1
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Iwaniec BW, Allegretti MM, Jackman JE. Metal ion requirement for catalysis by 3'-5' RNA polymerases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.21.644660. [PMID: 40166239 PMCID: PMC11957112 DOI: 10.1101/2025.03.21.644660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
The two-metal ion mechanism for catalysis of RNA and DNA synthesis by 5'-3' polymerases has been extensively characterized. The 3'-5' polymerase family of enzymes, consisting of tRNAHis guanylyltransferase (Thg1) and Thg1-like proteins (TLPs), perform a similar nucleotide addition reaction, but in the reverse direction, adding Watson-Crick base paired NTPs to the 5'-ends of RNA substrates, yet the effect of divalent cations beyond magnesium has not been described. Here, we examined the effects of five divalent cations (Mg2+, Mn2+, Co2+, Ni2+ and Ca2+) on templated nucleotide addition activity and kinetics of 5'-activation by ATP catalyzed by recombinantly purified, metal-free TLPs from organisms from diverse domains of life. This work revealed that different TLPs exhibit distinct dependencies on the concentration and identity of divalent metal ions that support effective catalysis. The patterns of metal ion usage demonstrated here for TLPs evince features that are characteristic of both canonical 5'-3' polymerases and DNA/RNA ligases. Similar to 5'-3' polymerases, some metals were also seen to be mutagenic in the context of TLP catalysis. Furthermore, we provide the first direct evidence that both ATP and the NTP poised for nucleotidyl transfer are present in the active site during the 5'-adenylylation. These results provide the first in-depth study of the role of the two-metal ion mechanism in TLP catalysis that was first suggested by structures of these enzymes.
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Affiliation(s)
- Brandon W.J. Iwaniec
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, 43210
- Center for RNA Biology and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Madison M. Allegretti
- Center for RNA Biology and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Jane E. Jackman
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, 43210
- Center for RNA Biology and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
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2
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Wilhelm SDP, Kakadia JH, Beharry A, Kenana R, Hoffman KS, O'Donoghue P, Heinemann IU. Transfer RNA supplementation rescues HARS deficiency in a humanized yeast model of Charcot-Marie-Tooth disease. Nucleic Acids Res 2024; 52:14043-14060. [PMID: 39530218 DOI: 10.1093/nar/gkae996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 09/13/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024] Open
Abstract
Aminoacyl-tRNA synthetases are indispensable enzymes in all cells, ensuring the correct pairing of amino acids to their cognate tRNAs to maintain translation fidelity. Autosomal dominant mutations V133F and Y330C in histidyl-tRNA synthetase (HARS) cause the genetic disorder Charcot-Marie-Tooth type 2W (CMT2W). Treatments are currently restricted to symptom relief, with no therapeutic available that targets the cause of disease. We previously found that histidine supplementation alleviated phenotypic defects in a humanized yeast model of CMT2W caused by HARS V155G and S356N that also unexpectedly exacerbated the phenotype of the two HARS mutants V133F and Y330C. Here, we show that V133F destabilizes recombinant HARS protein, which is rescued in the presence of tRNAHis. HARS V133F and Y330C cause mistranslation and cause changes to the proteome without activating the integrated stress response as validated by mass spectrometry and growth defects that persist with histidine supplementation. The growth defects and reduced translation fidelity caused by V133F and Y330C mutants were rescued by supplementation with human tRNAHis in a humanized yeast model. Our results demonstrate the feasibility of cognate tRNA as a therapeutic that rescues HARS deficiency and ameliorates toxic mistranslation generated by causative alleles for CMT.
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Affiliation(s)
- Sarah D P Wilhelm
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Jenica H Kakadia
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rosan Kenana
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Kyle S Hoffman
- Bioinformatics Solutions Inc, Waterloo, Ontario, N2L 3K8 Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
- Children's Health Research Institute, London, ON, N6C 4V3 Canada
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3
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Wilhelm SDP, Moresco AA, Rivero AD, Siu VM, Heinemann IU. Characterization of a novel heterozygous variant in the histidyl-tRNA synthetase gene associated with Charcot-Marie-Tooth disease type 2W. IUBMB Life 2024; 76:1125-1138. [PMID: 39352000 PMCID: PMC11580374 DOI: 10.1002/iub.2918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 09/01/2024] [Indexed: 10/03/2024]
Abstract
Heterozygous pathogenic variants in the histidyl-tRNA synthetase (HARS) gene are associated with Charcot-Marie-Tooth (CMT) type 2W disease, classified as an axonal peripheral neuropathy. To date, at least 60 variants causing CMT symptoms have been identified in seven different aminoacyl-tRNA synthetases, with eight being found in the catalytic domain of HARS. The genetic data clearly show a causative role of aminoacyl-tRNA synthetases in CMT; however, the cellular mechanisms leading to pathology can vary widely and are unknown in the case of most identified variants. Here we describe a novel HARS variant, c.412T>C; p.Y138H, identified through a CMT gene panel in a patient with peripheral neuropathy. To determine the effect of p.Y138H we employed a humanized HARS yeast model and recombinant protein biochemistry, which identified a deficiency in protein dimerization and a growth defect which shows mild but significant improvement with histidine supplementation. This raises the potential for a clinical trial of histidine.
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Affiliation(s)
- Sarah D. P. Wilhelm
- Department of BiochemistryThe University of Western OntarioLondonOntarioCanada
| | - Angelica A. Moresco
- Division of Medical Genetics, Department of PaediatricsThe University of Western OntarioLondonOntarioCanada
| | | | - Victoria Mok Siu
- Division of Medical Genetics, Department of PaediatricsThe University of Western OntarioLondonOntarioCanada
- Children's Health Research InstituteLondonOntarioCanada
| | - Ilka U. Heinemann
- Department of BiochemistryThe University of Western OntarioLondonOntarioCanada
- Children's Health Research InstituteLondonOntarioCanada
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4
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Qiu Y, Kenana R, Beharry A, Wilhelm SDP, Hsu SY, Siu VM, Duennwald M, Heinemann IU. Histidine supplementation can escalate or rescue HARS deficiency in a Charcot-Marie-Tooth disease model. Hum Mol Genet 2023; 32:810-824. [PMID: 36164730 PMCID: PMC9941834 DOI: 10.1093/hmg/ddac239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/30/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Aminoacyl-tRNA synthetases are essential enzymes responsible for charging amino acids onto cognate tRNAs during protein synthesis. In histidyl-tRNA synthetase (HARS), autosomal dominant mutations V133F, V155G, Y330C and S356N in the HARS catalytic domain cause Charcot-Marie-Tooth disease type 2 W (CMT2W), while tRNA-binding domain mutation Y454S causes recessive Usher syndrome type IIIB. In a yeast model, all human HARS variants complemented a genomic deletion of the yeast ortholog HTS1 at high expression levels. CMT2W associated mutations, but not Y454S, resulted in reduced growth. We show mistranslation of histidine to glutamine and threonine in V155G and S356N but not Y330C mutants in yeast. Mistranslating V155G and S356N mutants lead to accumulation of insoluble proteins, which was rescued by histidine. Mutants V133F and Y330C showed the most significant growth defect and decreased HARS abundance in cells. Here, histidine supplementation led to insoluble protein aggregation and further reduced viability, indicating histidine toxicity associated with these mutants. V133F proteins displayed reduced thermal stability in vitro, which was rescued by tRNA. Our data will inform future treatment options for HARS patients, where histidine supplementation may either have a toxic or compensating effect depending on the nature of the causative HARS variant.
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Affiliation(s)
- Yi Qiu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Rosan Kenana
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Sarah D P Wilhelm
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Sung Yuan Hsu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Victoria M Siu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Martin Duennwald
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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5
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Cognat V, Pawlak G, Pflieger D, Drouard L. PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1112-1119. [PMID: 36196656 DOI: 10.1111/tpj.15997] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
PlantRNA (http://plantrna.ibmp.cnrs.fr/) is a comprehensive database of transfer RNA (tRNA) gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms. In the first release (PlantRNA 1.0), tRNA genes from 11 organisms were annotated. In this second version, the annotation was implemented to 51 photosynthetic species covering the whole phylogenetic tree of photosynthetic organisms, from the most basal group of Archeplastida, the glaucophyte Cyanophora paradoxa, to various land plants. tRNA genes from lower photosynthetic organisms such as streptophyte algae or lycophytes as well as extremophile photosynthetic species such as Eutrema parvulum were incorporated in the database. As a whole, about 37 000 tRNA genes were accurately annotated. In the frame of the tRNA genes annotation from the genome of the Rhodophyte Chondrus crispus, non-canonical splicing sites in the D- or T-regions of tRNA molecules were identified and experimentally validated. As for PlantRNA 1.0, comprehensive biological information including 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences and tRNA mitochondrial import are included.
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Affiliation(s)
- Valérie Cognat
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084, Strasbourg, France
| | - Gael Pawlak
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084, Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084, Strasbourg, France
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084, Strasbourg, France
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6
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Patel KJ, Yourik P, Jackman JE. Fidelity of base-pair recognition by a 3'-5' polymerase: mechanism of the Saccharomyces cerevisiae tRNA His guanylyltransferase. RNA (NEW YORK, N.Y.) 2021; 27:683-693. [PMID: 33790044 PMCID: PMC8127993 DOI: 10.1261/rna.078686.121] [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] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
The tRNAHis guanylyltransferase (Thg1) was originally discovered in Saccharomyces cerevisiae where it catalyzes 3'-5' addition of a single nontemplated guanosine (G-1) to the 5' end of tRNAHis In addition to this activity, S. cerevisiae Thg1 (SceThg1) also catalyzes 3'-5' polymerization of Watson-Crick (WC) base pairs, utilizing nucleotides in the 3'-end of a tRNA as the template for addition. Subsequent investigation revealed an entire class of enzymes related to Thg1, called Thg1-like proteins (TLPs). TLPs are found in all three domains of life and preferentially catalyze 3'-5' polymerase activity, utilizing this unusual activity to repair tRNA, among other functions. Although both Thg1 and TLPs utilize the same chemical mechanism, the molecular basis for differences between WC-dependent (catalyzed by Thg1 and TLPs) and non-WC-dependent (catalyzed exclusively by Thg1) reactions has not been fully elucidated. Here we investigate the mechanism of base-pair recognition by 3'-5' polymerases using transient kinetic assays, and identify Thg1-specific residues that play a role in base-pair discrimination. We reveal that, regardless of the identity of the opposing nucleotide in the RNA "template," addition of a non-WC G-1 residue is driven by a unique kinetic preference for GTP. However, a secondary preference for forming WC base pairs is evident for all possible templating residues. Similar to canonical 5'-3' polymerases, nucleotide addition by SceThg1 is driven by the maximal rate rather than by NTP substrate affinity. Together, these data provide new insights into the mechanism of base-pair recognition by 3'-5' polymerases.
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Affiliation(s)
- Krishna J Patel
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Paul Yourik
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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7
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A Temporal Order in 5'- and 3'- Processing of Eukaryotic tRNA His. Int J Mol Sci 2019; 20:ijms20061384. [PMID: 30893886 PMCID: PMC6470698 DOI: 10.3390/ijms20061384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/21/2019] [Accepted: 03/15/2019] [Indexed: 01/27/2023] Open
Abstract
For flawless translation of mRNA sequence into protein, tRNAs must undergo a series of essential maturation steps to be properly recognized and aminoacylated by aminoacyl-tRNA synthetase, and subsequently utilized by the ribosome. While all tRNAs carry a 3'-terminal CCA sequence that includes the site of aminoacylation, the additional 5'-G-1 position is a unique feature of most histidine tRNA species, serving as an identity element for the corresponding synthetase. In eukaryotes including yeast, both 3'-CCA and 5'-G-1 are added post-transcriptionally by tRNA nucleotidyltransferase and tRNAHis guanylyltransferase, respectively. Hence, it is possible that these two cytosolic enzymes compete for the same tRNA. Here, we investigate substrate preferences associated with CCA and G-1-addition to yeast cytosolic tRNAHis, which might result in a temporal order to these important processing events. We show that tRNA nucleotidyltransferase accepts tRNAHis transcripts independent of the presence of G-1; however, tRNAHis guanylyltransferase clearly prefers a substrate carrying a CCA terminus. Although many tRNA maturation steps can occur in a rather random order, our data demonstrate a likely pathway where CCA-addition precedes G-1 incorporation in S. cerevisiae. Evidently, the 3'-CCA triplet and a discriminator position A73 act as positive elements for G-1 incorporation, ensuring the fidelity of G-1 addition.
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8
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Nakamura A, Wang D, Komatsu Y. Molecular mechanism of substrate recognition and specificity of tRNA His guanylyltransferase during nucleotide addition in the 3'-5' direction. RNA (NEW YORK, N.Y.) 2018; 24:1583-1593. [PMID: 30111535 PMCID: PMC6191723 DOI: 10.1261/rna.067330.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/09/2018] [Indexed: 05/06/2023]
Abstract
The tRNAHis guanylyltransferase (Thg1) transfers a guanosine triphosphate (GTP) in the 3'-5' direction onto the 5'-terminal of tRNAHis, opposite adenosine at position 73 (A73). The guanosine at the -1 position (G-1) serves as an identity element for histidyl-tRNA synthetase. To investigate the mechanism of recognition for the insertion of GTP opposite A73, first we constructed a two-stranded tRNAHis molecule composed of a primer and a template strand through division at the D-loop. Next, we evaluated the structural requirements of the incoming GTP from the incorporation efficiencies of GTP analogs into the two-piece tRNAHis Nitrogen at position 7 and the 6-keto oxygen of the guanine base were important for G-1 addition; however, interestingly, the 2-amino group was found not to be essential from the highest incorporation efficiency of inosine triphosphate. Furthermore, substitution of the conserved A73 in tRNAHis revealed that the G-1 addition reaction was more efficient onto the template containing the opposite A73 than onto the template with cytidine (C73) or other bases forming canonical Watson-Crick base-pairing. Some interaction might occur between incoming GTP and A73, which plays a role in the prevention of continuous templated 3'-5' polymerization. This study provides important insights into the mechanism of accurate tRNAHis maturation.
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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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9
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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: 0.6] [Reference Citation Analysis] [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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10
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Shigematsu M, Kirino Y. 5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves. RNA (NEW YORK, N.Y.) 2017; 23:161-168. [PMID: 27879434 PMCID: PMC5238791 DOI: 10.1261/rna.058024.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
Transfer RNAs (tRNAs) are fundamental adapter components of translational machinery. tRNAs can further serve as a source of tRNA-derived noncoding RNAs that play important roles in various biological processes beyond translation. Among all species of tRNAs, tRNAHisGUG has been known to uniquely contain an additional guanosine residue at the -1 position (G-1) of its 5'-end. To analyze this -1 nucleotide in detail, we developed a TaqMan qRT-PCR method that can distinctively quantify human mature cytoplasmic tRNAHisGUG containing G-1, U-1, A-1, or C-1 or lacking the -1 nucleotide (starting from G1). Application of this method to the mature tRNA fraction of BT-474 breast cancer cells revealed the presence of tRNAHisGUG containing U-1 as well as the one containing G-1 Moreover, tRNA lacking the -1 nucleotide was also detected, thus indicating the heterogeneous expression of 5'-tRNAHisGUG variants. A sequence library of sex hormone-induced 5'-tRNA halves (5'-SHOT-RNAs), identified via cP-RNA-seq of a BT-474 small RNA fraction, also demonstrated the expression of 5'-tRNAHisGUG halves containing G-1, U-1, or G1 as 5'-terminal nucleotides. Although the detected 5'-nucleotide species were identical, the relative abundances differed widely between mature tRNA and 5'-half from the same BT-474 cells. The majority of mature tRNAs contained the -1 nucleotide, whereas the majority of 5'-halves lacked this nucleotide, which was biochemically confirmed using a primer extension assay. These results reveal the novel identities of tRNAHisGUG molecules and provide insights into tRNAHisGUG maturation and the regulation of tRNA half production.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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11
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Burroughs AM, Aravind L. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Nucleic Acids Res 2016; 44:8525-8555. [PMID: 27536007 PMCID: PMC5062991 DOI: 10.1093/nar/gkw722] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/08/2016] [Indexed: 12/16/2022] Open
Abstract
RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of systems which repair or ‘heal’ this damage has only recently become apparent. Here, we summarize the known effectors, their modes of action, and RNA targets before surveying the diverse systems which counter this damage from a comparative genomics viewpoint. RNA-repair systems show a modular organization with extensive shuffling and displacement of the constituent domains; however, a general ‘syntax’ is strongly maintained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nucleotidyltransferases, enzymes modifying RNA-termini for ligation (phosphatases and kinases) or protection (methylases), and scaffold or cofactor proteins. We highlight poorly-understood or previously-uncharacterized repair systems and components, e.g. potential scaffolding cofactors (Rot/TROVE and SPFH/Band-7 modules) with their respective cognate non-coding RNAs (YRNAs and a novel tRNA-like molecule) and a novel nucleotidyltransferase associating with diverse ligases. These systems have been extensively disseminated by lateral transfer between distant prokaryotic and microbial eukaryotic lineages consistent with intense inter-organismal conflict. Components have also often been ‘institutionalized’ for non-conflict roles, e.g. in RNA-splicing and in RNAi systems (e.g. in kinetoplastids) which combine a distinct family of RNA-acting prim-pol domains with DICER-like proteins.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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12
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Long Y, Abad MG, Olson ED, Carrillo EY, Jackman JE. Identification of distinct biological functions for four 3'-5' RNA polymerases. Nucleic Acids Res 2016; 44:8395-406. [PMID: 27484477 PMCID: PMC5041481 DOI: 10.1093/nar/gkw681] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/22/2016] [Indexed: 12/19/2022] Open
Abstract
The superfamily of 3'-5' polymerases synthesize RNA in the opposite direction to all other DNA/RNA polymerases, and its members include eukaryotic tRNA(His) guanylyltransferase (Thg1), as well as Thg1-like proteins (TLPs) of unknown function that are broadly distributed, with family members in all three domains of life. Dictyostelium discoideum encodes one Thg1 and three TLPs (DdiTLP2, DdiTLP3 and DdiTLP4). Here, we demonstrate that depletion of each of the genes results in a significant growth defect, and that each protein catalyzes a unique biological reaction, taking advantage of specialized biochemical properties. DdiTLP2 catalyzes a mitochondria-specific tRNA(His) maturation reaction, which is distinct from the tRNA(His) maturation reaction typically catalyzed by Thg1 enzymes on cytosolic tRNA. DdiTLP3 catalyzes tRNA repair during mitochondrial tRNA 5'-editing in vivo and in vitro, establishing template-dependent 3'-5' polymerase activity of TLPs as a bona fide biological activity for the first time since its unexpected discovery more than a decade ago. DdiTLP4 is cytosolic and, surprisingly, catalyzes robust 3'-5' polymerase activity on non-tRNA substrates, strongly implying further roles for TLP 3'-5' polymerases in eukaryotes.
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Affiliation(s)
- Yicheng Long
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Maria G Abad
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Erik D Olson
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Elisabeth Y Carrillo
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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13
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Tian Q, Wang C, Liu Y, Xie W. Structural basis for recognition of G-1-containing tRNA by histidyl-tRNA synthetase. Nucleic Acids Res 2015; 43:2980-90. [PMID: 25722375 PMCID: PMC4357726 DOI: 10.1093/nar/gkv129] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in protein translation by linking tRNAs with cognate amino acids. Among all the tRNAs, only tRNAHis bears a guanine base at position -1 (G-1), and it serves as a major recognition element for histidyl-tRNA synthetase (HisRS). Despite strong interests in the histidylation mechanism, the tRNA recognition and aminoacylation details are not fully understood. We herein present the 2.55 Å crystal structure of HisRS complexed with tRNAHis, which reveals that G-1 recognition is principally nonspecific interactions on this base and is made possible by an enlarged binding pocket consisting of conserved glycines. The anticodon triplet makes additional specific contacts with the enzyme but the rest of the loop is flexible. Based on the crystallographic and biochemical studies, we inferred that the uniqueness of histidylation system originates from the enlarged binding pocket (for the extra base G-1) on HisRS absent in other aaRSs, and this structural complementarity between the 5′ extremity of tRNA and enzyme is probably a result of coevolution of both.
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Affiliation(s)
- Qingnan Tian
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou 510275, People's Republic of China Center for Cellular & Structural biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou 510006, People's Republic of China
| | - Caiyan Wang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou 510275, People's Republic of China Center for Cellular & Structural biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou 510006, People's Republic of China
| | - Yuhuan Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Wei Xie
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou 510275, People's Republic of China Center for Cellular & Structural biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou 510006, People's Republic of China
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14
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Rao BS, Jackman JE. Life without post-transcriptional addition of G-1: two alternatives for tRNAHis identity in Eukarya. RNA (NEW YORK, N.Y.) 2015; 21:243-53. [PMID: 25505023 PMCID: PMC4338351 DOI: 10.1261/rna.048389.114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/06/2014] [Indexed: 05/23/2023]
Abstract
The identity of tRNA(His) is strongly associated with the presence of an additional 5'-guanosine residue (G-1) in all three domains of life. The critical nature of the G-1 residue is underscored by the fact that two entirely distinct mechanisms for its acquisition are observed, with cotranscriptional incorporation observed in Bacteria, while post-transcriptional addition of G-1 occurs in Eukarya. Here, through our investigation of eukaryotes that lack obvious homologs of the post-transcriptional G-1-addition enzyme Thg1, we identify alternative pathways to tRNA(His) identity that controvert these well-established rules. We demonstrate that Trypanosoma brucei, like Acanthamoeba castellanii, lacks the G-1 identity element on tRNA(His) and utilizes a noncanonical G-1-independent histidyl-tRNA synthetase (HisRS). Purified HisRS enzymes from A. castellanii and T. brucei exhibit a mechanism of tRNA(His) recognition that is distinct from canonical G-1-dependent synthetases. Moreover, noncanonical HisRS enzymes genetically complement the loss of THG1 in Saccharomyces cerevisiae, demonstrating the biological relevance of the G-1-independent aminoacylation activity. In contrast, in Caenorhabditis elegans, which is another Thg1-independent eukaryote, the G-1 residue is maintained, but here its acquisition is noncanonical. In this case, the G-1 is encoded and apparently retained after 5' end processing, which has so far only been observed in Bacteria and organelles. Collectively, these observations unearth a widespread and previously unappreciated diversity in eukaryotic tRNA(His) identity mechanisms.
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Affiliation(s)
- Bhalchandra S Rao
- Molecular, Cellular and Developmental Biology Program, Center for RNA Biology and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jane E Jackman
- Molecular, Cellular and Developmental Biology Program, Center for RNA Biology and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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15
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Abstract
Nucleotide polymerization proceeds in the forward (5'-3') direction. This tenet of the central dogma of molecular biology is found in diverse processes including transcription, reverse transcription, DNA replication, and even in lagging strand synthesis where reverse polymerization (3'-5') would present a "simpler" solution. Interestingly, reverse (3'-5') nucleotide addition is catalyzed by the tRNA maturation enzyme tRNA(His) guanylyltransferase, a structural homolog of canonical forward polymerases. We present a Candida albicans tRNA(His) guanylyltransferase-tRNA(His) complex structure that reveals the structural basis of reverse polymerization. The directionality of nucleotide polymerization is determined by the orientation of approach of the nucleotide substrate. The tRNA substrate enters the enzyme's active site from the opposite direction (180° flip) compared with similar nucleotide substrates of canonical 5'-3' polymerases, and the finger domains are on opposing sides of the core palm domain. Structural, biochemical, and phylogenetic data indicate that reverse polymerization appeared early in evolution and resembles a mirror image of the forward process.
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16
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Smith BA, Jackman JE. Kinetic analysis of 3'-5' nucleotide addition catalyzed by eukaryotic tRNA(His) guanylyltransferase. Biochemistry 2011; 51:453-65. [PMID: 22136300 DOI: 10.1021/bi201397f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tRNA(His) guanylyltransferase (Thg1) catalyzes the incorporation of a single guanosine residue at the -1 position (G(-1)) of tRNA(His), using an unusual 3'-5' nucleotidyl transfer reaction. Thg1 and Thg1 orthologs known as Thg1-like proteins (TLPs), which catalyze tRNA repair and editing, are the only known enzymes that add nucleotides in the 3'-5' direction. Thg1 enzymes share no identifiable sequence similarity with any other known enzyme family that could be used to suggest the mechanism for catalysis of the unusual 3'-5' addition reaction. The high-resolution crystal structure of human Thg1 revealed remarkable structural similarity between canonical DNA/RNA polymerases and eukaryotic Thg1; nevertheless, questions regarding the molecular mechanism of 3'-5' nucleotide addition remain. Here, we use transient kinetics to measure the pseudo-first-order forward rate constants for the three steps of the G(-1) addition reaction catalyzed by yeast Thg1: adenylylation of the 5' end of the tRNA (k(aden)), nucleotidyl transfer (k(ntrans)), and removal of pyrophosphate from the G(-1)-containing tRNA (k(ppase)). This kinetic framework, in conjunction with the crystal structure of nucleotide-bound Thg1, suggests a likely role for two-metal ion chemistry in all three chemical steps of the G(-1) addition reaction. Furthermore, we have identified additional residues (K44 and N161) involved in adenylylation and three positively charged residues (R27, K96, and R133) that participate primarily in the nucleotidyl transfer step of the reaction. These data provide a foundation for understanding the mechanism of 3'-5' nucleotide addition in tRNA(His) maturation.
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Affiliation(s)
- Brian A Smith
- Department of Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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17
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Heinemann IU, Nakamura A, O'Donoghue P, Eiler D, Söll D. tRNAHis-guanylyltransferase establishes tRNAHis identity. Nucleic Acids Res 2011; 40:333-44. [PMID: 21890903 PMCID: PMC3245924 DOI: 10.1093/nar/gkr696] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Histidine transfer RNA (tRNA) is unique among tRNA species as it carries an additional nucleotide at its 5' terminus. This unusual G(-1) residue is the major tRNA(His) identity element, and essential for recognition by the cognate histidyl-tRNA synthetase to allow efficient His-tRNA(His) formation. In many organisms G(-1) is added post-transcriptionally as part of the tRNA maturation process. tRNA(His) guanylyltransferase (Thg1) specifically adds the guanylyate residue by recognizing the tRNA(His) anticodon. Thg1 homologs from all three domains of life have been the subject of exciting research that gave rise to a detailed biochemical, structural and phylogenetic enzyme characterization. Thg1 homologs are phylogenetically classified into eukaryal- and archaeal-type enzymes differing characteristically in their cofactor requirements and specificity. Yeast Thg1 displays a unique but limited ability to add 2-3 G or C residues to mutant tRNA substrates, thus catalyzing a 3' → 5' RNA polymerization. Archaeal-type Thg1, which has been horizontally transferred to certain bacteria and few eukarya, displays a more relaxed substrate range and may play additional roles in tRNA editing and repair. The crystal structure of human Thg1 revealed a fascinating structural similarity to 5' → 3' polymerases, indicating that Thg1 derives from classical polymerases and evolved to assume its specific function in tRNA(His) processing.
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Affiliation(s)
- Ilka U Heinemann
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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18
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Su D, Lieberman A, Lang BF, Simonović M, Söll D, Ling J. An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine. Nucleic Acids Res 2011; 39:4866-74. [PMID: 21321019 PMCID: PMC3113583 DOI: 10.1093/nar/gkr073] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 01/27/2011] [Accepted: 01/28/2011] [Indexed: 11/14/2022] Open
Abstract
The standard genetic code is used by most living organisms, yet deviations have been observed in many genomes, suggesting that the genetic code has been evolving. In certain yeast mitochondria, CUN codons are reassigned from leucine to threonine, which requires an unusual tRNA(Thr) with an enlarged 8-nt anticodon loop ( ). To trace its evolutionary origin we performed a comprehensive phylogenetic analysis which revealed that evolved from yeast mitochondrial tRNA(His). To understand this tRNA identity change, we performed mutational and biochemical experiments. We show that Saccharomyces cerevisiae mitochondrial threonyl-tRNA synthetase (MST1) could attach threonine to both and the regular , but not to the wild-type tRNA(His). A loss of the first nucleotide (G(-1)) in tRNA(His) converts it to a substrate for MST1 with a K(m) value (0.7 μM) comparable to that of (0.3 μM), and addition of G(-1) to allows efficient histidylation by histidyl-tRNA synthetase. We also show that MST1 from Candida albicans, a yeast in which CUN codons remain assigned to leucine, could not threonylate , suggesting that MST1 has coevolved with . Our work provides the first clear example of a recent recoding event caused by alloacceptor tRNA gene recruitment.
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MESH Headings
- Base Sequence
- Codon
- Evolution, Molecular
- Histidine-tRNA Ligase/metabolism
- Mitochondria/enzymology
- Molecular Sequence Data
- Phylogeny
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Mitochondrial
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, His/chemistry
- RNA, Transfer, His/genetics
- RNA, Transfer, His/metabolism
- RNA, Transfer, Thr/chemistry
- RNA, Transfer, Thr/genetics
- RNA, Transfer, Thr/metabolism
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Sequence Alignment
- Threonine/metabolism
- Threonine-tRNA Ligase/metabolism
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Affiliation(s)
- Dan Su
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Département de Biochimie, Robert Cedergren Centre, Université de Montréal, Montréal, Québec, Canada, Department of Biochemistry and Molecular Genetics, University of Illinois, 900 S. Ashland Avenue, MBRB 1170, Chicago, IL 60607 and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Allyson Lieberman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Département de Biochimie, Robert Cedergren Centre, Université de Montréal, Montréal, Québec, Canada, Department of Biochemistry and Molecular Genetics, University of Illinois, 900 S. Ashland Avenue, MBRB 1170, Chicago, IL 60607 and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - B. Franz Lang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Département de Biochimie, Robert Cedergren Centre, Université de Montréal, Montréal, Québec, Canada, Department of Biochemistry and Molecular Genetics, University of Illinois, 900 S. Ashland Avenue, MBRB 1170, Chicago, IL 60607 and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Miljan Simonović
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Département de Biochimie, Robert Cedergren Centre, Université de Montréal, Montréal, Québec, Canada, Department of Biochemistry and Molecular Genetics, University of Illinois, 900 S. Ashland Avenue, MBRB 1170, Chicago, IL 60607 and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Département de Biochimie, Robert Cedergren Centre, Université de Montréal, Montréal, Québec, Canada, Department of Biochemistry and Molecular Genetics, University of Illinois, 900 S. Ashland Avenue, MBRB 1170, Chicago, IL 60607 and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Jiqiang Ling
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Département de Biochimie, Robert Cedergren Centre, Université de Montréal, Montréal, Québec, Canada, Department of Biochemistry and Molecular Genetics, University of Illinois, 900 S. Ashland Avenue, MBRB 1170, Chicago, IL 60607 and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
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19
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You T, Coghill GM, Brown AJP. A quantitative model for mRNA translation in Saccharomyces cerevisiae. Yeast 2011; 27:785-800. [PMID: 20306461 DOI: 10.1002/yea.1770] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Messenger RNA (mRNA) translation is an essential step in eukaryotic gene expression that contributes to the regulation of this process. We describe a deterministic model based on ordinary differential equations that describe mRNA translation in Saccharomyces cerevisiae. This model, which was parameterized using published data, was developed to examine the kinetic behaviour of translation initiation factors in response to amino acid availability. The model predicts that the abundance of the eIF1-eIF3-eIF5 complex increases under amino acid starvation conditions, suggesting a possible auxiliary role for these factors in modulating translation initiation in addition to the known mechanisms involving eIF2. Our analyses of the robustness of the mRNA translation model suggest that individual cells within a randomly generated population are sensitive to external perturbations (such as changes in amino acid availability) through Gcn2 signalling. However, the model predicts that individual cells exhibit robustness against internal perturbations (such as changes in the abundance of translation initiation factors and kinetic parameters). Gcn2 appears to enhance this robustness within the system. These findings suggest a trade-off between the robustness and performance of this biological network. The model also predicts that individual cells exhibit considerable heterogeneity with respect to their absolute translation rates, due to random internal perturbations. Therefore, averaging the kinetic behaviour of cell populations probably obscures the dynamic robustness of individual cells. This highlights the importance of single-cell measurements for evaluating network properties.
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Affiliation(s)
- Tao You
- Physics Department, School of Natural and Computing Sciences, University of Aberdeen, Aberdeen, UK
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20
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Yuan J, Gogakos T, Babina AM, Söll D, Randau L. Change of tRNA identity leads to a divergent orthogonal histidyl-tRNA synthetase/tRNAHis pair. Nucleic Acids Res 2010; 39:2286-93. [PMID: 21087993 PMCID: PMC3064791 DOI: 10.1093/nar/gkq1176] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Mature tRNAHis has at its 5′-terminus an extra guanylate, designated as G−1. This is the major recognition element for histidyl-tRNA synthetase (HisRS) to permit acylation of tRNAHis with histidine. However, it was reported that tRNAHis of a subgroup of α-proteobacteria, including Caulobacter crescentus, lacks the critical G−1 residue. Here we show that recombinant C. crescentus HisRS allowed complete histidylation of a C. crescentus tRNAHis transcript (lacking G−1). The addition of G−1 did not improve aminoacylation by C. crescentus HisRS. However, mutations in the tRNAHis anticodon caused a drastic loss of in vitro histidylation, and mutations of bases A73 and U72 also reduced charging. Thus, the major recognition elements in C. crescentus tRNAHis are the anticodon, the discriminator base and U72, which are recognized by the divergent (based on sequence similarity) C. crescentus HisRS. Transplantation of these recognition elements into an Escherichia coli tRNAHis template, together with addition of base U20a, created a competent substrate for C. crescentus HisRS. These results illustrate how a conserved tRNA recognition pattern changed during evolution. The data also uncovered a divergent orthogonal HisRS/tRNAHis pair.
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Affiliation(s)
- Jing Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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21
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tRNA(His) guanylyltransferase (THG1), a unique 3'-5' nucleotidyl transferase, shares unexpected structural homology with canonical 5'-3' DNA polymerases. Proc Natl Acad Sci U S A 2010; 107:20305-10. [PMID: 21059936 DOI: 10.1073/pnas.1010436107] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All known DNA and RNA polymerases catalyze the formation of phosphodiester bonds in a 5' to 3' direction, suggesting this property is a fundamental feature of maintaining and dispersing genetic information. The tRNA(His) guanylyltransferase (Thg1) is a member of a unique enzyme family whose members catalyze an unprecedented reaction in biology: 3'-5' addition of nucleotides to nucleic acid substrates. The 2.3-Å crystal structure of human THG1 (hTHG1) reported here shows that, despite the lack of sequence similarity, hTHG1 shares unexpected structural homology with canonical 5'-3' DNA polymerases and adenylyl/guanylyl cyclases, two enzyme families known to use a two-metal-ion mechanism for catalysis. The ability of the same structural architecture to catalyze both 5'-3' and 3'-5' reactions raises important questions concerning selection of the 5'-3' mechanism during the evolution of nucleotide polymerases.
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22
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Rao BS, Maris EL, Jackman JE. tRNA 5'-end repair activities of tRNAHis guanylyltransferase (Thg1)-like proteins from Bacteria and Archaea. Nucleic Acids Res 2010; 39:1833-42. [PMID: 21051361 PMCID: PMC3061083 DOI: 10.1093/nar/gkq976] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The tRNAHis guanylyltransferase (Thg1) family comprises a set of unique 3′–5′ nucleotide addition enzymes found ubiquitously in Eukaryotes, where they function in the critical G−1 addition reaction required for tRNAHis maturation. However, in most Bacteria and Archaea, G−1 is genomically encoded; thus post-transcriptional addition of G−1 to tRNAHis is not necessarily required. The presence of highly conserved Thg1-like proteins (TLPs) in more than 40 bacteria and archaea therefore suggests unappreciated roles for TLP-catalyzed 3′–5′ nucleotide addition. Here, we report that TLPs from Bacillus thuringiensis (BtTLP) and Methanosarcina acetivorans (MaTLP) display biochemical properties consistent with a prominent role in tRNA 5′-end repair. Unlike yeast Thg1, BtTLP strongly prefers addition of missing N+1 nucleotides to 5′-truncated tRNAs over analogous additions to full-length tRNA (kcat/KM enhanced 5–160-fold). Moreover, unlike for −1 addition, BtTLP-catalyzed additions to truncated tRNAs are not biased toward addition of G, and occur with tRNAs other than tRNAHis. Based on these distinct biochemical properties, we propose that rather than functioning solely in tRNAHis maturation, bacterial and archaeal TLPs are well-suited to participate in tRNA quality control pathways. These data support more widespread roles for 3′–5′ nucleotide addition reactions in biology than previously expected.
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Affiliation(s)
- Bhalchandra S Rao
- Department of Biochemistry and Center for RNA Biology and Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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23
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Abstract
tRNA biology has come of age, revealing an unprecedented level of understanding and many unexpected discoveries along the way. This review highlights new findings on the diverse pathways of tRNA maturation, and on the formation and function of a number of modifications. Topics of special focus include the regulation of tRNA biosynthesis, quality control tRNA turnover mechanisms, widespread tRNA cleavage pathways activated in response to stress and other growth conditions, emerging evidence of signaling pathways involving tRNA and cleavage fragments, and the sophisticated intracellular tRNA trafficking that occurs during and after biosynthesis.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA.
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24
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Placido A, Sieber F, Gobert A, Gallerani R, Giegé P, Maréchal-Drouard L. Plant mitochondria use two pathways for the biogenesis of tRNAHis. Nucleic Acids Res 2010; 38:7711-7. [PMID: 20660484 PMCID: PMC2995067 DOI: 10.1093/nar/gkq646] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
All tRNAHis possess an essential extra G–1 guanosine residue at their 5′ end. In eukaryotes after standard processing by RNase P, G–1 is added by a tRNAHis guanylyl transferase. In prokaryotes, G–1 is genome-encoded and retained during maturation. In plant mitochondria, although trnH genes possess a G–1 we find here that both maturation pathways can be used. Indeed, tRNAHis with or without a G–1 are found in a plant mitochondrial tRNA fraction. Furthermore, a recombinant Arabidopsis mitochondrial RNase P can cleave tRNAHis precursors at both positions G+1 and G–1. The G–1 is essential for recognition by plant mitochondrial histidyl-tRNA synthetase. Whether, as shown in prokaryotes and eukaryotes, the presence of uncharged tRNAHis without G–1 has a function or not in plant mitochondrial gene regulation is an open question. We find that when a mutated version of a plant mitochondrial trnH gene containing no encoded extra G is introduced and expressed into isolated potato mitochondria, mature tRNAHis with a G–1 are recovered. This shows that a previously unreported tRNAHis guanylyltransferase activity is present in plant mitochondria.
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Affiliation(s)
- Antonio Placido
- Dipartimento di Biochimica e Biologia Molecolare Ernesto Quagliariello, Universita' degli Studi di Bari Aldo Moro, Via Orabona 4, 70126 Bari, Italy
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25
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Preston MA, Phizicky EM. The requirement for the highly conserved G-1 residue of Saccharomyces cerevisiae tRNAHis can be circumvented by overexpression of tRNAHis and its synthetase. RNA (NEW YORK, N.Y.) 2010; 16:1068-77. [PMID: 20360392 PMCID: PMC2856879 DOI: 10.1261/rna.2087510] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 02/12/2010] [Indexed: 05/23/2023]
Abstract
Nearly all tRNA(His) species have an additional 5' guanine nucleotide (G(-1)). G(-1) is encoded opposite C(73) in nearly all prokaryotes and in some archaea, and is added post-transcriptionally by tRNA(His) guanylyltransferase (Thg1) opposite A(73) in eukaryotes, and opposite C(73) in other archaea. These divergent mechanisms of G(-1) conservation suggest that G(-1) might have an important cellular role, distinct from its role in tRNA(His) charging. Thg1 is also highly conserved and is essential in the yeast Saccharomyces cerevisiae. However, the essential roles of Thg1 are unclear since Thg1 also interacts with Orc2 of the origin recognition complex, is implicated in the cell cycle, and catalyzes an unusual template-dependent 3'-5' (reverse) polymerization in vitro at the 5' end of activated tRNAs. Here we show that thg1-Delta strains are viable, but only if histidyl-tRNA synthetase and tRNA(His) are overproduced, demonstrating that the only essential role of Thg1 is its G(-1) addition activity. Since these thg1-Delta strains have severe growth defects if cytoplasmic tRNA(His) A(73) is overexpressed, and distinct, but milder growth defects, if tRNA(His) C(73) is overexpressed, these results show that the tRNA(His) G(-1) residue is important, but not absolutely essential, despite its widespread conservation. We also show that Thg1 catalyzes 3'-5' polymerization in vivo on tRNA(His) C(73), but not on tRNA(His) A(73), demonstrating that the 3'-5' polymerase activity is pronounced enough to have a biological role, and suggesting that eukaryotes may have evolved to have cytoplasmic tRNA(His) with A(73), rather than C(73), to prevent the possibility of 3'-5' polymerization.
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MESH Headings
- Base Sequence
- Conserved Sequence
- Gene Expression
- Genes, Fungal
- Histidine-tRNA Ligase/genetics
- Histidine-tRNA Ligase/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Nucleotidyltransferases/genetics
- Nucleotidyltransferases/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer, His/chemistry
- RNA, Transfer, His/genetics
- RNA, Transfer, His/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- Melanie A Preston
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
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26
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Computational analysis of tRNA identity. FEBS Lett 2009; 584:325-33. [PMID: 19944694 DOI: 10.1016/j.febslet.2009.11.084] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 11/20/2009] [Accepted: 11/20/2009] [Indexed: 11/22/2022]
Abstract
I review recent developments in computational analysis of tRNA identity. I suggest that the tRNA-protein interaction network is hierarchically organized, and coevolutionarily flexible. Its functional specificity of recognition and discrimination persists despite generic structural constraints and perturbative evolutionary forces. This flexibility comes from its arbitrary nature as a self-recognizing shape code. A revisualization of predicted Proteobacterial tRNA identity highlights open research problems. tRNA identity elements and their coevolution with proteins must be mapped structurally over the Tree of Life. These traits can also resolve deep roots in the Tree. I show that histidylation identity elements phylogenetically reposition Pelagibacter ubique within alpha-Proteobacteria.
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27
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Mallick B, Ghosh Z, Chakrabarti J. Structural determinants characteristic to AARS subclasses and tRNA-splicing endonuclease in eukaryotes. J Biomol Struct Dyn 2008; 26:223-34. [PMID: 18597544 DOI: 10.1080/07391102.2008.10507238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We compare and analyse the whole set of cytoplasmic, nonorganellar transfer RNA genes from 22 eukaryal genomes. Grouping this whole set into sets of isoacceptors we have elucidated structural elements that are characteristic to individual isoacceptor tRNAs within the subclasses of aminoacyl tRNA synthetases. Further, we have observed structural motifs straddling the exon-intron boundaries, which includes selective occurrence of both symmetric- 3-4-3 and asymmetric-3-4-(4, 5) bulge-helix-bulge-like structural motifs. Among all the tRNA isoacceptors, Ile, Leu, Ser, Pro, Met, Arg, and Tyr harbor BHB-like secondary structures at exon-intron boundaries. The structural signatories at the exon-intron boundaries appear to contribute to the specificity of splice site recognition.
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Affiliation(s)
- Bibekanand Mallick
- Computational Biology Group, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700032, India.
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Jackman JE, Phizicky EM. Identification of critical residues for G-1 addition and substrate recognition by tRNA(His) guanylyltransferase. Biochemistry 2008; 47:4817-25. [PMID: 18366186 DOI: 10.1021/bi702517q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The yeast tRNA(His) guanylyltransferase (Thg1) is an essential enzyme in yeast. Thg1 adds a single G residue to the 5' end of tRNA(His) (G(-1)), which serves as a crucial determinant for aminoacylation of tRNA(His). Thg1 is the only known gene product that catalyzes the 3'-5' addition of a single nucleotide via a normal phosphodiester bond, and since there is no identifiable sequence similarity between Thg1 and any other known enzyme family, the mechanism by which Thg1 catalyzes this unique reaction remains unclear. We have altered 29 highly conserved Thg1 residues to alanine, and using three assays to assess Thg1 catalytic activity and substrate specificity, we have demonstrated that the vast majority of these highly conserved residues (24/29) affect Thg1 function in some measurable way. We have identified 12 Thg1 residues that are critical for G(-1) addition, based on significantly decreased ability to add G(-1) to tRNA(His) in vitro and significant defects in complementation of a thg1Delta yeast strain. We have also identified a single Thg1 alteration (D68A) that causes a dramatic decrease in the rigorous specificity of Thg1 for tRNA(His). This single alteration enhances the k(cat)/K(M) for ppp-tRNA(Phe) by nearly 100-fold relative to that of wild-type Thg1. These results suggest that Thg1 substrate recognition is at least in part mediated by preventing recognition of incorrect substrates for nucleotide addition.
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Affiliation(s)
- Jane E Jackman
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, NY 14642, USA.
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Vasil'eva IA, Moor NA. Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition. BIOCHEMISTRY (MOSCOW) 2007; 72:247-63. [PMID: 17447878 DOI: 10.1134/s0006297907030029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review summarizes results of numerous (mainly functional) studies that have been accumulated over recent years on the problem of tRNA recognition by aminoacyl-tRNA synthetases. Development and employment of approaches that use synthetic mutant and chimeric tRNAs have demonstrated general principles underlying highly specific interaction in different systems. The specificity of interaction is determined by a certain number of nucleotides and structural elements of tRNA (constituting the set of recognition elements or specificity determinants), which are characteristic of each pair. Crystallographic structures available for many systems provide the details of the molecular basis of selective interaction. Diversity and identity of biochemical functions of the recognition elements make substantial contribution to the specificity of such interactions.
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Affiliation(s)
- I A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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