Céline Henry

In deep‐sea hydrothermal vents, sulfur compounds are central for microbial bioenergetics. Despite its significant impact on the global sulfur cycle, anaerobic sulfur compound disproportionation remains the least understood metabolism, with only three bacterial strains having been investigated at the proteomic level for their sulfur disproportionation metabolism to date. Here, we present a comparative proteomics study of the chemolithoautotrophic sulfur‐cycling species Dissulfuribacter thermophilus S69ᵀ. Upon thiosulfate disproportionation conditions, proteomics revealed a high abundance of a cytoplasmic thiosulfate reductase AB homologue (PhsAB‐like) that might reductively cleave thiosulfate into sulfide and sulfite. Subsequent steps might involve enzymes from the dissimilatory sulfate reduction, with Apr and Sat potentially functioning in reverse to produce sulfate. Strain S69 ^T exhibited enhanced growth under sulfite/dihydrogen, likely due to both sulfite respiration and disproportionation. Here, a range of new enzymes were more abundant. These included an enzyme containing NrfD, the MolyAB as well as two membranous tetrathionate reductase homologues. Other membranous oxidoreductases such as QmoABC, DsrMKJOP and Complex I, may contribute to the pathway, while autotrophic growth is likely sustained by the Wood–Ljungdahl pathway. These findings highlight the distinct enzymatic features of strain S69ᵀ compared to previously proteomically characterised sulfur‐disproportionating strains, revealing novel enzymes that warrant further analysis.

The nucleoprotein N of the human respiratory syncytial virus (HRSV) encases the viral genome, forming a flexible N–RNA nucleocapsid helix that serves as template for the viral polymerase L. Recent structural analysis revealed a non-canonical helical nucleocapsid arrangement that modulates RNA accessibility, yet its impact on polymerase function remains unknown. Here, we identified symmetric dimethylation of residue R27 of N as a critical modulator of nucleocapsid architecture and viral replication. We also showed that the methylase PRMT5 interacts with N and likely catalyses R27 methylation. Molecular dynamics simulations of RNA-free N dimers indicate that R27 methylation enhances opening and closing of the RNA-binding cavity, whereas a methylation-mimicking R27M substitution favours a closed state. Cryo-electron microscopy reveals a canonical, markedly straight R27M helix with increased rise and pitch. These findings demonstrate that post-translational modifications fine-tune interactions between N protomers, shaping nucleocapsid assembly, structure and dynamics, and thereby controlling HRSV replication.

MAM (Microbial-Anti-Inflammatory Molecule) is a key effector protein with anti-inflammatory properties in Faecalibacterium duncaniae, a critical human gut microbiota species. Despite its importance, MAM function and molecular features remain poorly understood. This study elucidates MAM's physiological importance by examining its cellular localization, secretion dynamics, and structural organization. Mass spectrometry and immunogold labeling confirmed MAM as the most abundant protein in the cell envelope and the second most abundant in the overall proteome, localizing it to the bacterial surface. Bioinformatic and in silico analyses suggest that MAM contains an N-terminal leader peptide with motifs recognized by a Peptidase-domain-Containing ABC Transporter (PCAT), enabling cargo transport to the cell envelope. After N-terminal excision, the cargo protein could be transported to the cell envelope via this PCAT, where it could assemble into a hexameric structure, as revealed by docking and AlphaFold3 modeling. Such results were supported by electron microscopy showing a lattice-like organization on the bacterial surface. This work introduces a novel discussion about the singular organization of the F. duncaniae cell envelope, having MAM as a key component for the bacteria, supporting the understanding of the unique biology of F. duncaniae and its potential as a next-generation probiotic or live biotherapeutic.

Bacterial pathogens employ multiple strategies to invade and damage host tissues while evading immune defenses. Recent studies highlight flagella as crucial contributors to bacterial virulence, not only by facilitating motility, but also by regulating the secretion of virulence factors. However, the role of the flagella-dependent secretome remains largely unexplored. We have recently shown that FliK, a key regulator that defines substrate specificity in the flagellar export apparatus, is essential for the resistance of Bacillus thuringiensis (B. thuringiensis) against antimicrobial peptides (AMPs) and its virulence in a Drosophila infection model. In this study, we used liquid chromatography–tandem mass spectrometry to conduct a large-scale comparative analysis of the proteins secreted in culture supernatant or associated with the cell wall of the ΔfliK mutant and its reference strain. Our results reveal significant differences in the secretome and surfaceome of the ΔfliK mutant compared to the reference strain. These findings emphasize the role of FliK in regulating the production and secretion of several proteins, underscoring the importance of flagella in controlling various biological processes. This work provides valuable insights into the functional characterization of potential candidate proteins involved in B. thuringiensis virulence and AMP resistance mechanisms. Overall, these results open new perspectives for understanding the molecular processes that govern bacterial resistance to AMPs.

Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state‐of‐the‐art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.

Giardiasis, a widespread intestinal parasitosis affecting humans and animals, is a growing concern due to the emergence of drug-resistant strains of G. intestinalis. Probiotics offer a promising alternative for preventing and treating giardiasis. Recent studies have shown that the probiotic Lactobacillus johnsonii CNCM I-4884 inhibits G. intestinalis growth both in vitro and in vivo. This protective effect is largely mediated by bile salt hydrolase (BSH) enzymes, which convert conjugated bile acids (BAs) into free forms that are toxic to the parasite. The objective of this study was to use adaptive evolution to develop stress-resistant derivatives of L. johnsonii CNCM I-4884, with the aim of improving its anti-Giardia activity. Twelve derivatives with enhanced resistance to BAs and reduced autolysis were generated. Among them, derivative M11 exhibited the highest in vitro anti-Giardia effect with enhanced BSH activity. Genomic and proteomic analyses of M11 revealed two SNPs and the upregulation of the global stress response by SigB, which likely contributed to its increased BAs resistance and BSH overproduction. Finally, the anti-Giardia efficacy of M11 was validated in a murine model of giardiasis. In conclusion, our results demonstrate that adaptive evolution is an effective strategy to generate robust food-grade bacteria with improved health benefits.

Phospholipids are essential components of most cell membranes. In Staphylococcus aureus , PlsX acyltransferase is considered indispensable for initiating phospholipid synthesis, unless exogenous fatty acids (FAs) are available to bypass this requirement. We report that S. aureus can capture internal FA sources to overcome PlsX essentiality in a Δ plsX mutant via point mutations in either of two genes: fabF , which encodes the FA synthesis enzyme 3-oxoacyl-(acyl-carrier-protein) synthase II, or fadM , which encodes an understudied bifunctional acyl-CoA thioesterase and ACP binding protein. Despite growth rescue, both Δ plsX suppressors differ from the parental strain by producing phospholipids with shortened FA lengths suggesting that both suppressors lead to premature FA release during synthesis. Additionally, both suppressors display increased sensitivity to β-lactam antibiotics. The similar behavior of both suppressors led us to show that fabF suppressors require the presence of fadM , indicative of FabF-FadM cooperation. We propose that reduced processivity of FabF suppressor variants, or greater availability of FadM for ACP binding in FadM variants, facilitates FA release from FabF-acyl-ACP intermediates. A FabF-FadM relay leading to FA release may contribute to homeostasis between FASII and phospholipid synthesis pathways. Significance: Phospholipids are vital cell membrane components. The essential Staphylococcus aureus phospholipid synthesis enzyme PlsX uses acyl-ACP, the end-product of fatty acid (FA) synthesis (FASII), to initiate phospholipid production. Despite its central role, PlsX can be substituted by exogenous FAs whose phosphorylation yields the same product. We discovered that without FA supplementation, mutants arise that rescue growth, indicating that internal FAs are released. Mutations occurred in either FabF, a FASII enzyme, or in FadM, an incompletely characterized protein. Our analyses give evidence that FabF and FadM proteins cooperate, and facilitate FA availability when either protein is mutated. We propose that in normal conditions, FadM might act as an “overflow valve” by releasing FAs from the FabF intermediate, which prevents buildup of FASII intermediates, and ensures FA-phospholipid balance. Remarkably, while this pathway rescues S. aureus growth, it sensitizes the MRSA strain to β-lactam antibiotics.

Ribosomally synthesized and posttranslationally 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 RiPP family called bufferins. With thousands of homologous biosynthetic gene clusters throughout the bacterial phylogenetic tree, bufferins form by far the largest family of RiPPs modified by multinuclear nonheme 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 rare examples of bacterial RiPPs found to feature an N-terminal Sec signal peptide allowing them to be exported by the ubiquitous Sec pathway. 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 complexing excess metal ions. Our study thus describes a large family of RiPP metallophores and unveils a widespread but overlooked metal homeostasis mechanism in bacteria.

Dual-fraction proteomics reveals a novel class of proteins impacted by nanoparticle exposure. Background: Nanoparticles (NPs) interact with cellular proteomes, altering biological processes. Understanding these interactions requires comprehensive analyses beyond solely characterizing the NP corona. Methods: We utilized a dual-fraction mass spectrometry (MS) approach to analyze both NP-bound and unbound proteins in Saccharomyces cerevisiae sp. protein extracts exposed to silica nanoparticles (SiNPs). We identified unique protein signatures for each fraction and quantified protein abundance changes using spectral counts. Results: Strong correlations were observed between protein profiles in each fraction and non-exposed controls, while minimal correlation existed between the fractions themselves. Linear models demonstrated equal contributions from both fractions in predicting control sample abundance. Combining both fractions revealed a larger proteomic response to SiNP exposure compared to single-fraction analysis. We identified 302/56 proteins bound/unbound to SiNPs and an additional 196 “impacted” proteins demonstrably affected by SiNPs. Conclusion: This dual-fraction MS approach provides a more comprehensive understanding of nanoparticle interactions with cellular proteomes. It reveals a novel class of “impacted” proteins, potentially undergoing conformational changes or aggregation due to NP exposure. Further research is needed to elucidate their biological functions and the mechanisms underlying their impact.

Dual-fraction proteomics reveals a novel class of proteins impacted by nanoparticle exposure. Background: Nanoparticles (NPs) interact with cellular proteomes, altering biological processes. Understanding these interactions requires comprehensive analyses beyond solely characterizing the NP corona. Methods: We utilized a dual-fraction mass spectrometry (MS) approach analyzing both NP-bound and unbound proteins in Saccharomyces cerevisiae sp. protein extracts exposed to silica nanoparticles (SiNPs). We identified unique protein signatures for each fraction and quantified protein abundance changes using spectral counts. Results: Strong correlations were observed between protein profiles in each fraction and non-exposed controls, while minimal correlation existed between the fractions themselves. Linear models demonstrated equal contributions from both fractions in predicting control sample abundance. Combining both fractions revealed a larger proteomic response to SiNP exposure compared to single-fraction analysis. We identified 302/56 proteins bound/unbound to SiNPs and an additional 196 "impacted" proteins demonstrably affected by SiNPs. Conclusion: This dual-fraction MS approach provides a more comprehensive understanding of nanoparticle interactions with cellular proteomes. It reveals a novel class of "impacted" proteins, potentially undergoing conformational changes or aggregation due to NP exposure. Further research is needed to elucidate their biological functions and the mechanisms underlying their impact.