Metabolic Profiling of Rhizobacteria Serratia plymuthica and Bacillus subtilis Revealed Intra- and Interspecific Differences and Elicitation of Plipastatins and Short Peptides Due to Co-cultivation

Genome-driven discovery of new serrawettin W2 analogues from Serratia fonticola DSM 4576

By expressing a multimodular NRPS gene sefA from Serratia fonticola DSM 4576 in E. coli, four new serrawettin W2 analogues, namely sefopeptides A-D (1-4), were isolated and structurally characterized and their biosynthesis was proposed. A bioactivity assay showed that sefopeptide C (3) exhibits moderate cytotoxic activity against acute promyelocytic leukemia NB4 cells.

Underexplored bacteria as reservoirs of novel antimicrobial lipopeptides

Natural products derived from microorganisms play a prominent role in drug discovery as potential anti-infective agents. Over the past few decades, lipopeptides produced by particularly Bacillus, Pseudomonas, Streptomyces, Paenibacillus, and cyanobacteria species, have been extensively studied for their antimicrobial potential. Subsequently, daptomycin and polymyxin B were approved by the Food and Drug Administration as lipopeptide antibiotics. Recent studies have however, indicated that Serratia, Brevibacillus, and Burkholderia, as well as predatory bacteria such as Myxococcus, Lysobacter, and Cystobacter, hold promise as relatively underexplored sources of novel classes of lipopeptides. This review will thus highlight the structures and the newly discovered scaffolds of lipopeptide families produced by these bacterial genera, with potential antimicrobial activities. Additionally, insight into the mode of action and biosynthesis of these lipopeptides will be provided and the application of a genome mining approach, to ascertain the biosynthetic gene cluster potential of these bacterial genera (genomes available on the National Center for Biotechnology Information) for their future pharmaceutical exploitation, will be discussed.

Metabolomics and Genomics Approach for the Discovery of Serrawettin W2 Lipopeptides from Serratia marcescens NP2

A metabolomics/peptidomics and genomics approach, using UPLC-MS^E, molecular networking, and genome mining, was used to describe the serrawettin W2 lipopeptide family produced by Serratia marcescens NP2. Seven known serrawettin W2 analogues were structurally elucidated along with 17 new analogues, which varied based on the first (fatty acyl length of C₈, C₁₀, C₁₂, or C_12:1), fifth (Phe, Tyr, Trp, or Leu/Ile), and sixth (Leu, Ile, or Val) residues. Tandem MS results suggested that the previously classified serrawettin W3 may be an analogue of serrawettin W2, with a putative structure of cyclo(C₁₀H₁₈O₂-Leu-Ser-Thr-Leu/Ile-Val). Chiral phase amino acid analysis enabled the distinction between l/d-Leu and l-Ile residues within nine purified compounds. ¹H and ¹³C NMR analyses confirmed the structures of four purified new analogues. Additionally, genome mining was conducted using Serratia genome sequences available on the NCBI database to identify the swrA gene using the antiSMASH software. NRPSpredictor2 predicted the specificity score of the adenylation-domain within swrA with 100% for the first, second, and third modules (Leu-Ser-Thr), 60-70% for the fourth module (Phe/Trp/Tyr/Val), and 70% for the fifth module (Val/Leu/Ile), confirming MS^E data. Finally, antibacterial activity was observed for compounds 6 and 11 against a clinical Enterococcus faecium strain.

Metabolome and transcriptome related dataset for pheromone biosynthesis in an aggressive forest pest Ips typographus

Eurasian spruce bark beetle, Ips typographus, is an aggressive pest among spruce vegetation. I. typographus host trees colonization is mediated by aggregation pheromone, consisting of 2-methyl-3-buten-2-ol and cis-verbenol produced in the beetle gut. Other biologically active compounds such as ipsdienol and verbenone have also been detected. 2-Methyl-3-buten-2-ol and ipsdienol are produced de-novo in the mevalonate pathway and cis-verbenol is oxidized from α-pinene sequestrated from the host. The pheromone production is presumably connected with further changes in the primary and secondary metabolisms in the beetle. To evaluate such possibilities, we obtained qualitative metabolomic data from the analysis of beetle guts in different life stages. We used Ultra-high-performance liquid chromatography-electrospray ionization-high resolution tandem mass spectrometry (UHPLC-ESI-HRMS/MS). The data were dereplicated using metabolomic software (XCMS, Camera, and Bio-Conductor) and approximately 3000 features were extracted. The metabolite was identified using GNPS databases and de-novo annotation in Sirius program followed by manual curation.

Further, we obtained differential gene expression (DGE) of RNA sequencing data for mevalonate pathway genes and CytochromeP450 (CyP450) genes from the gut tissue of the beetle to delineate their role on life stage-specific pheromone biosynthesis. CyP450 gene families were classified according to subclasses and given individual expression patterns as heat maps. Three mevalonate pathway genes and five CyP450 gene relative expressions were analyzed using quantitative real-time (qRT) PCR, from the gut tissue of different life stage male/female beetles, as extended knowledge of related research article (Ramakrishnan et al., 2022). This data provides essential information on pheromone biosynthesis at the molecular level and supports further research on pheromone biosynthesis and detoxification in conifer bark beetles.

Screening of Antimicrobial Activities and Lipopeptide Production of Endophytic Bacteria Isolated from Vetiver Roots

The exploration of certain microbial resources such as beneficial endophytic microorganisms is considered a promising strategy for the discovery of new antimicrobial compounds for the pharmaceutical industries and agriculture. Thirty-one endophytic bacterial strains affiliated with Bacillus, Janthinobacterium, Yokenella, Enterobacter, Pseudomonas, Serratia, and Microbacterium were previously isolated from vetiver (Chrysopogon zizanioides (L.) Roberty) roots. These endophytes showed antifungal activity against Fusarium graminearum and could be a source of antimicrobial metabolites. In this study, in particular, using high-throughput screening, we analyzed their antagonistic activities and those of their cell-free culture supernatants against three species of Fusarium plant pathogens, a bacterial strain of Escherichia coli, and a yeast strain of Saccharomyces cerevisiae, as well as their capacity to produce lipopeptides. The results showed that the culture supernatants of four strains close to B. subtilis species exhibited antimicrobial activities against Fusarium species and E. coli. Using mass spectrometry analyses, we identified two groups of lipopeptides (surfactins and plipastatins) in their culture supernatants. Whole-genome sequencing confirmed that these bacteria possess NRPS gene clusters for surfactin and plipastatin. In vitro tests confirmed the inhibitory effect of plipastatin alone or in combination with surfactin against the three Fusarium species.