1
|
Raghunandanan S, Priya R, Alanazi F, Lybecker MC, Schlax P, Yang X. A Fur family protein BosR is a novel RNA-binding protein that controls rpoS RNA stability in the Lyme disease pathogen. Nucleic Acids Res 2024; 52:5320-5335. [PMID: 38366569 PMCID: PMC11109971 DOI: 10.1093/nar/gkae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
The σ54-σS sigma factor cascade plays a central role in regulating differential gene expression during the enzootic cycle of Borreliella burgdorferi, the Lyme disease pathogen. In this pathway, the primary transcription of rpoS (which encodes σS) is under the control of σ54 which is activated by a bacterial enhancer-binding protein (EBP), Rrp2. The σ54-dependent activation in B. burgdorferi has long been thought to be unique, requiring an additional factor, BosR, a homologue of classical Fur/PerR repressor/activator. However, how BosR is involved in this σ54-dependent activation remains unclear and perplexing. In this study, we demonstrate that BosR does not function as a regulator for rpoS transcriptional activation. Instead, it functions as a novel RNA-binding protein that governs the turnover rate of rpoS mRNA. We further show that BosR directly binds to the 5' untranslated region (UTR) of rpoS mRNA, and the binding region overlaps with a region required for rpoS mRNA degradation. Mutations within this 5'UTR region result in BosR-independent RpoS production. Collectively, these results uncover a novel role of Fur/PerR family regulators as RNA-binding proteins and redefine the paradigm of the σ54-σS pathway in B. burgdorferi.
Collapse
Affiliation(s)
- Sajith Raghunandanan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Raj Priya
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Fuad Alanazi
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
| | - Meghan C Lybecker
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Center for Disease Control and Prevention, Fort Collins, CO, USA
| | - Paula Jean Schlax
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - X Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| |
Collapse
|
2
|
Lejars M, Hajnsdorf E. Bacterial RNase III: Targets and physiology. Biochimie 2024; 217:54-65. [PMID: 37482092 DOI: 10.1016/j.biochi.2023.07.009] [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: 04/21/2023] [Revised: 06/28/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
Bacteria can rapidly adapt to changes in their environment thanks to the innate flexibility of their genetic expression. The high turnover rate of RNAs, in particular messenger and regulatory RNAs, provides an important contribution to this dynamic adjustment. Recycling of RNAs is ensured by ribonucleases, among which RNase III is the focus of this review. RNase III enzymes are highly conserved from prokaryotes to eukaryotes and have the specific ability to cleave double-stranded RNAs. The role of RNase III in bacterial physiology has remained poorly explored for a long time. However, transcriptomic approaches recently uncovered a large impact of RNase III in gene expression in a wide range of bacteria, generating renewed interest in the physiological role of RNase III. In this review, we first describe the RNase III targets identified from global approaches in 8 bacterial species within 4 Phyla. We then present the conserved and unique functions of bacterial RNase III focusing on growth, resistance to stress, biofilm formation, motility and virulence. Altogether, this review highlights the underestimated impact of RNase III in bacterial adaptation.
Collapse
Affiliation(s)
- Maxence Lejars
- Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.
| | - Eliane Hajnsdorf
- UMR8261, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005, Paris, France.
| |
Collapse
|
3
|
Börner J, Friedrich T, Klug G. RNase III participates in control of quorum sensing, pigmentation and oxidative stress resistance in Rhodobacter sphaeroides. Mol Microbiol 2023; 120:874-892. [PMID: 37823424 DOI: 10.1111/mmi.15181] [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: 07/21/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
RNase III is a dsRNA-specific endoribonuclease, highly conserved in bacteria and eukarya. In this study, we analysed the effects of inactivation of RNase III on the transcriptome and the phenotype of the facultative phototrophic α-proteobacterium Rhodobacter sphaeroides. RNA-seq revealed an unexpectedly high amount of genes with increased expression located directly downstream to the rRNA operons. Chromosomal insertion of additional transcription terminators restored wild type-like expression of the downstream genes, indicating that RNase III may modulate the rRNA transcription termination in R. sphaeroides. Furthermore, we identified RNase III as a major regulator of quorum-sensing autoinducer synthesis in R. sphaeroides. It negatively controls the expression of the autoinducer synthase CerI by reducing cerI mRNA stability. In addition, RNase III inactivation caused altered resistance against oxidative stress and impaired formation of photosynthetically active pigment-protein complexes. We also observed an increase in the CcsR small RNAs that were previously shown to promote resistance to oxidative stress. Taken together, our data present interesting insights into RNase III-mediated regulation and expand the knowledge on the function of this important enzyme in bacteria.
Collapse
Affiliation(s)
- Janek Börner
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tobias Friedrich
- Biomedical Informatics and Systems Medicine, Justus-Liebig-University Giessen, Giessen, Germany
- Institute of Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Germany
| |
Collapse
|
4
|
Petroni E, Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi. Nat Commun 2023; 14:3931. [PMID: 37402717 DOI: 10.1038/s41467-023-39576-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023] Open
Abstract
Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. Here, we use several RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi - the etiological agent of Lyme disease. We identify complex gene arrangements and operons, untranslated regions and small RNAs. We predict intrinsic terminators and experimentally test examples of Rho-dependent transcription termination. Remarkably, 63% of RNA 3' ends map upstream of or internal to open reading frames (ORFs), including genes involved in the unique infectious cycle of B. burgdorferi. We suggest these RNAs result from premature termination, processing and regulatory events such as cis-acting regulation. Furthermore, the polyamine spermidine globally influences the generation of truncated mRNAs. Collectively, our findings provide insights into transcription termination and uncover an abundance of potential RNA regulators in B. burgdorferi.
Collapse
Affiliation(s)
- Emily Petroni
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Daniel Tetreault
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA.
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD, 20892, USA.
- Independent Research Scholar Program, Intramural Research Program, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
5
|
RNase III, Ribosome Biogenesis and Beyond. Microorganisms 2021; 9:microorganisms9122608. [PMID: 34946208 PMCID: PMC8708148 DOI: 10.3390/microorganisms9122608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 12/17/2022] Open
Abstract
The ribosome is the universal catalyst for protein synthesis. Despite extensive studies, the diversity of structures and functions of this ribonucleoprotein is yet to be fully understood. Deciphering the biogenesis of the ribosome in a step-by-step manner revealed that this complexity is achieved through a plethora of effectors involved in the maturation and assembly of ribosomal RNAs and proteins. Conserved from bacteria to eukaryotes, double-stranded specific RNase III enzymes play a large role in the regulation of gene expression and the processing of ribosomal RNAs. In this review, we describe the canonical role of RNase III in the biogenesis of the ribosome comparing conserved and unique features from bacteria to eukaryotes. Furthermore, we report additional roles in ribosome biogenesis re-enforcing the importance of RNase III.
Collapse
|
6
|
Samuels DS, Lybecker MC, Yang XF, Ouyang Z, Bourret TJ, Boyle WK, Stevenson B, Drecktrah D, Caimano MJ. Gene Regulation and Transcriptomics. Curr Issues Mol Biol 2020; 42:223-266. [PMID: 33300497 DOI: 10.21775/cimb.042.223] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Borrelia (Borreliella) burgdorferi, along with closely related species, is the etiologic agent of Lyme disease. The spirochete subsists in an enzootic cycle that encompasses acquisition from a vertebrate host to a tick vector and transmission from a tick vector to a vertebrate host. To adapt to its environment and persist in each phase of its enzootic cycle, B. burgdorferi wields three systems to regulate the expression of genes: the RpoN-RpoS alternative sigma factor cascade, the Hk1/Rrp1 two-component system and its product c-di-GMP, and the stringent response mediated by RelBbu and DksA. These regulatory systems respond to enzootic phase-specific signals and are controlled or fine- tuned by transcription factors, including BosR and BadR, as well as small RNAs, including DsrABb and Bb6S RNA. In addition, several other DNA-binding and RNA-binding proteins have been identified, although their functions have not all been defined. Global changes in gene expression revealed by high-throughput transcriptomic studies have elucidated various regulons, albeit technical obstacles have mostly limited this experimental approach to cultivated spirochetes. Regardless, we know that the spirochete, which carries a relatively small genome, regulates the expression of a considerable number of genes required for the transitions between the tick vector and the vertebrate host as well as the adaptation to each.
Collapse
Affiliation(s)
- D Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Meghan C Lybecker
- Department of Biology, University of Colorado, Colorado Springs, CO 80918, USA
| | - X Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Zhiming Ouyang
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Travis J Bourret
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, 68105 USA
| | - William K Boyle
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, 68105 USA
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY 40536, USA
| | - Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Melissa J Caimano
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
| |
Collapse
|