Biology subjects

Baltenneck, J.

Publications and source records attributed to Baltenneck, J..

6 recordsLinked to original sources

bioRxiv2026

A widespread NADase domain links bacterial immunity with human TEP1

Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune systems therefore have the potential to illuminate fundamental biological mechanisms throughout the tree of life. Here, we report that DUF4062 domains - which we rename NIR (NADase in bacterial immunity and vault ribonucleoproteins) - function in bacterial immunity against phages. We first identified NIR as an effector of Avs defense proteins, where it depletes cellular NAD+ to block viral infection. We then show that NIR domains are recurrently found as effectors in diverse defense systems. We use this association to uncover Vulcan and Vesta, two defense systems which trigger NAD+ depletion upon sensing distinct viral signals. Remarkably, NIR domains are widespread in eukaryotes where they are embedded in multiple NLR-like proteins. In particular, we identified a NIR domain with conserved NADase activity in the human TEP1 protein, a component of the telomerase complex and vault ribonucleoproteins. Together, these findings reveal an enzymatic activity shared between bacterial immunity and enigmatic eukaryotic machineries.

microbiology↗

bioRxiv2026

Widespread immune systems protect bacteria against conjugative plasmids

Conjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipients, they may also behave as genetic parasites. Bacteria would thus be expected to have evolved barriers to plasmid conjugation. However, the distribution of these barriers and their underlying mechanisms remain poorly understood. Here, we performed a large-scale analysis of 364 diverse strains of the opportunistic pathogen Acinetobacter baumannii as recipients of the broad-host-range conjugative plasmids R388 and RP4. Major variations in host susceptibilities to conjugation, with limited phylogenetic association, suggested multiple and fast-evolving plasmid-specific barriers. Functional genetic analyses revealed a role for core genes, pointing to epistasis or genetic background effects. This is illustrated by the previously unrecognized role of H-NS expression in alleviating conjugation barriers in a strain-dependent manner. Most importantly, we identified three novel immune systems protecting bacteria against conjugation by R388 and RP4. Their patchy distribution within the species, and that of their homologs across bacteria, indicate that they are part of a dynamic repertoire of immune systems against conjugation. While the Ishtar system promotes plasmid loss through putative HEPN nuclease domains, Namtar and Attar sense distinct components of the R388 type IV secretion system (T4SS) to trigger a non-proliferative, energetically depleted state, analogously to the abortive infection response of anti-phage defenses. Live imaging of conjugation showed Namtar halting cell division in Escherichia coli recipients, conferring population-level immunity against plasmid spread via horizontal and vertical transmission. The existence of immune systems specifically targeting T4SS components suggests that conjugative plasmids impose a selective disadvantage greater than previously thought. This work reveals an additional layer of bacterial immunity directed at a class of genetic elements driving dissemination of antibiotic resistance.

microbiology↗

bioRxiv2025

Comparative essentialome analysis of six Pectobacteriaceae strains using the TNSEEK pipeline identifies conserved and strain-specific fitness determinants

Transposon sequencing (Tn-seq) is a powerful technique for defining the essential genes required for bacterial survival. However, gene essentiality can vary significantly across taxonomic levels, and comparing large Tn-seq datasets from multiple strains presents considerable analytical challenges. To address this, we developed TNSEEK, a fully automated bioinformatics pipeline for the systematic and comparative analysis of transposon sequencing experiments. We applied TNSEEK to analyze six Soft Rot Pectobacteriaceae (SRP) strains, encompassing species from the Dickeya and Pectobacterium genera, grown in a rich medium. This approach identified a core essentialome of 225 genes, primarily involved in fundamental cellular maintenance, conserved across all six strains, a set comparable in size to that of the broader Enterobacteriaceae family. Only a few genus-specific essential genes were found highlighting interesting distinct metabolic capabilities between Dickeya and Pectobacterium genera. In striking contrast, we discovered a large variable essentialome comprising 181 strain-specific genes, many of which of unknown function. A portion of these strain-specific essential genes are components of defense systems and prophage genomic regions. The unexpected essentiality of these modules suggests they form a constitutively active frontline defense. Furthermore, a comparison with the E. coli essentialome demonstrates that discrepancies in gene essentiality can often be attributed to differences in growth conditions, particularly temperature, as well as variations in genetic redundancy. In conclusion, the TNSEEK pipeline is a robust tool for exploring functional genomics across multiple strains. IMPORTANCEDickeya and Pectobacterium are two genera of the Pectobacteriaceae family that contain mainly plant pathogenic bacteria. To analyze the diversity within bacteria of this family, we performed a Tn-seq analysis on six strains representing a range of ecological niches. To this aim we developed a bioinformatics pipeline, termed TNSEEK which allows the comparative analysis of results across diverse experimental conditions and multiple strains. Applied to growth in rich medium of the tested strains, it allowed the identification of an essentialome of 225 genes at the family level, few genus-specific essential genes but a large essentialome comprising 181 strain-specific genes, many of which of unknown function. Thus, TNSEEK proved its ability to analyze a large data set coming from different Tn-seq experiments and it offers an unparalleled flexibility in handling any number of strains and experiments.

genomics↗

bioRxiv2025

Beyond kin killing: Dickeya-derived phage-tail-like bacteriocin P2D1 targets phylogenetically distant Pseudomonas spp.

Tailocins, phage-tail-derived bacteriocins, are increasingly recognized as potent mediators of microbial antagonism, yet their ecological scope beyond kin-targeting remains poorly understood. Here, we investigated whether P2D1, a tailocin produced by the plant pathogen Dickeya dadantii 3937, can act against environmental bacteria phylogenetically distant from Dickeya spp. Screening 480 soil and rhizosphere isolates from three distinct plant-associated habitats in Poland, we identified nine Pseudomonas spp. strains susceptible to tailocin P2D1. Whole-genome sequencing and phenotype profiling revealed that these isolates spanned multiple clades, including taxa related to P. germanica, P. tensinigenes, and P. parakoreensis. The D. dadantii mutant lacking genes encoding tailocin sheath and tube proteins lost antagonistic activity against Pseudomonas isolates, confirming that tailocins alone mediate the observed killing. Plant tissue assays revealed that six of the P2D1-susceptible strains were non-pathogenic and could mitigate D. dadantii-induced soft rot on potato. In contrast, three isolates related to P. tensinigenes were able to cause rot on their own under permissive conditions. Together, these findings demonstrate that P2D1 tailocin extends its activity to ecologically co-occurring but taxonomically distant Pseudomonas, suggesting that conserved receptors underline cross-genus targeting. More broadly, our results add to the limited evidence for tailocin activity beyond kin killing and therefore challenge the prevailing paradigm of kin-restricted tailocin specificity. They further suggest that tailocins may influence microbial community assembly across taxonomic boundaries, while their in vivo roles remain understudied.

microbiology↗

bioRxiv2025

Ancient convergence with prokaryote defense and recent adaptations to lentiviruses in primates characterize the ancestral immune factors SAMD9s

Human SAMD9 and SAMD9L are duplicated genes that encode innate immune proteins restricting poxviruses and lentiviruses, such as HIV, and implicated in life-threatening genetic diseases and cancer. Here, we combined structural similarity searches, phylogenetics and population genomics with experimental assays of SAMD9/9L functions to resolve the evolutionary and functional dynamics of these immune proteins, spanning from prokaryotes to primates. We discovered structural analogs of SAMD9/9L in the anti-bacteriophage defense system Avs, resulting from convergent evolution. Further, the predicted nuclease active site was conserved in bacterial analogs and was essential for cell death functions, suggesting a fundamental role in defense across different life kingdoms. Despite this ancestral immunity, we identified genomic signatures of evolutionary arms-races in mammals, with remarkable gene copy number variations targeted by natural selection. We further unveiled that the absence of SAMD9 in bonobos corresponds to a recent gene loss still segregating in the population. Finally, we found that chimp and bonobo SAMD9Ls have enhanced anti-HIV-1 functions, and that bonobo-specific SAMD9L polymorphisms confer increased anti-HIV-1 activity to human SAMD9L without compromising its effect on cell translation. These SAMD9/9L adaptations likely resulted from strong viral selective pressures, including by primate lentiviruses, and could contribute to lentiviral resistance in bonobos. Altogether, this study elucidates the interplay between ancient immune convergence across kingdoms and species-specific adaptations within the Avs9 and SAMD9/9L antiviral shared immunity. Significance statementThe SAMD9 gene family encodes antiviral factors of poxviruses and lentiviruses/HIV and is implicated in genetic diseases. Here, we found strong structural similarity with proteins from the Avs anti-bacteriophage system and uncovered ancient functional convergence in immune strategies between prokaryotes and metazoans. Within mammals, and more importantly in primates, we describe a highly dynamic evolutionary history of the SAMD9 gene family that underwent adaptive episodic gene losses. Unlike humans and chimps, some bonobos lack the SAMD9 gene entirely. Bonobos and chimps also possess unique variants of SAMD9L enhancing anti-HIV-1 activity without compromising cell functions, suggesting super-restrictors. This could also participate in shaping SIVcpz evolution and contribute to the absence of lentivirus-infected bonobos. Overall, the seeming dichotomy between the ancient evolutionary convergence in different kingdoms and recent functional adaptation within primates highlights the arms-races between key immune defense systems and viruses. This study paves the way for evolutionary medicine, where evolutionary-based discoveries may have application to human health, providing a deeper understanding of how the immune system adapts to fight viral infections over billion years of evolution.

evolutionary biology↗

bioRxiv2025

Genetic Determinants of pOXA-48 Plasmid Maintenance and Propagation in Escherichia coli

Conjugative plasmids are the main drivers of antibiotic resistance dissemination contributing to the emergence and extensive spread of multidrug resistance clinical bacterial pathogens. pOXA-48 plasmids, belonging to the IncL group, have emerged as the primary vehicle for carbapenem resistance in Enterobacteriaceae. Despite the problematic prevalence of pOXA-48, most research has focused on epidemiology and genomics, leaving gaps in our understanding of the mechanisms behind its propagation. In this study, we used a transposon sequencing approach to identify genetic elements critical for plasmid stability, replication, and conjugative transfer. Our results identified a novel type I toxin-antitoxin system, new essential maintenance factors, and components of the type IV secretion system and regulatory elements crucial for conjugation. This study advances our understanding of pOXA-48 biology, providing key insights into the genetic factors underlying its successful maintenance and spread in bacterial populations.

microbiology↗