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Smith SA, Maurer-Alcalá XX, Yan Y, Katz LA, Santoferrara LF, McManus GB. Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion. Genome Biol Evol 2020; 12:1616-1622. [PMID: 32870974 PMCID: PMC7523726 DOI: 10.1093/gbe/evaa185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 12/04/2022] Open
Abstract
Schmidingerella arcuata is an ecologically important tintinnid ciliate that has long served as a model species in plankton trophic ecology. We present a partial micronuclear genome and macronuclear transcriptome resource for S. arcuata, acquired using single-cell techniques, and we report on pilot analyses including functional annotation and genome architecture. Our analysis shows major fragmentation, elimination, and scrambling in the micronuclear genome of S. arcuata. This work introduces a new nonmodel genome resource for the study of ciliate ecology and genomic biology and provides a detailed functional counterpart to ecological research on S. arcuata.
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Affiliation(s)
- Susan A Smith
- Department of Marine Sciences, University of Connecticut, Groton
| | | | - Ying Yan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Luciana F Santoferrara
- Department of Marine Sciences, University of Connecticut, Groton.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton
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Bezerra AR, Guimarães AR, Santos MAS. Non-Standard Genetic Codes Define New Concepts for Protein Engineering. Life (Basel) 2015; 5:1610-28. [PMID: 26569314 PMCID: PMC4695839 DOI: 10.3390/life5041610] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/12/2015] [Accepted: 10/21/2015] [Indexed: 11/16/2022] Open
Abstract
The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally designated as immutable and universal due to its conservation in most organisms, but sequencing of genes from the human mitochondrial genomes revealed deviations in codon assignments. Since then, alternative codes have been reported in both nuclear and mitochondrial genomes and genetic code engineering has become an important research field. Here, we review the most recent concepts arising from the study of natural non-standard genetic codes with special emphasis on codon re-assignment strategies that are relevant to engineering genetic code in the laboratory. Recent tools for synthetic biology and current attempts to engineer new codes for incorporation of non-standard amino acids are also reviewed in this article.
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Affiliation(s)
- Ana R Bezerra
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
| | - Ana R Guimarães
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
| | - Manuel A S Santos
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
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Abstract
SIGNIFICANCE Selenium is an essential trace element that is incorporated in the small but vital family of proteins, namely the selenoproteins, as the selenocysteine amino acid residue. In humans, 25 selenoprotein genes have been characterized. The most remarkable trait of selenoprotein biosynthesis is the cotranslational insertion of selenocysteine by the recoding of a UGA codon, normally decoded as a stop signal. RECENT ADVANCES In eukaryotes, a set of dedicated cis- and trans-acting factors have been identified as well as a variety of regulatory mechanisms, factors, or elements that control the selenoprotein expression at the level of the UGA-selenocysteine recoding process, offering a fascinating playground in the field of translational control. It appeared that the central players are two RNA molecules: the selenocysteine insertion sequence (SECIS) element within selenoprotein mRNA and the selenocysteine-tRNA([Ser]Sec); and their interacting partners. CRITICAL ISSUES After a couple of decades, despite many advances in the field and the discovery of many essential and regulatory components, the precise mechanism of UGA-selenocysteine recoding remains elusive and more complex than anticipated, with many layers of control. This review offers an update of selenoproteome biosynthesis and regulation in eukaryotes. FUTURE DIRECTIONS The regulation of selenoproteins in response to a variety of pathophysiological conditions and cellular stressors, including selenium levels, oxidative stress, replicative senescence, or cancer, awaits further detailed investigation. Clearly, the efficiency of UGA-selenocysteine recoding is the limiting stage of selenoprotein synthesis. The sequence of events leading Sec-tRNA([Ser]Sec) delivery to ribosomal A site awaits further analysis, notably at the level of a three-dimensional structure.
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Affiliation(s)
- Anne-Laure Bulteau
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, IPREM , CNRS/UPPA, UMR5254, Pau, France
| | - Laurent Chavatte
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement, IPREM , CNRS/UPPA, UMR5254, Pau, France
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A Single Amino Acid Substitution Alters Omnipotent eRF1 of Dileptus to Euplotes-type Dualpotent eRF1: Standard Codon Usage May be Advantageous in Raptorial Ciliates. Protist 2013; 164:440-9. [DOI: 10.1016/j.protis.2013.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 02/19/2013] [Accepted: 02/19/2013] [Indexed: 11/23/2022]
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Conard SE, Buckley J, Dang M, Bedwell GJ, Carter RL, Khass M, Bedwell DM. Identification of eRF1 residues that play critical and complementary roles in stop codon recognition. RNA (NEW YORK, N.Y.) 2012; 18:1210-21. [PMID: 22543865 PMCID: PMC3358643 DOI: 10.1261/rna.031997.111] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 03/15/2012] [Indexed: 05/31/2023]
Abstract
The initiation and elongation stages of translation are directed by codon-anticodon interactions. In contrast, a release factor protein mediates stop codon recognition prior to polypeptide chain release. Previous studies have identified specific regions of eukaryotic release factor one (eRF1) that are important for decoding each stop codon. The cavity model for eukaryotic stop codon recognition suggests that three binding pockets/cavities located on the surface of eRF1's domain one are key elements in stop codon recognition. Thus, the model predicts that amino acid changes in or near these cavities should influence termination in a stop codon-dependent manner. Previous studies have suggested that the TASNIKS and YCF motifs within eRF1 domain one play important roles in stop codon recognition. These motifs are highly conserved in standard code organisms that use UAA, UAG, and UGA as stop codons, but are more divergent in variant code organisms that have reassigned a subset of stop codons to sense codons. In the current study, we separately introduced TASNIKS and YCF motifs from six variant code organisms into eRF1 of Saccharomyces cerevisiae to determine their effect on stop codon recognition in vivo. We also examined the consequences of additional changes at residues located between the TASNIKS and YCF motifs. Overall, our results indicate that changes near cavities two and three frequently mediated significant effects on stop codon selectivity. In particular, changes in the YCF motif, rather than the TASNIKS motif, correlated most consistently with variant code stop codon selectivity.
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Affiliation(s)
- Sara E. Conard
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Jessica Buckley
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Mai Dang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Gregory J. Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Richard L. Carter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Mohamed Khass
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - David M. Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Eliseev BD, Alkalaeva EZ, Kryuchkova PN, Lekomtsev SA, Wang W, Liang AH, Frolova LY. Translation termination factor eRF1 of the ciliate Blepharisma japonicum recognizes all three stop codons. Mol Biol 2011. [DOI: 10.1134/s0026893311040030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Fidelity in archaeal information processing. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2010; 2010. [PMID: 20871851 PMCID: PMC2943090 DOI: 10.1155/2010/960298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Accepted: 07/12/2010] [Indexed: 12/30/2022]
Abstract
A key element during the flow of genetic information in living systems is fidelity. The accuracy of DNA replication influences the genome size as well as the rate of genome evolution. The large amount of energy invested in gene expression implies that fidelity plays a major role in fitness. On the other hand, an increase in fidelity generally coincides with a decrease in velocity. Hence, an important determinant of the evolution of life has been the establishment of a delicate balance between fidelity and variability. This paper reviews the current knowledge on quality control in archaeal information processing. While the majority of these processes are homologous in Archaea, Bacteria, and Eukaryotes, examples are provided of nonorthologous factors and processes operating in the archaeal domain. In some instances, evidence for the existence of certain fidelity mechanisms has been provided, but the factors involved still remain to be identified.
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Chaudhry R, Shakoori AR. Isolation and characterization of a novel copper-inducible metallothionein gene of a ciliate, Tetrahymena tropicalis lahorensis. J Cell Biochem 2010; 110:630-44. [PMID: 20512924 DOI: 10.1002/jcb.22573] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The two isoforms of copper metallothionein (CuMT) gene of a copper resistant ciliate, Tetrahymena tropicalis lahorensis (Ttl), have been isolated and characterized. The molecular cloning and nucleotide sequencing of cDNAs coding for the two CuMT isoforms revealed that TtlCuMT1 gene has 300, while TtlCuMT2 has 327 nucleotides, both with ATG as the initiation codon and TGA as the translational termination codon. TAG codes for glutamine in TtlCuMT2 gene which is peculiar to Tetrahymena. The deduced or translated TtlCuMT1 and TtlCuMT2 peptide sequences contain 100 and 108 amino acid residues including 28 and 32 cysteine residues, respectively. The amino acid sequences of TtlCuMT1 and TtlCuMT2 have special features of two and three CXCXXCXCXXCXC intragenic tandem repeats with a conserved structural pattern of cysteine, respectively. The predicted tertiary structures of these two isoforms indicate two domains. Domain I and the initial part of domain II showed >98% homology with other Tetrahymena CuMT. On the basis of the differences in the domain II, the metallothionein subfamily 7b can be divided into two groups, one (TtlCuMT1) comprising >100 amino acids and the other (TtlCuMT2) comprising <100 amino acids. This is a novel finding of the present study as no such report on this type of classification exists at the moment. TtlCuMT1 has 95%, while TtlCuMT2 has 97% resemblance with the previously reported CuMT genes of Tetrahymena spp. SDS-PAGE analysis using fluorescent probe as well as coomassie brilliant blue staining also confirmed the presence of metallothionein.
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Affiliation(s)
- Raheela Chaudhry
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
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Grosjean H, de Crécy-Lagard V, Marck C. Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes. FEBS Lett 2010; 584:252-64. [PMID: 19931533 DOI: 10.1016/j.febslet.2009.11.052] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 11/11/2009] [Accepted: 11/16/2009] [Indexed: 10/20/2022]
Abstract
The strategies organisms use to decode synonymous codons in cytosolic protein synthesis are not uniform. The complete isoacceptor tRNA repertoire and the type of modified nucleoside found at the wobble position 34 of their anticodons were analyzed in all kingdoms of life. This led to the identification of four main decoding strategies that are diversely used in Bacteria, Archaea and Eukarya. Many of the modern tRNA modification enzymes acting at position 34 of tRNAs are present only in specific domains and obviously have arisen late during evolution. In an evolutionary fine-tuning process, these enzymes must have played an essential role in the progressive introduction of new amino acids, and in the refinement and standardization of the canonical nuclear genetic code observed in all extant organisms (functional convergent evolutionary hypothesis).
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Affiliation(s)
- Henri Grosjean
- Université Paris-Sud, CNRS, UMR8621, Institut de Génétique et de Microbiologie, Orsay F-91405, France.
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Namy O, Rousset JP. Specification of Standard Amino Acids by Stop Codons. RECODING: EXPANSION OF DECODING RULES ENRICHES GENE EXPRESSION 2010. [DOI: 10.1007/978-0-387-89382-2_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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11
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Alkalaeva E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov FA, Gundllapalli S, Frolova L, Söll D, Kisselev L. Translation termination in pyrrolysine-utilizing archaea. FEBS Lett 2009; 583:3455-60. [PMID: 19796638 DOI: 10.1016/j.febslet.2009.09.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 09/24/2009] [Indexed: 10/20/2022]
Abstract
Although some data link archaeal and eukaryotic translation, the overall mechanism of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1) and eukaryotic (eRF1) single release factors recognize all three stop codons. The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis of the last stage of archaeal translation in pyrrolysine-utilizing species. We demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses activity and recognizes all three stop codons. The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed.
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Affiliation(s)
- Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
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12
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Vallabhaneni H, Fan-Minogue H, Bedwell DM, Farabaugh PJ. Connection between stop codon reassignment and frequent use of shifty stop frameshifting. RNA (NEW YORK, N.Y.) 2009; 15:889-897. [PMID: 19329535 PMCID: PMC2673066 DOI: 10.1261/rna.1508109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 02/05/2009] [Indexed: 05/27/2023]
Abstract
Ciliated protozoa of the genus Euplotes have undergone genetic code reassignment, redefining the termination codon UGA to encode cysteine. In addition, Euplotes spp. genes very frequently employ shifty stop frameshifting. Both of these phenomena involve noncanonical events at a termination codon, suggesting they might have a common cause. We recently demonstrated that Euplotes octocarinatus peptide release factor eRF1 ignores UGA termination codons while continuing to recognize UAA and UAG. Here we show that both the Tetrahymena thermophila and E. octocarinatus eRF1 factors allow efficient frameshifting at all three termination codons, suggesting that UGA redefinition also impaired UAA/UAG recognition. Mutations of the Euplotes factor restoring a phylogenetically conserved motif in eRF1 (TASNIKS) reduced programmed frameshifting at all three termination codons. Mutation of another conserved residue, Cys124, strongly reduces frameshifting at UGA while actually increasing frameshifting at UAA/UAG. We will discuss these results in light of recent biochemical characterization of these mutations.
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Affiliation(s)
- Haritha Vallabhaneni
- Program in Molecular and Cell Biology, Department of Biological Sciences, University of Maryland Baltimore County, Baltimore,Maryland 21250, USA
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13
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The life in science. Mol Biol 2008. [DOI: 10.1134/s0026893308050026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kim OTP, Sakurai A, Saito K, Ito K, Ikehara K, Harumoto T. Ciliates use both variant and universal genetic codes: Evidence of omnipotent eRF1s in the class Litostomatea. Gene 2008; 417:51-8. [DOI: 10.1016/j.gene.2008.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Revised: 03/21/2008] [Accepted: 03/25/2008] [Indexed: 11/30/2022]
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Lekomtsev SA, Kolosov PM, Frolova LY, Bidou L, Rousset JP, Kisselev LL. How does Euplotes translation termination factor eRF1 fail to recognize the UGA stop codon? Mol Biol 2007. [DOI: 10.1134/s002689330706009x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Lekomtsev S, Kolosov P, Bidou L, Frolova L, Rousset JP, Kisselev L. Different modes of stop codon restriction by the Stylonychia and Paramecium eRF1 translation termination factors. Proc Natl Acad Sci U S A 2007; 104:10824-9. [PMID: 17573528 PMCID: PMC1904165 DOI: 10.1073/pnas.0703887104] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Indexed: 11/18/2022] Open
Abstract
In universal-code eukaryotes, a single-translation termination factor, eukaryote class-1 polypeptide release factor (eRF1), decodes the three stop codons: UAA, UAG, and UGA. In some ciliates, like Stylonychia and Paramecium, eRF1s exhibit UGA-only decoding specificity, whereas UAG and UAA are reassigned as sense codons. Because variant-code ciliates may have evolved from universal-code ancestor(s), structural features should exist in ciliate eRF1s that restrict their stop codon recognition. In omnipotent eRF1s, stop codon recognition is associated with the N-terminal domain of the protein. Using both in vitro and in vivo assays, we show here that chimeric molecules composed of the N-terminal domain of Stylonychia eRF1 fused to the core domain (MC domain) of human eRF1 retained specificity toward UGA; this unambiguously associates eRF1 stop codon specificity to the nature of its N-terminal domain. Functional analysis of eRF1 chimeras constructed by swapping ciliate N-terminal domain sequences with the matching ones from the human protein highlighted the crucial role of the tripeptide QFM in restricting Stylonychia eRF1 specificity toward UGA. Using the site-directed mutagenesis, we show that Paramecium eRF1 specificity toward UGA resides within the NIKS (amino acids 61-64) and YxCxxxF (amino acids 124-131) motifs. Thus, we establish that eRF1 from two different ciliates relies on different molecular mechanisms to achieve specificity toward the UGA stop codon. This finding suggests that eRF1 restriction of specificity to only UGA might have been an early event occurring in independent instances in ciliate evolutionary history, possibly facilitating the reassignment of UAG and UAA to sense codons.
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Affiliation(s)
- Sergey Lekomtsev
- *Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Unité Mixte de Recherche 8621, Institut de Génétique et Microbiologie, Université Paris-Sud, F-91405 Orsay, France; and
| | - Petr Kolosov
- *Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Laure Bidou
- Unité Mixte de Recherche 8621, Institut de Génétique et Microbiologie, Université Paris-Sud, F-91405 Orsay, France; and
- Centre National de la Recherche Scientifique, F-91405 Orsay, France
| | - Ludmila Frolova
- *Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Jean-Pierre Rousset
- Unité Mixte de Recherche 8621, Institut de Génétique et Microbiologie, Université Paris-Sud, F-91405 Orsay, France; and
- Centre National de la Recherche Scientifique, F-91405 Orsay, France
| | - Lev Kisselev
- *Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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Song L, Wang Y, Chai B, Wang W, Liang A. C-terminal 76 amino acids of eRF3 are not required for the binding of release factor eRF1a from Euplotes octocarinatus. J Genet Genomics 2007; 34:486-90. [PMID: 17601607 DOI: 10.1016/s1673-8527(07)60053-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Accepted: 12/11/2006] [Indexed: 05/16/2023]
Abstract
Termination of translation in eukaryotes requires two polypeptide chain-release factors, eRF1 and eRF3. eRF1 recognizes stop signals, whereas eRF3 is a ribosome-dependent and eRF1-dependent GTPase. Polypeptide release factor eRF3 consists of N-terminal variable region and C-terminal conserved part. C-terminal part of eRF3 is responsible for termination of the translation. In the present study, the C-terminal of Euplotes octocarinatus eRF3 (eRF3C) and truncate eRF3C lacking 76 amino acids in C-terminal (eRF3Ct) were expressed in Escherichia coli. The recombinant GST-eRF3C and GST-eRF3Ct polypeptides were purified by affinity chromatography using glutathione Sepharose 4B column. After enzymatic cleavage of GST tail, the eRF3C and eRF3Ct protein were obtained. Pull-down analysis showed that the recombinant GST-eRF3C and GST-eRF3Ct polypeptides interacted with E. octocarinatus polypeptide chain release factor eRF1a. This result suggested that the C-terminal of eRF3 having 76 amino acids were not required for the binding of eRF1a in Euplotes octocarinatus.
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Affiliation(s)
- Li Song
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
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19
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Bogdanov AA, Karpov VL. RNA-protein interactions at the initial and terminal stages of protein biosynthesis as investigated by Lev Kisselev (on the occasion of his 70th anniversary). BIOCHEMISTRY (MOSCOW) 2006; 71:915-24. [PMID: 16978156 DOI: 10.1134/s0006297906080141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review highlights studies by Lev L. Kisselev and his colleagues on the initial and terminal stages of protein biosynthesis, which cover the period of the last 45 years (1961-2006). They investigated spatial structure of tRNAs, structure and functions of aminoacyl-tRNA-synthetases of higher organisms, and the final step of protein synthesis, termination of translation. L. Kisselev and his team have made three major contributions to these fields of molecular biology; (i) they proposed the hypothesis on the role of anticodon triplet of tRNA in recognition by cognate aminoacyl-tRNA synthetase, which has been experimentally confirmed and is now included in textbooks; (ii) identified primary structures and functions of two eukaryotic protein factors (eRF1 and eRF3) playing a pivotal role in translation termination; (iii) characterized a structural basis for stop codon recognition by eRF1 within the ribosome and discovered the negative structural elements of eRF1, limiting its recognition of one or two stop-codons.
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Affiliation(s)
- A A Bogdanov
- Lomonosov Moscow State University, Moscow, 119992, Russia.
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20
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Song L, Chai BF, Wang W, Liang AH. Identification of translational release factor eRF1a binding sites on eRF3 in Euplotes octocarinatus. Res Microbiol 2006; 157:842-50. [PMID: 16963230 DOI: 10.1016/j.resmic.2006.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 07/24/2006] [Accepted: 07/25/2006] [Indexed: 11/19/2022]
Abstract
Translation termination in eukaryotes is mediated by two polypeptide chain-release factors, eRF1 and eRF3. eRF1 recognizes stop signals, while eRF3 is a ribosome-dependent and eRF1-dependent GTPase. eRF1 forms a stable complex with eRF3 in vivo and in vitro. In the present study, a variety of truncated forms of Euplotes octocarinatus eRF3 were created, and systematic analysis of the interaction between E. octocarinatus eRF1a and these eRF3 mutants was performed by employing both in vivo a yeast two-hybrid assay and in vitro a pull-down assay. The results demonstrated that a short portion of the C-terminal domain of eRF3 is sufficient for eRF1a binding in E. octocarinatus. Specifically, the eRF1a-binding sites on eRF3 are located at a region containing amino acid residues 640-723 in E. octocarinatus eRF3. Amino acid sequence analysis of eRF3 from E. octocarinatus, humans and yeast showed that the eRF1a binding domain on E. octocarinatus eRF3 was similar to that of yeast eRF3 but different from that of human eRF3.
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Affiliation(s)
- Li Song
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
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21
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Alkalaeva EZ, Pisarev AV, Frolova LY, Kisselev LL, Pestova TV. In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3. Cell 2006; 125:1125-36. [PMID: 16777602 DOI: 10.1016/j.cell.2006.04.035] [Citation(s) in RCA: 230] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Revised: 03/21/2006] [Accepted: 04/18/2006] [Indexed: 10/24/2022]
Abstract
Eukaryotic translation termination is triggered by peptide release factors eRF1 and eRF3. Whereas eRF1 recognizes all three termination codons and induces hydrolysis of peptidyl tRNA, eRF3's function remains obscure. Here, we reconstituted all steps of eukaryotic translation in vitro using purified ribosomal subunits; initiation, elongation, and termination factors; and aminoacyl tRNAs. This allowed us to investigate termination using pretermination complexes assembled on mRNA encoding a tetrapeptide and to propose a model for translation termination that accounts for the cooperative action of eRF1 and eRF3 in ensuring fast release of nascent polypeptide. In this model, binding of eRF1, eRF3, and GTP to pretermination complexes first induces a structural rearrangement that is manifested as a 2 nucleotide forward shift of the toeprint attributed to pretermination complexes that leads to GTP hydrolysis followed by rapid hydrolysis of peptidyl tRNA. Cooperativity between eRF1 and eRF3 required the eRF3 binding C-terminal domain of eRF1.
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Affiliation(s)
- Elena Z Alkalaeva
- Department of Microbiology and Immunology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
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22
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Klobutcher LA. Sequencing of random Euplotes crassus macronuclear genes supports a high frequency of +1 translational frameshifting. EUKARYOTIC CELL 2006; 4:2098-105. [PMID: 16339727 PMCID: PMC1317503 DOI: 10.1128/ec.4.12.2098-2105.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Programmed translational frameshifts have been identified in genes from a broad range of organisms, but typically only a very few genes in a given organism require a frameshift for expression. In contrast, a recent analysis of gene sequences available in GenBank from ciliates in the genus Euplotes indicated that >5% required one or more +1 translational frameshifts to produce their predicted protein products. However, this sample of genes was nonrandom, biased, and derived from multiple Euplotes species. To test whether there truly is an abundance of frameshift genes in Euplotes, and to more accurately assess their frequency, we sequenced a random sample of 25 cloned genes/macronuclear DNA molecules from Euplotes crassus. Three new candidate +1 frameshift genes were identified in the sample that encode a membrane occupation and recognition nexus (MORN) repeat protein, a C(2)H(2)-type zinc finger protein, and a Ser/Thr protein kinase. Reverse transcription-PCR analyses indicate that all three genes are expressed in vegetatively proliferating cells and that the mRNAs retain the requirement of a frameshift. Although the sample of sequenced genes is relatively small, the results indicate that the frequency of genes requiring frameshifts in E. crassus is between 3.7% and 31.7% (at a 95% confidence interval). The current and past data also indicate that frameshift sites are found predominantly in genes that likely encode nonabundant proteins in the cell.
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Affiliation(s)
- Lawrence A Klobutcher
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06032, USA.
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23
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Salas-Marco J, Fan-Minogue H, Kallmeyer AK, Klobutcher LA, Farabaugh PJ, Bedwell DM. Distinct paths to stop codon reassignment by the variant-code organisms Tetrahymena and Euplotes. Mol Cell Biol 2006; 26:438-47. [PMID: 16382136 PMCID: PMC1346903 DOI: 10.1128/mcb.26.2.438-447.2006] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The reassignment of stop codons is common among many ciliate species. For example, Tetrahymena species recognize only UGA as a stop codon, while Euplotes species recognize only UAA and UAG as stop codons. Recent studies have shown that domain 1 of the translation termination factor eRF1 mediates stop codon recognition. While it is commonly assumed that changes in domain 1 of ciliate eRF1s are responsible for altered stop codon recognition, this has never been demonstrated in vivo. To carry out such an analysis, we made hybrid proteins that contained eRF1 domain 1 from either Tetrahymena thermophila or Euplotes octocarinatus fused to eRF1 domains 2 and 3 from Saccharomyces cerevisiae. We found that the Tetrahymena hybrid eRF1 efficiently terminated at all three stop codons when expressed in yeast cells, indicating that domain 1 is not the sole determinant of stop codon recognition in Tetrahymena species. In contrast, the Euplotes hybrid facilitated efficient translation termination at UAA and UAG codons but not at the UGA codon. Together, these results indicate that while domain 1 facilitates stop codon recognition, other factors can influence this process. Our findings also indicate that these two ciliate species used distinct approaches to diverge from the universal genetic code.
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Affiliation(s)
- Joe Salas-Marco
- Department of Microbiology, BBRB 432/Box 8, 1530 Third Avenue South, The University of Alabama at Birmingham, Birmingham, Alabama 35294-2170, USA
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24
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Liu Q. Comparative analysis of base biases around the stop codons in six eukaryotes. Biosystems 2006; 81:281-9. [PMID: 15979780 DOI: 10.1016/j.biosystems.2005.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Revised: 05/11/2005] [Accepted: 05/14/2005] [Indexed: 11/17/2022]
Abstract
Using full-length cDNA sequences, a comparative analysis of sequence patterns around the stop codons in six eukaryotes was performed. Here, it was showed that the codon immediately before and after the stop codons (defined as -1 codon and +1 codon, respectively) were much more biased than other examined positions, especially at the second position of -1 codons and the first position of +1 codons which were rich in As/Us and purines, respectively, for most species. The author speculated that strongly biased sequence pattern from position -2 to +4 might act as an extended translation termination signal. Translation termination was catalyzed by release factors that recognized the stop codons. The multiple amino acid sequence alignment of eukaryotic release factor 1 (eRF1) of 20 species showed that there were 16 residue sites that were strictly conserved, especially the invariant amino acids Ile70 and Lys71. Accordingly, it could be inferred that those candidate amino acids might involve in the recognition process. Moreover, the possible stop signal recognition hypothesis was also discussed herein.
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Affiliation(s)
- Qingpo Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China.
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25
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Kolosov P, Frolova L, Seit-Nebi A, Dubovaya V, Kononenko A, Oparina N, Justesen J, Efimov A, Kisselev L. Invariant amino acids essential for decoding function of polypeptide release factor eRF1. Nucleic Acids Res 2005; 33:6418-25. [PMID: 16282590 PMCID: PMC1283522 DOI: 10.1093/nar/gki927] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Revised: 10/08/2005] [Accepted: 10/08/2005] [Indexed: 11/12/2022] Open
Abstract
In eukaryotic ribosome, the N domain of polypeptide release factor eRF1 is involved in decoding stop signals in mRNAs. However, structure of the decoding site remains obscure. Here, we specifically altered the stop codon recognition pattern of human eRF1 by point mutagenesis of the invariant Glu55 and Tyr125 residues in the N domain. The 3D structure of generated eRF1 mutants was not destabilized as demonstrated by calorimetric measurements and calculated free energy perturbations. In mutants, the UAG response was most profoundly and selectively affected. Surprisingly, Glu55Arg mutant completely retained its release activity. Substitution of the aromatic ring in position 125 reduced response toward all stop codons. This result demonstrates the critical importance of Tyr125 for maintenance of the intact structure of the eRF1 decoding site. The results also suggest that Tyr125 is implicated in recognition of the 3d stop codon position and probably forms an H-bond with Glu55. The data point to a pivotal role played by the YxCxxxF motif (positions 125-131) in purine discrimination of the stop codons. We speculate that eRF1 decoding site is formed by a 3D network of amino acids side chains.
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Affiliation(s)
- Petr Kolosov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences119991 Moscow, Russia
- Institute of Molecular Biology, Aarhus UniversityDenmark
- Institute of Protein ResearchPustchino, 142290 Moscow Region, Russia
| | - Ludmila Frolova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences119991 Moscow, Russia
- Institute of Molecular Biology, Aarhus UniversityDenmark
- Institute of Protein ResearchPustchino, 142290 Moscow Region, Russia
| | - Alim Seit-Nebi
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences119991 Moscow, Russia
- Institute of Molecular Biology, Aarhus UniversityDenmark
- Institute of Protein ResearchPustchino, 142290 Moscow Region, Russia
| | - Vera Dubovaya
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences119991 Moscow, Russia
- Institute of Molecular Biology, Aarhus UniversityDenmark
- Institute of Protein ResearchPustchino, 142290 Moscow Region, Russia
| | - Artem Kononenko
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences119991 Moscow, Russia
- Institute of Molecular Biology, Aarhus UniversityDenmark
- Institute of Protein ResearchPustchino, 142290 Moscow Region, Russia
| | - Nina Oparina
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences119991 Moscow, Russia
- Institute of Molecular Biology, Aarhus UniversityDenmark
- Institute of Protein ResearchPustchino, 142290 Moscow Region, Russia
| | - Just Justesen
- Institute of Molecular Biology, Aarhus UniversityDenmark
| | - Alexandr Efimov
- Institute of Protein ResearchPustchino, 142290 Moscow Region, Russia
| | - Lev Kisselev
- To whom correspondence should be addressed. Tel: +7 095 1356009; Fax: +7 095 1351405;
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26
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Oparina NJ, Kalinina OV, Gelfand MS, Kisselev LL. Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications. Nucleic Acids Res 2005; 33:5226-34. [PMID: 16162810 PMCID: PMC1214553 DOI: 10.1093/nar/gki841] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Termination of protein synthesis is promoted in ribosomes by proper stop codon discrimination by class 1 polypeptide release factors (RFs). A large set of prokaryotic RFs differing in stop codon specificity, RF1 for UAG and UAA, and RF2 for UGA and UAA, was analyzed by means of a recently developed computational method allowing identification of the specificity-determining positions (SDPs) in families composed of proteins with similar but not identical function. Fifteen SDPs were identified within the RF1/2 superdomain II/IV known to be implicated in stop codon decoding. Three of these SDPs had particularly high scores. Five residues invariant for RF1 and RF2 [invariant amino acid residues (IRs)] were spatially clustered with the highest-scoring SDPs that in turn were located in two zones within the SDP/IR area. Zone 1 (domain II) included PxT and SPF motifs identified earlier by others as ‘discriminator tripeptides’. We suggest that IRs in this zone take part in the recognition of U, the first base of all stop codons. Zone 2 (domain IV) possessed two SDPs with the highest scores not identified earlier. Presumably, they also take part in stop codon binding and discrimination. Elucidation of potential functional role(s) of the newly identified SDP/IR zones requires further experiments.
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Affiliation(s)
- Nina J. Oparina
- To whom correspondence should be addressed. Tel: +7 095 1351419; Fax: +7 095 1351405;
| | - Olga V. Kalinina
- Department of Bioengineering and Bioinformatics, Moscow State UniversityVorob'evy Gory, 1-73, Moscow 119992, Russia
| | - Mikhail S. Gelfand
- Institute for Information Transmission Problems, Russian Academy of SciencesBolshoi Karetnyi per., 19, Moscow 127994, Russia
- State Scientific Centre GosNIIGenetika1st Dorozhny pr. 1, Moscow, 113545, Russia
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27
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Liang H, Wong JY, Bao Q, Cavalcanti ARO, Landweber LF. Decoding the decoding region: analysis of eukaryotic release factor (eRF1) stop codon-binding residues. J Mol Evol 2005; 60:337-44. [PMID: 15871044 DOI: 10.1007/s00239-004-0211-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Accepted: 10/18/2004] [Indexed: 10/25/2022]
Abstract
Peptide synthesis in eukaryotes terminates when eukaryotic release factor 1 (eRF1) binds to an mRNA stop codon and occupies the ribosomal A site. Domain 1 of the eRF1 protein has been implicated in stop codon recognition in a number of experimental studies. In order to further pinpoint the residues of this protein involved in stop codon recognition, we sequenced and compared eRF1 genes from a variety of ciliated protozoan species. We then performed a series of computational analyses to evaluate the conservation, accessibility, and structural environment of each amino acid located in domain 1. With this new dataset and methodology, we were able to identify eight specific amino acid sites important for stop codon recognition and also to propose a set of cooperative paired substitutions that may underlie stop codon reassignment. Our results are more consistent with current experimental data than previously described models.
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Affiliation(s)
- Han Liang
- Department of Chemistry, Princeton University, NJ 08544, USA.
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28
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Zhang Y, Baranov PV, Atkins JF, Gladyshev VN. Pyrrolysine and Selenocysteine Use Dissimilar Decoding Strategies. J Biol Chem 2005; 280:20740-51. [PMID: 15788401 DOI: 10.1074/jbc.m501458200] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Selenocysteine (Sec) and pyrrolysine (Pyl) are known as the 21st and 22nd amino acids in protein. Both are encoded by codons that normally function as stop signals. Sec specification by UGA codons requires the presence of a cis-acting selenocysteine insertion sequence (SECIS) element. Similarly, it is thought that Pyl is inserted by UAG codons with the help of a putative pyrrolysine insertion sequence (PYLIS) element. Herein, we analyzed the occurrence of Pyl-utilizing organisms, Pyl-associated genes, and Pyl-containing proteins. The Pyl trait is restricted to several microbes, and only one organism has both Pyl and Sec. We found that methanogenic archaea that utilize Pyl have few genes that contain in-frame UAG codons, and many of these are followed with nearby UAA or UGA codons. In addition, unambiguous UAG stop signals could not be identified. This bias was not observed in Sec-utilizing organisms and non-Pyl-utilizing archaea, as well as with other stop codons. These observations as well as analyses of the coding potential of UAG codons, overlapping genes, and release factor sequences suggest that UAG is not a typical stop signal in Pyl-utilizing archaea. On the other hand, searches for conserved Pyl-containing proteins revealed only four protein families, including methylamine methyltransferases and transposases. Only methylamine methyltransferases matched the Pyl trait and had conserved Pyl, suggesting that this amino acid is used primarily by these enzymes. These findings are best explained by a model wherein UAG codons may have ambiguous meaning and Pyl insertion can effectively compete with translation termination for UAG codons obviating the need for a specific PYLIS structure. Thus, Sec and Pyl follow dissimilar decoding and evolutionary strategies.
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Affiliation(s)
- Yan Zhang
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA
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29
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Kim OTP, Yura K, Go N, Harumoto T. Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions. Gene 2005; 346:277-86. [PMID: 15716103 DOI: 10.1016/j.gene.2004.11.046] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Revised: 11/04/2004] [Accepted: 11/26/2004] [Indexed: 11/18/2022]
Abstract
The genetic code of nuclear genes in some ciliates was found to differ from that of other organisms in the assignment of UGA, UAG, and UAA codons, which are normally assigned as stop codons. In some ciliate species, the universal stop codons UAA and UAG instead encode glutamine. In some other ciliates, the universal stop codon UGA appears to be translated as cysteine or tryptophan. Eukaryotic release factor 1 (eRF1) is a key protein in stop codon recognition, thus, the protein is believed to play an important role in the stop codon reassignment in ciliates. We have cloned, sequenced, and analyzed the cDNA of eRF1 from four ciliate species of three different classes: Karyorelictea (Loxodes striatus), Heterotrichea (Blepharisma musculus), and Litostomatea (Didinium nasutum, Dileptus margaritifer). Phylogenetic analysis of these eRF1s supports the hypothesis that the genetic code in ciliates has deviated independently several times from the universal genetic code, and that different ciliate eRF1s may have undergone different processes to change the codon specificity. Using computational methods, we have also suggested areas on the surface of eRF1s that are important for stop codon recognition in ciliate eRF1s.
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Affiliation(s)
- Oanh Thi Phuong Kim
- The Division of Human Environmental Sciences, Graduate School of Human Culture, Nara Women's University, Kitauoyanishi-machi, Nara 630-8506, Japan
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30
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Chapman B, Brown C. Translation termination in Arabidopsis thaliana: characterisation of three versions of release factor 1. Gene 2004; 341:219-25. [PMID: 15474304 DOI: 10.1016/j.gene.2004.06.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2004] [Revised: 05/14/2004] [Accepted: 06/29/2004] [Indexed: 10/26/2022]
Abstract
Translation termination is mediated in all eukaryotes by the two release factors eRF1 and eRF3. Most organisms have a single eRF1 gene, however, three isogenes of eRF1 are found in Arabidopsis thaliana. They have no introns in the coding region which may indicate that some are pseudogenes. However, each was expressed and able to rescue a temperature sensitive eRF1-mutant of Saccharomyces cerevisiae indicating functional redundancy in A. thaliana. While normally a highly accurate process, translation termination can be directed to fail by sequence elements within an messenger RNA (mRNA). Interestingly, a well-characterised readthrough element follows the stop codon in one of these three isogenes (designated eRF1-1). This element was shown to be capable of inducing readthrough in an in vitro assay using a dual luciferase reporter, but surprisingly readthrough could not be detected using the complete gene context. The results highlight the diversity and duplication of genes within plant genomes, but also emphasize the conservation of the translation process across kingdoms.
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Affiliation(s)
- Bernice Chapman
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
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31
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Abstract
Great advances have been made in the past three decades in understanding the molecular mechanics underlying protein synthesis in bacteria, but our understanding of the corresponding events in eukaryotic organisms is only beginning to catch up. In this review we describe the current state of our knowledge and ignorance of the molecular mechanics underlying eukaryotic translation. We discuss the mechanisms conserved across the three kingdoms of life as well as the important divergences that have taken place in the pathway.
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Affiliation(s)
- Lee D Kapp
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205-2185, USA.
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32
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Mora L, Zavialov A, Ehrenberg M, Buckingham RH. Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli. Mol Microbiol 2003; 50:1467-76. [PMID: 14651631 DOI: 10.1046/j.1365-2958.2003.03799.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Release factors RF1 and RF2 recognize stop codons present at the A-site of the ribosome and activate hydrolysis of peptidyl-tRNA to release the peptide chain. Interactions with RF3, a ribosome-dependent GTPase, then initiate a series of reactions that accelerate the dissociation of RF1 or RF2 and their recycling between ribosomes. Two regions of Escherichia coli RF1 and RF2 were identified previously as involved in stop codon recognition and peptidyl-tRNA hydrolysis. We show here that removing the N-terminal domain of RF1 or RF2 or exchanging this domain between the two factors does not affect RF specificity but has different effects on the activity of RF1 and RF2: truncated RF1 remains highly active and able to support rapid cell growth, whereas cells with truncated RF2 grow only poorly. Transplanting a loop of 13 amino acid residues from RF2 to RF1 switches the stop codon specificity. The interaction of the truncated factors with RF3 on the ribosome is defective: they fail to stimulate guanine nucleotide exchange on RF3, recycling is not stimulated by RF3, and nucleotide-free RF3 fails to stabilize the binding of RF1 or RF2 to the ribosome. However, the N-terminal domain seems not to be required for the expulsion of RF1 or RF2 by RF3:GTP.
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Affiliation(s)
- Liliana Mora
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
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33
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Bulygin KN, A Demeshkina N, Frolova LY, Graifer DM, Ven'yaminova AG, Kisselev LL, Karpova GG. The ribosomal A site-bound sense and stop codons are similarly positioned towards the A1823-A1824 dinucleotide of the 18S ribosomal RNA. FEBS Lett 2003; 548:97-102. [PMID: 12885414 DOI: 10.1016/s0014-5793(03)00755-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Positioning of the mRNA codon towards the 18S ribosomal RNA in the A site of human 80S ribosomes has been studied applying short mRNA analogs containing either the stop codon UAA or the sense codon UCA with a perfluoroaryl azide group at the uridine residue. Bound to the ribosomal A site, a modified codon crosslinks exclusively to the 40S subunits under mild UV irradiation. This result is inconsistent with the hypothesis [Ivanov et al. (2001) RNA 7, 1683-1692] which requires direct contact between the large rRNA and the stop codon of the mRNA as recognition step at translation termination. Both sense and stop codons crosslink to the same A1823/A1824 invariant dinucleotide in helix 44 of 18S rRNA. The data point to the resemblance between the ternary complexes formed at elongation (sense codon.aminoacyl-tRNA.AA dinucleotide of 18S rRNA) and termination (stop codon.eRF1.AA dinucleotide of 18S rRNA) steps of protein synthesis and support the view that eRF1 may be considered as a functional mimic of aminoacyl-tRNA.
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MESH Headings
- Azides
- Base Sequence
- Binding Sites
- Codon
- Codon, Terminator
- Cross-Linking Reagents
- Dinucleoside Phosphates
- Oligoribonucleotides/metabolism
- Protein Biosynthesis/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/metabolism
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/metabolism
- RNA, Transfer, Amino Acyl
- RNA, Transfer, Phe
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Affiliation(s)
- Konstantin N Bulygin
- Novosibirsk Institute of Bioorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
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34
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Chavatte L, Kervestin S, Favre A, Jean-Jean O. Stop codon selection in eukaryotic translation termination: comparison of the discriminating potential between human and ciliate eRF1s. EMBO J 2003; 22:1644-53. [PMID: 12660170 PMCID: PMC152891 DOI: 10.1093/emboj/cdg146] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
During eukaryotic translation termination, eRF1 responds to three stop codons. However, in ciliates with variant genetic codes, only one or two codons function as a stop signal. To localize the region of ciliate eRF1 implicated in stop codon discrimination, we have constructed ciliate-human hybrid eRF1s by swapping regions of human eRF1 for the equivalent region of ciliate Euplotes eRF1. We have examined the formation of a cross-link between recombinant eRF1s and mRNA analogs containing the photoactivable 4-thiouridine (s(4)U) at the first position of stop and control sense codons. With human eRF1, this cross-link can be detected only when either stop or UGG codons are located in the ribosomal A site. Here we show that the cross-link of the Euplotes-human hybrid eRF1 is restricted to mRNAs containing UAG and UAA codons, and that the entire N-terminal domain of Euplotes eRF1 is involved in discriminating against UGA and UGG. On the basis of these results, we discuss the steps of the selection process that determine the accuracy of stop codon recognition in eukaryotes.
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Affiliation(s)
- Laurent Chavatte
- Institut Jacques Monod, UMR 7592 CNRS-Universités Paris 7-Paris 6, France
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35
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Abstract
The mechanism of translation termination has long been a puzzle. Recent crystallographic evidence suggests that the eukaryotic release factor (eRF1), the bacterial release factor (RF2) and the ribosome recycling factor (RRF) all mimic a tRNA structure, whereas biochemical and genetic evidence supports the idea of a tripeptide 'anticodon' in bacterial release factors RF1 and RF2. However, the suggested structural mimicry of RF2 is not in agreement with the tripeptide 'anticodon' hypothesis and, furthermore, recently determined structures using cryo-electron microscopy show that, when bound to the ribosome, RF2 has a conformation that is distinct from the RF2 crystal structure. In addition, hydroxyl-radical probings of RRF on the ribosome are not in agreement with the simple idea that RRF mimics tRNA in the ribosome A-site. All of this evidence seriously questions the simple concept of structural mimicry between proteins and RNA and, thus, leaves only functional mimicry of protein factors of translation to be investigated.
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Affiliation(s)
- Yoshikazu Nakamura
- Department of Basic Medical Sciences, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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36
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Kisselev L, Ehrenberg M, Frolova L. Termination of translation: interplay of mRNA, rRNAs and release factors? EMBO J 2003; 22:175-82. [PMID: 12514123 PMCID: PMC140092 DOI: 10.1093/emboj/cdg017] [Citation(s) in RCA: 190] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Termination of translation in eukaryotes has focused recently on functional anatomy of polypeptide chain release factor, eRF1, by using a variety of different approaches. The tight correlation between the domain structure and different functions of eRF1 has been revealed. Independently, the role of prokaryotic RF1/2 in GTPase activity of RF3 has been deciphered, as well as RF3 function itself.
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Affiliation(s)
- Lev Kisselev
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia and
Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, S75124 Uppsala, Sweden Corresponding author e-mail:
| | - Måns Ehrenberg
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia and
Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, S75124 Uppsala, Sweden Corresponding author e-mail:
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37
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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.
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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:
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Seit-Nebi A, Frolova L, Kisselev L. Conversion of omnipotent translation termination factor eRF1 into ciliate-like UGA-only unipotent eRF1. EMBO Rep 2002; 3:881-6. [PMID: 12189178 PMCID: PMC1084231 DOI: 10.1093/embo-reports/kvf178] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In eukaryotic ribosomes, termination of translation is triggered by class 1 polypeptide release factor, eRF1. In organisms with a universal code, eRF1 responds to three stop codons, whereas, in ciliates with variant codes, only one or two codon(s) remain(s) as stop signals. By mutagenesis of the Y-C-F minidomain of the N domain, we converted an omnipotent human eRF1 recognizing all three stop codons into a unipotent 'ciliate-like' UGA-only eRF1. The conserved Cys127 located in the Y-C-F minidomain plays a critical role in stop codon recognition. The UGA-only response has also been achieved by concomitant substitutions of four other amino acids located at the Y-C-F and NIKS minidomains of eRF1. We suggest that for eRF1 the stop codon decoding is of a non-linear (non-protein-anticodon) type and explores a combination of positive and negative determinants. We assume that stop codon recognition is profoundly different by eukaryotic and prokaryotic class 1 RFs.
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Affiliation(s)
- Alim Seit-Nebi
- Engelhardt Institute of Molecular Biology, Moscow, Russia
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Kervestin S, Garnier OA, Karamyshev AL, Ito K, Nakamura Y, Meyer E, Jean-Jean O. Isolation and expression of two genes encoding eukaryotic release factor 1 from Paramecium tetraurelia. J Eukaryot Microbiol 2002; 49:374-82. [PMID: 12425524 DOI: 10.1111/j.1550-7408.2002.tb00215.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Paramecium tetraurelia, like some other ciliate species, uses an alternative nuclear genetic code where UAA and UAG are translated as glutamine and UGA is the only stop codon. It has been postulated that the use of stop codons as sense codons is dependent on the presence of specific tRNAs and on modification of eukaryotic release factor one (eRF1), a factor involved in stop codon recognition during translation termination. We describe here the isolation and characterisation of two genes, eRF1-a and eRF1 b, coding for eRF1 in P. tetraurelia. The two genes are very similar, both in genomic organization and in sequence, and might result from a recent duplication event. The two coding sequences are 1,314 nucleotides long, and encode two putative proteins of 437 amino acids with 98.5% identity. Interestingly, when compared with the eRF1 sequences either of ciliates having the same variant genetic code, or of other eukaryotes, the eRF1 of P. tetraurelia exhibits significant differences in the N-terminal region, which is thought to interact with stop codons. We discuss here the consequences of these changes in the light of recent models proposed to explain the mechanism of stop codon recognition in eukaryotes. Besides, analysis of the expression of the two genes by Northern blotting and primer extension reveals that these genes exhibit a differential expression during vegetative growth and autogamy.
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Affiliation(s)
- Stephanie Kervestin
- Unité de Biochimie Cellulaire, CNRS UMR 7098, Université Pierre et Marie Curie, Paris, France.
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Ito K, Frolova L, Seit-Nebi A, Karamyshev A, Kisselev L, Nakamura Y. Omnipotent decoding potential resides in eukaryotic translation termination factor eRF1 of variant-code organisms and is modulated by the interactions of amino acid sequences within domain 1. Proc Natl Acad Sci U S A 2002; 99:8494-9. [PMID: 12084909 PMCID: PMC124286 DOI: 10.1073/pnas.142690099] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In eukaryotes, a single translational release factor, eRF1, deciphers three stop codons, although its decoding mechanism remains puzzling. In the ciliate Tetrahymena thermophila, UAA and UAG codons are reassigned to Gln codons. A yeast eRF1-domain swap containing Tetrahymena domain 1 responded only to UGA in vitro and failed to complement a defect in yeast eRF1 in vivo at 37 degrees C. This finding demonstrates that decoding specificity of eRF1 from variant code organisms resides at domain 1. However, the wild-type eRF1 hybrid fully restored the growth of eRF1-deficient yeast at 30 degrees C. Tetrahymena eRF1 contains a variant sequence, KATNIKD, at the tip of domain 1. The TASNIKD variant of hybrid eRF1 rendered the eRF1-nullified yeast viable, although in an in vitro assay, the same hybrid eRF1 responded only to UGA. Nevertheless, the yeast eRF1 bearing the KATNIKD motif instead of the TASNIKS heptapeptide present in higher eukaryotes remains omnipotent in vivo. Collectively, these data suggest that variant genetic code organisms like Tetrahymena have an intrinsic potential to decode three stop codons in vivo, and that interaction within domain 1 between the KAT tripeptide and other sequences modulates the decoding specificity of Tetrahymena eRF1.
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Affiliation(s)
- Koichi Ito
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Bulygin KN, Repkova MN, Ven'yaminova AG, Graifer DM, Karpova GG, Frolova LY, Kisselev LL. Positioning of the mRNA stop signal with respect to polypeptide chain release factors and ribosomal proteins in 80S ribosomes. FEBS Lett 2002; 514:96-101. [PMID: 11904189 DOI: 10.1016/s0014-5793(02)02304-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
To study positioning of the mRNA stop signal with respect to polypeptide chain release factors (RFs) and ribosomal components within human 80S ribosomes, photoreactive mRNA analogs were applied. Derivatives of the UUCUAAA heptaribonucleotide containing the UUC codon for Phe and the stop signal UAAA, which bore a perfluoroaryl azido group at either the fourth nucleotide or the 3'-terminal phosphate, were synthesized. The UUC codon was directed to the ribosomal P site by the cognate tRNA(Phe), targeting the UAA stop codon to the A site. Mild UV irradiation of the ternary complexes consisting of the 80S ribosome, the mRNA analog and tRNA resulted in tRNA-dependent crosslinking of the mRNA analogs to the 40S ribosomal proteins and the 18S rRNA. mRNA analogs with the photoreactive group at the fourth uridine (the first base of the stop codon) crosslinked mainly to protein S15 (and much less to S2). For the 3'-modified mRNA analog, the major crosslinking target was protein S2, while protein S15 was much less crosslinked. Crosslinking of eukaryotic (e) RF1 was entirely dependent on the presence of a stop signal in the mRNA analog. eRF3 in the presence of eRF1 did not crosslink, but decreased the yield of eRF1 crosslinking. We conclude that (i) proteins S15 and S2 of the 40S ribosomal subunit are located near the A site-bound codon; (ii) eRF1 can induce spatial rearrangement of the 80S ribosome leading to movement of protein L4 of the 60S ribosomal subunit closer to the codon located at the A site; (iii) within the 80S ribosome, eRF3 in the presence of eRF1 does not contact the stop codon at the A site and is probably located mostly (if not entirely) on the 60S subunit.
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Affiliation(s)
- Konstantin N Bulygin
- Novosibirsk Institute of Bioorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentieva 8, 630090, Novosibirsk, Russia
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Moreira D, Kervestin S, Jean-Jean O, Philippe H. Evolution of Eukaryotic Translation Elongation and Termination Factors: Variations of Evolutionary Rate and Genetic Code Deviations. Mol Biol Evol 2002; 19:189-200. [PMID: 11801747 DOI: 10.1093/oxfordjournals.molbev.a004071] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Translation is carried out by the ribosome and several associated protein factors through three consecutive steps: initiation, elongation, and termination. Termination remains the least understood of them, partly because of the nonuniversality of the factors involved. To get some insights on the evolution of eukaryotic translation termination, we have compared the phylogeny of the release factors eRF1 and eRF3 to that of the elongation factors EF-1alpha and EF-2, with special focus on ciliates. Our results show that these four translation proteins have experienced different modes of evolution. This is especially evident for the EF-1alpha, EF-2, and eRF1 ciliate sequences. Ciliates appear as monophyletic in the EF-2 phylogenetic tree but not in the EF-1alpha and eRF1 phylogenetic trees. This seems to be mainly because of phylogeny reconstruction artifacts (the long-branch attraction) produced by the acceleration of evolutionary rate of ciliate EF-1alpha and eRF1 sequences. Interaction with the highly divergent actin found in ciliates, or on the contrary, loss of interaction, could explain the acceleration of the evolutionary rate of the EF-1alpha sequences. In the case of ciliate eRF1 sequences, their unusually high evolutionary rate may be related to the deviations in the genetic code usage found in diverse ciliates. These deviations involve a relaxation (or even abolition) of the recognition of one or two stop codons by eRF1. To achieve this, structural changes in eRF1 are needed, and this may affect its evolutionary rate. Eukaryotic translation seems to have followed a mosaic evolution, with its different elements governed by different selective pressures. However, a correlation analysis shows that, beneath the disagreement shown by the different translation proteins, their concerted evolution can still be made apparent when they are compared with other proteins that are not involved in translation.
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Affiliation(s)
- David Moreira
- Phylogénie, Bioinformatique et Génome, UMR 7622 CNRS, Paris, France
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Frolova L, Seit-Nebi A, Kisselev L. Highly conserved NIKS tetrapeptide is functionally essential in eukaryotic translation termination factor eRF1. RNA (NEW YORK, N.Y.) 2002; 8:129-36. [PMID: 11911360 PMCID: PMC1370237 DOI: 10.1017/s1355838202013262] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Class-1 polypeptide chain release factors (RFs) play a key role in translation termination. Eukaryotic (eRF1) and archaeal class-1 RFs possess a highly conserved Asn-Ile-Lys-Ser (NIKS) tetrapeptide located at the N-terminal domain of human eRF1. In the three-dimensional structure, NIKS forms a loop between helices. The universal occurrence and exposed nature of this motif provoke the appearance of hypotheses postulating an essential role of this tetrapeptide in stop codon recognition and ribosome binding. To approach this problem experimentally, site-directed mutagenesis of the NIKS (positions 61-64) in human eRF1 and adjacent amino acids has been applied followed by determination of release activity and ribosome-binding capacity of mutants. Substitutions of Asn61 and Ile62 residues of the NIKS cause a decrease in the ability of eRF1 mutants to promote termination reaction in vitro, but to a different extent depending on the stop codon specificity, position, and nature of the substituting residues. This observation points to a possibility that Asn-Ile dipeptide modulates the specific recognition of the stop codons by eRF1. Some replacements at positions 60, 63, and 64 cause a negligible (if any) effect in contrast to what has been deduced from some current hypotheses predicting the structure of the termination codon recognition site in eRF1. Reduction in ribosome binding revealed for Ile62, Ser64, Arg65, and Arg68 mutants argues in favor of the essential role played by the right part of the NIKS loop in interaction with the ribosome, most probably with ribosomal RNA.
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Abstract
Although the eukaryotic (eRF1) and prokaryotic (RF2) polypeptide release (translation termination) factors are functionally similar, they turn out to be very different in overall shape and architecture and in the location of key functional elements.
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Affiliation(s)
- Lev Kisselev
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
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Seit-Nebi A, Frolova L, Justesen J, Kisselev L. Class-1 translation termination factors: invariant GGQ minidomain is essential for release activity and ribosome binding but not for stop codon recognition. Nucleic Acids Res 2001; 29:3982-7. [PMID: 11574680 PMCID: PMC60236 DOI: 10.1093/nar/29.19.3982] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Previously, we have shown that all class-1 polypeptide release factors (RFs) share a common glycine-glycine-glutamine (GGQ) motif, which is critical for RF activity. Here, we subjected to site-directed mutagenesis two invariant amino acids, Gln185 and Arg189, situated in the GGQ minidomain of human eRF1, followed by determination of RF activity and the ribosome binding capacity for mutant eRF1. We show that replacement of Gln185 with polar amino acid residues causes partial inactivation of RF activity; Gln185Ile, Arg189Ala and Arg189Gln mutants are completely inactive; all mutants that retain partial RF activity respond similarly to three stop codons. We suggest that loss of RF activity for Gln185 and Arg189 mutants is caused by distortion of the conformation of the GGQ minidomain but not by damage of the stop codon recognition site of eRF1. Our data are inconsistent with the model postulating direct involvement of Gln185 side chain in orientation of water molecule toward peptidyl-tRNA ester bond at the ribosomal peptidyl transferase centre. Most of the Gln185 mutants exhibit reduced ability to bind to the ribosome, probably, to rRNA and/or (peptidyl)-tRNA(s). The data suggest that the GGQ motif is implicated both in promoting peptidyl-tRNA hydrolysis and binding to the ribosome.
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Affiliation(s)
- A Seit-Nebi
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
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