Analysis of the microbial proteome

Current Opinion in Microbiology

Volumn 3, Issue 3, 2000, Pages 292-297

  Washburn, Michael P ^a   Yates III, John R ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

BIOTECHNOLOGY; GEL ELECTROPHORESIS; MICROBIAL GENETICS; NONHUMAN; PROTEIN ANALYSIS; PROTEIN EXPRESSION; QUANTITATIVE ASSAY; REVIEW;

EID: 0034094451     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(00)00092-8     Document Type: Review

References (46)

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38. ••].
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40. 14N. Via mass spectrometry, the resulting difference in mass of identical peptides from each sample allowed the authors to determine the relative abundance of proteins whose expression levels changed by knocking out Cln2. Although powerful, this method can only be applied to organisms that can be grown under the defined conditions.
41. Gygi S., Rist B., Gerber S., Turecek F., Gelb M., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 17:1999;994-999. Again using isotopic labeling, Gygi et al. developed a general method of quantitative proteomics. After growing yeast on either ethanol or galactose (a carbon source), the cysteine residues of each sample were modified by a 'heavy' or a 'light' reagent. Again, the resulting mass difference of identical peptides from each sample allowed for the relative abundance of proteins in each sample to be determined by mass spectrometry. Because the isotopically labeled reagent is added after cell growth, this method can be applied to any system.
42. Wilkins M., Gasteiger E., Gooley A., Herbert B., Molly M., Binz P-A., Ou K., Sanchez J-C., Bairoch A., Williams K., Hochstrasser D. High-throughput mass spectrometric discovery of protein post-translational modifications. J Mol Biol. 289:1999;645-657. Few proteomic approaches to post-translational modifications have been carried out. Part of the problem has been the lack of high-throughput software tools to interpret mass spectrometry data. Wilkins et al. have designed a software tool - FindMod - that can simultaneously search for 22 different post-translational modifications. Although it has only been applied to individual proteins, FindMod may allow for high-throughput identification of post-translational modifications.
43. Soskic V., Görlach M., Poznanovic S., Boehmer F., Godovac-Zimmermann J. Functional proteomics analysis of signal transduction pathways of the platelet-derived growth factor β receptor. Biochemistry. 38:1999;1757-1764.
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45. Rout M., Aitchison J., Suprapto A., Hjertaas K., Zhao Y., Chait B. The yeast nuclear pore complex: composition, architecture, and transport mechansim. J Cell Biol. 148:2000;635-651. By combining proteomic methods with molecular biology, and immunolocalization, Rout et al. mapped the nuclear pore complex in yeast and proposed a detailed transport mechanism. They first separated proteins from a highly enriched nuclear pore complex fraction by HPLC and SDS-PAGE. Proteins were digested and their identities determined by mass spectrometry. From an initial set of 174 identified proteins, they searched databases to determine the function and localization of as many proteins in this set as possible. Several proteins were obviously contaminants, but they carried out classification assays to determine that about 30 of the remaining proteins were part of the nuclear pore complex. Tagged proteins were localized by immunoelectron microscopy and they generated a stoichometric map of the nuclear pore complex. This is a remarkable study that demonstrates the true power of proteomics when it is combined with other methods available to modern biologists.
46. Langen H., Takacs B., Evers S., Berndt P., Lahm H., Wipf B., Gray C., Fountoulakis M. Two-dimensional map of the proteome of Haemophilus influenzae. Electrophoresis. 21:2000;411-429. In an impressive long-term study, Langen et al. detected and identified 502 proteins from the proteome of Haemophilus influenzae. They utilized several different types of 2D gels to visualise large amounts of proteins from specific pH regions and proteins from the cell envelope. Furthermore, Langen et al. detected and identified many low abundance proteins by enriching fractions via several chromatographic methods. This is one of the most comprehensive 2D gel/proteomics projects to date, and an excellent model for future comprehensive analysis of proteomes.