1
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Vialetto E, Miele S, Goren MG, Yu J, Yu Y, Collias D, Beamud B, Osbelt L, Lourenço M, Strowig T, Brisse S, Barquist L, Qimron U, Bikard D, Beisel CL. Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity. Nucleic Acids Res 2024:gkae281. [PMID: 38661215 DOI: 10.1093/nar/gkae281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 03/24/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
CRISPR-Cas systems can be utilized as programmable-spectrum antimicrobials to combat bacterial infections. However, how CRISPR nucleases perform as antimicrobials across target sites and strains remains poorly explored. Here, we address this knowledge gap by systematically interrogating the use of CRISPR antimicrobials using multidrug-resistant and hypervirulent strains of Klebsiella pneumoniae as models. Comparing different Cas nucleases, DNA-targeting nucleases outperformed RNA-targeting nucleases based on the tested targets. Focusing on AsCas12a that exhibited robust targeting across different strains, we found that the elucidated modes of escape varied widely, restraining opportunities to enhance killing. We also encountered individual guide RNAs yielding different extents of clearance across strains, which were linked to an interplay between improper gRNA folding and strain-specific DNA repair and survival. To explore features that could improve targeting across strains, we performed a genome-wide screen in different K. pneumoniae strains that yielded guide design rules and trained an algorithm for predicting guide efficiency. Finally, we showed that Cas12a antimicrobials can be exploited to eliminate K. pneumoniae when encoded in phagemids delivered by T7-like phages. Altogether, our results highlight the importance of evaluating antimicrobial activity of CRISPR antimicrobials across relevant strains and define critical parameters for efficient CRISPR-based targeting.
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Affiliation(s)
- Elena Vialetto
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Solange Miele
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Moran G Goren
- Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Jiaqi Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Daphne Collias
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Beatriz Beamud
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Lisa Osbelt
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Till Strowig
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
- University of Würzburg, Medical Faculty, 97080 Würzburg, Germany
| | - Udi Qimron
- Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - David Bikard
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- University of Würzburg, Medical Faculty, 97080 Würzburg, Germany
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Gawlitt S, Collins SP, Yu Y, Blackman SA, Barquist L, Beisel CL. Expanding the flexibility of base editing for high-throughput genetic screens in bacteria. Nucleic Acids Res 2024; 52:4079-4097. [PMID: 38499498 DOI: 10.1093/nar/gkae174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/07/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide screens have become powerful tools for elucidating genotype-to-phenotype relationships in bacteria. Of the varying techniques to achieve knockout and knockdown, CRISPR base editors are emerging as promising options. However, the limited number of available, efficient target sites hampers their use for high-throughput screening. Here, we make multiple advances to enable flexible base editing as part of high-throughput genetic screening in bacteria. We first co-opt the Streptococcus canis Cas9 that exhibits more flexible protospacer-adjacent motif recognition than the traditional Streptococcus pyogenes Cas9. We then expand beyond introducing premature stop codons by mutating start codons. Next, we derive guide design rules by applying machine learning to an essentiality screen conducted in Escherichia coli. Finally, we rescue poorly edited sites by combining base editing with Cas9-induced cleavage of unedited cells, thereby enriching for intended edits. The efficiency of this dual system was validated through a conditional essentiality screen based on growth in minimal media. Overall, expanding the scope of genome-wide knockout screens with base editors could further facilitate the investigation of new gene functions and interactions in bacteria.
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Affiliation(s)
- Sandra Gawlitt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Scott P Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Samuel A Blackman
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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3
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Sullivan GJ, Barquist L, Cain AK. A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria. mSystems 2024; 9:e0066523. [PMID: 38470252 PMCID: PMC11019837 DOI: 10.1128/msystems.00665-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Functional genomics techniques, such as transposon insertion sequencing and RNA-sequencing, are key to studying relative differences in bacterial mutant fitness or gene expression under selective conditions. However, certain stress conditions, mutations, or antibiotics can directly interfere with DNA synthesis, resulting in systematic changes in local DNA copy numbers along the chromosome. This can lead to artifacts in sequencing-based functional genomics data when comparing antibiotic treatment to an unstressed control. Further, relative differences in gene-wise read counts may result from alterations in chromosomal replication dynamics, rather than selection or direct gene regulation. We term this artifact "chromosomal location bias" and implement a principled statistical approach to correct it by calculating local normalization factors along the chromosome. These normalization factors are then directly incorporated into statistical analyses using standard RNA-sequencing analysis methods without modifying the read counts themselves, preserving important information about the mean-variance relationship in the data. We illustrate the utility of this approach by generating and analyzing a ciprofloxacin-treated transposon insertion sequencing data set in Escherichia coli as a case study. We show that ciprofloxacin treatment generates chromosomal location bias in the resulting data, and we further demonstrate that failing to correct for this bias leads to false predictions of mutant drug sensitivity as measured by minimum inhibitory concentrations. We have developed an R package and user-friendly graphical Shiny application, ChromoCorrect, that detects and corrects for chromosomal bias in read count data, enabling the application of functional genomics technologies to the study of antibiotic stress.IMPORTANCEAltered gene dosage due to changes in DNA replication has been observed under a variety of stresses with a variety of experimental techniques. However, the implications of changes in gene dosage for sequencing-based functional genomics assays are rarely considered. We present a statistically principled approach to correcting for the effect of changes in gene dosage, enabling testing for differences in the fitness effects or regulation of individual genes in the presence of confounding differences in DNA copy number. We show that failing to correct for these effects can lead to incorrect predictions of resistance phenotype when applying functional genomics assays to investigate antibiotic stress, and we provide a user-friendly application to detect and correct for changes in DNA copy number.
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Affiliation(s)
- Geraldine J. Sullivan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Lars Barquist
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Amy K. Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, Australia
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4
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Jenniches L, Michaux C, Popella L, Reichardt S, Vogel J, Westermann AJ, Barquist L. Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives. Proc Natl Acad Sci U S A 2024; 121:e2308814121. [PMID: 38527194 PMCID: PMC10998600 DOI: 10.1073/pnas.2308814121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in posttranscriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. We developed a hierarchical Bayesian model that corrects for confounding factors in rifampicin RNA stability assays and enables us to identify differentially decaying transcripts transcriptome-wide. Our analysis revealed that the median RNA half-life in Salmonella in early stationary phase is less than 1 min, a third of previous estimates. We found that over half of the 500 most long-lived transcripts are bound by at least one major RBP, suggesting a general role for RBPs in shaping the transcriptome. Integrating differential stability estimates with cross-linking and immunoprecipitation followed by RNA sequencing (CLIP-seq) revealed that approximately 30% of transcripts with ProQ binding sites and more than 40% with CspC/E binding sites in coding or 3' untranslated regions decay differentially in the absence of the respective RBP. Analysis of differentially destabilized transcripts identified a role for ProQ in the oxidative stress response. Our findings provide insights into posttranscriptional regulation by ProQ and CspC/E, and the importance of RBPs in regulating gene expression.
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Affiliation(s)
- Laura Jenniches
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg97080, Germany
| | - Charlotte Michaux
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Linda Popella
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Sarah Reichardt
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg97080, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg97080, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
- Faculty of Medicine, University of Würzburg, Würzburg97080, Germany
| | - Alexander J. Westermann
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg97080, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg97080, Germany
- Faculty of Medicine, University of Würzburg, Würzburg97080, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, ONL5L 1C6Canada
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5
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Ryan D, Bornet E, Prezza G, Alampalli SV, Franco de Carvalho T, Felchle H, Ebbecke T, Hayward RJ, Deutschbauer AM, Barquist L, Westermann AJ. An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity. Nat Microbiol 2024; 9:1130-1144. [PMID: 38528147 PMCID: PMC10994844 DOI: 10.1038/s41564-024-01642-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 02/07/2024] [Indexed: 03/27/2024]
Abstract
Plasticity in gene expression allows bacteria to adapt to diverse environments. This is particularly relevant in the dynamic niche of the human intestinal tract; however, transcriptional networks remain largely unknown for gut-resident bacteria. Here we apply differential RNA sequencing (RNA-seq) and conventional RNA-seq to the model gut bacterium Bacteroides thetaiotaomicron to map transcriptional units and profile their expression levels across 15 in vivo-relevant growth conditions. We infer stress- and carbon source-specific transcriptional regulons and expand the annotation of small RNAs (sRNAs). Integrating this expression atlas with published transposon mutant fitness data, we predict conditionally important sRNAs. These include MasB, which downregulates tetracycline tolerance. Using MS2 affinity purification and RNA-seq, we identify a putative MasB target and assess its role in the context of the MasB-associated phenotype. These data-publicly available through the Theta-Base web browser ( http://micromix.helmholtz-hiri.de/bacteroides/ )-constitute a valuable resource for the microbiome community.
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Affiliation(s)
- Daniel Ryan
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Elise Bornet
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Gianluca Prezza
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Shuba Varshini Alampalli
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Taís Franco de Carvalho
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Hannah Felchle
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
- Department of Radiation Oncology, Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Munich, Germany
| | - Titus Ebbecke
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Regan J Hayward
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany.
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6
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Ghosh C, Popella L, Dhamodharan V, Jung J, Dietzsch J, Barquist L, Höbartner C, Vogel J. A comparative analysis of peptide-delivered antisense antibiotics employing diverse nucleotide mimics. RNA 2024:rna.079969.124. [PMID: 38413166 DOI: 10.1261/rna.079969.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/29/2024]
Abstract
Antisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes have great potential for counteracting antimicrobial resistance and for precision microbiome editing. To date, the development of such antisense antibiotics has primarily focused on using phosphorodiamidate morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical modalities that have spurred the success of ASO-based human therapy. Here, we directly compare the activities of seven chemically distinct 10mer ASOs, all designed to target the essential gene acpP upon delivery with a KFF-peptide carrier into Salmonella. Our systematic analysis of PNA, PMO, phosphorothioate-modified DNA (PTO), 2'-methylated RNA (RNA-OMe), 2'-methoxyethylated RNA (RNA-MOE), 2'-fluorinated RNA (RNA-F) and 2'-4'-locked RNA (LNA) is based on a variety of in vitro and in vivo methods to evaluate ASO uptake, target pairing and inhibition of bacterial growth. Our data show that only PNA and PMO are efficiently delivered by the KFF peptide into Salmonella to inhibit bacterial growth. Nevertheless, the strong target binding affinity and in vitro translational repression activity of LNA and RNA-MOE make them promising modalities for antisense antibiotics that will require the identification of an effective carrier.
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Affiliation(s)
| | - Linda Popella
- University of Würzburg, Institute of Molecular Infection Biology (IMIB)
| | | | - Jakob Jung
- Helmholtz Institute for RNA-based Infection Research (HIRI)
| | - Julia Dietzsch
- University of Würzburg, Institute of Organic Chemistry, and Center for Nanosystems Chemistry
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research
| | - Claudia Höbartner
- University of Würzburg, Institute of Organic Chemistry, and Center for Nanosystems Chemistry
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7
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Yu Y, Gawlitt S, de Andrade E Sousa LB, Merdivan E, Piraud M, Beisel CL, Barquist L. Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration. Genome Biol 2024; 25:13. [PMID: 38200565 PMCID: PMC10782694 DOI: 10.1186/s13059-023-03153-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
CRISPR interference (CRISPRi) is the leading technique to silence gene expression in bacteria; however, design rules remain poorly defined. We develop a best-in-class prediction algorithm for guide silencing efficiency by systematically investigating factors influencing guide depletion in genome-wide essentiality screens, with the surprising discovery that gene-specific features substantially impact prediction. We develop a mixed-effect random forest regression model that provides better estimates of guide efficiency. We further apply methods from explainable AI to extract interpretable design rules from the model. This study provides a blueprint for predictive models for CRISPR technologies where only indirect measurements of guide activity are available.
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Affiliation(s)
- Yanying Yu
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, 97080, Germany
| | - Sandra Gawlitt
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, 97080, Germany
| | | | - Erinc Merdivan
- Helmholtz AI, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Marie Piraud
- Helmholtz AI, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, 97080, Germany
- Medical Faculty, University of Würzburg, Würzburg, 97080, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, 97080, Germany.
- Medical Faculty, University of Würzburg, Würzburg, 97080, Germany.
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8
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Schumacher K, Gelhausen R, Kion-Crosby W, Barquist L, Backofen R, Jung K. Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress. mSystems 2023; 8:e0103723. [PMID: 37909716 PMCID: PMC10746267 DOI: 10.1128/msystems.01037-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Bacteria react very differently to survive in acidic environments, such as the human gastrointestinal tract. Escherichia coli is one of the extremely acid-resistant bacteria and has a variety of acid-defense mechanisms. Here, we provide the first genome-wide overview of the adaptations of E. coli K-12 to mild and severe acid stress at both the transcriptional and translational levels. Using ribosome profiling and RNA sequencing, we uncover novel adaptations to different degrees of acidity, including previously hidden stress-induced small proteins and novel key transcription factors for acid defense, and report mRNAs with pH-dependent differential translation efficiency. In addition, we distinguish between acid-specific adaptations and general stress response mechanisms using denoising autoencoders. This workflow represents a powerful approach that takes advantage of next-generation sequencing techniques and machine learning to systematically analyze bacterial stress responses.
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Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Willow Kion-Crosby
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
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9
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Reuter C, Hauf L, Imdahl F, Sen R, Vafadarnejad E, Fey P, Finger T, Jones NG, Walles H, Barquist L, Saliba AE, Groeber-Becker F, Engstler M. Vector-borne Trypanosoma brucei parasites develop in artificial human skin and persist as skin tissue forms. Nat Commun 2023; 14:7660. [PMID: 37996412 PMCID: PMC10667367 DOI: 10.1038/s41467-023-43437-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Transmission of Trypanosoma brucei by tsetse flies involves the deposition of the cell cycle-arrested metacyclic life cycle stage into mammalian skin at the site of the fly's bite. We introduce an advanced human skin equivalent and use tsetse flies to naturally infect the skin with trypanosomes. We detail the chronological order of the parasites' development in the skin by single-cell RNA sequencing and find a rapid activation of metacyclic trypanosomes and differentiation to proliferative parasites. Here we show that after the establishment of a proliferative population, the parasites enter a reversible quiescent state characterized by slow replication and a strongly reduced metabolism. We term these quiescent trypanosomes skin tissue forms, a parasite population that may play an important role in maintaining the infection over long time periods and in asymptomatic infected individuals.
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Affiliation(s)
- Christian Reuter
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, Wuerzburg, Germany
| | - Laura Hauf
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Fabian Imdahl
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
- Core Unit Systems Medicine, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Rituparno Sen
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Ehsan Vafadarnejad
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Philipp Fey
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Tamara Finger
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Nicola G Jones
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Heike Walles
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
- Core Facility Tissue Engineering, Otto-von-Guericke University, Magdeburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Wuerzburg, Germany
- Institute of Molecular Infection Biology (IMIB), Faculty of Medicine, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany
| | - Florian Groeber-Becker
- Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, Wuerzburg, Germany
- Translational Center Regenerative Therapies, Fraunhofer ISC, Wuerzburg, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, Julius-Maximilians-Universitaet of Wuerzburg, Wuerzburg, Germany.
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10
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Maharjan RP, Sullivan GJ, Adams F, Shah B, Hawkey J, Delgado N, Semenec L, Dinh H, Li L, Short F, Parkhill J, Paulsen I, Barquist L, Eijkelkamp B, Cain A. DksA is a conserved master regulator of stress response in Acinetobacter baumannii. Nucleic Acids Res 2023; 51:6101-6119. [PMID: 37158230 PMCID: PMC10325922 DOI: 10.1093/nar/gkad341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
Abstract
Coordination of bacterial stress response mechanisms is critical for long-term survival in harsh environments for successful host infection. The general and specific stress responses of well-studied Gram-negative pathogens like Escherichia coli are controlled by alternative sigma factors, archetypically RpoS. The deadly hospital pathogen Acinetobacter baumannii is notoriously resistant to environmental stresses, yet it lacks RpoS, and the molecular mechanisms driving this incredible stress tolerance remain poorly defined. Here, using functional genomics, we identified the transcriptional regulator DksA as a master regulator for broad stress protection and virulence in A. baumannii. Transcriptomics, phenomics and in vivo animal studies revealed that DksA controls ribosomal protein expression, metabolism, mutation rates, desiccation, antibiotic resistance, and host colonization in a niche-specific manner. Phylogenetically, DksA was highly conserved and well-distributed across Gammaproteobacteria, with 96.6% containing DksA, spanning 88 families. This study lays the groundwork for understanding DksA as a major regulator of general stress response and virulence in this important pathogen.
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Affiliation(s)
- Ram P Maharjan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Geraldine J Sullivan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Felise G Adams
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Bhumika S Shah
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Victoria, Australia
| | - Natasha Delgado
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Lucie Semenec
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Hue Dinh
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Liping Li
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Francesca L Short
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080Würzburg, Germany
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
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11
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Jung J, Popella L, Do PT, Pfau P, Vogel J, Barquist L. Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server. RNA 2023; 29:570-583. [PMID: 36750372 PMCID: PMC10158992 DOI: 10.1261/rna.079263.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 01/10/2023] [Indexed: 05/06/2023]
Abstract
Antisense oligomers (ASOs), such as peptide nucleic acids (PNAs), designed to inhibit the translation of essential bacterial genes, have emerged as attractive sequence- and species-specific programmable RNA antibiotics. Yet, potential drawbacks include unwanted side effects caused by their binding to transcripts other than the intended target. To facilitate the design of PNAs with minimal off-target effects, we developed MASON (make antisense oligomers now), a web server for the design of PNAs that target bacterial mRNAs. MASON generates PNA sequences complementary to the translational start site of a bacterial gene of interest and reports critical sequence attributes and potential off-target sites. We based MASON's off-target predictions on experiments in which we treated Salmonella enterica serovar Typhimurium with a series of 10-mer PNAs derived from a PNA targeting the essential gene acpP but carrying two serial mismatches. Growth inhibition and RNA-sequencing (RNA-seq) data revealed that PNAs with terminal mismatches are still able to target acpP, suggesting wider off-target effects than anticipated. Comparison of these results to an RNA-seq data set from uropathogenic Escherichia coli (UPEC) treated with eleven different PNAs confirmed that our findings are not unique to Salmonella We believe that MASON's off-target assessment will improve the design of specific PNAs and other ASOs.
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Affiliation(s)
- Jakob Jung
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Linda Popella
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Phuong Thao Do
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Patrick Pfau
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
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12
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Ryan D, Bornet E, Prezza G, Alampalli SV, de Carvalho TF, Felchle H, Ebbecke T, Hayward R, Deutschbauer AM, Barquist L, Westermann AJ. An integrated transcriptomics-functional genomics approach reveals a small RNA that modulates Bacteroides thetaiotaomicron sensitivity to tetracyclines. bioRxiv 2023:2023.02.16.528795. [PMID: 36824877 PMCID: PMC9949090 DOI: 10.1101/2023.02.16.528795] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Gene expression plasticity allows bacteria to adapt to diverse environments, tie their metabolism to available nutrients, and cope with stress. This is particularly relevant in a niche as dynamic and hostile as the human intestinal tract, yet transcriptional networks remain largely unknown in gut Bacteroides spp. Here, we map transcriptional units and profile their expression levels in Bacteroides thetaiotaomicron over a suite of 15 defined experimental conditions that are relevant in vivo , such as variation of temperature, pH, and oxygen tension, exposure to antibiotic stress, and growth on simple carbohydrates or on host mucin-derived glycans. Thereby, we infer stress- and carbon source-specific transcriptional regulons, including conditional expression of capsular polysaccharides and polysaccharide utilization loci, and expand the annotation of small regulatory RNAs (sRNAs) in this organism. Integrating this comprehensive expression atlas with transposon mutant fitness data, we identify conditionally important sRNAs. One example is MasB, whose inactivation led to increased bacterial tolerance of tetracyclines. Using MS2 affinity purification coupled with RNA sequencing, we predict targets of this sRNA and discuss their potential role in the context of the MasB-associated phenotype. Together, this transcriptomic compendium in combination with functional sRNA genomics-publicly available through a new iteration of the 'Theta-Base' web browser (www.helmholtz-hiri.de/en/datasets/bacteroides-v2)-constitutes a valuable resource for the microbiome and sRNA research communities alike.
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13
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Michaux C, Gerovac M, Hansen EE, Barquist L, Vogel J. Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens. Microlife 2022; 4:uqac027. [PMID: 37223738 PMCID: PMC10117718 DOI: 10.1093/femsml/uqac027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/24/2022] [Indexed: 05/25/2023]
Abstract
Enterococcus faecalis and Enterococcus faecium are major nosocomial pathogens. Despite their relevance to public health and their role in the development of bacterial antibiotic resistance, relatively little is known about gene regulation in these species. RNA-protein complexes serve crucial functions in all cellular processes associated with gene expression, including post-transcriptional control mediated by small regulatory RNAs (sRNAs). Here, we present a new resource for the study of enterococcal RNA biology, employing the Grad-seq technique to comprehensively predict complexes formed by RNA and proteins in E. faecalis V583 and E. faecium AUS0004. Analysis of the generated global RNA and protein sedimentation profiles led to the identification of RNA-protein complexes and putative novel sRNAs. Validating our data sets, we observe well-established cellular RNA-protein complexes such as the 6S RNA-RNA polymerase complex, suggesting that 6S RNA-mediated global control of transcription is conserved in enterococci. Focusing on the largely uncharacterized RNA-binding protein KhpB, we use the RIP-seq technique to predict that KhpB interacts with sRNAs, tRNAs, and untranslated regions of mRNAs, and might be involved in the processing of specific tRNAs. Collectively, these datasets provide departure points for in-depth studies of the cellular interactome of enterococci that should facilitate functional discovery in these and related Gram-positive species. Our data are available to the community through a user-friendly Grad-seq browser that allows interactive searches of the sedimentation profiles (https://resources.helmholtz-hiri.de/gradseqef/).
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Affiliation(s)
| | | | | | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße, 97080, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Jörg Vogel
- Corresponding author. Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, 97080, Würzburg, Germany. Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße, 97080, Würzburg, Germany. E-mail:
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14
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Hör J, Jung J, Ðurica-Mitić S, Barquist L, Vogel J. INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors. Nucleic Acids Res 2022; 50:e128. [PMID: 36229039 PMCID: PMC9825163 DOI: 10.1093/nar/gkac838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/11/2022] [Accepted: 09/19/2022] [Indexed: 01/29/2023] Open
Abstract
Ribosome profiling (Ribo-seq) is a powerful method for the transcriptome-wide assessment of protein synthesis rates and the study of translational control mechanisms. Yet, Ribo-seq also has limitations. These include difficulties with the analysis of translation-modulating molecules such as antibiotics, which are often toxic or challenging to deliver into living cells. Here, we have developed in vitro Ribo-seq (INRI-seq), a cell-free method to analyze the translational landscape of a fully customizable synthetic transcriptome. Using Escherichia coli as an example, we show how INRI-seq can be used to analyze the translation initiation sites of a transcriptome of interest. We also study the global impact of direct translation inhibition by antisense peptide nucleic acid (PNA) to analyze PNA off-target effects. Overall, INRI-seq presents a scalable, sensitive method to study translation initiation in a transcriptome-wide manner without the potentially confounding effects of extracting ribosomes from living cells.
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Affiliation(s)
- Jens Hör
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Jakob Jung
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Svetlana Ðurica-Mitić
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), D-97080 Würzburg, Germany,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- To whom correspondence should be addressed. Tel: +49 931 3182576;
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15
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Homberger C, Barquist L, Vogel J. Ushering in a new era of single-cell transcriptomics in bacteria. Microlife 2022; 3:uqac020. [PMID: 37223351 PMCID: PMC10117829 DOI: 10.1093/femsml/uqac020] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/17/2022] [Indexed: 05/25/2023]
Abstract
Transcriptome analysis of individual cells by single-cell RNA-seq (scRNA-seq) has become routine for eukaryotic tissues, even being applied to whole multicellular organisms. In contrast, developing methods to read the transcriptome of single bacterial cells has proven more challenging, despite a general perception of bacteria as much simpler than eukaryotes. Bacterial cells are harder to lyse, their RNA content is about two orders of magnitude lower than that of eukaryotic cells, and bacterial mRNAs are less stable than their eukaryotic counterparts. Most importantly, bacterial transcripts lack functional poly(A) tails, precluding simple adaptation of popular standard eukaryotic scRNA-seq protocols that come with the double advantage of specific mRNA amplification and concomitant depletion of rRNA. However, thanks to very recent breakthroughs in methodology, bacterial scRNA-seq is now feasible. This short review will discuss recently published bacterial scRNA-seq approaches (MATQ-seq, microSPLiT, and PETRI-seq) and a spatial transcriptomics approach based on multiplexed in situ hybridization (par-seqFISH). Together, these novel approaches will not only enable a new understanding of cell-to-cell variation in bacterial gene expression, they also promise a new microbiology by enabling high-resolution profiling of gene activity in complex microbial consortia such as the microbiome or pathogens as they invade, replicate, and persist in host tissue.
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Affiliation(s)
- Christina Homberger
- Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Jörg Vogel
- Corresponding author: Institute of Molecular Infection Biology, Josef-Schneider-Straße 2, D15, DE-97080 Wuerzburg, Germany. Tel: +49-931-3182575; Fax: +49-931-3182578; E-mail:
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16
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Vialetto E, Yu Y, Collins SP, Wandera KG, Barquist L, Beisel CL. A target expression threshold dictates invader defense and prevents autoimmunity by CRISPR-Cas13. Cell Host Microbe 2022; 30:1151-1162.e6. [PMID: 35690065 PMCID: PMC9590104 DOI: 10.1016/j.chom.2022.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/30/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022]
Abstract
CRISPR-Cas systems must enact robust immunity against foreign genetic material without inducing cytotoxic autoimmunity. For type VI systems that use Cas13 nucleases and recognize RNA targets, immune activation requires extensive CRISPR RNA (crRNA) guide-target complementarity and a target-flanking motif. Here, we report a third requirement shaping the immune response: the expression of the target transcript exceeding a threshold. We found that endogenous non-essential transcripts targeted by crRNAs rarely elicited autoimmunity. Instead, autoimmune induction required over-expressing the targeted transcripts above a threshold. A genome-wide screen confirmed target expression levels as a global determinant of cytotoxic autoimmunity and revealed that this threshold shifts with each guide-target pair. This threshold further ensured defense against a lytic bacteriophage yet allowed the tolerance of a targeted beneficial gene expressed from an invading plasmid. These findings establish target expression levels as an additional criterion for immune defense by RNA-targeting CRISPR-Cas systems, preventing autoimmunity and distinguishing pathogenic and benign invaders.
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Affiliation(s)
- Elena Vialetto
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Scott P Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Katharina G Wandera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany.
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17
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Popella L, Jung J, Do PT, Hayward RJ, Barquist L, Vogel J. Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli. Nucleic Acids Res 2022; 50:6435-6452. [PMID: 35687096 PMCID: PMC9226493 DOI: 10.1093/nar/gkac362] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/05/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022] Open
Abstract
Antisense peptide nucleic acids (PNAs) that target mRNAs of essential bacterial genes exhibit specific bactericidal effects in several microbial species, but our mechanistic understanding of PNA activity and their target gene spectrum is limited. Here, we present a systematic analysis of PNAs targeting 11 essential genes with varying expression levels in uropathogenic Escherichia coli (UPEC). We demonstrate that UPEC is susceptible to killing by peptide-conjugated PNAs, especially when targeting the widely-used essential gene acpP. Our evaluation yields three additional promising target mRNAs for effective growth inhibition, i.e.dnaB, ftsZ and rpsH. The analysis also shows that transcript abundance does not predict target vulnerability and that PNA-mediated growth inhibition is not universally associated with target mRNA depletion. Global transcriptomic analyses further reveal PNA sequence-dependent but also -independent responses, including the induction of envelope stress response pathways. Importantly, we show that 9mer PNAs are generally as effective in inhibiting bacterial growth as their 10mer counterparts. Overall, our systematic comparison of a range of PNAs targeting mRNAs of different essential genes in UPEC suggests important features for PNA design, reveals a general bacterial response to PNA conjugates and establishes the feasibility of using PNA antibacterials to combat UPEC.
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Affiliation(s)
- Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany
| | - Phuong Thao Do
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany
| | - Regan J Hayward
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080, Würzburg, Germany
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18
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Prezza G, Ryan D, Mädler G, Reichardt S, Barquist L, Westermann AJ. Comparative genomics provides structural and functional insights into Bacteroides RNA biology. Mol Microbiol 2021; 117:67-85. [PMID: 34379855 DOI: 10.1111/mmi.14793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022]
Abstract
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 the RNA biology in an understudied gut bacterium. We investigate putative RNA-binding proteins and predict a Bacteroides cold-shock protein homologue 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 co-conservation 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.
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Affiliation(s)
- Gianluca Prezza
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Daniel Ryan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Gohar Mädler
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Sarah Reichardt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.,Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
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19
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Ponath F, Tawk C, Zhu Y, Barquist L, Faber F, Vogel J. RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum. Nat Microbiol 2021; 6:1007-1020. [PMID: 34239075 DOI: 10.1038/s41564-021-00927-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 05/24/2021] [Indexed: 12/14/2022]
Abstract
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.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Caroline Tawk
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Yan Zhu
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Franziska Faber
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany. .,Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany. .,Faculty of Medicine, University of Würzburg, Würzburg, Germany.
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20
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Popella L, Jung J, Popova K, Ðurica-Mitić S, Barquist L, Vogel J. Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics. Nucleic Acids Res 2021; 49:4705-4724. [PMID: 33849070 PMCID: PMC8096218 DOI: 10.1093/nar/gkab242] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes provide a straight-forward way to repurpose our knowledge of bacterial regulatory RNAs for development of programmable species-specific antibiotics. While there is ample proof of PNA efficacy, their target selectivity and impact on bacterial physiology are poorly understood. Moreover, while antibacterial PNAs are typically designed to block mRNA translation, effects on target mRNA levels are not well-investigated. Here, we pioneer the use of global RNA-seq analysis to decipher PNA activity in a transcriptome-wide manner. We find that PNA-based antisense oligomer conjugates robustly decrease mRNA levels of the widely-used target gene, acpP, in Salmonella enterica, with limited off-target effects. Systematic analysis of several different PNA-carrier peptides attached not only shows different bactericidal efficiency, but also activation of stress pathways. In particular, KFF-, RXR- and Tat-PNA conjugates especially induce the PhoP/Q response, whereas the latter two additionally trigger several distinct pathways. We show that constitutive activation of the PhoP/Q response can lead to Tat-PNA resistance, illustrating the utility of RNA-seq for understanding PNA antibacterial activity. In sum, our study establishes an experimental framework for the design and assessment of PNA antimicrobials in the long-term quest to use these for precision editing of microbiota.
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Affiliation(s)
- Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Kristina Popova
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Svetlana Ðurica-Mitić
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
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21
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Abd El Ghany M, Barquist L, Clare S, Brandt C, Mayho M, Joffre´ E, Sjöling Å, Turner AK, Klena JD, Kingsley RA, Hill-Cawthorne GA, Dougan G, Pickard D. Functional analysis of colonization factor antigen I positive enterotoxigenic Escherichia coli identifies genes implicated in survival in water and host colonization. Microb Genom 2021; 7:000554. [PMID: 34110281 PMCID: PMC8461466 DOI: 10.1099/mgen.0.000554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) expressing the colonization pili CFA/I are common causes of diarrhoeal infections in humans. Here, we use a combination of transposon mutagenesis and transcriptomic analysis to identify genes and pathways that contribute to ETEC persistence in water environments and colonization of a mammalian host. ETEC persisting in water exhibit a distinct RNA expression profile from those growing in richer media. Multiple pathways were identified that contribute to water survival, including lipopolysaccharide biosynthesis and stress response regulons. The analysis also indicated that ETEC growing in vivo in mice encounter a bottleneck driving down the diversity of colonizing ETEC populations.
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Affiliation(s)
- Moataz Abd El Ghany
- The Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
- The Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Simon Clare
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Cordelia Brandt
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Mayho
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Enrique Joffre´
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - A. Keith Turner
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - John D. Klena
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Robert A. Kingsley
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Gordon Dougan
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Derek Pickard
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
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22
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Jiao C, Sharma S, Dugar G, Peeck NL, Bischler T, Wimmer F, Yu Y, Barquist L, Schoen C, Kurzai O, Sharma CM, Beisel CL. Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9. Science 2021; 372:941-948. [PMID: 33906967 PMCID: PMC8224270 DOI: 10.1126/science.abe7106] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/09/2021] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas systems recognize foreign genetic material using CRISPR RNAs (crRNAs). In type II systems, a trans-activating crRNA (tracrRNA) hybridizes to crRNAs to drive their processing and utilization by Cas9. While analyzing Cas9-RNA complexes from Campylobacter jejuni, we discovered tracrRNA hybridizing to cellular RNAs, leading to formation of "noncanonical" crRNAs capable of guiding DNA targeting by Cas9. Our discovery inspired the engineering of reprogrammed tracrRNAs that link the presence of any RNA of interest to DNA targeting with different Cas9 orthologs. This capability became the basis for a multiplexable diagnostic platform termed LEOPARD (leveraging engineered tracrRNAs and on-target DNAs for parallel RNA detection). LEOPARD allowed simultaneous detection of RNAs from different viruses in one test and distinguished severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its D614G (Asp614→Gly) variant with single-base resolution in patient samples.
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Affiliation(s)
- Chunlei Jiao
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Sahil Sharma
- Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg. 97080 Würzburg, Germany
| | - Gaurav Dugar
- Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg. 97080 Würzburg, Germany
| | - Natalia L Peeck
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Franziska Wimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
| | - Christoph Schoen
- Institute for Hygiene and Microbiology, University of Würzburg, 97080 Würzburg, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, 97080 Würzburg, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, 07745 Germany
| | - Cynthia M Sharma
- Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg. 97080 Würzburg, Germany.
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany.
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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23
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Chihara K, Barquist L, Takasugi K, Noda N, Tsuneda S. Global identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq. RNA Biol 2021; 18:2401-2416. [PMID: 33866926 DOI: 10.1080/15476286.2021.1917184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Pseudomonas aeruginosa harbours two redundant RNA-binding proteins RsmA/RsmN (RsmA/N), which play a critical role in balancing acute and chronic infections. However, in vivo binding sites on target transcripts and the overall impact on the physiology remains unclear. In this study, we applied in vivo UV crosslinking immunoprecipitation followed by RNA-sequencing (UV CLIP-seq) to detect RsmA/N-binding sites at single-nucleotide resolution and mapped more than 500 binding sites to approximately 400 genes directly bound by RsmA/N in P. aeruginosa. This also verified the ANGGA sequence in apical loops skewed towards 5'UTRs as a consensus motif for RsmA/N binding. Genetic analysis combined with CLIP-seq results suggested previously unrecognized RsmA/N targets involved in LPS modification. Moreover, the RsmA/N-titrating RNAs RsmY/RsmZ may be positively regulated by the RsmA/N-mediated translational repression of their upstream regulators, thus providing a possible mechanistic explanation for homoeostasis of the Rsm system. Thus, our study provides a detailed view of RsmA/N-RNA interactions and a resource for further investigation of the pleiotropic effects of RsmA/N on gene expression in P. aeruginosa.
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Affiliation(s)
- Kotaro Chihara
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Kenichi Takasugi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Naohiro Noda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
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24
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Michaux C, Hansen EE, Jenniches L, Gerovac M, Barquist L, Vogel J. Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium. Front Cell Infect Microbiol 2020; 10:600325. [PMID: 33324581 PMCID: PMC7724050 DOI: 10.3389/fcimb.2020.600325] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 10/19/2020] [Indexed: 12/19/2022] Open
Abstract
Enterococcus faecalis and faecium are two major representative clinical strains of the Enterococcus genus and are sadly notorious to be part of the top agents responsible for nosocomial infections. Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. Analyzing bacteria in late exponential phase, we capture ~40% (E. faecalis) and 43% (E. faecium) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. The transcriptome maps revealed sRNA candidates in both bacteria, some found in previous studies and new ones. Expression of candidate sRNAs is being confirmed under biologically relevant environmental conditions. This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse.
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Affiliation(s)
- Charlotte Michaux
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Elisabeth E Hansen
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Laura Jenniches
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Milan Gerovac
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
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25
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Venturini E, Svensson SL, Maaß S, Gelhausen R, Eggenhofer F, Li L, Cain AK, Parkhill J, Becher D, Backofen R, Barquist L, Sharma CM, Westermann AJ, Vogel J. A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence. Microlife 2020; 1:uqaa002. [PMID: 37223003 PMCID: PMC10117436 DOI: 10.1093/femsml/uqaa002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/14/2020] [Indexed: 05/25/2023]
Abstract
Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of comprehensive characterization in microbes other than Escherichia coli. We have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. We merged the annotated small proteome of Salmonella with new small proteins predicted with in silico and experimental approaches. We then exploited existing and newly generated global datasets that provide information on small open reading frame expression during infection of epithelial cells (dual RNA-seq), contribution to bacterial fitness inside macrophages (Transposon-directed insertion sequencing), and potential engagement in molecular interactions (Grad-seq). This integrative approach suggested a new role for the small protein MgrB beyond its known function in regulating PhoQ. We demonstrate a virulence and motility defect of a Salmonella ΔmgrB mutant and reveal an effect of MgrB in regulating the Salmonella transcriptome and proteome under infection-relevant conditions. Our study highlights the power of interpreting available 'omics' datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.
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Affiliation(s)
- Elisa Venturini
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Sarah L Svensson
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, 97080, Würzburg, Germany
| | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße, 17489, Greifswald, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee, 79110, Freiburg, Germany
| | - Florian Eggenhofer
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee, 79110, Freiburg, Germany
| | - Lei Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Guangqiao Road, Guangming District, 518131, Shenzhen, China
| | - Amy K Cain
- Department of Molecular Sciences, Macquarie University, Balaclava Road, Macquarie Park, New South Wales, 2109, Sydney, Australia
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, Cambridge, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, CB3 0ES, Cambridge, UK
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße, 17489, Greifswald, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee, 79110, Freiburg, Germany
| | - Lars Barquist
- Corresponding author: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße, 97080, Würzburg, Germany. E-mail:
| | - Cynthia M Sharma
- Corresponding author: Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, 97080, Würzburg, Germany. Tel: +49-9313182560; Fax: +49-9313182578; E-mail:
| | - Alexander J Westermann
- Corresponding author: Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany. Tel: +49 931 3182 575; E-mail:
| | - Jörg Vogel
- Corresponding author: Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany. Tel: +49 931 3182 575; E-mail:
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26
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Gerovac M, El Mouali Y, Kuper J, Kisker C, Barquist L, Vogel J. Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein. RNA 2020; 26:1448-1463. [PMID: 32646969 PMCID: PMC7491321 DOI: 10.1261/rna.076992.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 05/20/2023]
Abstract
RNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here establish glycerol gradient sedimentation with RNase treatment and mass spectrometry (GradR). Applied to Salmonella enterica, GradR confirms many known RBPs such as CsrA, Hfq, and ProQ by their RNase-sensitive sedimentation profiles, and discovers the FopA protein as a new member of the emerging family of FinO/ProQ-like RBPs. FopA, encoded on resistance plasmid pCol1B9, primarily targets a small RNA associated with plasmid replication. The target suite of FopA dramatically differs from the related global RBP ProQ, revealing context-dependent selective RNA recognition by FinO-domain RBPs. Numerous other unexpected RNase-induced changes in gradient profiles suggest that cellular RNA helps to organize macromolecular complexes in bacteria. By enabling poly(A)-independent generic RBP discovery, GradR provides an important element in the quest to build a comprehensive catalog of microbial RBPs.
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Affiliation(s)
- Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Youssef El Mouali
- Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
| | - Jochen Kuper
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
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27
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Elliott AG, Huang JX, Neve S, Zuegg J, Edwards IA, Cain AK, Boinett CJ, Barquist L, Lundberg CV, Steen J, Butler MS, Mobli M, Porter KM, Blaskovich MAT, Lociuro S, Strandh M, Cooper MA. An amphipathic peptide with antibiotic activity against multidrug-resistant Gram-negative bacteria. Nat Commun 2020; 11:3184. [PMID: 32576824 PMCID: PMC7311426 DOI: 10.1038/s41467-020-16950-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/03/2020] [Indexed: 11/09/2022] Open
Abstract
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. Peptide antibiotics often display a very narrow therapeutic index. Here, the authors present an optimized peptide antibiotic with broad-spectrum in vitro activities, in vivo efficacy in multiple disease models against multidrug-resistant Gram-negative infections, and reduced toxicity.
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Affiliation(s)
- Alysha G Elliott
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Johnny X Huang
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia.,School of Life Science and Technology, Weifang Medical University, Weifang, 261053, China
| | - Søren Neve
- Orphazyme, Ole Maaloesvej 3, 2200, Copenhagen, Denmark
| | - Johannes Zuegg
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Ingrid A Edwards
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Amy K Cain
- Wellcome Sanger Institute, Hinxton, UK.,Department of Molecular Sciences, Macquarie University, NSW, 2109, Australia
| | | | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | | | - Jason Steen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Queensland, Qld, Australia
| | - Mark S Butler
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, Queensland, Qld, Australia
| | - Kaela M Porter
- Adenium Biotech ApS, Ole Maaloesvej 3, 2200, Copenhagen, Denmark
| | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Sergio Lociuro
- BioVersys AG, Hochbergerstrasse 60C, Technology Park, 4057, Basel, Switzerland
| | - Magnus Strandh
- Adenium Biotech ApS, Ole Maaloesvej 3, 2200, Copenhagen, Denmark
| | - Matthew A Cooper
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia. .,Trinity College Dublin, Dublin, Ireland.
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28
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Abstract
It has been 10 years since the introduction of modern transposon-insertion sequencing (TIS) methods, which combine genome-wide transposon mutagenesis with high-throughput sequencing to estimate the fitness contribution or essentiality of each genetic component in a bacterial genome. Four TIS variations were published in 2009: transposon sequencing (Tn-Seq), transposon-directed insertion site sequencing (TraDIS), insertion sequencing (INSeq) and high-throughput insertion tracking by deep sequencing (HITS). TIS has since become an important tool for molecular microbiologists, being one of the few genome-wide techniques that directly links phenotype to genotype and ultimately can assign gene function. In this Review, we discuss the recent applications of TIS to answer overarching biological questions. We explore emerging and multidisciplinary methods that build on TIS, with an eye towards future applications. In this Review, several experts discuss progress in the decade since the development of transposon-based approaches for bacterial genetic screens. They describe how advances in both experimental technologies and analytical strategies are resulting in insights into diverse biological processes.
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Affiliation(s)
- Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Andrew L Goodman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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29
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Kingsley RA, Langridge G, Smith SE, Makendi C, Fookes M, Wileman TM, El Ghany MA, Keith Turner A, Dyson ZA, Sridhar S, Pickard D, Kay S, Feasey N, Wong V, Barquist L, Dougan G. Functional analysis of Salmonella Typhi adaptation to survival in water. Environ Microbiol 2019; 20:4079-4090. [PMID: 30450829 PMCID: PMC6282856 DOI: 10.1111/1462-2920.14458] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/16/2018] [Accepted: 10/21/2018] [Indexed: 11/28/2022]
Abstract
Contaminated water is a major risk factor associated with the transmission of Salmonella enterica serovar Typhi (S. Typhi), the aetiological agent of human typhoid. However, little is known about how this pathogen adapts to living in the aqueous environment. We used transcriptome analysis (RNA‐seq) and transposon mutagenesis (TraDIS) to characterize these adaptive changes and identify multiple genes that contribute to survival. Over half of the genes in the S. Typhi genome altered expression level within the first 24 h following transfer from broth culture to water, although relatively few did so in the first 30 min. Genes linked to central metabolism, stress associated with arrested proton motive force and respiratory chain factors changed expression levels. Additionally, motility and chemotaxis genes increased expression, consistent with a scavenging lifestyle. The viaB‐associated gene tviC encoding a glcNAc epimerase that is required for Vi polysaccharide biosynthesis was, along with several other genes, shown to contribute to survival in water. Thus, we define regulatory adaptation operating in S. Typhi that facilitates survival in water.
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Affiliation(s)
| | - Gemma Langridge
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Sarah E Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Carine Makendi
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Maria Fookes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Tom M Wileman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Moataz Abd El Ghany
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - A Keith Turner
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Zoe A Dyson
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Sushmita Sridhar
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Derek Pickard
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Sally Kay
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Vanessa Wong
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
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30
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Ondari EM, Klemm EJ, Msefula CL, El Ghany MA, Heath JN, Pickard DJ, Barquist L, Dougan G, Kingsley RA, MacLennan CA. Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313. Wellcome Open Res 2019; 4:74. [PMID: 31231691 PMCID: PMC6560496 DOI: 10.12688/wellcomeopenres.15059.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2019] [Indexed: 11/20/2022] Open
Abstract
Background:
Salmonella Typhimurium ST313 exhibits signatures of adaptation to invasive human infection, including higher resistance to humoral immune responses than gastrointestinal isolates. Full resistance to antibody-mediated complement killing (serum resistance) among nontyphoidal
Salmonellae is uncommon, but selection of highly resistant strains could compromise vaccine-induced antibody immunity. Here, we address the hypothesis that serum resistance is due to a distinct genotype or transcriptome response in
S. Typhimurium ST313. Methods: Six
S. Typhimurium ST313 bloodstream isolates, three of which were antibody resistant, were studied. Genomic content (single nucleotide polymorphisms and larger chromosomal modifications) of the strains was determined by Illumina and PACBIO sequencing, and functionally characterized using RNA-seq, transposon directed insertion site sequencing (TraDIS), targeted gene deletion and transfer of selected point mutations in an attempt to identify features associated with serum resistance.
Results: Sequence polymorphisms in genes from strains with atypical serum susceptibility when transferred from strains that were highly resistant or susceptible to a strain that exhibited intermediate susceptibility did not significantly alter serum killing phenotype. No large chromosomal modifications typified serum resistance or susceptibility. Genes required for resistance to serum identified by TraDIS and RNA-seq included those involved in exopolysaccharide synthesis, iron scavenging and metabolism. Most of the down-regulated genes were associated with membrane proteins. Resistant and susceptible strains had distinct transcriptional responses to serum, particularly related to genes responsible for polysaccharide biosynthesis. There was higher upregulation of
wca locus genes, involved in the biosynthesis of colanic acid exopolysaccharide, in susceptible strains and increased expression of
fepE, a regulator of very long-chain lipopolysaccharide in resistant strains. Conclusion: Clinical isolates of
S. Typhimurium ST313 exhibit distinct antibody susceptibility phenotypes that may be associated with changes in gene expression on exposure to serum.
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Affiliation(s)
- Edna M Ondari
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Novartis Vaccines Institute for Global Health, Siena, Italy.,Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Chisomo L Msefula
- Wellcome Trust Sanger Institute, Hinxton, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Institute, Blantyre, Malawi.,Department of Microbiology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Moataz Abd El Ghany
- Wellcome Trust Sanger Institute, Hinxton, UK.,The Westmead Institute for Medical Research and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead, Australia.,King Abdullah University of Science and Technology , Thuwal, Saudi Arabia
| | - Jennifer N Heath
- Institute of Immunology and Immuotherapy, University of Birmingham, Birmingham, UK
| | | | - Lars Barquist
- Wellcome Trust Sanger Institute, Hinxton, UK.,Helmholtz Institute for RNA-based Infection Research , Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, UK.,Department of Medicine, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, UK
| | | | - Calman A MacLennan
- Institute of Immunology and Immuotherapy, University of Birmingham, Birmingham, UK.,Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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31
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Nolan LM, Whitchurch CB, Barquist L, Katrib M, Boinett CJ, Mayho M, Goulding D, Charles IG, Filloux A, Parkhill J, Cain AK. A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa. Microb Genom 2018; 4. [PMID: 30383525 PMCID: PMC6321873 DOI: 10.1099/mgen.0.000229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is an extremely successful pathogen able to cause both acute and chronic infections in a range of hosts, utilizing a diverse arsenal of cell-associated and secreted virulence factors. A major cell-associated virulence factor, the Type IV pilus (T4P), is required for epithelial cell adherence and mediates a form of surface translocation termed twitching motility, which is necessary to establish a mature biofilm and actively expand these biofilms. P. aeruginosa twitching motility-mediated biofilm expansion is a coordinated, multicellular behaviour, allowing cells to rapidly colonize surfaces, including implanted medical devices. Although at least 44 proteins are known to be involved in the biogenesis, assembly and regulation of the T4P, with additional regulatory components and pathways implicated, it is unclear how these components and pathways interact to control these processes. In the current study, we used a global genomics-based random-mutagenesis technique, transposon directed insertion-site sequencing (TraDIS), coupled with a physical segregation approach, to identify all genes implicated in twitching motility-mediated biofilm expansion in P. aeruginosa. Our approach allowed identification of both known and novel genes, providing new insight into the complex molecular network that regulates this process in P. aeruginosa. Additionally, our data suggest that the flagellum-associated gene products have a differential effect on twitching motility, based on whether components are intra- or extracellular. Overall the success of our TraDIS approach supports the use of this global genomic technique for investigating virulence genes in bacterial pathogens.
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Affiliation(s)
- Laura M Nolan
- 1MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Cynthia B Whitchurch
- 2The ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Lars Barquist
- 3Institute for Molecular Infection Biology, University of Würzburg, Würzburg D-97080, Germany.,4Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Marilyn Katrib
- 2The ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Christine J Boinett
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,†Present address: Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Matthew Mayho
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - David Goulding
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ian G Charles
- 6Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UA, UK
| | - Alain Filloux
- 1MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Julian Parkhill
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Amy K Cain
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,‡Present address: Chemical and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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32
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Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M, Mayho M, Ellington MJ, Goulding D, Pickard D, Wick RR, Holt KE, Parkhill J, Thomson NR. Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin. Sci Rep 2018; 8:9868. [PMID: 29959380 PMCID: PMC6026146 DOI: 10.1038/s41598-018-28199-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 06/08/2018] [Indexed: 11/09/2022] Open
Abstract
Colistin remains one of the few antibiotics effective against multi-drug resistant (MDR) hospital pathogens, such as Klebsiella pneumoniae. Yet resistance to this last-line drug is rapidly increasing. Characterized mechanisms of colR in K. pneumoniae are largely due to chromosomal mutations in two-component regulators, although a plasmid-mediated colR mechanism has recently been uncovered. However, the effects of intrinsic colistin resistance are yet to be characterized on a whole-genome level. Here, we used a genomics-based approach to understand the mechanisms of adaptive colR acquisition in K. pneumoniae. In controlled directed-evolution experiments we observed two distinct paths to colistin resistance acquisition. Whole genome sequencing identified mutations in two colistin resistance genes: in the known colR regulator phoQ which became fixed in the population and resulted in a single amino acid change, and unstable minority variants in the recently described two-component sensor crrB. Through RNAseq and microscopy, we reveal the broad range of effects that colistin exposure has on the cell. This study is the first to use genomics to identify a population of minority variants with mutations in a colR gene in K. pneumoniae.
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Affiliation(s)
- Amy K Cain
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia.
| | - Christine J Boinett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Würzburg, D-97080, Germany
| | - Janina Dordel
- Department of Biology, Drexel University, Philadelphia, 19104, PA, USA
| | - Maria Fookes
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthew Mayho
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | | - David Goulding
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ryan R Wick
- Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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33
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Holmqvist E, Li L, Bischler T, Barquist L, Vogel J. Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3′ Ends. Mol Cell 2018; 70:971-982.e6. [DOI: 10.1016/j.molcel.2018.04.017] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/05/2018] [Accepted: 04/19/2018] [Indexed: 12/17/2022]
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34
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Wheeler NE, Gardner PP, Barquist L. Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica. PLoS Genet 2018; 14:e1007333. [PMID: 29738521 PMCID: PMC5940178 DOI: 10.1371/journal.pgen.1007333] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/24/2018] [Indexed: 11/18/2022] Open
Abstract
Emerging pathogens are a major threat to public health, however understanding how pathogens adapt to new niches remains a challenge. New methods are urgently required to provide functional insights into pathogens from the massive genomic data sets now being generated from routine pathogen surveillance for epidemiological purposes. Here, we measure the burden of atypical mutations in protein coding genes across independently evolved Salmonella enterica lineages, and use these as input to train a random forest classifier to identify strains associated with extraintestinal disease. Members of the species fall along a continuum, from pathovars which cause gastrointestinal infection and low mortality, associated with a broad host-range, to those that cause invasive infection and high mortality, associated with a narrowed host range. Our random forest classifier learned to perfectly discriminate long-established gastrointestinal and invasive serovars of Salmonella. Additionally, it was able to discriminate recently emerged Salmonella Enteritidis and Typhimurium lineages associated with invasive disease in immunocompromised populations in sub-Saharan Africa, and within-host adaptation to invasive infection. We dissect the architecture of the model to identify the genes that were most informative of phenotype, revealing a common theme of degradation of metabolic pathways in extraintestinal lineages. This approach accurately identifies patterns of gene degradation and diversifying selection specific to invasive serovars that have been captured by more labour-intensive investigations, but can be readily scaled to larger analyses.
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Affiliation(s)
- Nicole E. Wheeler
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- * E-mail: (NEW); (LB)
| | - Paul P. Gardner
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Lars Barquist
- Institute for Molecular Infection Biology, University of Wuerzburg, Wuerzburg, Germany
- Helmholtz Institute for RNA-based Infection Research, Wuerzburg, Germany
- * E-mail: (NEW); (LB)
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35
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Barquist L, Westermann AJ, Vogel J. Molecular phenotyping of infection-associated small non-coding RNAs. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0081. [PMID: 27672158 DOI: 10.1098/rstb.2016.0081] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2016] [Indexed: 02/07/2023] Open
Abstract
Infection is a complicated balance, with both pathogen and host struggling to tilt the result in their favour. Bacterial infection biology has relied on forward genetics for many of its advances, defining phenotype in terms of replication in model systems. However, many known virulence factors fail to produce robust phenotypes, particularly in the systems most amenable to genetic manipulation, such as cell-culture models. This has particularly been limiting for the study of the bacterial regulatory small RNAs (sRNAs) in infection. We argue that new sequencing-based technologies can work around this problem by providing a 'molecular phenotype', defined in terms of the specific transcriptional dysregulation in the infection system induced by gene deletion. We illustrate this using the example of our recent study of the PinT sRNA using dual RNA-seq, that is, simultaneous RNA sequencing of host and pathogen during infection. We additionally discuss how other high-throughput technologies, in particular genetic interaction mapping using transposon insertion sequencing, may be used to further dissect molecular phenotypes. We propose a strategy for how high-throughput technologies can be integrated in the study of non-coding regulators as well as bacterial virulence factors, enhancing our ability to rapidly generate hypotheses with regards to their function.This article is part of the themed issue 'The new bacteriology'.
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Affiliation(s)
- Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
| | - Alexander J Westermann
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97070 Würzburg, Germany
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36
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Heidrich N, Bauriedl S, Barquist L, Li L, Schoen C, Vogel J. The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. Nucleic Acids Res 2017; 45:6147-6167. [PMID: 28334889 PMCID: PMC5449619 DOI: 10.1093/nar/gkx168] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/02/2017] [Indexed: 12/15/2022] Open
Abstract
Neisseria meningitidis is a human commensal that can also cause life-threatening meningitis and septicemia. Despite growing evidence for RNA-based regulation in meningococci, their transcriptome structure and output of regulatory small RNAs (sRNAs) are incompletely understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptome of N. meningitidis strain 8013. Annotation of 1625 transcriptional start sites defines transcription units for most protein-coding genes but also reveals a paucity of classical σ70-type promoters, suggesting the existence of activators that compensate for the lack of −35 consensus sequences in N. meningitidis. The transcriptome maps also reveal 65 candidate sRNAs, a third of which were validated by northern blot analysis. Immunoprecipitation with the RNA chaperone Hfq drafts an unexpectedly large post-transcriptional regulatory network in this organism, comprising 23 sRNAs and hundreds of potential mRNA targets. Based on this data, using a newly developed gfp reporter system we validate an Hfq-dependent mRNA repression of the putative colonization factor PrpB by the two trans-acting sRNAs RcoF1/2. Our genome-wide RNA compendium will allow for a better understanding of meningococcal transcriptome organization and riboregulation with implications for colonization of the human nasopharynx.
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Affiliation(s)
- Nadja Heidrich
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Saskia Bauriedl
- Institute for Hygiene and Microbiology (IHM), University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Lei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christoph Schoen
- Institute for Hygiene and Microbiology (IHM), University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), D-97080 Würzburg, Germany
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37
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Abstract
The transcriptome is a powerful proxy for the physiological state of a cell, healthy or diseased. As a result, transcriptome analysis has become a key tool in understanding the molecular changes that accompany bacterial infections of eukaryotic cells. Until recently, such transcriptomic studies have been technically limited to analyzing mRNA expression changes in either the bacterial pathogen or the infected eukaryotic host cell. However, the increasing sensitivity of high-throughput RNA sequencing now enables "dual RNA-seq" studies, simultaneously capturing all classes of coding and noncoding transcripts in both the pathogen and the host. In the five years since the concept of dual RNA-seq was introduced, the technique has been applied to a range of infection models. This has not only led to a better understanding of the physiological changes in pathogen and host during the course of an infection but has also revealed hidden molecular phenotypes of virulence-associated small noncoding RNAs that were not visible in standard infection assays. Here, we use the knowledge gained from these recent studies to suggest experimental and computational guidelines for the design of future dual RNA-seq studies. We conclude this review by discussing prospective applications of the technique.
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Affiliation(s)
- Alexander J. Westermann
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- * E-mail:
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38
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Wheeler NE, Barquist L, Kingsley RA, Gardner PP. A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. Bioinformatics 2016; 32:3566-3574. [PMID: 27503221 PMCID: PMC5181535 DOI: 10.1093/bioinformatics/btw518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/17/2016] [Accepted: 08/02/2016] [Indexed: 02/04/2023] Open
Abstract
Motivation: Next generation sequencing technologies have provided us with a wealth of information on genetic variation, but predicting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics. Results: We present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms. Availability and Implementation: A program implementing DBS for pairwise genome comparisons is freely available at: https://github.com/UCanCompBio/deltaBS. Contact:nicole.wheeler@pg.canterbury.ac.nz or lars.barquist@uni-wuerzburg.de Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicole E Wheeler
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Lars Barquist
- Institute for Molecular Infection Biology, University of Wuerzburg, Wuerzburg, Germany
| | - Robert A Kingsley
- Institute of Food Research, Norwich Research Park, Norwich, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - Paul P Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Bio-protection Research Centre, University of Canterbury, Christchurch, New Zealand
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39
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Read HM, Mills G, Johnson S, Tsai P, Dalton J, Barquist L, Print CG, Patrick WM, Wiles S. The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium. PeerJ 2016; 4:e2130. [PMID: 27366640 PMCID: PMC4924136 DOI: 10.7717/peerj.2130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 05/24/2016] [Indexed: 11/30/2022] Open
Abstract
Bioluminescent reporter genes, such as those from fireflies and bacteria, let researchers use light production as a non-invasive and non-destructive surrogate measure of microbial numbers in a wide variety of environments. As bioluminescence needs microbial metabolites, tagging microorganisms with luciferases means only live metabolically active cells are detected. Despite the wide use of bioluminescent reporter genes, very little is known about the impact of continuous (also called constitutive) light expression on tagged bacteria. We have previously made a bioluminescent strain of Citrobacter rodentium, a bacterium which infects laboratory mice in a similar way to how enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC) infect humans. In this study, we compared the growth of the bioluminescent C. rodentium strain ICC180 with its non-bioluminescent parent (strain ICC169) in a wide variety of environments. To understand more about the metabolic burden of expressing light, we also compared the growth profiles of the two strains under approximately 2,000 different conditions. We found that constitutive light expression in ICC180 was near-neutral in almost every non-toxic environment tested. However, we also found that the non-bioluminescent parent strain has a competitive advantage over ICC180 during infection of adult mice, although this was not enough for ICC180 to be completely outcompeted. In conclusion, our data suggest that constitutive light expression is not metabolically costly to C. rodentium and supports the view that bioluminescent versions of microbes can be used as a substitute for their non-bioluminescent parents to study bacterial behaviour in a wide variety of environments.
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Affiliation(s)
- Hannah M Read
- Bioluminescent Superbugs Lab, University of Auckland, Auckland, New Zealand; Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Grant Mills
- Bioluminescent Superbugs Lab, University of Auckland, Auckland, New Zealand; Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Sarah Johnson
- Bioluminescent Superbugs Lab, University of Auckland, Auckland, New Zealand; Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Peter Tsai
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand; Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - James Dalton
- Bioluminescent Superbugs Lab, University of Auckland, Auckland, New Zealand; Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand
| | - Lars Barquist
- Institute for Molecular Infection Biology, University of Würzburg , Würzburg , Germany
| | - Cristin G Print
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand; Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand
| | - Wayne M Patrick
- Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand; Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, University of Auckland, Auckland, New Zealand; Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand
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Barquist L, Burge SW, Gardner PP. Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. Curr Protoc Bioinformatics 2016; 54:12.13.1-12.13.25. [PMID: 27322404 PMCID: PMC5010141 DOI: 10.1002/cpbi.4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Emerging high-throughput technologies have led to a deluge of putative non-coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology detection is critical to making maximal use of functional information gathered about ncRNAs: identifying homologous sequence allows us to transfer information gathered in one organism to another quickly and with a high degree of confidence. ncRNA presents a challenge for homology detection, as the primary sequence is often poorly conserved and de novo secondary structure prediction and search remain difficult. This unit introduces methods developed by the Rfam database for identifying "families" of homologous ncRNAs starting from single "seed" sequences, using manually curated sequence alignments to build powerful statistical models of sequence and structure conservation known as covariance models (CMs), implemented in the Infernal software package. We provide a step-by-step iterative protocol for identifying ncRNA homologs and then constructing an alignment and corresponding CM. We also work through an example for the bacterial small RNA MicA, discovering a previously unreported family of divergent MicA homologs in genus Xenorhabdus in the process. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Lars Barquist
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, D-97080 Germany
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA United Kingdom; Fax: +44 (0)1223 494919
| | - Sarah W. Burge
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA United Kingdom; Fax: +44 (0)1223 494919
| | - Paul P. Gardner
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
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Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J. Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo. EMBO J 2016; 35:991-1011. [PMID: 27044921 PMCID: PMC5207318 DOI: 10.15252/embj.201593360] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/26/2016] [Indexed: 12/22/2022] Open
Abstract
The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein target sites. We have applied CLIP‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single‐nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during their interactions with hundreds of cellular transcripts. This reveals 3′‐located Rho‐independent terminators as a universal motif involved in Hfq–RNA interactions. Additionally, Hfq preferentially binds 5′ to sRNA‐target sites in mRNAs, and 3′ to seed sequences in sRNAs, reflecting a simple logic in how Hfq facilitates sRNA–mRNA interactions. Importantly, global knowledge of Hfq sites significantly improves sRNA‐target predictions. CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs. Overall, our generic CLIP‐seq approach will bring new insights into post‐transcriptional gene regulation by RNA‐binding proteins in diverse bacterial species.
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Affiliation(s)
- Erik Holmqvist
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Patrick R Wright
- Bioinformatics Group, Department of Computer Science, Albert Ludwig University Freiburg, Freiburg, Germany
| | - Lei Li
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Thorsten Bischler
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert Ludwig University Freiburg, Freiburg, Germany BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ, Page AJ, Langridge GC, Quail MA, Keane JA, Parkhill J. The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. Bioinformatics 2016; 32:1109-11. [PMID: 26794317 PMCID: PMC4896371 DOI: 10.1093/bioinformatics/btw022] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/13/2016] [Indexed: 12/05/2022] Open
Abstract
Summary: Transposon insertion sequencing is a high-throughput technique for assaying large libraries of otherwise isogenic transposon mutants providing insight into gene essentiality, gene function and genetic interactions. We previously developed the Transposon Directed Insertion Sequencing (TraDIS) protocol for this purpose, which utilizes shearing of genomic DNA followed by specific PCR amplification of transposon-containing fragments and Illumina sequencing. Here we describe an optimized high-yield library preparation and sequencing protocol for TraDIS experiments and a novel software pipeline for analysis of the resulting data. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. This article can serve as a general reference for the application of the TraDIS methodology. Availability and implementation: The optimized sequencing protocol is included as supplementary information. The Bio-Tradis analysis pipeline is available under a GPL license at https://github.com/sanger-pathogens/Bio-Tradis Contact:parkhill@sanger.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lars Barquist
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and Institute for Molecular Infection Biology, University of Würzburg, Würzburg D-97080, Germany
| | - Matthew Mayho
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Carla Cummins
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | | | - Andrew J Page
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Gemma C Langridge
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Michael A Quail
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | | | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
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Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J. Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions. Nature 2016; 529:496-501. [PMID: 26789254 DOI: 10.1038/nature16547] [Citation(s) in RCA: 325] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/18/2015] [Indexed: 12/12/2022]
Abstract
Bacteria express many small RNAs for which the regulatory roles in pathogenesis have remained poorly understood due to a paucity of robust phenotypes in standard virulence assays. Here we use a generic 'dual RNA-seq' approach to profile RNA expression simultaneously in pathogen and host during Salmonella enterica serovar Typhimurium infection and reveal the molecular impact of bacterial riboregulators. We identify a PhoP-activated small RNA, PinT, which upon bacterial internalization temporally controls the expression of both invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity causes pervasive changes in coding and noncoding transcripts of the host. Interspecies correlation analysis links PinT to host cell JAK-STAT signalling, and we identify infection-specific alterations in multiple long noncoding RNAs. Our study provides a paradigm for a sensitive RNA-based analysis of intracellular bacterial pathogens and their hosts without physical separation, as well as a new discovery route for hidden functions of pathogen genes.
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Affiliation(s)
- Alexander J Westermann
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany
| | - Konrad U Förstner
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany.,University of Würzburg, Core Unit Systems Medicine, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany
| | - Fabian Amman
- University of Leipzig, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Härtelstraße 16-18, D-04107 Leipzig, Germany.,University of Vienna, Theoretical Biochemistry Group, Institute for Theoretical Chemistry, Währinger Straße 17, A-1090 Vienna, Austria
| | - Lars Barquist
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany
| | - Yanjie Chao
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany
| | - Leon N Schulte
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany
| | - Lydia Müller
- University of Leipzig, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Peter F Stadler
- University of Leipzig, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Härtelstraße 16-18, D-04107 Leipzig, Germany.,University of Vienna, Theoretical Biochemistry Group, Institute for Theoretical Chemistry, Währinger Straße 17, A-1090 Vienna, Austria.,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.,Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, New Mexico 87501, USA
| | - Jörg Vogel
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany.,Research Centre for Infectious Diseases (ZINF), University of Würzburg, D-97070 Würzburg, Germany
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Abstract
Over the past decade, bacterial small RNAs (sRNAs) have gone from a biological curiosity to being recognized as a major class of regulatory molecules. High-throughput methods for sampling the transcriptional output of bacterial cells demonstrate that sRNAs are universal features of bacterial transcriptomes, are plentiful, and appear to vary extensively over evolutionary time. With ever more bacteria coming under study, the question becomes how can we accelerate the discovery and functional characterization of sRNAs in diverse organisms. New technologies built on high-throughput sequencing are emerging that can rapidly provide global insight into the numbers and functions of sRNAs in bacteria of interest, providing information that can shape hypotheses and guide research. In this review, we describe recent developments in transcriptomics (RNA-seq) and functional genomics that we expect to help us develop an integrated, systems-level view of sRNA biology in bacteria.
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Affiliation(s)
- Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
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Okoro CK, Barquist L, Connor TR, Harris SR, Clare S, Stevens MP, Arends MJ, Hale C, Kane L, Pickard DJ, Hill J, Harcourt K, Parkhill J, Dougan G, Kingsley RA. Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa. PLoS Negl Trop Dis 2015; 9:e0003611. [PMID: 25803844 PMCID: PMC4372345 DOI: 10.1371/journal.pntd.0003611] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/10/2015] [Indexed: 12/16/2022] Open
Abstract
Two lineages of Salmonella enterica serovar Typhimurium (S. Typhimurium) of multi-locus sequence type ST313 have been linked with the emergence of invasive Salmonella disease across sub-Saharan Africa. The expansion of these lineages has a temporal association with the HIV pandemic and antibiotic usage. We analysed the whole genome sequence of 129 ST313 isolates representative of the two lineages and found evidence of lineage-specific genome degradation, with some similarities to that observed in S. Typhi. Individual ST313 S. Typhimurium isolates exhibit a distinct metabolic signature and modified enteropathogenesis in both a murine and cattle model of colitis, compared to S. Typhimurium outside of the ST313 lineages. These data define phenotypes that distinguish ST313 isolates from other S. Typhimurium and may represent adaptation to a distinct pathogenesis and lifestyle linked to an-immuno-compromised human population.
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Affiliation(s)
- Chinyere K. Okoro
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lars Barquist
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Institute for Molecular Infection Biology, University of Wurzburg, Wuerzburg, Germany
| | - Thomas R. Connor
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Simon R. Harris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Simon Clare
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mark P. Stevens
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Mark J. Arends
- Department of Pathology, University of Cambridge, Addenbrokes Hospital, Cambridge, United Kingdom
- Edinburgh Cancer Research Centre, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Christine Hale
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Leanne Kane
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek J. Pickard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jennifer Hill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Katherine Harcourt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Robert A. Kingsley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Institute of Food Research, Norwich Research Park, Norwich, Norfolk, United Kingdom
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Lindgreen S, Umu SU, Lai ASW, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP. Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Comput Biol 2014; 10:e1003907. [PMID: 25357249 PMCID: PMC4214555 DOI: 10.1371/journal.pcbi.1003907] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/11/2014] [Indexed: 02/03/2023] Open
Abstract
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA elements in bacterial and archaeal genomes is hampered by the difficulty of de novo identification. The emergence of new technologies for characterizing transcriptome outputs, notably RNA-seq, are improving noncoding RNA identification and expression quantification. However, a major challenge is to robustly distinguish functional outputs from transcriptional noise. To establish whether annotation of existing transcriptome data has effectively captured all functional outputs, we analysed over 400 publicly available RNA-seq datasets spanning 37 different Archaea and Bacteria. Using comparative tools, we identify close to a thousand highly-expressed candidate noncoding RNAs. However, our analyses reveal that capacity to identify noncoding RNA outputs is strongly dependent on phylogenetic sampling. Surprisingly, and in stark contrast to protein-coding genes, the phylogenetic window for effective use of comparative methods is perversely narrow: aggregating public datasets only produced one phylogenetic cluster where these tools could be used to robustly separate unannotated noncoding RNAs from a null hypothesis of transcriptional noise. Our results show that for the full potential of transcriptomics data to be realized, a change in experimental design is paramount: effective transcriptomics requires phylogeny-aware sampling. We have analysed more than 400 public transcriptomes, generated using RNA-seq, from almost 40 strains of Bacteria and Archaea. We discovered that the capacity to identify noncoding RNA outputs from this data is strongly dependent on phylogenetic sampling. Our results show that, for the full potential of transcriptomics data as a discovery tool to be realized, a change in experimental design is critical: effective comparative transcriptomics requires phylogeny-aware sampling. We also examined how comparative transcriptomics experiments can be used to effectively identify RNA elements. We find that, for RNA element discovery, a phylogeny-informed sampling approach is more effective than analyses of individual species. Phylogeny-informed sampling reveals a narrow ‘Goldilocks Zone’ (where species are not too similar and not too divergent) for RNA identification using clusters of related species. In stark contrast to protein-coding genes, not only is the phylogenetic window for the effective use of comparative methods for noncoding RNA identification perversely narrow, but few existing datasets sit within this Goldilocks Zone: by aggregating public datasets, we were only able to create one phylogenetic cluster where comparative tools could be used to confidently separate unannotated noncoding RNAs from transcriptional noise.
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MESH Headings
- Archaea/genetics
- Bacteria/genetics
- Cluster Analysis
- Computational Biology
- Databases, Genetic
- Gene Expression Profiling/methods
- Phylogeny
- RNA, Archaeal/chemistry
- RNA, Archaeal/classification
- RNA, Archaeal/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/classification
- RNA, Bacterial/genetics
- RNA, Untranslated/chemistry
- RNA, Untranslated/classification
- RNA, Untranslated/genetics
- Transcriptome/genetics
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Affiliation(s)
- Stinus Lindgreen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sinan Uğur Umu
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Alicia Sook-Wei Lai
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Hisham Eldai
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Wenting Liu
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Stephanie McGimpsey
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Nicole E. Wheeler
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Patrick J. Biggs
- Institute of Veterinary, Animal & Biomedical Sciences, Massey University, Palmerston North, New Zealand
- Allan Wilson Centre for Molecular Ecology & Evolution, Massey University, Palmerston North, New Zealand
| | - Nick R. Thomson
- Pathogen Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Lars Barquist
- Pathogen Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Institute for Molecular Infection Biology, University of Wuerzburg, Wuerzburg, Germany
| | - Anthony M. Poole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Allan Wilson Centre for Molecular Ecology & Evolution, Massey University, Palmerston North, New Zealand
- * E-mail: (AMP); (PPG)
| | - Paul P. Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- * E-mail: (AMP); (PPG)
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Pettit LJ, Browne HP, Yu L, Smits WK, Fagan RP, Barquist L, Martin MJ, Goulding D, Duncan SH, Flint HJ, Dougan G, Choudhary JS, Lawley TD. Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism. BMC Genomics 2014; 15:160. [PMID: 24568651 PMCID: PMC4028888 DOI: 10.1186/1471-2164-15-160] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/14/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Clostridium difficile is an anaerobic, Gram-positive bacterium that can reside as a commensal within the intestinal microbiota of healthy individuals or cause life-threatening antibiotic-associated diarrhea in immunocompromised hosts. C. difficile can also form highly resistant spores that are excreted facilitating host-to-host transmission. The C. difficile spo0A gene encodes a highly conserved transcriptional regulator of sporulation that is required for relapsing disease and transmission in mice. RESULTS Here we describe a genome-wide approach using a combined transcriptomic and proteomic analysis to identify Spo0A regulated genes. Our results validate Spo0A as a positive regulator of putative and novel sporulation genes as well as components of the mature spore proteome. We also show that Spo0A regulates a number of virulence-associated factors such as flagella and metabolic pathways including glucose fermentation leading to butyrate production. CONCLUSIONS The C. difficile spo0A gene is a global transcriptional regulator that controls diverse sporulation, virulence and metabolic phenotypes coordinating pathogen adaptation to a wide range of host interactions. Additionally, the rich breadth of functional data allowed us to significantly update the annotation of the C. difficile 630 reference genome which will facilitate basic and applied research on this emerging pathogen.
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Croucher NJ, Mitchell AM, Gould KA, Inverarity D, Barquist L, Feltwell T, Fookes MC, Harris SR, Dordel J, Salter SJ, Browall S, Zemlickova H, Parkhill J, Normark S, Henriques-Normark B, Hinds J, Mitchell TJ, Bentley SD. Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection. PLoS Genet 2013; 9:e1003868. [PMID: 24130509 PMCID: PMC3794909 DOI: 10.1371/journal.pgen.1003868] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 08/24/2013] [Indexed: 01/12/2023] Open
Abstract
Streptococcus pneumoniae of serotype 3 possess a mucoid capsule and cause disease associated with high mortality rates relative to other pneumococci. Phylogenetic analysis of a complete reference genome and 81 draft sequences from clonal complex 180, the predominant serotype 3 clone in much of the world, found most sampled isolates belonged to a clade affected by few diversifying recombinations. However, other isolates indicate significant genetic variation has accumulated over the clonal complex's entire history. Two closely related genomes, one from the blood and another from the cerebrospinal fluid, were obtained from a patient with meningitis. The pair differed in their behaviour in a mouse model of disease and in their susceptibility to antimicrobials, with at least some of these changes attributable to a mutation that up-regulated the patAB efflux pump. This indicates clinically important phenotypic variation can accumulate rapidly through small alterations to the genotype.
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Affiliation(s)
- Nicholas J. Croucher
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail: (NJC); (TJM)
| | - Andrea M. Mitchell
- Institute of Microbiology and Infection and School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Katherine A. Gould
- Bacterial Microarray Group, Division of Clinical Sciences, St. George's Hospital, University of London, London, United Kingdom
| | - Donald Inverarity
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Lars Barquist
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Theresa Feltwell
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Maria C. Fookes
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Simon R. Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Janina Dordel
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Susannah J. Salter
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sarah Browall
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Dept. of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Staffan Normark
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Dept. of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Dept. of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Jason Hinds
- Bacterial Microarray Group, Division of Clinical Sciences, St. George's Hospital, University of London, London, United Kingdom
| | - Tim J. Mitchell
- Institute of Microbiology and Infection and School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail: (NJC); (TJM)
| | - Stephen D. Bentley
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
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Abstract
In this review, we discuss transposon-insertion sequencing, variously known in the literature as TraDIS, Tn-seq, INSeq, and HITS. By monitoring a large library of single transposon-insertion mutants with high-throughput sequencing, these methods can rapidly identify genomic regions that contribute to organismal fitness under any condition assayable in the laboratory with exquisite resolution. We discuss the various protocols that have been developed and methods for analysis. We provide an overview of studies that have examined the reproducibility and accuracy of these methods, as well as studies showing the advantages offered by the high resolution and dynamic range of high-throughput sequencing over previous methods. We review a number of applications in the literature, from predicting genes essential for in vitro growth to directly assaying requirements for survival under infective conditions in vivo. We also highlight recent progress in assaying non-coding regions of the genome in addition to known coding sequences, including the combining of RNA-seq with high-throughput transposon mutagenesis.
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Affiliation(s)
- Lars Barquist
- Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK; EMBL-European Bioinformatics Institute; Hinxton, Cambridge, UK
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Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP. A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. Nucleic Acids Res 2013; 41:4549-64. [PMID: 23470992 PMCID: PMC3632133 DOI: 10.1093/nar/gkt148] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Salmonella Typhi and Typhimurium diverged only ∼50 000 years ago, yet have very different host ranges and pathogenicity. Despite the availability of multiple whole-genome sequences, the genetic differences that have driven these changes in phenotype are only beginning to be understood. In this study, we use transposon-directed insertion-site sequencing to probe differences in gene requirements for competitive growth in rich media between these two closely related serovars. We identify a conserved core of 281 genes that are required for growth in both serovars, 228 of which are essential in Escherichia coli. We are able to identify active prophage elements through the requirement for their repressors. We also find distinct differences in requirements for genes involved in cell surface structure biogenesis and iron utilization. Finally, we demonstrate that transposon-directed insertion-site sequencing is not only applicable to the protein-coding content of the cell but also has sufficient resolution to generate hypotheses regarding the functions of non-coding RNAs (ncRNAs) as well. We are able to assign probable functions to a number of cis-regulatory ncRNA elements, as well as to infer likely differences in trans-acting ncRNA regulatory networks.
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Affiliation(s)
- Lars Barquist
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
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