1
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Saha S, Mukherjee B, Banerjee P, Das D. The 'Not-So-Famous Five' in tumorigenesis: tRNAs, tRNA fragments, and tRNA epitranscriptome in concert with AARSs and AIMPs. Biochimie 2024; 222:45-62. [PMID: 38401639 DOI: 10.1016/j.biochi.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
RNA profiling studies have revealed that ∼75% of the human genome is transcribed to RNA but only a meagre fraction of it is translated to proteins. Majority of transcribed RNA constitute a specialized pool of non-coding RNAs. Human genome contains approximately 506 genes encoding a set of 51 different tRNAs, constituting a unique class of non-coding RNAs that not only have essential housekeeping functions as translator molecules during protein synthesis, but have numerous uncharted regulatory functions. Intriguing findings regarding a variety of non-canonical functions of tRNAs, tRNA derived fragments (tRFs), esoteric epitranscriptomic modifications of tRNAs, along with aminoacyl-tRNA synthetases (AARSs) and ARS-interacting multifunctional proteins (AIMPs), envision a 'peripheral dogma' controlling the flow of genetic information in the backdrop of qualitative information wrung out of the long-live central dogma of molecular biology, to drive cells towards either proliferation or differentiation programs. Our review will substantiate intriguing peculiarities of tRNA gene clusters, atypical tRNA-transcription from internal promoters catalysed by another distinct RNA polymerase enzyme, dynamically diverse tRNA epitranscriptome, intricate mechanism of tRNA-charging by AARSs governing translation fidelity, epigenetic regulation of gene expression by tRNA fragments, and the role of tRNAs and tRNA derived/associated molecules as quantitative determinants of the functional proteome, covertly orchestrating the process of tumorigenesis, through a deregulated tRNA-ome mediating selective codon-biased translation of cancer related gene transcripts.
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Affiliation(s)
- Sutapa Saha
- Department of Life Sciences, Presidency University, 86/1, College Street, Kolkata, 700073, WB, India.
| | - Biyas Mukherjee
- Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata, 700064, India
| | - Proma Banerjee
- Department of Life Sciences, Presidency University, 86/1, College Street, Kolkata, 700073, WB, India
| | - Debadrita Das
- Department of Life Sciences, Presidency University, 86/1, College Street, Kolkata, 700073, WB, India
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2
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Yin X, Dong Q, Fan S, Yang L, Li H, Jin Y, Laurentinah MR, Chen X, Sysa A, Fang H, Lyu J, Yu Y, Wang Y. A novel pathogenic mitochondrial DNA variant m.4344T>C in tRNA Gln causes developmental delay. J Hum Genet 2024:10.1038/s10038-024-01254-5. [PMID: 38730005 DOI: 10.1038/s10038-024-01254-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Mitochondrial diseases are a group of genetic diseases caused by mutations in mitochondrial DNA and nuclear DNA. However, the genetic spectrum of this disease is not yet complete. In this study, we identified a novel variant m.4344T>C in mitochondrial tRNAGln from a patient with developmental delay. The mutant loads of m.4344T>C were 95% and 89% in the patient's blood and oral epithelial cells, respectively. Multialignment analysis showed high evolutionary conservation of this nucleotide. TrRosettaRNA predicted that m.4344T>C variant would introduce an additional hydrogen bond and alter the conformation of the T-loop. The transmitochondrial cybrid-based study demonstrated that m.4344T>C variant impaired the steady-state level of mitochondrial tRNAGln and decreased the contents of mitochondrial OXPHOS complexes I, III, and IV, resulting in defective mitochondrial respiration, elevated mitochondrial ROS production, reduced mitochondrial membrane potential and decreased mitochondrial ATP levels. Altogether, this is the first report in patient carrying the m.4344T>C variant. Our data uncover the pathogenesis of the m.4344T>C variant and expand the genetic mutation spectrum of mitochondrial diseases, thus contributing to the clinical diagnosis of mitochondrial tRNAGln gene variants-associated mitochondrial diseases.
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Affiliation(s)
- Xiaojie Yin
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Qiyu Dong
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Shuanglong Fan
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Lina Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yijun Jin
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Mahlatsi Refiloe Laurentinah
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Xiandan Chen
- International Sakharov Environmental Institute of Belarusian State University, Minsk, 220070, Republic of Belarus
| | - Aliaksei Sysa
- International Sakharov Environmental Institute of Belarusian State University, Minsk, 220070, Republic of Belarus
| | - Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310053, Zhejiang, China.
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, 200092, China.
- Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, 200092, China.
| | - Ya Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
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3
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Kim Y, Cho S, Kim JC, Park HS. tRNA engineering strategies for genetic code expansion. Front Genet 2024; 15:1373250. [PMID: 38516376 PMCID: PMC10954879 DOI: 10.3389/fgene.2024.1373250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
The advancement of genetic code expansion (GCE) technology is attributed to the establishment of specific aminoacyl-tRNA synthetase/tRNA pairs. While earlier improvements mainly focused on aminoacyl-tRNA synthetases, recent studies have highlighted the importance of optimizing tRNA sequences to enhance both unnatural amino acid incorporation efficiency and orthogonality. Given the crucial role of tRNAs in the translation process and their substantial impact on overall GCE efficiency, ongoing efforts are dedicated to the development of tRNA engineering techniques. This review explores diverse tRNA engineering approaches and provides illustrative examples in the context of GCE, offering insights into the user-friendly implementation of GCE technology.
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Affiliation(s)
| | | | | | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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4
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Lee S, Hoyt S, Wu X, Garvie C, McGaunn J, Shekhar M, Tötzl M, Rees MG, Cherniack AD, Meyerson M, Greulich H. Velcrin-induced selective cleavage of tRNA Leu(TAA) by SLFN12 causes cancer cell death. Nat Chem Biol 2023; 19:301-310. [PMID: 36302897 DOI: 10.1038/s41589-022-01170-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 09/08/2022] [Indexed: 11/08/2022]
Abstract
Velcrin compounds kill cancer cells expressing high levels of phosphodiesterase 3A (PDE3A) and Schlafen family member 12 (SLFN12) by inducing complex formation between these two proteins, but the mechanism of cancer cell killing by the PDE3A-SLFN12 complex is not fully understood. Here, we report that the physiological substrate of SLFN12 RNase is tRNALeu(TAA). SLFN12 selectively digests tRNALeu(TAA), and velcrin treatment promotes the cleavage of tRNALeu(TAA) by inducing PDE3A-SLFN12 complex formation in vitro. We found that distinct sequences in the variable loop and acceptor stem of tRNALeu(TAA) are required for substrate digestion. Velcrin treatment of sensitive cells results in downregulation of tRNALeu(TAA), ribosome pausing at Leu-TTA codons and global inhibition of protein synthesis. Velcrin-induced cleavage of tRNALeu(TAA) by SLFN12 and the concomitant global inhibition of protein synthesis thus define a new mechanism of apoptosis initiation.
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Affiliation(s)
- Sooncheol Lee
- Cancer Program, Broad Institute, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Xiaoyun Wu
- Cancer Program, Broad Institute, Cambridge, MA, USA
- Astra-Zeneca, Waltham, MA, USA
| | - Colin Garvie
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | | | - Mrinal Shekhar
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Marcus Tötzl
- Cancer Program, Broad Institute, Cambridge, MA, USA
- Children's Cancer Research Institute, Vienna, Austria
| | | | - Andrew D Cherniack
- Cancer Program, Broad Institute, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew Meyerson
- Cancer Program, Broad Institute, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Heidi Greulich
- Cancer Program, Broad Institute, Cambridge, MA, USA.
- Dana-Farber Cancer Institute, Boston, MA, USA.
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5
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Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
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Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
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6
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Mohanty BK, Maples V, Kushner SR. OUP accepted manuscript. Nucleic Acids Res 2022; 50:1639-1649. [PMID: 35061897 PMCID: PMC8860583 DOI: 10.1093/nar/gkab1260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/22/2021] [Accepted: 12/09/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Bijoy K Mohanty
- Department of Genetics and Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Valerie Maples
- Department of Genetics and Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Sidney R Kushner
- To whom correspondence should be addressed. Tel: +1 706 542 8000;
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7
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Sopko B, Tejral G, Bitti G, Abate M, Medvedikova M, Hajduch M, Chloupek J, Fajmonova J, Skoric M, Amler E, Erban T. Glyphosate Interaction with eEF1α1 Indicates Altered Protein Synthesis: Evidence for Reduced Spermatogenesis and Cytostatic Effect. ACS OMEGA 2021; 6:14848-14857. [PMID: 34151066 PMCID: PMC8209799 DOI: 10.1021/acsomega.1c00449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
The broad-spectrum herbicide, glyphosate, is considered safe for animals because it selectively affects the shikimate pathway that is specific to plants and microorganisms. We sought a previously unknown mechanism to explain the concerns that glyphosate exposure can negatively affect animals, including humans. Computer modeling showed a probable interaction between glyphosate and eukaryotic translation elongation factor 1 subunit alpha 1 (eEF1α1), which was confirmed by microcalorimetry. Only restricted, nondisrupted spermatogenesis in rats was observed after chronic glyphosate treatments (0.7 and 7 mg/L). Cytostatic and antiproliferative effects of glyphosate in GC-1 and SUP-B15 cells were indicated. Meta-analysis of public health data suggested a possible effect of glyphosate use on sperm count. The in silico, in vitro, and in vivo experimental results as well as the metastatistics indicate side effects of chronic glyphosate exposure. Together, these findings indicate that glyphosate delays protein synthesis through an interaction with eEF1α1, thereby suppressing spermatogenesis and cell growth.
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Affiliation(s)
- Bruno Sopko
- Crop
Research Institute, Prague 161 06, Czechia
- Department
of Medical Chemistry and Clinical Biochemistry, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague 150 06, Czechia
- Laboratory
of Tissue Engineering, Institute of Experimental
Medicine, Academy of Sciences of the Czech Republic, Prague 142 20, Czechia
- Biomedicine
and Advanced Biomaterials Department, University Center for Energy
Efficient Buildings, The Czech Technical
University in Prague, Prague, Bustehrad 273 43, Czechia
| | - Gracian Tejral
- Laboratory
of Tissue Engineering, Institute of Experimental
Medicine, Academy of Sciences of the Czech Republic, Prague 142 20, Czechia
- Biomedicine
and Advanced Biomaterials Department, University Center for Energy
Efficient Buildings, The Czech Technical
University in Prague, Prague, Bustehrad 273 43, Czechia
- Department
of Biophysics, 2nd Faculty of Medicine, Charles University, Prague 150 06, Czechia
| | - Guissepe Bitti
- Laboratory
of Tissue Engineering, Institute of Experimental
Medicine, Academy of Sciences of the Czech Republic, Prague 142 20, Czechia
- Biomedicine
and Advanced Biomaterials Department, University Center for Energy
Efficient Buildings, The Czech Technical
University in Prague, Prague, Bustehrad 273 43, Czechia
| | - Marianna Abate
- Department
of Precision Medicine, University of Campania
“Luigi Vanvitelli”, Naples 80131, Italy
| | - Martina Medvedikova
- Institute
of Molecular and Translation Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc 779 00, Czechia
| | - Marian Hajduch
- Institute
of Molecular and Translation Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc 779 00, Czechia
| | - Jan Chloupek
- Department
of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences
Brno, Brno 612 42, Czechia
| | - Jolana Fajmonova
- Department
of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences
Brno, Brno 612 42, Czechia
| | - Misa Skoric
- Department
of Pathological Morphology and Parasitology, Faculty of Veterinary
Medicine, University of Veterinary and Pharmaceutical
Sciences Brno, Brno 612 42, Czechia
| | - Evzen Amler
- Biomedicine
and Advanced Biomaterials Department, University Center for Energy
Efficient Buildings, The Czech Technical
University in Prague, Prague, Bustehrad 273 43, Czechia
- Department
of Biophysics, 2nd Faculty of Medicine, Charles University, Prague 150 06, Czechia
| | - Tomas Erban
- Crop
Research Institute, Prague 161 06, Czechia
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8
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Phillips JB, Ardell DH. Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure-Function Map. J Mol Evol 2021; 89:103-116. [PMID: 33528599 PMCID: PMC7884595 DOI: 10.1007/s00239-021-09995-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/11/2021] [Indexed: 10/29/2022]
Abstract
The evolution of tRNA multigene families remains poorly understood, exhibiting unusual phenomena such as functional conversions of tRNA genes through anticodon shift substitutions. We improved FlyBase tRNA gene annotations from twelve Drosophila species, incorporating previously identified ortholog sets to compare substitution rates across tRNA bodies at single-site and base-pair resolution. All rapidly evolving sites fell within the same metal ion-binding pocket that lies at the interface of the two major stacked helical domains. We applied our tRNA Structure-Function Mapper (tSFM) method independently to each Drosophila species and one outgroup species Musca domestica and found that, although predicted tRNA structure-function maps are generally highly conserved in flies, one tRNA Class-Informative Feature (CIF) within the rapidly evolving ion-binding pocket-Cytosine 17 (C17), ancestrally informative for lysylation identity-independently gained asparaginylation identity and substituted in parallel across tRNAAsn paralogs at least once, possibly multiple times, during evolution of the genus. In D. melanogaster, most tRNALys and tRNAAsn genes are co-arrayed in one large heterologous gene cluster, suggesting that heterologous gene conversion as well as structural similarities of tRNA-binding interfaces in the closely related asparaginyl-tRNA synthetase (AsnRS) and lysyl-tRNA synthetase (LysRS) proteins may have played a role in these changes. A previously identified Asn-to-Lys anticodon shift substitution in D. ananassae may have arisen to compensate for the convergent and parallel gains of C17 in tRNAAsn paralogs in that lineage. Our results underscore the functional and evolutionary relevance of our tRNA structure-function map predictions and illuminate multiple genomic and structural factors contributing to rapid, parallel and compensatory evolution of tRNA multigene families.
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Affiliation(s)
- Julie Baker Phillips
- Quantitative and Systems Biology Program, University of California, Merced, CA, 95343, USA
- Department of Biology, Cumberland University, 1 Cumberland Square, Lebanon, TN, 37087, USA
| | - David H Ardell
- Quantitative and Systems Biology Program, University of California, Merced, CA, 95343, USA.
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA.
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9
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Kaiser F, Krautwurst S, Salentin S, Haupt VJ, Leberecht C, Bittrich S, Labudde D, Schroeder M. The structural basis of the genetic code: amino acid recognition by aminoacyl-tRNA synthetases. Sci Rep 2020; 10:12647. [PMID: 32724042 PMCID: PMC7387524 DOI: 10.1038/s41598-020-69100-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/06/2020] [Indexed: 12/29/2022] Open
Abstract
Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. We extensively characterize how these enzymes distinguish all natural amino acids based on the computational analysis of crystallographic structure data. The results of this meta-analysis show that the correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric effects.
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Affiliation(s)
- Florian Kaiser
- Biotechnology Center (BIOTEC), TU Dresden, 01307, Dresden, Germany. .,PharmAI GmbH, Tatzberg 47, 01307, Dresden, Germany.
| | - Sarah Krautwurst
- University of Applied Sciences Mittweida, 09648, Mittweida, Germany
| | | | - V Joachim Haupt
- Biotechnology Center (BIOTEC), TU Dresden, 01307, Dresden, Germany.,PharmAI GmbH, Tatzberg 47, 01307, Dresden, Germany
| | | | | | - Dirk Labudde
- University of Applied Sciences Mittweida, 09648, Mittweida, Germany
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10
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Mohanty BK, Agrawal A, Kushner SR. Generation of pre-tRNAs from polycistronic operons is the essential function of RNase P in Escherichia coli. Nucleic Acids Res 2020; 48:2564-2578. [PMID: 31993626 PMCID: PMC7049720 DOI: 10.1093/nar/gkz1188] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 12/05/2019] [Accepted: 01/27/2020] [Indexed: 11/14/2022] Open
Abstract
Ribonuclease P (RNase P) is essential for the 5′-end maturation of tRNAs in all kingdoms of life. In Escherichia coli, temperature sensitive mutations in either its protein (rnpA49) and or RNA (rnpB709) subunits lead to inviability at nonpermissive temperatures. Using the rnpA49 temperature sensitive allele, which encodes a partially defective RNase P at the permissive temperature, we show here for the first time that the processing of RNase P-dependent polycistronic tRNA operons to release pre-tRNAs is the essential function of the enzyme, since the majority of 5′-immature tRNAs can be aminoacylated unless their 5′-extensions ≥8 nt. Surprisingly, the failure of 5′-end maturation elicits increased polyadenylation of some pre-tRNAs by poly(A) polymerase I (PAP I), which exacerbates inviability. The absence of PAP I led to improved aminoacylation of 5′-immature tRNAs. Our data suggest a more dynamic role for PAP I in maintaining functional tRNA levels in the cell.
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Affiliation(s)
- Bijoy K Mohanty
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Ankit Agrawal
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Sidney R Kushner
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
- To whom correspondence should be addressed. Tel: +706 542 1440; Fax: +706 542 1439;
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11
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Zamudio GS, Palacios-Pérez M, José MV. Information theory unveils the evolution of tRNA identity elements in the three domains of life. Theory Biosci 2019; 139:77-85. [PMID: 31535331 DOI: 10.1007/s12064-019-00301-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 09/03/2019] [Indexed: 11/26/2022]
Abstract
We determined the identity elements of each tRNA isoacceptor for the three domains of life: Eubacteria, Archaea, and Eukarya. Our analyses encompass the most updated and curated available databases using an information theory approach. We obtained a collection of identity clusters for each of the isoacceptors of the 20 canonical amino acids for the three major domains of life. The identity clusters for all isoacceptors are compared within and among the three domains to determine their pattern of differentiation and to shed light on the evolution of the identity elements.
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Affiliation(s)
- Gabriel S Zamudio
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, C.P. 04510, Mexico City, CDMX, Mexico.
| | - Miryam Palacios-Pérez
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, C.P. 04510, Mexico City, CDMX, Mexico
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, C.P. 04510, Mexico City, CDMX, Mexico.
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12
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Zhao X, Han J, Zhu L, Xiao Y, Wang C, Hong F, Jiang P, Guan MX. Overexpression of human mitochondrial alanyl-tRNA synthetase suppresses biochemical defects of the mt-tRNA Ala mutation in cybrids. Int J Biol Sci 2018; 14:1437-1444. [PMID: 30262995 PMCID: PMC6158735 DOI: 10.7150/ijbs.27043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/17/2018] [Indexed: 11/13/2022] Open
Abstract
Mutations of mitochondrial transfer RNAs (mt-tRNAs) play a major role in a wide range of mitochondrial diseases because of the vital role of these molecules in mitochondrial translation. It has previously been reported that the overexpression of mitochondrial aminoacyl tRNA synthetases is effective at partially suppressing the defects resulting from mutations in their cognate mt-tRNAs in cells. Here we report a detailed analysis of the suppressive activities of mitochondrial alanyl-tRNA synthetase (AARS2) on mt-tRNAAla 5655 A>G mutant. Mitochondrial defects in respiration, activity of oxidative phosphorylation complexes, ATP production, mitochondrial superoxide, and membrane potential were consistently rescued in m.5655A>G cybrids upon AARS2 expression. However, AARS2 overexpression did not result in a detectable increase in mutated mt-tRNAAla but caused an increase incharged mt-tRNAAla in mutant cybrids, leading to enhanced mitochondrial translation. This indicated that AARS2 improved the aminoacylation activity in the case of m.5655A>G, rather than having a stabilizing effect on the tRNA structure. The data presented in this paper deepen our understanding of the pathogenesis of mt-tRNA diseases.
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Affiliation(s)
- Xiaoxu Zhao
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Institute of Genetics Zhejiang University, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jiamin Han
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Institute of Genetics Zhejiang University, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Ling Zhu
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yun Xiao
- Institute of Genetics Zhejiang University, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Chenghui Wang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Institute of Genetics Zhejiang University, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Fang Hong
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Pingping Jiang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Institute of Genetics Zhejiang University, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Institute of Genetics Zhejiang University, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, China
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