Evolution of photosynthetic prokaryotes: A maximum-likelihood mapping approach

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 358, Issue 1429, 2003, Pages 223-230

  Raymond, Jason ^a   Zhaxybayeva, Olga ^b   Gogarten, J Peter ^b   Blankenship, Robert E ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Evolution; Photosynthetic bacteria; Whole genome comparison

Indexed keywords

EVOLUTION; PHOTOSYNTHESIS; PROKARYOTE;

BACTERIA (MICROORGANISMS); PHOTOBACTERIA; PROKARYOTA;

EID: 0037471701     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.2002.1181     Document Type: Conference Paper

References (47)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. 1990 Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
2. Aravind, L., Tatusov, R. L., Wolf, Y. I., Walker, D. R. & Koonin, E. V. 1998 Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14, 442-444.
3. Asai, T., Zaporojets, D., Squires, C. & Squires, C. L. 1999 An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Proc. Natl Acad. Sci. USA 96, 1971-1976.
4. Baymann, F., Brugna, M., Muhlenhoff, U. & Nitschke, W. 2001 Daddy, where did (PS) I come from? Biochim. Biophys. Acta Bioenergetics 1507, 291-310.
5. Bellemare, G., Vigne, R. & Jordan, B. R. 1973 Interaction between Escherichia coli ribosomal proteins and 5S RNA molecules: recognition of prokaryotic 5S RNAs and rejection of eukaryotic 5S RNAs. Biochimie 55, 29-35.
6. Bergthorsson, U. & Ochman, H. 1998 Distribution of chromosome length variation in natural isolates of Escherichia coli. Mol. Biol. Evol. 15, 6-16.
7. Blankenship, R. E. 2002 Molecular mechanisms of photosynthesis. Oxford: Blackwell Science.
8. Blankenship, R. E. & Hartman, H. 1998 The origin and evolution of oxygenic photosynthesis. Trends Biochem. Sci. 23, 94-97.
9. Boucher, Y., Nesbo, C. L. & Doolittle, W. F. 2001 Microbial genomes: dealing with diversity. Curr. Opin. Microbiol. 4, 285-289.
10. Daya-Grosjean, L., Geisser, M., Stoffler, G. & Garret, R. A. 1973 Heterologous protein-RNA interactions in bacterial ribosomes. FEBS Lett. 37, 17-20.
11. Des Marais, D. J. 2000 Evolution. When did photosynthesis emerge on Earth? Science 289, 1703-1705.
12. Doolittle, W. F. 1999 Lateral genomics. Trends Cell Biol. 9, M5-M8.
13. Drummond, A. & Strimmer, K. 2001 PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 17, 662-663.
14. Felsenstein, J. 1989 PHYLIP: phylogeny inference package (v. 3.2). Cladistics 5, 164-166.
15. Gaidos, E. J., Nealson, K. H. & Kirschvink, J. L. 1999 Life in ice-covered oceans. Science 284, 1631-1633.
16. Gest, H. & Favinger, J. L. 1983 Heliobacterium chlorum, an anoxygenic brownish-green photosynthetic bacterium containing a new form of bacteriochlorophyll. Arch. Microbiol. 136, 11-16.
17. Gogarten, J. P. & Olendzenski, L. 1999 Orthologs, paralogs and genome comparisons. Curr. Opin. Genet. Dev. 9, 630-636.
18. Gupta, R. S., Mukhtar, T. & Singh, B. 1999 Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis. Mol. Microbiol. 32, 893-906.
19. Hall, T. A. 1999 BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95-98.
20. Igarashi, N., Harada, J., Nagashima, S., Matsuura, K., Shimada, K. & Nagashima, K. V. 2001 Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria. J. Mol. Evol. 52, 333-341.
21. Jain, R., Rivera, M. C. & Lake, J. A. 1999 Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl Acad. Sci. USA 96, 3801-3806.
22. Kumar, S., Tamura, K. & Nei, M. 1994 MEGA: molecular evolutionary genetics analysis software for microcomputers. Comput. Appl. Biosci. 10, 189-191.
23. Lawrence, J. 1999 Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9, 642-648.
24. Maidak, B. L., Cole, J. R., Lilburn, T. G., Parker Jr, C. T., Saxman, P. R., Farris, R. J., Garrity, G. M., Olsen, G. J., Schmidt, T. M. & Tiedje, J. M. 2001 The RDP-II (ribosomal database project). Nucleic Acids Res. 29, 173-174.
25. Naylor, G. W., Addlesee, H. A., Gibson, L. C. D. & Hunter, C. N. 1999 The photosynthesis gene cluster of Rhodobacter sphaeroides. Photosynthesis Res. 62, 121-139.
26. Nesbo, C. L, Boucher, Y. & Doolittle, W. F. 2001 Defining the core of nontransferable prokaryotic genes: the euryarchaeal core. J. Mol. Evol. 53, 340-350.
27. Nomura, M., Traub, P. & Bechmann, H. 1968 Hybrid 30S ribosomal particles reconstituted from components of different bacterial origins. Nature 219, 793-799.
28. Olson, J. M. & Pierson, B. K. 1987 Evolution of reaction centers in photosynthetic prokaryotes. Int. Rev. Cytol. 108, 209-248.
29. Overmann, J. & Schubert, K. 2002 Phototrophic consortia: model systems for symbiotic interrelations between prokaryotes. Arch. Microbiol. 177, 201-208.
30. Oyaizu, H., Debrunner-Vossbrinck, B., Mandelco, L., Studier, J. A. & Woese, C. R. 1987 The green non-sulfur bacteria: a deep branching in the eubacterial line of descent. Syst. Appl. Microbiol. 9, 47-53.
31. Perna, N. T. (and 27 others) 2001 Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529-533.
32. Raymond, J., Zhaxybayeva, O., Gogarten, J. P., Gerdes, S. Y. & Blankenship, R. E. 2002 Whole genome analysis of photosynthetic prokaryotes. Science. (In the press.)
33. Rye, R. & Holland, H.D. 1998 Paleosols and the evolution of atmospheric oxygen: a critical review. Am. J. Sci. 298, 621-672.
34. Schmidt, H. A., Strimmer, K., Vingron, M. & von Haeseler, A. 2002 TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-504.
35. Strimmer, K. & von Haeseler, A. 1997 Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl Acad. Sci. USA 94, 6815-6819.
36. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. 1997 A genomic perspective on protein families. Science 278, 631-637.
37. Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. 2000 The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33-36.
38. Walker, D. R. & Koonin, E. V. 1997 SEALS: a system for easy analysis of lots of sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5, 333-339.
39. Woese, C. R. 1987 Bacterial evolution. Microbiol. Rev. 51, 221-271.
40. Woese, C. R. 2000 Interpreting the universal phylogenetic tree. Proc. Natl Acad. Sci. USA 97, 8392-8396.
41. Wolstencroft, R. D. & Raven, J. A. 2002 Photosynthesis: likelihood of occurrence and possibility of detection on Earth-like planets. Icarus 157, 535-548.
42. Wrede, P. & Erdmann, V. A. 1973 Activities of B. stearothermophilus 50 S ribosomes reconstituted with prokaryotic and eukaryotic 5 S RNA. FEBS Lett. 33, 315-319.
43. Xiong, J. & Bauer, C. E. 2002 Complex evolution of photosynthesis. A. Rev. Plant Physiol. Plant Mol. Biol. 53, 503-521.
44. Xiong, J., Inoue, K. & Bauer, C. E. 1998 Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis. Proc. Natl Acad. Sci. USA 95, 14 851-14 856.
45. Xiong, J., Fischer, W. M., Inoue, K., Nakahara, M. & Bauer, C. E. 2000 Molecular evidence for the early evolution of photosynthesis. Science 289, 1724-1730.
46. Yap, W. H., Zhang, Z. & Wang, Y. 1999 Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J. Bacteriol. 181, 5201-5209.
47. Zhaxybayeva, O. & Gogarten, J. P. 2002 Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses. BMC Genomics 3, 4.