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Sharts DM, Almanza MT, Banks AV, Castellanos AM, Hernandez CGO, Lopez ML, Rodriguez D, Tong AY, Segeberg MR, Passalacqua LFM, Abdelsayed MM. Robo-Therm, a pipeline to RNA thermometer discovery and validation. RNA (NEW YORK, N.Y.) 2024; 30:760-769. [PMID: 38565243 PMCID: PMC11182007 DOI: 10.1261/rna.079980.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
RNA thermometers are highly structured noncoding RNAs located in the 5'-untranslated regions (UTRs) of genes that regulate expression by undergoing conformational changes in response to temperature. The discovery of RNA thermometers through bioinformatics is difficult because there is little sequence conservation among their structural elements. Thus, the abundance of these thermosensitive regulatory structures remains unclear. Herein, to advance the discovery and validation of RNA thermometers, we developed Robo-Therm, a pipeline that combines an adaptive and user-friendly in silico motif search with a well-established reporter system. Through our application of Robo-Therm, we discovered two novel RNA thermometers in bacterial and bacteriophage genomes found in the human gut. One of these thermometers is present in the 5'-UTR of a gene that codes for σ 70 RNA polymerase subunit in the bacteria Mediterraneibacter gnavus and Bacteroides pectinophilus, and in the bacteriophage Caudoviricetes, which infects B. pectinophilus The other thermometer is in the 5'-UTR of a tetracycline resistance gene (tetR) in the intestinal bacteria Escherichia coli and Shigella flexneri Our Robo-Therm pipeline can be applied to discover multiple RNA thermometers across various genomes.
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Affiliation(s)
- Davis M Sharts
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Maria T Almanza
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Andrea V Banks
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Alyssa M Castellanos
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | | | - Monica L Lopez
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Daniela Rodriguez
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Alina Y Tong
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Maximilian R Segeberg
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Luiz F M Passalacqua
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael M Abdelsayed
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
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Kienbeck K, Malfertheiner L, Zelger-Paulus S, Johannsen S, von Mering C, Sigel RKO. Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages. Nat Commun 2024; 15:1559. [PMID: 38378708 PMCID: PMC10879173 DOI: 10.1038/s41467-024-45653-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Trillions of microorganisms, collectively known as the microbiome, inhabit our bodies with the gut microbiome being of particular interest in biomedical research. Bacteriophages, the dominant virome constituents, can utilize suppressor tRNAs to switch to alternative genetic codes (e.g., the UAG stop-codon is reassigned to glutamine) while infecting hosts with the standard bacterial code. However, what triggers this switch and how the bacteriophage manipulates its host is poorly understood. Here, we report the discovery of a subgroup of minimal hepatitis delta virus (HDV)-like ribozymes - theta ribozymes - potentially involved in the code switch leading to the expression of recoded lysis and structural phage genes. We demonstrate their HDV-like self-scission behavior in vitro and find them in an unreported context often located with their cleavage site adjacent to tRNAs, indicating a role in viral tRNA maturation and/or regulation. Every fifth associated tRNA is a suppressor tRNA, further strengthening our hypothesis. The vast abundance of tRNA-associated theta ribozymes - we provide 1753 unique examples - highlights the importance of small ribozymes as an alternative to large enzymes that usually process tRNA 3'-ends. Our discovery expands the short list of biological functions of small HDV-like ribozymes and introduces a previously unknown player likely involved in the code switch of certain recoded gut bacteriophages.
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Affiliation(s)
- Kasimir Kienbeck
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland
| | | | - Silke Johannsen
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland.
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Tong A, Caudill EE, Jones AR, F. M. Passalacqua L, Abdelsayed MM. Characterization of a FourU RNA Thermometer in the 5' Untranslated Region of Autolysin Gene blyA in the Bacillus subtilis 168 Prophage SPβ. Biochemistry 2023; 62:2902-2907. [PMID: 37699513 PMCID: PMC10586365 DOI: 10.1021/acs.biochem.3c00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/28/2023] [Indexed: 09/14/2023]
Abstract
RNA thermometers are noncoding RNA structures located in the 5' untranslated regions (UTRs) of genes that regulate gene expression through temperature-dependent conformational changes. The fourU class of RNA thermometers contains a specific motif in which four consecutive uracil nucleotides are predicted to base pair with the Shine-Dalgarno (SD) sequence in a stem. We employed a bioinformatic search to discover a fourU RNA thermometer in the 5'-UTR of the blyA gene of the Bacillus subtilis phage SPβc2, a bacteriophage that infects B. subtilis 168. blyA encodes an autolysin enzyme, N-acetylmuramoyl-l-alanine amidase, which is involved in the lytic life cycle of the SPβ prophage. We have biochemically validated the predicted RNA thermometer in the 5'-UTR of the blyA gene. Our study suggests that RNA thermometers may play an underappreciated yet critical role in the lytic life cycle of bacteriophages.
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Affiliation(s)
- Alina
Y. Tong
- Department
of Biology, California Lutheran University, Thousand Oaks, California 91360, United States
| | - Emma E. Caudill
- Department
of Biology, California Lutheran University, Thousand Oaks, California 91360, United States
| | - Alexis R. Jones
- Department
of Biology, California Lutheran University, Thousand Oaks, California 91360, United States
| | - Luiz F. M. Passalacqua
- Laboratory
of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Michael M. Abdelsayed
- Department
of Biology, California Lutheran University, Thousand Oaks, California 91360, United States
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Cole KH, Lupták A. High-throughput methods in aptamer discovery and analysis. Methods Enzymol 2019; 621:329-346. [PMID: 31128787 DOI: 10.1016/bs.mie.2019.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Aptamers are small, functional nucleic acids that bind a variety of targets, often with high specificity and affinity. Genomic aptamers constitute the ligand-binding domains of riboswitches, whereas synthetic aptamers find applications as diagnostic and therapeutic tools, and as ligand-binding domains of regulatory RNAs in synthetic biology. Discovery and characterization of aptamers has been limited by a lack of high-throughput approaches that uncover the target-binding domains and the biochemical properties of individual sequences. With the advent of high-throughput sequencing, large-scale analysis of in vitro selected populations of aptamers (and catalytic nucleic acids, such as ribozymes and DNAzmes) became possible. In recent years the development of new experimental approaches and software tools has led to significant streamlining of the selection-pool analysis. This article provides an overview of post-selection data analysis and describes high-throughput methods that facilitate rapid discovery and biochemical characterization of aptamers.
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Affiliation(s)
- Kyle H Cole
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Andrej Lupták
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States; Department of Pharmaceutical Sciences, University of California, Irvine, CA, United States; Department of Chemistry, University of California, Irvine, CA, United States.
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Webb CHT, Lupták A. Kinetic Parameters of trans Scission by Extended HDV-like Ribozymes and the Prospect for the Discovery of Genomic trans-Cleaving RNAs. Biochemistry 2018; 57:1440-1450. [PMID: 29388767 DOI: 10.1021/acs.biochem.7b00789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hepatitis delta virus (HDV)-like ribozymes are self-cleaving catalytic RNAs with a widespread distribution in nature and biological roles ranging from self-scission during rolling-circle replication in viroids to co-transcriptional processing of eukaryotic retrotransposons, among others. The ribozymes fold into a double pseudoknot with a common catalytic core motif and highly variable peripheral domains. Like other self-cleaving ribozymes, HDV-like ribozymes can be converted into trans-acting catalytic RNAs by bisecting the self-cleaving variants at non-essential loops. Here we explore the trans-cleaving activity of ribozymes derived from the largest examples of the ribozymes (drz-Agam-2 family), which contain an extended domain between the substrate strand and the rest of the RNA. When this peripheral domain is bisected at its distal end, the substrate strand is recognized through two helices, rather than just one 7 bp helix common among the HDV ribozymes, resulting in stronger binding and increased sequence specificity. Kinetic characterization of the extended trans-cleaving ribozyme revealed an efficient trans-cleaving system with a surprisingly high KM', supporting a model that includes a recently proposed activation barrier related to the assembly of the catalytically competent ribozyme. The ribozymes also exhibit a very long koff for the products (∼2 weeks), resulting in a trade-off between sequence specificity and turnover. Finally, structure-based searches for the catalytic cores of these ribozymes in the genome of the mosquito Anopheles gambiae, combined with sequence searches for their putative substrates, revealed two potential ribozyme-substrate pairs that may represent examples of natural trans-cleaving ribozymes.
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Affiliation(s)
- Chiu-Ho T Webb
- Department of Molecular Biology and Biochemistry , University of California-Irvine , Irvine , California 92697 , United States
| | - Andrej Lupták
- Department of Molecular Biology and Biochemistry , University of California-Irvine , Irvine , California 92697 , United States.,Department of Pharmaceutical Sciences , University of California-Irvine , Irvine , California 92697 , United States.,Department of Chemistry , University of California-Irvine , Irvine , California 92697 , United States
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