An algorithmic framework for genome-wide modeling and analysis of translation networks

Biophysical Journal

Volumn 90, Issue 4, 2006, Pages 1136-1146

  Mehra, Amit ^a   Hatzimanikatis, Vassily ^a  

^a Northwestern University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ALGORITHM; ARTICLE; CODON; GENOME ANALYSIS; MATHEMATICAL MODEL; MODEL; PROTEIN SYNTHESIS; RIBOSOME; TRANSLATION INITIATION; BACTERIAL GENOME; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; GENETICS; THEORETICAL MODEL;

ALGORITHMS; ESCHERICHIA COLI; GENOME, BACTERIAL; MODELS, THEORETICAL; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EID: 33645775569     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.062521     Document Type: Article

References (35)

1. Miller, O. L., Jr., B. A. Hamkalo, and C. A. Thomas, Jr. 1970. Visualization of bacterial genes in action. Science. 169:392-395.
2. Brown, P. O., and D. Botstein. 1999. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21:33-37.
3. Lockhart, D. J., and E. A. Winzeler. 2000. Genomics, gene expression and DNA arrays. Nature. 405:827-836.
4. Selinger, D. W., K. J. Cheung, R. Mei, E. M. Johansson, C. S. Richmond, F. R. Blattner, D. J. Lockhart, and G. M. Church. 2000. RNA expression analysis using a 30-basepair resolution Escherichia coli genome array. Nat. Biotechnol. 18:1262-1268.
5. Anderson, N. L., and N. G. Anderson. 1998. Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis. 19:1853-1861.
6. Lahm, H. W., and H. Langen. 2000. Mass spectrometry: a tool for the identification of proteins separated by gels. Electrophoresis. 21:2105-2114.
7. Zong, Q., M. Schummer, L. Hood, and D. R. Morris. 1999. Messenger RNA translation state: the second dimension of high-throughput expression screening. Proc. Natl. Acad. Sci. USA. 96:10632-10636.
8. Arava, Y., Y. L. Wang, J. D. Storey, C. L. Liu, P. O. Brown, and D. Herschlag. 2003. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 100:3889-3894.
9. Dittmar, K. A., E. M. Mobley, A. J. Radek, and T. Pan. 2004. Exploring the regulation of tRNA distribution on the genomic scale. J. Mol. Biol. 337:31-47.
10. Gasch, A. P., P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D. Botstein, and P. O. Brown. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell. 11:4241-4257.
11. Ideker, T., V. Thorsson, J. A. Ranish, R. Christmas, J. Buhler, J. K. Eng, R. Bumgarner, D. R. Goodlett, R. Aebersold, and L. Hood. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 292:929-934.
12. Lee, P. S., L. B. Shaw, L. H. Choe, A. Mehra, V. Hatzimanikatis, and K. H. Lee. 2003. Insights into the relation between mRNA and protein expression patterns: II. Experimental observations in Escherichia coli. Biotechnol. Bioeng. 84:834-841.
13. Anderson, L., and J. Seilhamer. 1997. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis. 18:533-537.
14. Gygi, S. P., Y. Rochon, B. R. Franza, and R. Aebersold. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19:1720-1730.
15. Mehra, A., K. H. Lee, and V. Hatzimanikatis. 2003. Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations. Biotechnol. Bioeng. 84:822-833.
16. Heinrich, R., and T. A. Rapoport. 1980. Mathematical-modeling of translation of messenger-RNA in eukaryotes - steady-states, time-dependent processes and application to reticulocytes. J. Theor. Biol. 86:279-313.
17. MacDonald, C. T., J. H. Gibbs, and A. C. Pipkin. 1968. Kinetics of biopolymerization on nucleic acid templates. Biopolymers. 6:1-25.
18. MacDonald, C. T., and J. H. Gibbs. 1969. Concerning kinetics of polypeptide synthesis on polyribosomes. Biopolymers. 7:707-725.
19. Jacob, W. F., M. Santer, and A. E. Dahlberg. 1987. A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins. Proc. Natl. Acad. Sci. USA. 84:4757-4761.
20. Hui, A., and H. A. de Boer. 1987. Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli. Proc. Natl. Acad. Sci. USA. 84:4762-4766.
21. Byrd, R. H., M. E. Hribar, and J. Nocedal. 1999. An interior point algorithm for large-scale nonlinear programming. SIAM J. Optim. 9:877-900.
22. Byrd, R. H., J. C. Gilbert, and J. Nocedal. 2000. A trust region method based on interior point techniques for nonlinear programming. Math. Progr. 89:149-185.
23. Byrd, R. H., N. I. M. Gould, J. Nocedal, and R. A. Waltz. 2004. An algorithm for nonlinear optimization using linear programming and equality constrained subproblems. Math. Progr. 100:27-48.
24. Waltz, R. A. 2004. KNITRO 4.0 User's Manual. Ziena Optimization, Evanston, IL.
25. Bremer, H., and P. P. Dennis. 1996. Modulation of chemical composition and other parameters of the cell by growth rate. In Escherichia coli and Salmonella. F. C. Neidhart, editor. ASM Press, Washington, DC. 1553-1569.
26. Kacser, H., and J. A. Burns. 1973. The control of flux. Symp. Soc. Exp. Biol. 27:65-104.
27. Fell, D. A. 1992. Metabolic control analysis - a survey of its theoretical and experimental development. Biochem. J. 286:313-330.
28. Hershey, J. 1987. Protein synthesis. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. F.Neidhart, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger, editors. American Society for Microbiology, Washington, DC.
29. Helmann, J. D., M. F. Wu, P. A. Kobel, F. J. Gamo, M. Wilson, M. M. Morshedi, M. Navre, and C. Paddon. 2001. Global transcriptional response of Bacillus subtilis to heat shock. J. Bacteriol. 183:7318-7328.
30. Richmond, C. S., J. D. Glasner, R. Mau, H. Jin, and F. R. Blattner. 1999. Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res. 27:3821-3835.
31. Notterman, D. A., U. Alon, A. J. Sierk, and A. J. Levine. 2001. Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays. Cancer Res. 61:3124-3130.
32. Magee, J. A., T. Araki, S. Patil, T. Ehrig, L. True, P. A. Humphrey, W. J. Catalona, M. A. Watson, and J. Milbrandt. 2001. Expression profiling reveals hepsin overexpression in prostate cancer. Cancer Res. 61:5692-5696.
33. Vind, J., M. A. Sorensen, M. D. Rasmussen, and S. Pedersen. 1993. Synthesis of proteins in Escherichia coli is limited by the concentration of free ribosomes. Expression from reporter genes does not always reflect functional mRNA levels. J. Mol. Biol. 231:678-688.
34. Kacser, H., and J. A. Burns. 1979. Molecular democracy: who shares the controls? Biochem. Soc. Trans. 7:1149-1160.
35. Iyer, V., and K. Struhl. 1996. Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 93:5208-5212.