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Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. Cell Syst 2024; 15:388-408.e4. [PMID: 38636458 PMCID: PMC11075746 DOI: 10.1016/j.cels.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/21/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
Genome-wide measurement of ribosome occupancy on mRNAs has enabled empirical identification of translated regions, but high-confidence detection of coding regions that overlap annotated coding regions has remained challenging. Here, we report a sensitive and robust algorithm that revealed the translation of 388 N-terminally truncated proteins in budding yeast-more than 30-fold more than previously known. We extensively experimentally validated them and defined two classes. The first class lacks large portions of the annotated protein and tends to be produced from a truncated transcript. We show that two such cases, Yap5truncation and Pus1truncation, have condition-specific regulation and distinct functions from their respective annotated isoforms. The second class of truncated protein isoforms lacks only a small region of the annotated protein and is less likely to be produced from an alternative transcript isoform. Many display different subcellular localizations than their annotated counterpart, representing a common strategy for dual localization of otherwise functionally identical proteins. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Andrea L Higdon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nathan H Won
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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2
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Nishimura A, Yoon S, Matsunaga T, Ida T, Jung M, Ogata S, Morita M, Yoshitake J, Unno Y, Barayeu U, Takata T, Takagi H, Motohashi H, van der Vliet A, Akaike T. Longevity control by supersulfide-mediated mitochondrial respiration and regulation of protein quality. Redox Biol 2024; 69:103018. [PMID: 38199039 PMCID: PMC10821618 DOI: 10.1016/j.redox.2023.103018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/24/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Supersulfides, which are defined as sulfur species with catenated sulfur atoms, are increasingly being investigated in biology. We recently identified pyridoxal phosphate (PLP)-dependent biosynthesis of cysteine persulfide (CysSSH) and related supersulfides by cysteinyl-tRNA synthetase (CARS). Here, we investigated the physiological role of CysSSH in budding yeast (Saccharomyces cerevisiae) by generating a PLP-binding site mutation K109A in CRS1 (the yeast ortholog of CARS), which decreased the synthesis of CysSSH and related supersulfides and also led to reduced chronological aging, effects that were associated with an increased endoplasmic reticulum stress response and impaired mitochondrial bioenergetics. Reduced chronological aging in the K109A mutant could be rescued by using exogenous supersulfide donors. Our findings indicate important roles for CARS in the production and metabolism of supersulfides-to mediate mitochondrial function and to regulate longevity.
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Affiliation(s)
- Akira Nishimura
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan; Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan.
| | - Sunghyeon Yoon
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tetsuro Matsunaga
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomoaki Ida
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan; Organization for Research Promotion, Osaka Metropolitan University, Osaka, Japan
| | - Minkyung Jung
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Seiryo Ogata
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masanobu Morita
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Jun Yoshitake
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuka Unno
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Uladzimir Barayeu
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tsuyoshi Takata
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Takaaki Akaike
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan.
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3
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Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548938. [PMID: 37503254 PMCID: PMC10369987 DOI: 10.1101/2023.07.13.548938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Genome-wide measurements of ribosome occupancy on mRNA transcripts have enabled global empirical identification of translated regions. These approaches have revealed an unexpected diversity of protein products, but high-confidence identification of new coding regions that entirely overlap annotated coding regions - including those that encode truncated protein isoforms - has remained challenging. Here, we develop a sensitive and robust algorithm focused on identifying N-terminally truncated proteins genome-wide, identifying 388 truncated protein isoforms, a more than 30-fold increase in the number known in budding yeast. We perform extensive experimental validation of these truncated proteins and define two general classes. The first set lack large portions of the annotated protein sequence and tend to be produced from a truncated transcript. We show two such cases, Yap5 truncation and Pus1 truncation , to have condition-specific regulation and functions that appear distinct from their respective annotated isoforms. The second set of N-terminally truncated proteins lack only a small region of the annotated protein and are less likely to be regulated by an alternative transcript isoform. Many localize to different subcellular compartments than their annotated counterpart, representing a common strategy for achieving dual localization of otherwise functionally identical proteins.
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4
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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.
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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
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5
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Bittner E, Stehlik T, Freitag J. Sharing the wealth: The versatility of proteins targeted to peroxisomes and other organelles. Front Cell Dev Biol 2022; 10:934331. [PMID: 36225313 PMCID: PMC9549241 DOI: 10.3389/fcell.2022.934331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are eukaryotic organelles with critical functions in cellular energy and lipid metabolism. Depending on the organism, cell type, and developmental stage, they are involved in numerous other metabolic and regulatory pathways. Many peroxisomal functions require factors also relevant to other cellular compartments. Here, we review proteins shared by peroxisomes and at least one different site within the cell. We discuss the mechanisms to achieve dual targeting, their regulation, and functional consequences. Characterization of dual targeting is fundamental to understand how peroxisomes are integrated into the metabolic and regulatory circuits of eukaryotic cells.
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6
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Chatrath A, Kumar M, Prasad R. Comparative proteomics and variations in extracellular matrix of Candida tropicalis biofilm in response to citral. PROTOPLASMA 2022; 259:263-275. [PMID: 33959808 DOI: 10.1007/s00709-021-01658-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Candida tropicalis is an opportunistic human pathogen with an ability to cause superficial as well as systemic infections in immunocompromised patients. The formation of biofilm by C. tropicalis can cause dreadful and persistent infections which are difficult to treat due to acquired resistance. Presently, available anti-Candida drugs exhibit a high frequency of resistance, low specificity and toxicity at a higher dosage. In addition, the discovery of natural or synthetic anti-Candida drugs is slow paced and often does not pass clinical trials. Citral, a monoterpene aldehyde, has shown effective antimicrobial activities against various microorganisms. However, only few studies have elaborated the action of citral against the biofilm of C. tropicalis. In the present work, the aim was to study the fungicidal effect, differential expression of proteome and changes in extracellular matrix in response to the sub-lethal concentration (16 µg/mL) of citral. The administration of citral on C. tropicalis biofilm leads to a fungicidal effect. Furthermore, the differential expression of proteome has revealed twenty-five proteins in C. tropicalis biofilm, which were differentially expressed in the presence of citral. Among these, amino acid biosynthesis (Met6p, Gln1p, Pha2p); nucleotide biosynthesis (Xpt1p); carbohydrate metabolism (Eno1p, Fba1p, Gpm1p); sterol biosynthesis (Mvd1p/Erg19p, Hem13p); energy metabolism (Dnm1p, Coa1p, Ndk1p, Atp2p, Atp4p, Hts1p); oxidative stress (Hda2p, Gre22p, Tsa1p, Pst2p, Sod2p) and biofilm-specific (Adh1p, Ape1p, Gsp1p) proteins were identified. The overexpression of oxidative stress-related proteins indicates the response of biofilm cell to combating oxidative stress during citral treatment. Moreover, the upregulation of Adh1p is of particular interest because it subsidizes the biofilm inhibition through ethanol production as a cellular response. The augmented expression of Mvd1p/Erg19p signifies the effect of citral on ergosterol biosynthesis. The presence of citral has also shown an increment in hexosamine and ergosterol component in extracellular matrix of C. tropicalis biofilm. Hence, it is indicated that the cellular response towards citral acts through multifactorial processes. This study will further help in the interpretation of the effect of citral on C. tropicalis biofilm and development of novel antifungal agents against these potential protein targets.
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Affiliation(s)
- Apurva Chatrath
- Molecular Biology & Proteomics Laboratory, Department of Biotechnology, Indian Institute of Technology, Roorkee, 247667, Uttarakhand, India
| | - Manish Kumar
- Protein Structural & Molecular Dynamics Laboratory, Department of Biotechnology, Indian Institute of Technology, Roorkee, 247667, Uttarakhand, India
| | - Ramasare Prasad
- Molecular Biology & Proteomics Laboratory, Department of Biotechnology, Indian Institute of Technology, Roorkee, 247667, Uttarakhand, India.
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7
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Ghifari AS, Teixeira PF, Kmiec B, Singh N, Glaser E, Murcha MW. The dual-targeted prolyl aminopeptidase PAP1 is involved in proline accumulation in response to stress and during pollen development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:78-93. [PMID: 34460901 DOI: 10.1093/jxb/erab397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Plant endosymbiotic organelles such as mitochondria and chloroplasts harbour a wide array of biochemical reactions. As a part of protein homeostasis to maintain organellar activity and stability, unwanted proteins and peptides need to be completely degraded in a stepwise mechanism termed the processing pathway, where at the last stage single amino acids are released by aminopeptidases. Here, we determined the molecular and physiological functions of a prolyl aminopeptidase homologue PAP1 (At2g14260) that is able to release N-terminal proline. Transcript analyses demonstrate that an alternative transcription start site gives rise to two alternative transcripts, generating two in-frame proteins PAP1.1 and PAP1.2. Subcellular localization studies revealed that the longer isoform PAP1.1, which contains a 51 residue N-terminal extension, is exclusively targeted to chloroplasts, while the truncated isoform PAP1.2 is located in the cytosol. Distinct expression patterns in different tissues and developmental stages were observed. Investigations into the physiological role of PAP1 using loss-of-function mutants revealed that PAP1 activity may be involved in proline homeostasis and accumulation, required for pollen development and tolerance to osmotic stress. Enzymatic activity, subcellular location, and expression patterns of PAP1 suggest a role in the chloroplastic peptide processing pathway and proline homeostasis.
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Affiliation(s)
- Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth WA, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth WA, Australia
| | - Pedro F Teixeira
- Department of Biochemistry and Biophysics, Arrhenius Laboratory for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Beata Kmiec
- Department of Biochemistry and Biophysics, Arrhenius Laboratory for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Neha Singh
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth WA, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth WA, Australia
| | - Elzbieta Glaser
- Department of Biochemistry and Biophysics, Arrhenius Laboratory for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth WA, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth WA, Australia
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8
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Antika TR, Chrestella DJ, Ivanesthi IR, Rida G, Chen KY, Liu FG, Lee YC, Chen YW, Tseng YK, Wang CC. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2190-2200. [PMID: 35100402 PMCID: PMC8887476 DOI: 10.1093/nar/gkac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/14/2021] [Accepted: 01/11/2022] [Indexed: 11/14/2022] Open
Abstract
Unlike many other aminoacyl-tRNA synthetases, alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout biology. While Caenorhabditis elegans cytoplasmic AlaRS (CeAlaRSc) retains the prototype structure, its mitochondrial counterpart (CeAlaRSm) contains only a residual C-terminal domain (C-Ala). We demonstrated herein that the C-Ala domain from CeAlaRSc robustly binds both tRNA and DNA. It bound different tRNAs but preferred tRNAAla. Deletion of this domain from CeAlaRSc sharply reduced its aminoacylation activity, while fusion of this domain to CeAlaRSm selectively and distinctly enhanced its aminoacylation activity toward the elbow-containing (or L-shaped) tRNAAla. Phylogenetic analysis showed that CeAlaRSm once possessed the C-Ala domain but later lost most of it during evolution, perhaps in response to the deletion of the T-arm (part of the elbow) from its cognate tRNA. This study underscores the evolutionary gain of C-Ala for docking AlaRS to the L-shaped tRNAAla.
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Affiliation(s)
- Titi Rindi Antika
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 32001, Taiwan
| | - Dea Jolie Chrestella
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 32001, Taiwan
| | - Indira Rizqita Ivanesthi
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 32001, Taiwan
| | - Gita Riswana Nawung Rida
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 32001, Taiwan
| | - Kuan-Yu Chen
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 32001, Taiwan
| | - Fu-Guo Liu
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 32001, Taiwan
| | - Yi-Chung Lee
- Department of Neurology, Taipei Veterans General Hospital, Beitou District, Taipei 11217, Taiwan
| | - Yu-Wei Chen
- Department of Neurology, Landseed International Hospital, Pingzhen District, Taoyuan 32449, Taiwan
| | - Yi-Kuan Tseng
- Graduate Institute of Statistics, National Central University, Zhongli District, Taoyuan 32001, Taiwan
| | - Chien-Chia Wang
- To whom correspondence should be addressed. Tel: +886 3 426 0840; Fax: +886 3 422 8482;
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9
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Figuccia S, Degiorgi A, Ceccatelli Berti C, Baruffini E, Dallabona C, Goffrini P. Mitochondrial Aminoacyl-tRNA Synthetase and Disease: The Yeast Contribution for Functional Analysis of Novel Variants. Int J Mol Sci 2021; 22:ijms22094524. [PMID: 33926074 PMCID: PMC8123711 DOI: 10.3390/ijms22094524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/14/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
In most eukaryotes, mitochondrial protein synthesis is essential for oxidative phosphorylation (OXPHOS) as some subunits of the respiratory chain complexes are encoded by the mitochondrial DNA (mtDNA). Mutations affecting the mitochondrial translation apparatus have been identified as a major cause of mitochondrial diseases. These mutations include either heteroplasmic mtDNA mutations in genes encoding for the mitochondrial rRNA (mtrRNA) and tRNAs (mttRNAs) or mutations in nuclear genes encoding ribosomal proteins, initiation, elongation and termination factors, tRNA-modifying enzymes, and aminoacyl-tRNA synthetases (mtARSs). Aminoacyl-tRNA synthetases (ARSs) catalyze the attachment of specific amino acids to their cognate tRNAs. Differently from most mttRNAs, which are encoded by mitochondrial genome, mtARSs are encoded by nuclear genes and then imported into the mitochondria after translation in the cytosol. Due to the extensive use of next-generation sequencing (NGS), an increasing number of mtARSs variants associated with large clinical heterogeneity have been identified in recent years. Being most of these variants private or sporadic, it is crucial to assess their causative role in the disease by functional analysis in model systems. This review will focus on the contributions of the yeast Saccharomyces cerevisiae in the functional validation of mutations found in mtARSs genes associated with human disorders.
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Affiliation(s)
| | | | | | | | - Cristina Dallabona
- Correspondence: (C.D.); (P.G.); Tel.: +39-0521-905600 (C.D.); +39-0521-905107 (P.G.)
| | - Paola Goffrini
- Correspondence: (C.D.); (P.G.); Tel.: +39-0521-905600 (C.D.); +39-0521-905107 (P.G.)
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10
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Chia M, Li C, Marques S, Pelechano V, Luscombe NM, van Werven FJ. High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. Genome Biol 2021; 22:34. [PMID: 33446241 PMCID: PMC7807719 DOI: 10.1186/s13059-020-02245-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely elusive. We perform an integrative analysis of multiple highly synchronized cell-fate transitions and quantitative genomic techniques in Saccharomyces cerevisiae to identify regulatory functions associated with transcribing alternative isoforms. RESULTS Cell-fate transitions feature widespread elevated expression of alternative TSS and, to a lesser degree, TES usage. These dynamically regulated alternative TSSs are located mostly upstream of canonical TSSs, but also within gene bodies possibly encoding for protein isoforms. Increased upstream alternative TSS usage is linked to various effects on canonical TSS levels, which range from co-activation to repression. We identified two key features linked to these outcomes: an interplay between alternative and canonical promoter strengths, and distance between alternative and canonical TSSs. These two regulatory properties give a plausible explanation of how locally transcribed alternative TSSs control gene transcription. Additionally, we find that specific chromatin modifiers Set2, Set3, and FACT play an important role in mediating gene repression via alternative TSSs, further supporting that the act of upstream transcription drives the local changes in gene transcription. CONCLUSIONS The integrative analysis of multiple cell-fate transitions suggests the presence of a regulatory control system of alternative TSSs that is important for dynamic tuning of gene expression. Our work provides a framework for understanding how TSS heterogeneity governs eukaryotic gene expression, particularly during cell-fate changes.
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Affiliation(s)
- Minghao Chia
- The Francis Crick Institute, London, UK
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Cai Li
- The Francis Crick Institute, London, UK
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sueli Marques
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Vicente Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- Okinawa Institute of Science & Technology Graduate University, Okinawa, 904-0495, Japan
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
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11
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Garin S, Levi O, Cohen B, Golani-Armon A, Arava YS. Localization and RNA Binding of Mitochondrial Aminoacyl tRNA Synthetases. Genes (Basel) 2020; 11:genes11101185. [PMID: 33053729 PMCID: PMC7600831 DOI: 10.3390/genes11101185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondria contain a complete translation machinery that is used to translate its internally transcribed mRNAs. This machinery uses a distinct set of tRNAs that are charged with cognate amino acids inside the organelle. Interestingly, charging is executed by aminoacyl tRNA synthetases (aaRS) that are encoded by the nuclear genome, translated in the cytosol, and need to be imported into the mitochondria. Here, we review import mechanisms of these enzymes with emphasis on those that are localized to both mitochondria and cytosol. Furthermore, we describe RNA recognition features of these enzymes and their interaction with tRNA and non-tRNA molecules. The dual localization of mitochondria-destined aaRSs and their association with various RNA types impose diverse impacts on cellular physiology. Yet, the breadth and significance of these functions are not fully resolved. We highlight here possibilities for future explorations.
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12
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Bader G, Enkler L, Araiso Y, Hemmerle M, Binko K, Baranowska E, De Craene JO, Ruer-Laventie J, Pieters J, Tribouillard-Tanvier D, Senger B, di Rago JP, Friant S, Kucharczyk R, Becker HD. Assigning mitochondrial localization of dual localized proteins using a yeast Bi-Genomic Mitochondrial-Split-GFP. eLife 2020; 9:56649. [PMID: 32657755 PMCID: PMC7358010 DOI: 10.7554/elife.56649] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/11/2020] [Indexed: 12/31/2022] Open
Abstract
A single nuclear gene can be translated into a dual localized protein that distributes between the cytosol and mitochondria. Accumulating evidences show that mitoproteomes contain lots of these dual localized proteins termed echoforms. Unraveling the existence of mitochondrial echoforms using current GFP (Green Fluorescent Protein) fusion microscopy approaches is extremely difficult because the GFP signal of the cytosolic echoform will almost inevitably mask that of the mitochondrial echoform. We therefore engineered a yeast strain expressing a new type of Split-GFP that we termed Bi-Genomic Mitochondrial-Split-GFP (BiG Mito-Split-GFP). Because one moiety of the GFP is translated from the mitochondrial machinery while the other is fused to the nuclear-encoded protein of interest translated in the cytosol, the self-reassembly of this Bi-Genomic-encoded Split-GFP is confined to mitochondria. We could authenticate the mitochondrial importability of any protein or echoform from yeast, but also from other organisms such as the human Argonaute 2 mitochondrial echoform.
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Affiliation(s)
- Gaétan Bader
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Ludovic Enkler
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Yuhei Araiso
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Marine Hemmerle
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Krystyna Binko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Emilia Baranowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Johan-Owen De Craene
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | | | - Jean Pieters
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Bruno Senger
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, Bordeaux, France
| | - Sylvie Friant
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Hubert Dominique Becker
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
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13
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Wallace EWJ, Maufrais C, Sales-Lee J, Tuck LR, de Oliveira L, Feuerbach F, Moyrand F, Natarajan P, Madhani HD, Janbon G. Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom. Nucleic Acids Res 2020; 48:2312-2331. [PMID: 32020195 PMCID: PMC7049704 DOI: 10.1093/nar/gkaa060] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5' and 3' ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-mediated mRNA decay. Transcript leaders in Cryptococcus and other fungi are substantially longer and more AUG-dense than in Saccharomyces. Numerous Cryptococcus mRNAs encode predicted dual-localized proteins, including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Analysis of other fungal species shows that such dual-localization is also predicted to be common in the ascomycete mould, Neurospora crassa. Kozak-controlled regulation is correlated with insertions in translational initiation factors in fidelity-determining regions that contact the initiator tRNA. Thus, start codon context is a signal that quantitatively programs both the expression and the structures of proteins in diverse fungi.
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Affiliation(s)
- Edward W J Wallace
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, UK
| | - Corinne Maufrais
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
- Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, F-75015 Paris, France
| | - Jade Sales-Lee
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Laura R Tuck
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, UK
| | - Luciana de Oliveira
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
| | - Frank Feuerbach
- Institut Pasteur, Unité Génétique des Interactions Macromoléculaire, Département Génome et Génétique, F-75015 Paris, France
| | - Frédérique Moyrand
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
| | - Prashanthi Natarajan
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Guilhem Janbon
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
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14
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Demain LAM, Gerkes EH, Smith RJH, Molina-Ramirez LP, O'Keefe RT, Newman WG. A recurrent missense variant in HARS2 results in variable sensorineural hearing loss in three unrelated families. J Hum Genet 2020; 65:305-311. [PMID: 31827252 PMCID: PMC7500128 DOI: 10.1038/s10038-019-0706-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 11/14/2019] [Accepted: 12/02/2019] [Indexed: 01/31/2023]
Abstract
HARS2 encodes mitochondrial histidyl-tRNA synthetase (HARS2), which links histidine to its cognate tRNA in the mitochondrial matrix. Biallelic variants in HARS2 are associated with Perrault syndrome, a rare recessive condition characterized by sensorineural hearing loss in both sexes and primary ovarian insufficiency in 46,XX females. Some individuals with Perrault syndrome have a broader phenotypic spectrum with neurological features, including ataxia and peripheral neuropathy. Here, we report a recurrent variant in HARS2 in association with sensorineural hearing loss. In affected individuals from three unrelated families, the variant HARS2 c.1439G>A p.(Arg480His) is present as a heterozygous variant in trans to a putative pathogenic variant. The low prevalence of the allele HARS2 c.1439G>A p.(Arg480His) in the general population and its presence in three families with hearing loss, confirm the pathogenicity of this variant and illustrate the presentation of Perrault syndrome as nonsyndromic hearing loss in males and prepubertal females.
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Affiliation(s)
- Leigh A M Demain
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- NW Genomic Laboratory hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories and the Department of Otolaryngology-Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Leslie P Molina-Ramirez
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- NW Genomic Laboratory hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- NW Genomic Laboratory hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
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15
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De Nijs Y, De Maeseneire SL, Soetaert WK. 5' untranslated regions: the next regulatory sequence in yeast synthetic biology. Biol Rev Camb Philos Soc 2019; 95:517-529. [PMID: 31863552 DOI: 10.1111/brv.12575] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/08/2019] [Accepted: 11/28/2019] [Indexed: 01/10/2023]
Abstract
When developing industrial biotechnology processes, Saccharomyces cerevisiae (baker's yeast or brewer's yeast) is a popular choice as a microbial host. Many tools have been developed in the fields of synthetic biology and metabolic engineering to introduce heterologous pathways and tune their expression in yeast. Such tools mainly focus on controlling transcription, whereas post-transcriptional regulation is often overlooked. Herein we discuss regulatory elements found in the 5' untranslated region (UTR) and their influence on protein synthesis. We provide not only an overall picture, but also a set of design rules on how to engineer a 5' UTR. The reader is also referred to currently available models that allow gene expression to be tuned predictably using different 5' UTRs.
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Affiliation(s)
- Yatti De Nijs
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Sofie L De Maeseneire
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wim K Soetaert
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
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16
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Monteuuis G, Miścicka A, Świrski M, Zenad L, Niemitalo O, Wrobel L, Alam J, Chacinska A, Kastaniotis AJ, Kufel J. Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins. Nucleic Acids Res 2019; 47:5777-5791. [PMID: 31216041 PMCID: PMC6582344 DOI: 10.1093/nar/gkz301] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 12/15/2022] Open
Abstract
Utilization of non-AUG alternative translation start sites is most common in bacteria and viruses, but it has been also reported in other organisms. This phenomenon increases proteome complexity by allowing expression of multiple protein isoforms from a single gene. In Saccharomyces cerevisiae, a few described cases concern proteins that are translated from upstream near-cognate start codons as N-terminally extended variants that localize to mitochondria. Using bioinformatics tools, we provide compelling evidence that in yeast the potential for producing alternative protein isoforms by non-AUG translation initiation is much more prevalent than previously anticipated and may apply to as many as a few thousand proteins. Several hundreds of candidates are predicted to gain a mitochondrial targeting signal (MTS), generating an unrecognized pool of mitochondrial proteins. We confirmed mitochondrial localization of a subset of proteins previously not identified as mitochondrial, whose standard forms do not carry an MTS. Our data highlight the potential of non-canonical translation initiation in expanding the capacity of the mitochondrial proteome and possibly also other cellular features.
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Affiliation(s)
- Geoffray Monteuuis
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Anna Miścicka
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Michał Świrski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Lounis Zenad
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Olli Niemitalo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Lidia Wrobel
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Jahangir Alam
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Agnieszka Chacinska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Alexander J Kastaniotis
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
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17
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Nishimura A, Nasuno R, Yoshikawa Y, Jung M, Ida T, Matsunaga T, Morita M, Takagi H, Motohashi H, Akaike T. Mitochondrial cysteinyl-tRNA synthetase is expressed via alternative transcriptional initiation regulated by energy metabolism in yeast cells. J Biol Chem 2019; 294:13781-13788. [PMID: 31350340 DOI: 10.1074/jbc.ra119.009203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/23/2019] [Indexed: 11/06/2022] Open
Abstract
Eukaryotes typically utilize two distinct aminoacyl-tRNA synthetase isoforms, one for cytosolic and one for mitochondrial protein synthesis. However, the genome of budding yeast (Saccharomyces cerevisiae) contains only one cysteinyl-tRNA synthetase gene (YNL247W, also known as CRS1). In this study, we report that CRS1 encodes both cytosolic and mitochondrial isoforms. The 5' complementary DNA end method and GFP reporter gene analyses indicated that yeast CRS1 expression yields two classes of mRNAs through alternative transcription starts: a long mRNA containing a mitochondrial targeting sequence and a short mRNA lacking this targeting sequence. We found that the mitochondrial Crs1 is the product of translation from the first initiation AUG codon on the long mRNA, whereas the cytosolic Crs1 is produced from the second in-frame AUG codon on the short mRNA. Genetic analysis and a ChIP assay revealed that the transcription factor heme activator protein (Hap) complex, which is involved in mitochondrial biogenesis, determines the transcription start sites of the CRS1 gene. We also noted that Hap complex-dependent initiation is regulated according to the needs of mitochondrial energy production. The results of our study indicate energy-dependent initiation of alternative transcription of CRS1 that results in production of two Crs1 isoforms, a finding that suggests Crs1's potential involvement in mitochondrial energy metabolism in yeast.
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Affiliation(s)
- Akira Nishimura
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Ryo Nasuno
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Yuki Yoshikawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Minkyung Jung
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Tomoaki Ida
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Tetsuro Matsunaga
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Masanobu Morita
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Takaaki Akaike
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
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18
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Lee YH, Lo YT, Chang CP, Yeh CS, Chang TH, Chen YW, Tseng YK, Wang CC. Naturally occurring dual recognition of tRNA His substrates with and without a universal identity element. RNA Biol 2019; 16:1275-1285. [PMID: 31179821 DOI: 10.1080/15476286.2019.1626663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The extra 5' guanine nucleotide (G-1) on tRNAHis is a nearly universal feature that specifies tRNAHis identity. The G-1 residue is either genome encoded or post-transcriptionally added by tRNAHis guanylyltransferase (Thg1). Despite Caenorhabditis elegans being a Thg1-independent organism, its cytoplasmic tRNAHis (CetRNAnHis) retains a genome-encoded G-1. Our study showed that this eukaryote possesses a histidyl-tRNA synthetase (CeHisRS) gene encoding two distinct HisRS isoforms that differ only at their N-termini. Most interestingly, its mitochondrial tRNAHis (CetRNAmHis) lacks G-1, a scenario never observed in any organelle. This tRNA, while lacking the canonical identity element, can still be efficiently aminoacylated in vivo. Even so, addition of G-1 to CetRNAmHis strongly enhanced its aminoacylation efficiency in vitro. Overexpression of CeHisRS successfully bypassed the requirement for yeast THG1 in the presence of CetRNAnHis without G-1. Mutagenesis assays showed that the anticodon takes a primary role in CetRNAHis identity recognition, being comparable to the universal identity element. Consequently, simultaneous introduction of both G-1 and the anticodon of tRNAHis effectively converted a non-cognate tRNA to a tRNAHis-like substrate. Our study suggests that a new balance between identity elements of tRNAHis relieves HisRS from the absolute requirement for G-1.
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Affiliation(s)
- Yi-Hsueh Lee
- a Department of Life Sciences, National Central University , Taoyuan , Taiwan
| | - Ya-Ting Lo
- a Department of Life Sciences, National Central University , Taoyuan , Taiwan
| | - Chia-Pei Chang
- a Department of Life Sciences, National Central University , Taoyuan , Taiwan
| | - Chung-Shu Yeh
- b Genomics Research Center, Academia Sinica , Taipei , Taiwan
| | | | - Yu-Wei Chen
- c Department of Neurology, Landseed International Hospital , Taoyuan , Taiwan
| | - Yi-Kuan Tseng
- d Graduate Institute of Statistics, National Central University , Taoyuan , Taiwan
| | - Chien-Chia Wang
- a Department of Life Sciences, National Central University , Taoyuan , Taiwan
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19
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Yakobov N, Debard S, Fischer F, Senger B, Becker HD. Cytosolic aminoacyl-tRNA synthetases: Unanticipated relocations for unexpected functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:387-400. [PMID: 29155070 DOI: 10.1016/j.bbagrm.2017.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/13/2022]
Abstract
Prokaryotic and eukaryotic cytosolic aminoacyl-tRNA synthetases (aaRSs) are essentially known for their conventional function of generating the full set of aminoacyl-tRNA species that are needed to incorporate each organism's repertoire of genetically-encoded amino acids during ribosomal translation of messenger RNAs. However, bacterial and eukaryotic cytosolic aaRSs have been shown to exhibit other essential nonconventional functions. Here we review all the subcellular compartments that prokaryotic and eukaryotic cytosolic aaRSs can reach to exert either a conventional or nontranslational role. We describe the physiological and stress conditions, the mechanisms and the signaling pathways that trigger their relocation and the new functions associated with these relocating cytosolic aaRS. Finally, given that these relocating pools of cytosolic aaRSs participate to a wide range of cellular pathways beyond translation, but equally important for cellular homeostasis, we mention some of the pathologies and diseases associated with the dis-regulation or malfunctioning of these nontranslational functions.
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Affiliation(s)
- Nathaniel Yakobov
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Sylvain Debard
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Frédéric Fischer
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Bruno Senger
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Hubert Dominique Becker
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France.
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20
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A single Danio rerio hars gene encodes both cytoplasmic and mitochondrial histidyl-tRNA synthetases. PLoS One 2017; 12:e0185317. [PMID: 28934368 PMCID: PMC5608375 DOI: 10.1371/journal.pone.0185317] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/11/2017] [Indexed: 12/16/2022] Open
Abstract
Histidyl tRNA Synthetase (HARS) is a member of the aminoacyl tRNA synthetase (ARS) family of enzymes. This family of 20 enzymes is responsible for attaching specific amino acids to their cognate tRNA molecules, a critical step in protein synthesis. However, recent work highlighting a growing number of associations between ARS genes and diverse human diseases raises the possibility of new and unexpected functions in this ancient enzyme family. For example, mutations in HARS have been linked to two different neurological disorders, Usher Syndrome Type IIIB and Charcot Marie Tooth peripheral neuropathy. These connections raise the possibility of previously undiscovered roles for HARS in metazoan development, with alterations in these functions leading to complex diseases. In an attempt to establish Danio rerio as a model for studying HARS functions in human disease, we characterized the Danio rerio hars gene and compared it to that of human HARS. Using a combination of bioinformatics, molecular biology, and cellular approaches, we found that while the human genome encodes separate genes for cytoplasmic and mitochondrial HARS protein, the Danio rerio genome encodes a single hars gene which undergoes alternative splicing to produce the respective cytoplasmic and mitochondrial versions of Hars. Nevertheless, while the HARS genes of humans and Danio differ significantly at the genomic level, we found that they are still highly conserved at the amino acid level, underscoring the potential utility of Danio rerio as a model organism for investigating HARS function and its link to human diseases in vivo.
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21
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Lee YH, Chang CP, Cheng YJ, Kuo YY, Lin YS, Wang CC. Evolutionary gain of highly divergent tRNA specificities by two isoforms of human histidyl-tRNA synthetase. Cell Mol Life Sci 2017; 74:2663-2677. [PMID: 28321488 PMCID: PMC11107585 DOI: 10.1007/s00018-017-2491-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 02/16/2017] [Accepted: 02/20/2017] [Indexed: 11/28/2022]
Abstract
The discriminator base N73 is a key identity element of tRNAHis. In eukaryotes, N73 is an "A" in cytoplasmic tRNAHis and a "C" in mitochondrial tRNAHis. We present evidence herein that yeast histidyl-tRNA synthetase (HisRS) recognizes both A73 and C73, but somewhat prefers A73 even within the context of mitochondrial tRNAHis. In contrast, humans possess two distinct yet closely related HisRS homologues, with one encoding the cytoplasmic form (with an extra N-terminal WHEP domain) and the other encoding its mitochondrial counterpart (with an extra N-terminal mitochondrial targeting signal). Despite these two isoforms sharing high sequence similarities (81% identity), they strongly preferred different discriminator bases (A73 or C73). Moreover, only the mitochondrial form recognized the anticodon as a strong identity element. Most intriguingly, swapping the discriminator base between the cytoplasmic and mitochondrial tRNAHis isoacceptors conveniently switched their enzyme preferences. Similarly, swapping seven residues in the active site between the two isoforms readily switched their N73 preferences. This study suggests that the human HisRS genes, while descending from a common ancestor with dual function for both types of tRNAHis, have acquired highly specialized tRNA recognition properties through evolution.
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Affiliation(s)
- Yi-Hsueh Lee
- Department of Life Sciences, National Central University, Jungli District, Taoyuan, 32001, Taiwan
| | - Chia-Pei Chang
- Department of Life Sciences, National Central University, Jungli District, Taoyuan, 32001, Taiwan
| | - Yu-Ju Cheng
- Department of Life Sciences, National Central University, Jungli District, Taoyuan, 32001, Taiwan
| | - Yi-Yi Kuo
- Department of Life Sciences, National Central University, Jungli District, Taoyuan, 32001, Taiwan
| | - Yeong-Shin Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Chien-Chia Wang
- Department of Life Sciences, National Central University, Jungli District, Taoyuan, 32001, Taiwan.
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22
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Debard S, Bader G, De Craene JO, Enkler L, Bär S, Laporte D, Hammann P, Myslinski E, Senger B, Friant S, Becker HD. Nonconventional localizations of cytosolic aminoacyl-tRNA synthetases in yeast and human cells. Methods 2017; 113:91-104. [DOI: 10.1016/j.ymeth.2016.09.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 09/27/2016] [Accepted: 09/30/2016] [Indexed: 11/26/2022] Open
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23
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Kastaniotis AJ, Autio KJ, Kerätär JM, Monteuuis G, Mäkelä AM, Nair RR, Pietikäinen LP, Shvetsova A, Chen Z, Hiltunen JK. Mitochondrial fatty acid synthesis, fatty acids and mitochondrial physiology. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:39-48. [PMID: 27553474 DOI: 10.1016/j.bbalip.2016.08.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/20/2016] [Accepted: 08/17/2016] [Indexed: 02/07/2023]
Abstract
Mitochondria and fatty acids are tightly connected to a multiplicity of cellular processes that go far beyond mitochondrial fatty acid metabolism. In line with this view, there is hardly any common metabolic disorder that is not associated with disturbed mitochondrial lipid handling. Among other aspects of mitochondrial lipid metabolism, apparently all eukaryotes are capable of carrying out de novo fatty acid synthesis (FAS) in this cellular compartment in an acyl carrier protein (ACP)-dependent manner. The dual localization of FAS in eukaryotic cells raises the questions why eukaryotes have maintained the FAS in mitochondria in addition to the "classic" cytoplasmic FAS and what the products are that cannot be substituted by delivery of fatty acids of extramitochondrial origin. The current evidence indicates that mitochondrial FAS is essential for cellular respiration and mitochondrial biogenesis. Although both β-oxidation and FAS utilize thioester chemistry, CoA acts as acyl-group carrier in the breakdown pathway whereas ACP assumes this role in the synthetic direction. This arrangement metabolically separates these two pathways running towards opposite directions and prevents futile cycling. A role of this pathway in mitochondrial metabolic sensing has recently been proposed. This article is part of a Special Issue entitled: Lipids of Mitochondria edited by Guenther Daum.
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Affiliation(s)
- Alexander J Kastaniotis
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Kaija J Autio
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Juha M Kerätär
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Geoffray Monteuuis
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anne M Mäkelä
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Remya R Nair
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Laura P Pietikäinen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Antonina Shvetsova
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Zhijun Chen
- State Key Laboratory of Supramolecular Structure and Materials and Institute of Theoretical Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland; State Key Laboratory of Supramolecular Structure and Materials and Institute of Theoretical Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China.
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Chang CY, Chang CP, Chakraborty S, Wang SW, Tseng YK, Wang CC. Modulating the Structure and Function of an Aminoacyl-tRNA Synthetase Cofactor by Biotinylation. J Biol Chem 2016; 291:17102-11. [PMID: 27330079 DOI: 10.1074/jbc.m116.734343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Indexed: 12/20/2022] Open
Abstract
Arc1p is a yeast-specific tRNA-binding protein that forms a ternary complex with glutamyl-tRNA synthetase (GluRSc) and methionyl-tRNA synthetase (MetRS) in the cytoplasm to regulate their catalytic activities and subcellular distributions. Despite Arc1p not being involved in any known biotin-dependent reaction, it is a natural target of biotin modification. Results presented herein show that biotin modification had no obvious effect on the growth-supporting activity, subcellular distribution, tRNA binding, or interactions of Arc1p with GluRSc and MetRS. Nevertheless, biotinylation of Arc1p was temperature dependent; raising the growth temperature from 30 to 37 °C drastically reduced its biotinylation level. As a result, Arc1p purified from a yeast culture that had been grown overnight at 37 °C was essentially biotin free. Non-biotinylated Arc1p was more heat stable, more flexible in structure, and more effective than its biotinylated counterpart in promoting glutamylation activity of the otherwise inactive GluRSc at 37 °C in vitro Our study suggests that the structure and function of Arc1p can be modulated via biotinylation in response to temperature changes.
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Affiliation(s)
| | | | - Shruti Chakraborty
- the Department of Biotechnology, University of Calcutta, Kolkata 700019, India, and
| | - Shao-Win Wang
- the Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli 35053, Taiwan
| | - Yi-Kuan Tseng
- the Graduate Institute of Statistics, National Central University, Jungli District, Taoyuan 32001, Taiwan
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25
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Chang CY, Chien CI, Chang CP, Lin BC, Wang CC. A WHEP Domain Regulates the Dynamic Structure and Activity of Caenorhabditis elegans Glycyl-tRNA Synthetase. J Biol Chem 2016; 291:16567-75. [PMID: 27298321 DOI: 10.1074/jbc.m116.730812] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Indexed: 11/06/2022] Open
Abstract
WHEP domains exist in certain eukaryotic aminoacyl-tRNA synthetases and play roles in tRNA or protein binding. We present evidence herein that cytoplasmic and mitochondrial forms of Caenorhabditis elegans glycyl-tRNA synthetase (CeGlyRS) are encoded by the same gene (CeGRS1) through alternative initiation of translation. The cytoplasmic form possessed an N-terminal WHEP domain, whereas its mitochondrial isoform possessed an extra N-terminal sequence consisting of an mitochondrial targeting signal and an appended domain. Cross-species complementation assays showed that CeGRS1 effectively rescued the cytoplasmic and mitochondrial defects of a yeast GRS1 knock-out strain. Although both forms of CeGlyRS efficiently charged the cytoplasmic tRNAs(Gly) of C. elegans, the mitochondrial form was much more efficient than its cytoplasmic counterpart in charging the mitochondrial tRNA(Gly) isoacceptor, which carries a defective TψC hairpin. Despite the WHEP domain per se lacking tRNA binding activity, deletion of this domain reduced the catalytic efficiency of the enzyme. Most interestingly, the deletion mutant possessed a higher thermal stability and a somewhat lower structural flexibility. Our study suggests a role for the WHEP domain as a regulator of the dynamic structure and activity of the enzyme.
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Affiliation(s)
- Chih-Yao Chang
- From the Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Chin-I Chien
- From the Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Chia-Pei Chang
- From the Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Bo-Chun Lin
- From the Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Chien-Chia Wang
- From the Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
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26
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Kartvelishvili E, Peretz M, Tworowski D, Moor N, Safro M. Chimeric human mitochondrial PheRS exhibits editing activity to discriminate nonprotein amino acids. Protein Sci 2015; 25:618-26. [PMID: 26645192 DOI: 10.1002/pro.2855] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/10/2015] [Indexed: 11/11/2022]
Abstract
Mitochondria are considered as the primary source of reactive oxygen species (ROS) in nearly all eukaryotic cells during respiration. The harmful effects of these compounds range from direct neurotoxicity to incorporation into proteins producing aberrant molecules with multiple physiological problems. Phenylalanine exposure to ROS produces multiple oxidized isomers: tyrosine, Levodopa, ortho-Tyr, meta-Tyr (m-Tyr), and so on. Cytosolic phenylalanyl-tRNA synthetase (PheRS) exerts control over the translation accuracy, hydrolyzing misacylated products, while monomeric mitochondrial PheRS lacks the editing activity. Recently we showed that "teamwork" of cytosolic and mitochondrial PheRSs cannot prevent incorporation of m-Tyr and l-Dopa into proteins. Here, we present human mitochondrial chimeric PheRS with implanted editing module taken from EcPheRS. The monomeric mitochondrial chimera possesses editing activity, while in bacterial and cytosolic PheRSs this type of activity was detected for the (αβ)2 architecture only. The fusion protein catalyzes aminoacylation of tRNA(Phe) with cognate phenylalanine and effectively hydrolyzes the noncognate aminoacyl-tRNAs: Tyr-tRNA(Phe) and m-Tyr-tRNA(Phe) .
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Affiliation(s)
| | - Moshe Peretz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dmitry Tworowski
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nina Moor
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, 630090, Russia
| | - Mark Safro
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
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27
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Chang CP, Chang CY, Lee YH, Lin YS, Wang CC. Divergent Alanyl-tRNA Synthetase Genes of Vanderwaltozyma polyspora Descended from a Common Ancestor through Whole-Genome Duplication Followed by Asymmetric Evolution. Mol Cell Biol 2015; 35:2242-53. [PMID: 25896914 PMCID: PMC4456443 DOI: 10.1128/mcb.00018-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/14/2015] [Accepted: 04/14/2015] [Indexed: 11/20/2022] Open
Abstract
Cytoplasmic and mitochondrial forms of a eukaryotic aminoacyl-tRNA synthetase (aaRS) are generally encoded by two distinct nuclear genes, one of eukaryotic origin and the other of mitochondrial origin. However, in most known yeasts, only the mitochondrial-origin alanyl-tRNA synthetase (AlaRS) gene is retained and plays a dual-functional role. Here, we present a novel scenario of AlaRS evolution in the yeast Vanderwaltozyma polyspora. V. polyspora possesses two significantly diverged AlaRS gene homologues, one encoding the cytoplasmic form and the other its mitochondrial counterpart. Clever selection of transcription and translation initiation sites enables the two isoforms to be localized and thus functional in their respective cellular compartments. However, the two isoforms can also be stably expressed and function in the reciprocal compartments by insertion or removal of a mitochondrial targeting signal. Synteny and phylogeny analyses revealed that the AlaRS homologues of V. polyspora arose from a dual-functional common ancestor through whole-genome duplication (WGD). Moreover, the mitochondrial form had higher synonymous (1.6-fold) and nonsynonymous (2.8-fold) substitution rates than did its cytoplasmic counterpart, presumably due to a lesser constraint imposed on components of the mitochondrial translational apparatus. Our study suggests that asymmetric evolution confers the divergence between the AlaRS paralogues of V. polyspora.
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Affiliation(s)
- Chia-Pei Chang
- Department of Life Sciences, National Central University, Jungli, Taiwan
| | - Chih-Yao Chang
- Department of Life Sciences, National Central University, Jungli, Taiwan
| | - Yi-Hsueh Lee
- Department of Life Sciences, National Central University, Jungli, Taiwan
| | - Yeong-Shin Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, Taiwan
| | - Chien-Chia Wang
- Department of Life Sciences, National Central University, Jungli, Taiwan
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28
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Giordano C, Morea V, Perli E, d'Amati G. The phenotypic expression of mitochondrial tRNA-mutations can be modulated by either mitochondrial leucyl-tRNA synthetase or the C-terminal domain thereof. Front Genet 2015; 6:113. [PMID: 25852750 PMCID: PMC4370040 DOI: 10.3389/fgene.2015.00113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/04/2015] [Indexed: 11/23/2022] Open
Abstract
Mutations in mitochondrial (mt) DNA determine important human diseases. The majority of the known pathogenic mutations are located in transfer RNA (tRNA) genes and are responsible for a wide range of currently untreatable disorders. Experimental evidence both in yeast and in human cells has shown that the detrimental effects of mt-tRNA point mutations can be attenuated by increasing the expression of the cognate mt-aminoacyl-tRNA synthetases (aaRSs). In addition, constitutive high levels of isoleucyl-tRNA syntethase have been shown to reduce the penetrance of a homoplasmic mutation in mt-tRNAIle in a small kindred. More recently, we showed that the isolated carboxy-terminal domain of human mt-leucyl tRNA synthetase (LeuRS-Cterm) localizes to mitochondria and ameliorates the energetic defect in transmitochondrial cybrids carrying mutations either in the cognate mt-tRNALeu(UUR) or in the non-cognate mt-tRNAIle gene. Since the mt-LeuRS-Cterm does not possess catalytic activity, its rescuing ability is most likely mediated by a chaperon-like effect, consisting in the stabilization of the tRNA structure altered by the mutation. All together, these observations open potential therapeutic options for mt-tRNA mutations-associated diseases.
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Affiliation(s)
- Carla Giordano
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome Rome, Italy
| | - Veronica Morea
- National Research Council of Italy, Institute of Molecular Biology and Pathology, Department of Biochemical Sciences, Sapienza University of Rome Rome, Italy
| | - Elena Perli
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome Rome, Italy
| | - Giulia d'Amati
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome Rome, Italy ; Pasteur Institute-Cenci Bolognetti Foundation Rome, Italy
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29
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Vanderwaltozyma polyspora possesses two glycyl-tRNA synthetase genes: one constitutive and one inducible. Fungal Genet Biol 2015; 76:47-56. [PMID: 25683380 DOI: 10.1016/j.fgb.2015.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/14/2015] [Accepted: 02/02/2015] [Indexed: 11/22/2022]
Abstract
Aminoacyl-tRNA synthetases are housekeeping enzymes essential for protein synthesis. We herein present evidence that the yeast Vanderwaltozyma polyspora possesses two paralogous glycyl-tRNA synthetase (GlyRS) genes-GRS1 and GRS2. Paradoxically, GRS1 provided functions in both the cytoplasm and mitochondria, while GRS2 was essentially silent under normal growth conditions. Expression of GRS2 could be activated by stresses such as high pH or ethanol and most effectively by high temperature. The expressed GlyRS2 protein was exclusively found in the cytoplasm and more stable under heat-shock conditions (37°C) than under normal growth conditions (30°C) in vivo. In addition, GRS2 effectively rescued the cytoplasmic defect of a Saccharomyces cerevisiae GRS1 knockout strain when expressed from a constitutive promoter. Moreover, the purified GlyRS2 enzyme was fairly active at both 30°C and 37°C in glycylation of yeast tRNA in vitro. However, unexpectedly, the purified GlyRS2 enzyme was practically inactive at temperature above 40°C in vitro. Our study suggests that GRS2 is an inducible gene that acts under stress conditions where GlyRS1 may be insufficient, unavailable, or rendered inactive.
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30
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Suomi F, Menger KE, Monteuuis G, Naumann U, Kursu VAS, Shvetsova A, Kastaniotis AJ. Expression and evolution of the non-canonically translated yeast mitochondrial acetyl-CoA carboxylase Hfa1p. PLoS One 2014; 9:e114738. [PMID: 25503745 PMCID: PMC4263661 DOI: 10.1371/journal.pone.0114738] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 11/13/2014] [Indexed: 12/16/2022] Open
Abstract
The Saccharomyces cerevisiae genome encodes two sequence related acetyl-CoA carboxylases, the cytosolic Acc1p and the mitochondrial Hfa1p, required for respiratory function. Several aspects of expression of the HFA1 gene and its evolutionary origin have remained unclear. Here, we determined the HFA1 transcription initiation sites by 5' RACE analysis. Using a novel "Stop codon scanning" approach, we mapped the location of the HFA1 translation initiation site to an upstream AUU codon at position -372 relative to the annotated start codon. This upstream initiation leads to production of a mitochondrial targeting sequence preceding the ACC domains of the protein. In silico analyses of fungal ACC genes revealed conserved "cryptic" upstream mitochondrial targeting sequences in yeast species that have not undergone a whole genome duplication. Our Δhfa1 baker's yeast mutant phenotype rescue studies using the protoploid Kluyveromyces lactis ACC confirmed functionality of the cryptic upstream mitochondrial targeting signal. These results lend strong experimental support to the hypothesis that the mitochondrial and cytosolic acetyl-CoA carboxylases in S. cerevisiae have evolved from a single gene encoding both the mitochondrial and cytosolic isoforms. Leaning on a cursory survey of a group of genes of our interest, we propose that cryptic 5' upstream mitochondrial targeting sequences may be more abundant in eukaryotes than anticipated thus far.
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Affiliation(s)
- Fumi Suomi
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Katja E Menger
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Geoffray Monteuuis
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Uta Naumann
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - V A Samuli Kursu
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Antonina Shvetsova
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Alexander J Kastaniotis
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
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Di Micco P, Fazzi D'Orsi M, Morea V, Frontali L, Francisci S, Montanari A. The yeast model suggests the use of short peptides derived from mt LeuRS for the therapy of diseases due to mutations in several mt tRNAs. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:3065-74. [PMID: 25261707 DOI: 10.1016/j.bbamcr.2014.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 01/23/2023]
Abstract
We have previously established a yeast model of mitochondrial (mt) diseases. We showed that defective respiratory phenotypes due to point-mutations in mt tRNA(Leu(UUR)), tRNA(Ile) and tRNA(Val) could be relieved by overexpression of both cognate and non-cognate nuclearly encoded mt aminoacyl-tRNA synthetases (aaRS) LeuRS, IleRS and ValRS. More recently, we showed that the isolated carboxy-terminal domain (Cterm) of yeast mt LeuRS, and even short peptides derived from the human Cterm, have the same suppressing abilities as the whole enzymes. In this work, we extend these results by investigating the activity of a number of mt aaRS from either class I or II towards a panel of mt tRNAs. The Cterm of both human and yeast mt LeuRS has the same spectrum of activity as mt aaRS belonging to class I and subclass a, which is the most extensive among the whole enzymes. Yeast Cterm is demonstrated to be endowed with mt targeting activity. Importantly, peptide fragments β30_31 and β32_33, derived from the human Cterm, have even higher efficiency as well as wider spectrum of activity, thus opening new avenues for therapeutic intervention. Bind-shifting experiments show that the β30_31 peptide directly interacts with human mt tRNA(Leu(UUR)) and tRNA(Ile), suggesting that the rescuing activity of isolated peptide fragments is mediated by a chaperone-like mechanism. Wide-range suppression appears to be idiosyncratic of LeuRS and its fragments, since it is not shared by Cterminal regions derived from human mt IleRS or ValRS, which are expected to have very different structures and interactions with tRNAs.
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Affiliation(s)
- Patrizio Di Micco
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Mario Fazzi D'Orsi
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Veronica Morea
- National Research Council of Italy (CNR) - Institute of Biology, Molecular Medicine and Nanobiotechnology (IBMN), Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Laura Frontali
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy; Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Silvia Francisci
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy; Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Arianna Montanari
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy.
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Functional substitution of a eukaryotic glycyl-tRNA synthetase with an evolutionarily unrelated bacterial cognate enzyme. PLoS One 2014; 9:e94659. [PMID: 24743154 PMCID: PMC3990555 DOI: 10.1371/journal.pone.0094659] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/18/2014] [Indexed: 12/03/2022] Open
Abstract
Two oligomeric types of glycyl-tRNA synthetase (GlyRS) are found in nature: a α2 type and a α2β2 type. The former has been identified in all three kingdoms of life and often pairs with tRNAGly that carries an A73 discriminator base, while the latter is found only in bacteria and chloroplasts and is almost always coupled with tRNAGly that contains U73. In the yeast Saccharomyces cerevisiae, a single GlyRS gene, GRS1, provides both the cytoplasmic and mitochondrial functions, and tRNAGly isoacceptors in both compartments possess A73. We showed herein that Homo sapiens and Arabidopsis thaliana cytoplasmic GlyRSs (both α2-type enzymes) can rescue both the cytoplasmic and mitochondrial defects of a yeast grs1- strain, while Escherichia coli GlyRS (a α2β2-type enzyme) and A. thaliana organellar GlyRS (a (αβ)2-type enzyme) failed to rescue either defect of the yeast mull allele. However, a head-to-tail αβ fusion of E. coli GlyRS effectively supported the mitochondrial function. Our study suggests that a α2-type eukaryotic GlyRS may be functionally substituted with a α2β2-type bacterial cognate enzyme despite their remote evolutionary relationships.
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33
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Idiosyncrasies in decoding mitochondrial genomes. Biochimie 2014; 100:95-106. [PMID: 24440477 DOI: 10.1016/j.biochi.2014.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 01/06/2014] [Indexed: 11/24/2022]
Abstract
Mitochondria originate from the α-proteobacterial domain of life. Since this unique event occurred, mitochondrial genomes of protozoans, fungi, plants and metazoans have highly derived and diverged away from the common ancestral DNA. These resulting genomes highly differ from one another, but all present-day mitochondrial DNAs have a very reduced coding capacity. Strikingly however, ATP production coupled to electron transport and translation of mitochondrial proteins are the two common functions retained in all mitochondrial DNAs. Paradoxically, most components essential for these two functions are now expressed from nuclear genes. Understanding how mitochondrial translation evolved in various eukaryotic models is essential to acquire new knowledge of mitochondrial genome expression. In this review, we provide a thorough analysis of the idiosyncrasies of mitochondrial translation as they occur between organisms. We address this by looking at mitochondrial codon usage and tRNA content. Then, we look at the aminoacyl-tRNA-forming enzymes in terms of peculiarities, dual origin, and alternate function(s). Finally we give examples of the atypical structural properties of mitochondrial tRNAs found in some organisms and the resulting adaptive tRNA-protein partnership.
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An insertion peptide in yeast glycyl-tRNA synthetase facilitates both productive docking and catalysis of cognate tRNAs. Mol Cell Biol 2013; 33:3515-23. [PMID: 23816885 DOI: 10.1128/mcb.00122-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The yeast Saccharomyces cerevisiae possesses two distinct glycyl-tRNA synthetase (GlyRS) genes: GRS1 and GRS2. GRS1 is dually functional, encoding both cytoplasmic and mitochondrial activities, while GRS2 is dysfunctional and not required for growth. The protein products of these two genes, GlyRS1 and GlyRS2, are much alike but are distinguished by an insertion peptide of GlyRS1, which is absent from GlyRS2 and other eukaryotic homologues. We show that deletion or mutation of the insertion peptide modestly impaired the enzyme's catalytic efficiency in vitro (with a 2- to 3-fold increase in Km and a 5- to 8-fold decrease in kcat). Consistently, GRS2 can be conveniently converted to a functional gene via codon optimization, and the insertion peptide is dispensable for protein stability and the rescue activity of GRS1 at 30°C in vivo. A phylogenetic analysis further showed that GRS1 and GRS2 are paralogues that arose from a gene duplication event relatively recently, with GRS1 being the predecessor. These results indicate that GlyRS2 is an active enzyme essentially resembling the insertion peptide-deleted form of GlyRS1. Our study suggests that the insertion peptide represents a novel auxiliary domain, which facilitates both productive docking and catalysis of cognate tRNAs.
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Liao CC, Lin CH, Chen SJ, Wang CC. Trans-kingdom rescue of Gln-tRNAGln synthesis in yeast cytoplasm and mitochondria. Nucleic Acids Res 2012; 40:9171-81. [PMID: 22821561 PMCID: PMC3467082 DOI: 10.1093/nar/gks689] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aminoacylation of transfer RNAGln (tRNAGln) is performed by distinct mechanisms in different kingdoms and represents the most diverged route of aminoacyl-tRNA synthesis found in nature. In Saccharomyces cerevisiae, cytosolic Gln-tRNAGln is generated by direct glutaminylation of tRNAGln by glutaminyl-tRNA synthetase (GlnRS), whereas mitochondrial Gln-tRNAGln is formed by an indirect pathway involving charging by a non-discriminating glutamyl-tRNA synthetase and the subsequent transamidation by a specific Glu-tRNAGln amidotransferase. Previous studies showed that fusion of a yeast non-specific tRNA-binding cofactor, Arc1p, to Escherichia coli GlnRS enables the bacterial enzyme to substitute for its yeast homologue in vivo. We report herein that the same fusion enzyme, upon being imported into mitochondria, substituted the indirect pathway for Gln-tRNAGln synthesis as well, despite significant differences in the identity determinants of E. coli and yeast cytosolic and mitochondrial tRNAGln isoacceptors. Fusion of Arc1p to the bacterial enzyme significantly enhanced its aminoacylation activity towards yeast tRNAGln isoacceptors in vitro. Our study provides a mechanism by which trans-kingdom rescue of distinct pathways of Gln-tRNAGln synthesis can be conferred by a single enzyme.
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Affiliation(s)
- Chih-Chi Liao
- Department of Life Sciences, National Central University, Jung-li 32001, Taiwan, Republic of China
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36
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Paul MF, Alushin GM, Barros MH, Rak M, Tzagoloff A. The putative GTPase encoded by MTG3 functions in a novel pathway for regulating assembly of the small subunit of yeast mitochondrial ribosomes. J Biol Chem 2012; 287:24346-55. [PMID: 22621929 PMCID: PMC3397861 DOI: 10.1074/jbc.m112.363309] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 05/22/2012] [Indexed: 11/06/2022] Open
Abstract
Very little is known about biogenesis of mitochondrial ribosomes. The GTPases encoded by the nuclear MTG1 and MTG2 genes of Saccharomyces cerevisiae have been reported to play a role in assembly of the ribosomal 54 S subunit. In the present study biochemical screens of a collection of respiratory deficient yeast mutants have enabled us to identify a third gene essential for expression of mitochondrial ribosomes. This gene codes for a member of the YqeH family of GTPases, which we have named MTG3 in keeping with the earlier convention. Mutations in MTG3 cause the accumulation of the 15 S rRNA precursor, previously shown to have an 80-nucleotide 5' extension. Sucrose gradient sedimentation of mitochondrial ribosomes from temperature-sensitive mtg3 mutants grown at the permissive and restrictive temperatures, combined with immunobloting with subunit-specific antibodies, indicate that Mtg3p is required for assembly of the 30 S but not 54 S ribosomal subunit. The respiratory deficient growth phenotype of an mtg3 null mutant is partially rescued by overexpression of the Mrpl4p constituent located at the peptide exit site of the 54 S subunit. The rescue is accompanied by an increase in processed 15 S rRNA. This suggests that Mtg3p and Mrpl4p jointly regulate assembly of the small subunit by modulating processing of the 15 S rRNA precursor.
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Affiliation(s)
- Marie-Françoise Paul
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Gregory M. Alushin
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Mario H. Barros
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Malgorzata Rak
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Alexander Tzagoloff
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
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37
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Chen SJ, Wu YH, Huang HY, Wang CC. Saccharomyces cerevisiae possesses a stress-inducible glycyl-tRNA synthetase gene. PLoS One 2012; 7:e33363. [PMID: 22438917 PMCID: PMC3306390 DOI: 10.1371/journal.pone.0033363] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 02/13/2012] [Indexed: 12/04/2022] Open
Abstract
Aminoacyl-tRNA synthetases are a large family of housekeeping enzymes that are pivotal in protein translation and other vital cellular processes. Saccharomyces cerevisiae possesses two distinct nuclear glycyl-tRNA synthetase (GlyRS) genes, GRS1 and GRS2. GRS1 encodes both cytoplasmic and mitochondrial activities, while GRS2 is essentially silent and dispensable under normal conditions. We herein present evidence that expression of GRS2 was drastically induced upon heat shock, ethanol or hydrogen peroxide addition, and high pH, while expression of GRS1 was somewhat repressed under those conditions. In addition, GlyRS2 (the enzyme encoded by GRS2) had a higher protein stability and a lower KM value for yeast tRNAGly under heat shock conditions than under normal conditions. Moreover, GRS2 rescued the growth defect of a GRS1 knockout strain when highly expressed by a strong promoter at 37°C, but not at the optimal temperature of 30°C. These results suggest that GRS2 is actually an inducible gene that may function to rescue the activity of GRS1 under stress conditions.
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Affiliation(s)
| | | | | | - Chien-Chia Wang
- Department of Life Sciences, National Central University, Jung-li, Taiwan
- * E-mail:
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Jackson KE, Pham JS, Kwek M, De Silva NS, Allen SM, Goodman CD, McFadden GI, Ribas de Pouplana L, Ralph SA. Dual targeting of aminoacyl-tRNA synthetases to the apicoplast and cytosol in Plasmodium falciparum. Int J Parasitol 2012; 42:177-86. [DOI: 10.1016/j.ijpara.2011.11.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 11/16/2022]
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Chen SJ, Lee CY, Lin ST, Wang CC. Rescuing a dysfunctional homologue of a yeast glycyl-tRNA synthetase gene. ACS Chem Biol 2011; 6:1182-7. [PMID: 21877692 DOI: 10.1021/cb200240a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The yeast Saccharomyces cerevisiae contains two distinct nuclear glycyl-tRNA synthetase (GlyRS) genes, GRS1 and GRS2. GRS1 is dual functional in that possesses both cytoplasmic and mitochondrial activities, whereas GRS2 is pseudogene-like. GlyRS1 and GlyRS2 are highly similar on the whole but are distinguished by a lysine-rich insertion domain of 44 amino acid residues, present only in GlyRS1. We herein present evidence that whereas the insertion domain is dispensable for the complementary activity of GRS1in vivo, deletion of this domain from GlyRS1 reduced its aminoacylation activity by up to 9-fold. On the other hand, fusion of a constitutive ADH promoter to GRS2 failed to confer a functional phenotype to the gene, but further fusion of ARC1 (a yeast gene encoding a tRNA-binding protein, Arc1p) to this hybrid gene successfully rescued its activity. Most intriguingly, purified GlyRS2 retained a substantial level of aminoacylation activity. Fusion of Arc1p to this enzyme further enhanced its activity and stability. These findings highlight not only the structural integrity of the pseudogene-encoded enzyme but also the necessity of obtaining an auxiliary tRNA-binding domain for functioning of a yeast tRNA synthetase.
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Affiliation(s)
- Shun-Jia Chen
- Department of Life Sciences, National Central University, 300 Jung-da Rd., Jung-li 32001, Taiwan
| | - Chih-Ying Lee
- Department of Life Sciences, National Central University, 300 Jung-da Rd., Jung-li 32001, Taiwan
| | - Szu-Ting Lin
- Department of Life Sciences, National Central University, 300 Jung-da Rd., Jung-li 32001, Taiwan
| | - Chien-Chia Wang
- Department of Life Sciences, National Central University, 300 Jung-da Rd., Jung-li 32001, Taiwan
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Rettig J, Wang Y, Schneider A, Ochsenreiter T. Dual targeting of isoleucyl-tRNA synthetase in Trypanosoma brucei is mediated through alternative trans-splicing. Nucleic Acids Res 2011; 40:1299-306. [PMID: 21976735 PMCID: PMC3273800 DOI: 10.1093/nar/gkr794] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNAs with their cognate amino acids. They are an essential part of each translation system and in eukaryotes are therefore found in both the cytosol and mitochondria. Thus, eukaryotes either have two distinct genes encoding the cytosolic and mitochondrial isoforms of each of these enzymes or a single gene encoding dually localized products. Trypanosomes require trans-splicing of a cap containing leader sequence onto the 5′-untranslated region of every mRNA. Recently we speculated that alternative trans-splicing could lead to the expression of proteins having amino-termini of different lengths that derive from the same gene. We now demonstrate that alternative trans-splicing, creating a long and a short spliced variant, is the mechanism for dual localization of trypanosomal isoleucyl-tRNA synthetase (IleRS). The protein product of the longer spliced variant possesses an amino-terminal presequence and is found exclusively in mitochondria. In contrast, the shorter spliced variant is translated to a cytosol-specific isoform lacking the presequence. Furthermore, we show that RNA stability is one mechanism determining the differential abundance of the two spliced isoforms.
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Affiliation(s)
- Jochen Rettig
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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41
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Chang CP, Tseng YK, Ko CY, Wang CC. Alanyl-tRNA synthetase genes of Vanderwaltozyma polyspora arose from duplication of a dual-functional predecessor of mitochondrial origin. Nucleic Acids Res 2011; 40:314-22. [PMID: 21908394 PMCID: PMC3245939 DOI: 10.1093/nar/gkr724] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In eukaryotes, the cytoplasmic and mitochondrial forms of a given aminoacyl-tRNA synthetase (aaRS) are typically encoded by two orthologous nuclear genes, one of eukaryotic origin and the other of mitochondrial origin. We herein report a novel scenario of aaRS evolution in yeast. While all other yeast species studied possess a single nuclear gene encoding both forms of alanyl-tRNA synthetase (AlaRS), Vanderwaltozyma polyspora, a yeast species descended from the same whole-genome duplication event as Saccharomyces cerevisiae, contains two distinct nuclear AlaRS genes, one specifying the cytoplasmic form and the other its mitochondrial counterpart. The protein sequences of these two isoforms are very similar to each other. The isoforms are actively expressed in vivo and are exclusively localized in their respective cellular compartments. Despite the presence of a promising AUG initiator candidate, the gene encoding the mitochondrial form is actually initiated from upstream non-AUG codons. A phylogenetic analysis further revealed that all yeast AlaRS genes, including those in V. polyspora, are of mitochondrial origin. These findings underscore the possibility that contemporary AlaRS genes in V. polyspora arose relatively recently from duplication of a dual-functional predecessor of mitochondrial origin.
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Affiliation(s)
- Chia-Pei Chang
- Department of Life Sciences, National Central University, Jungli 32001, Taiwan
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42
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Two proteins with different functions are derived from the KlHEM13 gene. EUKARYOTIC CELL 2011; 10:1331-9. [PMID: 21821717 DOI: 10.1128/ec.05108-11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two proteins that differ at the N terminus (l-KlCpo and s-KlCpo) are derived from KlHEM13, a single-copy-number gene in the haploid genome of Kluyveromyces lactis. Two transcriptional start site (tss) pools are detectable using primer extension, and their selection is heme dependent. One of these tss pools is located 5' of the first translation initiation codon (TIC) in the open reading frame of KlHEM13, while the other is located between the first and second TICs. In terms of functional significance, only s-KlCpo complements the heme deficiency caused by the Δhem13 deletion in K. lactis. Data obtained from immune detection in subcellular fractions, directed mutagenesis, chromatin immunoprecipitation (ChIP) assays, and the functional relevance of ΔKlhem13 deletion for KlHEM13 promoter activity suggest that l-KlCpo regulates KlHEM13 transcription. A hypothetical model of the evolutionary origins and coexistence of these two proteins in K. lactis is discussed.
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Mutations in mitochondrial histidyl tRNA synthetase HARS2 cause ovarian dysgenesis and sensorineural hearing loss of Perrault syndrome. Proc Natl Acad Sci U S A 2011; 108:6543-8. [PMID: 21464306 DOI: 10.1073/pnas.1103471108] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Perrault syndrome is a genetically heterogeneous recessive disorder characterized by ovarian dysgenesis and sensorineural hearing loss. In a nonconsanguineous family with five affected siblings, linkage analysis and genomic sequencing revealed the genetic basis of Perrault syndrome to be compound heterozygosity for mutations in the mitochondrial histidyl tRNA synthetase HARS2 at two highly conserved amino acids, L200V and V368L. The nucleotide substitution creating HARS2 p.L200V also created an alternate splice leading to deletion of 12 codons from the HARS2 message. Affected family members thus carried three mutant HARS2 transcripts. Aminoacylation activity of HARS2 p.V368L and HARS2 p.L200V was reduced and the deletion mutant was not stably expressed in mammalian mitochondria. In yeast, lethality of deletion of the single essential histydyl tRNA synthetase HTS1 was fully rescued by wild-type HTS1 and by HTS1 p.L198V (orthologous to HARS2 p.L200V), partially rescued by HTS1 p.V381L (orthologous to HARS2 p.V368L), and not rescued by the deletion mutant. In Caenorhabditis elegans, reduced expression by RNAi of the single essential histydyl tRNA synthetase hars-1 severely compromised fertility. Together, these data suggest that Perrault syndrome in this family was caused by reduction of HARS2 activity. These results implicate aberrations of mitochondrial translation in mammalian gonadal dysgenesis. More generally, the relationship between HARS2 and Perrault syndrome illustrates how causality may be demonstrated for extremely rare inherited mutations in essential, highly conserved genes.
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A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J 2011; 30:882-93. [PMID: 21285948 DOI: 10.1038/emboj.2010.363] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 12/21/2010] [Indexed: 11/09/2022] Open
Abstract
The YgjD/Kae1 family (COG0533) has been on the top-10 list of universally conserved proteins of unknown function for over 5 years. It has been linked to DNA maintenance in bacteria and mitochondria and transcription regulation and telomere homeostasis in eukaryotes, but its actual function has never been found. Based on a comparative genomic and structural analysis, we predicted this family was involved in the biosynthesis of N(6)-threonylcarbamoyl adenosine, a universal modification found at position 37 of tRNAs decoding ANN codons. This was confirmed as a yeast mutant lacking Kae1 is devoid of t(6)A. t(6)A(-) strains were also used to reveal that t(6)A has a critical role in initiation codon restriction to AUG and in restricting frameshifting at tandem ANN codons. We also showed that YaeZ, a YgjD paralog, is required for YgjD function in vivo in bacteria. This work lays the foundation for understanding the pleiotropic role of this universal protein family.
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Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV. Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Res 2011; 39:4220-34. [PMID: 21266472 PMCID: PMC3105428 DOI: 10.1093/nar/gkr007] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In eukaryotes, it is generally assumed that translation initiation occurs at the AUG codon closest to the messenger RNA 5' cap. However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG, UUG, GUG, ACG, AUA and AUU. While non-AUG initiation has been experimentally verified for a handful of human genes, the full extent to which this phenomenon is utilized--both for increased coding capacity and potentially also for novel regulatory mechanisms--remains unclear. To address this issue, and hence to improve the quality of existing coding sequence annotations, we developed a methodology based on phylogenetic analysis of predicted 5' untranslated regions from orthologous genes. We use evolutionary signatures of protein-coding sequences as an indicator of translation initiation upstream of annotated coding sequences. Our search identified novel conserved potential non-AUG-initiated N-terminal extensions in 42 human genes including VANGL2, FGFR1, KCNN4, TRPV6, HDGF, CITED2, EIF4G3 and NTF3, and also affirmed the conservation of known non-AUG-initiated extensions in 17 other genes. In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data.
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Affiliation(s)
- Ivaylo P Ivanov
- BioSciences Institute, University College Cork, Cork, Ireland.
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46
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Lin CH, Lin G, Chang CP, Wang CC. A tryptophan-rich peptide acts as a transcription activation domain. BMC Mol Biol 2010; 11:85. [PMID: 21078206 PMCID: PMC2992532 DOI: 10.1186/1471-2199-11-85] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Accepted: 11/16/2010] [Indexed: 11/23/2022] Open
Abstract
Background Eukaryotic transcription activators normally consist of a sequence-specific DNA-binding domain (DBD) and a transcription activation domain (AD). While many sequence patterns and motifs have been defined for DBDs, ADs do not share easily recognizable motifs or structures. Results We report herein that the N-terminal domain of yeast valyl-tRNA synthetase can function as an AD when fused to a DNA-binding protein, LexA, and turn on reporter genes with distinct LexA-responsive promoters. The transcriptional activity was mainly attributed to a five-residue peptide, WYDWW, near the C-terminus of the N domain. Remarkably, the pentapeptide per se retained much of the transcriptional activity. Mutations which substituted tryptophan residues for both of the non-tryptophan residues in the pentapeptide (resulting in W5) significantly enhanced its activity (~1.8-fold), while mutations which substituted aromatic residues with alanine residues severely impaired its activity. Accordingly, a much more active peptide, pentatryptophan (W7), was produced, which elicited ~3-fold higher activity than that of the native pentapeptide and the N domain. Further study indicated that W7 mediates transcription activation through interacting with the general transcription factor, TFIIB. Conclusions Since W7 shares no sequence homology or features with any known transcription activators, it may represent a novel class of AD.
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Affiliation(s)
- Chen-Huan Lin
- Department of Life Science, National Central University, Jung-li 32001, Taiwan
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47
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Abstract
tRNA biology has come of age, revealing an unprecedented level of understanding and many unexpected discoveries along the way. This review highlights new findings on the diverse pathways of tRNA maturation, and on the formation and function of a number of modifications. Topics of special focus include the regulation of tRNA biosynthesis, quality control tRNA turnover mechanisms, widespread tRNA cleavage pathways activated in response to stress and other growth conditions, emerging evidence of signaling pathways involving tRNA and cleavage fragments, and the sophisticated intracellular tRNA trafficking that occurs during and after biosynthesis.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA.
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48
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Montanari A, De Luca C, Frontali L, Francisci S. Aminoacyl-tRNA synthetases are multivalent suppressors of defects due to human equivalent mutations in yeast mt tRNA genes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:1050-7. [DOI: 10.1016/j.bbamcr.2010.05.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 04/22/2010] [Accepted: 05/05/2010] [Indexed: 12/01/2022]
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49
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Yogev O, Pines O. Dual targeting of mitochondrial proteins: mechanism, regulation and function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:1012-20. [PMID: 20637721 DOI: 10.1016/j.bbamem.2010.07.004] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Revised: 07/04/2010] [Accepted: 07/07/2010] [Indexed: 01/25/2023]
Abstract
One solution found in evolution to increase the number of cellular functions, without increasing the number of genes, is distribution of single gene products to more than one cellular compartment. It is well documented that in eukaryotic cells, molecules of one protein can be located in several subcellular locations, a phenomenon termed dual targeting, dual localization, or dual distribution. The differently localized proteins are coined in this review "echoforms" indicating repetitious forms of the same protein (echo in Greek denotes repetition) distinctly placed in the cell. This term replaces the term to "isoproteins" or "isoenzymes" which are reserved for proteins with the same activity but different amino acid sequences. Echoforms are identical or nearly identical, even though, as referred to in this review may, in some cases, surprisingly have a totally different function in the different compartments. With regard to mitochondria, our operational definition of dual targeted proteins refers to situations in which one of the echoforms is translocated through/into a mitochondrial membrane. In this review we ask how, when and why mitochondrial proteins are dual localized in the cell. We describe mechanisms of dual targeting of proteins between mitochondria and other compartments of the eukaryotic cell. In particular, we have paid attention to situations in which dual localization is regulated in time, location or function. In addition, we have attempted to provide a broader view concerning the phenomenon of dual localization of proteins by looking at mechanisms that are beyond our simple definition of dual targeting. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
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Affiliation(s)
- Ohad Yogev
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
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50
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Chang CP, Chen SJ, Lin CH, Wang TL, Wang CC. A single sequence context cannot satisfy all non-AUG initiator codons in yeast. BMC Microbiol 2010; 10:188. [PMID: 20618922 PMCID: PMC2909995 DOI: 10.1186/1471-2180-10-188] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Accepted: 07/09/2010] [Indexed: 11/17/2022] Open
Abstract
Background Previous studies in Saccharomyces cerevisiae showed that ALA1 (encoding alanyl-tRNA synthetase) and GRS1 (encoding glycyl-tRNA synthetase) respectively use ACG and TTG as their alternative translation initiator codons. To explore if any other non-ATG triplets can act as initiator codons in yeast, ALA1 was used as a reporter for screening. Results We show herein that except for AAG and AGG, all triplets that differ from ATG by a single nucleotide were able to serve as initiator codons in ALA1. Among these initiator codons, TTG, CTG, ACG, and ATT had ~50% initiating activities relative to that of ATG, while GTG, ATA, and ATC had ~20% initiating activities relative to that of ATG. Unexpectedly, these non-AUG initiator codons exhibited different preferences toward various sequence contexts. In particular, GTG was one of the most efficient non-ATG initiator codons, while ATA was essentially inactive in the context of GRS1. Conclusion This finding indicates that a sequence context that is favorable for a given non-ATG initiator codon might not be as favorable for another.
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Affiliation(s)
- Chia-Pei Chang
- Department of Life Science, National Central University, Jung-li, Taiwan
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