1
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Lahry K, Datta M, Varshney U. Genetic analysis of translation initiation in bacteria: An initiator tRNA-centric view. Mol Microbiol 2024. [PMID: 38410838 DOI: 10.1111/mmi.15243] [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: 12/19/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/28/2024]
Abstract
Translation of messenger RNA (mRNA) in bacteria occurs in the steps of initiation, elongation, termination, and ribosome recycling. The initiation step comprises multiple stages and uses a special transfer RNA (tRNA) called initiator tRNA (i-tRNA), which is first aminoacylated and then formylated using methionine and N10 -formyl-tetrahydrofolate (N10 -fTHF), respectively. Both methionine and N10 -fTHF are produced via one-carbon metabolism, linking translation initiation with active cellular metabolism. The fidelity of i-tRNA binding to the ribosomal peptidyl-site (P-site) is attributed to the structural features in its acceptor stem, and the highly conserved three consecutive G-C base pairs (3GC pairs) in the anticodon stem. The acceptor stem region is important in formylation of the amino acid attached to i-tRNA and in its initial binding to the P-site. And, the 3GC pairs are crucial in transiting the i-tRNA through various stages of initiation. We utilized the feature of 3GC pairs to investigate the nuanced layers of scrutiny that ensure fidelity of translation initiation through i-tRNA abundance and its interactions with the components of the translation apparatus. We discuss the importance of i-tRNA in the final stages of ribosome maturation, as also the roles of the Shine-Dalgarno sequence, ribosome heterogeneity, initiation factors, ribosome recycling factor, and coevolution of the translation apparatus in orchestrating a delicate balance between the fidelity of initiation and/or its leakiness to generate proteome plasticity in cells to confer growth fitness advantages in response to the dynamic nutritional states.
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Affiliation(s)
- Kuldeep Lahry
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Madhurima Datta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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2
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Lahry K, Gopal A, Sah S, Shah RA, Varshney U. Metabolic Flux of N 10-Formyltetrahydrofolate Plays a Critical Role in the Fidelity of Translation Initiation in Escherichia coli. J Mol Biol 2020; 432:5473-5488. [PMID: 32795532 DOI: 10.1016/j.jmb.2020.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/27/2020] [Accepted: 08/04/2020] [Indexed: 12/20/2022]
Abstract
One-carbon metabolism produces methionine and N10-formyl-tetrahydrofolate (N10-fTHF) required for aminoacylation and formylation of initiator tRNA (i-tRNA), respectively. In Escherichia coli, N10-fTHF is made from 5, 10-methylene-THF by a two-step reaction using 5,10-methylene-THF dehydrogenase/cyclohydrolase (FolD). The i-tRNAs from all domains of life possess a highly conserved sequence of three consecutive G-C base pairs (3GC pairs) in their anticodon stem. A 3GC mutant i-tRNA (wherein the 3GC pairs are mutated to those found in elongator tRNAMet) is incompetent in initiation in E. coli (even though it is efficiently aminoacylated and formylated). Here, we show that E. coli strains having mutations in FolD (G122D or C58Y or P140L) allow a plasmid encoded 3GC mutant i-tRNA to participate in initiation. In vitro, the FolD mutants are highly compromised in their dehydrogenase/cyclohydrolase activities leading to reduced production of N10-fTHF and decreased rates of i-tRNA formylation. The perturbation of one-carbon metabolism by trimethoprim (inhibitor of dihydrofolate reductase) phenocopies FolD deficiency and allows initiation with the 3GC mutant i-tRNA. This study reveals an important crosstalk between one-carbon metabolism and the fidelity of translation initiation via formylation of i-tRNA, and suggests that augmentation of the age old sulfa drugs with FolD inhibitors could be an important antibacterial strategy.
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Affiliation(s)
- Kuldeep Lahry
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Aiswarya Gopal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Shivjee Sah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Riyaz Ahmad Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India.
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3
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Shah RA, Varada R, Sah S, Shetty S, Lahry K, Singh S, Varshney U. Rapid formylation of the cellular initiator tRNA population makes a crucial contribution to its exclusive participation at the step of initiation. Nucleic Acids Res 2019; 47:1908-1919. [PMID: 30608556 PMCID: PMC6393288 DOI: 10.1093/nar/gky1310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/09/2018] [Accepted: 12/21/2018] [Indexed: 01/13/2023] Open
Abstract
Initiator tRNAs (i-tRNAs) possess highly conserved three consecutive GC base pairs (GC/GC/GC, 3GC pairs) in their anticodon stems. Additionally, in bacteria and eukaryotic organelles, the amino acid attached to i-tRNA is formylated by Fmt to facilitate its targeting to 30S ribosomes. Mutations in GC/GC/GC to UA/CG/AU in i-tRNACUA/3GC do not affect its formylation. However, the i-tRNACUA/3GC is non-functional in initiation. Here, we characterised an Escherichia coli strain possessing an amber mutation in its fmt gene (fmtam274), which affords initiation with i-tRNACUA/3GC. Replacement of fmt with fmtam274 in the parent strain results in production of truncated Fmt, accumulation of unformylated i-tRNA, and a slow growth phenotype. Introduction of i-tRNACUA/3GC into the fmtam274 strain restores accumulation of formylated i-tRNAs and rescues the growth defect of the strain. We show that i-tRNACUA/3GC causes a low level suppression of am274 in fmtam274. Low levels of cellular Fmt lead to compromised efficiency of formylation of i-tRNAs, which in turn results in distribution of the charged i-tRNAs between IF2 and EF-Tu allowing the plasmid borne i-tRNACUA/3GC to function at both the initiation and elongation steps. We show that a speedy formylation of i-tRNA population is crucial for its preferential binding (and preventing other tRNAs) into the P-site.
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Affiliation(s)
- Riyaz Ahmad Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Rajagopal Varada
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Shivjee Sah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Sunil Shetty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Kuldeep Lahry
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Sudhir Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
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4
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Gampe C, White ACS, Siva S, Zécri F, Diener J. 3'-Modification stabilizes mRNA and increases translation in cells. Bioorg Med Chem Lett 2018; 28:2451-2453. [PMID: 29907393 DOI: 10.1016/j.bmcl.2018.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 01/19/2023]
Abstract
Successful implementation of mRNA gene therapy is facing many hurdles, for example poor expression levels of the exogenously delivered mRNA transcripts. Herein we describe the synthesis of various 3'-modified RNA oligonucleotides, and we show that 3'-modification drastically stabilizes these oligonucleotides in cell extracts. Modification of the 3'-terminus of gaussia luciferase mRNA results in 3-fold increased and extended (>48 h) translation of the mRNA. Our findings suggest 3'-modification of RNA-transcripts as a valid approach to increase expression levels for application in mRNA gene therapy.
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Affiliation(s)
- Christian Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Ave., Cambridge, MA 02139, USA.
| | - Amy C Seila White
- Novartis Institutes for BioMedical Research, 181 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Swetha Siva
- Novartis Institutes for BioMedical Research, 181 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Frédéric Zécri
- Novartis Institutes for BioMedical Research, 181 Massachusetts Ave., Cambridge, MA 02139, USA
| | - John Diener
- Novartis Institutes for BioMedical Research, 181 Massachusetts Ave., Cambridge, MA 02139, USA
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5
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Chafe SC, Mangroo D. Scyl1 facilitates nuclear tRNA export in mammalian cells by acting at the nuclear pore complex. Mol Biol Cell 2010; 21:2483-99. [PMID: 20505071 PMCID: PMC2903676 DOI: 10.1091/mbc.e10-03-0176] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We provide evidence that Scyl1 is also a cytoplasmic component of the nuclear aminoacylation-dependent tRNA export pathway. Scyl1, like the Saccharomyces cerevisiae Cex1p, may collect aminoacyl-tRNAs from the nuclear tRNA export receptors at the cytoplasmic side of the NPC and channel them to eEF-1A for use in protein synthesis. Scyl1 is an evolutionarily conserved N-terminal protein kinase-like domain protein that plays a role in COP1-mediated retrograde protein trafficking in mammalian cells. Furthermore, loss of Scyl1 function has been shown to result in neurodegenerative disorders in mice. Here, we report that Scyl1 is also a cytoplasmic component of the mammalian nuclear tRNA export machinery. Like exportin-t, overexpression of Scyl1 restored export of a nuclear export-defective serine amber suppressor tRNA mutant in COS-7 cells. Scyl1 binds tRNA saturably, and associates with the nuclear pore complex by interacting, in part, with Nup98. Scyl1 copurifies with the nuclear tRNA export receptors exportin-t and exportin-5, the RanGTPase, and the eukaryotic elongation factor eEF-1A, which transports aminoacyl-tRNAs to the ribosomes. Scyl1 interacts directly with exportin-t and RanGTP but not with eEF-1A or RanGDP in vitro. Moreover, exportin-t containing tRNA, Scyl1, and RanGTP form a quaternary complex in vitro. Biochemical characterization also suggests that the nuclear aminoacylation-dependent pathway is primarily responsible for tRNA export in mammalian cells. These findings together suggest that Scyl1 participates in the nuclear aminoacylation-dependent tRNA export pathway and may unload aminoacyl-tRNAs from the nuclear tRNA export receptor at the cytoplasmic side of the nuclear pore complex and channels them to eEF-1A.
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Affiliation(s)
- Shawn C Chafe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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6
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Eswara MB, McGuire AT, Pierce JB, Mangroo D. Utp9p facilitates Msn5p-mediated nuclear reexport of retrograded tRNAs in Saccharomyces cerevisiae. Mol Biol Cell 2009; 20:5007-25. [PMID: 19812255 PMCID: PMC2785743 DOI: 10.1091/mbc.e09-06-0490] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 09/18/2009] [Accepted: 09/25/2009] [Indexed: 11/11/2022] Open
Abstract
Utp9p is a nucleolar protein that is part of a subcomplex containing several U3 snoRNA-associated proteins including Utp8p, which is a protein that shuttles aminoacyl-tRNAs from the nucleolus to the nuclear tRNA export receptors Los1p and Msn5p in Saccharomyces cerevisiae. Here we show that Utp9p is also an intranuclear component of the Msn5p-mediated nuclear tRNA export pathway. Depletion of Utp9p caused nuclear accumulation of mature tRNAs derived from intron-containing precursors, but not tRNAs made from intronless pre-tRNAs. Utp9p binds tRNA directly and saturably, and copurifies with Utp8p, Gsp1p, and Msn5p, but not with Los1p or aminoacyl-tRNA synthetases. Utp9p interacts directly with Utp8p, Gsp1p, and Msn5p in vitro. Furthermore, Gsp1p forms a complex with Msn5p and Utp9p in a tRNA-dependent manner. However, Utp9p does not shuttle between the nucleus and the cytoplasm. Because tRNA splicing occurs in the cytoplasm and the spliced tRNAs are retrograded back to the nucleus, we propose that Utp9p facilitates nuclear reexport of retrograded tRNAs. Moreover, the data suggest that Utp9p together with Utp8p translocate aminoacyl-tRNAs from the nucleolus to Msn5p and assist with formation of the Msn5p-tRNA-Gsp1p-GTP export complex.
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Affiliation(s)
- Manoja B.K. Eswara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Andrew T. McGuire
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Jacqueline B. Pierce
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Dev Mangroo
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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7
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McGuire AT, Mangroo D. Cex1p is a novel cytoplasmic component of the Saccharomyces cerevisiae nuclear tRNA export machinery. EMBO J 2007; 26:288-300. [PMID: 17203074 PMCID: PMC1783447 DOI: 10.1038/sj.emboj.7601493] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Accepted: 11/15/2006] [Indexed: 11/08/2022] Open
Abstract
The Saccharomyces cerevisiae Yor112wp, which we named Cex1p, was identified using a yeast tRNA three-hybrid interaction approach and an in vivo nuclear tRNA export assay as a cytoplasmic component of the nuclear tRNA export machinery. Cex1p binds tRNA saturably, and associates with the nuclear pore complex by interacting directly with Nup116p. Cex1p co-purifies with the nuclear tRNA export receptors Los1p and Msn5p, the eukaryotic elongation factor eEF-1A, which delivers aminoacylated tRNAs to the ribosome, and the RanGTPase Gsp1p, but not with Cca1p, a tRNA maturation enzyme that facilitates translocation of non-aminoacylated tRNAs across the nuclear pore complex. Depletion of Cex1p and eEF-1A or Los1p significantly reduced the efficiency of nuclear tRNA export. Cex1p interacts with Los1p but not with eEF-1A in vitro. These findings suggest that Cex1p is a component of the nuclear aminoacylation-dependent tRNA export pathway in S. cerevisiae. They also suggest that Cex1p collects aminoacyl-tRNAs from the nuclear export receptors at the cytoplasmic side of the nuclear pore complex, and transfers them to eEF-1A using a channelling mechanism.
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Affiliation(s)
- Andrew T McGuire
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Dev Mangroo
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1. Tel.: +1 519 824 4120, Ext. 53432; Fax: +1 519 837 1802; E-mail:
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8
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Zhou L, Civitello ER, Gupta N, Silverman RH, Molinaro RJ, Anderson DE, Torrence PF. Endowing RNase H-inactive antisense with catalytic activity: 2-5A-morphants. Bioconjug Chem 2005; 16:383-90. [PMID: 15769093 DOI: 10.1021/bc049778q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A convergent synthetic approach was used to conjugate 2',5'-oligoadenylate (2-5A, p5'A2' [p5'A2'](n)()p5'A) to phosphorodiamidate morpholino oligomers (morphants). To provide requisite quantities of 2-5A starting material, commercially and readily available synthons for solid-phase synthesis were adapted for larger scale solution synthesis. Thus, the tetranucleotide 5'-phosphoryladenylyl(2'-->5')adenylyl(2'-->5')adenylyl(2'-->5')adenosine (p5'A2'p5'A2'](2)p5'A2', tetramer 2-5A, 9) was synthesized starting with 2',3'-O-dibenzoyl-N(6),N(6)-dibenzoyl adenosine prepared from commercially available 5'-O-(4-monomethoxytrityl) adenosine. Coupling with N(6)-benzoyl-5'-O-(4,4'-dimethoxytrityl)-3'-O-(tert-butyldimethylsilyl) adenosine-2'-(N,N-diisopropyl-2-cyanoethyl)phosphoramidite, followed by oxidization and deprotection, generated 5'-deprotected dimer 2-5A. Similar procedures lengthened the chain to form protected tetramer 2-5 A. The title product 9 p5'A(2'p5'A)(3) (tetramer 2-5A) was obtained through phosphorylation of the terminal 5'-hydroxy of the protected tetramer and removal of remaining protecting groups using concentrated ammonium hydroxide-ethanol (3:1, v/v) at 55 degrees C and tetrabutylammonium fluoride (TBAF) in THF at room temperature, respectively. The 2-5A-phosphorodiamidate morpholino antisense chimera 11 (2-5A-morphant) was synthesized by covalently linking an aminolinker-functionalized phosphorodiamidate morpholino oligomer with periodate oxidized 2-5A tetramer (p5'A2'[p5'A2'](2)p5'A). The resulting Schiff base was reduced with cyanoborohydride thereby transforming the ribose of the 2'-terminal nucleotide of 2-5A N-substituted morpholine. RNase L assays demonstrated that this novel 2-5A-antisense chimera had significant biological activity, thereby providing another potential tool for RNA ablation.
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Affiliation(s)
- Longhu Zhou
- Department of Chemistry, Northern Arizona University, Box 5698, Flagstaff, Arizona 86011-5698, USA
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9
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Steiner-Mosonyi M, Leslie DM, Dehghani H, Aitchison JD, Mangroo D. Utp8p is an essential intranuclear component of the nuclear tRNA export machinery of Saccharomyces cerevisiae. J Biol Chem 2003; 278:32236-45. [PMID: 12794079 DOI: 10.1074/jbc.m302779200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A yeast tRNA three-hybrid interaction approach and an in vivo nuclear tRNA export assay based on amber suppression was used to identify proteins that participate in the nuclear tRNA export process in Saccharomyces cerevisiae. One of the proteins identified by this strategy is Utp8p, an essential 80-kDa nucleolar protein that has been implicated in 18 S ribosomal RNA biogenesis. Our characterization indicated that the major function of Utp8p is in nuclear tRNA export. Like the S. cerevisiae Los1p and the mammalian exportin-t, which are proteins known to facilitate nuclear tRNA export, overexpression of Utp8p restored export of tRNAamTyr mutants defective in nuclear export. Furthermore, depletion of Utp8p blocked nuclear export of mature tRNAs derived from both intronless and intron-containing pre-tRNAs but did not affect tRNA and rRNA maturation, nuclear export of mRNA and ribosomes, or nuclear tRNA aminoacylation. Overexpression of Utp8p also alleviated nuclear retention of non-aminoacylated tRNATyr in a tyrosyl-tRNA synthetase mutant strain. Utp8p binds tRNA directly and saturably, indicating that it has a tRNA-binding site. Utp8p does not appear to function as a tRNA export receptor, because it does not shuttle between the nucleus and the cytoplasm. Taken together, the results suggest that Utp8p is an essential intranuclear component of the nuclear tRNA export machinery, which may channel tRNA to the various tRNA export pathways operating in S. cerevisiae.
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Affiliation(s)
- Marta Steiner-Mosonyi
- Guelph-Waterloo Center for Graduate Work in Chemistry and Biochemistry, Department of Chemistry and Biochemistry, University of Guelph, Ontario N1G 2W1, Canada
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10
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Mayer C, Stortchevoi A, Köhrer C, Varshney U, RajBhandary UL. Initiator tRNA and its role in initiation of protein synthesis. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:195-206. [PMID: 12762022 DOI: 10.1101/sqb.2001.66.195] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- C Mayer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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11
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Mayer C, RajBhandary UL. Conformational change of Escherichia coli initiator methionyl-tRNA(fMet) upon binding to methionyl-tRNA formyl transferase. Nucleic Acids Res 2002; 30:2844-50. [PMID: 12087168 PMCID: PMC117066 DOI: 10.1093/nar/gkf411] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The specific formylation of initiator methionyl-tRNA (Met-tRNA) by methionyl-tRNA formyltransferase (MTF) is important for the initiation of protein synthesis in Escherichia coli. The determinants for formylation are located in the acceptor stem and in the dihydrouridine (D) stem of the initiator tRNA (tRNA(fMet)). Here, we have used ethylation interference analysis to study the interactions between the Met-tRNA(fMet) and MTF in solution. We have identified three clusters of phosphates in the tRNA that, when ethylated, interfere with binding of MTF. Interference due to ethylation of phosphates in the acceptor stem and in the D stem is most likely due to the close proximity of the protein as seen in the crystal structure of the MTF.fMet-tRNA(fMet) complex. The third cluster of phosphates, whose ethylation interferes with binding of MTF, is dispersed along the anticodon stem, which is distal to the sites of tRNA protein contacts. Interestingly, these latter positions correspond to sites of increased cleavages by RNase V1 in RNA footprinting experiments. Together, these results suggest that in addition to the protein, which binds to the substrate tRNA in an induced fit mechanism, the tRNA also undergoes induced structural changes during its binding to MTF.
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Affiliation(s)
- Christine Mayer
- Department of Biology, 68-671A, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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12
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Wang Z, Chen L, Bayly SF, Torrence PF. Convergent synthesis of ribonuclease L-active 2',5'-oligoadenylate-peptide nucleic acids. Bioorg Med Chem Lett 2000; 10:1357-60. [PMID: 10890163 DOI: 10.1016/s0960-894x(00)00240-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
2-5A was conjugated to N-(2-aminoethyl)-glycyl PNA by periodate oxidization, followed by coupling with amino-derivatized PNA and final cyanoborohydride reduction. An adduct of 2-5A pentamer with tetrameric thymine PNA activated RNase L with the same potency as earlier versions of 2-5A-PNA or 2-5A-DNA.
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Affiliation(s)
- Z Wang
- Section on Biomedical Chemistry, Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive antd Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0805, USA
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13
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Gite S, Mamaev S, Olejnik J, Rothschild K. Ultrasensitive fluorescence-based detection of nascent proteins in gels. Anal Biochem 2000; 279:218-25. [PMID: 10706791 DOI: 10.1006/abio.1999.4472] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The most common method of analysis of proteins synthesized in a cell-free translation system (e.g., nascent proteins) involves the use of radioactive amino acids such as [(35)S]methionine or [(14)C]leucine. We report a sensitive, nonisotopic, fluorescence-based method for the detection of nascent proteins directly in polyacrylamide gels. A fluorescent reporter group is incorporated at the N-terminus of nascent proteins using an Escherichia coli initiator tRNA(fmet) misaminoacylated with methionine modified at the alpha-amino group. In addition to the normal formyl group, we find that the protein translational machinery accepts BODIPY-FL, a relatively small fluorophore with a high fluorescent quantum yield, as an N-terminal modification. Under the optimal conditions, fluorescent bands from nanogram levels of in vitro-produced proteins could be detected directly in gels using a conventional UV-transilluminator. Higher sensitivity ( approximately 100-fold) could be obtained using a laser-based fluorescent gel scanner. The major advantages of this approach include elimination of radioactivity and the rapid detection of the protein bands immediately after electrophoresis without any downstream processing. The ability to rapidly synthesize nascent proteins containing an N-terminal tag facilitates many biotechnological applications including functional analysis of gene products, drug discovery, and mutation screening.
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Affiliation(s)
- S Gite
- AmberGen, Inc., 1106, Commonwealth Avenue, Boston, Massachusetts, 02215, USA
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14
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Gite S, Li Y, Ramesh V, RajBhandary UL. Escherichia coli methionyl-tRNA formyltransferase: role of amino acids conserved in the linker region and in the C-terminal domain on the specific recognition of the initiator tRNA. Biochemistry 2000; 39:2218-26. [PMID: 10694387 DOI: 10.1021/bi9926072] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The formylation of initiator methionyl-tRNA by methionyl-tRNA formyltransferase (MTF) is important for the initiation of protein synthesis in eubacteria. We are studying the molecular mechanisms of recognition of the initiator tRNA by Escherichia coli MTF. MTF from eubacteria contains an approximately 100-amino acid C-terminal extension that is not found in the E. coli glycinamide ribonucleotide formyltransferase, which, like MTF, use N(10)-formyltetrahydrofolate as a formyl group donor. This C-terminal extension, which forms a distinct structural domain, is attached to the N-terminal domain through a linker region. Here, we describe the effect of (i) substitution mutations on some nineteen basic, aromatic and other conserved amino acids in the linker region and in the C-terminal domain of MTF and (ii) deletion mutations from the C-terminus on enzyme activity. We show that the positive charge on two of the lysine residues in the linker region leading to the C-terminal domain are important for enzyme activity. Mutation of some of the basic amino acids in the C-terminal domain to alanine has mostly small effects on the kinetic parameters, whereas mutation to glutamic acid has large effects. However, the deletion of 18, 20, or 80 amino acids from the C-terminus has very large effects on enzyme activity. Overall, our results support the notion that the basic amino acid residues in the C-terminal domain provide a positively charged channel that is used for the nonspecific binding of tRNA, whereas some of the amino acids in the linker region play an important role in activity of MTF.
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Affiliation(s)
- S Gite
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Larive CK, Lunte SM, Zhong M, Perkins MD, Wilson GS, Gokulrangan G, Williams T, Afroz F, Schöneich C, Derrick TS, Middaugh CR, Bogdanowich-Knipp S. Separation and analysis of peptides and proteins. Anal Chem 1999; 71:389R-423R. [PMID: 10409086 DOI: 10.1021/a1990013o] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C K Larive
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
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16
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Ramesh V, Mayer C, Dyson MR, Gite S, RajBhandary UL. Induced fit of a peptide loop of methionyl-tRNA formyltransferase triggered by the initiator tRNA substrate. Proc Natl Acad Sci U S A 1999; 96:875-80. [PMID: 9927661 PMCID: PMC15318 DOI: 10.1073/pnas.96.3.875] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A 16-aa insertion loop present in eubacterial methionyl-tRNA formyltransferases (MTF) is critical for specific recognition of the initiator tRNA in Escherichia coli. We have studied the interactions between this region of the E. coli enzyme and initiator methionyl-tRNA (Met-tRNA) by using two complementary protection experiments: protection of MTF against proteolytic cleavage by tRNA and protection of tRNA against nucleolytic cleavage by MTF. The insertion loop in MTF is uniquely sensitive to cleavage by trypsin. We show that the substrate initiator Met-tRNA protects MTF against trypsin cleavage, whereas a formylation-defective mutant initiator Met-tRNA, which binds to MTF with approximately the same affinity, does not. Also, mutants of MTF within the insertion loop (which are defective in formylation) are not protected by the initiator Met-tRNA. Thus, a functional enzyme-substrate complex is necessary for protection of MTF against trypsin cleavage. Along with other data, these results strongly suggest that a segment of the insertion loop, which is exposed and unstructured in MTF, undergoes an induced fit in the functional MTF.Met-tRNA complex but not in the nonfunctional one. Footprinting experiments show that MTF specifically protects the acceptor stem and the 3'-end region of the initiator Met-tRNA against cleavage by double and single strand-specific nucleases. This protection also depends on formation of a functional MTF.Met-tRNA complex. Thus, the insertion loop interacts mostly with the acceptor stem of the initiator Met-tRNA, which contains the critical determinants for formylation.
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Affiliation(s)
- V Ramesh
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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17
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Schmitt E, Panvert M, Blanquet S, Mechulam Y. Crystal structure of methionyl-tRNAfMet transformylase complexed with the initiator formyl-methionyl-tRNAfMet. EMBO J 1998; 17:6819-26. [PMID: 9843487 PMCID: PMC1171029 DOI: 10.1093/emboj/17.23.6819] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The crystal structure of Escherichia coli methionyl-tRNAfMet transformylase complexed with formyl-methionyl-tRNAfMet was solved at 2.8 A resolution. The formylation reaction catalyzed by this enzyme irreversibly commits methionyl-tRNAfMet to initiation of translation in eubacteria. In the three-dimensional model, the methionyl-tRNAfMet formyltransferase fills in the inside of the L-shaped tRNA molecule on the D-stem side. The anticodon stem and loop are away from the protein. An enzyme loop is wedged in the major groove of the acceptor helix. As a result, the C1-A72 mismatch characteristic of the initiator tRNA is split and the 3' arm bends inside the active centre. This recognition mechanism is markedly distinct from that of elongation factor Tu, which binds the acceptor arm of aminoacylated elongator tRNAs on the T-stem side.
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Affiliation(s)
- E Schmitt
- Laboratoire de Biochimie, Unité Mixte de Recherche No. 7654 du Centre National de la Recherche Scientifique, Ecole Polytechnique, F-91128 Palaiseau cedex, France
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18
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Takeuchi N, Kawakami M, Omori A, Ueda T, Spremulli LL, Watanabe K. Mammalian mitochondrial methionyl-tRNA transformylase from bovine liver. Purification, characterization, and gene structure. J Biol Chem 1998; 273:15085-90. [PMID: 9614118 DOI: 10.1074/jbc.273.24.15085] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian mitochondrial methionyl-tRNA transformylase (MTFmt) was partially purified 2,200-fold from bovine liver mitochondria using column chromatography. The polypeptide responsible for MTFmt activity was excised from a sodium dodecyl sulfate-polyacrylamide gel and the amino acid sequences of several peptides were determined. The cDNA encoding bovine MTFmt was obtained and its nucleotide sequence was determined. The deduced amino acid sequence of the mature form of MTFmt consists of 357 amino acid residues. This sequence is about 30% identical to the corresponding Escherichia coli and yeast mitochondrial MTFs. Kinetic parameters governing the formylation of various tRNAs were obtained. Bovine MTFmt formylates its homologous mitochondrial methionyl-tRNA and the E. coli initiator methionyl-tRNA (Met-tRNAfMet) with essentially equal efficiency. The E. coli elongator methionyl-tRNA (Met-tRNAmMet) was also formylated although with somewhat less favorable kinetics. These results suggest that the substrate specificity of MTFmt is not as rigid as that of the E. coli MTF which clearly discriminates between the bacterial initiator and elongator Met-tRNAs. These observations are discussed in terms of the presence of a single tRNAMet gene in mammalian mitochondria.
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Affiliation(s)
- N Takeuchi
- Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113, Japan
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19
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Crain PF, McCloskey JA. Applications of mass spectrometry to the characterization of oligonucleotides and nucleic acids. Curr Opin Biotechnol 1998; 9:25-34. [PMID: 9503584 DOI: 10.1016/s0958-1669(98)80080-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry-based techniques continue to undergo active development for applications to nucleic acids, fueled by methods based on electrospray and matrix-assisted laser desorption ionization. In the past two years, notable advances have occurred in multiple interrelated areas, including sequencing techniques for oligonucleotides, approaches to mixture analysis, microscale sample handling and targeted DNA assays, and improvements in instrumentation for greater sensitivity and mass resolution.
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Affiliation(s)
- P F Crain
- University of Utah, Department of Medicinal Chemistry, Salt Lake City 84112-5820, USA.
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20
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Ramesh V, Gite S, Li Y, RajBhandary UL. Suppressor mutations in Escherichia coli methionyl-tRNA formyltransferase: role of a 16-amino acid insertion module in initiator tRNA recognition. Proc Natl Acad Sci U S A 1997; 94:13524-9. [PMID: 9391059 PMCID: PMC28339 DOI: 10.1073/pnas.94.25.13524] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The specific formylation of initiator methionyl-tRNA by methionyl-tRNA formyltransferase (MTF; EC 2.1.2.9) is important for the initiation of protein synthesis in eubacteria and in eukaryotic organelles. The determinants for formylation in the tRNA are clustered mostly in the acceptor stem. As part of studies on the molecular mechanism of recognition of the initiator tRNA by MTF, we report here on the isolation and characterization of suppressor mutations in Escherichia coli MTF, which compensate for the formylation defect of a mutant initiator tRNA, lacking a critical determinant in the acceptor stem. We show that the suppressor mutant in MTF has a glycine-41 to arginine change within a 16-amino acid insertion found in MTF from many sources. A mutant with glycine-41 changed to lysine also acts as a suppressor, whereas mutants with changes to aspartic acid, glutamine, and leucine do not. The kinetic parameters of the purified wild-type and mutant Arg-41 and Lys-41 enzymes, determined by using the wild-type and mutant tRNAs as substrates, show that the Arg-41 and Lys-41 mutant enzymes compensate specifically for the strong negative effect of the acceptor stem mutation on formylation. These and other considerations suggest that the 16-amino acid insertion in MTF plays an important role in the specific recognition of the determinants for formylation in the acceptor stem of the initiator tRNA.
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MESH Headings
- Amino Acid Sequence
- Binding Sites/genetics
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Genes, Bacterial
- Hydroxymethyl and Formyl Transferases/genetics
- Hydroxymethyl and Formyl Transferases/metabolism
- Kinetics
- Molecular Sequence Data
- Mutagenesis, Insertional
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/genetics
- RNA, Transfer, Met/metabolism
- Sequence Homology, Amino Acid
- Suppression, Genetic
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Affiliation(s)
- V Ramesh
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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