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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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2
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Sun Q, Ma J, Basit RA, Fu Z, Liu X, Fan G. Screening of a Saccharomyces cerevisiae Strain with High 3-Methylthio-1-Propanol Yield and Optimization of Its Fermentation Conditions. Foods 2024; 13:1296. [PMID: 38731667 PMCID: PMC11083530 DOI: 10.3390/foods13091296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
3-Methylthio-1-propanol (3-Met) is an important flavor compound in various alcoholic beverages such as Baijiu and Huangjiu. To maintain the content of 3-Met in these alcoholic beverages, it is necessary to screen a micro-organism with high yield of 3-Met from the brewing environment. In this study, the ability of yeast strains from the Baijiu brewing to produce 3-Met was analyzed, aiming to obtain yeast with high-yield 3-Met, and its fermentation conditions were optimized. Firstly, 39 yeast strains were screened using 3-Met conversion medium. The results showed that the majority of the strains from Baijiu brewing sources could produce 3-Met, and nearly half of the strains produced more than 0.5 g/L of 3-Met. Among these, yeast F10404, Y03401, and Y8#01, produced more than 1.0 g/L of 3-Met, with yeast Y03401 producing the highest amount at 1.30 g/L. Through morphological observation, physiological and biochemical analysis, and molecular biological identification, it was confirmed that yeast Y03401 was a Saccharomyces cerevisiae. Subsequently, the optimal fermentation conditions for 3-Met production by this yeast were obtained through single-factor designs, Plackett-Burman test, steepest ascent path design and response surface methodology. When the glucose concentration was 60 g/L, yeast extract concentration was 0.8 g/L, L-methionine concentration was 3.8 g/L, initial pH was 4, incubation time was 63 h, inoculum size was 1.6%, shaking speed was 150 rpm, loading volume was 50 mL/250 mL, and temperature was 26 °C, the content of 3-Met produced by S. cerevisiae Y03401 reached a high level of 3.66 g/L. It was also noteworthy that, in contrast to other study findings, this yeast was able to create substantial amounts of 3-Met even in the absence of L-methionine precursor. Based on the clear genome of S. cerevisiae and its characteristics in 3-Met production, S. cerevisiae Y03401 had broad prospects for application in alcoholic beverages such as Baijiu.
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Affiliation(s)
- Qi Sun
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; (Q.S.); (J.M.); (R.A.B.); (X.L.)
| | - Jinghao Ma
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; (Q.S.); (J.M.); (R.A.B.); (X.L.)
| | - Rana Abdul Basit
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; (Q.S.); (J.M.); (R.A.B.); (X.L.)
| | - Zhilei Fu
- School of Biology and Food Science, Hebei Normal University for Nationalities, Chengde 067000, China;
| | - Xiaoyan Liu
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; (Q.S.); (J.M.); (R.A.B.); (X.L.)
| | - Guangsen Fan
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; (Q.S.); (J.M.); (R.A.B.); (X.L.)
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
- Sweet Code Nutrition & Health Institute, Zibo 256306, China
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3
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Zhang Y, Sun Q, Liu X, Basit RA, Ma J, Fu Z, Cheng L, Fan G, Teng C. Screening, Identification, and Fermentation Condition Optimization of a High-Yield 3-Methylthiopropanol Yeast and Its Aroma-Producing Characteristics. Foods 2024; 13:418. [PMID: 38338553 PMCID: PMC10855053 DOI: 10.3390/foods13030418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
A high-yield 3-methylthiopropanol (3-Met) yeast Y1402 was obtained from sesame-flavored Daqu, and it was identified as Saccharomycopsis fibuligera. S. fibuligera Y1402 showed a broad range of growth temperatures and pH, as well as the maximum tolerance to glucose, NaCl, nicotine, and 3-Met at 50% (w/w), 15% (w/v), 1.2 g/L, and 18 g/L, respectively. After optimization using single-factor experiments, a Plackett-Burman design, a steepest ascent test, and a Box-Behnken design, the 3-Met yield reached 4.03 g/L by S. fibuligera Y1402 under the following optimal conditions: glucose concentration of 40 g/L, yeast extract concentration of 0.63 g/L, Tween 80 concentration of 2 g/L, L-methionine concentration of 5 g/L, liquid volume of 25 mL/250 mL, initial pH of 5.3, fermentation temperature of 32 °C, inoculum size of 0.8%, shaking speed of 210 rpm, and fermentation time of 54 h. The fermentation was scaled up to a 3 L fermenter under the optimized conditions, and the yield of 3-Met reached 0.71 g/L. Additionally, an aroma analysis revealed that the flavor substances produced by S. fibuligera Y1402 in sorghum hydrolysate medium was mainly composed of compounds with floral, sweet, creamy, roasted nut, and clove-like aromas. Therefore, S. fibuligera has great potential for application in the brewing of Baijiu and other fermented foods.
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Affiliation(s)
- Yujiao Zhang
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China; (Y.Z.); (Q.S.); (X.L.); (R.A.B.); (J.M.); (L.C.); (C.T.)
| | - Qi Sun
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China; (Y.Z.); (Q.S.); (X.L.); (R.A.B.); (J.M.); (L.C.); (C.T.)
| | - Xiaoyan Liu
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China; (Y.Z.); (Q.S.); (X.L.); (R.A.B.); (J.M.); (L.C.); (C.T.)
| | - Rana Abdul Basit
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China; (Y.Z.); (Q.S.); (X.L.); (R.A.B.); (J.M.); (L.C.); (C.T.)
| | - Jinghao Ma
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China; (Y.Z.); (Q.S.); (X.L.); (R.A.B.); (J.M.); (L.C.); (C.T.)
| | - Zhilei Fu
- Department of Biology and Food Science, Hebei Normal University for Nationalities, Chengde 067000, China;
| | - Liujie Cheng
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China; (Y.Z.); (Q.S.); (X.L.); (R.A.B.); (J.M.); (L.C.); (C.T.)
| | - Guangsen Fan
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China; (Y.Z.); (Q.S.); (X.L.); (R.A.B.); (J.M.); (L.C.); (C.T.)
| | - Chao Teng
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China; (Y.Z.); (Q.S.); (X.L.); (R.A.B.); (J.M.); (L.C.); (C.T.)
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4
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Anbalagan S. Temperature-sensing riboceptors. RNA Biol 2024; 21:1-6. [PMID: 39016038 PMCID: PMC11259075 DOI: 10.1080/15476286.2024.2379118] [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] [Accepted: 07/08/2024] [Indexed: 07/18/2024] Open
Abstract
Understanding how cells sense temperature is a fundamental question in biology and is pivotal for the evolution of life. In numerous organisms, temperature is not only sensed but also generated due to cellular processes. Consequently, the mechanisms governing temperature sensation in various organisms have been experimentally elucidated. Extending upon others' proposals and demonstration of protein- and nucleic acid-based thermosensors, and utilizing a colonial India 'punkah-wallahs' analogy, I present my rationale for the necessity of temperature sensing in every organelle in a cell. Finally, I propose temperature-sensing riboceptors (ribonucleic acid receptors) to integrate all the RNA molecules (mRNA, non-coding RNA, and so forth) capable of sensing temperature and triggering a signaling event, which I call as thermocrine signaling. This approach could enable the identification of riboceptors in every cell of almost every organism, not only for temperature but also for other classes of ligands, including gaseous solutes, and water.
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Affiliation(s)
- Savani Anbalagan
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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5
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Screening of Yeasts Isolated from Baijiu Environments for Producing 3-Methylthio-1-propanol and Optimizing Production Conditions. Foods 2022; 11:foods11223616. [PMID: 36429207 PMCID: PMC9689521 DOI: 10.3390/foods11223616] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
3-Methylthio-1-propanol (3-Met) is widely used as a flavoring substance and an essential aroma ingredient in many foods. Producing 3-Met by microbial transformation is green and eco-friendly. In the present study, one strain, YHM-G, which produced a high level of 3-Met, was isolated from the Baijiu-producing environment. Strain YHM-G was identified as Hyphopichia burtonii according to its morphological properties, physiological and biochemical characteristics, and ribosomal large subunit 26S rRNA gene D1/D2 domain sequence analysis. The optimal conditions for 3-Met production by YHM-G were obtained by single factor design, Plackett-Burman design, steepest ascent path design and response surface methodology as follows: 42.7 g/L glucose, pH 6, 0.9 g/L yeast extract, 6 g/L L-methionine (L-Met), culture temperature 28 °C, shaking speed 210 rpm, loading volume 50 mL/250 mL, inoculum size 0.5% (v/v), culturing period 48 h and 2.5 g/L Tween-80. Under these optimal conditions, the 3-Met production by strain YHM-G was 3.16 g/L, a value 88.1% higher than that before optimization. Strain YHM-G can also produce a variety of flavor compounds that are important for many foods. This strain thus has the potential to increase the abundance of 3-Met in some fermented foods and enhance their aroma profiles.
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Abstract
RNA viruses include respiratory viruses, such as coronaviruses and influenza viruses, as well as vector-borne viruses, like dengue and West Nile virus. RNA viruses like these encounter various environments when they copy themselves and spread from cell to cell or host to host. Ex vivo differences, such as geographical location and humidity, affect their stability and transmission, while in vivo differences, such as pH and host gene expression, impact viral receptor binding, viral replication, and the host immune response against the viral infection. A critical factor affecting RNA viruses both ex vivo and in vivo, and defining the outcome of viral infections and the direction of viral evolution, is temperature. In this minireview, we discuss the impact of temperature on viral replication, stability, transmission, and adaptation, as well as the host innate immune response. Improving our understanding of how RNA viruses function, survive, and spread at different temperatures will improve our models of viral replication and transmission risk analyses.
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Affiliation(s)
- Karishma Bisht
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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7
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Tetz V, Tetz G. Novel prokaryotic system employing previously unknown nucleic acids-based receptors. Microb Cell Fact 2022; 21:202. [PMID: 36195904 PMCID: PMC9531389 DOI: 10.1186/s12934-022-01923-0] [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: 08/24/2022] [Accepted: 09/16/2022] [Indexed: 12/26/2022] Open
Abstract
The present study describes a previously unknown universal system that orchestrates the interaction of bacteria with the environment, named the Teazeled receptor system (TR-system). The identical system was recently discovered within eukaryotes. The system includes DNA- and RNA-based molecules named "TezRs", that form receptor's network located outside the membrane, as well as reverse transcriptases and integrases. TR-system takes part in the control of all major aspects of bacterial behavior, such as intra cellular communication, growth, biofilm formation and dispersal, utilization of nutrients including xenobiotics, virulence, chemo- and magnetoreception, response to external factors (e.g., temperature, UV, light and gas content), mutation events, phage-host interaction, and DNA recombination activity. Additionally, it supervises the function of other receptor-mediated signaling pathways. Importantly, the TR-system is responsible for the formation and maintenance of cell memory to preceding cellular events, as well the ability to "forget" preceding events. Transcriptome and biochemical analysis revealed that the loss of different TezRs instigates significant alterations in gene expression and proteins synthesis.
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Affiliation(s)
- Victor Tetz
- Human Microbiology Institute, New York, NY, 10013, USA
| | - George Tetz
- Human Microbiology Institute, New York, NY, 10013, USA.
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8
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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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9
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Ruffini N, Klingenberg S, Heese R, Schweiger S, Gerber S. The Big Picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach. Front Aging Neurosci 2022; 14:866886. [PMID: 35832065 PMCID: PMC9271745 DOI: 10.3389/fnagi.2022.866886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/13/2022] [Indexed: 12/12/2022] Open
Abstract
The common features of all neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis (ALS), and Huntington's disease, are the accumulation of aggregated and misfolded proteins and the progressive loss of neurons, leading to cognitive decline and locomotive dysfunction. Still, they differ in their ultimate manifestation, the affected brain region, and the kind of proteinopathy. In the last decades, a vast number of processes have been described as associated with neurodegenerative diseases, making it increasingly harder to keep an overview of the big picture forming from all those data. In this meta-study, we analyzed genomic, transcriptomic, proteomic, and epigenomic data of the aforementioned diseases using the data of 234 studies in a network-based approach to study significant general coherences but also specific processes in individual diseases or omics levels. In the analysis part, we focus on only some of the emerging findings, but trust that the meta-study provided here will be a valuable resource for various other researchers focusing on specific processes or genes contributing to the development of neurodegeneration.
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Affiliation(s)
- Nicolas Ruffini
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Leibniz Institute for Resilience Research, Leibniz Association, Mainz, Germany
| | - Susanne Klingenberg
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Raoul Heese
- Fraunhofer Institute for Industrial Mathematics (ITWM), Kaiserslautern, Germany
| | - Susann Schweiger
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
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10
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Micic J, Rodríguez-Galán O, Babiano R, Fitzgerald F, Fernández-Fernández J, Zhang Y, Gao N, Woolford JL, de la Cruz J. Ribosomal protein eL39 is important for maturation of the nascent polypeptide exit tunnel and proper protein folding during translation. Nucleic Acids Res 2022; 50:6453-6473. [PMID: 35639884 PMCID: PMC9226512 DOI: 10.1093/nar/gkac366] [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: 08/19/2021] [Revised: 04/04/2022] [Accepted: 05/12/2022] [Indexed: 11/29/2022] Open
Abstract
During translation, nascent polypeptide chains travel from the peptidyl transferase center through the nascent polypeptide exit tunnel (NPET) to emerge from 60S subunits. The NPET includes portions of five of the six 25S/5.8S rRNA domains and ribosomal proteins uL4, uL22, and eL39. Internal loops of uL4 and uL22 form the constriction sites of the NPET and are important for both assembly and function of ribosomes. Here, we investigated the roles of eL39 in tunnel construction, 60S biogenesis, and protein synthesis. We show that eL39 is important for proper protein folding during translation. Consistent with a delay in processing of 27S and 7S pre-rRNAs, eL39 functions in pre-60S assembly during middle nucleolar stages. Our biochemical assays suggest the presence of eL39 in particles at these stages, although it is not visualized in them by cryo-electron microscopy. This indicates that eL39 takes part in assembly even when it is not fully accommodated into the body of pre-60S particles. eL39 is also important for later steps of assembly, rotation of the 5S ribonucleoprotein complex, likely through long range rRNA interactions. Finally, our data strongly suggest the presence of alternative pathways of ribosome assembly, previously observed in the biogenesis of bacterial ribosomal subunits.
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Affiliation(s)
- Jelena Micic
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Reyes Babiano
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Fiona Fitzgerald
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - José Fernández-Fernández
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Yunyang Zhang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
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11
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Paulose AK, Huang C, Chen P, Tripathi A, Chen P, Huang Y, Wang Y. A Rapid Detection of COVID-19 Viral RNA in Human Saliva Using Electrical Double Layer-Gated Field-Effect Transistor-Based Biosensors. ADVANCED MATERIALS TECHNOLOGIES 2022; 7:2100842. [PMID: 34901383 PMCID: PMC8646907 DOI: 10.1002/admt.202100842] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/11/2021] [Indexed: 05/15/2023]
Abstract
In light of the swift outspread and considerable mortality, coronavirus disease 2019 (COVID-19) necessitates a rapid screening tool and a precise diagnosis. Saliva is considered as an alternative specimen to detect the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since the viral load is comparable to what are found in a throat and a nasal cavity. The electrical double layer (EDL)-gated field-effect transistor-based biosensor (BioFET) emerges as a promising candidate for salivary COVID-19 tests due to a high sensitivity, a portable configuration, a label-free operation, and a matrix insensitivity. In this work, the authors utilize EDL-gated BioFETs to detect complementary DNAs (cDNAs) and viral RNAs with various testing conditions such as switches of probes, temperature treatments, and matrices. The selectivity is confirmed with cDNA and noncomplementary DNA (ncDNA), exhibiting an eightfold difference in electrical signals. The matrix insensitivity is evaluated, and BioFETs successfully validate the detection of SARS-CoV-2 N-gene RNA down to 1 fm in diluted human saliva with a 95°C- and a 25°C-treatment, respectively. This proposed system has a high potential to be deployed for an on-site COVID-19 screening, improving the disease control and benefitting frontline healthcare system.
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Affiliation(s)
- Akhil K. Paulose
- Institute of Nanoengineering and MicrosystemsNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Chih‐Cheng Huang
- Institute of Nanoengineering and MicrosystemsNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Po‐Hsuan Chen
- Institute of Nanoengineering and MicrosystemsNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Adarsh Tripathi
- Institute of Molecular MedicineNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Pin‐Hsuan Chen
- Department of Power Mechanical EngineeringNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Yu‐Shan Huang
- Institute of Nanoengineering and MicrosystemsNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Yu‐Lin Wang
- Institute of Nanoengineering and MicrosystemsNational Tsing Hua UniversityHsinchu30013Taiwan
- Department of Power Mechanical EngineeringNational Tsing Hua UniversityHsinchu30013Taiwan
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12
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Structural insights into assembly of the ribosomal nascent polypeptide exit tunnel. Nat Commun 2020; 11:5111. [PMID: 33037216 PMCID: PMC7547690 DOI: 10.1038/s41467-020-18878-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/14/2020] [Indexed: 11/08/2022] Open
Abstract
The nascent polypeptide exit tunnel (NPET) is a major functional center of 60S ribosomal subunits. However, little is known about how the NPET is constructed during ribosome assembly. We utilized molecular genetics, biochemistry, and cryo-electron microscopy (cryo-EM) to investigate the functions of two NPET-associated proteins, ribosomal protein uL4 and assembly factor Nog1, in NPET assembly. Structures of mutant pre-ribosomes lacking the tunnel domain of uL4 reveal a misassembled NPET, including an aberrantly flexible ribosomal RNA helix 74, resulting in at least three different blocks in 60S assembly. Structures of pre-ribosomes lacking the C-terminal extension of Nog1 demonstrate that this extension scaffolds the tunnel domain of uL4 in the NPET to help maintain stability in the core of pre-60S subunits. Our data reveal that uL4 and Nog1 work together in the maturation of ribosomal RNA helix 74, which is required to ensure proper construction of the NPET and 60S ribosomal subunits. The nascent polypeptide exit tunnel (NPET) is a functional center of the large ribosomal subunit through which the nascent polypeptide chains travel from the peptidyltransferase center (PTC). Here the authors provide structural insight into NPET maturation and how it is linked to other aspects of ribosome biogenesis.
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13
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Dong X, Qu G, Piazza CL, Belfort M. Group II intron as cold sensor for self-preservation and bacterial conjugation. Nucleic Acids Res 2020; 48:6198-6209. [PMID: 32379323 PMCID: PMC7293003 DOI: 10.1093/nar/gkaa313] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/20/2020] [Indexed: 01/18/2023] Open
Abstract
Group II introns are self-splicing ribozymes and mobile genetic elements. Splicing is required for both expression of the interrupted host gene and intron retromobility. For the pRS01 plasmid-encoded Lactococcus lactis group II intron, Ll.LtrB, splicing enables expression of the intron's host relaxase protein. Relaxase, in turn, initiates horizontal transfer of the conjugative pRS01 plasmid and stimulates retrotransposition of the intron. Little is known about how splicing of bacterial group II introns is influenced by environmental conditions. Here, we show that low temperatures can inhibit Ll.LtrB intron splicing. Whereas autocatalysis is abolished in the cold, splicing is partially restored by the intron-encoded protein (IEP). Structure profiling reveals cold-induced disruptions of key tertiary interactions, suggesting that a kinetic trap prevents the intron RNA from assuming its native state. Interestingly, while reduced levels of transcription and splicing lead to a paucity of excised intron in the cold, levels of relaxase mRNA are maintained, partially due to diminished intron-mediated mRNA targeting, allowing intron spread by conjugal transfer. Taken together, this study demonstrates not only the intrinsic cold sensitivity of group II intron splicing and the role of the IEP for cold-stress adaptation, but also maintenance of horizontal plasmid and intron transfer under cold-shock.
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Affiliation(s)
- Xiaolong Dong
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Guosheng Qu
- College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Carol Lyn Piazza
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY 12222, USA
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14
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Abstract
Temperature variation is one of the multiple parameters a microbial pathogen encounters when it invades a warm-blooded host. To survive and thrive at host body temperature, human pathogens have developed various strategies to sense and respond to their ambient temperature. An instantaneous response is mounted by RNA thermometers (RNATs), which are integral sensory structures in mRNAs that modulate translation efficiency. At low temperatures outside the host, the folded RNA blocks access of the ribosome to the translation initiation region. The temperature shift upon entering the host destabilizes the RNA structure and thus permits ribosome binding. This reversible zipper-like mechanism of RNATs is ideally suited to fine-tune virulence gene expression when the pathogen enters or exits the body of its host. This review summarizes our present knowledge on virulence-related RNATs and discusses recent developments in the field.
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15
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Qi F, Frishman D. Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions. Nucleic Acids Res 2017; 45:6109-6118. [PMID: 28335026 PMCID: PMC5449622 DOI: 10.1093/nar/gkx161] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/24/2017] [Indexed: 11/13/2022] Open
Abstract
Secondary structure elements in the coding regions of mRNAs play an important role in gene expression and regulation, but distinguishing functional from non-functional structures remains challenging. Here we investigate the dependence of sequence–structure relationships in the coding regions on temperature based on the recent PARTE data by Wan et al. Our main finding is that the regions with high and low thermostability (high Tm and low Tm regions) are under evolutionary pressure to preserve RNA secondary structure and primary sequence, respectively. Sequences of low Tm regions display a higher degree of evolutionary conservation compared to high Tm regions. Low Tm regions are under strong synonymous constraint, while high Tm regions are not. These findings imply that high Tm regions contain thermo-stable functionally important RNA structures, which impose relaxed evolutionary constraint on sequence as long as the base-pairing patterns remain intact. By contrast, low thermostability regions contain single-stranded functionally important conserved RNA sequence elements accessible for binding by other molecules. We also find that theoretically predicted structures of paralogous mRNA pairs become more similar with growing temperature, while experimentally measured structures tend to diverge, which implies that the melting pathways of RNA structures cannot be fully captured by current computational approaches.
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Affiliation(s)
- Fei Qi
- Department of Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany.,St Petersburg State Polytechnic University, St Petersburg 195251, Russia
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16
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Ignatov D, Johansson J. RNA-mediated signal perception in pathogenic bacteria. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28792118 DOI: 10.1002/wrna.1429] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 11/09/2022]
Abstract
Bacterial pathogens encounter several different environments during an infection, many of them possibly being detrimental. In order to sense its surroundings and adjust the gene expression accordingly, different regulatory schemes are undertaken. With these, the bacterium appropriately can differentiate between various environmental cues to express the correct virulence factor at the appropriate time and place. An attractive regulator device is RNA, which has an outstanding ability to alter its structure in response to external stimuli, such as metabolite concentration or alterations in temperature, to control its downstream gene expression. This review will describe the function of riboswitches and thermometers, with a particular emphasis on regulatory RNAs being important for bacterial pathogenicity. WIREs RNA 2017, 8:e1429. doi: 10.1002/wrna.1429 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Dmitriy Ignatov
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Jörgen Johansson
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
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17
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Rivas-Aravena A, Muñoz P, Jorquera P, Diaz A, Reinoso C, González-Catrilelbún S, Sandino AM. Study of RNA-A Initiation Translation of The Infectious Pancreatic Necrosis Virus. Virus Res 2017; 240:121-129. [PMID: 28743463 DOI: 10.1016/j.virusres.2017.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/08/2017] [Accepted: 07/12/2017] [Indexed: 01/24/2023]
Abstract
The infectious pancreatic necrosis virus (IPNV) is a salmonid pathogen that causes significant economic losses to the aquaculture industry. IPNV is a non-enveloped virus containing two uncapped and non-polyadenylated double strand RNA genomic segments, RNA-A and RNA-B. The viral protein Vpg is covalently attached to the 5' end of both segments. There is little knowledge about its viral cycle, particularly about the translation of the RNAs. Through experiments using mono and bicistronic reporters, in this work we show that the 120-nucleotide-long 5'-UTR of RNA-A contains an internal ribosome entry site (IRES) that functions efficiently both in vitro and in salmon cells. IRES activity is strongly dependent on temperature. Also, the IRES structure is confined to the 5'UTR and is not affected by the viral coding sequence. This is the first report of IRES activity in a fish virus and can give us tools to generate antivirals to attack the virus without affecting fish directly.
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Affiliation(s)
- Andrea Rivas-Aravena
- Comisión Chilena de Energía Nuclear, Departamento de Aplicaciones Nucleares, Laboratorio de Radiobiología Celular y Molecular. Nueva Bilbao 12501, Las Condes, Santiago, Chile; Universidad San Sebastián, Facultad de Ciencias, Lota 2465, Providencia, Santiago, Chile.
| | - Patricio Muñoz
- Universidad de Santiago de Chile, Centro de Biotecnología Acuícola, Laboratorio de Virología,Av. Bernardo O'Higgins 3303, Estación Central, Santiago, Chile
| | - Patricia Jorquera
- Universidad de Santiago de Chile, Centro de Biotecnología Acuícola, Laboratorio de Virología,Av. Bernardo O'Higgins 3303, Estación Central, Santiago, Chile
| | - Alvaro Diaz
- Universidad de Santiago de Chile, Centro de Biotecnología Acuícola, Laboratorio de Virología,Av. Bernardo O'Higgins 3303, Estación Central, Santiago, Chile
| | - Claudia Reinoso
- Universidad de Santiago de Chile, Centro de Biotecnología Acuícola, Laboratorio de Virología,Av. Bernardo O'Higgins 3303, Estación Central, Santiago, Chile
| | - Sebastián González-Catrilelbún
- Comisión Chilena de Energía Nuclear, Departamento de Aplicaciones Nucleares, Laboratorio de Radiobiología Celular y Molecular. Nueva Bilbao 12501, Las Condes, Santiago, Chile; Universidad de Santiago de Chile, Centro de Biotecnología Acuícola, Laboratorio de Virología,Av. Bernardo O'Higgins 3303, Estación Central, Santiago, Chile
| | - Ana María Sandino
- Universidad de Santiago de Chile, Centro de Biotecnología Acuícola, Laboratorio de Virología,Av. Bernardo O'Higgins 3303, Estación Central, Santiago, Chile.
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18
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Zhang L, Tripathi A. Archaeal RNA ligase from thermoccocus kodakarensis for template dependent ligation. RNA Biol 2016; 14:36-44. [PMID: 27715457 DOI: 10.1080/15476286.2016.1239688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Nicking-sealing RNA ligases play a significant biological role in host defense and cellular repair, and have become an important molecular tool in biomedical engineering. Due to the propensity for RNA to form secondary structures, RNA modifying enzymes with elevated optimum temperatures are highly desired. Current characterized double stranded RNA ligases, such as the bacteriophage T4 RNA ligase 2, while possessing good template dependency, are not active at elevated temperatures. The few characterized RNA ligases from thermophiles exhibit high template independency. We synthesize and characterize here, KOD RNA ligase (KOD1Rnl), a thermostable and template dependent RNA ligase from the archaeon, Thermoccocus Kodakarensis. We disclose that a 13 time reduction in template independent ligation can be achieved with the addition of a single stranded DNase, such as RecJ. We also elucidate the effects of the presence of blood proteins on the activity of KOD1Rnl. Template dependent and thermostable RNA ligases, such as KOD RNA ligase, can be utilized in RNA detection, modification and sequencing.
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Affiliation(s)
- Lei Zhang
- a Center for Biomedical Engineering, School of Engineering, Brown University , Providence , RI , USA
| | - Anubhav Tripathi
- a Center for Biomedical Engineering, School of Engineering, Brown University , Providence , RI , USA
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19
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Garcia-Martin JA, Dotu I, Fernandez-Chamorro J, Lozano G, Ramajo J, Martinez-Salas E, Clote P. RNAiFold2T: Constraint Programming design of thermo-IRES switches. Bioinformatics 2016; 32:i360-i368. [PMID: 27307638 PMCID: PMC4908349 DOI: 10.1093/bioinformatics/btw265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
MOTIVATION RNA thermometers (RNATs) are cis-regulatory elements that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resource in synthetic biology, where engineered RNATs could prove to be useful tools in biosensors and conditional gene regulation. RESULTS Solving the 2-temperature inverse folding problem is critical for RNAT engineering. Here we introduce RNAiFold2T, the first Constraint Programming (CP) and Large Neighborhood Search (LNS) algorithms to solve this problem. Benchmarking tests of RNAiFold2T against existent programs (adaptive walk and genetic algorithm) inverse folding show that our software generates two orders of magnitude more solutions, thus allowing ample exploration of the space of solutions. Subsequently, solutions can be prioritized by computing various measures, including probability of target structure in the ensemble, melting temperature, etc. Using this strategy, we rationally designed two thermosensor internal ribosome entry site (thermo-IRES) elements, whose normalized cap-independent translation efficiency is approximately 50% greater at 42 °C than 30 °C, when tested in reticulocyte lysates. Translation efficiency is lower than that of the wild-type IRES element, which on the other hand is fully resistant to temperature shift-up. This appears to be the first purely computational design of functional RNA thermoswitches, and certainly the first purely computational design of functional thermo-IRES elements. AVAILABILITY RNAiFold2T is publicly available as part of the new release RNAiFold3.0 at https://github.com/clotelab/RNAiFold and http://bioinformatics.bc.edu/clotelab/RNAiFold, which latter has a web server as well. The software is written in C ++ and uses OR-Tools CP search engine. CONTACT clote@bc.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Ivan Dotu
- Department of Experimental and Health Sciences, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra. Dr. Aiguader 88, Barcelona, Spain
| | - Javier Fernandez-Chamorro
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Gloria Lozano
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Jorge Ramajo
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Encarnacion Martinez-Salas
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Peter Clote
- Biology Department, Boston College, Chestnut Hill, MA 02467, USA
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20
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González Plaza JJ, Hulak N, Zhumadilov Z, Akilzhanova A. Fever as an important resource for infectious diseases research. Intractable Rare Dis Res 2016; 5:97-102. [PMID: 27195192 PMCID: PMC4869589 DOI: 10.5582/irdr.2016.01009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/26/2016] [Accepted: 04/04/2016] [Indexed: 02/07/2023] Open
Abstract
Fever or pyrexia is a process where normal body temperature is raised over homeostasis conditions. Although many effects of fever over the immune system have been known for a long time, it has not been until recent studies when these effects have been evaluated in several infection processes. Results have been promising, as they have reported new ways of regulation, especially in RNA molecules. In light of these new studies, it seems important to start to evaluate the effects of pyrexia in current research efforts in host-pathogen interactions. Viruses and bacteria are responsible for different types of infectious diseases, and while it is of paramount importance to understand the mechanisms of infection, potential effects of fever on this process may have been overlooked. This is especially relevant because during the course of many infectious diseases the organism develops fever. Due to the lack of specific treatments for many of those afflictions, experimental evaluation in fever-like conditions can potentially bring new insights into the infection process and can ultimately help to develop treatments. The aim of this review is to present evidence that the temperature increase during fever affects the way the infection takes place, for both the pathogen and the host.
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Affiliation(s)
- Juan José González Plaza
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
- Research Department, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Zagreb, Croatia
| | - Nataša Hulak
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Zhaxybay Zhumadilov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, PI “National Laboratory Astana”, AOE “Nazarbayev University”, Astana, Kazakhstan
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, PI “National Laboratory Astana”, AOE “Nazarbayev University”, Astana, Kazakhstan
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21
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Hoynes-O'Connor A, Hinman K, Kirchner L, Moon TS. De novo design of heat-repressible RNA thermosensors in E. coli. Nucleic Acids Res 2015; 43:6166-79. [PMID: 25979263 PMCID: PMC4499127 DOI: 10.1093/nar/gkv499] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/04/2015] [Indexed: 11/15/2022] Open
Abstract
RNA-based temperature sensing is common in bacteria that live in fluctuating environments. Most naturally-occurring RNA thermosensors are heat-inducible, have long sequences, and function by sequestering the ribosome binding site in a hairpin structure at lower temperatures. Here, we demonstrate the de novo design of short, heat-repressible RNA thermosensors. These thermosensors contain a cleavage site for RNase E, an enzyme native to Escherichia coli and many other organisms, in the 5′ untranslated region of the target gene. At low temperatures, the cleavage site is sequestered in a stem–loop, and gene expression is unobstructed. At high temperatures, the stem–loop unfolds, allowing for mRNA degradation and turning off expression. We demonstrated that these thermosensors respond specifically to temperature and provided experimental support for the central role of RNase E in the mechanism. We also demonstrated the modularity of these RNA thermosensors by constructing a three-input composite circuit that utilizes transcriptional, post-transcriptional, and post-translational regulation. A thorough analysis of the 24 thermosensors allowed for the development of design guidelines for systematic construction of similar thermosensors in future applications. These short, modular RNA thermosensors can be applied to the construction of complex genetic circuits, facilitating rational reprogramming of cellular processes for synthetic biology applications.
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Affiliation(s)
- Allison Hoynes-O'Connor
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kristina Hinman
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lukas Kirchner
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tae Seok Moon
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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22
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Delvillani F, Sciandrone B, Peano C, Petiti L, Berens C, Georgi C, Ferrara S, Bertoni G, Pasini ME, Dehò G, Briani F. Tet-Trap, a genetic approach to the identification of bacterial RNA thermometers: application to Pseudomonas aeruginosa. RNA (NEW YORK, N.Y.) 2014; 20:1963-1976. [PMID: 25336583 PMCID: PMC4238360 DOI: 10.1261/rna.044354.114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 09/10/2014] [Indexed: 06/04/2023]
Abstract
Modulation of mRNA translatability either by trans-acting factors (proteins or sRNAs) or by in cis-acting riboregulators is widespread in bacteria and controls relevant phenotypic traits. Unfortunately, global identification of post-transcriptionally regulated genes is complicated by poor structural and functional conservation of regulatory elements and by the limitations of proteomic approaches in protein quantification. We devised a genetic system for the identification of post-transcriptionally regulated genes and we applied this system to search for Pseudomonas aeruginosa RNA thermometers, a class of regulatory RNA that modulates gene translation in response to temperature changes. As P. aeruginosa is able to thrive in a broad range of environmental conditions, genes differentially expressed at 37 °C versus lower temperatures may be involved in infection and survival in the human host. We prepared a plasmid vector library with translational fusions of P. aeruginosa DNA fragments (PaDNA) inserted upstream of TIP2, a short peptide able to inactivate the Tet repressor (TetR) upon expression. The library was assayed in a streptomycin-resistant merodiploid rpsL(+)/rpsL31 Escherichia coli strain in which the dominant rpsL(+) allele, which confers streptomycin sensitivity, was repressed by TetR. PaDNA fragments conferring thermosensitive streptomycin resistance (i.e., expressing PaDNA-TIP2 fusions at 37°C, but not at 28°C) were sequenced. We identified four new putative thermosensors. Two of them were validated with conventional reporter systems in E. coli and P. aeruginosa. Interestingly, one regulates the expression of ptxS, a gene implicated in P. aeruginosa pathogenesis.
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Affiliation(s)
- Francesco Delvillani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Barbara Sciandrone
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Clelia Peano
- Istituto di Tecnologie Biomediche, CNR, 20090 Segrate, Italy
| | - Luca Petiti
- Istituto di Tecnologie Biomediche, CNR, 20090 Segrate, Italy Doctoral Program of Molecular and Translational Medicine, Università degli Studi di Milano, 20133 Milano, Italy
| | - Christian Berens
- Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Christiane Georgi
- Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Silvia Ferrara
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Giovanni Bertoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Maria Enrica Pasini
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Gianni Dehò
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
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23
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Righetti F, Narberhaus F. How to find RNA thermometers. Front Cell Infect Microbiol 2014; 4:132. [PMID: 25279353 PMCID: PMC4166951 DOI: 10.3389/fcimb.2014.00132] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/02/2014] [Indexed: 11/27/2022] Open
Abstract
Temperature is one of the decisive signals that a mammalian pathogen has entered its warm-blooded host. Among the many ways to register temperature changes, bacteria often use temperature-modulated structures in the untranslated region of mRNAs. In this article, we describe how such RNA thermometers (RNATs) have been discovered one by one upstream of heat shock and virulence genes in the past, and how next-generation sequencing approaches are able to reveal novel temperature-responsive RNA structures on a global scale.
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24
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Churkin A, Avihoo A, Shapira M, Barash D. RNAthermsw: direct temperature simulations for predicting the location of RNA thermometers. PLoS One 2014; 9:e94340. [PMID: 24718440 PMCID: PMC3981793 DOI: 10.1371/journal.pone.0094340] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 03/14/2014] [Indexed: 11/18/2022] Open
Abstract
The mechanism of RNA thermometers is a subject of growing interest. Also known as RNA thermosensors, these temperature-sensitive segments of the mRNA regulate gene expression by changing their secondary structure in response to temperature fluctuations. The detection of RNA thermometers in various genes of interest is valuable as it could lead to the discovery of new thermometers participating in fundamental processes such as preferential translation during heat-shock. RNAthermsw is a user-friendly webserver for predicting the location of RNA thermometers using direct temperature simulations. It operates by analyzing dotted figures generated as a result of a moving window that performs successive energy minimization folding predictions. Inputs include the RNA sequence, window size, and desired temperature change. RNAthermsw can be freely accessed at http://www.cs.bgu.ac.il/~rnathemsw/RNAthemsw/ (with the slash sign at the end). The website contains a help page with explanations regarding the exact usage.
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Affiliation(s)
- Alexander Churkin
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
| | | | - Michal Shapira
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
- * E-mail:
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