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Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria.

Letzel AC, Pidot SJ, Hertweck C - BMC Genomics (2014)

Bottom Line: More than 25% of anaerobes are capable of producing RiPPs either alone or in conjunction with other secondary metabolites, such as polyketides or non-ribosomal peptides.Amongst the analyzed genomes, several gene clusters encode uncharacterized RiPPs, whilst others show similarity with known RiPPs.These include a number of potential class II lanthipeptides; head-to-tail cyclized peptides and lactococcin 972-like RiPP.

View Article: PubMed Central - PubMed

Affiliation: Leibniz Institute for Natural Product Research and Infection Biology HKI, Beutenbergstr, 11a, Jena 07745, Germany. christian.hertweck@hki-jena.de.

ABSTRACT

Background: Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a diverse group of biologically active bacterial molecules. Due to the conserved genomic arrangement of many of the genes involved in their synthesis, these secondary metabolite biosynthetic pathways can be predicted from genome sequence data. To date, however, despite the myriad of sequenced genomes covering many branches of the bacterial phylogenetic tree, such an analysis for a broader group of bacteria like anaerobes has not been attempted.

Results: We investigated a collection of 211 complete and published genomes, focusing on anaerobic bacteria, whose potential to encode RiPPs is relatively unknown. We showed that the presence of RiPP-genes is widespread among anaerobic representatives of the phyla Actinobacteria, Proteobacteria and Firmicutes and that, collectively, anaerobes possess the ability to synthesize a broad variety of different RiPP classes. More than 25% of anaerobes are capable of producing RiPPs either alone or in conjunction with other secondary metabolites, such as polyketides or non-ribosomal peptides.

Conclusion: Amongst the analyzed genomes, several gene clusters encode uncharacterized RiPPs, whilst others show similarity with known RiPPs. These include a number of potential class II lanthipeptides; head-to-tail cyclized peptides and lactococcin 972-like RiPP. This study presents further evidence in support of anaerobic bacteria as an untapped natural products reservoir.

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Detected circularin A-like RiPPs. A Circularin A gene cluster (cir) of C. beijerinckii ATCC 25752 in comparison to putative circularin A like gene cluster of C. bescii Z-1320 and C. perfringens SM 101; Numbers represent the locus tag for each gene within the genome sequence of each organism. B Alignment of circularin A precursor sequence (CirA) and circularin A-like precursor sequences of C. bescii Z-1320 (Athe_2617), C. saccharolyticus DSM 8903 (Csac_0526) and C. perfringens SM 101 (CPR_0761) C Amino acid structure of circularin A.
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Fig11: Detected circularin A-like RiPPs. A Circularin A gene cluster (cir) of C. beijerinckii ATCC 25752 in comparison to putative circularin A like gene cluster of C. bescii Z-1320 and C. perfringens SM 101; Numbers represent the locus tag for each gene within the genome sequence of each organism. B Alignment of circularin A precursor sequence (CirA) and circularin A-like precursor sequences of C. bescii Z-1320 (Athe_2617), C. saccharolyticus DSM 8903 (Csac_0526) and C. perfringens SM 101 (CPR_0761) C Amino acid structure of circularin A.

Mentions: Relatively few HtT-cyclized peptides were identified amongst the genomes analyzed here. Those that were identified were found in the phyla Firmicutes and Chloroflexi (Table 10), with several exhibiting homology to circularin A (Figure 11A), a previously characterized peptide of Clostridium beijerinckii ATCC 25752[85, 86] (Figure 11C). The gene order in the Caldicellulosiruptor gene clusters is identical to each other and the precursor sequences differ by only a few amino acids (Figure 11B). The putative circularin A gene cluster of C. perfringens SM 101 is quite different, however, and it has limited conservation with the circularin A gene cluster in C. beijerinckii ATCC 25752 and is flanked by numerous transposases (Figure 11A).Table 10


Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria.

Letzel AC, Pidot SJ, Hertweck C - BMC Genomics (2014)

Detected circularin A-like RiPPs. A Circularin A gene cluster (cir) of C. beijerinckii ATCC 25752 in comparison to putative circularin A like gene cluster of C. bescii Z-1320 and C. perfringens SM 101; Numbers represent the locus tag for each gene within the genome sequence of each organism. B Alignment of circularin A precursor sequence (CirA) and circularin A-like precursor sequences of C. bescii Z-1320 (Athe_2617), C. saccharolyticus DSM 8903 (Csac_0526) and C. perfringens SM 101 (CPR_0761) C Amino acid structure of circularin A.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4289311&req=5

Fig11: Detected circularin A-like RiPPs. A Circularin A gene cluster (cir) of C. beijerinckii ATCC 25752 in comparison to putative circularin A like gene cluster of C. bescii Z-1320 and C. perfringens SM 101; Numbers represent the locus tag for each gene within the genome sequence of each organism. B Alignment of circularin A precursor sequence (CirA) and circularin A-like precursor sequences of C. bescii Z-1320 (Athe_2617), C. saccharolyticus DSM 8903 (Csac_0526) and C. perfringens SM 101 (CPR_0761) C Amino acid structure of circularin A.
Mentions: Relatively few HtT-cyclized peptides were identified amongst the genomes analyzed here. Those that were identified were found in the phyla Firmicutes and Chloroflexi (Table 10), with several exhibiting homology to circularin A (Figure 11A), a previously characterized peptide of Clostridium beijerinckii ATCC 25752[85, 86] (Figure 11C). The gene order in the Caldicellulosiruptor gene clusters is identical to each other and the precursor sequences differ by only a few amino acids (Figure 11B). The putative circularin A gene cluster of C. perfringens SM 101 is quite different, however, and it has limited conservation with the circularin A gene cluster in C. beijerinckii ATCC 25752 and is flanked by numerous transposases (Figure 11A).Table 10

Bottom Line: More than 25% of anaerobes are capable of producing RiPPs either alone or in conjunction with other secondary metabolites, such as polyketides or non-ribosomal peptides.Amongst the analyzed genomes, several gene clusters encode uncharacterized RiPPs, whilst others show similarity with known RiPPs.These include a number of potential class II lanthipeptides; head-to-tail cyclized peptides and lactococcin 972-like RiPP.

View Article: PubMed Central - PubMed

Affiliation: Leibniz Institute for Natural Product Research and Infection Biology HKI, Beutenbergstr, 11a, Jena 07745, Germany. christian.hertweck@hki-jena.de.

ABSTRACT

Background: Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a diverse group of biologically active bacterial molecules. Due to the conserved genomic arrangement of many of the genes involved in their synthesis, these secondary metabolite biosynthetic pathways can be predicted from genome sequence data. To date, however, despite the myriad of sequenced genomes covering many branches of the bacterial phylogenetic tree, such an analysis for a broader group of bacteria like anaerobes has not been attempted.

Results: We investigated a collection of 211 complete and published genomes, focusing on anaerobic bacteria, whose potential to encode RiPPs is relatively unknown. We showed that the presence of RiPP-genes is widespread among anaerobic representatives of the phyla Actinobacteria, Proteobacteria and Firmicutes and that, collectively, anaerobes possess the ability to synthesize a broad variety of different RiPP classes. More than 25% of anaerobes are capable of producing RiPPs either alone or in conjunction with other secondary metabolites, such as polyketides or non-ribosomal peptides.

Conclusion: Amongst the analyzed genomes, several gene clusters encode uncharacterized RiPPs, whilst others show similarity with known RiPPs. These include a number of potential class II lanthipeptides; head-to-tail cyclized peptides and lactococcin 972-like RiPP. This study presents further evidence in support of anaerobic bacteria as an untapped natural products reservoir.

Show MeSH