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Pseudomonas aeruginosa, a ubiquitous opportunistic pathogen, coordinates virulence gene expression primarily through three quorum-sensing (QS) systems: Las, Rhl, and Pqs. Despite the functions of QS systems in P. aeruginosa being relatively well-documented, the regulatory mechanisms modulating their activities remain largely unexplored. Here, we isolated and characterized a Las-null strain, PA_HN008, which overproduces pyocyanin (PYO) at the late growth stage due to its active RhlI-RhlR-PqsE pathway. Leveraging PYO production as a phenotypic marker, we conducted a genome-wide screening for upstream QS modulators and successfully identified PA5348 (designated as HupA), the α subunit of the nucleoid-associated protein HU, as a specific activator of the Pqs system and PYO production. RNA-seq and protein-DNA interaction assays further revealed that HupA directly binds to the promoters of pqs and phz genes, thereby inducing PqsE expression and PYO production. This study demonstrates that HupA acts as a novel transcriptional factor to control QS activity and virulence gene expression in P. aeruginosa, which not only reveals the regulatory function of the HU subunit HupA on virulence factor production but also uncovers the sequence-specific DNA-binding capability of HupA for stimulating gene transcription.IMPORTANCEThe nucleoid-associated protein HU is abundant and evolutionarily conserved in bacteria, which typically binds DNA in a sequence-nonspecific manner with high affinity to abnormal DNA structures during DNA damage and then contributes to DNA compaction, replication, recombination, and other physiological functions. However, the potential involvement of HU in regulating quorum sensing (QS), a critical cell-to-cell communication system governing bacterial virulence factor production, is poorly understood. In this study, we demonstrated that the α subunit of the HU protein, namely HupA, is a key regulator that activates the Pqs system and pyocyanin production through genome-wide screening in a clinical isolate PA_HN008. This study reveals the capability of the HU subunit to selectively bind target DNA sequences and stimulate QS activity as well as virulence factor production. Our findings provide novel insights into the biochemical properties of the HU subunit and its regulatory role in bacterial virulence.
Pubmed ID: 41801021
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Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.
View all literature mentionsOriginal SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsA software package for the mapping of short reads from illumina sequencing machines onto a reference genome. It''s recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features: * Maps single, paired-end and mate pair Illumina reads to a reference genome * Fast: about 20 Gbase per hour in hybrid mode (using BWA) * Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome * High sensitivity for indels and divergent reads, up to 10-15% * Low mapping bias for reads with SNPs * Well calibrated mapping quality scores * Input: Fastq and Fasta; gzipped or plain * Output: SAM, Maq''s map file * Optionally calculates per-base alignment posteriors * Optionally processes part of the input * Handles reads of up to 4500 bases
View all literature mentionsDatabase of peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome expanded to include all Pseudomonas species to facilitate cross-strain and cross-species genome comparisons with high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. The current annotation is updated using recent research literature and peer-reviewed submissions by a worldwide community of PseudoCAP (Pseudomonas aeruginosa Community Annotation Project) participating researchers. If you are interested in participating, you are invited to get involved. Many annotations, DNA sequences, Orthologs, Intergenic DNA, and Protein sequences are available for download.
View all literature mentionsSoftware package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.
View all literature mentionsSoftware Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.
View all literature mentionsDatabase for molecular typing and microbial genome diversity.
View all literature mentionsSoftware package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionsSoftware tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.
View all literature mentionsSoftware to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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