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Comparative genome analysis of the closely related Synechocystis strains PCC 6714 and PCC 6803.

Kopf M, Klähn S, Pade N, Weingärtner C, Hagemann M, Voß B, Hess WR - DNA Res. (2014)

Bottom Line: PCC 6714.Genome information for Synechocystis sp.PCC 6714 has been deposited in Genbank (accession no AMZV01000000).

View Article: PubMed Central - PubMed

Affiliation: Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany.

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Prophage Psy1 inserted into the trnFGAA gene (labelled by the green stars) of Synechocystis 6714. Genome position is drawn along the x-axis. Protein coding genes are shown in red if conserved in Synechocystis 6803 and in blue if not; trnFGAA is shown in green. Transcriptome read counts per 100 million for the forward strand are plotted above and for the reverse strand below the CDS features. The GC % content is indicated by the green bars (each representing 1000 nt). The following genes were annotated as coding for bacteriophage-related proteins and are mentioned in the text: sly1027640, HK97 family phage portal protein; sly1027490, bacteriophage lysozyme-like protein; sly1027670 and sly1027680, remotely similar to bacteriophage Cro repressor; sly1027700, D5 N terminal like domain-containing protein of phage D5 proteins and bacteriophage P4 DNA primases; sly1027750, phage integrase.
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DST055F3: Prophage Psy1 inserted into the trnFGAA gene (labelled by the green stars) of Synechocystis 6714. Genome position is drawn along the x-axis. Protein coding genes are shown in red if conserved in Synechocystis 6803 and in blue if not; trnFGAA is shown in green. Transcriptome read counts per 100 million for the forward strand are plotted above and for the reverse strand below the CDS features. The GC % content is indicated by the green bars (each representing 1000 nt). The following genes were annotated as coding for bacteriophage-related proteins and are mentioned in the text: sly1027640, HK97 family phage portal protein; sly1027490, bacteriophage lysozyme-like protein; sly1027670 and sly1027680, remotely similar to bacteriophage Cro repressor; sly1027700, D5 N terminal like domain-containing protein of phage D5 proteins and bacteriophage P4 DNA primases; sly1027750, phage integrase.

Mentions: A further difference between Synechocystis 6714 and 6803 genomes is the presence of a prophage in the former but its lack in the latter (Fig. 3). As this prophage has not been previously described, we called it Psy1, for prophage in Synechocystis 1. The genomic DNA of Psy1 has integrated into the trnF (phenylalanine-specific tRNAGAA) gene, duplicating its 3′ half but restoring the gene to be functional intact. This insertion might have occurred only recently as the duplicated segment of the trnF gene is still sequence identical with the original prophage host gene. Although the Psy1 genome is with a total length of 20 660 nt quite short for a prophage, genomes of comparable size have recently been reported for siphoviruses, which infect marine cyanobacteria (e.g. S-CBS1 infecting Synechococcus strains CB0201, CB0204, CB0202, and CB0101).31 The annotation of Psy1 adds another 27 genes unique for strain 6714 (Supplementary Table S6). Most of these genes have no closely related homologues in database searches, indicating that Psy1 might belong to a novel group of bacteriophages. Clear homologues exist for Sly1027750, an integrase with several homologues in other cyanobacterial genomes; Sly1027640, an HK97 family phage portal protein with the tail sheath protein from the Pseudomonas transducing phage PhiPA3 as the best matching protein in the bacteriophage database (BlastP E-value 7e−16);32 Sly1027490, a lysozyme superfamily protein with the putative endolysin from Acinetobacter phage phiAC-1 as the best matching bacteriophage protein (BlastP E-value 2e-30);33 Sly1027700, a D5 N terminal like domain-containing protein of phage D5 proteins and bacteriophage P4 DNA primases (Fig. 3).Figure 3.


Comparative genome analysis of the closely related Synechocystis strains PCC 6714 and PCC 6803.

Kopf M, Klähn S, Pade N, Weingärtner C, Hagemann M, Voß B, Hess WR - DNA Res. (2014)

Prophage Psy1 inserted into the trnFGAA gene (labelled by the green stars) of Synechocystis 6714. Genome position is drawn along the x-axis. Protein coding genes are shown in red if conserved in Synechocystis 6803 and in blue if not; trnFGAA is shown in green. Transcriptome read counts per 100 million for the forward strand are plotted above and for the reverse strand below the CDS features. The GC % content is indicated by the green bars (each representing 1000 nt). The following genes were annotated as coding for bacteriophage-related proteins and are mentioned in the text: sly1027640, HK97 family phage portal protein; sly1027490, bacteriophage lysozyme-like protein; sly1027670 and sly1027680, remotely similar to bacteriophage Cro repressor; sly1027700, D5 N terminal like domain-containing protein of phage D5 proteins and bacteriophage P4 DNA primases; sly1027750, phage integrase.
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Related In: Results  -  Collection

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DST055F3: Prophage Psy1 inserted into the trnFGAA gene (labelled by the green stars) of Synechocystis 6714. Genome position is drawn along the x-axis. Protein coding genes are shown in red if conserved in Synechocystis 6803 and in blue if not; trnFGAA is shown in green. Transcriptome read counts per 100 million for the forward strand are plotted above and for the reverse strand below the CDS features. The GC % content is indicated by the green bars (each representing 1000 nt). The following genes were annotated as coding for bacteriophage-related proteins and are mentioned in the text: sly1027640, HK97 family phage portal protein; sly1027490, bacteriophage lysozyme-like protein; sly1027670 and sly1027680, remotely similar to bacteriophage Cro repressor; sly1027700, D5 N terminal like domain-containing protein of phage D5 proteins and bacteriophage P4 DNA primases; sly1027750, phage integrase.
Mentions: A further difference between Synechocystis 6714 and 6803 genomes is the presence of a prophage in the former but its lack in the latter (Fig. 3). As this prophage has not been previously described, we called it Psy1, for prophage in Synechocystis 1. The genomic DNA of Psy1 has integrated into the trnF (phenylalanine-specific tRNAGAA) gene, duplicating its 3′ half but restoring the gene to be functional intact. This insertion might have occurred only recently as the duplicated segment of the trnF gene is still sequence identical with the original prophage host gene. Although the Psy1 genome is with a total length of 20 660 nt quite short for a prophage, genomes of comparable size have recently been reported for siphoviruses, which infect marine cyanobacteria (e.g. S-CBS1 infecting Synechococcus strains CB0201, CB0204, CB0202, and CB0101).31 The annotation of Psy1 adds another 27 genes unique for strain 6714 (Supplementary Table S6). Most of these genes have no closely related homologues in database searches, indicating that Psy1 might belong to a novel group of bacteriophages. Clear homologues exist for Sly1027750, an integrase with several homologues in other cyanobacterial genomes; Sly1027640, an HK97 family phage portal protein with the tail sheath protein from the Pseudomonas transducing phage PhiPA3 as the best matching protein in the bacteriophage database (BlastP E-value 7e−16);32 Sly1027490, a lysozyme superfamily protein with the putative endolysin from Acinetobacter phage phiAC-1 as the best matching bacteriophage protein (BlastP E-value 2e-30);33 Sly1027700, a D5 N terminal like domain-containing protein of phage D5 proteins and bacteriophage P4 DNA primases (Fig. 3).Figure 3.

Bottom Line: PCC 6714.Genome information for Synechocystis sp.PCC 6714 has been deposited in Genbank (accession no AMZV01000000).

View Article: PubMed Central - PubMed

Affiliation: Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany.

Show MeSH
Related in: MedlinePlus