The genomic pattern of tDNA operon expression in e. coli

PLoS Computational Biology

Volumn 1, Issue 1, 2005, Pages 0086-0099

  Ardell, David H ^a,c   Kirsebom, Leif A ^b  

^a Uppsala University ^*

^b UPPSALA UNIVERSITY   (Sweden)

^c UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI; GENE EXPRESSION; LOCATION;

CO-EXPRESSION; CONCENTRATION PROFILES; E. COLI; EXPRESSION VARIATIONS; GENE DOSAGE; GENETIC BASIS; GENOMIC PATTERNS; LEAST SQUARE; MULTIPLE REGRESSIONS; REANALYSIS;

GROWTH RATE;

EID: 33645052751     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0010012     Document Type: Article

References (43)

1. Ikemura T(1982) Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs.J Mol Biol 158: 573-597.
2. Dong HJ, Nilsson L, Kurland CG (1996) Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol 260: 649-663.
3. Ehrenberg M, Kurland CG (1984) Costs of accuracy determined by a maximal growth rate constraint. Q Rev Biophys 17: 45-82.
4. Emilsson V, Kurland CG (1990) Growth rate dependence of transfer RNA abundance in Escherichia coli. Embo J 9: 4359-4366.
5. Emilsson V, Naslund AK, Kurland CG (l993) Growth-rate-dependent accumulation of twelve tRNA species in Escherichia coli.] Mol Biol 230: 483491.
6. Akashi H, Eyre-Walker A (1998) Translational selection and molecular evolution. Curr Opin Genet Dev 8: 688-693.
7. Percudani R, Pavesi A, Ottonello S (1997) Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J Mol Biol 268: 322-330.
8. Kanaya S, Yamada Y, Kudo Y, Ikemura T (1999) Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: Gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene 238: 143-155.
9. Rocha EP (2004) Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization. Genome Res 14: 2279-2286.
10. Keener J, Nomura M (1996) Regulation of ribosome synthesis. In: Neidhardt F, Curtiss III R, Ingraham JL, Lin EC, Brooks, Low K, et al., editors. Escherichia coli and Salmonella'. Cellular and molecular biology, 2nd ed. Washington, D.C.: ASM Press, pp. 1417-1431.
11. Condon C, Philips J, Fu ZY, Squires C, Squires CL (1992) Comparison of the expression of the seven ribosomal RNA operons in Escherichia coli. Embo J 11: 4175-4185.
12. Cooper S, Helmstetter CE (1968) Chromosome replication and the division cycle of Escherichia coli B/r. J Mol Biol 31: 519-540.
13. Sueoka N, Yoshikawa H (1965) The chromosome of Bacillus subtilis. I. Theory of marker frequency analysis. Genetics 52: 747-757.
14. Chandler MG, Pritchard RH (1975) The effect of gene concentration and relative gene dosage on gene output in Escherichia coli. Mol Gen Genet 138: 127-141.
15. Bremer H, Churchward G (1977) An examination of the CooperHelmstetter theory of DNA replication in bacteria and its underlying assumptions. J Theor Biol 69: 645-654.
16. Schmid MB, Roth JR (1987) Gene location affects expression level in Salmonella typhimurium. J Bacteriol 169: 2872-2875.
17. Donachie WD, Robinson AC (1987) Cell division: Parameter values and the process. In: Neidhardt F, Ingraham JL, Low KB, Magasanik B, Schaechter M, et al., editors. Escherichia coli and Salmonella typhimurium, 1st ed. Washington, DC: American Society for Microbiology, pp. 1578-1593.
18. Dennis PP, Ehrenberg M, Bremer H (2004) Control of rRNA synthesis in Escherichia coli: A systems biology approach. Microbiol Mol Biol Rev 68: 639668.
19. Paul BJ, Ross W, Gaal T, Course RL (2004) rRNA transcription in Escherichia coli. Annu Rev Genet 38: 749-770.
20. Gralla JD (2005) Escherichia coli ribosomal RNA transcription: Regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein. Mol Microbiol 55: 973-977.
21. Dennis PP (1971) Regulation of stable RNA synthesis in Escherichia coli. Nat New Biol 232: 43-47.
22. Dittmar KA, Mobley EM, Radek AJ, Pan T (2004) Exploring the regulation of tRNA distribution on the genomic scale. J Mol Biol 337: 31-47.
23. Berg OG, Kurland CG (1997) Growth rate-optimised tRNA abundance and codon usage.] Mol Biol 270: 544-550.
24. Emilsson V, Kurland CG (1990) Growth-rate dependence of global aminoacid-composition. Biochim Biophys Acta 1050: 248-251.
25. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1474.
26. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
27. Kenri T, Imamoto F, Kano Y (1994) Three tandemly repeated structural genes encoding tRNA(flMet) in the metZ operon of Escherichia coli K-12. Gene 138: 261-262.
28. Inokuchi H, Yamao F (1995) Structure and expression of prokaryotic tRNA genes. In: Soil D, RajBhandary UL, editors. tRNA: Structure, biosynthesis and function. Washington, D.C.: ASM Press, pp. 17-30.
29. Champagne N, LapointeJ (1998) Influence of FIS on the transcription from closely spaced and non-overlapping divergent promoters for an aminoacyltRNA synthetase gene (gltX) and a tRNA operon (valU) in Escherichia coli. Mol Microbiol 27: 1141-1156.
30. Ow MC, Kushner SR (2002) Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Genes Dev 16: 1102-1115.
31. Pettersson BM, Ardell DH, Kirsebom LA (2005) The length of the 5' leader of Escherichia coli tRNA precursors influences bacterial growth. J Mol Biol: In press.
32. Zar JH (1999) Biostatistical analysis. Saddle River (New Jersey): PrenticeHall.
33. Bipatnath M, Dennis PP, Bremer H (1998) Initiation and velocity of chromosome replication in Escherichia coli B/r and K-12. J Bacteriol 180: 265-273.
34. Michelsen O, Teixeira de Mattos MJ, Jensen PR, Hansen FG (2003) Precise determinations of C and D periods by flow cytometry in Escherichia coli K-12 and B/r. Microbiology 149: 1001-1010.
35. Zhang X, Bremer H (1996) Effects of Fis on ribosome synthesis and activity and on rRNA promoter activities in Escherichia coli.J Mol Biol 259: 27-40.
36. Batschelet E (1981) Circular statistics in biology. Sibson R, Cohen JE, editors. London: Academic Press. 371 p.
37. Rocha EP (2004) The replication-related organization of bacterial genomes. Microbiology 150: 1609-1627.
38. Rocha EP, Danchin A (2003) Essentiality, not expressiveness, drives genestrand bias in bacteria. Nat Genet 34: 377-378.
39. R Development Core Team (2004) R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
40. Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2: 13-34.
41. Efron B, Tibshirani RJ (1993) An introduction to the bootstrap. New York: Chapman and Hall.
42. Hirvonen CA, Ross W, Wozniak CE, Marasco E, Anthony JR, et al. (2001) Contributions of UP elements and the transcription factor FIS to expression from the seven rrn PI promoters in Escherichia coli.] Bacteriol 183: 6305-6314.
43. Brunschede H, Dove TL, Bremer H (1977) Establishment of exponential growth after a nutritional shift-up in Escherichia coli B/r: Accumulation of deoxyribonucleic acid, ribonucleic acid, and protein. J Bacteriol 129: 10201033.