Comparative studies on the structure of cyanobacterial genomes

A comparison of gene order in completely sequenced bacterial genomes from distantly related taxa including Synechocystis PCC 6803 has revealed that at least 19 clusters of two or more genes are widely preserved in (eu)Bacteria. These are presumed to reflect conserved elements of coordinated gene expression that require gene proximity. Most relate to the translation machinery. Seven of these gene orders are essentially conserved in the Archaea as well. Overall, the results lend further support to the idea that entities with an RNA genome preceded the first DNA based common ancestor.; Six complete cyanobacterial genomes, Synechocystis PCC 6803 (3.6Mb), Synechococcus WH8102 (2.72Mb), Prochlorococcus marinus MED4 (1.6Mb), Prochlorococcus marinus MIT9313 (2.4Mb), and Nostoc punctiforme (9.2Mb), were compared. A set of 957 proteins was found to be shared by all six genomes. This set was narrowed to 170, which are unique to cyanobacteria. The set of unique genes contains 11 clusters of 2 or 3 genes also common to all six genomes. Most of the known genes, (61%) in the signature set are related to photosynthesis, with the majority of genes (70.8%) being of unknown function. The functional categories of the core set of cyanobacterial proteins support the view of what distinguishes photosynthetic bacteria from eubacterial genomes in general. The fact that these genes are also present in the chloroplasts of land plants further supports the endosymbiotic theory concerning chloroplast origins.; Sample sequencing was used to compare the genome of Synechococcus PCC 7002 to the completely sequenced genome of Synechocystis PCC 6803. A library consisting of 207 cosmids was used for sample sequencing. Sequencing from the ends of cosmids has produced information covering 12% of the genome of Synechococcus PCC 7002. Approximately 295,000 bases of sequence, which includes 195 coding regions were generated. These sequences have a mean read of 500 bases with an average spacing of 4200 by over the 2.7Mb genome. Sequence similarity determined utilizing BLAST servers at the NCBI along with Cyanobase (the database of Synechocystis PCC 6803), has revealed that approximately 70% of the discovered genes have a high similarity to Synechocystis PCC 6803. Even in these closely related bacteria, there has been extensive gene shuffling consistent with our earlier studies of gene order.