1461 research outputs found
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Streptococcus anginosus orchestrates antibacterial potential of NETs facilitating survival of accompanying pathogens
Full text linkStreptococcus anginosus is considered an emerging opportunistic pathogen causing life-threatening infections, including abscesses and empyema. Noticeably, clinical data revealed that S. anginosus also constitutes an important component of polymicrobial infections. Here, we showed for the first time that S. anginosus inactivates the antibacterial potential of neutrophil extracellular traps (NETs). The process is determined by a cell wall-anchored nuclease referred to as SanA, which high expression dominates in clinical strains isolated from severe infections. Nuclease activity protects S. anginosus against the antibacterial activity of NETs, supporting at the same time the survival of coexisting highly pathogenic species of Enterobacteriales. Obtained data suggest that SanA nuclease should be recognized as a critical S. anginosus virulence factor determining severe monospecies purulent infections but also shielding other pathogens promoting the development of polymicrobial infections
Transcription Kinetics in the Coronavirus Life Cycle
Full text linkCoronaviruses utilize a positive-sense single-strand RNA, functioning simultaneously as mRNA and the genome. An RNA-dependent RNA polymerase (RdRP) plays a dual role in transcribing genes and replicating the genome, making RdRP a critical target in therapies against coronaviruses. This review explores recent advancements in understanding the coronavirus transcription machinery, discusses it within virus infection context, and incorporates kinetic considerations on RdRP activity. We also address steric limitations in coronavirus replication, particularly during early infection phases, and outline hypothesis regarding translation–transcription conflicts, postulating the existence of mechanisms that resolve these issues. In cells infected by coronaviruses, abundant structural proteins are synthesized from subgenomic RNA fragments (sgRNAs) produced via discontinuous transcription. During elongation, RdRP can skip large sections of the viral genome, resulting in the creation of shorter sgRNAs that reflects the stoichiometry of viral structural proteins. Although the precise mechanism of discontinuous transcription remains unknown, we discuss recent hypotheses involving long-distance RNA–RNA interactions, helicase-mediated RdRP backtracking, dissociation and reassociation of RdRP, and RdRP dimerization
Non-dikarya fungi share the TORC1 pathway with animals, not with Saccharomyces cerevisiae
Full text linkTarget of rapamycin (TOR), discovered in Saccharomyces cerevisiae, is a highly conserved serine/threonine kinase acting as a regulatory hub between the cell and its environment. Like mammals, in fungi, the TOR complex 1 (TORC1) pathway is essential for coordinating cell growth in response to nutrient availability. The activation of TORC1 is similar in yeast and mammals, while its inhibition is more complex in mammals. This divergence of TORC1 regulation opens the question of how common are the yeast and mammalian variants in the fungal kingdom. In this work, we trace the evolutionary history of TORC1 components throughout the fungal kingdom. Our findings show that these fungi contain the mammalian-specific KICSTOR complex for TORC1 inhibition. They also possess orthologs of serine, arginine and methionine sensors of TORC1 pathway that orchestrate the response to nutrient starvation in mammals. The Rheb-TSC mediated activation of mammalian TORC1 that was lost in Saccharomycotina was also conserved in non-Dikarya. These findings indicate that the TORC1 pathway in non-Dikarya fungi resembles mammalian TORC1. Saccharomycotina lost many of the inhibitory components and evolved alternate regulatory mechanisms. Furthermore, our work highlights the limitations of using S. cerevisiae as a fungal model while putting forward other fungi as possible research models
Effects of CDC45 mutations on DNA replication and genome stability
Full text linkCdc45 is a non-catalytic subunit of the CMG helicase complex that is recruited to the autonomously replicating
sequence at the onset of DNA replication. The Cdc45 protein is required for the initiation of DNA replication as
well as for nascent DNA strand synthesis. It interacts with Mcm2 and Psf1 elements of CMG helicase, as well as
with Sld3, an initiation factor, and Pol2, the catalytic subunit of DNA polymerase epsilon (Pol ε). In this study, we
analyzed the effects of amino acid substitutions in the Cdc45 region involved in the interaction of this protein
with Mcm2–7 (Cdc45-1), Psf1 (Cdc45-26), and Sld3 (Cdc45-25, Cdc45-35). We found that mutations in CDC45
resulted in defective DNA replication. Under permissive conditions, delayed DNA synthesis was observed. At
restrictive temperatures, the mutant cells were unable to efficiently replicate DNA. However, after the initiation
of DNA replication under permissive conditions, the four analyzed CDC45 mutants exhibited DNA synthesis
under the restrictive conditions. Moreover, we observed increased mutation rates, mainly dependent on DNA
polymerase zeta (Pol ζ), as well as increased incidence of replication errors. These findings confirm the essential
function of Cdc45 in DNA replication initiation and demonstrate that impaired Cdc45 subunit has an impact on
the fidelity of the nascent DNA strand synthesis. The changes in cell function observed in this study, related to
defects in Cdc45 function, may help understand some diseases associated with CDC45
Co-Fermentation and Genomic Insights into Lactic Acid Bacteria for Enhanced Propionic Acid Production Using a Non-GMO Approach
Full text linkPropionic acid (PA) is an important organic acid with applications in food preservation, feed additives, and bio-based chemical production. While industrial PA is mostly derived from petrochemical processes, sustainable microbial alternatives are gaining attention. In this study, we explored a co-fermentation strategy using lactic acid bacteria (LAB) with complementary metabolic capabilities to enhance PA biosynthesis via the 1,2-propanediol (PDO) pathway. Genome-based screening identified a metabolic division between strains capable of producing PDO (e.g., Carnobacterium maltaromaticum IBB3447) and those converting PDO to PA (e.g., Levilactobacillus brevis IBB3735). Notably, we discovered that C. maltaromaticum IBB3447 is capable of PDO 24 biosynthesis, a function previously undescribed in this species. Phenotypic assays confirmed glycerol metabolism and acid tolerance among strains. In co-culture fermentation trials, the highest PA concentration (6.87 mM) was achieved using simultaneous fermentation in a fructose–sorbitol–glucose (FRC-SOR-GLC) medium, accompanied by prior PDO accumulation (up to 13.13 mM). No single strain produced PA independently, confirming that metabolic cooperation is required. These findings reveal a novel LAB-based bioprocess for sustainable PA and PDO production, using cross-feeding interactions and the valorization of industrial waste streams. The study supports future optimization and scale-up for circular bioeconomy applications
The BRAHMA-associated SWI/SNF chromatin remodeling complex controls Arabidopsis seed quality and physiology
Full text linkThe SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complex is involved in various aspects of plant development and stress responses. Here, we investigated the role of BRM (BRAHMA), a core catalytic subunit of the SWI/SNF complex, in Arabidopsis thaliana seed biology. brm-3 seeds exhibited enlarged size, reduced yield, increased longevity, and enhanced secondary dormancy, but did not show changes in primary dormancy or salt tolerance. Some of these phenotypes depended on the expression of DOG1, a key regulator of seed dormancy, as they were restored in the brm-3 dog1-4 double mutant. Transcriptomic and metabolomic analyses revealed that BRM and DOG1 synergistically modulate the expression of numerous genes. Some of the changes observed in the brm-3 mutant, including increased glutathione levels, depended on a functional DOG1. We demonstrated that the BRM-containing chromatin remodeling complex directly controls secondary dormancy through DOG1 by binding and remodeling its 3′ region, where the promoter of the long noncoding RNA asDOG1 is located. Our results suggest that BRM and DOG1 cooperate to control seed physiological properties and that BRM regulates DOG1 expression through asDOG1. This study reveals chromatin remodeling at the DOG1 locus as a molecular mechanism controlling the interplay between seed viability and dormancy
Structural and functional insights into Gp21 as a new SF4 helicase of prolate-headed Lactococcus lactis phage 94p4
Full text linkThe Gp21 protein is encoded in the early gene region of the lytic, prolate-headed (Ceduovirus type) Lactococcus lactis bacteriophage 94p4 genome. By in silico modelling we found that the protein shares significant structural and motif-specific homology with superfamily 4 (SF4) replicative helicases, such as Escherichia coli DnaB, phage T4 Gp41, and phage T7 Gp4. Our study demonstrates that Gp21 possesses robust DNA unwinding activity, efficiently separating strands of DNA heteroduplexes in a 5′ to 3′ direction. Biochemical characterization revealed that Gp21 forms hexamers and requires ATP and Mg2+ as cofactors for optimal activity. Site-directed mutagenesis of conserved residues within Gp21 impaired both its unwinding activity and hexamer formation, further supporting its classification as an SF4 helicase. The functional and structural similarity of Gp21 to SF4 replicative DNA helicases strongly suggests its role in DNA replication. This discovery identifies Gp21 as the first functionally confirmed SF4 helicase in Ceduovirus phages, offering new insights into the replication of this phage family
Integrated proteome and lipidome analyses place OCIAD1 at mitochondria-peroxisome intersection balancing lipid metabolism
Full text linkOCIAD1 (Ovarian Cancer Immunoreactive Antigen Domain Containing 1) is a membrane protein largely localized to mitochondria, however, its function in health or disease is not well understood. To comprehensively characterize the molecular changes upon lack of OCIAD1, we used mass spectrometry to study the mitochondrial and cellular proteome and lipidome. We find extensive lipidome rearrangement in OCIAD1 KO cells, characterized by two main phenotypes of decreased ether phospholipids and decreased phospholipids with an odd number of carbons. The lipidomic changes suggest alterations in peroxisomal lipid metabolism. At the same time, proteins responsible for mitochondrial fatty acid β oxidation are significantly increased. Together with a global loss in peroxisomal proteins, aberrant peroxisomal morphology, and a meta-analysis of proximity labeling data, this gives a function to the previously observed partial localization of OCIAD1 to peroxisomes. We suggest a role for OCIAD1 in balancing mitochondrial and peroxisomal lipid metabolism, and a direct impact on the key enzymes FAR1 and ABCD3
LILRB1-directed CAR-T cells for the treatment of hematological malignancies
Full text linkCD19 CAR-T cells have established a new standard for relapsed/refractory B-cell malignancies. However, the treatment fails in 50% of patients, often due to CD19 antigen loss. Alternative immunotherapies targeting other antigens are being tested but show limited efficacy, especially in cases of lineage switching or loss of B-cell phenotype, highlighting the need for novel targets. Herein, we identified leukocyte-immunoglobulin-like-receptor-B1 (LILRB1, CD85j) as a novel target for CAR-T cells through cell surface proteomics on patient-derived samples of high-risk B-cell acute lymphoblastic leukemia (B-ALL). LILRB1, an immune inhibitory receptor, is normally expressed only on monocytes and B-cells. We observed stable LILRB1 expression in B-ALL and B-cell non-Hodgkin lymphoma (B-NHL), even after CD20/CD19-based immunotherapies. LILRB1 CAR-T cells showed antigen-specific antitumor activity in vitro against B-ALL/B-NHL cells, including those resistant to CD19 CAR-T-cells, and in vivo in B-ALL xenografts. Additionally, we identified LILRB1 in monocytic acute myeloid leukemia (AML) and demonstrated LILRB1 CAR-T cell cytotoxicity against AML cell lines in vitro and in vivo. These findings establish LILRB1 as a novel target for cancer immunotherapy and show evidence for the preclinical efficacy of LILRB1 CAR-T cells against haematological malignancies, including cases resistant to previous lines of immunotherapy, thus holding promise for further clinical development
Symmetric adenine methylation is an essential DNA modification in the early-diverging fungus Rhizopus microsporus
Full text linkThe discovery of N6-methyladenine (6mA) in eukaryotic genomes, typically found in prokaryotic DNA, has revolutionized epigenetics. Here, we show that symmetric 6mA is essential in the early diverging fungus Rhizopus microsporus, as the absence of the MT-A70 complex (MTA1c) responsible for this modification results in a lethal phenotype. 6mA is present in 70% of the genes, correlating with the presence of H3K4me3 and H2A.Z in open euchromatic regions. This modification is found predominantly in nucleosome linker regions, influencing the nucleosome positioning around the transcription start sites of highly expressed genes. Controlled downregulation of MTA1c reduces symmetric 6mA sites affecting nucleosome positioning and histone modifications, leading to altered gene expression, which is likely the cause of the severe phenotypic changes observed. Our study highlights the indispensable role of the DNA 6mA in a multicellular organism and delineates the mechanisms through which this epigenetic mark regulates gene expression in a eukaryotic genome