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Geslain R, Pan T. Functional analysis of human tRNA isodecoders. J Mol Biol 2009; 396:821-31. [PMID: 20026070 DOI: 10.1016/j.jmb.2009.12.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 12/02/2009] [Accepted: 12/10/2009] [Indexed: 11/16/2022]
Abstract
tRNA isodecoders share the same anticodon but have differences in their body sequence. An unexpected result from genome sequencing projects is the identification of a large number of tRNA isodecoder genes in mammalian genomes. In the reference human genome, more than 270 isodecoder genes are present among the approximately 450 tRNA genes distributed among 49 isoacceptor families. Whether sequence diversity among isodecoder tRNA genes reflects functional variability is an open question. To address this, we developed a method to quantify the efficiency of tRNA isodecoders in stop-codon suppression in human cell lines. First, a green fluorescent protein (GFP) gene that contains a single UAG stop codon at two distinct locations is introduced. GFP is only produced when a tRNA suppressor containing CUA anticodon is co-transfected with the GFP gene. The suppression efficiency is examined for 31 tRNA isodecoders (all contain CUA anticodon), 21 derived from four isoacceptor families of tRNASer genes, 7 from five families of tRNALeu genes, and 3 from three families of tRNAAla genes. We found that isodecoder tRNAs display a large difference in their suppression efficiency. Among those with above background suppression activity, differences of up to 20-fold were observed. We were able to tune tRNA suppression efficiency by subtly adjusting the tRNA sequence and inter-convert poor suppressors into potent ones. We also demonstrate that isodecoder tRNAs with varying suppression efficiencies have similar stability and exhibit similar levels of aminoacylation in vivo. Our results indicate that naturally occurring tRNA isodecoders can have large functional variations and suggest that some tRNA isodecoders may perform a function distinct from translation.
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Affiliation(s)
- Renaud Geslain
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
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McClain WH, Gabriel K, Lee D, Otten S. Structure-function analysis of tRNA(Gln) in an Escherichia coli knockout strain. RNA (NEW YORK, N.Y.) 2004; 10:795-804. [PMID: 15100435 PMCID: PMC1370570 DOI: 10.1261/rna.5271404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Accepted: 02/02/2004] [Indexed: 05/24/2023]
Abstract
The diverse and highly specific interaction between RNAs and proteins plays an essential role in many important biological processes. In the glutamine aminoacylation system, crystal structures of the free and ligated macromolecules have provided a description of the tRNA-protein interactions at the molecular level. This data lays the foundation for genetic, biochemical, and structural analyses to delineate the set of key interactions that governs the structure-function relationships of the two macromolecules. To this end the chromosomal tRNA(Gln) genes were disrupted in Escherichia coli to produce a tRNA(Gln) knockout strain that depends upon expression of a functional tRNA(Gln) from a plasmid for cell viability. Mutants of an inactive tester tRNA derived from tRNA(Ala) were generated by hydroxylamine mutagenesis, and the active derivatives were selected by their ability to support knockout cell growth. Two of the mutants contained substitutions in the first base pair of the acceptor stem that likely facilitate the formation of a hairpin loop that places A76 in the active site. The third mutation was located at position 13 in the D loop region of the tRNA, and suggests that an interaction with residue 13 contributes to a specific conformational change in unliganded GlnRS, which helps configure the enzyme active site in its catalytically proficient form. This work demonstrates the efficacy of an integrated approach that combines genetic selections and biochemical analyses with the physical data from crystal structures to reveal molecular steps that control the specificity of RNA-protein interactions.
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Affiliation(s)
- William H McClain
- Department of Bacteriology, University of Wisconsin, 420 Henry Mall, Madison, WI 53706-1569, USA.
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Geslain R, Martin F, Camasses A, Eriani G. A yeast knockout strain to discriminate between active and inactive tRNA molecules. Nucleic Acids Res 2003; 31:4729-37. [PMID: 12907713 PMCID: PMC169964 DOI: 10.1093/nar/gkg685] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Here we report the construction of a yeast genetic screen designed to identify essential residues in tRNA(Arg). The system consists of a tRNA(Arg) knockout strain and a set of vectors designed to rescue and select for variants of tRNA(Arg). By plasmid shuffling we selected inactive tRNA mutants that were further analyzed by northern blotting. The mutational analysis focused on the tRNA D and anticodon loops that contact the aminoacyl-tRNA synthetase. The anticodon triplet was excluded from the analysis because of its role in decoding the Arg codons. Most of the inactivating mutations are residues involved in tertiary interactions. These mutations had dramatic effects on tRNA(Arg) abundance. Other inactivating mutations were located in the anticodon loop, where they did not affect transcription and aminoacylation but probably altered interaction with the translation machinery. No lethal effects were observed when residues 16, 20 and 38 were individually mutated, despite the fact that they are involved in sequence-specific interactions with the aminoacyl-tRNA synthetase. However, the steady-state levels of the aminoacylated forms of U20A and U20G were decreased by a factor of 3.5-fold in vivo. This suggests that, unlike in the Escherichia coli tRNA(Arg):ArgRS system where residue 20 (A) is a major identity element, in yeast this position is of limited consequence.
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Affiliation(s)
- Renaud Geslain
- UPR 9002 SMBMR du CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 Rue René Descartes, 67084 Strasbourg, France
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Choi H, Gabriel K, Schneider J, Otten S, McClain WH. Recognition of acceptor-stem structure of tRNA(Asp) by Escherichia coli aspartyl-tRNA synthetase. RNA (NEW YORK, N.Y.) 2003; 9:386-393. [PMID: 12649491 PMCID: PMC1370406 DOI: 10.1261/rna.2139703] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2002] [Accepted: 12/16/2002] [Indexed: 05/23/2023]
Abstract
Protein-RNA recognition between aminoacyl-tRNA synthetases and tRNA is highly specific and essential for cell viability. We investigated the structure-function relationships involved in the interaction of the Escherichia coli tRNA(Asp) acceptor stem with aspartyl-tRNA synthetase. The goal was to isolate functionally active mutants and interpret them in terms of the crystal structure of the synthetase-tRNA(Asp) complex. Mutants were derived from Saccharomyces cerevisiae tRNA(Asp), which is inactive with E. coli aspartyl-tRNA synthetase, allowing a genetic selection of active tRNAs in a tRNA(Asp) knockout strain of E. coli. The mutants were obtained by directed mutagenesis or library selections that targeted the acceptor stem of the yeast tRNA(Asp) gene. The mutants provide a rich source of tRNA(Asp) sequences, which show that the sequence of the acceptor stem can be extensively altered while allowing the tRNA to retain substantial aminoacylation and cell-growth functions. The predominance of tRNA backbone-mediated interactions observed between the synthetase and the acceptor stem of the tRNA in the crystal and the mutability of the acceptor stem suggest that many of the corresponding wild-type bases are replaceable by alternative sequences, so long as they preserve the initial backbone structure of the tRNA. Backbone interactions emerge as an important functional component of the tRNA-synthetase interaction.
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Affiliation(s)
- Hyunsic Choi
- Department of Bacteriology, University of Wisconsin, Madison, Madison, Wisconsin 53706-1567, USA
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Moulinier L, Eiler S, Eriani G, Gangloff J, Thierry JC, Gabriel K, McClain W, Moras D. The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism. EMBO J 2001; 20:5290-301. [PMID: 11566892 PMCID: PMC125622 DOI: 10.1093/emboj/20.18.5290] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 2.6 A resolution crystal structure of an inactive complex between yeast tRNA(Asp) and Escherichia coli aspartyl-tRNA synthetase reveals the molecular details of a tRNA-induced mechanism that controls the specificity of the reaction. The dimer is asymmetric, with only one of the two bound tRNAs entering the active site cleft of its subunit. However, the flipping loop, which controls the proper positioning of the amino acid substrate, acts as a lid and prevents the correct positioning of the terminal adenosine. The structure suggests that the acceptor stem regulates the loop movement through sugar phosphate backbone- protein interactions. Solution and cellular studies on mutant tRNAs confirm the crucial role of the tRNA three-dimensional structure versus a specific recognition of bases in the control mechanism.
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Affiliation(s)
| | | | - G. Eriani
- UPR 9004, Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP 163, 67404 Illkirch Cedex, C.U. de Strasbourg,
UPR9002, IBMC, 15 rue René Descartes, 67084 Strasbourg, France and Department of Bacteriology, University of Wisconsin, Madison, WI 53706-1567, USA Corresponding author e-mail:
| | - J. Gangloff
- UPR 9004, Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP 163, 67404 Illkirch Cedex, C.U. de Strasbourg,
UPR9002, IBMC, 15 rue René Descartes, 67084 Strasbourg, France and Department of Bacteriology, University of Wisconsin, Madison, WI 53706-1567, USA Corresponding author e-mail:
| | | | - K. Gabriel
- UPR 9004, Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP 163, 67404 Illkirch Cedex, C.U. de Strasbourg,
UPR9002, IBMC, 15 rue René Descartes, 67084 Strasbourg, France and Department of Bacteriology, University of Wisconsin, Madison, WI 53706-1567, USA Corresponding author e-mail:
| | - W.H. McClain
- UPR 9004, Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP 163, 67404 Illkirch Cedex, C.U. de Strasbourg,
UPR9002, IBMC, 15 rue René Descartes, 67084 Strasbourg, France and Department of Bacteriology, University of Wisconsin, Madison, WI 53706-1567, USA Corresponding author e-mail:
| | - D. Moras
- UPR 9004, Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP 163, 67404 Illkirch Cedex, C.U. de Strasbourg,
UPR9002, IBMC, 15 rue René Descartes, 67084 Strasbourg, France and Department of Bacteriology, University of Wisconsin, Madison, WI 53706-1567, USA Corresponding author e-mail:
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Abstract
Determining the functional activity of an essential RNA in vivo presents special challenges. We have devised an in vivo analysis of alternative forms of an essential tRNA gene in Escherichia coli knockout cells using either a plasmid switch or a regulated two-plasmid system. The model system is presented together with a description of the new plasmids and procedures necessary to effect these analyses. The system is readily adaptable to non-essential RNAs.
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MESH Headings
- Arabinose/metabolism
- Blotting, Northern
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Gene Deletion
- Genes, Essential/genetics
- Genetic Markers/genetics
- Genetic Vectors/genetics
- Glucose/metabolism
- Plasmids/genetics
- Promoter Regions, Genetic/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- Replication Origin/genetics
- Terminator Regions, Genetic/genetics
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Affiliation(s)
- K Gabriel
- Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, E. B. Fred Hall, Madison, WI 53706-1567, USA
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