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Birkholz N, Kamata K, Feussner M, Wilkinson ME, Cuba Samaniego C, Migur A, Kimanius D, Ceelen M, Went SC, Usher B, Blower TR, Brown CM, Beisel CL, Weinberg Z, Fagerlund RD, Jackson SA, Fineran PC. Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein. Nature 2024; 631:670-677. [PMID: 38987591 DOI: 10.1038/s41586-024-07644-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/31/2024] [Indexed: 07/12/2024]
Abstract
In all organisms, regulation of gene expression must be adjusted to meet cellular requirements and frequently involves helix-turn-helix (HTH) domain proteins1. For instance, in the arms race between bacteria and bacteriophages, rapid expression of phage anti-CRISPR (acr) genes upon infection enables evasion from CRISPR-Cas defence; transcription is then repressed by an HTH-domain-containing anti-CRISPR-associated (Aca) protein, probably to reduce fitness costs from excessive expression2-5. However, how a single HTH regulator adjusts anti-CRISPR production to cope with increasing phage genome copies and accumulating acr mRNA is unknown. Here we show that the HTH domain of the regulator Aca2, in addition to repressing Acr synthesis transcriptionally through DNA binding, inhibits translation of mRNAs by binding conserved RNA stem-loops and blocking ribosome access. The cryo-electron microscopy structure of the approximately 40 kDa Aca2-RNA complex demonstrates how the versatile HTH domain specifically discriminates RNA from DNA binding sites. These combined regulatory modes are widespread in the Aca2 family and facilitate CRISPR-Cas inhibition in the face of rapid phage DNA replication without toxic acr overexpression. Given the ubiquity of HTH-domain-containing proteins, it is anticipated that many more of them elicit regulatory control by dual DNA and RNA binding.
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Affiliation(s)
- Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Kotaro Kamata
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
| | - Maximilian Feussner
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Max E Wilkinson
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Angela Migur
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | | | - Marijn Ceelen
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute for Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Sam C Went
- Department of Biosciences, Durham University, Durham, UK
| | - Ben Usher
- Department of Biosciences, Durham University, Durham, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Durham, UK
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.
- Genetics Otago, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.
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2
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Raghunandanan S, Priya R, Alanazi F, Lybecker MC, Schlax P, Yang X. A Fur family protein BosR is a novel RNA-binding protein that controls rpoS RNA stability in the Lyme disease pathogen. Nucleic Acids Res 2024; 52:5320-5335. [PMID: 38366569 PMCID: PMC11109971 DOI: 10.1093/nar/gkae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
The σ54-σS sigma factor cascade plays a central role in regulating differential gene expression during the enzootic cycle of Borreliella burgdorferi, the Lyme disease pathogen. In this pathway, the primary transcription of rpoS (which encodes σS) is under the control of σ54 which is activated by a bacterial enhancer-binding protein (EBP), Rrp2. The σ54-dependent activation in B. burgdorferi has long been thought to be unique, requiring an additional factor, BosR, a homologue of classical Fur/PerR repressor/activator. However, how BosR is involved in this σ54-dependent activation remains unclear and perplexing. In this study, we demonstrate that BosR does not function as a regulator for rpoS transcriptional activation. Instead, it functions as a novel RNA-binding protein that governs the turnover rate of rpoS mRNA. We further show that BosR directly binds to the 5' untranslated region (UTR) of rpoS mRNA, and the binding region overlaps with a region required for rpoS mRNA degradation. Mutations within this 5'UTR region result in BosR-independent RpoS production. Collectively, these results uncover a novel role of Fur/PerR family regulators as RNA-binding proteins and redefine the paradigm of the σ54-σS pathway in B. burgdorferi.
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Affiliation(s)
- Sajith Raghunandanan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Raj Priya
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Fuad Alanazi
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
| | - Meghan C Lybecker
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Center for Disease Control and Prevention, Fort Collins, CO, USA
| | - Paula Jean Schlax
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - X Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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3
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Monti M, Herman R, Mancini L, Capitanchik C, Davey K, Dawson CS, Ule J, Thomas GH, Willis AE, Lilley KS, Villanueva E. Interrogation of RNA-protein interaction dynamics in bacterial growth. Mol Syst Biol 2024; 20:573-589. [PMID: 38531971 PMCID: PMC11066096 DOI: 10.1038/s44320-024-00031-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Characterising RNA-protein interaction dynamics is fundamental to understand how bacteria respond to their environment. In this study, we have analysed the dynamics of 91% of the Escherichia coli expressed proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mostly present in Proteobacteria, two of them are orthologs of human mitochondrial proteins associated with rare metabolic disorders. Moreover, we reveal novel RBP functions for proteins such as the chaperone HtpG, a new stationary phase tRNA-binding protein. For the first time, the dynamics of the bacterial RBPome have been interrogated, showcasing how this approach can reveal the function of uncharacterised proteins and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.
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Affiliation(s)
- Mie Monti
- MRC Toxicology Unit, University of Cambridge, University of Cambridge, CB2 1QR, Cambridge, UK
| | - Reyme Herman
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Leonardo Mancini
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Charlotte Capitanchik
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- UK Dementia Research Institute at King's College London, The Wohl, 5 Cutcombe Road, London, SE5 9RX, UK
| | - Karen Davey
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- UK Dementia Research Institute at King's College London, The Wohl, 5 Cutcombe Road, London, SE5 9RX, UK
| | - Charlotte S Dawson
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- UK Dementia Research Institute at King's College London, The Wohl, 5 Cutcombe Road, London, SE5 9RX, UK
| | - Gavin H Thomas
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, University of Cambridge, CB2 1QR, Cambridge, UK.
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK.
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK.
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Zhu Y, Ponath F, Cosi V, Vogel J. A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum. Nucleic Acids Res 2024; 52:3950-3970. [PMID: 38281181 DOI: 10.1093/nar/gkae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024] Open
Abstract
The common oral microbe Fusobacterium nucleatum has recently drawn attention after it was found to colonize tumors throughout the human body. Fusobacteria are also interesting study systems for bacterial RNA biology as these early-branching species encode many small noncoding RNAs (sRNAs) but lack homologs of the common RNA-binding proteins (RBPs) CsrA, Hfq and ProQ. To search for alternate sRNA-associated RBPs in F. nucleatum, we performed a systematic mass spectrometry analysis of proteins that co-purified with 19 different sRNAs. This approach revealed strong enrichment of the KH domain proteins KhpA and KhpB with nearly all tested sRNAs, including the σE-dependent sRNA FoxI, a regulator of several envelope proteins. KhpA/B act as a dimer to bind sRNAs with low micromolar affinity and influence the stability of several of their target transcripts. Transcriptome studies combined with biochemical and genetic analyses suggest that KhpA/B have several physiological functions, including being required for ethanolamine utilization. Our RBP search and the discovery of KhpA/B as major RBPs in F. nucleatum are important first steps in identifying key players of post-transcriptional control at the root of the bacterial phylogenetic tree.
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Affiliation(s)
- Yan Zhu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Valentina Cosi
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
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5
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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] [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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6
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Stenum TS, Holmqvist E. Global Identification of RNA-Binding Proteins in Bacteria. Methods Mol Biol 2024; 2741:347-361. [PMID: 38217662 DOI: 10.1007/978-1-0716-3565-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
RNA-binding proteins (RBPs) are at the heart of many biological processes and are therefore essential for cellular life. Following identification of single RBPs by classical genetics and molecular biology methods, approaches for RBP discovery on a systems level have recently emerged. For instance, RNA interactome capture (RIC) enables the global purification of RBPs cross-linked to polyadenylated RNA using oligo(dT) probes. RIC was originally developed for eukaryotic organisms but was recently established for capturing RBPs in bacteria. In this chapter, we provide a detailed step-by-step protocol for performing RIC in bacteria. The protocol is based on its application to Escherichia coli but should be amenable for charting other genetically tractable bacterial species.
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Affiliation(s)
| | - Erik Holmqvist
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden.
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7
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Wu W, Pang CNI, Tree JJ, Mediati DG. Profiling the in vivo RNA interactome associated with the endoribonuclease RNase III in Staphylococcus aureus. Methods Enzymol 2023; 692:299-324. [PMID: 37925184 DOI: 10.1016/bs.mie.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Regulatory small RNA (sRNA) have been extensively studied in model Gram-negative bacteria, but the functional characterisation of these post-transcriptional gene regulators in Gram-positives remains a major challenge. Our previous work in enterohaemorrhagic E. coli utilised the proximity-dependant ligation technique termed CLASH (UV-crosslinking, ligation, and sequencing of hybrids) for direct high-throughput sequencing of the regulatory sRNA-RNA interactions within the cell. Recently, we adapted the CLASH technique and demonstrated that UV-crosslinking and RNA proximity-dependant ligation can be applied to Staphylococcus aureus, which uncovered the first RNA-RNA interaction network in a Gram-positive bacterium. In this chapter, we describe modifications to the CLASH technique that were developed to capture the RNA interactome associated with the double-stranded endoribonuclease RNase III in two clinical isolates of S. aureus. To briefly summarise our CLASH methodology, regulatory RNA-RNA interactions were first UV-crosslinked in vivo to the RNase III protein and protein-RNA complexes were affinity-purified using the His6-TEV-FLAG tags. Linkers were ligated to RNase III-bound RNA during library preparation and duplexed RNA-RNA species were ligated together to form a single contiguous RNA 'hybrid'. The RNase III-RNA binding sites and RNA-RNA interactions occurring on RNase III (RNA hybrids) were then identified by paired-end sequencing technology. RNase III-CLASH represents a step towards a systems-level understanding of regulatory RNA in Gram-positive bacteria.
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Affiliation(s)
- Winton Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Chi Nam Ignatius Pang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia; Children's Medical Research Institute, Westmead, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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Chihara K, Gerovac M, Hör J, Vogel J. Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq). RNA (NEW YORK, N.Y.) 2022; 29:rna.079439.122. [PMID: 36328526 PMCID: PMC9808575 DOI: 10.1261/rna.079439.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
New methods for the global identification of RNA-protein interactions have led to greater recognition of the abundance and importance of RNA-binding proteins (RBPs) in bacteria. Here, we expand this tool kit by developing SEC-seq, a method based on a similar concept as the established Grad-seq approach. In Grad-seq, cellular RNA and protein complexes of a bacterium of interest are separated in a glycerol gradient, followed by high-throughput RNA-sequencing and mass spectrometry analyses of individual gradient fractions. New RNA-protein complexes are predicted based on the similarity of their elution profiles. In SEC-seq, we have replaced the glycerol gradient with separation by size exclusion chromatography, which shortens operation times and offers greater potential for automation. Applying SEC-seq to Escherichia coli, we find that the method provides a higher resolution than Grad-seq in the lower molecular weight range up to ~500 kDa. This is illustrated by the ability of SEC-seq to resolve two distinct, but similarly sized complexes of the global translational repressor CsrA with either of its antagonistic small RNAs, CsrB and CsrC. We also characterized changes in the SEC-seq profiles of the small RNA MicA upon deletion of its RNA chaperones Hfq and ProQ and investigated the redistribution of these two proteins upon RNase treatment. Overall, we demonstrate that SEC-seq is a tractable and reproducible method for the global profiling of bacterial RNA-protein complexes that offers the potential to discover yet-unrecognized associations between bacterial RNAs and proteins.
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Affiliation(s)
- Kotaro Chihara
- Helmholtz Institute for RNA-based Infection Research, Würzburg, Germany
| | | | - Jens Hör
- Weizmann Institute, Rehovot, Israel
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9
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Sun L, Cao B, Liu Y, Shi P, Zheng Y, Wang B, Zhang Q. TripDesign: A DNA Triplex Design Approach Based on Interaction Forces. J Phys Chem B 2022; 126:8708-8719. [PMID: 36260921 DOI: 10.1021/acs.jpcb.2c05611] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A DNA triplex has the advantages of improved nanostructure stability and pH environment responsiveness compared with single-stranded and double-stranded nucleic acids. However, sequence stability and low design efficiency hinder the application of DNA triplexes. Therefore, a DNA triplex design approach (TripDesign) based on interaction forces is proposed. First, we present the stacking force constraint, torsional stress constraint, and G-quadruplex motif constraint and then use an improved memetic algorithm to design triplex sequences under combinatorial constraints. Finally, to quantify the process of triplex formation, we also explore the minimum length of the triplex-forming oligos (TFOs) required to form the triplex and the factors that produce depletion in cyclic pH-jump experiments. The experimental results show that the sequences produced by TripDesign have high stability and reversibility, and the proposed approach achieves efficient and automatic sequence design. In addition, this study characterizes multiple basic parameters of DNA triplex formation and promotes the wider application of DNA triplexes in nanotechnology.
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Affiliation(s)
- Lijun Sun
- The Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian116622, China
| | - Ben Cao
- School of Computer Science and Technology, Dalian University of Technology, Dalian116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian116024, China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of Technology, Dalian116024, China
| | - Yanfen Zheng
- School of Computer Science and Technology, Dalian University of Technology, Dalian116024, China
| | - Bin Wang
- The Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian116622, China
| | - Qiang Zhang
- The Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian116622, China
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