Variation in biosynthesis and metal-binding properties of isonitrile-containing peptides produced by Mycobacteria versus Streptomyces

Bioinformatic, structural, and biochemical analysis leads to the discovery of novel isonitrilases and decodes their substrate selectivity

Bacterial species, such as Mycobacterium tuberculosis, utilize isonitrile-containing peptides (INPs) for trace metal trafficking, e.g., copper or zinc. Despite their importance, very few INP structures have been characterized to date. Reported INPs consist of a peptide backbone and β-isonitrile amide moieties. While the peptide backbone can be annotated using an adenylation domain predictor of non-ribosomal peptide synthetase (NRPS), determining the alkyl chain of β-isonitrile amide moieties remains challenging via conventional analytical techniques. In this study, we focus on non-heme iron and 2-oxoglutarate (Fe/2OG) dependent isonitrilases that exhibit inherent selectivity toward the alkyl chain length of the substrate, thus enabling the structural elucidation of INPs. Based on two known isonitrilase structures, we identified eight residue positions that control substrate selectivity. Using a custom Python program that we developed, BioSynthNexus, over 350 Fe/2OG isonitrilase genes were identified. One of these enzymes was engineered through mutations at eight selected positions, effectively modifying its substrate preference to favor either a shorter or a longer alkyl chain. Furthermore, by examining several annotated isonitrilases at eight selected positions, substrate preferences of several isonitrilases were predicted and validated through biochemical assays. Together, these findings allow for effective identification of isonitrilases and INPs, and establish a predictive framework for determining the preferred alkyl chain of β-isonitrile amide moieties.

Chalkophore mediated respiratory oxidase flexibility controls M. tuberculosis virulence

Oxidative phosphorylation has emerged as a critical therapeutic vulnerability of M. tuberculosis (Mtb). However, it is unknown how intracellular bacterial pathogens such as Mtb maintain respiration during infection despite the chemical effectors of host immunity. Mtb synthesizes diisonitrile lipopeptides that tightly chelate copper, but the role of these chalkophores in host-pathogen interactions is also unknown. We demonstrate that M. tuberculosis chalkophores maintain the function of the heme-copper bcc:aa 3 respiratory supercomplex under copper limitation. Chalkophore deficiency impairs Mtb survival, respiration to oxygen, and ATP production under copper deprivation in culture, effects that are exacerbated by loss of the heme dependent Cytochrome BD respiratory oxidase. Our genetic analyses indicate that maintenance of respiration is the only cellular target of chalkophore mediated copper acquisition. M. tuberculosis lacking chalkophore biosynthesis is attenuated in mice, a phenotype that is also severely exacerbated by loss of the CytBD respiratory oxidase. We find that the host immune pressure that attenuates chalkophore deficient Mtb is independent of adaptive immunity and neutrophils. These data demonstrate that chalkophores counter host inflicted copper deprivation and highlight a multilayered system by which M. tuberculosis maintains respiration during infection.

Copper-chelating natural products

Bacteria and fungi produce natural products that coordinate copper for a variety of functions. Many copper-binding natural products function as copper-chelating metallophores, or chalkophores, that scavenge copper from the environment to meet cellular needs. By contrast, some compounds sequester toxic levels of environmental copper to protect the producing microorganism. These copper-binding compounds often have antimicrobial activities as well. In recent years, a number of new copper-coordinating natural products have been reported, including both ribosomally and non-ribosomally synthesized molecules. There have also been significant advances in understanding the biosynthesis of these and previously known copper chelators, leading to the discovery of new enzyme families. This review summarizes the recently discovered copper-binding natural products, their biosynthetic pathways, and their functions. By highlighting key biosynthetic enzymes, we hope to inspire the discovery of new copper-coordinating natural products that may be used as therapeutics and antimicrobial agents.

Biosynthesis of isonitrile lipopeptides

Isonitrile lipopeptides discovered from Actinobacteria have attracted wide attention due to their fascinating biosynthetic pathways and relevance to the virulence of many human pathogens including Mycobacterium tuberculosis. Specifically, the identification of the new class of isonitrile-forming enzymes that belong to non-heme iron (II) and α-ketoglutarate dependent dioxygenases has intrigued several research groups to investigate their catalytic mechanism. Here we summarize the recent studies on the biosynthesis of isonitrile lipopeptides from Streptomyces and Mycobacterium. The latest research on the core and tailoring enzymes involved in the pathway as well as the isonitrile metabolic enzymes are discussed in this review.