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Zhang D, Wu J, Yuan Y, Li X, Gao X, Kang D, Zhang X, Huang SS, Dai P. Mitochondrial tRNA Ser(UCN) mutations associated non-syndromic sensorineural hearing loss in Chinese families. Heliyon 2024; 10:e27041. [PMID: 38501023 PMCID: PMC10945119 DOI: 10.1016/j.heliyon.2024.e27041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 12/29/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
Mitochondrial transfer RNA mutation is one of the most important causes of hereditary hearing loss in humans. Mitochondrial transfer RNASer (UCN) gene is another hot spot for mutations associated with non-syndromic hearing loss, besides the 12S ribosomal RNA gene. In this study, we assessed the clinical phenotype and the molecular characteristics of two Chinese families with non-syndromic hearing loss. Mutational analysis revealed that 7445A > G and 7510T > C mutations in the mitochondrial transfer RNASer (UCN) gene were the molecular etiology of Family 1 and Family 2, respectively. However, the clinical and genetic characteristics of the two families carrying the above mutations in the transfer RNASer (UCN) gene exhibited a variable expression of hearing loss and an incomplete penetrance. Sequencing analysis of the complete mitochondrial genome showed the presence of transfer RNATrp 5568A > G and NADH-ubiquinone oxidoreductase chain 4 11696G > A mutations in Family 1. The mitochondrial haplotype analysis showed that the two families belonged to Asian D4 and M80'D haplotypes, respectively, and no pathogenic variations were found in the nuclear genes. To our knowledge, our study is the first to report 7445A > G and 7510T > C mutations in the mitochondrial transfer RNASer (UCN) gene, in multi-generation non-syndromic hearing loss pedigrees from China. Our study suggests that 5568A > G and 11696G > A mutations may enhance the penetrance of hearing loss in Chinese Family 1, while mitochondrial haplotypes and known nuclear genes may not be modifiers for the phenotypic expression of 7445A > G and 7510T > C mutations in these Chinese families.
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Affiliation(s)
- Dejun Zhang
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
- ColIege of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China
- State Key Lab of Hearing Science, Ministry of Education, National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Jie Wu
- ColIege of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China
- State Key Lab of Hearing Science, Ministry of Education, National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Yongyi Yuan
- ColIege of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China
- State Key Lab of Hearing Science, Ministry of Education, National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Xiaohong Li
- Department of Otolaryngology, Head and Neck Surgery, National Children's Medical Center/Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xue Gao
- Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Dongyang Kang
- ColIege of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China
- State Key Lab of Hearing Science, Ministry of Education, National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Xin Zhang
- ColIege of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China
- State Key Lab of Hearing Science, Ministry of Education, National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Sha-sha Huang
- ColIege of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China
- State Key Lab of Hearing Science, Ministry of Education, National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Pu Dai
- ColIege of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China
- State Key Lab of Hearing Science, Ministry of Education, National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
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Davey-Young J, Hasan F, Tennakoon R, Rozik P, Moore H, Hall P, Cozma E, Genereaux J, Hoffman KS, Chan PP, Lowe TM, Brandl CJ, O’Donoghue P. Mistranslating the genetic code with leucine in yeast and mammalian cells. RNA Biol 2024; 21:1-23. [PMID: 38629491 PMCID: PMC11028032 DOI: 10.1080/15476286.2024.2340297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Translation fidelity relies on accurate aminoacylation of transfer RNAs (tRNAs) by aminoacyl-tRNA synthetases (AARSs). AARSs specific for alanine (Ala), leucine (Leu), serine, and pyrrolysine do not recognize the anticodon bases. Single nucleotide anticodon variants in their cognate tRNAs can lead to mistranslation. Human genomes include both rare and more common mistranslating tRNA variants. We investigated three rare human tRNALeu variants that mis-incorporate Leu at phenylalanine or tryptophan codons. Expression of each tRNALeu anticodon variant in neuroblastoma cells caused defects in fluorescent protein production without significantly increased cytotoxicity under normal conditions or in the context of proteasome inhibition. Using tRNA sequencing and mass spectrometry we confirmed that each tRNALeu variant was expressed and generated mistranslation with Leu. To probe the flexibility of the entire genetic code towards Leu mis-incorporation, we created 64 yeast strains to express all possible tRNALeu anticodon variants in a doxycycline-inducible system. While some variants showed mild or no growth defects, many anticodon variants, enriched with G/C at positions 35 and 36, including those replacing Leu for proline, arginine, alanine, or glycine, caused dramatic reductions in growth. Differential phenotypic defects were observed for tRNALeu mutants with synonymous anticodons and for different tRNALeu isoacceptors with the same anticodon. A comparison to tRNAAla anticodon variants demonstrates that Ala mis-incorporation is more tolerable than Leu at nearly every codon. The data show that the nature of the amino acid substitution, the tRNA gene, and the anticodon are each important factors that influence the ability of cells to tolerate mistranslating tRNAs.
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Affiliation(s)
- Josephine Davey-Young
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Farah Hasan
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Rasangi Tennakoon
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Peter Rozik
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Henry Moore
- Department of Biomolecular Engineering, Baskin School of Engineering & UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Peter Hall
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Ecaterina Cozma
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | | | - Patricia P. Chan
- Department of Biomolecular Engineering, Baskin School of Engineering & UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Todd M. Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering & UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Christopher J. Brandl
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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Yuan C, Li Z, Luo X, Huang P, Guo L, Lu M, Xia J, Xiao Y, Zhou XL, Chen M. Mammalian trans-editing factor ProX is able to deacylate tRNA Thr mischarged with alanine. Int J Biol Macromol 2023; 253:127121. [PMID: 37778588 DOI: 10.1016/j.ijbiomac.2023.127121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/16/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The precise coupling of tRNAs with their cognate amino acids, known as tRNA aminoacylation, is a stringently regulated process that governs translation fidelity. To ensure fidelity, organisms deploy multiple layers of editing mechanisms to correct mischarged tRNAs. Prior investigations have unveiled the propensity of eukaryotic AlaRS to erroneously attach alanine onto tRNACys and tRNAThr featuring the G4:U69 base pair. In light of this, and given ProXp-ala's capacity in deacylating Ala-tRNAPro, we embarked on exploring whether this trans-editing factor could extend its corrective function to encompass these mischarged tRNAs. Our in vitro deacylation assays demonstrate that murine ProXp-ala (mProXp-ala) is able to efficiently hydrolyze Ala-tRNAThr, while Ala-tRNACys remains unaffected. Subsequently, we determined the first structure of eukaryotic ProXp-ala, revealing a dynamic helix α2 involved in substrate binding. By integrating molecular dynamics simulations and biochemical assays, we pinpointed the pivotal interactions between mProXp-ala and Ala-tRNA, wherein the basic regions of mProXp-ala as well as the C3-G70 plays essential role in recognition. These observations collectively provide a cogent rationale for mProXp-ala's deacylation proficiency against Ala-tRNAThr. Our findings offer valuable insights into the translation quality control within higher eukaryotic organisms, where the fidelity of translation is safeguarded by the multi-functionality of extensively documented proteins.
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Affiliation(s)
- Chen Yuan
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zihan Li
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyu Luo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Pingping Huang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lijie Guo
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Meiling Lu
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yibei Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China.
| | - Xiao-Long Zhou
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Meirong Chen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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Bhowal P, Roy B, Ganguli S, Igloi GL, Banerjee R. Elucidating the structure-function attributes of a trypanosomal arginyl-tRNA synthetase. Mol Biochem Parasitol 2023; 256:111597. [PMID: 37852416 DOI: 10.1016/j.molbiopara.2023.111597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/20/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are fundamental components of the protein translation machinery. In light of their pivotal role in protein synthesis and structural divergence among species, they have always been considered potential targets for the development of antimicrobial compounds. Arginyl-tRNA synthetase from Trypanosoma cruzi (TcArgRS), the parasite responsible for causing Chagas Disease, contains a 100-amino acid insertion that was found to be completely absent in the human counterpart of similar length, as ascertained from multiple sequence alignment results. Thus, we were prompted to perform a preliminary characterization of TcArgRS using biophysical, biochemical, and bioinformatics tools. We expressed the protein in E. coli and validated its in-vitro enzymatic activity. Additionally, analysis of DTNB kinetics, Circular dichroism (CD) spectra, and ligand-binding studies using intrinsic tryptophan fluorescence measurements aided us to understand some structural features in the absence of available crystal structures. Our study indicates that TcArgRS can discriminate between L-arginine and its analogues. Among the many tested substrates, only L-canavanine and L-thioarginine, a synthetic arginine analogue exhibited notable activation. The binding of various substrates was also determined using in silico methods. This study may provide a viable foundation for studying small compounds that can be targeted against TcArgRS.
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Affiliation(s)
- Pratyasha Bhowal
- Department of Biotechnology and Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, India
| | - Bappaditya Roy
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sayak Ganguli
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Park Street, Mullick Bazar, Kolkata 700 016, India.
| | - Gabor L Igloi
- Institute of Biology III, University of Freiburg, Schänzlestr 1, D-79104 Freiburg, Germany
| | - Rajat Banerjee
- Department of Biotechnology and Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, India.
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5
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Saquib M, Agnihotri P, Biswas S. Interrelated grid of non-coding RNA: An important aspect in Rheumatoid Arthritis pathogenesis. Mol Biol Rep 2023:10.1007/s11033-023-08543-w. [PMID: 37294467 DOI: 10.1007/s11033-023-08543-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
Inflammation and autoimmunity are the root cause of rheumatoid arthritis, a destructive disease of joints. Multiple biomolecules are involved in the pathogenesis of RA and are related to various events of molecular biology. RNA is a versatile biomolecule, playing numerous roles at structural, functional, and regulatory stages to maintain cellular homeostasis. The involvement of RNA (coding/non-coding) in disease development and progression has left a wide whole to fill with newer approaches. Non-coding RNAs belong to the housekeeping and regulatory categories and both have their specific roles, and their alteration causes specific implications in disease pathogenesis. Housekeeping RNAs, rRNA, tRNA and regulatory RNA, micro-RNA, circular RNA, piRNA and long non-coding RNA were found to be important regulators of inflammation. They work at the pre-and post-transcriptional levels and were found to be more intriguing to study their regulatory impact on disease pathogenesis. The review addresses a question on how the non-coding RNA gets involved in early RA pathogenesis and can be utilized to know their targets to understand the disease better and make way towards the unresolved mystery of RA development.
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Affiliation(s)
- Mohd Saquib
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prachi Agnihotri
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sagarika Biswas
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Integrative and Functional Biology Department CSIR- Institute of Genomics & Integrative Biology, Mall Road, Delhi, 110 007, India.
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Yamagami R, Hori H. Functional analysis of tRNA modification enzymes using mutational profiling. Methods Enzymol 2023; 692:69-101. [PMID: 37925188 DOI: 10.1016/bs.mie.2023.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Transfer RNA (tRNA) delivers amino acids to the ribosome and functions as an essential adapter molecule for decoding codons on the messenger RNA (mRNA) during protein synthesis. Before attaining their proper activity, tRNAs undergo multiple post-transcriptional modifications with highly diversified roles such as stabilization of the tRNA structure, recognition of aminoacyl tRNA synthetases, precise codon-anticodon recognition, support of viral replication and onset of immune responses. The synthesis of the majority of modified nucleosides is catalyzed by a site-specific tRNA modification enzyme. This chapter provides a detailed protocol for using mutational profiling to analyze the enzymatic function of a tRNA methyltransferase in a high-throughput manner. In a previous study, we took tRNA m1A22 methyltransferase TrmK from Geobacillus stearothermophilus as a model tRNA methyltransferase and applied this protocol to gain mechanistic insights into how TrmK recognizes the substrate tRNAs. In theory, this protocol can be used unaltered for studying enzymes that catalyze modifications at the Watson-Crick face such as 1-methyladenosine (m1A), 3-methylcytosine (m3C), 3-methyluridine (m3U), 1-methylguanosine (m1G), and N2,N2-dimethylguanosine (m22G).
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Affiliation(s)
- Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
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Bommisetti P, Young A, Bandarian V. Elucidation of the substrate of tRNA-modifying enzymes MnmEG leads to in vitro reconstitution of an evolutionarily conserved uridine hypermodification. J Biol Chem 2022; 298:102548. [PMID: 36181794 PMCID: PMC9626948 DOI: 10.1016/j.jbc.2022.102548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022] Open
Abstract
The evolutionarily conserved bacterial proteins MnmE and MnmG collectively install a carboxymethylaminomethyl (cmnm) group at the fifth position of wobble uridines of several tRNA species. While the reaction catalyzed by MnmEG is one of the central steps in the biosynthesis of the methylaminomethyl (mnm) posttranscriptional tRNA modification, details of the reaction remain elusive. Glycine is known to be the source of the carboxy methylamino moiety of cmnm, and a tetrahydrofolate (THF) analog is thought to supply the one carbon that is appended to the fifth position of U. However, the nature of the folate analog remains unknown. This article reports the in vitro biochemical reconstitution of the MnmEG reaction. Using isotopically labeled methyl and methylene THF analogs, we demonstrate that methylene THF is the true substrate. We also show that reduced FAD is required for the reaction and that DTT can replace the NADH in its role as a reductant. We discuss the implications of these methylene-THF and reductant requirements on the mechanism of this key tRNA modification catalyzed by MnmEG.
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Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Anthony Young
- Soliome Inc, 479 Jessie Street, San Francisco, CA 94103, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States.
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Fu X, He X, Yang Y, Jiang S, Wang S, Peng X, Tang G, Zong T, Li X, Zhang Y, Zou Y, Yu T. Identification of transfer RNA-derived fragments and their potential roles in aortic dissection. Genomics 2021; 113:3039-49. [PMID: 34214628 DOI: 10.1016/j.ygeno.2021.06.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/19/2021] [Accepted: 06/27/2021] [Indexed: 12/15/2022]
Abstract
Emerging evidence suggests that majority of the transfer RNA (tRNA)-derived small RNA, including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), play a significant role in the molecular mechanisms underlying some human diseases. However, expression of tRFs/tiRNAs and their potential roles in aortic dissection (AD) remain unclear. This study examined the expression characteristics and explored the functional roles of tRFs/tiRNAs in AD using RNA-sequencing, bioinformatics, real-time quantitative reverse transcription polymerase chain reaction, and loss- and gain-of-function analysis. Results revealed that a total of 41 tRFs/tiRNAs were dysregulated in the AD group compared to the control group. Among them, 12 were upregulated and 29 were downregulated (fold change≥1.5 and p < 0.05). RT-qPCR results revealed that expressions of tRF-1:30-chrM.Met-CAT was significantly upregulated, while that of tRF-54:71-chrM.Trp-TCA and tRF-1:32-chrM.Cys-GCA were notably downregulated; expression patterns were consistent with the RNA sequencing data. Bioinformatic analysis showed that a variety of related pathways might be involved in the pathogenesis of AD. Functionally, tRF-1:30-chrM.Met-CAT could facilitate proliferation, migration, and phenotype switching in vascular smooth muscle cells (VSMCs), which might serve as a significant regulator in the progression of AD. In summary, the study illustrated that tRFs/tiRNAs expressed in AD tissues have potential biological functions and may act as promising biomarkers or therapeutic targets for AD.
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Wang ZS, Zhou HC, Wei CY, Wang ZH, Hao X, Zhang LH, Li JZ, Wang ZL, Wang H. Global survey of miRNAs and tRNA-derived small RNAs from the human parasitic protist Trichomonas vaginalis. Parasit Vectors 2021; 14:87. [PMID: 33514387 PMCID: PMC7844918 DOI: 10.1186/s13071-020-04570-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/28/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Small non-coding RNAs play critical regulatory roles in post-transcription. However, their characteristics in Trichomonas vaginalis, the causative agent of human sexually transmitted trichomoniasis, still remain to be determined. METHODS Small RNA transcriptomes from Trichomonas trophozoites were deep sequenced using the Illumina NextSeq 500 system and comprehensively analyzed to identify Trichomonas microRNAs (miRNAs) and transfer RNA (tRNA)-derived small RNAs (tsRNAs). The tsRNA candidates were confirmed by stem-loop quantitative reverse transcription-PCR, and motifs to guide the cleavage of tsRNAs were predicted using the GLAM2 algorithm. RESULTS The miRNAs were found to be present in T. vaginalis but at an extremely low abundance (0.0046%). Three categories of endogenous Trichomonas tsRNAs were identified, namely 5'tritsRNAs, mid-tritsRNAs and 3'tritsRNAs, with the 5'tritsRNAs constituting the dominant category (67.63%) of tsRNAs. Interestingly, the cleavage site analysis verified both conventional classes of tRNA-derived fragments (tRFs) and tRNA-halves in tritsRNAs, indicating the expression of tRNA-halves in the non-stress condition. A total of 25 tritsRNAs were experimentally confirmed, accounting for 78.1% of all tested candidates. Three motifs were predicted to guide the production of tritsRNAs. The results prove the expression of tRFs and tRNA-halves in the T. vaginalis transcriptome. CONCLUSIONS This is the first report of genome-wide investigation of small RNAs, particularly tsRNAs and miRNAs, from Trichomonas parasites. Our findings demonstrate the expression profile of tsRNAs in T. vaginalis, while miRNA was barely detected. These results may promote further research aimed at gaining a better understanding of the evolution of small non-coding RNA in T. vaginalis and their functions in the pathogenesis of trichomoniasis.
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Affiliation(s)
- Zhen-Sheng Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China.,NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Hong-Chang Zhou
- School of Medicine, Huzhou University and Huzhou Central Hospital, Huzhou, 313000, Zhejiang province, China
| | - Chun-Yan Wei
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China
| | - Zhi-Hua Wang
- Department of Immunology, Guilin Medical University, Guilin, 541000, Guangxi province, China
| | - Xiao Hao
- Blood Chamber, Blood Station of Jinan, Jinan, 250000, Shandong province, China
| | - Lian-Hui Zhang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China
| | - Jing-Zhong Li
- NHC Key Laboratory of Echinococcosis Prevention and Control, #21 linkuo North Road, Chengguan District, Lhasa, 850000, Tibet Autonomous Region, People's Republic of China
| | - Zeng-Lei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
| | - Heng Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China.
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Abstract
During their biosynthesis, transfer RNAs (tRNAs) are decorated with a large number of posttranscriptional chemical modifications. Methods to directly detect the introduction of posttranscriptional modifications during tRNA maturation are rare and do not provide information on the temporality of modification events. Here, we report a methodology, using NMR as a tool to monitor tRNA maturation in a nondisruptive and continuous fashion in cellular extracts. This method requires the production of substrate tRNA transcripts devoid of modifications and active cell extracts containing the necessary cellular enzymatic activities to modify RNA. The present protocol describes these different aspects of our method and reports the time-resolved NMR monitoring of the yeast tRNAPhe maturation as an example. The NMR-based methodology presented here could be adapted to investigate diverse features in tRNA maturation.
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Affiliation(s)
- Alexandre Gato
- Expression génétique microbienne, UMR 8261, CNRS, Université de Paris, Institut de biologie physico-chimique (IBPC), Paris, France
| | - Marjorie Catala
- Expression génétique microbienne, UMR 8261, CNRS, Université de Paris, Institut de biologie physico-chimique (IBPC), Paris, France
| | - Carine Tisné
- Expression génétique microbienne, UMR 8261, CNRS, Université de Paris, Institut de biologie physico-chimique (IBPC), Paris, France
| | - Pierre Barraud
- Expression génétique microbienne, UMR 8261, CNRS, Université de Paris, Institut de biologie physico-chimique (IBPC), Paris, France.
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Zhang ZY, Zhang CH, Yang JJ, Xu PP, Yi PJ, Hu ML, Peng WJ. Genome-wide analysis of hippocampal transfer RNA-derived small RNAs identifies new potential therapeutic targets of Bushen Tiansui formula against Alzheimer's disease. J Integr Med 2020; 19:135-143. [PMID: 33334712 DOI: 10.1016/j.joim.2020.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Bushen Tiansui formula (BSTSF), a traditional Chinese medicine prescription, has been widely used to treat Alzheimer's disease (AD). However, the mechanisms underlying its effects remain largely unknown. In this study, a rat AD model was used to study the effects of BSTSF on cognitive performance and expression of transfer RNA-derived small RNAs (tsRNAs) in the hippocampus, to determine whether treatment of AD with BSTSF could regulate the expression of tsRNAs, a novel small non-coding RNA. METHODS To generate a validated AD model, oligomeric amyloid-β1-42 (Aβ1-42) was injected intracerebroventricularly into rats. The Morris water maze (MWM) test was used to evaluate rat cognitive performance, and tsRNA-sequencing was conducted to examine tsRNA expression in the rat hippocampus. Potential targets were validated by quantitative real-time polymerase chain reaction (qRT-PCR). Bioinformatic analyses were conducted to investigate the biological function of candidate tsRNAs. RESULTS The learning and memory deficits of Aβ1-42-induced AD rats, assessed by MWM tests, were clearly ameliorated by BSTSF treatment. A total of 387 tsRNAs were detected in the rat hippocampus. Among them, 13 were significantly dysregulated in AD rats compared with sham control rats, while 57 were markedly altered by BSTSF treatment, relative to untreated AD rats (fold change ≥ 2 and P < 0.05). Moreover, six BSTSF treatment-related tsRNAs were identified and validated by qRT-PCR. Bioinformatic analyses indicated that the six treatment-related tsRNAs had potential therapeutic roles, via multiple signaling pathways and Gene Ontology biological functions, including cyclic adenosine monophosphate and retrograde endocannabinoid signaling. CONCLUSION This study identified a previously uncharacterized mechanism underlying the effects of BSTSF in alleviating the learning and memory deficits in Aβ1-42-induced AD rats, demonstrating that tsRNAs are potential therapeutic targets of BSTSF in the treatment of AD.
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Affiliation(s)
- Zhe-Yu Zhang
- Department of Integrated Traditional Chinese & Western Medicine, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan Province, China
| | - Chun-Hu Zhang
- Department of Integrated Traditional Chinese & Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Jing-Jing Yang
- Department of Integrated Traditional Chinese & Western Medicine, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Pan-Pan Xu
- Department of Integrated Traditional Chinese & Western Medicine, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan Province, China
| | - Peng-Ji Yi
- Department of Integrated Traditional Chinese & Western Medicine, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan Province, China
| | - Mu-Li Hu
- Department of Scientific Research, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan Province, China
| | - Wei-Jun Peng
- Department of Integrated Traditional Chinese & Western Medicine, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan Province, China.
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Green JA, Ansari MY, Ball H, Haqqi TM. tRNA-derived fragments (tRFs) regulate post-transcriptional gene expression via AGO-dependent mechanism in IL-1β stimulated chondrocytes. Osteoarthritis Cartilage 2020; 28:1102-1110. [PMID: 32407895 PMCID: PMC8418333 DOI: 10.1016/j.joca.2020.04.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVES Recent studies have shown that tRNA-derived RNA fragments (tRFs) are novel regulators of post-transcriptional gene expression. However, the expression profiles and their role in post-transcriptional gene regulation in chondrocytes is unknown. Here, we determined tRFs expression profile and explored tRF-3003a role in post-transcriptional gene regulation in IL-1β stimulated chondrocytes. METHODS We used qPCR arrays to determine tRNAs and tRFs expression in age- and sex-matched primary human OA chondrocytes and TC28/I2 cells stimulated with IL-1β. Chondrocytes were transfected with tRNA-CysGCA overexpression plasmid or tRF-3003a mimic and 3'UTR luciferase reporter plasmids of mRNAs harboring predicted tRF target "seed sequence". The AGO-RNA-induced silencing complex (AGO-RISC)-dependent repressive activity of tRF-3003a was determined by siRNA-mediated knockdown of AGO2. RESULTS IL-1β increased the expression levels of specific tRNAs and of tRF-3003a, a type 3 tRF produced by the cleavage of tRNA-CysGCA. tRF-3003a "seed sequence" was identified in the 3'UTR of JAK3 mRNA and tRNA-CysGCA overexpression or transfection of a tRF-3003a mimic in chondrocytes downregulated JAK3 expression and significantly reduced the activity of the 3'UTR reporter. RIP assay showed enrichment of tRF-3003a into AGO2/RISC in IL-1β treated chondrocytes. The suppressive effect of tRF-3003a on JAK3 3'UTR reporter was abrogated with siRNA-mediated depletion of AGO2. CONCLUSIONS We demonstrate that under pathological conditions chondrocytes display perturbations in the expression profile of specific tRNAs and tRFs. Furthermore, a specific tRF namely tRF-3003a can post-transcriptionally regulate JAK3 expression via AGO/RISC formation in chondrocytes. Identification of this novel mechanism may be of value in the design of precision therapies for OA.
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Affiliation(s)
- J. A. Green
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272
| | - M. Y. Ansari
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272
| | - H.C. Ball
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272
| | - T. M. Haqqi
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272,Corresponding author: Prof. Dr. Tariq M. Haqqi; Department of Anatomy & Neurobiology, Northeast Ohio Medical University, 4209 St Rt 44, Rootstown, OH 44272
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Catala M, Gato A, Tisné C, Barraud P. Preparation of Yeast tRNA Sample for NMR Spectroscopy. Bio Protoc 2020; 10:e3646. [PMID: 33659318 DOI: 10.21769/bioprotoc.3646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 11/02/2022] Open
Abstract
Transfer RNAs (tRNAs) are heavily decorated with post-transcriptional modifications during their biosynthesis. To fulfil their functions within cells, tRNAs undergo a tightly controlled biogenesis process leading to the formation of mature tRNAs. In addition, functions of tRNAs are often modulated by their modifications. Although the biological importance of post-transcriptional RNA modifications is widely appreciated, methods to directly detect their introduction during RNA biosynthesis are rare and do not easily provide information on the temporal nature of events. To obtain information on the tRNA maturation process, we have developed a methodology, using NMR as a tool to monitor tRNA maturation in a non-disruptive and continuous fashion in cellular extracts. By following the maturation of a model yeast tRNA with time-resolved NMR, we showed that modifications are introduced in a defined sequential order, and that the chronology is controlled by cross-talk between modification events. The implementation of this method requires the production for NMR spectroscopy of tRNA samples with different modification status, in order to identify the NMR signature of individual modifications. The production of tRNA samples for the analysis of modification pathways with NMR spectroscopy will be presented here and examplified on the yeast tRNAPhe, but can be extended to any other tRNA by changing the sequence of the construct. The protocol describes the production of unmodified tRNA samples by in vitro transcription, and the production of modified tRNA samples by recombinant expression of tRNAs in E. coli.
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Affiliation(s)
- Marjorie Catala
- Expression génétique microbienne, UMR 8261, CNRS, Université de Paris, Institut de biologie physico-chimique (IBPC), 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Alexandre Gato
- Expression génétique microbienne, UMR 8261, CNRS, Université de Paris, Institut de biologie physico-chimique (IBPC), 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Carine Tisné
- Expression génétique microbienne, UMR 8261, CNRS, Université de Paris, Institut de biologie physico-chimique (IBPC), 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Pierre Barraud
- Expression génétique microbienne, UMR 8261, CNRS, Université de Paris, Institut de biologie physico-chimique (IBPC), 13 rue Pierre et Marie Curie, 75005 Paris, France
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Janin M, Coll-SanMartin L, Esteller M. Disruption of the RNA modifications that target the ribosome translation machinery in human cancer. Mol Cancer 2020; 19:70. [PMID: 32241281 PMCID: PMC7114786 DOI: 10.1186/s12943-020-01192-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic and epigenetic changes deregulate RNA and protein expression in cancer cells. In this regard, tumors exhibit an abnormal proteome in comparison to the corresponding normal tissues. Translation control is a crucial step in the regulation of gene expression regulation under normal and pathological conditions that ultimately determines cellular fate. In this context, evidence shows that transfer and ribosomal RNA (tRNA and rRNA) modifications affect the efficacy and fidelity of translation. The number of RNA modifications increases with the complexity of organisms, suggesting an evolutionary diversification of the possibilities for fine-tuning the functions of coding and non-coding RNAs. In this review, we focus on alterations of modifications of transfer and ribosomal RNA that affect translation in human cancer. This variation in the RNA modification status can be the result of altered modifier expression (writers, readers or erasers), but also due to components of the machineries (C/D or H/ACA boxes) or alterations of proteins involved in modifier expression. Broadening our understanding of the mechanisms by which site-specific modifications modulate ribosome activity in the context of tumorigenesis will enable us to enrich our knowledge about how ribosomes can influence cell fate and form the basis of new therapeutic opportunities.
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Affiliation(s)
- Maxime Janin
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Laia Coll-SanMartin
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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15
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de Farias ST, José MV. Transfer RNA: The molecular demiurge in the origin of biological systems. Prog Biophys Mol Biol 2020; 153:28-34. [PMID: 32105652 DOI: 10.1016/j.pbiomolbio.2020.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 01/24/2023]
Abstract
Herein, we review recent works on the role that the tRNA molecule played in the early origins of biological systems. tRNAs gave origin to the first genes (mRNA), the peptidyl transferase center (PTC), the 16S ribosomal molecule, proto-tRNAs were at the core of a proto-translation system, and the anticodon and operational codes appeared in tRNAs molecules. Metabolic pathways emerged from evolutionary pressures of the decoding systems. The transitions from the RNA world to the ribonucleoprotein world to modern biological systems were driven by two kinds of tRNAs transitions, to wit, tRNAs leading to both mRNA and rRNA.
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Affiliation(s)
- Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Brazil.
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México CDMX, C.P. 04510, Mexico.
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16
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Su Z, Frost EL, Lammert CR, Przanowska RK, Lukens JR, Dutta A. tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal-immune-activation autism model. RNA Biol 2020; 17:1183-1195. [PMID: 31983265 DOI: 10.1080/15476286.2020.1721047] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
tRNA-derived small fragments (tRFs) and tRNA halves have emerging functions in different biological pathways, such as regulating gene expression, protein translation, retrotransposon activity, transgenerational epigenetic changes and response to environmental stress. However, small RNAs like tRFs and microRNAs in the maternal-fetal interface during gestation have not been studied extensively. Here we investigated the small RNA composition of mouse placenta/decidua, which represents the interface where the mother communicates with the foetus, to determine whether there are specific differences in tRFs and microRNAs during fetal development and in response to maternal immune activation (MIA). Global tRF expression pattern, just like microRNAs, can distinguish tissue types among placenta/decidua, fetal brain and fetal liver. In particular, 5' tRNA halves from tRNAGly, tRNAGlu, tRNAVal and tRNALys are abundantly expressed in the normal mouse placenta/decidua. Moreover, tRF and microRNA levels in the maternal-fetal interface change dynamically over the course of embryonic development. To see if stress alters non-coding RNA expression at the maternal-fetal interface, we treated pregnant mice with a viral infection mimetic, which has been shown to promote autism-related phenotypes in the offspring. Acute changes in the levels of specific tRFs and microRNAs were observed 3-6 h after MIA and are suppressed thereafter. A group of 5' tRNA halves is down-regulated by MIA, whereas a group of 18-nucleotide tRF-3a is up-regulated. In conclusion, tRFs show tissue-specificity, developmental changes and acute response to environmental stress, opening the possibility of them having a role in the fetal response to MIA.
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Affiliation(s)
- Zhangli Su
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia , Charlottesville, VA, USA
| | - Elizabeth L Frost
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia , Charlottesville, VA, USA
| | - Catherine R Lammert
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia , Charlottesville, VA, USA
| | - Roza K Przanowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia , Charlottesville, VA, USA
| | - John R Lukens
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia , Charlottesville, VA, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia , Charlottesville, VA, USA
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17
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Zhu C, Tian L, Yang H, Chen P, Li Y, Liu Y. Mitochondrial outer membrane voltage-dependent anion channel is involved in renal dysfunction in a spontaneously hypertensive rat carrying transfer RNA mutations. Eur J Pharmacol 2019; 865:172622. [PMID: 31618620 DOI: 10.1016/j.ejphar.2019.172622] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 08/13/2019] [Accepted: 08/20/2019] [Indexed: 11/18/2022]
Abstract
Mitochondrial DNA mutations promote hypertensive renal dysfunction, but the molecular mechanism remains unclear. This study compared renal damage between spontaneously hypertensive rats (SHR) and SHR with mitochondrial transfer (t)RNA mutations. To investigate the role of mitochondrial outer membrane voltage-dependent anion channel 1 (VDAC1) in the process of tRNA-promoting mitochondrial dysfunction, we treated HK-2 cells with H2O2, cyclosporine (CsA), or atractylodin (Atr) to observe the association between VDAC1 and mitochondrial function. Intriguingly, the mitochondrial structure of SHR carrying tRNA mutations was obviously disordered, and reactive oxygen species production and VDAC1 and Bax expression and binding were increased, which was associated with marked renal dysfunction. The expression of VDAC1 and Bax was also up-regulated in HK-2 cells by H2O2 treatment. However, CsA and Atr had no significant effect on the expression of VDAC1 and Bax. H2O2 caused mitochondrial membrane potential collapse, while CsA could increase the mitochondrial membrane potential and Atr had the opposite effect. Treatment with H2O2 significantly decreased ATP synthesis, which was improved by intervention with Atr. H2O2 also decreased the maximum oxygen consumption rate, while CsA and Atr had no significant effect. We found that H2O2 promoted the colocalization of VDAC1 and Bax, which was partially inhibited by intervention with CsA or Atr. In conclusion, we found that tRNA mutations promoted hypertensive renal insufficiency. Increased reactive oxygen species was an important associated mechanism, which inhibited mitochondrial function by affecting VDAC1 expression and function.
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Affiliation(s)
- Chao Zhu
- Cardiac Department, Institute of Geriatric Cardiology, PLA General Hospital, Beijing, 100853, China; Department of Cardiology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Liuyang Tian
- Cardiac Department, Institute of Geriatric Cardiology, PLA General Hospital, Beijing, 100853, China; Department of Cardiology, Tianjin Union Medical Center, Tianjin, 300121, China
| | - Huanwan Yang
- Cardiac Department, Institute of Geriatric Cardiology, PLA General Hospital, Beijing, 100853, China
| | - Pu Chen
- National Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yang Li
- Cardiac Department, Institute of Geriatric Cardiology, PLA General Hospital, Beijing, 100853, China.
| | - Yuqi Liu
- Cardiac Department, Institute of Geriatric Cardiology, PLA General Hospital, Beijing, 100853, China; National Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing, 100853, China; Department of Cardiology & National Clinical Research Center of Geriatric Disease, Chinese PLA General Hospital, Beijing, 100853, China; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, 100853, China.
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18
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Abstract
Transfer RNAs (tRNAs) are key components of the translation machinery. They read codons on messenger RNAs (mRNAs) and deliver the appropriate amino acid to the ribosome for protein synthesis. The human genome encodes more than 500 tRNA genes but their individual contribution to the cellular tRNA pool is unclear. In recent years, novel methods were developed to improve the quantification of tRNA gene expression, most of which rely on next-generation sequencing such as small RNA-Seq applied to tRNAs (tRNA-Seq). In a previous study, we presented a bioinformatics strategy to analyse tRNA-Seq datasets that we named 'isodecoder-specific tRNA gene contribution profiling' (Iso-tRNA-CP). Using Iso-tRNA-CP, we showed that tRNA gene expression is cell type- and tissue-specific and that this process can regulate tRNA-derived fragments abundance. An additional observation that stems from that work is that approximately half of human tRNA genes appeared silent or poorly expressed. In this commentary, I discuss this finding in light of the current literature and speculate on potential functions that transcriptionally silent tRNA genes may play. Studying silent tRNA genes may offer a unique opportunity to unravel novel mechanisms of cell regulation associated to tRNA biology.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
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19
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Magee R, Londin E, Rigoutsos I. TRNA-derived fragments as sex-dependent circulating candidate biomarkers for Parkinson's disease. Parkinsonism Relat Disord 2019; 65:203-209. [PMID: 31402278 DOI: 10.1016/j.parkreldis.2019.05.035] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Parkinson's Disease (PD) is diagnosed clinically. Reliable non-invasive PD biomarkers are actively sought. Transfer RNAs produce short non-coding RNAs, the tRNA-derived fragments (tRF). tRF have been shown to play diverse roles, including in amyotrophic lateral sclerosis, and the response to ischemic stroke. Rich tRF populations are being reported in biofluids. We explored the possibility that tRF can serve as non-invasive biomarkers for PD. METHODS We collected existing RNA-seq samples and re-analyzed a total of 254 legacy datasets from 3 previous studies, from male and female PD patients and controls that belong to three categories: prefrontal cortex samples from 29 patients and 33 controls; cerebrospinal fluid (CSF) samples from 63 patients and 64 controls; and, serum samples from 34 patients and 31 controls. First, we identified tRF exhaustively and deterministically in every dataset. Second, we determined tRF that are differentially abundant (DA) between PD and control samples, using uncorrected t-tests. Lastly, we assessed all the DA tRF from the previous step with Partial Least Squares - Discriminant Analysis (PLS-DA) to stringently sub-select tRF that can distinguish PD patients from controls. RESULTS We show that PLS-DA identified tRF from prefrontal cortex, CSF, and serum that can distinguish PD patients from controls. A handful of identified tRF were previously investigated in neurological contexts. Signatures built from relatively few tRF suffice to distinguish PD from control in each category of samples with high sensitivity (89-100%) and specificity (79-98%). CONCLUSION tRF-based signatures are promising candidates that warrant further evaluation as non-invasive PD biomarkers.
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Affiliation(s)
- Rogan Magee
- Computational Medicine Center, Jefferson Alumni Hall #M81, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Eric Londin
- Computational Medicine Center, Jefferson Alumni Hall #M81, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Jefferson Alumni Hall #M81, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
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Lee HH, Wang YN, Hung MC. Functional roles of the human ribonuclease A superfamily in RNA metabolism and membrane receptor biology. Mol Aspects Med 2019; 70:106-116. [PMID: 30902663 DOI: 10.1016/j.mam.2019.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/17/2019] [Indexed: 02/08/2023]
Abstract
The human ribonuclease A (hRNase A) superfamily is comprised of 13 members of secretory RNases, most of which are recognized as catabolic enzymes for their ribonucleolytic activity to degrade ribonucleic acids (RNAs) in the extracellular space, where they play a role in innate host defense and physiological homeostasis. Interestingly, human RNases 9-13, which belong to a non-canonical subgroup of the hRNase A superfamily, are ribonucleolytic activity-deficient proteins with unclear biological functions. Moreover, accumulating evidence indicates that secretory RNases, such as human RNase 5, can be internalized into cells facilitated by membrane receptors like the epidermal growth factor receptor to regulate intracellular RNA species, in particular non-coding RNAs, and signaling pathways by either a ribonucleolytic activity-dependent or -independent manner. In this review, we summarize the classical role of hRNase A superfamily in the metabolism of extracellular and intracellular RNAs and update its non-classical function as a cognate ligand of membrane receptors. We further discuss the biological significance and translational potential of using secretory RNases as predictive biomarkers or therapeutic agents in certain human diseases and the pathological settings for future investigations.
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Affiliation(s)
- Heng-Huan Lee
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Unit 108, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Ying-Nai Wang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Unit 108, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Unit 108, 1515 Holcombe Boulevard, Houston, TX, 77030, USA; Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, China Medical University, Taichung, 404, Taiwan; Department of Biotechnology, Asia University, Taichung 413, Taiwan.
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21
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Wang Z, Wei C, Hao X, Deng W, Zhang L, Wang Z, Wang H. Genome-wide identification and characterization of transfer RNA-derived small RNAs in Plasmodium falciparum. Parasit Vectors 2019; 12:36. [PMID: 30646930 PMCID: PMC6332904 DOI: 10.1186/s13071-019-3301-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/07/2019] [Indexed: 01/16/2023] Open
Abstract
Background Transfer RNA (tRNA)-derived fragments (tRFs) have been widely identified in nature, functioning in diverse biological and pathological situations. Yet, the presence of these small RNAs in Plasmodium spp. remains unknown. Systematic identification and characterization of tRFs is therefore highly needed to understand further their roles in Plasmodium parasites, particularly in the virulent Plasmodium falciparum parasite. Results Genome-wide small RNAs with sizes ranging from 18–30 nucleotides from P. falciparum were deep-sequenced via Illumina HiSeq 2000 technology. In-depth analysis revealed the presence of a vast number of small RNAs originating from tRNA-coding genes, responsible for 22.4% of the total reads as the second predominant group. Three P. falciparum-derived tRF types (ptRFs) were identified as 5'ptRFs, mid-ptRFs and 3'ptRFs. The majority (90%) of ptRFs were derived from tRNAs that coded eight amino acids: Pro, Phe, Asn, Gly, Cys, Gln, His and Ala. Stem-loop reverse transcription polymerase chain reaction further confirmed the presence of tRFs in the blood stages of P. falciparum. Four new motifs with an enriched G/C feature were determined at cleavage sites that might guide the generation of ptRFs. Conclusions To our knowledge, this is the first report of a genome-wide investigation of ptRFs from Plasmodium species. The identification of ptRFs reveals a complex small RNA system manipulated by the malaria parasite, and might promote research on the function of tRFs in the pathogenesis of Plasmodium infections. Electronic supplementary material The online version of this article (10.1186/s13071-019-3301-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhensheng Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 5# Dong Dan San Tiao, Beijing, 100005, People's Republic of China
| | - Chunyan Wei
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 5# Dong Dan San Tiao, Beijing, 100005, People's Republic of China
| | - Xiao Hao
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 5# Dong Dan San Tiao, Beijing, 100005, People's Republic of China
| | - Weiwei Deng
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 5# Dong Dan San Tiao, Beijing, 100005, People's Republic of China
| | - Lianhui Zhang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 5# Dong Dan San Tiao, Beijing, 100005, People's Republic of China
| | - Zenglei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
| | - Heng Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 5# Dong Dan San Tiao, Beijing, 100005, People's Republic of China.
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22
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Abstract
Transfer RNAs are the largest, most complex non-coding RNA family, universal to all living organisms. tRNAscan-SE has been the de facto tool for predicting tRNA genes in whole genomes. The newly developed version 2.0 has incorporated advanced methodologies with improved probabilistic search software and a suite of new gene models, enabling better functional classification of predicted genes. This chapter describes the use of the UNIX command-driven and online web versions, illustrating different search modes and options.
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Affiliation(s)
- Patricia P Chan
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
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Wang D, Ning C, Xiang H, Zheng X, Kong M, Yin T, Liu J, Zhao X. Polymorphism of mitochondrial tRNA genes associated with the number of pigs born alive. J Anim Sci Biotechnol 2018; 9:86. [PMID: 30534375 PMCID: PMC6260895 DOI: 10.1186/s40104-018-0299-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/17/2018] [Indexed: 11/13/2022] Open
Abstract
Background Mutations in mitochondrial tRNA genes have been widely reported association with human reproductions. It is also important to explore the effect on the number of piglets born alive (NBA). Here, 1017 sows were used to investigate the association between polymorphisms in mitochondrial tRNA genes and NBA. Results In total, 16 mutations were found in mitochondrial tRNA genes, of which 13 mutations were significantly associated with NBA (P < 0.05). The reproductions of mutant carriers were significantly greater than that of wild carriers by 0.989 piglets born alive/sow farrowing. To test whether the mutations altered the structure of mitochondrial tRNAs, the secondary and tertiary structures were predicted. In result, C2255T changed the secondary structure of tRNA-Val by elongating the T stem and shrinking the T loop, and C2255T and G2259A in the tRNA-Val gene, C6217T and T6219C in the tRNA-Ala gene, and T15283C in the tRNA-Glu gene altered the tertiary structure of their tRNAs, respectively by changing the folding form of the T arm, and C16487T in the tRNA-Thr gene changed the tertiary structure of mitochondrial tRNA-Thr by influencing the folding form of the acceptor arm. Conclusions Results highlight the effect of mitochondrial tRNA genes on the number of piglets born alive, and suggest that polymorphic sites of the tRNA genes be genetic markers for selection of pig reproduction. Electronic supplementary material The online version of this article (10.1186/s40104-018-0299-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dan Wang
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Chao Ning
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Hai Xiang
- 2School of Life Science and Engineering, Foshan University, Foshan, 528225 China
| | - Xianrui Zheng
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Minghua Kong
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Tao Yin
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Jianfeng Liu
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Xingbo Zhao
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
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Lobue PA, Yu N, Jora M, Abernathy S, Limbach PA. Improved application of RNAModMapper - An RNA modification mapping software tool - For analysis of liquid chromatography tandem mass spectrometry (LC-MS/MS) data. Methods 2018; 156:128-138. [PMID: 30366097 DOI: 10.1016/j.ymeth.2018.10.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/02/2018] [Accepted: 10/21/2018] [Indexed: 12/21/2022] Open
Abstract
Research into post-transcriptional processing and modification of RNA continues to speed forward, as their ever-emerging role in the regulation of gene expression in biological systems continues to unravel. Liquid chromatography tandem mass spectrometry (LC-MS/MS) has proven for over two decades to be a powerful ally in the elucidation of RNA modification identity and location, but the technique has not proceeded without its own unique technical challenges. The throughput of LC-MS/MS modification mapping experiments continues to be impeded by tedious and time-consuming spectral interpretation, particularly during for the analysis of complex RNA samples. RNAModMapper was recently developed as a tool to improve the interpretation and annotation of LC-MS/MS data sets from samples containing post-transcriptionally modified RNAs. Here, we delve deeper into the methodology and practice of RNAModMapper to provide greater insight into its utility, and remaining hurdles, in current RNA modification mapping experiments.
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Affiliation(s)
- Peter A Lobue
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH 45221-0172, United States
| | - Ningxi Yu
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH 45221-0172, United States
| | - Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH 45221-0172, United States
| | - Scott Abernathy
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH 45221-0172, United States.
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Nakamura A, Wang D, Komatsu Y. Biochemical analysis of human tRNA His guanylyltransferase in mitochondrial tRNA His maturation. Biochem Biophys Res Commun 2018; 503:2015-2021. [PMID: 30093107 DOI: 10.1016/j.bbrc.2018.07.150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 07/30/2018] [Indexed: 11/29/2022]
Abstract
Mitochondria contain their own protein synthesis machinery, which includes mitochondrial tRNA maturation. It has been suggested that mammalian mitochondrial tRNAHis (mtRNAHis) is matured by post-transcriptional addition of guanosine at the -1 position (G-1), which serves as an identity element for mitochondrial histidyl-tRNA synthetase. However, the exact maturation process of mammalian mtRNAHis remains unclear. In cytoplasmic tRNAHis (ctRNAHis) maturation, tRNAHis guanylyltransferase (Thg1) adds a GTP onto the 5'-terminal of ctRNAHis and then removes the 5'-pyrophosphate to yield the mature 5'-monophospholylated G-1-ctRNAHis (pG-1-ctRNAHis). Although mammalian Thg1 is localized to both the cytoplasm and mitochondria, it remains unclear whether mammalian Thg1 plays a role in mtRNAHis maturation in mitochondria. Here, we demonstrated that human Thg1 (hThg1) catalyzes the G-1 addition reaction for both human ctRNAHis and mtRNAHis through recognition of the anticodon. While hThg1 catalyzed consecutive GTP additions to mtRNAHisin vitro, it did not exhibit any activity toward mature pG-1-mtRNAHis. We further found that hThg1 could add a GMP directly to the 5'-terminal of mtRNAHis in a template-dependent manner, but fungal Thg1 could not. Therefore, we hypothesized that acceleration of the pyrophosphate removal activity before or after the G-1 addition reaction is a key feature of hThg1 for maintaining a normal 5'-terminal of mtRNAHis in human mitochondria. This study provided a new insight into the differences between tRNAHis maturation in the cytoplasm and mitochondria of humans.
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Affiliation(s)
- Akiyoshi Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan
| | - Daole Wang
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan; Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.
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Sørensen MA, Fehler AO, Lo Svenningsen S. Transfer RNA instability as a stress response in Escherichia coli: Rapid dynamics of the tRNA pool as a function of demand. RNA Biol 2018; 15:586-593. [PMID: 29023189 PMCID: PMC6103710 DOI: 10.1080/15476286.2017.1391440] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Production of the translation apparatus of E. coli is carefully matched to the demand for protein synthesis posed by a given growth condition. For example, the fraction of RNA polymerases that transcribe rRNA and tRNA drops from 80% during rapid growth to 24% within minutes of a sudden amino acid starvation. We recently reported in Nucleic Acids Research that the tRNA pool is more dynamically regulated than previously thought. In addition to the regulation at the level of synthesis, we found that tRNAs are subject to demand-based regulation at the level of their degradation. In this point-of-view article we address the question of why this phenomenon has not previously been described. We also present data that expands on the mechanism of tRNA degradation, and we discuss the possible implications of tRNA instability for the ability of E. coli to cope with stresses that affect the translation process.
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Pilotte J, Chan SW, Farnum JB, Thomas WM, Smilansky Z, Vanderklish PW. A heterogeneous tRNA granule structure exhibiting rapid, bi-directional neuritic transport. Eur J Cell Biol 2018; 97:168-79. [PMID: 29482850 DOI: 10.1016/j.ejcb.2018.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/09/2018] [Accepted: 02/12/2018] [Indexed: 11/23/2022] Open
Abstract
mRNA translation is regulated by diverse mechanisms that converge at the initiation and elongation steps to determine the rate, profile, and localization of proteins synthesized. A consistently relevant feature of these mechanisms is the spatial re-distribution of translation machinery, a process of particular importance in neural cells. This process has, however, been largely overlooked with respect to its potential role in regulating the local concentration of cytoplasmic tRNAs, even as a multitude of data suggest that spatial regulation of the tRNA pool may help explain the remarkably high rates of peptide elongation. Here, we report that Cy3/Cy5-labeled bulk tRNAs transfected into neural cells distribute into granule-like structures - "tRNA granules" - that exhibit dynamic mixing of tRNAs between granules and rapid, bi-directional vectorial movement within neurites. Imaging of endogenous tRNAgly and tRNAlys by fluorescent in situ hybridization revealed a similar granular distribution of tRNAs in somata and neurites; this distribution was highly overlapping with granules imaged by introduction of exogenous Cy5-tRNAthr and Cy3-tRNAval. A subset of tRNA granules located in the cell body, neurite branch points and growth cones displayed fluorescence resonance energy transfer (FRET) between Cy3 and Cy5-labeled tRNAs indicative of translation, and co-localization with elongation machinery. A population of smaller, rapidly trafficked granules in neurites lacked FRET and showed poor colocalization with translation initiation and elongation factors, suggesting that they are a translationally inactive tRNA transport particle. Our data suggest that tRNAs are packaged into granules that are rapidly transported to loci where translation is needed, where they may greatly increase the local concentration of tRNAs in support of efficient elongation. The potential implications of this newly described structure for channeling of elongation, local translation, and diseases associated with altered tRNA levels or function are discussed.
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Loher P, Telonis AG, Rigoutsos I. Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap. Methods Mol Biol 2018; 1680:237-55. [PMID: 29030853 DOI: 10.1007/978-1-4939-7339-2_16] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
There is an increasing interest within the scientific community in identifying tRNA-derived fragments (tRFs) and elucidating the roles they play in the cell. Such endeavors can be greatly facilitated by mining the numerous datasets from many cellular contexts that exist publicly. However, the standard mapping tools cannot be used for the purpose. Several factors complicate this endeavor including: the presence of multiple identical or nearly identical isodecoders at various genomic locations; the presence of identical sequence segments that are shared by isodecoders of the same or even different anticodons; the existence of numerous partial tRNA sequences across the genome; the existence of hundreds of "lookalike" sequences that resemble true tRNAs; and others. This is generating a need for specialized tools that can mine deep sequencing data to identify and quantify tRFs. We discuss the various complicating factors and their ramifications, and how to use and run MINTmap, a tool that addresses these considerations.
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Alamos P, Tello M, Bustamante P, Gutiérrez F, Shmaryahu A, Maldonado J, Levicán G, Orellana O. Functionality of tRNAs encoded in a mobile genetic element from an acidophilic bacterium. RNA Biol 2017; 15:518-527. [PMID: 28708455 DOI: 10.1080/15476286.2017.1349049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The genome of the acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans, strain ATCC 23270, contains 95 predicted tRNA genes. Thirty-six of these genes (all 20 species) are clustered within an actively excising integrative-conjugative element (ICEAfe1). We speculated that these tRNA genes might have a role in adapting the bacterial tRNA pool to the codon usage of ICEAfe1 genes. To answer this question, we performed theoretical calculations of the global tRNA adaptation index to the entire A. ferrooxidans genome with and without the ICEAfe1 encoded tRNA genes. Based on these calculations, we observed that tRNAs encoded in ICEAfe1 negatively contribute to adapt the tRNA pool to the codon use in A. ferrooxidans. Although some of the tRNAs encoded in ICEAfe1 are functional in aminoacylation or protein synthesis, we found that they are expressed at low levels. These findings, along with the identification of a tRNA-like RNA encoded in the same cluster, led us to speculate that tRNA genes encoded in the mobile genetic element ICEAfe1 might have acquired mutations that would result in either inactivation or the acquisition of new functions.
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Affiliation(s)
- Pamela Alamos
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Mario Tello
- b Centro de Biotecnología Acuícola, Departamento de Biología , Facultad de Química y Biología, Universidad de Santiago de Chile
| | - Paula Bustamante
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Fernanda Gutiérrez
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Amir Shmaryahu
- c Fundación Ciencia y Vida , Zañartu 1482, Santiago , Chile
| | - Juan Maldonado
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Gloria Levicán
- d Departamento de Biología , Facultad de Química y Biología, Universidad de Santiago de Chile , Santiago , Chile
| | - Omar Orellana
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
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Reynolds NM, Vargas-Rodriguez O, Söll D, Crnković A. The central role of tRNA in genetic code expansion. Biochim Biophys Acta Gen Subj 2017; 1861:3001-3008. [PMID: 28323071 DOI: 10.1016/j.bbagen.2017.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND The development of orthogonal translation systems (OTSs) for genetic code expansion (GCE) has allowed for the incorporation of a diverse array of non-canonical amino acids (ncAA) into proteins. Transfer RNA, the central molecule in the translation of the genetic message into proteins, plays a significant role in the efficiency of ncAA incorporation. SCOPE OF REVIEW Here we review the biochemical basis of OTSs for genetic code expansion. We focus on the role of tRNA and discuss strategies used to engineer tRNA for the improvement of ncAA incorporation into proteins. MAJOR CONCLUSIONS The engineering of orthogonal tRNAs for GCE has significantly improved the incorporation of ncAAs. However, there are numerous unintended consequences of orthogonal tRNA engineering that cannot be predicted ab initio. GENERAL SIGNIFICANCE Genetic code expansion has allowed for the incorporation of a great diversity of ncAAs and novel chemistries into proteins, making significant contributions to our understanding of biological molecules and interactions. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
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Hoffman KS, O'Donoghue P, Brandl CJ. Mistranslation: from adaptations to applications. Biochim Biophys Acta Gen Subj 2017; 1861:3070-80. [PMID: 28153753 DOI: 10.1016/j.bbagen.2017.01.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness. In studies of model organisms, mistranslation often acts as an adaptive response. These studies reveal evolutionary conserved mechanisms to maintain proteostasis even during high rates of mistranslation. SCOPE OF REVIEW This review discusses the evolutionary basis of altered genetic codes, how mistranslation is identified, and how deviations to the genetic code are exploited. We revisit early discoveries of genetic code deviations and provide examples of adaptive mistranslation events in nature. Lastly, we highlight innovations in synthetic biology to expand the genetic code. MAJOR CONCLUSIONS The genetic code is still evolving. Mistranslation increases proteomic diversity that enables cells to survive stress conditions or suppress a deleterious allele. Genetic code variants have been identified by genome and metagenome sequence analyses, suppressor genetics, and biochemical characterization. GENERAL SIGNIFICANCE Understanding the mechanisms of translation and genetic code deviations enables the design of new codes to produce novel proteins. Engineering the translation machinery and expanding the genetic code to incorporate non-canonical amino acids are valuable tools in synthetic biology that are impacting biomedical research. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Xu Y, MacKerell AD Jr, Nilsson L. Structural effects of modified ribonucleotides and magnesium in transfer RNAs. Bioorg Med Chem 2016; 24:4826-34. [PMID: 27364608 DOI: 10.1016/j.bmc.2016.06.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 11/20/2022]
Abstract
Modified nucleotides are ubiquitous and important to tRNA structure and function. To understand their effect on tRNA conformation, we performed a series of molecular dynamics simulations on yeast tRNAPhe and tRNAinit, Escherichia coli tRNAinit and HIV tRNALys. Simulations were performed with the wild type modified nucleotides, using the recently developed CHARMM compatible force field parameter set for modified nucleotides (J. Comput. Chem.2016, 37, 896), or with the corresponding unmodified nucleotides, and in the presence or absence of Mg2+. Results showed a stabilizing effect associated with the presence of the modifications and Mg2+ for some important positions, such as modified guanosine in position 37 and dihydrouridines in 16/17 including both structural properties and base interactions. Some other modifications were also found to make subtle contributions to the structural properties of local domains. While we were not able to investigate the effect of adenosine 37 in tRNAinit and limitations were observed in the conformation of E. coli tRNAinit, the presence of the modified nucleotides and of Mg2+ better maintained the structural features and base interactions of the tRNA systems than in their absence indicating the utility of incorporating the modified nucleotides in simulations of tRNA and other RNAs.
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Fernández-Millán P, Schelcher C, Chihade J, Masquida B, Giegé P, Sauter C. Transfer RNA: From pioneering crystallographic studies to contemporary tRNA biology. Arch Biochem Biophys 2016; 602:95-105. [PMID: 26968773 DOI: 10.1016/j.abb.2016.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/29/2016] [Accepted: 03/03/2016] [Indexed: 12/17/2022]
Abstract
Transfer RNAs (tRNAs) play a key role in protein synthesis as adaptor molecules between messenger RNA and protein sequences on the ribosome. Their discovery in the early sixties provoked a worldwide infatuation with the study of their architecture and their function in the decoding of genetic information. tRNAs are also emblematic molecules in crystallography: the determination of the first tRNA crystal structures represented a milestone in structural biology and tRNAs were for a long period the sole source of information on RNA folding, architecture, and post-transcriptional modifications. Crystallographic data on tRNAs in complex with aminoacyl-tRNA synthetases (aaRSs) also provided the first insight into protein:RNA interactions. Beyond the translation process and the history of structural investigations on tRNA, this review also illustrates the renewal of tRNA biology with the discovery of a growing number of tRNA partners in the cell, the involvement of tRNAs in a variety of regulatory and metabolic pathways, and emerging applications in biotechnology and synthetic biology.
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Benítez AA, Hernández Cifre JG, Díaz Baños FG, de la Torre JG. Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA. BMC Biophys 2015; 8:11. [PMID: 26629336 PMCID: PMC4666080 DOI: 10.1186/s13628-015-0025-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 11/18/2015] [Indexed: 12/02/2022]
Abstract
Background The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational scheme for predicting global properties and mimicking the internal dynamics of RNA molecules in solution. A simple coarse-grained model with one bead per nucleotide and two types of intra-molecular interactions (elastic interactions and excluded volume interactions) is used to represent the RNA chain. The elastic interactions are modeled by a set of Hooke springs that form a minimalist elastic network. The Brownian dynamics technique is employed to simulate the time evolution of the RNA conformations. Results That scheme is applied to the 5S ribosomal RNA of E. Coli and the yeast phenylalanine transfer RNA. From the Brownian trajectory, several solution properties (radius of gyration, translational diffusion coefficient, and a rotational relaxation time) are calculated. For the case of yeast phenylalanine transfer RNA, the time evolution and the probability distribution of the inter-arm angle is also computed. Conclusions The general good agreement between our results and some experimental data indicates that the model is able to capture the tertiary structure of RNA in solution. Our simulation results also compare quite well with other numerical data. An advantage of the scheme described here is the possibility of visualizing the real time macromolecular dynamics. Electronic supplementary material The online version of this article (doi:10.1186/s13628-015-0025-7) contains supplementary material, which is available to authorized users.
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Yong HS, Song SL, Eamsobhana P, Goh SY, Lim PE. Complete mitochondrial genome reveals genetic diversity of Angiostrongylus cantonensis (Nematoda: Angiostrongylidae). Acta Trop 2015; 152:157-164. [PMID: 26348256 DOI: 10.1016/j.actatropica.2015.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/31/2015] [Accepted: 09/01/2015] [Indexed: 12/31/2022]
Abstract
Angiostrongylus cantonensis is a zoonotic parasite that causes eosinophilic meningitis in humans. Earlier work on its mitochondrial genome was based on long polymerase chain reaction method. To date, only the mitogenome of the isolates from China has been studied. We report here the complete mitogenome of the Thailand isolate based on next generation sequencing and compare the genetic diversity with other isolates. The mitogenome of the Thailand isolate (13,519bp) is longer than those of the China isolates (13,497-13,502bp). Five protein-coding genes (atp6, cox1, cox2, cob, nad2) show variations in length among the isolates. The stop codon of the Thailand isolate differs from the China and Taiwan isolates in 4 genes (atp6, cob, nad2, nad6). Additionally, the Thailand isolate has 4 incomplete T stop codon compared to 3 in the China and Taiwan isolates. The control region is longer in the Thailand isolate (258bp) than the China (230-236bp) and Taiwan (237bp) isolates. The intergenic sequence between nad4 and cox1 genes in the Thailand isolate lacks 2bp (indels) at the 5'-end of the sequence as well as differs at 7 other sites compared to the China and Taiwan isolates. In the Thailand isolate, 18 tRNAs lack the entire TΨC-arm, compared to 17 in the China isolate and 16 in the Taiwan isolate. Phylogenetic analyses based on 36 mt-genes, 12 PCGs, 2 rRNA genes, 22 tRNA genes and control region all indicate closer genetic affinity between the China and Taiwan isolates compared to the Thailand isolate. Based on 36 mt-genes, the inter-isolate genetic distance varies from p=3.2% between China and Taiwan isolates to p=11.6% between Thailand and China isolates. The mitogenome will be useful for population, phylogenetics and phylogeography studies.
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Abstract
A maximal C(3) self-complementary trinucleotide circular code X is identified in genes of bacteria, eukaryotes, plasmids and viruses (Michel, 2015; Arquès and Michel, 1996). A translation (framing) code based on the circular code was proposed in Michel (2012) with the identification of several X circular code motifs (X motifs shortly) in both ribosomal RNAs (rRNAs) and their decoding center, and transfer RNAs (tRNAs). We extended these results in two ways. First, three universal X motifs were determined in the ribosome decoding center: the X motif mAA containing the conserved nucleotides A1492 and A1493, the X motif mG containing the conserved nucleotide G530 and the X motif m with unknown biological function (El Soufi and Michel, 2014). Secondly, statistical analysis of X motifs of greatest lengths performed on different and large tRNA populations according to taxonomy, tRNA length and tRNA score showed that these X motifs have occurrence probabilities in the 5' and/or 3' regions of 16 isoaccepting tRNAs of prokaryotes and eukaryotes greater than the random case (Michel, 2013). We continue here the previous works with the identification of X motifs in rRNAs of prokaryotes and eukaryotes near the ribosome decoding center. Seven X motifs PrRNAXm conserved in 16S rRNAs of prokaryotes P and four X motifs ErRNAXm conserved in 18S rRNAs of eukaryotes E are identified near the ribosome decoding center. Furthermore, four very large X motifs of length greater than or equal to 20 nucleotides, 14 large X motifs of length between 16 and 19 nucleotides and several X motifs of length greater or equal to 9 nucleotides are found in tRNAs of prokaryotes. Some properties of these X motifs in tRNAs are described. These new results strengthen the concept of a translation code based on the circular code (Michel, 2012).
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Affiliation(s)
- Karim El Soufi
- Theoretical Bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France.
| | - Christian J Michel
- Theoretical Bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France.
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Root-Bernstein M, Root-Bernstein R. The ribosome as a missing link in the evolution of life. J Theor Biol 2014; 367:130-158. [PMID: 25500179 DOI: 10.1016/j.jtbi.2014.11.025] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 11/15/2014] [Accepted: 11/20/2014] [Indexed: 12/27/2022]
Abstract
Many steps in the evolution of cellular life are still mysterious. We suggest that the ribosome may represent one important missing link between compositional (or metabolism-first), RNA-world (or genes-first) and cellular (last universal common ancestor) approaches to the evolution of cells. We present evidence that the entire set of transfer RNAs for all twenty amino acids are encoded in both the 16S and 23S rRNAs of Escherichia coli K12; that nucleotide sequences that could encode key fragments of ribosomal proteins, polymerases, ligases, synthetases, and phosphatases are to be found in each of the six possible reading frames of the 16S and 23S rRNAs; and that every sequence of bases in rRNA has information encoding more than one of these functions in addition to acting as a structural component of the ribosome. Ribosomal RNA, in short, is not just a structural scaffold for proteins, but the vestigial remnant of a primordial genome that may have encoded a self-organizing, self-replicating, auto-catalytic intermediary between macromolecules and cellular life.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Biological Evolution
- Escherichia coli K12/enzymology
- Escherichia coli K12/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Probability
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- Ribosomes/metabolism
- Transcription, Genetic
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Affiliation(s)
- Meredith Root-Bernstein
- School of Geography and the Environment, Oxford University, South Parks Road, Oxford, Oxfordshire OX1 3QY, United Kingdom
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38
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Abstract
Transfer RNA (tRNA) is traditionally considered to be an adaptor molecule that helps ribosomes to decode messenger RNA (mRNA) and synthesize protein. Recent studies have demonstrated that tRNAs also serve as a major source of small non-coding RNAs that possess distinct and varied functions. These tRNA fragments are heterogeneous in size, nucleotide composition, biogenesis and function. Here we describe multiple roles that tRNA fragments play in cell physiology and discuss their relevance to human health and disease.
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Affiliation(s)
- Paul Anderson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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39
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Abstract
The regulation of gene expression in response to stress is an essential cellular protection mechanism. Recent advances in tRNA modification analysis and genome-based codon bias analytics have facilitated studies that lead to a novel model for translational control, with translation elongation dynamically regulated during stress responses. Stress-induced increases in specific anticodon wobble bases are required for the optimal translation of stress response transcripts that are significantly biased in the use of degenerate codons keyed to these modified tRNA bases. These findings led us to introduce the notion of tRNA modification tunable transcripts (MoTTs - transcripts whose translation is regulated by tRNA modifications), which are identifiable using genome-wide codon counting algorithms. In support of this general model of translational control of stress response, studies making use of detailed measures of translation, tRNA methyltransferase mutants, and computational and mass spectrometry approaches reveal that stress reprograms tRNA modifications to translationally regulate MoTTs linked to arginine and leucine codons, which helps cells survive insults by damaging agents. These studies highlight how tRNA methyltransferase activities and MoTTs are key components of the cellular stress response.
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Affiliation(s)
- Chen Gu
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas J Begley
- State University of New York - College of Nanoscale Science and Engineering, Albany, NY, United States; The RNA Institute at the University at Albany, Albany, NY, United States.
| | - Peter C Dedon
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States; Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
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40
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Torres AG, Piñeyro D, Filonava L, Stracker TH, Batlle E, Ribas de Pouplana L. A-to-I editing on tRNAs: biochemical, biological and evolutionary implications. FEBS Lett 2014; 588:4279-86. [PMID: 25263703 DOI: 10.1016/j.febslet.2014.09.025] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/16/2014] [Accepted: 09/16/2014] [Indexed: 12/13/2022]
Abstract
Inosine on transfer RNAs (tRNAs) are post-transcriptionally formed by a deamination mechanism of adenosines at positions 34, 37 and 57 of certain tRNAs. Despite its ubiquitous nature, the biological role of inosine in tRNAs remains poorly understood. Recent developments in the study of nucleotide modifications are beginning to indicate that the dynamics of such modifications are used in the control of specific genetic programs. Likewise, the essentiality of inosine-modified tRNAs in genome evolution and animal biology is becoming apparent. Here we review our current understanding on the role of inosine in tRNAs, the enzymes that catalyze the modification and the evolutionary link between such enzymes and other deaminases.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain
| | - David Piñeyro
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain
| | - Liudmila Filonava
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), P/ Lluís Companys 23, Barcelona 08010, Catalonia, Spain
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), P/ Lluís Companys 23, Barcelona 08010, Catalonia, Spain.
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41
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Biswal DK, Chatterjee A, Bhattacharya A, Tandon V. The mitochondrial genome of Paragonimus westermani (Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda). PeerJ 2014; 2:e484. [PMID: 25165620 PMCID: PMC4137670 DOI: 10.7717/peerj.484] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 06/23/2014] [Indexed: 11/20/2022] Open
Abstract
Among helminth parasites, Paragonimus (zoonotic lung fluke) gains considerable importance from veterinary and medical points of view because of its diversified effect on its host. Nearly fifty species of Paragonimus have been described across the globe. It is estimated that more than 20 million people are infected worldwide and the best known species is Paragonimus westermani, whose type locality is probably India and which infects millions of people in Asia causing disease symptoms that mimic tuberculosis. Human infections occur through eating raw crustaceans containing metacercarie or ingestion of uncooked meat of paratenic hosts such as pigs. Though the fluke is known to parasitize a wide range of mammalian hosts representing as many as eleven families, the status of its prevalence, host range, pathogenic manifestations and its possible survivors in nature from where the human beings contract the infection is not well documented in India. We took advantage of the whole genome sequence data for P. westermani, generated by Next Generation Sequencing, and its comparison with the existing data for the P. westermani for comparative mt DNA phylogenomic analyses. Specific primers were designed for the 12 protein coding genes with the aid of existing P. westermani mtDNA as the reference. The Ion torrent next generation sequencing platform was harnessed to completely sequence the mitochondrial genome, and applied innovative approaches to bioinformatically assemble and annotate it. A strategic PCR primer design utilizing the whole genome sequence data from P. westermani enabled us to design specific primers capable of amplifying all regions of the mitochondrial genome from P. westermani. Assembly of NGS data from libraries enriched in mtDNA sequence by PCR gave rise to a total of 11 contigs spanning the entire 14.7 kb mt DNA sequence of P. westermani available at NCBI. We conducted gap-filling by traditional Sanger sequencing to fill in the gaps. Annotation of non-protein coding genes successfully identified tRNA regions for the 24 tRNAs coded in mtDNA and 12 protein coding genes. Bayesian phylogenetic analyses of the concatenated protein coding genes placed P. westermani within the family Opisthorchida. The complete mtDNA sequence of P. westermani is 15,004 base pairs long; the lung fluke is the major etiological agent of paragonimiasis and the first Indian representative for the family Paragonimidae to be fully sequenced that provides important genetic markers for ecological, population and biogeographical studies and molecular diagnostic of digeneans that cause trematodiases.
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Affiliation(s)
- Devendra K Biswal
- Bioinformatics Centre, North-Eastern Hill University , Shillong, Meghalaya , India
| | - Anupam Chatterjee
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University , Shillong, Meghalaya , India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University , New Delhi , India
| | - Veena Tandon
- Bioinformatics Centre, North-Eastern Hill University , Shillong, Meghalaya , India ; Department of Zoology, North-Eastern Hill University , Shillong, Meghalaya , India
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Huot JL, Enkler L, Megel C, Karim L, Laporte D, Becker HD, Duchêne AM, Sissler M, Maréchal-Drouard L. Idiosyncrasies in decoding mitochondrial genomes. Biochimie 2014; 100:95-106. [PMID: 24440477 DOI: 10.1016/j.biochi.2014.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 01/06/2014] [Indexed: 11/24/2022]
Abstract
Mitochondria originate from the α-proteobacterial domain of life. Since this unique event occurred, mitochondrial genomes of protozoans, fungi, plants and metazoans have highly derived and diverged away from the common ancestral DNA. These resulting genomes highly differ from one another, but all present-day mitochondrial DNAs have a very reduced coding capacity. Strikingly however, ATP production coupled to electron transport and translation of mitochondrial proteins are the two common functions retained in all mitochondrial DNAs. Paradoxically, most components essential for these two functions are now expressed from nuclear genes. Understanding how mitochondrial translation evolved in various eukaryotic models is essential to acquire new knowledge of mitochondrial genome expression. In this review, we provide a thorough analysis of the idiosyncrasies of mitochondrial translation as they occur between organisms. We address this by looking at mitochondrial codon usage and tRNA content. Then, we look at the aminoacyl-tRNA-forming enzymes in terms of peculiarities, dual origin, and alternate function(s). Finally we give examples of the atypical structural properties of mitochondrial tRNAs found in some organisms and the resulting adaptive tRNA-protein partnership.
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Abstract
Oregano (Origanum vulgare L., Lamiaceae) is a medicinal and aromatic plant maybe best known for flavouring pizza. New applications e.g. as natural antioxidants for food are emerging due to the plants' high antibacterial and antioxidant activity. The complete chloroplast (cp) genome of Origanum vulgare (GenBank/EBML/DDBJ accession number: JX880022) consists of 151,935 bp and includes a pair of inverted repeats (IR) of 25,527 bp separated by one small and one large single copy region (SSC and LSC) of 17,745 and 83,136 bp, respectively. The genome with an overall GC content of 38% hosts 114 genes that covering 63% of the genome of which 8% were introns. The comparison of the Origanum cp genome with the cp genomes of two other core lamiales (Salvia miltiorrhiza Bunge and Sesamum indicum L.) revealed completely conserved protein-coding regions in the IR region but also in the LSC and SSC regions. Phylogenetic analysis of the lamiids based on 56 protein-coding genes give a hint at the basic structure of the Lamiales. However, further genomes will be necessary to clarify this taxonomically complicated order. The variability of the cp within the genus Origanum, studied exemplarily on 16 different chloroplast DNA regions, demonstrated that in 14 regions analyzed, the variability was extremely low (max. 0.7%), while only two regions showed a moderate variability of up to 2.3%. The cp genome of Origanum vulgare contains 27 perfect mononucleotide repeats (number of repeats>9) consisting exclusively of the nucleotides A or T. 34 perfect repeats (repeat lengths>1 and number of repeats>3) were found, of which 32 were di-, and 2 were trinucleotide repeats.
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Affiliation(s)
- Brigitte Lukas
- Institute for Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
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44
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Abstract
To measure the size and amount of RNA transcribed from a specific gene of interest.
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