Signature proteins for the major clades of Cyanobacteria

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Gupta, Radhey S ^a   Mathews, Divya W ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKER; CLADISTICS; CYANOBACTERIUM; ECOTYPE; GENOMICS; LIGHT INTENSITY; PHYLOGENY; PROTEIN; TAXONOMY;

CHROOCOCCALES; CYANOBACTERIA; NOSTOC; NOSTOCALES; OSCILLATORIALES; PROCHLOROCOCCUS; SYNECHOCOCCUS; SYNECHOCYSTIS;

BACTERIAL DNA; BACTERIAL PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; CLASSIFICATION; DNA SEQUENCE; GENETICS; INDEL MUTATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROCHLOROCOCCUS; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; SYNECHOCOCCUS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CONSERVED SEQUENCE; DNA, BACTERIAL; GENOME, BACTERIAL; INDEL MUTATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROCHLOROCOCCUS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SYNECHOCOCCUS;

EID: 77149149384     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-24     Document Type: Article

References (85)

1. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. R Rippka J Deruelles JB Waterbury M Herdman RY Stanier, J Gen Microbiol 1979 111 1 61
2. The Phototrophic Prokaryotes. EN Kondratieva N Pfennig HG Truper, The Prokaryotes New York: Springer-Verlag, Balows A, Truper HG, Dworkin M, Harder W, Schleifer KH, 1992 312 330
3. Phylum BX. Cyanobacteria: Oxygenic Photosynthetic Bacteria. RW Castenholz, Bergey's Manual of Systematic Bacteriology New York: Springer, Boone DR, Castenholz RW, 2001 474 487
4. Morphological and habitat evolution in the Cyanobacteria using a compartmentalization approach. P Sanchez-Baracaldo PK Hayes CE Blank, Geobiology 2005 3 145 165 10.1111/j.1472-4669.2005.00050.x (Pubitemid 43942995)
5. Morphological and genetic criteria in the taxonomy of Cyanophyta/Cyanobacteria. A Wilmotte S Golubic, Arhciv fur Hydrobiologie 1991 64 1 24
6. Phylogenetic Relationships among the Cyanobacteria Based on 16S rRNA Sequences. A Wilmotte M Herdman, Bergey's Manual of Systematic Bacteriology New York: Springer, Boone DR, Castenholz RW, 2001 487 493
7. The RDP-II (Ribosomal Database Project). BL Maidak JR Cole TG Lilburn CT Parker Jr PR Saxman RJ Farris GM Garrity GJ Olsen TM Schmidt JM Tiedje, Nucleic Acids Res 2001 29 173 174 10.1093/nar/29.1.173 11125082
8. The Revised Road Map to the Manual. GM Garrity JA Bell TG Lilburn, Bergey's Manual of Systematic Bacteriology, Part A, Introductory Essays New York: Springer, Brenner DJ, Krieg NR, Staley JT, 2005 2 159 220 full-text
9. A proposal for further integration of the cyanobacteria under the Bacteriological Code. A Oren, Int J Syst Evol Microbiol 2004 54 1895 1902 10.1099/ijs.0.03008-0 15388760
10. Nomenclature of Cyanophyta/Cyanobacteria: roundtable on the unification of the nomenclature under the Botanical and Bacteriological Codes. L Hoffmann, Algological Studies 2005 117 13 29 10.1127/1864-1318/2005/0117-0013
11. Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families. WD Swingley RE Blankenship J Raymond, Mol Biol Evol 2008 25 643 654 10.1093/molbev/msn034 18296704
12. Genome evolution in cyanobacteria: the stable core and the variable shell. T Shi PG Falkowski, Proc Natl Acad Sci USA 2008 105 2510 2515 10.1073/pnas.0711165105 18268351
13. Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. O Zhaxybayeva JP Gogarten RL Charlebois WF Doolittle RT Papke, Genome Res 2006 16 1099 1108 10.1101/gr.5322306 16899658
14. Prokaryote taxonomy online: challenges ahead. A Oren E Stackebrandt, Nature 2002 419 15 10.1038/419015c 12214210
15. System of Cyanoprokaryotes (Cyanobacteria) - State in 2004. L Hoffmann J Komarek J kastovsky, Algological Studies 2005 95 1155 10.1127/1864-1318/2005/ 0117-0095
16. Critical Issues in Bacterial Phylogenies. RS Gupta E Griffiths, Theor Popul Biol 2002 61 423 434 10.1006/tpbi.2002.1589 12167362
17. Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships Among Archaebacteria, Eubacteria, and Eukaryotes. RS Gupta, Microbiol Mol Biol Rev 1998 62 1435 1491 9841678
18. The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes. RS Gupta, FEMS Microbiol Rev 2000 24 367 402 10.1111/j.1574-6976.2000.tb00547.x 10978543
19. Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids. CF Delwiche M Kuhsel JD Palmer, Mol Phylogenet Evol 1995 4 110 128 10.1006/mpev.1995.1012 7663757
20. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. MC Rivera JA Lake, Science 1992 257 74 76 10.1126/science.1621096 1621096
21. Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae. E Griffiths RS Gupta, Microbiology 2007 153 2648 2654 10.1099/mic.0.2007/009118-0 17660429
22. Molecular signatures in protein sequences that are characteristic of Cyanobacteria and plastid homologues. RS Gupta M Pereira C Chandrasekera V Johari, Int J Syst Evol Microbiol 2003 53 1833 1842 10.1099/ijs.0.02720-0 14657112
23. Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades. RS Gupta, Int J Syst Evol Microbiol 2009 59 2510 2526 10.1099/ijs.0.005678-0 19622649
24. The origin and evolution of plastids and their genomes. JD Palmer CF Delwiche, Molecular Systematics of Plants II DNA Sequencing Norwell, MA, USA. Kluwer Academic Publishers, Sotis DE, Soltis PE, Doyle JJ, 1998 375 409
25. Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups. B Gao R Parmanathan RS Gupta, Antonie van Leeuwenhoek 2006 90 69 91 10.1007/s10482-006-9061-2 16670965
26. Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species. RS Gupta E Lorenzini, BMC Evol Biol 2007 7 71 10.1186/1471-2148-7-71 17488508
27. Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups. RS Gupta A Mok, BMC Microbiol 2007 7 106 10.1186/1471-2180-7-106 18045498
28. Signature genes as a phylogenomic tool. BE Dutilh B Snel TJ Ettema MA Huynen, Mol Biol Evol 2008 25 1659 1667 10.1093/molbev/msn115 18492663
29. Cyanobacterial signatures genes. KA Martin JL Siefert S Yerrapragada Y Lu TZ McNeill PA Moreno GM Weinstock WR Widger GE Fox, Photosynth Res 2003 75 211 221 10.1023/A:1023990402346 16228602
30. The cyanobacterial genome core and the origin of photosynthesis. AY Mulkidjanian EV Koonin KS Makarova SL Mekhedov A Sorokin YI Wolf A Dufresne F Partensky H Burd D Kaznadzey R Haselkorn MY Galperin, Proc Natl Acad Sci USA 2006 103 13126 13131 10.1073/pnas.0605709103 16924101
31. Toward automatic reconstruction of a highly resolved tree of life. FD Ciccarelli T Doerks C von Mering CJ Creevey B Snel P Bork, Science 2006 311 1283 1287 10.1126/science.1123061 16513982
32. Horizontal gene transfer, genome innovation and evolution. JP Gogarten JP Townsend, Nat Rev Microbiol 2005 3 679 687 10.1038/nrmicro1204 16138096
33. Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus. O Zhaxybayeva WF Doolittle RT Papke JP Gogarten, Genome Biology and Evolution 2009 1 325 339 10.1093/gbe/evp032
34. Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria). JT Herbeck PH Degnan JJ Wernegreen, Mol Biol Evol 2005 22 520 532 10.1093/molbev/msi036 15525700
35. The genetic core of the universal ancestor. JK Harris ST Kelley GB Spiegelman NR Pace, Genome Res 2003 13 407 412 10.1101/gr.652803 12618371
36. Complete genome structure of Gloeobacter violaceus PCC a cyanobacterium that lacks thylakoids. Y Nakamura T Kaneko S Sato M Mimuro H Miyashita T Tsuchiya S Sasamoto A Watanabe K Kawashima Y Kishida C Kiyokawa M Kohara M Matsumoto A Matsuno N Nakazaki S Shimpo C Takeuchi M Yamada S Tabata, DNA Res 7421 10 137 145 10.1093/dnares/10.4.137
37. Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains. D Honda A Yokota J Sugiyama, J Mol Evol 1999 48 723 739 10.1007/PL00006517 10229577
38. Evolutionary relationships among cyanobacteria and green chloroplasts. SJ Giovannoni S Turner GJ Olsen S Barns DJ Lane NR Pace, J Bacteriol 1988 170 3584 3592 3136142
39. The phylogenetic relationships of cyanobacteria inferred from 16S rRNA, gyrB, rpoC1 and rpoD1 gene sequences. PS Seo A Yokota, J Gen Appl Microbiol 2003 49 191 203 10.2323/jgam.49.191 12949700
40. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. G Rocap FW Larimer J Lamerdin S Malfatti P Chain NA Ahlgren A Arellano M Coleman L Hauser WR Hess ZI Johnson M Land D Lindell AF Post W Regala M Shah SL Shaw C Steglich MB Sullivan CS Ting A Tolonen EA Webb ER Zinser SW Chisholm, Nature 2003 424 1042 1047 10.1038/nature01947 12917642
41. Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. G Rocap DL Distel JB Waterbury SW Chisholm, Appl Environ Microbiol 2002 68 1180 1191 10.1128/AEM.68.3.1180-1191.2002 11872466
42. Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria. B Gao R Mohan RS Gupta, Int J Syst Evol Microbiol 2009 59 234 247 10.1099/ijs.0.002741-0 19196760
43. Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. B Gao RS Gupta, BMC Genomics 2007 8 86 10.1186/1471-2164-8-86 17394648
44. Evolutionary Origins of Genomic Repertoires in Bacteria. E Lerat V Daubin H Ochman NA Moran, PLoS Biol 2005 3 130 10.1371/journal.pbio.0030130 15799709
45. Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina. WD Swingley M Chen PC Cheung AL Conrad LC Dejesa J Hao BM Honchak LE Karbach A Kurdoglu S Lahiri SD Mastrian H Miyashita L Page P Ramakrishna S Satoh WM Sattley Y Shimada HL Taylor T Tomo T Tsuchiya ZT Wang J Raymond M Mimuro RE Blankenship JW Touchman, Proc Natl Acad Sci USA 2008 105 2005 2010 10.1073/pnas.0709772105 18252824
46. Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. Y Nakamura T Kaneko S Sato M Ikeuchi H Katoh S Sasamoto A Watanabe M Iriguchi K Kawashima T Kimura Y Kishida C Kiyokawa M Kohara M Matsumoto A Matsuno N Nakazaki S Shimpo M Sugimoto C Takeuchi M Yamada S Tabata, DNA Research 2002 9 123 130 10.1093/dnares/9.4.123 12240834 (Pubitemid 36307035)
47. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. S Turner KM Pryer VP Miao JD Palmer, J Eukaryot Microbiol 1999 46 327 338 10.1111/j.1550-7408.1999.tb04612.x 10461381
48. Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. T Kaneko Y Nakamura CP Wolk T Kuritz S Sasamoto A Watanabe M Iriguchi A Ishikawa K Kawashima T Kimura Y Kishida M Kohara M Matsumoto A Matsuno A Muraki N Nakazaki S Shimpo M Sugimoto M Takazawa M Yamada M Yasuda S Tabata, DNA Res 2001 8 205 213 10.1093/dnares/8.5.205 11759840
49. Distribution of split DnaE inteins in cyanobacteria. J Caspi G Amitai O Belenkiy S Pietrokovski, Mol Microbiol 2003 50 1569 1577 10.1046/j.1365-2958. 2003.03825.x 14651639
50. Heterocyst formation in cyanobacteria. DG Adams, Curr Opin Microbiol 2000 3 618 624 10.1016/S1369-5274(00)00150-8 11121783
51. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. A Dufresne M Salanoubat F Partensky F Artiguenave IM Axmann V Barbe S Duprat MY Galperin EV Koonin F Le Gall KS Makarova M Ostrowski S Oztas C Robert IB Rogozin DJ Scanlan NT De Marsac J Weissenbach P Wincker YI Wolf WR Hess, Proc Natl Acad Sci USA 2003 100 10020 10025 10.1073/pnas.1733211100 12917486
52. The genome of a motile marine Synechococcus. B Palenik B Brahamsha FW Larimer M Land L Hauser P Chain J Lamerdin W Regala EE Allen J McCarren I Paulsen A Dufresne F Partensky EA Webb J Waterbury, Nature 2003 424 1037 1042 10.1038/nature01943 12917641
53. Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. B Palenik Q Ren CL Dupont GS Myers JF Heidelberg JH Badger R Madupu WC Nelson LM Brinkac RJ Dodson AS Durkin SC Daugherty SA Sullivan H Khouri Y Mohamoud R Halpin IT Paulsen, Proc Natl Acad Sci USA 2006 103 13555 13559 10.1073/pnas.0602963103 16938853
54. Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme. M Sugishima CT Migita X Zhang T Yoshida K Fukuyama, Eur J Biochem 2004 271 4517 4525 10.1111/j.1432-1033.2004.04411.x 15560792
55. Conformational changes in the catalytic cycle of protochlorophyllide oxidoreductase: what lessons can be learnt from dihydrofolate reductase? DJ Heyes NS Scrutton, Biochem Soc Trans 2009 37 354 357 10.1042/BST0370354 19290861
56. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. LR Moore G Rocap SW Chisholm, Nature 1998 393 464 467 10.1038/30965 9624000
57. Niche adaptation in ocean cyanobacteria. MJ Ferris B Palenik, Nature 1998 396 226 228 10.1038/24297 (Pubitemid 28541378)
58. Structural features and the persistence of acquired proteins. HP Narra MH Cordes H Ochman, Proteomics 2008 8 4772 4781 10.1002/pmic.200800061 18924109
59. Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria. B Gao R Mohan RS Gupta, Int J Syst Evol Microbiol 2009 59 234 247 10.1099/ijs.0.002741-0 19196760
60. Analysis of singleton ORFans in fully sequenced microbial genomes. N Siew D Fischer, Proteins 2003 53 241 251 10.1002/prot.10423 14517975
61. The fate of new bacterial genes. CH Kuo H Ochman, FEMS Microbiol Rev 2009 33 38 43 10.1111/j.1574-6976.2008.00140.x 19054121
62. Persistence drives gene clustering in bacterial genomes. G Fang EP Rocha A Danchin, BMC Genomics 2008 9 4 10.1186/1471-2164-9-4 18179692
63. Molecular signatures (unique proteins and conserved Indels) that are specific for the epsilon proteobacteria (Campylobacterales). RS Gupta, BMC Genomics 2006 7 167 10.1186/1471-2164-7-167 16817973
64. Chlamydiae-specific proteins and indels: novel tools for studies. RS Gupta E Griffiths, Trends Microbiol 2006 14 527 535 10.1016/j.tim.2006.10.002 17049238
65. Prokaryotic evolution in light of gene transfer. JP Gogarten WF Doolittle JG Lawrence, Mol Biol Evol 2002 19 2226 2238 12446813
66. Whole-genome analysis of photosynthetic prokaryotes. J Raymond O Zhaxybayeva JP Gogarten SY Gerdes RE Blankenship, Science 2002 298 1616 1620 10.1126/science.1075558 12446909
67. Rare genomic changes as a tool for phylogenetics. A Rokas PW Holland, Trends Ecol Evol 2000 15 454 459 10.1016/S0169-5347(00)01967-4 11050348
68. Ancient gene transfer as a tool in phylogenetic reconstruction. J Huang JP Gogarten, Methods Mol Biol 2009 532 127 139 full-text 19271182
69. Quantitative phylogenetic assessment of microbial communities in diverse environments. C von Mering P Hugenholtz J Raes SG Tringe T Doerks LJ Jensen N Ward P Bork, Science 2007 315 1126 1130 10.1126/science.1133420 17272687
70. Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. T Doerks C von Mering P Bork, Nucleic Acids Res 2004 32 6321 6326 10.1093/nar/gkh973 15576358
71. How essential are nonessential genes? G Fang E Rocha A Danchin, Mol Biol Evol 2005 22 2147 2156 10.1093/molbev/msi211 16014871
72. The power of phylogenetic comparison in revealing protein function. Z Yang, Proc Natl Acad Sci USA 2005 102 3179 3180 10.1073/pnas.0500371102 15728394
73. Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth. B Singh RS Gupta, Mol Genet Genomics 2009 281 361 373 10.1007/s00438-008-0417-3 19127371
74. Identifying protein function - a call for community action. RJ Roberts, PLoS Biol 2004 2 42 10.1371/journal.pbio.0020042 15024411
75. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. MY Galperin EV Koonin, Nucleic Acids Res 2004 32 5452 5463 10.1093/nar/gkh885 15479782
76. From protein sequence to function. A Danchin, Curr Opin Struct Biol 1999 9 363 367 10.1016/S0959-440X(99)80049-9 10408894
77. Multiple sequence alignment with Clustal x. F Jeanmougin JD Thompson M Gouy DG Higgins TJ Gibson, Trends Biochem Sci 1998 23 403 405 10.1016/S0968-0004(98)01285-7 9810230
78. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. J Castresana, Mol Biol Evol 2000 17 540 552 10742046
79. M Kimura, The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press 1983
80. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Y Van de Peer R De Wachter, Comput Appl Biosci 1994 10 569 570 7828077
81. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. HA Schmidt K Strimmer M Vingron A von Haeseler, Bioinformatics 2002 18 502 504 10.1093/bioinformatics/18.3.502 11934758
82. Gapped BLAST and PSI-BLAST: a new generation of protein databases search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Research 1997 25 3389 3402 10.1093/nar/25.17.3389 9254694
83. Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization. C Sugita K Ogata M Shikata H Jikuya J Takano M Furumichi M Kanehisa T Omata M Sugiura M Sugita, Photosynth Res 2007 93 55 67 10.1007/s11120-006-9122-4 17211581
84. Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. A Dufresne M Ostrowski DJ Scanlan L Garczarek S Mazard BP Palenik IT Paulsen NT De Marsac P Wincker C Dossat S Ferriera J Johnson AF Post WR Hess F Partensky, Genome Biol 2008 9 90 10.1186/gb-2008-9-5-r90 18507822
85. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. T Kaneko S Sato H Kotani A Tanaka E Asamizu Y Nakamura N Miyajima M Hirosawa M Sugiura S Sasamoto T Kimura T Hosouchi A Matsuno A Muraki N Nakazaki K Naruo S Okumura S Shimpo C Takeuchi T Wada A Watanabe M Yamada M Yasuda S Tabata, DNA Research 1996 3 109 136 10.1093/dnares/3.3.109 8905231 (Pubitemid 126682789)