A putative lipopeptide biosynthetic gene cluster is conserved in many species of Actinobacteria, including Mycobacterium tuberculosis and M. marinum, but the specific function of the encoding proteins has been elusive. Using both in vivo heterologous reconstitution and in vitro biochemical analyses, we have revealed that the five encoding biosynthetic enzymes are capable of synthesizing a family of isonitrile lipopeptides (INLPs) through a thio-template mechanism. The biosynthesis features the generation of isonitrile from a single precursor Gly promoted by a thioesterase and a nonheme iron(II)-dependent oxidase homolog and the acylation of both amino groups of Lys by the same isonitrile acyl chain facilitated by a single condensation domain of a nonribosomal peptide synthetase. In addition, the deletion of INLP biosynthetic genes in M. marinum has decreased the intracellular metal concentration, suggesting the role of this biosynthetic gene cluster in metal transport.biosynthetic enzymes | mycobacteria | metal transport S mall-molecule secondary metabolites are produced by microbes as chemical weapons to combat competing organisms or as communication signals to control complex processes such as virulence, morphological differentiation, biofilm formation, and metal acquisition (1-3). One of the most important classes of secondary metabolites are nonribosomal peptides, which are typically biosynthesized by modular nonribosomal peptide synthetases (NRPSs) in an assembly-line manner (4). Two NRPS-encoding gene clusters (mbt and Rv0096-0101) have been identified from the genome of Mycobacterium tuberculosis, the leading causative agent of tuberculosis that currently infects one-third of the world's population. Although the cluster of mbt has been characterized to biosynthesize mycobactin siderophores that form mycobactin-Fe(III) complexes for iron sequestration (5), the role of Rv0096-0101 remains obscure despite various biological studies that have indicated the production of a virulence factor by this gene cluster (6-14). For example, using transposon-site hybridization, Rv0098 to Rv0101 were predicted to be required for M. tuberculosis survival in a mouse model of infection (10). Consistently, a transposon insertion of Rv0097 attenuated M. tuberculosis growth and survival in mice (7).An in silico homology search has revealed that gene clusters homologous to Rv0096-0101 are conserved in pathogenic mycobacteria, such as M. bovis, M. leprae, M. marinum, M. ulcerans, and M. abscessus (Fig. 1), but absent in nonpathogenic mycobacteria such as M. smegmatis, providing further indication of the virulenceassociated nature of the locus product in mycobacteria. Interestingly, in addition to the genus of Mycobacterium, related operons are found in the phylum of Actinobacteria across genera including Streptomyces, Kutzneria, Nocardia, and Rhodococcus (Fig. 1), suggesting a widespread presence of this cluster. Further bioinformatic analysis has shown that five genes (Rv0097-0101) are conserved across all identified gene cluste...
1-Alkenes are important platform chemicals that are almost exclusively produced from fossil hydrocarbons. Bioproduction of 1-alkenes can mitigate our dependence on declining petrochemical resources, thereby representing an important step in the field of green chemistry. Here, we report the discovery of a new family of membrane-bound desaturase-like enzymes that convert medium-chain fatty acids (10−16 carbons) into the corresponding 1-alkenes through oxidative decarboxylation. We further show that these desaturase-like enzymes could be efficient in transforming lauric acid to 1-undecene in E. coli compared to the existing 1-alkene biosynthetic enzymes. This work expands the enzyme inventory for the transformation of fatty acid precursors to hydrocarbons and promotes the industrial production of mediumchain 1-alkenes through microbial fermentation.
The electron-rich isonitrile is an important functionality in bioactive natural products, but its biosynthesis has been restricted to the IsnA family of isonitrile synthases. We here provide the first structural and biochemical evidence of an alternative mechanism for isonitrile formation. ScoE, a putative non-heme iron(II)-dependent enzyme from Streptomyces coeruleorubidus, was shown to catalyze the conversion of (R)-3-((carboxymethyl)amino)butanoic acid to (R)-3-isocyanobutanoic acid through an oxidative decarboxylation mechanism. This work further provides a revised scheme for the biosynthesis of a unique class of isonitrile lipopeptides, of which several members are critical for the virulence of pathogenic mycobacteria.
P. putida lysine metabolism can produce multiple commodity chemicals, conferring great biotechnological value. Despite much research, the connection of lysine catabolism to central metabolism in P. putida remained undefined. Here, we used random barcode transposon sequencing to fill the gaps of lysine metabolism in P. putida. We describe a route of 2-oxoadipate (2OA) catabolism, which utilizes DUF1338-containing protein P. putida 5260 (PP_5260) in bacteria. Despite its prevalence in many domains of life, DUF1338-containing proteins have had no known biochemical function. We demonstrate that PP_5260 is a metalloenzyme which catalyzes an unusual route of decarboxylation of 2OA to d-2-hydroxyglutarate (d-2HG). Our screen also identified a recently described novel glutarate metabolic pathway. We validate previous results and expand the understanding of glutarate hydroxylase CsiD by showing that can it use either 2OA or 2KG as a cosubstrate. Our work demonstrated that biological novelty can be rapidly identified using unbiased experimental genetics and that RB-TnSeq can be used to rapidly validate previous results.
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