Saccharomyces cerevisiae proteomics

J. S. Crawford, E. Mortz, M. Boutry, Subproteomics identification of plasma membrane proteins from the yeast Saccharomyces cerevisiae, Proteomics 12 (2002), 1706-1714. 

L. Lu, A. K. Arakaki, H. Lu, and J. Skolnick, Genome Res., 13, 1146-1154 (2003). Multimeric Threading-based Prediction of Protein-Protein Interactions on a Genomic Scale Application to the Saccharomyces cerevisiae Proteome. 

Pardo M et al. A proteomic approach for the study of Saccharomyces cerevisiae cell wall biogenesis. Electrophoresis 2000 21 3396-3410. 

Ross, P.L., Huang, Y.N., Marchese, J.N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., and Pappin, D.J. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154-1169. 

Fig. 6. Distribution of the most common folds in selected bacterial, archaeal, and eukaryotic proteomes. The vertical axis shows the fraction of all predicted folds in the respective proteome. Fold name abbreviations FAD/NAD, FAD/NAD(P)-binding Rossman-like domains TIM, TIM-barrel domains SAM-MTR, S-adenosylmethionine-dependent methyltransferases PK, serine-threonine protein kinases PP-Loop, ATP pyrophosphatases. mge, Mycoplasma genitalium rpr, Rickettsiaprowazekii hh x, Borrelia burgdorferi ctr, Chlamydia trachomatis hpy, Helicobacter pylori tma, Thermotoga maritima ssp, Synechocystis sp. mtu, Mycobacterium tuberculosis eco, Escherichia coli mja, Methanococcus jannaschii pho, Pyrococcus horikoshii see, Saccharomyces cerevisiae, cel, Caenorhabditis elegans.

Holz, C., Prinz, B., Bolotina, N., Sievert, V, Bussow, K., Simon, B., Stahl, U. and Lang, C. (20(B). EstabUshing the yeast Saccharomyces cerevisiae as a system for expression of human proteins on a proteome-scale. J. Struct. Fund. Genomics 4,97-108. 

Staudt LM, Brown PO. Genomic views of the immune system. Annu Rev Immunol 2000 18 829-859. Grigoriev A. A relationship between gene expression and protein interactions on the proteome scale analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2001 29 3513-3519. 

Sickmann A, Reinders J, Wagner Y, Joppich C, Zahedi R, Meyer HE, Schonfisch B, Perschil I, Chacinska A, Guiard B, Rehling P, Pfanner N, Meisinger C (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci USA 100 13207-13212... 

Rotte C, Henze K, Muller M, Martin W (2000) Origins of hydrogenosomes and mitochondria -commentary. Curr Opin Microbiol 3 481-486 Saraste M (1999) Oxidative phosphorylation at the fin de siecle. Science 283 1488-1493 Sickmann A, Reinders J, Wagner Y, Joppich C, Zahedi R, Meyer HE, Schonfisch B, Perschil I, Chacinska A, Guiard B, Rehling P, Pfanner N, Meisinger C (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci USA 100 13207-13212 Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147 195-197... 

The discussion in this chapter focussed at developments in the field of protein characterization, and provided an overview of the technology developed to enable proteomics studies (Ch. 18). The strategies outline above have been applied to increasingly complex samples. Some examples are the detection and identification of human leucocyte antigen peptides related to the major histocompatibility complex [166], and the unattended identification of 90 proteins from the yeast Saccharomyces cerevisiae by means of an integrated workstation for LC-MS-MS under DDA and with database searching [34]. 

Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics 2002 l(4) 323-33. 

Vido K, Spector D, Lagniel G, Lopez S, Toledano MB, Labarre J. A proteome analysis of the cadmium response in Saccharomyces cerevisiae. J Biol Chem 2001 276(ll) 8469-74. 

De Nobel, H., Lawrie, L., Brul, S., et al. 2001. Parallel and comparative analysis of the proteome and transcriptome of sorbic acid stressed Saccharomyces cerevisiae. Yeast 18 1413-1428. 

Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S et al (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3(12) 1154-1169... 

Trabalzini, L., Paffetti, A., Scalioni, A., Talamo, F., Ferro, E., Coratza, G., Bovalini, L., Lusini, P., Martelli, P., and Santucci, A. 2003. Proteomic response to physiological fermentation stresses in a wild type wine strain of Saccharomyces cerevisiae. Biochem. J. 370,35-46. 

Consortium for the Functional Genomics of Microbial Eukaryotes. University of Manchester, U.K URL http //www. cogeme.man.ac.uk. Analysis of the transcriptome and proteome of Saccharomyces cerevisiae (yeast) and a ntunber of plant and human fungal pathogens together with a bioinformatics centre. 

A. C. Gavin, M. Bosche, R. Krause et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415 (2002), 141 Y. Ho, A. Gruhler, A. Heilbut et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spcclrometry. Nature, 415 (2002), 180. 

Widespread use of mass spectrometry to analyze large numbers of spots from two-dimensional gels has also brought out another apparent shortcoming of 2DE. Articles on proteome-wide analyses of Saccharomyces cerevisiae point to a growing awareness in the literature and community of another shortcoming of 2DE, namely that no spots with low abundance can be identified from silver stained two-dimensional gels. °-"... 

Using proteomic technologies (tandem affinity purification and MS) to discover protein-protein interactions, a substantial number of proteins have been identified as potential SPT2 (LCB2)-associated proteins in Saccharomyces cerevisiae (A.C. Gavin,... 

Kim H, Melen K, Osterherg M, von Heijne G (2006) A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc Natl Acad Sci USA 103 11142-11147... 

Figure 5.9 shows a snapshot of an LC CID MS/MS analysis of a tryptic digest of a standard six-protein mixture. The top mass spectrum (scan 1345 in this experiment) is an FT-ICR survey scan. In the subsequent scan ( 1346), CID MS/MS of the precursor ion m/z 524.9 is performed in the linear ion trap. That precursor ion is the most abundant ion in the survey scan that has not been subjected previously to MS/MS, that is, is not on the exclusion list. Scan 1347 is the CID mass spectrum of precursor mJz 6253, the second most abundant ion, not on the exclusion list, in the survey scan. The sequence ends with CID of precursor m/z 707.6, the third most abundant ion, not on the exclusion list, in the survey scan. The subsequent scan (not shown) is an FT-ICR survey scan. An alternative workflow favored by some researchers is one FT-ICR survey MS scan followed by CID in the linear ion trap of the 10 most-abundant ions [107]. These parallel-processing approaches have been applied to a diverse range of studies including analysis of the chicken egg white proteome [108], the low molecular weight proteome of Halobacterium salinarum [109], the endocervical mucas proteome [110], sumoylation in Saccharomyces cerevisiae [111], and the tear fluid proteome [112]. 

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