Genome-enabled informatics and biochemical genetics in marine cyanobacteria

Cyanobacteria are oxygenic photosynthetic bacteria that have shaped the chemical and biological evolution of Earth. They are one of the largest groups of bacteria and the oldest known fossils on Earth, as well as significant players in global carbon, nitrogen and oxygen cycles. Despite the progress in cyanobacterial physiology, ecology and biogeochemistry in the past decades, the molecular evolution of cyanobacteria, particularly the origin and evolution of oxygenic photosynthesis, has not been well studied. This is partially due to a lack of sufficient sequence information across all photosynthetic lineages. Molecular technologies have only been applied to a few available genes in studying the acclimation of oceanic cyanobacteria to environmental stimuli. The availability of complete genome sequences of cyanobacteria now provides the first opportunity to study the origin and evolution of these oxygenic photoautotrophs, as well as their adaptation to the contemporary oligotrophic ocean. In the work presented here, I exploit the full power of this rapidly accumulating information to (1) demonstrate the mode and pattern of genome evolution in cyanobacteria and its implications to oxygenic photosynthesis; (2) examine the effects of iron limitation on the regulation of photosynthetic and nitrogen fixation genes in Trichodesmium erythraeum IMS101.; I demonstrate phylogenetic incongruence among 682 orthologous protein families from 13 genomes of cyanobacteria. I identify a core set of 321 genes that share similar evolutionary histories, and hence establish a foundation for reconstructing robust organismal phylogeny. The core set is extremely conservative in protein variability, and is comprised largely of informational genes as well as a number of genes encoding core proteins in photosynthetic pathway. The finding is consistent with the complexity hypothesis, that is, genes coding for large complex systems that have more macromolecular interactions are less subject to horizontal transfers than genes coding for small assemblies of a few gene products (Jain et al., 1999). I test this hypothesis by analyzing the correspondence in genetic distance matrices between all possible pair-wise combinations of 82 photosynthetic genes in 10 species of cyanobacteria. I discover significant correlations between proteins linked in a conserved gene order, and between structurally identified interacting protein scaffolds that coordinate the binding of cofactors involved in photosynthetic electron transport. The tempo of evolution of genes encoding core metabolic processes in the photosynthetic apparatus is highly constrained by protein interactions and this acts as an internal selection pressure governing the conservation of clusters of photosynthetic genes in oxygenic prokaryotic photoautotrophs. In effect, these core proteins have become "frozen metabolic accidents", that is, the metabolic functions the proteins mediate are not only energetically inefficient, but also apparently cannot be significantly altered via selection. Finally, to examine how the photosynthesis and nitrogen fixation machineries acclimate to iron availability, I perform iron deprivation and reconstitution experiments using axenic cultures of Trichodesmium erythraeum IMS101. I show that the major metalloprotein encoding genes in both photosynthesis and nitrogen fixation machinery are transcriptionally regulated by Fe availability. Both physiological and molecular responses suggest that nitrogen fixation is much more sensitive to Fe limitation than photosynthesis.