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Peng G, He Y, Wang M, Ashraf MF, Liu Z, Zhuang C, Zhou H. The structural characteristics and the substrate recognition properties of RNase Z S1. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:83-90. [PMID: 33302124 DOI: 10.1016/j.plaphy.2020.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
TMS5 encodes an RNase ZS1 protein that can process ubiquitin-60S ribosomal protein L40 family (UbL40) mRNAs to regulate thermo-sensitive genic male sterility in rice. Despite the importance of this protein, the structural characteristics and substrate recognition properties of RNase ZS1 remain unclear. Here, we found that the variations in several conservative amino acids alter the activation of RNase ZS1, and its recognition of RNA substrates depends on the structure of RNA. RNase ZS1 acts as a homodimer. The conserved amino acids in or adjacent to enzyme center play a critical role in the enzyme activity of RNase ZS1 and the conserved amino acids that far from active center have little impact on its enzyme activity. The cleavage efficiency of RNase ZS1 for pre-tRNA-MetCAU35 and UbL401 mRNA with cloverleaf-like structure was higher than that of pre-tRNA-AspAUC9 and UbL404 mRNA with imperfect cloverleaf-like structure. This difference implies that the enzyme activity of RNase ZS1 depends on the cloverleaf-like structure of the RNA. Furthermore, the RNase ZS1 activity was not inhibited by the 5' leader sequence and 3' CCA motif of pre-tRNA. These findings provide new insights for studying the cleavage characteristics and substrate recognition properties of RNase ZS.
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Affiliation(s)
- Guoqing Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Ying He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Mumei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Muhammad Furqan Ashraf
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China.
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Saoura M, Powell CA, Kopajtich R, Alahmad A, AL‐Balool HH, Albash B, Alfadhel M, Alston CL, Bertini E, Bonnen PE, Bratkovic D, Carrozzo R, Donati MA, Di Nottia M, Ghezzi D, Goldstein A, Haan E, Horvath R, Hughes J, Invernizzi F, Lamantea E, Lucas B, Pinnock K, Pujantell M, Rahman S, Rebelo‐Guiomar P, Santra S, Verrigni D, McFarland R, Prokisch H, Taylor RW, Levinger L, Minczuk M. Mutations in ELAC2 associated with hypertrophic cardiomyopathy impair mitochondrial tRNA 3'-end processing. Hum Mutat 2019; 40:1731-1748. [PMID: 31045291 PMCID: PMC6764886 DOI: 10.1002/humu.23777] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 04/09/2019] [Accepted: 04/29/2019] [Indexed: 12/16/2022]
Abstract
Mutations in either the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA metabolism, including ELAC2. The ELAC2 gene codes for the mitochondrial RNase Z, responsible for endonucleolytic cleavage of the 3' ends of mitochondrial pre-tRNAs. Here, we report the identification of 16 novel ELAC2 variants in individuals presenting with mitochondrial respiratory chain deficiency, hypertrophic cardiomyopathy (HCM), and lactic acidosis. We provide evidence for the pathogenicity of the novel missense variants by studying the RNase Z activity in an in vitro system. We also modeled the residues affected by a missense mutation in solved RNase Z structures, providing insight into enzyme structure and function. Finally, we show that primary fibroblasts from the affected individuals have elevated levels of unprocessed mitochondrial RNA precursors. Our study thus broadly confirms the correlation of ELAC2 variants with severe infantile-onset forms of HCM and mitochondrial respiratory chain dysfunction. One rare missense variant associated with the occurrence of prostate cancer (p.Arg781His) impairs the mitochondrial RNase Z activity of ELAC2, suggesting a functional link between tumorigenesis and mitochondrial RNA metabolism.
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Affiliation(s)
| | | | - Robert Kopajtich
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsTechnische Universität MünchenMunichGermany
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Ahmad Alahmad
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- Kuwait Medical Genetics CenterKuwait CityKuwait
| | | | | | - Majid Alfadhel
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research CentreKing Saud bin Abdulaziz University for Health SciencesRiyadhSaudi Arabia
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Enrico Bertini
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Penelope E. Bonnen
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Drago Bratkovic
- Metabolic ClinicWomen's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Rosalba Carrozzo
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | | | - Michela Di Nottia
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Daniele Ghezzi
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
- Department of Pathophysiology and TransplantationUniversity of MilanMilanItaly
| | - Amy Goldstein
- Mitochondrial Medicine Frontier ProgramChildren's Hospital of PhiladelphiaPhiladelphiaUSA
| | - Eric Haan
- Metabolic ClinicWomen's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Rita Horvath
- Wellcome Centre for Mitochondrial Research, Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUK
| | - Joanne Hughes
- National Centre for Inherited Metabolic DisordersTemple Street Children's University HospitalDublinIreland
| | - Federica Invernizzi
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Eleonora Lamantea
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Benjamin Lucas
- York CollegeThe City University of New YorkJamaicaNew York
| | | | | | - Shamima Rahman
- Mitochondrial Research GroupUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Pedro Rebelo‐Guiomar
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
- Graduate Program in Areas of Basic and Applied BiologyUniversity of PortoPortoPortugal
| | - Saikat Santra
- Department of Clinical Inherited Metabolic DisordersBirmingham Children's HospitalBirminghamUK
| | - Daniela Verrigni
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Robert McFarland
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Holger Prokisch
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsTechnische Universität MünchenMunichGermany
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Louis Levinger
- York CollegeThe City University of New YorkJamaicaNew York
| | - Michal Minczuk
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
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Shang J, Wu L, Yang Y, Li Y, Liu Z, Huang Y. Overexpression of Schizosaccharomyces pombe tRNA 3′-end processing enzyme Trz2 leads to an increased cellular iron level and apoptotic cell death. Fungal Genet Biol 2019; 122:11-20. [DOI: 10.1016/j.fgb.2018.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 10/10/2018] [Accepted: 10/23/2018] [Indexed: 01/18/2023]
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Saoura M, Pinnock K, Pujantell-Graell M, Levinger L. Substitutions in conserved regions preceding and within the linker affect activity and flexibility of tRNase ZL, the long form of tRNase Z. PLoS One 2017; 12:e0186277. [PMID: 29045449 PMCID: PMC5646807 DOI: 10.1371/journal.pone.0186277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/28/2017] [Indexed: 11/19/2022] Open
Abstract
The enzyme tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes 3' trailers from precursor tRNAs, preparing them for CCA addition and aminoacylation. The short form of tRNase Z, tRNase ZS, functions as a homodimer and is found in all prokaryotes and some eukaryotes. The long form, tRNase ZL, related to tRNase ZS through tandem duplication and found only in eukaryotes, possesses ~2,000-fold greater catalytic efficiency than tRNase ZS. tRNase ZL consists of related but diverged amino and carboxy domains connected by a flexible linker (also referred to as a flexible tether) and functions as a monomer. The amino domain retains the flexible arm responsible for substrate recognition and binding while the carboxy domain retains the active site. The linker region was explored by Ala-scanning through two conserved regions of D. melanogaster tRNase Z: NdomTprox, located at the carboxy end of the amino domain proximal to the linker, and Tflex, a flexible site in the linker. Periodic substitutions in a hydrophobic patch (F329 and L332) at the carboxy end of NdomTprox show 2,700 and 670-fold impairment relative to wild type, respectively, accompanied by reduced linker flexibility at N-T inside the Ndom- linker boundary. The Ala substitution for N378 in the Tflex region has 10-fold higher catalytic efficiency than wild type and locally decreased flexibility, while the Ala substitution at R382 reduces catalytic efficiency ~50-fold. These changes in pre-tRNA processing kinetics and protein flexibility are interpreted in light of a recent crystal structure for S. cerevisiae tRNase Z, suggesting transmission of local changes in hydrophobicity into the skeleton of the amino domain.
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Affiliation(s)
- Makenzie Saoura
- York College of The City University of New York, Jamaica, New York, United States of America
| | - Kyla Pinnock
- York College of The City University of New York, Jamaica, New York, United States of America
| | - Maria Pujantell-Graell
- York College of The City University of New York, Jamaica, New York, United States of America
| | - Louis Levinger
- York College of The City University of New York, Jamaica, New York, United States of America
- * E-mail:
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5
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Wilson C, Ramai D, Serjanov D, Lama N, Levinger L, Chang EJ. Tethered domains and flexible regions in tRNase Z(L), the long form of tRNase Z. PLoS One 2013; 8:e66942. [PMID: 23874404 PMCID: PMC3714273 DOI: 10.1371/journal.pone.0066942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/13/2013] [Indexed: 11/30/2022] Open
Abstract
tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes the pre-tRNA 3′ trailer in a step central to tRNA maturation. The short form (tRNase ZS) is the only one found in bacteria and archaebacteria and is also present in some eukaryotes. The homologous long form (tRNase ZL), exclusively found in eukaryotes, consists of related amino- and carboxy-domains, suggesting that tRNase ZL arose from a tandem duplication of tRNase ZS followed by interdependent divergence of the domains. X-ray crystallographic structures of tRNase ZS reveal a flexible arm (FA) extruded from the body of tRNase Z remote from the active site that binds tRNA far from the scissile bond. No tRNase ZL structures have been solved; alternative biophysical studies are therefore needed to illuminate its functional characteristics. Structural analyses of tRNase ZL performed by limited proteolysis, two dimensional gel electrophoresis and mass spectrometry establish stability of the amino and carboxy domains and flexibility of the FA and inter-domain tether, with implications for tRNase ZL function.
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Affiliation(s)
- Christopher Wilson
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Daryl Ramai
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
| | - Dmitri Serjanov
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Neema Lama
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
| | - Louis Levinger
- Department of Biology, York College of The City University of New York, Jamaica, New York, United States of America
| | - Emmanuel J. Chang
- Department of Chemistry, York College of The City University of New York, Jamaica, New York, United States of America
- * E-mail:
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He SM, Wathier M, Podzelinska K, Wong M, McSorley FR, Asfaw A, Hove-Jensen B, Jia Z, Zechel DL. Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway. Biochemistry 2011; 50:8603-15. [PMID: 21830807 DOI: 10.1021/bi2005398] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PhnP is a phosphodiesterase that plays an important role within the bacterial carbon-phosphorus lyase (CP-lyase) pathway by recycling a "dead-end" intermediate, 5-phospho-α-d-ribosyl 1,2-cyclic phosphate, that is formed during organophosphonate catabolism. As a member of the metallo-β-lactamase superfamily, PhnP is most homologous in sequence and structure to tRNase Z phosphodiesterases. X-ray structural analysis of PhnP complexed with orthovanadate to 1.5 Å resolution revealed this inhibitor bound in a tetrahedral geometry by the two catalytic manganese ions and the putative general acid residue H200. Guided by this structure, we probed the contributions of first- and second-sphere active site residues to catalysis and metal ion binding by site-directed mutagenesis, kinetic analysis, and ICP-MS. Alteration of H200 to alanine resulted in a 6-33-fold decrease in k(cat)/K(M) with substituted methyl phenylphosphate diesters with leaving group pK(a) values ranging from 4 to 8.4. With bis(p-nitrophenyl)phosphate as a substrate, there was a 10-fold decrease in k(cat)/K(M), primarily the result of a large increase in K(M). Moreover, the nickel ion-activated H200A PhnP displayed a bell-shaped pH dependence for k(cat)/K(M) with pK(a) values (pK(a1) = 6.3; pK(a2) = 7.8) that were comparable to those of the wild-type enzyme (pK(a1) = 6.5; pK(a2) = 7.8). Such modest effects are counter to what is expected for a general acid catalyst and suggest an alternate role for H200 in this enzyme. A Brønsted analysis of the PhnP reaction with a series of substituted phenyl methyl phosphate esters yielded a linear correlation, a β(lg) of -1.06 ± 0.1, and a Leffler α value of 0.61, consistent with a synchronous transition state for phosphoryl transfer. On the basis of these data, we propose a mechanism for PhnP.
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Affiliation(s)
- Shu-Mei He
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
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7
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Fan L, Wang Z, Liu J, Guo W, Yan J, Huang Y. A survey of green plant tRNA 3'-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2. BMC Evol Biol 2011; 11:219. [PMID: 21781332 PMCID: PMC3161902 DOI: 10.1186/1471-2148-11-219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Accepted: 07/23/2011] [Indexed: 11/10/2022] Open
Abstract
Background tRNase Z removes the 3'-trailer sequences from precursor tRNAs, which is an essential step preceding the addition of the CCA sequence. tRNase Z exists in the short (tRNase ZS) and long (tRNase ZL) forms. Based on the sequence characteristics, they can be divided into two major types: bacterial-type tRNase ZS and eukaryotic-type tRNase ZL, and one minor type, Thermotoga maritima (TM)-type tRNase ZS. The number of tRNase Zs is highly variable, with the largest number being identified experimentally in the flowering plant Arabidopsis thaliana. It is unknown whether multiple tRNase Zs found in A. thaliana is common to the plant kingdom. Also unknown is the extent of sequence and structural conservation among tRNase Zs from the plant kingdom. Results We report the identification and analysis of candidate tRNase Zs in 27 fully sequenced genomes of green plants, the great majority of which are flowering plants. It appears that green plants contain multiple distinct tRNase Zs predicted to reside in different subcellular compartments. Furthermore, while the bacterial-type tRNase ZSs are present only in basal land plants and green algae, the TM-type tRNase ZSs are widespread in green plants. The protein sequences of the TM-type tRNase ZSs identified in green plants are similar to those of the bacterial-type tRNase ZSs but have distinct features, including the TM-type flexible arm, the variant catalytic HEAT and HST motifs, and a lack of the PxKxRN motif involved in CCA anti-determination (inhibition of tRNase Z activity by CCA), which prevents tRNase Z cleavage of mature tRNAs. Examination of flowering plant chloroplast tRNA genes reveals that many of these genes encode partial CCA sequences. Based on our results and previous studies, we predict that the plant TM-type tRNase ZSs may not recognize the CCA sequence as an anti-determinant. Conclusions Our findings substantially expand the current repertoire of the TM-type tRNase ZSs and hint at the possibility that these proteins may have been selected for their ability to process chloroplast pre-tRNAs with whole or partial CCA sequences. Our results also support the coevolution of tRNase Zs and tRNA 3'-trailer sequences in plants.
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Affiliation(s)
- Lijuan Fan
- Laboratory of Yeast Genetics and Molecular Biology, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
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Functional conservation of tRNase ZL among Saccharomyces cerevisiae, Schizosaccharomyces pombe and humans. Biochem J 2009; 422:483-92. [PMID: 19555350 DOI: 10.1042/bj20090743] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Although tRNase Z from various organisms was shown to process nuclear tRNA 3' ends in vitro, only a very limited number of studies have reported its in vivo biological functions. tRNase Z is present in a short form, tRNase Z(S), and a long form, tRNase Z(L). Unlike Saccharomyces cerevisiae, which contains one tRNase Z(L) gene (scTRZ1) and humans, which contain one tRNase Z(L) encoded by the prostate-cancer susceptibility gene ELAC2 and one tRNase Z(S), Schizosaccharomyces pombe contains two tRNase Z(L) genes, designated sptrz1(+) and sptrz2(+). We report that both sptrz1(+) and sptrz2(+) are essential for growth. Moreover, sptrz1(+) is required for cell viability in the absence of Sla1p, which is thought to be required for endonuclease-mediated maturation of pre-tRNA 3' ends in yeast. Both scTRZ1 and ELAC2 can complement a temperature-sensitive allele of sptrz1(+), sptrz1-1, but not the sptrz1 null mutant, indicating that despite exhibiting species specificity, tRNase Z(L)s are functionally conserved among S. cerevisiae, S. pombe and humans. Overexpression of sptrz1(+), scTRZ1 and ELAC2 can increase suppression of the UGA nonsense mutation ade6-704 through facilitating 3' end processing of the defective suppressor tRNA that mediates suppression. Our findings reveal that 3' end processing is a limiting step for defective tRNA maturation and demonstrate that overexpression of sptrz1(+), scTRZ1 and ELAC2 can promote defective tRNA 3' processing in vivo. Our results also support the notion that yeast tRNase Z(L) is absolutely required for 3' end processing of at least a few pre-tRNAs even in the absence of Sla1p.
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Liao RZ, Himo F, Yu JG, Liu RZ. Theoretical Study of the RNA Hydrolysis Mechanism of the Dinuclear Zinc Enzyme RNase Z. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900202] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Levinger L, Hopkinson A, Desetty R, Wilson C. Effect of changes in the flexible arm on tRNase Z processing kinetics. J Biol Chem 2009; 284:15685-91. [PMID: 19351879 DOI: 10.1074/jbc.m900745200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
tRNAs are transcribed as precursors and processed in a series of reactions culminating in aminoacylation and translation. Central to tRNA maturation, the 3' end trailer can be endonucleolytically removed by tRNase Z. A flexible arm (FA) extruded from the body of tRNase Z consists of a structured alphaalphabetabeta hand that binds the elbow of pre-tRNA. Deleting the FA hand causes an almost 100-fold increase in Km with little change in kcat, establishing its contribution to substrate recognition/binding. Remarkably, a 40-residue Ala scan through the FA hand reveals a conserved leucine at the ascending stalk/hand boundary that causes practically the same increase in Km as the hand deletion, thus nearly eliminating its ability to bind substrate. Km also increases with substitutions in the GP (alpha4-alpha5) loop and at other conserved residues in the FA hand predicted to contact substrate based on the co-crystal structure. Substitutions that reduce kcat are clustered in the beta10-beta11 loop.
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Affiliation(s)
- Louis Levinger
- Department of Biology, York College of the City University of New York, Jamaica, New York 11451, USA.
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11
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Takaku H, Nashimoto M. Escherichia coli tRNase Z can shut down growth probably by removing amino acids from aminoacyl-tRNAs. Genes Cells 2009; 13:1087-97. [PMID: 18823332 DOI: 10.1111/j.1365-2443.2008.01230.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In most organisms, tRNase Z is considered to be essential for 3' processing of tRNA molecules. The Escherichia coli tRNase Z gene, however, appears to be dispensable under normal growth conditions, and its existence remained an enigma. Here we intensively examined various (pre-)tRNAs for good substrates of E. coli tRNase Z in vitro, and found that the enzyme can remove the 3' terminal CCA residues from mature tRNAs regardless of their nucleotide modifications. Furthermore, we discovered that E. coli tRNase Z, when sufficiently expressed in the cell, can shut down growth probably by removing amino acids from aminoacyl-tRNAs. We confirmed in vitro that E. coli tRNase Z exceptionally possesses the activity that cleaves off the 3' terminal residues charging an amino acid from an aminoacyl-tRNA molecule. The current data suggest that tRNase Z might help modulate a cell growth rate by repressing translation under some stressful conditions.
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Affiliation(s)
- Hiroaki Takaku
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan
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12
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Hartmann RK, Gössringer M, Späth B, Fischer S, Marchfelder A. The making of tRNAs and more - RNase P and tRNase Z. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:319-68. [PMID: 19215776 DOI: 10.1016/s0079-6603(08)00808-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transfer-RNA (tRNA) molecules are essential players in protein biosynthesis. They are transcribed as precursors, which have to be extensively processed at both ends to become functional adaptors in protein synthesis. Two endonucleases that directly interact with the tRNA moiety, RNase P and tRNase Z, remove extraneous nucleotides on the molecule's 5'- and 3'-side, respectively. The ribonucleoprotein enzyme RNase P was identified almost 40 years ago and is considered a vestige from the "RNA world". Here, we present the state of affairs on prokaryotic RNase P, with a focus on recent findings on its role in RNA metabolism. tRNase Z was only identified 6 years ago, and we do not yet have a comprehensive understanding of its function. The current knowledge on prokaryotic tRNase Z in tRNA 3'-processing is reviewed here. A second, tRNase Z-independent pathway of tRNA 3'-end maturation involving 3'-exonucleases will also be discussed.
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Affiliation(s)
- Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany
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13
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Elbarbary RA, Takaku H, Nashimoto M. Functional analyses for tRNase Z variants: an aspartate and a histidine in the active site are essential for the catalytic activity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:2079-85. [PMID: 18809514 DOI: 10.1016/j.bbapap.2008.08.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2008] [Revised: 08/22/2008] [Accepted: 08/25/2008] [Indexed: 10/21/2022]
Abstract
We performed functional analyses for various single amino-acid substitution variants of Escherichia coli, Bacillus subtilis, and human tRNase Zs. The well-conserved six histidine, His(I)-His(VI), and two aspartate, Asp(I) and Asp(II), residues together with metal ions are thought to form the active site of tRNase Z. The Mn(2+)-rescue analysis for Thermotoga maritima tRNase Z(S) has suggested that Asp(I) and His(V) directly contribute the proton transfer for the catalysis, and a catalytic mechanism has been proposed. However, experimental evidence supporting the proposed mechanism was limited. Here we intensively examined E. coli and B. subtilis tRNase Z(S) variants and human tRNase Z(L) variants for cleavage activities on pre-tRNAs in the presence of Mg(2+) or Mn(2+) ions. We observed that the Mn(2+) ions cannot rescue the activities of Asp(I)Ala and His(V)Ala variants from each species, which are lost in the presence of Mg(2+). This observation may support the proposed catalytic mechanism.
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Affiliation(s)
- Reyad A Elbarbary
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata 956-8603, Japan
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14
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Takahashi M, Takaku H, Nashimoto M. Regulation of the human tRNase ZSgene expression. FEBS Lett 2008; 582:2532-6. [DOI: 10.1016/j.febslet.2008.06.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Revised: 05/11/2008] [Accepted: 06/13/2008] [Indexed: 10/21/2022]
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15
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Minagawa A, Ishii R, Takaku H, Yokoyama S, Nashimoto M. The flexible arm of tRNase Z is not essential for pre-tRNA binding but affects cleavage site selection. J Mol Biol 2008; 381:289-99. [PMID: 18602113 DOI: 10.1016/j.jmb.2008.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2007] [Revised: 05/02/2008] [Accepted: 05/08/2008] [Indexed: 10/22/2022]
Abstract
tRNase Z is an enzyme responsible for removing a 3' trailer from pre-tRNA. Although most tRNase Zs cleave pre-tRNAs immediately after the discriminator nucleotide with the exception of Thermotoga maritima tRNase Z, which cleaves after the (74)CCA(76) sequence, our knowledge was limited about how the cleavage site in pre-tRNA is selected. Bacterial tRNase Zs contain a unique domain termed flexible arm, which extends from the core domain. Using various tRNase Z variants, here we examined how the flexible arm affects the cleavage site selection. T. maritima tRNase Z variants with modified flexible arms shifted the cleavage site and a Bacillus subtilis tRNase Z variant with no flexible arm showed an anomalous cleavage activity. Some of the T. maritima/B. subtilis chimeric enzymes had both properties: they recognized (74)CCA(76)-containing pre-tRNA and cleaved it after the discriminator. Taken together, the present data indicate that the flexible arm is not essential for pre-tRNA binding but affects the cleavage site selection probably by pushing the distal region of the T arm in such a way that the discriminator nucleotide becomes closer to the catalytic site.
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Affiliation(s)
- Asako Minagawa
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan
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16
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Karkashon S, Hopkinson A, Levinger L. tRNase Z catalysis and conserved residues on the carboxy side of the His cluster. Biochemistry 2007; 46:9380-7. [PMID: 17655328 PMCID: PMC2526284 DOI: 10.1021/bi700578v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
tRNAs are transcribed as precursors and processed in a series of required reactions leading to aminoacylation and translation. The 3'-end trailer can be removed by the pre-tRNA processing endonuclease tRNase Z, an ancient, conserved member of the beta-lactamase superfamily of metal-dependent hydrolases. The signature sequence of this family, the His domain (HxHxDH, Motif II), and histidines in Motifs III and V and aspartate in Motif IV contribute seven side chains for the coordination of two divalent metal ions. We previously investigated the effects on catalysis of substitutions in Motif II and in the PxKxRN loop and Motif I on the amino side of Motif II. Herein, we present the effects of substitutions on the carboxy side of Motif II within Motifs III, IV, the HEAT and HST loops, and Motif V. Substitution of the Motif IV aspartate reduces catalytic efficiency more than 10,000-fold. Histidines in Motif III, V, and the HST loop are also functionally important. Strikingly, replacement of Glu in the HEAT loop with Ala reduces efficiency by approximately 1000-fold. Proximity and orientation of this Glu side chain relative to His in the HST loop and the importance of both residues for catalysis suggest that they function as a duo in proton transfer at the final stage of reaction, characteristic of the tRNase Z class of RNA endonucleases.
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Affiliation(s)
| | | | - Louis Levinger
- *to whom correspondence should be addressed: Phone: 718-262-2704 FAX: 718-262-2652
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17
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Dominski Z. Nucleases of the metallo-beta-lactamase family and their role in DNA and RNA metabolism. Crit Rev Biochem Mol Biol 2007; 42:67-93. [PMID: 17453916 DOI: 10.1080/10409230701279118] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Proteins of the metallo-beta-lactamase family with either demonstrated or predicted nuclease activity have been identified in a number of organisms ranging from bacteria to humans and has been shown to be important constituents of cellular metabolism. Nucleases of this family are believed to utilize a zinc-dependent mechanism in catalysis and function as 5' to 3' exonucleases and or endonucleases in such processes as 3' end processing of RNA precursors, DNA repair, V(D)J recombination, and telomere maintenance. Examples of metallo-beta-lactamase nucleases include CPSF-73, a known component of the cleavage/polyadenylation machinery, which functions as the endonuclease in 3' end formation of both polyadenylated and histone mRNAs, and Artemis that opens DNA hairpins during V(D)J recombination. Mutations in two metallo-beta-lactamase nucleases have been implicated in human diseases: tRNase Z required for 3' processing of tRNA precursors has been linked to the familial form of prostate cancer, whereas inactivation of Artemis causes severe combined immunodeficiency (SCID). There is also a group of as yet uncharacterized proteins of this family in bacteria and archaea that based on sequence similarity to CPSF-73 are predicted to function as nucleases in RNA metabolism. This article reviews the cellular roles of nucleases of the metallo-beta-lactamase family and the recent advances in studying these proteins.
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Affiliation(s)
- Zbigniew Dominski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
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18
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Nakashima A, Takaku H, Shibata HS, Negishi Y, Takagi M, Tamura M, Nashimoto M. Gene silencing by the tRNA maturase tRNase ZL under the direction of small-guide RNA. Gene Ther 2007; 14:78-85. [PMID: 16885998 DOI: 10.1038/sj.gt.3302841] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Revised: 05/30/2006] [Accepted: 06/28/2006] [Indexed: 11/08/2022]
Abstract
We have been developing a unique system for the downregulation of a gene expression through cutting a specific mRNA by the long form of tRNA 3'-processing endoribonuclease (tRNase Z(L)) under the direction of small-guide RNA (sgRNA). However, the efficacy of this system and the involvement of tRNase Z(L) in the living cells were not clear. Here we show, by targeting the exogenous luciferase gene, that the efficacy of the sgRNA/tRNase Z(L) method can become comparable to that of the RNA interference technology and that the gene silencing is owing to tRNase Z(L) directed by sgRNA not owing to a simple antisense effect. We also show that tRNase Z(L) together with sgRNA can downregulate expression of the endogenous human genes Bcl-2 and glycogen synthase kinase-3beta by degrading their mRNAs in cell culture. Furthermore, we demonstrate that a gene expression in the livers of postnatal mice can be inhibited by an only seven-nucleotide sgRNA. These data suggest that sgRNA might be utilized as therapeutic agents to treat diseases such as cancers and AIDS.
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Affiliation(s)
- A Nakashima
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, Japan
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19
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Minagawa A, Takaku H, Ishii R, Takagi M, Yokoyama S, Nashimoto M. Identification by Mn2+ rescue of two residues essential for the proton transfer of tRNase Z catalysis. Nucleic Acids Res 2006; 34:3811-8. [PMID: 16916792 PMCID: PMC1540738 DOI: 10.1093/nar/gkl517] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Thermotoga maritima tRNase Z cleaves pre-tRNAs containing the 74CCA76 sequence precisely after the A76 residue to create the mature 3' termini. Its crystal structure has revealed a four-layer alphabeta/betaalpha sandwich fold that is typically found in the metallo-beta-lactamase superfamily. The well-conserved six histidine and two aspartate residues together with metal ions are assumed to form the tRNase Z catalytic center. Here, we examined tRNase Z variants containing single amino acid substitutions in the catalytic center for pre-tRNA cleavage. Cleavage by each variant in the presence of Mg2+ was hardly detected, although it is bound to pre-tRNA. Surprisingly, however, Mn2+ ions restored the lost Mg2+-dependent activity with two exceptions of the Asp52Ala and His222Ala substitutions, which abolished the activity almost completely. These results provide a piece of evidence that Asp-52 and His-222 directly contribute the proton transfer for the catalysis.
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Affiliation(s)
| | | | - Ryohei Ishii
- RIKEN Genomic Sciences CenterTsurumi, Yokohama 230-0045, Japan
| | | | - Shigeyuki Yokoyama
- RIKEN Genomic Sciences CenterTsurumi, Yokohama 230-0045, Japan
- RIKEN Harima Institute at SPring-8Sayo-gun, Hyogo 679-5148, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of TokyoBunkyo-ku, Tokyo 113-0033, Japan
| | - Masayuki Nashimoto
- To whom correspondence should be addressed. Tel: +81 250 25 5119; Fax: +81 250 25 5021;
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20
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Vogel A, Schilling O, Späth B, Marchfelder A. The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties. Biol Chem 2006; 386:1253-64. [PMID: 16336119 DOI: 10.1515/bc.2005.142] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
tRNase Z is the endoribonuclease that generates the mature 3'-end of tRNA molecules by removal of the 3'-trailer elements of precursor tRNAs. This enzyme has been characterized from representatives of all three domains of life (Bacteria, Archaea and Eukarya), as well as from mitochondria and chloroplasts. tRNase Z enzymes come in two forms: short versions (280-360 amino acids in length), present in all three kingdoms, and long versions (750-930 amino acids), present only in eukaryotes. The recently solved crystal structure of the bacterial tRNase Z provides the structural basis for the understanding of central functional elements. The substrate is recognized by an exosite that protrudes from the main protein body and consists of a metallo-beta-lactamase domain. Cleavage of the precursor tRNA occurs at the binuclear zinc site located in the other subunit of the functional homodimer. The first gene of the tRNase Z family was cloned in 2002. Since then a comprehensive set of data has been acquired concerning this new enzyme, including detailed functional studies on purified recombinant enzymes, mutagenesis studies and finally the determination of the crystal structure of three bacterial enzymes. This review summarizes the current knowledge about these exciting enzymes.
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Affiliation(s)
- Andreas Vogel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim, Germany
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21
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Shibata HS, Minagawa A, Takaku H, Takagi M, Nashimoto M. Unstructured RNA is a substrate for tRNase Z. Biochemistry 2006; 45:5486-92. [PMID: 16634630 DOI: 10.1021/bi051972s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
tRNase Z, which exists in almost all cells, is believed to be working primarily for tRNA 3' maturation. In Escherichia coli, however, the tRNase Z gene appears to be dispensable under normal growth conditions, and its physiological role is not clear. Here, to investigate a possibility that E. coli tRNase Z cleaves RNAs other than pre-tRNAs, we tested several unstructured RNAs for cleavage. Surprisingly, all these substrates were cleaved very efficiently at multiple sites by a recombinant E. coli enzyme in vitro. tRNase Zs from Bacillus subtilis and Thermotoga maritima also cleaved various unstructured RNAs. The E. coli and B. subtilis enzymes seem to have a tendency to cleave after cytidine or before uridine, while cleavage by the T. maritima enzyme inevitably occurred after CCA in addition to the other cleavages. Assays to determine optimal conditions indicated that metal ion requirements differ between B. subtilis and T. maritima tRNase Zs. There was no significant difference in the observed rate constant between unstructured RNA and pre-tRNA substrates, while the K(d) value of a tRNase Z/unstructured RNA complex was much higher than that of an enzyme/pre-tRNA complex. Furthermore, eukaryotic tRNase Zs from yeast, pig, and human cleaved unstructured RNA at multiple sites, but an archaeal tRNase Z from Pyrobaculum aerophilum did not.
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Affiliation(s)
- Hirotaka S Shibata
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata 956-8603, Japan
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22
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Zareen N, Hopkinson A, Levinger L. Residues in two homology blocks on the amino side of the tRNase Z His domain contribute unexpectedly to pre-tRNA 3' end processing. RNA (NEW YORK, N.Y.) 2006; 12:1104-15. [PMID: 16618969 PMCID: PMC1464858 DOI: 10.1261/rna.4206] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
tRNase Z, which can endonucleolytically remove pre-tRNA 3'-end trailers, possesses the signature His domain (HxHxDH; Motif II) of the beta-lactamase family of metal-dependent hydrolases. Motif II combines with Motifs III-V on its carboxy side to coordinate two divalent metal ions, constituting the catalytic core. The PxKxRN loop and Motif I on the amino side of Motif II have been suggested to modulate tRNase Z activity, including the anti-determinant effect of CCA in mature tRNA. Ala walks through these two homology blocks reveal residues in which the substitutions unexpectedly reduce catalytic efficiency. While substitutions in Motif II can drastically affect k(cat) without affecting k(M), five- to 15-fold increases in k(M) are observed with substitutions in several conserved residues in the PxKxRN loop and Motif I. These increases in k(M) suggest a model for substrate binding. Expressed tRNase Z processes mature tRNA with CCA at the 3' end approximately 80 times less efficiently than a pre-tRNA possessing natural sequence of the 3'-end trailer, due to reduced k(cat) with no effect on k(M), showing the CCA anti-determinant to be a characteristic of this enzyme.
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Affiliation(s)
- Neela Zareen
- York College of The City University of New York, Jamaica, 11451, USA
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23
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Minagawa A, Takaku H, Shibata HS, Ishii R, Takagi M, Yokoyama S, Nashimoto M. Substrate recognition ability differs among various prokaryotic tRNase Zs. Biochem Biophys Res Commun 2006; 345:385-93. [PMID: 16681995 DOI: 10.1016/j.bbrc.2006.04.105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 04/18/2006] [Indexed: 11/20/2022]
Abstract
There exists a significant difference in pre-tRNA preference among prokaryotic tRNase Zs. This is an enigma, because pre-tRNAs should form the common L-shaped structure and tRNase Zs should form the common structure based on the alphabeta/betaalpha-fold. To address this issue, we examined six different eubacterial and archaeal tRNase Zs including two newly isolated tRNase Zs for cleavage of 18 different pre-tRNA substrates. Two Thermotoga maritima, one Thermus thermophilus, one Bacillus subtilis, one Thermoplasma acidophilum, and one Pyrobaculum aerophilum enzymes were tested. To our surprise, the newly isolated proteins T. maritima and T. thermophilus showed the weak tRNase Z activity, even though their primary amino acid sequences are, on the whole, quite different from those of the typical tRNase Zs. We confirmed that substrate recognition ability is quite different among those tRNase Zs. In addition, we found that the optimal conditions as a whole differ significantly among the enzymes. From these results, we provided several clues to solve the enigma by showing the potential importance of the 74th-76th nucleotide sequence of pre-tRNA, the flexible arm length of tRNase Z, the divalent metal ion species, and the histidine corresponding His222 in T. maritima tRNase Z.
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Affiliation(s)
- Asako Minagawa
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata 956-8603, Japan
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24
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Yan H, Zareen N, Levinger L. Naturally occurring mutations in human mitochondrial pre-tRNASer(UCN) can affect the transfer ribonuclease Z cleavage site, processing kinetics, and substrate secondary structure. J Biol Chem 2005; 281:3926-35. [PMID: 16361254 DOI: 10.1074/jbc.m509822200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
tRNAs are transcribed as precursors with a 5' end leader and a 3' end trailer. The 5' end leader is processed by RNase P, and in most organisms in all three kingdoms, transfer ribonuclease (tRNase) Z can endonucleolytically remove the 3' end trailer. Long ((L)) and short ((S)) forms of the tRNase Z gene are present in the human genome. tRNase Z(L) processes a nuclear-encoded pre-tRNA approximately 1600-fold more efficiently than tRNase Z(S) and is predicted to have a strong mitochondrial transport signal. tRNase Z(L) could, thus, process both nuclear- and mitochondrially encoded pre-tRNAs. More than 150 pathogenesis-associated mutations have been found in the mitochondrial genome, most of them in the 22 mitochondrially encoded tRNAs. All the mutations investigated in human mitochondrial tRNA(Ser(UCN)) affect processing efficiency, and some affect the cleavage site and secondary structure. These changes could affect tRNase Z processing of mutant pre-tRNAs, perhaps contributing to mitochondrial disease.
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Affiliation(s)
- Hua Yan
- York College of The City University of New York, Jamaica, 11451, USA
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25
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Späth B, Kirchner S, Vogel A, Schubert S, Meinlschmidt P, Aymanns S, Nezzar J, Marchfelder A. Analysis of the functional modules of the tRNA 3' endonuclease (tRNase Z). J Biol Chem 2005; 280:35440-7. [PMID: 16118225 DOI: 10.1074/jbc.m506418200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
tRNA 3' processing is one of the essential steps during tRNA maturation. The tRNA 3'-processing endonuclease tRNase Z was only recently isolated, and its functional domains have not been identified so far. We performed an extensive mutational study to identify amino acids and regions involved in dimerization, tRNA binding, and catalytic activity. 29 deletion and point variants of the tRNase Z enzyme were generated. According to the results obtained, variants can be sorted into five different classes. The first class still had wild type activity in all three respects. Members of the second and third class still formed dimers and bound tRNAs but had reduced catalytic activity (class two) or no catalytic activity (class three). The fourth class still formed dimers but did not bind the tRNA and did not process precursors. Since this class still formed dimers, it seems that the amino acids mutated in these variants are important for RNA binding. The fifth class did not have any activity anymore. Several conserved amino acids could be mutated without or with little loss of activity.
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Affiliation(s)
- Bettina Späth
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
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