Complementing genomics with proteomics: The membrane subproteome of Pseudomonas aeruginosa PAO1

With the completion of many genome projects, a shift is now occurring from the acquisition of gene sequence to understanding the role and context of g ene products within the genome. The opportunistic pathogen Pseudomonas aeru ginosa is one organism for which a genome sequence is now available, includ ing the annotation of open reading frames (ORFs). However, approximately on e third of the ORFs are as yet undefined in function. Proteomics can comple ment genomics, by characterising gene products and their response to a vari ety of biological and environmental influences. In this study we have estab lished the first two-dimensional gel electrophoresis reference map of prote ins from the membrane fraction of P. aeruginosa strain PA01. A total of 189 proteins have been identified and correlated with 104 genes from the P. ae ruginosa genome. Annotated membrane proteins could be grouped into three di stinct categories: (i) those with functions previously characterised in P. aeruginosa (38%); (ii) those with significant sequence similarity to protei ns with assigned function or hypothetical proteins in other organisms (46%) ; and (iii) those with unknown function (16%). Transmembrane prediction alg orithms showed that each identified protein sequence contained at least one membrane-spanning region. Furthermore, the current methodology used to iso late the membrane fraction was shown to be highly specific since no contami nating cytosolic proteins were characterised. Preliminary analysis showed t hat at least 15 gel spots may be glycosylated in vivo, including three prot eins that have not previously been functionally characterised. The referenc e map of membrane proteins from this organism is now the basis for determin ing surface molecules associated with antibiotic resistance and efflux, cel l-cell signalling and pathogen-host interactions in a variety of P. aerugin osa strains.