Chapter 26 : From Genetics to Genomics

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From Genetics to Genomics, Page 1 of 2

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While Barry's career has focused on the analysis of genomes, that mantra still rings in his head, and he has found that what is true for genetics is also true for genomics. The link between genotype and phenotype provided the framework for most genetics research prior to the genomics era. Biology and most sciences develop in a standard technology arc: description, simple testing, complex testing, and finally full-scale implementation. The first papers in the genomics field described the basic attributes of the technology and genome architecture. Microbiology is currently undergoing a revolution brought on by large-scale sequencing technology and the reality of dauntingly large data sets. Just 4 years after the genome was sequenced, forward-thinking biologists like Lee Hartwell began proposing a new paradigm, initially called “modular biology,” for genomics research. These ideas and frameworks have since launched the fields of systems biology, synthetic biology, and functional genomics. Much like the early genome papers in the mid-1990s, the earliest metagenomics papers also reported on our ability to sequence and make sense of environmental metagenomes. As a result, comparative metagenomics approaches may be the most fruitful approaches for analyzing such data sets. The authors also believe that only by studying the full continuum of metabolic and ecological interactions in a niche, and their reflection in the total genetic complement of all organisms of that niche (what we call the “nicheome”), can we understand the forces shaping microbial evolution.

Citation: Suen G, Aylward F, Slater S, Goldman B. 2011. From Genetics to Genomics, p 257-266. In Maloy S, Hughes K, Casadesús J (ed), The Lure of Bacterial Genetics. ASM Press, Washington, DC. doi: 10.1128/9781555816810.ch26

Key Concept Ranking

Horizontal Gene Transfer
Microbial Ecology
Bacterial Genetics
Microbial Evolution
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1. Andersson, S. G.,, A. Zomorodipour,, J. O. Andersson,, T. Sicheritz-Pontén,, U. C. Alsmark,, R. M. Podowski,, A. K. Nslund,, A.-S. Eriksson,, H. H. Winkler, and, C. G. Kurland. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133140.
2. Avery, O. T.,, C. M. MacLeod, and, M. McCarty. 1944. Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III.J. Exp. Med. 79:137158.
3. Bai, X.,, J. Zhang,, A. Ewing,, S. A. Miller,, A. J. Radek,, D. V. Shevchenko,, K. Tsukerman,, T. Walunas,, A. Lapidus,, J. W. Campbell, and, S. A. Hogenhout. 2006. Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J. Bacteriol. 188:36823696.
4. Baas-Becking, L. G. M. 1934. Geobiologie of Inleiding Tot de Milieukunde. W. P. van Stockum & Zoon, The Hague, The Netherlands.
5. Beijerinck, M. W. 1901. Enrichment culture studies with urea bacteria. Zentbl. Bakteriol. Part II, 7, 33.
6. Bergey, D. H.,, F. C. Harrison,, R. S. Breed,, B. W. Hammer, and, F. M. Huntoon. 1923. Bergey’s Manual of Determinative Bacteriology. Williams and Wilkins Company, Baltimore, MD.
7. Brock, T. 1990. The Emergence of Bacterial Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
8. Brzuszkiewicz, E.,, H. Bruggemann,, H. Liese-gang,, M. Emmerth,, T. Ölschläger,, G. Nagy,, K. Albermann,, C. Wagner,, C. Buchrieser,, L. Emödy,, G. Gottschalk,, J. Hacker, and, U. Dobrindt. 2006. How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc. Natl.Acad. Sci. USA 103:1287912884.
9. Callister, S. J.,, L. A. McCue,, J. E. Turse,, M. E. Monroe,, K. J. Auberry,, R. D. Smith,, J. N. Adkins, and, M. S. Lipton. 2008. Comparative bacterial proteomics: analysis of the core genome concept. PLoS ONE 3:e1542.
10. Chan, C. K.,, A. L. Hsu,, S. K. Halgamuge, and, S.-L. Tang. 2008. Binning sequences using very sparse labels within a metagenome. BMC Bioinformatics 9:215.
11. Cohan, F. M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56:457487.
12. Cohen, S. N.,, C. A. C. Chang,, H. W. Boyer, and, R. B. Helling. 1973. Construction of biologically functional bacterial plasmids in vitro. Proc. Natl. Acad. Sci. USA 70:32403244.
13. Coleman, M. L.,, M. B. Sullivan,, A. C. Martiny,, C. Steglich,, K. Barry,, E. F. DeLong, and, S. W. Chisholm. 2006. Genomic islands and the ecology and evolution of Prochlorococcus. Science 311:17681770.
14. Daims, H.,, F. Maixner,, S. Lücker,, K. Stoecker,, K. Hace, and, M. Wagner. 2006. Ecophysiology and niche differentiation of Nitrospira-like bacteria, the key nitrite oxidizers in wastewater treatment plants. Water Sci. Technol. 54:2127.
15. Dale, C., and, N. A. Moran. 2006. Molecular interactions between bacterial symbionts and their hosts. Cell 126:453465.
16. Dale, C.,, B. Wang,, N. Moran, and, H. Ochman. 2003. Loss of DNA recombinational repair enzymes in the initial stages of genome degeneration. Mol. Biol. Evol. 20:11881194.
17. Dawkins, R. 1976. The Selfish Gene. Oxford University Press, Oxford, United Kingdom.
18. de Wit, R., and, T. Bouvier. 2006. “Everything is everywhere, but, the environment selects”; what did Baas Becking and Beijerinck really say? Environ. Microbiol. 8:755758.
19. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:21242129.
20. Field, D.,, J. Hughes, and, E. R. Moxon. 2004. Using the genome to understand pathogenicity. Methods Mol. Biol. 266:261287.
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. Sutton,, W. Fitz-Hugh,, C. Fields,, J. D. Gocayne,, J. Scott,, R. Shirley,, L. 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. T. Nguyen,, D. M. Saudek,, R. C. Brandon,, L. D. Fine,, J. L. Fritchman,, J. L. Fuhrmann,, N. S. M. Geoghagen,, C. L. Gnehm,, L. A. McDonald,, K. V. Small,, C. M. Fraser,, H. O. Smith, and, J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
22. Franklin, R., and, R. G. Gosling. 1953. Molecular configuration in sodium thymonucleate. Nature 171:740741.
23. Handelsman, J.,, M. R. Rondon,, S. F. Brady,, J. Clardy, and, R. M. Goodman. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5:R245R249.
24. Hartwell, L. H.,, J. J. Hopfield,, S. Leibler, and, A. W. Murray. 1999. From molecular to modular cell biology. Nature 402:C47C52.
25. Hochhut, B.,, U. Dobrindt, and, J. Hacker. 2005. Pathogenicity islands and their role in bacterial virulence and survival. Contrib. Microbiol. 12:234254.
26. Hugenholtz, P. 2002. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3:REVIEWS0003.
27. Jacob, F., and, J. Monod. 1961. Genetic regulatory mechanisms in the synthesis of proteins.J. Mol. Biol. 3:318356.
28. Jacob, F., and, J. Monod. 1961. On the regulation of gene activity. Cold Spring Harbor Symp. Quant. Biol. 26:193209.
29. Lawrence, J. 1999. Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9:642648.
30. Lawrence, J. G., and, J. R. Roth. 1996. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143:18431860.
31. Lerat, E.,, V. Daubin, and, N. A. Moran. 2003. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS Biol. 1:E19.
32. Lobban, P. E., and, A. D. Kaiser. 1973. Enzymatic end-to-end joining of DNA molecules. J. Mol. Biol. 78:18.
33. Losick, R., and, J. Pero. 1981. Cascades of sigma factors. Cell 25:582584.
34. Luria, S. E., and, M. Delbruck. 1953. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28:491511.
35. Marcotte, E. M.,, M. Pellegrini,, H.-L. Ng,, D. W. Rice,, T. O. Yeates, and, D. Eisenberg. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285:751753.
36. Martiny, J. B.,, B. J. Bohannan,, J. H. Brown,, R. K. Colwell,, J. A. Fuhrman,, J. L. Green,, M. C. Horner-Devine,, M. Kane,, J. A. Krumins,, C. R. Kuske,, P. J. Morin,, S. Naeem,, L. Ovres,, A. L. Reysenbach,, V. H. Smith, and, J.T. Staley. 2006. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4:102112.
37. Martiny, J. B., and, D. Field. 2005. Ecological perspectives on the sequenced genome collection. Ecol. Lett. 8:13341345.
38. Maxam, A. M., and, W. Gilbert. 1977. A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA 74:560564.
39. McHardy, A. C.,, H. G. Martin,, A. Tsirigos,, P. Hugenholtz, and, I. Rigoutsos. 2007. Accurate phylogenetic classification of variable-length DNA fragments. Nat. Methods 4:6372.
40. Meselson, M., and, F. W. Stahl. 1958. The replication of DNA in Escherichia coli. Proc. Natl. Acad. Sci. USA 44:671682.
41. Moran, N. A.,, J. P. McCutcheon, and, A. Nakabachi. 2008. Genomics and evolution of heritable bacterial symbionts. Annu. Rev. Genet. 42:165190.
42. Nadon, R., and, J. Shoemaker. 2002. Statistical issues with microarrays: processing and analysis. Trends Genet. 18:265271.
43. Nakabachi, A.,, A. Yamashita,, H. Toh,, H. Ishikawa,, H. E. Dunbar,, N. A. Moran, and, M. Hattori. 2006. The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314:267.
44. Ochman, H.,, J. G. Lawrence, and, E. A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299304.
45. Oelschlaeger, T. A.,, U. Dobrindt, and, J. Hacker. 2002. Pathogenicity islands of uro-pathogenic E. coli and the evolution of virulence. Int. J. Antimicrob. Agents 19:517521.
46. Pedros-Alio, C. 2006. Genomics and marine microbial ecology. Int. Microbiol. 9:191197.
47. Pellegrini, M. 2001. Computational methods for protein function analysis. Curr. Opin. Chem. Biol. 5:4650.
48. Pellegrini, M.,, M. Thompson,, J. Fierro, and, P. Bowers. 2001. Computational method to assign microbial genes to pathways.J. Cell Biochem. Suppl. 37:106109.
49. Perna, N. T.,, G. Plunkett III,, V. Burland,, B. Mau,, J. D. Glasner,, D. J. Rose,, G. F. Mayhew,, P. S. Evans,, J. Gregor,, H. A. Kirkpatrick,, G. Pósfai,, J. Hackett,, S. Klink,, A. Boutin,, Y. Shao,, L. Miller,, E. J. Grotbeck,, N. W. Davis,, A. Lim,, E. T. Dimalanta,, K. D. Potamousis,, J. Apodaca,, T. S. Anantharaman,, J. Lin,, G. Yen,, D. C. Schwartz,, R. A. Welch, and, F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529533.
50. Saiki, R. K.,, D. H. Gelfand,, S. Stoffel,, S. J. Scharf,, R. Higuchi,, G. T. Horn,, K. B. Mullis, and, H. A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487491.
51. Sanger, F.,, G. M. Air,, B. G. Barrell,, N. L. Brown,, A. R. Coulson,, C. A. Fiddes,, C. A. Hutchison,, P. M. Slocombe, and, M. Smith. 1977. Nucleotide sequence of bacteriophage phiX174 DNA. Nature 265:687695.
52. Sanger, F., and, A. R. Coulson. 1975. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 94:441448.
53. Service, R. F. 2006. Gene sequencing. The race for the $1000 genome. Science 311:15441546.
54. Singh, S.,, J. Stavrinides,, D. Christendat, and, D. S. Guttman. 2008. A phylogenomic analysis of the shikimate dehydrogenases reveals broadscale functional diversification and identifies one functionally distinct subclass. Mol. Biol. Evol. 25:22212232.
55. Slonim, D. K. 2002. From patterns to pathways: gene expression data analysis comes of age. Nat. Genet. 32 (Suppl):502508.
56. Srinivasan, B. S.,, N. B. Caberoy,, G. Suen,, R. G. Taylor,, R. Shah,, F. Tengra,, B. S. Goldman,, A. G. Garza, and, R. D. Welch. 2005. Functional genome annotation through phylogenomic mapping. Nat. Biotechnol. 23:691698.
57. Staley, J. T., and, A. Konopka. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39:321346.
58. Suen, G.,, B. S. Goldman, and, R. D. Welch. 2007. Predicting prokaryotic ecological niches using genome sequence analysis. PLoS One 2: e743.
59. Tringe, S. G.,, C. von Mering,, A. Kobayashi,, A. A. Salamov,, K. Chen,, H. W. Chang,, M. Podar,, J. M. Short,, E. J. Mathur,, J. C. Detter,, P. Bork,, P. Hugenholtz, and, E. M. Rubin. 2005. Comparative metagenomics of microbial communities. Science 308:554557.
60. Tyson, G. W.,, J. Chapman,, P. Hugenholtz,, E. E. Allen,, R. J. Ram,, P. M. Richardson,, V. V. Solovyev,, E. M. Rubin,, D. S. Rokhsar, and, J. F. Banfield. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 3743.
61. Venter, J. C.,, K. Remington,, J. F. Heidelberg,, A. L. Halpern,, D. Rusch,, J. A. Eisen,, D. Wu,, I. Paulsen,, K. E. Nelson,, W. Nelson,, D. E. Fouts,, S. Levy,, A. H. Knap,, M. W. Lomas,, K. Nealson,, O. White,, J. Peterson,, J. Hoffman,, R. Parsons,, H. Baden-Tillson,, C. Pfannkoch,, Y. H. Rogers, and, H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:6674.
62. von Mering, C.,, P. Hugenholtz,, J. Raes,, S. G. Tringe,, T. Doerks,, L. J. Jensen,, N. Ward, and, P. Bork. 2007. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315:11261130.
63. Warnecke, F.,, P. Luginbühl,, N. Ivanova,, M. Ghassemian,, T. H. Richardson,, J. T. Stege,, M. Cayouette,, A. C. McHardy,, G. Djordjevic,, N. Aboushadi,, R. Sorek,, S. G. Tringe,, M. Podar,, H. G. Martin,, V. Kunin,, D. Dalevi,, J. Madejska,, E. Kirton,, D. Platt,, E. Szeto,, A. Salamov,, K. Barry,, N. Mikhailova,, N. C. Kyrpides,, E. G. Matson,, E. A. Ottesen,, X. Zhang,, M. Hernández,, C. Murillo,, L. G. Acosta,, I. Rigoutsos,, G. Tamayo,, B. D. Green,, C. Chang,, E. M. Rubin,, E. J. Mathur,, D. E. Robertson,, P. Hugenholtz, and, J. R. Lead-better. 2007. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560565.
64. Watson, J. D., and, F. H. C. Crick. 1953. A structure for deoxyribose nucleic acid. Nature 171:737738.
65. Welch, R. A.,, V. Burland,, G. Plunkett III,, P. Redford,, P. Roesch,, D. Rasko,, E. L. Buckles,, S.-R. Liou,, A. Boutin,, J. Hackett,, D. Stroud,, G. F. Mayhew,, D. J. Rose,, S. Zhou,, D. C. Schwartz,, N. T. Perna,, H. L. T. Mobley,, M. S. Donnenberg, and, F. R. Blattner. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99:1702017024.
66. Wernegreen, J. J. 2002. Genome evolution in bacterial endosymbionts of insects. Nat. Rev. Genet. 3:850861.
67. Whitaker, R. J., and, J. F. Banfield. 2006. Population genomics in natural microbial communities. Trends Ecol. Evol. 21:508516.
68. Wilkins, M. H. F.,, A. R. Stokes, and, H. R. Wilson. 1953. Molecular structure of deoxypentose nucleic acids. Nature 171:738740.
69. Woese, C. R.,, O. Kandler, and, M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:45764579.
70. Zilber-Rosenberg, I., and, E. Rosenberg. 2008. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev. 32:723735.
71. Zinder, N. D., and, J. Lederberg. 1952. Genetic exchange in Salmonella. J. Bacteriol. 64:679699.

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