1
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Pérez-Ortín JE, Jordán-Pla A, Zhang Y, Moreno-García J, Bassot C, Barba-Aliaga M, de Campos-Mata L, Choder M, Díez J, Piazza I, Pelechano V, García-Martínez J. Comparison of Xrn1 and Rat1 5' → 3' exoribonucleases in budding yeast supports the specific role of Xrn1 in cotranslational mRNA decay. Yeast 2024. [PMID: 38874348 DOI: 10.1002/yea.3968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
The yeast Saccharomyces cerevisiae and most eukaryotes carry two 5' → 3' exoribonuclease paralogs. In yeast, they are called Xrn1, which shuttles between the nucleus and the cytoplasm, and executes major cytoplasmic messenger RNA (mRNA) decay, and Rat1, which carries a strong nuclear localization sequence (NLS) and localizes to the nucleus. Xrn1 is 30% identical to Rat1 but has an extra ~500 amino acids C-terminal extension. In the cytoplasm, Xrn1 can degrade decapped mRNAs during the last round of translation by ribosomes, a process referred to as "cotranslational mRNA decay." The division of labor between the two enzymes is still enigmatic and serves as a paradigm for the subfunctionalization of many other paralogs. Here we show that Rat1 is capable of functioning in cytoplasmic mRNA decay, provided that Rat1 remains cytoplasmic due to its NLS disruption (cRat1). This indicates that the physical segregation of the two paralogs plays roles in their specific functions. However, reversing segregation is not sufficient to fully complement the Xrn1 function. Specifically, cRat1 can partially restore the cell volume, mRNA stability, the proliferation rate, and 5' → 3' decay alterations that characterize xrn1Δ cells. Nevertheless, cotranslational decay is only slightly complemented by cRat1. The use of the AlphaFold prediction for cRat1 and its subsequent docking with the ribosome complex and the sequence conservation between cRat1 and Xrn1 suggest that the tight interaction with the ribosome observed for Xrn1 is not maintained in cRat1. Adding the Xrn1 C-terminal domain to Rat1 does not improve phenotypes, which indicates that lack of the C-terminal is not responsible for partial complementation. Overall, during evolution, it appears that the two paralogs have acquired specific characteristics to make functional partitioning beneficial.
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Affiliation(s)
- José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Antonio Jordán-Pla
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
| | - Yujie Zhang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Jorge Moreno-García
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
| | - Claudio Bassot
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| | - Marina Barba-Aliaga
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
| | - Leire de Campos-Mata
- Virology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mordechai Choder
- Department of Molecular Microbiology, Technion-Israel Institute of Technology, Rappaport Faculty of Medicine, Haifa, Israel
| | - Juana Díez
- Virology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - José García-Martínez
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, Burjassot, Spain
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2
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Tomaz da Silva P, Zhang Y, Theodorakis E, Martens LD, Yépez VA, Pelechano V, Gagneur J. Cellular energy regulates mRNA degradation in a codon-specific manner. Mol Syst Biol 2024; 20:506-520. [PMID: 38491213 PMCID: PMC11066088 DOI: 10.1038/s44320-024-00026-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/18/2024] Open
Abstract
Codon optimality is a major determinant of mRNA translation and degradation rates. However, whether and through which mechanisms its effects are regulated remains poorly understood. Here we show that codon optimality associates with up to 2-fold change in mRNA stability variations between human tissues, and that its effect is attenuated in tissues with high energy metabolism and amplifies with age. Mathematical modeling and perturbation data through oxygen deprivation and ATP synthesis inhibition reveal that cellular energy variations non-uniformly alter the effect of codon usage. This new mode of codon effect regulation, independent of tRNA regulation, provides a fundamental mechanistic link between cellular energy metabolism and eukaryotic gene expression.
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Affiliation(s)
- Pedro Tomaz da Silva
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Yujie Zhang
- Scilifelab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Evangelos Theodorakis
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Laura D Martens
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Vicente A Yépez
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Vicent Pelechano
- Scilifelab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
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3
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Huch S, Nersisyan L, Ropat M, Barrett D, Wu M, Wang J, Valeriano VD, Vardazaryan N, Huerta-Cepas J, Wei W, Du J, Steinmetz LM, Engstrand L, Pelechano V. Atlas of mRNA translation and decay for bacteria. Nat Microbiol 2023:10.1038/s41564-023-01393-z. [PMID: 37217719 DOI: 10.1038/s41564-023-01393-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 04/19/2023] [Indexed: 05/24/2023]
Abstract
Regulation of messenger RNA stability is pivotal for programmed gene expression in bacteria and is achieved by a myriad of molecular mechanisms. By bulk sequencing of 5' monophosphorylated mRNA decay intermediates (5'P), we show that cotranslational mRNA degradation is conserved among both Gram-positive and -negative bacteria. We demonstrate that, in species with 5'-3' exonucleases, the exoribonuclease RNase J tracks the trailing ribosome to produce an in vivo single-nucleotide toeprint of the 5' position of the ribosome. In other species lacking 5'-3' exonucleases, ribosome positioning alters endonucleolytic cleavage sites. Using our metadegradome (5'P degradome) sequencing approach, we characterize 5'P mRNA decay intermediates in 96 species including Bacillus subtilis, Escherichia coli, Synechocystis spp. and Prevotella copri and identify codon- and gene-level ribosome stalling responses to stress and drug treatment. We also apply 5'P sequencing to complex clinical and environmental microbiomes and demonstrate that metadegradome sequencing provides fast, species-specific posttranscriptional characterization of responses to drug or environmental perturbations. Finally we produce a degradome atlas for 96 species to enable analysis of mechanisms of RNA degradation in bacteria. Our work paves the way for the application of metadegradome sequencing to investigation of posttranscriptional regulation in unculturable species and complex microbial communities.
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Affiliation(s)
- Susanne Huch
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Lilit Nersisyan
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia
| | - Maria Ropat
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Donal Barrett
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Mengjun Wu
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Jing Wang
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Valerie D Valeriano
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Nelli Vardazaryan
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia
| | - Jaime Huerta-Cepas
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo-UPM, Madrid, Spain
| | - Wu Wei
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Juan Du
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
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4
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Hughes LA, Rudler DL, Siira SJ, McCubbin T, Raven SA, Browne JM, Ermer JA, Rientjes J, Rodger J, Marcellin E, Rackham O, Filipovska A. Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation. Nat Commun 2023; 14:2210. [PMID: 37072429 PMCID: PMC10113395 DOI: 10.1038/s41467-023-37843-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/29/2023] [Indexed: 04/20/2023] Open
Abstract
The number of tRNA isodecoders has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both individually and combinatorially. Using ATAC-Seq, RNA-seq, ribo-profiling and proteomics we observed distinct molecular consequences of single tRNA deletions. We show that tRNA-Phe-1-1 is required for neuronal function and its loss is partially compensated by increased expression of other tRNAs but results in mistranslation. In contrast, the other tRNA-Phe isodecoder genes buffer the loss of each of the remaining six tRNA-Phe genes. In the tRNA-Phe gene family, the expression of at least six tRNA-Phe alleles is required for embryonic viability and tRNA-Phe-1-1 is most important for development and survival. Our results reveal that the multi-copy configuration of tRNA genes is required to buffer translation and viability in mammals.
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Affiliation(s)
- Laetitia A Hughes
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Danielle L Rudler
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Samuel A Raven
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Jasmin M Browne
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Judith A Ermer
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Jeanette Rientjes
- Monash Genome Modification Platform, Monash University, 35 Rainforest Walk, Clayton, VIC, 3800, Australia
| | - Jennifer Rodger
- School of Biological Sciences (Physiology), The University of Western Australia, Crawley, WA, 6009, Australia
- Perron Institute for Neurological and Translational Sciences, Nedlands, WA, 6009, Australia
| | - Esteban Marcellin
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, 4072, QLD, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Perth, WA, Australia.
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia.
- Curtin Medical School, Curtin University, Bentley, WA, 6102, Australia.
- Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, 6102, Australia.
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia.
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Perth, WA, Australia.
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia.
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia.
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia.
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5
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Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics. Nat Commun 2022; 13:1860. [PMID: 35387982 PMCID: PMC8987054 DOI: 10.1038/s41467-022-29274-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 03/02/2022] [Indexed: 12/27/2022] Open
Abstract
PoxtA and OptrA are ATP binding cassette (ABC) proteins of the F subtype (ABCF). They confer resistance to oxazolidinone and phenicol antibiotics, such as linezolid and chloramphenicol, which stall translating ribosomes when certain amino acids are present at a defined position in the nascent polypeptide chain. These proteins are often encoded on mobile genetic elements, facilitating their rapid spread amongst Gram-positive bacteria, and are thought to confer resistance by binding to the ribosome and dislodging the bound antibiotic. However, the mechanistic basis of this resistance remains unclear. Here we refine the PoxtA spectrum of action, demonstrate alleviation of linezolid-induced context-dependent translational stalling, and present cryo-electron microscopy structures of PoxtA in complex with the Enterococcus faecalis 70S ribosome. PoxtA perturbs the CCA-end of the P-site tRNA, causing it to shift by ∼4 Å out of the ribosome, corresponding to a register shift of approximately one amino acid for an attached nascent polypeptide chain. We postulate that the perturbation of the P-site tRNA by PoxtA thereby alters the conformation of the attached nascent chain to disrupt the drug binding site. PoxtA confers resistance to ribosome-targeting oxazolidinone (linezolid) and chloramphenicol antibiotics. Here, Crowe-McAuliffe et al. provide structural insights into how binding of PoxtA to the ribosome indirectly promotes drug dissociation.
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6
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Abstract
mRNA degradation is connected to the translation process up to the degree that 5'-3' mRNA degradation follows the last translating ribosome. To study 5'-3'co-translational mRNA decay and the associated ribosome dynamics, here we present an improved high-throughput 5'P degradome RNA sequencing protocol (HT-5Pseq). We exemplify its application in Saccharomyces cerevisiae, but in principle, it could be applied to any other eukaryotic organism. HT-5Pseq is easy, scalable, and uses affordable duplex-specific nuclease-based rRNA depletion. For complete details on the use and execution of this protocol, please refer to Zhang and Pelechano (2021).
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Affiliation(s)
- Yujie Zhang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
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7
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Carpentier MC, Bousquet-Antonelli C, Merret R. Fast and Efficient 5'P Degradome Library Preparation for Analysis of Co-Translational Decay in Arabidopsis. PLANTS 2021; 10:plants10030466. [PMID: 33804539 PMCID: PMC7998949 DOI: 10.3390/plants10030466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/20/2022]
Abstract
The recent development of high-throughput technologies based on RNA sequencing has allowed a better description of the role of post-transcriptional regulation in gene expression. In particular, the development of degradome approaches based on the capture of 5′monophosphate decay intermediates allows the discovery of a new decay pathway called co-translational mRNA decay. Thanks to these approaches, ribosome dynamics could now be revealed by analysis of 5′P reads accumulation. However, library preparation could be difficult to set-up for non-specialists. Here, we present a fast and efficient 5′P degradome library preparation for Arabidopsis samples. Our protocol was designed without commercial kit and gel purification and can be easily done in one working day. We demonstrated the robustness and the reproducibility of our protocol. Finally, we present the bioinformatic reads-outs necessary to assess library quality control.
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Affiliation(s)
- Marie-Christine Carpentier
- CNRS-LGDP UMR 5096, 58 avenue Paul Alduy, 66860 Perpignan, France; (M.-C.C.); (C.B.-A.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 58 avenue Paul Alduy, 66860 Perpignan, France
| | - Cécile Bousquet-Antonelli
- CNRS-LGDP UMR 5096, 58 avenue Paul Alduy, 66860 Perpignan, France; (M.-C.C.); (C.B.-A.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 58 avenue Paul Alduy, 66860 Perpignan, France
| | - Rémy Merret
- CNRS-LGDP UMR 5096, 58 avenue Paul Alduy, 66860 Perpignan, France; (M.-C.C.); (C.B.-A.)
- Université de Perpignan Via Domitia, LGDP-UMR5096, 58 avenue Paul Alduy, 66860 Perpignan, France
- Correspondence:
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