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Fan L, Wang Y, Huang H, Wang Z, Liang C, Yang X, Ye P, Lin J, Shi W, Zhou Y, Yan H, Long Z, Wang Z, Liu L, Qian J. RNA binding motif 4 inhibits the replication of ebolavirus by directly targeting 3'-leader region of genomic RNA. Emerg Microbes Infect 2024; 13:2300762. [PMID: 38164794 PMCID: PMC10773643 DOI: 10.1080/22221751.2023.2300762] [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: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Ebola virus (EBOV) belongs to Filoviridae family possessing single-stranded negative-sense RNA genome, which is a serious threat to human health. Nowadays, no therapeutics have been proven to be successful in efficiently decreasing the mortality rate. RNA binding proteins (RBPs) are reported to participate in maintaining cell integrity and regulation of viral replication. However, little is known about whether and how RBPs participate in regulating the life cycle of EBOV. In our study, we found that RNA binding motif protein 4 (RBM4) inhibited the replication of EBOV in HEK293T and Huh-7 cells by suppressing viral mRNA production. Such inhibition resulted from the direct interaction between the RRM1 domain of RBM4 and the "CU" enrichment elements located in the PE1 and TSS of the 3'-leader region within the viral genome. Simultaneously, RBM4 could upregulate the expression of some cytokines involved in the host innate immune responses to synergistically exert its antiviral function. The findings therefore suggest that RBM4 might serve as a novel target of anti-EBOV strategy.
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Affiliation(s)
- Linjin Fan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Yulong Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Hongxin Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Zequn Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Chudan Liang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Xiaofeng Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Pengfei Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Jingyan Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Wendi Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Yuandong Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Huijun Yan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Zhenyu Long
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zhongyi Wang
- Beijing Institute of Biotechnology, Beijing, People’s Republic of China
| | - Linna Liu
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jun Qian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
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Chu LC, Christopoulou N, McCaughan H, Winterbourne S, Cazzola D, Wang S, Litvin U, Brunon S, Harker PJ, McNae I, Granneman S. pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data. Life Sci Alliance 2024; 7:e202402787. [PMID: 39079742 PMCID: PMC11289467 DOI: 10.26508/lsa.202402787] [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: 04/22/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
High-throughput proteomics approaches have revolutionised the identification of RNA-binding proteins (RBPome) and RNA-binding sequences (RBDome) across organisms. Yet, the extent of noise, including false positives, associated with these methodologies, is difficult to quantify as experimental approaches for validating the results are generally low throughput. To address this, we introduce pyRBDome, a pipeline for enhancing RNA-binding proteome data in silico. It aligns the experimental results with RNA-binding site (RBS) predictions from distinct machine-learning tools and integrates high-resolution structural data when available. Its statistical evaluation of RBDome data enables quick identification of likely genuine RNA-binders in experimental datasets. Furthermore, by leveraging the pyRBDome results, we have enhanced the sensitivity and specificity of RBS detection through training new ensemble machine-learning models. pyRBDome analysis of a human RBDome dataset, compared with known structural data, revealed that although UV-cross-linked amino acids were more likely to contain predicted RBSs, they infrequently bind RNA in high-resolution structures. This discrepancy underscores the limitations of structural data as benchmarks, positioning pyRBDome as a valuable alternative for increasing confidence in RBDome datasets.
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Affiliation(s)
- Liang-Cui Chu
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Niki Christopoulou
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Hugh McCaughan
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Sophie Winterbourne
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Davide Cazzola
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
| | - Shichao Wang
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Ulad Litvin
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Salomé Brunon
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris, France
| | - Patrick Jb Harker
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Cancer Biomarker Centre, University of Manchester, Manchester, UK
| | - Iain McNae
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
| | - Sander Granneman
- https://ror.org/01nrxwf90 Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK
- https://ror.org/01nrxwf90 Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
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3
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Peng W, Xu Y, Yin Y, Xie J, Ma R, Song G, Zhang Z, Quan Q, Jiang Q, Li M, Li B. Biological characteristics of manganese transporter MntP in Klebsiella pneumoniae. mSphere 2024; 9:e0037724. [PMID: 38888334 PMCID: PMC11288033 DOI: 10.1128/msphere.00377-24] [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: 05/05/2024] [Accepted: 05/29/2024] [Indexed: 06/20/2024] Open
Abstract
Klebsiella pneumoniae is an important opportunistic pathogen that causes a variety of infections. It is critical for bacteria to maintain metal homeostasis during infection. By using an isogenic mntP deletion mutant of K. pneumoniae strain NTUH-K2044, we found that MntP was a manganese efflux pump. Manganese increased the tolerance to oxidative stress, and oxidative stress could increase the intracellular manganese concentration. In oxidative stress, the mntP deletion mutant exhibited significantly higher sensitivity to manganese. Furthermore, iron could increase the tolerance of the mntP deletion mutant to manganese. Inductively coupled plasma mass spectrometry analysis revealed that the mntP deletion mutant had higher intracellular manganese and iron concentrations than wild-type and complementary strains. These findings suggested that iron could increase manganese tolerance in K. pneumoniae. This work elucidated the role of MntP in manganese detoxification and Mn/Fe homeostasis in K. pneumoniae.IMPORTANCEMetal homeostasis plays an important role during the process of bacterial infection. Herein, we revealed that MntP was involved in intracellular manganese homeostasis. Manganese promoted resistance to oxidative stress in Klebsiella pneumoniae. Furthermore, we demonstrated that the mntP deletion mutant exhibited significantly lower survival under manganese and H2O2 conditions. Oxidative stress increased the intracellular manganese content of the mntP deletion mutant. MntP played a critical role in maintaining intracellular manganese and iron concentrations. MntP contributed to manganese detoxification and Mn/Fe homeostasis in K. pneumoniae.
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Affiliation(s)
- Wei Peng
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yafei Xu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yilin Yin
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
| | - Jichen Xie
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
| | - Renhui Ma
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
| | - Guoyuan Song
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zhiqiang Zhang
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
| | - Qiuhang Quan
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
| | - Qinggen Jiang
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
| | - Moran Li
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
| | - Bei Li
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, Hubei, China
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Lawaetz AC, Cowley LA, Denham EL. Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets. Microb Genom 2024; 10. [PMID: 38668652 DOI: 10.1099/mgen.0.001239] [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: 05/16/2024] Open
Abstract
Accurate annotation to single-nucleotide resolution of the transcribed regions in genomes is key to optimally analyse RNA-seq data, understand regulatory events and for the design of experiments. However, currently most genome annotations provided by GenBank generally lack information about untranslated regions. Additionally, information regarding genomic locations of non-coding RNAs, such as sRNAs, or anti-sense RNAs is frequently missing. To provide such information, diverse RNA-seq technologies, such as Rend-seq, have been developed and applied to many bacterial species. However, incorporating this vast amount of information into annotation files has been limited and is bioinformatically challenging, resulting in UTRs and other non-coding elements being overlooked or misrepresented. To overcome this problem, we present pyRAP (python Rend-seq Annotation Pipeline), a software package that analyses Rend-seq datasets to accurately resolve transcript boundaries genome-wide. We report the use of pyRAP to find novel transcripts, transcript isoforms, and RNase-dependent sRNA processing events. In Bacillus subtilis we uncovered 63 novel transcripts and provide genomic coordinates with single-nucleotide resolution for 2218 5'UTRs, 1864 3'UTRs and 161 non-coding RNAs. In Escherichia coli, we report 117 novel transcripts, 2429 5'UTRs, 1619 3'UTRs and 91 non-coding RNAs, and in Staphylococcus aureus, 16 novel transcripts, 664 5'UTRs, 696 3'UTRs, and 81 non-coding RNAs. Finally, we use pyRAP to produce updated annotation files for B. subtilis 168, E. coli K-12 MG1655, and S. aureus 8325 for use in the wider microbial genomics research community.
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Affiliation(s)
- Andreas C Lawaetz
- Life Sciences Department, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Lauren A Cowley
- Life Sciences Department, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- Milner Centre for Evolution, Life Sciences Department, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Emma L Denham
- Life Sciences Department, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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5
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Reslane I, Handke LD, Watson GF, Shinde D, Ahn JS, Endres JL, Razvi F, Gilbert EA, Bayles KW, Thomas VC, Lehman MK, Fey PD. Glutamate -dependent arginine biosynthesis requires the inactivation of spoVG, sarA, and ahrC in Staphylococcus aureus. J Bacteriol 2024; 206:e0033723. [PMID: 38299858 PMCID: PMC10883023 DOI: 10.1128/jb.00337-23] [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: 10/13/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Genome sequencing has demonstrated that Staphylococcus aureus encodes arginine biosynthetic genes argDCJBFGH synthesizing proteins that mediate arginine biosynthesis using glutamate as a substrate. Paradoxically, however, S. aureus does not grow in a defined, glutamate-replete medium lacking arginine and glucose (CDM-R). Studies from our laboratory have found that specific mutations are selected by S. aureus that facilitate growth in CDM-R. However, these selected mutants synthesize arginine utilizing proline as a substrate rather than glutamate. In this study, we demonstrate that the ectopic expression of the argDCJB operon supports the growth of S. aureus in CDM-R, thus documenting the functionality of this pathway. Furthermore, suppressor mutants of S. aureus JE2 putA::Tn, which is defective in synthesizing arginine from proline, were selected on CDM-R agar. Genome sequencing revealed that these mutants had compensatory mutations within both spoVG, encoding an ortholog of the Bacillus subtilis stage V sporulation protein, and sarA, encoding the staphylococcal accessory regulator. Transcriptional studies document that argD expression is significantly increased when JE2 spoVG sarA was grown in CDM-R. Lastly, we found that a mutation in ahrC was required to induce argD expression in JE2 spoVG sarA when grown in an arginine-replete medium (CDM), suggesting that AhrC also functions to repress argDCJB in an arginine-dependent manner. In conclusion, these data indicate that the argDCJB operon is functional when transcribed in vitro and that SNPs within potential putative regulatory proteins are required to alleviate the repression.IMPORTANCEAlthough Staphylococcus aureus has the capability to synthesize all 20 amino acids, it is phenotypically auxotrophic for several amino acids including arginine. This work identifies putative regulatory proteins, including SpoVG, SarA, and AhrC, that function to inhibit the arginine biosynthetic pathways using glutamate as a substrate. Understanding the ultimate mechanisms of why S. aureus is selected to repress arginine biosynthetic pathways even in the absence of arginine will add to the growing body of work assessing the interactions between metabolism and S. aureus pathogenesis.
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Affiliation(s)
- Itidal Reslane
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Luke D. Handke
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Gabrielle F. Watson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Dhananjay Shinde
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jong-Sam Ahn
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jennifer L. Endres
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Fareha Razvi
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Emily A. Gilbert
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kenneth W. Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Vinai C. Thomas
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - McKenzie K. Lehman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
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6
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Quendera AP, Pinto SN, Pobre V, Antunes W, Bonifácio VDB, Arraiano CM, Andrade JM. The ribonuclease PNPase is a key regulator of biofilm formation in Listeria monocytogenes and affects invasion of host cells. NPJ Biofilms Microbiomes 2023; 9:34. [PMID: 37286543 PMCID: PMC10247797 DOI: 10.1038/s41522-023-00397-1] [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: 10/25/2022] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Abstract
Biofilms provide an environment that protects microorganisms from external stresses such as nutrient deprivation, antibiotic treatments, and immune defences, thereby creating favorable conditions for bacterial survival and pathogenesis. Here we show that the RNA-binding protein and ribonuclease polynucleotide phosphorylase (PNPase) is a positive regulator of biofilm formation in the human pathogen Listeria monocytogenes, a major responsible for food contamination in food-processing environments. The PNPase mutant strain produces less biofilm biomass and exhibits an altered biofilm morphology that is more susceptible to antibiotic treatment. Through biochemical assays and microscopical analysis, we demonstrate that PNPase is a previously unrecognized regulator of the composition of the biofilm extracellular matrix, greatly affecting the levels of proteins, extracellular DNA, and sugars. Noteworthy, we have adapted the use of the fluorescent complex ruthenium red-phenanthroline for the detection of polysaccharides in Listeria biofilms. Transcriptomic analysis of wild-type and PNPase mutant biofilms reveals that PNPase impacts many regulatory pathways associated with biofilm formation, particularly by affecting the expression of genes involved in the metabolism of carbohydrates (e.g., lmo0096 and lmo0783, encoding PTS components), of amino acids (e.g., lmo1984 and lmo2006, encoding biosynthetic enzymes) and in the Agr quorum sensing-like system (lmo0048-49). Moreover, we show that PNPase affects mRNA levels of the master regulator of virulence PrfA and PrfA-regulated genes, and these results could help to explain the reduced bacterial internalization in human cells of the ΔpnpA mutant. Overall, this work demonstrates that PNPase is an important post-transcriptional regulator for virulence and adaptation to the biofilm lifestyle of Gram-positive bacteria and highlights the expanding role of ribonucleases as critical players in pathogenicity.
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Affiliation(s)
- Ana Patrícia Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal
| | - Sandra Nunes Pinto
- Institute for Bioengineering and Biosciences (IBB) and Associate Laboratory-Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal
| | - Wilson Antunes
- Laboratório de Imagem, Nanomorfologia e Espectroscopia de Raios-X (Linx) da Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Instituto Universitário Militar, Centro de Investigação, Inovação e Desenvolvimento da Academia Militar, Av. Dr Alfredo Bensaúde, 1100-471, Lisboa, Portugal
| | - Vasco D B Bonifácio
- Institute for Bioengineering and Biosciences (IBB) and Associate Laboratory-Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
- Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Cecília Maria Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal
| | - José Marques Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal.
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7
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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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8
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Michaux C, Gerovac M, Hansen EE, Barquist L, Vogel J. Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens. MICROLIFE 2022; 4:uqac027. [PMID: 37223738 PMCID: PMC10117718 DOI: 10.1093/femsml/uqac027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/24/2022] [Indexed: 05/25/2023]
Abstract
Enterococcus faecalis and Enterococcus faecium are major nosocomial pathogens. Despite their relevance to public health and their role in the development of bacterial antibiotic resistance, relatively little is known about gene regulation in these species. RNA-protein complexes serve crucial functions in all cellular processes associated with gene expression, including post-transcriptional control mediated by small regulatory RNAs (sRNAs). Here, we present a new resource for the study of enterococcal RNA biology, employing the Grad-seq technique to comprehensively predict complexes formed by RNA and proteins in E. faecalis V583 and E. faecium AUS0004. Analysis of the generated global RNA and protein sedimentation profiles led to the identification of RNA-protein complexes and putative novel sRNAs. Validating our data sets, we observe well-established cellular RNA-protein complexes such as the 6S RNA-RNA polymerase complex, suggesting that 6S RNA-mediated global control of transcription is conserved in enterococci. Focusing on the largely uncharacterized RNA-binding protein KhpB, we use the RIP-seq technique to predict that KhpB interacts with sRNAs, tRNAs, and untranslated regions of mRNAs, and might be involved in the processing of specific tRNAs. Collectively, these datasets provide departure points for in-depth studies of the cellular interactome of enterococci that should facilitate functional discovery in these and related Gram-positive species. Our data are available to the community through a user-friendly Grad-seq browser that allows interactive searches of the sedimentation profiles (https://resources.helmholtz-hiri.de/gradseqef/).
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Affiliation(s)
- Charlotte Michaux
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Milan Gerovac
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Elisabeth E Hansen
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße, 97080, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße, 97080, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
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9
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Chihara K, Gerovac M, Hör J, Vogel J. Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq). RNA (NEW YORK, N.Y.) 2022; 29:rna.079439.122. [PMID: 36328526 PMCID: PMC9808575 DOI: 10.1261/rna.079439.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
New methods for the global identification of RNA-protein interactions have led to greater recognition of the abundance and importance of RNA-binding proteins (RBPs) in bacteria. Here, we expand this tool kit by developing SEC-seq, a method based on a similar concept as the established Grad-seq approach. In Grad-seq, cellular RNA and protein complexes of a bacterium of interest are separated in a glycerol gradient, followed by high-throughput RNA-sequencing and mass spectrometry analyses of individual gradient fractions. New RNA-protein complexes are predicted based on the similarity of their elution profiles. In SEC-seq, we have replaced the glycerol gradient with separation by size exclusion chromatography, which shortens operation times and offers greater potential for automation. Applying SEC-seq to Escherichia coli, we find that the method provides a higher resolution than Grad-seq in the lower molecular weight range up to ~500 kDa. This is illustrated by the ability of SEC-seq to resolve two distinct, but similarly sized complexes of the global translational repressor CsrA with either of its antagonistic small RNAs, CsrB and CsrC. We also characterized changes in the SEC-seq profiles of the small RNA MicA upon deletion of its RNA chaperones Hfq and ProQ and investigated the redistribution of these two proteins upon RNase treatment. Overall, we demonstrate that SEC-seq is a tractable and reproducible method for the global profiling of bacterial RNA-protein complexes that offers the potential to discover yet-unrecognized associations between bacterial RNAs and proteins.
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Affiliation(s)
- Kotaro Chihara
- Helmholtz Institute for RNA-based Infection Research, Würzburg, Germany
| | | | - Jens Hör
- Weizmann Institute, Rehovot, Israel
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10
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Bheemireddy S, Sandhya S, Srinivasan N, Sowdhamini R. Computational tools to study RNA-protein complexes. Front Mol Biosci 2022; 9:954926. [PMID: 36275618 PMCID: PMC9585174 DOI: 10.3389/fmolb.2022.954926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
RNA is the key player in many cellular processes such as signal transduction, replication, transport, cell division, transcription, and translation. These diverse functions are accomplished through interactions of RNA with proteins. However, protein–RNA interactions are still poorly derstood in contrast to protein–protein and protein–DNA interactions. This knowledge gap can be attributed to the limited availability of protein-RNA structures along with the experimental difficulties in studying these complexes. Recent progress in computational resources has expanded the number of tools available for studying protein-RNA interactions at various molecular levels. These include tools for predicting interacting residues from primary sequences, modelling of protein-RNA complexes, predicting hotspots in these complexes and insights into derstanding in the dynamics of their interactions. Each of these tools has its strengths and limitations, which makes it significant to select an optimal approach for the question of interest. Here we present a mini review of computational tools to study different aspects of protein-RNA interactions, with focus on overall application, development of the field and the future perspectives.
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Affiliation(s)
- Sneha Bheemireddy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Sankaran Sandhya
- Department of Biotechnology, Faculty of Life and Allied Health Sciences, M.S. Ramaiah University of Applied Sciences, Bengaluru, India
- *Correspondence: Sankaran Sandhya, ; Ramanathan Sowdhamini,
| | | | - Ramanathan Sowdhamini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
- *Correspondence: Sankaran Sandhya, ; Ramanathan Sowdhamini,
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11
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Erkorkmaz BA, Kırtel O, Abaramak G, Nikerel E, Öner ET. UV and Chemically Induced Halomonas smyrnensis Mutants for Enhanced Levan Productivity. J Biotechnol 2022; 356:19-29. [PMID: 35914617 DOI: 10.1016/j.jbiotec.2022.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/14/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Halomonas smyrnensis AAD6T is a moderately halophilic bacterium proven to be a powerful biotechnological tool with its ability to accumulate valuable biopolymers such as levan and poly(3-hydroxybutyrate) (PHB). Levan is a fructose homopolymer with β-2,6 fructofuranosidic linkages on the polymer backbone, and its distinctive applications in various industries such as food, pharmaceutical, medical, and chemical have been well-defined. On the other hand, PHB is a promising raw material to produce biodegradable plastics. Although it was shown in our previous studies that H. smyrnensis AAD6T exhibits one of the highest conversion yields of sucrose to levan reported to date, novel strategies are required to overcome high costs of levan production. In this study, we aimed at increasing levan productivity of H. smyrnensis AAD6T cultures using random mutagenesis techniques combined (i.e., ethyl methanesulfate treatment and/or ultraviolet irradiation). After several consecutive treatments, mutant strains BAE2, BAE5 and BAE6 were selected as efficient levan producers, as BAE2 standing out as the most efficient one not only in sucrose utilization and levan production rates, but also in final PHB concentrations. The mutants' whole genome sequences were analysed to determine the mutations occurred. Several mutations in genes related to central carbon metabolism and osmoregulation were found. Our results suggest that random mutagenesis can be a facile and efficient strategy to enhance the performance of extremophiles in adverse conditions.
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Affiliation(s)
- Burak Adnan Erkorkmaz
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey; Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Onur Kırtel
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey
| | - Gülbahar Abaramak
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey
| | - Emrah Nikerel
- Department of Genetics and Bioengineering, Yeditepe University, 34755 Istanbul, Turkey
| | - Ebru Toksoy Öner
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey.
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12
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McKellar SW, Ivanova I, Arede P, Zapf RL, Mercier N, Chu LC, Mediati DG, Pickering AC, Briaud P, Foster RG, Kudla G, Fitzgerald JR, Caldelari I, Carroll RK, Tree JJ, Granneman S. RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression. Nat Commun 2022; 13:3560. [PMID: 35732654 PMCID: PMC9217828 DOI: 10.1038/s41467-022-31173-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/03/2022] [Indexed: 01/13/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen responsible for significant human morbidity and mortality. Post-transcriptional regulation by small RNAs (sRNAs) has emerged as an important mechanism for controlling virulence. However, the functionality of the majority of sRNAs during infection is unknown. To address this, we performed UV cross-linking, ligation, and sequencing of hybrids (CLASH) in MRSA to identify sRNA-RNA interactions under conditions that mimic the host environment. Using a double-stranded endoribonuclease III as bait, we uncovered hundreds of novel sRNA-RNA pairs. Strikingly, our results suggest that the production of small membrane-permeabilizing toxins is under extensive sRNA-mediated regulation and that their expression is intimately connected to metabolism. Additionally, we also uncover an sRNA sponging interaction between RsaE and RsaI. Taken together, we present a comprehensive analysis of sRNA-target interactions in MRSA and provide details on how these contribute to the control of virulence in response to changes in metabolism.
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Affiliation(s)
- Stuart W McKellar
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Ivayla Ivanova
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Pedro Arede
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Rachel L Zapf
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA
| | - Noémie Mercier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Liang-Cui Chu
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Amy C Pickering
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh, Scotland, UK
| | - Paul Briaud
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA
| | - Robert G Foster
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - J Ross Fitzgerald
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh, Scotland, UK
| | - Isabelle Caldelari
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Ronan K Carroll
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA
- The Infectious and Tropical Disease Institute, Ohio University, Athens, OH, 45701, USA
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Sander Granneman
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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13
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PerR-Regulated Manganese Import Contributes to Oxidative Stress Defense in Streptococcus suis. Appl Environ Microbiol 2022; 88:e0008622. [PMID: 35465691 DOI: 10.1128/aem.00086-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Streptococcus suis has been increasingly recognized as a porcine zoonotic pathogen that threatens the health of both pigs and humans. Metal homeostasis plays a critical role in the antioxidative capability of bacteria, thus facilitating the escape of pathogenic species from the innate immunity systems of hosts. Here, we revealed that manganese increased the ability of S. suis to resist oxidative stress. RNA sequencing was used to identify potential candidate genes involved in the maintenance of intracellular manganese homeostasis. Four genes, termed troABCD, were identified by NCBI BLASTp analysis. The troA, troB, troC, and troD deletion mutant strains exhibited decreased intracellular manganese content and tolerance to H2O2 compared to the wild-type strain. Thus, troABCD were determined to be involved in manganese uptake and played an important role in H2O2 tolerance in S. suis. Furthermore, the inactivation of perR increased the survival of H2O2-pulsed S. suis 2.18-fold and elevated the intracellular manganese content. H2O2-pulsed S. suis and perR deletion mutants upregulated troABCD. This finding suggested that H2O2 released the suppression of troABCD by perR. In addition, an electrophoretic mobility shift assay (EMSA) showed that PerR at 500 ng binds to the troABCD promoter, indicating that troABCD were directly regulated by PerR. In conclusion, this study revealed that manganese increases tolerance to H2O2 by upregulating the expression of troABCD. Moreover, PerR-regulated Mn import in S. suis and increased the tolerance of S. suis to oxidative stress by regulating troABCD. IMPORTANCE During infection, it is extremely important for bacteria to defend against oxidative stress. While manganese plays an important role in this process, its role is unclear in S. suis. Here, we demonstrated that manganese increased S. suis tolerance to oxidative stress. Four manganese ABC transporter genes, troABCD, were identified. Oxidative stress increased the content of manganese in the cell. Furthermore, PerR increased the tolerance to oxidative stress of S. suis by regulating troABCD. Manganese played an important role in bacterial defense against oxidative stress. These findings provide novel insight into the mechanism by which S. suis resists oxidative stress and approaches to inhibit bacterial infection by limiting manganese intake.
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14
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Boutet E, Djerroud S, Perreault J. Small RNAs beyond Model Organisms: Have We Only Scratched the Surface? Int J Mol Sci 2022; 23:ijms23084448. [PMID: 35457265 PMCID: PMC9029176 DOI: 10.3390/ijms23084448] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 01/27/2023] Open
Abstract
Small RNAs (sRNAs) are essential regulators in the adaptation of bacteria to environmental changes and act by binding targeted mRNAs through base complementarity. Approximately 550 distinct families of sRNAs have been identified since their initial characterization in the 1980s, accelerated by the emergence of RNA-sequencing. Small RNAs are found in a wide range of bacterial phyla, but they are more prominent in highly researched model organisms compared to the rest of the sequenced bacteria. Indeed, Escherichia coli and Salmonella enterica contain the highest number of sRNAs, with 98 and 118, respectively, with Enterobacteriaceae encoding 145 distinct sRNAs, while other bacteria families have only seven sRNAs on average. Although the past years brought major advances in research on sRNAs, we have perhaps only scratched the surface, even more so considering RNA annotations trail behind gene annotations. A distinctive trend can be observed for genes, whereby their number increases with genome size, but this is not observable for RNAs, although they would be expected to follow the same trend. In this perspective, we aimed at establishing a more accurate representation of the occurrence of sRNAs in bacteria, emphasizing the potential for novel sRNA discoveries.
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15
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Evdokimova V. Y-box Binding Protein 1: Looking Back to the Future. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S5-S145. [PMID: 35501983 DOI: 10.1134/s0006297922140024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding protein 1 is a member of the cold shock domain (CSD) protein family and one of the most studied proteins associated with a large number of human diseases. This review aims to critically reassess the growing number of pathological functions ascribed to YB-1 in the past decades. The focus is given on the important role of YB-1 and related CSD proteins in the physiology of normal cells. The functional significance of these proteins is highlighted by their high evolutionary conservation from bacteria to men, where they are ubiquitously expressed and involved in coordinating all steps of mRNA biogenesis, including transcription, translation, storage, and degradation. Their activities are especially important under conditions requiring rapid change in the gene expression programs, such as early embryonic development, differentiation, stress, and adaptation to new environments. Therefore, to define a precise role of YB-1 in tumorigenic transformation and in other pathological conditions, it is important to understand its basic properties and functions in normal cells, and how they are interrupted in complex diseases including cancer.
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16
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Charbonnier M, González-Espinoza G, Kehl-Fie TE, Lalaouna D. Battle for Metals: Regulatory RNAs at the Front Line. Front Cell Infect Microbiol 2022; 12:952948. [PMID: 35865816 PMCID: PMC9294342 DOI: 10.3389/fcimb.2022.952948] [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: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Metal such as iron, zinc, manganese, and nickel are essential elements for bacteria. These nutrients are required in crucial structural and catalytic roles in biological processes, including precursor biosynthesis, DNA replication, transcription, respiration, and oxidative stress responses. While essential, in excess these nutrients can also be toxic. The immune system leverages both of these facets, to limit bacterial proliferation and combat invaders. Metal binding immune proteins reduce the bioavailability of metals at the infection sites starving intruders, while immune cells intoxicate pathogens by providing metals in excess leading to enzyme mismetallation and/or reactive oxygen species generation. In this dynamic metal environment, maintaining metal homeostasis is a critical process that must be precisely coordinated. To achieve this, bacteria utilize diverse metal uptake and efflux systems controlled by metalloregulatory proteins. Recently, small regulatory RNAs (sRNAs) have been revealed to be critical post-transcriptional regulators, working in conjunction with transcription factors to promote rapid adaptation and to fine-tune bacterial adaptation to metal abundance. In this mini review, we discuss the expanding role for sRNAs in iron homeostasis, but also in orchestrating adaptation to the availability of other metals like manganese and nickel. Furthermore, we describe the sRNA-mediated interdependency between metal homeostasis and oxidative stress responses, and how regulatory networks controlled by sRNAs contribute to survival and virulence.
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Affiliation(s)
- Mathilde Charbonnier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | | | - Thomas E Kehl-Fie
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana IL, United States.,Carl R. Woese Institute for Genomic Biology University of Illinois Urbana-Champaign, Urbana IL, United States
| | - David Lalaouna
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
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17
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Xu Q, Chen H, Sun W, Zhang Y, Zhu D, Rai KR, Chen JL, Chen Y. sRNA23, a novel small RNA, regulates to the pathogenesis of Streptococcus suis serotype 2. Virulence 2021; 12:3045-3061. [PMID: 34882070 PMCID: PMC8667912 DOI: 10.1080/21505594.2021.2008177] [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] [Indexed: 11/02/2022] Open
Abstract
ABBREVIATION sRNA: small noncoding RNA; FBA: fructose diphosphate aldolase; rplB: 50S ribosomal protein L2; RACE: rapid amplification of cDNA ends; EMSA: electrophoretic mobility shift assay; THB: Todd-Hewitt broth; FBS: fetal bovine serum; BIP: 2,2'-Bipyridine.
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Affiliation(s)
- Quanming Xu
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong Chen
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wen Sun
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongyi Zhang
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dewen Zhu
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kul Raj Rai
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ji-Long Chen
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Chen
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
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18
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Barrientos L, Mercier N, Lalaouna D, Caldelari I. Assembling the Current Pieces: The Puzzle of RNA-Mediated Regulation in Staphylococcus aureus. Front Microbiol 2021; 12:706690. [PMID: 34367109 PMCID: PMC8334554 DOI: 10.3389/fmicb.2021.706690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/30/2021] [Indexed: 01/16/2023] Open
Abstract
The success of the major opportunistic human Staphylococcus aureus relies on the production of numerous virulence factors, which allow rapid colonization and dissemination in any tissues. Indeed, regulation of its virulence is multifactorial, and based on the production of transcriptional factors, two-component systems (TCS) and small regulatory RNAs (sRNAs). Advances in high-throughput sequencing technologies have unveiled the existence of hundreds of potential RNAs with regulatory functions, but only a fraction of which have been validated in vivo. These discoveries have modified our thinking and understanding of bacterial physiology and virulence fitness by placing sRNAs, alongside transcriptional regulators, at the center of complex and intertwined regulatory networks that allow S. aureus to rapidly adapt to the environmental cues present at infection sites. In this review, we describe the recently acquired knowledge of characterized regulatory RNAs in S. aureus that are associated with metal starvation, nutrient availability, stress responses and virulence. These findings highlight the importance of sRNAs for the comprehension of S. aureus infection processes while raising questions about the interplay between these key regulators and the pathways they control.
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Affiliation(s)
- Laura Barrientos
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Noémie Mercier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - David Lalaouna
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Isabelle Caldelari
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
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