Microbial proteomics: how far have we come?

Abstract

It is now over 15 years since the beginning of the microbial genome era. At that time, great interest was invested in the idea of understanding bacterial genome dynamics via the analysis of their protein components or 'proteomes'. As bacterial analysis had driven the early advances in genomic squencing, these organisms were amongst the first subjected to protein-based studies. it is fair to suggest in hindsight that the original hype did not match the outcomes. At that time the term proteome was coined, en masse protein analysis meant little more than two-dimensional electrophoresis gels and mainly Edman sequencing for protein identification. As such, only the most abundant cellular constituents could be analysed and interest soon turned for many researchers towards microarray-based transcriptomics where a much greater percentage of the genome could be surveyed. Despite this, substantial and continuing evidence has demonstrated that transcript and protein levels (and, of course, the associated substrates and products of the predicted protein functions) often do not correlate. Therefore, a truly ‘systems biology’ organism-wide approach is necessary, where genomics, transcriptomics, proteomics and metabolomics are integrated to understand how microbes respond to changes in their genetic or physiological environments, and thus generate new hypotheses for functional understanding. This article will examine how proteomics technology has evolved to the stage at which the total proteome can be elucidated, and provide a guide for ‘best practice’ for undertaking successful proteomics analyses.