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Yang X, Yang J, Huang H, Yan X, Li X, Lin Z. Achieving robust synthetic tolerance in industrial E. coli through negative auto-regulation of a DsrA-Hfq module. Synth Syst Biotechnol 2024; 9:462-469. [PMID: 38634002 PMCID: PMC11021974 DOI: 10.1016/j.synbio.2024.04.003] [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: 02/05/2024] [Revised: 03/29/2024] [Accepted: 04/06/2024] [Indexed: 04/19/2024] Open
Abstract
In industrial fermentation processes, microorganisms often encounter acid stress, which significantly impact their productivity. This study focused on the acid-resistant module composed of small RNA (sRNA) DsrA and the sRNA chaperone Hfq. Our previous study had shown that this module improved the cell growth of Escherichia coli MG1655 at low pH, but failed to obtain this desired phenotype in industrial strains. Here, we performed a quantitative analysis of DsrA-Hfq module to determine the optimal expression mode. We then assessed the potential of the CymR-based negative auto-regulation (NAR) circuit for industrial application, under different media, strains and pH levels. Growth assay at pH 4.5 revealed that NAR-05D04H circuit was the best acid-resistant circuit to improve the cell growth of E. coli MG1655. This circuit was robust and worked well in the industrial lysine-producing strain E. coli SCEcL3 at a starting pH of 6.8 and without pH control, resulting in a 250 % increase in lysine titer and comparable biomass in shaking flask fermentation compared to the parent strain. This study showed the practical application of NAR circuit in regulating DsrA-Hfq module, effectively and robustly improving the acid tolerance of industrial strains, which provides a new approach for breeding industrial strains with tolerance phenotype.
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Affiliation(s)
- Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jingduan Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Haozheng Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiaofang Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiaofan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- School of Biomedicine, Guangdong University of Technology, Guangzhou 510006, China
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2
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Humphrey ED, Sukhodolets MV. Isolation and Partial Characterization of Novel, Structurally Uniform (Hfq 6) n≥8 Assemblies Carrying Accessory Transcription and Translation Factors. Biochemistry 2024; 63:1647-1662. [PMID: 38869079 DOI: 10.1021/acs.biochem.3c00728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
In growing E. coli cells, the transcription-translation complexes (TTCs) form characteristic foci; however, the exact molecular composition of these superstructures is not known with certainty. Herein, we report that, during our recently developed "fast" procedures for purification of E. coli RNA polymerase (RP), a fraction of the RP's α/RpoA subunits is displaced from the core RP complexes and copurifies with multiprotein superstructures carrying the nucleic acid-binding protein Hfq and the ribosomal protein S6. We show that the main components of these large multiprotein assemblies are fixed protein copy-number (Hfq6)n≥8 complexes; these complexes have a high level of structural uniformity and are distinctly unlike the previously described (Hfq6)n "head-to-tail" polymers. We describe purification of these novel, structurally uniform (Hfq6)n≥8 complexes to near homogeneity and show that they also contain small nonprotein molecules and accessory S6. We demonstrate that Hfq, S6, and RP have similar solubility profiles and present evidence pointing to a role of the Hfq C-termini in superstructure formation. Taken together, our data offer new insights into the composition of the macromolecular assemblies likely acting as scaffolds for transcription complexes and ribosomes during bacterial cells' active growth.
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Affiliation(s)
- Elijah D Humphrey
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States
| | - Maxim V Sukhodolets
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States
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3
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Sett A, Dubey V, Bhowmik S, Pathania R. Decoding Bacterial Persistence: Mechanisms and Strategies for Effective Eradication. ACS Infect Dis 2024. [PMID: 38940498 DOI: 10.1021/acsinfecdis.4c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
The ability of pathogenic bacteria to evade antibiotic treatment is an intricate and multifaceted phenomenon. Over the years, treatment failure among patients due to determinants of antimicrobial resistance (AMR) has been the focal point for the research and development of new therapeutic agents. However, the survival of bacteria by persisting under antibiotic stress has largely been overlooked. Bacterial persisters are a subpopulation of sensitive bacterial cells exhibiting a noninheritable drug-tolerant phenotype. They are linked to the recalcitrance of infections in healthcare settings, in turn giving rise to AMR variants. The importance of bacterial persistence in recurring infections has been firmly recognized. Fundamental work over the past decade has highlighted numerous unique tolerance factors contributing to the persister phenotype in many clinically relevant pathogens. This review summarizes contributing factors that could aid in developing new strategies against bacterial antibiotic persisters.
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Affiliation(s)
- Abhiroop Sett
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Vineet Dubey
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Somok Bhowmik
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
- Centre of Excellence in Disaster Mitigation and Management, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
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4
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Fernando CM, Breaker RR. Bioinformatic prediction of proteins relevant to functions of the bacterial OLE ribonucleoprotein complex. mSphere 2024; 9:e0015924. [PMID: 38771028 DOI: 10.1128/msphere.00159-24] [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: 02/23/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
OLE (ornate, large, extremophilic) RNAs are members of a noncoding RNA class present in many Gram-positive, extremophilic bacteria. The large size, complex structure, and extensive sequence conservation of OLE RNAs are characteristics consistent with the hypothesis that they likely function as ribozymes. The OLE RNA representative from Halalkalibacterium halodurans is known to localize to the phospholipid membrane and requires at least three essential protein partners: OapA, OapB, and OapC. However, the precise biochemical functions of this unusual ribonucleoprotein (RNP) complex remain unknown. Genetic disruption of OLE RNA or its partners revealed that the complex is beneficial under diverse stress conditions. To search for additional links between OLE RNA and other cellular components, we used phylogenetic profiling to identify proteins that are either correlated or anticorrelated with the presence of OLE RNA in various bacterial species. This analysis revealed strong correlations between the essential protein-binding partners of OLE RNA and organisms that carry the ole gene. Similarly, proteins involved in sporulation are correlated, suggesting a potential role for the OLE RNP complex in spore formation. Intriguingly, the Mg2+ transporter MpfA is strongly anticorrelated with OLE RNA. Evidence indicates that MpfA is structurally related to OapA and therefore MpfA may serve as a functional replacement for some contributions otherwise performed by the OLE RNP complex in species that lack this device. Indeed, OLE RNAs might represent an ancient RNA class that enabled primitive organisms to sense and respond to major cellular stresses.IMPORTANCEOLE (ornate, large, extremophilic) RNAs were first reported nearly 20 years ago, and they represent one of the largest and most intricately folded noncoding RNA classes whose biochemical function remains to be established. Other RNAs with similar size, structural complexity, and extent of sequence conservation have proven to catalyze chemical transformations. Therefore, we speculate that OLE RNAs likewise operate as ribozymes and that they might catalyze a fundamental reaction that has persisted since the RNA World era-a time before the emergence of proteins in evolution. To seek additional clues regarding the function of OLE RNA, we undertook a computational effort to identify potential protein components of the OLE ribonucleoprotein (RNP) complex or other proteins that have functional links to this device. This analysis revealed known protein partners and several additional proteins that might be physically or functionally linked to the OLE RNP complex. Finally, we identified a Mg2+ transporter protein, MpfA, that strongly anticorrelates with the OLE RNP complex. This latter result suggests that MpfA might perform at least some functions that are like those carried out by the OLE RNP complex.
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Affiliation(s)
- Chrishan M Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
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5
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Bastet L, Korepanov A, Jagodnik J, Grondin J, Lamontagne AM, Guillier M, Lafontaine D. Riboswitch and small RNAs modulate btuB translation initiation in Escherichia coli and trigger distinct mRNA regulatory mechanisms. Nucleic Acids Res 2024; 52:5852-5865. [PMID: 38742638 PMCID: PMC11162775 DOI: 10.1093/nar/gkae347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 03/19/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Small RNAs (sRNAs) and riboswitches represent distinct classes of RNA regulators that control gene expression upon sensing metabolic or environmental variations. While sRNAs and riboswitches regulate gene expression by affecting mRNA and protein levels, existing studies have been limited to the characterization of each regulatory system in isolation, suggesting that sRNAs and riboswitches target distinct mRNA populations. We report that the expression of btuB in Escherichia coli, which is regulated by an adenosylcobalamin (AdoCbl) riboswitch, is also controlled by the small RNAs OmrA and, to a lesser extent, OmrB. Strikingly, we find that the riboswitch and sRNAs reduce mRNA levels through distinct pathways. Our data show that while the riboswitch triggers Rho-dependent transcription termination, sRNAs rely on the degradosome to modulate mRNA levels. Importantly, OmrA pairs with the btuB mRNA through its central region, which is not conserved in OmrB, indicating that these two sRNAs may have specific targets in addition to their common regulon. In contrast to canonical sRNA regulation, we find that OmrA repression of btuB is lost using an mRNA binding-deficient Hfq variant. Together, our study demonstrates that riboswitch and sRNAs modulate btuB expression, providing an example of cis- and trans-acting RNA-based regulatory systems maintaining cellular homeostasis.
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Affiliation(s)
- Laurène Bastet
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Alexey P Korepanov
- Expression Génétique Microbienne, UMR8261 CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005Paris, France
| | - Jonathan Jagodnik
- Expression Génétique Microbienne, UMR8261 CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005Paris, France
| | - Jonathan P Grondin
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Anne-Marie Lamontagne
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Maude Guillier
- Expression Génétique Microbienne, UMR8261 CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005Paris, France
| | - Daniel A Lafontaine
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
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6
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Garg R, Manhas I, Chaturvedi D. Unveiling the orchestration: mycobacterial small RNAs as key mediators in host-pathogen interactions. Front Microbiol 2024; 15:1399280. [PMID: 38903780 PMCID: PMC11188477 DOI: 10.3389/fmicb.2024.1399280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Small RNA (sRNA) molecules, a class of non-coding RNAs, have emerged as pivotal players in the regulation of gene expression and cellular processes. Mycobacterium tuberculosis and other pathogenic mycobacteria produce diverse small RNA species that modulate bacterial physiology and pathogenesis. Recent advances in RNA sequencing have enabled identification of novel small RNAs and characterization of their regulatory functions. This review discusses the multifaceted roles of bacterial small RNAs, covering their biogenesis, classification, and functional diversity. Small RNAs (sRNAs) play pivotal roles in orchestrating diverse cellular processes, ranging from gene silencing to epigenetic modifications, across a broad spectrum of organisms. While traditionally associated with eukaryotic systems, recent research has unveiled their presence and significance within bacterial domains as well. Unlike their eukaryotic counterparts, which primarily function within the context of RNA interference (RNAi) pathways, bacterial sRNAs predominantly act through base-pairing interactions with target mRNAs, leading to post-transcriptional regulation. This fundamental distinction underscores the necessity of elucidating the unique roles and regulatory mechanisms of bacterial sRNAs in bacterial adaptation and survival. By doing these myriad functions, they regulate bacterial growth, metabolism, virulence, and drug resistance. In Mycobacterium tuberculosis, apart from having various roles in the bacillus itself, small RNA molecules have emerged as key regulators of gene expression and mediators of host-pathogen interactions. Understanding sRNA regulatory networks in mycobacteria can drive our understanding of significant role they play in regulating virulence and adaptation to the host environment. Detailed functional characterization of Mtb sRNAs at the host-pathogen interface is required to fully elucidate the complex sRNA-mediated gene regulatory networks deployed by Mtb, to manipulate the host. A deeper understanding of this aspect could pave the development of novel diagnostic and therapeutic strategies for tuberculosis.
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Affiliation(s)
- Rajni Garg
- Department of Human Genetics and Molecular Medicine, Amity School of Health Sciences, Amity University, Mohali, Punjab, India
| | - Ishali Manhas
- Department of Biotechnology, Amity School of Biological Sciences, Amity University, Mohali, Punjab, India
| | - Diksha Chaturvedi
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, Odisha, India
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7
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Zion S, Katz S, Hershberg R. Escherichia coli adaptation under prolonged resource exhaustion is characterized by extreme parallelism and frequent historical contingency. PLoS Genet 2024; 20:e1011333. [PMID: 38885285 PMCID: PMC11213340 DOI: 10.1371/journal.pgen.1011333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 06/28/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
Like many other non-sporulating bacterial species, Escherichia coli is able to survive prolonged periods of resource exhaustion, by entering a state of growth called long-term stationary phase (LTSP). In July 2015, we initiated a set of evolutionary experiments aimed at characterizing the dynamics of E. coli adaptation under LTSP. In these experiments populations of E. coli were allowed to initially grow on fresh rich media, but were not provided with any new external growth resources since their establishment. Utilizing whole genome sequencing data obtained for hundreds of clones sampled at 12 time points spanning the first six years of these experiments, we reveal several novel aspects of the dynamics of adaptation. First, we show that E. coli continuously adapts genetically, up to six years under resource exhaustion, through the highly convergent accumulation of mutations. We further show that upon entry into LTSP, long-lasting lineages are established. This lineage structure is in itself convergent, with similar lineages arising across independently evolving populations. The high parallelism with which adaptations occur under LTSP, combined with the LTSP populations' lineage structure, enable us to screen for pairs of loci displaying a significant association in the occurrence of mutations, suggestive of a historical contingency. We find that such associations are highly frequent and that a third of convergently mutated loci are involved in at least one such association. Combined our results demonstrate that LTSP adaptation is characterized by remarkably high parallelism and frequent historical contingency.
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Affiliation(s)
- Shira Zion
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Sophia Katz
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ruth Hershberg
- Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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8
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Goh KJ, Altuvia Y, Argaman L, Raz Y, Bar A, Lithgow T, Margalit H, Gan YH. RIL-seq reveals extensive involvement of small RNAs in virulence and capsule regulation in hypervirulent Klebsiella pneumoniae. Nucleic Acids Res 2024:gkae440. [PMID: 38804271 DOI: 10.1093/nar/gkae440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 04/29/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) can infect healthy individuals, in contrast to classical strains that commonly cause nosocomial infections. The recent convergence of hypervirulence with carbapenem-resistance in K. pneumoniae can potentially create 'superbugs' that are challenging to treat. Understanding virulence regulation of hvKp is thus critical. Accumulating evidence suggest that posttranscriptional regulation by small RNAs (sRNAs) plays a role in bacterial virulence, but it has hardly been studied in K. pneumoniae. We applied RIL-seq to a prototypical clinical isolate of hvKp to unravel the Hfq-dependent RNA-RNA interaction (RRI) network. The RRI network is dominated by sRNAs, including predicted novel sRNAs, three of which we validated experimentally. We constructed a stringent subnetwork composed of RRIs that involve at least one hvKp virulence-associated gene and identified the capsule gene loci as a hub target where multiple sRNAs interact. We found that the sRNA OmrB suppressed both capsule production and hypermucoviscosity when overexpressed. Furthermore, OmrB base-pairs within kvrA coding region and partially suppresses translation of the capsule regulator KvrA. This agrees with current understanding of capsule as a major virulence and fitness factor. It emphasizes the intricate regulatory control of bacterial phenotypes by sRNAs, particularly of genes critical to bacterial physiology and virulence.
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Affiliation(s)
- Kwok Jian Goh
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yair Raz
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yunn-Hwen Gan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
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9
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Lee CY, Joshi M, Wang A, Myong S. 5'UTR G-quadruplex structure enhances translation in size dependent manner. Nat Commun 2024; 15:3963. [PMID: 38729943 PMCID: PMC11087576 DOI: 10.1038/s41467-024-48247-8] [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: 09/13/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Translation initiation in bacteria is frequently regulated by various structures in the 5' untranslated region (5'UTR). Previously, we demonstrated that G-quadruplex (G4) formation in non-template DNA enhances transcription. In this study, we aim to explore how G4 formation in mRNA (RG4) at 5'UTR impacts translation using a T7-based in vitro translation system and in E. coli. We show that RG4 strongly promotes translation efficiency in a size-dependent manner. Additionally, inserting a hairpin upstream of the RG4 further enhances translation efficiency, reaching up to a 12-fold increase. We find that the RG4-dependent effect is not due to increased ribosome affinity, ribosome binding site accessibility, or mRNA stability. We propose a physical barrier model in which bulky structures in 5'UTR biases ribosome movement toward the downstream start codon, thereby increasing the translation output. This study provides biophysical insights into the regulatory role of 5'UTR structures in in vitro and bacterial translation, highlighting their potential applications in tuning gene expression.
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Affiliation(s)
- Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Meera Joshi
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ashley Wang
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, IL, 61801, USA.
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10
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Zhu Y, Ponath F, Cosi V, Vogel J. A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum. Nucleic Acids Res 2024; 52:3950-3970. [PMID: 38281181 DOI: 10.1093/nar/gkae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024] Open
Abstract
The common oral microbe Fusobacterium nucleatum has recently drawn attention after it was found to colonize tumors throughout the human body. Fusobacteria are also interesting study systems for bacterial RNA biology as these early-branching species encode many small noncoding RNAs (sRNAs) but lack homologs of the common RNA-binding proteins (RBPs) CsrA, Hfq and ProQ. To search for alternate sRNA-associated RBPs in F. nucleatum, we performed a systematic mass spectrometry analysis of proteins that co-purified with 19 different sRNAs. This approach revealed strong enrichment of the KH domain proteins KhpA and KhpB with nearly all tested sRNAs, including the σE-dependent sRNA FoxI, a regulator of several envelope proteins. KhpA/B act as a dimer to bind sRNAs with low micromolar affinity and influence the stability of several of their target transcripts. Transcriptome studies combined with biochemical and genetic analyses suggest that KhpA/B have several physiological functions, including being required for ethanolamine utilization. Our RBP search and the discovery of KhpA/B as major RBPs in F. nucleatum are important first steps in identifying key players of post-transcriptional control at the root of the bacterial phylogenetic tree.
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Affiliation(s)
- Yan Zhu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Valentina Cosi
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
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11
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Zhang J, Zhang S, Zhou W, Zhang X, Li G, Li R, Lin X, Chen Z, Liu F, Shen P, Zhou X, Gao Y, Chen Z, Chao Y, Wang C. A widely conserved protein Rof inhibits transcription termination factor Rho and promotes Salmonella virulence program. Nat Commun 2024; 15:3187. [PMID: 38622116 PMCID: PMC11018607 DOI: 10.1038/s41467-024-47438-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024] Open
Abstract
Transcription is crucial for the expression of genetic information and its efficient and accurate termination is required for all living organisms. Rho-dependent termination could rapidly terminate unwanted premature RNAs and play important roles in bacterial adaptation to changing environments. Although Rho has been discovered for about five decades, the regulation mechanisms of Rho-dependent termination are still not fully elucidated. Here we report that Rof is a conserved antiterminator and determine the cryogenic electron microscopy structure of Rho-Rof antitermination complex. Rof binds to the open-ring Rho hexamer and inhibits the initiation of Rho-dependent termination. Rof's N-terminal α-helix undergoes conformational changes upon binding with Rho, and is key in facilitating Rof-Rho interactions. Rof binds to Rho's primary binding site (PBS) and excludes Rho from binding with PBS ligand RNA at the initiation step. Further in vivo analyses in Salmonella Typhimurium show that Rof is required for virulence gene expression and host cell invasion, unveiling a physiological function of Rof and transcription termination in bacterial pathogenesis.
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Affiliation(s)
- Jing Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Shuo Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhou
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xiang Zhang
- The Fifth People's Hospital, Institutes of Biomedical Sciences, School of Public Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Guanjin Li
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruoxuan Li
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xingyu Lin
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziying Chen
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- The Fifth People's Hospital, Institutes of Biomedical Sciences, School of Public Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Fang Liu
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Pan Shen
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xiaogen Zhou
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Yue Gao
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Zhenguo Chen
- The Fifth People's Hospital, Institutes of Biomedical Sciences, School of Public Health, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Yanjie Chao
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
| | - Chengyuan Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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12
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Vogt LN, Panis G, Schäpers A, Peschek N, Huber M, Papenfort K, Viollier PH, Fröhlich KS. Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus. mBio 2024; 15:e0315323. [PMID: 38511926 PMCID: PMC11005374 DOI: 10.1128/mbio.03153-23] [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: 11/21/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The alphaproteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. crescentus. Small RNAs (sRNAs) are a prominent class of regulators of bacterial gene expression, and most sRNAs characterized today engage in direct base-pairing interactions to modulate the translation and/or stability of target mRNAs. In many cases, the ubiquitous RNA chaperone, Hfq, contributes to the establishment of RNA-RNA interactions. Although the deletion of the hfq gene is associated with a severe loss of fitness in C. crescentus, the RNA ligands of the chaperone have remained largely unexplored. Here we report on the identification of coding and non-coding transcripts associated with Hfq in C. crescentus and demonstrate Hfq-dependent post-transcriptional regulation in this organism. We show that the Hfq-bound sRNA RusT is transcriptionally controlled by the NtrYX two-component system and induced in response to iron starvation. By combining RusT pulse expression with whole-genome transcriptome analysis, we determine 16 candidate target transcripts that are deregulated, many of which encode outer membrane transporters. We hence suggest RusT to support remodeling of the C. crescentus cell surface when iron supplies are limited.IMPORTANCEThe conserved RNA-binding protein Hfq contributes significantly to the adaptation of bacteria to different environmental conditions. Hfq not only stabilizes associated sRNAs but also promotes inter-molecular base-pairing interactions with target transcripts. Hfq plays a pivotal role for growth and survival, controlling central metabolism and cell wall synthesis in the oligotroph Caulobacter crescentus. However, direct evidence for Hfq-dependent post-transcriptional regulation and potential oligotrophy in C. crescentus has been lacking. Here, we identified sRNAs and mRNAs associated with Hfq in vivo, and demonstrated the requirement of Hfq for sRNA-mediated regulation, particularly of outer membrane transporters in C. crescentus.
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Affiliation(s)
- Laura N. Vogt
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Anna Schäpers
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Nikolai Peschek
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michaela Huber
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kai Papenfort
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Kathrin S. Fröhlich
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
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13
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Guo D, Xiong Y, Fu B, Sha Z, Li B, Wu H. Liquid-Liquid phase separation in bacteria. Microbiol Res 2024; 281:127627. [PMID: 38262205 DOI: 10.1016/j.micres.2024.127627] [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] [Received: 10/17/2023] [Revised: 12/16/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
Cells are the essential building blocks of living organisms, responsible for carrying out various biochemical reactions and performing specific functions. In eukaryotic cells, numerous membrane organelles have evolved to facilitate these processes by providing specific spatial locations. In recent years, it has also been discovered that membraneless organelles play a crucial role in the subcellular organization of bacteria, which are single-celled prokaryotic microorganisms characterized by their simple structure and small size. These membraneless organelles in bacteria have been found to undergo Liquid-Liquid phase separation (LLPS), a molecular mechanism that allows for their assembly. Through extensive research, the occurrence of LLPS and its role in the spatial organization of bacteria have been better understood. Various biomacromolecules have been identified to exhibit LLPS properties in different bacterial species. LLPS which is introduced into synthetic biology applies to bacteria has important implications, and three recent research reports have shed light on its potential applications in this field. Overall, this review investigates the molecular mechanisms of LLPS occurrence and its significance in bacteria while also considering the future prospects of implementing LLPS in synthetic biology.
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Affiliation(s)
- Dong Guo
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhou Sha
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Bohao Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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14
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Kuzminov A. Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma. J Bacteriol 2024; 206:e0021123. [PMID: 38358278 PMCID: PMC10994824 DOI: 10.1128/jb.00211-23] [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] [Indexed: 02/16/2024] Open
Abstract
Bacterial chromosome, the nucleoid, is traditionally modeled as a rosette of DNA mega-loops, organized around proteinaceous central scaffold by nucleoid-associated proteins (NAPs), and mixed with the cytoplasm by transcription and translation. Electron microscopy of fixed cells confirms dispersal of the cloud-like nucleoid within the ribosome-filled cytoplasm. Here, I discuss evidence that the nucleoid in live cells forms DNA phase separate from riboprotein phase, the "riboid." I argue that the nucleoid-riboid interphase, where DNA interacts with NAPs, transcribing RNA polymerases, nascent transcripts, and ssRNA chaperones, forms the transcription zone. An active part of phase separation, transcription zone enforces segregation of the centrally positioned information phase (the nucleoid) from the surrounding action phase (the riboid), where translation happens, protein accumulates, and metabolism occurs. I speculate that HU NAP mostly tiles up the nucleoid periphery-facilitating DNA mobility but also supporting transcription in the interphase. Besides extruding plectonemically supercoiled DNA mega-loops, condensins could compact them into solenoids of uniform rings, while HU could support rigidity and rotation of these DNA rings. The two-phase cytoplasm arrangement allows the bacterial cell to organize the central dogma activities, where (from the cell center to its periphery) DNA replicates and segregates, DNA is transcribed, nascent mRNA is handed over to ribosomes, mRNA is translated into proteins, and finally, the used mRNA is recycled into nucleotides at the inner membrane. The resulting information-action conveyor, with one activity naturally leading to the next one, explains the efficiency of prokaryotic cell design-even though its main intracellular transportation mode is free diffusion.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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15
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McQuail J, Matera G, Gräfenhan T, Bischler T, Haberkant P, Stein F, Vogel J, Wigneshweraraj S. Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery. Nucleic Acids Res 2024; 52:2323-2339. [PMID: 38142457 PMCID: PMC10954441 DOI: 10.1093/nar/gkad1211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/17/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023] Open
Abstract
The RNA binding protein Hfq has a central role in the post-transcription control of gene expression in many bacteria. Numerous studies have mapped the transcriptome-wide Hfq-mediated RNA-RNA interactions in growing bacteria or bacteria that have entered short-term growth-arrest. To what extent post-transcriptional regulation underpins gene expression in growth-arrested bacteria remains unknown. Here, we used nitrogen (N) starvation as a model to study the Hfq-mediated RNA interactome as Escherichia coli enter, experience, and exit long-term growth arrest. We observe that the Hfq-mediated RNA interactome undergoes extensive changes during N starvation, with the conserved SdsR sRNA making the most interactions with different mRNA targets exclusively in long-term N-starved E. coli. Taking a proteomics approach, we reveal that in growth-arrested cells SdsR influences gene expression far beyond its direct mRNA targets. We demonstrate that the absence of SdsR significantly compromises the ability of the mutant bacteria to recover growth competitively from the long-term N-starved state and uncover a conserved post-transcriptional regulatory axis which underpins this process.
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Affiliation(s)
- Josh McQuail
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
| | - Gianluca Matera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Tom Gräfenhan
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Institute for Molecular Infection Biology (IMIB), Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Sivaramesh Wigneshweraraj
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
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16
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Hu W, Huo X, Bai H, Chen Z, Zhang J, Yang H, Feng S. Insights into the complementation potential of the extreme acidophile's orthologue in replacing Escherichia coli hfq gene-particularly in bacterial resistance to environmental stress. World J Microbiol Biotechnol 2024; 40:105. [PMID: 38386219 DOI: 10.1007/s11274-024-03924-0] [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: 12/17/2023] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
Acidithiobacillus caldus is a typical extreme acidophile widely used in the biohydrometallurgical industry, which often experiences extreme environmental stress in its natural habitat. Hfq, an RNA-binding protein, typically functions as a global regulator involved in various cellular physiological processes. Yet, the biological functions of Hfq derived from such extreme acidophile have not been extensively investigated. In this study, the recombinant strain Δhfq/Achfq, constructed by CRISPR/Cas9-mediated chromosome integration, fully or partially restored the phenotypic defects caused by hfq deletion in Escherichia coli, including impaired growth performance, abnormal cell morphology, impaired swarming motility, decreased stress resistance, decreased intracellular ATP and free amino acid levels, and attenuated biofilm formation. Particularly noteworthy, the intracellular ATP level and biofilm production of the recombinant strain were increased by 12.2% and 7.0%, respectively, compared to the Δhfq mutant. Transcriptomic analysis revealed that even under heterologous expression, AcHfq exerted global regulatory effects on multiple cellular processes, including metabolism, environmental signal processing, and motility. Finally, we established a potential working model to illustrate the regulatory mechanism of AcHfq in bacterial resistance to environmental stress.
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Affiliation(s)
- Wenbo Hu
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xingyu Huo
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Haochen Bai
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Zongling Chen
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Jianxin Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Hailin Yang
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Shoushuai Feng
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
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17
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Wicke D, Neumann P, Gößringer M, Chernev A, Davydov S, Poehlein A, Daniel R, Urlaub H, Hartmann R, Ficner R, Stülke J. The previously uncharacterized RnpM (YlxR) protein modulates the activity of ribonuclease P in Bacillus subtilis in vitro. Nucleic Acids Res 2024; 52:1404-1419. [PMID: 38050972 PMCID: PMC10853771 DOI: 10.1093/nar/gkad1171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023] Open
Abstract
Even though Bacillus subtilis is one of the most studied organisms, no function has been identified for about 20% of its proteins. Among these unknown proteins are several RNA- and ribosome-binding proteins suggesting that they exert functions in cellular information processing. In this work, we have investigated the RNA-binding protein YlxR. This protein is widely conserved in bacteria and strongly constitutively expressed in B. subtilis suggesting an important function. We have identified the RNA subunit of the essential RNase P as the binding partner of YlxR. The main activity of RNase P is the processing of 5' ends of pre-tRNAs. In vitro processing assays demonstrated that the presence of YlxR results in reduced RNase P activity. Chemical cross-linking studies followed by in silico docking analysis and experiments with site-directed mutant proteins suggest that YlxR binds to the region of the RNase P RNA that is important for binding and cleavage of the pre-tRNA substrate. We conclude that the YlxR protein is a novel interaction partner of the RNA subunit of RNase P that serves to finetune RNase P activity to ensure appropriate amounts of mature tRNAs for translation. We rename the YlxR protein RnpM for RNase P modulator.
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Affiliation(s)
- Dennis Wicke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Markus Gößringer
- Institute for the Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Swetlana Davydov
- Institute for the Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, GZMB, University Medical Centre Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Georg-August-University Göttingen, Germany
| | - Roland K Hartmann
- Institute for the Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
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18
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Du Y, Wang Y, Geng J, Long J, Yang H, Duan G, Chen S. Molecular mechanism of Hfq-dependent sRNA1039 and sRNA1600 regulating antibiotic resistance and virulence in Shigella sonnei. Int J Antimicrob Agents 2024; 63:107070. [PMID: 38141834 DOI: 10.1016/j.ijantimicag.2023.107070] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
Bacillary dysentery caused by Shigella spp. is a significant concern for human health. Small non-coding RNA (sRNA) plays a crucial role in regulating antibiotic resistance and virulence in Shigella spp. However, the specific mechanisms behind this phenomenon are still not fully understood. This study discovered two sRNAs (sRNA1039 and sRNA1600) that may be involved in bacterial resistance and virulence. By constructing deletion mutants (WT/ΔSR1039 and WT/ΔSR1600), this study found that the WT/ΔSR1039 mutants caused a two-fold increase in sensitivity to ampicillin, gentamicin and cefuroxime, and the WT/ΔSR1600 mutants caused a two-fold increase in sensitivity to cefuroxime. Furthermore, the WT/ΔSR1600 mutants caused a decrease in the adhesion and invasion of bacteria to HeLa cells (P<0.01), and changed the oxidative stress level of bacteria to reduce their survival rate (P<0.001). Subsequently, this study explored the molecular mechanisms by which sRNA1039 and sRNA1600 regulate antibiotic resistance and virulence. The deletion of sRNA1039 accelerated the degradation of target gene cfa mRNA and reduced its expression, thereby regulating the expression of pore protein gene ompD indirectly and negatively to increase bacterial sensitivity to ampicillin, gentamicin and cefuroxime. The inactivation of sRNA1600 reduced the formation of persister cells to reduce resistance to cefuroxime, and reduced the expression of type-III-secretion-system-related genes to reduce bacterial virulence by reducing the expression of target gene tomB. These results provide new insights into Hfq-sRNA-mRNA regulation of the resistance and virulence network of Shigella sonnei, which could potentially promote the development of more effective treatment strategies.
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Affiliation(s)
- Yazhe Du
- Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Ya Wang
- Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Juan Geng
- Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Jinzhao Long
- Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Haiyan Yang
- Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Guangcai Duan
- Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Shuaiyin Chen
- Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China.
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19
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Turbant F, Machiels Q, Waeytens J, Wien F, Arluison V. The Amyloid Assembly of the Bacterial Hfq Is Lipid-Driven and Lipid-Specific. Int J Mol Sci 2024; 25:1434. [PMID: 38338713 PMCID: PMC10855545 DOI: 10.3390/ijms25031434] [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: 12/27/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Under specific conditions, some proteins can self-assemble into fibrillar structures called amyloids. Initially, these proteins were associated with neurodegenerative diseases in eucaryotes. Nevertheless, they have now been identified in the three domains of life. In bacteria, they are involved in diverse biological processes and are usually useful for the cell. For this reason, they are classified as "functional amyloids". In this work, we focus our analysis on a bacterial functional amyloid called Hfq. Hfq is a pleiotropic regulator that mediates several aspects of genetic expression, mainly via the use of small noncoding RNAs. Our previous work showed that Hfq amyloid-fibrils interact with membranes. This interaction influences Hfq amyloid structure formation and stability, but the specifics of the lipid on the dynamics of this process is unknown. Here, we show, using spectroscopic methods, how lipids specifically drive and modulate Hfq amyloid assembly or, conversely, its disassembly. The reported effects are discussed in light of the consequences for bacterial cell life.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Quentin Machiels
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- SDV Department, Université Paris Cité, 75006 Paris, France
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20
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Kho ZY, Azad MAK, Zhu Y, Han ML, Zhou QT, Velkov T, Naderer T, Li J. Transcriptomic interplay between Acinetobacter baumannii , human macrophage and polymyxin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576770. [PMID: 38328180 PMCID: PMC10849618 DOI: 10.1101/2024.01.23.576770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Optimization of antibiotic therapy has been hindered by our dearth of understanding on the mechanism of the host-pathogen-drug interactions. Here, we employed dual RNA-sequencing to examine transcriptomic perturbations in response to polymyxin B in a co-culture infection model of Acinetobacter baumannii and human macrophages. Our findings revealed that polymyxin B treatment induced significant transcriptomic response in macrophage-interacting A. baumannii , exacerbating bacterial oxidative stress, disrupting metal homeostasis, affecting osmoadaptation, triggering stringent stress response, and influencing pathogenic factors. Moreover, infected macrophages adapt heme catabolism, coagulation cascade, and hypoxia-inducible signaling to confront bacterial invasion. Disrupting rcnB , ompW , and traR/dksA genes in A. baumannii impairs metal homeostasis, osmotic stress defense and stringent responses, thereby enhancing antibacterial killing by polymyxin. These findings shed light on the global stress adaptations at the network level during host-pathogen-drug interactions, revealing promising therapeutic targets for further investigation. IMPORTANCE In the context of the development of bacterial resistance during the course of antibiotic therapy, the role of macrophages in shaping bacterial response to antibiotic killing remains enigmatic. Herein we employed dual RNA-sequencing and an in vitro tripartite model to delve into the unexplored transcriptional networks of the Acinetobacter baumannii -macrophage-polymyxin axis. Our findings uncovered the potential synergy between macrophages and polymyxin B which appear to act in co-operation to disrupt multiple stress tolerance mechanisms in A. baumannii . Notably, we discovered the critical roles of bacterial nickel/cobalt homeostasis ( rcnB family), osmotic stress defense ( ompW family), and stringent response regulator ( traR/dksA C4-type zinc finger) in tolerating the last-line antibiotic polymyxin B. Our findings may lead to potential targets for the development of novel therapeutics against the problematic pathogen A. baumannii .
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21
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Moreno R, Rojo F. What are the signals that control catabolite repression in Pseudomonas? Microb Biotechnol 2024; 17:e14407. [PMID: 38227132 PMCID: PMC10832556 DOI: 10.1111/1751-7915.14407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Metabolically versatile bacteria exhibit a global regulatory response known as carbon catabolite repression (CCR), which prioritizes some carbon sources over others when all are present in sufficient amounts. This optimizes growth by distributing metabolite fluxes, but can restrict yields in biotechnological applications. The molecular mechanisms and preferred substrates for CCR vary between bacterial groups. Escherichia coli prioritizes glucose whereas Pseudomonas sp. prefer certain organic acids or amino acids. A significant issue in understanding (and potentially bypassing) CCR is the lack of information about the signals that trigger this regulatory response. In E. coli, several key compounds act as flux sensors, governing the flow of metabolites through catabolic pathways and preventing imbalances. These flux sensors can also modulate the CCR response. It has been suggested that the order of substrate preference is determined by carbon uptake flux rather than substrate identity. For Pseudomonas, much less information is available, as the signals that induce CCR are poorly understood. This article briefly discusses the available evidence on the signals that trigger CCR and the questions that remain to be answered in Pseudomonas.
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Affiliation(s)
- Renata Moreno
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Fernando Rojo
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
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22
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Payá G, Bautista V, Pastor-Soler S, Camacho M, Esclapez J, Bonete MJ. Analysis of Lsm Protein-Mediated Regulation in the Haloarchaeon Haloferax mediterranei. Int J Mol Sci 2024; 25:580. [PMID: 38203750 PMCID: PMC10779274 DOI: 10.3390/ijms25010580] [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: 10/05/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq found in the Eukarya, Archaea, and Bacteria domains. Archaeal Lsm proteins have been shown to bind sRNAs and are probably involved in various cellular processes, suggesting a similar function in regulating sRNAs by Hfq in bacteria. Moreover, archaeal Lsm proteins probably represent the ancestral Lsm domain from which eukaryotic Sm proteins have evolved. In this work, Haloferax mediterranei was used as a model organism because it has been widely used to investigate the nitrogen cycle and its regulation in Haloarchaea. Predicting this protein's secondary and tertiary structures has resulted in a three-dimensional model like the solved Lsm protein structure of Archaeoglobus fulgidus. To obtain information on the oligomerization state of the protein, homologous overexpression and purification by means of molecular exclusion chromatography have been performed. The results show that this protein can form hexameric complexes, which can aggregate into 6 or 12 hexameric rings depending on the NaCl concentration and without RNA. In addition, the study of transcriptional expression via microarrays has allowed us to obtain the target genes regulated by the Lsm protein under nutritional stress conditions: nitrogen or carbon starvation. Microarray analysis has shown the first universal stress proteins (USP) in this microorganism that mediate survival in situations of nitrogen deficiency.
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Affiliation(s)
| | | | | | | | | | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; (G.P.); (V.B.); (S.P.-S.); (M.C.); (J.E.)
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23
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Turbant F, Mosca K, Busi F, Arluison V, Wien F. Circular and Linear Dichroism for the Analysis of Small Noncoding RNA Properties. Methods Mol Biol 2024; 2741:399-416. [PMID: 38217665 DOI: 10.1007/978-1-0716-3565-0_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Useful structural information about the conformation of nucleic acids can be quickly acquired by circular and linear dichroism (CD/LD) spectroscopy. These techniques, rely on the differential absorption of polarised light and are indeed extremely sensitive to subtle changes in the structure of chiral biomolecules. Many CD analyses of DNA or DNA:protein complexes have been conducted with substantial data acquisitions. Conversely, CD RNA analysis are still scarce, despite the fact that RNA plays a wide cellular function. This chapter seeks to introduce the reader to the use of circular, linear dichroism and in particular the use of Synchrotron Radiation for such samples. The use of these techniques on small noncoding RNA (sRNA) will be exemplified by analyzing changes in base stacking and/or helical parameters for the understanding of sRNA structure and function, especially by translating the dynamics of RNA:RNA annealing but also to access RNA stability or RNA:RNA alignment. The effect of RNA remodeling proteins will also be addressed. These analyses are especially useful to decipher the mechanisms by which sRNA will adopt the proper conformation thanks to the action of proteins such as Hfq or ProQ in the regulation of the expression of their target mRNAs.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, CEA Saclay, Gif-sur-Yvette, France
- Synchrotron SOLEIL, L'Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France
| | - Kevin Mosca
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, CEA Saclay, Gif-sur-Yvette, France
- Synchrotron SOLEIL, L'Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France
- SANOFI, Marcy-l'Etoile, France
| | - Florent Busi
- Université Paris Cité, Paris, France
- BFA, UMR 8251, Université Paris cité, CNRS, Paris, France
| | - Véronique Arluison
- CEA Saclay, Laboratoire LeÇon Brillouin LLB, CEA/CNRS, Gif-sur-Yvette, France
- Université Paris Cité, Paris, France
| | - Frank Wien
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, CEA Saclay, Gif-sur-Yvette, France.
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24
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King KA, Benton AH, Caudill MT, Stoyanof ST, Kang L, Michalak P, Lahmers KK, Dunman PM, DeHart TG, Ahmad SS, Jutras BL, Poncin K, De Bolle X, Caswell CC. Post-transcriptional control of the essential enzyme MurF by a small regulatory RNA in Brucella abortus. Mol Microbiol 2024; 121:129-141. [PMID: 38082493 DOI: 10.1111/mmi.15207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 01/15/2024]
Abstract
Brucella abortus is a facultative, intracellular, zoonotic pathogen that resides inside macrophages during infection. This is a specialized niche where B. abortus encounters various stresses as it navigates through the macrophage. In order to survive this harsh environment, B. abortus utilizes post-transcriptional regulation of gene expression through the use of small regulatory RNAs (sRNAs). Here, we characterize a Brucella sRNAs called MavR (for MurF- and virulence-regulating sRNA), and we demonstrate that MavR is required for the full virulence of B. abortus in macrophages and in a mouse model of chronic infection. Transcriptomic and proteomic studies revealed that a major regulatory target of MavR is MurF. MurF is an essential protein that catalyzes the final cytoplasmic step in peptidoglycan (PG) synthesis; however, we did not detect any differences in the amount or chemical composition of PG in the ΔmavR mutant. A 6-nucleotide regulatory seed region within MavR was identified, and mutation of this seed region resulted in dysregulation of MurF production, as well as significant attenuation of infection in a mouse model. Overall, the present study underscores the importance of sRNA regulation in the physiology and virulence of Brucella.
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Affiliation(s)
- Kellie A King
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Angela H Benton
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Mitchell T Caudill
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - S Tristan Stoyanof
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Lin Kang
- Department of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, USA
- College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana, USA
- Center for One Health Research, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, USA
| | - Pawel Michalak
- Department of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, USA
- Center for One Health Research, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, USA
- Institute for Evolution, University of Haifa, Haifa, Israel
| | - Kevin K Lahmers
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Paul M Dunman
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Tanner G DeHart
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Saadman S Ahmad
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Brandon L Jutras
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Katy Poncin
- URBM, Narilis, University of Namur, Namur, Belgium
| | | | - Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
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25
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Ormazábal A, Palma J, Pierdominici-Sottile G. Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods. Methods Mol Biol 2024; 2741:207-238. [PMID: 38217656 DOI: 10.1007/978-1-0716-3565-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Molecular dynamics simulations have proved extremely useful in investigating the functioning of proteins with atomic-scale resolution. Many applications to the study of RNA also exist, and their number increases by the day. However, implementing MD simulations for RNA molecules in solution faces challenges that the MD practitioner must be aware of for the appropriate use of this tool. In this chapter, we present the fundamentals of MD simulations, in general, and the peculiarities of RNA simulations, in particular. We discuss the strengths and limitations of the technique and provide examples of its application to elucidate small RNA's performance.
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Affiliation(s)
- Agustín Ormazábal
- Departmento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Godoy Cruz, CABA, Argentina
| | - Juliana Palma
- Departmento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Godoy Cruz, CABA, Argentina
| | - Gustavo Pierdominici-Sottile
- Departmento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Godoy Cruz, CABA, Argentina.
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26
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García-Tomsig NI, Lagares A, Becker A, Valverde C, Jiménez-Zurdo JI. An Integrated Affinity Chromatography-Based Approach to Unravel the sRNA Interactome in Nitrogen-Fixing Rhizobia. Methods Mol Biol 2024; 2741:363-380. [PMID: 38217663 DOI: 10.1007/978-1-0716-3565-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
The activity mechanism and function of bacterial base-pairing small non-coding RNA regulators (sRNAs) are largely shaped by their main interacting cellular partners, i.e., proteins and mRNAs. We describe here an MS2 affinity chromatography-based procedure adapted to unravel the sRNA interactome in nitrogen-fixing legume endosymbiotic bacteria. The method consists of tagging of the bait sRNA at its 5'-end with the MS2 aptamer followed by pulse overexpression and immobilization of the chimeric transcript from cell lysates by an MS2-MBP fusion protein conjugated to an amylose resin. The sRNA-binding proteins and target mRNAs are further profiled by mass spectrometry and RNAseq, respectively.
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Affiliation(s)
- Natalia Isabel García-Tomsig
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Antonio Lagares
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas (LFGBBP), Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Argentina
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas (LFGBBP), Centro de Bioquímica y Microbiología del Suelo (CBMS), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires, Argentina
| | - José Ignacio Jiménez-Zurdo
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
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27
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Turbant F, Esnouf E, Rosaz F, Wien F, Węgrzyn G, Chauvet H, Arluison V. Role of the Bacterial Amyloid-like Hfq in Fluoroquinolone Fluxes. Microorganisms 2023; 12:53. [PMID: 38257880 PMCID: PMC10819720 DOI: 10.3390/microorganisms12010053] [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: 11/29/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Due to their two-cell membranes, Gram-negative bacteria are particularly resistant to antibiotics. Recent investigations aimed at exploring new target proteins involved in Gram-negative bacteria adaptation helped to identify environmental changes encountered during infection. One of the most promising approaches in finding novel targets for antibacterial drugs consists of blocking noncoding RNA-based regulation using the protein cofactor, Hfq. Although Hfq is important in many bacterial pathogens, its involvement in antibiotics response is still unclear. Indeed, Hfq may mediate drug resistance by regulating the major efflux system in Escherichia coli, but it could also play a role in the influx of antibiotics. Here, using an imaging approach, we addressed this problem quantitatively at the single-cell level. More precisely, we analyzed how Hfq affects the dynamic influx and efflux of ciprofloxacin, an antibiotic from the group of fluoroquinolones that is used to treat bacterial infections. Our results indicated that the absence of either whole Hfq or its C-terminal domain resulted in a more effective accumulation of ciprofloxacin, irrespective of the presence of the functional AcrAB-TolC efflux pump. However, overproduction of the MicF small regulatory RNA, which reduces the efficiency of expression of the ompF gene (coding for a porin involved in antibiotics influx) in a Hfq-dependent manner, resulted in impaired accumulation of ciprofloxacin. These results led us to propose potential mechanisms of action of Hfq in the regulation of fluoroquinolone fluxes across the E. coli envelope.
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Affiliation(s)
- Florian Turbant
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.); (H.C.)
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| | - Emeline Esnouf
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
| | - Francois Rosaz
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.); (H.C.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| | - Hugo Chauvet
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.); (H.C.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
- UFR SDV, Université Paris Cité, 75013 Paris, France
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28
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Bloch S, Lewandowska N, Zwolenkiewicz J, Mach P, Łukasiak A, Olejniczak M, Donaldson LW, Węgrzyn G, Nejman-Faleńczyk B. Bacteriophage-encoded 24B_1 molecule resembles herpesviral microRNAs and plays a crucial role in the development of both the virus and its host. PLoS One 2023; 18:e0296038. [PMID: 38117844 PMCID: PMC10732415 DOI: 10.1371/journal.pone.0296038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/01/2023] [Indexed: 12/22/2023] Open
Abstract
The 24B_1 small non-coding RNA molecule has been identified in Escherichia coli after induction of Shiga toxin-converting bacteriophage Φ24B. In this work, we focused on its direct role during phage and bacterial host development. We observed that in many aspects, this phage sRNA resembles herpesviral microRNAs. Similar to microRNAs, the mature 24B_1 is a short molecule, consisting of just 20 nucleotides. It is generated by cleaving the 80-nt long precursor transcript, and likely it undergoes a multi-step maturation process in which the Hfq protein plays an important role, as confirmed by demonstration of its binding to the 24B_1 precursor, but not to the 24B_1 mature form. Moreover, 24B_1 plays a significant role in maintaining the prophage state and reprogramming the host's energy metabolism. We proved that overproduction of this molecule causes the opposite physiological effects to the mutant devoid of the 24B_1 gene, and thus, favors the lysogenic pathway. Furthermore, the 24B_1 overrepresentation significantly increases the efficiency of expression of phage genes coding for proteins CI, CII, and CIII which are engaged in the maintenance of the prophage. It seems that through binding to mRNA of the sdhB gene, coding for the succinate dehydrogenase subunit, the 24B_1 alters the central carbon metabolism and causes a drop in the ATP intracellular level. Interestingly, a similar effect, called the Warburg switch, is caused by herpesviral microRNAs and it is observed in cancer cells. The advantage of the Warburg effect is still unclear, however, it was proposed that the metabolism of cancer cells, and all rapidly dividing cells, is adopted to convert nutrients such as glucose and glutamine faster and more efficiently into biomass. The availability of essential building blocks, such as nucleotides, amino acids, and lipids, is crucial for effective cell proliferation which in turn is essential for the prophage and its host to stay in the lysogenic state.
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Affiliation(s)
- Sylwia Bloch
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | | | - Joanna Zwolenkiewicz
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Paulina Mach
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | | | - Mikołaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | | | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
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29
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Liu F, Chen Z, Zhang S, Wu K, Bei C, Wang C, Chao Y. In vivo RNA interactome profiling reveals 3'UTR-processed small RNA targeting a central regulatory hub. Nat Commun 2023; 14:8106. [PMID: 38062076 PMCID: PMC10703908 DOI: 10.1038/s41467-023-43632-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Small noncoding RNAs (sRNAs) are crucial regulators of gene expression in bacteria. Acting in concert with major RNA chaperones such as Hfq or ProQ, sRNAs base-pair with multiple target mRNAs and form large RNA-RNA interaction networks. To systematically investigate the RNA-RNA interactome in living cells, we have developed a streamlined in vivo approach iRIL-seq (intracellular RIL-seq). This generic approach is highly robust, illustrating the dynamic sRNA interactomes in Salmonella enterica across multiple stages of growth. We have identified the OmpD porin mRNA as a central regulatory hub that is targeted by a dozen sRNAs, including FadZ cleaved from the conserved 3'UTR of fadBA mRNA. Both ompD and FadZ are activated by CRP, constituting a type I incoherent feed-forward loop in the fatty acid metabolism pathway. Altogether, we have established an approach to profile RNA-RNA interactomes in live cells, highlighting the complexity of RNA regulatory hubs and RNA networks.
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Affiliation(s)
- Fang Liu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ziying Chen
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center & Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shuo Zhang
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kejing Wu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cheng Bei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
| | - Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China.
| | - Yanjie Chao
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China.
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
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30
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Luo X, Zhang A, Tai CH, Chen J, Majdalani N, Storz G, Gottesman S. An acetyltranferase moonlights as a regulator of the RNA binding repertoire of the RNA chaperone Hfq in Escherichia coli. Proc Natl Acad Sci U S A 2023; 120:e2311509120. [PMID: 38011569 PMCID: PMC10710024 DOI: 10.1073/pnas.2311509120] [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: 07/07/2023] [Accepted: 10/23/2023] [Indexed: 11/29/2023] Open
Abstract
Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with their target mRNAs. In Escherichia coli and many other bacteria, this process is dependent on the RNA chaperone Hfq, a mediator for sRNA-mRNA annealing. YhbS (renamed here as HqbA), a putative Gcn5-related N-acetyltransferase (GNAT), was previously identified as a silencer of sRNA signaling in a genomic library screen. Here, we studied how HqbA regulates sRNA signaling and investigated its physiological roles in modulating Hfq activity. Using fluorescent reporter assays, we found that HqbA overproduction suppressed all tested Hfq-dependent sRNA signaling. Direct interaction between HqbA and Hfq was demonstrated both in vivo and in vitro, and mutants that blocked the interaction interfered with HqbA suppression of Hfq. However, an acetylation-deficient HqbA mutant still disrupted sRNA signaling, and HqbA interacted with Hfq at a site far from the active site. This suggests that HqbA may be bifunctional, with separate roles for regulating via Hfq interaction and for acetylation of undefined substrates. Gel shift assays revealed that HqbA strongly reduced the interaction between the Hfq distal face and low-affinity RNAs but not high-affinity RNAs. Comparative RNA immunoprecipitation of Hfq and sequencing showed enrichment of two tRNA precursors, metZWV and proM, by Hfq in mutants that lost the HqbA-Hfq interaction. Our results suggest that HqbA provides a level of quality control for Hfq by competing with low-affinity RNA binders.
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Affiliation(s)
- Xing Luo
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Aixia Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD20892-4417
| | - Chin-Hsien Tai
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Jiandong Chen
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Nadim Majdalani
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD20892-4417
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20892
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31
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Rojano-Nisimura AM, Simmons TR, Leistra AN, Mihailovic MK, Buchser R, Ekdahl AM, Joseph I, Curtis NC, Contreras LM. CsrA selectively modulates sRNA-mRNA regulator outcomes. Front Mol Biosci 2023; 10:1249528. [PMID: 38116378 PMCID: PMC10729762 DOI: 10.3389/fmolb.2023.1249528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/10/2023] [Indexed: 12/21/2023] Open
Abstract
Post-transcriptional regulation, by small RNAs (sRNAs) as well as the global Carbon Storage Regulator A (CsrA) protein, play critical roles in bacterial metabolic control and stress responses. The CsrA protein affects selective sRNA-mRNA networks, in addition to regulating transcription factors and sigma factors, providing additional avenues of cross talk between other stress-response regulators. Here, we expand the known set of sRNA-CsrA interactions and study their regulatory effects. In vitro binding assays confirm novel CsrA interactions with ten sRNAs, many of which are previously recognized as key regulatory nodes. Of those 10 sRNA, we identify that McaS, FnrS, SgrS, MicL, and Spot42 interact directly with CsrA in vivo. We find that the presence of CsrA impacts the downstream regulation of mRNA targets of the respective sRNA. In vivo evidence supports enhanced CsrA McaS-csgD mRNA repression and showcases CsrA-dependent repression of the fucP mRNA via the Spot42 sRNA. We additionally identify SgrS and FnrS as potential new sRNA sponges of CsrA. Overall, our results further support the expanding impact of the Csr system on cellular physiology via CsrA impact on the regulatory roles of these sRNAs.
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Affiliation(s)
| | - Trevor R. Simmons
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Abigail N. Leistra
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Mia K. Mihailovic
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Ryan Buchser
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Alyssa M. Ekdahl
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Isabella Joseph
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Nicholas C. Curtis
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Lydia M. Contreras
- Biochemistry Graduate Program, University of Texas at Austin, Austin, TX, United States
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
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32
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Deng Y, Zang S, Lin Z, Xu L, Cheng C, Feng J. The Pleiotropic Phenotypes Caused by an hfq Null Mutation in Vibrio harveyi. Microorganisms 2023; 11:2741. [PMID: 38004752 PMCID: PMC10672845 DOI: 10.3390/microorganisms11112741] [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: 10/24/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Hfq is a global regulator and can be involved in multiple cellular processes by assisting small regulatory RNAs (sRNAs) to target mRNAs. To gain insight into the virulence regulation of Hfq in Vibrio harveyi, the hfq null mutant, ∆hfq, was constructed in V. harveyi strain 345. Compared with the wild-type strain, the mortality of pearl gentian sharply declined from 80% to 0% in ∆hfq when infected with a dose that was 7.5-fold the median lethal dose (LD50). Additionally, ∆hfq led to impairments of bacterial growth, motility, and biofilm formation and resistance to reactive oxygen species, chloramphenicol, and florfenicol. A transcriptome analysis indicated that the expression of 16.39% genes on V. harveyi 345 were significantly changed after the deletion of hfq. Without Hfq, the virulence-related pathways, including flagellar assembly and bacterial chemotaxis, were repressed. Moreover, eleven sRNAs, including sRNA0405, sRNA0078, sRNA0419, sRNA0145, and sRNA0097, which, respectively, are involved in chloramphenicol/florfenicol resistance, outer membrane protein synthesis, electron transport, amino acid metabolism, and biofilm formation, were significantly down-regulated. In general, Hfq contributes to the virulence of V. harveyi 345 probably via positively regulating bacterial motility and biofilm formation. It is involved in flagellar assembly and bacterial chemotaxis by binding sRNAs and regulating the target mRNAs.
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Affiliation(s)
| | | | | | | | | | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (Y.D.); (S.Z.); (Z.L.); (L.X.); (C.C.)
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33
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Nandana V, Rathnayaka-Mudiyanselage IW, Muthunayake NS, Hatami A, Mousseau CB, Ortiz-Rodríguez LA, Vaishnav J, Collins M, Gega A, Mallikaarachchi KS, Yassine H, Ghosh A, Biteen JS, Zhu Y, Champion MM, Childers WS, Schrader JM. The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions. Cell Rep 2023; 42:113229. [PMID: 37815915 PMCID: PMC10842194 DOI: 10.1016/j.celrep.2023.113229] [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: 02/17/2023] [Revised: 07/16/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Bacterial ribonucleoprotein bodies (BR-bodies) are non-membrane-bound structures that facilitate mRNA decay by concentrating mRNA substrates with RNase E and the associated RNA degradosome machinery. However, the full complement of proteins enriched in BR-bodies has not been defined. Here, we define the protein components of BR-bodies through enrichment of the bodies followed by mass spectrometry-based proteomic analysis. We find 111 BR-body-enriched proteins showing that BR-bodies are more complex than previously assumed. We identify five BR-body-enriched proteins that undergo RNA-dependent phase separation in vitro with a complex network of condensate mixing. We observe that some RNP condensates co-assemble with preferred directionality, suggesting that RNA may be trafficked through RNP condensates in an ordered manner to facilitate mRNA processing/decay, and that some BR-body-associated proteins have the capacity to dissolve the condensate. Altogether, these results suggest that a complex network of protein-protein and protein-RNA interactions controls BR-body phase separation and RNA processing.
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Affiliation(s)
- Vidhyadhar Nandana
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Imalka W Rathnayaka-Mudiyanselage
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA; Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | | | - Ali Hatami
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
| | - C Bruce Mousseau
- Department of Chemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Jamuna Vaishnav
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
| | - Michael Collins
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Alisa Gega
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | | | - Hadi Yassine
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Aishwarya Ghosh
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yingxi Zhu
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
| | - Matthew M Champion
- Department of Chemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jared M Schrader
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA.
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34
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Reichelt R, Rothmeier T, Grünberger F, Willkomm S, Bruckmann A, Hausner W, Grohmann D. The archaeal Lsm protein from Pyrococcus furiosus binds co-transcriptionally to poly(U)-rich target RNAs. Biol Chem 2023; 404:1085-1100. [PMID: 37709673 DOI: 10.1515/hsz-2023-0215] [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] [Received: 05/14/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
Posttranscriptional processes in Bacteria include the association of small regulatory RNAs (sRNA) with a target mRNA. The sRNA/mRNA annealing process is often mediated by an RNA chaperone called Hfq. The functional role of bacterial and eukaryotic Lsm proteins is partially understood, whereas knowledge about archaeal Lsm proteins is scarce. Here, we used the genetically tractable archaeal hyperthermophile Pyrococcus furiosus to identify the protein interaction partners of the archaeal Sm-like proteins (PfuSmAP1) using mass spectrometry and performed a transcriptome-wide binding site analysis of PfuSmAP1. Most of the protein interaction partners we found are part of the RNA homoeostasis network in Archaea including ribosomal proteins, the exosome, RNA-modifying enzymes, but also RNA polymerase subunits, and transcription factors. We show that PfuSmAP1 preferentially binds messenger RNAs and antisense RNAs recognizing a gapped poly(U) sequence with high affinity. Furthermore, we found that SmAP1 co-transcriptionally associates with target RNAs. Our study reveals that in contrast to bacterial Hfq, PfuSmAP1 does not affect the transcriptional activity or the pausing behaviour of archaeal RNA polymerases. We propose that PfuSmAP1 recruits antisense RNAs to target mRNAs and thereby executes its putative regulatory function on the posttranscriptional level.
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Affiliation(s)
- Robert Reichelt
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Tamara Rothmeier
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Felix Grünberger
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Sarah Willkomm
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology (Biochemistry I), Protein Mass Spectrometry Laboratory, University of Regensburg, D-93053 Regensburg, Germany
| | - Winfried Hausner
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, D-93053 Regensburg, Germany
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35
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Zhu W, Xi L, Qiao J, Du D, Wang Y, Morigen. Involvement of OxyR and Dps in the repression of replication initiation by DsrA small RNA in Escherichia coli. Gene 2023; 882:147659. [PMID: 37482259 DOI: 10.1016/j.gene.2023.147659] [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] [Received: 06/27/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023]
Abstract
Regulation of the cell cycle process is an effective measure to ensure the stability and fidelity of genetic material during the reproduction of bacteria under different stresses. The small RNA DsrA helps bacteria adapt to environments by binding to multiple targets, but its association with the cell cycle remains unclear. Detection by flow cytometry, we first found that the knockout of dsrA promoted replication initiation, and corresponding overexpression of DsrA inhibited replication initiation in Escherichia coli. The absence of the chaperone protein Hfq, the DNA replication negative regulator protein Dps, or the transcription factor OxyR, was found to cause DsrA to no longer inhibit replication initiation. Excess DsrA promotes expression of the oxyR and dps gene, whereas β-galactosidase activity assay showed that deleting oxyR limited the enhancement of dps promoter transcriptional activity by DsrA. OxyR is a known positive regulator of Dps. Our data suggests that the effect of DsrA on replication initiation requires Hfq and that the upregulation of Dps expression by OxyR in response to DsrA levels may be a potential regulatory pathway for the negative regulation of DNA replication initiation.
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Affiliation(s)
- Weiwei Zhu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Lingjun Xi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Jiaxin Qiao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Dongdong Du
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yao Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Morigen
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China.
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36
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Myong S, Lee CY, Joshi M, Wang A. 5'UTR G-quadruplex structure enhances translation in size dependent manner. RESEARCH SQUARE 2023:rs.3.rs-3352233. [PMID: 37790436 PMCID: PMC10543253 DOI: 10.21203/rs.3.rs-3352233/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Translation initiation in bacteria is frequently regulated by various structures in the 5' untranslated region (5'UTR). Previously, we demonstrated that G-quadruplex (G4) formation in non-template DNA enhances transcription. In this study, we aimed to explore how G4 formation in mRNA (RG4) at 5'UTR impacts translation using a T7-based in vitro translation system and in E. coli. We showed that RG4 strongly promotes translation efficiency in a size-dependent manner. Additionally, inserting a hairpin upstream of the RG4 further enhances translation efficiency, reaching up to a 12-fold increase. We found that the RG4-dependent effect is not due to increased ribosome affinity, ribosome binding site accessibility, or mRNA stability. We proposed a physical barrier model in which bulky structures in 5'UTR prevent ribosome dislodging and thereby increase the translation output. This study provides biophysical insights into the regulatory role of 5'UTR structures in bacterial translation, highlighting their potential applications in tuning gene expression.
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Affiliation(s)
- Sua Myong
- Boston Children's Hospital/Harvard Medical School
| | | | - Meera Joshi
- Boston Children's Hospital/Harvard Medical School
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37
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Fodor A, Hess C, Ganas P, Boros Z, Kiss J, Makrai L, Dublecz K, Pál L, Fodor L, Sebestyén A, Klein MG, Tarasco E, Kulkarni MM, McGwire BS, Vellai T, Hess M. Antimicrobial Peptides (AMP) in the Cell-Free Culture Media of Xenorhabdus budapestensis and X. szentirmaii Exert Anti-Protist Activity against Eukaryotic Vertebrate Pathogens including Histomonas meleagridis and Leishmania donovani Species. Antibiotics (Basel) 2023; 12:1462. [PMID: 37760758 PMCID: PMC10525888 DOI: 10.3390/antibiotics12091462] [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: 07/31/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Anti-microbial peptides provide a powerful toolkit for combating multidrug resistance. Combating eukaryotic pathogens is complicated because the intracellular drug targets in the eukaryotic pathogen are frequently homologs of cellular structures of vital importance in the host organism. The entomopathogenic bacteria (EPB), symbionts of entomopathogenic-nematode species, release a series of non-ribosomal templated anti-microbial peptides. Some may be potential drug candidates. The ability of an entomopathogenic-nematode/entomopathogenic bacterium symbiotic complex to survive in a given polyxenic milieu is a coevolutionary product. This explains that those gene complexes that are responsible for the biosynthesis of different non-ribosomal templated anti-microbial protective peptides (including those that are potently capable of inactivating the protist mammalian pathogen Leishmania donovanii and the gallinaceous bird pathogen Histomonas meleagridis) are co-regulated. Our approach is based on comparative anti-microbial bioassays of the culture media of the wild-type and regulatory mutant strains. We concluded that Xenorhabdus budapestensis and X. szentirmaii are excellent sources of non-ribosomal templated anti-microbial peptides that are efficient antagonists of the mentioned pathogens. Data on selective cytotoxicity of different cell-free culture media encourage us to forecast that the recently discovered "easy-PACId" research strategy is suitable for constructing entomopathogenic-bacterium (EPB) strains producing and releasing single, harmless, non-ribosomal templated anti-microbial peptides with considerable drug, (probiotic)-candidate potential.
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Affiliation(s)
- András Fodor
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter. sétány 1C, H-1117 Budapest, Hungary; (Z.B.); (T.V.)
| | - Claudia Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine (Vetmeduni Vienna), 1210 Vienna, Austria; (C.H.); (P.G.)
| | - Petra Ganas
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine (Vetmeduni Vienna), 1210 Vienna, Austria; (C.H.); (P.G.)
| | - Zsófia Boros
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter. sétány 1C, H-1117 Budapest, Hungary; (Z.B.); (T.V.)
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Páter Károly utca 1, H-2100 Gödöllő, Hungary;
| | - János Kiss
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Páter Károly utca 1, H-2100 Gödöllő, Hungary;
| | | | - Károly Dublecz
- Institute of Physiology and Nutrition, Georgikon Campus, Hungarian University of Agriculture and Life Sciences (MATE), Deák Ferenc utca 16, H-8360 Keszthely, Hungary; (K.D.); (L.P.)
| | - László Pál
- Institute of Physiology and Nutrition, Georgikon Campus, Hungarian University of Agriculture and Life Sciences (MATE), Deák Ferenc utca 16, H-8360 Keszthely, Hungary; (K.D.); (L.P.)
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, H-1143 Budapest, Hungary;
| | - Anna Sebestyén
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest, Hungary;
| | - Michael G. Klein
- USDA-ARS & Department of Entomology, The Ohio State University, 13416 Claremont Ave, Cleveland, OH 44130, USA;
| | - Eustachio Tarasco
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy;
| | - Manjusha M. Kulkarni
- Division of Infectious Diseases, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA; (M.M.K.); (B.S.M.)
| | - Bradford S. McGwire
- Division of Infectious Diseases, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA; (M.M.K.); (B.S.M.)
| | - Tibor Vellai
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter. sétány 1C, H-1117 Budapest, Hungary; (Z.B.); (T.V.)
| | - Michael Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine (Vetmeduni Vienna), 1210 Vienna, Austria; (C.H.); (P.G.)
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Abstract
Small regulatory RNA (sRNAs) are key mediators of posttranscriptional gene control in bacteria. Assisted by RNA-binding proteins, a single sRNA often modulates the expression of dozens of genes, and thus sRNAs frequently adopt central roles in regulatory networks. Posttranscriptional regulation by sRNAs comes with several unique features that cannot be achieved by transcriptional regulators. However, for optimal network performance, transcriptional and posttranscriptional control mechanisms typically go hand-in-hand. This view is reflected by the ever-growing class of mixed network motifs involving sRNAs and transcription factors, which are ubiquitous in biology and whose regulatory properties we are beginning to understand. In addition, sRNA activity can be antagonized by base-pairing with sponge RNAs, adding yet another layer of complexity to these networks. In this article, we summarize the regulatory concepts underlying sRNA-mediated gene control in bacteria and discuss how sRNAs shape the output of a network, focusing on several key examples.
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Affiliation(s)
- Kai Papenfort
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany;
- Microverse Cluster, Friedrich Schiller University Jena, Jena, Germany
| | - Sahar Melamed
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel;
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39
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Trouillon J, Attrée I, Elsen S. The regulation of bacterial two-partner secretion systems. Mol Microbiol 2023; 120:159-177. [PMID: 37340956 DOI: 10.1111/mmi.15112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023]
Abstract
Two-partner secretion (TPS) systems, also known as Type Vb secretion systems, allow the translocation of effector proteins across the outer membrane of Gram-negative bacteria. By secreting different classes of effectors, including cytolysins and adhesins, TPS systems play important roles in bacterial pathogenesis and host interactions. Here, we review the current knowledge on TPS systems regulation and highlight specific and common regulatory mechanisms across TPS functional classes. We discuss in detail the specific regulatory networks identified in various bacterial species and emphasize the importance of understanding the context-dependent regulation of TPS systems. Several regulatory cues reflecting host environment during infection, such as temperature and iron availability, are common determinants of expression for TPS systems, even across relatively distant species. These common regulatory pathways often affect TPS systems across subfamilies with different effector functions, representing conserved global infection-related regulatory mechanisms.
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Affiliation(s)
- Julian Trouillon
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
| | - Ina Attrée
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
| | - Sylvie Elsen
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
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40
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Nandana V, Rathnayaka-Mudiyanselage IW, Muthunayak NS, Hatami A, Mousseau CB, Ortiz-Rodríguez LA, Vaishnav J, Collins M, Gega A, Mallikaarachchi KS, Yassine H, Ghosh A, Biteen JS, Zhu Y, Champion MM, Childers WS, Schrader JM. The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524314. [PMID: 36712072 PMCID: PMC9882336 DOI: 10.1101/2023.01.18.524314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Bacterial RNP bodies (BR-bodies) are non-membrane-bound structures that facilitate mRNA decay by concentrating mRNA substrates with RNase E and the associated RNA degradosome machinery. However, the full complement of proteins enriched in BR-bodies has not been defined. Here we define the protein components of BR-bodies through enrichment of the bodies followed by mass spectrometry-based proteomic analysis. We found 111 BR-body enriched proteins, including several RNA binding proteins, many of which are also recruited directly to in vitro reconstituted RNase E droplets, showing BR-bodies are more complex than previously assumed. While most BR-body enriched proteins that were tested cannot phase separate, we identified five that undergo RNA-dependent phase separation in vitro, showing other RNP condensates interface with BR-bodies. RNA degradosome protein clients are recruited more strongly to RNase E droplets than droplets of other RNP condensates, implying that client specificity is largely achieved through direct protein-protein interactions. We observe that some RNP condensates assemble with preferred directionally, suggesting that RNA may be trafficked through RNP condensates in an ordered manner to facilitate mRNA processing/decay, and that some BR-body associated proteins have the capacity to dissolve the condensate. Finally, we find that RNA dramatically stimulates the rate of RNase E phase separation in vitro, explaining the dissolution of BR-bodies after cellular mRNA depletion observed previously. Altogether, these results suggest that a complex network of protein-protein and protein-RNA interactions controls BR-body phase separation and RNA processing.
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Affiliation(s)
- V Nandana
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - I W Rathnayaka-Mudiyanselage
- Wayne State University, Department of Biological Sciences, Detroit, MI
- Wayne State University, Department of Chemistry, Detroit, MI
| | - N S Muthunayak
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - A Hatami
- Wayne State University, Department of Chemical Engineering and Materials Science, Detroit, MI
| | - C B Mousseau
- University of Notre Dame, Department of Chemistry, Notre Dame, IN
| | | | - J Vaishnav
- Wayne State University, Department of Chemical Engineering and Materials Science, Detroit, MI
| | - M Collins
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA
| | - A Gega
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | | | - H Yassine
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - A Ghosh
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - J S Biteen
- University of Michigan, Department of Chemistry, Ann Arbor, MI
| | - Y Zhu
- Wayne State University, Department of Chemical Engineering and Materials Science, Detroit, MI
| | - M M Champion
- University of Notre Dame, Department of Chemistry, Notre Dame, IN
| | - W S Childers
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA
| | - J M Schrader
- Wayne State University, Department of Biological Sciences, Detroit, MI
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41
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Turbant F, Waeytens J, Blache A, Esnouf E, Raussens V, Węgrzyn G, Achouak W, Wien F, Arluison V. Interactions and Insertion of Escherichia coli Hfq into Outer Membrane Vesicles as Revealed by Infrared and Orientated Circular Dichroism Spectroscopies. Int J Mol Sci 2023; 24:11424. [PMID: 37511182 PMCID: PMC10379585 DOI: 10.3390/ijms241411424] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
The possible carrier role of Outer Membrane Vesicles (OMVs) for small regulatory noncoding RNAs (sRNAs) has recently been demonstrated. Nevertheless, to perform their function, these sRNAs usually need a protein cofactor called Hfq. In this work we show, by using a combination of infrared and circular dichroism spectroscopies, that Hfq, after interacting with the inner membrane, can be translocated into the periplasm, and then be exported in OMVs, with the possibility to be bound to sRNAs. Moreover, we provide evidence that Hfq interacts with and is inserted into OMV membranes, suggesting a role for this protein in the release of sRNA outside the vesicle. These findings provide clues to the mechanism of host-bacteria interactions which may not be defined solely by protein-protein and protein-outer membrane contacts, but also by the exchange of RNAs, and in particular sRNAs.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Anaïs Blache
- Lab of Microbial Ecology of the Rhizosphere, (LEMiRE), BIAM, CEA, CNRS, Aix Marseille University, 13115 Saint Paul Lez Durance, France
| | - Emeline Esnouf
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Vincent Raussens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Wafa Achouak
- Lab of Microbial Ecology of the Rhizosphere, (LEMiRE), BIAM, CEA, CNRS, Aix Marseille University, 13115 Saint Paul Lez Durance, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, 75006 Paris, France
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42
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Jaworska K, Konarska J, Gomza P, Rożen P, Nieckarz M, Krawczyk-Balska A, Brzostek K, Raczkowska A. Interplay between the RNA Chaperone Hfq, Small RNAs and Transcriptional Regulator OmpR Modulates Iron Homeostasis in the Enteropathogen Yersinia enterocolitica. Int J Mol Sci 2023; 24:11157. [PMID: 37446335 DOI: 10.3390/ijms241311157] [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: 06/19/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Iron is both essential for and potentially toxic to bacteria, so the precise maintenance of iron homeostasis is necessary for their survival. Our previous study indicated that in the human enteropathogen Yersinia enterocolitica, the regulator OmpR directly controls the transcription of the fur, fecA and fepA genes, encoding the ferric uptake repressor and two transporters of ferric siderophores, respectively. This study was undertaken to determine the significance of the RNA chaperone Hfq and the small RNAs OmrA and RyhB1 in the post-transcriptional control of the expression of these OmpR targets. We show that Hfq silences fur, fecA and fepA expression post-transcriptionally and negatively affects the production of FLAG-tagged Fur, FecA and FepA proteins. In addition, we found that the fur gene is under the negative control of the sRNA RyhB1, while fecA and fepA are negatively regulated by the sRNA OmrA. Finally, our data revealed that the role of OmrA results from a complex interplay of transcriptional and post-transcriptional effects in the feedback circuit between the regulator OmpR and the sRNA OmrA. Thus, the expression of fur, fecA and fepA is subject to complex transcriptional and post-transcriptional regulation in order to maintain iron homeostasis in Y. enterocolitica.
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Affiliation(s)
- Karolina Jaworska
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Julia Konarska
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Patrycja Gomza
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Paula Rożen
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Marta Nieckarz
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Agata Krawczyk-Balska
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Katarzyna Brzostek
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Adrianna Raczkowska
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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Bode E, Assmann D, Happel P, Meyer E, Münch K, Rössel N, Bode HB. easyPACId, a Simple Method for Induced Production, Isolation, Identification, and Testing of Natural Products from Proteobacteria. Bio Protoc 2023; 13:e4709. [PMID: 37449040 PMCID: PMC10336570 DOI: 10.21769/bioprotoc.4709] [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: 12/15/2022] [Revised: 02/21/2023] [Accepted: 04/21/2023] [Indexed: 07/18/2023] Open
Abstract
The easyPACId (easy Promoter Activation and Compound Identification) approach is focused on the targeted activation of natural product biosynthetic gene clusters (BGCs) encoding non-ribosomal peptide synthetases (NRPS), polyketide synthases (PKS), NRPS-PKS hybrids, or other BGC classes. It was applied to entomopathogenic bacteria of the genera Xenorhabdus and Photorhabdus by exchanging the natural promoter of desired BGCs against the L-arabinose inducible PBAD promoter in ∆hfq mutants of the respective strains. The crude (culture) extracts of the cultivated easyPACId mutants are enriched with the single compound or compound class and can be tested directly against various target organisms without further purification of the produced natural products. Furthermore, isolation and identification of compounds from these mutants is simplified due to the reduced background in the ∆hfq strains. The approach avoids problems often encountered in heterologous expression hosts, chemical synthesis, or tedious extraction of desired compounds from wild-type crude extracts. This protocol describes easyPACId for Xenorhabdus and Photorhabdus, but it was also successfully adapted to Pseudomonas entomophila and might be suitable for other proteobacteria that carry hfq.
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Affiliation(s)
- Edna Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniela Assmann
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Petra Happel
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Elmar Meyer
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Karin Münch
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Rössel
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Helge B. Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Molecular Biotechnology, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Chemical Biology, Department of Chemistry, Philipps University Marburg, Marburg, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- SYNMIKRO (Zentrum für Synthetische Mikrobiologie), Marburg, Germany
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44
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Gebhardt MJ, Farland EA, Basu P, Macareno K, Melamed S, Dove SL. Hfq-licensed RNA-RNA interactome in Pseudomonas aeruginosa reveals a keystone sRNA. Proc Natl Acad Sci U S A 2023; 120:e2218407120. [PMID: 37285605 PMCID: PMC10214189 DOI: 10.1073/pnas.2218407120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/08/2023] [Indexed: 06/09/2023] Open
Abstract
The RNA chaperone Hfq plays important regulatory roles in many bacteria by facilitating the base pairing between small RNAs (sRNAs) and their cognate mRNA targets. In the gram-negative opportunistic pathogen Pseudomonas aeruginosa, over a hundred putative sRNAs have been identified but for most, their regulatory targets remained unknown. Using RIL-seq with Hfq in P. aeruginosa, we identified the mRNA targets for dozens of previously known and unknown sRNAs. Strikingly, hundreds of the RNA-RNA interactions we discovered involved PhrS. This sRNA was thought to mediate its effects by pairing with a single target mRNA and regulating the abundance of the transcription regulator MvfR required for the synthesis of the quorum sensing signal PQS. We present evidence that PhrS controls many transcripts by pairing with them directly and employs a two-tiered mechanism for governing PQS synthesis that involves control of an additional transcription regulator called AntR. Our findings in P. aeruginosa expand the repertoire of targets for previously known sRNAs, reveal potential regulatory targets for previously unknown sRNAs, and suggest that PhrS may be a keystone sRNA with the ability to pair with an unusually large number of transcripts in this organism.
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Affiliation(s)
- Michael J. Gebhardt
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Elizabeth A. Farland
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Pallabi Basu
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Keven Macareno
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Sahar Melamed
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem9112102, Israel
| | - Simon L. Dove
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA02115
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45
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Thereza Fiori-Duarte A, Bitencourt de Souza Ferreira L, Sanches Ascencio A, Fábio Kawano D. Modulation of Pseudomonas aeruginosa quorum sensing by ajoene through direct competition with small RNAs for binding at the proximal site of Hfq - a structure-based perspective. Gene 2023:147506. [PMID: 37224934 DOI: 10.1016/j.gene.2023.147506] [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: 03/14/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/26/2023]
Abstract
Bacteria can communicate to each other via quorum sensing, a cell density-dependent gene regulation system that stimulates the expression of virulence factors in the neighboring cells. Although the interaction of the natural product ajoene with the Hfq protein has been associated with the disruption of the quorum sensing system in Pseudomonas aeruginosa, there is no information concerning the corresponding ligand-target interaction process. Herein we observed a strong correlation (p < 0.00001) between the estimated affinities for the binding of 23 ajoene analogues at the proximal site of the Hfq protein of P. aeruginosa and their corresponding IC50 values, which reflect the reduction in the transcription of a virulence factor after quorum sensing inhibition. In this concern, our analyses reinforces previous propositions suggesting that ajoene could target the Hfq protein and affects its interaction with RNAs. Based on docking simulations, we tried to elucidate the binding mode of ajoene into the proximal Hfq site and the also to established the minimum set of groups that would be necessary for a good interaction at this site, which includes a single hydrogen bond acceptor feature surrounded by groups that interact via π-sulfur (i.e., disulfide sulfurs) and/or π-alkyl/π-π stacking interactions (e.g., vinyl or small aryl/heteroaryl/heterocyclic groups). Because of the widespread role of Hfq as a matchmaker between messenger and small regulatory RNAs in Gram-negatives, we believe the discussion here provided for P. aeruginosa could be extrapolated for Gram-negatives in general, while the interaction of ajoene over the Hfq protein of Gram-positives would still remain more controversial.
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Affiliation(s)
- Ana Thereza Fiori-Duarte
- Group on the Research & Development of Bioactive Compounds (GR&DBC), Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Cândido Portinari 200, 13083-871 Campinas-SP, Brazil
| | - Luciana Bitencourt de Souza Ferreira
- Group on the Research & Development of Bioactive Compounds (GR&DBC), Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Cândido Portinari 200, 13083-871 Campinas-SP, Brazil
| | - Amanda Sanches Ascencio
- Group on the Research & Development of Bioactive Compounds (GR&DBC), Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Cândido Portinari 200, 13083-871 Campinas-SP, Brazil
| | - Daniel Fábio Kawano
- Group on the Research & Development of Bioactive Compounds (GR&DBC), Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Cândido Portinari 200, 13083-871 Campinas-SP, Brazil.
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46
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Cossey SM, Velicer GJ, Yu YTN. Ribonuclease D Processes a Small RNA Regulator of Multicellular Development in Myxobacteria. Genes (Basel) 2023; 14:genes14051061. [PMID: 37239421 DOI: 10.3390/genes14051061] [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: 04/04/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
By targeting mRNA transcripts, non-coding small RNAs (sRNAs) regulate the expression of genes governing a wide range of bacterial functions. In the social myxobacterium Myxococcus xanthus, the sRNA Pxr serves as a gatekeeper of the regulatory pathway controlling the life-cycle transition from vegetative growth to multicellular fruiting body development. When nutrients are abundant, Pxr prevents the initiation of the developmental program, but Pxr-mediated inhibition is alleviated when cells starve. To identify genes essential for Pxr function, a developmentally defective strain in which Pxr-mediated blockage of development is constitutively active (strain "OC") was transposon-mutagenized to identify suppressor mutations that inactivate or bypass Pxr inhibition and thereby restore development. One of the four loci in which a transposon insertion restored development is rnd, encoding the Ribonuclease D protein (RNase D). RNase D is an exonuclease important for tRNA maturation. Here, we show that disruption of rnd abolishes the accumulation of Pxr-S, the product of Pxr processing from a longer precursor form (Pxr-L) and the active inhibitor of development. Additionally, the decrease in Pxr-S caused by rnd disruption was associated with increased accumulation primarily of a longer novel Pxr-specific transcript (Pxr-XL) rather than of Pxr-L. The introduction of a plasmid expressing rnd reverted cells back to OC-like phenotypes in development and Pxr accumulation, indicating that a lack of RNase D alone suppresses the developmental defect of OC. Moreover, an in vitro Pxr-processing assay demonstrated that RNase D processes Pxr-XL into Pxr-L; this implies that overall, Pxr sRNA maturation requires a sequential two-step processing. Collectively, our results indicate that a housekeeping ribonuclease plays a central role in a model form of microbial aggregative development. To our knowledge, this is the first evidence implicating RNase D in sRNA processing.
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Affiliation(s)
- Sarah M Cossey
- Institute for Integrative Biology, Department of Environmental Systems Science, ETH Zürich, 8092 Zurich, Switzerland
| | - Gregory J Velicer
- Institute for Integrative Biology, Department of Environmental Systems Science, ETH Zürich, 8092 Zurich, Switzerland
| | - Yuen-Tsu Nicco Yu
- Institute for Integrative Biology, Department of Environmental Systems Science, ETH Zürich, 8092 Zurich, Switzerland
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47
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Payá G, Bautista V, Camacho M, Esclapez J, Bonete MJ. Comprehensive Bioinformatics Analysis of the Biodiversity of Lsm Proteins in the Archaea Domain. Microorganisms 2023; 11:1196. [PMID: 37317170 DOI: 10.3390/microorganisms11051196] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq proteins. Sm and Lsm proteins are found in the Eukarya and Archaea domains, respectively, while Hfq proteins exist in the Bacteria domain. Even though Sm and Hfq proteins have been extensively studied, archaeal Lsm proteins still require further exploration. In this work, different bioinformatics tools are used to understand the diversity and distribution of 168 Lsm proteins in 109 archaeal species to increase the global understanding of these proteins. All 109 archaeal species analyzed encode one to three Lsm proteins in their genome. Lsm proteins can be classified into two groups based on molecular weight. Regarding the gene environment of lsm genes, many of these genes are located adjacent to transcriptional regulators of the Lrp/AsnC and MarR families, RNA-binding proteins, and ribosomal protein L37e. Notably, only proteins from species of the class Halobacteria conserved the internal and external residues of the RNA-binding site identified in Pyrococcus abyssi, despite belonging to different taxonomic orders. In most species, the Lsm genes show associations with 11 genes: rpl7ae, rpl37e, fusA, flpA, purF, rrp4, rrp41, hel308, rpoD, rpoH, and rpoN. We propose that most archaeal Lsm proteins are related to the RNA metabolism, and the larger Lsm proteins could perform different functions and/or act through other mechanisms of action.
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Affiliation(s)
- Gloria Payá
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Vanesa Bautista
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Mónica Camacho
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Julia Esclapez
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
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48
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Tanniche I, Nazem-Bokaee H, Scherr DM, Schlemmer S, Senger RS. A novel synthetic sRNA promoting protein overexpression in cell-free systems. Biotechnol Prog 2023; 39:e3324. [PMID: 36651906 DOI: 10.1002/btpr.3324] [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] [Received: 06/02/2022] [Revised: 10/31/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Bacterial small RNAs (sRNAs) that regulate gene expression have been engineered for uses in synthetic biology and metabolic engineering. Here, we designed a novel non-Hfq-dependent sRNA scaffold that uses a modifiable 20 nucleotide antisense binding region to target mRNAs selectively and influence protein expression. The system was developed for regulation of a fluorescent reporter in vivo using Escherichia coli, but the system was found to be more responsive and produced statistically significant results when applied to protein synthesis using in vitro cell-free systems (CFS). Antisense binding sequences were designed to target not only translation initiation regions but various secondary structures in the reporter mRNA. Targeting a high-energy stem loop structure and the 3' end of mRNA yielded protein expression knock-downs that approached 70%. Notably, targeting a low-energy stem structure near a potential RNase E binding site led to a statistically significant 65% increase in protein expression (p < 0.05). These results were not obtainable in vivo, and the underlying mechanism was translated from the reporter system to achieve better than 75% increase in recombinant diaphorase expression in a CFS. It is possible the designs developed here can be applied to improve/regulate expression of other proteins in a CFS.
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Affiliation(s)
- Imen Tanniche
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
- School of Plant & Environmental Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Hadi Nazem-Bokaee
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
- CSIRO, Black Mountain Science & Innovation Park, Canberra, Australia
| | - David M Scherr
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Sara Schlemmer
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Ryan S Senger
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia, USA
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49
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Lorenzetti APR, Kusebauch U, Zaramela LS, Wu WJ, de Almeida JPP, Turkarslan S, L. G. de Lomana A, Gomes-Filho JV, Vêncio RZN, Moritz RL, Koide T, Baliga NS. A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon. mSystems 2023; 8:e0081622. [PMID: 36912639 PMCID: PMC10134880 DOI: 10.1128/msystems.00816-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2023] Open
Abstract
The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation in environmental acclimation are underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating the transcriptome-wide locations of transcript processing sites (TPSs) and SmAP1 binding, the genome-wide locations of antisense RNAs (asRNAs), and the consequences of RNase_2099C knockout on the differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely being regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (transcriptome sequencing [RNA-Seq]) and protein levels (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry [SWATH-MS]) for 2,579 genes over four phases of batch culture growth in complex medium generated additional evidence for the conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation under anoxic conditions and modulate the frequency of transposition by insertion sequence (IS) elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public Web resource (https://halodata.systemsbiology.net). IMPORTANCE While the transcriptional regulation landscape of archaea has been extensively investigated, we currently have limited knowledge about post-transcriptional regulation and its driving mechanisms in this domain of life. In this study, we collected and integrated omics data from multiple sources and technologies to infer post-transcriptionally regulated genes and the putative mechanisms modulating their expression at the protein level in Halobacterium salinarum NRC-1. The results suggest that post-transcriptional regulation may drive environmental acclimation by regulating hallmark biological processes. To foster discoveries by other research groups interested in the topic, we extended our integrated data to the public in the form of an interactive atlas (https://halodata.systemsbiology.net).
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Affiliation(s)
- Alan P. R. Lorenzetti
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- Institute for Systems Biology, Seattle, Washington, USA
| | | | - Lívia S. Zaramela
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, Washington, USA
| | - João P. P. de Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | | | - José V. Gomes-Filho
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Ricardo Z. N. Vêncio
- Department of Computation and Mathematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Tie Koide
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA
- Lawrence Berkeley National Lab, Berkeley, California, USA
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50
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Zeng S, Shi Q, Liu Y, Li M, Lin D, Zhang S, Li Q, Pu J, Shen C, Huang B, Chen C, Zeng J. The small RNA PrrH of Pseudomonas aeruginosa regulates hemolysis and oxidative resistance in bloodstream infection. Microb Pathog 2023; 180:106124. [PMID: 37105322 DOI: 10.1016/j.micpath.2023.106124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 04/29/2023]
Abstract
Small regulatory RNAs (sRNAs) regulate multiple physiological functions in bacteria, and sRNA PrrH can regulate iron homeostasis and virulence. However, the function of PrrH in Pseudomonas aeruginosa (P. aeruginosa) bloodstream infection (BSI) is largely unknown. The aim of this study was to investigate the role of PrrH in P. aeruginosa BSI model. First, P. aeruginosa PAO1 was co-cultured with peripheral blood cells for 6 h qRT-PCR results showed a transient up-regulation of PrrH expression at 1 h. Simultaneously, the expression of iron uptake genes fpvA, pvdS and phuR was upregulated. In addition, the use of iron chelator 2,2'-dipyridyl to create low-iron conditions caused up-regulation of PrrH expression, a result similar to the BSI model. Furthermore, the addition of FeCl3 was found to decrease PrrH expression. These results support the hypothesis that the expression of PrrH is regulated by iron in BSI model. Then, to clarify the effect of PrrH on major cells in the blood, we used PrrH mutant, overexpressing and wild-type strains to act separately on erythrocytes and neutrophils. On one hand, the hemolysis assay revealed that PrrH contributes to the hemolytic activity of PAO1, and its effect was dependent on the T3SS system master regulator gene exsA, yet had no association with the hemolytic phospholipase C (plcH), pldA, and lasB elastase genes. On the other hand, PrrH mutant enhanced the oxidative resistance of PAO1 in the neutrophils co-culture assay, H2O2-treated growth curve and conventional plate spotting assays. Furthermore, the katA was predicted to be a target gene of PrrH by bioinformatics software, and then verified by qPCR and GFP reporter system. In summary, dynamic changes in the expression of prrH are iron-regulated during PAO1 bloodstream infection. In addition, PrrH promotes the hemolytic activity of P. aeruginosa in an exsA-dependent manner and negatively regulates katA to reduce the oxidative tolerance of P. aeruginosa.
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Affiliation(s)
- Shenghe Zeng
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510000, China; The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - Qixuan Shi
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510000, China; The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - YinZhen Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510000, China; The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - Mo Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510000, China
| | - Dongling Lin
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510000, China
| | - Shebin Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510000, China
| | - Qiwei Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510000, China
| | - Jieying Pu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510000, China
| | - Cong Shen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510000, China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510000, China.
| | - Cha Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510000, China.
| | - Jianming Zeng
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510000, China.
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