New approaches to the problem of generating coherent, reproducible phenotypes
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- 作者：Vic Norris (1)
Ghislain Gangwe Nana (2)
Jean-Nicolas Audinot (3) - 关键词：Phenotypic diversity ; Cell division ; Bacteria ; Computing ; Module ; Equilibrium
- 刊名：Theory in Biosciences
- 出版年：2014
- 出版时间：March 2014
- 年：2014
- 卷：133
- 期：1
- 页码：47-61
- 全文大小：1,123 KB
- 参考文献：1. Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S (2004) Bacterial persistence as a phenotypic switch. Science (New York) 305:1622鈥?625
2. Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell鈥檚 functional organization. Nat Rev Genet 5(2):101鈥?13. doi:10.1038/nrg1272
3. Battesti A, Majdalani N, Gottesman S (2011) The RpoS-mediated general stress response in / Escherichia coli. Annu Rev Microbiol 65:189鈥?13. doi:10.1146/annurev-micro-090110-102946
4. Benford G (1995) Old legends. In: Bear G (ed) New legends. Legend Books, London, pp 292鈥?06
5. Berger M, Farcas A, Geertz M, Zhelyazkova P, Brix K, Travers A, Muskhelishvili G (2010) Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU. EMBO Rep 11(1):59鈥?4. doi:10.1038/embor.2009.232
6. Binenbaum Z, Parola AH, Zaritsky A, Fishov I (1999) Transcription- and translation-dependent changes in membrane dynamics in bacteria: testing the transertion model for domain formation. Mol Microbiol 32:1173鈥?182
7. Booth IR (2002) Stress and the single cell: intrapopulation diversity is a mechanism to ensure survival upon exposure to stress. Int J Food Microbiol 78:19鈥?0
8. Boxer SG, Kraft ML, Weber PK (2009) Advances in imaging secondary ion mass spectrometry for biological samples. Annu Rev Biophys 38:53鈥?4. doi:10.1146/annurev.biophys.050708.133634
9. Bray D (2012) The propagation of allosteric states in large multiprotein complexes. J Mol Biol. doi:10.1016/j.jmb.2012.12.008
10. Briers Y, Staubli T, Schmid MC, Wagner M, Schuppler M, Loessner MJ (2012) Intracellular vesicles as reproduction elements in cell wall-deficient L-form bacteria. PloS one 7(6):e38514. doi:10.1371/journal.pone.0038514
11. Cabin-Flaman A, Monnier AF, Coffinier Y, Audinot JN, Gibouin D, Wirtz T, Boukherroub R, Migeon HN, Bensimon A, Janniere L, Ripoll C, Norris V (2011) Combed single DNA molecules imaged by secondary ion mass spectrometry. Anal Chem 83(18):6940鈥?947. doi:10.1021/ac201685t
12. Cabrera JE, Jin DJ (2003) The distribution of RNA polymerase in / Escherichia coli is dynamic and sensitive to environmental cues. Mol Microbiol 50:1493鈥?505
13. Cabrera JE, Cagliero C, Quan S, Squires CL, Jin DJ (2009) Active transcription of rRNA operons condenses the nucleoid in / Escherichia coli: examining the effect of transcription on nucleoid structure in the absence of transertion. J Bacteriol 191(13):4180鈥?185. doi:10.1128/JB.01707-08
14. Cheng S, Liu Y, Crowley CS, Yeates TO, Bobik TA (2008) Bacterial microcompartments: their properties and paradoxes. BioEssays 30(11鈥?2):1084鈥?095
15. Cooper S, Shedden K, Vu-Phan D (2009) Invariant mRNA and mitotic protein breakdown solves the Russian Doll problem of the cell cycle. Cell Biol Int 33(1):10鈥?8. doi:10.1016/j.cellbi.2008.10.004
16. Defeu Soufo HJ, Reimold C, Linne U, Knust T, Gescher J, Graumann PL (2010) Bacterial translation elongation factor EF-Tu interacts and colocalizes with actin-like MreB protein. Proc Natl Acad Sci USA 107(7):3163鈥?168
17. Demarty M, Gleyse B, Raine D, Ripoll C, Norris V (2003) Modelling autocatalytic networks with artificial microbiology. Comptes Rendus de l鈥橝cademie des Sciences 326:459鈥?66
18. Echtenkamp PL, Wilson DB, Shuler ML (2009) Cell cycle progression in / Escherichia coli B/r affects transcription of certain genes: implications for synthetic genome design. Biotechnol Bioeng 102(3):902鈥?09. doi:10.1002/bit.22098
19. Eden E, Geva-Zatorsky N, Issaeva I, Cohen A, Dekel E, Danon T, Cohen L, Mayo A, Alon U (2011) Proteomehalf-life dynamics in living human cells. Science (New York) 331(6018):764鈥?68. doi:10.1126/science.1199784
20. Espeli O, Mercier R, Boccard F (2008) DNA dynamics vary according to macrodomain topography in the / E. coli chromosome. Mol Microbiol 68(6):1418鈥?427
21. Exley R, Zouine M, Pernelle J鈥揓, Beloin C, Le Hegarat F, Deneubourg AM (2001) A possible role for L24 of / Bacillus subtilis in nucleoid organization and segregation. Biochimie 83:269鈥?75
22. Fell DA, Wagner A (2000) The small world of metabolism. Nat Biotechnol 18(11):1121鈥?122. doi:10.1038/81025
23. Ferguson ML, Le Coq D, Jules M, Aymerich S, Radulescu O, Declerck N, Royer CA (2012) Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states. Proc Natl Acad Sci USA 109(1):155鈥?60. doi:10.1073/pnas.1110541108
24. Fishov I, Norris V (2012) Membrane heterogeneity created by transertion is a global regulator in bacteria. Curr Opin Microbiol 15(6):724鈥?30. doi:10.1016/j.mib.2012.11.001
25. Fishov I, Zaritsky A, Grover NB (1995) On microbial states of growth. Mol Microbiol 15:789鈥?94
26. Gangwe Nana G, Gibouin D, Lefebvre F, Delaune A, Janni猫re L, Ripoll C, Cabin-Flaman A, Norris V (2012) Intracellular and population heterogeneity in / Bacillus subtilis revealed by secondary ion mass spectrometry. In: Amar P, K茅p猫s F, Norris V (eds) Modelling complex biological systems in the context of genomics. EDP Sciences, Evry, pp 79鈥?4
27. Garcia-Betancur JC, Yepes A, Schneider J, Lopez D (2012) Single-cell analysis of Bacillus subtilis biofilms using fluorescence microscopy and flow cytometry. J Vis Exp 15(60):1鈥?. doi:10.3791/3796
28. Ghosh S, Sureka K, Ghosh B, Bose I, Basu J, Kundu M (2011) Phenotypic heterogeneity in mycobacterial stringent response. BMC Syst Biol 5:18. doi:10.1186/1752-0509-5-18
29. Godin M, Delgado FF, Son S, Grover WH, Bryan AK, Tzur A, Jorgensen P, Payer K, Grossman AD, Kirschner MW, Manalis SR (2010) Using buoyant mass to measure the growth of single cells. Nat Methods 7(5):387鈥?90. doi:10.1038/nmeth.1452
30. Gowrishankar J, Harinarayanan R (2004) Why is transcription coupled to translation in bacteria? Mol Microbiol 54:598鈥?03
31. Guelzim N, Bottani S, Bourgine P, Kepes F (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 31:60鈥?3
32. Guerquin-Kern JL, Wu TD, Quintana C, Croisy A (2005) Progress in analytical imaging of the cell by dynamic secondary ion mass spectrometry (SIMS microscopy). Biochim Biophys Acta 1724(3):228鈥?38
33. Herskovits AA, Seluanov A, Rajsbaum R, ten Hagen-Jongman CM, Henrichs T, Bochkareva ES, Phillips GJ, Probst FJ, Nakae T, Ehrmann M, Luirink J, Bibi E (2001) Evidence for coupling of membrane targeting and function of the signal recognition particle (SRP) receptor FtsY. EMBO Rep 2(11):1040鈥?046. doi:10.1093/embo-reports/kve226
34. Hintze A, Adami C (2008) Evolution of complex modular biological networks. PLoS Comput Biol 4(2):e23. doi:10.1371/journal.pcbi.0040023
35. Huang R, Reusch RN (1996) Poly(3-hydroxybutyrate) is associated with specific proteins in the cytoplasm and membranes of / Escherichia coli. J Biol Chem 271:22196鈥?2202
36. Hunding A, Kepes F, Lancet D, Minsky A, Norris V, Raine D, Sriram K, Root-Bernstein R (2006) Compositional complementarity and prebiotic ecology in the origin of life. BioEssays 28(4):399鈥?12
37. Iost I, Dreyfus M (1995) The stability of / Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation. EMBO J 14(13):3252鈥?261
38. Junier I, Martin O, Kepes F (2010) Spatial and topological organization of DNA chains induced by gene co-localization. PLoS Comput Biol 6(2):e1000678. doi:10.1371/journal.pcbi.1000678
39. Kaprelyants AS, Mukamolova GV, Davey HM, Kell DB (1996) Quantitative analysis of the physiological heterogeneity within starved cultures of micrococcus luteus by flow cytometry and cell sorting. Appl Environ Microbiol 62(4):1311鈥?316
40. Kashtan N, Mayo AE, Kalisky T, Alon U (2009) An analytically solvable model for rapid evolution of modular structure. PLoS Comput Biol 5(4):e1000355. doi:10.1371/journal.pcbi.1000355
41. Kauffman S (1996) At home in the universe, the search for the laws of complexity. Penguin, London
42. Kaufmann SA (1993) The origins of order. Oxford University Press, New York
43. Kogoma T (1997) Stable DNA replication: interplay between DNA replication, homologous recombination and transcription. Microbiol Mol Biol Rev 61:212鈥?38
44. Lambert G, Liao D, Vyawahare S, Austin RH (2011) Anomalous spatial redistribution of competing bacteria under starvation conditions. J Bacteriol 193(8):1878鈥?883. doi:10.1128/JB.01430-10
45. Leaver M, Dominguez-Cuevas P, Coxhead JM, Daniel RA, Errington J (2009) Life without a wall or division machine in / Bacillus subtilis. Nature 457(7231):849鈥?53
46. Lechene C, Hillion F, McMahon G, Benson D, Kleinfeld AM, Kampf JP, Distel D, Luyten Y, Bonventre J, Hentschel D, Park KM, Ito S, Schwartz M, Benichou G, Slodzian G (2006) High-resolution quantitative imaging of mammalian and bacterial cells using stable isotope mass spectrometry. J Biol 5(6):20
47. Lemke JL (2000) Opening up closure. Semiotics across scales. Ann NY Acad Sci 901:100鈥?11
48. Libby EA, Roggiani M, Goulian M (2012) Membrane protein expression triggers chromosomal locus repositioning in bacteria. Proc Natl Acad Sci USA 109(19):7445鈥?450. doi:10.1073/pnas.1109479109
49. Livolant FY, Bouligand Y (1978) New observations on the twisted arrangement of dinoflagellate chromosomes. Chromosoma 68:21鈥?4
50. Lynch AS, Wang JC (1993) Anchoring of DNA to the bacterial cytoplasmic membrane through co-transcriptional synthesis of polypeptides encoding membrane proteins or proteins for export : a mechanism of plasmid hypernegative supercoiling in mutants deficient in DNA topoisomerase I. J Bacteriol 175:1645鈥?655
51. Mathieu LG, Sonea S (1995) A powerful bacterial world. Endeavour 19:112鈥?17
52. Matsuhashi M, Pankrushina AN, Takeuchi S, Ohshima H, Miyoi H, Endoh K, Murayama K, Watanabe H, Endo S, Tobi M, Mano Y, Hyodo M, Kobayashi T, Kaneko T, Otani S, Yoshimura S, Harata A, Sawada T (1998) Production of sound waves by bacterial cells and the response of bacterial cells to sound. J Gen Appl Microbiol 44(1):49鈥?5
53. Matsumoto K, Kusaka J, Nishibori A, Hara H (2006) Lipid domains in bacterial membranes. Mol Microbiol 61(5):1110鈥?117
54. Mayer F (2006) Cytoskeletal elements in bacteria / Mycoplasma pneumoniae, Thermoanaerobacterium sp., and / Escherichia coli as revealed by electron microscopy. J Mol Microbiol Biotechnol 11(3鈥?):228鈥?43
55. Mileykovskaya E, Dowhan W (2000) Visualization of phospholipid domains in / Escherichia coli by using the cardiolipin-specific fluorescent dye 10-N-nonyl acridine orange. J Bacteriol 182:1172鈥?175
56. Mileykovskaya E, Dowhan W (2009) Cardiolipin membrane domains in prokaryotes and eukaryotes. Biochim Biophys Acta 1788(10):2084鈥?091. doi:10.1016/j.bbamem.2009.04.003
57. Miller OL Jr, Hamkalo BA, Thomas CA Jr (1970) Visualization of bacterial genes in action. Science (New York) 169(943):392鈥?95
58. Minsky A, Shimoni E, Frenkiel-Krispin D (2002) Stress, order and survival. Nat Rev Mol Cell Biol 3:50鈥?0
59. Musat N, Halm H, Winterholler B, Hoppe P, Peduzzi S, Hillion F, Horreard F, Amann R, Jorgensen BB, Kuypers MM (2008) A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc Natl Acad Sci USA 105(46):17861鈥?7866. doi:10.1073/pnas.0809329105
60. Musat N, Foster R, Vagner T, Adam B, Kuypers MM (2012) Detecting metabolic activities in single cells, with emphasis on nanoSIMS. FEMS Microbiol Rev 36(2):486鈥?11. doi:10.1111/j.1574-6976.2011.00303.x
61. Naseem R, Wann KT, Holland IB, Campbell AK (2009) ATP regulates calcium efflux and growth in / E. coli. J Mol Biol 391(1):42鈥?6. doi:10.1016/j.jmb.2009.05.064
62. Norris V (1995) Hypothesis: chromosome separation in / E. coli involves autocatalytic gene expression, transertion and membrane domain formation. Mol Microbiol 16:1051鈥?057
63. Norris V (1998) Modelling / E. coli: the concept of competitive coherence. Comptes Rendus de l鈥橝cademie des Sciences 321:777鈥?87
64. Norris V (2007) Could phase oscillations occur in bacteria? In: Amar P, Kepes F, Norris V, Bernot G (eds) Modelling complex biological systems in the context of genomics. EDP Sciences, Evry, pp 89鈥?8
65. Norris V (2011) Speculations on the initiation of chromosome replication in / Escherichia coli: the dualism hypothesis. Med Hypotheses 76(5):706鈥?16. doi:S0306-9877(11)00053-310.1016/j.mehy.2011.02.002
66. Norris V (2012) Competitive coherence. In: Azari NP, Runehov A, Oviedo L (eds) Encyclopedia of sciences and religions. Springer, New York
67. Norris V, Amar P (2012) Chromosome replication in / Escherichia coli: life on the scales. Life 2(4):286鈥?12
68. Norris V, Hyland GJ (1997) Do bacteria 鈥渟ing鈥? Mol Microbiol 24:879鈥?80
69. Norris V, Raine DJ (1998) A fission-fusion origin for life. Orig Life Evol Biosph 28:523鈥?37
70. Norris V, Cabin A, Zemirline A (2005) Hypercomplexity. Acta Biotheor 53(4):313鈥?30
71. Norris V, Blaauwen TD, Doi RH, Harshey RM, Janniere L, Jimenez-Sanchez A, Jin DJ, Levin PA, Mileykovskaya E, Minsky A, Misevic G, Ripoll C, Saier M Jr., Skarstad K, Thellier M (2007) Toward a hyperstructure taxonomy. Ann Rev Microbiol 61:309-329
72. Norris V, Hunding A, Kepes F, Lancet D, Minsky A, Raine D, Root-Bernstein R, Sriram K (2007b) Question 7: the first units of life were not simple cells. Orig Life Evol Biosph 37(4鈥?):429鈥?32
73. Norris V, Zemirline A, Amar P, Audinot JN, Ballet P, Ben-Jacob E, Bernot G, Beslon G, Cabin A, Fanchon E, Giavitto JL, Glade N, Greussay P, Grondin Y, Foster JA, Hutzler G, Jost J, Kepes F, Michel O, Molina F, Signorini J, Stano P, Thierry AR (2011) Computing with bacterial constituents, cells and populations: from bioputing to bactoputing. Theory Biosci 130(3):211鈥?28. doi:10.1007/s12064-010-0118-4
74. Norris V, Engel M, Demarty M (2012a) Modelling biological systems with competitive coherence. Adv Artif Neural Syst 2012:1鈥?0. doi:10.1155/2012/703878
75. Norris V, Loutelier-Bourhis C, Thierry A (2012b) How did metabolism and genetic replication get married? Orig Life Evol Biosph. doi:10.1007/s11084-012-9312-3
76. Norris V, Menu-Bouaouiche L, Becu J-M, Legendre R, Norman R, Rosenzweig JA (2012c) Hyperstructure interactions influence the virulence of the Type 3 secretion system in yersiniae and other bacteria. Appl Microbiol Biotechnol 96(1):23鈥?6. doi:10.1007/s00253-012-4325-4
77. Norris V, Amar P, Legent G, Ripoll C, Thellier M, Ovadi J (2013) Sensor potency of the moonlighting enzyme-decorated cytoskeleton. BMC Biochem 14:3. doi:10.1186/1471-2091-14-3
78. Ogden GB, Pratt MJ, Schaechter M (1988) The replicative origin of the / E. coli chromosome binds to cell membrane only when hemi-methylated. Cell 54:127鈥?35
79. Onoda T, Enokizono J, Kaya H, Oshima A, Freestone P, Norris V (2000) Effects of calcium and calcium chelators on growth and morphology of / Escherichia coli L-form NC-7. J Bacteriol 182:1419鈥?422
80. Pelling AE, Sehati S, Gralla EB, Valentine JS, Gimzewski JK (2004) Local nanomechanical motion of the cell wall of / Saccharomyces cerevisiae. Science (New York) 305:1147鈥?150
81. Popa R, Weber PK, Pett-Ridge J, Finzi JA, Fallon SJ, Hutcheon ID, Nealson KH, Capone DG (2007) Carbon and nitrogen fixation and metabolite exchange in and between individual cells of / Anabaena oscillarioides. ISME J 1(4):354鈥?60. doi:10.1038/ismej.2007.44
82. Potrykus K, Murphy H, Philippe N, Cashel M (2011) ppGpp is the major source of growth rate control in / E. coli. Environ Microbiol 13(3):563鈥?75. doi:10.1111/j.1462-2920.2010.02357.x
83. Raine DJ, Norris V (2000) Metabolic cycles and self-organised criticality. Interjournal of complex systems paper 361. http://www.interjournal.org
84. Raine DJ, Norris V (2007) Lipid domain boundaries as prebiotic catalysts of peptide bond formation. J Theor Biol 246(1):176鈥?85
85. Rao NN, Gomez-Garcia MR, Kornberg A (2009) Inorganic polyphosphate: essential for growth and survival. Annu Rev Biochem 78:605鈥?47. doi:10.1146/annurev.biochem.77.083007.093039
86. Reshes G, Vanounou S, Fishov I, Feingold M (2008) Timing the start of division in / E. coli: a single-cell study. Phys Biol 5(4):46001
87. Rocha E, Fralick J, Vediyappan G, Danchin A, Norris V (2003) A strand-specific model for chromosome segregation in bacteria. Mol Microbiol 49:895鈥?03
88. Root-Bernstein RS, Dillon PF (1997) Molecular complementarity I: the complementarity theory of the origin and evolution of life. J Theor Biol 188(4):447鈥?79
89. Salthe S (1985) Evolving hierarchical systems. Columbia University Press, New York
90. Scolari VF, Bassetti B, Sclavi B, Lagomarsino MC (2011) Gene clusters reflecting macrodomain structure respond to nucleoid perturbations. Mol BioSyst 7(3):878鈥?88. doi:10.1039/c0mb00213e
91. Segre D, Ben-Eli D, Lancet D (2000) Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies. Proc Natl Acad Sci USA 97:4112鈥?117
92. Sekimizu K, Kornberg A (1988) Cardiolipin activation of dnaA protein, the initiation protein of replication in / Escherichia coli. J Biol Chem 263(15):7131鈥?135
93. Shoval O, Sheftel H, Shinar G, Hart Y, Ramote O, Mayo A, Dekel E, Kavanagh K, Alon U (2012) Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space. Science (New York) 336(6085):1157鈥?160. doi:10.1126/science.1217405
94. Simon HA (1962) The architecture of complexity. Proc Am Philos Soc 106(6):467鈥?82
95. Smits WK, Kuipers OP, Veening JW (2006) Phenotypic variation in bacteria: the role of feedback regulation. Nat Rev Microbiol 4(4):259鈥?71
96. Sobetzko P, Travers A, Muskhelishvili G (2012) Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle. Proc Natl Acad Sci USA 109(2):E42鈥揈50. doi:10.1073/pnas.1108229109
97. Son S, Tzur A, Weng Y, Jorgensen P, Kim J, Kirschner MW, Manalis SR (2012) Direct observation of mammalian cell growth and size regulation. Nat Methods 9(9):910鈥?12. doi:10.1038/nmeth.2133
98. Steinhauser ML, Bailey AP, Senyo SE, Guillermier C, Perlstein TS, Gould AP, Lee RT, Lechene CP (2012) Multi-isotope imaging mass spectrometry quantifies stem cell division and metabolism. Nature 481(7382):516鈥?19. doi:10.1038/nature10734
99. Stewart MK, Cummings LA, Johnson ML, Berezow AB, Cookson BT (2011) Regulation of phenotypic heterogeneity permits Salmonella evasion of the host caspase-1 inflammatory response. Proc Natl Acad Sci USA 108(51):20742鈥?0747. doi:10.1073/pnas.1108963108
100. Terui Y, Akiyama M, Sakamoto A, Tomitori H, Yamamoto K, Ishihama A, Igarashi K, Kashiwagi K (2012) Increase in cell viability by polyamines through stimulation of the synthesis of ppGpp regulatory protein and omega protein of RNA polymerase in / Escherichia coli. Int J Biochem Cell Biol 44(2):412鈥?22. doi:10.1016/j.biocel.2011.11.017
101. Trouillon R, Passarelli MK, Wang J, Kurczy ME, Ewing AG (2013) Chemical analysis of single cells. Anal Chem 85(2):522鈥?42. doi:10.1021/ac303290s
102. Tyler BJ, Bruening C, Rangaranjan S, Arlinghaus HF (2011) TOF-SIMS imaging of adsorbed proteins on topographically complex surfaces with Bi(3) (+) primary ions. Biointerphases 6(3):135. doi:10.1116/1.3622347
103. Vohradsky J, Ramsden JJ (2001) Genome resource utilization during prokaryotic development. FASEB J 15:2054鈥?056
104. Vos-Scheperkeuter GH, Witholt B (1982) Co-translational insertion of envelope proteins; theoretical considerations and implications. Ann Inst Pasteur 133A:129鈥?38
105. Wada A, Mikkola R, Kurland CG, Ishihama A (2000) Growth phase-coupled changes of the ribosome profile in natural isolates and laboratory strains of / Escherichia coli. J Bacteriol 182:2893鈥?899
106. Wagner M (2009) Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging. Annu Rev Microbiol 63:411鈥?29. doi:10.1146/annurev.micro.091208.073233
107. Wahl A, Schuth N, Pfeiffer D, Nussberger S, Jendrossek D (2012) PHB granules are attached to the nucleoid via PhaM in / Ralstonia eutropha. BMC Microbiol 12:262. doi:1471-2180-12-26210.1186/1471-2180-12-262
108. Weart RB, Lee AH, Chien AC, Haeusser DP, Hill NS, Levin PA (2007) A metabolic sensor governing cell size in bacteria. Cell 130(2):335鈥?47
109. Woldringh CL, Nanninga N (1985) Structure of the nucleoid and cytoplasm in the intact cell. In: Nanninga N (ed) Molecular cytology of / Escherichia coli. Academic Press, London, pp 161鈥?97
110. Wolf SG, Frenkiel D, Arad T, Finkel SE, Kolter R, Minsky A (1999) DNA protection by stress-induced biocrystallization. Nature 400:83鈥?5
111. Zhou P, Bogan JA, Welch K, Pickett SR, Wang H-J, Zaritsky A, Helmstetter CE (1997) Gene transcription and chromosome replication in / Escherichia coli. J Bacteriol 179:163鈥?69 - 作者单位：Vic Norris (1)
Ghislain Gangwe Nana (2)
Jean-Nicolas Audinot (3)
1. Theoretical Biology Unit, University of Rouen, 76821, Mont Saint Aignan, France
2. EA3829, Department of Biology, University of Rouen, 76821, Mont Saint Aignan, France
3. D茅partement Science et Analyse des Mat茅riaux, Centre de Recherche Public-Gabriel Lippmann, 4422, Belvaux, Luxembourg - ISSN：1611-7530
文摘
Fundamental, unresolved questions in biology include how a bacterium generates coherent phenotypes, how a population of bacteria generates a coherent set of such phenotypes, how the cell cycle is regulated and how life arose. To try to help answer these questions, we have developed the concepts of hyperstructures, competitive coherence and life on the scales of equilibria. Hyperstructures are large assemblies of macromolecules that perform functions. Competitive coherence describes the way in which organisations such as cells select a subset of their constituents to be active in determining their behaviour; this selection results from a competition between a process that is responsible for a historical coherence and another process responsible for coherence with the current environment. Life on the scales of equilibria describes how bacteria depend on the cell cycle to negotiate phenotype space and, in particular, to satisfy the conflicting constraints of having to grow in favourable conditions so as to reproduce yet not grow in hostile conditions so as to survive. Both competitive coherence and life on the scales deal with the problem of reconciling conflicting constraints. Here, we bring together these concepts in the common framework of hyperstructures and make predictions that may be tested using a learning program, Coco, and secondary ion mass spectrometry.