Sequence Analysis of the Genome of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC6803. II. Sequence Determination of the Entire Genome and Assignment of Potential Protein-coding Regions

Abstract

The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was completed. The total length of the genome finally confirmed was 3,573,470 bp, including the previously reported sequence of 1,003,450 bp from map position 64% to 92% of the genome. The entire sequence was assembled from the sequences of the physical map-based contigs of cosmid clones and of lambda clones and long PCR products which were used for gap-filling. The accuracy of the sequence was guaranteed by analysis of both strands of DNA through the entire genome. The authenticity of the assembled sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA using the assembled sequence data. To predict the potential protein-coding regions, analysis of open reading frames (ORFs), analysis by the GeneMark program and similarity search to databases were performed. As a result, a total of 3,168 potential protein genes were assigned on the genome, in which 145 (4.6%) were identical to reported genes and 1,257 (39.6%) and 340 (10.8%) showed similarity to reported and hypothetical genes, respectively. The remaining 1,426 (45.0%) had no apparent similarity to any genes in databases. Among the potential protein genes assigned, 128 were related to the genes participating in photosynthetic reactions. The sum of the sequences coding for potential protein genes occupies 87% of the genome length. By adding rRNA and tRNA genes, therefore, the genome has a very compact arrangement of protein- and RNA-coding regions. A notable feature on the gene organization of the genome was that 99 ORFs, which showed similarity to transposase genes and could be classified into 6 groups, were found spread all over the genome, and at least 26 of them appeared to remain intact. The result implies that rearrangement of the genome occurred frequently during and after establishment of this species.

A putative HCO−3 transporter in the cyanobacterium Synechococcus sp. strain PCC 79421

“…U62616) identi¢ed several open reading frames (identi¢ed in the legend of Fig. 1), some are similar to those identi¢ed in Synechocystis PCC 6803 [23]. Comparison of the DNA sequence in the wild type with those in the two repeated regions (due to the single crossover) in mutant IL-2, identi¢ed several alterations in the latter.…”

“…Sll**** and slr**** are the homologous genes in Synechocystis PCC 6803 [23]; YZ02-myctu, accession no. Q10536; ICC, accession no.…”

Identification and nitrogen regulation of the cyanase gene from the cyanobacteria Synechocystis sp. strain PCC 6803 and Synechococcus sp. strain PCC 7942

“…strain PCC 7942 (25), Synechocystis sp. strain PCC 6803 (giP1652570) (15), and Phormidium laminosum (21). It is also similar to CmpB, the integral membrane component of another cyanobacterial ABC transporter closely related to the nitrate-nitrite transporter, from strain PCC 7942 (giP11019379) (24) and strain PCC 6803 (giP1001317) (16).…”

The Escherichia coli phage‐shock‐protein (psp) operon

“…None of these resembles other proteins in the database closely enough to provide strong, sequencebased clues to their function. The first (5Ј-proximal) 25.5 kDa protein, PspA, has three known homologues: PspB, a cold-shock protein from Bacillus subtilis (Graumann et al, 1996), a protein (SYCSLRD) from Synechocystis (Kaneko et al, 1995), and another protein (IM30) from pea chloroplast (Li et al, 1994). The function of none of these homologous proteins is known.…”