1
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Evans MM, Liu S, Krautner JS, Seguin CG, Leung R, Ronald JA. Evaluation of DNA minicircles for delivery of adenine and cytosine base editors using activatable gene on "GO" reporter imaging systems. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102248. [PMID: 39040503 PMCID: PMC11260848 DOI: 10.1016/j.omtn.2024.102248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 06/07/2024] [Indexed: 07/24/2024]
Abstract
Over 30,000 point mutations are associated with debilitating diseases, including many cancer types, underscoring a critical need for targeted genomic solutions. CRISPR base editors, like adenine base editors (ABEs) and cytosine base editors (CBEs), enable precise modifications by converting adenine to guanine and cytosine to thymine, respectively. Challenges in efficiency and safety concerns regarding viral vectors used in delivery limit the scope of base editing. This study introduces non-viral minicircles, bacterial-backbone-free plasmids, as a delivery vehicle for ABEs and CBEs. The research uses cells engineered with the "Gene On" (GO) reporter gene systems for tracking minicircle-delivered ABEs, CBEs, or Cas9 nickase (control), using green fluorescent protein (GFPGO), bioluminescence reporter firefly luciferase (LUCGO), or a highly sensitive Akaluciferase (AkalucGO) designed in this study. The results show that transfection of minicircles expressing CBE or ABE resulted in significantly higher GFP expression and luminescence signals over controls, with minicircles demonstrating the most substantial editing. This study presents minicircles as a new strategy for base editor delivery and develops an enhanced bioluminescence imaging reporter system for tracking ABE activity. Future studies aim to evaluate the use of minicircles in preclinical cancer models, facilitating potential clinical applications.
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Affiliation(s)
- Melissa M. Evans
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Shirley Liu
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Joshua S. Krautner
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Caroline G. Seguin
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Rajan Leung
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, University of Western Ontario, London, ON N6A 5C1, Canada
| | - John A. Ronald
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, University of Western Ontario, London, ON N6A 5C1, Canada
- Lawson Health Research Institute, London, ON N6C 2R5, Canada
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2
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Takallou S, Hajikarimlou M, Al-Gafari M, Wang J, Kazmirchuk TDD, Said KB, Samanfar B, Golshani A. The Involvement of YNR069C in Protein Synthesis in the Baker's Yeast, Saccharomyces cerevisiae. BIOLOGY 2024; 13:138. [PMID: 38534408 DOI: 10.3390/biology13030138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
Maintaining translation fidelity is a critical step within the process of gene expression. It requires the involvement of numerous regulatory elements to ensure the synthesis of functional proteins. The efficient termination of protein synthesis can play a crucial role in preserving this fidelity. Here, we report on investigating a protein of unknown function, YNR069C (also known as BSC5), for its activity in the process of translation. We observed a significant increase in the bypass of premature stop codons upon the deletion of YNR069C. Interestingly, the genomic arrangement of this ORF suggests a compatible mode of expression reliant on translational readthrough, incorporating the neighboring open reading frame. We also showed that the deletion of YNR069C results in an increase in the rate of translation. Based on our results, we propose that YNR069C may play a role in translation fidelity, impacting the overall quantity and quality of translation. Our genetic interaction analysis supports our hypothesis, associating the role of YNR069C to the regulation of protein synthesis.
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Affiliation(s)
- Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Mustafa Al-Gafari
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jiashu Wang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Thomas David Daniel Kazmirchuk
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Kamaledin B Said
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Hail 55476, Saudi Arabia
| | - Bahram Samanfar
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, ON K1A 0C6, Canada
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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3
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Lahiri P, Martin MS, Lino BR, Scheck RA, Van Deventer JA. Dual Noncanonical Amino Acid Incorporation Enabling Chemoselective Protein Modification at Two Distinct Sites in Yeast. Biochemistry 2023; 62:2098-2114. [PMID: 37377426 PMCID: PMC11146674 DOI: 10.1021/acs.biochem.2c00711] [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] [Indexed: 06/29/2023]
Abstract
Incorporation of more than one noncanonical amino acid (ncAA) within a single protein endows the resulting construct with multiple useful features such as augmented molecular recognition or covalent cross-linking capabilities. Herein, for the first time, we demonstrate the incorporation of two chemically distinct ncAAs into proteins biosynthesized in Saccharomyces cerevisiae. To complement ncAA incorporation in response to the amber (TAG) stop codon in yeast, we evaluated opal (TGA) stop codon suppression using three distinct orthogonal translation systems. We observed selective TGA readthrough without detectable cross-reactivity from host translation components. Readthrough efficiency at TGA was modulated by factors including the local nucleotide environment, gene deletions related to the translation process, and the identity of the suppressor tRNA. These observations facilitated systematic investigation of dual ncAA incorporation in both intracellular and yeast-displayed protein constructs, where we observed efficiencies up to 6% of wild-type protein controls. The successful display of doubly substituted proteins enabled the exploration of two critical applications on the yeast surface─(A) antigen binding functionality and (B) chemoselective modification with two distinct chemical probes through sequential application of two bioorthogonal click chemistry reactions. Lastly, by utilizing a soluble form of a doubly substituted construct, we validated the dual incorporation system using mass spectrometry and demonstrated the feasibility of conducting selective labeling of the two ncAAs sequentially using a "single-pot" approach. Overall, our work facilitates the addition of a 22nd amino acid to the genetic code of yeast and expands the scope of applications of ncAAs for basic biological research and drug discovery.
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Affiliation(s)
- Priyanka Lahiri
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Meghan S. Martin
- Chemistry Department, Tufts University, Medford, Massachusetts 02155, USA
| | - Briana R. Lino
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Rebecca A. Scheck
- Chemistry Department, Tufts University, Medford, Massachusetts 02155, USA
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
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4
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Kobayashi S, Kaji A, Kaji H. A novel function for eukaryotic elongation factor 3: Inhibition of stop codon readthrough in yeast. Arch Biochem Biophys 2023; 740:109580. [PMID: 36948349 DOI: 10.1016/j.abb.2023.109580] [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: 11/26/2022] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 03/24/2023]
Abstract
Eukaryotic elongation factor 3 (eEF3) is one of the essential yeast ribosome-associated ATP-binding cassette type F (ABCF) ATPases. Previously, we found that eEF3 stimulates release of mRNA from puromycin-treated polysomes. In this study, we used a cell-free cricket paralysis virus (CrPV) internal ribosome entry site (IRES)-mediated firefly luciferase bicistronic mRNA translation system with yeast S30 extract. When eEF3 was partially removed from the crude extract, the product from the downstream ORF was increased by the readthrough of a UAA stop codon in the upstream ORF. eEF3 enhanced the release of luciferase from the polysome by eukaryotic release factor (eRF)1 and eRF3. These results suggest that eEF3 is a factor that assists eRFs in performing normal protein synthesis termination in yeast.
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Affiliation(s)
- Soushi Kobayashi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA; Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
| | - Akira Kaji
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA.
| | - Hideko Kaji
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
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5
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Manjunath LE, Singh A, Som S, Eswarappa SM. Mammalian proteome expansion by stop codon readthrough. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1739. [PMID: 35570338 DOI: 10.1002/wrna.1739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 12/20/2022]
Abstract
Recognition of a stop codon by translation machinery as a sense codon results in translational readthrough instead of termination. This recoding process, termed stop codon readthrough (SCR) or translational readthrough, is found in all domains of life including mammals. The context of the stop codon, local mRNA topology, and molecules that interact with the mRNA region downstream of the stop codon determine SCR. The products of SCR can have localization, stability, and function different from those of the canonical isoforms. In this review, we discuss how recent technological and computational advances have increased our understanding of the SCR process in the mammalian system. Based on the known molecular events that occur during SCR of multiple mRNAs, we propose transient molecular roadblocks on an mRNA downstream of the stop codon as a possible mechanism for the induction of SCR. We argue, with examples, that the insights gained from the natural SCR events can guide us to develop novel strategies for the treatment of diseases caused by premature stop codons. This article is categorized under: Translation > Regulation.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
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6
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Zackin MT, Stieglitz JT, Van Deventer JA. Genome-Wide Screen for Enhanced Noncanonical Amino Acid Incorporation in Yeast. ACS Synth Biol 2022; 11:3669-3680. [PMID: 36346914 PMCID: PMC10065164 DOI: 10.1021/acssynbio.2c00267] [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] [Indexed: 11/09/2022]
Abstract
Numerous applications of noncanonical amino acids (ncAAs) in basic biology and therapeutic development require efficient protein biosynthesis using an expanded genetic code. However, achieving such incorporation at repurposed stop codons in cells is generally inefficient and limited by complex cellular processes that preserve the fidelity of protein synthesis. A more comprehensive understanding of the processes that contribute to ncAA incorporation would aid in the development of genomic engineering strategies for augmenting genetic code manipulation. In this work, we used a series of fluorescent reporters to screen a pooled Saccharomyces cerevisiae molecular barcoded yeast knockout (YKO) collection. Fluorescence-activated cell sorting enabled isolation of strains encoding single-gene deletions exhibiting improved ncAA incorporation efficiency in response to the amber (TAG) stop codon; 55 unique candidate deletions were identified. The deleted genes encoded for proteins that participate in diverse cellular processes, including many genes that have no known connection with protein translation. We then verified that two knockouts, yil014c-aΔ and alo1Δ, exhibited improved ncAA incorporation efficiency starting from independently acquired strains possessing the knockouts. Using additional orthogonal translation systems and ncAAs, we determined that yil014c-aΔ and alo1Δ enhance ncAA incorporation efficiency without loss of fidelity over a wide range of conditions. Our findings highlight opportunities for further modulating gene expression with genetic, genomic, and synthetic biology approaches to improve ncAA incorporation efficiency. In addition, these discoveries have the potential to enhance our fundamental understanding of protein translation. Ultimately, cells that efficiently biosynthesize ncAA-containing proteins will streamline the realization of applications utilizing expanded genetic codes ranging from basic biology to drug discovery.
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Affiliation(s)
- Matthew T. Zackin
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
| | - Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
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7
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Zhang J, Xu C. Gene product diversity: adaptive or not? Trends Genet 2022; 38:1112-1122. [PMID: 35641344 PMCID: PMC9560964 DOI: 10.1016/j.tig.2022.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 01/24/2023]
Abstract
One gene does not equal one RNA or protein. The genomic revolution has revealed numerous different RNA and protein molecules that can be produced from one gene, such as circular RNAs generated by back-splicing, proteins with residues mismatching the genomic encoding because of RNA editing, and proteins extended in the C terminus via stop codon readthrough in translation. Are these diverse products results of exquisite gene regulations or imprecise biological processes? While there are cases where the gene product diversity appears beneficial, genome-scale patterns suggest that much of this diversity arises from nonadaptive, molecular errors. This finding has important implications for studying the functions of diverse gene products and for understanding the fundamental properties and evolution of cellular life.
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Affiliation(s)
- Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Chuan Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
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8
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Egbert S, Hoffman JR, McMullin RT, Lendemer JC, Sorensen JL. Unraveling usnic acid: a comparison of biosynthetic gene clusters between two reindeer lichen (Cladonia rangiferina and C. uncialis). Fungal Biol 2022; 126:697-706. [PMID: 36517138 DOI: 10.1016/j.funbio.2022.08.007] [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: 03/31/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 01/07/2023]
Abstract
Lichenized fungi are known for their production of a diversity of secondary metabolites, many of which have broad biological and pharmacological applications. By far the most well-studied of these metabolites is usnic acid. While this metabolite has been well-known and researched for decades, the gene cluster responsible for its production was only recently identified from the species Cladonia uncialis. Usnic acid production varies considerably in the genus Cladonia, even among closely related taxa, and many species, such as C. rangiferina, have been inferred to be incapable of producing the metabolite based on analysis by thin-layer chromatography (TLC). We sequenced and examined the usnic acid biosynthetic gene clusters, or lack thereof, from four closely related Cladonia species (C. oricola, C. rangiferina, C. stygia, and C. subtenuis), and compare them against those of C. uncialis. We complement this comparison with tiered chemical profile analyses to confirm the presence or absence of usnic acid in select samples, using both HPLC and LC-MS. Despite long-standing reporting that C. rangiferina lacks the ability to produce usnic acid, we observed functional gene clusters from the species and detected usnic acid when extracts were examined by LC-MS. By contrast, C. stygia and C. oricola, have been previously described as lacking the ability to produce usnic acid, lacked the gene cluster entirely, and no usnic acid could be detected in C. oricola extracts via HPLC or LC-MS. This work suggests that chemical profiles attained through inexpensive and low-sensitivity methods like TLC may fail to detect low abundance metabolites that can be taxonomically informative. This study also bolsters understanding of the usnic acid gene cluster in lichens, revealing differences among domains of the polyketide synthase which may explain observed differences in expression. These results reinforce the need for comprehensive characterization of lichen secondary metabolite profiles with sensitive LC-MS methods.
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Affiliation(s)
- Susan Egbert
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Jordan R Hoffman
- Department of Biology, Graduate Center, City University of New York, The New York, USA; Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
| | - R Troy McMullin
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, K1P 6P4, Canada
| | - James C Lendemer
- Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA.
| | - John L Sorensen
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
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9
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New opportunities for genetic code expansion in synthetic yeast. Curr Opin Biotechnol 2022; 75:102691. [DOI: 10.1016/j.copbio.2022.102691] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/23/2021] [Accepted: 01/18/2022] [Indexed: 12/19/2022]
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10
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Influence of novel readthrough agents on myelin protein zero translation in the peripheral nervous system. Neuropharmacology 2022; 211:109059. [DOI: 10.1016/j.neuropharm.2022.109059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/24/2022] [Accepted: 04/06/2022] [Indexed: 12/22/2022]
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11
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Cillingová A, Tóth R, Mojáková A, Zeman I, Vrzoňová R, Siváková B, Baráth P, Neboháčová M, Klepcová Z, Brázdovič F, Lichancová H, Hodorová V, Brejová B, Vinař T, Mutalová S, Vozáriková V, Mutti G, Tomáška Ľ, Gácser A, Gabaldón T, Nosek J. Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources. PLoS Genet 2022; 18:e1009815. [PMID: 35255079 PMCID: PMC8929692 DOI: 10.1371/journal.pgen.1009815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/17/2022] [Accepted: 02/22/2022] [Indexed: 11/19/2022] Open
Abstract
Many fungal species utilize hydroxyderivatives of benzene and benzoic acid as carbon sources. The yeast Candida parapsilosis metabolizes these compounds via the 3-oxoadipate and gentisate pathways, whose components are encoded by two metabolic gene clusters. In this study, we determine the chromosome level assembly of the C. parapsilosis strain CLIB214 and use it for transcriptomic and proteomic investigation of cells cultivated on hydroxyaromatic substrates. We demonstrate that the genes coding for enzymes and plasma membrane transporters involved in the 3-oxoadipate and gentisate pathways are highly upregulated and their expression is controlled in a substrate-specific manner. However, regulatory proteins involved in this process are not known. Using the knockout mutants, we show that putative transcriptional factors encoded by the genes OTF1 and GTF1 located within these gene clusters function as transcriptional activators of the 3-oxoadipate and gentisate pathway, respectively. We also show that the activation of both pathways is accompanied by upregulation of genes for the enzymes involved in β-oxidation of fatty acids, glyoxylate cycle, amino acid metabolism, and peroxisome biogenesis. Transcriptome and proteome profiles of the cells grown on 4-hydroxybenzoate and 3-hydroxybenzoate, which are metabolized via the 3-oxoadipate and gentisate pathway, respectively, reflect their different connection to central metabolism. Yet we find that the expression profiles differ also in the cells assimilating 4-hydroxybenzoate and hydroquinone, which are both metabolized in the same pathway. This finding is consistent with the phenotype of the Otf1p-lacking mutant, which exhibits impaired growth on hydroxybenzoates, but still utilizes hydroxybenzenes, thus indicating that additional, yet unidentified transcription factor could be involved in the 3-oxoadipate pathway regulation. Moreover, we propose that bicarbonate ions resulting from decarboxylation of hydroxybenzoates also contribute to differences in the cell responses to hydroxybenzoates and hydroxybenzenes. Finally, our phylogenetic analysis highlights evolutionary paths leading to metabolic adaptations of yeast cells assimilating hydroxyaromatic substrates.
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Affiliation(s)
- Andrea Cillingová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Renáta Tóth
- HCEMM-USZ Department of Microbiology, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Anna Mojáková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Igor Zeman
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Romana Vrzoňová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Barbara Siváková
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Neboháčová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Zuzana Klepcová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Filip Brázdovič
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Hana Lichancová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Viktória Hodorová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Broňa Brejová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tomáš Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Sofia Mutalová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Giacomo Mutti
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Atilla Gácser
- HCEMM-USZ Department of Microbiology, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
- * E-mail:
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12
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Stieglitz JT, Potts KA, Van Deventer JA. Broadening the Toolkit for Quantitatively Evaluating Noncanonical Amino Acid Incorporation in Yeast. ACS Synth Biol 2021; 10:3094-3104. [PMID: 34730946 DOI: 10.1021/acssynbio.1c00370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic code expansion is a powerful approach for advancing critical fields such as biological therapeutic discovery. However, the machinery for genetically encoding noncanonical amino acids (ncAAs) is only available in limited plasmid formats, constraining potential applications. In extreme cases, the introduction of two separate plasmids, one containing an orthogonal translation system (OTS) to facilitate ncAA incorporation and a second for expressing a ncAA-containing protein of interest, is not possible due to a lack of the available selection markers. One strategy to circumvent this challenge is to express the OTS and protein of interest from a single vector. For what we believe is the first time in yeast, we describe here several sets of single plasmid systems (SPSs) for performing genetic code manipulation and compare the ncAA incorporation capabilities of these plasmids against the capabilities of previously described dual plasmid systems (DPSs). For both dual fluorescent protein reporters and yeast display reporters tested with multiple OTSs and ncAAs, measured ncAA incorporation efficiencies with SPSs were determined to be equal to efficiencies determined with DPSs. Click chemistry on yeast cells displaying ncAA-containing proteins was also shown to be feasible in both formats, although differences in reactivity between formats suggest the need for caution when using such approaches. Additionally, we investigated whether these reporters would support the separation of yeast strains known to exhibit distinct ncAA incorporation efficiencies. Model sorts conducted with mixtures of two strains transformed with the same SPS or DPS both led to the enrichment of a strain known to support a higher efficiency ncAA incorporation, suggesting that these reporters will be suitable for conducting screens for strains exhibiting enhanced ncAA incorporation efficiencies. Overall, our results confirm that SPSs are well behaved in yeast and provide a convenient alternative to DPSs. SPSs are expected to be invaluable for conducting high-throughput investigations of the effects of genetic or genomic changes on ncAA incorporation efficiency and, more fundamentally, the eukaryotic translation apparatus.
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Affiliation(s)
- Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Kelly A. Potts
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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13
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Zhang S, Chen Y, Wang Y, Zhang P, Chen G, Zhou Y. Insights Into Translatomics in the Nervous System. Front Genet 2021; 11:599548. [PMID: 33408739 PMCID: PMC7779767 DOI: 10.3389/fgene.2020.599548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
Most neurological disorders are caused by abnormal gene translation. Generally, dysregulation of elements involved in the translational process disrupts homeostasis in neurons and neuroglia. Better understanding of how the gene translation process occurs requires detailed analysis of transcriptomic and proteomic profile data. However, a lack of strictly direct correlations between mRNA and protein levels limits translational investigation by combining transcriptomic and proteomic profiling. The much better correlation between proteins and translated mRNAs than total mRNAs in abundance and insufficiently sensitive proteomics approach promote the requirement of advances in translatomics technology. Translatomics which capture and sequence the mRNAs associated with ribosomes has been effective in identifying translational changes by genetics or projections, ribosome stalling, local translation, and transcript isoforms in the nervous system. Here, we place emphasis on the main three translatomics methods currently used to profile mRNAs attached to ribosome-nascent chain complex (RNC-mRNA). Their prominent applications in neurological diseases including glioma, neuropathic pain, depression, fragile X syndrome (FXS), neurodegenerative disorders are outlined. The content reviewed here expands our understanding on the contributions of aberrant translation to neurological disease development.
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Affiliation(s)
- Shuxia Zhang
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yeru Chen
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongjie Wang
- Key Laboratory of Elemene Anti-Cancer Medicine of Zhejiang Province and Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou, China
| | - Piao Zhang
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Gang Chen
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Youfa Zhou
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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14
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Manjunath LE, Singh A, Sahoo S, Mishra A, Padmarajan J, Basavaraju CG, Eswarappa SM. Stop codon read-through of mammalian MTCH2 leading to an unstable isoform regulates mitochondrial membrane potential. J Biol Chem 2020; 295:17009-17026. [PMID: 33028634 PMCID: PMC7863902 DOI: 10.1074/jbc.ra120.014253] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Stop codon read-through (SCR) is a process of continuation of translation beyond a stop codon. This phenomenon, which occurs only in certain mRNAs under specific conditions, leads to a longer isoform with properties different from that of the canonical isoform. MTCH2, which encodes a mitochondrial protein that regulates mitochondrial metabolism, was selected as a potential read-through candidate based on evolutionary conservation observed in the proximal region of its 3' UTR. Here, we demonstrate translational read-through across two evolutionarily conserved, in-frame stop codons of MTCH2 using luminescence- and fluorescence-based assays, and by analyzing ribosome-profiling and mass spectrometry (MS) data. This phenomenon generates two isoforms, MTCH2x and MTCH2xx (single- and double-SCR products, respectively), in addition to the canonical isoform MTCH2, from the same mRNA. Our experiments revealed that a cis-acting 12-nucleotide sequence in the proximal 3' UTR of MTCH2 is the necessary signal for SCR. Functional characterization showed that MTCH2 and MTCH2x were localized to mitochondria with a long t1/2 (>36 h). However, MTCH2xx was found predominantly in the cytoplasm. This mislocalization and its unique C terminus led to increased degradation, as shown by greatly reduced t1/2 (<1 h). MTCH2 read-through-deficient cells, generated using CRISPR-Cas9, showed increased MTCH2 expression and, consistent with this, decreased mitochondrial membrane potential. Thus, double-SCR of MTCH2 regulates its own expression levels contributing toward the maintenance of normal mitochondrial membrane potential.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sarthak Sahoo
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Ashutosh Mishra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Jinsha Padmarajan
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | | | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India.
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15
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Kurilla A, Szőke A, Auber A, Káldi K, Silhavy D. Expression of the translation termination factor eRF1 is autoregulated by translational readthrough and 3'UTR intron-mediated NMD in Neurospora crassa. FEBS Lett 2020; 594:3504-3517. [PMID: 32869294 DOI: 10.1002/1873-3468.13918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/30/2020] [Accepted: 08/17/2020] [Indexed: 01/24/2023]
Abstract
Eukaryotic release factor 1 (eRF1) is a translation termination factor that binds to the ribosome at stop codons. The expression of eRF1 is strictly controlled, since its concentration defines termination efficiency and frequency of translational readthrough. Here, we show that eRF1 expression in Neurospora crassa is controlled by an autoregulatory circuit that depends on the specific 3'UTR structure of erf1 mRNA. The stop codon context of erf1 promotes readthrough that protects the mRNA from its 3'UTR-induced nonsense-mediated mRNA decay (NMD). High eRF1 concentration leads to inefficient readthrough, thereby allowing NMD-mediated erf1 degradation. We propose that eRF1 expression is controlled by similar autoregulatory circuits in many fungi and seed plants and discuss the evolution of autoregulatory systems of different translation termination factors.
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Affiliation(s)
- Anita Kurilla
- Department of Genetics, NARIC, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Anita Szőke
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Andor Auber
- Department of Genetics, NARIC, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Krisztina Káldi
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Dániel Silhavy
- Department of Genetics, NARIC, Agricultural Biotechnology Institute, Gödöllő, Hungary.,Biological Research Centre, Institute of Plant Biology, Szeged, Hungary
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16
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Ghosh S, Guimaraes JC, Lanzafame M, Schmidt A, Syed AP, Dimitriades B, Börsch A, Ghosh S, Mittal N, Montavon T, Correia AL, Danner J, Meister G, Terracciano LM, Pfeffer S, Piscuoglio S, Zavolan M. Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation. EMBO J 2020; 39:e103922. [PMID: 32812257 PMCID: PMC7507497 DOI: 10.15252/embj.2019103922] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 06/27/2020] [Accepted: 07/07/2020] [Indexed: 01/05/2023] Open
Abstract
Translational readthrough, i.e., elongation of polypeptide chains beyond the stop codon, was initially reported for viral RNA, but later found also on eukaryotic transcripts, resulting in proteome diversification and protein‐level modulation. Here, we report that AGO1x, an evolutionarily conserved translational readthrough isoform of Argonaute 1, is generated in highly proliferative breast cancer cells, where it curbs accumulation of double‐stranded RNAs (dsRNAs) and consequent induction of interferon responses and apoptosis. In contrast to other mammalian Argonaute protein family members with primarily cytoplasmic functions, AGO1x exhibits nuclear localization in the vicinity of nucleoli. We identify AGO1x interaction with the polyribonucleotide nucleotidyltransferase 1 (PNPT1) and show that the depletion of this protein further augments dsRNA accumulation. Our study thus uncovers a novel function of an Argonaute protein in buffering the endogenous dsRNA‐induced interferon responses, different than the canonical function of AGO proteins in the miRNA effector pathway. As AGO1x expression is tightly linked to breast cancer cell proliferation, our study thus suggests a new direction for limiting tumor growth.
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Affiliation(s)
- Souvik Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Joao C Guimaraes
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Manuela Lanzafame
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Afzal Pasha Syed
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Beatrice Dimitriades
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Anastasiya Börsch
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Shreemoyee Ghosh
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Nitish Mittal
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Montavon
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Ana Luisa Correia
- Department of Biomedicine, University of Basel/University Hospital Basel, Basel, Switzerland
| | - Johannes Danner
- Department of Biochemistry, Department of Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Department of Biochemistry, Department of Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | | | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Salvatore Piscuoglio
- Institute of Pathology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel/University Hospital Basel, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
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17
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Premature termination codon readthrough in Drosophila varies in a developmental and tissue-specific manner. Sci Rep 2020; 10:8485. [PMID: 32444687 PMCID: PMC7244557 DOI: 10.1038/s41598-020-65348-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/31/2020] [Indexed: 12/29/2022] Open
Abstract
Despite their essential function in terminating translation, readthrough of stop codons occurs more frequently than previously supposed. However, little is known about the regulation of stop codon readthrough by anatomical site and over the life cycle of animals. Here, we developed a set of reporters to measure readthrough in Drosophila melanogaster. A focused RNAi screen in whole animals identified upf1 as a mediator of readthrough, suggesting that the stop codons in the reporters were recognized as premature termination codons (PTCs). We found readthrough rates of PTCs varied significantly throughout the life cycle of flies, being highest in older adult flies. Furthermore, readthrough rates varied dramatically by tissue and, intriguingly, were highest in fly brains, specifically neurons and not glia. This was not due to differences in reporter abundance or nonsense-mediated mRNA decay (NMD) surveillance between these tissues. Readthrough rates also varied within neurons, with cholinergic neurons having highest readthrough compared with lowest readthrough rates in dopaminergic neurons. Overall, our data reveal temporal and spatial variation of PTC-mediated readthrough in animals, and suggest that readthrough may be a potential rescue mechanism for PTC-harboring transcripts when the NMD surveillance pathway is inhibited.
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18
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Otani Y, Ohno N, Cui J, Yamaguchi Y, Baba H. Upregulation of large myelin protein zero leads to Charcot-Marie-Tooth disease-like neuropathy in mice. Commun Biol 2020; 3:121. [PMID: 32170207 PMCID: PMC7070019 DOI: 10.1038/s42003-020-0854-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 02/24/2020] [Indexed: 01/01/2023] Open
Abstract
Charcot-Marie-Tooth (CMT) disease is a hereditary neuropathy mainly caused by gene mutation of peripheral myelin proteins including myelin protein zero (P0, MPZ). Large myelin protein zero (L-MPZ) is an isoform of P0 that contains an extended polypeptide synthesized by translational readthrough at the C-terminus in tetrapods, including humans. The physiological role of L-MPZ and consequences of an altered L-MPZ/P0 ratio in peripheral myelin are not known. To clarify this, we used genome editing to generate a mouse line (L-MPZ mice) that produced L-MPZ instead of P0. Motor tests and electrophysiological, immunohistological, and electron microscopy analyses show that homozygous L-MPZ mice exhibit CMT-like phenotypes including thin and/or loose myelin, increased small-caliber axons, and disorganized axo-glial interactions. Heterozygous mice show a milder phenotype. These results highlight the importance of an appropriate L-MPZ/P0 ratio and show that aberrant readthrough of a myelin protein causes neuropathy.
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Affiliation(s)
- Yoshinori Otani
- Department of Molecular Neurobiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, Japan
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Japan
| | - Jingjing Cui
- Department of Molecular Neurobiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Yoshihide Yamaguchi
- Department of Molecular Neurobiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan.
| | - Hiroko Baba
- Department of Molecular Neurobiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
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19
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Potts KA, Stieglitz JT, Lei M, Van Deventer JA. Reporter system architecture affects measurements of noncanonical amino acid incorporation efficiency and fidelity. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2020; 5:573-588. [PMID: 33791108 PMCID: PMC8009230 DOI: 10.1039/c9me00107g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ability to genetically encode noncanonical amino acids (ncAAs) within proteins supports a growing number of applications ranging from fundamental biological studies to enhancing the properties of biological therapeutics. Currently, our quantitative understanding of ncAA incorporation systems is confounded by the diverse set of characterization and analysis approaches used to quantify ncAA incorporation events. While several effective reporter systems support such measurements, it is not clear how quantitative results from different reporters relate to one another, or which details influence measurements most strongly. Here, we evaluate the quantitative performance of single-fluorescent protein reporters, dual-fluorescent protein reporters, and cell surface-displayed protein reporters of ncAA insertion in response to the TAG (amber) codon in yeast. While different reporters support varying levels of apparent readthrough efficiencies, flow cytometry-based evaluations with dual reporters yielded measurements exhibiting consistent quantitative trends and precision across all evaluated conditions. Further investigations of dual-fluorescent protein reporter architecture revealed that quantitative outputs are influenced by stop codon location and N- and C-terminal fluorescent protein identity. Both dual-fluorescent protein reporters and a "drop-in" version of yeast display support quantification of ncAA incorporation in several single-gene knockout strains, revealing strains that enhance ncAA incorporation efficiency without compromising fidelity. Our studies reveal critical details regarding reporter system performance in yeast and how to effectively deploy such reporters. These findings have substantial implications for how to engineer ncAA incorporation systems-and protein translation apparatuses-to better accommodate alternative genetic codes for expanding the chemical diversity of biosynthesized proteins.
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Affiliation(s)
- K A Potts
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - J T Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - M Lei
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - J A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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20
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Michorowska S, Giebułtowicz J, Wolinowska R, Konopka A, Wilkaniec A, Krajewski P, Bulska E, Wroczyński P. Detection of ALDH3B2 in Human Placenta. Int J Mol Sci 2019; 20:E6292. [PMID: 31847104 PMCID: PMC6941052 DOI: 10.3390/ijms20246292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 01/28/2023] Open
Abstract
Aldehyde dehydrogenase 3B2 (ALDH3B2) gene contains a premature termination codon, which can be skipped or suppressed resulting in full-length protein expression. Alternatively, the longest putative open reading frame starting with the second in-frame start codon would encode short isoform. No unequivocal evidence of ALDH3B2 expression in healthy human tissues is available. The aim of this study was to confirm its expression in human placenta characterized by the highest ALDH3B2 mRNA abundance. ALDH3B2 DNA and mRNA were sequenced. The expression was investigated using western blot. The identity of the protein was confirmed using mass spectrometry (MS). The predicted tertiary and quaternary structures, subcellular localization, and phosphorylation sites were assessed using bioinformatic analyses. All DNA and mRNA isolates contained the premature stop codon. In western blot analyses, bands corresponding to the mass of full-length protein were detected. MS analysis led to the identification of two unique peptides, one of which is encoded by the nucleotide sequence located upstream the second start codon. Bioinformatic analyses suggest cytoplasmic localization and several phosphorylation sites. Despite premature stop codon in DNA and mRNA sequences, full-length ALDH3B2 was found. It can be formed as a result of premature stop codon readthrough, complex phenomenon enabling stop codon circumvention.
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Affiliation(s)
- Sylwia Michorowska
- Department of Bioanalysis and Drug Analysis, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.G.); (P.W.)
| | - Joanna Giebułtowicz
- Department of Bioanalysis and Drug Analysis, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.G.); (P.W.)
| | - Renata Wolinowska
- Department of Pharmaceutical Microbiology, Centre for Preclinical Research and Technology (CePT), Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland;
| | - Anna Konopka
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 02-097 Warsaw, Poland; (A.K.); (E.B.)
| | - Anna Wilkaniec
- Department of Cellular Signaling, Mossakowski Research Centre, Polish Academy of Sciences, Pawińskiego 5, 02-106 Warsaw, Poland;
| | - Paweł Krajewski
- Forensic Medicine Department, First Faculty of Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland;
| | - Ewa Bulska
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, 02-097 Warsaw, Poland; (A.K.); (E.B.)
| | - Piotr Wroczyński
- Department of Bioanalysis and Drug Analysis, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.G.); (P.W.)
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21
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Beißel C, Neumann B, Uhse S, Hampe I, Karki P, Krebber H. Translation termination depends on the sequential ribosomal entry of eRF1 and eRF3. Nucleic Acids Res 2019; 47:4798-4813. [PMID: 30873535 PMCID: PMC6511868 DOI: 10.1093/nar/gkz177] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/28/2019] [Accepted: 03/08/2019] [Indexed: 01/16/2023] Open
Abstract
Translation termination requires eRF1 and eRF3 for polypeptide- and tRNA-release on stop codons. Additionally, Dbp5/DDX19 and Rli1/ABCE1 are required; however, their function in this process is currently unknown. Using a combination of in vivo and in vitro experiments, we show that they regulate a stepwise assembly of the termination complex. Rli1 and eRF3-GDP associate with the ribosome first. Subsequently, Dbp5-ATP delivers eRF1 to the stop codon and in this way prevents a premature access of eRF3. Dbp5 dissociates upon placing eRF1 through ATP-hydrolysis. This in turn enables eRF1 to contact eRF3, as the binding of Dbp5 and eRF3 to eRF1 is mutually exclusive. Defects in the Dbp5-guided eRF1 delivery lead to premature contact and premature dissociation of eRF1 and eRF3 from the ribosome and to subsequent stop codon readthrough. Thus, the stepwise Dbp5-controlled termination complex assembly is essential for regular translation termination events. Our data furthermore suggest a possible role of Dbp5/DDX19 in alternative translation termination events, such as during stress response or in developmental processes, which classifies the helicase as a potential drug target for nonsense suppression therapy to treat cancer and neurodegenerative diseases.
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Affiliation(s)
- Christian Beißel
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Bettina Neumann
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Simon Uhse
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Irene Hampe
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
| | - Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Germany
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22
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Li C, Zhang J. Stop-codon read-through arises largely from molecular errors and is generally nonadaptive. PLoS Genet 2019; 15:e1008141. [PMID: 31120886 PMCID: PMC6550407 DOI: 10.1371/journal.pgen.1008141] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/05/2019] [Accepted: 04/16/2019] [Indexed: 12/02/2022] Open
Abstract
Stop-codon read-through refers to the phenomenon that a ribosome goes past the stop codon and continues translating into the otherwise untranslated region (UTR) of a transcript. Recent ribosome-profiling experiments in eukaryotes uncovered widespread stop-codon read-through that also varies among tissues, prompting the adaptive hypothesis that stop-codon read-through is an important, regulated mechanism for generating proteome diversity. Here we propose and test a competing hypothesis that stop-codon read-through arises mostly from molecular errors and is largely nonadaptive. The error hypothesis makes distinct predictions about the probability of read-through, frequency of sequence motifs for read-through, and conservation of the read-through region, each of which is supported by genome-scale data from yeasts and fruit flies. Thus, except for the few cases with demonstrated functions, stop-codon read-through is generally nonadaptive. This finding, along with other molecular errors recently quantified, reveals a much less precise or orderly cellular life than is commonly thought.
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Affiliation(s)
- Chuan Li
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
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23
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Xu Y, Ju HJ, DeBlasio S, Carino EJ, Johnson R, MacCoss MJ, Heck M, Miller WA, Gray SM. A Stem-Loop Structure in Potato Leafroll Virus Open Reading Frame 5 (ORF5) Is Essential for Readthrough Translation of the Coat Protein ORF Stop Codon 700 Bases Upstream. J Virol 2018; 92:e01544-17. [PMID: 29514911 PMCID: PMC5952135 DOI: 10.1128/jvi.01544-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/06/2018] [Indexed: 11/20/2022] Open
Abstract
Translational readthrough of the stop codon of the capsid protein (CP) open reading frame (ORF) is used by members of the Luteoviridae to produce their minor capsid protein as a readthrough protein (RTP). The elements regulating RTP expression are not well understood, but they involve long-distance interactions between RNA domains. Using high-resolution mass spectrometry, glutamine and tyrosine were identified as the primary amino acids inserted at the stop codon of Potato leafroll virus (PLRV) CP ORF. We characterized the contributions of a cytidine-rich domain immediately downstream and a branched stem-loop structure 600 to 700 nucleotides downstream of the CP stop codon. Mutations predicted to disrupt and restore the base of the distal stem-loop structure prevented and restored stop codon readthrough. Motifs in the downstream readthrough element (DRTE) are predicted to base pair to a site within 27 nucleotides (nt) of the CP ORF stop codon. Consistent with a requirement for this base pairing, the DRTE of Cereal yellow dwarf virus was not compatible with the stop codon-proximal element of PLRV in facilitating readthrough. Moreover, deletion of the complementary tract of bases from the stop codon-proximal region or the DRTE of PLRV prevented readthrough. In contrast, the distance and sequence composition between the two domains was flexible. Mutants deficient in RTP translation moved long distances in plants, but fewer infection foci developed in systemically infected leaves. Selective 2'-hydroxyl acylation and primer extension (SHAPE) probing to determine the secondary structure of the mutant DRTEs revealed that the functional mutants were more likely to have bases accessible for long-distance base pairing than the nonfunctional mutants. This study reveals a heretofore unknown combination of RNA structure and sequence that reduces stop codon efficiency, allowing translation of a key viral protein.IMPORTANCE Programmed stop codon readthrough is used by many animal and plant viruses to produce key viral proteins. Moreover, such "leaky" stop codons are used in host mRNAs or can arise from mutations that cause genetic disease. Thus, it is important to understand the mechanism(s) of stop codon readthrough. Here, we shed light on the mechanism of readthrough of the stop codon of the coat protein ORFs of viruses in the Luteoviridae by identifying the amino acids inserted at the stop codon and RNA structures that facilitate this "leakiness" of the stop codon. Members of the Luteoviridae encode a C-terminal extension to the capsid protein known as the readthrough protein (RTP). We characterized two RNA domains in Potato leafroll virus (PLRV), located 600 to 700 nucleotides apart, that are essential for efficient RTP translation. We further determined that the PLRV readthrough process involves both local structures and long-range RNA-RNA interactions. Genetic manipulation of the RNA structure altered the ability of PLRV to translate RTP and systemically infect the plant. This demonstrates that plant virus RNA contains multiple layers of information beyond the primary sequence and extends our understanding of stop codon readthrough. Strategic targets that can be exploited to disrupt the virus life cycle and reduce its ability to move within and between plant hosts were revealed.
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Affiliation(s)
- Yi Xu
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, New York, USA
| | - Ho-Jong Ju
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, New York, USA
| | - Stacy DeBlasio
- Emerging Pests and Pathogens Research Unit, USDA, ARS, Ithaca, New York, USA
| | - Elizabeth J Carino
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michelle Heck
- Emerging Pests and Pathogens Research Unit, USDA, ARS, Ithaca, New York, USA
- Boyce Thompson Institute, Ithaca, New York, USA
| | - W Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Stewart M Gray
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, New York, USA
- Emerging Pests and Pathogens Research Unit, USDA, ARS, Ithaca, New York, USA
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24
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Loughran G, Jungreis I, Tzani I, Power M, Dmitriev RI, Ivanov IP, Kellis M, Atkins JF. Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. J Biol Chem 2018; 293:4434-4444. [PMID: 29386352 PMCID: PMC5868278 DOI: 10.1074/jbc.m117.818526] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/30/2018] [Indexed: 12/25/2022] Open
Abstract
Although stop codon readthrough is used extensively by viruses to expand their gene expression, verified instances of mammalian readthrough have only recently been uncovered by systems biology and comparative genomics approaches. Previously, our analysis of conserved protein coding signatures that extend beyond annotated stop codons predicted stop codon readthrough of several mammalian genes, all of which have been validated experimentally. Four mRNAs display highly efficient stop codon readthrough, and these mRNAs have a UGA stop codon immediately followed by CUAG (UGA_CUAG) that is conserved throughout vertebrates. Extending on the identification of this readthrough motif, we here investigated stop codon readthrough, using tissue culture reporter assays, for all previously untested human genes containing UGA_CUAG. The readthrough efficiency of the annotated stop codon for the sequence encoding vitamin D receptor (VDR) was 6.7%. It was the highest of those tested but all showed notable levels of readthrough. The VDR is a member of the nuclear receptor superfamily of ligand-inducible transcription factors, and it binds its major ligand, calcitriol, via its C-terminal ligand-binding domain. Readthrough of the annotated VDR mRNA results in a 67 amino acid-long C-terminal extension that generates a VDR proteoform named VDRx. VDRx may form homodimers and heterodimers with VDR but, compared with VDR, VDRx displayed a reduced transcriptional response to calcitriol even in the presence of its partner retinoid X receptor.
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Affiliation(s)
- Gary Loughran
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland,
| | - Irwin Jungreis
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, and
| | - Ioanna Tzani
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Michael Power
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ruslan I Dmitriev
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ivaylo P Ivanov
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, and
| | - John F Atkins
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland, .,Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112-5330
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25
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Jamar NH, Kritsiligkou P, Grant CM. The non-stop decay mRNA surveillance pathway is required for oxidative stress tolerance. Nucleic Acids Res 2017; 45:6881-6893. [PMID: 28472342 PMCID: PMC5499853 DOI: 10.1093/nar/gkx306] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/12/2017] [Indexed: 01/09/2023] Open
Abstract
Reactive oxygen species (ROS) are toxic by-products of normal aerobic metabolism. ROS can damage mRNAs and the translational apparatus resulting in translational defects and aberrant protein production. Three mRNA quality control systems monitor mRNAs for translational errors: nonsense-mediated decay, non-stop decay (NSD) and no-go decay (NGD) pathways. Here, we show that factors required for the recognition of NSD substrates and components of the SKI complex are required for oxidant tolerance. We found an overlapping requirement for Ski7, which bridges the interaction between the SKI complex and the exosome, and NGD components (Dom34/Hbs1) which have been shown to function in both NSD and NGD. We show that ski7 dom34 and ski7 hbs1 mutants are sensitive to hydrogen peroxide stress and accumulate an NSD substrate. We further show that NSD substrates are generated during ROS exposure as a result of aggregation of the Sup35 translation termination factor, which increases stop codon read-through allowing ribosomes to translate into the 3΄-end of mRNAs. Overexpression of Sup35 decreases stop codon read-through and rescues oxidant tolerance consistent with this model. Our data reveal an unanticipated requirement for the NSD pathway during oxidative stress conditions which prevents the production of aberrant proteins from NSD mRNAs.
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Affiliation(s)
- Nur H Jamar
- The University of Manchester, Faculty of Biology, Medicine and Health, Manchester M13 9PT, UK.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Paraskevi Kritsiligkou
- The University of Manchester, Faculty of Biology, Medicine and Health, Manchester M13 9PT, UK
| | - Chris M Grant
- The University of Manchester, Faculty of Biology, Medicine and Health, Manchester M13 9PT, UK
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26
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Phylogenetically Conserved Sequences Around Myelin P0 Stop Codon are Essential for Translational Readthrough to Produce L-MPZ. Neurochem Res 2017; 43:227-237. [PMID: 29081003 DOI: 10.1007/s11064-017-2423-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/14/2017] [Accepted: 10/19/2017] [Indexed: 02/02/2023]
Abstract
Myelin protein zero (P0, MPZ) is the main cell adhesion molecule in peripheral myelin, the sequence of which is evolutionarily highly conserved. Large myelin protein zero (L-MPZ) is a novel translational readthrough molecule in mammals in a physiological status and is encoded by the P0 mRNA with an extra domain. The sequence similarities in the L-MPZ-specific region are found in humans and frogs but not in fish P0 cDNA. Actual synthesis of L-MPZ has been detected in rat and mouse sciatic nerve but not yet evaluated in frogs and humans. The production mechanism and physiological functions of L-MPZ remain unknown. Additionally, the sequence context around the canonical stop codon is significant for readthrough in viruses and yeast, but the correlation between the sequence around P0 stop codon and L-MPZ synthesis is unclear. Here, we focused on the phylogenetic pathways in L-MPZ synthesis. We have shown that L-MPZ is widely produced from frogs to humans using western blotting against L-MPZ. Mutation analysis of the sequence around the stop codon for L-MPZ synthesis using a mammalian in vitro transcription/translation system revealed that the evolutionarily conserved sequence around P0 stop codon is susceptible to readthrough and is similar to the consensus motif in viruses and yeast UAG stop codon type molecules. Our results demonstrate that the phylogenetically conserved sequence around the canonical P0 stop codon is essential for L-MPZ synthesis, suggesting that phylogenetic emergence of L-MPZ in amphibians may be related to particular distribution and/or function in the PNS myelin.
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27
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O'Doherty PJ, Khan A, Johnson AJ, Rogers PJ, Bailey TD, Wu MJ. Proteomic response to linoleic acid hydroperoxide in Saccharomyces cerevisiae. FEMS Yeast Res 2017; 17:3752509. [PMID: 28449083 DOI: 10.1093/femsyr/fox022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 04/20/2017] [Indexed: 12/12/2022] Open
Abstract
Yeast AP-1 transcription factor (Yap1p) and the enigmatic oxidoreductases Oye2p and Oye3p are involved in counteracting lipid oxidants and their unsaturated breakdown products. In order to uncover the response to linoleic acid hydroperoxide (LoaOOH) and the roles of Oye2p, Oye3p and Yap1p, we carried out proteomic analysis of the homozygous deletion mutants oye3Δ, oye2Δ and yap1Δ alongside the diploid parent strain BY4743. The findings demonstrate that deletion of YAP1 narrowed the response to LoaOOH, as the number of proteins differentially expressed in yap1Δ was 70% of that observed in BY4743. The role of Yap1p in regulating the major yeast peroxiredoxin Tsa1p was demonstrated by the decreased expression of Tsa1p in yap1Δ. The levels of Ahp1p and Hsp31p, previously shown to be regulated by Yap1p, were increased in LoaOOH-treated yap1Δ, indicating their expression is also regulated by another transcription factor(s). Relative to BY4743, protein expression differed in oye3Δ and oye2Δ under LoaOOH, underscored by superoxide dismutase (Sod1p), multiple heat shock proteins (Hsp60p, Ssa1p, and Sse1p), the flavodoxin-like protein Pst2p and the actin stabiliser tropomyosin (Tpm1p). Proteins associated with glycolysis were increased in all strains following treatment with LoaOOH. Together, the dataset reveals, for the first time, the yeast proteomic response to LoaOOH, highlighting the significance of carbohydrate metabolism, as well as distinction between the roles of Oye3p, Oye2p and Yap1p.
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Affiliation(s)
- Patrick J O'Doherty
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Alamgir Khan
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney NSW 2109 Australia
| | - Adam J Johnson
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Peter J Rogers
- School of Biomolecular and Physical Sciences, Griffith University, Nathan QLD 4111, Australia
| | - Trevor D Bailey
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Ming J Wu
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
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28
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Nyikó T, Auber A, Szabadkai L, Benkovics A, Auth M, Mérai Z, Kerényi Z, Dinnyés A, Nagy F, Silhavy D. Expression of the eRF1 translation termination factor is controlled by an autoregulatory circuit involving readthrough and nonsense-mediated decay in plants. Nucleic Acids Res 2017; 45:4174-4188. [PMID: 28062855 PMCID: PMC5397192 DOI: 10.1093/nar/gkw1303] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/24/2016] [Accepted: 12/28/2016] [Indexed: 12/28/2022] Open
Abstract
When a ribosome reaches a stop codon, the eukaryotic Release Factor 1 (eRF1) binds to the A site of the ribosome and terminates translation. In yeasts and plants, both over- and underexpression of eRF1 lead to altered phenotype indicating that eRF1 expression should be strictly controlled. However, regulation of eRF1 level is still poorly understood. Here we show that expression of plant eRF1 is controlled by a complex negative autoregulatory circuit, which is based on the unique features of the 3΄untranslated region (3΄UTR) of the eRF1-1 transcript. The stop codon of the eRF1-1 mRNA is in a translational readthrough promoting context, while its 3΄UTR induces nonsense-mediated decay (NMD), a translation termination coupled mRNA degradation mechanism. We demonstrate that readthrough partially protects the eRF1-1 mRNA from its 3΄UTR induced NMD, and that elevated eRF1 levels inhibit readthrough and stimulate NMD. Thus, high eRF1 level leads to reduced eRF1-1 expression, as weakened readthrough fails to protect the eRF1-1 mRNA from the more intense NMD. This eRF1 autoregulatory circuit might serve to finely balance general translation termination efficiency.
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Affiliation(s)
- Tünde Nyikó
- Department of Genetics, Agricultural Biotechnology Institute, Gödöllő, Szent-Györgyi 4, H-2100, Hungary
| | - Andor Auber
- Department of Genetics, Agricultural Biotechnology Institute, Gödöllő, Szent-Györgyi 4, H-2100, Hungary
| | - Levente Szabadkai
- Department of Genetics, Agricultural Biotechnology Institute, Gödöllő, Szent-Györgyi 4, H-2100, Hungary
| | - Anna Benkovics
- Department of Genetics, Agricultural Biotechnology Institute, Gödöllő, Szent-Györgyi 4, H-2100, Hungary
| | - Mariann Auth
- Department of Genetics, Agricultural Biotechnology Institute, Gödöllő, Szent-Györgyi 4, H-2100, Hungary
| | - Zsuzsanna Mérai
- Department of Genetics, Agricultural Biotechnology Institute, Gödöllő, Szent-Györgyi 4, H-2100, Hungary
| | - Zoltán Kerényi
- Department of Genetics, Agricultural Biotechnology Institute, Gödöllő, Szent-Györgyi 4, H-2100, Hungary
| | - Andrea Dinnyés
- Department of Genetics, Agricultural Biotechnology Institute, Gödöllő, Szent-Györgyi 4, H-2100, Hungary
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Temesvári 62, H-6726, Hungary
| | - Dániel Silhavy
- Department of Genetics, Agricultural Biotechnology Institute, Gödöllő, Szent-Györgyi 4, H-2100, Hungary
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29
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Kompella PS, Moses AM, Peisajovich SG. Introduction of Premature Stop Codons as an Evolutionary Strategy To Rescue Signaling Network Function. ACS Synth Biol 2017; 6:446-454. [PMID: 27935292 DOI: 10.1021/acssynbio.6b00142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The cellular concentrations of key components of signaling networks are tightly regulated, as deviations from their optimal ranges can have negative effects on signaling function. For example, overexpression of the yeast mating pathway mitogen-activated protein kinase (MAPK) Fus3 decreases pathway output, in part by sequestering individual components away from functional multiprotein complexes. Using a synthetic biology approach, we investigated potential mechanisms by which selection could compensate for a decrease in signaling activity caused by overexpression of Fus3. We overexpressed a library of random mutants of Fus3 and used cell sorting to select variants that rescued mating pathway activity. Our results uncovered that one remarkable way in which selection can compensate for protein overexpression is by introducing premature stop codons at permitted positions. Because of the low efficiency with which premature stop codons are read through, the resulting cellular concentration of active Fus3 returns to values within the range required for proper signaling. Our results underscore the importance of interpreting genotypic variation at the systems rather than at the individual gene level, as mutations can have opposite effects on protein and network function.
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Affiliation(s)
- Purnima S. Kompella
- Department of Cell and Systems
Biology, University of Toronto 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada
| | - Alan M. Moses
- Department of Cell and Systems
Biology, University of Toronto 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada
| | - Sergio G. Peisajovich
- Department of Cell and Systems
Biology, University of Toronto 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada
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30
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Widespread and dynamic translational control of red blood cell development. Blood 2016; 129:619-629. [PMID: 27899360 DOI: 10.1182/blood-2016-09-741835] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/19/2016] [Indexed: 11/20/2022] Open
Abstract
Cell development requires tight yet dynamic control of protein production. Here, we use parallel RNA and ribosome profiling to study translational regulatory dynamics during murine terminal erythropoiesis. Our results uncover pervasive translational control of protein synthesis, with widespread alternative translation initiation and termination, robust discrimination of long noncoding from micropeptide-encoding RNAs, and dynamic use of upstream open reading frames. Further, we identify hundreds of messenger RNAs (mRNAs) whose translation efficiency is dynamically controlled during erythropoiesis and that enrich for target sites of RNA-binding proteins that are specific to hematopoietic cells, thus unraveling potential regulators of erythroid translational programs. A major such program involves enhanced decoding of specific mRNAs that are depleted in terminally differentiating/enucleating cells with decreasing transcriptional capacity. We find that RBM38, an erythroid-specific RNA-binding protein previously implicated in splicing, interacts with the general translation initiation factor eIF4G and promotes translation of a subset of these irreplaceable mRNAs. Inhibition of RBM38 compromises translation in erythroblasts and impairs their maturation, highlighting a key function for this protein during erythropoiesis. These findings thus reveal critical roles for dynamic translational control in supporting specialized mammalian cell formation.
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31
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Lujan E, Bornemann DJ, Rottig C, Bayless BA, Stocker H, Hafen E, Arora K, Warrior R. Analysis of novel alleles of brother of tout-velu, the drosophila ortholog of human EXTL3 using a newly developed FRT42D ovo D chromosome. Genesis 2016; 54:573-581. [PMID: 27636555 DOI: 10.1002/dvg.22981] [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: 08/30/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 11/08/2022]
Abstract
The FLP/FRT system permits rapid phenotypic screening of homozygous lethal mutations in the context of a viable mosaic fly. Combining this system with ovoD dominant female-sterile transgenes enables efficient production of embryos derived from mutant germline clones lacking maternal contribution from a gene of interest. Two distinct sets of FRT chromosomes, carrying either the mini-white (w + mW.hs ), or rosy (ry+ ) and neomycin (neoR ) transgenes are in common use. Parallel ovoD lines were developed using w + mW.hs FRT insertions on the X and chromosomes 2R and 3L, as well as ry+ , neoR FRT insertions on 2L and 3R. Consequently, mutations isolated on the X, 2R and 3L chromosomes in a ry+ , neoR FRT background, are not amenable to germline clonal analysis without labor-intensive recombination onto chromosome arms containing a w + mW.hs FRT. Here we report the creation of a new ovoD line for the ry+ , neoR FRT insertion at position FRT42D on chromosome 2R, through induced recombination in males. To establish the developmental relevance of this reagent we characterized the maternal-effect phenotypes of novel brother of tout-velu alleles generated on an FRT42D chromosome in a somatic mosaic screen. We find that an apparent null mutation that causes severe defects in somatic tissues has a much milder effect on embryonic patterning, emphasizing the necessity of analyzing mutant phenotypes at multiple developmental stages.
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Affiliation(s)
- Ernesto Lujan
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, 92697
| | - Douglas J Bornemann
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, 92697.,Developmental Biology Center, University of California Irvine, Irvine, CA, 92697
| | - Carmen Rottig
- Department of Biology, ETH Zurich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, Zurich, 8093, Switzerland
| | - Brian A Bayless
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, 92697
| | - Hugo Stocker
- Department of Biology, ETH Zurich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, Zurich, 8093, Switzerland
| | - Ernst Hafen
- Department of Biology, ETH Zurich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, Zurich, 8093, Switzerland
| | - Kavita Arora
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, 92697.,Developmental Biology Center, University of California Irvine, Irvine, CA, 92697
| | - Rahul Warrior
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, 92697.,Developmental Biology Center, University of California Irvine, Irvine, CA, 92697
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32
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Jungreis I, Chan CS, Waterhouse RM, Fields G, Lin MF, Kellis M. Evolutionary Dynamics of Abundant Stop Codon Readthrough. Mol Biol Evol 2016; 33:3108-3132. [PMID: 27604222 PMCID: PMC5100048 DOI: 10.1093/molbev/msw189] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species. Using improved comparative genomics methods for detecting readthrough, we identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector, Anopheles gambiae, and of 51 additional Drosophila melanogaster stop codons, including several cases of double and triple readthrough and of readthrough of two adjacent stop codons. We find that most differences between the readthrough repertoires of the two species arose from readthrough gain or loss in existing genes, rather than birth of new genes or gene death; that readthrough-associated RNA structures are sometimes gained or lost while readthrough persists; that readthrough is more likely to be lost at TAA and TAG stop codons; and that readthrough is under continued purifying evolutionary selection in mosquito, based on population genetic evidence. We also determine readthrough-associated gene properties that predate readthrough, and identify differences in the characteristic properties of readthrough genes between clades. We estimate more than 600 functional readthrough stop codons in mosquito and 900 in fruit fly, provide evidence of readthrough control of peroxisomal targeting, and refine the phylogenetic extent of abundant readthrough as following divergence from centipede.
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Affiliation(s)
- Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Clara S Chan
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Robert M Waterhouse
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA.,Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, Geneva, Switzerland.,Swiss Institute of Bioinformatics, rue Michel-Servet 1, Geneva, Switzerland
| | | | | | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
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33
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Pancsa R, Macossay-Castillo M, Kosol S, Tompa P. Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing. Sci Rep 2016; 6:32142. [PMID: 27561673 PMCID: PMC4999894 DOI: 10.1038/srep32142] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/21/2016] [Indexed: 01/21/2023] Open
Abstract
In translational readthrough (TR) the ribosome continues extending the nascent protein beyond the first in-frame termination codon. Due to the lack of dedicated analyses of eukaryotic TR cases, the associated functional-evolutionary advantages are still unclear. Here, based on a variety of computational methods, we describe the structural and functional properties of previously proposed D. melanogaster and S. cerevisiae TR proteins and extensions. We found that in D. melanogaster TR affects long proteins in mainly regulatory roles. Their TR-extensions are structurally disordered and rich in binding motifs, which, together with their cell-type- and developmental stage-dependent inclusion, suggest that similarly to alternatively spliced exons they rewire cellular interaction networks in a temporally and spatially controlled manner. In contrast, yeast TR proteins are rather short and fulfil mainly housekeeping functions, like translation. Yeast extensions usually lack disorder and linear motifs, which precludes elucidating their functional relevance with sufficient confidence. Therefore we propose that by being much more restricted and by lacking clear functional hallmarks in yeast as opposed to fruit fly, TR shows remarkable parallels with alternative splicing. Additionally, the lack of conservation of TR extensions among orthologous TR proteins suggests that TR-mediated functions may be generally specific to lower taxonomic levels.
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Affiliation(s)
- Rita Pancsa
- Flanders Institute for Biotechnology (VIB), Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Pleinlaan 2, Brussels, Belgium
| | - Mauricio Macossay-Castillo
- Flanders Institute for Biotechnology (VIB), Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Pleinlaan 2, Brussels, Belgium
| | - Simone Kosol
- Flanders Institute for Biotechnology (VIB), Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Pleinlaan 2, Brussels, Belgium
| | - Peter Tompa
- Flanders Institute for Biotechnology (VIB), Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Pleinlaan 2, Brussels, Belgium.,Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, 1117 Budapest, Hungary
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34
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Dabrowski M, Bukowy-Bieryllo Z, Zietkiewicz E. Translational readthrough potential of natural termination codons in eucaryotes--The impact of RNA sequence. RNA Biol 2016; 12:950-8. [PMID: 26176195 PMCID: PMC4615788 DOI: 10.1080/15476286.2015.1068497] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Termination of protein synthesis is not 100% efficient. A number of natural mechanisms that suppress translation termination exist. One of them is STOP codon readthrough, the process that enables the ribosome to pass through the termination codon in mRNA and continue translation to the next STOP codon in the same reading frame. The efficiency of translational readthrough depends on a variety of factors, including the identity of the termination codon, the surrounding mRNA sequence context, and the presence of stimulating compounds. Understanding the interplay between these factors provides the necessary background for the efficient application of the STOP codon suppression approach in the therapy of diseases caused by the presence of premature termination codons.
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Affiliation(s)
- Maciej Dabrowski
- a Institute of Human Genetics; Polish Academy of Sciences ; Poznan , Poland
| | | | - Ewa Zietkiewicz
- a Institute of Human Genetics; Polish Academy of Sciences ; Poznan , Poland
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35
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Abstract
The TTT complex is composed of the three essential proteins Tel2, Tti1, and Tti2 The complex is required to maintain steady state levels of phosphatidylinositol 3-kinase-related kinase (PIKK) proteins, including mTOR, ATM/Tel1, ATR/Mec1, and TRRAP/Tra1, all of which serve as regulators of critical cell signaling pathways. Due to their association with heat shock proteins, and with newly synthesized PIKK peptides, components of the TTT complex may act as cochaperones. Here, we analyze the consequences of depleting the cellular level of Tti2 in Saccharomyces cerevisiae We show that yeast expressing low levels of Tti2 are viable under optimal growth conditions, but the cells are sensitive to a number of stress conditions that involve PIKK pathways. In agreement with this, depleting Tti2 levels decreased expression of Tra1, Mec1, and Tor1, affected their localization and inhibited the stress responses in which these molecules are involved. Tti2 expression was not increased during heat shock, implying that it does not play a general role in the heat shock response. However, steady state levels of Hsp42 increase when Tti2 is depleted, and tti2L187P has a synthetic interaction with exon 1 of the human Huntingtin gene containing a 103 residue polyQ sequence, suggesting a general role in protein quality control. We also find that overexpressing Hsp90 or its cochaperones is synthetic lethal when Tti2 is depleted, an effect possibly due to imbalanced stoichiometry of a complex required for PIKK assembly. These results indicate that Tti2 does not act as a general chaperone, but may have a specialized function in PIKK folding and/or complex assembly.
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36
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Abstract
Although prions were first discovered through their link to severe brain degenerative diseases in animals, the emergence of prions as regulators of the phenotype of the yeast Saccharomyces cerevisiae and the filamentous fungus Podospora anserina has revealed a new facet of prion biology. In most cases, fungal prions are carried without apparent detriment to the host cell, representing a novel form of epigenetic inheritance. This raises the question of whether or not yeast prions are beneficial survival factors or actually gives rise to a "disease state" that is selected against in nature. To date, most studies on the impact of fungal prions have focused on laboratory-cultivated "domesticated" strains of S. cerevisiae. At least eight prions have now been described in this species, each with the potential to impact on a wide range of cellular processes. The discovery of prions in nondomesticated strains of S. cerevisiae and P. anserina has confirmed that prions are not simply an artifact of "domestication" of this species. In this review, I describe what we currently know about the phenotypic impact of fungal prions. I then describe how the interplay between host genotype and the prion-mediated changes can generate a wide array of phenotypic diversity. How such prion-generated diversity may be of benefit to the host in survival in a fluctuating, often hazardous environment is then outlined. Prion research has now entered a new phase in which we must now consider their biological function and evolutionary significance in the natural world.
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Affiliation(s)
- Mick F Tuite
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom.
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Beznosková P, Gunišová S, Valášek LS. Rules of UGA-N decoding by near-cognate tRNAs and analysis of readthrough on short uORFs in yeast. RNA (NEW YORK, N.Y.) 2016; 22:456-66. [PMID: 26759455 PMCID: PMC4748822 DOI: 10.1261/rna.054452.115] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/10/2015] [Indexed: 05/13/2023]
Abstract
The molecular mechanism of stop codon recognition by the release factor eRF1 in complex with eRF3 has been described in great detail; however, our understanding of what determines the difference in termination efficiencies among various stop codon tetranucleotides and how near-cognate (nc) tRNAs recode stop codons during programmed readthrough in Saccharomyces cerevisiae is still poor. Here, we show that UGA-C as the only tetranucleotide of all four possible combinations dramatically exacerbated the readthrough phenotype of the stop codon recognition-deficient mutants in eRF1. Since the same is true also for UAA-C and UAG-C, we propose that the exceptionally high readthrough levels that all three stop codons display when followed by cytosine are partially caused by the compromised sampling ability of eRF1, which specifically senses cytosine at the +4 position. The difference in termination efficiencies among the remaining three UGA-N tetranucleotides is then given by their varying preferences for nc-tRNAs. In particular, UGA-A allows increased incorporation of Trp-tRNA whereas UGA-G and UGA-C favor Cys-tRNA. Our findings thus expand the repertoire of general decoding rules by showing that the +4 base determines the preferred selection of nc-tRNAs and, in the case of cytosine, it also genetically interacts with eRF1. Finally, using an example of the GCN4 translational control governed by four short uORFs, we also show how the evolution of this mechanism dealt with undesirable readthrough on those uORFs that serve as the key translation reinitiation promoting features of the GCN4 regulation, as both of these otherwise counteracting activities, readthrough versus reinitiation, are mediated by eIF3.
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Affiliation(s)
- Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, 142 20 Prague, Czech Republic Faculty of Science, Charles University in Prague, 128 43 Prague, Czech Republic
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, 142 20 Prague, Czech Republic
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, 142 20 Prague, Czech Republic
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Kalstrup T, Blunck R. Reinitiation at non-canonical start codons leads to leak expression when incorporating unnatural amino acids. Sci Rep 2015; 5:11866. [PMID: 26153354 PMCID: PMC4648390 DOI: 10.1038/srep11866] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/05/2015] [Indexed: 12/31/2022] Open
Abstract
With the rapid development of a continuously growing selection of unnatural amino acids (UAAs), UAA insertion becomes increasingly popular for investigating proteins. However, it can prove problematic to ensure the homogeneity of the expressed proteins, when homogeneity is compromised by “leak expression”. Here, we show that leak expression may be mediated by reinitiation and can result in unwanted proteins when stop codons for UAA insertion are mutated into the N-terminus of proteins. We demonstrate that up to 25% of leak expression occurs through reinitiation in the Shaker-Kv channel when stop codons are located within the first 70 amino acids. Several non-canonical start codons were identified as translation reinitaition sites, and by removing the start codons, we were able to decrease leak expression to less than 1%. Our study emphasizes the need to carefully inspect for leak expression when inserting UAAs and demonstrates how leak expression can be eliminated.
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Affiliation(s)
- Tanja Kalstrup
- Groupe d'Études des Protéines Membranaires (GÉPROM), Departments of Physics and of Physiology, Université de Montréal, Montréal, QC, Canada
| | - Rikard Blunck
- Groupe d'Études des Protéines Membranaires (GÉPROM), Departments of Physics and of Physiology, Université de Montréal, Montréal, QC, Canada
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Abstract
In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads.
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Beznosková P, Wagner S, Jansen ME, von der Haar T, Valášek LS. Translation initiation factor eIF3 promotes programmed stop codon readthrough. Nucleic Acids Res 2015; 43:5099-111. [PMID: 25925566 PMCID: PMC4446449 DOI: 10.1093/nar/gkv421] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/18/2015] [Indexed: 12/21/2022] Open
Abstract
Programmed stop codon readthrough is a post-transcription regulatory mechanism specifically increasing proteome diversity by creating a pool of C-terminally extended proteins. During this process, the stop codon is decoded as a sense codon by a near-cognate tRNA, which programs the ribosome to continue elongation. The efficiency of competition for the stop codon between release factors (eRFs) and near-cognate tRNAs is largely dependent on its nucleotide context; however, the molecular mechanism underlying this process is unknown. Here, we show that it is the translation initiation (not termination) factor, namely eIF3, which critically promotes programmed readthrough on all three stop codons. In order to do so, eIF3 must associate with pre-termination complexes where it interferes with the eRF1 decoding of the third/wobble position of the stop codon set in the unfavorable termination context, thus allowing incorporation of near-cognate tRNAs with a mismatch at the same position. We clearly demonstrate that efficient readthrough is enabled by near-cognate tRNAs with a mismatch only at the third/wobble position. Importantly, the eIF3 role in programmed readthrough is conserved between yeast and humans.
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Affiliation(s)
- Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic Faculty of Science, Charles University, Vinicna 5, Prague 128 44, the Czech Republic
| | - Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Myrte Esmeralda Jansen
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | | | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
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41
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Stiebler AC, Freitag J, Schink KO, Stehlik T, Tillmann BAM, Ast J, Bölker M. Ribosomal readthrough at a short UGA stop codon context triggers dual localization of metabolic enzymes in Fungi and animals. PLoS Genet 2014; 10:e1004685. [PMID: 25340584 PMCID: PMC4207609 DOI: 10.1371/journal.pgen.1004685] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/18/2014] [Indexed: 11/21/2022] Open
Abstract
Translation of mRNA into a polypeptide chain is a highly accurate process. Many prokaryotic and eukaryotic viruses, however, use leaky termination of translation to optimize their coding capacity. Although growing evidence indicates the occurrence of ribosomal readthrough also in higher organisms, a biological function for the resulting extended proteins has been elucidated only in very few cases. Here, we report that in human cells programmed stop codon readthrough is used to generate peroxisomal isoforms of cytosolic enzymes. We could show for NAD-dependent lactate dehydrogenase B (LDHB) and NAD-dependent malate dehydrogenase 1 (MDH1) that translational readthrough results in C-terminally extended protein variants containing a peroxisomal targeting signal 1 (PTS1). Efficient readthrough occurs at a short sequence motif consisting of a UGA termination codon followed by the dinucleotide CU. Leaky termination at this stop codon context was observed in fungi and mammals. Comparative genome analysis allowed us to identify further readthrough-derived peroxisomal isoforms of metabolic enzymes in diverse model organisms. Overall, our study highlights that a defined stop codon context can trigger efficient ribosomal readthrough to generate dually targeted protein isoforms. We speculate that beyond peroxisomal targeting stop codon readthrough may have also other important biological functions, which remain to be elucidated.
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Affiliation(s)
- Alina C. Stiebler
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE Excellence Cluster for Integrative Fungal Research (IPF), Senckenberg Society, Frankfurt am Main, Germany
| | - Kay O. Schink
- Faculty of Medicine, Centre for Cancer Biomedicine, University of Oslo, Montebello, Oslo, Norway
- Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, Montebello, Oslo, Norway
| | - Thorsten Stehlik
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | | | - Julia Ast
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Michael Bölker
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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42
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Eswarappa SM, Potdar AA, Koch WJ, Fan Y, Vasu K, Lindner D, Willard B, Graham LM, DiCorleto PE, Fox PL. Programmed translational readthrough generates antiangiogenic VEGF-Ax. Cell 2014; 157:1605-18. [PMID: 24949972 DOI: 10.1016/j.cell.2014.04.033] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/21/2014] [Accepted: 04/04/2014] [Indexed: 12/20/2022]
Abstract
Translational readthrough, observed primarily in less complex organisms from viruses to Drosophila, expands the proteome by translating select transcripts beyond the canonical stop codon. Here, we show that vascular endothelial growth factor A (VEGFA) mRNA in mammalian endothelial cells undergoes programmed translational readthrough (PTR) generating VEGF-Ax, an isoform containing a unique 22-amino-acid C terminus extension. A cis-acting element in the VEGFA 3' UTR serves a dual function, not only encoding the appended peptide but also directing the PTR by decoding the UGA stop codon as serine. Heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 binds this element and promotes readthrough. Remarkably, VEGF-Ax exhibits antiangiogenic activity in contrast to the proangiogenic activity of VEGF-A. Pathophysiological significance of VEGF-Ax is indicated by robust expression in multiple human tissues but depletion in colon adenocarcinoma. Furthermore, genome-wide analysis revealed AGO1 and MTCH2 as authentic readthrough targets. Overall, our studies reveal a novel protein-regulated PTR event in a vertebrate system.
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Affiliation(s)
- Sandeepa M Eswarappa
- Department of Cellular and Molecular Medicine, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Alka A Potdar
- Department of Cellular and Molecular Medicine, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA
| | - William J Koch
- Department of Cellular and Molecular Medicine, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yi Fan
- Department of Cellular and Molecular Medicine, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kommireddy Vasu
- Department of Cellular and Molecular Medicine, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Daniel Lindner
- Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Belinda Willard
- Mass Spectrometry Laboratory for Protein Sequencing, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Linda M Graham
- Department of Biomedical Engineering, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul E DiCorleto
- Department of Cellular and Molecular Medicine, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul L Fox
- Department of Cellular and Molecular Medicine, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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Liu W, Mellado L, Espeso EA, Sealy-Lewis HM. In Aspergillus nidulans the suppressors suaA and suaC code for release factors eRF1 and eRF3 and suaD codes for a glutamine tRNA. G3 (BETHESDA, MD.) 2014; 4:1047-57. [PMID: 24727290 PMCID: PMC4065248 DOI: 10.1534/g3.114.010702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 03/25/2014] [Indexed: 11/24/2022]
Abstract
In Aspergillus nidulans, after extensive mutagenesis, a collection of mutants was obtained and four suppressor loci were identified genetically that could suppress mutations in putative chain termination mutations in different genes. Suppressor mutations in suaB and suaD have a similar restricted spectrum of suppression and suaB111 was previously shown to be an alteration in the anticodon of a gln tRNA. We have shown that like suaB, a suaD suppressor has a mutation in the anticodon of another gln tRNA allowing suppression of UAG mutations. Mutations in suaA and suaC had a broad spectrum of suppression. Four suaA mutations result in alterations in the coding region of the eukaryotic release factor, eRF1, and another suaA mutation has a mutation in the upstream region of eRF1 that prevents splicing of the first intron within the 5'UTR. Epitope tagging of eRF1 in this mutant results in 20% of the level of eRF1 compared to the wild-type. Two mutations in suaC result in alterations in the eukaryotic release factor, eRF3. This is the first description in Aspergillus nidulans of an alteration in eRF3 leading to suppression of chain termination mutations.
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Affiliation(s)
- Wen Liu
- Department of Biological, Biomedical and Environmental Sciences, University of Hull, Hull HU6 7RX, United Kingdom
| | - Laura Mellado
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Eduardo A Espeso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Heather M Sealy-Lewis
- Department of Biological, Biomedical and Environmental Sciences, University of Hull, Hull HU6 7RX, United Kingdom
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Abstract
Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged far behind. Here we have applied ribosome profiling—which measures both global mRNA levels and their translation rates—to two species of Saccharomyces yeast and their interspecific hybrid in order to assess the relative contributions of changes in mRNA abundance and translation to regulatory evolution. We report that both cis- and trans-acting regulatory divergence in translation are abundant, affecting at least 35% of genes. The majority of translational divergence acts to buffer changes in mRNA abundance, suggesting a widespread role for stabilizing selection acting across regulatory levels. Nevertheless, we observe evidence of lineage-specific selection acting on several yeast functional modules, including instances of reinforcing selection acting at both levels of regulation. Finally, we also uncover multiple instances of stop-codon readthrough that are conserved between species. Our analysis reveals the underappreciated complexity of post-transcriptional regulatory divergence and indicates that partitioning the search for the locus of selection into the binary categories of “coding” versus “regulatory” may overlook a significant source of selection, acting at multiple regulatory levels along the path from genotype to phenotype.
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Affiliation(s)
- Carlo G Artieri
- Department of Biology, Stanford University, Stanford, California 94305, USA
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45
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Zhao G, Yao Y, Chen W, Cao X. Comparison and analysis of the genomes of two Aspergillus oryzae strains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:7805-7809. [PMID: 23889147 DOI: 10.1021/jf400080g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A. oryzae 3.042 (China) and A. oryzae RIB40 (Japan) used for soy sauce fermentation show some regional differences. We sequenced the genome of A. oryzae 3.042 and compared it to A. oryzae RIB40 in an attempt to understand why different features are shown by these two A. oryzae strains. We predict 11,399 protein-coding genes in A. oryzae 3.042. The genomes of these two A. oryzae strains are collinear revealed by MUMmer analysis, indicating that the differences are not obvious between them. Several strain-specific genes of two strains are identified by genome sequences' comparison, and they are classified into some groups, which have the relationship with cell growth, cellular response and regulation, resistance, energy metabolism, salt tolerance, and flavor formation. A. oryzae 3.042 showed stronger potential for mycelial growth and environmental stress resistance, such as the genes of chitinase and quinone reductase. Some genes unique to A. oryzae RIB40 were related to energy metabolism and salt tolerance, especially genes for Na(+) and K(+) transport, while others were associated with signal transduction and flavor formation. The genome sequence of A. oryzae 3.042 will facilitate the identification of the genetic basis of traits in A. oryzae 3.042, and accelerate our understanding of the different genetic traits of the two A. oryzae strains.
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Affiliation(s)
- Guozhong Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University , 1800 Lihu Road, Wuxi 214122, Jiangsu Province, People's Republic of China
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Bauer JW, Brandl C, Haubenreisser O, Wimmer B, Weber M, Karl T, Klausegger A, Breitenbach M, Hintner H, von der Haar T, Tuite MF, Breitenbach-Koller L. Specialized yeast ribosomes: a customized tool for selective mRNA translation. PLoS One 2013; 8:e67609. [PMID: 23861776 PMCID: PMC3704640 DOI: 10.1371/journal.pone.0067609] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 05/25/2013] [Indexed: 11/23/2022] Open
Abstract
Evidence is now accumulating that sub-populations of ribosomes - so-called specialized ribosomes - can favour the translation of subsets of mRNAs. Here we use a large collection of diploid yeast strains, each deficient in one or other copy of the set of ribosomal protein (RP) genes, to generate eukaryotic cells carrying distinct populations of altered ‘specialized’ ribosomes. We show by comparative protein synthesis assays that different heterologous mRNA reporters based on luciferase are preferentially translated by distinct populations of specialized ribosomes. These mRNAs include reporters carrying premature termination codons (PTC) thus allowing us to identify specialized ribosomes that alter the efficiency of translation termination leading to enhanced synthesis of the wild-type protein. This finding suggests that these strains can be used to identify novel therapeutic targets in the ribosome. To explore this further we examined the translation of the mRNA encoding the extracellular matrix protein laminin β3 (LAMB3) since a LAMB3-PTC mutant is implicated in the blistering skin disease Epidermolysis bullosa (EB). This screen identified specialized ribosomes with reduced levels of RP L35B as showing enhanced synthesis of full-length LAMB3 in cells expressing the LAMB3-PTC mutant. Importantly, the RP L35B sub-population of specialized ribosomes leave both translation of a reporter luciferase carrying a different PTC and bulk mRNA translation largely unaltered.
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Affiliation(s)
- Johann W. Bauer
- Department of Cell Biology, University of Salzburg, Salzburg, Austria
- Department of Dermatology, General Hospital Salzburg/PMU, Salzburg, Austria
| | - Clemens Brandl
- Department of Cell Biology, University of Salzburg, Salzburg, Austria
| | | | - Bjoern Wimmer
- Department of Cell Biology, University of Salzburg, Salzburg, Austria
| | - Manuela Weber
- Department of Cell Biology, University of Salzburg, Salzburg, Austria
| | - Thomas Karl
- Department of Cell Biology, University of Salzburg, Salzburg, Austria
| | - Alfred Klausegger
- Department of Dermatology, General Hospital Salzburg/PMU, Salzburg, Austria
| | | | - Helmut Hintner
- Department of Cell Biology, University of Salzburg, Salzburg, Austria
- Department of Dermatology, General Hospital Salzburg/PMU, Salzburg, Austria
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Mick F. Tuite
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
- * E-mail: (MFT); (LB-K)
| | - Lore Breitenbach-Koller
- Department of Cell Biology, University of Salzburg, Salzburg, Austria
- * E-mail: (MFT); (LB-K)
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Ligabue-Braun R, Andreis FC, Verli H, Carlini CR. 3-to-1: unraveling structural transitions in ureases. Naturwissenschaften 2013; 100:459-67. [PMID: 23619940 DOI: 10.1007/s00114-013-1045-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/05/2013] [Accepted: 04/05/2013] [Indexed: 01/08/2023]
Abstract
Ureases are nickel-dependent enzymes which catalyze the hydrolysis of urea to ammonia and carbamate. Despite the apparent wealth of data on ureases, many crucial aspects regarding these enzymes are still unknown, or constitute matter for ongoing debates. One of these is most certainly their structural organization: ureases from plants and fungi have a single unit, while bacterial and archaean ones have three-chained structures. However, the primitive state of these proteins--single- or three-chained--is yet unknown, despite many efforts in the field. Through phylogenetic inference using three different datasets and two different algorithms, we were able to observe chain number transitions displayed in a 3-to-1 fashion. Our results imply that the ancestral state for ureases is the three-chained organization, with single-chained ureases deriving from them. The two-chained variants are not evolutionary intermediates. A fusion process, different from those already studied, may explain this structural transition.
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Affiliation(s)
- Rodrigo Ligabue-Braun
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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48
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O'Connor STF, Lan J, North M, Loguinov A, Zhang L, Smith MT, Gu AZ, Vulpe C. Genome-Wide Functional and Stress Response Profiling Reveals Toxic Mechanism and Genes Required for Tolerance to Benzo[a]pyrene in S. cerevisiae. Front Genet 2013; 3:316. [PMID: 23403841 PMCID: PMC3567348 DOI: 10.3389/fgene.2012.00316] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 12/20/2012] [Indexed: 12/29/2022] Open
Abstract
Benzo[a]pyrene (BaP) is a ubiquitous, potent, and complete carcinogen resulting from incomplete organic combustion. BaP can form DNA adducts but other mechanisms may play a role in toxicity. We used a functional toxicology approach in S. cerevisiae to assess the genetic requirements for cellular resistance to BaP. In addition, we examined translational activities of key genes involved in various stress response pathways. We identified multiple genes and processes involved in modulating BaP toxicity in yeast which support DNA damage as a primary mechanism of toxicity, but also identify other potential toxicity pathways. Gene ontology enrichment analysis indicated that DNA damage and repair as well as redox homeostasis and oxidative stress are key processes in cellular response to BaP suggesting a similar mode of action of BaP in yeast and mammals. Interestingly, toxicant export is also implicated as a potential novel modulator of cellular susceptibility. In particular, we identified several transporters with human orthologs (solute carrier family 22) which may play a role in mammalian systems.
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49
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Bordeira-Carriço R, Pêgo AP, Santos M, Oliveira C. Cancer syndromes and therapy by stop-codon readthrough. Trends Mol Med 2012; 18:667-78. [PMID: 23044248 DOI: 10.1016/j.molmed.2012.09.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 08/10/2012] [Accepted: 09/17/2012] [Indexed: 12/19/2022]
Abstract
Several hereditary cancer syndromes are associated with nonsense mutations that create premature termination codons (PTC). Therapeutic strategies involving readthrough induction partially restore expression of proteins with normal function from nonsense-mutated genes, and small molecules such as aminoglycosides and PTC124 have exhibited promising results for treating patients with cystic fibrosis and Duchenne muscular dystrophy. Transgenic expression of suppressor-tRNAs and depleting translation termination factors are, among others, potential strategies for treating PTC-associated diseases. In this review, the potential of using readthrough strategies as a therapy for cancer syndromes is discussed, and we consider the effect of nonsense-mediated decay and other factors on readthrough efficiency.
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50
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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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