Correlation between Protein and mRNA Abundance in Yeast

REFERENCES

• Aebersold, R. H., J. Leavitt, R. A. Saavedra, L. E. Hood, and J. Kent 1987. Internal amino acid sequence analysis of proteins separated by one- or two-dimensional gel electrophoresis after in situ protease digestion on nitrocellulose. Proc. Natl. Acad. Sci. USA 84:6970–6974.
   PubMed Web of Science ®Google Scholar
• Aebersold, R. H., D. B. Teplow, L. E. Hood, and J. Kent 1986. Electroblotting onto activated glass. High efficiency preparation of proteins from analytical sodium dodecyl sulfate-polyacrylamide gels for direct sequence analysis. Eur. J. Biochem. 261:4229–4238.
   Google Scholar
• Bennetzen, J. L., and J. Hall 1982. Codon selection in yeast. J. Biol. Chem. 257:3026–3031.
   PubMed Web of Science ®Google Scholar
• Boucherie, H., G. Dujardin, M. Kermorgant, C. Monribot, P. Slonimski, and J. Perrot 1995. Two-dimensional protein map of Saccharomyces cerevisiae: construction of a gene-protein index. Yeast 11:601–613.
   PubMed Web of Science ®Google Scholar
• Boucherie, H., F. Sagliocco, R. Joubert, I. Maillet, J. Labarre, and J. Perrot 1996. Two-dimensional gel protein database of Saccharomyces cerevisiae. Electrophoresis 17:1683–1699.
   PubMedGoogle Scholar
• Carmen, A. A., P. K. Brindle, C. S. Park, and J. Holland 1995. Transcriptional regulation by an upstream repression sequence from the yeast enolase gene ENO1. Yeast 11:1031–1043.
   PubMedGoogle Scholar
• Ducret, A., I. VanOostveen, J. K. Eng, J. R. Yates, and J. Aebersold 1998. High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry. Protein Sci. 7:706–719.
   PubMed Web of Science ®Google Scholar
• Eng, J., A. McCormack, and J. Yates 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5:976–989.
   PubMed Web of Science ®Google Scholar
• Figeys, D., A. Ducret, J. R. Yates, and J. Aebersold 1996. Protein identification by solid phase microextraction-capillary zone electrophoresis-microelectrospray-tandem mass spectrometry. Nat. Biotechnol. 14:1579–1583.
   PubMedGoogle Scholar
• Figeys, D., I. VanOostveen, A. Ducret, and J. Aebersold 1996. Protein identification by capillary zone electrophoresis/microelectrospray ionization-tandem mass spectrometry at the subfemtomole level. Anal. Chem. 68:1822–1828.
   PubMedGoogle Scholar
• Fraser, C. M., and J. Fleischmann 1997. Strategies for whole microbial genome sequencing and analysis. Electrophoresis 18:1207–1216.
   PubMedGoogle Scholar
• Garrels, J. I., B. Futcher, R. Kobayashi, G. I. Latter, B. Schwender, T. Volpe, J. R. Warner, and J. McLaughlin 1994. Protein identifications for a Saccharomyces cerevisiae protein database. Electrophoresis 15:1466–1486.
   PubMedGoogle Scholar
• Garrels, J. I., C. S. McLaughlin, J. R. Warner, B. Futcher, G. I. Latter, R. Kobayashi, B. Schwender, T. Volpe, D. S. Anderson, F. Mesquita-Fuentes, and J. Payne 1997. Proteome studies of Saccharomyces cerevisiae: identification and characterization of abundant proteins. Electrophoresis 18:1347–1360.
   PubMed Web of Science ®Google Scholar
• Gygi, S. P., R. Aebersold 1998. Absolute quantitation of 2-DE protein spots, p. 417–421. In A. J. Link (ed.), 2-D protocols for proteome analysis. Humana Press, Totowa, N.J.
   Google Scholar
• Harford, J. B., D. R. Morris 1997. Post-transcriptional gene regulation. Wiley-Liss, Inc., New York, N.Y.
   Google Scholar
• Hereford, L. M., and J. Rosbash 1977. Number and distribution of polyadenylated RNA sequences in yeast. Cell 10:453–462.
   PubMed Web of Science ®Google Scholar
• Hodges, P. E., W. E. Payne, and J. Garrels 1998. The Yeast Protein Database (YPD): a curated proteome database for Saccharomyces cerevisiae. Nucleic Acids Res. 26:68–72.
   PubMedGoogle Scholar
• Klose, J., and J. Kobalz 1995. Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis 16:1034–1059.
   PubMed Web of Science ®Google Scholar
• Kurland, C. G. 1991. Codon bias and gene expression. FEBS Lett. 285:165–169.
   PubMed Web of Science ®Google Scholar
• Lashkari, D. A., J. L. DeRisi, J. H. McCusker, A. F. Namath, C. Gentile, S. Y. Hwang, P. O. Brown, and J. Davis 1997. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. USA 94:13057–13062.
   PubMed Web of Science ®Google Scholar
• Liang, P., and J. Pardee 1992. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257:967–971.
   PubMed Web of Science ®Google Scholar
• Link, A. J., L. G. Hays, E. B. Carmack, J. R. Yates III.. 1997. Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143. Electrophoresis 18:1314–1334.
   PubMed Web of Science ®Google Scholar
• Nawrocki, A., M. R. Larsen, A. V. Podtelejnikov, O. N. Jensen, M. Mann, P. Roepstorff, A. Gorg, S. J. Fey, and J. Larsen 1998. Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification. Electrophoresis 19:1024–1035.
   PubMed Web of Science ®Google Scholar
• O’Farrell, P. H. 1975. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250:4007–4021.
   PubMed Web of Science ®Google Scholar
• OWL Protein Sequence Database. 2 August 1998, posting date. [Online.] http://bmbsgi11.leeds.ac.uk/bmb5dp/owl.html [8 January 1999, last date accessed.]
   Google Scholar
• Patterson, S. D., and J. Aebersold 1995. Mass spectrometric approaches for the identification of gel-separated proteins. Electrophoresis 16:1791–1814.
   PubMed Web of Science ®Google Scholar
• Pennington, S. R., M. R. Wilkins, D. F. Hochstrasser, and J. Dunn 1997. Proteome analysis: from protein characterization to biological function. Trends Cell Biol. 7:168–173.
   PubMed Web of Science ®Google Scholar
• Shalon, D., S. J. Smith, and J. Brown 1996. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6:639–645.
   PubMed Web of Science ®Google Scholar
• Shevchenko, A., O. N. Jensen, A. V. Podtelejnikov, F. Sagliocco, M. Wilm, O. Vorm, P. Mortensen, H. Boucherie, and J. Mann 1996. Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. USA 93:14440–14445.
   PubMed Web of Science ®Google Scholar
• Shevchenko, A., M. Wilm, O. Vorm, and J. Mann 1996. Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal. Chem. 68:850–858.
   PubMed Web of Science ®Google Scholar
• Sikorski, R. S., and J. Hieter 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19–27.
   PubMed Web of Science ®Google Scholar
• Tsunasawa, S., J. W. Stewart, and J. Sherman 1985. Amino-terminal processing of mutant forms of yeast iso-1-cytochrome c. The specificities of methionine aminopeptidase and acetyltransferase. J. Biol. Chem. 260:5382–5391.
   PubMedGoogle Scholar
• Urlinger, S., K. Kuchler, T. H. Meyer, S. Uebel, and J. Tamp’e 1997. Intracellular location, complex formation, and function of the transporter associated with antigen processing in yeast. Eur. J. Biochem. 245:266–272.
   PubMedGoogle Scholar
• Varshavsky, A. 1996. The N-end rule: functions, mysteries, uses. Proc. Natl. Acad. Sci. USA 93:12142–12149.
   PubMed Web of Science ®Google Scholar
• Velculescu, V. E., L. Zhang, B. Vogelstein, and J. Kinzler 1995. Serial analysis of gene expression. Science 270:484–487.
   PubMed Web of Science ®Google Scholar
• Velculescu, V. E., L. Zhang, W. Zhou, J. Vogelstein, M. A. Basrai, D. E. Bassett Jr., P. Hieter, B. Vogelstein, and J. Kinzler 1997. Characterization of the yeast transcriptome. Cell 88:243–251.
   PubMed Web of Science ®Google Scholar
• Wilkins, M. R., K. L. Williams, R. D. Appel, D. F. Hochstrasser 1997. Proteome research: new frontiers in functional genomics. Springer-Verlag, Berlin, Germany.
   Google Scholar
• Wilm, M., A. Shevchenko, T. Houthaeve, S. Breit, L. Schweigerer, T. Fotsis, and J. Mann 1996. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379:466–469.
   PubMed Web of Science ®Google Scholar
• Yan, J. X., M. R. Wilkins, K. Ou, A. A. Gooley, K. L. Williams, J. C. Sanchez, O. Golaz, C. Pasquali, and J. Hochstrasser 1996. Large-scale amino-acid analysis for proteome studies. J. Chromatogr. A 736:291–302.
   PubMedGoogle Scholar
• YPD Website. 6 March 1998, revision date. [Online.] Proteome, Inc. http://www.proteome.com/YPDhome.html [8 January 1999, last date accessed.]
   Google Scholar