L. Barquist

The RNA-binding protein RbpB is a central regulator of polysaccharide utilization in gut Bacteroides

This study identifies RbpB as a key RNA-binding protein regulating polysaccharide utilization in gut Bacteroides through post-transcriptional control of PULs.

A side-by-side comparison of peptide-delivered antisense antibiotics employing different nucleotide mimics

This study compares seven chemically distinct antisense oligomers targeting Salmonella acpP, finding only PNA and PMO are effectively delivered by a KFF peptide to inhibit bacterial growth.

Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have sub-minute half-lives

The paper develops a Bayesian model to estimate RNA stability in Salmonella, revealing most transcripts have sub-minute half-lives and RBPs significantly affect decay rates.

Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress

This study uses ribosome profiling and RNA sequencing to analyze E. coli's response to mild and severe acid stress, identifying new genes, pathways, and sORFs.

Improved bacterial single-cell RNA-seq through automated MATQ-seq and Cas9-based removal of rRNA reads

This paper improves bacterial single-cell RNA-seq by automating MATQ-seq and using Cas9 to remove rRNA, enhancing gene detection and reducing cell loss.

Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens

This study uses Grad-seq to identify RNA-protein complexes and novel sRNAs in E. faecalis and E. faecium, revealing conserved regulatory mechanisms and potential roles of KhpB in RNA processing.

High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality

The paper uses transposon mutagenesis across Enterobacteriaceae species to identify core essential genes and shows rapid turnover of essentiality across related strains.

INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors

The paper introduces INRI-seq, a cell-free Ribo-seq method to study translation initiation and off-target effects of antisense inhibitors in E. coli.

Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli

This study systematically evaluates PNA-based antisense antibiotics targeting essential genes in UPEC, identifying effective targets and revealing bacterial responses to PNA conjugates.

Global identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq

This study identifies RsmA/N binding sites in Pseudomonas aeruginosa using UV CLIP-seq, revealing over 500 binding peaks and a consensus motif, and shows their role in gene regulation and homeostasis.

An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important Gram-positive bacterium

This study maps the transcriptome of C. difficile and reveals Hfq's role in post-transcriptional regulation through RNA-centric techniques and Hfq RIP-seq.

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

The paper introduces GradR, a method combining RNase treatment and mass spectrometry to discover bacterial RNA-binding proteins, identifying FopA as a new FinO domain RBP with distinct RNA targets.

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

The paper identifies and characterizes small proteins in Salmonella Typhimurium using integrated omics data, revealing a new role for MgrB in virulence and motility.

Dual RNA-seq provides insight into the biology of the neglected intracellular human pathogen Orientia tsutsugamushi

The paper uses dual RNA-seq to study the transcriptional architecture and host-pathogen interactions of Orientia tsutsugamushi, identifying antisense regulation and strain-specific immune responses.