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

Yasmin Neves Vieira Sabino,Thaynara Da Silva Lopes,Sharon Ann Huws,Sofia Magalhães Moreira,Katialaine Corrêa De Araújo,Tiago Antônio De Oliveira Mendes,Fábia Giovana Do Val De Assis,Hilário C Mantovani

doi:10.3389/fmicb.2020.576738

Yasmin Neves Vieira Sabino, Thaynara Da Silva Lopes + Show 6 more

Open Access

https://doi.org/10.3389/fmicb.2020.576738

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Abstract

Studies of rumen microbial ecology suggest that the capacity to produce antimicrobial peptides could be a useful trait in species competing for ecological niches in the ruminal ecosystem. However, little is known about the synthesis of lasso peptides by ruminal microorganisms. Here we analyzed the distribution and diversity of lasso peptide gene clusters in 425 bacterial genomes from the rumen ecosystem. Genome mining was performed using antiSMASH 5, BAGEL4, and a database of well-known precursor sequences. The genomic context of the biosynthetic clusters was investigated to identify putative lasA genes and protein sequences from enzymes of the biosynthetic machinery were evaluated to identify conserved motifs. Metatranscriptome analysis evaluated the expression of the biosynthetic genes in the rumen microbiome. Several incomplete (n = 23) and complete (n = 11) putative lasso peptide clusters were detected in the genomes of ruminal bacteria. The complete gene clusters were exclusively found within the phylum Firmicutes, mainly (48%) in strains of the genus Butyrivibrio. The analysis of the genetic organization of complete putative lasso peptide clusters revealed the presence of co-occurring genes, including kinases (85%), transcriptional regulators (49%), and glycosyltransferases (36%). Moreover, a conserved pattern of cluster organization was detected between strains of the same genus/species. The maturation enzymes LasB, LasC, and LasD showed regions highly conserved, including the presence of a transglutaminase core in LasB, an asparagine synthetase domain in LasC, and an ABC-type transporter system in LasD. Phylogenetic trees of the essential biosynthetic proteins revealed that sequences split into monophyletic groups according to their shared single common ancestor. Metatranscriptome analyses indicated the expression of the lasso peptides biosynthetic genes within the active rumen microbiota. Overall, our in silico screening allowed the discovery of novel biosynthetic gene clusters in the genomes of ruminal bacteria and revealed several strains with the genetic potential to synthesize lasso peptides, suggesting that the ruminal microbiota represents a potential source of these promising peptides.

Highlights

Natural products have improved human quality of life and play a noteworthy role in drug discovery and development (Newman and Cragg, 2016)
We performed data mining in 425 bacterial genomes representing the major species of bacteria from the rumen microbiome in an attempt to identify biosynthetic gene clusters (BGCs) potentially associated with the production of lasso peptides
Computational tools were applied to search for sequences in the rumen bacterial genomes with similarities to genes that are known to be associated with the biosynthesis of lasso peptides

Summary

Introduction

Natural products have improved human quality of life and play a noteworthy role in drug discovery and development (Newman and Cragg, 2016). Traditional culture-based strategies for the screening of new molecules have been responsible for the discovery of many relevant enzymes and metabolites (Steele and Stowers, 1991; Winter et al, 2011) These approaches are largely driven by chance, making costly, time-consuming, and often limited regarding the number of strains that can be used in large-scale screening endeavors (Tietz et al, 2017). The advent of microbial genomics and the increasing availability of computational tools to perform genome mining has evidenced the underexplored potential of some microbial species as alternative sources of new therapeutic agents (Winter et al, 2011) These tools and resources emerged as an alternative approach to identify novel biosynthetic gene clusters (BGCs) encoding putative bioactive metabolites and to assess the genetic potential of producer strains (Weber and Kim, 2016). Besides the discovery of new products, genome mining contributes to understanding the connection between metabolites and the gene sequences that encode them, providing ecological insights about the role of individual microbial populations in the microbiome (Bachmann et al, 2014)

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