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Cyanobacteria are important participants in global biogeochemical process, but their metabolic processes and genomic functions are incompletely understood. In particular, operon structure, which can provide valuable metabolic and genomic insight, is difficult to determine experimentally, and algorithmic operon predictions probably underestimate actual operon extent. A software method is presented for enhancing current operon predictions by incorporating information from whole-genome time-series expression studies, using a Machine Learning classifier. Results are presented for the marine cyanobacterium . A total of 15 operon enhancements are proposed. The source code is publicly available.
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http://dx.doi.org/10.7717/peerj.13259 | DOI Listing |
Brief Bioinform
August 2025
Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
Spliced leader (SL) trans-splicing occurs in a wide range of eukaryotes and plays a critical role in processing mRNAs derived from operon structures. However, current research on this mechanism remains limited, partly due to the difficulty in accurately identifying genuine SL trans-splicing events. The advent of long-read RNA sequencing technologies, such as direct RNA sequencing by Oxford Nanopore Technologies, offers a more promising avenue for detecting these events with greater resolution.
View Article and Find Full Text PDFJ Biol Chem
September 2025
Research Unit in Biology of Microorganisms (URBM), Department of Biology, Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
Metals like copper (Cu), zinc, and nickel exhibit dual nature, necessitating a tight regulation of their cellular homeostasis to meet physiological demands while preventing toxicity. In bacteria, metal homeostasis involves inner membrane (IM) P-type ATPases and ABC transporters, envelope-spanning tripartite efflux pumps, and outer membrane (OM) pore-forming proteins. Four decades ago, the OM β-barrel protein PcoB was shown to provide an additional layer of Cu resistance in an Escherichia coli strain isolated from the gut of swine fed with Cu supplements.
View Article and Find Full Text PDFbioRxiv
August 2025
Microbiology, School of Biological and Chemical Sciences, University of Galway, Ireland.
Alanine transport and metabolism impact MRSA pathophysiology by dictating the availability of d-alanine for cell wall synthesis, the target of β-lactam antibiotics. Furthermore -dependent alanine transport controls MRSA β-lactam susceptibility in chemically defined medium (CDM) in a glucose-dependent manner. Here we report that was auxotrophic for l-alanine in CDM, and that this growth defect was rescued by glucose (or compensatory mutations), but only when the alanine racemase () and d-alanine aminotransferase () genes were functional.
View Article and Find Full Text PDFAntibiotics (Basel)
July 2025
Department of Microbiology, Medical School, University of Athens, 11527 Athens, Greece.
: Among , OXA-48-like-producing strains have been scarcely detected. Herein, we characterized a -harbouring strain recovered from Greece (Pm GR-1), while phylogenomics and comparative genomics analyses with previously published carriers were also assessed. : Characterization of Pm GR-1 was performed by the Vitek Compact and Mass Spectrometry systems, antimicrobial susceptibility testing, detection of beta-lactamases, multilocus-sequence typing (MLST), and whole-genome sequencing (WGS).
View Article and Find Full Text PDFNucleic Acids Res
July 2025
School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, 2033, Australia.
RNA-binding proteins (RBPs) play key roles in regulating virulence gene expression in pathogenic enterohaemorrhagic Escherichia coli (EHEC). To capture the RNA-binding proteome in EHEC, total RNA-associated protein purification (TRAPP) was employed and identified 443 RNA-associated proteins. These included 35 encoded within pathogenicity islands, with RNA-binding confirmed in vitro for four, including RhsFI.
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