Biology subjects

Zirah, S.

Publications and source records attributed to Zirah, S..

7 recordsLinked to original sources

bioRxiv2025

Tiarins, a diverse family of natural Trojan-horse aminoacyl-tRNA synthetase inhibitors discovered by genome mining

Trifolitoxin (TFX) is a ribosomally synthesized and post-translationally modified peptide antibiotic produced by Rhizobium anhuiense T24. Although discovered more than half a century ago, its mechanism of action has remained elusive. Here we demonstrate that TFX inhibits arginyl-tRNA synthetase (ArgRS), an essential translation enzyme. TFX acts as a Trojan-horse antibiotic: it enters cells via the inner membrane oligopeptide transporter YejABEF and then undergoes partial proteolysis by the aminopeptidase PepN to release a "warhead" that binds ArgRS and arrests translation. A systematic analysis of prokaryotic genomes revealed that TFX belongs to a widespread family of modified peptides that we designate the tiarins. In addition to ArgRS inhibitors, the tiarin family includes compounds that specifically target at least seven other aminoacyl-tRNA synthetases. These findings define a previously unrecognized family of natural antibiotics and provide a framework for developing a new class of inhibitors targeting various tRNA synthetases.

molecular biology↗

bioRxiv2025

Multinuclear non-heme iron dependent oxidative enzymes: Landscape of their substrates, partner proteins and biosynthetic gene clusters

Proteins of the multinuclear non-heme iron-dependent oxidative (MNIO) enzyme superfamily catalyze various modification reactions on the precursors of ribosomally synthesized, post-translationally modified peptides (RiPPs). We recently identified two large families of MNIO-modified RiPPs called bufferins, which enhance bacterial growth under copper stress by chelating the excess metal ions. Here, we explored the diversity of potential MNIO substrates by performing extensive in silico studies. Analyses of MNIO-coding biosynthetic gene clusters (BGCs) identified various groups of putative precursors most of which are characterized by specific Cys-containing motifs, throughout the eubacterial phylogenetic tree. The precursors of most MNIO-modified RiPPs harbor N-terminal Sec-dependent signal peptides, a rare feature among bacterial RiPPs. Some precursors are very long relative to those of typical RiPPs, indicating that MNIO enzymes could modify both peptide and protein substrates. We also identified a distinct family of integral membrane proteins with large predicted extra-cytoplasmic domains mostly found in Actinomycetota, frequently but not systematically associated with MNIOs. Most MNIO BGCs harbor genes coding for DUF2063 domain-containing proteins or structurally related proteins, serving as partners of the enzymes for precursor modification. We uncovered a correlation between the presence or the absence of Sec signal peptides in the precursors and the types of partner proteins of the MNIO enzymes. This study depicts the global landscape of potential MNIO-dependent natural products by unveiling groups of peptides and proteins genetically associated with MNIOs. It reveals a treasure trove of potential new RiPP precursors which likely represent a widespread bacterial strategy to deal with copper stress, and most likely other stresses, in natural environments. Impact statementThe multinuclear non-heme iron-dependent oxidative (MNIO) enzymes belong to an emerging superfamily of modification enzymes that catalyze various oxidation reactions on ribosomally synthesized post-translationally modified peptides (RiPP) precursors. The largest families of MNIO-modified RiPPs, called bufferins, are involved in copper homeostasis. In this work we performed extensive in silico analyses to explore the diversity of RiPP precursors genetically associated with MNIO enzymes and identified major families. Some precursors are much larger than typical RiPP precursors, indicating that MNIO enzymes may also modify proteins. We defined subtypes of MNIO enzymes partner proteins dedicated to specific families of precursors. Our analyses of the biosynthetic gene clusters unveiled functions beyond copper homeostasis, likely for the response to other metal stresses. The global landscape of MNIO-modified RiPP precursors will be a basis for investigations into new RiPP families and will undoubtedly lead to the discovery of new modifications and new functions.

bioinformatics↗

bioRxiv2024

A family of lanthipeptides with anti-phage function

Bacteria synthesize natural products to adapt to their environment, where phage-bacteria interactions play a crucial role in bacterial ecology. Although a few natural products have been shown to protect bacteria from phage infection, the prevalence and diversity of chemical anti-phage defense remain largely unexplored. Here, we uncover a novel family of over 2000 lanthipeptide biosynthetic gene clusters from Actinobacteria that participate in anti-phage defense, which we named lanthiphages. Lanthiphages colocalize with other anti-phage systems in defense islands. We demonstrate that native lanthiphage expression protects the model strain Streptomyces coelicolor against diverse phages. Heterologous expression of four additional lanthiphage pathways shows that the anti-phage function is conserved across this family of biosynthetic gene clusters. Finally, we demonstrate that lanthiphage expression leads to the production of a novel compound and alters phage transcription. Our findings highlight that biosynthetic gene clusters with anti-phage functions can be successfully identified through genomic analysis. This work paves the way for the systematic mining of anti-phage natural products, which could constitute a novel reservoir of antiviral drugs.

microbiology↗

bioRxiv2024

A widespread family of ribosomal peptide metallophores involved in bacterial adaptation to copper stress

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse group of natural products that bacteria employ in their survival strategies. Herein, we characterized the structure, the biosynthetic pathway and the mode of action of a new RiPP family called bufferins. With thousands of homologous biosynthetic gene clusters throughout the eubacterial phylogenetic tree, bufferins form by far the largest family of RiPPs modified by multinuclear non-heme iron-dependent oxidases (MNIO, DUF692 family). Using Caulobacter vibrioides bufferins as a model, we showed that the conserved Cys residues of their precursors are transformed into 5-thiooxazoles, further expanding the reaction range of MNIO enzymes. This rare modification is installed in conjunction with a partner protein of the DUF2063 family. Bufferin precursors are the first examples of bacterial RiPPs found to feature an N-terminal Sec signal peptide and thus to be exported by the ubiquitous Sec pathway, a new paradigm in the RiPP field. Other original features of bufferins are their large size and protein-like fold, which blurs the line between modified peptides and proteins. We reveal that bufferins are involved in copper homeostasis, and their metal-binding propensity requires the thiooxazole heterocycles. Bufferins enhance bacterial growth under copper stress by sequestering excess metal ions in the periplasm. Our study thus describes a large family of RiPP metallophores and unveils a widespread but overlooked metal homeostasis mechanism in eubacteria likely to be relevant to One-Health strategies. Significance statementCopper is both essential and toxic in excess. Bacteria face copper in their environments, notably in phagocytes, hence they have developed several defense mechanisms. We discovered a widespread strategy of protection from copper, through the biosynthesis of natural products that we call bufferins. Bufferins are ribosomally synthesized post-translationally modified peptides (RiPPs), natural products with key roles in bacterial physiology and ecology. Bufferins enhance bacterial growth under copper stress by complexing with the metal using thiooxazole heterocycles that result from enzymatic modification of cysteine residues. With thousands of homologs throughout the eubacterial phylogenetic tree, bufferins represent a highly prevalent strategy of adaptation to metal stress. They are larger in size than most RiPPs, expanding the concept of RiPPs to modified proteins.

microbiology↗

bioRxiv2022

Molecular Acclimation of Halobacterium salinarum to Halite Brine Inclusions

1Halophilic microorganisms have long been known to survive within the brine inclusions of salt crystals, as evidenced by the change in color for salt crystals containing pigmented halophiles. However, the molecular mechanisms allowing this survival has remained an open question for decades. While protocols for the surface sterilization of halite (NaCl) have enabled isolation of cells and DNA from within halite brine inclusions, "-omics" based approaches have faced two main technical challenges: (1) removal of all contaminating organic biomolecules (including proteins) from halite surfaces, and (2) performing selective biomolecule extractions directly from cells contained within halite brine inclusions with sufficient speed to avoid modifications in gene expression during extraction. In this study, we present methods to resolve these two technical challenges. In addition, we apply these methods to perform the first examination of the early acclimation of a model haloarchaeon (Halobacterium salinarum NRC-1) to halite brine inclusions. Examinations of the proteome of Halobacterium cells two months post-evaporation revealed a high degree of similarity with stationary phase liquid cultures, but with a sharp down-regulation of ribosomal proteins. Low quantities of RNA from halite brine inclusions corroborate the hypothesis of low transcriptional and translational activities. While proteins for central metabolism were part of the shared proteome between liquid cultures and halite brine inclusions, proteins involved in cell mobility (archaellum, gas vesicles) were either absent or less abundant in halite samples. Proteins unique to cells within brine inclusions included transporters, suggesting modified interactions between cells and the surrounding brine inclusion microenvironment. The methods and hypotheses presented here enable future studies of the survival of halophiles in both culture model and natural halite systems.

microbiology↗

bioRxiv2018

Novel Mechanism for Surface Layer Shedding and Regenerating in Bacteria Exposed to Metal-Contaminated Conditions

Surface layers (S-layers) are self-assembling, ordered structures composed of repeating protein subunits found as components of the cell walls throughout the Bacteria and the Archaea. S-layers act as an interface between prokaryotic cells and their surrounding environment, and provide protection for microorganisms against diverse environmental stresses including heavy metal stress. We have previously characterized the process by which S-layers serve as a nucleation site for metal mineralization in the presence of high concentration of metals. Here, we test the hypothesis originally proposed in cyanobacteria that a \"shedding\" mechanism exists in prokaryotes for replacing S-layers that have become mineral-encrusted. We used a metallotolerant gram-positive bacterium bearing an S-layer, Lysinibacillus sp. TchIII 20n38, as a model organism. We characterize for the first time a mechanism for resistance to metals through S-layer shedding and regeneration. S-layers nucleate the formation of Fe-mineral on the cell surface, leading to the encrustation of the S-layer. Using a combination of scanning electron microscopy (SEM) and nanoSIMS, we show that mineral-encrusted S-layers are shed by the bacterial cells, and the emerging cells regenerate new S-layers as part of their cell wall structure. This novel mechanism for the survival of prokaryotes in metal-contaminated environments may also provide elements necessary for the development of renewable systems for metal bioremediation.

microbiology↗

bioRxiv2018

Global metabolomic characterizations of Microcystis spp. highlights clonal diversity in natural bloom-forming populations and expands metabolite structural diversity

Cyanobacteria are photosynthetic prokaryotes that are able to synthetize a wild rang of secondary metabolites exhibiting noticeable bioactivity, comprising toxicity. Microcystis represents one of the most common cyanobacteria taxa constituting the intensive blooms that arise nowadays in freshwater ecosystems worldwide. They produce numerous cyanotoxins (toxic metabolites), which are potentially harmful to Human health and aquatic organisms. In order to better understand the variations in cyanotoxins production between clones of the Microcystis, we investigate the diversity of several strains isolated from the same blooms, from different populations in various geographical area.\n\nTwenty-four clonal strains were compared by genotyping with 16S-ITS fragment sequencing and metabolites chemotyping using LC ESI-qTOF mass spectrometry. While, genotyping can only discriminate between the different species, the global metabolomes reveal clear discriminant molecular profiles between strains. These profiles can be clustered primarily according to their global metabolite content, then to their genotype, and finally to their sampling localities. A global molecular network of all metabolites highlights the production of a wide set of chemically diverse metabolites, comprising only few microcystins, but many aeruginosins, cyanopeptolins and microginins, along with a large set of unknown molecules. They represent the molecular biodiversity that still remain to be investigated and characterized at their structure as well as at their potential bioactivity or toxicity levels.

microbiology↗