Atkinson, G. | bioRxiv Science

bioRxiv2026

Nucleoid-associated proteins sense phage-induced genome damage to elicit abortive infection

Bacteria have evolved diverse immune strategies to detect and neutralize bacteriophage infection. Here, we describe an unprecedented paradigm in which a chromosome-architecting nucleoid-associated protein (NAP) is repurposed as a viral infection sensor. When phage attack leads to genome degradation, the NAP sensor is released from the nucleoid to the cytoplasm, where it binds and activates diverse immune effectors. One such effector is a nucleotide-modifying toxin normally existing as an inactive homotetramer. NAP binding converts it into a catalytically active heterotrimer that halts both transcription and translation. Phylogenetic analyses unveiled the high modularity, polyphyletic origin, and wide distribution of NAP-mediated defenses. Collectively, we define a distinct class of defense systems in which bacteria sense phage-induced genome damage through NAP relocation, highlighting an unexpected but essential role for these proteins as sentinels of genome integrity.

microbiology↗

bioRxiv2024

Host-derived Interleukin 1α induces an immunosuppressive tumor microenvironment via regulating monocyte-to-macrophage differentiation

Tumor-associated macrophages exhibit high heterogeneity and contribute to the establishment of an immunosuppressive tumor microenvironment (TME). Although numerous studies have demonstrated that extracellular factors promote macrophage proliferation and polarization, the regulatory mechanisms governing the differentiation process to generate phenotypically, and functionally diverse macrophage subpopulations remain largely unexplored. In this study, we examined the influence of interleukin 1 (IL-1) on the development of an immunosuppressive TME using orthotopic transplantation murine models of breast cancer. Deletion of host Il1 led to the rejection of inoculated congenic tumors. Single-cell sequencing analysis revealed that CX3CR1+ macrophage cells were the primary sources of IL-1 in the TME. The absence of IL-1 reprogrammed the monocyte-to-macrophage differentiation process within the TME, characterized by a notable decrease in the subset of CX3CR+ ductal-like macrophages and an increase in iNOS-expressing inflammatory cells. Comparative analysis of gene signatures in both human and mouse macrophage subsets suggested that IL-1 deficiency shifted the macrophage polarization from M2 to M1 phenotypes, leading to enhanced cytotoxic T lymphocyte activity in the TME. Importantly, elevated levels of IL-1 in human cancers were associated with worse prognosis following immunotherapy. These findings underscore the pivotal role of IL-1 in shaping an immune-suppressive TME through the regulation of macrophage differentiation and activity, highlighting IL-1 as a potential target for breast cancer treatment. TeaserInterleukin 1 dictates macrophage behavior, influencing an immunosuppressive microenvironment in breast cancer, suggesting it as a treatment target.

cancer biology↗

bioRxiv2017

ABCF ATPases involved in protein synthesis, ribosome assembly and antibiotic resistance: structural and functional diversification across the tree of life

Within the larger ABC superfamily of ATPases, ABCF family members eEF3 in Saccharomyces cerevisiae and EttA in Escherichia coli have been found to function as ribosomal translation factors. Several other ABCFs including biochemically characterised VgaA, LsaA and MsrE confer resistance to antibiotics that target the peptidyl transferase centre and exit tunnel of the ribosome. However, the diversity of ABCF subfamilies, the relationships among subfamilies and the evolution of antibiotic resistance factors from other ABCFs have not been explored. To address this, we analysed the presence of ABCFs and their domain architectures in 4505 genomes across the tree of life. We find 45 distinct subfamilies of ABCFs that are widespread across bacterial and eukaryotic phyla, suggesting they were present in the last common ancestor of both. Surprisingly, currently known antibiotic resistance (ARE) ABCFs are not confined to a distinct lineage of the ABCF family tree. This suggests that either antibiotic resistance is a pervasive feature of bacterial ABCFs, or it is relatively easy to evolve antibiotic resistance from other ABCF functions. Our data suggest there are a number of previously unidentified ARE ABCFs in antibiotic producers and important human pathogens. We also find that ATPase-deficient mutants of all four E. coli ABCFs (EttA, YbiT, YheS and Uup) inhibit protein synthesis, indicative of their ribosomal function, and demonstrate a genetic interaction of ABCFs Uup and YheS with translational GTPase BipA involved in assembly of the 50S ribosome subunit. Finally, we show that Bacillus subtilis VmlR is a ribosome-binding resistance factor localised to the cytoplasm.\n\nAuthor summaryIsolated members of the ABCF protein family of ATP-hydrolysing enzymes have been found to have important roles in protein synthesis and antibiotic resistance. However, their full diversity across the tree of life, and their evolutionary histories have never been examined. Therefore, we analysed the presence of ABCFs and their constituent domains in genomes across the tree of life, discovering 45 distinct subfamilies of ABCFs that are widespread across bacterial and eukaryotic phyla. This includes several subfamilies that we predict comprise novel antibiotic resistance (ARE) ABCFs, present in antibiotic producers and important human pathogens. There are significant gaps in our knowledge about the functional capabilities of different ABCF families. To address this, we have made ATPase domain mutants of all four Escherichia coli ABCFs, showing that they inhibit protein synthesis and indicating a role on the ribosome. Furthermore, we demonstrate a genetic interaction of two E. coli ABCFs with the GTPase BipA, involved in ribosome assembly. Finally, we show that Bacillus subtilis VmlR in the ARE2 subfamily is a ribosome-binding resistance factor localised to the cytoplasm. As more is discovered about the function of individual ABCFs, the more it will be possible to predict functions of uncharacterised members, using the ABCF family tree as a framework.

molecular biology↗