Limits...
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.

Show MeSH

Related in: MedlinePlus

A likely genomic island in two Synechocystis strains. A genomic segment of ∼40 kb from Synechocystis 6803 is shown with some genes annotated for orientation (EPS, exopolysaccharide export protein; CmcI, Cephalosporin hydroxylase protein; GT1, GT1 family of glycosyltransferases; GTA-GTB, fusion protein joining a glycosyltransferase family A with a glycosyltransferase family B domain; Norf2 is a 68 amino acid peptide-encoding gene originally predicted on basis of transcriptome data indicating the presence of an mRNA for this conserved reading frame).19 Adjacent genes to this region are in the two strains of the gene pairs slr0976/slr0977 and sly1015510/sly1015500 encoding a DUF820 protein and an ABC transporter permease component; left side in 6803) and slr1084/slr1085 and sly1015040/sly1015030 (encoding a WcaF-type acyl transferase and a glycosyltransferase; right side in 6803). The GC % content, indicated by the green bars (each representing 1000 nt), drops considerably within this region. Thus, this region has features of a genomic island. The nucleotide identity to matching segments in the Synechocystis 6714 genome is colour coded (red >90%, light red >70%). The corresponding stretch in the Synechocystis 6714 genome encompasses genes sly1015490– sly1015020, almost entirely belonging to the list of unique genes in that strain (Supplementary Table S6). The proteins encoded by these genes are annotated as hypothetical proteins, UDP-glucose 4-epimerase, several different glycosyltransferases, rhamnogalacturonides degradation protein RhiN, dTDP-glucose 4′6′-dehydratase, methylase/methyltransferase, ABC transporter, GDP-mannose 4′6′dehydratase and as NAD-dependent epimerase/dehydratase.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4060947&req=5

DST055F2: A likely genomic island in two Synechocystis strains. A genomic segment of ∼40 kb from Synechocystis 6803 is shown with some genes annotated for orientation (EPS, exopolysaccharide export protein; CmcI, Cephalosporin hydroxylase protein; GT1, GT1 family of glycosyltransferases; GTA-GTB, fusion protein joining a glycosyltransferase family A with a glycosyltransferase family B domain; Norf2 is a 68 amino acid peptide-encoding gene originally predicted on basis of transcriptome data indicating the presence of an mRNA for this conserved reading frame).19 Adjacent genes to this region are in the two strains of the gene pairs slr0976/slr0977 and sly1015510/sly1015500 encoding a DUF820 protein and an ABC transporter permease component; left side in 6803) and slr1084/slr1085 and sly1015040/sly1015030 (encoding a WcaF-type acyl transferase and a glycosyltransferase; right side in 6803). The GC % content, indicated by the green bars (each representing 1000 nt), drops considerably within this region. Thus, this region has features of a genomic island. The nucleotide identity to matching segments in the Synechocystis 6714 genome is colour coded (red >90%, light red >70%). The corresponding stretch in the Synechocystis 6714 genome encompasses genes sly1015490– sly1015020, almost entirely belonging to the list of unique genes in that strain (Supplementary Table S6). The proteins encoded by these genes are annotated as hypothetical proteins, UDP-glucose 4-epimerase, several different glycosyltransferases, rhamnogalacturonides degradation protein RhiN, dTDP-glucose 4′6′-dehydratase, methylase/methyltransferase, ABC transporter, GDP-mannose 4′6′dehydratase and as NAD-dependent epimerase/dehydratase.

Mentions: The higher number of transposon genes in Synechocystis 6803 is correlated with a low degree of syntheny between the two strains. Another situation exists with the rfb-gene cluster that differs entirely between the two strains and encodes several glycosyltransferases possibly involved in cell wall biosynthesis and the modification of cell surface properties. This region has features of a genomic island, since the adjacent genes are conserved between the two Synechocystis strains, but the GC content drops considerably (from 48 to 35%) within this region in both strains (Fig. 2). Genomic islands consist of sets of genes that become laterally transferred, belong to the flexible gene pool of a bacterial phylum and frequently provide a certain fitness advantage.30 Accordingly, the most closely related homologues matching to these proteins are found in a wide variety of organisms. For the 50 genes located in the Synechocystis 6714 rfb gene cluster, the phylogenetically top-matching proteins belong to groups as diverse as Zetaproteobacteria, Bacilli, Clostridia, Armatimonadetes, Rhodopirellula, and Stigonematales cyanobacteria. The top-matching proteins against the Synechocystis 6803 rfb gene cluster proteins are of comparable diversity. A particular example is also the norf2 gene which was annotated on the basis of transcriptome data.19 The most closely related proteins to Norf2 (Fig. 2) are annotated in Thiocapsa marina (69% identical and 86% similar residues) and several Thioalkalivibrio species, pointing further to the alien origin of this genomic region.Figure 2.


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)

A likely genomic island in two Synechocystis strains. A genomic segment of ∼40 kb from Synechocystis 6803 is shown with some genes annotated for orientation (EPS, exopolysaccharide export protein; CmcI, Cephalosporin hydroxylase protein; GT1, GT1 family of glycosyltransferases; GTA-GTB, fusion protein joining a glycosyltransferase family A with a glycosyltransferase family B domain; Norf2 is a 68 amino acid peptide-encoding gene originally predicted on basis of transcriptome data indicating the presence of an mRNA for this conserved reading frame).19 Adjacent genes to this region are in the two strains of the gene pairs slr0976/slr0977 and sly1015510/sly1015500 encoding a DUF820 protein and an ABC transporter permease component; left side in 6803) and slr1084/slr1085 and sly1015040/sly1015030 (encoding a WcaF-type acyl transferase and a glycosyltransferase; right side in 6803). The GC % content, indicated by the green bars (each representing 1000 nt), drops considerably within this region. Thus, this region has features of a genomic island. The nucleotide identity to matching segments in the Synechocystis 6714 genome is colour coded (red >90%, light red >70%). The corresponding stretch in the Synechocystis 6714 genome encompasses genes sly1015490– sly1015020, almost entirely belonging to the list of unique genes in that strain (Supplementary Table S6). The proteins encoded by these genes are annotated as hypothetical proteins, UDP-glucose 4-epimerase, several different glycosyltransferases, rhamnogalacturonides degradation protein RhiN, dTDP-glucose 4′6′-dehydratase, methylase/methyltransferase, ABC transporter, GDP-mannose 4′6′dehydratase and as NAD-dependent epimerase/dehydratase.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4060947&req=5

DST055F2: A likely genomic island in two Synechocystis strains. A genomic segment of ∼40 kb from Synechocystis 6803 is shown with some genes annotated for orientation (EPS, exopolysaccharide export protein; CmcI, Cephalosporin hydroxylase protein; GT1, GT1 family of glycosyltransferases; GTA-GTB, fusion protein joining a glycosyltransferase family A with a glycosyltransferase family B domain; Norf2 is a 68 amino acid peptide-encoding gene originally predicted on basis of transcriptome data indicating the presence of an mRNA for this conserved reading frame).19 Adjacent genes to this region are in the two strains of the gene pairs slr0976/slr0977 and sly1015510/sly1015500 encoding a DUF820 protein and an ABC transporter permease component; left side in 6803) and slr1084/slr1085 and sly1015040/sly1015030 (encoding a WcaF-type acyl transferase and a glycosyltransferase; right side in 6803). The GC % content, indicated by the green bars (each representing 1000 nt), drops considerably within this region. Thus, this region has features of a genomic island. The nucleotide identity to matching segments in the Synechocystis 6714 genome is colour coded (red >90%, light red >70%). The corresponding stretch in the Synechocystis 6714 genome encompasses genes sly1015490– sly1015020, almost entirely belonging to the list of unique genes in that strain (Supplementary Table S6). The proteins encoded by these genes are annotated as hypothetical proteins, UDP-glucose 4-epimerase, several different glycosyltransferases, rhamnogalacturonides degradation protein RhiN, dTDP-glucose 4′6′-dehydratase, methylase/methyltransferase, ABC transporter, GDP-mannose 4′6′dehydratase and as NAD-dependent epimerase/dehydratase.
Mentions: The higher number of transposon genes in Synechocystis 6803 is correlated with a low degree of syntheny between the two strains. Another situation exists with the rfb-gene cluster that differs entirely between the two strains and encodes several glycosyltransferases possibly involved in cell wall biosynthesis and the modification of cell surface properties. This region has features of a genomic island, since the adjacent genes are conserved between the two Synechocystis strains, but the GC content drops considerably (from 48 to 35%) within this region in both strains (Fig. 2). Genomic islands consist of sets of genes that become laterally transferred, belong to the flexible gene pool of a bacterial phylum and frequently provide a certain fitness advantage.30 Accordingly, the most closely related homologues matching to these proteins are found in a wide variety of organisms. For the 50 genes located in the Synechocystis 6714 rfb gene cluster, the phylogenetically top-matching proteins belong to groups as diverse as Zetaproteobacteria, Bacilli, Clostridia, Armatimonadetes, Rhodopirellula, and Stigonematales cyanobacteria. The top-matching proteins against the Synechocystis 6803 rfb gene cluster proteins are of comparable diversity. A particular example is also the norf2 gene which was annotated on the basis of transcriptome data.19 The most closely related proteins to Norf2 (Fig. 2) are annotated in Thiocapsa marina (69% identical and 86% similar residues) and several Thioalkalivibrio species, pointing further to the alien origin of this genomic region.Figure 2.

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