VimR is a conserved master transcription regulator controlling virulence and metabolism in Pseudomonas.

Pseudomonas syringae, a highly destructive plant bacterial pathogen causing severe disease and significant yield losses in agriculture globally, has complex regulatory systems involving many transcriptional factors (TFs). Although the LysR-type transcriptional regulator (LTTR) protein family is a well-known group of TFs involved in diverse physiological functions, the roles of LTTRs in P. syringae remain largely unknown.

Comprehensive comparison of the third-generation sequencing tools for bacterial 6mA profiling.

DNA N-methyladenine (6mA) serves as an intrinsic and principal epigenetic marker in prokaryotes, impacting various biological processes. To date, limited advanced sequencing technologies and analyzing tools are available for bacterial DNA 6mA. Here, we evaluate eight tools designed for the 6mA identification or de novo methylation detection.

Architecture of genome-wide transcriptional regulatory network reveals dynamic functions and evolutionary trajectories in .

The model Gram-negative plant pathogen utilises hundreds of transcription factors (TFs) to regulate its functional processes, including virulence and metabolic pathways that control its ability to infect host plants. Although the molecular mechanisms of regulators have been studied for decades, a comprehensive understanding of genome-wide TFs in 1448A remains limited. Here, we investigated the binding characteristics of 170 of 301 annotated TFs through chromatin immunoprecipitation sequencing (ChIP-seq).

DNA methylome regulates virulence and metabolism in .

Bacterial pathogens employ epigenetic mechanisms, including DNA methylation, to adapt to environmental changes, and these mechanisms play important roles in various biological processes. is a model phytopathogenic bacterium, but its methylome is less well known than that of other species. In this study, we conducted single-molecule real-time sequencing to profile the DNA methylation landscape in three model pathovars of .

Hfq mediates transcriptome-wide RNA structurome reprogramming under virulence-inducing conditions in a phytopathogen.

Although RNA structures play important roles in regulating gene expression, the mechanism and function of mRNA folding in plant bacterial pathogens remain elusive. Therefore, we perform dimethyl sulfate sequencing (DMS-seq) on the Pseudomonas syringae under nutrition-rich and -deficient conditions, revealing that the mRNA structure changes substantially in the minimal medium (MM) that tunes global translation efficiency (TE), thereby inducing virulence. This process is led by the increased expression of hfq, which is directly activated by transcription regulators RpoS and CysB.

Osteoclast-targeted delivery of anti-miRNA oligonucleotides by red blood cell extracellular vesicles.

Osteoporosis (OP) affects millions worldwide but currently cannot be cured. Suppressing the level of miR-214 in osteoclasts by the anti-miRNA oligonucleotide (AMO) anti-miR-214 reverses bone absorption and provides a potential treatment. Here we report a peptide-guided delivery strategy using red blood cell extracellular vesicles (RBCEVs) as the vehicle to realize osteoclast-targeted delivery of anti-miR-214.

Virulence-related regulatory network of .

Transcription factors (TFs) play important roles in regulating multiple biological processes by binding to promoter regions and regulating the global gene transcription levels. is a Gram-negative phytopathogenic bacterium harbouring 301 putative TFs in its genome, approximately 50 of which are responsible for virulence-related gene and pathway regulation. Over the past decades, RNA sequencing, chromatin immunoprecipitation sequencing, high-throughput systematic evolution of ligands by exponential enrichment, and other technologies have been applied to identify the functions of master regulators and their interactions in virulence-related pathways.

Bacterial Transcription Factors Bind to Coding Regions and Regulate Internal Cryptic Promoters.

Transcription factors (TFs) regulate transcription by binding to the specific sequences at the promoter region. However, the mechanisms and functions of TFs binding within the coding sequences (CDS) remain largely elusive in prokaryotes. To this end, we collected 409 data sets for bacterial TFs, including 104 chromatin immunoprecipitation sequencing (ChIP-seq) assays and 305 data sets from the systematic evolution of ligands by exponential enrichment (SELEX) in seven model bacteria.

Maintenance of tRNA and elongation factors supports T3SS proteins translational elongations in pathogenic bacteria during nutrient starvation.

Background: Sufficient nutrition contributes to rapid translational elongation and protein synthesis in eukaryotic cells and prokaryotic bacteria. Fast synthesis and accumulation of type III secretion system (T3SS) proteins conduce to the invasion of pathogenic bacteria into the host cells. However, the translational elongation patterns of T3SS proteins in pathogenic bacteria under T3SS-inducing conditions remain unclear.

Regulation of uric acid and glyoxylate metabolism by UgmR protein in Pseudomonas aeruginosa.

The opportunistic pathogen Pseudomonas aeruginosa has evolved several systems to adapt to complex environments. The GntR family proteins play important roles in the regulation of metabolic processes and bacterial pathogenesis. In this study, we uncovered that the gene clusters of PA1513-PA1518 and PA1498-PA1502 in P.