Project description:PacBio HiFi sequencing was used to characterize genome-wide DNA base modifications and methylation motifs in Alicyclobacillus acidocaldarius subsp. acidocaldarius strain KCTC 1825 (DSM 446). Base-modification kinetics were mapped to the complete genome assembly and analyzed for m6A and m4C signals. The processed dataset provides per-base modification calls, motif-associated calls, and motif summaries linked to the public genome assembly and SRA run.
Project description:Quorum sensing (QS) is a cell-to-cell communication mechanism that enables bacteria to coordinate collective behaviors in response to population density. The BraI/R QS system is conserved among Burkholderia and Paraburkholderia species, and its regulatory role is still unknown. In this study, the BraI/R QS of P. kururiensis was investigated for biological control of another bacterial species. The results demonstrate that the functional BraI/R system influences interbacterial competition, as braI and braR mutant strains failed to inhibit the growth of Escherichia coli, in contrast to the wild-type strain. These findings suggest that the BraI/R QS system plays a regulatory role in modulating interspecies antagonism. Comparative exoproteome analyses were performed for the wild-type and the BraI/R QS-mutant P. kururiensis strains, revealing distinct protein populations, including structural and effector proteins of the Type VI secretion system (T6SS). Genomic mapping revealed that two of those T6SS-proteins were encoded within a specific T6SS gene cluster (T6SS-3), while others originate outside any major T6SS gene cluster. The identification of exoproteome targets regulated by the BraI/R QS system represents a significant advance toward the understanding of the molecular mechanisms underpinning P. kururiensis interactions with competing bacteria, further supporting its potential as a biological control agent against phytopathogenic and/or free-living species.
Project description:Clavibacter michiganensis subsp. michiganensis is an important Gram-positive phytopathogenic bacteria that causes bacterial wilt and canker in tomato. The genome of the type strain, NCPPB382, has been sequenced and annotated, however comparative genomics suggests that certain regions are under- or misannotated. In order to improve the genome annotation, we have undertaken a proteogenomic study of this important pathogen. Samples were grown in culture and the proteome of the pellet and supernatant were analyzed separately using shotgun HPLC-MS/MS. These proteomics datasets were analyzed and a number of missing gene were found and a number of existing gene calls were modified.
Project description:This study investigated the transcriptomic response of Paraburkholderia busanensis P39 during exposure to fungal biomass of Colletotrichum scovillei KC05. RNA-seq was used to compare P39 grown alone with P39 exposed to fungal biomass, with three biological replicates per condition. The study aimed to identify transcriptional changes associated with fungal-biomass adaptation, nutrient scavenging, cell-envelope remodeling, regulatory responses, and interface-associated functions. Reads were aligned to the Paraburkholderia busanensis P39 genome represented by GenBank accessions CP058248 and CP058249.
Project description:Streptococcus gallolyticus subsp. gallolyticus is a commensal of the human gastrointestinal tract and a pathogen of infective endocarditis and other biofilm-associated infections with exposed collagen. Therefore, this study focuses on the characterization of the biofilm formation and collagen adhesion of S. gallolyticus subsp. gallolyticus under different conditions. It has been observed that lysozyme triggers biofilm formation divergently in the analyzed S. gallolyticus subsp. gallolyticus strains. The transcriptome analysis was performed for two strains which form more biofilm in the presence of lysozyme. Lysozyme leads to higher expression of genes of transcription and translation, of the dlt operon (cell wall modification), of hydrogen peroxide resistance proteins and of two immunity proteins which could be involved in biofilm formation. Furthermore, the adhesion ability of 73 different S. gallolyticus subsp. gallolyticus strains to collagen type I and IV was analyzed. High adhesion ability was observed for the strain UCN 34, whereas the strain DSM 16831 adhered only marginally to collagen. The full genome microarray analysis revealed strain-dependent gene expression due to adhesion. The expression of genes of a transposon and a phage region in strain DSM 16831 were increased, which corresponds to lateral gene transfer. Adherence to collagen leads to a change in the expression of genes of nutrients uptake in the strain UCN 34.