1
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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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2
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Doublet V, Ubrig E, Alioua A, Bouchon D, Marcadé I, Maréchal-Drouard L. Large gene overlaps and tRNA processing in the compact mitochondrial genome of the crustacean Armadillidium vulgare. RNA Biol 2015; 12:1159-68. [PMID: 26361137 DOI: 10.1080/15476286.2015.1090078] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
A faithful expression of the mitochondrial DNA is crucial for cell survival. Animal mitochondrial DNA (mtDNA) presents a highly compact gene organization. The typical 16.5 kbp animal mtDNA encodes 13 proteins, 2 rRNAs and 22 tRNAs. In the backyard pillbug Armadillidium vulgare, the rather small 13.9 kbp mtDNA encodes the same set of proteins and rRNAs as compared to animal kingdom mtDNA, but seems to harbor an incomplete set of tRNA genes. Here, we first confirm the expression of 13 tRNA genes in this mtDNA. Then we show the extensive repair of a truncated tRNA, the expression of tRNA involved in large gene overlaps and of tRNA genes partially or fully integrated within protein-coding genes in either direct or opposite orientation. Under selective pressure, overlaps between genes have been likely favored for strong genome size reduction. Our study underlines the existence of unknown biochemical mechanisms for the complete gene expression of A. vulgare mtDNA, and of co-evolutionary processes to keep overlapping genes functional in a compacted mitochondrial genome.
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Affiliation(s)
- Vincent Doublet
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Elodie Ubrig
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
| | - Abdelmalek Alioua
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
| | - Didier Bouchon
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Isabelle Marcadé
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Laurence Maréchal-Drouard
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
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3
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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: 1.1] [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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4
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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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5
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Wende S, Platzer EG, Jühling F, Pütz J, Florentz C, Stadler PF, Mörl M. Biological evidence for the world's smallest tRNAs. Biochimie 2013; 100:151-8. [PMID: 23958440 DOI: 10.1016/j.biochi.2013.07.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 07/24/2013] [Indexed: 11/15/2022]
Abstract
Due to their function as adapters in translation, tRNA molecules share a common structural organization in all kingdoms and organelles with ribosomal protein biosynthesis. A typical tRNA has a cloverleaf-like secondary structure, consisting of acceptor stem, D-arm, anticodon arm, a variable region, and T-arm, with an average length of 73 nucleotides. In several mitochondrial genomes, however, tRNA genes encode transcripts that show a considerable deviation of this standard, having reduced D- or T-arms or even completely lack one of these elements, resulting in tRNAs as small as 66 nts. An extreme case of such truncations is found in the mitochondria of Enoplea. Here, several tRNA genes are annotated that lack both the D- and the T-arm, suggesting even shorter transcripts with a length of only 42 nts. However, direct evidence for these exceptional tRNAs, which were predicted by purely computational means, has been lacking so far. Here, we demonstrate that several of these miniaturized armless tRNAs consisting only of acceptor- and anticodon-arms are indeed transcribed and correctly processed by non-encoded CCA addition in the mermithid Romanomermis culicivorax. This is the first direct evidence for the existence and functionality of the smallest tRNAs ever identified so far. It opens new possibilities towards exploration/assessment of minimal structural motifs defining a functional tRNA and their evolution.
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Affiliation(s)
- Sandra Wende
- University of Leipzig, Institute for Biochemistry, Leipzig, Germany
| | - Edward G Platzer
- University of California, Riverside, Department of Nematology, Riverside, CA 92521, USA
| | - Frank Jühling
- University of Leipzig, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig, Germany
| | - Joern Pütz
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Catherine Florentz
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Peter F Stadler
- University of Leipzig, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig, Germany; Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany; Fraunhofer Institut für Zelltherapie und Immunologie - IZI, Leipzig, Germany; Department of Theoretical Chemistry, University of Vienna, Vienna, Austria; Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark; Santa Fe Institute, Santa Fe, NM, USA
| | - Mario Mörl
- University of Leipzig, Institute for Biochemistry, Leipzig, Germany.
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6
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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: 2.5] [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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7
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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: 1.7] [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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8
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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: 25] [Impact Index Per Article: 1.8] [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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9
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Abstract
tRNA(His) has thus far always been found with one of the most distinctive of tRNA features, an extra 5' nucleotide that is usually a guanylate. tRNA(His) genes in a disjoint alphaproteobacterial group comprising the Rhizobiales, Rhodobacterales, Caulobacterales, Parvularculales, and Pelagibacter generally fail to encode this extra guanylate, unlike those of other alphaproteobacteria and bacteria in general. Rather than adding an extra 5' guanylate posttranscriptionally as eukaryotes do, evidence is presented here that two of these species, Sinorhizobium meliloti and Caulobacter crescentus, simply lack any extra nucleotide on tRNA(His). This loss correlates with changes at the 3' end sequence of tRNA(His) and at many sites in histidyl-tRNA synthetase that might be expected to affect tRNA(His) recognition, in the flipping loop, the insertion domain, the anticodon-binding domain, and the motif 2 loop. The altered tRNA charging system may have affected other tRNA charging systems in these bacteria; for example, a site in tRNA(Glu) sequences was found to covary with tRNA(His) among alphaproteobacteria.
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Affiliation(s)
- Chunxia Wang
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg VA 24061, USA
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10
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Gu W, Hurto RL, Hopper AK, Grayhack EJ, Phizicky EM. Depletion of Saccharomyces cerevisiae tRNA(His) guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m(5)C. Mol Cell Biol 2005; 25:8191-201. [PMID: 16135808 PMCID: PMC1234336 DOI: 10.1128/mcb.25.18.8191-8201.2005] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The essential Saccharomyces cerevisiae tRNA(His) guanylyltransferase (Thg1p) is responsible for the unusual G(-1) addition to the 5' end of cytoplasmic tRNA(His). We report here that tRNA(His) from Thg1p-depleted cells is uncharged, although histidyl tRNA synthetase is active and the 3' end of the tRNA is intact, suggesting that G(-1) is a critical determinant for aminoacylation of tRNA(His) in vivo. Thg1p depletion leads to activation of the GCN4 pathway, most, but not all, of which is Gcn2p dependent, and to the accumulation of tRNA(His) in the nucleus. Surprisingly, tRNA(His) in Thg1p-depleted cells accumulates additional m(5)C modifications, which are delayed relative to the loss of G(-1) and aminoacylation. The additional modification is likely due to tRNA m(5)C methyltransferase Trm4p. We developed a new method to map m(5)C residues in RNA and localized the additional m(5)C to positions 48 and 50. This is the first documented example of the accumulation of additional modifications in a eukaryotic tRNA species.
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Affiliation(s)
- Weifeng Gu
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, 601 Elmwood Avenue, Rochester, NY 14642, USA
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11
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Connolly SA, Rosen AE, Musier-Forsyth K, Francklyn CS. G-1:C73 recognition by an arginine cluster in the active site of Escherichia coli histidyl-tRNA synthetase. Biochemistry 2004; 43:962-9. [PMID: 14744140 DOI: 10.1021/bi035708f] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aminoacylation of a transfer RNA (tRNA) by its cognate aminoacyl-tRNA synthetase relies upon the recognition of specific nucleotides as well as conformational features within the tRNA by the synthetase. In Escherichia coli, the aminoacylation of tRNA(His) by histidyl-tRNA synthetase (HisRS) is highly dependent upon the recognition of the unique G-1:C73 base pair and the 5'-monophosphate. This work investigates the RNA-protein interactions between the HisRS active site and these critical recognition elements. A homology model of the tRNA(His)-HisRS complex was generated and used to design site-specific mutants of possible G-1:C73 contacts. Aminoacylation assays were performed with these HisRS mutants and N-1:C73 tRNA(His) and microhelix(His) variants. Complete suppression of the negative effect of 5'-phosphate deletion by R123A HisRS, as well as the increased discrimination of Q118E HisRS against a 5'-triphosphate, suggests a possible interaction between the 5'-phosphate and active-site residues Arg123 and Gln118 in which these residues create a sterically and electrostatically favorable pocket for the binding of the negatively charged phosphate group. Additionally, a network of interactions appears likely between G-1 and Arg116, Arg123, and Gln118 because mutation of these residues significantly reduced the sensitivity of HisRS to changes at G-1. Our studies also support an interaction previously proposed between Gln118 and C73. Defining the RNA-protein interactions critical for efficient aminoacylation by E. coli HisRS helps to further characterize the active site of this enzyme and improves our understanding of how the unique identity elements in the acceptor stem of tRNA(His) confer specificity.
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Affiliation(s)
- Susan A Connolly
- Department of Biochemistry, University of Vermont, Health Sciences Complex, Burlington 05405, USA
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12
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Gu W, Jackman JE, Lohan AJ, Gray MW, Phizicky EM. tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5' end of tRNAHis. Genes Dev 2003; 17:2889-901. [PMID: 14633974 PMCID: PMC289149 DOI: 10.1101/gad.1148603] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
All tRNAHis molecules are unusual in having an extra 5' GMP residue (G(-1)) that, in eukaryotes, is added after transcription and RNase P cleavage. Incorporation of this G(-1) residue is a rare example of nucleotide addition occurring at an RNA 5' end in a normal phosphodiester linkage. We show here that the essential Saccharomyces cerevisiae ORF YGR024c (THG1) is responsible for this guanylyltransferase reaction. Thg1p was identified by survey of a genomic collection of yeast GST-ORF fusion proteins for addition of [alpha-32P]GTP to tRNAHis. End analysis confirms the presence of G(-1). Thg1p is required for tRNAHis guanylylation in vivo, because cells depleted of Thg1p lack G(-1) in their tRNAHis. His6-Thg1p purified from Escherichia coli catalyzes the guanylyltransferase step of G(-1) addition using a ppp-tRNAHis substrate, and appears to catalyze the activation step using p-tRNAHis and ATP. Thg1p is highlye conserved in eukaryotes, where G(-1) addition is necessary, and is not found in eubacteria, where G(-1) is genome-encoded. Thus, Thg1p is the first member of a new family of enzymes that can catalyze phosphodiester bond formation at the 5' end of RNAs, formally in a 3'-5' direction. Surprisingly, despite its varied activities, Thg1p contains no recognizable catalytic or functional domains.
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Affiliation(s)
- Weifeng Gu
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
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13
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Castresana J, Feldmaier-Fuchs G, Yokobori S, Satoh N, Pääbo S. The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria. Genetics 1998; 150:1115-23. [PMID: 9799263 PMCID: PMC1460392 DOI: 10.1093/genetics/150.3.1115] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The complete nucleotide sequence of the mitochondrial genome of the hemichordate Balanoglossus carnosus (acorn worm) was determined. The arrangement of the genes encoding 13 protein, 22 tRNA, and 2 rRNA genes is essentially the same as in vertebrates, indicating that the vertebrate and hemichordate mitochondrial gene arrangement is close to that of their common ancestor, and, thus, that it has been conserved for more than 600 million years, whereas that of echinoderms has been rearranged extensively. The genetic code of hemichordate mitochondria is similar to that of echinoderms in that ATA encodes isoleucine and AGA serine, whereas the codons AAA and AGG, whose amino acid assignments also differ between echinoderms and vertebrates, are absent from the B. carnosus mitochondrial genome. There are three noncoding regions of length 277, 41, and 32 bp: the larger one is likely to be equivalent to the control region of other deuterostomes, while the two others may contain transcriptional promoters for genes encoded on the minor coding strand. Phylogenetic trees estimated from the inferred protein sequences indicate that hemichordates are a sister group of echinoderms.
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Affiliation(s)
- J Castresana
- Institute of Zoology, University of Munich, D-80333 Munich, Germany.
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14
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Abstract
Mature tRNAs are remarkably similar in all cells. However, the primary transcripts from tRNA genes can vary considerably due to differences in gene organization. RNase P must be able to recognize the elements that are common to all tRNA precursors to accurately remove the 5'-leader sequences.
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Affiliation(s)
- C J Green
- SRI International, Menlo Park, CA, USA
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15
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Chang YS, Huang FL, Lo TB. The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J Mol Evol 1994; 38:138-55. [PMID: 8169959 DOI: 10.1007/bf00166161] [Citation(s) in RCA: 240] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The complete sequence of the carp mitochondrial genome of 16,575 base pairs has been determined. The carp mitochondrial genome encodes the same set of genes (13 proteins, 2 rRNAs, and 22 tRNAs) as do other vertebrate mitochondrial DNAs. Comparison of this teleostean mitochondrial genome with those of other vertebrates reveals a similar gene order and compact genomic organization. The codon usage of proteins of carp mitochondrial genome is similar to that of other vertebrates. The phylogenetic relationship for mitochondrial protein genes is more apparent than that for the mitochondrial tRNA and rRNA genes.
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Affiliation(s)
- Y S Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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16
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Jahn D, Pande S. Histidine tRNA guanylyltransferase from Saccharomyces cerevisiae. II. Catalytic mechanism. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54429-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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17
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Pande S, Jahn D, Söll D. Histidine tRNA guanylyltransferase from Saccharomyces cerevisiae. I. Purification and physical properties. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54428-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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18
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Covello PS, Gray MW. Sequence analysis of wheat mitochondrial transcripts capped in vitro: definitive identification of transcription initiation sites. Curr Genet 1991; 20:245-51. [PMID: 1718611 DOI: 10.1007/bf00326239] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To identify transcription initiation sites in wheat mitochondria, the nascent 5'-ends of transcripts were specifically labeled by incubation of wheat mitochondrial RNA with [alpha-32P]GTP in the presence of the enzyme guanylyltransferase. After separation of the resulting capped transcripts by electrophoresis in polyacrylamide gels, individual RNAs were recovered and directly sequenced. Four RNA sequences obtained in this way were localized upstream of the protein-coding genes atpA, coxII, coxIII and orf25. Comparison of mRNA and gene sequences allowed precise positioning of transcription initiation sites for these four genes. Sequence similarities immediately upstream of these sites define a conserved motif that we suggest as a candidate regulatory element in wheat mtDNA. The relationship between this motif and putative mitochondrial promoters in other plant species is discussed.
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Affiliation(s)
- P S Covello
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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19
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L'Abbé D, Duhaime J, Lang B, Morais R. The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)99096-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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20
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Krupp G, Kahle D, Vogt T, Char S. Sequence changes in both flanking sequences of a pre-tRNA influence the cleavage specificity of RNase P. J Mol Biol 1991; 217:637-48. [PMID: 1706437 DOI: 10.1016/0022-2836(91)90522-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The cleavage specificities of the RNase P holoenzymes from Escherichia coli and the yeast Schizosaccharomyces pombe and of the catalytic M1 RNA from E. coli were analyzed in 5'-processing experiments using a yeast serine pre-tRNA with mutations in both flanking sequences. The template DNAs were obtained by enzymatic reactions in vitro and transcribed with phage SP6 or T7 RNA polymerase. The various mutations did not alter the cleavage specificity of the yeast RNase P holoenzyme; cleavage always occurred predominantly at position G + 1, generating the typical seven base-pair acceptor stem. In contrast, the specificity of the prokaryotic RNase P activities, i.e. the catalytic M1 RNA and the RNase P holoenzyme from E. coli, was influenced by some of the mutated pre-tRNA substrates, which resulted in an unusual cleavage pattern, generating extended acceptor stems. The bases G - 1 and C + 73, forming the eighth base pair in these extended acceptor stems, were an important motif in promoting the unusual cleavage pattern. It was found only in some natural pre-tRNAs, including tRNA(SeCys) from E. coli, and tRNAs(His) from bacteria and chloroplasts. Also, the corresponding mature tRNAs in vivo contain an eight base pair acceptor stem. The presence of the CCA sequence at the 3' end of the tRNA moiety is known to enhance the cleavage efficiency with the catalytic M1 RNA. Surprisingly, the presence or absence of this sequence in two of our substrate mutants drastically altered the cleavage specificity of M1 RNA and of the E. coli holoenzyme, respectively. Possible reasons for the different cleavage specificities of the enzymes, the influence of sequence alterations and the importance of stacking forces in the acceptor stems are discussed.
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Affiliation(s)
- G Krupp
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, F.R.G
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21
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Desjardins P, Morais R. Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome. J Mol Evol 1991; 32:153-61. [PMID: 1706782 DOI: 10.1007/bf02515387] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Segments of the Japanese quail mitochondrial genome encompassing many tRNA and protein genes, the small and part of the large rRNA genes, and the control region have been cloned and sequenced. Analysis of the relative position of these genes confirmed that the tRNA(Glu) and ND6 genes in galliform mitochondrial DNA are located immediately adjacent to the control region of the molecule instead of between the cytochrome b and ND5 genes as in other vertebrates. Japanese quail and chicken display another distinctive characteristic, that is, they both lack an equivalent to the light-strand replication origin found between the tRNA(Cys) and tRNA(Asn) genes in all vertebrate mitochondrial genomes sequenced thus far. Comparison of the protein-encoding genes revealed that a great proportion of the substitutions are silent and involve mainly transitions. This bias toward transitions also occurs in the tRNA and rRNA genes but is not observed in the control region where transversions account for many of the substitutions. Sequence alignment indicated that the two avian control regions evolve mainly through base substitutions but are also characterized by the occurrence of a 57-bp deletion/addition event at their 5' end. The overall sequence divergence between the two gallinaceous birds suggests that avian mitochondrial genomes evolve at a similar rate to other vertebrate mitochondrial DNAs.
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Affiliation(s)
- P Desjardins
- Département de biochimie, Faculté de médecine, Université de Montréal, Québec, Canada
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22
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Blum B, Simpson L. Guide RNAs in kinetoplastid mitochondria have a nonencoded 3' oligo(U) tail involved in recognition of the preedited region. Cell 1990; 62:391-7. [PMID: 1695552 DOI: 10.1016/0092-8674(90)90375-o] [Citation(s) in RCA: 197] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Maxicircle-encoded guide RNAs (gRNAs) for cytochrome b and maxicircle unidentified reading frames 2 and 3 (MURF2 and MURF3) were isolated by hybrid selection and sequenced. All three gRNAs contained nonencoded 3' oligo(U) tails 5-24 nucleotides in length, with a mean length of approximately 15 nucleotides. Secondary structure calculations indicate a functional role of the 3' oligo(U) tail in stabilizing the initial hybrid formed between the gRNA and the preedited mRNA, and allowed the identification of potential mRNA recognition sites for an editing complex. In addition, isolated MURF2 gRNA-II could be 5' capped with [alpha-32P]-GTP and guanylyltransferase, suggesting that at least some gRNAs represent primary transcripts.
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Affiliation(s)
- B Blum
- Department of Biology, University of California, Los Angeles 90024-1606
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