In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides

Sabino, Yasmin Neves Vieira; Araújo, Katialaine Corrêa de; Assis, Fábia Giovana do Val de; Moreira, Sofia Magalhães; Lopes, Thaynara da Silva; Mendes, Tiago Antônio de Oliveira; Huws, Sharon; Mantovani, Hilário Cuquetto

doi:10.3389/fmicb.2020.576738

Cited by 12 publications

(11 citation statements)

References 80 publications

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“…In silico analyses of bacterial genomes have shown a frequent co-occurrence of genes encoding diverse enzymes associated with the RiPP BGCs, such as lasso peptide BGCs in rumen bacteria. 81 Both primary and tailoring modifications are subtended by a large array of enzymes. 44,55,82 If many of them have been shown to fall into canonical classes, many other biosynthetic enzymes, including the post-tailoring ones, catalyse unprecedented modifications, which involve chemically difficult reactions and novel mechanisms.…”

Section: Ribosomally Synthesized Peptides In Their Producersmentioning

confidence: 99%

“…The increasing interest in microbiota and their roles in human and animal health has triggered descriptions of the potential of microbiota (gut, skin, rumen, …) as a source of antimicrobials, many of which are RSPs. 81,146,193–197 Despite this rich context, and although among the secondary metabolites RSPs probably play a major role in microbial communities living in association with all organisms, unfortunately, in many cases there is no solid evidence of a mutualistic relationship between the organisms and the microorganisms or the role played by RSPs from the hosted microbiota. Conclusive examples of the different roles played by RSPs in various hosts and contexts have been selected and are described in the following.…”

Section: Cross-talks In Holobionts: Rsps As Weaponsmentioning

confidence: 99%

“…It involves both exploring novel niches, such as those provided by extreme environments and underexplored microbiota. For instance, the rumen microbiota has been shown recently to be a rich source of RiPPs 81 but has not been extensively studied yet, or the pulmonary microbiota, which is much lesser studied than the gut microbiota due probably to its lower richness. Other under-considered microbiota in various terrestrial, marine, and fresh-water environments and organisms, or in the human body should be explored.…”

Section: Current Standpoints To Future Directions: From Microbial Eco...mentioning

confidence: 99%

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Ribosomally synthesized peptides, foreground players in microbial interactions: recent developments and unanswered questions

Rebuffat

2022

Nat. Prod. Rep.

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Section: Ribosomally Synthesized Peptides In Their Producersmentioning

confidence: 99%

Section: Cross-talks In Holobionts: Rsps As Weaponsmentioning

confidence: 99%

Section: Current Standpoints To Future Directions: From Microbial Eco...mentioning

confidence: 99%

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Ribosomally synthesized peptides, foreground players in microbial interactions: recent developments and unanswered questions

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2022

Nat. Prod. Rep.

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“…These AMPs demonstrated potential antibacterial activity against several MDR pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and , S. aureus. Moreover, a recent study by Sabino et al (2020) unveiled another AMPs from lasso peptides group. The ruminal bacteria and fungi have been noted to have a vital role in degrading polysaccharides in the rumen.…”

Section: Resultsmentioning

confidence: 99%

Bioprospecting of cow's ruminal microbiota from a slaughterhouse in Ambarawa, Central Java, Indonesia

et al. 2021

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Abstract. Murwani R, Sibero MT, Silitonga PRA, Ambariyanto A. 2021. Bioprospecting of cow's ruminal microbiota from a slaughterhouse in Ambarawa, Central Java, Indonesia. Biodiversitas 22: 5030-5038. Ruminal microorganisms play essential roles in maintaining ruminant health. However, most studies focused only on ruminal lactic acid bacteria (LAB), although other ruminal microorganisms might have biological properties for biotechnological purposes. Therefore, the current study aimed to isolate ruminal bacteria (LAB and non-LAB) and fungi from ruminal material and conducted a bioprospecting study to understand their ability to produce antibacterial compounds and polysaccharide-degrading enzymes. The ruminal bacteria were isolated on MRS and ISP4 agar, while PDA was used to isolate the different fungi. The antibacterial property was tested against multidrug-resistant Escherichia coli and Salmonella enterica ser. Typhi. The ability to produce agarase, alginate-lyase, and carrageenase was screened. Prospective isolates were identified using DNA barcoding approach. Twelve bacteria were isolated using MRS agar, six from ISP4 agar, and four fungi from PDA. Among twelve bacteria from MRS agar, eleven were considered LAB, which consisted of Lactobacillus plantarum and Pediococcus acidilactici. Several classes of bacteria such as actinobacteria, firmicutes, ?-proteobacteria, and ?-proteobacteria were isolated during this study. In addition, three fungal classes, namely Saccharomycetes, Eurotiomycetes, and Mucoromycetes were also isolated. All bacteria from MRS agar were suggested to have potential compounds with antimicrobial activity, while all ruminal fungi exhibited potential sources of polysaccharide-degrading enzymes.

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“…In several previous genome mining campaigns, ,, a unique lasso peptide subclade was noticed that is predominantly found in Firmicutes. The defining feature of this subclade is that the BGCs encode bifunctional proteins (B2/D), containing both N-terminal leader peptidase and C-terminal ABC transporter domains, that are not present in other lasso peptide operons.…”

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confidence: 99%

A Bifunctional Leader Peptidase/ABC Transporter Protein Is Involved in the Maturation of the Lasso Peptide Cochonodin I from Streptococcus suis

et al. 2021

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Lasso peptides are members of the natural product superfamily of ribosomally synthesized and post-translationally modified peptides (RiPPs). Here, we describe the first lasso peptide originating from a biosynthetic gene cluster belonging to a unique lasso peptide subclade defined by the presence of a bifunctional protein harboring both a leader peptidase (B2) and an ABC transporter (D) domain. Bioinformatic analysis revealed that these clusters also encode homologues of the NisR/NisK regulatory system and the NisF/NisE/NisG immunity factors, which are usually associated with the clusters of antimicrobial class I lanthipeptides, such as nisin, another distinct RiPP subfamily. The cluster enabling the heterologous production of the lasso peptide cochonodin I in E. coli originated from Streptococcus suis LSS65, and the threaded structure of cochonodin I was evidenced through extensive MS/MS analysis and stability assays. It was shown that the ABC transporter domain from SsuB2/D is not essential for lasso peptide maturation. By extensive genome mining dedicated exclusively to other lasso peptide biosynthetic gene clusters featuring bifunctional B2/D proteins, it was furthermore revealed that many bacteria associated with human or animal microbiota hold the biosynthetic potential to produce cochonodin-like lasso peptides, implying that these natural products might play roles in human and animal health.

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In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides

Cited by 12 publications

References 80 publications

Ribosomally synthesized peptides, foreground players in microbial interactions: recent developments and unanswered questions

Ribosomally synthesized peptides, foreground players in microbial interactions: recent developments and unanswered questions

Bioprospecting of cow's ruminal microbiota from a slaughterhouse in Ambarawa, Central Java, Indonesia

A Bifunctional Leader Peptidase/ABC Transporter Protein Is Involved in the Maturation of the Lasso Peptide Cochonodin I from Streptococcus suis

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