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.