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- Title
Shotgun proteomics of cyanobacteria--applications of experimental and data-mining techniques.
- Authors
Barrios-Llerena, Martin E.; Poh Kuan Chong; Chee Sian Gan; Snijders, Ambrosius P. L.; Reardon, Kenneth F.; Wright, Phillip C.
- Abstract
Cyanobacteria are photosynthetic bacteria notable for their ability to produce hydrogen and a variety of interesting secondary metabolites. As a result of the growing number of completed cyanobacterial genome projects, the development of post-genomics analysis for this important group has been accelerating. DNA microarrays and classical two-dimensional gel electrophoresis (2DE) were the first technologies applied in such analyses. In many other systems, 'shotgun' proteomics employing multi-dimensional liquid chromatography and tandem mass spectrometry has proven to be a powerful tool. However, this approach has been relatively under-utilized in cyanobacteria. This study assesses progress in cyanobacterial shotgun proteomics to date, and adds a new perspective by developing a protocol for the shotgun proteomic analysis of the filamentous cyanobacterium Anabaena variabilis ATCC 29413, a model for N2 fixation. Using approaches for enhanced protein extraction, 646 proteins were identified, which is more than double the previous results obtained using 2DE. Notably, the improved extraction method and shotgun approach resulted in a significantly higher representation of basic and hydrophobic proteins. The use of protein bioinformatics tools to further mine these shotgun data is illustrated through the application of PSORTb for localization, the grand average hydropathy (GRAVY) index for hyclrophobicity, LipoP for lipoproteins and the exponentially modified protein abundance index (emPAI) for abundance, The results are compared with the most well-studied cyanobacterium, Synechocystis sp. PCC 6803. Some general issues in shotgun proteome identification and quantification are then addressed.
- Subjects
PROTEOMICS; CYANOBACTERIA; PROKARYOTES; ANABAENA variabilis; RESEARCH
- Publication
Briefings in Functional Genomics & Proteomics, 2006, Vol 5, Issue 2, p121
- ISSN
1473-9550
- Publication type
Article
- DOI
10.1093/bfgp/ell021