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Genome mining demonstrates the widespread occurrence of gene clusters encoding bacteriocins in cyanobacteria.

Wang H, Fewer DP, Sivonen K - PLoS ONE (2011)

Bottom Line: They ranged in length from 28 to 164 amino acids with very little sequence conservation of the core peptide.This classification is supported by phylogenetic analysis, which further indicated independent evolutionary trajectories of gene clusters in different groups.Our data suggests that cyanobacteria are a prolific source of low-molecular weight post-translationally modified peptides.

View Article: PubMed Central - PubMed

Affiliation: Division of Microbiology, Department of Food and Environment Sciences, University of Helsinki, Helsinki, Finland.

ABSTRACT
Cyanobacteria are a rich source of natural products with interesting biological activities. Many of these are peptides and the end products of a non-ribosomal pathway. However, several cyanobacterial peptide classes were recently shown to be produced through the proteolytic cleavage and post-translational modification of short precursor peptides. A new class of bacteriocins produced through the proteolytic cleavage and heterocyclization of precursor proteins was recently identified from marine cyanobacteria. Here we show the widespread occurrence of bacteriocin gene clusters in cyanobacteria through comparative analysis of 58 cyanobacterial genomes. A total of 145 bacteriocin gene clusters were discovered through genome mining. These clusters encoded 290 putative bacteriocin precursors. They ranged in length from 28 to 164 amino acids with very little sequence conservation of the core peptide. The gene clusters could be classified into seven groups according to their gene organization and domain composition. This classification is supported by phylogenetic analysis, which further indicated independent evolutionary trajectories of gene clusters in different groups. Our data suggests that cyanobacteria are a prolific source of low-molecular weight post-translationally modified peptides.

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Organization of cyanobacterial bacteriocin gene clusters.The putatively identified gene clusters in this study were classified into seven groups (from I to VII) based on their gene organization and domain composition. ORF sizes and directions are shown in relative scale with color definition as precursor in red, ABC transporter in blue, HlyD in orange, SurA in green, LanM in pink, S8 peptidase-containing protein in yellow, other modification enzymes in purple, adjacent ORFs in black, and tRNA gene in light green. Domains involved in cyanobacterial bacteriocin production and modification are demonstrated within the ORFs with different colors, domain names are derived from the Conserved Domain Database [35]. (I) An example structure of group I from strain Synechococcus PCC 7335, and the locus_tag of hlyD is S7335_4080. (II) from Anabaena variabilis ATCC 29413, and the locus_tag of hlyD is Ava_4382. (III) from Nostoc sp. 7120, and the locus_tag of hlyD is alr5148. (IV) from Nostoc punctiforme PCC 73102, and the locus_tag of hlyD is Npun_F5048. (V) from Nostoc punctiforme PCC 73102, and the locus_tag of hlyD is Npun_R1804. (VI) from Anabaena variabilis ATCC 29413, and the locus_tag of the S8 peptidase domain-containing protein is Ava_4226. (VII) from Trichodesmium erythraeum IMS101, and the locus_tag of hlyD is Tery_0894.
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pone-0022384-g002: Organization of cyanobacterial bacteriocin gene clusters.The putatively identified gene clusters in this study were classified into seven groups (from I to VII) based on their gene organization and domain composition. ORF sizes and directions are shown in relative scale with color definition as precursor in red, ABC transporter in blue, HlyD in orange, SurA in green, LanM in pink, S8 peptidase-containing protein in yellow, other modification enzymes in purple, adjacent ORFs in black, and tRNA gene in light green. Domains involved in cyanobacterial bacteriocin production and modification are demonstrated within the ORFs with different colors, domain names are derived from the Conserved Domain Database [35]. (I) An example structure of group I from strain Synechococcus PCC 7335, and the locus_tag of hlyD is S7335_4080. (II) from Anabaena variabilis ATCC 29413, and the locus_tag of hlyD is Ava_4382. (III) from Nostoc sp. 7120, and the locus_tag of hlyD is alr5148. (IV) from Nostoc punctiforme PCC 73102, and the locus_tag of hlyD is Npun_F5048. (V) from Nostoc punctiforme PCC 73102, and the locus_tag of hlyD is Npun_R1804. (VI) from Anabaena variabilis ATCC 29413, and the locus_tag of the S8 peptidase domain-containing protein is Ava_4226. (VII) from Trichodesmium erythraeum IMS101, and the locus_tag of hlyD is Tery_0894.

Mentions: A total of 145 putative bacteriocin gene clusters were identified in 43 cyanobacteria (Figure 1, Table 1), by analyzing 58 complete and partial genomes from strains with diverse genomic structures and various morphologies (Table S1). These gene clusters were classified into seven groups by comparison of their diverse gene organization and domain composition (Figure 2).


Genome mining demonstrates the widespread occurrence of gene clusters encoding bacteriocins in cyanobacteria.

Wang H, Fewer DP, Sivonen K - PLoS ONE (2011)

Organization of cyanobacterial bacteriocin gene clusters.The putatively identified gene clusters in this study were classified into seven groups (from I to VII) based on their gene organization and domain composition. ORF sizes and directions are shown in relative scale with color definition as precursor in red, ABC transporter in blue, HlyD in orange, SurA in green, LanM in pink, S8 peptidase-containing protein in yellow, other modification enzymes in purple, adjacent ORFs in black, and tRNA gene in light green. Domains involved in cyanobacterial bacteriocin production and modification are demonstrated within the ORFs with different colors, domain names are derived from the Conserved Domain Database [35]. (I) An example structure of group I from strain Synechococcus PCC 7335, and the locus_tag of hlyD is S7335_4080. (II) from Anabaena variabilis ATCC 29413, and the locus_tag of hlyD is Ava_4382. (III) from Nostoc sp. 7120, and the locus_tag of hlyD is alr5148. (IV) from Nostoc punctiforme PCC 73102, and the locus_tag of hlyD is Npun_F5048. (V) from Nostoc punctiforme PCC 73102, and the locus_tag of hlyD is Npun_R1804. (VI) from Anabaena variabilis ATCC 29413, and the locus_tag of the S8 peptidase domain-containing protein is Ava_4226. (VII) from Trichodesmium erythraeum IMS101, and the locus_tag of hlyD is Tery_0894.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3140520&req=5

pone-0022384-g002: Organization of cyanobacterial bacteriocin gene clusters.The putatively identified gene clusters in this study were classified into seven groups (from I to VII) based on their gene organization and domain composition. ORF sizes and directions are shown in relative scale with color definition as precursor in red, ABC transporter in blue, HlyD in orange, SurA in green, LanM in pink, S8 peptidase-containing protein in yellow, other modification enzymes in purple, adjacent ORFs in black, and tRNA gene in light green. Domains involved in cyanobacterial bacteriocin production and modification are demonstrated within the ORFs with different colors, domain names are derived from the Conserved Domain Database [35]. (I) An example structure of group I from strain Synechococcus PCC 7335, and the locus_tag of hlyD is S7335_4080. (II) from Anabaena variabilis ATCC 29413, and the locus_tag of hlyD is Ava_4382. (III) from Nostoc sp. 7120, and the locus_tag of hlyD is alr5148. (IV) from Nostoc punctiforme PCC 73102, and the locus_tag of hlyD is Npun_F5048. (V) from Nostoc punctiforme PCC 73102, and the locus_tag of hlyD is Npun_R1804. (VI) from Anabaena variabilis ATCC 29413, and the locus_tag of the S8 peptidase domain-containing protein is Ava_4226. (VII) from Trichodesmium erythraeum IMS101, and the locus_tag of hlyD is Tery_0894.
Mentions: A total of 145 putative bacteriocin gene clusters were identified in 43 cyanobacteria (Figure 1, Table 1), by analyzing 58 complete and partial genomes from strains with diverse genomic structures and various morphologies (Table S1). These gene clusters were classified into seven groups by comparison of their diverse gene organization and domain composition (Figure 2).

Bottom Line: They ranged in length from 28 to 164 amino acids with very little sequence conservation of the core peptide.This classification is supported by phylogenetic analysis, which further indicated independent evolutionary trajectories of gene clusters in different groups.Our data suggests that cyanobacteria are a prolific source of low-molecular weight post-translationally modified peptides.

View Article: PubMed Central - PubMed

Affiliation: Division of Microbiology, Department of Food and Environment Sciences, University of Helsinki, Helsinki, Finland.

ABSTRACT
Cyanobacteria are a rich source of natural products with interesting biological activities. Many of these are peptides and the end products of a non-ribosomal pathway. However, several cyanobacterial peptide classes were recently shown to be produced through the proteolytic cleavage and post-translational modification of short precursor peptides. A new class of bacteriocins produced through the proteolytic cleavage and heterocyclization of precursor proteins was recently identified from marine cyanobacteria. Here we show the widespread occurrence of bacteriocin gene clusters in cyanobacteria through comparative analysis of 58 cyanobacterial genomes. A total of 145 bacteriocin gene clusters were discovered through genome mining. These clusters encoded 290 putative bacteriocin precursors. They ranged in length from 28 to 164 amino acids with very little sequence conservation of the core peptide. The gene clusters could be classified into seven groups according to their gene organization and domain composition. This classification is supported by phylogenetic analysis, which further indicated independent evolutionary trajectories of gene clusters in different groups. Our data suggests that cyanobacteria are a prolific source of low-molecular weight post-translationally modified peptides.

Show MeSH
Related in: MedlinePlus