1
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Bushhouse DZ, Fu J, Lucks JB. RNA folding kinetics control riboswitch sensitivity in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587317. [PMID: 38585885 PMCID: PMC10996619 DOI: 10.1101/2024.03.29.587317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Riboswitches are ligand-responsive gene-regulatory RNA elements that perform key roles in maintaining cellular homeostasis. Understanding how riboswitch sensitivity is controlled is critical to understanding how highly conserved aptamer domains are deployed in a variety of contexts with different sensitivity demands. Here we uncover new roles by which RNA folding dynamics control riboswitch sensitivity in cells. By investigating the Clostridium beijerinckii pfl ZTP riboswitch, we identify multiple mechanistic routes of altering expression platform sequence and structure to slow RNA folding, all of which enhance riboswitch sensitivity. Applying these methods to riboswitches with diverse aptamer architectures that regulate transcription and translation with ON and OFF logic demonstrates the generality of our findings, indicating that any riboswitch that operates in a kinetic regime can be sensitized by slowing expression platform folding. Comparison of the most sensitized versions of these switches to equilibrium aptamer:ligand dissociation constants suggests a limit to the sensitivities achievable by kinetic RNA switches. Our results add to the growing suite of knowledge and approaches that can be used to rationally program cotranscriptional RNA folding for biotechnology applications, and suggest general RNA folding principles for understanding dynamic RNA systems in other areas of biology.
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Affiliation(s)
- David Z. Bushhouse
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
| | - Jiayu Fu
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
| | - Julius B. Lucks
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA
- Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, Illinois 60208, USA
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, USA
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2
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Blechar J, de Jesus V, Fürtig B, Hengesbach M, Schwalbe H. Shine-Dalgarno Accessibility Governs Ribosome Binding to the Adenine Riboswitch. ACS Chem Biol 2024; 19:607-618. [PMID: 38412235 DOI: 10.1021/acschembio.3c00435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Translational riboswitches located in the 5' UTR of the messenger RNA (mRNA) regulate translation through variation of the accessibility of the ribosome binding site (RBS). These are the result of conformational changes in the riboswitch RNA governed by ligand binding. Here, we use a combination of single-molecule colocalization techniques (Single-Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) and Single-Molecule Kinetic Analysis of Ribosome Binding (SiM-KARB)) and microscale thermophoresis (MST) to investigate the adenine-sensing riboswitch in Vibrio vulnificus, focusing on the changes of accessibility between the ligand-free and ligand-bound states. We show that both methods faithfully report on the accessibility of the RBS within the riboswitch and that both methods identify an increase in accessibility upon adenine binding. Expanding on the regulatory context, we show the impact of the ribosomal protein S1 on the unwinding of the RNA secondary structure, thereby favoring ribosome binding even for the apo state. The determined rate constants suggest that binding of the ribosome is faster than the time required to change from the ON state to the OFF state, a prerequisite for efficient regulation decision.
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Affiliation(s)
- Julius Blechar
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
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3
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Salvail H, Balaji A, Roth A, Breaker RR. A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine. Cell Rep 2023; 42:113571. [PMID: 38096053 PMCID: PMC10853860 DOI: 10.1016/j.celrep.2023.113571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Natural polyamines such as spermidine and spermine cations have characteristics that make them highly likely to be sensed by riboswitches, such as their general affinity to polyanionic RNA and their broad contributions to cell physiology. Despite previous claims that polyamine riboswitches exist, evidence of their biological functions has remained unconvincing. Here, we report that rare variants of bacterial S-adenosylmethionine-I (SAM-I) riboswitches reject SAM and have adapted to selectively sense spermidine. These spermidine-sensing riboswitch variants are associated with genes whose protein products are directly involved in the production of spermidine and other polyamines. Biochemical and genetic assays demonstrate that representatives of this riboswitch class robustly function as genetic "off" switches, wherein spermidine binding causes premature transcription termination to suppress the expression of polyamine biosynthetic genes. These findings confirm the existence of natural spermidine-sensing riboswitches in bacteria and expand the list of variant riboswitch classes that have adapted to bind different ligands.
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Affiliation(s)
- Hubert Salvail
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Aparaajita Balaji
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Adam Roth
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA.
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4
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Huang Y, Chen M, Hu G, Wu B, He M. Elimination of editing plasmid mediated by theophylline riboswitch in Zymomonas mobilis. Appl Microbiol Biotechnol 2023; 107:7151-7163. [PMID: 37728624 DOI: 10.1007/s00253-023-12783-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/23/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023]
Abstract
Zymomonas mobilis is regarded as a potential chassis for the production of platform chemicals. Genome editing using the CRISPR-Cas system could meet the need for gene modification in metabolic engineering. However, the low curing efficiency of CRISPR editing plasmid is a common bottleneck in Z. mobilis. In this study, we utilized a theophylline-dependent riboswitch to regulate the expression of the replicase gene of the editing plasmid, thereby promoting the elimination of exogeneous plasmid. The riboswitch D (RSD) with rigorous regulatory ability was identified as the optimal candidate by comparing the transformation efficiency of four theophylline riboswitch-based backbone editing plasmids, and the optimal theophylline concentration for inducing RSD was determined to be 2 mM. A highly effective method for eliminating the editing plasmid, cells with RSD-based editing plasmid which were cultured in liquid and solid RM media in alternating passages at 37 °C without shaking, was established by testing the curing efficiency of backbone editing plasmids pMini and pMini-RSD in RM medium with or without theophylline at 30 °C or 37 °C. Finally, the RSD-based editing plasmid was applied to genome editing, resulting in an increase of more than 10% in plasmid elimination efficiency compared to that of pMini-based editing plasmid. KEY POINTS: • An effective strategy for curing CRISPR editing plasmid has been established in Z. mobilis. • Elimination efficiency of the CRISPR editing plasmid was enhanced by 10% to 20% under the regulation of theophylline-dependent riboswitch RSD.
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Affiliation(s)
- Yuhuan Huang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Mao Chen
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, China.
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, China.
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5
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Xu J, Hou J, Ding M, Wang Z, Chen T. Riboswitches, from cognition to transformation. Synth Syst Biotechnol 2023; 8:357-370. [PMID: 37325181 PMCID: PMC10265488 DOI: 10.1016/j.synbio.2023.05.008] [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: 03/01/2023] [Revised: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
Riboswitches are functional RNA elements that regulate gene expression by directly detecting metabolites. Twenty years have passed since it was first discovered, researches on riboswitches are becoming increasingly standardized and refined, which could significantly promote people's cognition of RNA function as well. Here, we focus on some representative orphan riboswitches, enumerate the structural and functional transformation and artificial design of riboswitches including the coupling with ribozymes, hoping to attain a comprehensive understanding of riboswitch research.
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Affiliation(s)
- Jingdong Xu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Junyuan Hou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Mengnan Ding
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Zhiwen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Tao Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300350, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
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6
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Kumar A, Vashisth H. Mechanism of Ligand Discrimination by the NMT1 Riboswitch. J Chem Inf Model 2023; 63:4864-4874. [PMID: 37486304 PMCID: PMC11088486 DOI: 10.1021/acs.jcim.3c00835] [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] [Indexed: 07/25/2023]
Abstract
Riboswitches are conserved functional domains in mRNA that almost exclusively exist in bacteria. They regulate the biosynthesis and transport of amino acids and essential metabolites such as coenzymes, nucleobases, and their derivatives by specifically binding small molecules. Due to their ability to precisely discriminate between different cognate molecules as well as their common existence in bacteria, riboswitches have become potential antibacterial drug targets that could deliver urgently needed antibiotics with novel mechanisms of action. In this work, we report the recognition mechanisms of four oxidization products (XAN, AZA, UAC, and HPA) generated during purine degradation by an RNA motif termed the NMT1 riboswitch. Specifically, we investigated the physical interactions between the riboswitch and the oxidized metabolites by computing the changes in the free energy on mutating key nucleobases in the ligand binding pocket of the riboswitch. We discovered that the electrostatic interactions are central to ligand discrimination by this riboswitch. The relative binding free energies of the mutations further indicated that some of the mutations can also strengthen the binding affinities of the ligands (AZA, UAC, and HPA). These mechanistic details are also potentially relevant in the design of novel compounds targeting riboswitches.
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Affiliation(s)
- Amit Kumar
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire 03824, United States
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7
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Wakchaure PD, Ganguly B. Exploring the structure, function of thiamine pyrophosphate riboswitch, and designing small molecules for antibacterial activity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1774. [PMID: 36594112 DOI: 10.1002/wrna.1774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/10/2022] [Accepted: 12/15/2022] [Indexed: 01/04/2023]
Abstract
During the last decade, riboswitches emerged as new small-molecule sensing RNA in bacteria. Thiamine pyrophosphate (TPP) riboswitch is widely distributed and occurs in plants, bacteria, fungi, and archaea. Extensive biochemical, structural, and genetic studies have been carried out to elucidate the recognition mechanism of TPP riboswitches. However, a comprehensive report summarizing all information on recognition principles and newly designed ligands for TPP riboswitch is scarce in the literature. This review gives a comprehensive understanding of the TPP riboswitch's structure, mechanism, and methods applied to design ligands for the TPP riboswitch. The ligand-bound TPP riboswitch was studied with various experimental and theoretical techniques to elucidate the conformational dynamics. The mutation studies shed light on the significance of pyrimidine sensing helix for the binding of ligands. Further, the structure-activity relationship study and fragment-based approach lead to the development of ligands with Kd values at the sub-micromolar level. However, there is a need to design more potent inhibitors for TPP riboswitch for therapeutic applications. The recent advancements in ligand design highlight the TPP riboswitch as a promising target for developing new antibiotics. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Riboswitches Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Padmaja D Wakchaure
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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8
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Tanniche I, Nazem-Bokaee H, Scherr DM, Schlemmer S, Senger RS. A novel synthetic sRNA promoting protein overexpression in cell-free systems. Biotechnol Prog 2023; 39:e3324. [PMID: 36651906 DOI: 10.1002/btpr.3324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/31/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Bacterial small RNAs (sRNAs) that regulate gene expression have been engineered for uses in synthetic biology and metabolic engineering. Here, we designed a novel non-Hfq-dependent sRNA scaffold that uses a modifiable 20 nucleotide antisense binding region to target mRNAs selectively and influence protein expression. The system was developed for regulation of a fluorescent reporter in vivo using Escherichia coli, but the system was found to be more responsive and produced statistically significant results when applied to protein synthesis using in vitro cell-free systems (CFS). Antisense binding sequences were designed to target not only translation initiation regions but various secondary structures in the reporter mRNA. Targeting a high-energy stem loop structure and the 3' end of mRNA yielded protein expression knock-downs that approached 70%. Notably, targeting a low-energy stem structure near a potential RNase E binding site led to a statistically significant 65% increase in protein expression (p < 0.05). These results were not obtainable in vivo, and the underlying mechanism was translated from the reporter system to achieve better than 75% increase in recombinant diaphorase expression in a CFS. It is possible the designs developed here can be applied to improve/regulate expression of other proteins in a CFS.
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Affiliation(s)
- Imen Tanniche
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
- School of Plant & Environmental Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Hadi Nazem-Bokaee
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
- CSIRO, Black Mountain Science & Innovation Park, Canberra, Australia
| | - David M Scherr
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Sara Schlemmer
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Ryan S Senger
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia, USA
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9
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Amadei F, Reichenbach M, Gallo S, Sigel RKO. The structural features of the ligand-free moaA riboswitch and its ion-dependent folding. J Inorg Biochem 2023; 242:112153. [PMID: 36774787 DOI: 10.1016/j.jinorgbio.2023.112153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/02/2023]
Abstract
Riboswitches are structural elements of mRNA involved in the regulation of gene expression by responding to specific cellular metabolites. To fulfil their regulatory function, riboswitches prefold into an active state, the so-called binding competent form, that guarantees metabolite binding and allows a consecutive refolding of the RNA. Here, we describe the folding pathway to the binding competent form as well as the ligand free structure of the moaA riboswitch of E. coli. This RNA proposedly responds to the molybdenum cofactor (Moco), a highly oxygen-sensitive metabolite, essential in the carbon and sulfur cycles of eukaryotes. K+- and Mg2+-dependent footprinting assays and spectroscopic investigations show a high degree of structure formation of this RNA already at very low ion-concentrations. Mg2+ facilitates additionally a general compaction of the riboswitch towards its proposed active structure. We show that this fold agrees with the earlier suggested secondary structure which included also a long-range tetraloop/tetraloop-receptor like interaction. Metal ion cleavage assays revealed specific Mg2+-binding pockets within the moaA riboswitch. These Mg2+ binding pockets are good indicators for the potential Moco binding site, since in riboswitches, Mg2+ was shown to be necessary to bind phosphate-carrying metabolites. The importance of the phosphate and of other functional groups of Moco is highlighted by binding assays with tetrahydrobiopterin, the reduced and oxygen-sensitive core moiety of Moco. We demonstrate that the general molecular shape of pterin by its own is insufficient for the recognition by the riboswitch.
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Affiliation(s)
- Fabio Amadei
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - María Reichenbach
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sofia Gallo
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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10
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Kim W, Kim M, Park W. Unlocking the mystery of lysine toxicity on Microcystis aeruginosa. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130932. [PMID: 36860069 DOI: 10.1016/j.jhazmat.2023.130932] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Lysine toxicity on certain groups of bacterial cells has been recognized for many years, but the detailed molecular mechanisms that drive this phenomenon have not been elucidated. Many cyanobacteria including Microcystis aeruginosa cannot efficiently export and degrade lysine, although they have evolved to maintain a single copy of the lysine uptake system through which arginine or ornithine can also be transported into the cytoplasm. Autoradiographic analysis using 14C-l-lysine confirmed that lysine was competitively uptaken into cells with arginine or ornithine, which explained the arginine or ornithine-mediated alleviation of lysine toxicity in M. aeruginosa. A relatively non-specific MurE amino acid ligase could incorporate l-lysine into the 3rd position of UDP-N-acetylmuramyl-tripeptide by replacing meso-diaminopimelic acid during the stepwise addition of amino acids on peptidoglycan (PG) biosynthesis. However, further transpeptidation was blocked because lysine substitution at the pentapeptide of the cell wall inhibited the activity of transpeptidases. The leaky PG structure caused irreversible damage to the photosynthetic system and membrane integrity. Collectively, our results suggest that a lysine-mediated coarse-grained PG network and the absence of concrete septal PG lead to the death of slow-growing cyanobacteria.
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Affiliation(s)
- Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea.
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11
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Lu B, Guo Z, Zhong K, Osire T, Sun Y, Jiang L. State of the art in CRISPR/Cas system-based signal conversion and amplification applied in the field of food analysis. Trends Food Sci Technol 2023. [DOI: 10.1016/j.tifs.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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12
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Mao C, Mao Y, Zhu X, Chen G, Feng C. Synthetic biology-based bioreactor and its application in biochemical analysis. Crit Rev Anal Chem 2023:1-18. [PMID: 36803337 DOI: 10.1080/10408347.2023.2180319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
In the past few years, synthetic biologists have established some biological elements and bioreactors composed of nucleotides under the guidance of engineering methods. Following the concept of engineering, the common bioreactor components in recent years are introduced and compared. At present, biosensors based on synthetic biology have been applied to water pollution monitoring, disease diagnosis, epidemiological monitoring, biochemical analysis and other detection fields. In this paper, the biosensor components based on synthetic bioreactors and reporters are reviewed. In addition, the applications of biosensors based on cell system and cell-free system in the detection of heavy metal ions, nucleic acid, antibiotics and other substances are presented. Finally, the bottlenecks faced by biosensors and the direction of optimization are also discussed.
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Affiliation(s)
- Changqing Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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13
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Wang X, Fang C, Wang Y, Shi X, Yu F, Xiong J, Chou SH, He J. Systematic Comparison and Rational Design of Theophylline Riboswitches for Effective Gene Repression. Microbiol Spectr 2023; 11:e0275222. [PMID: 36688639 PMCID: PMC9927458 DOI: 10.1128/spectrum.02752-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Riboswitches are promising regulatory tools in synthetic biology. To date, 25 theophylline riboswitches have been developed for regulation of gene expression in bacteria. However, no one has systematically evaluated their regulatory effects. To promote efficient selection and application of theophylline riboswitches, we examined 25 theophylline riboswitches in Escherichia coli MG1655 and found that they varied widely in terms of activation/repression ratios and expression levels in the absence of theophylline. Of the 20 riboswitches that activate gene expression, only one exhibited a high activation ratio (63.6-fold) and low expression level without theophylline. Furthermore, none of the five riboswitches that repress gene expression were more than 2.0-fold efficient. To obtain an effective repression system, we rationally designed a novel theophylline riboswitch to control a downstream gene or genes by premature transcription termination. This riboswitch allowed theophylline-dependent downregulation of the TurboRFP reporter in a dose- and time-dependent manner. Its performance profile exceeded those of previously described repressive theophylline riboswitches. We then introduced as the second part a RepA tag (protein degradation tag) coding sequence fused at the 5'-terminal end of the turborfp gene, which further reduced protein level, while not reducing the repressive effect of the riboswitch. By combining two tandem theophylline riboswitches with a RepA tag, we constructed a regulatory cassette that represses the expression of the gene(s) of interest at both the transcriptional and posttranslational levels. This regulatory cassette can be used to repress the expression of any gene of interest and represents a crucial step toward harnessing theophylline riboswitches and expanding the synthetic biology toolbox. IMPORTANCE A variety of gene expression regulation tools with significant regulatory effects are essential for the construction of complex gene circuits in synthetic biology. Riboswitches have received wide attention due to their unique biochemical, structural, and genetic properties. Here, we have not only systematically and precisely characterized the regulatory properties of previously developed theophylline riboswitches but also engineered a novel repressive theophylline riboswitch acting at the transcriptional level. By introducing coding sequences of a tandem riboswitch and a RepA protein degradation tag at the 5' end of the reporter gene, we successfully constructed a simple and effective regulatory cassette for gene regulation. Our work provides useful biological components for the construction of synthetic biology gene circuits.
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Affiliation(s)
- Xun Wang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Can Fang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Yifei Wang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Xinyu Shi
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Fan Yu
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Jin Xiong
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
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14
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Kavita K, Breaker RR. Discovering riboswitches: the past and the future. Trends Biochem Sci 2023; 48:119-141. [PMID: 36150954 PMCID: PMC10043782 DOI: 10.1016/j.tibs.2022.08.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 01/25/2023]
Abstract
Riboswitches are structured noncoding RNA domains used by many bacteria to monitor the concentrations of target ligands and regulate gene expression accordingly. In the past 20 years over 55 distinct classes of natural riboswitches have been discovered that selectively sense small molecules or elemental ions, and thousands more are predicted to exist. Evidence suggests that some riboswitches might be direct descendants of the RNA-based sensors and switches that were likely present in ancient organisms before the evolutionary emergence of proteins. We provide an overview of the current state of riboswitch research, focusing primarily on the discovery of riboswitches, and speculate on the major challenges facing researchers in the field.
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Affiliation(s)
- Kumari Kavita
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA.
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15
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Xu L, Xiao Y, Zhang J, Fang X. Structural insights into translation regulation by the THF-II riboswitch. Nucleic Acids Res 2023; 51:952-965. [PMID: 36620887 PMCID: PMC9881143 DOI: 10.1093/nar/gkac1257] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
In bacteria, expression of folate-related genes is controlled by the tetrahydrofolate (THF) riboswitch in response to specific binding of THF and its derivatives. Recently, a second class of THF riboswitches, named THF-II, was identified in Gram-negative bacteria, which exhibit distinct architecture from the previously characterized THF-I riboswitches found in Gram-positive bacteria. Here, we present the crystal structures of the ligand-bound THF-II riboswitch from Mesorhizobium loti. These structures exhibit a long rod-like fold stabilized by continuous base pair and base triplet stacking across two helices of P1 and P2 and their interconnecting ligand-bound binding pocket. The pterin moiety of the ligand docks into the binding pocket by forming hydrogen bonds with two highly conserved pyrimidines in J12 and J21, which resembles the hydrogen-bonding pattern at the ligand-binding site FAPK in the THF-I riboswitch. Using small-angle X-ray scattering and isothermal titration calorimetry, we further characterized the riboswitch in solution and reveal that Mg2+ is essential for pre-organization of the binding pocket for efficient ligand binding. RNase H cleavage assay indicates that ligand binding reduces accessibility of the ribosome binding site in the right arm of P1, thus down-regulating the expression of downstream genes. Together, these results provide mechanistic insights into translation regulation by the THF-II riboswitch.
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Affiliation(s)
| | | | - Jie Zhang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China,Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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16
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Serrano-Gutiérrez M, Merino E. Antisense-acting riboswitches: A poorly characterized yet important model of transcriptional regulation in prokaryotic organisms. PLoS One 2023; 18:e0281744. [PMID: 36809273 PMCID: PMC9943018 DOI: 10.1371/journal.pone.0281744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Riboswitches are RNA elements involved in regulating genes that participate in the biosynthesis or transport of essential metabolites. They are characterized by their ability to recognize their target molecules with high affinity and specificity. Riboswitches are commonly cotranscribed with their target genes and are located at the 5' end of their transcriptional units. To date, only two exceptional cases of riboswitches being situated at the 3' end and transcribing in the antisense direction of their regulated genes have been described. The first case involves a SAM riboswitch located at the 3' end of the ubiG-mccB-mccA operon in Clostridium acetobutylicum involved in converting methionine to cysteine. The second case concerns a Cobalamin riboswitch in Listeria monocytogenes that regulates the transcription factor PocR related to this organism's pathogenic process. In almost a decade since the first descriptions of antisense-acting riboswitches, no new examples have been described. In this work, we performed a computational analysis to identify new examples of antisense-acting riboswitches. We found 292 cases in which, according to the available information, we infer that the expected regulation of the riboswitch is consistent with the signaling molecule it senses and the metabolic function of the regulated gene. The metabolic implications of this novel type of regulation are thoroughly discussed.
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Affiliation(s)
- Mariela Serrano-Gutiérrez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Enrique Merino
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail:
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17
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Sherlock ME, Higgs G, Yu D, Widner DL, White NA, Sudarsan N, Sadeeshkumar H, Perkins KR, Mirihana Arachchilage G, Malkowski SN, King CG, Harris KA, Gaffield G, Atilho RM, Breaker RR. Architectures and complex functions of tandem riboswitches. RNA Biol 2022; 19:1059-1076. [PMID: 36093908 PMCID: PMC9481103 DOI: 10.1080/15476286.2022.2119017] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Riboswitch architectures that involve the binding of a single ligand to a single RNA aptamer domain result in ordinary dose-response curves that require approximately a 100-fold change in ligand concentration to cover nearly the full dynamic range for gene regulation. However, by using multiple riboswitches or aptamer domains in tandem, these ligand-sensing structures can produce additional, complex gene control outcomes. In the current study, we have computationally searched for tandem riboswitch architectures in bacteria to provide a more complete understanding of the diverse biological and biochemical functions of gene control elements that are made exclusively of RNA. Numerous different arrangements of tandem homologous riboswitch architectures are exploited by bacteria to create more ‘digital’ gene control devices, which operate over a narrower ligand concentration range. Also, two heterologous riboswitch aptamers are sometimes employed to create two-input Boolean logic gates with various types of genetic outputs. These findings illustrate the sophisticated genetic decisions that can be made by using molecular sensors and switches based only on RNA.
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Affiliation(s)
- Madeline E. Sherlock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Research-1S, Aurora, CO, USA
| | - Gadareth Higgs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Diane Yu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Danielle L. Widner
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Neil A. White
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Harini Sadeeshkumar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Kevin R. Perkins
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Gayan Mirihana Arachchilage
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
- PTC Therapeutics, Inc, South Plainfield, NJ, USA
| | | | - Christopher G. King
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Glenn Gaffield
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Ruben M. Atilho
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Ronald R. Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
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18
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Rütten A, Kirchner T, Musiol-Kroll EM. Overview on Strategies and Assays for Antibiotic Discovery. Pharmaceuticals (Basel) 2022; 15:1302. [PMID: 36297414 PMCID: PMC9607151 DOI: 10.3390/ph15101302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
The increase in antibiotic resistance poses a major threat to global health. Actinomycetes, the Gram-positive bacteria of the order Actinomycetales, are fertile producers of bioactive secondary metabolites, including antibiotics. Nearly two-thirds of antibiotics that are used for the treatment of bacterial infections were originally isolated from actinomycetes strains belonging to the genus Streptomyces. This emphasizes the importance of actinomycetes in antibiotic discovery. However, the identification of a new antimicrobial compound and the exploration of its mode of action are very challenging tasks. Therefore, different approaches that enable the "detection" of an antibiotic and the characterization of the mechanisms leading to the biological activity are indispensable. Beyond bioinformatics tools facilitating the identification of biosynthetic gene clusters (BGCs), whole cell-screenings-in which cells are exposed to actinomycete-derived compounds-are a common strategy applied at the very early stage in antibiotic drug development. More recently, target-based approaches have been established. In this case, the drug candidates were tested for interactions with usually validated targets. This review focuses on the bioactivity-based screening methods and provides the readers with an overview on the most relevant assays for the identification of antibiotic activity and investigation of mechanisms of action. Moreover, the article includes examples of the successful application of these methods and suggestions for improvement.
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Affiliation(s)
- Anika Rütten
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Teresa Kirchner
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Ewa Maria Musiol-Kroll
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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19
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Sharma P, Mondal K, Kumar S, Tamang S, Najar IN, Das S, Thakur N. RNA thermometers in bacteria: Role in thermoregulation. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022; 1865:194871. [DOI: 10.1016/j.bbagrm.2022.194871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 04/09/2023]
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20
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RNA secondary structure packages evaluated and improved by high-throughput experiments. Nat Methods 2022; 19:1234-1242. [PMID: 36192461 PMCID: PMC9839360 DOI: 10.1038/s41592-022-01605-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Despite the popularity of computer-aided study and design of RNA molecules, little is known about the accuracy of commonly used structure modeling packages in tasks sensitive to ensemble properties of RNA. Here, we demonstrate that the EternaBench dataset, a set of more than 20,000 synthetic RNA constructs designed on the RNA design platform Eterna, provides incisive discriminative power in evaluating current packages in ensemble-oriented structure prediction tasks. We find that CONTRAfold and RNAsoft, packages with parameters derived through statistical learning, achieve consistently higher accuracy than more widely used packages in their standard settings, which derive parameters primarily from thermodynamic experiments. We hypothesized that training a multitask model with the varied data types in EternaBench might improve inference on ensemble-based prediction tasks. Indeed, the resulting model, named EternaFold, demonstrated improved performance that generalizes to diverse external datasets including complete messenger RNAs, viral genomes probed in human cells and synthetic designs modeling mRNA vaccines.
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21
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Giarimoglou N, Kouvela A, Maniatis A, Papakyriakou A, Zhang J, Stamatopoulou V, Stathopoulos C. A Riboswitch-Driven Era of New Antibacterials. Antibiotics (Basel) 2022; 11:antibiotics11091243. [PMID: 36140022 PMCID: PMC9495366 DOI: 10.3390/antibiotics11091243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/26/2022] Open
Abstract
Riboswitches are structured non-coding RNAs found in the 5′ UTR of important genes for bacterial metabolism, virulence and survival. Upon the binding of specific ligands that can vary from simple ions to complex molecules such as nucleotides and tRNAs, riboswitches change their local and global mRNA conformations to affect downstream transcription or translation. Due to their dynamic nature and central regulatory role in bacterial metabolism, riboswitches have been exploited as novel RNA-based targets for the development of new generation antibacterials that can overcome drug-resistance problems. During recent years, several important riboswitch structures from many bacterial representatives, including several prominent human pathogens, have shown that riboswitches are ideal RNA targets for new compounds that can interfere with their structure and function, exhibiting much reduced resistance over time. Most interestingly, mainstream antibiotics that target the ribosome have been shown to effectively modulate the regulatory behavior and capacity of several riboswitches, both in vivo and in vitro, emphasizing the need for more in-depth studies and biological evaluation of new antibiotics. Herein, we summarize the currently known compounds that target several main riboswitches and discuss the role of mainstream antibiotics as modulators of T-box riboswitches, in the dawn of an era of novel inhibitors that target important bacterial regulatory RNAs.
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Affiliation(s)
- Nikoleta Giarimoglou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Adamantia Kouvela
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Alexandros Maniatis
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi, 15341 Athens, Greece
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
- Correspondence: ; Tel.: +30-2610-997932
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22
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Streptococcus suis TrpX is part of a tryptophan uptake system, and its expression is regulated by a T-box regulatory element. Sci Rep 2022; 12:13920. [PMID: 35978073 PMCID: PMC9382623 DOI: 10.1038/s41598-022-18227-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
Streptococcus suis, a common member of the porcine respiratory microbiota, can cause life-threatening diseases in pigs as well as humans. A previous study identified the gene trpX as conditionally essential for in vivo survival by intrathecal infection of pigs with a transposon library of S. suis strain 10. Here, we characterized trpX, encoding a putative tryptophan/tyrosine transport system substrate-binding protein, in more detail. We compared growth capacities of the isogenic trpX-deficient mutant derivative strain 10∆trpX with its parent. Growth experiments in chemically defined media (CDM) revealed that growth of 10∆trpX depended on tryptophan concentration, suggesting TrpX involvement in tryptophan uptake. We demonstrated that trpX is part of an operon structure and co-transcribed with two additional genes encoding a putative permease and ATPase, respectively. Bioinformatics analysis identified a putative tryptophan T-box riboswitch in the 5′ untranslated region of this operon. Finally, qRT-PCR and a reporter activation assay revealed trpX mRNA induction under tryptophan-limited conditions. In conclusion, our study showed that TrpX is part of a putative tryptophan ABC transporter system regulated by a T-box riboswitch probably functioning as a substrate-binding protein. Due to the tryptophan auxotrophy of S. suis, TrpX plays a crucial role for metabolic adaptation and growth during infection.
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23
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Spangler JR, Leski TA, Schultzhaus Z, Wang Z, Stenger DA. Large scale screening of CRISPR guide RNAs using an optimized high throughput robotics system. Sci Rep 2022; 12:13953. [PMID: 35977955 PMCID: PMC9385653 DOI: 10.1038/s41598-022-17474-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
All CRISPR/CAS systems utilize CRISPR guide RNAs (crRNAs), the design of which depend on the type of CAS protein, genetic target and the environment/matrix. While machine learning approaches have recently been developed to optimize some crRNA designs, candidate crRNAs must still be screened for efficacy under relevant conditions. Here, we demonstrate a high-throughput method to screen hundreds of candidate crRNAs for activation of Cas13a collateral RNA cleavage. Entire regions of a model gene transcript (Y. pestis lcrV gene) were tiled to produce overlapping crRNA sets. We tested for possible effects that included crRNA/target sequence, size and secondary structures, and the commercial source of DNA oligomers used to generate crRNAs. Detection of a 981 nt target RNA was initially successful with 271 out of 296 tested guide RNAs, and that was improved to 287 out of 296 (97%) after protocol optimizations. For this specific example, we determined that crRNA efficacy did not strongly depend on the target region or crRNA physical properties, but was dependent on the source of DNA oligomers used for RNA preparation. Our high-throughput methods for screening crRNAs has general applicability to the optimization of Cas12 and Cas13 guide RNA designs.
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Affiliation(s)
- J R Spangler
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA.
| | - T A Leski
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
| | - Z Schultzhaus
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Z Wang
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
| | - D A Stenger
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
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24
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Arney JW, Weeks KM. RNA-Ligand Interactions Quantified by Surface Plasmon Resonance with Reference Subtraction. Biochemistry 2022; 61:1625-1632. [PMID: 35802500 PMCID: PMC9357220 DOI: 10.1021/acs.biochem.2c00177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structured RNAs bind ligands and are attractive targets for small-molecule drugs. A wide variety of analytical methods have been used to characterize RNA-ligand interactions, but our experience is that most have significant limitations in terms of material requirements and applicability to complex RNAs. Surface plasmon resonance (SPR) potentially overcomes these limitations, but we find that the standard experimental framework measures notable nonspecific electrostatic-mediated interactions, frustrating analysis of weak RNA binders. SPR measurements are typically quantified relative to a non-target reference channel. Here, we show that referencing to a channel containing a non-binding control RNA enables subtraction of nonspecific binding contributions, allowing measurements of accurate and specific binding affinities. We validated this approach for small-molecule binders of two riboswitch RNAs with affinities ranging from nanomolar to millimolar, including low-molecular-mass fragment ligands. SPR implemented with reference subtraction reliably discriminates specific from nonspecific binding, uses RNA and ligand material efficiently, and enables rapid exploration of the ligand-binding landscape for RNA targets.
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Affiliation(s)
- J. Winston Arney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
27599-3290
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
27599-3290
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25
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Ray S, Dandpat SS, Chatterjee S, Walter NG. Precise tuning of bacterial translation initiation by non-equilibrium 5'-UTR unfolding observed in single mRNAs. Nucleic Acids Res 2022; 50:8818-8833. [PMID: 35892287 PMCID: PMC9410914 DOI: 10.1093/nar/gkac635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/15/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
Noncoding, structured 5′-untranslated regions (5′-UTRs) of bacterial messenger RNAs (mRNAs) can control translation efficiency by forming structures that either recruit or repel the ribosome. Here we exploit a 5′-UTR embedded preQ1-sensing, pseudoknotted translational riboswitch to probe how binding of a small ligand controls recruitment of the bacterial ribosome to the partially overlapping Shine-Dalgarno (SD) sequence. Combining single-molecule fluorescence microscopy with mutational analyses, we find that the stability of 30S ribosomal subunit binding is inversely correlated with the free energy needed to unfold the 5′-UTR during mRNA accommodation into the mRNA binding cleft. Ligand binding to the riboswitch stabilizes the structure to both antagonize 30S recruitment and accelerate 30S dissociation. Proximity of the 5′-UTR and stability of the SD:anti-SD interaction both play important roles in modulating the initial 30S-mRNA interaction. Finally, depletion of small ribosomal subunit protein S1, known to help resolve structured 5′-UTRs, further increases the energetic penalty for mRNA accommodation. The resulting model of rapid standby site exploration followed by gated non-equilibrium unfolding of the 5′-UTR during accommodation provides a mechanistic understanding of how translation efficiency is governed by riboswitches and other dynamic structure motifs embedded upstream of the translation initiation site of bacterial mRNAs.
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Affiliation(s)
- Sujay Ray
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shiba S Dandpat
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Surajit Chatterjee
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G Walter
- Single-Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
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26
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Mukherjee S, Kuang Z, Ghosh S, Detroja R, Carmi G, Tripathy S, Barash D, Frenkel-Morgenstern M, Nevo E, Li K. Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis. BIOLOGY 2022; 11:biology11081110. [PMID: 35892966 PMCID: PMC9331176 DOI: 10.3390/biology11081110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/09/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022]
Abstract
Simple Summary The microevolutionary dynamics of soil bacteria under microclimatic differences are largely unexplored in contrast to our improving knowledge of their vast diversity. In this study, we performed a comparative metagenomic analysis of two sharply divergent rocks and soil types at the Evolution Plateau (EP) in eastern Upper Galilee, Israel. We have identified the significant differences in bacterial taxonomic diversity, functions, and patterns of RNA-based gene regulation between the bacteria from two different soil types. Furthermore, we have identified several species with a significant genetic divergence of the same species between the two soil types, highlighting the soil bacteria’s incipient sympatric speciation. Abstract Soil bacteria respond rapidly to changes in new environmental conditions. For adaptation to the new environment, they could mutate their genome, which impacts the alternation of the functional and regulatory landscape. Sometimes, these genetic and ecological changes may drive the bacterial evolution and sympatric speciation. Although sympatric speciation has been controversial since Darwin suggested it in 1859, there are several strong theoretical or empirical evidences to support it. Sympatric speciation associated with soil bacteria remains largely unexplored. Here, we provide potential evidence of sympatric speciation of soil bacteria by comparison of metagenomics from two sharply contrasting abutting divergence rock and soil types (Senonian chalk and its rendzina soil, and abutting Pleistocene basalt rock and basalt soil). We identified several bacterial species with significant genetic differences in the same species between the two soil types and ecologies. We show that the bacterial community composition has significantly diverged between the two soils; correspondingly, their functions were differentiated in order to adapt to the local ecological stresses. The ecologies, such as water availability and pH value, shaped the adaptation and speciation of soil bacteria revealed by the clear-cut genetic divergence. Furthermore, by a novel analysis scheme of riboswitches, we highlight significant differences in structured non-coding RNAs between the soil bacteria from two divergence soil types, which could be an important driver for functional adaptation. Our study provides new insight into the evolutionary divergence and incipient sympatric speciation of soil bacteria under microclimatic ecological differences.
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Affiliation(s)
- Sumit Mukherjee
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel;
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3498838, Israel;
- Correspondence: (S.M.); (K.L.)
| | - Zhuoran Kuang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
| | - Samrat Ghosh
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata 700054, India; (S.G.); (S.T.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201009, India
| | - Rajesh Detroja
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Gon Carmi
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata 700054, India; (S.G.); (S.T.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201009, India
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel;
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3498838, Israel;
| | - Kexin Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
- Correspondence: (S.M.); (K.L.)
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27
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Crielaard S, Maassen R, Vosman T, Rempkens I, Velema WA. Affinity-Based Profiling of the Flavin Mononucleotide Riboswitch. J Am Chem Soc 2022; 144:10462-10470. [PMID: 35666649 PMCID: PMC9204756 DOI: 10.1021/jacs.2c02685] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Riboswitches are
structural RNA elements that control gene expression.
These naturally occurring RNA sensors are of continued interest as
antibiotic targets, molecular sensors, and functional elements of
synthetic circuits. Here, we describe affinity-based profiling of
the flavin mononucleotide (FMN) riboswitch to characterize ligand
binding and structural folding. We designed and synthesized photoreactive
ligands and used them for photoaffinity labeling. We showed selective
labeling of the FMN riboswitch and used this covalent interaction
to quantitatively measure ligand binding, which we demonstrate with
the naturally occurring antibiotic roseoflavin. We measured conditional
riboswitch folding as a function of temperature and cation concentration.
Furthermore, combining photoaffinity labeling with reverse transcription
revealed ligand binding sites within the aptamer domain with single-nucleotide
resolution. The photoaffinity probe was applied to cellular extracts
of Bacillus subtilis to demonstrate conditional folding
of the endogenous low-abundant ribD FMN riboswitch
in biologically derived samples using quantitative PCR. Lastly, binding
of the riboswitch-targeting antibiotic roseoflavin to the FMN riboswitch
was measured in live bacteria using the photoaffinity probe.
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Affiliation(s)
- Stefan Crielaard
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Rick Maassen
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tess Vosman
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Ivy Rempkens
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Willem A Velema
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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28
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An allosteric ribozyme generator and an inverse folding ribozyme generator: Two computer programs for automated computational design of oligonucleotide-sensing allosteric hammerhead ribozymes with YES Boolean logic function based on experimentally validated algorithms. Comput Biol Med 2022; 145:105469. [DOI: 10.1016/j.compbiomed.2022.105469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 11/18/2022]
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29
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Hamal Dhakal S, Panchapakesan SSS, Slattery P, Roth A, Breaker RR. Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2'-deoxyguanosine. Proc Natl Acad Sci U S A 2022; 119:e2120246119. [PMID: 35622895 PMCID: PMC9295807 DOI: 10.1073/pnas.2120246119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/12/2022] [Indexed: 12/30/2022] Open
Abstract
The aptamer portions of previously reported riboswitch classes that sense guanine, adenine, or 2′-deoxyguanosine are formed by a highly similar three-stem junction with distinct nucleotide sequences in the regions joining the stems. The nucleotides in these joining regions form the major features of the selective ligand-binding pocket for each aptamer. Previously, we reported the existence of additional, rare variants of the predominant guanine-sensing riboswitch class that carry nucleotide differences in the ligand-binding pocket, suggesting that these RNAs have further diversified their structures and functions. Herein, we report the discovery and analysis of three naturally occurring variants of guanine riboswitches that are narrowly distributed across Firmicutes. These RNAs were identified using comparative sequence analysis methods, which also revealed that some of the gene associations for these variants are atypical for guanine riboswitches or their previously known natural variants. Binding assays demonstrate that the newfound variant riboswitch representatives recognize xanthine, guanine, or 2′-deoxyguanosine, with the guanine class exhibiting greater discrimination against related purines than the more common guanine riboswitch class reported previously. These three additional variant classes, together with the four previously discovered riboswitch classes that employ the same three-stem junction architecture, reveal how a simple structural framework can be diversified to expand the range of purine-based ligands sensed by RNA.
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Affiliation(s)
- Siddhartha Hamal Dhakal
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
| | | | - Paul Slattery
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
| | - Adam Roth
- HHMI, Yale University, New Haven, CT 06520-8103
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103
- HHMI, Yale University, New Haven, CT 06520-8103
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103
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30
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Hoetzel J, Suess B. Structural changes in aptamers are essential for synthetic riboswitch engineering. J Mol Biol 2022; 434:167631. [PMID: 35595164 DOI: 10.1016/j.jmb.2022.167631] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/19/2022]
Abstract
Synthetic riboswitches are powerful tools in synthetic biology in which sensing and execution are consolidated in a single RNA molecule. By using SELEX to select aptamers in vitro, synthetic riboswitches can in theory be engineered against any ligand of choice. Surprisingly, very few in vitro selected aptamers have been used for the engineering of synthetic riboswitches. In-depth studies of these aptamers suggest that the key characteristics of such regulatory active RNAs are their structural switching abilities and their binding dynamics. Conventional SELEX approaches seem to be inadequate to select for these characteristics, which may explain the lack of in vitro selected aptamers suited for engineering of synthetic riboswitches. In this review, we explore the functional principles of synthetic riboswitches, identify key characteristics of regulatory active in vitro selected aptamers and integrate these findings in context with available in vitro selection methods. Based on these insights, we propose to use a combination of capture-SELEX and subsequent functional screening for a more successful in vitro selection of aptamers that can be applied for the engineering of synthetic riboswitches.
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Affiliation(s)
- Janis Hoetzel
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany. https://www.twitter.com/J_Hoetzel
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany; Center for Synthetic Biology, Technical University of Darmstadt, Germany.
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31
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Abstract
More than 55 distinct classes of riboswitches that respond to small metabolites or elemental ions have been experimentally validated to date. The ligands sensed by these riboswitches are biased in favor of fundamental compounds or ions that are likely to have been relevant to ancient forms of life, including those that might have populated the "RNA World", which is a proposed biochemical era that predates the evolutionary emergence of DNA and proteins. In the following text, I discuss the various types of ligands sensed by some of the most common riboswitches present in modern bacterial cells and consider implications for ancient biological processes centered on the proven capabilities of these RNA-based sensors. Although most major biochemical aspects of metabolism are represented by known riboswitch classes, there are striking sensory gaps in some key areas. These gaps could reveal weaknesses in the performance capabilities of RNA that might have hampered RNA World evolution, or these could highlight opportunities to discover additional riboswitch classes that sense essential metabolites.
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Affiliation(s)
- Ronald R. Breaker
- Corresponding Author: Ronald R. Breaker - Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, United States; Phone: 203-432-9389; , Twitter: @RonBreaker
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32
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Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information. BMC Genomics 2022; 23:68. [PMID: 35062881 PMCID: PMC8780764 DOI: 10.1186/s12864-022-08314-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 01/12/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The gram-positive bacterium, Streptomyces avermitilis, holds industrial importance as the producer of avermectin, a widely used anthelmintic agent, and a heterologous expression host of secondary metabolite-biosynthetic gene clusters. Despite its industrial importance, S. avermitilis’ genome organization and regulation of gene expression remain poorly understood. In this study, four different types of Next-Generation Sequencing techniques, including dRNA-Seq, Term-Seq, RNA-Seq and ribosome profiling, were applied to S. avermitilis to determine transcription units of S. avermitilis at a genome-wide level and elucidate regulatory elements for transcriptional and translational control of individual transcription units.
Result
By applying dRNA-Seq and Term-Seq to S. avermitilis MA-4680, a total of 2361 transcription start sites and 2017 transcript 3′-end positions were identified, respectively, leading to determination of 1601 transcription units encoded in S. avermitilis’ genome. Cataloguing the transcription units and integrated analysis of multiple high-throughput data types revealed the presence of diverse regulatory elements for gene expression, such as promoters, 5′-UTRs, terminators, 3′-UTRs and riboswitches. The conserved promoter motifs were identified from 2361 transcription start sites as 5′-TANNNT and 5′-BTGACN for the − 10 and − 35 elements, respectively. The − 35 element and spacer lengths between − 10 and − 35 elements were critical for transcriptional regulation of functionally distinct genes, suggesting the involvement of unique sigma factors. In addition, regulatory sequences recognized by antibiotic regulatory proteins were identified from the transcription start site information. Analysis of the 3′-end of RNA transcript revealed that stem structure formation is a major determinant for transcription termination of most transcription units.
Conclusions
The transcription unit architecture elucidated from the transcripts’ boundary information provides insights for unique genetic regulatory mechanisms of S. avermitilis. Our findings will elevate S. avermitilis’ potential as a production host for a diverse set of secondary metabolites.
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33
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Kameda T, Awazu A, Togashi Y. Molecular dynamics analysis of biomolecular systems including nucleic acids. Biophys Physicobiol 2022; 19:e190027. [DOI: 10.2142/biophysico.bppb-v19.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University
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34
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Sanbonmatsu K. Towards Molecular Mechanism in Long Non-coding RNAs: Linking Structure and Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:23-32. [DOI: 10.1007/978-3-030-92034-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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35
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Bialy RM, Mainguy A, Li Y, Brennan JD. Functional nucleic acid biosensors utilizing rolling circle amplification. Chem Soc Rev 2022; 51:9009-9067. [DOI: 10.1039/d2cs00613h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.
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Affiliation(s)
- Roger M. Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Alexa Mainguy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D. Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
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36
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Zhang G, Ren X, Liang X, Wang Y, Feng D, Zhang Y, Xian M, Zou H. Improving the Microbial Production of Amino Acids: From Conventional Approaches to Recent Trends. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0390-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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37
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Sanbonmatsu K. Getting to the bottom of lncRNA mechanism: structure-function relationships. Mamm Genome 2021; 33:343-353. [PMID: 34642784 PMCID: PMC8509902 DOI: 10.1007/s00335-021-09924-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
Abstract
While long non-coding RNAs are known to play key roles in disease and development, relatively few structural studies have been performed for this important class of RNAs. Here, we review functional studies of long non-coding RNAs and expose the need for high-resolution 3-D structural studies, discussing the roles of long non-coding RNAs in the cell and how structure–function relationships might be used to elucidate further understanding. We then describe structural studies of other classes of RNAs using chemical probing, nuclear magnetic resonance, small-angle X-ray scattering, X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Next, we review early structural studies of long non-coding RNAs to date and describe the way forward for the structural biology of long non-coding RNAs in terms of cryo-EM.
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38
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Peng H, Latifi B, Müller S, Lupták A, Chen IA. Self-cleaving ribozymes: substrate specificity and synthetic biology applications. RSC Chem Biol 2021; 2:1370-1383. [PMID: 34704043 PMCID: PMC8495972 DOI: 10.1039/d0cb00207k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Various self-cleaving ribozymes appearing in nature catalyze the sequence-specific intramolecular cleavage of RNA and can be engineered to catalyze cleavage of appropriate substrates in an intermolecular fashion, thus acting as true catalysts. The mechanisms of the small, self-cleaving ribozymes have been extensively studied and reviewed previously. Self-cleaving ribozymes can possess high catalytic activity and high substrate specificity; however, substrate specificity is also engineerable within the constraints of the ribozyme structure. While these ribozymes share a common fundamental catalytic mechanism, each ribozyme family has a unique overall architecture and active site organization, indicating that several distinct structures yield this chemical activity. The multitude of catalytic structures, combined with some flexibility in substrate specificity within each family, suggests that such catalytic RNAs, taken together, could access a wide variety of substrates. Here, we give an overview of 10 classes of self-cleaving ribozymes and capture what is understood about their substrate specificity and synthetic applications. Evolution of these ribozymes in an RNA world might be characterized by the emergence of a new ribozyme family followed by rapid adaptation or diversification for specific substrates. Self-cleaving ribozymes have become important tools of synthetic biology. Here we summarize the substrate specificity and applications of the main classes of these ribozymes.![]()
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Affiliation(s)
- Huan Peng
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
| | - Brandon Latifi
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
| | - Sabine Müller
- Institute for Biochemistry, University Greifswald 17487 Greifswald Germany
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
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39
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Zhang J, Pang Q, Wang Q, Qi Q, Wang Q. Modular tuning engineering and versatile applications of genetically encoded biosensors. Crit Rev Biotechnol 2021; 42:1010-1027. [PMID: 34615431 DOI: 10.1080/07388551.2021.1982858] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Genetically encoded biosensors have a diverse range of detectable signals and potential applications in many fields, including metabolism control and high-throughput screening. Their ability to be used in situ with minimal interference to the bioprocess of interest could revolutionize synthetic biology and microbial cell factories. The performance and functions of these biosensors have been extensively studied and have been rapidly improved. We review here current biosensor tuning strategies and attempt to unravel how to obtain ideal biosensor functions through experimental adjustments. Strategies for expanding the biosensor input signals that increases the number of detectable compounds have also been summarized. Finally, different output signals and their practical requirements for biotechnology and biomedical applications and environmental safety concerns have been analyzed. This in-depth review of the responses and regulation mechanisms of genetically encoded biosensors will assist to improve their design and optimization in various application scenarios.
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Affiliation(s)
- Jian Zhang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qingxiao Pang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qi Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qingsheng Qi
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China.,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China.,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P. R. China
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40
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Bahoua B, Sevdalis SE, Soto AM. Effect of Sequence on the Interactions of Divalent Cations with M-Box Riboswitches from Mycobacterium tuberculosis and Bacillus subtilis. Biochemistry 2021; 60:2781-2794. [PMID: 34472844 DOI: 10.1021/acs.biochem.1c00371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA is highly negatively charged and often acquires complex structures that require the presence of divalent cations. Subtle changes in conformation resulting from changes in sequence can affect the way ions associate with RNA. Riboswitches are RNA molecules that are involved in the control of gene expression in bacteria and are excellent systems for testing the effects of sequence variations on the conformation of RNA because they contain a highly conserved binding pocket but present sequence variability among different organisms. In this work, we have compared the aptamer domain of a proposed M-box riboswitch from Mycobacterium tuberculosis with the aptamer domain of a validated M-box riboswitch from Bacillus subtilis. We have in vitro transcribed and purified wild-type (WT) M-box riboswitches from M. tuberculosis and B. subtilis as well as a variety of mutated aptamers in which regions from one riboswitch have been replaced with regions from the other riboswitch. We have used ultraviolet unfolding experiments and circular dichroism to characterize the interactions of WT and related M-box riboswitches with divalent cations. Our results show that M-box from M. tuberculosis associates with Mg2+ and Sr2+ in a similar fashion while M-box from B. subtilis discriminates between these two ions and appears to associate better with Mg2+. Our overall results show that M-box from M. tuberculosis interacts differently with cations than M-box from B. subtilis and suggest conformational differences between these two riboswitches.
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41
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Brewer KI, Gaffield GJ, Puri M, Breaker RR. DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria. Bioinformatics 2021; 38:533-535. [PMID: 34524415 PMCID: PMC8723152 DOI: 10.1093/bioinformatics/btab624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 05/07/2021] [Accepted: 09/10/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY Recent efforts to identify novel bacterial structured noncoding RNA (ncRNA) motifs through searching long, GC-rich intergenic regions (IGRs) have revealed several new classes, including the recently validated HMP-PP riboswitch. The DIMPL (Discovery of Intergenic Motifs PipeLine) discovery pipeline described herein enables rapid extraction and selection of bacterial IGRs that are enriched for structured ncRNAs. Moreover, DIMPL automates the subsequent computational steps necessary for their functional identification. AVAILABILITY AND IMPLEMENTATION The DIMPL pipeline is freely available as a Docker image with an accompanying set of Jupyter notebooks. Full instructions for download and use are available at https://github.com/breakerlab/dimpl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kenneth I Brewer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA
| | - Glenn J Gaffield
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA
| | - Malavika Puri
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
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42
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Wei C, Wang S, Liu P, Cheng ST, Qian G, Wang S, Fu Y, Qian W, Sun W. The PdeK-PdeR two-component system promotes unipolar localization of FimX and pilus extension in Xanthomonas oryzae pv. oryzicola. Sci Signal 2021; 14:eabi9589. [PMID: 34520229 DOI: 10.1126/scisignal.abi9589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Chao Wei
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, and Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Shanzhi Wang
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, and Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Pengwei Liu
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Shou-Ting Cheng
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoliang Qian
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Shuwei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wei Qian
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenxian Sun
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, and Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing 100193, China.,College of Plant Protection, Jilin Agricultural University, Changchun 130118, Jilin, China
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43
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Zhang J, Liu G, Zhang X, Chang Y, Wang S, He W, Sun W, Chen D, Murchie AIH. Aminoglycoside riboswitch control of the expression of integron associated aminoglycoside resistance adenyltransferases. Virulence 2021; 11:1432-1442. [PMID: 33103573 PMCID: PMC7588185 DOI: 10.1080/21505594.2020.1836910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The proliferation of antibiotic resistance has its origins in horizontal gene transfer. The class 1 integrons mediate gene transfer by assimilating antibiotic-resistance genes through site-specific recombination. For the class 1 integrons the first assimilated gene normally encodes an aminoglycoside antibiotic resistance protein which is either an aminoglycoside acetyltransferase (AAC), nucleotidyltransferase - (ANT), or adenyl transferase (AAD). An aminoglycoside-sensing riboswitch RNA in the leader RNA of AAC/AAD that controls the expression of aminoglycoside resistance genes has been previously described. Here we explore the relationship between the recombinant products of integron recombination and a series of candidate riboswitch RNAs in the 5' UTR of aad (aminoglycoside adenyltransferases) genes. The RNA sequences from the 5' UTR of the aad genes from pathogenic strains that are the products of site-specific DNA recombination by class 1 integrons were investigated. Reporter assays, MicroScale Thermophoresis (MST) and covariance analysis revealed that a functional aminoglycoside-sensing riboswitch was selected at the DNA level through integron-mediated site-specific recombination. This study explains the close association between integron recombination and the aminoglycoside-sensing riboswitch RNA.
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Affiliation(s)
- Jun Zhang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Getong Liu
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Xuhui Zhang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Yaowen Chang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Shasha Wang
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Weizhi He
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Wenxia Sun
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Dongrong Chen
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
| | - Alastair I H Murchie
- Key Laboratory of Medical Epigenetics and Metabolism, Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University , Shanghai, PR China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University , Shanghai, PR China
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44
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Sugimoto N, Endoh T, Takahashi S, Tateishi-Karimata H. Chemical Biology of Double Helical and Non-Double Helical Nucleic Acids: “To B or Not To B, That Is the Question”. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210131] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
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45
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Elghondakly A, Wu CH, Klupt S, Goodson J, Winkler WC. A NusG Specialized Paralog That Exhibits Specific, High-Affinity RNA-Binding Activity. J Mol Biol 2021; 433:167100. [PMID: 34119489 DOI: 10.1016/j.jmb.2021.167100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/17/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
Bacterial NusG associates with RNA polymerase (RNAP) through its N-terminal domain, while the C-terminal domain (CTD) forms dynamic interactions with Rho, S10, NusB and NusA to affect transcription elongation. While virtually all bacteria encode for a core NusG, many also synthesize paralogs that transiently bind RNAP to alter expression of targeted genes. Yet, despite the importance of the genes they regulate, most of the subfamilies of NusG paralogs (e.g., UpxY, TaA, ActX and LoaP) have not been investigated in depth. Herein, we discover that LoaP requires a small RNA hairpin located within the 5' leader region of its targeted operons. LoaP binds the RNA element with nanomolar affinity and high specificity, in contrast to other NusG proteins, which have not been shown to exhibit RNA-binding activity. These data reveal a sequence feature that can be used to identify LoaP-regulated operons. This discovery also expands the repertoire of macromolecular interactions exhibited by the NusG CTD during transcription elongation to include an RNA ligand.
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Affiliation(s)
- Amr Elghondakly
- The University of Maryland, Department of Chemistry and Biochemistry, College Park, MD, United States
| | - Chih Hao Wu
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States
| | - Steven Klupt
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States
| | - Jonathan Goodson
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States
| | - Wade C Winkler
- The University of Maryland, Department of Chemistry and Biochemistry, College Park, MD, United States; The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States.
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46
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Miguel-Arribas A, Val-Calvo J, Gago-Córdoba C, Izquierdo JM, Abia D, Wu LJ, Errington J, Meijer WJJ. A novel bipartite antitermination system widespread in conjugative elements of Gram-positive bacteria. Nucleic Acids Res 2021; 49:5553-5567. [PMID: 33999173 PMCID: PMC8191782 DOI: 10.1093/nar/gkab360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/09/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022] Open
Abstract
Transcriptional regulation allows adaptive and coordinated gene expression, and is essential for life. Processive antitermination systems alter the transcription elongation complex to allow the RNA polymerase to read through multiple terminators in an operon. Here, we describe the discovery of a novel bipartite antitermination system that is widespread among conjugative elements from Gram-positive bacteria, which we named conAn. This system is composed of a large RNA element that exerts antitermination, and a protein that functions as a processivity factor. Besides allowing coordinated expression of very long operons, we show that these systems allow differential expression of genes within an operon, and probably contribute to strict regulation of the conjugation genes by minimizing the effects of spurious transcription. Mechanistic features of the conAn system are likely to decisively influence its host range, with important implications for the spread of antibiotic resistance and virulence genes.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - César Gago-Córdoba
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - José M Izquierdo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular "Severo Ochoa", (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
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47
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Brewer KI, Greenlee EB, Higgs G, Yu D, Mirihana Arachchilage G, Chen X, King N, White N, Breaker RR. Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes. RNA Biol 2021; 18:2417-2432. [PMID: 33970790 PMCID: PMC8632094 DOI: 10.1080/15476286.2021.1917891] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
Comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding RNAs (ncRNAs) from bacterial genomic DNA sequence datasets. Previously, we developed a computational pipeline to more comprehensively identify structured ncRNA representatives from individual bacterial genomes. This search process exploits the fact that genomic regions serving as templates for the transcription of structured RNAs tend to be present in longer than average noncoding 'intergenic regions' (IGRs) that are enriched in G and C nucleotides compared to the remainder of the genome. In the present study, we apply this computational pipeline to identify structured ncRNA candidates from 26 diverse bacterial species. Numerous novel structured ncRNA motifs were discovered, including several riboswitch candidates, one whose ligand has been identified and others that have yet to be experimentally validated. Our findings support recent predictions that hundreds of novel ribo-switch classes and other ncRNAs remain undiscovered among the limited number of bacterial species whose genomes have been completely sequenced.
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Affiliation(s)
- Kenneth I Brewer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Etienne B Greenlee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Gadareth Higgs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Diane Yu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Xi Chen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Nicholas King
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Neil White
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
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48
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Pandey A, Boros E. Coordination Complexes to Combat Bacterial Infections: Recent Developments, Current Directions and Future Opportunities. Chemistry 2021; 27:7340-7350. [PMID: 33368662 DOI: 10.1002/chem.202004822] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/22/2020] [Indexed: 12/29/2022]
Abstract
Drug discovery aimed at the efficient eradication of life-threatening bacterial infections, especially in light of the emergence of multi-drug resistance of pathogenic bacteria, has remained a challenge for medicinal chemists over the past several decades. As nutrient acquisition and metabolism at the host-pathogen interface become better elucidated, new drug targets continue to emerge. Metal homeostasis is among these processes, and thus provides opportunities for medicinal inorganic chemists to alter or disrupt these processes selectively to impart bacteriostatic or bacteriotoxic effects. In this minireview, we showcase some of the recent work from the field of metal-based antibacterial agents and highlight divergent strategies and mechanisms of action.
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Affiliation(s)
- Apurva Pandey
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, 11794, USA
| | - Eszter Boros
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, 11794, USA
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49
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Panchapakesan SSS, Breaker RR. The case of the missing allosteric ribozymes. Nat Chem Biol 2021; 17:375-382. [PMID: 33495645 PMCID: PMC8880209 DOI: 10.1038/s41589-020-00713-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/13/2020] [Indexed: 01/28/2023]
Abstract
The RNA World theory encompasses the hypothesis that sophisticated ribozymes and riboswitches were the primary drivers of metabolic processes in ancient organisms. Several types of catalytic RNAs and many classes of ligand-sensing RNA switches still exist in modern cells. Curiously, allosteric ribozymes formed by the merger of RNA enzyme and RNA switch components are largely absent in today's biological systems. This is true despite the striking abundances of various classes of both self-cleaving ribozymes and riboswitch aptamers. Here we present the known types of ligand-controlled ribozymes and riboswitches and discuss the possible reasons why fused ribozyme-aptamer constructs have been disfavored through evolution.
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Affiliation(s)
- Shanker S. S. Panchapakesan
- Department of Molecular, Cellular and Developmental
Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental
Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA.,Howard Hughes Medical Institute, Yale University, P.O. Box
208103, New Haven, CT 06520-8103, USA.,Department of Molecular Biophysics and Biochemistry, Yale
University, P.O. Box 208103, New Haven, CT 06520-8103, USA
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50
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Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene. Int J Mol Sci 2021; 22:ijms22063234. [PMID: 33810132 PMCID: PMC8004769 DOI: 10.3390/ijms22063234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism.
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