Chapter 6 : Comparing Microbial Genomes: How the Gene Set Determines the Lifestyle

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Sequencing of complete microbial genomes, pioneered in 1995 by J. C. Venter and colleagues, continues at an ever-increasing pace. The availability of complete genome sequences has had a major impact on the view of microbial evolution. Comparative analysis of the complete genomes of several diverse microorganisms on the basis of such properties as codon usage, open reading frame (ORF) density, and the lengths of coding regions shows many common trends in their organization. Comparison of the complete genomes of closely related bacterial species, and , showed a significant degree of synteny between these organisms. Homologous genes and their products can be classified into orthologs, related by vertical descent (e.g., speciation), and paralogs, related by duplication. Pathogenic bacteria import a variety of metabolites from their hosts, which allows them to shed genes encoding enzymes for some of the metabolic pathways. Comparative analysis of the available microbial genomes reveals both conservation of protein families and diversity of gene repertoires and gene organization among organisms that belong to diverse phylogenetic lineages. In many cases, bacterial genes seem to have substituted for the original genes of the archaeal-eukaryotic lineage, making phylogenetic reconstructions extremely complicated.

Citation: Galperin M, Tatusov R, Koonin E. 1999. Comparing Microbial Genomes: How the Gene Set Determines the Lifestyle, p 91-108. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch6
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Image of FIGURE 1

Lengths of proteins encoded in completely sequenced genomes. The lengths of predicted ORFs were averaged over 50-amino-acid intervals and plotted as fractions of the total number of ORFs predicted in each particular organism. The plots were normalized so that the total area under each curve is the same. Data for sp., and were added to the plots of length distributions in proteobacteria (A), low-G+C gram-positive bacteria (B), and archaea (C), respectively, for illustrative purposes. sp.; .

Citation: Galperin M, Tatusov R, Koonin E. 1999. Comparing Microbial Genomes: How the Gene Set Determines the Lifestyle, p 91-108. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch6
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Image of FIGURE 2

Functional roles of conserved proteins in completely sequenced genomes. Each pie chart represents the numbers of proteins in each genome that are not included in the current set of COGs (the largest sector in every genome), and clockwise, the numbers of proteins that are responsible for (i) information storage and processing, including transcription, translation, DNA replication, recombination, and repair, and ribosome biogenesis; (ii) cellular processes, such as membrane and cell wall biogenesis, protein folding, and secretion; (iii) cellular metabolism, including carbohydrate, amino acid, lipid, and nucleotide metabolism and energy production and conversion. The last sector indicates poorly characterized conserved proteins. The total number is larger than the number of proteins in each particular genome, as different domains of the same protein may be included in different COGs.

Citation: Galperin M, Tatusov R, Koonin E. 1999. Comparing Microbial Genomes: How the Gene Set Determines the Lifestyle, p 91-108. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch6
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Image of FIGURE 3

Conservation of the pyrimidine biosynthesis pathway in various microorganisms. The enzymes are listed under gene names. The COG numbers are from the COG database (www.ncbi.nlm.nih.gov/COG [ ]). The designations of species in the phylogenetic patterns are as follows: E, H, U, X, B, G, M. P, R, O, L, I, C. Q, C, sp.; M, ; T, M. A, K, P. Y, . The uppercase letters indicate organisms that have proteins in a corresponding COG; the lowercase letters indicate the organisms that are not represented in a given COG. Nonorthologous enzymes catalyzing the same biochemical reaction are shown side by side, where known. Different subunits or conserved domains of the same enzyme are shown in the same frame, one under the other.

Citation: Galperin M, Tatusov R, Koonin E. 1999. Comparing Microbial Genomes: How the Gene Set Determines the Lifestyle, p 91-108. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch6
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Image of FIGURE 4

Conservation of the purine biosynthesis pathway in various microorganisms. For an explanation of the symbols, see the legend to Fig. 3 .

Citation: Galperin M, Tatusov R, Koonin E. 1999. Comparing Microbial Genomes: How the Gene Set Determines the Lifestyle, p 91-108. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch6
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1. Andersson, S. G.,, A. Zomorodipour,, J. O. Andersson,, T. Sicheritz-Ponten,, U. C. Alsmark,, R. M. Podowski,, A. K. Naslund,, A. S. Eriksson,, H. H. Winkler,, and C. G. Kurland. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396: 133 140.
2. Arndt, E. 1990. Nucleotide sequence of four genes encoding ribosomal proteins from the 'S10 and spectinomycin' operon equivalent region in the archaebacterium Halobacterium marismortui . FEBS Lett. 267: 193 198.
3. Auer, J.,, G. Spicker,, and A. Bock. 1989. Organization and structure of the Methanococcus transcriptional unit homologous to the Escherichia coli "spectinomycin operon." Implications for the evolutionary relationship of 70 S and 80 S ribosomes. J. Mol. Biol. 209: 21 36.
4. Basrai, M. A.,, P. Hieter,, and J. D. Boeke. 1997. Small open reading frames: beautiful needles in the haystack. Genome Res. 7: 768 771.
5. Blattner, F. R.,, G. Plunkett III,, C. A. Bloch,, N. T. Perna,, V. Burland,, M. Riley,, J. Collado-Vides,, J. D. Glasner,, C. K. Rode,, G. F. Mayhew,, J. Gregor,, N. W. Davis,, H. A. Kirkpatrick,, M. A. Goeden,, D. J. Rose,, B. Mau,, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453 1474.
6. Bocchetta, M.,, E. Ceccarelli,, R. Creti,, A. M. Sanangelantoni,, O. Tiboni,, and P. Cammarano. 1995. Arrangement and nucleotide sequence of the gene ( fus) encoding elongation factor G (EF-G) from the hyperthermophilic bacterium Aquifex pyrophilus: phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the EF-G/fus sequences. J. Mol. Evol 41: 803 812.
7. Braun, E. L.,, E. K. Fuge,, P. A. Padilla,, and M. Werner-Washburne. 1996. A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family. J. Bacteriol. 178: 6865 6872.
8. Brenner, S. E.,, T. Hubbard,, A. Murzin,, and C. Chothia. 1995. Gene duplications in H. influenzae . Nature 378: 140.
9. Brown, J. R.,, and W. F. Doolittle. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61: 456 502.
10. Bult, C. J.,, O. White,, G. J. Olsen,, L. Zhou,, R. D. Fleischmann,, G. G. Sutton,, J. A. Blake,, L. M. FitzGerald,, R. A. Clayton,, J. D. Gocayne,, A. R. Kerlavage,, B. A. Dougherty,, J.-F. Tomb,, M. D. Adams,, C. I. Reich,, R. Overbeek,, E. F. Kirkness,, K. G. Weinstock,, J. M. Merrick,, A. Glodek,, J. L. Scott,, N. S. M. Geoghagen,, J. F. Weidman,, J. L. Fuhrmann,, D. Nguyen,, T. R. Utterback,, J. M. Kelley,, J. D. Peterson,, P. W. Sadow,, M. C. Hanna,, M. D. Cotton,, K. M. Roberts,, M. A. Hurst,, B. P. Kaine,, M. Borodovsky,, H.-P. Klenk,, C. M. Fraser,, H. O. Smith,, C. R. Woese,, and J. C. Venter. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii . Science 273: 1058 1073.
11. Clayton, R. A.,, O. White,, K. A. Ketchum,, and J. C. Venter. 1997. The first genome from the third domain of life. Nature 387: 459 462.
12. Cole, S. T.,, R. Brosch,, J. Parkhill,, T. Garnier,, C. Churcher,, D. Harris,, S. V. Gordon,, K. Eiglmeier,, S. Gas,, C. E. Barry III,, F. Tekaia,, K. Badcock,, D. Basham,, D. Brown,, T. Chillingworth,, R. Connor,, R. Davies,, K. Devlin,, T. Feltwell,, S. Gentles,, N. Hamlin,, S. Holroyd,, T. Hornsby,, K. Jagels,, and B. G. Barrell. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537 544.
13. Dandekar, T.,, B. Snel,, M. Huynen,, and P. Bork. 1998. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23: 324 328.
14. Das, S.,, L. Yu,, C. Gaitatzes,, R. Rogers,, J. Freeman,, J. Bienkowska,, R. M. Adams,, T. F. Smith,, and J. Lindelien. 1997. Biology's new Rosetta stone. Nature 385: 29 30.
15. Deckert, G.,, P. V. Warren,, T. Gaasterland,, W. G. Young,, A. L. Lenox,, D. E. Graham,, R. Overbeek,, M. A. Snead,, M. Keller,, M. Aujay,, R. Huber,, R. A. Feldman,, J. M. Short,, G.J. Olsen,, and R. V. Swanson. 1998. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus . Nature 392: 353 358.
16. Doerks, T.,, A. Bairoch,, and P. Bork. 1998. Protein annotation: detective work for function prediction. Trends Genet. 14: 248 250.
17. Edgell, D. R.,, and W. F. Doolittle. 1997. Archaea and the origin(s) of DNA replication proteins. Cell 89: 995 998.
18. Elagoz, A.,, A. Abdi,, J. C. Hubert,, and B. Kammerer. 1996. Structure and organisation of the pyrimidine biosynthesis pathway genes in Lactobacillus plantarum: a PCR strategy for sequencing without cloning. Gene 182: 37 43.
19. Fitch, W. M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19: 99 113.
20. Fitch, W. M. 1995. Uses for evolutionary trees. Phil. Trans. R. Soc. Lond. B 349: 93 102.
21. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J.-F. Tomb,, B. A. Dougherty,, J. M. Merrick,, K. McKenney,, G. G. Sutton,, W. FitzHugh,, C. Fields,, J. D. Gocayne,, J. Scott,, R. Shirley,, L.-I. Liu,, A. Glodek,, J. M. Kelley,, J. F. Weidman,, C. A. Phillips,, T. Spriggs,, E. Hedblom,, M. D. Cotton,, T. R. Utterback,, M. C. Hanna,, D. Nguyen,, D. M. Saudek,, R. C. Brandon,, L. D. Fine,, J. L. Frichtman,, J. L. Fuhrmann,, N. S. M. Geoghagen,, C. L. Gnehm,, L. A. McDonald,, K. V. Small,, C. M. Fräser,, H. O. Smith,, and J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496 512.
22. Fraser, C. M.,, S. Casjens,, W. M. Huang,, G. G. Sutton,, R. Clayton,, R. Lathigra,, O. White,, K. A. Ketchum,, R. Dodson,, E. K. Hickey,, M. Gwinn,, B. Dougherty,, J.-F. Tomb,, R. D. Fleischmann,, D. Richardson,, J. Peterson,, A. R. Kerlavage,, J. Quackenbush,, S. Salzberg,, M. Hanson,, R. van Vugt,, N. Palmer,, M. D. Adams,, J. Gocayne,, J. Weidman,, T. Utterback,, L. Watthey,, L. McDonald,, P. Artiach,, C. Bowman,, S. Garland,, C. Fujii,, M. D. Cotton,, K. Horst,, K. Roberts,, B. Hatch,, H. O. Smith,, and J. C. Venter. 1997. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390: 580 586.
23. Fraser, C. M.,, J. D. Gocayne,, O. White,, M. D. Adams,, R. A. Clayton,, R. D. Fleischmann,, C. J. Bult,, A. R. Kerlavage,, G. Sutton,, J. M. Kelley,, J. L. Fritchman,, J. F. Weidman,, K. V. Small,, M. Sandusky,, J. Fuhrmann,, D. Nguyen,, T. R. Utterback,, D. M. Saudek,, C. A. Phillips,, J. M. Merrick,, J.-F. Tomb,, B. A. Dougherty,, K. F. Bott,, P.-C. Hu,, T. S. Lucier,, S. N. Peterson,, H. O. Smith,, C. A. Hutchinson III,, and J. C. Venter. 1995. The minimal gene complement of Mycoplasma genitalium . Science 270: 397 403.
24. Galperin, M. Y.,, and E. V. Koonin. 1997. A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity. Protein Sci. 6: 2639 2643.
25. Galperin, M. Y.,, and E. V. Koonin. 1997. Sequence analysis of an exceptionally conserved operon suggests enzymes for a new link between histidine and purine biosynthesis. Mol. Microbiol. 24: 443 445.
26. Gelfand, M. S.,, and E. V. Koonin. 1997. Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. Nucleic Acids Res. 25: 2430 2439.
27. Ghim, S. Y.,, and J. Neuhard. 1994. The pyrimidine biosynthesis Operon of the thermophile Bacillus caldolyticus includes genes for uracil phosphoribosyltransferase and uracil permease. J. Bacteriol. 176: 3698 3707.
28. Goffeau, A.,, B. G. Barrell,, H. Bussey,, R. W. Davis,, B. Dujon,, H. Feldmann,, F. Galibert,, J. D. Hoheisel,, C. Jacq,, M. Johnston,, E. J. Louis,, H. W. Mewes,, Y. Murakami,, P. Philippsen,, H. Tettelin,, and S. G. Oliver. 1996. Life with 6000 genes. Science 274: 546 567.
29. Himmelreich, R.,, H. Hilbert,, H. Plagens,, E. Pirkl,, B. C. Li,, and R. Herrmann. 1996. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae . Nucleic Acids Res. 24: 4420 4449.
30. Himmelreich, R.,, H. Plagens,, H. Hilbert,, B. Reiner,, and R. Herrmann. 1997. Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium . Nucleic Acids Res. 25: 701 712.
31. Huynen, M. A.,, and P. Bork. 1998. Measuring genome evolution. Proc. Natl. Acad. Sci. USA. 95: 5849 5856.
32. Itoh, T. 1988. Complete nucleotide sequence of the ribosomal 'A' protein Operon from the archaebacterium, Halobacterium halobium . Eur. J. Biochem. 176: 297 303.
33. Kaneko, T.,, 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,, and S. Tabata. 1996. 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. DNA Res. 3: 109 136.
34. Karlin, S.,, J. Mrazek,, and A. M. Campbell. 1997. Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol. 179: 3899 3913.
35. Kawarabayasi, Y.,, M. Sawada,, H. Horikawa,, Y. Haikawa,, Y. Hino,, S. Yamamoto,, M. Sekine,, S. Baba,, H. Kosugi,, A. Hosoyama,, Y. Nagai,, M. Sakai,, K. Ogura,, R. Otsuka,, H. Nakazawa,, M. Takamiya,, Y. Ohfuku,, T. Funahashi,, T. Tanaka,, Y. Kudoh,, J. Yamazaki,, N. Kushida,, A. Oguchi,, K. Aoki,, and H. Kikuchi. 1998. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5: 147 155.
36. Klenk, H.-P.,, R. A. Clayton,, J.-F. Tomb,, O. White,, K. E. Nelson,, K. A. Ketchum,, R. J. Dodson,, M. Gwinn,, E. K. Hickey,, J. D. Peterson,, D. L. Richardson,, A. R. Kerlavage,, D. E. Graham,, N. C. Kyrpides,, R. D. Fleischmann,, J. Quackenbush,, N. H. Lee,, G. G. Sutton,, S. Gill,, E. F. Kirkness,, B. A. Dougherty,, K. McKenney,, M. D. Adams,, B. Loftus,, J. D. Peterson,, C. I. Reich,, L. K. McNeil,, J. H. Badger,, A. Glodek,, L. Zhou,, R. Overbeek,, J. D. Gocayne,, J. F. Weidman,, L. McDonald,, T. R. Utterback,, M. D. Cotton,, T. Spriggs,, P. Artiach,, B. P. Kaine,, S. M. Sykes,, P. W. Sadow,, K. P. D'Andrea,, C. Bowman,, C. Fujii,, S. A. Garland,, T. M. Mason,, G. J. Olsen,, C. M. Fraser,, H. O. Smith,, C. R. Woese,, and J. C. Venter. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus . Nature 390: 364 370.
37. Kolsto, A. B. 1997. Dynamic bacterial genome organization. Mol. Microbiol. 24: 241 248.
38. Koonin, E. V. 1997. Evidence for a family of archaeal ATPases. Science 275: 1489 1490.
39. Koonin, E. V.,, A. R. Mushegian,, and P. Bork. 1996. Non-orthologous gene displacement. Trends Genet. 12: 334 336.
40. Koonin, E. V.,, A. R. Mushegian,, M. Y. Galperin,, and D. R. Walker. 1997. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol. 25: 619 637.
41. Koonin, E. V.,, R. L. Tatusov,, and M. Y. Galperin. 1998. Beyond the complete genomes: from sequences to structure and function. Curr. Opin. Struct. Biol. 8: 355 363.
42. Koonin, E. V.,, R. L. Tatusov,, and K. E. Rudd. 1995. Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications. Proc. Natl. Acad. Sci. USA 92: 11921 11925.
43. Kunst, F.,, N. Ogasawara,, I. Moszer,, A. M. Albertini,, G. Alloni,, V. Azevedo,, M. G. Bertero,, P. Bessieres,, A. Bolotin,, S. Borchert,, R. Borriss,, L. Boursier,, A. Brans,, M. Braun,, S. C. Brignell,, S. Bron,, S. Brouillet,, C. V. Bruschi,, B. Caldwell,, V. Capuano,, N. M. Carter,, S.-K. Choi,, J.-J. Codani,, I. F. Connerton,, N. J. Cummings,, R. A. Daniel,, F. Denizot,, K. M. Devine,, A. Düsterhoft,, S. D. Ehrlich,, P. T. Emmerson,, K. D. Entian,, J. Errington,, C. Fabret,, E. Ferrari,, D. Foulger,, C. Fritz,, M. Fujita,, Y. Fujita,, S. Fuma,, A. Galizzi,, N. Galleron,, S.-Y. Ghim,, P. Glaser,, A. Gofieau,, E. J. Golightly,, G. Grandi,, G. Guiseppi,, B. J. Guy,, K. Haga,, J. Haiech,, C. R. Harwood,, A. Hénaut,, H. Hilbert,, S. Holsappel,, S. Hosono,, M.-F. Hullo,, M. Itaya,, L. Jones,, B. Joris,, D. Karamata,, Y. Kasahara,, M. Klaerr-Blanchard,, C. Klein,, Y. Kobayashi,, P. Koetter,, G. Koningstein,, S. Krogh,, M. Kumano,, K. Kurita,, A. Lapidus,, S. Lardinois,, J. Lauber,, V. Lazarevic,, S.-M. Lee,, A. Levine,, H. Liu,, S. Masuda,, C. Mauel,, C. Medigue,, N. Medina,, R. P. Meilado,, M. Mizuno,, D. Moestl,, S. Nakai,, M. Noback,, D. Noone,, M. O'Reilly,, K. Ogawa,, A. Ogiwara,, B. Oudega,, S.-H. Park,, V. Parro,, T. M. Pohl,, D. Portetelle,, S. Porwollik,, A. M. Prescott,, E. Presecan,, P. Pujic,, B. Purnelle,, G. Rapoport,, M. Rey,, S. Reynolds,, M. Rieger,, C. Rivolta,, E. Rocha,, B. Roche,, M. Rose,, Y. Sadaie,, T. Sato,, E. Scanlan,, S. Schleich,, R. Schroeter,, F. Scoffone,, J. Sekiguchi,, A. Sekowska,, S. J. Seror,, P. Serror,, B.-S. Shin,, B. Soldo,, A. Sorokin,, E. Tacconi,, T. Takagi,, H. Takahashi,, K. Takemaru,, M. Takeuchi,, A. Tamakoshi,, T. Tanaka,, P. Perpstra,, A. Tognoni,, V. Tosato,, S. Uchiyama,, M. Vandenbol,, F. Vannier,, A. Vassarotti,, A. Viari,, R. Wambutt,, E. Wedler,, H. Wedler,, T. Weitzenegger,, P. Winters,, A. Wipat,, H. Yamamoto,, K. Yamane,, K. Yasumoto,, K. Yata,, K. Yoshida,, H.-F. Yoshikawa,, E. Zumstein,, H. Yoshikawa,, and A. Danchin. 1997. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis . Nature 390: 249 256.
44. Labedan, B.,, and M. Riley. 1995. Gene products of Escherichia coli: sequence comparisons and common ancestries. Mol. Biol. Evol. 12: 980 987.
45. Labedan, B.,, and M. Riley. 1995. Widespread protein sequence similarities: origins of Escherichia coli genes. J. Bacteriol. 177: 1585 1588.
46. Lawrence, J. G.,, and J. R. Roth. 1996. Selfish Operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143: 1843 1860.
47. Lechner, K.,, G. Heller,, and A. Bock. 1989. Organization and nucleotide sequence of a transcriptional unit of Methanococcus vannielii comprising genes for protein synthesis elongation factors and ribosomal proteins. J. Mol. Evol. 29: 20 27.
48. Li, X.,, G. M. Weinstock,, and B. E. Murray. 1995. Generation of auxotrophic mutants of Enterococcus faecalis . J. Bacteriol. 177: 6866 6873.
49. Maidak, B. L.,, G. J. Olsen,, N. Larsen,, R. Overbeek,, M. J. McCaughey,, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25: 109 111.
50. Mankin, A. S. 1989. The nucleotide sequence of the genes coding for the S19 and L22 equivalent ribosomal proteins from Halobacterium halobium . FEBS Lett. 246: 13 16.
51. Meyer, E.,, N. J. Leonard,, B. Bhat,, J. Stubbe,, and J. M. Smith. 1992. Purification and characterization of the purE, purK, and purC gene products: identification of a previously unrecognized energy requirement in the purine biosynthetic pathway. Biochemistry 31: 5022 5032.
52. Mushegian, A. R.,, and E. V. Koonin. 1996. Gene order is not conserved in bacterial evolution. Trends Genet. 12: 289 290.
53. Olsen, G. J.,, and C. R. Woese. 1997. Archaeal genomics: an overview. Cell 89: 991 994.
54. Olsen, G. J.,, C. R. Woese,, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176: 1 6.
55. Overbeek, R.,, N. Larsen,, W. Smith,, N. Maltsev,, and E. Selkov. 1997. Representation of function: the next step. Gene 191: GC1 GC9.
56. Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276: 734 740.
57. Padilla, P. A.,, E. K. Fuge,, M. E. Crawford,, A. Errett,, and M. Werner-Washburne. 1998. The highly conserved, coregulated SNO and SNZ gene families in Saccharomyces cerevisiae respond to nutrient limitation. J. Bacteriol. 180: 5718 5726.
58. Pitulle, C.,, Y. Yang,, M. Marchiani,, E. R. Moore,, J. L. Siefert,, M. Aragno,, P. Jurtshuk, Jr.,, and G. E. Fox. 1994. Phylogenetic position of the genus Hydrogenobacter . Int. J. Syst. Bacteriol. 44: 620 626.
59. Quinn, C. L.,, B. T. Stephenson,, and R. L. Switzer. 1991. Functional organization and nucleotide sequence of the Bacillus subtilis pyrimidine biosynthetic Operon. J. Biol. Chem. 266: 9113 9127.
60. Ramirez, C.,, L. C. Shimmin,, P. Leggatt,, and A. T. Matheson. 1994. Structure and transcription of the L11-L1-L10-L12 ribosomal protein gene operon from the extreme thermophilic archaeon Sulfolobus acidocaldarius . J. Mol. Biol. 244: 242 249.
61. Riley, M.,, and B. Labedan. 1997. Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module. J. Mol. Biol. 268: 857 868.
62. Schenk-Groninger, R.,, J. Becker,, and M. Brendel. 1995. Cloning, sequencing, and characterizing the Lactobacillus leichmannii pyrC gene encoding dihydroorotase. Biochimie 77: 265 272.
63. Schricker, R.,, V. Magdolen,, A. Kaniak,, K. Wolf,, and W. Bandlow. 1992. The adenylate kinase family in yeast: identification of URA6 as a multicopy suppressor of deficiency in major AMP kinase. Gene 122: 111 118.
64. Smith, D. R.,, L. A. Doucette-Stamm,, C. Deloughery,, H. Lee,, J. Dubois,, T. Aldredge,, R. Bashirzadeh,, D. Blakely,, R. Cook,, K. Gilbert,, D. Harrison,, L. Hoang,, P. Keagle,, W. Lumm,, B. Pothier,, D. Qiu,, R. Spadafora,, R. Vicaire,, Y. Wang,, J. Wierzbowski,, R. Gibson,, N. Jiwani,, A. Caruso,, D. Bush,, H. Safer,, D. Patwell,, S. Prabhakar,, S. McDougall,, G. Shimer,, A. Goyal,, S. Pietrokovsky,, G. M. Church,, C. J. Daniels,, J.-I. Mao,, P. Rice,, J. Nolling,, and J. N. Reeve. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum AH: functional analysis and comparative genomics. J. Bacteriol 179: 7135 7155.
65. Stephens, R. S.,, S. Kaiman,, C. Lammel,, J. Fan,, R. Marathe,, L. Aravind,, W. Mitchell,, L. Olinger,, R. L. Tatusov,, Q. Zhao,, E. V. Koonin,, and R. W. Davis. 1998. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis . Science 282: 754 759.
66. Takase, K.,, S. Kakinuma,, I. Yamato,, K. Konishi,, K. Igarashi,, and Y. Kakinuma. 1994. Sequencing and characterization of the ntp gene cluster for vacuolar-type Na(+)-translocating ATPase of Enterococcus hirae . J. Biol Chem. 269: 11037 11044.
67. Tatusov, R. L.,, E. V. Koonin,, and D.J. Lipman. 1997. A genomic perspective on protein families. Science 278: 631 637.
68. Tatusov, R. L.,, A. R. Mushegian,, P. Bork,, N. P. Brown,, W. S. Hayes,, M. Borodovsky,, K. E. Rudd,, and E. V. Koonin. 1996. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli . Curr. Biol. 6: 279 291.
69. Tomb, J.-F.,, O. White,, A. R. Kerlavage,, R. A. Clayton,, G. G. Sutton,, R. F. Fleishmann,, K. A. Ketchum,, H. P. Klenk,, S. Gill,, B. A. Dougherty,, K. A. Nelson,, J. Quackenbush,, L. Zhou,, E. F. Kirkness,, S. Peterson,, B. Loftus,, D. Richardson,, R. Dodson,, H. G. Khalak,, A. Glodek,, K. McKenney,, L. M. Fitzgerald,, N. Lee,, M. D. Adams,, E. K. Hickey,, D. E. Berg,, J. D. Gocayne,, T. R. Utterback,, J. D. Peterson,, J. M. Kelley,, M. D. Cotton,, J. M. Weidman,, C. Fujii,, C. Bowman,, L. Watthey,, E. Wallin,, W. S. Hayes,, M. Borodovsky,, P. D. Karp,, H. O. Smith,, C. M. Fraser,, and J. C. Venter. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori . Nature 388: 539 547.
70. Walker, J. E.,, and N. J. Gay. 1983. Analysis of Escherichia coli ATP synthase subunits by DNA and protein sequencing. Methods Enzymol. 97: 195 218.
71. Watanabe, H.,, H. Mori,, T. Itoh,, and T. Gojobori. 1997. Genome plasticity as a paradigm of eubacteria evolution. J. Mol. Evol. 44: 57 64.
72. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221 271.
73. Woese, C. R. 1994. There must be a prokaryote somewhere: microbiology's search for itself. Microbiol. Rev. 58: 1 9.
74. Woese, C. R.,, O. Kandier,, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87: 4576 4579.


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Universally conserved gene strings (operons) in bacteria and archaea

Citation: Galperin M, Tatusov R, Koonin E. 1999. Comparing Microbial Genomes: How the Gene Set Determines the Lifestyle, p 91-108. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch6
Generic image for table

Conservation of ATP synthase operons in microbial genomes

Citation: Galperin M, Tatusov R, Koonin E. 1999. Comparing Microbial Genomes: How the Gene Set Determines the Lifestyle, p 91-108. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch6

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