1
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Mitchener M, Begley TJ, Dedon PC. Molecular Coping Mechanisms: Reprogramming tRNAs To Regulate Codon-Biased Translation of Stress Response Proteins. Acc Chem Res 2023; 56:3504-3514. [PMID: 37992267 PMCID: PMC10702489 DOI: 10.1021/acs.accounts.3c00572] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023]
Abstract
As part of the classic central dogma of molecular biology, transfer RNAs (tRNAs) are integral to protein translation as the adaptor molecules that link the genetic code in messenger RNA (mRNA) to the amino acids in the growing peptide chain. tRNA function is complicated by the existence of 61 codons to specify 20 amino acids, with most amino acids coded by two or more synonymous codons. Further, there are often fewer tRNAs with unique anticodons than there are synonymous codons for an amino acid, with a single anticodon able to decode several codons by "wobbling" of the base pairs arising between the third base of the codon and the first position on the anticodon. The complications introduced by synonymous codons and wobble base pairing began to resolve in the 1960s with the discovery of dozens of chemical modifications of the ribonucleotides in tRNA, which, by analogy to the epigenome, are now collectively referred to as the epitranscriptome for not changing the genetic code inherent to all RNA sequences. tRNA modifications were found to stabilize codon-anticodon interactions, prevent misinitiation of translation, and promote translational fidelity, among other functions, with modification deficiencies causing pathological phenotypes. This led to hypotheses that modification-dependent tRNA decoding efficiencies might play regulatory roles in cells. However, it was only with the advent of systems biology and convergent "omic" technologies that the higher level function of synonymous codons and tRNA modifications began to emerge.Here, we describe our laboratories' discovery of tRNA reprogramming and codon-biased translation as a mechanism linking tRNA modifications and synonymous codon usage to regulation of gene expression at the level of translation. Taking a historical approach, we recount how we discovered that the 8-10 modifications in each tRNA molecule undergo unique reprogramming in response to cellular stresses to promote translation of mRNA transcripts with unique codon usage patterns. These modification tunable transcripts (MoTTs) are enriched with specific codons that are differentially decoded by modified tRNAs and that fall into functional families of genes encoding proteins necessary to survive the specific stress. By developing and applying systems-level technologies, we showed that cells lacking specific tRNA modifications are sensitized to certain cellular stresses by mistranslation of proteins, disruption of mitochondrial function, and failure to translate critical stress response proteins. In essence, tRNA reprogramming serves as a cellular coping strategy, enabling rapid translation of proteins required for stress-specific cell response programs. Notably, this phenomenon has now been characterized in all organisms from viruses to humans and in response to all types of environmental changes. We also elaborate on recent findings that cancer cells hijack this mechanism to promote their own growth, metastasis, and chemotherapeutic resistance. We close by discussing how understanding of codon-biased translation in various systems can be exploited to develop new therapeutics and biomanufacturing processes.
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Affiliation(s)
- Michelle
M. Mitchener
- Antimicrobial
Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
| | - Thomas J. Begley
- Department
of Biological Sciences, University at Albany, Albany, New York 12222, United States
- RNA
Institute, University at Albany, Albany, New York 12222, United States
| | - Peter C. Dedon
- Antimicrobial
Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Lee WL, Sinha A, Lam LN, Loo HL, Liang J, Ho P, Cui L, Chan CSC, Begley T, Kline KA, Dedon P. An RNA modification enzyme directly senses reactive oxygen species for translational regulation in Enterococcus faecalis. Nat Commun 2023; 14:4093. [PMID: 37433804 DOI: 10.1038/s41467-023-39790-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
Bacteria possess elaborate systems to manage reactive oxygen and nitrogen species (ROS) arising from exposure to the mammalian immune system and environmental stresses. Here we report the discovery of an ROS-sensing RNA-modifying enzyme that regulates translation of stress-response proteins in the gut commensal and opportunistic pathogen Enterococcus faecalis. We analyze the tRNA epitranscriptome of E. faecalis in response to reactive oxygen species (ROS) or sublethal doses of ROS-inducing antibiotics and identify large decreases in N2-methyladenosine (m2A) in both 23 S ribosomal RNA and transfer RNA. This we determine to be due to ROS-mediated inactivation of the Fe-S cluster-containing methyltransferase, RlmN. Genetic knockout of RlmN gives rise to a proteome that mimics the oxidative stress response, with an increase in levels of superoxide dismutase and decrease in virulence proteins. While tRNA modifications were established to be dynamic for fine-tuning translation, here we report the discovery of a dynamically regulated, environmentally responsive rRNA modification. These studies lead to a model in which RlmN serves as a redox-sensitive molecular switch, directly relaying oxidative stress to modulating translation through the rRNA and the tRNA epitranscriptome, adding a different paradigm in which RNA modifications can directly regulate the proteome.
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Affiliation(s)
- Wei Lin Lee
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Ameya Sinha
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Ling Ning Lam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Hooi Linn Loo
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Jiaqi Liang
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- School of Chemistry, Chemical Engineering and Biotechnology, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Peiying Ho
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Liang Cui
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Cheryl Siew Choo Chan
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- Critical Analytics for Manufacturing Personalized-Medicine IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Thomas Begley
- Department of Biological Sciences and The RNA Institute, University at Albany, Albany, NY, USA
| | - Kimberly Ann Kline
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Peter Dedon
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore.
- Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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3
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Mycobacterium tuberculosis whiB3 and Lipid Metabolism Genes Are Regulated by Host Induced Oxidative Stress. Microorganisms 2022; 10:microorganisms10091821. [PMID: 36144423 PMCID: PMC9506551 DOI: 10.3390/microorganisms10091821] [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: 08/15/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/23/2022] Open
Abstract
The physiological state of the human macrophage may impact the metabolism and the persistence of Mycobacterium tuberculosis. This pathogen senses and counters the levels of O2, CO, reactive oxygen species (ROS), and pH in macrophages. M. tuberculosis responds to oxidative stress through WhiB3. The goal was to determine the effect of NADPH oxidase (NOX) modulation and oxidative agents on the expression of whiB3 and genes involved in lipid metabolism (lip-Y, Icl-1, and tgs-1) in intracellular mycobacteria. Human macrophages were first treated with NOX modulators such as DPI (ROS inhibitor) and PMA (ROS activator), or with oxidative agents (H2O2 and generator system O2•-), and then infected with mycobacteria. We determined ROS production, cell viability, and expression of whiB3, as well as genes involved in lipid metabolism. PMA, H2O2, and O2•- increased ROS production in human macrophages, generating oxidative stress in bacteria and augmented the gene expression of whiB3, lip-Y, Icl-1, and tgs-1. Our results suggest that ROS production in macrophages induces oxidative stress in intracellular bacteria inducing whiB3 expression. This factor may activate the synthesis of reserve lipids produced to survive in the latency state, which allows its persistence for long periods within the host.
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4
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Hu JF, Yim D, Ma D, Huber SM, Davis N, Bacusmo JM, Vermeulen S, Zhou J, Begley TJ, DeMott MS, Levine SS, de Crécy-Lagard V, Dedon PC, Cao B. Quantitative mapping of the cellular small RNA landscape with AQRNA-seq. Nat Biotechnol 2021; 39:978-988. [PMID: 33859402 PMCID: PMC8355021 DOI: 10.1038/s41587-021-00874-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/25/2021] [Indexed: 12/23/2022]
Abstract
Current next-generation RNA-sequencing (RNA-seq) methods do not provide accurate quantification of small RNAs within a sample, due to sequence-dependent biases in capture, ligation and amplification during library preparation. We present a method, absolute quantification RNA-sequencing (AQRNA-seq), that minimizes biases and provides a direct, linear correlation between sequencing read count and copy number for all small RNAs in a sample. Library preparation and data processing were optimized and validated using a 963-member microRNA reference library, oligonucleotide standards of varying length, and RNA blots. Application of AQRNA-seq to a panel of human cancer cells revealed >800 detectable miRNAs that varied during cancer progression, while application to bacterial transfer RNA pools, with the challenges of secondary structure and abundant modifications, revealed 80-fold variation in tRNA isoacceptor levels, stress-induced site-specific tRNA fragmentation, quantitative modification maps, and evidence for stress-induced, tRNA-driven, codon-biased translation. AQRNA-seq thus provides a versatile means to quantitatively map the small RNA landscape in cells.
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Affiliation(s)
- Jennifer F Hu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Bristol Myers Squibb, Seattle, WA, USA
| | - Daniel Yim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- A*STAR Genome Institute of Singapore, Singapore, Singapore
| | - Duanduan Ma
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sabrina M Huber
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Laboratory of Toxicology, ETH Zürich, Zürich, Switzerland
| | - Nick Davis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Theon Therapeutics, Cambridge, MA, USA
| | - Jo Marie Bacusmo
- Department of Microbiology & Cell Science, University of Florida, Gainesville, FL, USA
| | - Sidney Vermeulen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jieliang Zhou
- KK Research Center, KK Women's and ChildrenBristol Myers Squibb's Hospital, Singapore, Singapore
| | - Thomas J Begley
- The RNA Institute and Department of Biology, University at Albany, Albany, NY, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stuart S Levine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance IRG, Singapore, Singapore.
| | - Bo Cao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance IRG, Singapore, Singapore.
- College of Life Sciences, Qufu Normal University, Qufu, China.
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5
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Hadizadeh Tasbiti A, Yari S, Siadat SD, Karimipoor M, Badmasti F, Masoumi M, Abdolrahimi F, Khanipour S, Hassanzadeh SM, Ghalami Nobar M, Yari F. Comparing mRNA expression and protein abundance in MDR Mycobacterium tuberculosis: Novel protein candidates, Rv0443, Rv0379 and Rv0147 as TB potential diagnostic or therapeutic targets. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 30:e00641. [PMID: 34189062 PMCID: PMC8220328 DOI: 10.1016/j.btre.2021.e00641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 11/25/2022]
Abstract
Tuberculosis (TB) is a sizable public health threat in the world. This study was conducted to determine the differential protein composition between susceptible and MDRTB strains. Tuberculosis proteins were extracted by Triton™ X-114 and ammonium sulfate. Two-dimensional gel electrophoresis protein spots were selected for identification by mass spectrometry and mRNA expression levels were measured by real- time PCR. 2DE-Western blot and T cell epitope prediction for identified proteins were made by the IEDB server. The result shows at least six protein spots (Rv0147, Rv3597c, Rv0379, Rv3699, Rv1392 and Rv0443) were differentially expressed in MDRTB isolates. However, difference in mRNA gene expression was not found in the six mRNA genes. 2DE-Western blot procedures indicated strong reaction against MDRTB proteins corresponds to 13, 16 and 55 kDa areas that might be used as new diagnostic tools. In conclusion, these MDRTB proteins identified in this study could be reliable TB diagnostic candidates or therapeutic targets.
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Affiliation(s)
- Alireza Hadizadeh Tasbiti
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shamsi Yari
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Morteza Masoumi
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
| | - Farid Abdolrahimi
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
| | - Sharareh Khanipour
- Tuberculosis and Pulmonary Research Dept. Pasteur Institute of Iran, Tehran, Iran
| | | | - Mostafa Ghalami Nobar
- Reference Health Laboratory, Iran Ministry of Health and Medical Education, Tehran, Iran
| | - Fatemeh Yari
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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6
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Machado MC, Vimbela GV, Silva-Oliveira TT, Bose A, Tripathi A. The response of Synechococcus sp. PCC 7002 to micro-/nano polyethylene particles - Investigation of a key anthropogenic stressor. PLoS One 2020; 15:e0232745. [PMID: 32609722 PMCID: PMC7329024 DOI: 10.1371/journal.pone.0232745] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/27/2020] [Indexed: 01/09/2023] Open
Abstract
Microplastics or plastic particles less than 5 mm in size are a ubiquitous and damaging pollutant in the marine environment. However, the interactions between these plastic particles and marine microorganisms are just starting to be understood. The objective of this study was to measure the responses of a characteristic marine organism (Synechococcus sp. PCC 7002) to an anthropogenic stressor (polyethelene nanoparticles and microparticles) using molecular techniques. This investigation showed that polyethylene microparticles and nanoparticles have genetic, enzymatic and morphological effects on Synechococcus sp. PCC 7002. An RT-PCR analysis showed increases in the expression of esterase and hydrolase genes at 5 days of exposure to polyethylene nanoparticles and at 10 days of exposure to polyethylene microparticles. A qualitative enzymatic assay also showed esterase activity in nanoparticle exposed samples. Cryo-scanning electron microscopy was used to assess morphological changes in exopolymer formation resulting from exposure to polyethylene microparticles and nanoparticles. The data from this paper suggests that microplastic and nanoplastics could be key microbial stressors and should be investigated in further detail.
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Affiliation(s)
- Mary C. Machado
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, United States of America
| | - Gina V. Vimbela
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, United States of America
| | | | - Arijit Bose
- University of Rhode Island, Kingston, Rhode Island, United States of America
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, United States of America
- * E-mail:
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7
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Dhar BC, Reed AJ, Mitra S, Rodriguez Sanchez P, Nedorezova DD, Connelly RP, Rohde KH, Gerasimova YV. Cascade of deoxyribozymes for the colorimetric analysis of drug resistance in Mycobacterium tuberculosis. Biosens Bioelectron 2020; 165:112385. [PMID: 32729510 DOI: 10.1016/j.bios.2020.112385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 02/01/2023]
Abstract
A visual cascade detection system has been applied to the detection and analysis of drug-resistance profile of Mycobacterium tuberculosis complex (MTC), a causative agent of tuberculosis. The cascade system utilizes highly selective split RNA-cleaving deoxyribozyme (sDz) sensors. When activated by a complementary nucleic acid, sDz releases the peroxidase-like deoxyribozyme apoenzyme, which, in complex with a hemin cofactor, catalyzes the color change of the sample's solution. The excellent selectivity of the cascade has allowed for the detection of point mutations in the sequences of the MTC rpoB, katG, and gyrA genes, which are responsible for resistance to rifampin, isoniazid, and fluoroquinolone, respectively. When combined with isothermal nucleic acid sequence based amplification (NASBA), the assay was able to detect amplicons of 16S rRNA and katG mRNA generated from 0.1 pg and 10 pg total RNA taken for NASBA, respectively, in less than 2 h, producing a signal detectable with the naked eye. The proposed assay may become a prototype for point-of-care diagnosis of drug resistant bacteria with visual signal output.
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Affiliation(s)
- Bidhan C Dhar
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Adam J Reed
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Suvra Mitra
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | | | - Daria D Nedorezova
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Ryan P Connelly
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Kyle H Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA.
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8
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Deng H, Zhou X, Liu Q, Li B, Liu H, Huang R, Xing D. Paperfluidic Chip Device for Small RNA Extraction, Amplification, and Multiplexed Analysis. ACS APPLIED MATERIALS & INTERFACES 2017; 9:41151-41158. [PMID: 29116747 DOI: 10.1021/acsami.7b12637] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Small RNAs have been considered as potential biomarkers of various human diseases. Sensitive and multiplexed determination of small RNAs with point-of-care (POC) assay would be of great significance. Herein, an integrated paperfluidic chip device for multiplexed small RNA analysis was developed for the first time. In this system, the extraction and purification of small RNA was completed through a poly(ether sulfone) (PES) paper chip without the need for centrifugation. Subsequently, a newly designed hairpin probe-exponential amplification reaction (HP-EXPAR) was directly performed within the extraction paper chip. For the simultaneous realization of multiple detection, a multilayer paper chip was designed in a foldable manner with more portability and usability. Quantum dots (QDs) were employed as signal labels, which endowed this assay with high optical detection efficiency. Moreover, magnetic sheets were introduced as an alternative method for layer stacking, not only guaranteeing adjacent layers are in contact but also facilitating the sample dispersion. With these outstanding characteristics, our platform obtained a satisfactory sensitivity range from 3 × 105 to 3 × 108 copies with a limit of 3 × 106 copies. Additionally, the multiplex small RNA analyses from various cancer cells were in good agreement with the results of the real-time polymerase chain reaction (qRT-PCR). More importantly, simultaneous analysis of two types of miRNAs from clinical tumor samples demonstrated the clinical applicability of the system. Therefore, the proposed paper-based device shows great promise for POC applications in the future.
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Affiliation(s)
- Huaping Deng
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University , Guangzhou 510631, China
| | - Xiaoming Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University , Guangzhou 510631, China
| | - Qianwen Liu
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine , Guangzhou 510060, China
| | - Bofan Li
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University , Guangzhou 510631, China
| | - Hongxing Liu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University , Guangzhou 510631, China
| | - Ru Huang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University , Guangzhou 510631, China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University , Guangzhou 510631, China
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9
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tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence. Nat Commun 2016; 7:13302. [PMID: 27834374 PMCID: PMC5114619 DOI: 10.1038/ncomms13302] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 09/21/2016] [Indexed: 02/07/2023] Open
Abstract
Microbial pathogens adapt to the stress of infection by regulating transcription, translation and protein modification. We report that changes in gene expression in hypoxia-induced non-replicating persistence in mycobacteria—which models tuberculous granulomas—are partly determined by a mechanism of tRNA reprogramming and codon-biased translation. Mycobacterium bovis BCG responded to each stage of hypoxia and aerobic resuscitation by uniquely reprogramming 40 modified ribonucleosides in tRNA, which correlate with selective translation of mRNAs from families of codon-biased persistence genes. For example, early hypoxia increases wobble cmo5U in tRNAThr(UGU), which parallels translation of transcripts enriched in its cognate codon, ACG, including the DosR master regulator of hypoxic bacteriostasis. Codon re-engineering of dosR exaggerates hypoxia-induced changes in codon-biased DosR translation, with altered dosR expression revealing unanticipated effects on bacterial survival during hypoxia. These results reveal a coordinated system of tRNA modifications and translation of codon-biased transcripts that enhance expression of stress response proteins in mycobacteria. Mycobacteria can adapt to the stress of human infection by entering a dormant state. Here the authors show that hypoxia-induced dormancy in M. bovis BCG involves the reprogramming of tRNA wobble modifications and copy numbers, coupled with biased use of synonymous codons in survival genes.
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10
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Oh TS, Kang HY, Nam YS, Kim YJ, You EK, Lee MY, Cho SY, Lee HJ. An Effective Method of RNA Extraction from Mycobacterium tuberculosis. ANNALS OF CLINICAL MICROBIOLOGY 2016. [DOI: 10.5145/acm.2016.19.1.20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Tae Sang Oh
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Hee Yoon Kang
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - You Sun Nam
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Eun Kyung You
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Min Young Lee
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Sun Young Cho
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Hee Joo Lee
- Department of Laboratory Medicine, Kyung Hee University School of Medicine, Seoul, Korea
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11
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Cai WM, Chionh YH, Hia F, Gu C, Kellner S, McBee ME, Ng CS, Pang YLJ, Prestwich EG, Lim KS, Babu IR, Begley TJ, Dedon PC. A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. Methods Enzymol 2015; 560:29-71. [PMID: 26253965 DOI: 10.1016/bs.mie.2015.03.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. This chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: (1) RNA isolation, (2) RNA purification, (3) RNA hydrolysis to individual ribonucleosides, (4) chromatographic resolution of ribonucleosides, (5) identification of the full set of modified ribonucleosides, (6) mass spectrometric quantification of ribonucleosides, (6) interrogation of ribonucleoside datasets, and (7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision, and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response. The methods described here should find wide use in virtually any analysis involving RNA modifications.
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Affiliation(s)
- Weiling Maggie Cai
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Yok Hian Chionh
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Fabian Hia
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chee Sheng Ng
- Singapore-MIT Alliance for Research and Technology, Singapore; School of Biological Sciences, Nanyang Technological Institute, Singapore
| | - Yan Ling Joy Pang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kok Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - I Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Thomas J Begley
- College of Nanoscale Engineering and Science, State University of New York, Albany, New York, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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