. Mol Biol Evol 25:643–654
  Article CAS PubMed Google Scholar
• Swingley WD, Chen M, Cheung PC, Conrad AL, Dejesa LC, Hao J, Honchak BM, Karbach LE, Kurdoglu A, Lahiri S, Mastrian SD, Miyashita H, Page L, Ramakrishna P, Satoh S, Sattley WM, Shimada Y, Taylor HL, Tomo T, Tsuchiya T, Wang ZT, Raymond J, Mimuro M, Blankenship RE, Touchman JW (2008b) Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina. Proc Natl Acad Sci USA 105:2005–2010
  Article CAS PubMed Google Scholar
• Tsukatani Y, Wen J, Blankenship RE, Bryant DA (2010) Characterization of the FMO protein from the aerobic chlorophototroph, Candidatus Chloracidobacterium thermophilum. Photosynth Res. doi:10.1007/s11120-00909517-0)
• Vassiliev IR, Antonkine ML, Golbeck JH (2001) Iron-sulfur clusters in type I reaction centers. Biochim Biophys Acta 1507:139–160
  Article CAS PubMed Google Scholar
• Vermaas WFJ (1994) Evolution of heliobacteria: implications for photosynthetic reaction center complexes. Photosynth Res 41:285–294
  Article CAS PubMed Google Scholar
• Walker CJ, Willows RD (1997) Mechanism and regulation of Mg-chelatase. Biochem J 327(Pt 2):321–333
  CAS PubMed Google Scholar
• Wall JD, Weaver PF, Gest H (1975) Gene transfer agents, bacteriophages, and bacteriocins of Rhodopseudomonas capsulata. Arch Microbiol 105:217–224
  Article CAS PubMed Google Scholar
• Williams KP, Sobral BW, Dickerman AW (2007) A robust species tree for the Alphaproteobacteria. J Bacteriol 189:4578–4586
  Article CAS PubMed Google Scholar
• Willows RD (2003) Biosynthesis of chlorophylls from protoporphyrin IX. Nat Prod Rep 20:327–341
  Article CAS PubMed Google Scholar
• Wilmotte A, Golubic S (1991) Morphological and genetic criteria in the taxonomy of Cyanophyta/Cyanobacteria. Archiv fur Hydrobiologie 64:1–24
  Google Scholar
• Wilmotte A, Herdman M (2001) Phylogenetic relationships among the Cyanobacteria based on 16S rRNA sequences. In: Boone DR, Castenholz RW (eds) Bergey’s manual of systematic bacteriology. Springer, New York, pp 487–493
  Google Scholar
• Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA (2009) Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One 4:e4207
  Article PubMed Google Scholar
• Yildiz FH, Gest H, Bauer CE (1991) Attenuated effect of oxygen on photopigment synthesis in Rhodospirillum centenum. J Bacteriol 173:5502–5506
  CAS PubMed Google Scholar
• Yurkov VV, Beatty JT (1998) Aerobic anoxygenic phototrophic bacteria. Microbiol Mol Biol Rev 62:695–724
  CAS PubMed Google Scholar
• Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT (2006) Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res 16:1099–1108
  Article CAS PubMed Google Scholar
• Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP (2009) Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus. Genome Biology and Evolution 1:325–339
  Article Google Scholar