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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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Distribution of different RiPP biosynthetic gene clusters by habitat and pathogenicity. Animal (yellow); human (blue), environment (soil/mud) (red); extreme (green); other (purple); pathogenic (orange); non- pathogenic (black).
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Fig2: Distribution of different RiPP biosynthetic gene clusters by habitat and pathogenicity. Animal (yellow); human (blue), environment (soil/mud) (red); extreme (green); other (purple); pathogenic (orange); non- pathogenic (black).

Mentions: When it comes to the kind of RiPPs which are produced by the respective strains lanthipeptides, sactipeptides and linear azol(in)e-containing peptides (LAP) are the most common types (each group of RiPPs is explained in further detail below). LAP- and lactococcin-like genes are present predominantly in human pathogenic strains, whilst strains from extreme environments tend to contain DNA encoding head-to-tail cyclized peptides, as well as lanthipeptides and sactipeptides (Table 2, Figure 2). Lasso peptide biosynthetic loci appear to be mainly contained within non-pathogen genomes, and the lanthipeptides also appear to follow a similar distribution. Proteobacteria predominantly contain lasso peptide gene clusters and these are also more common in non-clostridia Firmicutes as well as head-to-tail cyclized peptides (Table 2, Figure 2).Table 2


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

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

Distribution of different RiPP biosynthetic gene clusters by habitat and pathogenicity. Animal (yellow); human (blue), environment (soil/mud) (red); extreme (green); other (purple); pathogenic (orange); non- pathogenic (black).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Distribution of different RiPP biosynthetic gene clusters by habitat and pathogenicity. Animal (yellow); human (blue), environment (soil/mud) (red); extreme (green); other (purple); pathogenic (orange); non- pathogenic (black).
Mentions: When it comes to the kind of RiPPs which are produced by the respective strains lanthipeptides, sactipeptides and linear azol(in)e-containing peptides (LAP) are the most common types (each group of RiPPs is explained in further detail below). LAP- and lactococcin-like genes are present predominantly in human pathogenic strains, whilst strains from extreme environments tend to contain DNA encoding head-to-tail cyclized peptides, as well as lanthipeptides and sactipeptides (Table 2, Figure 2). Lasso peptide biosynthetic loci appear to be mainly contained within non-pathogen genomes, and the lanthipeptides also appear to follow a similar distribution. Proteobacteria predominantly contain lasso peptide gene clusters and these are also more common in non-clostridia Firmicutes as well as head-to-tail cyclized peptides (Table 2, Figure 2).Table 2

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