By way of introduction: Some constraints of the cell physics that are usually forgotten, but should be taken into account for in silico genome analysis

Biochimie

Volumn 78, Issue 5, 1996, Pages 299-301

  Danchin, A ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

Cytoplasmic proton concentration; Knots; Transcription; Translation

Indexed keywords

PROTON;

ARTICLE; BACTERIUM; BIOPHYSICS; COMPUTER ANALYSIS; DNA TRANSCRIPTION; GENETIC ANALYSIS; GENOME; RNA TRANSLATION;

BACTERIA (MICROORGANISMS);

EID: 0029805446     PISSN: 03009084     EISSN: None     Source Type: Journal    
DOI: 10.1016/0300-9084(96)84760-2     Document Type: Article

References (20)

1. 1 Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb J-F, Dougherty BA, Merrick JM, McKenney K, Sutton G, FitzHugh W, Fields CA, Gocayne JD, Scott JD, Shirley R, Liu L-I, Glodek A, Kelley JM, Weidman JF, Phillips CA, Spriggs T, Hedblom E, Cotton MD, Utterback TR, Hanna MC, Nguyen DT, Saudek DM, Brandon RC, Fine LD, Fritchman JL, Fuhrmann JL, Geoghagen NSM, Gnehm CL, McDonald LA, Small KV, Fraser CM, Smith HO, Venter JC (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512
2. 2 Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage R, Sutton G, Kelley JM, Fritchman JL, Weidman JF, Small KV, Sandusky M, Fuhrmann J, Nguyen D, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu PC, Lucier TS, Peterson SN, Smith HO, Hutchison III CA, Venter JC (1995) The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403
3. 3 Shellman V, Pettijohn D (1991) Introduction of proteins into living bacterial cells: distribution of labeled HU protein in Escherichia coli. J Bacteriol 173, 3047-3059
4. 4 Merchante R, Pooley H, Karamata D (1995) A periplasm in Bacillus subtilis. J Bacteriol 177, 6176-6183
5. 5 Koch AL (1988) Biophysics of bacterial walls viewed as stress-bearing fabric. Microbiol Rev 52, 337-353
6. 6 Negrutskii BS, Deutscher MP (1991) Channeling of aminoacyl-tRNA for protein synthesis in vivo. Proc Natl Acad Sci USA 88, 4991-4995
7. 7 Negrutskii BS, Deutscher MP (1992) A sequestered pool of aminoacyl-tRNA in mammalian cells. Proc Natl Acad Sci USA 89, 3601-3604
8. 8 Norris V, Turnock G, Sigee D (1996) The Escherichia coli enzoskeleton. Mol Microbiol 19, 197-204
9. 9 Ovadi J (1991) Physiological significance of metabolic channeling. J Theor Biol 152, 1-22
10. 10 Worcel A, Burgi E (1972) On the structure of the folded chromosome of Escherichia coli. J Mol Biol 71, 127-147
11. 11 Worcel A, Burgi E (1974) Properties of a membrane-attached form of the folded chromosome of Escherichia coli. J Mol Biol 82, 91-105
12. 12 Delius H, Worcel A (1974) Electron microscopic studies on the folded chromosome of Escherichia coli. Cold Spring Harb Symp Quant Biol 38, 53-58
13. 13 Timsit Y, Moras D (1994) DNA self-fitting: the double helix directs the geometry of its supramolecular assembly. EMBO J 13, 2737-2746
14. 14 Kuzminov A (1995) Collapse and repair of replication forks in Escherichia coli. Mol Microbiol 16, 373-384
15. 15 Yamanaka K, Ogura T, Niki H, Hiraga S (1992) Identification and characterization of the smbA gene, a suppressor of the mukB null mutant of Escherichia coli. J Bacteriol 174, 7517-7526
16. 16 Yamanaka K, Ogura T, Koonin EV, Niki H, Hiraga S (1994) Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia coli. Mol Gen Genet 243, 9-16
17. 17 Felsenfeld G (1992) Chromatin as an essential part of the transcriptional mechanism. Nature 355, 219-224
18. 18 Heggeler-Bordier BT, Wahli W, Adrian M, Stasiak A, Dubochet J (1992) The apical localization of transcribing RNA polymerases on supercoiled DNA prevents their rotation around the template. EMBO J 11, 667-672
19. 19 French S (1993) With heavy traffic on the genome, one-way travel is the key. ASM News 59, 437-443
20. 20 Danchin A (1987) The significance of split genes to developmental genetics. Adv Genet 24, 243-284