Defining the genome and metalloproteome of microorganisms
Lancaster, William Andrew
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The genome revolution and advent of omic-based approaches have resulted in a dramatic increase in the availability of biological data in just the last few years. The analysis and interpretation of these data can address fundamental questions and reveal unexpected aspects of biology. One such question that is key to the emerging field of synthetic biology is: “What is the minimum complement of genes necessary to sustain life?” Herein it is shown that the answer depends upon the lifestyle of the organism, which in turn directly influences the minimal size of a microbial cell. The ‘omics’ revolution has also resulted in a dramatic reduction in the cost of DNA sequencing, changing the paradigm from availability of genomes of a few model organisms to a world in which strains, populations and even single cells are completely genotyped. In the current work the sequencing of a recently-isolated genetically tractable strain of Pyrococcus furiosus revealed a highly dynamic genome with extensive transposon-mediated rearrangement compared to the model strain. Moreover, disruption of some genes did not result in expected phenotypic changes, indicating greater metabolic redundancy than previously appreciated. It is also shown here that a fundamental aspect of biology that cannot be comprehensively addressed by genome sequence alone is the requirement of specific metal cofactors by proteins for proper structure and function. The coupling of metallomics and proteomics revealed that the metalloproteomes of microorganisms remain largely uncharacterized. It was shown that P. furiosus contains an unexpectedly large number of proteins that bind a metal but were not predicted to be metalloproteins. A bioinformatic analysis of the co-occurrence of metals and proteins during the non-denaturing fractionation of native P. furiosus biomass led to the prediction of many potential novel metalloproteins. The study of uptake and utilization of metals by microbes is especially significant in the field of bioremediation. A metallomic and genomic comparison of two model organisms, Desulfovibrio vulgaris strain Hildenborough and Pelosinus fermentans strain A11 revealed surprising and fundamental differences in metal uptake, providing results that will guide future research into the metal assimilation by these organisms potentially including the characterization of uranium-containing proteins.