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Book Summary:
With the advent of whole genome sequencing, a new era of biology was ushered in allowing for “systems-biology” approaches to characterizing microbial systems. The field of systems biology aims to catalogue and understand all of the biological components, their functions, and all of their interactions in a living system as well as communities of living systems. The developments of technologies to use genome sequence information and probe the functional components of microbes at a global level are being developed. One of the applications is to simultaneously measure and compare the expression of all the proteins present in a microbial system. This is the field of proteomics. With the development of electrospray ionization, rapid tandem mass spectrometry and database-searching algorithms, mass spectrometry (MS) has become the leader in the attempts to decipher proteomes. The goal of the work described here was to build a state-of-the-art robust MS-based proteomics platform for the characterization of microbial proteomes from isolates to communities. Proteome analyses of the metal-reducing bacteria Shewanella oneidensis and the metabolically versatile bacteria Rhodopseudomonas palustris are given as examples of the power of this technology to elucidate proteins important to different metabolic states at a global level. The analysis of microbial proteomes from isolates is only the first step of the challenge. In nature, microbial species do not act alone but are always found in mixtures with other species where their intricate interactions are critical for survival. These studies conclude with some of the first efforts to develop methodologies to measure proteomes of simple controlled mixtures of microbial species and then present the first attempt at measuring the proteome of a natural microbial community, a biofilm from an acid mine drainage system. This microbial system illustrates life at the extreme of nature where life not only exists but flourishes in very acidic conditions with high metal concentrations and high temperatures. The technologies developed through these studies were applied to the first deep characterization of an environmental microbial community proteome, the deciphering of the expressed proteome of the acid mine drainage biofilm. |
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