Bacteria as computers making computers

FEMS Microbiology Reviews

Volumn 33, Issue 1, 2009, Pages 3-26

  Danchin, Antoine ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

ADAR; Algorithmic complexity; APOBEC; Junk DNA; Minimal genome; Operating system

Indexed keywords

BACTERIAL DNA;

BACTERIAL CHROMOSOME; BACTERIAL GENETICS; BACTERIUM; COMPUTER; DNA REPLICATION; DNA TRANSCRIPTION; GENE EXPRESSION; GENE MUTATION; GENOME; MOLECULAR BIOLOGY; NONHUMAN; REVIEW;

BACTERIA; GENOME, BACTERIAL; MEDICAL INFORMATICS; MOLECULAR BIOLOGY; PHYLOGENY; SYSTEMS BIOLOGY;

EID: 57549101206     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1111/j.1574-6976.2008.00137.x     Document Type: Review

References (216)

1. Adam H, Jouannic S, Morcillo F, Verdeil JL, Duval Y Tregear JW (2007) Determination of flower structure in Elaeis guineensis: do palms use the same homeotic genes as other species? Ann Bot (London) 100 : 1 12.
2. Allen C, Bekoff M Lauder G (1998) Nature's Purposes. MIT Press, Cambridge, MA.
3. Alon U (2006) An Introduction to Systems Biology. Design Principles of Biological Circuits. Chapman & Hall, London.
4. Ara K, Ozaki K, Nakamura K, Yamane K, Sekiguchi J Ogasawara N (2007) Bacillus minimum genome factory: effective utilization of microbial genome information. Biotechnol Appl Bioc 46 : 169 178.
5. Arifuzzaman M, Maeda M, Itoh A et al 2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 16 : 686 691.
6. Ayala FJ (2008) Science, evolution, and creationism. P Natl Acad Sci USA 105 : 3 4.
7. Bachiller D, Macias A, Duboule D Morata G (1994) Conservation of a functional hierarchy between mammalian and insect Hox/HOM genes. EMBO J 13 : 1930 1941.
8. Bailly-Bechet M, Danchin A, Iqbal M, Marsili M Vergassola M (2006) Codon usage domains over bacterial chromosomes. PLoS Comput Biol 2 : e37.
9. Baker MD, Wolanin PM Stock JB (2006) Systems biology of bacterial chemotaxis. Curr Opin Microbiol 9 : 187 192.
10. Bankhead T, Kobryn K Chaconas G (2006) Unexpected twist: harnessing the energy in positive supercoils to control telomere resolution. Mol Microbiol 62 : 895 905.
11. Barendregt H (1984) The Lambda Calculus: its Syntax and Semantics. Studies in Logic and the Foundations of Mathematics (Barendregt H, ed). North-Holland, Amsterdam.
12. Barrett CL, Kim TY, Kim HU, Palsson BO Lee SY (2006) Systems biology as a foundation for genome-scale synthetic biology. Curr Opin Biotech 17 : 488 492.
13. Baumler AJ (1997) The record of horizontal gene transfer in Salmonella. Trends Microbiol 5 : 318 322.
14. Bennett C (1988a) Logical depth and physical complexity. The Universal Turing Machine: A Half-Century Survey (Herken R, ed), pp. 227 257. Oxford University Press, Oxford.
15. Bennett C (1988b) Notes on the history of reversible computation. IBM J Res Dev 44 : 270 277.
16. Ben-Yehuda S, Rudner DZ Losick R (2003) RacA, a bacterial protein that anchors chromosomes to the cell poles. Science 299 : 532 536.
17. Berger B, Pridmore RD, Barretto C, Delmas-Julien F, Schreiber K, Arigoni F Brussow H (2007) Similarity and differences in the Lactobacillus acidophilus group identified by polyphasic analysis and comparative genomics. J Bacteriol 189 : 1311 1321.
18. Bingle LE, Bailey CM Pallen MJ (2008) Type VI secretion: a beginner's guide. Curr Opin Microbiol 11 : 3 8.
19. Brochard-Wyart F, Tanaka T, Borghi N de Gennes PG (2005) Semiflexible polymers confined in soft tubes. Langmuir 21 : 4144 4148.
20. Bruggeman FJ Westerhoff HV (2007) The nature of systems biology. Trends Microbiol 15 : 45 50.
21. Brzuszkiewicz E, Bruggemann H, Liesegang H et al 2006) How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. P Natl Acad Sci USA 103 : 12879 12884.
22. Buchler NE, Gerland U Hwa T (2003) On schemes of combinatorial transcription logic. P Natl Acad Sci USA 100 : 5136 5141.
23. Burrus V Waldor MK (2004) Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 155 : 376 386.
24. Cairns J, Overbaugh J Miller S (1988) The origin of mutants. Nature 335 : 142 145.
25. Carbone A (2006) Computational prediction of genomic functional cores specific to different microbes. J Mol Evol 63 : 733 746.
26. Cavalier-Smith T (2002) The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Micr 52 : 7 76.
27. Cavalier-Smith T (2006) Cell evolution and Earth history: stasis and revolution. Philos T Roy Soc B 361 : 969 1006.
28. Chaitin G (2007) Speculations on biology, information and complexity. EATCS Bull 91 : 231 237.
29. Changeux JP, Courrège P Danchin A (1973) A theory of the epigenesis of neuronal networks by selective stabilization of synapses. P Natl Acad Sci USA 70 : 2974 2978.
30. Cohen SS (1960) A hypothesis on a possible competitive relation between DNA synthesis and protein synthesis. Cancer Res 20 : 698 699.
31. Cole ST Guest JR (1979) Production of a soluble form of fumarate reductase by multiple gene duplication in Escherichia coli K12. Eur J Biochem 102 : 65 71.
32. Corbellini G (1998) La definizione informazionale della specificità biologica. L' Informazione nelle Scienze dalla Vita (Continenza B Gagliasso E, eds), pp. 66 99. Franco Angeli, Milano.
33. Cornish-Bowden A Cardenas ML (2007) The threat from creationism to the rational teaching of biology. Biol Res 40 : 113 122.
34. Corre J Louarn JM (2005) Extent of the activity domain and possible roles of FtsK in the Escherichia coli chromosome terminus. Mol Microbiol 56 : 1539 1548.
35. Couturier E Rocha EP (2006) Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes. Mol Microbiol 59 : 1506 1518.
36. Cover T Thomas J (1991) Elements of Information Theory. Wiley, New York.
37. Danchin A (1983) L'Œuf et la Poule. Histoires du Code Génétique. Fayard, Paris.
38. Danchin A (1986) Order and necessity. From enzyme adaptation to natural philosophy: heritage from Jacques Monod. Symposium J Monod and Molecular Biology, Yesterday and Today, Trani, Italy, 13-15 December 1986. Elsevier Sciences Publishers, Amsterdam, pp. 187 196.
39. Danchin A (1988a) Complete genome sequencing: future and prospects. BAP 1988-1989 (Goffeau A, ed), pp. 1 24. Commission of the European Communities, Brussels.
40. Danchin A (1988b) Origin of mutants disputed. Nature 336 : 527.
41. Danchin A (1989) Homeotopic transformation and the origin of translation. Prog Biophys Mol Bio 54 : 81 86.
42. Danchin A (1993 (2007)) Bacteria are not lamarckian. HAL arXiv: q-bio.GN/0702032:hal-00130797.
43. Danchin A (1995) Why sequence genomes? The Escherichia coli imbroglio. Mol Microbiol 18 : 371 376.
44. Danchin A (1996) On genomes and cosmologies. Integrative Approaches to Molecular Biology (Collado-Vides J, Magasanik B Smith T, eds), pp. 91 111. The MIT Press, Cambridge, MA.
45. Danchin A (1999) From protein sequence to function. Curr Opin Struc Biol 9 : 363 367.
46. Danchin A (2003) The Delphic Boat. What Genomes Tell Us. Harvard University Press, Cambridge, MA.
47. Danchin A (2007) Archives or palimpsests? Bacterial genomes unveil a scenario for the origin of life. Biological Theory 2 : 52 61.
48. Danchin A (2008a) Natural selection and immortality. Biogerontology 9. EPub ahead of print.
49. Danchin A (2008b) A phylogenetic view of bacterial ribonucleases. Prog Biophys Mol Bio 83, in press.
50. Danchin A Hénaut A (1997) The map of the cell is in the chromosome. Curr Opin Genet Dev 7 : 852 854.
51. Danchin A, Médigue C, Gascuel O, Soldano H Hénaut A (1991) From data banks to data bases. Res Microbiol 142 : 913 916.
52. Danchin A, Guerdoux-Jamet P, Moszer I Nitschké P (2000) Mapping the bacterial cell architecture into the chromosome. Philos T Roy Soc B 355 : 179 190.
53. Danchin A, Fang G Noria S (2007) The extant core bacterial proteome is an archive of the origin of life. Proteomics 7 : 875 889.
54. D'Ari R Thomas R (2003) Hardware (DNA) circuits. C R Biol 326 : 215 217.
55. Daudin H (1926 1927) De Linné à Lamarck. Méthodes de la classification et idée de série en botanique et en zoologie (1740-1790). Félix Alcan, Paris.
56. de Lorenzo V Danchin A (2008) The discovery of new worlds and new words. EMBO Rep 9 : 822 827.
57. de Marco A (2008) Minimal information: an urgent need to assess the functional reliability of recombinant proteins used in biological experiments. Microb Cell Fact 7 : 20.
58. den Blaauwen T, de Pedro MA, Nguyen-Disteche M Ayala JA (2008) Morphogenesis of rod-shaped sacculi. FEMS Microbiol Rev 32 : 321 344.
59. Diels H (1902) Die Fragmente der Vorsokratiker. Weidmansche Buchhandlung, Berlin.
60. Dobrindt U, Hentschel U, Kaper JB Hacker J (2002) Genome plasticity in pathogenic and nonpathogenic enterobacteria. Curr Top Microbiol 264 : 157 175.
61. Dyson FJ (1985) Origins of Life. Cambridge University Press, Cambridge, UK.
62. Edsall JT (1953) Some comments on proteins and protein structure. P Roy Soc Lond B Bio 141 : 97 103.
63. Egelman EH (2003) Cell walls, cell shape, and bacterial actin homologs. Dev Cell 5 : 4 5.
64. Elowitz MB Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403 : 335 338.
65. Errington J (2003) Dynamic proteins and a cytoskeleton in bacteria. Nat Cell Biol 5 : 175 178.
66. Esnault E, Valens M, Espeli O Boccard F (2007) Chromosome structuring limits genome plasticity in Escherichia coli. PLoS Genet 3 : e226.
67. Fang G, Rocha EP Danchin A (2005) How essential are nonessential genes? Mol Biol Evol 22 : 2147 2156.
68. Fang G, Rocha EP Danchin A (2008) Persistence drives gene clustering in bacterial genomes. BMC Genomics 9 : 4.
69. Fijalkowska IJ, Jonczyk P, Tkaczyk MM, Bialoskorska M Schaaper RM (1998) Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome. P Natl Acad Sci USA 95 : 10020 10025.
70. Fong SS Palsson BO (2004) Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 36 : 1056 1058.
71. Foster PL Cairns J (1992) Mechanisms of directed mutation. Genetics 131 : 783 789.
72. French S (1992) Consequences of replication fork movement through transcription units in vivo. Science 258 : 1362 1365.
73. Fuglsang A (2003) Strong associations between gene function and codon usage. APMIS 111 : 843 847.
74. Gene-ontology-consortium (2001) Creating the gene ontology resource: design and implementation. Genome Res 11 : 1425 1433.
75. Gene-ontology-consortium (2008) The Gene Ontology project in 2008. Nucleic Acids Res 36 : D440 D444.
76. Gibson DG, Benders GA, Andrews-Pfannkoch C et al 2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319 : 1215 1220.
77. Glaser P, Kunst F, Arnaud M et al 1993) Bacillus subtilis genome project: cloning and sequencing of the 97 kb region from 325 degrees to 333 degrees. Mol Microbiol 10 : 371 384.
78. Gorini L (1958) Régulation en retour (feedback control) de la synthèse de l'arginine chez Escherichia coli. B Soc Chim Biol 40 : 1939 1952.
79. Gouy M Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10 : 7055 7074.
80. Grantham R, Gautier C, Gouy M, Mercier R Pave A (1980) Codon catalog usage and the genome hypothesis. Nucleic Acids Res 8 : r49 r62.
81. Guerdoux-Jamet P, Henaut A, Nitschke P, Risler JL Danchin A (1997) Using codon usage to predict genes origin: is the Escherichia coli outer membrane a patchwork of products from different genomes? DNA Res 4 : 257 265.
82. Gupta RS (1998) Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol R 62 : 1435 1491.
83. Gupta RS (2000) The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24 : 367 402.
84. Haebel PW, Gutmann S Ban N (2004) Dial tm for rescue: tmRNA engages ribosomes stalled on defective mRNAs. Curr Opin Struc Biol 14 : 58 65.
85. Hall BG (1998) Adaptive mutagenesis: a process that generates almost exclusively beneficial mutations. Genetica 102-103 : 109 125.
86. Handrigan GR Wassersug RJ (2007) The anuran Bauplan: a review of the adaptive, developmental, and genetic underpinnings of frog and tadpole morphology. Biol Rev 82 : 1 25.
87. Haran TE, Kahn JD Crothers DM (1994) Sequence elements responsible for DNA curvature. J Mol Biol 244 : 135 143.
88. Harold FM (2007) Bacterial morphogenesis: learning how cells make cells. Curr Opin Microbiol 10 : 591 595.
89. Hayes W (1952) Recombination in Bact. coli K-12: unidirectional transfer of genetic material. Nature 169 : 118 119.
90. Heard E Bickmore W (2007) The ins and outs of gene regulation and chromosome territory organisation. Curr Opin Cell Biol 19 : 311 316.
91. Hénaut A Danchin A (1996) Analysis and predictions from Escherichia coli sequences or E. coli in silico. Escherichia coli and Salmonella, Cellular and Molecular Biology, Vol. 1 (Neidhardt F, ed), pp. 2047 2065. ASM Press, Washington, DC.
92. Herbert SI (1995) Informatics for care protocols and guidelines: towards a European knowledge model. Stud Health Technol Inform 16 : 27 42.
93. Hilario E Gogarten JP (1993) Horizontal transfer of ATPase genes-the tree of life becomes a net of life. Biosystems 31 : 111 119.
94. Hofstadter D (1979) Gödel, Escher, Bach: An Eternal Golden Braid. Basic Books, New York.
95. Hogg T, Mechold U, Malke H, Cashel M Hilgenfeld R (2004) Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response. Cell 117 : 57 68.
96. Holmes RK, Malim MH Bishop KN (2007) APOBEC-mediated viral restriction: not simply editing? Trends Biochem Sci 32 : 118 128.
97. Horimoto K, Fukuchi S Mori K (2001) Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomes. Bioinformatics 17 : 791 802.
98. Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, Fraser CM, Smith HO Venter JC (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286 : 2165 2169.
99. Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y Bork P (1998) Homology-based fold predictions for Mycoplasma genitalium proteins. J Mol Biol 280 : 323 326.
100. Iimura T Pourquie O (2007) Hox genes in time and space during vertebrate body formation. Dev Growth Differ 49 : 265 275.
101. Itaya M, Tsuge K, Koizumi M Fujita K (2005) Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. P Natl Acad Sci USA 102 : 15971 15976.
102. Iyer LM, Aravind L, Bork P, Hofmann K, Mushegian AR, Zhulin IB Koonin EV (2001) Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Genome Biol 2, RESEARCH0051.
103. Jayaram M (2007) Split target specificity of ResT: a design for protein delivery, site selectivity and regulation of enzyme activity? Mol Microbiol 64 : 575 579.
104. Jeong KS, Ahn J Khodursky AB (2004) Spatial patterns of transcriptional activity in the chromosome of Escherichia coli. Genome Biol 5 : R86.
105. Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO Agarwalla S (2006) Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol 188 : 8259 8271.
106. Jun S Mulder B (2006) Entropy-driven spatial organization of highly confined polymers: lessons for the bacterial chromosome. P Natl Acad Sci USA 103 : 12388 12393.
107. Karwath A De Raedt L (2006) SMIREP: predicting chemical activity from SMILES. J Chem Inf Model 46 : 2432 2444.
108. Kebbekus P, Draper DE Hagerman P (1995) Persistence length of RNA. Biochemistry 34 : 4354 4357.
109. Kobayashi K, Ehrlich SD, Albertini A et al 2003) Essential Bacillus subtilis genes. P Natl Acad Sci USA 100 : 4678 4683.
110. Kuldell N (2007) Authentic teaching and learning through synthetic biology. J Biol Eng 1 : 8.
111. Landauer R (1961) Irreversibility and heat generation in the computing process. IBM J Res Dev 3 : 184 191.
112. Larsabal E Danchin A (2005) Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns". BMC Bioinformatics 6 : 206.
113. Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA III., Smith HO Venter JC (2007) Genome transplantation in bacteria: changing one species to another. Science 317 : 632 638.
114. Laub MT, Shapiro L McAdams HH (2007) Systems biology of Caulobacter. Annu Rev Genet 41 : 429 441.
115. Lawrence JG Roth JR (1996) Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143 : 1843 1860.
116. Ledwig M (2006) Common knowledge in game theory. Int J Knowl Cult Change Manage 6 : 43 48.
117. Lewis P Errington J (1997) Direct evidence for active segregation of oriC regions of the Bacillus subtilis chromosome and co-localization with the SpoOJ partitioning protein. Mol Microbiol 25 : 945 954.
118. Lewis RA, Wakimoto BT, Denell RE Kaufman TC (1980) Genetic analysis of the antennapedia gene complex (Ant-C) and adjacent chromosomal regions of Drosophila melanogaster. II. Polytene chromosome segments 84A-84B1,2. Genetics 95 : 383 397.
119. Lewontin RC (1993) The Doctrine of DNA: Biology as Ideology. Penguin Books, London.
120. Liberman EA (1979) Analog-digital molecular cell computer. Biosystems 11 : 111 124.
121. Liberman EA Minina SV (1996) Cell molecular computers and biological information as the foundation of nature's laws. Biosystems 38 : 173 177.
122. Lifson S (2005) What the book say: what is information for molecular biology? BioEssays 16 : 373 375.
123. Lindroos H, Vinnere O, Mira A, Repsilber D, Naslund K Andersson SG (2006) Genome rearrangements, deletions, and amplifications in the natural population of Bartonella henselae. J Bacteriol 188 : 7426 7439.
124. Lobry JR (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13 : 660 665.
125. Lobry JR Louarn JM (2003) Polarisation of prokaryotic chromosomes. Curr Opin Microbiol 6 : 101 108.
126. Luijsterburg MS, Noom MC, Wuite GJ Dame RT (2006) The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J Struct Biol 156 : 262 272.
127. Maeder DL, Anderson I, Brettin TS et al 2006) The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J Bacteriol 188 : 7922 7931.
128. Manchester KL (2008) Historical opinion: Erwin Chargaff and his 'rules' for the base composition of DNA: why did he fail to see the possibility of complementarity? Trends Biochem Sci 33 : 65 70.
129. Marles-Wright J Lewis RJ (2007) Stress responses of bacteria. Curr Opin Struc Biol 17 : 755 760.
130. Maynard-Smith J (2000) The concept of information in biology. Philos Sci 67 : 177 194.
131. Mayr E (1998) Two empires or three? P Natl Acad Sci USA 95 : 9720 9723.
132. Médigue C, Rouxel T, Vigier P, Hénaut A Danchin A (1991) Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol 222 : 851 856.
133. Mingorance J, Tamames J Vicente M (2004) Genomic channeling in bacterial cell division. J Mol Recognit 17 : 481 487.
134. Mirkin EV Mirkin SM (2005) Mechanisms of transcription-replication collisions in bacteria. Mol Cell Biol 25 : 888 895.
135. Mitrophanov AY Groisman EA (2008) Positive feedback in cellular control systems. BioEssays 30 : 542 555.
136. Mizoguchi H, Mori H Fujio T (2007) Escherichia coli minimum genome factory. Biotechnol Appl Bioc 46 : 157 167.
137. Monod J (1971) Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology. Vintage, New York.
138. Moszer I, Rocha EP Danchin A (1999) Codon usage and lateral gene transfer in Bacillus subtilis. Curr Opin Microbiol 2 : 524 528.
139. Movila A, Uspenskaia I, Toderas I, Melnic V Conovalov J (2006) Prevalence of Borrelia burgdorferi sensu lato and Coxiella burnetti in ticks collected in different biocenoses in the Republic of Moldova. Int J Med Microbiol 296 : 172 176.
140. Muller D, Médigue C, Koechler S et al 2007) A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet 3 : e53.
141. Muller H (1932) Some genetic aspects of sex. Am Nat 66 : 118 128.
142. Mushegian AR Koonin EV (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. P Natl Acad Sci USA 93 : 10268 10273.
143. Myhill J (1952) Some philosophical implications of mathematical logic. Three classes of ideas. Rev Metaphys 6 : 165 198.
144. Nagel T (1998) Reductionism and antireductionism. Novartis Fdn Symp 213 : 3 10 discussion 10-14; 73-15.
145. Nitschké P, Guerdoux-Jamet P, Chiapello H, Faroux G, Hénaut C, Hénaut A Danchin A (1998) Indigo: a World-Wide-Web review of genomes and gene functions. FEMS Microbiol Rev 22 : 207 227.
146. Noria S Danchin A (2002) Just so genome stories: what does my neighbor tell me? Uehara Memorial Foundation Symposium: Genome Science: Towards a New Paradigm? (Yoshikawa H, Ogasawara N Satoh N, eds), pp. 3 13. Elsevier Science BV, Tokyo.
147. Offroy de la Mettrie J (translation 1996) Machine Man and other Writings. Cambridge University Press, Cambridge.
148. Oliver SG, van der Aart QJ, Agostoni-Carbone ML et al 1992) The complete DNA sequence of yeast chromosome III. Nature 357 : 38 46.
149. Orgel L (1963) The maintenance of the accuracy of protein synthesis and its relevance to aging. P Natl Acad Sci USA 49 : 517 521.
150. Overbeek R, Fonstein M, D'Souza M, Pusch GD Maltsev N (1999) The use of gene clusters to infer functional coupling. P Natl Acad Sci USA 96 : 2896 2901.
151. Palsson BO (2004) Two-dimensional annotation of genomes. Nat Biotechnol 22 : 1218 1219.
152. Parsot C (1986) Evolution of biosynthetic pathways: a common ancestor for threonine synthase, threonine dehydratase and D-serine dehydratase. EMBO J 5 : 3013 3019.
153. Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K Weng Z (2007) Nucleosome positioning signals in genomic DNA. Genome Res 17 : 1170 1177.
154. Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH Ussery DW (2000) A DNA structural atlas for Escherichia coli. J Mol Biol 299 : 907 930.
155. Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO Cozzarelli NR (2004) Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol 5 : R87.
156. Plantinga TH, van der Does C Driessen AJ (2004) Transporter's evolution and carbohydrate metabolic clusters. Trends Microbiol 12 : 4 7.
157. Posfai G, Plunkett G III., Feher T et al 2006) Emergent properties of reduced-genome Escherichia coli. Science 312 : 1044 1046.
158. Potvin E, Sanschagrin F Levesque RC (2008) Sigma factors in Pseudomonas aeruginosa. FEMS Microbiol Rev 32 : 38 55.
159. Price ND Shmulevich I (2007) Biochemical and statistical network models for systems biology. Curr Opin Biotech 18 : 365 370.
160. Quastler H (1953) Essays on the Use of Information Theory in Biology. University of Illinois Press, Urbana, IL.
161. Quastler H (1964) The Emergence of Biological Organization. Yale University Press, New York.
162. Quastler H, Platzman RL Yockey H (1958) Symposium on Information Theory in Biology. Pergamon Press, Oxford.
163. Rocha EP (2002) Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes? Trends Microbiol 10 : 393 395.
164. Rocha EP Danchin A (2001) Ongoing evolution of strand composition in bacterial genomes. Mol Biol Evol 18 : 1789 1799.
165. Rocha EP Danchin A (2002) Base composition bias might result from competition for metabolic resources. Trends Genet 18 : 291 294.
166. Rocha EP Danchin A (2003a) Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nat Genet 34 : 377 378.
167. Rocha EP Danchin A (2003b) Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res 31 : 6570 6577.
168. Rocha EP, Danchin A Viari A (1999) Universal replication biases in bacteria. Mol Microbiol 32 : 11 16.
169. Rocha EP, Sekowska A Danchin A (2000) Sulphur islands in the Escherichia coli genome: markers of the cell's architecture? FEBS Lett 476 : 8 11.
170. Rocha EP, Fralick J, Vediyappan G, Danchin A Norris V (2003) A strand-specific model for chromosome segregation in bacteria. Mol Microbiol 49 : 895 903.
171. Rogozin IB, Makarova KS, Murvai J, Czabarka E, Wolf YI, Tatusov RL, Szekely LA Koonin EV (2002) Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res 30 : 2212 2223.
172. Rokem JS, Lantz AE Nielsen J (2007) Systems biology of antibiotic production by microorganisms. Nat Prod Rep 24 : 1262 1287.
173. Rosenberg SM (1997) Mutation for survival. Curr Opin Genet Dev 7 : 829 834.
174. Rudolph CJ, Dhillon P, Moore T Lloyd RG (2007) Avoiding and resolving conflicts between DNA replication and transcription. DNA Repair (Amsterdam) 6 : 981 993.
175. Sanger F, Coulson AR, Hong GF, Hill DF Petersen GB (1982) Nucleotide sequence of bacteriophage lambda DNA. J Mol Biol 162 : 729 773.
176. Sarkar S (2005) Molecular Models of Life. Philosophical Papers on Molecular Biology. MIT Press, Cambridge, MA.
177. Sassetti CM, Boyd DH Rubin EJ (2003) Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48 : 77 84.
178. Savageau MA (1991) Reconstructionist molecular biology. New Biol 3 : 190 197.
179. Schrödinger E (1945) What is Life? The Physical Aspect of the Living Cell. The Macmillan Company, New York.
180. Schwartz YB Pirrotta V (2007) Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 8 : 9 22.
181. Sekowska A, Kung HF Danchin A (2000) Sulfur metabolism in Escherichia coli and related bacteria: facts and fiction. J Mol Microb Biotech 2 : 145 177.
182. Shannon C Weaver W (1949) The Mathematical Theory of Communication. University of Illinois, Urbana, IL.
183. Sharpe ME Errington J (1998) A fixed distance for separation of newly replicated copies of oriC in Bacillus subtilis: implications for co-ordination of chromosome segregation and cell division. Mol Microbiol 28 : 981 990.
184. Shi T Falkowski PG (2008) Genome evolution in cyanobacteria: the stable core and the variable shell. P Natl Acad Sci USA 105 : 2510 2515.
185. Smith HO, Tomb JF, Dougherty BA, Fleischmann RD Venter JC (1995) Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome. Science 269 : 538 540.
186. Snow CP (1993) The Two Cultures, 2nd edn, Cambridge University Press, Cambridge, UK.
187. Steane A (1998) Quantum computing. Rep Prog Phys 61 : 117 173.
188. Takeuchi F, Watanabe S, Baba T et al 2005) Whole-genome sequencing of Staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of human-colonizing staphylococcal species. J Bacteriol 187 : 7292 7308.
189. Takeyasu K, Kim J, Ohniwa RL, Kobori T, Inose Y, Morikawa K, Ohta T, Ishihama A Yoshimura SH (2004) Genome architecture studied by nanoscale imaging: analyses among bacterial phyla and their implication to eukaryotic genome folding. Cytogenet Genome Res 107 : 38 48.
190. Tamames J, Gonzalez-Moreno M, Mingorance J, Valencia A Vicente M (2001) Bringing gene order into bacterial shape. Trends Genet 17 : 124 126.
191. Tamames J, Moya A Valencia A (2007) Modular organization in the reductive evolution of protein-protein interaction networks. Genome Biol 8 : R94.
192. Thanaraj TA Argos P (1996) Ribosome-mediated translational pause and protein domain organization. Protein Sci 5 : 1594 1612.
193. Tolstorukov MY, Virnik KM, Adhya S Zhurkin VB (2005) A-tract clusters may facilitate DNA packaging in bacterial nucleoid. Nucleic Acids Res 33 : 3907 3918.
194. Tompkins JD, Nelson JL, Hazel JC, Leugers SL, Stumpf JD Foster PL (2003) Error-prone polymerase, DNA polymerase IV, is responsible for transient hypermutation during adaptive mutation in Escherichia coli. J Bacteriol 185 : 3469 3472.
195. Trautteur G Tamburrini G (2007) A note on discreteness and virtuality in analog computing. Theor Comput Sci 371 : 106 114.
196. Turing A (1936 1937) On computable numbers, with an application to the Entscheidungsproblem. P Lond Math Soc 42 : 230 265.
197. Turing A (1946 (1986 A. M. Turing's ACE Report of 1946 and other papers. Charles Babbage Institute Reprint Series for the History of Computing, Vol. 10 (Carpenter B Doran R, eds). MIT Press, Cambridge, MA.
198. Turing A (1952) The chemical basis of morphogenesis. Philos T Roy Soc B 237 : 37 72.
199. Valente L Nishikura K (2005) ADAR gene family and A-to-I RNA editing: diverse roles in posttranscriptional gene regulation. Prog Nucleic Acid Re 79 : 299 338.
200. Villarreal LP (2004) Are viruses alive? Sci Am 291 : 100 105.
201. von Neumann J (1958) The Computer and the Brain. Yale University Press, New Haven.
202. Waliszewski P, Molski M Konarski J (1998) On the holistic approach in cellular and cancer biology: nonlinearity, complexity, and quasi-determinism of the dynamic cellular network. J Surg Oncol 68 : 70 78.
203. Walsby AE (2005) Archaea with square cells. Trends Microbiol 13 : 193 195.
204. Wang JD, Berkmen MB Grossman AD (2007) Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis. P Natl Acad Sci USA 104 : 5608 5613.
205. Warren WC, Hillier LW, Marshall Graves JA et al 2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 453 : 175 183.
206. Watson JD Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171 : 737 738.
207. Webb CD, Graumann PL, Kahana JA, Teleman AA, Silver PA Losick R (1998) Use of time-lapse microscopy to visualize rapid movement of the replication origin region of the chromosome during the cell cycle in Bacillus subtilis. Mol Microbiol 28 : 883 892.
208. Wilmut I, Schnieke AE, McWhir J, Kind AJ Campbell KH (1997) Viable offspring derived from fetal and adult mammalian cells. Nature 385 : 810 813.
209. Woese CR (1972) The evolution of cellular tape reading processes and macromolecular complexity. Brookhaven Sym Biol 23 : 326 365.
210. Woese CR, Magrum LJ Fox GE (1978) Archaebacteria. J Mol Evol 11 : 245 251.
211. Woldringh CL Nanninga N (2006) Structural and physical aspects of bacterial chromosome segregation. J Struct Biol 156 : 273 283.
212. Wright BE (2004) Stress-directed adaptive mutations and evolution. Mol Microbiol 52 : 643 650.
213. Yarmolinsky MB (2000) A pot-pourri of plasmid paradoxes: effects of a second copy. Mol Microbiol 38 : 1 7.
214. Yockey H (1992) Information Theory and Molecular Biology. Cambridge University Press, Cambridge, UK.
215. Yockey H, Platzmann R Quastler H (1958) Symposium on Information Theory in Biology. Pergamon Press, New York.
216. Zimmerman SB (2006) Shape and compaction of Escherichia coli nucleoids. J Struct Biol 156 : 255 261.