Proteomics : a tool for understanding adaptation in environmentally significant microorganisms.

Understanding how microorganisms adapt to adverse environments is beneficial for a variety of reasons depending on the conditions under investigation. In this thesis, the ancient life forms, cyanobacteria, form the basis of the research. Research into salt tolerance is useful because agricultural practices are leading to increasing soil salinity, which prevent growth of susceptible crop species. In addition, elucidating adaptive mechanisms in possibly Earth's most abundant photosynthetic microorganism is important, due to its significant role in nutrient cycling and climate control. Proteins are synthesised in cells in response to environmental perturbations and are therefore essential for adaptation, and in this thesis proteomics is the principal method applied. Less pronounced protein expression changes are characteristic of long-term adaptive responses as opposed to immediate shock responses, and therefore techniques were developed and applied which could quantify with high accuracy (25 to 50% changes). Interpreting these changes into biological function required analysis of a sufficient fraction of the proteome, which was achieved through a variety of protein and peptide fractionation techniques. Protein separation through traditional 2DE was also optimised to overcome the detrimental effects of salt. These methods were applied to a well-studied model cyanobacterium, Synechocystis sp. PCC6803, which allowed a comparison to be made with present knowledge. Subsequently, an approach to investigate the unsequenced cyanobacterium, Euhalothece sp. BAAOO 1, was developed and revealed an unusual response to low salt. A direct comparison of these two cyanobacteria was then made relying on their high degree of proteome homology, which highlighted their shared and contrasting tolerance mechanisms. Finally, the methods were extended to characterise the proteome of Prochlorococcus marinus MED4, and increase our understanding of adaptation to varying light intensities characteristic of its oceanic niche.