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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 putative lanthipeptide gene clusters sorted by similar biosynthetic origin. Numbers represent the locus tag for each gene within the genome sequence of each organism.
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Fig4: Detected putative lanthipeptide gene clusters sorted by similar biosynthetic origin. Numbers represent the locus tag for each gene within the genome sequence of each organism.

Mentions: In total 15 putative lanthipeptide biosynthetic gene clusters were detected in the analysed bacterial genomes, with class II lanthipeptides being the most common (Table 3, Figures 3 and4). The lanthipeptides were once thought to be restricted to the Actinobacteria and Firmicutes phyla and in terms of anaerobes, this also appears to be the case[1]. Whilst some predicted lanthipeptide biosynthetic gene clusters exhibit similarity to previously characterized 2-component lanthipeptides, such as those for lichenicidin VK21 (Bacillus licheniformis VK21)[30] or lichenicidin (Bacillus licheniformis DSM 13 (ATCC 14580)), the remaining lanthipeptide gene clusters appear to be unique. The lichenicidins consist of two single peptides which gain their full activity only in combination[30] and they are encoded by two different precursor peptides as well as modified by two separate LanM enzymes. The leader sequence is removed during the transport out of the cell by the bifunctional enzyme LanT (transporter with N-terminal protease)[31].Table 3


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

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

Detected putative lanthipeptide gene clusters sorted by similar biosynthetic origin. Numbers represent the locus tag for each gene within the genome sequence of each organism.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Detected putative lanthipeptide gene clusters sorted by similar biosynthetic origin. Numbers represent the locus tag for each gene within the genome sequence of each organism.
Mentions: In total 15 putative lanthipeptide biosynthetic gene clusters were detected in the analysed bacterial genomes, with class II lanthipeptides being the most common (Table 3, Figures 3 and4). The lanthipeptides were once thought to be restricted to the Actinobacteria and Firmicutes phyla and in terms of anaerobes, this also appears to be the case[1]. Whilst some predicted lanthipeptide biosynthetic gene clusters exhibit similarity to previously characterized 2-component lanthipeptides, such as those for lichenicidin VK21 (Bacillus licheniformis VK21)[30] or lichenicidin (Bacillus licheniformis DSM 13 (ATCC 14580)), the remaining lanthipeptide gene clusters appear to be unique. The lichenicidins consist of two single peptides which gain their full activity only in combination[30] and they are encoded by two different precursor peptides as well as modified by two separate LanM enzymes. The leader sequence is removed during the transport out of the cell by the bifunctional enzyme LanT (transporter with N-terminal protease)[31].Table 3

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