1
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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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2
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Wiedermannová J, Julius C, Yuzenkova Y. The expanding field of non-canonical RNA capping: new enzymes and mechanisms. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201979. [PMID: 34017598 PMCID: PMC8131947 DOI: 10.1098/rsos.201979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Recent years witnessed the discovery of ubiquitous and diverse 5'-end RNA cap-like modifications in prokaryotes as well as in eukaryotes. These non-canonical caps include metabolic cofactors, such as NAD+/NADH, FAD, cell wall precursors UDP-GlcNAc, alarmones, e.g. dinucleotides polyphosphates, ADP-ribose and potentially other nucleoside derivatives. They are installed at the 5' position of RNA via template-dependent incorporation of nucleotide analogues as an initiation substrate by RNA polymerases. However, the discovery of NAD-capped processed RNAs in human cells suggests the existence of alternative post-transcriptional NC capping pathways. In this review, we compiled growing evidence for a number of these other mechanisms which produce various non-canonically capped RNAs and a growing repertoire of capping small molecules. Enzymes shown to be involved are ADP-ribose polymerases, glycohydrolases and tRNA synthetases, and may potentially include RNA 3'-phosphate cyclases, tRNA guanylyl transferases, RNA ligases and ribozymes. An emerging rich variety of capping molecules and enzymes suggests an unrecognized level of complexity of RNA metabolism.
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Affiliation(s)
| | | | - Yulia Yuzenkova
- Medical School, NUBI, Newcastle University, Newcastle upon Tyne, UK
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3
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Matlock AO, Smith BA, Jackman JE. Chemical footprinting and kinetic assays reveal dual functions for highly conserved eukaryotic tRNA His guanylyltransferase residues. J Biol Chem 2019; 294:8885-8893. [PMID: 31000629 DOI: 10.1074/jbc.ra119.007939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/16/2019] [Indexed: 01/28/2023] Open
Abstract
tRNAHis guanylyltransferase (Thg1) adds a single guanine to the -1 position of tRNAHis as part of its maturation. This seemingly modest addition of one nucleotide to tRNAHis ensures translational fidelity by providing a critical identity element for the histidyl aminoacyl tRNA synthetase (HisRS). Like HisRS, Thg1 utilizes the GUG anticodon for selective tRNAHis recognition, and Thg1-tRNA complex structures have revealed conserved residues that interact with anticodon nucleotides. Separately, kinetic analysis of alanine variants has demonstrated that many of these same residues are required for catalytic activity. A model in which loss of activity with the variants was attributed directly to loss of the critical anticodon interaction has been proposed to explain the combined biochemical and structural results. Here we used RNA chemical footprinting and binding assays to test this model and further probe the molecular basis for the requirement for two critical tRNA-interacting residues, His-152 and Lys-187, in the context of human Thg1 (hThg1). Surprisingly, we found that His-152 and Lys-187 alanine-substituted variants maintain a similar overall interaction with the anticodon region, arguing against the sufficiency of this interaction for driving catalysis. Instead, conservative mutagenesis revealed a new direct function for these residues in recognition of a non-Watson-Crick G-1:A73 bp, which had not been described previously. These results have important implications for the evolution of eukaryotic Thg1 from a family of ancestral promiscuous RNA repair enzymes to the highly selective enzymes needed for their essential function in tRNAHis maturation.
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Affiliation(s)
- Ashanti O Matlock
- From the Department of Chemistry and Biochemistry, Center for RNA Biology, and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210
| | - Brian A Smith
- From the Department of Chemistry and Biochemistry, Center for RNA Biology, and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210
| | - Jane E Jackman
- From the Department of Chemistry and Biochemistry, Center for RNA Biology, and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210
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4
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Dodbele S, Moreland B, Gardner SM, Bundschuh R, Jackman JE. 5'-End sequencing in Saccharomyces cerevisiae offers new insights into 5'-ends of tRNA H is and snoRNAs. FEBS Lett 2019; 593:971-981. [PMID: 30908619 DOI: 10.1002/1873-3468.13364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/07/2019] [Accepted: 03/12/2019] [Indexed: 01/19/2023]
Abstract
tRNAH is guanylyltransferase (Thg1) specifies eukaryotic tRNAH is identity by catalysing a 3'-5' non-Watson-Crick (WC) addition of guanosine to the 5'-end of tRNAH is . Thg1 family enzymes in Archaea and Bacteria, called Thg1-like proteins (TLPs), catalyse a similar but distinct 3'-5' addition in an exclusively WC-dependent manner. Here, a genetic system in Saccharomyces cerevisiae was employed to further assess the biochemical differences between Thg1 and TLPs. Utilizing a novel 5'-end sequencing pipeline, we find that a Bacillus thuringiensis TLP sustains the growth of a thg1Δ strain by maintaining a WC-dependent addition of U-1 across from A73 . Additionally, we observe 5'-end heterogeneity in S. cerevisiae small nucleolar RNAs (snoRNAs), an observation that may inform methods of annotation and mechanisms of snoRNA processing.
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Affiliation(s)
- Samantha Dodbele
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Blythe Moreland
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Physics, The Ohio State University, Columbus, OH, USA
| | - Spencer M Gardner
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Ralf Bundschuh
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Physics, The Ohio State University, Columbus, OH, USA.,Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Jane E Jackman
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
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5
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The Role of 3' to 5' Reverse RNA Polymerization in tRNA Fidelity and Repair. Genes (Basel) 2019; 10:genes10030250. [PMID: 30917604 PMCID: PMC6471195 DOI: 10.3390/genes10030250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 12/16/2022] Open
Abstract
The tRNAHis guanylyltransferase (Thg1) superfamily includes enzymes that are found in all three domains of life that all share the common ability to catalyze the 3′ to 5′ synthesis of nucleic acids. This catalytic activity, which is the reverse of all other known DNA and RNA polymerases, makes this enzyme family a subject of biological and mechanistic interest. Previous biochemical, structural, and genetic investigations of multiple members of this family have revealed that Thg1 enzymes use the 3′ to 5′ chemistry for multiple reactions in biology. Here, we describe the current state of knowledge regarding the catalytic features and biological functions that have been so far associated with Thg1 and its homologs. Progress toward the exciting possibility of utilizing this unusual protein activity for applications in biotechnology is also discussed.
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6
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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: 0.5] [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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7
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Desai R, Kim K, Büchsenschütz HC, Chen AW, Bi Y, Mann MR, Turk MA, Chung CZ, Heinemann IU. Minimal requirements for reverse polymerization and tRNA repair by tRNA His guanylyltransferase. RNA Biol 2017; 15:614-622. [PMID: 28901837 DOI: 10.1080/15476286.2017.1372076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
tRNAHis guanylyltransferase (Thg1) has unique reverse (3'-5') polymerase activity occurring in all three domains of life. Most eukaryotic Thg1 homologs are essential genes involved in tRNAHis maturation. These enzymes normally catalyze a single 5' guanylation of tRNAHis lacking the essential G-1 identity element required for aminoacylation. Recent studies suggest that archaeal type Thg1, which includes most archaeal and bacterial Thg1 enzymes is phylogenetically distant from eukaryotic Thg1. Thg1 is evolutionarily related to canonical 5'-3' forward polymerases but catalyzes reverse 3'-5'polymerization. Similar to its forward polymerase counterparts, Thg1 encodes the conserved catalytic palm domain and fingers domain. Here we investigate the minimal requirements for reverse polymerization. We show that the naturally occurring minimal Thg1 enzyme from Ignicoccus hospitalis (IhThg1), which lacks parts of the conserved fingers domain, is catalytically active. And adds all four natural nucleotides to RNA substrates, we further show that the entire fingers domain of Methanosarcina acetivorans Thg1 and Pyrobaculum aerophilum Thg1 (PaThg1) is dispensable for enzymatic activity. In addition, we identified residues in yeast Thg1 that play a part in preventing extended polymerization. Mutation of these residues with alanine resulted in extended reverse polymerization. PaThg1 was found to catalyze extended, template dependent tRNA repair, adding up to 13 nucleotides to a truncated tRNAHis substrate. Sequencing results suggest that PaThg1 fully restored the near correct sequence of the D- and acceptor stem, but also produced incompletely and incorrectly repaired tRNA products. This research forms the basis for future engineering efforts towards a high fidelity, template dependent reverse polymerase.
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Affiliation(s)
- Riddhi Desai
- a Department of Biochemistry , The University of Western Ontario , London , Canada
| | - Kunmo Kim
- a Department of Biochemistry , The University of Western Ontario , London , Canada
| | | | - Allan W Chen
- a Department of Biochemistry , The University of Western Ontario , London , Canada
| | - Yumin Bi
- a Department of Biochemistry , The University of Western Ontario , London , Canada
| | - Mitchell R Mann
- a Department of Biochemistry , The University of Western Ontario , London , Canada
| | - Matthew A Turk
- a Department of Biochemistry , The University of Western Ontario , London , Canada
| | - Christina Z Chung
- a Department of Biochemistry , The University of Western Ontario , London , Canada
| | - Ilka U Heinemann
- a Department of Biochemistry , The University of Western Ontario , London , Canada
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8
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Lee K, Lee EH, Son J, Hwang KY. Crystal structure of tRNA His guanylyltransferase from Saccharomyces cerevisiae. Biochem Biophys Res Commun 2017. [PMID: 28623126 DOI: 10.1016/j.bbrc.2017.06.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
tRNA maturation involves several steps, including processing, splicing, CCA addition, and posttranscriptional modifications. tRNAHis guanylyltransferase (Thg1) is the only enzyme known to catalyze templated nucleotide addition in the 3'-5' direction, unlike other DNA and RNA polymerases. For a better understanding of its unique catalytic mechanism at the molecular level, we determined the crystal structure of GTP-bound Thg1 from Saccharomyces cerevisiae at the maximum resolution of 3.0 Å. The structure revealed the enzyme to have a tetrameric conformation that is well conserved among different species, and the GTP molecule was clearly bound at the active site, coordinating with two magnesium ions. In addition, two flexible protomers at the potential binding site (PBS) for tRNAHis were observed. We suggest that the PBS of the tetramer could also be one of the sites for interaction with partner proteins.
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Affiliation(s)
- Kitaik Lee
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-791, Republic of Korea
| | - Eun Hye Lee
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-791, Republic of Korea
| | - Jonghyeon Son
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-791, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-791, Republic of Korea.
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9
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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: 1.6] [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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10
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Kimura S, Suzuki T, Chen M, Kato K, Yu J, Nakamura A, Tanaka I, Yao M. Template-dependent nucleotide addition in the reverse (3'-5') direction by Thg1-like protein. SCIENCE ADVANCES 2016; 2:e1501397. [PMID: 27051866 PMCID: PMC4820378 DOI: 10.1126/sciadv.1501397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/04/2016] [Indexed: 05/23/2023]
Abstract
Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5'-end of truncated transfer RNA (tRNA) species in a Watson-Crick template-dependent manner. The reaction proceeds in two steps: the activation of the 5'-end by adenosine 5'-triphosphate (ATP)/guanosine 5'-triphosphate (GTP), followed by nucleotide addition. Structural analyses of the TLP and its reaction intermediates have revealed the atomic detail of the template-dependent elongation reaction in the 3'-5' direction. The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg(2+) ions, and the two reactions are executed at the same reaction center in a stepwise fashion. When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3'-OH of the incoming nucleotide and the 5'-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. That the 3'-5' elongation enzyme performs this elaborate two-step reaction in one catalytic center suggests that these two reactions have been inseparable throughout the process of protein evolution. Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNA(His)-specific G-1 addition enzyme. Each tRNA(His) binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. Furthermore, mutational analyses show that tRNA(His) is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode.
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Affiliation(s)
- Shoko Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tateki Suzuki
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Meirong Chen
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Koji Kato
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Akiyoshi Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
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11
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Long Y, Jackman JE. In vitro substrate specificities of 3'-5' polymerases correlate with biological outcomes of tRNA 5'-editing reactions. FEBS Lett 2015; 589:2124-30. [PMID: 26143376 DOI: 10.1016/j.febslet.2015.06.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
Abstract
Protozoan mitochondrial tRNAs (mt-tRNAs) are repaired by a process known as 5'-editing. Mt-tRNA sequencing revealed organism-specific patterns of editing G-U base pairs, wherein some species remove G-U base pairs during 5'-editing, while others retain G-U pairs in the edited tRNA. We tested whether 3'-5' polymerases that catalyze the repair step of 5'-editing exhibit organism-specific preferences that explain the treatment of G-U base pairs. Biochemical and kinetic approaches revealed that a 3'-5' polymerase from Acanthamoeba castellanii tolerates G-U wobble pairs in editing substrates much more readily than several other enzymes, consistent with its biological pattern of editing.
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Affiliation(s)
- Yicheng Long
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, United States
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, United States.
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12
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Zhu W, Ausin I, Seleznev A, Méndez-Vigo B, Picó FX, Sureshkumar S, Sundaramoorthi V, Bulach D, Powell D, Seemann T, Alonso-Blanco C, Balasubramanian S. Natural Variation Identifies ICARUS1, a Universal Gene Required for Cell Proliferation and Growth at High Temperatures in Arabidopsis thaliana. PLoS Genet 2015; 11:e1005085. [PMID: 25951176 PMCID: PMC4423873 DOI: 10.1371/journal.pgen.1005085] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/20/2015] [Indexed: 12/17/2022] Open
Abstract
Plants are highly sensitive to environmental changes and even small variations in ambient temperature have severe consequences on their growth and development. Temperature affects multiple aspects of plant development, but the processes and mechanisms underlying thermo-sensitive growth responses are mostly unknown. Here we exploit natural variation in Arabidopsis thaliana to identify and characterize novel components and processes mediating thermo-sensitive growth responses in plants. Phenotypic screening of wild accessions identified several strains displaying pleiotropic growth defects, at cellular and organism levels, specifically at high ambient temperatures. Positional cloning and characterization of the underlying gene revealed that ICARUS1 (ICA1), which encodes a protein of the tRNAHis guanylyl transferase (Thg1) superfamily, is required for plant growth at high temperatures. Transcriptome and gene marker analyses together with DNA content measurements show that ICA1 loss-of-function results in down regulation of cell cycle associated genes at high temperatures, which is linked with a block in G2/M transition and endoreduplication. In addition, plants with mutations in ICA1 show enhanced sensitivity to DNA damage. Characterization of additional strains that carry lesions in ICA1, but display normal growth, shows that alternative splicing is likely to alleviate the deleterious effects of some natural mutations. Furthermore, analyses of worldwide and regional collections of natural accessions indicate that ICA1 loss-of-function has arisen several times independently, and that these occur at high frequency in some local populations. Overall our results suggest that ICA1-mediated-modulation of fundamental processes such as tRNAHis maturation, modify plant growth responses to temperature changes in a quantitative and reversible manner, in natural populations. The increase in average temperatures across the globe has been predicted to have negative impacts on agricultural productivity. Therefore, there is a need to understand the molecular mechanisms that underlie plant growth responses to varying temperature regimes. At present, very little is known about the genes and pathways that modulate thermo-sensory growth responses in plants. In this article, the authors exploit natural variation in the commonly occurring weed thale cress (Arabidopsis thaliana) and identify a gene referred to as ICARUS1 to be required for plant growth at higher ambient temperatures. Plants carrying lesions in this gene stop growing at high temperatures and revert to growth when temperatures reduce. Using a combination of computational, molecular and cell biological approaches, the authors demonstrate that allelic variation at ICARUS1, which encodes an enzyme required for the fundamental biochemical process of tRNAHis maturation, underlies variation in thermo-sensory growth responses of A. thaliana. Furthermore, the authors discover that the deleterious impact of a natural mutation in ICARUS1 is suppressed through alternative splicing, thus suggesting the potential for alternative splicing to buffer the impacts of some natural mutations. These results support that modulation of fundamental processes, in addition to transcriptional regulation, mediate thermo-sensory growth responses in plants.
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Affiliation(s)
- Wangsheng Zhu
- School of Biological Sciences, Monash University, Victoria, Australia
| | - Israel Ausin
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Andrei Seleznev
- School of Biological Sciences, Monash University, Victoria, Australia
| | - Belén Méndez-Vigo
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F. Xavier Picó
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | | | | | - Dieter Bulach
- Victorian Bioinformatics Consortium, Monash University, Victoria, Australia
| | - David Powell
- Victorian Bioinformatics Consortium, Monash University, Victoria, Australia
| | - Torsten Seemann
- Victorian Bioinformatics Consortium, Monash University, Victoria, Australia
| | - Carlos Alonso-Blanco
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail: (CAB); (SB)
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13
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Abad MG, Long Y, Kinchen RD, Schindel ET, Gray MW, Jackman JE. Mitochondrial tRNA 5'-editing in Dictyostelium discoideum and Polysphondylium pallidum. J Biol Chem 2014; 289:15155-65. [PMID: 24737330 DOI: 10.1074/jbc.m114.561514] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Mitochondrial tRNA (mt-tRNA) 5'-editing was first described more than 20 years ago; however, the first candidates for 5'-editing enzymes were only recently identified in a eukaryotic microbe (protist), the slime mold Dictyostelium discoideum. In this organism, eight of 18 mt-tRNAs are predicted to be edited based on the presence of genomically encoded mismatched nucleotides in their aminoacyl-acceptor stem sequences. Here, we demonstrate that mt-tRNA 5'-editing occurs at all predicted sites in D. discoideum as evidenced by changes in the sequences of isolated mt-tRNAs compared with the expected sequences encoded by the mitochondrial genome. We also identify two previously unpredicted editing events in which G-U base pairs are edited in the absence of any other genomically encoded mismatches. A comparison of 5'-editing in D. discoideum with 5'-editing in another slime mold, Polysphondylium pallidum, suggests organism-specific idiosyncrasies in the treatment of U-G/G-U pairs. In vitro activities of putative D. discoideum editing enzymes are consistent with the observed editing reactions and suggest an overall lack of tRNA substrate specificity exhibited by the repair component of the editing enzyme. Although the presence of terminal mismatches in mt-tRNA sequences is highly predictive of the occurrence of mt-tRNA 5'-editing, the variability in treatment of U-G/G-U base pairs observed here indicates that direct experimental evidence of 5'-editing must be obtained to understand the complete spectrum of mt-tRNA editing events in any species.
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Affiliation(s)
- Maria G Abad
- From the Department of Chemistry and Biochemistry, Center for RNA Biology and
| | - Yicheng Long
- From the Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210 and
| | - R Dimitri Kinchen
- From the Department of Chemistry and Biochemistry, Center for RNA Biology and
| | - Elinor T Schindel
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jane E Jackman
- From the Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210 and
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14
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Smith BA, Jackman JE. Saccharomyces cerevisiae Thg1 uses 5'-pyrophosphate removal to control addition of nucleotides to tRNA(His.). Biochemistry 2014; 53:1380-91. [PMID: 24548272 PMCID: PMC3985462 DOI: 10.1021/bi4014648] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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In
eukaryotes, the tRNAHis guanylyltransferase (Thg1)
catalyzes 3′–5′ addition of a single guanosine
residue to the −1 position (G–1) of tRNAHis, across from a highly conserved adenosine at position 73
(A73). After addition of G–1, Thg1 removes
pyrophosphate from the tRNA 5′-end, generating 5′-monophosphorylated
G–1-containing tRNA. The presence of the 5′-monophosphorylated
G–1 residue is important for recognition of tRNAHis by its cognate histidyl-tRNA synthetase. In addition to
the single-G–1 addition reaction, Thg1 polymerizes
multiple G residues to the 5′-end of tRNAHis variants.
For 3′–5′ polymerization, Thg1 uses the 3′-end
of the tRNAHis acceptor stem as a template. The mechanism
of reverse polymerization is presumed to involve nucleophilic attack
of the 3′-OH from each incoming NTP on the intact 5′-triphosphate
created by the preceding nucleotide addition. The potential exists
for competition between 5′-pyrophosphate removal and 3′–5′
polymerase reactions that could define the outcome of Thg1-catalyzed
addition, yet the interplay between these competing reactions has
not been investigated for any Thg1 enzyme. Here we establish transient
kinetic assays to characterize the pyrophosphate removal versus nucleotide
addition activities of yeast Thg1 with a set of tRNAHis substrates in which the identity of the N–1:N73 base pair was varied to mimic various products of the N–1 addition reaction catalyzed by Thg1. We demonstrate
that retention of the 5′-triphosphate is correlated with efficient
3′–5′ reverse polymerization. A kinetic partitioning
mechanism that acts to prevent addition of nucleotides beyond the
−1 position with wild-type tRNAHis is proposed.
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Affiliation(s)
- Brian A Smith
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
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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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