1887

Abstract

A theoretical framework was established for the interpretation of microarray measurements. Mathematical equations were derived that link the molecular processes involved in the transcription and translation of an open reading frame (ORF) with the properties of a population of cells. The theory was applied to three published sets of microarray measurements related to the growth of . It was shown for strains growing at the same rate, for example wild-type and mutant strains, that the expression ratio obtained by microarray analysis for a particular ORF is equal to the ratio of the copy numbers of the encoded protein. The growth of in a batch culture was analysed at several time points over a period of 60 days. Several properties including the following were calculated for cells cultured for 60 days: μ≤0.008 h, there was a decrease in the number of ribosomes per cell to 26 % of the value at day 0, and only 40 % or less of this reduced number of ribosomes were estimated to be actively synthesizing protein. Profiles of the expression ratio observed for a particular ORF versus the period of cell culture were related to changes in the relative numbers of copies of the encoded protein per cell. Two profiles were found to have theoretical significance: profile I, exemplified by ORFs encoding proteins needed for DNA partition and DNA synthesis; and profile II, exemplified by ORFs encoding proteins (including ribosomal proteins) needed for protein synthesis. Data for a number of other genes including , , and were also analysed.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2007/005868-0
2007-10-01
2020-08-07
Loading full text...

Full text loading...

/deliver/fulltext/micro/153/10/3337.html?itemId=/content/journal/micro/10.1099/mic.0.2007/005868-0&mimeType=html&fmt=ahah

References

  1. Bacon J., James B. W., Wernisch L., Williams A., Morley K. A., Hatch G. J., Mangan J. A., Hinds J., Stoker N. G.. other authors 2004; The influence of reduced oxygen availability on pathogenicity and gene expression in Mycobacterium tuberculosis . Tuberculosis (Edinb84:205–217
    [Google Scholar]
  2. Beste D. J. V., Peters J., Hooper T., Avignone-Rossa C., Bushell M. E., McFadden J.. 2005; Compiling a molecular inventory for Mycobacterium bovis BCG at two growth rates: evidence for growth rate-mediated regulation of ribosome biosynthesis and lipid metabolism. J Bacteriol187:1677–1684
    [Google Scholar]
  3. Betts J. C., Lukey P. T., Robb L. C., McAdam R. A., Duncan K.. 2002; Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol43:717–731
    [Google Scholar]
  4. Bowtell D., Sambrook J.. 2000; DNA Microarrays: a Molecular Cloning Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press;
  5. Bremer H., Dennis P. P.. 1996; Modulation of chemical composition and other parameters of the cell growth rate . In Escherichia coli and Salmonella: Cellular and Molecular Biology , 2nd edn. pp1553–1568 Edited by Neidhardt F. C.. others Washington, DC: American Society for Microbiology Press;
  6. Butcher P. D.. 2004; Microarrays for Mycobacterium tuberculosis . Tuberculosis (Edinb84:131–137
    [Google Scholar]
  7. Byrne R., Levin J. G., Bladen H. A., Nirenberg M. W.. 1964; The in vitro formation of a DNA–ribosome complex. Proc Natl Acad Sci U S A52:140–148
    [Google Scholar]
  8. Cox R. A.. 2003; Correlation of the rate of protein synthesis and the third power of the RNA : protein ratio in Escherichia coli and Mycobacterium tuberculosis . Microbiology149:729–737
    [Google Scholar]
  9. Cox R. A.. 2004; Quantitative relationships for specific growth rates and macromolecular compositions of Mycobacterium tuberculosis, Streptomyces coelicolor A3(2) and Escherichia coli B/r: an integrative theoretical approach. Microbiology150:1413–1426
    [Google Scholar]
  10. Cox R. A., Cook G. M.. 2007; Growth regulation in the mycobacterial cell. Curr Mol Med7:231–245
    [Google Scholar]
  11. Feiss M., DeMoss R. D.. 1965; Protein synthesis and ribosome-bound tryptophanase. J Mol Biol14:283–287
    [Google Scholar]
  12. Grunberg-Manago M.. 1999; Messenger RNA stability and its role in the control of gene expression in bacteria and phages. Annu Rev Genet33:193–227
    [Google Scholar]
  13. Keener J., Nomura M.. 1996; Regulation of ribsosome synthesis In Escherichia coli an d Salmonella: Cellular and Molecular Biology . , 2nd edn. pp1417–1428 Edited by Neidhardt F. C.. others Washington, DC: American Society for Microbiology Press;
  14. Kendall S. L., Movahedzadeh F., Rison S. C., Wemisch L., Parish T., Duncan K., Betts J. C., Stoker N. G.. 2004; The Mycobacterium tuberculosis dosRS two-component system is induced by multiple stresses. Tuberculosis (Edinb84:247–255
    [Google Scholar]
  15. Khodursky A. B., Bernstein J. A.. 2003; Life after transcription – revisiting the fate of messenger RNA. Trends Genet19:113–115
    [Google Scholar]
  16. Lamichhane G., Zignol M., Blades N. J., Geiman D. E., Dougherty A., Grosset J., Broman K. W., Bishai W. R.. 2003; A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis . Proc Natl Acad Sci U S A100:7213–7218
    [Google Scholar]
  17. Leroy A., Vanzo N. F., Sousa S., Dreyfus M., Carpousis A. J.. 2002; Function in Escherichia coli of the non-catalytic part of RNase E: role in the degradation of ribosome-free mRNA. Mol Microbiol45:1231–1243
    [Google Scholar]
  18. Massey T. H., Mercogliano C. P., Yates J., Sherratt D. J., Lowe J.. 2006; Double-stranded DNA translocation: structure and mechanism of hexameric FtsK . Mol Cell23:457–469
    [Google Scholar]
  19. McCarthy B. J.. 1960; Variations in bacterial ribosomes. Biochim Biophys Acta39:563–564
    [Google Scholar]
  20. Miller O. L. Jr, Hamkalo B. A., Thomas C. A. Jr. 1970; Visualization of bacterial genes in action. Science169:392–395
    [Google Scholar]
  21. Nie L., Wu G., Zhang W.. 2006; Correlation between mRNA and protein abundance in Desulfovibrio vulgaris : a multiple regression to identify sources of variations. Biochem Biophys Res Commun339:603–610
    [Google Scholar]
  22. Noller H. E., Nomura M.. 1996; Ribosomes.. In Escherichia coli and Salmonella: Cellular and Molecular Biology , 2nd edn. pp167–186 Edited by Neidhardt F. C.. others Washington, DC: American Society for Microbiology Press;
  23. Ozoline O. N., Tsyganov M. A.. 1995; Structure of open promoter complexes with Escherichia coli RNA polymerase as revealed by the DNase I footprinting technique compilation analysis. Nucleic Acids Res23:4533–4541
    [Google Scholar]
  24. Pape T., Wintermeyer W., Rodnina M. V.. 1998; Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A-site of the E. coli ribosome. EMBO J17:7490–7497
    [Google Scholar]
  25. Régnier P., Arraiano C. M.. 2000; Degradation of mRNA in bacteria: emergence of ubiquitous features. Bioessays22:235–244
    [Google Scholar]
  26. Sassetti C. M., Boyd D. H., Rubin E. L.. 2003; Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol48:77–84
    [Google Scholar]
  27. Schaechter E., Maaløe O., Kjeldgaard N. O.. 1958; Dependence on medium and temperature of cell size and chemical composition during balanced growth of Salmonella typhimurium . J Gen Microbiol19:592–606
    [Google Scholar]
  28. Stent G. S.. 1964; The operon: on its third anniversary. Science144:816–820
    [Google Scholar]
  29. Verma A., Sampla A. K., Tyagi J. S.. 1999; Mycobacterium tuberculosis rrn promoters: differential usage and growth rate-dependent control. J Bacteriol181:4326–4333
    [Google Scholar]
  30. Voskuil M. I., Visconti K. C., Schoolnik G. K.. 2004; Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb84:218–227
    [Google Scholar]
  31. Wada A., Yamazaki Y., Fujita N., Ishihama A.. 1990; Structure and probable genetic location of a “ribosome modulation factor” associated with 100S ribosomes in stationary-phase Escherichia coli cells. Proc Natl Acad Sci U S A87:2657–2661
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2007/005868-0
Loading
/content/journal/micro/10.1099/mic.0.2007/005868-0
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error