The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms

Abstract

BackgroundCyanobacteria are among the most abundant organisms on Earth and represent one of the oldest and most widespread clades known in modern phylogenetics. As the only known prokaryotes capable of oxygenic photosynthesis, cyanobacteria are considered to be a promising resource for renewable fuels and natural products. Our efforts to harness the sun's energy using cyanobacteria would greatly benefit from an increased understanding of the genomic diversity across multiple cyanobacterial strains. In this respect, the advent of novel sequencing techniques and the availability of several cyanobacterial genomes offers new opportunities for understanding microbial diversity and metabolic organization and evolution in diverse environments.ResultsHere, we report a whole genome comparison of multiple phototrophic cyanobacteria. We describe genetic diversity found within cyanobacterial genomes, specifically with respect to metabolic functionality. Our results are based on pair-wise comparison of protein sequences and concomitant construction of clusters of likely ortholog genes. We differentiate between core, shared and unique genes and show that the majority of genes are associated with a single genome. In contrast, genes with metabolic function are strongly overrepresented within the core genome that is common to all considered strains. The analysis of metabolic diversity within core carbon metabolism reveals parts of the metabolic networks that are highly conserved, as well as highly fragmented pathways.ConclusionsOur results have direct implications for resource allocation and further sequencing projects. It can be extrapolated that the number of newly identified genes still significantly increases with increasing number of new sequenced genomes. Furthermore, genome analysis of multiple phototrophic strains allows us to obtain a detailed picture of metabolic diversity that can serve as a starting point for biotechnological applications and automated metabolic reconstructions.

Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth

“…Of particular interest are the energetic implications of carbon cycling (43), light damage and its repair, and the coupling of metabolic processes to the cell cycle, as well as the temporal segregation of incompatible metabolic processes, such as nitrogen fixation in certain cyanobacteria (44). We conjecture that global resource allocation models, together with the methodology described here, will allow us to assess the condition-dependent cost and benefit of individual genes (45) in the context of a growing cell, and thereby facilitate the study of metabolic adaptations and metabolic diversity of cyanobacteria (46) with the ultimate aim of understanding the limits of phototrophic growth in complex environments.…”

Long-Term Acclimation to Iron Limitation Reveals New Insights in Metabolism Regulation of Synechococcus sp. PCC7002

“…and Prochlorococcus marinus strains presented exclusive genes (absent in other cyanobacteria including Synechococcus sp. PCC7002) encoding for enzymes related to defense response, DNA integration and regulatory processes (Beck et al, 2012). Similarly, oceanic strains lack genes common to all the other strains (including Synechococcus sp.…”

“…These differences highlight specific adaptations to different environments (Sohm et al, 2016). However, pathways related to gene expression and central metabolism such as the Calvin-Benson-Bassham cycle, and nucleotide and amino acid biosynthesis and photosynthesis were highly conserved amongst cyanobacteria (Dufresne et al, 2008;Beck et al, 2012). Thus, despite the arguably suitability of Synechococcus sp.…”

Daily Expression Pattern of Protein-Encoding Genes and Small Noncoding RNAs in Synechocystis sp. Strain PCC 6803

“…Only transcripts classified as cyclic in both studies and with peak times of transcripts differing by less than 8 h were considered oscillating in Synechococcus. Gene homology between both species was investigated in a previous study (43).…”