Sequence Analysis of the Genome of the Unicellular Cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence Features in the 1 Mb Region from Map Positions 64% to 92% of the Genome

Abstract

The contiguous sequence of 1,003,450 bp spanning map positions 64% to 92% of the genome of Synechocystis sp. strain PCC6803 has been deduced. Computer analysis of the sequence predicts that this region contains at least 818 potential ORFs, in which 255 (31%) were either genes that had already been identified or their homologues, 84 (10%) were homologues to registered hypothetical genes, and 149 (18%) showed weak similarities to reported genes. The remaining 330 ORFs showed no apparent similarity to any reported genes or carried no significant protein motifs. The potential ORFs as a whole occupied 86% of the sequenced region, implying compact arrangement of genes in the genome. As to the structural RNA genes, one rRNA operon consisting of 5,028 bp and at least 11 species of tRNA genes were identified. It is noteworthy that 10 out of the 11 tRNA species showed significant sequence similarities to tRNAs reported in plant chloroplasts. As other notable unique sequences, three classes of IS-like elements each with characteristics typical of IS elements were identified, and a typical unit of WD(Trp-Asp)-repeats which have only been detected in the regulatory proteins of eukaryotes was identified within the large 5,079-bp ORF located at map position 69%.

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

“…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 extent of identity is 41 to 42% with the NrtB proteins and 39 to 40% with the CmpB proteins (alignment not shown).…”

“…A 0.8-kbp fragment of Synechocystis sp. strain PCC 6803 DNA, carrying the entire slr0899 ORF with 280 bases and 56 bases, respectively, of its 5Ј-and 3Ј-flanking sequences, was excised from an M13mp18 clone carrying the ORFs slr0898 and slr0899 (16) and cloned between the PstI and KpnI sites of pBluescriptII SK ϩ in the same orientation as that of lacZ on the vector. The resulting plasmid (pCY2), in which the slr0899 ORF was placed 250 bases downstream from a truncated LacZ ORF, was transformed into E. coli CSH26.…”

“…strain PCC 6803 DNA carrying the entire cynS gene, excised with NcoI and KpnI from the M13mp18 clone carrying the slr0898 and slr0899 ORFs (16); and the kanamycin resistance gene cartridge C.K1 (9) carrying nptII. The double-stranded DNA probes were labeled with 32 P as described by Feinberg and Vogelstein (10).…”

“…The open reading frame (ORF) slr0899 of Synechococcus sp. strain PCC 6803 (16) and its homolog of Synechocystis sp. strain PCC 7942, encoding cyanase-like sequences, were identified as the cyanobacterial cyanase gene (designated cynS) and shown to be repressed by ammonium.…”

The Sulfolobus solfataricus P2 genome project

“…Synechocystis sp. PCC6803, at an intermediate distance from the major model bacterial genomes, has 10% of ORFs matching hypothetical proteins [19]. It would seem that most of the highly conserved and ubiquitous gene families have already been identified, as has been previously suggested [20].…”