publications of working group Integrative Informatics for Infection Biology ([HIRI]IIIB)
http://hdl.handle.net/10033/621182
2024-02-19T07:30:55ZAn amphipathic peptide with antibiotic activity against multidrug-resistant Gram-negative bacteria.
http://hdl.handle.net/10033/623233
An amphipathic peptide with antibiotic activity against multidrug-resistant Gram-negative bacteria.
Elliott, Alysha G; Huang, Johnny X; Neve, Søren; Zuegg, Johannes; Edwards, Ingrid A; Cain, Amy K; Boinett, Christine J; Barquist, Lars; Lundberg, Carina Vingsbo; Steen, Jason; Butler, Mark S; Mobli, Mehdi; Porter, Kaela M; Blaskovich, Mark A T; Lociuro, Sergio; Strandh, Magnus; Cooper, Matthew A
Peptide antibiotics are an abundant and synthetically tractable source of molecular diversity,
but they are often cationic and can be cytotoxic, nephrotoxic and/or ototoxic, which has
limited their clinical development. Here we report structure-guided optimization of an
amphipathic peptide, arenicin-3, originally isolated from the marine lugworm Arenicola marina.
The peptide induces bacterial membrane permeability and ATP release, with serial passaging
resulting in a mutation in mlaC, a phospholipid transport gene. Structure-based design led to
AA139, an antibiotic with broad-spectrum in vitro activity against multidrug-resistant and
extensively drug-resistant bacteria, including ESBL, carbapenem- and colistin-resistant clinical
isolates. The antibiotic induces a 3–4 log reduction in bacterial burden in mouse models of
peritonitis, pneumonia and urinary tract infection. Cytotoxicity and haemolysis of the progenitor peptide is ameliorated with AA139, and the ‘no observable adverse effect level’
(NOAEL) dose in mice is ~10-fold greater than the dose generally required for efficacy in the
infection models
2020-06-23T00:00:00ZComparative genomics provides structural and functional insights into Bacteroides RNA biology.
http://hdl.handle.net/10033/623153
Comparative genomics provides structural and functional insights into Bacteroides RNA biology.
Prezza, Gianluca; Ryan, Daniel; Mädler, Gohar; Reichardt, Sarah; Barquist, Lars; Westermann, Alexander J
Bacteria employ noncoding RNA molecules for a wide range of biological processes, including scaffolding large molecular complexes, catalyzing chemical reactions, defending against phages, and controlling gene expression. Secondary structures, binding partners, and molecular mechanisms have been determined for numerous small noncoding RNAs (sRNAs) in model aerobic bacteria. However, technical hurdles have largely prevented analogous analyses in the anaerobic gut microbiota. While experimental techniques are being developed to investigate the sRNAs of gut commensals, computational tools and comparative genomics can provide immediate functional insight. Here, using Bacteroides thetaiotaomicron as a representative microbiota member, we illustrate how comparative genomics improves our understanding of RNA biology in an understudied gut bacterium. We investigate putative RNA-binding proteins and predict a Bacteroides cold-shock protein homolog to have an RNA-related function. We apply an in silico protocol incorporating both sequence and structural analysis to determine the consensus structures and conservation of nine Bacteroides noncoding RNA families. Using structure probing, we validate and refine these predictions and deposit them in the Rfam database. Through synteny analyses, we illustrate how genomic coconservation can serve as a predictor of sRNA function. Altogether, this work showcases the power of RNA informatics for investigating the RNA biology of anaerobic microbiota members.
2021-08-28T00:00:00ZRNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum.
http://hdl.handle.net/10033/623009
RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum.
Ponath, Falk; Tawk, Caroline; Zhu, Yan; Barquist, Lars; Faber, Franziska; Vogel, Jörg
Fusobacterium nucleatum, long known as a constituent of the oral microflora, has recently garnered renewed attention for its association with several different human cancers. The growing interest in this emerging cancer-associated bacterium contrasts with a paucity of knowledge about its basic gene expression features and physiological responses. As fusobacteria lack all established small RNA-associated proteins, post-transcriptional networks in these bacteria are also unknown. In the present study, using differential RNA-sequencing, we generate high-resolution global RNA maps for five clinically relevant fusobacterial strains-F. nucleatum subspecies nucleatum, animalis, polymorphum and vincentii, as well as F. periodonticum-for early, mid-exponential growth and early stationary phase. These data are made available in an online browser, and we use these to uncover fundamental aspects of fusobacterial gene expression architecture and a suite of non-coding RNAs. Developing a vector for functional analysis of fusobacterial genes, we discover a conserved fusobacterial oxygen-induced small RNA, FoxI, which serves as a post-transcriptional repressor of the major outer membrane porin FomA. Our findings provide a crucial step towards delineating the regulatory networks enabling F. nucleatum adaptation to different environments, which may elucidate how these bacteria colonize different compartments of the human body.
2021-07-08T00:00:00ZAn RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium.
http://hdl.handle.net/10033/622979
An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium.
Fuchs, Manuela; Lamm-Schmidt, Vanessa; Sulzer, Johannes; Ponath, Falk; Jenniches, Laura; Kirk, Joseph A; Fagan, Robert P; Barquist, Lars; Vogel, Jörg; Faber, Franziska
The gram-positive human pathogen Clostridioides difficile has emerged as the leading cause of antibiotic-associated diarrhea. However, little is known about the bacterium's transcriptome architecture and mechanisms of posttranscriptional control. Here, we have applied transcription start site and termination mapping to generate a single-nucleotide-resolution RNA map of C. difficile 5' and 3' untranslated regions, operon structures, and noncoding regulators, including 42 sRNAs. Our results indicate functionality of many conserved riboswitches and predict cis-regulatory RNA elements upstream of multidrug resistance (MDR)-type ATP-binding cassette (ABC) transporters and transcriptional regulators. Despite growing evidence for a role of Hfq in RNA-based gene regulation in C. difficile, the functions of Hfq-based posttranscriptional regulatory networks in gram-positive pathogens remain controversial. Using Hfq immunoprecipitation followed by sequencing of bound RNA species (RIP-seq), we identify a large cohort of transcripts bound by Hfq and show that absence of Hfq affects transcript stabilities and steady-state levels. We demonstrate sRNA expression during intestinal colonization by C. difficile and identify infection-related signals impacting its expression. As a proof of concept, we show that the utilization of the abundant intestinal metabolite ethanolamine is regulated by the Hfq-dependent sRNA CDIF630nc_085. Overall, our study lays the foundation for understanding clostridial riboregulation with implications for the infection process and provides evidence for a global role of Hfq in posttranscriptional regulation in a gram-positive bacterium.
2021-06-15T00:00:00Z