1
|
Shuvalov A, Klishin A, Biziaev N, Shuvalova E, Alkalaeva E. Functional Activity of Isoform 2 of Human eRF1. Int J Mol Sci 2024; 25:7997. [PMID: 39063238 PMCID: PMC11277123 DOI: 10.3390/ijms25147997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/29/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Eukaryotic release factor eRF1, encoded by the ETF1 gene, recognizes stop codons and induces peptide release during translation termination. ETF1 produces several different transcripts as a result of alternative splicing, from which two eRF1 isoforms can be formed. Isoform 1 codes well-studied canonical eRF1, and isoform 2 is 33 amino acid residues shorter than isoform 1 and completely unstudied. Using a reconstituted mammalian in vitro translation system, we showed that the isoform 2 of human eRF1 is also involved in translation. We showed that eRF1iso2 can interact with the ribosomal subunits and pre-termination complex. However, its codon recognition and peptide release activities have decreased. Additionally, eRF1 isoform 2 exhibits unipotency to UGA. We found that eRF1 isoform 2 interacts with eRF3a but stimulated its GTPase activity significantly worse than the main isoform eRF1. Additionally, we studied the eRF1 isoform 2 effect on stop codon readthrough and translation in a cell-free translation system. We observed that eRF1 isoform 2 suppressed stop codon readthrough of the uORFs and decreased the efficiency of translation of long coding sequences. Based on these data, we assumed that human eRF1 isoform 2 can be involved in the regulation of translation termination. Moreover, our data support previously stated hypotheses that the GTS loop is important for the multipotency of eRF1 to all stop codons. Whereas helix α1 of the N-domain eRF1 is proposed to be involved in conformational rearrangements of eRF1 in the A-site of the ribosome that occur after GTP hydrolysis by eRF3, which ensure hydrolysis of peptidyl-tRNA at the P site of the ribosome.
Collapse
Affiliation(s)
- Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexandr Klishin
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.)
| | - Nikita Biziaev
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.)
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (A.S.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
2
|
Salman A, Biziaev N, Shuvalova E, Alkalaeva E. mRNA context and translation factors determine decoding in alternative nuclear genetic codes. Bioessays 2024; 46:e2400058. [PMID: 38724251 DOI: 10.1002/bies.202400058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024]
Abstract
The genetic code is a set of instructions that determine how the information in our genetic material is translated into amino acids. In general, it is universal for all organisms, from viruses and bacteria to humans. However, in the last few decades, exceptions to this rule have been identified both in pro- and eukaryotes. In this review, we discuss the 16 described alternative eukaryotic nuclear genetic codes and observe theories of their appearance in evolution. We consider possible molecular mechanisms that allow codon reassignment. Most reassignments in nuclear genetic codes are observed for stop codons. Moreover, in several organisms, stop codons can simultaneously encode amino acids and serve as termination signals. In this case, the meaning of the codon is determined by the additional factors besides the triplets. A comprehensive review of various non-standard coding events in the nuclear genomes provides a new insight into the translation mechanism in eukaryotes.
Collapse
Affiliation(s)
- Ali Salman
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, Russia
| | - Nikita Biziaev
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, Russia
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
3
|
Stefanov BA, Ajuh E, Allen S, Nowacki M. Eukaryotic release factor 1 from Euplotes promotes frameshifting at premature stop codons in human cells. iScience 2024; 27:109413. [PMID: 38510117 PMCID: PMC10952039 DOI: 10.1016/j.isci.2024.109413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/23/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Human physiology is highly susceptible to frameshift mutations within coding regions, and many hereditary diseases and cancers are caused by such indels. Presently, therapeutic options to counteract them are limited and, in the case of direct genome editing, risky. Here, we show that release factor 1 (eRF1) from Euplotes, an aquatic protist known for frequent +1 frameshifts in its coding regions, can enhance +1 ribosomal frameshifting at slippery heptameric sequences in human cells without an apparent requirement for an mRNA secondary structure. We further show an increase in frameshifting rate at the premature termination sequence found in the HEXA gene of Tay-Sachs disease patients, or a breast cancer cell line that harbors a tumor-driving frameshift mutation in GATA3. Although the overall increase in frameshifting would need further improvement for clinical applications, our results underscore the potential of exogenous factors, such as Eu eRF1, to increase frameshifting in human cells.
Collapse
Affiliation(s)
| | - Elvis Ajuh
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Sarah Allen
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| |
Collapse
|
4
|
Williams TD, Rousseau A. Translation regulation in response to stress. FEBS J 2024. [PMID: 38308808 DOI: 10.1111/febs.17076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
Cell stresses occur in a wide variety of settings: in disease, during industrial processes, and as part of normal day-to-day rhythms. Adaptation to these stresses requires cells to alter their proteome. Cells modify the proteins they synthesize to aid proteome adaptation. Changes in both mRNA transcription and translation contribute to altered protein synthesis. Here, we discuss the changes in translational mechanisms that occur following the onset of stress, and the impact these have on stress adaptation.
Collapse
Affiliation(s)
- Thomas D Williams
- MRC-PPU, School of Life Sciences, University of Dundee, UK
- Sir William Dunn School of Pathology, University of Oxford, UK
| | | |
Collapse
|
5
|
McGowan J, Kilias ES, Alacid E, Lipscombe J, Jenkins BH, Gharbi K, Kaithakottil GG, Macaulay IC, McTaggart S, Warring SD, Richards TA, Hall N, Swarbreck D. Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids. PLoS Genet 2023; 19:e1010913. [PMID: 37796765 PMCID: PMC10553269 DOI: 10.1371/journal.pgen.1010913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/10/2023] [Indexed: 10/07/2023] Open
Abstract
The genetic code is one of the most highly conserved features across life. Only a few lineages have deviated from the "universal" genetic code. Amongst the few variants of the genetic code reported to date, the codons UAA and UAG virtually always have the same translation, suggesting that their evolution is coupled. Here, we report the genome and transcriptome sequencing of a novel uncultured ciliate, belonging to the Oligohymenophorea class, where the translation of the UAA and UAG stop codons have changed to specify different amino acids. Genomic and transcriptomic analyses revealed that UAA has been reassigned to encode lysine, while UAG has been reassigned to encode glutamic acid. We identified multiple suppressor tRNA genes with anticodons complementary to the reassigned codons. We show that the retained UGA stop codon is enriched in the 3'UTR immediately downstream of the coding region of genes, suggesting that there is functional drive to maintain tandem stop codons. Using a phylogenomics approach, we reconstructed the ciliate phylogeny and mapped genetic code changes, highlighting the remarkable number of independent genetic code changes within the Ciliophora group of protists. According to our knowledge, this is the first report of a genetic code variant where UAA and UAG encode different amino acids.
Collapse
Affiliation(s)
- Jamie McGowan
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Elisabet Alacid
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - James Lipscombe
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Iain C. Macaulay
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Seanna McTaggart
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Sally D. Warring
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| |
Collapse
|
6
|
Kachale A, Pavlíková Z, Nenarokova A, Roithová A, Durante IM, Miletínová P, Záhonová K, Nenarokov S, Votýpka J, Horáková E, Ross RL, Yurchenko V, Beznosková P, Paris Z, Valášek LS, Lukeš J. Short tRNA anticodon stem and mutant eRF1 allow stop codon reassignment. Nature 2023; 613:751-758. [PMID: 36631608 DOI: 10.1038/s41586-022-05584-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 11/18/2022] [Indexed: 01/13/2023]
Abstract
Cognate tRNAs deliver specific amino acids to translating ribosomes according to the standard genetic code, and three codons with no cognate tRNAs serve as stop codons. Some protists have reassigned all stop codons as sense codons, neglecting this fundamental principle1-4. Here we analyse the in-frame stop codons in 7,259 predicted protein-coding genes of a previously undescribed trypanosomatid, Blastocrithidia nonstop. We reveal that in this species in-frame stop codons are underrepresented in genes expressed at high levels and that UAA serves as the only termination codon. Whereas new tRNAsGlu fully cognate to UAG and UAA evolved to reassign these stop codons, the UGA reassignment followed a different path through shortening the anticodon stem of tRNATrpCCA from five to four base pairs (bp). The canonical 5-bp tRNATrp recognizes UGG as dictated by the genetic code, whereas its shortened 4-bp variant incorporates tryptophan also into in-frame UGA. Mimicking this evolutionary twist by engineering both variants from B. nonstop, Trypanosoma brucei and Saccharomyces cerevisiae and expressing them in the last two species, we recorded a significantly higher readthrough for all 4-bp variants. Furthermore, a gene encoding B. nonstop release factor 1 acquired a mutation that specifically restricts UGA recognition, robustly potentiating the UGA reassignment. Virtually the same strategy has been adopted by the ciliate Condylostoma magnum. Hence, we describe a previously unknown, universal mechanism that has been exploited in unrelated eukaryotes with reassigned stop codons.
Collapse
Affiliation(s)
- Ambar Kachale
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Zuzana Pavlíková
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Anna Nenarokova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.,School of Biological Sciences, University of Bristol, Bristol, UK
| | - Adriana Roithová
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Ignacio M Durante
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Petra Miletínová
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic.,Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Serafim Nenarokov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Jan Votýpka
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Institute of Microbiology, Czech Academy of Sciences, Třeboň, Czech Republic
| | | | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petra Beznosková
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic. .,Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
| | | | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic. .,Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
| |
Collapse
|
7
|
Wang C, Yan Y, Chen X, Al‐Farraj SA, El‐Serehy HA, Gao F. Further analyses on the evolutionary “key‐protist”
Halteria
(Protista, Ciliophora) based on transcriptomic data. ZOOL SCR 2019. [DOI: 10.1111/zsc.12380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chundi Wang
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
| | - Xiao Chen
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
- Department of Genetics and Development Columbia University Medical Center New York NY USA
| | - Saleh A. Al‐Farraj
- Zoology Department, College of Science King Saud University Riyadh Saudi Arabia
| | - Hamed A. El‐Serehy
- Zoology Department, College of Science King Saud University Riyadh Saudi Arabia
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
| |
Collapse
|
8
|
Ivanov A, Shuvalova E, Egorova T, Shuvalov A, Sokolova E, Bizyaev N, Shatsky I, Terenin I, Alkalaeva E. Polyadenylate-binding protein-interacting proteins PAIP1 and PAIP2 affect translation termination. J Biol Chem 2019; 294:8630-8639. [PMID: 30992367 DOI: 10.1074/jbc.ra118.006856] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 03/29/2019] [Indexed: 12/29/2022] Open
Abstract
Polyadenylate-binding protein (PABP) stimulates translation termination via interaction of its C-terminal domain with eukaryotic polypeptide chain release factor, eRF3. Additionally, two other proteins, poly(A)-binding protein-interacting proteins 1 and 2 (PAIP1 and PAIP2), bind the same domain of PABP and regulate its translation-related activity. To study the biochemistry of eRF3 and PAIP1/2 competition for PABP binding, we quantified the effects of PAIPs on translation termination in the presence or absence of PABP. Our results demonstrated that both PAIP1 and PAIP2 prevented translation termination at the premature termination codon, by controlling PABP activity. Moreover, PAIP1 and PAIP2 inhibited the activity of free PABP on translation termination in vitro However, after binding the poly(A) tail, PABP became insensitive to suppression by PAIPs and efficiently activated translation termination in the presence of eRF3a. Additionally, we revealed that PAIP1 binds eRF3 in solution, which stabilizes the post-termination complex. These results indicated that PAIP1 and PAIP2 participate in translation termination and are important regulators of readthrough at the premature termination codon.
Collapse
Affiliation(s)
- Alexandr Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ekaterina Shuvalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Tatiana Egorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey Shuvalov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nikita Bizyaev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ivan Shatsky
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ilya Terenin
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow 119234, Russia; Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow 119146, Russia.
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
| |
Collapse
|
9
|
Wada M, Ito K. Misdecoding of rare CGA codon by translation termination factors, eRF1/eRF3, suggests novel class of ribosome rescue pathway in S. cerevisiae. FEBS J 2019; 286:788-802. [PMID: 30471181 PMCID: PMC7379694 DOI: 10.1111/febs.14709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 10/24/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022]
Abstract
The CGA arginine codon is a rare codon in Saccharomyces cerevisiae. Thus, full-length mature protein synthesis from reporter genes with internal CGA codon repeats are markedly reduced, and the reporters, instead, produce short-sized polypeptides via an unknown mechanism. Considering the product size and similar properties between CGA sense and UGA stop codons, we hypothesized that eukaryote polypeptide-chain release factor complex eRF1/eRF3 catalyses polypeptide release at CGA repeats. Herein, we performed a series of analyses and report that the CGA codon can be, to a certain extent, decoded as a stop codon in yeast. This also raises an intriguing possibility that translation termination factors eRF1/eRF3 rescue ribosomes stalled at CGA codons, releasing premature polypeptides, and competing with canonical tRNAICG to the CGA codon. Our results suggest an alternative ribosomal rescue pathway in eukaryotes. The present results suggest that misdecoding of low efficient codons may play a novel role in global translation regulation in S. cerevisiae.
Collapse
Affiliation(s)
- Miki Wada
- Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoKashiwa‐cityJapan
- Technical officeThe Institute of Medical ScienceThe University of TokyoMinato‐kuJapan
| | - Koichi Ito
- Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoKashiwa‐cityJapan
| |
Collapse
|
10
|
Abstract
Termination of protein synthesis on the ribosome requires that mRNA stop codons are recognized with high fidelity. This is achieved by specific release factor proteins that are very different in bacteria and eukaryotes. Hence, while there are two release factors with overlapping specificity in bacteria, the single omnipotent eRF1 release factor in eukaryotes is able to read all three stop codons. This is particularly remarkable as it is able to select three out of four combinations of purine bases in the last two codon positions. With recently determined 3D structures of eukaryotic termination complexes, it has become possible to explore the origin of eRF1 specificity by computer simulations. Here, we report molecular dynamics free energy calculations on these termination complexes, where relative eRF1 binding free energies to different cognate and near-cognate codons are evaluated. The simulations show a high and uniform discrimination against the near-cognate codons, that differ from the cognate ones by a single nucleotide, and reveal the structural mechanisms behind the precise decoding by eRF1. The eukaryotic release factor eRF1 is able to recognize the three stop codons UAA, UAG and UGA with high accuracy, while discriminating against near-cognate codons. Here the authors use molecular dynamic simulation to provide insight into the molecular basis behind the remarkable codon specificity of eRF1.
Collapse
|
11
|
Alkalaeva E, Mikhailova T. Reassigning stop codons via translation termination: How a few eukaryotes broke the dogma. Bioessays 2016; 39. [PMID: 28009453 DOI: 10.1002/bies.201600213] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The genetic code determines how amino acids are encoded within mRNA. It is universal among the vast majority of organisms, although several exceptions are known. Variant genetic codes are found in ciliates, mitochondria, and numerous other organisms. All revealed genetic codes (standard and variant) have at least one codon encoding a translation stop signal. However, recently two new genetic codes with a reassignment of all three stop codons were revealed in studies examining the protozoa transcriptomes. Here, we discuss this finding and the recent studies of variant genetic codes in eukaryotes. We consider the possible molecular mechanisms allowing the use of certain codons as sense and stop signals simultaneously. The results obtained by studying these amazing organisms represent a new and exciting insight into the mechanism of stop codon decoding in eukaryotes. Also see the video abstract here.
Collapse
Affiliation(s)
- Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Mikhailova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
12
|
Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
Collapse
Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| |
Collapse
|
13
|
Swart EC, Serra V, Petroni G, Nowacki M. Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination. Cell 2016; 166:691-702. [PMID: 27426948 PMCID: PMC4967479 DOI: 10.1016/j.cell.2016.06.020] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 04/19/2016] [Accepted: 06/06/2016] [Indexed: 01/13/2023]
Abstract
The prevailing view of the nuclear genetic code is that it is largely frozen and unambiguous. Flexibility in the nuclear genetic code has been demonstrated in ciliates that reassign standard stop codons to amino acids, resulting in seven variant genetic codes, including three previously undescribed ones reported here. Surprisingly, in two of these species, we find efficient translation of all 64 codons as standard amino acids and recognition of either one or all three stop codons. How, therefore, does the translation machinery interpret a “stop” codon? We provide evidence, based on ribosomal profiling and “stop” codon depletion shortly before coding sequence ends, that mRNA 3′ ends may contribute to distinguishing stop from sense in a context-dependent manner. We further propose that such context-dependent termination/readthrough suppression near transcript ends enables genetic code evolution. Alternative nuclear genetic codes continue to be discovered in ciliates Genetic codes with stops and all their codons encoding standard amino acids exist Transcript ends may distinguish stop codons as such in ambiguous genetic codes The ability to resolve genetic code ambiguity may enable genetic code evolution
Collapse
Affiliation(s)
| | - Valentina Serra
- Department of Biology, University of Pisa, Pisa 56126, Italy
| | - Giulio Petroni
- Department of Biology, University of Pisa, Pisa 56126, Italy
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.
| |
Collapse
|
14
|
Chai B, Li C, Yu J, Hao Y, Guo P, Shen Q. Stop codon recognition in the early-diverged protozoans Giardia lamblia and Trichomonas vaginalis. Mol Biochem Parasitol 2015; 202:15-21. [PMID: 26310515 DOI: 10.1016/j.molbiopara.2015.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/25/2015] [Accepted: 08/18/2015] [Indexed: 10/23/2022]
Abstract
Two classes of polypeptide release factors (RFs) are responsible for maintaining accuracy in translation termination; however, their detailed mechanism of action and evolutionary history of these factors remain elusive. The structure and function of RFs vary in bacteria and eukaryotes, a fact that is suggestive of evolutionary changes in the translation termination system. Giardia lamblia (Diplomonada) and Trichomonas vaginalis (Parabasalia) are considered as early-diverged eukaryotes. The class II release factor, eRF3, of Giardia (Gl-eRF3) appears to have only one domain that corresponds to EF-1α and lacks the N-terminal domain, similar to that of eRF3 of other organisms. In the present study, we show that the chimeric molecules Gl/Sc eRF1 and Tv/Sc eRF1, which are composed of the N-terminal domain of Gl-eRF1 or Tv-eRF1, fused to the core domain (M and C domain) of Saccharomyces cerevisiae eRF1 (Sc-eRF1), resulting in loss of the RF properties of the N-terminal domain. This suggests that the conformation of eRF1 for stop codon recognition in Giardia and Trichomonas varies from the eRF1s of other eukaryotes, including ciliates and yeast. Further studies using intra-N-terminal chimeras of eRF1 indicated that the combination of the GTS loop and NIKS motif from Gl-eRF1 and the Y-C-F motif from Sc-eRF1within the N terminal domain of hybrid eRF1 could restore UGA, but not UAG and UGA recognition. In contrast, the combination of the GTS loop and the NIKS motif of Sc-eRF1 and the Y-C-F motif of Gl-eRF1 could restore UAG and UAA recognition, but not UGA recognition. Thus, these results confirm the findings of previous studies that three motifs in eRF1 are necessary for discrimination of the three bases of stop codons. The NIKS motif is responsible for recognition of the first two bases of UAA and UAG, and the Y-C-F motif identifies the second base of UGA by Gl-eRF1. Amino acid residue substitutions in Gl/Sc-eRF1 by corresponding residues of Sc-eRF1 could change and even restore RF activity, further suggesting different conformation of eRF1 are used for stop codon recognition in Giardia and in Saccharomyces.
Collapse
Affiliation(s)
- Baofeng Chai
- Key Laboratory of Chemical Biology and Molecular Engineering, Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China.
| | - Cui Li
- Faculty of Environment and Economics, Shanxi University of Finance and Economics, Taiyuan 030006, China
| | - Jingfei Yu
- Key Laboratory of Chemical Biology and Molecular Engineering, Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Yanrong Hao
- Key Laboratory of Chemical Biology and Molecular Engineering, Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Ping Guo
- Key Laboratory of Chemical Biology and Molecular Engineering, Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Quan Shen
- Key Laboratory of Chemical Biology and Molecular Engineering, Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| |
Collapse
|
15
|
Saito K, Ito K. Genetic analysis of L123 of the tRNA-mimicking eukaryote release factor eRF1, an amino acid residue critical for discrimination of stop codons. Nucleic Acids Res 2015; 43:4591-601. [PMID: 25897120 PMCID: PMC4482090 DOI: 10.1093/nar/gkv376] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/09/2015] [Indexed: 11/18/2022] Open
Abstract
In eukaryotes, the tRNA-mimicking polypeptide-chain release factor, eRF1, decodes stop codons on the ribosome in a complex with eRF3; this complex exhibits striking structural similarity to the tRNA–eEF1A–GTP complex. Although amino acid residues or motifs of eRF1 that are critical for stop codon discrimination have been identified, the details of the molecular mechanisms involved in the function of the ribosomal decoding site remain obscure. Here, we report analyses of the position-123 amino acid of eRF1 (L123 in Saccharomyces cerevisiae eRF1), a residue that is phylogenetically conserved among species with canonical and variant genetic codes. In vivo readthrough efficiency analysis and genetic growth complementation analysis of the residue-123 systematic mutants suggested that this amino acid functions in stop codon discrimination in a manner coupled with eRF3 binding, and distinctive from previously reported adjacent residues. Furthermore, aminoglycoside antibiotic sensitivity analysis and ribosomal docking modeling of eRF1 in a quasi-A/T state suggested a functional interaction between the side chain of L123 and ribosomal residues critical for codon recognition in the decoding site, as a molecular explanation for coupling with eRF3. Our results provide insights into the molecular mechanisms underlying stop codon discrimination by a tRNA-mimicking protein on the ribosome.
Collapse
Affiliation(s)
- Kazuki Saito
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-city, Chiba 277-8562, Japan
| | - Koichi Ito
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-city, Chiba 277-8562, Japan
| |
Collapse
|
16
|
Susorov D, Mikhailova T, Ivanov A, Sokolova E, Alkalaeva E. Stabilization of eukaryotic ribosomal termination complexes by deacylated tRNA. Nucleic Acids Res 2015; 43:3332-43. [PMID: 25753665 PMCID: PMC4381076 DOI: 10.1093/nar/gkv171] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/21/2015] [Indexed: 01/12/2023] Open
Abstract
Stabilization of the ribosomal complexes plays an important role in translational control. Mechanisms of ribosome stabilization have been studied in detail for initiation and elongation of eukaryotic translation, but almost nothing is known about stabilization of eukaryotic termination ribosomal complexes. Here, we present one of the mechanisms of fine-tuning of the translation termination process in eukaryotes. We show that certain deacylated tRNAs, remaining in the E site of the ribosome at the end of the elongation cycle, increase the stability of the termination and posttermination complexes. Moreover, only the part of eRF1 recognizing the stop codon is stabilized in the A site of the ribosome, and the stabilization is not dependent on the hydrolysis of peptidyl-tRNA. The determinants, defining this property of the tRNA, reside in the acceptor stem. It was demonstrated by site-directed mutagenesis of tRNAVal and construction of a mini-helix structure identical to the acceptor stem of tRNA. The mechanism of this stabilization is different from the fixation of the unrotated state of the ribosome by CCA end of tRNA or by cycloheximide in the E site. Our data allow to reveal the possible functions of the isodecoder tRNAs in eukaryotes.
Collapse
Affiliation(s)
- Denis Susorov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Tatiana Mikhailova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander Ivanov
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Elizaveta Sokolova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
17
|
Blanchet S, Rowe M, Von der Haar T, Fabret C, Demais S, Howard MJ, Namy O. New insights into stop codon recognition by eRF1. Nucleic Acids Res 2015; 43:3298-308. [PMID: 25735746 PMCID: PMC4381064 DOI: 10.1093/nar/gkv154] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/17/2015] [Indexed: 11/25/2022] Open
Abstract
In eukaryotes, translation termination is performed by eRF1, which recognizes stop codons via its N-terminal domain. Many previous studies based on point mutagenesis, cross-linking experiments or eRF1 chimeras have investigated the mechanism by which the stop signal is decoded by eRF1. Conserved motifs, such as GTS and YxCxxxF, were found to be important for termination efficiency, but the recognition mechanism remains unclear. We characterized a region of the eRF1 N-terminal domain, the P1 pocket, that we had previously shown to be involved in termination efficiency. We performed alanine scanning mutagenesis of this region, and we quantified in vivo readthrough efficiency for each alanine mutant. We identified two residues, arginine 65 and lysine 109, as critical for recognition of the three stop codons. We also demonstrated a role for the serine 33 and serine 70 residues in UGA decoding in vivo. NMR analysis of the alanine mutants revealed that the correct conformation of this region was controlled by the YxCxxxF motif. By combining our genetic data with a structural analysis of eRF1 mutants, we were able to formulate a new model in which the stop codon interacts with eRF1 through the P1 pocket.
Collapse
Affiliation(s)
- Sandra Blanchet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 400, 91400 Orsay, France
| | - Michelle Rowe
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | | | - Céline Fabret
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 400, 91400 Orsay, France
| | - Stéphane Demais
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 400, 91400 Orsay, France
| | - Mark J Howard
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 400, 91400 Orsay, France
| |
Collapse
|
18
|
Schmied WH, Elsässer SJ, Uttamapinant C, Chin JW. Efficient multisite unnatural amino acid incorporation in mammalian cells via optimized pyrrolysyl tRNA synthetase/tRNA expression and engineered eRF1. J Am Chem Soc 2014; 136:15577-83. [PMID: 25350841 PMCID: PMC4333590 DOI: 10.1021/ja5069728] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The efficient, site-specific introduction of unnatural amino acids into proteins in mammalian cells is an outstanding challenge in realizing the potential of genetic code expansion approaches. Addressing this challenge will allow the synthesis of modified recombinant proteins and augment emerging strategies that introduce new chemical functionalities into proteins to control and image their function with high spatial and temporal precision in cells. The efficiency of unnatural amino acid incorporation in response to the amber stop codon (UAG) in mammalian cells is commonly considered to be low. Here we demonstrate that tRNA levels can be limiting for unnatural amino acid incorporation efficiency, and we develop an optimized pyrrolysyl-tRNA synthetase/tRNACUA expression system, with optimized tRNA expression for mammalian cells. In addition, we engineer eRF1, that normally terminates translation on all three stop codons, to provide a substantial increase in unnatural amino acid incorporation in response to the UAG codon without increasing readthrough of other stop codons. By combining the optimized pyrrolysyl-tRNA synthetase/tRNACUA expression system and an engineered eRF1, we increase the yield of protein bearing unnatural amino acids at a single site 17- to 20-fold. Using the optimized system, we produce proteins containing unnatural amino acids with comparable yields to a protein produced from a gene that does not contain a UAG stop codon. Moreover, the optimized system increases the yield of protein, incorporating an unnatural amino acid at three sites, from unmeasurably low levels up to 43% of a no amber stop control. Our approach may enable the efficient production of site-specifically modified therapeutic proteins, and the quantitative replacement of targeted cellular proteins with versions bearing unnatural amino acids that allow imaging or synthetic regulation of protein function.
Collapse
Affiliation(s)
- Wolfgang H Schmied
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | | | | | | |
Collapse
|
19
|
Wada M, Ito K. A genetic approach for analyzing the co-operative function of the tRNA mimicry complex, eRF1/eRF3, in translation termination on the ribosome. Nucleic Acids Res 2014; 42:7851-66. [PMID: 24914055 PMCID: PMC4081094 DOI: 10.1093/nar/gku493] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During termination of translation in eukaryotes, a GTP-binding protein, eRF3, functions within a complex with the tRNA-mimicking protein, eRF1, to decode stop codons. It remains unclear how the tRNA-mimicking protein co-operates with the GTPase and with the functional sites on the ribosome. In order to elucidate the molecular characteristics of tRNA-mimicking proteins involved in stop codon decoding, we have devised a heterologous genetic system in Saccharomyces cerevisiae. We found that eRF3 from Pneumocystis carinii (Pc-eRF3) did not complement depletion of S. cerevisiae eRF3. The strength of Pc-eRF3 binding to Sc-eRF1 depends on the GTP-binding domain, suggesting that defects of the GTPase switch in the heterologous complex causes the observed lethality. We isolated mutants of Pc-eRF3 and Sc-eRF1 that restore cell growth in the presence of Pc-eRF3 as the sole source of eRF3. Mapping of these mutations onto the latest 3D-complex structure revealed that they were located in the binding-interface region between eRF1 and eRF3, as well as in the ribosomal functional sites. Intriguingly, a novel functional site was revealed adjacent to the decoding site of eRF1, on the tip domain that mimics the tRNA anticodon loop. This novel domain likely participates in codon recognition, coupled with the GTPase function.
Collapse
Affiliation(s)
- Miki Wada
- Technical office, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-city, Chiba, 277-8562, Japan
| | - Koichi Ito
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-city, Chiba, 277-8562, Japan
| |
Collapse
|
20
|
Xu L, Hao Y, Li C, Shen Q, Chai B, Wang W, Liang A. Identification of amino acids responsible for stop codon recognition for polypeptide chain release factor. Biochem Cell Biol 2013; 91:155-64. [PMID: 23668788 DOI: 10.1139/bcb-2012-0091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
One factor involved in eukaryotic translation termination is class 1 release factor in eukaryotes (eRF1), which functions to decode stop codons. Variant code species, such as ciliates, frequently exhibit altered stop codon recognition. Studies revealed that some class-specific residues in the eRF1 N-terminal domain are responsible for stop codon reassignment in ciliates. Here, we investigated the effects on stop codon recognition of chimeric eRF1s containing the N-terminal domain of Euplotes octocarinatus and Blepharisma japonicum eRF1 fused to Saccharomyces cerevisiae M and C domains using dual luciferase read-through assays. Mutation of class-specific residues in different eRF1 classes was also studied to identify key residues and motifs involved in stop codon decoding. As expected, our results demonstrate that 3 pockets within the eRF1 N-terminal domain were involved in decoding stop codon nucleotides. However, allocation of residues to each pocket was revalued. Our data suggest that hydrophobic and class-specific surface residues participate in different functions: modulation of pocket conformation and interaction with stop codon nucleotides, respectively. Residues conserved across all eRF1s determine the relative orientation of the 3 pockets according to stop codon nucleotides. However, quantitative analysis of variant ciliate and yeast eRF1 point mutants did not reveal any correlation between evolutionary conservation of class-specific residues and termination-related functional specificity and was limited in elucidating a detailed mechanism for ciliate stop codon reassignment. Thus, based on isolation of suppressor tRNAs from Euplotes and Tetrahymena, we propose that stop codon reassignment in ciliates may be controlled by cooperation between eRF1 and suppressor tRNAs.
Collapse
Affiliation(s)
- Lijun Xu
- a Key Laboratory of Chemical Biology and Molecular Engineering, Ministry of Education, China; and Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | | | | | | | | | | | | |
Collapse
|
21
|
Kryuchkova P, Grishin A, Eliseev B, Karyagina A, Frolova L, Alkalaeva E. Two-step model of stop codon recognition by eukaryotic release factor eRF1. Nucleic Acids Res 2013; 41:4573-86. [PMID: 23435318 PMCID: PMC3632111 DOI: 10.1093/nar/gkt113] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Release factor eRF1 plays a key role in the termination of protein synthesis in eukaryotes. The eRF1 consists of three domains (N, M and C) that perform unique roles in termination. Previous studies of eRF1 point mutants and standard/variant code eRF1 chimeras unequivocally demonstrated a direct involvement of the highly conserved N-domain motifs (NIKS, YxCxxxF and GTx) in stop codon recognition. In the current study, we extend this work by investigating the role of the 41 invariant and conserved N-domain residues in stop codon decoding by human eRF1. Using a combination of the conservative and non-conservative amino acid substitutions, we measured the functional activity of >80 mutant eRF1s in an in vitro reconstituted eukaryotic translation system and selected 15 amino acid residues essential for recognition of different stop codon nucleotides. Furthermore, toe-print analyses provide evidence of a conformational rearrangement of ribosomal complexes that occurs during binding of eRF1 to messenger RNA and reflects stop codon decoding activity of eRF1. Based on our experimental data and molecular modelling of the N-domain at the ribosomal A site, we propose a two-step model of stop codon decoding in the eukaryotic ribosome.
Collapse
Affiliation(s)
- Polina Kryuchkova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia
| | | | | | | | | | | |
Collapse
|
22
|
Betney R, de Silva E, Mertens C, Knox Y, Krishnan J, Stansfield I. Regulation of release factor expression using a translational negative feedback loop: a systems analysis. RNA (NEW YORK, N.Y.) 2012; 18:2320-34. [PMID: 23104998 PMCID: PMC3504682 DOI: 10.1261/rna.035113.112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The essential eukaryote release factor eRF1, encoded by the yeast SUP45 gene, recognizes stop codons during ribosomal translation. SUP45 nonsense alleles are, however, viable due to the establishment of feedback-regulated readthrough of the premature termination codon; reductions in full-length eRF1 promote tRNA-mediated stop codon readthrough, which, in turn, drives partial production of full-length eRF1. A deterministic mathematical model of this eRF1 feedback loop was developed using a staged increase in model complexity. Model predictions matched the experimental observation that strains carrying the mutant SUQ5 tRNA (a weak UAA suppressor) in combination with any of the tested sup45(UAA) nonsense alleles exhibit threefold more stop codon readthrough than that of an SUQ5 yeast strain. The model also successfully predicted that eRF1 feedback control in an SUQ5 sup45(UAA) mutant would resist, but not completely prevent, imposed changes in eRF1 expression. In these experiments, the introduction of a plasmid-borne SUQ5 copy into a sup45(UAA) SUQ5 mutant directed additional readthrough and full-length eRF1 expression, despite feedback. Secondly, induction of additional sup45(UAA) mRNA expression in a sup45(UAA) SUQ5 strain also directed increased full-length eRF1 expression. The autogenous sup45 control mechanism therefore acts not to precisely control eRF1 expression, but rather as a damping mechanism that only partially resists changes in release factor expression level. The validated model predicts that the degree of feedback damping (i.e., control precision) is proportional to eRF1 affinity for the premature stop codon. The validated model represents an important tool to analyze this and other translational negative feedback loops.
Collapse
MESH Headings
- Binding, Competitive
- Codon, Terminator/genetics
- Codon, Terminator/metabolism
- Feedback, Physiological
- Genes, Fungal
- Models, Biological
- Mutation
- Peptide Termination Factors/genetics
- Peptide Termination Factors/metabolism
- Protein Biosynthesis
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Systems Analysis
Collapse
Affiliation(s)
- Russell Betney
- University of Aberdeen, School of Medical Sciences, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Eric de Silva
- Chemical Engineering and Chemical Technology, Institute for Systems and Synthetic Biology, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Christina Mertens
- University of Aberdeen, School of Medical Sciences, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Yvonne Knox
- University of Aberdeen, School of Medical Sciences, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - J. Krishnan
- Chemical Engineering and Chemical Technology, Institute for Systems and Synthetic Biology, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Ian Stansfield
- University of Aberdeen, School of Medical Sciences, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
- Corresponding authorE-mail
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Hernández G, Proud CG, Preiss T, Parsyan A. On the Diversification of the Translation Apparatus across Eukaryotes. Comp Funct Genomics 2012; 2012:256848. [PMID: 22666084 PMCID: PMC3359775 DOI: 10.1155/2012/256848] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Accepted: 03/07/2012] [Indexed: 11/21/2022] Open
Abstract
Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Diversity is ingrained in all stages and echelons of life, namely, the occupancy of ecological niches, behavioral patterns, body plans and organismal complexity, as well as metabolic needs and genetics. In this review, we will discuss that diversity also exists in a key biochemical process, translation, across eukaryotes. Translation is a fundamental process for all forms of life, and the basic components and mechanisms of translation in eukaryotes have been largely established upon the study of traditional, so-called model organisms. By using modern genome-wide, high-throughput technologies, recent studies of many nonmodel eukaryotes have unveiled a surprising diversity in the configuration of the translation apparatus across eukaryotes, showing that this apparatus is far from being evolutionarily static. For some of the components of this machinery, functional differences between different species have also been found. The recent research reviewed in this article highlights the molecular and functional diversification the translational machinery has undergone during eukaryotic evolution. A better understanding of all aspects of organismal diversity is key to a more profound knowledge of life.
Collapse
Affiliation(s)
- Greco Hernández
- Division of Basic Research, National Institute for Cancer (INCan), Avenida San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080 Mexico City, Mexico
| | - Christopher G. Proud
- Centre for Biological Sciences, University of Southampton, Life Sciences Building (B85), Southampton SO17 1BJ, UK
| | - Thomas Preiss
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Building 131, Garran Road, Acton, Canberra, ACT 0200, Australia
| | - Armen Parsyan
- Goodman Cancer Centre and Department of Biochemistry, Faculty of Medicine, McGill University, 1160 Pine Avenue West, Montreal, QC, Canada H3A 1A3
- Division of General Surgery, Department of Surgery, Faculty of Medicine, McGill University Health Centre, Royal Victoria Hospital, 687 Pine Avenue West, Montreal, QC, Canada H3A 1A1
| |
Collapse
|
25
|
Polshakov VI, Eliseev BD, Birdsall B, Frolova LY. Structure and dynamics in solution of the stop codon decoding N-terminal domain of the human polypeptide chain release factor eRF1. Protein Sci 2012; 21:896-903. [PMID: 22517631 DOI: 10.1002/pro.2067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/15/2012] [Accepted: 03/17/2012] [Indexed: 11/07/2022]
Abstract
The high-resolution NMR structure of the N-domain of human eRF1, responsible for stop codon recognition, has been determined in solution. The overall fold of the protein is the same as that found in the crystal structure. However, the structures of several loops, including those participating in stop codon decoding, are different. Analysis of the NMR relaxation data reveals that most of the regions with the highest structural discrepancy between the solution and solid states undergo internal motions on the ps-ns and ms time scales. The NMR data show that the N-domain of human eRF1 exists in two conformational states. The distribution of the residues having the largest chemical shift differences between the two forms indicates that helices α2 and α3, with the NIKS loop between them, can switch their orientation relative to the β-core of the protein. Such structural plasticity may be essential for stop codon recognition by human eRF1.
Collapse
Affiliation(s)
- Vladimir I Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, MV Lomonosov Moscow State University, Moscow, Russia.
| | | | | | | |
Collapse
|
26
|
Wong LE, Li Y, Pillay S, Frolova L, Pervushin K. Selectivity of stop codon recognition in translation termination is modulated by multiple conformations of GTS loop in eRF1. Nucleic Acids Res 2012; 40:5751-65. [PMID: 22383581 PMCID: PMC3384315 DOI: 10.1093/nar/gks192] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Translation termination in eukaryotes is catalyzed by two release factors eRF1 and eRF3 in a cooperative manner. The precise mechanism of stop codon discrimination by eRF1 remains obscure, hindering drug development targeting aberrations at translation termination. By solving the solution structures of the wild-type N-domain of human eRF1 exhibited omnipotent specificity, i.e. recognition of all three stop codons, and its unipotent mutant with UGA-only specificity, we found the conserved GTS loop adopting alternate conformations. We propose that structural variability in the GTS loop may underline the switching between omnipotency and unipotency of eRF1, implying the direct access of the GTS loop to the stop codon. To explore such feasibility, we positioned N-domain in a pre-termination ribosomal complex using the binding interface between N-domain and model RNA oligonucleotides mimicking Helix 44 of 18S rRNA. NMR analysis revealed that those duplex RNA containing 2-nt internal loops interact specifically with helix α1 of N-domain, and displace C-domain from a non-covalent complex of N-domain and C-domain, suggesting domain rearrangement in eRF1 that accompanies N-domain accommodation into the ribosomal A site.
Collapse
Affiliation(s)
- Leo E Wong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | | | | | | | | |
Collapse
|
27
|
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]
|
28
|
Bulygin KN, Khairulina YS, Kolosov PM, Ven’yaminova AG, Graifer DM, Vorobjev YN, Frolova LY, Karpova GG. Adenine and guanine recognition of stop codon is mediated by different N domain conformations of translation termination factor eRF1. Nucleic Acids Res 2011; 39:7134-46. [PMID: 21602268 PMCID: PMC3167606 DOI: 10.1093/nar/gkr376] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Positioning of release factor eRF1 toward adenines and the ribose-phosphate backbone of the UAAA stop signal in the ribosomal decoding site was studied using messenger RNA (mRNA) analogs containing stop signal UAA/UAAA and a photoactivatable cross-linker at definite locations. The human eRF1 peptides cross-linked to these analogs were identified. Cross-linkers on the adenines at the 2nd, 3rd or 4th position modified eRF1 near the conserved YxCxxxF loop (positions 125–131 in the N domain), but cross-linker at the 4th position mainly modified the tripeptide 26-AAR-28. This tripeptide cross-linked also with derivatized 3′-phosphate of UAA, while the same cross-linker at the 3′-phosphate of UAAA modified both the 26–28 and 67–73 fragments. A comparison of the results with those obtained earlier with mRNA analogs bearing a similar cross-linker at the guanines indicates that positioning of eRF1 toward adenines and guanines of stop signals in the 80S termination complex is different. Molecular modeling of eRF1 in the 80S termination complex showed that eRF1 fragments neighboring guanines and adenines of stop signals are compatible with different N domain conformations of eRF1. These conformations vary by positioning of stop signal purines toward the universally conserved dipeptide 31-GT-32, which neighbors guanines but is oriented more distantly from adenines.
Collapse
Affiliation(s)
- Konstantin N. Bulygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, 119991, Russia
| | - Yulia S. Khairulina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, 119991, Russia
| | - Petr M. Kolosov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, 119991, Russia
| | - Aliya G. Ven’yaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, 119991, Russia
| | - Dmitri M. Graifer
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, 119991, Russia
| | - Yuri N. Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, 119991, Russia
| | - Ludmila Yu. Frolova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, 119991, Russia
| | - Galina G. Karpova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, 119991, Russia
- *To whom correspondence should be addressed. Tel: +7(383) 363 5140; Fax: +7(383) 363-5153;
| |
Collapse
|