Spirulina Genome Structure Analysis And Phycobiliproteins Adaptive Evolution

Spirulina (or Arthrospira) is a type of nonheterocystous and filamentous cyanobacteria found in most lakes, ponds and coastal water, which is proposed as an important mariculture crop both for food and food supplement, and as a potential chemical factory for a variety of useful products. Ongoing Spirulina genome project offers us a wealth of information concerning the sequence and organization of the Spirulina platensis genome, which expand our ability to analyze gene function, organization, and evolution and to examine how environmental parameters and specific mutations shape the photosynthetic genome and proteome.Till now, we have generated more than 7Mbp genomic sequences (45.6% G+C) with 8× coverage of redundancy from the Spirulina platensis shot-gun genome-sequencing project A total of 7,795 protein-coding genes were predicted, including many shorte r(coding for <120 aa) or partial genes. Of the protein-coding genes, nearly 39% are exclusive to Spirulina platensis and 389 are noncyanobacteria best-hit genes, which share less similarity with other cyanobacterial genes. Pfam domain analysis also reveals that Spirulina possesses many specific domains, e.g. Peptidase_MA, DMT, OB, ATP-grasp, Flavokinase.However, genetic studies on Spirulina were restricted by the absence of effective genetic transformation tools. Previous studies revealed that most of the Spirulina species have a high endonuclease activity, which makes the introduction of foreign DNA molecules very difficult. Hence, genome-wide identification of RM systems in Spirulina will undoubtedly help to develop an efficient gene transfer system in this organism. Here, we firstly retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina, and then performed a range of comparative and bioinforamtics analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RM genes, 11 putative Type II RM genes or the solitary methyltransferases, and 9HNH endonuclease genes in the Spirulina genome. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than that in unicellular species, and this expansion of RM systems in filamentous cyanobacteria should be related to their genome enlargement.Phycobiliproteins, together with the linker polypeptides and various chromophores, are basic building blocks of phycobilisomes, a supramolecular complex with a light-harvesting function in cyanobacteria and red algae. We employed evolutionary and bioinformatic tools to elucidate their evolutionary fates after the diversification of phycobiliproteins. We found that many sites with elevated d_n/d_s ratios in different phycobiliprotein lineages are located in the chromophore-binding domain and the helical hairpin domains (X and Y). Covariation analyses also reveal that these sites are significantly correlated, showing strong evidence of the functional-structural importance of interactions among these residues. The potential selective pressure driving the diversification of phycobiliproteins may be related to the phycobiliprotein-chromophore microenvironment formation and the subunits interaction.Moreover, we utilized a molecular population genetic approach for a large number of ppeB sequences with various vertical distributions to study the genetic structure of phycoerythrin and elucidate potential factors that shape phycoerythrin variation in different ecotypes of Prochlorococcus. Several neutrality statistical tests indicate an excess of rare frequency polymorphisms in the low light adapted (LL)-Prochlorococcus data, but an excess of intermediate frequency polymorphisms in the high light adapted (HL)-Prochlorococcus data. Distributions of the positively selected sites, when mapped onto the tertiary structure, reveal that HL- and LL-phycoerythrin should be under different selective patterns. These findings may provide insights into the likely role of selection at the phycoerythrin locus and motivate further research to unveil the structural-functional role of these residues and energy transfer through the chromophores.