1
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Ha N, Lee EJ. Manganese Transporter Proteins in Salmonella enterica serovar Typhimurium. J Microbiol 2023; 61:289-296. [PMID: 36862278 DOI: 10.1007/s12275-023-00027-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 03/03/2023]
Abstract
The metal cofactors are essential for the function of many enzymes. The host restricts the metal acquisition of pathogens for their immunity and the pathogens have evolved many ways to obtain metal ions for their survival and growth. Salmonella enterica serovar Typhimurium also needs several metal cofactors for its survival, and manganese has been found to contribute to Salmonella pathogenesis. Manganese helps Salmonella withstand oxidative and nitrosative stresses. In addition, manganese affects glycolysis and the reductive TCA, which leads to the inhibition of energetic and biosynthetic metabolism. Therefore, manganese homeostasis is crucial for full virulence of Salmonella. Here, we summarize the current information about three importers and two exporters of manganese that have been identified in Salmonella. MntH, SitABCD, and ZupT have been shown to participate in manganese uptake. mntH and sitABCD are upregulated by low manganese concentration, oxidative stress, and host NRAMP1 level. mntH also contains a Mn2+-dependent riboswitch in its 5' UTR. Regulation of zupT expression requires further investigation. MntP and YiiP have been identified as manganese efflux proteins. mntP is transcriptionally activated by MntR at high manganese levels and repressed its activity by MntS at low manganese levels. Regulation of yiiP requires further analysis, but it has been shown that yiiP expression is not dependent on MntS. Besides these five transporters, there might be additional transporters that need to be identified.
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Affiliation(s)
- Nakyeong Ha
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.
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2
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Uppalapati SR, Vazquez-Torres A. Manganese Utilization in Salmonella Pathogenesis: Beyond the Canonical Antioxidant Response. Front Cell Dev Biol 2022; 10:924925. [PMID: 35903545 PMCID: PMC9315381 DOI: 10.3389/fcell.2022.924925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
The metal ion manganese (Mn2+) is equally coveted by hosts and bacterial pathogens. The host restricts Mn2+ in the gastrointestinal tract and Salmonella-containing vacuoles, as part of a process generally known as nutritional immunity. Salmonella enterica serovar Typhimurium counteract Mn2+ limitation using a plethora of metal importers, whose expression is under elaborate transcriptional and posttranscriptional control. Mn2+ serves as cofactor for a variety of enzymes involved in antioxidant defense or central metabolism. Because of its thermodynamic stability and low reactivity, bacterial pathogens may favor Mn2+-cofactored metalloenzymes during periods of oxidative stress. This divalent metal catalyzes metabolic flow through lower glycolysis, reductive tricarboxylic acid and the pentose phosphate pathway, thereby providing energetic, redox and biosynthetic outputs associated with the resistance of Salmonella to reactive oxygen species generated in the respiratory burst of professional phagocytic cells. Combined, the oxyradical-detoxifying properties of Mn2+ together with the ability of this divalent metal cation to support central metabolism help Salmonella colonize the mammalian gut and establish systemic infections.
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Affiliation(s)
- Siva R. Uppalapati
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO, United States,*Correspondence: Siva R. Uppalapati, ; Andres Vazquez-Torres,
| | - Andres Vazquez-Torres
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO, United States,Veterans Affairs Eastern Colorado Health Care System, Denver, CO, United States,*Correspondence: Siva R. Uppalapati, ; Andres Vazquez-Torres,
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3
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Mahendran G, Jayasinghe OT, Thavakumaran D, Arachchilage GM, Silva GN. Key players in regulatory RNA realm of bacteria. Biochem Biophys Rep 2022; 30:101276. [PMID: 35592614 PMCID: PMC9111926 DOI: 10.1016/j.bbrep.2022.101276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022] Open
Abstract
Precise regulation of gene expression is crucial for living cells to adapt for survival in diverse environmental conditions. Among the common cellular regulatory mechanisms, RNA-based regulators play a key role in all domains of life. Discovery of regulatory RNAs have made a paradigm shift in molecular biology as many regulatory functions of RNA have been identified beyond its canonical roles as messenger, ribosomal and transfer RNA. In the complex regulatory RNA network, riboswitches, small RNAs, and RNA thermometers can be identified as some of the key players. Herein, we review the discovery, mechanism, and potential therapeutic use of these classes of regulatory RNAs mainly found in bacteria. Being highly adaptive organisms that inhabit a broad range of ecological niches, bacteria have adopted tight and rapid-responding gene regulation mechanisms. This review aims to highlight how bacteria utilize versatile RNA structures and sequences to build a sophisticated gene regulation network. The three major classes of prokaryotic ncRNAs and their characterized mechanisms of operation in gene regulation. sRNAs emerging as major players in global gene regulatory networks. Riboswitch mediated gene control mechanisms through on/off switches in response to ligand binding. RNA thermo sensors for temperature-dependent gene expression. Therapeutic importance of ncRNAs and computational approaches involved in the discovery of ncRNAs.
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Affiliation(s)
- Gowthami Mahendran
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, 46556, USA
| | - Oshadhi T. Jayasinghe
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Dhanushika Thavakumaran
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, 46556, USA
| | - Gayan Mirihana Arachchilage
- Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520-8103, USA
- PTC Therapeutics Inc, South Plainfield, NJ, 07080, USA
| | - Gayathri N. Silva
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Corresponding author.
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4
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Bosma EF, Rau MH, van Gijtenbeek LA, Siedler S. Regulation and distinct physiological roles of manganese in bacteria. FEMS Microbiol Rev 2021; 45:6284802. [PMID: 34037759 PMCID: PMC8632737 DOI: 10.1093/femsre/fuab028] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
Manganese (Mn2+) is an essential trace element within organisms spanning the entire tree of life. In this review, we provide an overview of Mn2+ transport and the regulation of its homeostasis in bacteria, with a focus on its functions beyond being a cofactor for enzymes. Crucial differences in Mn2+ homeostasis exist between bacterial species that can be characterized to have an iron- or manganese-centric metabolism. Highly iron-centric species require minimal Mn2+ and mostly use it as a mechanism to cope with oxidative stress. As a consequence, tight regulation of Mn2+ uptake is required, while organisms that use both Fe2+ and Mn2+ need other layers of regulation for maintaining homeostasis. We will focus in detail on manganese-centric bacterial species, in particular lactobacilli, that require little to no Fe2+ and use Mn2+ for a wider variety of functions. These organisms can accumulate extraordinarily high amounts of Mn2+ intracellularly, enabling the nonenzymatic use of Mn2+ for decomposition of reactive oxygen species while simultaneously functioning as a mechanism of competitive exclusion. We further discuss how Mn2+ accumulation can provide both beneficial and pathogenic bacteria with advantages in thriving in their niches.
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Affiliation(s)
- Elleke F Bosma
- Chr. Hansen A/S, Discovery, R&D, 2970 Hoersholm, Denmark
| | - Martin H Rau
- Chr. Hansen A/S, Discovery, R&D, 2970 Hoersholm, Denmark
| | | | - Solvej Siedler
- Corresponding author: Boege Allé 10-12, 2970 Hoersholm, Denmark. Tel: +45 52 18 08 25; E-mail:
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5
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Kim Y, Wower J, Maltseva N, Chang C, Jedrzejczak R, Wilamowski M, Kang S, Nicolaescu V, Randall G, Michalska K, Joachimiak A. Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2. Commun Biol 2021; 4:193. [PMID: 33564093 PMCID: PMC7873276 DOI: 10.1038/s42003-021-01735-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 Nsp15 is a uridine-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family that is highly conserved in coronaviruses. As endoribonuclease activity seems to be responsible for the interference with the innate immune response, Nsp15 emerges as an attractive target for therapeutic intervention. Here we report the first structures with bound nucleotides and show how the enzyme specifically recognizes uridine moiety. In addition to a uridine site we present evidence for a second base binding site that can accommodate any base. The structure with a transition state analog, uridine vanadate, confirms interactions key to catalytic mechanisms. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. This acquired knowledge was instrumental in identifying Tipiracil, an FDA approved drug that is used in the treatment of colorectal cancer, as a potential anti-COVID-19 drug. Using crystallography, biochemical, and whole-cell assays, we demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme’s active site. Our findings provide new insights for the development of uracil scaffold-based drugs. Youngchang Kim, Jacek Wower, and colleagues explore the sequence specificity, metal ion dependence and catalytic mechanism of the Nsp15 endoribonuclease NendoU from SARS-CoV-2. The authors also solve five new crystal structures of the enzyme in complex with 5’UMP, 3’UMP, 5’cGpU, uridine 2′,3′-vanadate (transition state analog) and Tipiracil (uracil mimic), and demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme’s active site.
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Affiliation(s)
- Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Jacek Wower
- Department of Animal Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Changsoo Chang
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Mateusz Wilamowski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA
| | - Soowon Kang
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, 60367, USA
| | - Vlad Nicolaescu
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, 60367, USA
| | - Glenn Randall
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, 60367, USA
| | - Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA. .,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA. .,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA.
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6
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Scull CE, Dandpat SS, Romero RA, Walter NG. Transcriptional Riboswitches Integrate Timescales for Bacterial Gene Expression Control. Front Mol Biosci 2021; 7:607158. [PMID: 33521053 PMCID: PMC7838592 DOI: 10.3389/fmolb.2020.607158] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022] Open
Abstract
Transcriptional riboswitches involve RNA aptamers that are typically found in the 5' untranslated regions (UTRs) of bacterial mRNAs and form alternative secondary structures upon binding to cognate ligands. Alteration of the riboswitch's secondary structure results in perturbations of an adjacent expression platform that controls transcription elongation and termination, thus turning downstream gene expression "on" or "off." Riboswitch ligands are typically small metabolites, divalent cations, anions, signaling molecules, or other RNAs, and can be part of larger signaling cascades. The interconnectedness of ligand binding, RNA folding, RNA transcription, and gene expression empowers riboswitches to integrate cellular processes and environmental conditions across multiple timescales. For a successful response to an environmental cue that may determine a bacterium's chance of survival, a coordinated coupling of timescales from microseconds to minutes must be achieved. This review focuses on recent advances in our understanding of how riboswitches affect such critical gene expression control across time.
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Affiliation(s)
| | | | | | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States
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7
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de Freitas EC, Ucci AP, Teixeira EC, Pedroso GA, Hilario E, Bertolazzi Zocca VF, de Paiva GB, Ferreira H, Pedrolli DB, Bertolini MC. The copper-inducible copAB operon in Xanthomonas citri subsp. citri is regulated at transcriptional and translational levels. MICROBIOLOGY-SGM 2019; 165:355-365. [PMID: 30689540 DOI: 10.1099/mic.0.000767] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Upstream open reading frames (ORFs) are frequently found in the 5'-flanking regions of genes and may have a regulatory role in gene expression. A small ORF (named cohL here) was identified upstream from the copAB copper operon in Xanthomonascitri subsp. citri (Xac). We previously demonstrated that copAB expression was induced by copper and that gene inactivation produced a mutant strain that was unable to grow in the presence of copper. Here, we address the role of cohL in copAB expression control. We demonstrate that cohL expression is induced by copper in a copAB-independent manner. Although cohL is transcribed, the CohL protein is either not expressed in vivo or is synthesized at undetectable levels. Inactivation of cohL (X. citri cohL polar mutant strain) leads to an inability to synthesize cohL and copAB transcripts and consequently the inability to grow in the presence of copper. Bioinformatic tools predicted a stem-loop structure for the cohL-copAB intergenic region and revealed that this region may arrange itself in a secondary structure. Using in vitro gene expression, we found out that the structured 5'-UTR mRNA of copAB is responsible for sequestering the ribosome-binding site that drives the translation of copA. However, copper alone was not able to release the sequence. Based on the results, we speculate that cohL plays a role as a regulatory RNA rather than as a protein-coding gene.
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Affiliation(s)
- Eliane Cristina de Freitas
- 1Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-900, Araraquara, SP, Brazil
| | - Amanda Piovesan Ucci
- 1Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-900, Araraquara, SP, Brazil
| | - Elaine Cristina Teixeira
- 1Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-900, Araraquara, SP, Brazil
| | - Gisele Audrei Pedroso
- 1Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-900, Araraquara, SP, Brazil
| | - Eduardo Hilario
- 1Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-900, Araraquara, SP, Brazil.,†Present address: Department of Biochemistry, University of California, Riverside, CA, 92521-0129, USA
| | - Vitória Fernanda Bertolazzi Zocca
- 2Departamento de Bioprocessos e Biotecnologia, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista, UNESP, 14800-903, Araraquara, Brazil
| | - Gabriela Barbosa de Paiva
- 2Departamento de Bioprocessos e Biotecnologia, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista, UNESP, 14800-903, Araraquara, Brazil
| | - Henrique Ferreira
- 3Departamento de Bioquímica e Microbiologia, Instituto de Biociências, UNESP, Universidade Estadual Paulista, 13506-900, Rio Claro, SP, Brazil
| | - Danielle Biscaro Pedrolli
- 2Departamento de Bioprocessos e Biotecnologia, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista, UNESP, 14800-903, Araraquara, Brazil
| | - Maria Célia Bertolini
- 1Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-900, Araraquara, SP, Brazil
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8
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Sherwood AV, Henkin TM. Riboswitch-Mediated Gene Regulation: Novel RNA Architectures Dictate Gene Expression Responses. Annu Rev Microbiol 2017; 70:361-74. [PMID: 27607554 DOI: 10.1146/annurev-micro-091014-104306] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Riboswitches are RNA elements that act on the mRNA with which they are cotranscribed to modulate expression of that mRNA. These elements are widely found in bacteria, where they have a broad impact on gene expression. The defining feature of riboswitches is that they directly recognize a physiological signal, and the resulting shift in RNA structure affects gene regulation. The majority of riboswitches respond to cellular metabolites, often in a feedback loop to repress synthesis of the enzymes used to produce the metabolite. Related elements respond to the aminoacylation status of a specific tRNA or to a physical parameter, such as temperature or pH. Recent studies have identified new classes of riboswitches and have revealed new insights into the molecular mechanisms of signal recognition and gene regulation. Application of structural and biophysical approaches has complemented previous genetic and biochemical studies, yielding new information about how different riboswitches operate.
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Affiliation(s)
- Anna V Sherwood
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210; .,Molecular, Cellular and Developmental Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - Tina M Henkin
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210;
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9
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McCown PJ, Corbino KA, Stav S, Sherlock ME, Breaker RR. Riboswitch diversity and distribution. RNA (NEW YORK, N.Y.) 2017; 23:995-1011. [PMID: 28396576 PMCID: PMC5473149 DOI: 10.1261/rna.061234.117] [Citation(s) in RCA: 317] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/04/2017] [Indexed: 05/04/2023]
Abstract
Riboswitches are commonly used by bacteria to detect a variety of metabolites and ions to regulate gene expression. To date, nearly 40 different classes of riboswitches have been discovered, experimentally validated, and modeled at atomic resolution in complex with their cognate ligands. The research findings produced since the first riboswitch validation reports in 2002 reveal that these noncoding RNA domains exploit many different structural features to create binding pockets that are extremely selective for their target ligands. Some riboswitch classes are very common and are present in bacteria from nearly all lineages, whereas others are exceedingly rare and appear in only a few species whose DNA has been sequenced. Presented herein are the consensus sequences, structural models, and phylogenetic distributions for all validated riboswitch classes. Based on our findings, we predict that there are potentially many thousands of distinct bacterial riboswitch classes remaining to be discovered, but that the rarity of individual undiscovered classes will make it increasingly difficult to find additional examples of this RNA-based sensory and gene control mechanism.
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Affiliation(s)
- Phillip J McCown
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Keith A Corbino
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Shira Stav
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Madeline E Sherlock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
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10
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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11
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Wedekind JE, Dutta D, Belashov IA, Jenkins JL. Metalloriboswitches: RNA-based inorganic ion sensors that regulate genes. J Biol Chem 2017; 292:9441-9450. [PMID: 28455443 DOI: 10.1074/jbc.r117.787713] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Divalent ions fulfill essential cellular roles and are required for virulence by certain bacteria. Free intracellular Mg2+ can approach 5 mm, but at this level Mn2+, Ni2+, or Co2+ can be growth-inhibitory, and magnesium fluoride is toxic. To maintain ion homeostasis, many bacteria have evolved ion sensors embedded in the 5'-leader sequences of mRNAs encoding ion uptake or efflux channels. Here, we review current insights into these "metalloriboswitches," emphasizing ion-specific binding by structured RNA aptamers and associated conformational changes in downstream signal sequences. This riboswitch-effector interplay produces a layer of gene regulatory feedback that has elicited interest as an antibacterial target.
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Affiliation(s)
- Joseph E Wedekind
- From the Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Debapratim Dutta
- From the Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Ivan A Belashov
- From the Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Jermaine L Jenkins
- From the Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
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12
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Sokurenko Y, Ulyanova V, Zelenikhin P, Kolpakov A, Blokhin D, Müller D, Klochkov V, Ilinskaya O. The Role of Metals in the Reaction Catalyzed by Metal-Ion-Independent Bacillary RNase. Bioinorg Chem Appl 2016; 2016:4121960. [PMID: 28096759 PMCID: PMC5209602 DOI: 10.1155/2016/4121960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/27/2016] [Accepted: 11/02/2016] [Indexed: 11/18/2022] Open
Abstract
Extracellular enzymes of intestinal microbiota are the key agents that affect functional activity of the body as they directly interact with epithelial and immune cells. Several species of the Bacillus genus, like Bacillus pumilus, a common producer of extracellular RNase binase, can populate the intestinal microbiome as a colonizing organism. Without involving metal ions as cofactors, binase depolymerizes RNA by cleaving the 3',5'-phosphodiester bond and generates 2',3'-cyclic guanosine phosphates in the first stage of a catalytic reaction. Maintained in the reaction mixture for more than one hour, such messengers can affect the human intestinal microflora and the human body. In the present study, we found that the rate of 2',3'-cGMP was growing in the presence of transition metals that stabilized the RNA structure. At the same time, transition metal ions only marginally reduced the amount of 2',3'-cGMP, blocking binase recognition sites of guanine at N7 of nucleophilic purine bases.
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Affiliation(s)
- Yulia Sokurenko
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya Str. 18, Kazan 420008, Russia
| | - Vera Ulyanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya Str. 18, Kazan 420008, Russia
| | - Pavel Zelenikhin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya Str. 18, Kazan 420008, Russia
| | - Alexey Kolpakov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya Str. 18, Kazan 420008, Russia
| | - Dmitriy Blokhin
- Institute of Physics, Kazan Federal University, Kremlevskaya Str. 16a, Kazan 420008, Russia
| | - Dieter Müller
- Institute for Anatomy and Cell Biology, Justus Liebig University Giessen, Aulweg 123, 35385 Giessen, Germany
| | - Vladimir Klochkov
- Institute of Physics, Kazan Federal University, Kremlevskaya Str. 16a, Kazan 420008, Russia
| | - Olga Ilinskaya
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya Str. 18, Kazan 420008, Russia
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13
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Saunders AM, DeRose VJ. Beyond Mg 2+: functional interactions between RNA and transition metals. Curr Opin Chem Biol 2016; 34:152-158. [PMID: 27616014 DOI: 10.1016/j.cbpa.2016.07.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
It is well-known that RNA structure and function depend heavily on cations, and the ability of Mg2+ to stabilize RNA structures has been emphasized. Recent studies, however, highlight the importance of transition metals in RNA function. Riboswitches that selectively bind Ni2+, Co2+, and Mn2+ have been discovered with specific RNA-metal sites that influence metal-related gene expression. Exogenous metals such as Pt(II) from therapeutics also bind and may inhibit cellular RNA function. Novel reports that RNA can host Fe(II) in catalytic sites are relevant to early life in pre-oxygenic atmospheres. These new observations emphasize the importance of transition metals in the field of RNA metallobiochemistry.
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Affiliation(s)
- Adam M Saunders
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon Eugene, OR 97403, United States
| | - Victoria J DeRose
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon Eugene, OR 97403, United States.
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14
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Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR. Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. Mol Cell 2016; 57:1088-1098. [PMID: 25794617 DOI: 10.1016/j.molcel.2015.02.009] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/17/2014] [Accepted: 02/03/2015] [Indexed: 11/19/2022]
Abstract
Bacteria regularly encounter widely varying metal concentrations in their surrounding environment. As metals become depleted or, conversely, accrue to toxicity, microbes will activate cellular responses that act to maintain metal homeostasis. A suite of metal-sensing regulatory ("metalloregulatory") proteins orchestrate these responses by allosterically coupling the selective binding of target metals to the activity of DNA-binding domains. However, we report here the discovery, validation, and structural details of a widespread class of riboswitch RNAs, whose members selectively and tightly bind the low-abundance transition metals, Ni(2+) and Co(2+). These riboswitches bind metal cooperatively, and with affinities in the low micromolar range. The structure of a Co(2+)-bound RNA reveals a network of molecular contacts that explains how it achieves cooperative binding between adjacent sites. These findings reveal that bacteria have evolved to utilize highly selective metalloregulatory riboswitches, in addition to metalloregulatory proteins, for detecting and responding to toxic levels of heavy metals.
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Affiliation(s)
- Kazuhiro Furukawa
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Arati Ramesh
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhiyuan Zhou
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Zasha Weinberg
- Howard Hughes Medical Institute, New Haven, CT 06520, USA
| | - Tenaya Vallery
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Wade C Winkler
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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15
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Dambach M, Sandoval M, Updegrove TB, Anantharaman V, Aravind L, Waters LS, Storz G. The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element. Mol Cell 2016; 57:1099-1109. [PMID: 25794618 DOI: 10.1016/j.molcel.2015.01.035] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/17/2014] [Accepted: 01/23/2015] [Indexed: 11/18/2022]
Abstract
The highly structured, cis-encoded RNA elements known as riboswitches modify gene expression upon binding a wide range of molecules. The yybP-ykoY motif was one of the most broadly distributed and numerous bacterial riboswitches for which the cognate ligand was unknown. Using a combination of in vivo reporter and in vitro expression assays, equilibrium dialysis, and northern analysis, we show that the yybP-ykoY motif responds directly to manganese ions in both Escherichia coli and Bacillus subtilis. The identification of the yybP-ykoY motif as a manganese ion sensor suggests that the genes that are preceded by this motif and encode a diverse set of poorly characterized membrane proteins have roles in metal homeostasis.
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Affiliation(s)
- Michael Dambach
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
| | - Melissa Sandoval
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
| | - Taylor B Updegrove
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Lauren S Waters
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
- Department of Chemistry, University of Wisconsin Oshkosh, Oshkosh, WI 54901, USA
| | - Gisela Storz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
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16
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Saunders AM, DeRose VJ. Beyond Mg(2+): functional interactions between RNA and transition metals. Curr Opin Chem Biol 2016; 31:153-9. [PMID: 27031926 DOI: 10.1016/j.cbpa.2016.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/25/2016] [Indexed: 12/19/2022]
Abstract
It is well-known that RNA structure and function depend heavily on cations, and the ability of Mg(2+) to stabilize RNA structures has been emphasized. Recent studies, however, highlight the importance of transition metals in RNA function. Riboswitches that selectively bind Ni(2+), Co(2+), and Mn(2+) have been discovered with specific RNA-metal sites that influence metal-related gene expression. Exogenous metals such as Pt(II) from therapeutics also bind and may inhibit cellular RNA. Novel reports that RNA can host Fe(II) in catalytic sites are relevant to early life in pre-oxygenic atmospheres. These new observations emphasize the importance of transition metals in the field of RNA metallobiochemistry.
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Affiliation(s)
- Adam M Saunders
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon Eugene, OR 97403, United States
| | - Victoria J DeRose
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon Eugene, OR 97403, United States.
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17
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Rinaldi AJ, Lund PE, Blanco MR, Walter NG. The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts. Nat Commun 2016; 7:8976. [PMID: 26781350 PMCID: PMC4735710 DOI: 10.1038/ncomms9976] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/21/2015] [Indexed: 01/20/2023] Open
Abstract
In response to intracellular signals in Gram-negative bacteria, translational riboswitches—commonly embedded in messenger RNAs (mRNAs)—regulate gene expression through inhibition of translation initiation. It is generally thought that this regulation originates from occlusion of the Shine-Dalgarno (SD) sequence upon ligand binding; however, little direct evidence exists. Here we develop Single Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) to investigate the ligand-dependent accessibility of the SD sequence of an mRNA hosting the 7-aminomethyl-7-deazaguanine (preQ1)-sensing riboswitch. Spike train analysis reveals that individual mRNA molecules alternate between two conformational states, distinguished by ‘bursts' of probe binding associated with increased SD sequence accessibility. Addition of preQ1 decreases the lifetime of the SD's high-accessibility (bursting) state and prolongs the time between bursts. In addition, ligand-jump experiments reveal imperfect riboswitching of single mRNA molecules. Such complex ligand sensing by individual mRNA molecules rationalizes the nuanced ligand response observed during bulk mRNA translation. In response to intracellular signals, bacterial translational riboswitches embedded in mRNAs can regulate gene expression through inhibition of translation initiation. Here, the authors describe SiM-KARTS, a novel approach for detecting changes in the structure of single RNA molecules in response to a ligand.
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Affiliation(s)
- Arlie J Rinaldi
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Paul E Lund
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Mario R Blanco
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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