1
|
Avila-Bonilla RG, Macias S. The molecular language of RNA 5' ends: guardians of RNA identity and immunity. RNA (NEW YORK, N.Y.) 2024; 30:327-336. [PMID: 38325897 PMCID: PMC10946433 DOI: 10.1261/rna.079942.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
RNA caps are deposited at the 5' end of RNA polymerase II transcripts. This modification regulates several steps of gene expression, in addition to marking transcripts as self to enable the innate immune system to distinguish them from uncapped foreign RNAs, including those derived from viruses. Specialized immune sensors, such as RIG-I and IFITs, trigger antiviral responses upon recognition of uncapped cytoplasmic transcripts. Interestingly, uncapped transcripts can also be produced by mammalian hosts. For instance, 5'-triphosphate RNAs are generated by RNA polymerase III transcription, including tRNAs, Alu RNAs, or vault RNAs. These RNAs have emerged as key players of innate immunity, as they can be recognized by the antiviral sensors. Mechanisms that regulate the presence of 5'-triphosphates, such as 5'-end dephosphorylation or RNA editing, prevent immune recognition of endogenous RNAs and excessive inflammation. Here, we provide a comprehensive overview of the complexity of RNA cap structures and 5'-triphosphate RNAs, highlighting their roles in transcript identity, immune surveillance, and disease.
Collapse
Affiliation(s)
- Rodolfo Gamaliel Avila-Bonilla
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - Sara Macias
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| |
Collapse
|
2
|
Ivanesthi IR, Rida GRN, Setiawibawa AA, Tseng YK, Muammar A, Wang CC. Recognition of tRNA His in an RNase P-Free Nanoarchaeum. Microbiol Spectr 2023; 11:e0462122. [PMID: 36840576 PMCID: PMC10100707 DOI: 10.1128/spectrum.04621-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
The 5' extra guanosine with 5'-monophosphate at position -1 (G-1) of tRNAHis (p-tRNAHis) is a nearly universal feature that establishes tRNAHis identity. G-1 is either genome encoded and retained after processing by RNase P (RNase P) or posttranscriptionally incorporated by tRNAHis guanylyltransferase (Thg1) after RNase P cleavage. However, RNase P is not found in the hyperthermophilic archaeum Nanoarchaeum equitans; instead, all of its tRNAs, including tRNAHis, are transcribed as leaderless tRNAs with 5'-triphosphate (ppp-tRNAs). How N. equitans histidyl-tRNA synthetase (NeHisRS) recognizes its cognate tRNA (NetRNAHis) is of particular interest. In this paper, we show that G-1 serves as the major identity element of NetRNAHis, with its anticodon performing a similar role, though to a lesser extent. Moreover, NeHisRS distinctly preferred p-tRNAHis over ppp-tRNAHis (~5-fold difference). Unlike other prokaryotic HisRSs, which strongly prefer tRNAHis with C73, this enzyme could charge tRNAsHis with A73 and C73 with nearly equal efficiency. As a result, mutation at the C73-recognition amino acid residue Q112 had only a minor effect (<2-fold reduction). This study suggests that NeHisRS has evolved to disregard C73, but it still maintains its evolutionarily preserved preference toward tRNAHis with 5'-monophosphate. IMPORTANCE Mature tRNAHis has, at its 5'-terminus, an extra guanosine with 5'-monophosphate, designated G-1. G-1 is the major recognition element for histidyl-tRNA synthetase (HisRS), regardless of whether it is of eukaryotic or prokaryotic origin. However, in the hyperthermophilic archaeum Nanoarchaeum equitans, all its tRNAs, including tRNAHis, are transcribed as leaderless tRNAs with 5'-triphosphate. This piqued our curiosity about whether N. equitans histidyl-tRNA synthetase (NeHisRS) prefers tRNAHis with 5'-triphosphate. We show herein that G-1 is still the major recognition element for NeHisRS. However, unlike other prokaryotic HisRSs, which strongly prefer tRNAHis with C73, this enzyme shows almost the same preference for C73 and A73. Most intriguingly, NeHisRS still prefers 5'-monophosphate over 5'-triphosphate. It thus appears that the preference of HisRS for tRNAHis with 5'-monophosphate emerged very early in evolution.
Collapse
Affiliation(s)
| | | | | | - Yi-Kuan Tseng
- Graduate Institute of Statistics, National Central University, Jungli District, Taoyuan, Taiwan
| | - Arief Muammar
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Chien-Chia Wang
- Department of Life Sciences, National Central University, Jungli District, Taoyuan, Taiwan
| |
Collapse
|
3
|
Ender A, Stadler PF, Mörl M, Findeiß S. RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing. Methods Mol Biol 2022; 2518:179-202. [PMID: 35666446 DOI: 10.1007/978-1-0716-2421-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Riboswitches are an attractive target for the directed design of RNA-based regulators by in silico prediction. These noncoding RNA elements consist of an aptamer platform for the highly selective ligand recognition and an expression platform which controls gene activity typically at the level of transcription or translation. In previous work, we could successfully apply RNA folding prediction to implement a new riboswitch mechanism regulating processing of a tRNA by RNase P. In this contribution, we present detailed information about our pipeline consisting of in silico design combined with the biochemical analysis for the verification of the implemented mechanism. Furthermore, we discuss the applicability of the presented biochemical in vivo and in vitro methods for the characterization of other artificial riboswitches.
Collapse
Affiliation(s)
- Anna Ender
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
- Max Planck Institute for Mathematics in the Science, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
- Santa Fe Institute, Santa Fe, NM, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany.
| |
Collapse
|
4
|
Erber L, Betat H, Mörl M. CCA-Addition Gone Wild: Unusual Occurrence and Phylogeny of Four Different tRNA Nucleotidyltransferases in Acanthamoeba castellanii. Mol Biol Evol 2021; 38:1006-1017. [PMID: 33095240 PMCID: PMC7947759 DOI: 10.1093/molbev/msaa270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
tRNAs are important players in the protein synthesis machinery, where they act as adapter molecules for translating the mRNA codons into the corresponding amino acid sequence. In a series of highly conserved maturation steps, the primary transcripts are converted into mature tRNAs. In the amoebozoan Acanthamoeba castellanii, a highly unusual evolution of some of these processing steps was identified that are based on unconventional RNA polymerase activities. In this context, we investigated the synthesis of the 3'-terminal CCA-end that is added posttranscriptionally by a specialized polymerase, the tRNA nucleotidyltransferase (CCA-adding enzyme). The majority of eukaryotic organisms carry only a single gene for a CCA-adding enzyme that acts on both the cytosolic and the mitochondrial tRNA pool. In a bioinformatic analysis of the genome of this organism, we identified a surprising multitude of genes for enzymes that contain the active site signature of eukaryotic/eubacterial tRNA nucleotidyltransferases. In vitro activity analyses of these enzymes revealed that two proteins represent bona fide CCA-adding enzymes, one of them carrying an N-terminal sequence corresponding to a putative mitochondrial target signal. The other enzymes have restricted activities and represent CC- and A-adding enzymes, respectively. The A-adding enzyme is of particular interest, as its sequence is closely related to corresponding enzymes from Proteobacteria, indicating a horizontal gene transfer. Interestingly, this unusual diversity of nucleotidyltransferase genes is not restricted to Acanthamoeba castellanii but is also present in other members of the Acanthamoeba genus, indicating an ancient evolutionary trait.
Collapse
Affiliation(s)
- Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| |
Collapse
|
5
|
Yu P, Zhou L, Yang WT, Miao LJ, Li Z, Zhang XJ, Wang Y, Gui JF. Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae. BMC Genomics 2021; 22:50. [PMID: 33446100 PMCID: PMC7809818 DOI: 10.1186/s12864-020-07360-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/29/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated characteristics were not elaborated. RESULTS In this study, we sequenced and analyzed the complete mitogenomes of a female Cobits macrostigma. Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of 58 Cobitinae mitogenomes, including C. macrostigma. Cobitinae mitogenomes display highly conserved tRNA secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were observed among different genus and significantly negative linear correlation between AT% and AT-skew were found among Cobitinae, genus Cobitis and Pangio mitogenomes, respectively. A specific 3 bp insertion (GCA) in the atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally, all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the paraphyly of Cobitis and polyphyly of Misgurnus. The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur (14.40 Ma) between ancestral species of Cobitis and ancestral species of Misgurnus. CONCLUSIONS The current study represents the first comparative mitogenomic and phylogenetic analyses within Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the cobitinae family.
Collapse
Affiliation(s)
- Peng Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Tao Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Jun Miao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
6
|
Warren JM, Sloan DB. Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria. Mitochondrion 2020; 52:144-156. [PMID: 32184120 DOI: 10.1016/j.mito.2020.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 01/31/2023]
Abstract
Transfer RNAs (tRNAs) remain one of the very few classes of genes still encoded in the mitochondrial genome. These key components of the protein translation system must interact with a large enzymatic network of nuclear-encoded gene products to maintain mitochondrial function. Plants have an evolutionarily dynamic mitochondrial tRNA population, including ongoing tRNA gene loss and replacement by both horizontal gene transfer from diverse sources and import of nuclear-expressed tRNAs from the cytosol. Thus, plant mitochondria represent an excellent model for understanding how anciently divergent genes can act as "interchangeable parts" during the evolution of complex molecular systems. In particular, understanding the integration of the mitochondrial translation system with elements of the corresponding machinery used in cytosolic protein synthesis is a key area for eukaryotic cellular evolution. Here, we review the increasingly detailed phylogenetic data about the evolutionary history of mitochondrial tRNA gene loss, transfer, and functional replacement that has created extreme variation in mitochondrial tRNA populations across plant species. We describe emerging tRNA-seq methods with promise for refining our understanding of the expression and subcellular localization of tRNAs. Finally, we summarize current evidence and identify open questions related to coevolutionary changes in nuclear-encoded enzymes that have accompanied turnover in mitochondrial tRNA populations.
Collapse
Affiliation(s)
- Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
|
9
|
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: 0.4] [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.
Collapse
|
10
|
Lant JT, Berg MD, Heinemann IU, Brandl CJ, O'Donoghue P. Pathways to disease from natural variations in human cytoplasmic tRNAs. J Biol Chem 2019; 294:5294-5308. [PMID: 30643023 DOI: 10.1074/jbc.rev118.002982] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Perfectly accurate translation of mRNA into protein is not a prerequisite for life. Resulting from errors in protein synthesis, mistranslation occurs in all cells, including human cells. The human genome encodes >600 tRNA genes, providing both the raw material for genetic variation and a buffer to ensure that resulting translation errors occur at tolerable levels. On the basis of data from the 1000 Genomes Project, we highlight the unanticipated prevalence of mistranslating tRNA variants in the human population and review studies on synthetic and natural tRNA mutations that cause mistranslation or de-regulate protein synthesis. Although mitochondrial tRNA variants are well known to drive human diseases, including developmental disorders, few studies have revealed a role for human cytoplasmic tRNA mutants in disease. In the context of the unexpectedly large number of tRNA variants in the human population, the emerging literature suggests that human diseases may be affected by natural tRNA variants that cause mistranslation or de-regulate tRNA expression and nucleotide modification. This review highlights examples relevant to genetic disorders, cancer, and neurodegeneration in which cytoplasmic tRNA variants directly cause or exacerbate disease and disease-linked phenotypes in cells, animal models, and humans. In the near future, tRNAs may be recognized as useful genetic markers to predict the onset or severity of human disease.
Collapse
Affiliation(s)
| | | | | | | | - Patrick O'Donoghue
- From the Departments of Biochemistry and .,Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| |
Collapse
|
11
|
Affiliation(s)
- Ines Teichert
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universitaet Bochum, Germany
- * E-mail:
| |
Collapse
|
12
|
Shang J, Yang Y, Wu L, Zou M, Huang Y. The S. pombe mitochondrial transcriptome. RNA (NEW YORK, N.Y.) 2018; 24:1241-1254. [PMID: 29954949 PMCID: PMC6097661 DOI: 10.1261/rna.064477.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 06/26/2018] [Indexed: 05/22/2023]
Abstract
Mitochondrial gene expression is largely controlled through post-transcriptional processes including mitochondrial RNA (mt-RNA) processing, modification, decay, and quality control. Defective mitochondrial gene expression results in mitochondrial oxidative phosphorylation (OXPHOS) deficiency and has been implicated in human disease. To fully understand mitochondrial transcription and RNA processing, we performed RNA-seq analyses of mt-RNAs from the fission yeast Schizosaccharomyces pombe RNA-seq analyses show that the abundance of mt-RNAs vary greatly. Analysis of data also reveals mt-RNA processing sites including an unusual RNA cleavage event by mitochondrial tRNA (mt-tRNA) 5'-end processing enzyme RNase P. Additionally, this analysis reveals previously unknown mitochondrial transcripts including the rnpB-derived fragment, mitochondrial small RNAs (mitosRNAs) such as mt-tRNA-derived fragments (mt-tRFs) and mt-tRNA halves, and mt-tRNAs marked with 3'-CCACCA/CCACC in S. pombe Finally, RNA-seq reveals that inactivation of trz2 encoding S. pombe mitochondrial tRNA 3'-end processing enzyme globally impairs mt-tRNA 3'-end processing, inhibits mt-mRNA 5'-end processing, and causes accumulation of unprocessed transcripts, demonstrating the feasibility of using RNA-seq to examine the protein known or predicted to be involved in mt-RNA processing in S. pombe Our work uncovers the complexity of a fungal mitochondrial transcriptome and provides a framework for future studies of mitochondrial gene expression using S. pombe as a model system.
Collapse
Affiliation(s)
- Jinjie Shang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yanmei Yang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Lin Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Mengting Zou
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| |
Collapse
|
13
|
Tomita K, Liu Y. Human BCDIN3D Is a Cytoplasmic tRNA His-Specific 5'-Monophosphate Methyltransferase. Front Genet 2018; 9:305. [PMID: 30127802 PMCID: PMC6088191 DOI: 10.3389/fgene.2018.00305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 07/18/2018] [Indexed: 01/17/2023] Open
Abstract
Bicoid interacting 3 domain containing RNA methyltransferase (BCDIN3D) is a member of the Bin3 methyltransferase family and is evolutionary conserved from worm to human. BCDIN3D is overexpressed in breast cancer, which is associated with poor prognosis of breast cancers. However, the biological functions and properties of BCDIN3D have been enigmatic. Recent studies have revealed that human BCDIN3D monomethylates 5'-monophsosphate of cytoplasmic tRNAHisin vivo and in vitro. BCDIN3D recognizes the unique and exceptional structural features of cytoplasmic tRNAHis and discriminates tRNAHis from other cytoplasmic tRNA species. Thus, BCDIN3D is a tRNAHis-specific 5'-monophosphate methyltransferase. Methylation of the 5'-phosphate group of tRNAHis does not significantly affect tRNAHis aminoacylation by histidyl-tRNA synthetase in vitro nor the steady state level or stability of tRNAHisin vivo. Hence, methylation of the 5'-phosphate group of tRNAHis by BCDIN3D or tRNAHis itself may be involved in certain unknown biological processes, beyond protein synthesis. This review discusses recent reports on BCDIN3D and the possible association between 5'-phosphate monomethylation of tRNAHis and the tumorigenic phenotype of breast cancer.
Collapse
Affiliation(s)
- Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Yining Liu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| |
Collapse
|
14
|
Irimie AI, Zimta AA, Ciocan C, Mehterov N, Dudea D, Braicu C, Berindan-Neagoe I. The Unforeseen Non-Coding RNAs in Head and Neck Cancer. Genes (Basel) 2018; 9:genes9030134. [PMID: 29494516 PMCID: PMC5867855 DOI: 10.3390/genes9030134] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 12/18/2022] Open
Abstract
Previously ignored non-coding RNAs (ncRNAs) have become the subject of many studies. However, there is an imbalance in the amount of consideration that ncRNAs are receiving. Some transcripts such as microRNAs (miRNAs) or small interfering RNAs (siRNAs) have gained much attention, but it is necessary to investigate other “pieces of the RNA puzzle”. These can offer a more complete view over normal and pathological cell behavior. The other ncRNA species are less studied, either due to their recent discovery, such as stable intronic sequence RNA (sisRNA), YRNA, miRNA-offset RNAs (moRNA), telomerase RNA component (TERC), natural antisense transcript (NAT), transcribed ultraconserved regions (T-UCR), and pseudogene transcript, or because they are still largely seen as non-coding transcripts with no relevance to pathogenesis. Moreover, some are still considered housekeeping RNAs, for instance small nucleolar RNAs (snoRNAs) and TERC. Our review summarizes the biogenesis, mechanism of action and potential role of less known ncRNAs in head and neck cancer, with a particular focus on the installment and progress for this particular cancer type.
Collapse
Affiliation(s)
- Alexandra Iulia Irimie
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutic, Aesthetic, "IuliuHatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Alina-Andreea Zimta
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cristina Ciocan
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University Plovdiv, BulVasilAprilov 15-А, Plovdiv 4002, Bulgaria.
- Technological Center for Emergency Medicine, BulVasilAprilov 15-А, Plovdiv 4002, Bulgaria.
| | - Diana Dudea
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutic, Aesthetic, "IuliuHatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics and Translational Medicine, "IuliuHatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Research Center for Functional Genomics and Translational Medicine, "IuliuHatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Republicii 34 Street, 400015 Cluj-Napoca, Romania.
| |
Collapse
|
15
|
Mistranslation: from adaptations to applications. Biochim Biophys Acta Gen Subj 2017; 1861:3070-3080. [PMID: 28153753 DOI: 10.1016/j.bbagen.2017.01.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness. In studies of model organisms, mistranslation often acts as an adaptive response. These studies reveal evolutionary conserved mechanisms to maintain proteostasis even during high rates of mistranslation. SCOPE OF REVIEW This review discusses the evolutionary basis of altered genetic codes, how mistranslation is identified, and how deviations to the genetic code are exploited. We revisit early discoveries of genetic code deviations and provide examples of adaptive mistranslation events in nature. Lastly, we highlight innovations in synthetic biology to expand the genetic code. MAJOR CONCLUSIONS The genetic code is still evolving. Mistranslation increases proteomic diversity that enables cells to survive stress conditions or suppress a deleterious allele. Genetic code variants have been identified by genome and metagenome sequence analyses, suppressor genetics, and biochemical characterization. GENERAL SIGNIFICANCE Understanding the mechanisms of translation and genetic code deviations enables the design of new codes to produce novel proteins. Engineering the translation machinery and expanding the genetic code to incorporate non-canonical amino acids are valuable tools in synthetic biology that are impacting biomedical research. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Moreira S, Valach M, Aoulad-Aissa M, Otto C, Burger G. Novel modes of RNA editing in mitochondria. Nucleic Acids Res 2016; 44:4907-19. [PMID: 27001515 PMCID: PMC4889940 DOI: 10.1093/nar/gkw188] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/10/2016] [Indexed: 11/20/2022] Open
Abstract
Gene structure and expression in diplonemid mitochondria are unparalleled. Genes are fragmented in pieces (modules) that are separately transcribed, followed by the joining of module transcripts to contiguous RNAs. Some instances of unique uridine insertion RNA editing at module boundaries were noted, but the extent and potential occurrence of other editing types remained unknown. Comparative analysis of deep transcriptome and genome data from Diplonema papillatum mitochondria reveals ∼220 post-transcriptional insertions of uridines, but no insertions of other nucleotides nor deletions. In addition, we detect in total 114 substitutions of cytosine by uridine and adenosine by inosine, amassed into unusually compact clusters. Inosines in transcripts were confirmed experimentally. This is the first report of adenosine-to-inosine editing of mRNAs and ribosomal RNAs in mitochondria. In mRNAs, editing causes mostly amino-acid additions and non-synonymous substitutions; in ribosomal RNAs, it permits formation of canonical secondary structures. Two extensively edited transcripts were compared across four diplonemids. The pattern of uridine-insertion editing is strictly conserved, whereas substitution editing has diverged dramatically, but still rendering diplonemid proteins more similar to other eukaryotic orthologs. We posit that RNA editing not only compensates but also sustains, or even accelerates, ultra-rapid evolution of genome structure and sequence in diplonemid mitochondria.
Collapse
Affiliation(s)
- Sandrine Moreira
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada
| | - Mohamed Aoulad-Aissa
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada
| | - Christian Otto
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, D-04109, Germany
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada
| |
Collapse
|
18
|
Transfer RNA: From pioneering crystallographic studies to contemporary tRNA biology. Arch Biochem Biophys 2016; 602:95-105. [PMID: 26968773 DOI: 10.1016/j.abb.2016.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/29/2016] [Accepted: 03/03/2016] [Indexed: 12/17/2022]
Abstract
Transfer RNAs (tRNAs) play a key role in protein synthesis as adaptor molecules between messenger RNA and protein sequences on the ribosome. Their discovery in the early sixties provoked a worldwide infatuation with the study of their architecture and their function in the decoding of genetic information. tRNAs are also emblematic molecules in crystallography: the determination of the first tRNA crystal structures represented a milestone in structural biology and tRNAs were for a long period the sole source of information on RNA folding, architecture, and post-transcriptional modifications. Crystallographic data on tRNAs in complex with aminoacyl-tRNA synthetases (aaRSs) also provided the first insight into protein:RNA interactions. Beyond the translation process and the history of structural investigations on tRNA, this review also illustrates the renewal of tRNA biology with the discovery of a growing number of tRNA partners in the cell, the involvement of tRNAs in a variety of regulatory and metabolic pathways, and emerging applications in biotechnology and synthetic biology.
Collapse
|
19
|
Zíková A, Hampl V, Paris Z, Týč J, Lukeš J. Aerobic mitochondria of parasitic protists: Diverse genomes and complex functions. Mol Biochem Parasitol 2016; 209:46-57. [PMID: 26906976 DOI: 10.1016/j.molbiopara.2016.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 02/08/2023]
Abstract
In this review the main features of the mitochondria of aerobic parasitic protists are discussed. While the best characterized organelles are by far those of kinetoplastid flagellates and Plasmodium, we also consider amoebae Naegleria and Acanthamoeba, a ciliate Ichthyophthirius and related lineages. The simplistic view of the mitochondrion as just a power house of the cell has already been abandoned in multicellular organisms and available data indicate that this also does not apply for protists. We discuss in more details the following mitochondrial features: genomes, post-transcriptional processing, translation, biogenesis of iron-sulfur complexes, heme metabolism and the electron transport chain. Substantial differences in all these core mitochondrial features between lineages are compatible with the view that aerobic protists harbor organelles that are more complex and flexible than previously appreciated.
Collapse
Affiliation(s)
- Alena Zíková
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice (Budweis), Czech Republic.
| | - Vladimír Hampl
- Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice (Budweis), Czech Republic; Canadian Institute for Advanced Research, Toronto, Canada.
| |
Collapse
|
20
|
Kolondra A, Labedzka-Dmoch K, Wenda JM, Drzewicka K, Golik P. The transcriptome of Candida albicans mitochondria and the evolution of organellar transcription units in yeasts. BMC Genomics 2015; 16:827. [PMID: 26487099 PMCID: PMC4618339 DOI: 10.1186/s12864-015-2078-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 10/13/2015] [Indexed: 02/06/2023] Open
Abstract
Background Yeasts show remarkable variation in the organization of their mitochondrial genomes, yet there is little experimental data on organellar gene expression outside few model species. Candida albicans is interesting as a human pathogen, and as a representative of a clade that is distant from the model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Unlike them, it encodes seven Complex I subunits in its mtDNA. No experimental data regarding organellar expression were available prior to this study. Methods We used high-throughput RNA sequencing and traditional RNA biology techniques to study the mitochondrial transcriptome of C. albicans strains BWP17 and SN148. Results The 14 protein-coding genes, two ribosomal RNA genes, and 24 tRNA genes are expressed as eight primary polycistronic transcription units. We also found transcriptional activity in the noncoding regions, and antisense transcripts that could be a part of a regulatory mechanism. The promoter sequence is a variant of the nonanucleotide identified in other yeast mtDNAs, but some of the active promoters show significant departures from the consensus. The primary transcripts are processed by a tRNA punctuation mechanism into the monocistronic and bicistronic mature RNAs. The steady state levels of various mature transcripts exhibit large differences that are a result of posttranscriptional regulation. Transcriptome analysis allowed to precisely annotate the positions of introns in the RNL (2), COB (2) and COX1 (4) genes, as well as to refine the annotation of tRNAs and rRNAs. Comparative study of the mitochondrial genome organization in various Candida species indicates that they undergo shuffling in blocks usually containing 2–3 genes, and that their arrangement in primary transcripts is not conserved. tRNA genes with their associated promoters, as well as GC-rich sequence elements play an important role in these evolutionary events. Conclusions The main evolutionary force shaping the mitochondrial genomes of yeasts is the frequent recombination, constantly breaking apart and joining genes into novel primary transcription units. The mitochondrial transcription units are constantly rearranged in evolution shaping the features of gene expression, such as the presence of secondary promoter sites that are inactive, or act as “booster” promoters, simplified transcriptional regulation and reliance on posttranscriptional mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2078-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Adam Kolondra
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Karolina Labedzka-Dmoch
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Joanna M Wenda
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Katarzyna Drzewicka
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Pawel Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland. .,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Haag S, Warda AS, Kretschmer J, Günnigmann MA, Höbartner C, Bohnsack MT. NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs. RNA (NEW YORK, N.Y.) 2015; 21:1532-43. [PMID: 26160102 PMCID: PMC4536315 DOI: 10.1261/rna.051524.115] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 06/01/2015] [Indexed: 05/04/2023]
Abstract
Many cellular RNAs require modification of specific residues for their biogenesis, structure, and function. 5-methylcytosine (m(5)C) is a common chemical modification in DNA and RNA but in contrast to the DNA modifying enzymes, only little is known about the methyltransferases that establish m(5)C modifications in RNA. The putative RNA methyltransferase NSUN6 belongs to the family of Nol1/Nop2/SUN domain (NSUN) proteins, but so far its cellular function has remained unknown. To reveal the target spectrum of human NSUN6, we applied UV crosslinking and analysis of cDNA (CRAC) as well as chemical crosslinking with 5-azacytidine. We found that human NSUN6 is associated with tRNAs and acts as a tRNA methyltransferase. Furthermore, we uncovered tRNA(Cys) and tRNA(Thr) as RNA substrates of NSUN6 and identified the cytosine C72 at the 3' end of the tRNA acceptor stem as the target nucleoside. Interestingly, target recognition in vitro depends on the presence of the 3'-CCA tail. Together with the finding that NSUN6 localizes to the cytoplasm and largely colocalizes with marker proteins for the Golgi apparatus and pericentriolar matrix, our data suggest that NSUN6 modifies tRNAs in a late step in their biogenesis.
Collapse
Affiliation(s)
- Sara Haag
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Ahmed S Warda
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Jens Kretschmer
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Manuel A Günnigmann
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, 37077 Göttingen, Germany
| | - Markus T Bohnsack
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, 37073 Göttingen, Germany
| |
Collapse
|
23
|
Wilusz JE. Controlling translation via modulation of tRNA levels. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:453-70. [PMID: 25919480 DOI: 10.1002/wrna.1287] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/13/2015] [Accepted: 04/06/2015] [Indexed: 12/22/2022]
Abstract
Transfer RNAs (tRNAs) are critical adaptor molecules that carry amino acids to a messenger RNA (mRNA) template during protein synthesis. Although tRNAs have commonly been viewed as abundant 'house-keeping' RNAs, it is becoming increasingly clear that tRNA expression is tightly regulated. Depending on a cell's proliferative status, the pool of active tRNAs is rapidly changed, enabling distinct translational programs to be expressed in differentiated versus proliferating cells. Here, I highlight several post-transcriptional regulatory mechanisms that allow the expression or functions of tRNAs to be altered. Modulating the modification status or structural stability of individual tRNAs can cause those specific tRNA transcripts to selectively accumulate or be degraded. Decay generally occurs via the rapid tRNA decay pathway or by the nuclear RNA surveillance machinery. In addition, the CCA-adding enzyme plays a critical role in determining the fate of a tRNA. The post-transcriptional addition of CCA to the 3' ends of stable tRNAs generates the amino acid attachment site, whereas addition of CCACCA to unstable tRNAs prevents aminoacylation and marks the tRNA for degradation. In response to various stresses, tRNAs can accumulate in the nucleus or be further cleaved into small RNAs, some of which inhibit translation. By implementing these various post-transcriptional control mechanisms, cells are able to fine-tune tRNA levels to regulate subsets of mRNAs as well as overall translation rates.
Collapse
Affiliation(s)
- Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| |
Collapse
|