Prokaryotic genomes: The emerging paradigm of genome-based microbiology

Current Opinion in Genetics and Development

Volumn 7, Issue 6, 1997, Pages 757-763

  Koonin, Eugene V ^a   Galperin, Michael Y ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIUM; EVOLUTION; GENE FUSION; GENE SEQUENCE; GENE TRANSFER; GENETIC CONSERVATION; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE; REVIEW;

EID: 0031459310     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(97)80037-8     Document Type: Article

References (52)

1. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269:1995;496-512.
2. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, et al. The minimal gene complement of Mycoplasma genitalium. Science. 270:1995;397-403.
3. Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC, Herrmann R. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:1996;4420-4449.
4. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. of outstanding interest Science. 273:1996;1058-1073 The first complete archaeal genome sequence, substantiating the view of the Archaea as the third domain of life. Original conservative analysis of protein sequences encoded in M. jannaschii genome resulted in function prediction for 44% of the 1,743 gene products.
5. Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, et al. 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. of outstanding interest DNA Res. 3:1996;109-136 The first fully sequenced genome of an autotrophic bacterium codes for 3,168 proteins - the second largest set after E. coli. Many cyanobacterial proteins have homologs among bacterial and/or chloroplast proteins. Analysis of this cyanobacterial genome will be a benchmark for all future plant genome sequencing projects.
6. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, et al. Life with 6000 genes. Science. 274:1996;546.
7. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, et al. Life with 6000 genes. Science. 274:1996;563-567.
8. Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew G, et al. The complete genome sequence of Escherichia coli K-12. of outstanding interest Science. 277:1997;1453-1462 With 4,639,221 base pairs and 4,288 predicted genes, the E. coli genome is the largest prokaryotic genome studied so far and is certainly the best studied one. This sequence should provide additional insight into the complex metabolic and regulatory networks of this bacterium. It will be a tremendous help in analyzing other genomes but much remains to be learnt about E. coli itself, given that the function of about one half of its genes are unknown.
9. Tomb J, White O, Kerlavage A, Clayton R, Sutton G, Fleishmann R, Ketchum K, Klenk H, Gill S, Dougherty B, et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. of outstanding interest Nature. 388:1997;539-547 The genomic sequence of the bacterium that causes peptic ulcers and is believed to infect up to a half of the human population. This organism survives in a highly acidic environment and should provide a clue to the general mechanisms of acid tolerance. As H. pylori belongs to an ancient branch of Proteobacteria, its genome will probably shed some light on the evolution of metabolic pathways in bacteria (and mitochondria).
10. Olsen GJ, Woese CR, Overbeek R. The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol. 176:1994;1-6.
11. Koonin EV. Big time for small genomes. Genome Res. 7:1997;418-421.
12. Koonin EV, Mushegian AR, Rudd KE. Sequencing and analysis of bacterial genomes. Curr Biol. 6:1996;404-416.
13. Doolittle RF. A bug with excess gastric avidity. Nature. 388:1997;515-516.
14. Neidhardt FC, Curtiss R III, Ingraham JL, Linn ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE. Escherichia coli and Salmonella. 1996;ASM Press, Washington, DC.
15. Mewes HW, Albermann K, Bahr M, Frishman D, Gleissner A, Hani J, Heumann K, Kleine K, Maierl A, Oliver SG, et al. Overview of the yeast genome. of special interest Nature. 387:1997;7-65 The first detailed description of the yeast genome. With 12,000 kb of DNA and >6,000 of predicted proteins, analysis of the yeast genome presents a major challenge for bioinformatics and an important step towards understanding the protein content of higher eukaryotes.
16. Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, Borodovsky M, Rudd KE, Koonin EV. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr Biol. 6:1996;279-291.
17. Huynen M, Diaz Y, Bork P. Differential display of genomes. Trends Genet. 13:1997;389-390 The first systematic application of the genome subtraction technique that is used to identify metabolic alterations and probable virulence factors in a parasitic organism (H. influenzae) by comparing it with a related free-living one (E. coli).
18. Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM. Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology. Mol Microbiol. 16:1995;955-967.
19. Koonin EV, Tatusov RL, Rudd KE. Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications. Proc Natl Acad Sci USA. 92:1995;11921-11925.
20. Scharf M, Schneider R, Casari G, Bork P, Valencia A, Ouzounis C, Sander C. GeneQuiz: a workbench for sequence analysis. Ismb. 2:1994;348-353.
21. Gaasterland T, Sensen CW. Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture. Biochimie. 78:1996;302-310.
22. Koonin EV, Mushegian AR, Galperin MY, Walker DR. Comparison archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for archaea. of special interest Mol Microbiol. 25:1997;619-637 A detailed analysis of the M. jannaschii genome, including new functional predictions for >300 gene products and reconstruction of certain metabolic pathways. As a result, homologs were identified for 73% of the M. jannaschii proteins and functions were predicted for ~70% of them. Comparison of M. jannaschii genome with three bacterial genomes resulted in elucidation of common trends regarding similar distribution of families of paralogs, similar representation of protein structural classes, and gene shuffling among archaeal and bacterial genomes.
23. of outstanding interest Doolittle RF. Computer methods for macromolecular sequence analysis. Meth Enzymol. 266:1996; This volume of Methods in Enzymology offers a series of detailed reviews on various aspects of computer methods in sequence analysis, from database searching to constructing multiple alignments and phylogenetic trees to predicting protein structure.
24. Henikoff S, Henikoff JG. Embedding strategies for effective use of information from multiple sequence alignments. Protein Sci. 6:1997;698-705.
25. Neuwald AF, Liu JS, Lipman DJ, Lawrence CE. Extracting protein alignment models from the sequence database. Nucleic Acids Res. 25:1997;1665-1677.
26. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zheng Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST - a new generation of protein database search programs. of outstanding interest Nuceic Acids Res. 25:1997;3389-3402 A complete description of recently developed programs that combine the advantages of the standard BLAST programs with the high sensitivity of the profile search methods at low computation costs. The increased sensitivity of database scanning is illustrated by two impressive examples. This set of programs is expected to replace previous versions of BLAST as the standard tool for database searching.
27. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 215:1990;403-410.
28. Mushegian AR, Bassett DE Jr, Boguski MS, Bork P, Koonin EV. Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. of special interest Proc Natl Acad Sci USA. 94:1997;5831-5836 Sequence analysis of 70 human genes associated with specific genetic diseases demonstrating the power of recently developed computer methods in identifying similarities between distant protein families. For most of the disease gene products, statistically significant sequence similarities were detected in model organisms (bacteria, yeast, and/or nematode).
29. Rost B. PHD: predicting one-dimensional protein structure by profile-based neural networks. Meth Enzymol. 266:1996;525-539.
30. Frishman D, Argos P. Seventy-five percent accuracy in protein secondary structure prediction. Proteins. 27:1997;329-335.
31. Rudd KE. Escherichia coli K-12 on the Internet. Trends Genet. 12:1996;156-157.
32. Fitch WM. Distinguishing homologous from analogous proteins. Syst Zool. 19:1970;99-113.
33. Koonin EV, Mushegian AR, Bork P. Non-orthologous gene displacement. Trends Genet. 12:1996;334-336.
34. Mushegian AR, Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. of special interest Proc Natl Acad Sci USA. 93:1996;10268-10273 Analysis of the proteins encoded in the genomes of both M. genitalium and H. influenzae with the aim of identifying the genes essential for cellular function and modeling a primitive cell that might have existed at a very early stage of evolution. The resulting set of 256 genes may be close to the minimal gene set that is necessary and sufficient to sustain the existence of a cell with the modern system of genome expression.
35. Labedan B, Riley M. Widespread protein sequence similarities: origins of Escherichia coli genes. J Bacteriol. 177:1995;1585-1588.
36. Labedan B, Riley M. Gene products of Escherichia coli: sequence comparisons and common ancestries. Mol Biol Evol. 12:1995;980-987.
37. Riley M, Labedan B. Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module. J Mol Biol. 268:1997;857-868.
38. Brenner SE, Hubbard T, Murzin A, Chothia C. Gene duplications in H. influenzae. Nature. 378:1995;140.
39. Saier MJ. Phylogenetic approaches to the identification and characterization of protein families and superfamilies. Microbial Comp Genomics. 1:1996;129-150.
40. Koonin EV. Evidence for a family of archaeal ATPases. Science. 275:1997;1489-1490.
41. Doolittle RF. Convergent evolution: the need to be explicit. Trends Biochem Sci. 19:1994;15-18.
42. Koonin EV, Mushegian AR. Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics. Curr Opin Genet Dev. 6:1996;757-762.
43. Himmelreich R, Plagens H, Hilbert H, Reiner B, Herrmann R. Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. of special interest Nucleic Acids Res. 25:1997;701-712 All the proteins encoded in the M. genitalium genome were found to also be encoded in the larger genome of M. pneumoniae. The order of orthologous genes is well conserved within individual segments of the genome, whereas the order of these segments in the two genomes was different.
44. Mushegian AR, Koonin EV. Gene order is not conserved in bacterial evolution. Trends Genet. 12:1996;289-290.
45. Kolsto AB. Dynamic bacterial genome organization. of special interest Mol Microbiol. 24:1997;241-248 A review of genome organization in various bacteria with special emphasis on the diverse functions of extrachromosomal elements in naturally-occurring bacteria.
46. Watanabe H, Mori H, Itoh T, Gojobori T. Genome plasticity as a paradigm of eubacteria evolution. of special interest J Mol Evol. 44:1997;57-64 A comparison of the location of orthologous genes in different genomes showing that dynamic rearrangements have occurred in eubacterial genomes with a frequency sufficient to break operon structures during evolution. The longest conserved regions contain operons coding for the ribosomal proteins, which might have been under strong structural constraints during evolution.
47. Olsen GJ, Woese CR. Archaeal genomics: an overview. Cell. 89:1997;991-994.
48. Edgell DR, Doolittle WF. Archaea and the origin(s) of DNA replication proteins. Cell. 89:1997;990-995.
49. Woese CR. There must be a prokaryote somewhere: microbiology's search for itself. Microbiol Rev. 58:1994;1-9.
50. Gogarten JP, Kibak H, Dittrich P, Taiz L, Bowman EJ, Bowman BJ, Manolson MF, Poole RJ, Date T, Oshima T, et al. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci USA. 86:1989;6661-6665.
51. Gray MW. Origin and evolution of organelle genomes. Curr Opin Genet Dev. 4:1993;884-890.
52. Keeling PJ, Doolittle WF. Evidence that eukaryotic triosephosphate isomerase is of alpha-proteobacterial origin. of special interest Proc Natl Acad Sci USA. 94:1997;1270-1275 Sequence analysis of the triosephosphate isomerase (tpi) genes from various bacteria, archaea, and eukaryotes suggests that eukaryotic tpi genes came from an alpha-proteobacterial genome (e.g. from the protomitochondrial endosymbiont) after the divergence of archaea and eukaryotes.