1
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König F, Svensson SL, Sharma CM. Interplay of two small RNAs fine-tunes hierarchical flagella gene expression in Campylobacter jejuni. Nat Commun 2024; 15:5240. [PMID: 38897989 PMCID: PMC11187230 DOI: 10.1038/s41467-024-48986-8] [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: 07/06/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024] Open
Abstract
Like for many bacteria, flagella are crucial for Campylobacter jejuni motility and virulence. Biogenesis of the flagellar machinery requires hierarchical transcription of early, middle (RpoN-dependent), and late (FliA-dependent) genes. However, little is known about post-transcriptional regulation of flagellar biogenesis by small RNAs (sRNAs). Here, we characterized two sRNAs with opposing effects on C. jejuni filament assembly and motility. We demonstrate that CJnc230 sRNA (FlmE), encoded downstream of the flagellar hook protein, is processed from the RpoN-dependent flgE mRNA by RNase III, RNase Y, and PNPase. We identify mRNAs encoding a flagella-interaction regulator and the anti-sigma factor FlgM as direct targets of CJnc230 repression. CJnc230 overexpression upregulates late genes, including the flagellin flaA, culminating in longer flagella and increased motility. In contrast, overexpression of the FliA-dependent sRNA CJnc170 (FlmR) reduces flagellar length and motility. Overall, our study demonstrates how the interplay of two sRNAs post-transcriptionally fine-tunes flagellar biogenesis through balancing of the hierarchically-expressed components.
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Affiliation(s)
- Fabian König
- University of Würzburg, Institute of Molecular Infection Biology, Department of Molecular Infection Biology II, 97080, Würzburg, Germany
| | - Sarah L Svensson
- University of Würzburg, Institute of Molecular Infection Biology, Department of Molecular Infection Biology II, 97080, Würzburg, Germany
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cynthia M Sharma
- University of Würzburg, Institute of Molecular Infection Biology, Department of Molecular Infection Biology II, 97080, Würzburg, Germany.
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2
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Man L, Soh PXY, McEnearney TE, Cain JA, Dale AL, Cordwell SJ. Multi-Omics of Campylobacter jejuni Growth in Chicken Exudate Reveals Molecular Remodelling Associated with Altered Virulence and Survival Phenotypes. Microorganisms 2024; 12:860. [PMID: 38792690 PMCID: PMC11123243 DOI: 10.3390/microorganisms12050860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Campylobacter jejuni is the leading cause of foodborne human gastroenteritis in the developed world. Infections are largely acquired from poultry produced for human consumption and poor food handling is thus a major risk factor. Chicken exudate (CE) is a liquid produced from defrosted commercial chicken products that facilitates C. jejuni growth. We examined the response of C. jejuni to growth in CE using a multi-omics approach. Changes in the C. jejuni proteome were assessed by label-based liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). We quantified 1328 and 1304 proteins, respectively, in experiments comparing 5% CE in Mueller-Hinton (MH) medium and 100% CE with MH-only controls. These proteins represent 81.8% and 80.3% of the predicted C. jejuni NCTC11168 proteome. Growth in CE induced profound remodelling of the proteome. These changes were typically conserved between 5% and 100% CE, with a greater magnitude of change observed in 100% CE. We confirmed that CE induced C. jejuni biofilm formation, as well as increasing motility and resistance against oxidative stress, consistent with changes to proteins representing those functions. Assessment of the C. jejuni metabolome showed CE also led to increased intracellular abundances of serine, proline, and lactate that were correlated with the elevated abundances of their respective transporters. Analysis of carbon source uptake showed prolonged culture supernatant retention of proline and succinate in CE-supplemented medium. Metabolomics data provided preliminary evidence for the uptake of chicken-meat-associated dipeptides. C. jejuni exposed to CE showed increased resistance to several antibiotics, including polymyxin B, consistent with changes to tripartite efflux system proteins and those involved in the synthesis of lipid A. The C. jejuni CE proteome was also characterised by very large increases in proteins associated with iron acquisition, while a decrease in proteins containing iron-sulphur clusters was also observed. Our data suggest CE is both oxygen- and iron-limiting and provide evidence of factors required for phenotypic remodelling to enable C. jejuni survival on poultry products.
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Affiliation(s)
- Lok Man
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Pamela X. Y. Soh
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Tess E. McEnearney
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Joel A. Cain
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ashleigh L. Dale
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Stuart J. Cordwell
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW 2006, Australia
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3
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Zheng J, Zuo G, Zhou Z, Shi Z, Guo H, Sun Z, Feng Y. Indole inhibited the expression of csrA gene in Escherichia coli. J GEN APPL MICROBIOL 2024; 69:239-248. [PMID: 37423745 DOI: 10.2323/jgam.2023.06.007] [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: 07/11/2023]
Abstract
Indole is a very important signal molecule which plays multiple regulatory roles in many physiological and biochemical processes of bacteria, but up to now, the reasons for its wide range of functions have not been revealed. In this study, we found that indole inhibits the motility, promotes glycogen accumulation and enhances starvation resistance of Escherichia coli. However, the regulatory effects of indole became insignificant while the global csrA gene was mutated. To reveal the regulatory relationship between indole and csrA, we studied the effects of indole on the transcription level of csrA, flhDC, glgCAP and cstA, and also the sensing of the promoters of the genes on indole. It was found that indole inhibited the transcription of csrA, and only the promoter of the csrA gene can sense indole. Namely, indole indirectly regulated the translation level of FlhDC, GlgCAP and CstA. These data indicates that indole regulation is related with the regulation of CsrA, which may throw light on the regulation mechanism research of indole.
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Affiliation(s)
- Jing Zheng
- School of Life Science, Beijing Institute of Technology
- School of Life Science, Langfang Normal University
| | - Guocai Zuo
- School of Life Science, Langfang Normal University
| | - Zhiguo Zhou
- School of Life Science, Langfang Normal University
| | - Zhenxia Shi
- School of Life Science, Langfang Normal University
| | - Huiying Guo
- School of Life Science, Langfang Normal University
| | - Zemin Sun
- School of Life Science, Beijing Institute of Technology
| | - Yongjun Feng
- School of Life Science, Beijing Institute of Technology
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4
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Kannaiah S, Goldberger O, Alam N, Barnabas G, Pozniak Y, Nussbaum-Shochat A, Schueler-Furman O, Geiger T, Amster-Choder O. MinD-RNase E interplay controls localization of polar mRNAs in E. coli. EMBO J 2024; 43:637-662. [PMID: 38243117 PMCID: PMC10897333 DOI: 10.1038/s44318-023-00026-9] [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: 02/03/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
The E. coli transcriptome at the cell's poles (polar transcriptome) is unique compared to the membrane and cytosol. Several factors have been suggested to mediate mRNA localization to the membrane, but the mechanism underlying polar localization of mRNAs remains unknown. Here, we combined a candidate system approach with proteomics to identify factors that mediate mRNAs localization to the cell poles. We identified the pole-to-pole oscillating protein MinD as an essential factor regulating polar mRNA localization, although it is not able to bind RNA directly. We demonstrate that RNase E, previously shown to interact with MinD, is required for proper localization of polar mRNAs. Using in silico modeling followed by experimental validation, the membrane-binding site in RNase E was found to mediate binding to MinD. Intriguingly, not only does MinD affect RNase E interaction with the membrane, but it also affects its mode of action and dynamics. Polar accumulation of RNase E in ΔminCDE cells resulted in destabilization and depletion of mRNAs from poles. Finally, we show that mislocalization of polar mRNAs may prevent polar localization of their protein products. Taken together, our findings show that the interplay between MinD and RNase E determines the composition of the polar transcriptome, thus assigning previously unknown roles for both proteins.
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Affiliation(s)
- Shanmugapriya Kannaiah
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA.
| | - Omer Goldberger
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Nawsad Alam
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Georgina Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
- Department of Pathology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yair Pozniak
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
| | - Anat Nussbaum-Shochat
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100001, Rehovot, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel.
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5
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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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6
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Guo Q, Zhang YX, Zheng LJ, Zhang MJ, Zheng SH, Chen WX, Fan LH, Zheng HD. Transporter mining and metabolic engineering of Escherichia coli for high-level D-allulose production from D-fructose by thermo-swing fermentation. Biotechnol J 2024; 19:e2300085. [PMID: 37789647 DOI: 10.1002/biot.202300085] [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: 02/21/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023]
Abstract
D-Allulose is an ultra-low-calorie sweetener with broad market prospects in the fields of food, beverage, health care, and medicine. The fermentative synthesis of D-allulose is still under development and considered as an ideal route to replace enzymatic approaches for large-scale production of D-allulose in the future. Generally, D-allulose is synthesized from D-fructose through Izumoring epimerization. This biological reaction is reversible, and a high temperature is beneficial to the conversion of D-fructose. Mild cell growth conditions seriously limit the efficiency of producing D-allulose through fermentation. FryABC permease was identified to be responsible for the transport of D-allulose in Escherichia coli by comparative transcriptomic analysis. A cell factory was then developed by expression of ptsG-F, dpe, and deletion of fryA, fruA, manXYZ, mak, and galE. The results show that the newly engineered E. coli was able to produce 32.33 ± 1.33 g L-1 of D-allulose through a unique thermo-swing fermentation process, with a yield of 0.94 ± 0.01 g g-1 on D-fructose.
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Affiliation(s)
- Qiang Guo
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
| | - Ya-Xing Zhang
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
| | - Ling-Jie Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
| | - Meng-Jun Zhang
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
| | - Shang-He Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
| | - Wei-Xiang Chen
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
| | - Li-Hai Fan
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
- Qingyuan Innovation Laboratory, Quanzhou, People's Republic of China
| | - Hui-Dong Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
- Qingyuan Innovation Laboratory, Quanzhou, People's Republic of China
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7
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Hauke M, Metz F, Rapp J, Faass L, Bats SH, Radziej S, Link H, Eisenreich W, Josenhans C. Helicobacter pylori Modulates Heptose Metabolite Biosynthesis and Heptose-Dependent Innate Immune Host Cell Activation by Multiple Mechanisms. Microbiol Spectr 2023; 11:e0313222. [PMID: 37129481 PMCID: PMC10269868 DOI: 10.1128/spectrum.03132-22] [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: 08/11/2022] [Accepted: 04/05/2023] [Indexed: 05/03/2023] Open
Abstract
Heptose metabolites including ADP-d-glycero-β-d-manno-heptose (ADP-heptose) are involved in bacterial lipopolysaccharide and cell envelope biosynthesis. Recently, heptoses were also identified to have potent proinflammatory activity on human cells as novel microbe-associated molecular patterns. The gastric pathogenic bacterium Helicobacter pylori produces heptose metabolites, which it transports into human cells through its Cag type 4 secretion system. Using H. pylori as a model, we have addressed the question of how proinflammatory ADP-heptose biosynthesis can be regulated by bacteria. We have characterized the interstrain variability and regulation of heptose biosynthesis genes and the modulation of heptose metabolite production by H. pylori, which impact cell-autonomous proinflammatory human cell activation. HldE, a central enzyme of heptose metabolite biosynthesis, showed strong sequence variability between strains and was also variably expressed between strains. Amounts of gene transcripts in the hldE gene cluster displayed intrastrain and interstrain differences, were modulated by host cell contact and the presence of the cag pathogenicity island, and were affected by carbon starvation regulator A (CsrA). We reconstituted four steps of the H. pylori lipopolysaccharide (LPS) heptose biosynthetic pathway in vitro using recombinant purified GmhA, HldE, and GmhB proteins. On the basis of one- and two-dimensional nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry, the structures of major reaction products were identified as β-d-ADP-heptose and β-heptose-1-monophosphate. A proinflammatory heptose-monophosphate variant was also identified for the first time as a novel cell-active product in H. pylori bacteria. Separate purified HldE subdomains and variant HldE allowed us to uncover additional strain variation in generating heptose metabolites. IMPORTANCE Bacterial heptose metabolites, intermediates of lipopolysaccharide (LPS) biosynthesis, are novel microbe-associated molecular patterns (MAMPs) that activate proinflammatory signaling. In the gastric pathogen Helicobacter pylori, heptoses are transferred into host cells by the Cag type IV secretion system, which is also involved in carcinogenesis. Little is known about how H. pylori, which is highly strain variable, regulates heptose biosynthesis and downstream host cell activation. We report here that the regulation of proinflammatory heptose production by H. pylori is strain specific. Heptose gene cluster activity is modulated by the presence of an active cag pathogenicity island (cagPAI), contact with human cells, and the carbon starvation regulator A. Reconstitution with purified biosynthesis enzymes and purified bacterial lysates allowed us to biochemically characterize heptose pathway products, identifying a heptose-monophosphate variant as a novel proinflammatory metabolite. These findings emphasize that the bacteria use heptose biosynthesis to fine-tune inflammation and also highlight opportunities to mine the heptose biosynthesis pathway as a potential therapeutic target against infection, inflammation, and cancer.
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Affiliation(s)
- Martina Hauke
- Max von Pettenkofer Institute, Ludwig Maximilians University Munich, München, Germany
| | - Felix Metz
- Max von Pettenkofer Institute, Ludwig Maximilians University Munich, München, Germany
| | - Johanna Rapp
- Bacterial Metabolomics, CMFI, University Tübingen, Tübingen, Germany
| | - Larissa Faass
- Max von Pettenkofer Institute, Ludwig Maximilians University Munich, München, Germany
| | - Simon H. Bats
- Max von Pettenkofer Institute, Ludwig Maximilians University Munich, München, Germany
| | - Sandra Radziej
- Bavarian NMR Center–Structural Membrane Biochemistry, Department of Chemistry, Technical University Munich, Garching, Germany
| | - Hannes Link
- Bacterial Metabolomics, CMFI, University Tübingen, Tübingen, Germany
| | - Wolfgang Eisenreich
- Bavarian NMR Center–Structural Membrane Biochemistry, Department of Chemistry, Technical University Munich, Garching, Germany
| | - Christine Josenhans
- Max von Pettenkofer Institute, Ludwig Maximilians University Munich, München, Germany
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8
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Gerber A, van Otterdijk S, Bruggeman FJ, Tutucci E. Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies. Transcription 2023; 14:105-126. [PMID: 37050882 PMCID: PMC10807504 DOI: 10.1080/21541264.2023.2199669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/14/2023] Open
Abstract
Across all kingdoms of life, gene regulatory mechanisms underlie cellular adaptation to ever-changing environments. Regulation of gene expression adjusts protein synthesis and, in turn, cellular growth. Messenger RNAs are key molecules in the process of gene expression. Our ability to quantitatively measure mRNA expression in single cells has improved tremendously over the past decades. This revealed an unexpected coordination between the steps that control the life of an mRNA, from transcription to degradation. Here, we provide an overview of the state-of-the-art imaging approaches for measurement and quantitative understanding of gene expression, starting from the early visualizations of single genes by electron microscopy to current fluorescence-based approaches in single cells, including live-cell RNA-imaging approaches to FISH-based spatial transcriptomics across model organisms. We also highlight how these methods have shaped our current understanding of the spatiotemporal coupling between transcriptional and post-transcriptional events in prokaryotes. We conclude by discussing future challenges of this multidisciplinary field.Abbreviations: mRNA: messenger RNA; rRNA: ribosomal rDNA; tRNA: transfer RNA; sRNA: small RNA; FISH: fluorescence in situ hybridization; RNP: ribonucleoprotein; smFISH: single RNA molecule FISH; smiFISH: single molecule inexpensive FISH; HCR-FISH: Hybridization Chain-Reaction-FISH; RCA: Rolling Circle Amplification; seqFISH: Sequential FISH; MERFISH: Multiplexed error robust FISH; UTR: Untranslated region; RBP: RNA binding protein; FP: fluorescent protein; eGFP: enhanced GFP, MCP: MS2 coat protein; PCP: PP7 coat protein; MB: Molecular beacons; sgRNA: single guide RNA.
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Affiliation(s)
- Alan Gerber
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Sander van Otterdijk
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J. Bruggeman
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Evelina Tutucci
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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9
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Gavrilov AA, Evko GS, Galitsyna AA, Ulianov SV, Kochetkova TV, Merkel AY, Tyakht AV, Razin SV. RNA-DNA interactomes of three prokaryotes uncovered by proximity ligation. Commun Biol 2023; 6:473. [PMID: 37120653 PMCID: PMC10148824 DOI: 10.1038/s42003-023-04853-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/19/2023] [Indexed: 05/01/2023] Open
Abstract
Proximity ligation approaches, which are widely used to study the spatial organization of the genome, also make it possible to reveal patterns of RNA-DNA interactions. Here, we use RedC, an RNA-DNA proximity ligation approach, to assess the distribution of major RNA types along the genomes of E. coli, B. subtilis, and thermophilic archaeon T. adornatum. We find that (i) messenger RNAs preferentially interact with their cognate genes and the genes located downstream in the same operon, which is consistent with polycistronic transcription; (ii) ribosomal RNAs preferentially interact with active protein-coding genes in both bacteria and archaea, indicating co-transcriptional translation; and (iii) 6S noncoding RNA, a negative regulator of bacterial transcription, is depleted from active genes in E. coli and B. subtilis. We conclude that the RedC data provide a rich resource for studying both transcription dynamics and the function of noncoding RNAs in microbial organisms.
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Affiliation(s)
- Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Grigory S Evko
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | | | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 117312, Moscow, Russia
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 117312, Moscow, Russia
| | - Alexander V Tyakht
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
- Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
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10
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Kurniyati K, Chang Y, Guo W, Liu J, Malkowski MG, Li C. Anti-σ 28 Factor FlgM Regulates Flagellin Gene Expression and Flagellar Polarity of Treponema denticola. J Bacteriol 2023; 205:e0046322. [PMID: 36715541 PMCID: PMC9945498 DOI: 10.1128/jb.00463-22] [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: 12/02/2022] [Accepted: 01/07/2023] [Indexed: 01/31/2023] Open
Abstract
FlgM, an antagonist of FliA (also known as σ28), inhibits transcription of bacterial class 3 flagellar genes. It does so primarily through binding to free σ28 to prevent it from forming a complex with core RNA polymerase. We recently identified an FliA homolog (FliATd) in the oral spirochete Treponema denticola; however, its antagonist FlgM remained uncharacterized. Herein, we provide several lines of evidence that TDE0201 functions as an antagonist of FliATd. TDE0201 is structurally similar to FlgM proteins, although its sequence is not conserved. Heterologous expression of TDE0201 in Escherichia coli inhibits its flagellin gene expression and motility. Biochemical and mutational analyses demonstrate that TDE0201 binds to FliATd and prevents it from binding to the σ28-dependent promoter. Deletions of flgM genes typically enhance bacterial class 3 flagellar gene expression; however, deletion of TDE0201 has an opposite effect (e.g., the mutant has a reduced level of flagellins). Follow-up studies revealed that deletion of TDE0201 leads to FliATd turnover, which in turn impairs the expression of flagellin genes. Swimming plate, cell tracking, and cryo-electron tomography analyses further disclosed that deletion of TDE0201 impairs spirochete motility and alters flagellar number and polarity: i.e., instead of having bipolar flagella, the mutant has flagella only at one end of cells. Collectively, these results indicate that TDE0201 is a FlgM homolog but acts differently from its counterparts in other bacteria. IMPORTANCE Spirochetes are a group of bacteria that cause several human diseases. A unique aspect of spirochetes is that they have bipolar periplasmic flagella (PFs), which bestow on the spirochetes a unique spiral shape and distinct swimming behaviors. While the structure and function of PFs have been extensively studied in spirochetes, the molecular mechanism that regulates the PFs' morphogenesis and assembly is poorly understood. In this report, FlgM, an anti-σ28 factor, is identified and functionally characterized in the oral spirochete Treponema denticola. Our results show that FlgM regulates the number and polarity of PFs via a unique mechanism. Identification of FliA and FlgM in T. denticola sets a benchmark to investigate their roles in other spirochetes.
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Affiliation(s)
- Kurni Kurniyati
- Department of Oral Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Yunjie Chang
- Department of Microbial Pathogenesis, Yale University, School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, School of Medicine, New Haven, Connecticut, USA
| | - Wangbiao Guo
- Department of Microbial Pathogenesis, Yale University, School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, School of Medicine, New Haven, Connecticut, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University, School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, School of Medicine, New Haven, Connecticut, USA
| | - Michael G. Malkowski
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, New York, USA
| | - Chunhao Li
- Department of Oral Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA
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11
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Guo Q, Liu MM, Zheng SH, Zheng LJ, Ma Q, Cheng YK, Zhao SY, Fan LH, Zheng HD. Methanol-Dependent Carbon Fixation for Irreversible Synthesis of d-Allulose from d-Xylose by Engineered Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14255-14263. [PMID: 36286250 DOI: 10.1021/acs.jafc.2c06616] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
d-Allulose is a rare hexose with great application potential, owing to its moderate sweetness, low energy, and unique physiological functions. The current strategies for d-allulose production, whether industrialized or under development, utilize six-carbon sugars such as d-glucose or d-fructose as a substrate and are usually based on the principle of reversible Izumoring epimerization. In this work, we designed a novel route that coupled the pathways of methanol reduction, pentose phosphate (PP), ribulose monophosphate (RuMP), and allulose monophosphate (AuMP) for Escherichia coli to irreversibly synthesize d-allulose from d-xylose and methanol. After improving the expression of AlsE by SUMO fusion and regulating the carbon fluxes by knockout of FrmRAB, RpiA, PfkA, and PfkB, the titer of d-allulose in fed-batch fermentation reached ≈70.7 mM, with a yield of ≈0.471 mM/mM on d-xylose or ≈0.512 mM/mM on methanol.
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Affiliation(s)
- Qiang Guo
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Mei-Ming Liu
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Shang-He Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Ling-Jie Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Qian Ma
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Ying-Kai Cheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Su-Ying Zhao
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, People's Republic of China
- Qingyuan Innovation Laboratory, Quanzhou 362801, People's Republic of China
| | - Li-Hai Fan
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, People's Republic of China
- Qingyuan Innovation Laboratory, Quanzhou 362801, People's Republic of China
| | - Hui-Dong Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou 350108, People's Republic of China
- Qingyuan Innovation Laboratory, Quanzhou 362801, People's Republic of China
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12
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Zheng LJ, Guo Q, Zhang YX, Liu CY, Fan LH, Zheng HD. Engineering of Escherichia coli for D-allose fermentative synthesis from D-glucose through izumoring cascade epimerization. Front Bioeng Biotechnol 2022; 10:1050808. [PMID: 36338116 PMCID: PMC9633178 DOI: 10.3389/fbioe.2022.1050808] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/11/2022] [Indexed: 10/13/2023] Open
Abstract
D-Allose is a potential alternative to sucrose in the food industries and a useful additive for the healthcare products in the future. At present, the methods for large-scale production of D-allose are still under investigation, most of which are based on in vitro enzyme-catalyzed Izumoring epimerization. In contrast, fermentative synthesis of D-allose has never been reported, probably due to the absence of available natural microorganisms. In this work, we co-expressed D-galactose: H+ symporter (GalP), D-glucose isomerase (DGI), D-allulose 3-epimerase (DAE), and ribose-5-phosphate isomerase (RPI) in Escherichia coli, thereby constructing an in vivo Izumoring pathway for yielding D-allose from D-glucose. The carbon fluxes and carbon catabolite repression (CCR) were rationally regulated by knockout of FruA, PtsG, Glk, Mak, PfkA, and PfkB involved in the pathways capable of phosphorylating D-fructose, D-glucose, and fructose-6-phosphate. Moreover, the native D-allose transporter was damaged by inactivation of AlsB, thus driving the reversible Izumoring reactions towards the target product. Fermentation was performed in the M9 medium supplemented with glycerol as a carbon source and D-glucose as a substrate. The results show that the engineered E. coli cell factory was able to produce approximately 127.35 mg/L of D-allose after 84 h. Our achievements in the fermentative production of D-allose in this work may further promote the green manufacturing of rare sugars.
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Affiliation(s)
- Ling-Jie Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
- Qingyuan Innovation Laboratory, Quanzhou, China
| | - Qiang Guo
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
| | - Ya-Xing Zhang
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
| | - Chen-Yang Liu
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
| | - Li-Hai Fan
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
- Qingyuan Innovation Laboratory, Quanzhou, China
| | - Hui-Dong Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China
- Qingyuan Innovation Laboratory, Quanzhou, China
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13
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Kurniyati K, Chang Y, Liu J, Li C. Transcriptional and functional characterizations of multiple flagellin genes in spirochetes. Mol Microbiol 2022; 118:175-190. [PMID: 35776658 PMCID: PMC9481697 DOI: 10.1111/mmi.14959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 11/28/2022]
Abstract
The flagellar filament is a helical propeller for bacterial locomotion. In external flagellates, the filaments are mostly homopolymers of a single flagellin protein. By contrast, the flagellar filaments of spirochetes are mostly heteropolymers of multiple flagellin proteins. This report seeks to investigate the role of multiple flagellin proteins using the oral spirochete Treponema denticola as a model. First, biochemical and genetic studies uncover that the flagellar filaments of T. denticola mainly comprise four proteins, FlaA, FlaB1, FlaB2, and FlaB3, in a defined stoichiometry. Second, transcriptional analyses reveal that the genes encoding these four proteins are regulated by two different transcriptional factors, sigma28 and sigma70 . Third, loss-of-function studies demonstrate that each individual flagellin protein contributes to spirochete motility, but none of them is absolutely required. Last, we provide genetic and structural evidence that FlaA forms a "seam"-like structure around the core and that deletion of individual flagellin protein alters the flagellar homeostasis. Collectively, these results demonstrate that T. denticola has evolved a unique mechanism to finely regulate its flagellar filament gene expression and assembly which renders the organelle with the right number, shape, strength, and structure for its distinct motility.
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Affiliation(s)
- Kurni Kurniyati
- Department of Oral Craniofacial Molecular Biology, School of DentistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Yunjie Chang
- Microbial Sciences InstituteYale UniversityWest HavenConnecticutUSA
- Department of Microbial PathogenesisYale School of MedicineNew HavenConnecticutUSA
| | - Jun Liu
- Microbial Sciences InstituteYale UniversityWest HavenConnecticutUSA
- Department of Microbial PathogenesisYale School of MedicineNew HavenConnecticutUSA
| | - Chunhao Li
- Department of Oral Craniofacial Molecular Biology, School of DentistryVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of Microbiology and Immunology, School of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA
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14
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Li S, Lam J, Souliotis L, Alam MT, Constantinidou C. Posttranscriptional Regulation in Response to Different Environmental Stresses in Campylobacter jejuni. Microbiol Spectr 2022; 10:e0020322. [PMID: 35678555 PMCID: PMC9241687 DOI: 10.1128/spectrum.00203-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/10/2022] [Indexed: 11/20/2022] Open
Abstract
The survival strategies that Campylobacter jejuni (C. jejuni) employ throughout its transmission and infection life cycles remain largely elusive. Specifically, there is a lack of understanding about the posttranscriptional regulation of stress adaptations resulting from small noncoding RNAs (sRNAs). Published C. jejuni sRNAs have been discovered in specific conditions but with limited insights into their biological activities. Many more sRNAs are yet to be discovered as they may be condition-dependent. Here, we have generated transcriptomic data from 21 host- and transmission-relevant conditions. The data uncovered transcription start sites, expression patterns and posttranscriptional regulation during various stress conditions. This data set helped predict a list of putative sRNAs. We further explored the sRNAs' biological functions by integrating differential gene expression analysis, coexpression analysis, and genome-wide sRNA target prediction. The results showed that the C. jejuni gene expression was influenced primarily by nutrient deprivation and food storage conditions. Further exploration revealed a putative sRNA (CjSA21) that targeted tlp1 to 4 under food processing conditions. tlp1 to 4 are transcripts that encode methyl-accepting chemotaxis proteins (MCPs), which are responsible for chemosensing. These results suggested CjSA21 inhibits chemotaxis and promotes survival under food processing conditions. This study presents the broader research community with a comprehensive data set and highlights a novel sRNA as a potential chemotaxis inhibitor. IMPORTANCE The foodborne pathogen C. jejuni is a significant challenge for the global health care system. It is crucial to investigate C. jejuni posttranscriptional regulation by small RNAs (sRNAs) in order to understand how it adapts to different stress conditions. However, limited data are available for investigating sRNA activity under stress. In this study, we generate gene expression data of C. jejuni under 21 stress conditions. Our data analysis indicates that one of the novel sRNAs mediates the adaptation to food processing conditions. Results from our work shed light on the posttranscriptional regulation of C. jejuni and identify an sRNA associated with food safety.
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Affiliation(s)
- Stephen Li
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Jenna Lam
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | - Mohammad Tauqeer Alam
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
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15
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Guo Q, Liu CY, Zheng LJ, Zheng SH, Zhang YX, Zhao SY, Zheng HD, Fan LH, Lin XC. Metabolically Engineered Escherichia coli for Conversion of D-Fructose to D-Allulose via Phosphorylation-Dephosphorylation. Front Bioeng Biotechnol 2022; 10:947469. [PMID: 35814008 PMCID: PMC9257026 DOI: 10.3389/fbioe.2022.947469] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
D-Allulose is an ultra-low calorie sweetener with broad market prospects. As an alternative to Izumoring, phosphorylation-dephosphorylation is a promising method for D-allulose synthesis due to its high conversion of substrate, which has been preliminarily attempted in enzymatic systems. However, in vitro phosphorylation-dephosphorylation requires polyphosphate as a phosphate donor and cannot completely deplete the substrate, which may limit its application in industry. Here, we designed and constructed a metabolic pathway in Escherichia coli for producing D-allulose from D-fructose via in vivo phosphorylation-dephosphorylation. PtsG-F and Mak were used to replace the fructose phosphotransferase systems (PTS) for uptake and phosphorylation of D-fructose to fructose-6-phosphate, which was then converted to D-allulose by AlsE and A6PP. The D-allulose titer reached 0.35 g/L and the yield was 0.16 g/g. Further block of the carbon flux into the Embden-Meyerhof-Parnas (EMP) pathway and introduction of an ATP regeneration system obviously improved fermentation performance, increasing the titer and yield of D-allulose to 1.23 g/L and 0.68 g/g, respectively. The E. coli cell factory cultured in M9 medium with glycerol as a carbon source achieved a D-allulose titer of ≈1.59 g/L and a yield of ≈0.72 g/g on D-fructose.
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Affiliation(s)
- Qiang Guo
- Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, College of Chemical Engineering, Fuzhou University, Fuzhou, China
| | - Chen-Yang Liu
- Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, College of Chemical Engineering, Fuzhou University, Fuzhou, China
| | - Ling-Jie Zheng
- Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, College of Chemical Engineering, Fuzhou University, Fuzhou, China
| | - Shang-He Zheng
- Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, College of Chemical Engineering, Fuzhou University, Fuzhou, China
| | - Ya-Xing Zhang
- Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, College of Chemical Engineering, Fuzhou University, Fuzhou, China
| | - Su-Ying Zhao
- Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, College of Chemical Engineering, Fuzhou University, Fuzhou, China
- Qingyuan Innovation Laboratory, Quanzhou, China
| | - Hui-Dong Zheng
- Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, College of Chemical Engineering, Fuzhou University, Fuzhou, China
- Qingyuan Innovation Laboratory, Quanzhou, China
| | - Li-Hai Fan
- Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, College of Chemical Engineering, Fuzhou University, Fuzhou, China
- Qingyuan Innovation Laboratory, Quanzhou, China
- *Correspondence: Li-Hai Fan, ; Xiao-Cheng Lin,
| | - Xiao-Cheng Lin
- Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, College of Chemical Engineering, Fuzhou University, Fuzhou, China
- *Correspondence: Li-Hai Fan, ; Xiao-Cheng Lin,
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16
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Sharma S, Sharma CM. Identification of RNA Binding Partners of CRISPR-Cas Proteins in Prokaryotes Using RIP-Seq. Methods Mol Biol 2022; 2404:111-133. [PMID: 34694606 DOI: 10.1007/978-1-0716-1851-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
CRISPR-Cas systems consist of a complex ribonucleoprotein (RNP) machinery encoded in prokaryotic genomes to confer adaptive immunity against foreign mobile genetic elements. Of these, especially the class 2, Type II CRISPR-Cas9 RNA-guided systems with single protein effector modules have recently received much attention for their application as programmable DNA scissors that can be used for genome editing in eukaryotes. While many studies have concentrated their efforts on improving RNA-mediated DNA targeting with these Type II systems, little is known about the factors that modulate processing or binding of the CRISPR RNA (crRNA) guides and the trans-activating tracrRNA to the nuclease protein Cas9, and whether Cas9 can also potentially interact with other endogenous RNAs encoded within the host genome. Here, we describe RIP-seq as a method to globally identify the direct RNA binding partners of CRISPR-Cas RNPs using the Cas9 nuclease as an example. RIP-seq combines co-immunoprecipitation (coIP) of an epitope-tagged Cas9 followed by isolation and deep sequencing analysis of its co-purified bound RNAs. This method can not only be used to study interactions of Cas9 with its known interaction partners, crRNAs and tracrRNA in native systems, but also to reveal potential additional RNA substrates of Cas9. For example, in RIP-seq analysis of Cas9 from the foodborne pathogen Campylobacter jejuni (CjeCas9), we recently identified several endogenous RNAs bound to CjeCas9 RNP in a crRNA-dependent manner, leading to the discovery of PAM-independent RNA cleavage activity of CjeCas9 as well as non-canonical crRNAs. RIP-seq can be easily adapted to any other effector RNP of choice from other CRISPR-Cas systems, allowing for the identification of target RNAs. Deciphering novel RNA-protein interactions for CRISPR-Cas proteins within host bacterial genomes will lead to a better understanding of the molecular mechanisms and functions of these systems and enable us to use the in vivo identified interaction rules as design principles for nucleic acid-targeting applications, fitted to each nuclease of interest.
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Affiliation(s)
- Sahil Sharma
- Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
| | - Cynthia M Sharma
- Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
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17
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Svensson SL, Sharma CM. RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist. eLife 2021; 10:69064. [PMID: 34843430 PMCID: PMC8687705 DOI: 10.7554/elife.69064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/28/2021] [Indexed: 12/27/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are important post-transcriptional regulators in stress responses and virulence. They can be derived from an expanding list of genomic contexts, such as processing from parental transcripts by RNase E. The role of RNase III in sRNA biogenesis is less well understood despite its well-known roles in rRNA processing, RNA decay, and cleavage of sRNA-mRNA duplexes. Here, we show that RNase III processes a pair of cis-encoded sRNAs (CJnc190 and CJnc180) of the food-borne pathogen Campylobacter jejuni. While CJnc180 processing by RNase III requires CJnc190, RNase III processes CJnc190 independent of CJnc180 via cleavage of an intramolecular duplex. We also show that CJnc190 directly represses translation of the colonization factor PtmG by targeting a G-rich ribosome-binding site, and uncover that CJnc180 is a cis-acting antagonist of CJnc190, indirectly affecting ptmG regulation. Our study highlights a role for RNase III in sRNA biogenesis and adds cis-encoded RNAs to the expanding diversity of transcripts that can antagonize bacterial sRNAs.
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Affiliation(s)
- Sarah Lauren Svensson
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Cynthia Mira Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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18
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Guo Q, Ullah I, Zheng LJ, Gao XQ, Liu CY, Zheng HD, Fan LH, Deng L. Intelligent self-control of carbon metabolic flux in SecY-engineered Escherichia coli for xylitol biosynthesis from xylose-glucose mixtures. Biotechnol Bioeng 2021; 119:388-398. [PMID: 34837379 DOI: 10.1002/bit.28002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 01/31/2023]
Abstract
Xylitol is a salutary sugar substitute that has been widely used in the food, pharmaceutical, and chemical industries. Co-fermentation of xylose and glucose by metabolically engineered cell factories is a promising alternative to chemical hydrogenation of xylose for commercial production of xylitol. Here, we engineered a mutant of SecY protein-translocation channel (SecY [ΔP]) in xylitol-producing Escherichia coli JM109 (DE3) as a passageway for xylose uptake. It was found that SecY (ΔP) channel could rapidly transport xylose without being interfered by XylB-catalyzed synthesis of xylitol-phosphate, which is impossible for native XylFGH and XylE transporters. More importantly, with the coaction of SecY (ΔP) channel and carbon catabolite repression (CCR), the flux of xylose to the pentose phosphate (PP) pathway and the xylitol synthesis pathway in E. coli could be automatically controlled in response to glucose, thereby ensuring that the mutant cells were able to fully utilize sugars with high xylitol yields. The E. coli cell factory developed in this study has been proven to be applicable to a broad range of xylose-glucose mixtures, which is conducive to simplifying the mixed-sugar fermentation process for efficient and economical production of xylitol.
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Affiliation(s)
- Qiang Guo
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People's Republic of China
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
| | - Irfan Ullah
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Ling-Jie Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People's Republic of China
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
| | - Xin-Quan Gao
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
| | - Chen-Yang Liu
- Qingyuan Innovation Laboratory, Fuzhou University, Quanzhou, People's Republic of China
| | - Hui-Dong Zheng
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
- Qingyuan Innovation Laboratory, Fuzhou University, Quanzhou, People's Republic of China
| | - Li-Hai Fan
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, People's Republic of China
- Qingyuan Innovation Laboratory, Fuzhou University, Quanzhou, People's Republic of China
| | - Li Deng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People's Republic of China
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19
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Oogai Y, Nakata M. Small regulatory RNAs of oral streptococci and periodontal bacteria. JAPANESE DENTAL SCIENCE REVIEW 2021; 57:209-216. [PMID: 34745393 PMCID: PMC8551640 DOI: 10.1016/j.jdsr.2021.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/27/2022] Open
Abstract
Small regulatory RNAs (sRNAs) belong to a family of non-coding RNAs, and many of which regulate expression of genes via interaction with mRNA. The recent popularity of high-throughput next generation sequencers have presented abundant sRNA-related data, including sRNAs of several different oral bacterial species. Some sRNA candidates have been validated in terms of their expression and interaction with target mRNAs. Since the oral cavity is an environment constantly exposed to various stimuli, such as fluctuations in temperature and pH, and osmotic pressure, as well as changes in nutrient availability, oral bacteria require rapid control of gene expression for adaptation to such diverse conditions, while regulation via interactions of sRNAs with mRNA provides advantages for rapid adaptation. This review summarizes methods effective for identification and validation of sRNAs, as well as sRNAs identified to be associated with oral bacterial species, including cariogenic and periodontal pathogens, together with their confirmed and putative target genes.
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Affiliation(s)
- Yuichi Oogai
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 890-8544, Japan
| | - Masanobu Nakata
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 890-8544, Japan
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20
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Zhang Y, Andrade MO, Wang W, Teper D, Romeo T, Wang N. Examination of the Global Regulon of CsrA in Xanthomonas citri subsp. citri Using Quantitative Proteomics and Other Approaches. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1236-1249. [PMID: 34282945 DOI: 10.1094/mpmi-05-21-0113-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The RNA-binding protein CsrA is a global posttranscriptional regulator and controls many physiological processes and virulence traits. Deletion of csrA caused loss of virulence, reduced motility and production of xanthan gum and substantial increase in glycogen accumulation, as well as enhanced bacterial aggregation and cell adhesion in Xanthomonas spp. How CsrA controls these traits is poorly understood. In this study, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis was conducted to compare the protein profile of wild-type strain Xanthomonas citri subsp. citri and the isogenic ΔcsrA strain. A total of 2,374 proteins were identified, and 284 were considered to be differentially expressed proteins (DEPS), among which 151 proteins were up-regulated and 133 were down-regulated in the ΔcsrA strain with respect to the wild-type strain. Enrichment analysis and a protein-protein interaction network analysis showed that CsrA regulates bacterial secretion systems, flagella, and xanthan gum biosynthesis. Several proteins encoded by the gumB operon were down-regulated, whereas proteins associated with flagellum assembly and the type IV secretion system were up-regulated in the ΔcsrA strain relative to the Xcc306 strain. These results were confirmed by β-glucuronidase assay or Western blot. RNA secondary structure prediction and a gel-shift assay indicated that CsrA binds to the Shine-Dalgarno sequence of virB5. In addition, the iTRAQ analysis identified 248 DEPs that were not previously identified in transcriptome analyses. Among them, CsrA regulates levels of eight regulatory proteins (ColR, GacA, GlpR, KdgR, MoxR, PilH, RecX, and YgiX), seven TonB-dependent receptors, four outer membrane proteins, and two ferric enterobactin receptors. Taken together, this study greatly expands understanding of the regulatory network of CsrA in X. citri subsp. citri.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Yanan Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred FL 33850, U.S.A
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, 655011, China
| | - Maxuel O Andrade
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred FL 33850, U.S.A
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Wenting Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred FL 33850, U.S.A
- Department of Plant Pathology, University of Florida, Gainesville FL 32611, U.S.A
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred FL 33850, U.S.A
| | - Tony Romeo
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville FL 32611, U.S.A
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred FL 33850, U.S.A
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21
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Reduced Infection Efficiency of Phage NCTC 12673 on Non-Motile Campylobacter jejuni Strains Is Related to Oxidative Stress. Viruses 2021; 13:v13101955. [PMID: 34696385 PMCID: PMC8540345 DOI: 10.3390/v13101955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/08/2021] [Accepted: 09/20/2021] [Indexed: 01/26/2023] Open
Abstract
Campylobacter jejuni is a Gram-negative foodborne pathogen that causes diarrheal disease and is associated with severe post-infectious sequelae. Bacteriophages (phages) are a possible means of reducing Campylobacter colonization in poultry to prevent downstream human infections. However, the factors influencing phage-host interactions must be better understood before this strategy can be predictably employed. Most studies have focused on Campylobacter phage binding to the host surface, with all phages classified as either capsule- or flagella-specific. Here we describe the characterization of a C. jejuni phage that requires functional flagellar glycosylation and motor genes for infection, without needing the flagella for adsorption to the cell surface. Through phage infectivity studies of targeted C. jejuni mutants, transcriptomic analysis of phage-resistant mutants, and genotypic and phenotypic analysis of a spontaneous phage variant capable of simultaneously overcoming flagellar gene dependence and sensitivity to oxidative stress, we have uncovered a link between oxidative stress, flagellar motility, and phage infectivity. Taken together, our results underscore the importance of understanding phage-host interactions beyond the cell surface and point to host oxidative stress state as an important and underappreciated consideration for future phage-host interaction studies.
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22
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Campa AR, Smith LM, Hampton HG, Sharma S, Jackson SA, Bischler T, Sharma CM, Fineran PC. The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems. Nucleic Acids Res 2021; 49:9508-9525. [PMID: 34403463 PMCID: PMC8450108 DOI: 10.1093/nar/gkab704] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022] Open
Abstract
CRISPR-Cas systems provide bacteria with adaptive immunity against phages and plasmids; however, pathways regulating their activity are not well defined. We recently developed a high-throughput genome-wide method (SorTn-seq) and used this to uncover CRISPR-Cas regulators. Here, we demonstrate that the widespread Rsm/Csr pathway regulates the expression of multiple CRISPR-Cas systems in Serratia (type I-E, I-F and III-A). The main pathway component, RsmA (CsrA), is an RNA-binding post-transcriptional regulator of carbon utilisation, virulence and motility. RsmA binds cas mRNAs and suppresses type I and III CRISPR-Cas interference in addition to adaptation by type I systems. Coregulation of CRISPR-Cas and flagella by the Rsm pathway allows modulation of adaptive immunity when changes in receptor availability would alter susceptibility to flagella-tropic phages. Furthermore, we show that Rsm controls CRISPR-Cas in other genera, suggesting conservation of this regulatory strategy. Finally, we identify genes encoding RsmA homologues in phages, which have the potential to manipulate the physiology of host bacteria and might provide an anti-CRISPR activity.
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Affiliation(s)
- Aroa Rey Campa
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Leah M Smith
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Hannah G Hampton
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Sahil Sharma
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Cynthia M Sharma
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand
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23
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CsrA Enhances Cyclic-di-GMP Biosynthesis and Yersinia pestis Biofilm Blockage of the Flea Foregut by Alleviating Hfq-Dependent Repression of the hmsT mRNA. mBio 2021; 12:e0135821. [PMID: 34340543 PMCID: PMC8406273 DOI: 10.1128/mbio.01358-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Plague-causing Yersinia pestis is transmitted through regurgitation when it forms a biofilm-mediated blockage in the foregut of its flea vector. This biofilm is composed of an extracellular polysaccharide substance (EPS) produced when cyclic-di-GMP (c-di-GMP) levels are elevated. The Y. pestis diguanylate cyclase enzymes HmsD and HmsT synthesize c-di-GMP. HmsD is required for biofilm blockage formation but contributes minimally to in vitro biofilms. HmsT, however, is necessary for in vitro biofilms and contributes to intermediate rates of biofilm blockage. C-di-GMP synthesis is regulated at the transcriptional and posttranscriptional levels. In this, the global RNA chaperone, Hfq, posttranscriptionally represses hmsT mRNA translation. How c-di-GMP levels and biofilm blockage formation is modulated by nutritional stimuli encountered in the flea gut is unknown. Here, the RNA-binding regulator protein CsrA, which controls c-di-GMP-mediated biofilm formation and central carbon metabolism responses in many Gammaproteobacteria, was assessed for its role in Y. pestis biofilm formation. We determined that CsrA was required for markedly greater c-di-GMP and EPS levels when Y. pestis was cultivated on alternative sugars implicated in flea biofilm blockage metabolism. Our assays, composed of mobility shifts, quantification of mRNA translation, stability, and abundance, and epistasis analyses of a csrA hfq double mutant strain substantiated that CsrA represses hfq mRNA translation, thereby alleviating Hfq-dependent repression of hmsT mRNA translation. Additionally, a csrA mutant exhibited intermediately reduced biofilm blockage rates, resembling an hmsT mutant. Hence, we reveal CsrA-mediated control of c-di-GMP synthesis in Y. pestis as a tiered, posttranscriptional regulatory process that enhances biofilm blockage-mediated transmission from fleas.
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24
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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: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [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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25
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A bacterial small RNA regulates the adaptation of Helicobacter pylori to the host environment. Nat Commun 2021; 12:2085. [PMID: 33837194 PMCID: PMC8035401 DOI: 10.1038/s41467-021-22317-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/10/2021] [Indexed: 12/15/2022] Open
Abstract
Long-term infection of the stomach with Helicobacter pylori can cause gastric cancer. However, the mechanisms by which the bacteria adapt to the stomach environment are poorly understood. Here, we show that a small non-coding RNA of H. pylori (HPnc4160, also known as IsoB or NikS) regulates the pathogen’s adaptation to the host environment as well as bacterial oncoprotein production. In a rodent model of H. pylori infection, the genomes of bacteria isolated from the stomach possess an increased number of T-repeats upstream of the HPnc4160-coding region, and this leads to reduced HPnc4160 expression. We use RNA-seq and iTRAQ analyses to identify eight targets of HPnc4160, including genes encoding outer membrane proteins and oncoprotein CagA. Mutant strains with HPnc4160 deficiency display increased colonization ability of the mouse stomach, in comparison with the wild-type strain. Furthermore, HPnc4160 expression is lower in clinical isolates from gastric cancer patients than in isolates derived from non-cancer patients, while the expression of HPnc4160’s targets is higher in the isolates from gastric cancer patients. Therefore, the small RNA HPnc4160 regulates H. pylori adaptation to the host environment and, potentially, gastric carcinogenesis. Long-term infection of the stomach with Helicobacter pylori can cause gastric cancer. Here, Kinoshita-Daitoku et al. show that a small non-coding RNA of H. pylori regulates bacterial adaptation to the stomach environment and bacterial oncoprotein production.
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26
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Gerovac M, Vogel J, Smirnov A. The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches. Front Mol Biosci 2021; 8:661448. [PMID: 33898526 PMCID: PMC8058203 DOI: 10.3389/fmolb.2021.661448] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
Macromolecular complexes of proteins and RNAs are essential building blocks of cells. These stable supramolecular particles can be viewed as minimal biochemical units whose structural organization, i.e., the way the RNA and the protein interact with each other, is directly linked to their biological function. Whether those are dynamic regulatory ribonucleoproteins (RNPs) or integrated molecular machines involved in gene expression, the comprehensive knowledge of these units is critical to our understanding of key molecular mechanisms and cell physiology phenomena. Such is the goal of diverse complexomic approaches and in particular of the recently developed gradient profiling by sequencing (Grad-seq). By separating cellular protein and RNA complexes on a density gradient and quantifying their distributions genome-wide by mass spectrometry and deep sequencing, Grad-seq charts global landscapes of native macromolecular assemblies. In this review, we propose a function-based ontology of stable RNPs and discuss how Grad-seq and related approaches transformed our perspective of bacterial and eukaryotic ribonucleoproteins by guiding the discovery of new RNA-binding proteins and unusual classes of noncoding RNAs. We highlight some methodological aspects and developments that permit to further boost the power of this technique and to look for exciting new biology in understudied and challenging biological models.
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Affiliation(s)
- Milan Gerovac
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Alexandre Smirnov
- UMR 7156—Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
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27
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Orooji Y, Movahedi A, Liu Z, Asadnia M, Ghasali E, Ganjkhanlou Y, Razmjou A, Karimi-Maleh H, Kiadeh NTH. Luminescent film: Biofouling investigation of tetraphenylethylene blended polyethersulfone ultrafiltration membrane. CHEMOSPHERE 2021; 267:128871. [PMID: 33308836 DOI: 10.1016/j.chemosphere.2020.128871] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/03/2020] [Accepted: 10/31/2020] [Indexed: 06/12/2023]
Abstract
Despite the huge contribution of membrane-based brine and wastewater purification systems in today's life, biofouling still affects sustainability of membrane engineering. Aimed at reducing membrane modules wastage, the need to study biofouling monitoring as one of contributory factors stemmed from the short time between initial attachment and irreversible biofoulant adhesion. Hence, a membrane for monitoring is introduced to determine the right cleaning time by using fluorescent sensing as a non-destructive and scalable approach. The classical solid-state emissive fluorophore, tetraphenylethylene (TPE), was introduced as a sustainable, safe and sensitive fluorescent indicator in order to show the potential of the method, and polyethersulfone (PES) and nonsolvent-induced phase separation method, the most popular material and method, are used to fabricate membrane in industry and academia. Since the employed filler has an aggregation-induced emission (AIE) characteristic, it can track the biofouling throughout the operation. The fabricated membranes have certain characterizations (i.e. morphology assessment, flux, antibiogram, flow cytometry, surface free energy, and protein adsorption) which indicate that hybrid membrane with 5 wt % of TPE has identical biofouling activity compared to neat PES membrane and its optimal luminescence properties make it an appropriate candidate for non-destructive and online biofouling monitoring.
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Affiliation(s)
- Yasin Orooji
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, PR China; Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, PR China.
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, 210037, PR China
| | - Zhipeng Liu
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, PR China; Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, PR China
| | - Mohsen Asadnia
- School of Engineering, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Ehsan Ghasali
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, PR China
| | - Yadolah Ganjkhanlou
- Department of Chemistry, NIS and INSTM Centers, Università di Torino, via P. Giuria 7, 10125, Turin, Italy
| | - Amir Razmjou
- Centre for Technology in Water and Wastewater (CTWW), School of Civil and Environmental Engineering, University of Technology Sydney (UTS), Australia
| | - Hassan Karimi-Maleh
- Department of Chemical Engineering, Laboratory of Nanotechnology, Quchan University of Technology, Quchan, Islamic Republic of Iran; School of Resources and Environment, University of Electronic Science and Technology of China, Xiyuan Ave, P. O. Box 611731, Chengdu, PR China; Department of Chemical Sciences, University of Johannesburg, Doornfontein Campus, P. O. Box 17011, Johannesburg, 2028, South Africa.
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28
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Liu J, Yu M, Ge Y, Tian Y, Hu B, Zhao Y. The RsmA RNA-Binding Proteins in Pseudomonas syringae Exhibit Distinct and Overlapping Roles in Modulating Virulence and Survival Under Different Nutritional Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:637595. [PMID: 33719314 PMCID: PMC7952654 DOI: 10.3389/fpls.2021.637595] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
The post-transcriptional regulator RsmA globally controls gene expression in bacteria. Previous studies showed that RsmA2 and RsmA3 played critical roles in regulating type III secretion system (T3SS), motility, syringafactin, and alginate productions in Pseudomonas syringae pv. tomato strain DC3000 (PstDC3000). In this study, we investigated global gene expression profiles of the wild-type PstDC3000, the rsmA3 mutant, and the rsmA2/A3 double mutant in the hrp-inducing minimum medium (HMM) and King's B (KB) medium. By comparing the rsmA2/A3 and rsmA3 mutants to PstDC3000, a total of 1358 and 1074 differentially expressed genes (DEGs) in HMM, and 870 and 1463 DEGs in KB were uncovered, respectively. When comparing the rsmA2/A3 mutant with the rsmA3 mutant, 277 and 741 DEGs in HMM and KB, respectively, were revealed. Transcriptomic analysis revealed that the rsmY, rsmZ, and rsmX1-5 non-coding small RNAs (ncsRNAs) were positively affected by RsmA2 and RsmA3, while RsmA3 positively regulates the expression of the rsmA2 gene and negatively regulates both rsmA1 and rsmA5 gene expression. Comparative transcriptomic analysis showed that RsmA2 and RsmA3 synergistically influenced the expression of genes involved in T3SS and alginate biosynthesis in HMM and chemotaxis in KB. RsmA2 and RsmA3 inversely affected genes involved in syringafactin production in HMM and ribosomal protein biosynthesis in KB. In addition, RsmA2 played a major role in influencing genes involved in sarcosine and thiamine biosynthesis in HMM and in mannitol and phosphate metabolism in KB. On the other hand, genes involved in fatty acid metabolism, cellulose biosynthesis, signal transduction, and stress responses were mainly impacted by RsmA3 in both HMM and KB; whereas RsmA3 played a major role in controlling genes involved in c-di-GMP, phosphate metabolism, chemotaxis, and capsular polysaccharide in HMM. Furthermore, regulation of syringafactin production and oxidative stress by RsmA2 and RsmA3 was experimentally verified. Our results suggested the potential interplay among the RsmA proteins, which exhibit distinct and overlapping roles in modulating virulence and survival in P. syringae under different nutritional conditions.
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Affiliation(s)
- Jun Liu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, China
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Menghao Yu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Yixin Ge
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, China
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Yanli Tian
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, China
| | - Baishi Hu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, China
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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29
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Irastortza-Olaziregi M, Amster-Choder O. Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises. Front Microbiol 2021; 11:624830. [PMID: 33552035 PMCID: PMC7858274 DOI: 10.3389/fmicb.2020.624830] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 01/17/2023] Open
Abstract
Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT occurs when ribosomes associate with and initiate translation of mRNAs whose transcription has not yet concluded, therefore forming "RNAP.mRNA.ribosome" complexes. CTT is a well-documented phenomenon that is involved in important gene regulation processes, such as attenuation and operon polarity. Despite the progress in our understanding of the cellular signals that coordinate CTT, certain aspects of its molecular architecture remain controversial. Additionally, new information on the spatial segregation between the transcriptional and the translational machineries in certain species, and on the capability of certain mRNAs to localize translation-independently, questions the unanimous occurrence of CTT. Furthermore, studies where transcription and translation were artificially uncoupled showed that transcription elongation can proceed in a translation-independent manner. Here, we review studies supporting the occurrence of CTT and findings questioning its extent, as well as discuss mechanisms that may explain both coupling and uncoupling, e.g., chromosome relocation and the involvement of cis- or trans-acting elements, such as small RNAs and RNA-binding proteins. These mechanisms impact RNA localization, stability, and translation. Understanding the two options by which genes can be expressed and their consequences should shed light on a new layer of control of bacterial transcripts fate.
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Affiliation(s)
- Mikel Irastortza-Olaziregi
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
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30
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Bogacz M, El Abbar FM, Cox CA, Li J, Fiedler JS, Tran LKH, Tran PMH, Daugherty CL, Blake KH, Wang Z, Azadi P, Thompson SA. Binding of Campylobacter jejuni FliW Adjacent to the CsrA RNA-Binding Pockets Modulates CsrA Regulatory Activity. Front Microbiol 2021; 11:531596. [PMID: 33505360 PMCID: PMC7829508 DOI: 10.3389/fmicb.2020.531596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 12/08/2020] [Indexed: 11/13/2022] Open
Abstract
Campylobacter jejuni CsrA is an mRNA-binding, post-transcriptional regulator that controls many metabolic- and virulence-related characteristics of this important pathogen. In contrast to E. coli CsrA, whose activity is modulated by binding to small non-coding RNAs (sRNAs), C. jejuni CsrA activity is controlled by binding to the CsrA antagonist FliW. In this study, we identified the FliW binding site on CsrA. Deletion of the C-terminus of C. jejuni CsrA, which is extended relative to sRNA-binding CsrA proteins, abrogated FliW binding. Bacterial two-hybrid experiments were used to assess the interaction of FliW with wild-type CsrA and mutants thereof, in which every amino acid was individually mutated. Two CsrA mutations (V51A and N55A) resulted in a significant decrease in FliW binding. The V51A and N55A mutants also showed a decrease in CsrA-FliW complex formation, as assessed by size-exclusion chromatography and surface plasmon resonance. These residues were highly conserved in bacterial species containing CsrA orthologs whose activities are predicted to be regulated by FliW. The location of FliW binding was immediately adjacent to the two RNA-binding sites of the CsrA homodimer, suggesting the model that FliW binding to CsrA modulates its ability to bind to its mRNA targets either by steric hindrance, electrostatic repulsion, or by altering the overall structure of the RNA-binding sites.
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Affiliation(s)
- Marek Bogacz
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Faiha M El Abbar
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Claudia A Cox
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Jiaqi Li
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Jarred S Fiedler
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Lynn K H Tran
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Paul M H Tran
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - C Luke Daugherty
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Kate H Blake
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Zhirui Wang
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, United States
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, United States
| | - Stuart A Thompson
- Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
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31
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Contact with the CsrA Core Is Required for Allosteric Inhibition by FliW in Bacillus subtilis. J Bacteriol 2020; 203:JB.00574-20. [PMID: 33106347 DOI: 10.1128/jb.00574-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 11/20/2022] Open
Abstract
The RNA-binding protein CsrA is a posttranscriptional regulator encoded by genomes throughout the bacterial phylogeny. In the gammaproteobacteria, the activity of CsrA is inhibited by small RNAs that competitively sequester CsrA binding. In contrast, the firmicute Bacillus subtilis encodes a protein inhibitor of CsrA called FliW, which noncompetitively inhibits CsrA activity but for which the precise mechanism of antagonism is unclear. Here, we take an unbiased genetic approach to identify residues of FliW important for CsrA inhibition and these residues fall into two distinct spatial and functional classes. Most loss-of-function alleles mutated FliW residues surrounding the critical regulatory CsrA residue N55 and abolished interaction between the two proteins. Two loss-of-function alleles, however, mutated FliW residues near the CsrA core dimerization domain and maintained interaction with CsrA. One of the FliW alleles reversed a residue charge to disrupt a salt bridge with the CsrA core, and a compensatory charge reversal in the CsrA partner residue restored both the salt bridge and antagonism. We propose a model in which the initial interaction between FliW and CsrA is necessary but not sufficient for antagonism, and for which salt bridge formation with, and deformation of, the CsrA core domain is likely required to allosterically abolish RNA-binding activity.IMPORTANCE CsrA is a small dimeric protein that binds RNA and is one of the few known examples of transcript-specific protein regulators of translation in bacteria. A protein called FliW binds to and antagonizes CsrA to govern flagellin homeostasis and flagellar assembly. Despite having a high-resolution three-dimensional structure of the FliW-CsrA complex, the mechanism of noncompetitive inhibition remains unresolved. Here, we identify FliW residues required for antagonism and we find that the residues make a linear connection in the complex from initial binding interaction with CsrA to a critical salt bridge near the core of the CsrA dimer. We propose that the salt bridge represents an allosteric contact that distorts the CsrA core to prevent RNA binding.
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Muleya V, Marondedze C. Functional Roles of RNA-Binding Proteins in Plant Signaling. Life (Basel) 2020; 10:life10110288. [PMID: 33217949 PMCID: PMC7698727 DOI: 10.3390/life10110288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022] Open
Abstract
RNA-binding proteins (RBPs) are typical proteins that bind RNA through single or multiple RNA-binding domains (RBDs). These proteins have a functional role in determining the fate or function of the bound RNAs. A few hundred RBPs were known through in silico prediction based on computational assignment informed by structural similarity and the presence of classical RBDs. However, RBPs lacking such conventional RBDs were omitted. Owing to the recent mRNA interactome capture technology based on UV-crosslinking and fixing proteins to their mRNA targets followed by affinity capture purification and identification of RBPs by tandem mass spectrometry, several hundreds of RBPs have recently been discovered. These proteome-wide studies have colossally increased the number of proteins implicated in RNA binding and unearthed hundreds of novel RBPs lacking classical RBDs, such as proteins involved in intermediary metabolism. These discoveries provide wide insights into the post-transcriptional gene regulation players and their role in plant signaling, such as environmental stress conditions. In this review, novel discoveries of RBPs are explored, particularly on the evolving knowledge of their role in stress responses. The molecular functions of these RBPs, particularly focusing on those that do not have classical RBDs, are also elucidated at the systems level.
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Affiliation(s)
- Victor Muleya
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Main Campus, Senga Road, Gweru P Bag 9055, Zimbabwe;
| | - Claudius Marondedze
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Main Campus, Senga Road, Gweru P Bag 9055, Zimbabwe;
- Rijk Zwaan, 2678 ZG De Lier, The Netherlands
- Correspondence: or or
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Ardissone S, Kint N, Petrignani B, Panis G, Viollier PH. Secretion Relieves Translational Co-repression by a Specialized Flagellin Paralog. Dev Cell 2020; 55:500-513.e4. [DOI: 10.1016/j.devcel.2020.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/28/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022]
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Pourciau C, Lai YJ, Gorelik M, Babitzke P, Romeo T. Diverse Mechanisms and Circuitry for Global Regulation by the RNA-Binding Protein CsrA. Front Microbiol 2020; 11:601352. [PMID: 33193284 PMCID: PMC7652899 DOI: 10.3389/fmicb.2020.601352] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
The carbon storage regulator (Csr) or repressor of stationary phase metabolites (Rsm) system of Gammaproteobacteria is among the most complex and best-studied posttranscriptional regulatory systems. Based on a small RNA-binding protein, CsrA and homologs, it controls metabolism, physiology, and bacterial lifestyle decisions by regulating gene expression on a vast scale. Binding of CsrA to sequences containing conserved GGA motifs in mRNAs can regulate translation, RNA stability, riboswitch function, and transcript elongation. CsrA governs the expression of dozens of transcription factors and other regulators, further expanding its influence on cellular physiology, and these factors can participate in feedback to the Csr system. Expression of csrA itself is subject to autoregulation via translational inhibition and indirect transcriptional activation. CsrA activity is controlled by small noncoding RNAs (sRNAs), CsrB and CsrC in Escherichia coli, which contain multiple high affinity CsrA binding sites that compete with those of mRNA targets. Transcription of CsrB/C is induced by certain nutrient limitations, cellular stresses, and metabolites, while these RNAs are targeted for degradation by the presence of a preferred carbon source. Consistent with these findings, CsrA tends to activate pathways and processes that are associated with robust growth and repress stationary phase metabolism and stress responses. Regulatory loops between Csr components affect the signaling dynamics of the Csr system. Recently, systems-based approaches have greatly expanded our understanding of the roles played by CsrA, while reinforcing the notion that much remains to be learned about the Csr system.
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Affiliation(s)
- Christine Pourciau
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Ying-Jung Lai
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Mark Gorelik
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Tony Romeo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
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Barnawi H, Masri N, Hussain N, Al-Lawati B, Mayasari E, Gulbicka A, Jervis AJ, Huang MH, Cavet JS, Linton D. RNA-based thermoregulation of a Campylobacter jejuni zinc resistance determinant. PLoS Pathog 2020; 16:e1009008. [PMID: 33064782 PMCID: PMC7592916 DOI: 10.1371/journal.ppat.1009008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 10/28/2020] [Accepted: 09/28/2020] [Indexed: 01/04/2023] Open
Abstract
RNA thermometers (RNATs) trigger bacterial virulence factor expression in response to the temperature shift on entering a warm-blooded host. At lower temperatures these secondary structures sequester ribosome-binding sites (RBSs) to prevent translation initiation, whereas at elevated temperatures they "melt" allowing translation. Campylobacter jejuni is the leading bacterial cause of human gastroenteritis worldwide yet little is known about how it interacts with the host including host induced gene regulation. Here we demonstrate that an RNAT regulates a C. jejuni gene, Cj1163c or czcD, encoding a member of the Cation Diffusion Facilitator family. The czcD upstream untranslated region contains a predicted stem loop within the mRNA that sequesters the RBS to inhibit translation at temperatures below 37°C. Mutations that disrupt or enhance predicted secondary structure have significant and predictable effects on temperature regulation. We also show that in an RNAT independent manner, CzcD expression is induced by Zn(II). Mutants lacking czcD are hypersensitive to Zn(II) and also over-accumulate Zn(II) relative to wild-type, all consistent with CzcD functioning as a Zn(II) exporter. Importantly, we demonstrate that C. jejuni Zn(II)-tolerance at 32°C, a temperature at which the RNAT limits CzcD production, is increased by RNAT disruption. Finally we show that czcD inactivation attenuates larval killing in a Galleria infection model and that at 32°C disrupting RNAT secondary structure to allow CzcD production can enhance killing. We hypothesise that CzcD regulation by metals and temperature provides a mechanism for C. jejuni to overcome innate immune system-mediated Zn(II) toxicity in warm-blooded animal hosts.
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Affiliation(s)
- Heba Barnawi
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Nader Masri
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Natasha Hussain
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Bushra Al-Lawati
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Evita Mayasari
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Microbiology Department, Faculty of Medicine, Universitas Sumatera Utara, Indonesia
| | - Aleksandra Gulbicka
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Adrian J. Jervis
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Min-Hsuan Huang
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Jennifer S. Cavet
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- * E-mail: (JSC); (DL)
| | - Dennis Linton
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- * E-mail: (JSC); (DL)
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Irastortza-Olaziregi M, Amster-Choder O. RNA localization in prokaryotes: Where, when, how, and why. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1615. [PMID: 32851805 DOI: 10.1002/wrna.1615] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/27/2020] [Accepted: 06/02/2020] [Indexed: 12/27/2022]
Abstract
Only recently has it been recognized that the transcriptome of bacteria and archaea can be spatiotemporally regulated. All types of prokaryotic transcripts-rRNAs, tRNAs, mRNAs, and regulatory RNAs-may acquire specific localization and these patterns can be temporally regulated. In some cases bacterial RNAs reside in the vicinity of the transcription site, but in many others, transcripts show distinct localizations to the cytoplasm, the inner membrane, or the pole of rod-shaped species. This localization, which often overlaps with that of the encoded proteins, can be achieved either in a translation-dependent or translation-independent fashion. The latter implies that RNAs carry sequence-level features that determine their final localization with the aid of RNA-targeting factors. Localization of transcripts regulates their posttranscriptional fate by affecting their degradation and processing, translation efficiency, sRNA-mediated regulation, and/or propensity to undergo RNA modifications. By facilitating complex assembly and liquid-liquid phase separation, RNA localization is not only a consequence but also a driver of subcellular spatiotemporal complexity. We foresee that in the coming years the study of RNA localization in prokaryotes will produce important novel insights regarding the fundamental understanding of membrane-less subcellular organization and lead to practical outputs with biotechnological and therapeutic implications. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Mikel Irastortza-Olaziregi
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Sobrero PM, Valverde C. Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas. Front Mol Biosci 2020; 7:127. [PMID: 32754614 PMCID: PMC7366521 DOI: 10.3389/fmolb.2020.00127] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/02/2020] [Indexed: 12/15/2022] Open
Abstract
Gene expression is adjusted according to cellular needs through a combination of mechanisms acting at different layers of the flow of genetic information. At the posttranscriptional level, RNA-binding proteins are key factors controlling the fate of nascent and mature mRNAs. Among them, the members of the CsrA family are small dimeric proteins with heterogeneous distribution across the bacterial tree of life, that act as global regulators of gene expression because they recognize characteristic sequence/structural motifs (short hairpins with GGA triplets in the loop) present in hundreds of mRNAs. The regulatory output of CsrA binding to mRNAs is counteracted in most cases by molecular mimic, non-protein coding RNAs that titrate the CsrA dimers away from the target mRNAs. In γ-proteobacteria, the regulatory modules composed by CsrA homologs and the corresponding antagonistic sRNAs, are mastered by two-component systems of the GacS-GacA type, which control the transcription and the abundance of the sRNAs, thus constituting the rather linear cascade Gac-Rsm that responds to environmental or cellular signals to adjust and coordinate the expression of a set of target genes posttranscriptionally. Within the γ-proteobacteria, the genus Pseudomonas has been shown to contain species with different number of active CsrA (RsmA) homologs and of molecular mimic sRNAs. Here, with the help of the increasing availability of genomic data we provide a comprehensive state-of-the-art picture of the remarkable multiplicity of CsrA lineages, including novel yet uncharacterized paralogues, and discuss evolutionary aspects of the CsrA subfamilies of the genus Pseudomonas, and implications of the striking presence of csrA alleles in natural mobile genetic elements (phages and plasmids).
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Affiliation(s)
- Patricio Martín Sobrero
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Buenos Aires, Argentina
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The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition. Nat Commun 2020; 11:2823. [PMID: 32499480 PMCID: PMC7272453 DOI: 10.1038/s41467-020-16650-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
FinO-domain proteins are a widespread family of bacterial RNA-binding proteins with regulatory functions. Their target spectrum ranges from a single RNA pair, in the case of plasmid-encoded FinO, to global RNA regulons, as with enterobacterial ProQ. To assess whether the FinO domain itself is intrinsically selective or promiscuous, we determine in vivo targets of Neisseria meningitidis, which consists of solely a FinO domain. UV-CLIP-seq identifies associations with 16 small non-coding sRNAs and 166 mRNAs. Meningococcal ProQ predominantly binds to highly structured regions and generally acts to stabilize its RNA targets. Loss of ProQ alters transcript levels of >250 genes, demonstrating that this minimal ProQ protein impacts gene expression globally. Phenotypic analyses indicate that ProQ promotes oxidative stress resistance and DNA damage repair. We conclude that FinO domain proteins recognize some abundant type of RNA shape and evolve RNA binding selectivity through acquisition of additional regions that constrain target recognition. FinO-domain proteins are bacterial RNA-binding proteins with a wide range of target specificities. Here, the authors employ UV CLIP-seq and show that minimal ProQ protein of Neisseria meningitidis binds to various small non-coding RNAs and mRNAs involved in virulence.
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Saha C, Mohanraju P, Stubbs A, Dugar G, Hoogstrate Y, Kremers GJ, van Cappellen WA, Horst-Kreft D, Laffeber C, Lebbink JH, Bruens S, Gaskin D, Beerens D, Klunder M, Joosten R, Demmers JAA, van Gent D, Mouton JW, van der Spek PJ, van der Oost J, van Baarlen P, Louwen R. Guide-free Cas9 from pathogenic Campylobacter jejuni bacteria causes severe damage to DNA. SCIENCE ADVANCES 2020; 6:eaaz4849. [PMID: 32596446 PMCID: PMC7299616 DOI: 10.1126/sciadv.aaz4849] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 05/06/2020] [Indexed: 05/11/2023]
Abstract
CRISPR-Cas9 systems are enriched in human pathogenic bacteria and have been linked to cytotoxicity by an unknown mechanism. Here, we show that upon infection of human cells, Campylobacter jejuni secretes its Cas9 (CjeCas9) nuclease into their cytoplasm. Next, a native nuclear localization signal enables CjeCas9 nuclear entry, where it catalyzes metal-dependent nonspecific DNA cleavage leading to cell death. Compared to CjeCas9, native Cas9 of Streptococcus pyogenes (SpyCas9) is more suitable for guide-dependent editing. However, in human cells, native SpyCas9 may still cause some DNA damage, most likely because of its ssDNA cleavage activity. This side effect can be completely prevented by saturation of SpyCas9 with an appropriate guide RNA, which is only partially effective for CjeCas9. We conclude that CjeCas9 plays an active role in attacking human cells rather than in viral defense. Moreover, these unique catalytic features may therefore make CjeCas9 less suitable for genome editing applications.
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Affiliation(s)
- Chinmoy Saha
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | | | - Andrew Stubbs
- Clinical Bioinformatics, Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Gaurav Dugar
- Institute of Molecular Infection Biology (IMIB)/Research Center for Infectious Diseases (ZINF), University of Würzburg, Würzburg, Germany
| | - Youri Hoogstrate
- Clinical Bioinformatics, Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Gert-Jan Kremers
- Optical Imaging Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | | | - Deborah Horst-Kreft
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Charlie Laffeber
- Department of Molecular Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Joyce H.G. Lebbink
- Department of Molecular Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Radiation Oncology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Serena Bruens
- Department of Molecular Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Duncan Gaskin
- Institute of Food Research, Gut Health and Food Safety Programme, Norwich Research Park, Norwich, UK
| | - Dior Beerens
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Maarten Klunder
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Rob Joosten
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Jeroen A. A. Demmers
- Proteomics Center, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Dik van Gent
- Department of Molecular Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Johan W. Mouton
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Peter J. van der Spek
- Clinical Bioinformatics, Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Peter van Baarlen
- Host-Microbe Interactomics Group, University of Wageningen, Wageningen, Netherlands
| | - Rogier Louwen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
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Alzheimer M, Svensson SL, König F, Schweinlin M, Metzger M, Walles H, Sharma CM. A three-dimensional intestinal tissue model reveals factors and small regulatory RNAs important for colonization with Campylobacter jejuni. PLoS Pathog 2020; 16:e1008304. [PMID: 32069333 PMCID: PMC7048300 DOI: 10.1371/journal.ppat.1008304] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 02/28/2020] [Accepted: 01/02/2020] [Indexed: 02/06/2023] Open
Abstract
The Gram-negative Epsilonproteobacterium Campylobacter jejuni is currently the most prevalent bacterial foodborne pathogen. Like for many other human pathogens, infection studies with C. jejuni mainly employ artificial animal or cell culture models that can be limited in their ability to reflect the in-vivo environment within the human host. Here, we report the development and application of a human three-dimensional (3D) infection model based on tissue engineering to study host-pathogen interactions. Our intestinal 3D tissue model is built on a decellularized extracellular matrix scaffold, which is reseeded with human Caco-2 cells. Dynamic culture conditions enable the formation of a polarized mucosal epithelial barrier reminiscent of the 3D microarchitecture of the human small intestine. Infection with C. jejuni demonstrates that the 3D tissue model can reveal isolate-dependent colonization and barrier disruption phenotypes accompanied by perturbed localization of cell-cell junctions. Pathogenesis-related phenotypes of C. jejuni mutant strains in the 3D model deviated from those obtained with 2D-monolayers, but recapitulated phenotypes previously observed in animal models. Moreover, we demonstrate the involvement of a small regulatory RNA pair, CJnc180/190, during infections and observe different phenotypes of CJnc180/190 mutant strains in 2D vs. 3D infection models. Hereby, the CJnc190 sRNA exerts its pathogenic influence, at least in part, via repression of PtmG, which is involved in flagellin modification. Our results suggest that the Caco-2 cell-based 3D tissue model is a valuable and biologically relevant tool between in-vitro and in-vivo infection models to study virulence of C. jejuni and other gastrointestinal pathogens. Enteric pathogens have evolved numerous strategies to successfully colonize and persist in the human gastrointestinal tract. However, especially for the research of virulence mechanisms of human pathogens, often only limited infection models are available. Here, we have applied and further advanced a tissue-engineered human intestinal tissue model based on an extracellular matrix scaffold reseeded with human cells that can faithfully mimic pathogenesis-determining processes of the zoonotic pathogen Campylobacter jejuni. Our three-dimensional (3D) intestinal infection model allows for the assessment of epithelial barrier function during infection as well as for the quantification of bacterial adherence, internalization, and transmigration. Investigation of C. jejuni mutant strains in our 3D tissue model revealed isolate-specific infection phenotypes, in-vivo relevant infection outcomes, and uncovered the involvement of a small RNA pair during C. jejuni pathogenesis. Overall, our results demonstrate the power of tissue-engineered models for studying host-pathogen interactions, and our model will also be helpful to investigate other gastrointestinal pathogens.
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Affiliation(s)
- Mona Alzheimer
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Sarah L. Svensson
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Fabian König
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Matthias Schweinlin
- Department of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Würzburg, Germany
| | - Marco Metzger
- Department of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Würzburg, Germany
- Fraunhofer-Institute for Silicate Research, Translational Centre Regenerative Therapies, Würzburg, Germany
| | - Heike Walles
- Department of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Würzburg, Germany
- Core Facility Tissue Engineering, Otto-von-Guericke University, Magdeburg, Germany
- * E-mail: (HW); (CMS)
| | - Cynthia M. Sharma
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- * E-mail: (HW); (CMS)
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Lambrecht SJ, Kanesaki Y, Fuss J, Huettel B, Reinhardt R, Steglich C. Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4. Sci Rep 2019; 9:14331. [PMID: 31586076 PMCID: PMC6778093 DOI: 10.1038/s41598-019-49881-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 09/02/2019] [Indexed: 01/22/2023] Open
Abstract
The sRNA Yfr1 and members of the Yfr2 sRNA family are almost universally present within cyanobacteria. The conserved motifs of these sRNAs are nearly complementary to each other, suggesting their ability to participate in crosstalk. The conserved motif of Yfr1 is shared by members of the Yfr10 sRNA family, members of which are otherwise less conserved in sequence, structure, and synteny compared to Yfr1. The different structural properties enable the discrimination of unique targets of Yfr1 and Yfr10. Unlike most studied regulatory sRNAs, Yfr1 gene expression only slightly changes under the tested stress conditions and is present at high levels at all times. In contrast, cellular levels of Yfr10 increase during the course of acclimation to darkness, and levels of Yfr2 increase when cells are shifted to high light or nitrogen limitation conditions. In this study, we investigated the targetomes of Yfr2, Yfr1, and Yfr10 in Prochlorococcus MED4, establishing CRAFD-Seq as a new method for identifying direct targets of these sRNAs that is applicable to all bacteria, including those that are not amenable to genetic modification. The results suggest that these sRNAs are integrated within a regulatory network of unprecedented complexity in the adjustment of carbon and nitrogen-related primary metabolism.
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Affiliation(s)
- S Joke Lambrecht
- University of Freiburg, Faculty of Biology, D-79104, Freiburg, Germany
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan.,Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Janina Fuss
- Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, D-50829, Köln, Germany
| | - Bruno Huettel
- Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, D-50829, Köln, Germany
| | - Richard Reinhardt
- Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, D-50829, Köln, Germany
| | - Claudia Steglich
- University of Freiburg, Faculty of Biology, D-79104, Freiburg, Germany.
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43
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Lee JH, Ancona V, Chatnaparat T, Yang HW, Zhao Y. The RNA-Binding Protein CsrA Controls Virulence in Erwinia amylovora by Regulating RelA, RcsB, and FlhD at the Posttranscriptional Level. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1448-1459. [PMID: 31140921 DOI: 10.1094/mpmi-03-19-0077-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
CsrA, an RNA-binding protein, binds to target transcripts and alters their translation or stability. In Erwinia amylovora, CsrA positively regulates the expression of type III secretion system (T3SS), exopolysaccharide amylovoran, and motility. In this study, the global effect of CsrA and its noncoding small RNA (ncsRNA) csrB in E. amylovora was determined by RNA-seq, and potential molecular mechanisms of CsrA-dependent virulence regulation were examined. Transcriptomic analyses under the T3SS-inducing condition revealed that mutation in the csrA gene led to differential expression of more than 20% of genes in the genome. Among them, T3SS genes and those required for cell growth and viability were significantly downregulated. On the other hand, the csrB mutant exhibited significant upregulation of most major virulence genes, suggesting an antagonistic effect of csrB on CsrA targets. Direct interaction between CsrA protein and csrB was further confirmed through the RNA electrophoretic mobility shift assay (REMSA). However, no direct interaction between CsrA and hrpL and hrpS transcripts was detected, suggesting that HrpL and HrpS are not targets of CsrA, whereas three CsrA targets (relA, rcsB, and flhD) were identified and confirmed by REMSA, site-directed mutagenesis, and LacZ reporter gene assays. These findings might partially explain how CsrA positively controls E. amylovora virulence by targeting major regulators at the posttranscriptional level.
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Affiliation(s)
- Jae Hoon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
| | - Veronica Ancona
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
| | - Tiyakhon Chatnaparat
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
| | - Ho-Wen Yang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
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Kannaiah S, Livny J, Amster-Choder O. Spatiotemporal Organization of the E. coli Transcriptome: Translation Independence and Engagement in Regulation. Mol Cell 2019; 76:574-589.e7. [PMID: 31540875 DOI: 10.1016/j.molcel.2019.08.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 06/28/2019] [Accepted: 08/13/2019] [Indexed: 12/22/2022]
Abstract
RNA localization in eukaryotes is a mechanism to regulate transcripts fate. Conversely, bacterial transcripts were not assumed to be specifically localized. We previously demonstrated that E. coli mRNAs may localize to where their products localize in a translation-independent manner, thus challenging the transcription-translation coupling extent. However, the scope of RNA localization in bacteria remained unknown. Here, we report the distribution of the E. coli transcriptome between the membrane, cytoplasm, and poles by combining cell fractionation with deep-sequencing (Rloc-seq). Our results reveal asymmetric RNA distribution on a transcriptome-wide scale, significantly correlating with proteome localization and prevalence of translation-independent RNA localization. The poles are enriched with stress-related mRNAs and small RNAs, the latter becoming further enriched upon stress in an Hfq-dependent manner. Genome organization may play a role in localizing membrane protein-encoding transcripts. Our results show an unexpected level of intricacy in bacterial transcriptome organization and highlight the poles as hubs for regulation.
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Affiliation(s)
- Shanmugapriya Kannaiah
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02140, USA
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel.
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45
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Abstract
RNA-binding proteins (RBPs) are central to most if not all cellular processes, dictating the fate of virtually all RNA molecules in the cell. Starting with pioneering work on ribosomal proteins, studies of bacterial RBPs have paved the way for molecular studies of RNA-protein interactions. Work over the years has identified major RBPs that act on cellular transcripts at the various stages of bacterial gene expression and that enable their integration into post-transcriptional networks that also comprise small non-coding RNAs. Bacterial RBP research has now entered a new era in which RNA sequencing-based methods permit mapping of RBP activity in a truly global manner in vivo. Moreover, the soaring interest in understudied members of host-associated microbiota and environmental communities is likely to unveil new RBPs and to greatly expand our knowledge of RNA-protein interactions in bacteria.
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Affiliation(s)
- Erik Holmqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany. .,Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
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46
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El Abbar FM, Li J, Owen HC, Daugherty CL, Fulmer CA, Bogacz M, Thompson SA. RNA Binding by the Campylobacter jejuni Post-transcriptional Regulator CsrA. Front Microbiol 2019; 10:1776. [PMID: 31447808 PMCID: PMC6692469 DOI: 10.3389/fmicb.2019.01776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/18/2019] [Indexed: 01/02/2023] Open
Abstract
Campylobacter jejuni is a Gram-negative rod-shaped bacterium that commensally inhabits the intestinal tracts of livestock and birds, and which also persists in surface waters. C. jejuni is a leading cause of foodborne gastroenteritis, and these infections are sometimes associated with the development of post-infection sequelae such as Guillain-Barré Syndrome. Flagella are considered a primary virulence factor in C. jejuni, as these organelles are required for pathogenicity-related phenotypes including motility, biofilm formation, host cell interactions, and host colonization. The post-transcriptional regulator CsrA regulates the expression of the major flagellin FlaA by binding to flaA mRNA and repressing its translation. Additionally, CsrA has previously been shown to regulate 120–150 proteins involved in diverse cellular processes. The amino acid sequence of C. jejuni CsrA is significantly different from that of Escherichia coli CsrA, and no previous research has defined the amino acids of C. jejuni CsrA that are critical for RNA binding. In this study, we used in vitro SELEX to identify the consensus RNA sequence mAwGGAs to which C. jejuni CsrA binds with high affinity. We performed saturating site-directed mutagenesis on C. jejuni CsrA and assessed the regulatory activity of these mutant proteins, using a reporter system encoding the 5′ untranslated region (5′ UTR) upstream of flaA linked translationally to the C. jejuni astA gene. These assays allowed us to identify 19 amino acids that were involved in RNA binding by CsrA, with many but not all of these amino acids clustered in predicted beta strands that are involved in RNA binding by E. coli CsrA. Decreased flaA mRNA binding by mutant CsrA proteins L2A and A36V was confirmed by electrophoretic mobility shift assays. The majority of the amino acids implicated in RNA binding were conserved among diverse Campylobacter species.
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Affiliation(s)
- Faiha M El Abbar
- Division of Infectious Diseases, Department of Medicine, Augusta University, Augusta, GA, United States
| | - Jiaqi Li
- Division of Infectious Diseases, Department of Medicine, Augusta University, Augusta, GA, United States
| | - Harry C Owen
- Division of Infectious Diseases, Department of Medicine, Augusta University, Augusta, GA, United States
| | - C Luke Daugherty
- Division of Infectious Diseases, Department of Medicine, Augusta University, Augusta, GA, United States
| | - Claudia A Fulmer
- Division of Infectious Diseases, Department of Medicine, Augusta University, Augusta, GA, United States
| | - Marek Bogacz
- Division of Infectious Diseases, Department of Medicine, Augusta University, Augusta, GA, United States
| | - Stuart A Thompson
- Division of Infectious Diseases, Department of Medicine, Augusta University, Augusta, GA, United States
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47
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Robust Stoichiometry of FliW-CsrA Governs Flagellin Homeostasis and Cytoplasmic Organization in Bacillus subtilis. mBio 2019; 10:mBio.00533-19. [PMID: 31113895 PMCID: PMC6529632 DOI: 10.1128/mbio.00533-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular concentration of flagellar filament protein Hag is restricted by the Hag-FliW-CsrA system in B. subtilis. Here we show that the Hag-FliW-CsrAdimer system functions at nearly 1:1:1 stoichiometry and that the system is both robust with respect to perturbation and hypersensitive to the Hag intracellular concentration. Moreover, restriction of cytoplasmic Hag levels is important for maintaining proper intracellular architecture, as artificial Hag hyperaccumulation led to generalized spatial defects and a high frequency of minicell production. The Hag-FliW-CsrA system is conserved in the deeper branches of bacterial phylogeny, and we note that the Hag-FliW-CsrA “homeostasis module” resembles a toxin-antitoxin system where, by analogy, CsrA is the “toxin,” FliW is the “antitoxin,” and Hag is the target. Flagellin (Hag) is one of the most abundant proteins in Bacillus subtilis. Here we show that each flagellar filament is assembled from ∼12,000 Hag monomers and that there is a cytoplasmic pool of Hag that is restricted to 5% of the total. Hag is thought to be restricted at the level of translation by a partner-switching mechanism involving FliW and the homodimeric RNA-binding protein CsrA (CsrAdimer). We further show that the mechanism of translation inhibition is hypersensitive due to a 1:1 ratio of Hag to FliW, a 1:1 inhibitory ratio of FliW to CsrAdimer, and a nearly 1:1 ratio of CsrAdimer to hag transcripts. Equimolarity of all components couples single-molecule detection of Hag export to compensatory translation and causes cytoplasmic Hag concentrations to oscillate around the level of FliW. We found that stoichiometry is ensured by genetic architecture, translational coupling, and the ability of CsrAdimer to restrict hag transcript accumulation. We further show that homeostasis prevents Hag hyperaccumulation that would otherwise cause severe defects in intracellular architecture, perhaps due to increased molecular crowding. We note that FliW-CsrA-mediated structural homeostasis has similarities to that seen with some toxin-antitoxin systems.
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48
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Babitzke P, Lai YJ, Renda AJ, Romeo T. Posttranscription Initiation Control of Gene Expression Mediated by Bacterial RNA-Binding Proteins. Annu Rev Microbiol 2019; 73:43-67. [PMID: 31100987 DOI: 10.1146/annurev-micro-020518-115907] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA-binding proteins play vital roles in regulating gene expression and cellular physiology in all organisms. Bacterial RNA-binding proteins can regulate transcription termination via attenuation or antitermination mechanisms, while others can repress or activate translation initiation by affecting ribosome binding. The RNA targets for these proteins include short repeated sequences, longer single-stranded sequences, RNA secondary or tertiary structure, and a combination of these features. The activity of these proteins can be influenced by binding of metabolites, small RNAs, or other proteins, as well as by phosphorylation events. Some of these proteins regulate specific genes, while others function as global regulators. As the regulatory mechanisms, components, targets, and signaling circuitry surrounding RNA-binding proteins have become better understood, in part through rapid advances provided by systems approaches, a sense of the true nature of biological complexity is becoming apparent, which we attempt to capture for the reader of this review.
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Affiliation(s)
- Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
| | - Ying-Jung Lai
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, USA; ,
| | - Andrew J Renda
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
| | - Tony Romeo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, USA; ,
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49
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Müller P, Gimpel M, Wildenhain T, Brantl S. A new role for CsrA: promotion of complex formation between an sRNA and its mRNA target in Bacillus subtilis. RNA Biol 2019; 16:972-987. [PMID: 31043113 PMCID: PMC6546359 DOI: 10.1080/15476286.2019.1605811] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
CsrA is a widely conserved, abundant small RNA binding protein that has been found in E. coli and other Gram-negative bacteria where it is involved in the regulation of carbon metabolism, biofilm formation and virulence. CsrA binds to single-stranded GGA motifs around the SD sequence of target mRNAs where it inhibits or activates translation or influences RNA processing. Small RNAs like CsrB or CsrC containing 13–22 GGA motifs can sequester CsrA, thereby abrogating the effect of CsrA on its target mRNAs. In B. subtilis, CsrA has so far only been found to regulate one target, hag mRNA and to be sequestered by a protein (FliW) and not by an sRNA. Here, we employ a combination of in vitro and in vivo methods to investigate the effect of CsrA on the small regulatory RNA SR1 from B. subtilis, its primary target ahrC mRNA and its downstream targets, the rocABC and rocDEF operons. We demonstrate that CsrA can promote the base-pairing interactions between SR1 and ahrC mRNA, a function that has so far only been found for Hfq or ProQ. Abbreviations: aa, amino acid; bp, basepair; nt, nucleotide; PAA, polyacrylamide; SD, Shine Dalgarno.
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Affiliation(s)
- Peter Müller
- a Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik , Friedrich-Schiller-Universität Jena , Jena , Germany
| | - Matthias Gimpel
- a Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik , Friedrich-Schiller-Universität Jena , Jena , Germany.,b Institut für Biotechnologie , Fachgebiet Bioverfahrenstechnik , Berlin , Germany
| | - Theresa Wildenhain
- a Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik , Friedrich-Schiller-Universität Jena , Jena , Germany
| | - Sabine Brantl
- a Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik , Friedrich-Schiller-Universität Jena , Jena , Germany
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50
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Abstract
Diverse mechanisms and functions of posttranscriptional regulation by small regulatory RNAs and RNA-binding proteins have been described in bacteria. In contrast, little is known about the spatial organization of RNAs in bacterial cells. In eukaryotes, subcellular localization and transport of RNAs play important roles in diverse physiological processes, such as embryonic patterning, asymmetric cell division, epithelial polarity, and neuronal plasticity. It is now clear that bacterial RNAs also can accumulate at distinct sites in the cell. However, due to the small size of bacterial cells, RNA localization and localization-associated functions are more challenging to study in bacterial cells, and the underlying molecular mechanisms of transcript localization are less understood. Here, we review the emerging examples of RNAs localized to specific subcellular locations in bacteria, with indications that subcellular localization of transcripts might be important for gene expression and regulatory processes. Diverse mechanisms for bacterial RNA localization have been suggested, including close association to their genomic site of transcription, or to the localizations of their protein products in translation-dependent or -independent processes. We also provide an overview of the state of the art of technologies to visualize and track bacterial RNAs, ranging from hybridization-based approaches in fixed cells to in vivo imaging approaches using fluorescent protein reporters and/or RNA aptamers in single living bacterial cells. We conclude with a discussion of open questions in the field and ongoing technological developments regarding RNA imaging in eukaryotic systems that might likewise provide novel insights into RNA localization in bacteria.
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