Biodiversity of genes encoding anti-microbial traits within plant associated microbes

Abstract

The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters.

Current knowledge and perspectives of Paenibacillus: a review

“…These are a family of peptides each consisting of a polycationic diaminobutyryl-containing heptapeptide ring and tripeptide side chain with a fatty acid derivative at the N-terminus [104]. Members of the family include polymyxin A, B, C, D, E (also called colistin), M (also called mattacin), P, S, and T [103–106].…”

“…polymyxin E 1 and E 2 ) differ in the lipid moiety and/or the amino acid at residue 7 [103]. Amino acid diversity is thought to arise from combinatorial chemistry, due to mixing and matching of alleles of the NRPS modular domains [104]. Polymyxin gene clusters found to date each encode three multi-modular NRPSs and two ABC transporters [103, 107].…”

Root-hair endophyte stacking in finger millet creates a physicochemical barrier to trap the fungal pathogen Fusarium graminearum

“…However, the emerging literature suggests that microbes that inhabit plants without themselves causing disease, defined as endophytes, may contribute to host resistance against fungal pathogens 11,12 . Endophytes suppress diseases through the induction of host resistance genes 13 , competition 14 and/or the production of antipathogenic compounds 15,16 .…”

Leveraging ecological theory to guide natural product discovery

“…However, although metagenomic analyses continue to expand our understanding of the incredible diversity of endophytic populations in both medicinal and non-medicinal plants, the roles of microbial NPs in the plant-microbe symbiosis remain poorly understood. Endophytic microbes have been reported to produce diverse NPs including polyketides, non-ribosomal peptides, alkaloids, terpenoids, and other compounds [68]. These compounds are hypothesized to influence plant fitness via diverse mechanisms, including in Fig.…”