1
|
Kutner J, Towpik J, Ginalski K, Boguta M. Mitochondrial release factor in yeast: interplay of functional domains. Curr Genet 2008; 53:185-92. [DOI: 10.1007/s00294-008-0177-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 01/10/2008] [Accepted: 01/11/2008] [Indexed: 10/22/2022]
|
2
|
Shaw JJ, Green R. Two distinct components of release factor function uncovered by nucleophile partitioning analysis. Mol Cell 2008; 28:458-67. [PMID: 17996709 DOI: 10.1016/j.molcel.2007.09.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/10/2007] [Accepted: 09/07/2007] [Indexed: 10/22/2022]
Abstract
During translation termination, release factor (RF) protein catalyzes a hydrolytic reaction in the large subunit peptidyl transferase center to release the finished polypeptide chain. While the mechanism of catalysis of peptide release remains obscure, important contributing factors have been identified, including conserved active-site nucleotides and a GGQ tripeptide motif in the RF. Here we describe pre-steady-state kinetic and nucleophile competition experiments to examine RF contributions to the rate and specificity of peptide release. We find that while unacylated tRNA stimulates release in a nondiscriminating manner, RF1 is very specific for water. Further analysis reveals that amino acid Q235 of the RF1 GGQ motif is critical for the observed specificity. These data lead to a model where RFs make two distinct contributions to catalysis--a relatively nonspecific activation of the catalytic center and specific selection of water as a nucleophile facilitated by Q235.
Collapse
Affiliation(s)
- Jeffrey J Shaw
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | |
Collapse
|
3
|
Bouakaz L, Bouakaz E, Murgola EJ, Ehrenberg M, Sanyal S. The role of ribosomal protein L11 in class I release factor-mediated translation termination and translational accuracy. J Biol Chem 2005; 281:4548-56. [PMID: 16371360 DOI: 10.1074/jbc.m510433200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It has been suggested from in vivo and cryoelectron micrographic studies that the large ribosomal subunit protein L11 and its N-terminal domain play an important role in peptide release by, in particular, the class I release factor RF1. In this work, we have studied in vitro the role of L11 in translation termination with ribosomes from a wild type strain (WT-L11), an L11 knocked-out strain (DeltaL11), and an L11 N terminus truncated strain (Cter-L11). Our data show 4-6-fold reductions in termination efficiency (k(cat)/K(m)) of RF1, but not of RF2, on DeltaL11 and Cter-L11 ribosomes compared with wild type. There is, at the same time, no effect of these L11 alterations on the maximal rate of ester bond cleavage by either RF1 or RF2. The rates of dissociation of RF2 but not of RF1 from the ribosome after peptide release are somewhat reduced by the L11 changes irrespective of the presence of RF3, and they cause a 2-fold decrease in the missense error. Our results suggest that the L11 modifications increase nonsense suppression at UAG codons because of the reduced termination efficiency of RF1 and that they decrease nonsense suppression at UGA codons because of a decreased missense error level.
Collapse
Affiliation(s)
- Lamine Bouakaz
- Institute of Cell and Molecular Biology, Uppsala University, Sweden
| | | | | | | | | |
Collapse
|
4
|
Chavatte L, Seit-Nebi A, Dubovaya V, Favre A. The invariant uridine of stop codons contacts the conserved NIKSR loop of human eRF1 in the ribosome. EMBO J 2002; 21:5302-11. [PMID: 12356746 PMCID: PMC129024 DOI: 10.1093/emboj/cdf484] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To unravel the region of human eukaryotic release factor 1 (eRF1) that is close to stop codons within the ribosome, we used mRNAs containing a single photoactivatable 4-thiouridine (s(4)U) residue in the first position of stop or control sense codons. Accurate phasing of these mRNAs onto the ribosome was achieved by the addition of tRNA(Asp). Under these conditions, eRF1 was shown to crosslink exclusively to mRNAs containing a stop or s(4)UGG codon. A procedure that yielded (32)P-labeled eRF1 deprived of the mRNA chain was developed; analysis of the labeled peptides generated after specific cleavage of both wild-type and mutant eRF1s maps the crosslink in the tripeptide KSR (positions 63-65 of human eRF1) and points to K63 located in the conserved NIKS loop as the main crosslinking site. These data directly show the interaction of the N-terminal (N) domain of eRF1 with stop codons within the 40S ribosomal subunit and provide strong support for the positioning of the eRF1 middle (M) domain on the 60S subunit. Thus, the N and M domains mimic the tRNA anticodon and acceptor arms, respectively.
Collapse
Affiliation(s)
- Laurent Chavatte
- Institut Jacques Monod, UMR 7592 CNRS-Universités Paris 7–Paris 6, 2 place Jussieu, F-75251 Paris cedex 05, France and Engelhardt Institute of Molecular Biology, Moscow 119991, Russia Present address: Cleveland Clinic Foundation, 9500 Euclid Avenue NC-10, Cleveland, OH 44195, USA Corresponding author e-mail:
| | - Alim Seit-Nebi
- Institut Jacques Monod, UMR 7592 CNRS-Universités Paris 7–Paris 6, 2 place Jussieu, F-75251 Paris cedex 05, France and Engelhardt Institute of Molecular Biology, Moscow 119991, Russia Present address: Cleveland Clinic Foundation, 9500 Euclid Avenue NC-10, Cleveland, OH 44195, USA Corresponding author e-mail:
| | - Vera Dubovaya
- Institut Jacques Monod, UMR 7592 CNRS-Universités Paris 7–Paris 6, 2 place Jussieu, F-75251 Paris cedex 05, France and Engelhardt Institute of Molecular Biology, Moscow 119991, Russia Present address: Cleveland Clinic Foundation, 9500 Euclid Avenue NC-10, Cleveland, OH 44195, USA Corresponding author e-mail:
| | - Alain Favre
- Institut Jacques Monod, UMR 7592 CNRS-Universités Paris 7–Paris 6, 2 place Jussieu, F-75251 Paris cedex 05, France and Engelhardt Institute of Molecular Biology, Moscow 119991, Russia Present address: Cleveland Clinic Foundation, 9500 Euclid Avenue NC-10, Cleveland, OH 44195, USA Corresponding author e-mail:
| |
Collapse
|
5
|
Mansell JB, Guévremont D, Poole ES, Tate WP. A dynamic competition between release factor 2 and the tRNA(Sec) decoding UGA at the recoding site of Escherichia coli formate dehydrogenase H. EMBO J 2001; 20:7284-93. [PMID: 11743004 PMCID: PMC125778 DOI: 10.1093/emboj/20.24.7284] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Factors affecting competition between termination and elongation in vivo during translation of the fdhF selenocysteine recoding site (UGA) were studied with wild-type and modified fdhF sequences. Altering sequences surrounding the recoding site UGA without affecting RNA secondary structure indicated that the kinetics of stop signal decoding have a significant influence on selenocysteine incorporation efficiency. The UGA in the wild-type fdhF sequence remains 'visible' to the factor and forms a site-directed cross-link when mRNA stem-loop secondary structure is absent, but not when it is present. The timing of the secondary structure unfolding during translation may be a critical feature of competition between release factor 2 and tRNA(Sec) for decoding UGA. Increasing the cellular concentration of either of these decoding molecules for termination or selenocysteine incorporation showed that they were able to compete for UGA by a kinetic competition that is dynamic and dependent on the Escherichia coli growth rate. The tRNA(Sec)-mediated decoding can compete more effectively for the UGA recoding site at lower growth rates, consistent with anaerobic induction of fdhF expression.
Collapse
Affiliation(s)
| | | | | | - Warren P. Tate
- Department of Biochemistry and Centre for Gene Research, University of Otago, PO Box 56, Dunedin, New Zealand
Corresponding author e-mail:
| |
Collapse
|
6
|
Chavatte L, Frolova L, Kisselev L, Favre A. The polypeptide chain release factor eRF1 specifically contacts the s(4)UGA stop codon located in the A site of eukaryotic ribosomes. ACTA ACUST UNITED AC 2001; 268:2896-904. [PMID: 11358506 DOI: 10.1046/j.1432-1327.2001.02177.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
It has been shown previously [Brown, C.M. & Tate, W.P. (1994) J. Biol. Chem. 269, 33164-33170.] that the polypeptide chain release factor RF2 involved in translation termination in prokaryotes was able to photocrossreact with mini-messenger RNAs containing stop signals in which U was replaced by 4-thiouridine (s4U). Here, using the same strategy we have monitored photocrosslinking to eukaryotic ribosomal components of 14-mer mRNA in the presence of tRNA(f)(Met), and 42-mer mRNA in the presence of tRNA(Asp) (tRNA(Asp) gene transcript). We show that: (a) both 14-mer and 42-mer mRNAs crossreact with ribosomal RNA and ribosomal proteins. The patterns of the crosslinked ribosomal proteins are similar with both mRNAs and sensitive to ionic conditions; (b) the crosslinking patterns obtained with 42-mer mRNAs show characteristic modification upon addition of tRNA(Asp) providing evidence for appropriate mRNA phasing onto the ribosome. Similar changes are not detected with the 14-mer mRNA.tRNA(f)(Met) pairs; (c) when eukaryotic polypeptide chain release factor 1 (eRF1) is added to the ribosome.tRNA(Asp) complex it crossreacts with the 42-mer mRNA containing the s(4)UGA stop codon located in the A site, but not with the s(4)UCA sense codon; this crosslink involves the N-terminal and middle domains of eRF1 but not the C domain which interacts with eukaryotic polypeptide chain release factor 3 (eRF3); (d) addition of eRF3 has no effect on the yield of eRF1-42-mer mRNA crosslinking and eRF3 does not crossreact with 42-mer mRNA. These experiments delineate the in vitro conditions allowing optimal phasing of mRNA on the eukaryotic ribosome and demonstrate a direct and specific contact of 'core' eRF1 and s(4)UGA stop codon within the ribosomal A site.
Collapse
Affiliation(s)
- L Chavatte
- Institut Jacques Monod, UMR 7592 CNRS-Universités Paris 7-Paris 6, France
| | | | | | | |
Collapse
|
7
|
Poole E, Tate W. Release factors and their role as decoding proteins: specificity and fidelity for termination of protein synthesis. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1493:1-11. [PMID: 10978500 DOI: 10.1016/s0167-4781(00)00162-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The decoding of stop signals in mRNA requires protein release factors. Two classes of factor are found in both prokaryotes and eukaryotes, a decoding factor and a stimulatory recycling factor. These factors form complexes at the active centre of the ribosome and mimic in overall shape the complexes found at other stages of protein synthesis. The decoding release factor is shaped like a tRNA and has a domain for codon recognition at the decoding site of the ribosome, and a domain for peptidyl-tRNA hydrolysis that is inferred to be near the peptidyltransferase centre. Initial interaction of the decoding factor with the ribosome is a low fidelity event involving multiple contacts with the ribosomal components. A subsequent discrimination step, at present poorly defined, ensures high fidelity of codon recognition.
Collapse
Affiliation(s)
- E Poole
- Department of Biochemistry and the Centre for Gene Research, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | | |
Collapse
|
8
|
Askarian-Amiri ME, Pel HJ, Guévremont D, McCaughan KK, Poole ES, Sumpter VG, Tate WP. Functional characterization of yeast mitochondrial release factor 1. J Biol Chem 2000; 275:17241-8. [PMID: 10748224 DOI: 10.1074/jbc.m910448199] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The yeast Saccharomyces cerevisiae mitochondrial release factor was expressed from the cloned MRF1 gene, purified from inclusion bodies, and refolded to give functional activity. The gene encoded a factor with release activity that recognized cognate stop codons in a termination assay with mitochondrial ribosomes and in an assay with Escherichia coli ribosomes. The noncognate stop codon, UGA, encoding tryptophan in mitochondria, was recognized weakly in the heterologous assay. The mitochondrial release factor 1 protein bound to bacterial ribosomes and formed a cross-link with the stop codon within a mRNA bound in a termination complex. The affinity was strongly dependent on the identity of stop signal. Two alleles of MRF1 that contained point mutations in a release factor 1 specific region of the primary structure and that in vivo compensated for mutations in the decoding site rRNA of mitochondrial ribosomes were cloned, and the expressed proteins were purified and refolded. The variant proteins showed impaired binding to the ribosome compared with mitochondrial release factor 1. This structural region in release factors is likely to be involved in codon-dependent specific ribosomal interactions.
Collapse
Affiliation(s)
- M E Askarian-Amiri
- Department of Biochemistry and Centre for Gene Research, University of Otago, P. O. Box 56, 9015 Dunedin, New Zealand
| | | | | | | | | | | | | |
Collapse
|
9
|
Song H, Mugnier P, Das AK, Webb HM, Evans DR, Tuite MF, Hemmings BA, Barford D. The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Cell 2000; 100:311-21. [PMID: 10676813 DOI: 10.1016/s0092-8674(00)80667-4] [Citation(s) in RCA: 341] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The release factor eRF1 terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase center. The crystal structure of human eRF1 to 2.8 A resolution, combined with mutagenesis analyses of the universal GGQ motif, reveals the molecular mechanism of release factor activity. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase center. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site.
Collapse
MESH Headings
- Amino Acid Sequence
- Codon, Terminator
- Crystallography
- Humans
- Hydrolysis
- Models, Molecular
- Molecular Mimicry
- Molecular Sequence Data
- Peptide Chain Termination, Translational
- Peptide Termination Factors/chemistry
- Peptide Termination Factors/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- Recombinant Proteins/chemistry
- Sequence Homology, Amino Acid
Collapse
Affiliation(s)
- H Song
- Section of Structural Biology, Institute of Cancer Research, London, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|