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Taylor AD, Hathaway QA, Kunovac A, Pinti MV, Newman MS, Cook CC, Cramer ER, Starcovic SA, Winters MT, Westemeier-Rice ES, Fink GK, Durr AJ, Rizwan S, Shepherd DL, Robart AR, Martinez I, Hollander JM. Mitochondrial sequencing identifies long noncoding RNA features that promote binding to PNPase. Am J Physiol Cell Physiol 2024; 327:C221-C236. [PMID: 38826135 DOI: 10.1152/ajpcell.00648.2023] [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: 11/27/2023] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/04/2024]
Abstract
Extranuclear localization of long noncoding RNAs (lncRNAs) is poorly understood. Based on machine learning evaluations, we propose a lncRNA-mitochondrial interaction pathway where polynucleotide phosphorylase (PNPase), through domains that provide specificity for primary sequence and secondary structure, binds nuclear-encoded lncRNAs to facilitate mitochondrial import. Using FVB/NJ mouse and human cardiac tissues, RNA from isolated subcellular compartments (cytoplasmic and mitochondrial) and cross-linked immunoprecipitate (CLIP) with PNPase within the mitochondrion were sequenced on the Illumina HiSeq and MiSeq, respectively. lncRNA sequence and structure were evaluated through supervised [classification and regression trees (CART) and support vector machines (SVM)] machine learning algorithms. In HL-1 cells, quantitative PCR of PNPase CLIP knockout mutants (KH and S1) was performed. In vitro fluorescence assays assessed PNPase RNA binding capacity and verified with PNPase CLIP. One hundred twelve (mouse) and 1,548 (human) lncRNAs were identified in the mitochondrion with Malat1 being the most abundant. Most noncoding RNAs binding PNPase were lncRNAs, including Malat1. lncRNA fragments bound to PNPase compared against randomly generated sequences of similar length showed stratification with SVM and CART algorithms. The lncRNAs bound to PNPase were used to create a criterion for binding, with experimental validation revealing increased binding affinity of RNA designed to bind PNPase compared to control RNA. The binding of lncRNAs to PNPase was decreased through the knockout of RNA binding domains KH and S1. In conclusion, sequence and secondary structural features identified by machine learning enhance the likelihood of nuclear-encoded lncRNAs binding to PNPase and undergoing import into the mitochondrion.NEW & NOTEWORTHY Long noncoding RNAs (lncRNAs) are relatively novel RNAs with increasingly prominent roles in regulating genetic expression, mainly in the nucleus but more recently in regions such as the mitochondrion. This study explores how lncRNAs interact with polynucleotide phosphorylase (PNPase), a protein that regulates RNA import into the mitochondrion. Machine learning identified several RNA structural features that improved lncRNA binding to PNPase, which may be useful in targeting RNA therapeutics to the mitochondrion.
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Affiliation(s)
- Andrew D Taylor
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Heart and Vascular Institute, West Virginia University, Morgantown, West Virginia, United States
- Department of Medical Education, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Amina Kunovac
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Mark V Pinti
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- West Virginia University School of Pharmacy, Morgantown, West Virginia, United States
| | - Mackenzie S Newman
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Chris C Cook
- Cardiovascular and Thoracic Surgery, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Evan R Cramer
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Sarah A Starcovic
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Michael T Winters
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University Cancer Institute, School of Medicine, Morgantown, West Virginia, United States
| | - Emily S Westemeier-Rice
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University Cancer Institute, School of Medicine, Morgantown, West Virginia, United States
| | - Garrett K Fink
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Andrya J Durr
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Saira Rizwan
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Danielle L Shepherd
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Aaron R Robart
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Ivan Martinez
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University Cancer Institute, School of Medicine, Morgantown, West Virginia, United States
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
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2
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Nikitchina N, Ulashchik E, Shmanai V, Heckel AM, Tarassov I, Mazunin I, Entelis N. Targeting of CRISPR-Cas12a crRNAs into human mitochondria. Biochimie 2024; 217:74-85. [PMID: 37690471 DOI: 10.1016/j.biochi.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/10/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
Mitochondrial gene editing holds great promise as a therapeutic approach for mitochondrial diseases caused by mutations in the mitochondrial DNA (mtDNA). Current strategies focus on reducing mutant mtDNA heteroplasmy levels through targeted cleavage or base editing. However, the delivery of editing components into mitochondria remains a challenge. Here we investigate the import of CRISPR-Cas12a system guide RNAs (crRNAs) into human mitochondria and study the structural requirements for this process by northern blot analysis of RNA isolated from nucleases-treated mitoplasts. To investigate whether the fusion of crRNA with known RNA import determinants (MLS) improve its mitochondrial targeting, we added MLS hairpin structures at 3'-end of crRNA and demonstrated that this did not impact crRNA ability to program specific cleavage of DNA in lysate of human cells expressing AsCas12a nuclease. Surprisingly, mitochondrial localization of the fused crRNA molecules was not improved compared to non-modified version, indicating that structured scaffold domain of crRNA can probably function as MLS, assuring crRNA mitochondrial import. Then, we designed a series of crRNAs targeting different regions of mtDNA and demonstrated their ability to program specific cleavage of mtDNA fragments in cell lysate and their partial localization in mitochondrial matrix in human cells transfected with these RNA molecules. We hypothesize that mitochondrial import of crRNAs may depend on their secondary structure/sequence. We presume that imported crRNA allow reconstituting the active crRNA/Cas12a system in human mitochondria, which can contribute to the development of effective strategies for mitochondrial gene editing and potential future treatment of mitochondrial diseases.
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Affiliation(s)
- Natalia Nikitchina
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, Strasbourg, 67000, France
| | - Egor Ulashchik
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, Minsk, 220072, Belarus
| | - Vadim Shmanai
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, Minsk, 220072, Belarus
| | - Anne-Marie Heckel
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, Strasbourg, 67000, France
| | - Ivan Tarassov
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, Strasbourg, 67000, France
| | - Ilya Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Nina Entelis
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, Strasbourg, 67000, France.
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3
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Bárria C, Athayde D, Hernandez G, Fonseca L, Casinhas J, Cordeiro TN, Archer M, Arraiano CM, Brito JA, Matos RG. Structure and function of Campylobacter jejuni polynucleotide phosphorylase (PNPase): Insights into the role of this RNase in pathogenicity. Biochimie 2024; 216:56-70. [PMID: 37806617 DOI: 10.1016/j.biochi.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/10/2023]
Abstract
Ribonucleases are in charge of the processing, degradation and quality control of all cellular transcripts, which makes them crucial factors in RNA regulation. This post-transcriptional regulation allows bacteria to promptly react to different stress conditions and growth phase transitions, and also to produce the required virulence factors in pathogenic bacteria. Campylobacter jejuni is the main responsible for human gastroenteritis in the world. In this foodborne pathogen, exoribonuclease PNPase (CjPNP) is essential for low-temperature cell survival, affects the synthesis of proteins involved in virulence and has an important role in swimming, cell adhesion/invasion ability, and chick colonization. Here we report the crystallographic structure of CjPNP, complemented with SAXS, which confirms the characteristic doughnut-shaped trimeric arrangement and evaluates domain arrangement and flexibility. Mutations in highly conserved residues were constructed to access their role in RNA degradation and polymerization. Surprisingly, we found two mutations that altered CjPNP into a protein that is only capable of degrading RNA even in conditions that favour polymerization. These findings will be important to develop new strategies to combat C. jejuni infections.
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Affiliation(s)
- Cátia Bárria
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Diogo Athayde
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Guillem Hernandez
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Leonor Fonseca
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Jorge Casinhas
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Tiago N Cordeiro
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Margarida Archer
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Cecília M Arraiano
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - José A Brito
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Rute G Matos
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
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4
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How RNases Shape Mitochondrial Transcriptomes. Int J Mol Sci 2022; 23:ijms23116141. [PMID: 35682820 PMCID: PMC9181182 DOI: 10.3390/ijms23116141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
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5
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Barbier M, Bahlo M, Pennisi A, Jacoupy M, Tankard RM, Ewenczyk C, Davies KC, Lino-Coulon P, Colace C, Rafehi H, Auger N, Ansell BRE, van der Stelt I, Howell KB, Coutelier M, Amor DJ, Mundwiller E, Guillot-Noël L, Storey E, Gardner RJM, Wallis MJ, Brusco A, Corti O, Rötig A, Leventer RJ, Brice A, Delatycki MB, Stevanin G, Lockhart PJ, Durr A. Heterozygous PNPT1 variants cause spinocerebellar ataxia type 25. Ann Neurol 2022; 92:122-137. [PMID: 35411967 DOI: 10.1002/ana.26366] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Dominant spinocerebellar ataxias (SCA) are characterized by genetic heterogeneity. Some mapped and named loci remain without a causal gene identified. Here we applied next generation sequencing (NGS) to uncover the genetic etiology of the SCA25 locus. METHODS Whole-exome and whole-genome sequencing were performed in families linked to SCA25, including the French family in which the SCA25 locus was originally mapped. Whole exome sequence data was interrogated in a cohort of 796 ataxia patients of unknown aetiology. RESULTS The SCA25 phenotype spans a slowly evolving sensory and cerebellar ataxia, in most cases attributed to ganglionopathy. A pathogenic variant causing exon skipping was identified in the gene encoding Polyribonucleotide Nucleotidyltransferase PNPase 1 (PNPT1) located in the SCA25 linkage interval. A second splice variant in PNPT1 was detected in a large Australian family with a dominant ataxia also mapping to SCA25. An additional nonsense variant was detected in an unrelated individual with ataxia. Both nonsense and splice heterozygous variants result in premature stop codons, all located in the S1-domain of PNPase. In addition, an elevated type I interferon response was observed in blood from all affected heterozygous carriers tested. PNPase notably prevents the abnormal accumulation of double-stranded mtRNAs in the mitochondria and leakage into the cytoplasm, associated with triggering a type I interferon response. INTERPRETATION This study identifies PNPT1 as a new SCA gene, responsible for SCA25, and highlights biological links between alterations of mtRNA trafficking, interferonopathies and ataxia. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mathieu Barbier
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Alessandra Pennisi
- Necker Hospital, APHP, Reference Center for Mitochondrial Diseases, Genetics Department, Institut Imagine, University of Paris, Paris, France.,Inserm UMR_S1163, Institut Imagine, Paris, France
| | - Maxime Jacoupy
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Rick M Tankard
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Claire Ewenczyk
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Kayli C Davies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Patricia Lino-Coulon
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Claire Colace
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Nicolas Auger
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Brendan R E Ansell
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Ivo van der Stelt
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Donders Centre for Neuroscience, Faculty of Science, Radboud University, The Netherlands
| | - Katherine B Howell
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, 3052, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Marie Coutelier
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - David J Amor
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Emeline Mundwiller
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Lena Guillot-Noël
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Elsdon Storey
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | | | - Mathew J Wallis
- Clinical Genetics Service, Austin Health, Melbourne, Australia; Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia.,School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Olga Corti
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Agnès Rötig
- Necker Hospital, APHP, Reference Center for Mitochondrial Diseases, Genetics Department, Institut Imagine, University of Paris, Paris, France.,Inserm UMR_S1163, Institut Imagine, Paris, France
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, 3052, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Victorian Clinical Genetics Service, Melbourne, 3052, Australia
| | - Giovanni Stevanin
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Alexandra Durr
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
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6
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Falchi FA, Pizzoccheri R, Briani F. Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase. Int J Mol Sci 2022; 23:ijms23031652. [PMID: 35163574 PMCID: PMC8836086 DOI: 10.3390/ijms23031652] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Polynucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. Human PNPase (hPNPase) is located in mitochondria and is essential for mitochondrial function and homeostasis. Not surprisingly, mutations in the PNPT1 gene, encoding hPNPase, cause serious diseases. hPNPase has been implicated in a plethora of processes taking place in different cell compartments and involving other proteins, some of which physically interact with hPNPase. This paper reviews hPNPase RNA binding and catalytic activity in relation with the protein structure and in comparison, with the activity of bacterial PNPases. The functions ascribed to hPNPase in different cell compartments are discussed, highlighting the gaps that still need to be filled to understand the physiological role of this ancient protein in human cells.
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7
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Hosseini Bereshneh A, Rezaei Z, Jafarinia E, Rajabi F, Ashrafi MR, Tavasoli AR, Garshasbi M. Crystallographic modeling of the PNPT1:c.1453A>G variant as a cause of mitochondrial dysfunction and autosomal recessive deafness; expanding the neuroimaging and clinical features. Mitochondrion 2021; 59:1-7. [PMID: 33812062 DOI: 10.1016/j.mito.2021.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/21/2022]
Abstract
Deficiency of the proteins involved in oxidative phosphorylation (OXPHOS) can lead to mitochondrial dysfunction. Polyribonucleotide nucleotidyltransferase 1 (PNPT1) is one of the genes involved in the OXPHOS and encodes the mitochondrial polynucleotide phosphorylase (PNPase) which is implicated in RNA-processing exoribonuclease activity. Herein, we report a 34-month-old boy who presented with global developmental delay, muscular hypotonia, hearing impairment, and movement disorders including chorea and dystonia. Mitochondrial genome sequencing and whole-exome sequencing (WES) were performed and a variant in PNPT1:c.1453A>G; p. (Met485Val) was identified. A number of patient's neurologic problems had been already reported in previous studies, however, lower limbs spasticity and bulbar dysfunction were novel phenotypic findings. In addition, delayed myelination during infancy, progressive basal ganglia atrophy, and brain stem abnormal signals including transverse pontine fibers and superior colliculus involvement were also novel neuroimaging findings in this case. Different crystallographic modeling and stereochemical analysis of the c.1453A>G; p. (Met485Val) variant showed this variant affects the active site of the protein and disrupts the normal protein function.
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Affiliation(s)
- Ali Hosseini Bereshneh
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran; Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Prenatal Diagnosis and Genetic Research Center, Dastgheib Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Rezaei
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Jafarinia
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Rajabi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahmoud Reza Ashrafi
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Reza Tavasoli
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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8
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Bamborschke D, Kreutzer M, Koy A, Koerber F, Lucas N, Huenseler C, Herkenrath P, Lee-Kirsch MA, Cirak S. PNPT1 mutations may cause Aicardi-Goutières-Syndrome. Brain Dev 2021; 43:320-324. [PMID: 33158637 DOI: 10.1016/j.braindev.2020.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Aicardi-Goutières syndrome (AGS) is a clinically and genetically heterogenous autoinflammatory disorder caused by constitutive activation of the type I interferon axis. It has been associated with the genes TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR1, IFIH1. The clinical diagnosis of AGS is usually made in the context of early-onset encephalopathy in combination with basal ganglia calcification or white matter abnormalities on cranial MRI and laboratory prove of interferon I activation. CASE PRESENTATION We report a patient with early-onset encephalopathy, severe neurodevelopmental regression, progressive secondary microcephaly, epilepsy, movement disorder, and white matter hyperintensities on T2 weighted MRI images. Via whole-exome sequencing, we identified a novel homozygous missense variant (c.1399C > T, p.Pro467Ser) in PNPT1 (NM_033109). Longitudinal assessment of the interferon signature showed a massively elevated interferon score and chronic type I interferon-mediated autoinflammation. CONCLUSION Bi-allelic mutations in PNPT1 have been reported in early-onset encephalopathy. Insufficient nuclear RNA import into mitochondria with consecutive disruption of the respiratory chain was proposed as the main underlying pathomechanism. Recent studies have shown that PNPT1 deficiency causes an accumulation of double-stranded mtRNAs in the cytoplasm, leading to aberrant type I interferon activation, however, longitudinal assessment has been lacking. Here, we present a case of AGS with continuously elevated type I interferon signature with a novel likely-pathogenic homozygous PNTP1 variant. We highlight the clinical value of assessing the interferon signature in children with encephalopathy of unknown origin and suggest all patients presenting with a phenotype of AGS should be screened for mutations in PNPT1.
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Affiliation(s)
- Daniel Bamborschke
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Mona Kreutzer
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Anne Koy
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Friederike Koerber
- Department of Pediatric Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Nadja Lucas
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Christoph Huenseler
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Peter Herkenrath
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sebahattin Cirak
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
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9
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Sharma P, Bharat, Dogra N, Singh S. Small Regulatory Molecules Acting Big in Cancer: Potential Role of Mito-miRs in Cancer. Curr Mol Med 2020; 19:621-631. [PMID: 31340735 DOI: 10.2174/1566524019666190723165357] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/08/2019] [Accepted: 07/15/2019] [Indexed: 12/13/2022]
Abstract
MicroRNAs [miRNAs] are short, non-coding, single stranded RNA molecules regulating gene expression of their targets at the posttranscriptional level by either degrading mRNA or by inhibiting translation. Previously, miRNAs have been reported to be present inside the mitochondria and these miRNAs have been termed as mito-miRs. Origin of these mito-miRs may either be from mitochondrial genome or import from nucleus. The second class of mito-miRs makes it important to unravel the involvement of miRNAs in crosstalk between nucleus and mitochondria. Since miRNAs are involved in various physiological processes, their deregulation is often associated with disease progression, including cancer. The current review focuses on the involvement of miRNAs in different mitochondrial mediated processes. It also highlights the importance of exploring the interaction of miRNAs with mitochondrial genome, which may lead to the development of small regulatory RNA based therapeutic options.
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Affiliation(s)
- Praveen Sharma
- Laboratory of Molecular Medicine, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Mansa Road, Bathinda 151001, Punjab, India
| | - Bharat
- Laboratory of Molecular Medicine, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Mansa Road, Bathinda 151001, Punjab, India
| | - Nilambra Dogra
- Centre for Systems Biology and Bioinformatics, Panjab University, Sector-25, Chandigarh 160014, India
| | - Sandeep Singh
- Laboratory of Molecular Medicine, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Mansa Road, Bathinda 151001, Punjab, India
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10
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Current perspectives on the clinical implications of oxidative RNA damage in aging research: challenges and opportunities. GeroScience 2020; 43:487-505. [PMID: 32529593 PMCID: PMC8110629 DOI: 10.1007/s11357-020-00209-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/28/2020] [Indexed: 02/05/2023] Open
Abstract
Ribonucleic acid (RNA) molecules can be easily attacked by reactive oxygen species (ROS), which are produced during normal cellular metabolism and under various oxidative stress conditions. Numerous findings report that the amount of cellular 8-oxoG, the most abundant RNA damage biomarker, is a promising target for the sensitive measurement of oxidative stress and aging-associated diseases, including neuropsychiatric disorders. Most importantly, available data suggest that RNA oxidation has important implications for various signaling pathways and gene expression regulation in aging-related diseases, highlighting the necessity of using combinations of RNA oxidation adducts in both experimental studies and clinical trials. In this review, we primarily describe evidence for the effect of oxidative stress on RNA integrity modulation and possible quality control systems. Additionally, we discuss the profiles and clinical implications of RNA oxidation products that have been under intensive investigation in several aging-associated medical disorders.
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11
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Rius R, Van Bergen NJ, Compton AG, Riley LG, Kava MP, Balasubramaniam S, Amor DJ, Fanjul-Fernandez M, Cowley MJ, Fahey MC, Koenig MK, Enns GM, Sadedin S, Wilson MJ, Tan TY, Thorburn DR, Christodoulou J. Clinical Spectrum and Functional Consequences Associated with Bi-Allelic Pathogenic PNPT1 Variants. J Clin Med 2019; 8:jcm8112020. [PMID: 31752325 PMCID: PMC6912252 DOI: 10.3390/jcm8112020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 02/01/2023] Open
Abstract
PNPT1 (PNPase—polynucleotide phosphorylase) is involved in multiple RNA processing functions in the mitochondria. Bi-allelic pathogenic PNPT1 variants cause heterogeneous clinical phenotypes affecting multiple organs without any established genotype–phenotype correlations. Defects in PNPase can cause variable combined respiratory chain complex defects. Recently, it has been suggested that PNPase can lead to activation of an innate immune response. To better understand the clinical and molecular spectrum of patients with bi-allelic PNPT1 variants, we captured detailed clinical and molecular phenotypes of all 17 patients reported in the literature, plus seven new patients, including a 78-year-old male with the longest reported survival. A functional follow-up of genomic sequencing by cDNA studies confirmed a splicing defect in a novel, apparently synonymous, variant. Patient fibroblasts showed an accumulation of mitochondrial unprocessed PNPT1 transcripts, while blood showed an increased interferon response. Our findings suggest that functional analyses of the RNA processing function of PNPase are more sensitive than testing downstream defects in oxidative phosphorylation (OXPHPOS) enzyme activities. This research extends our knowledge of the clinical and functional consequences of bi-allelic pathogenic PNPT1 variants that may guide management and further efforts into understanding the pathophysiological mechanisms for therapeutic development.
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Affiliation(s)
- Rocio Rius
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Nicole J. Van Bergen
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alison G. Compton
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Lisa G. Riley
- Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2050, Australia
| | - Maina P. Kava
- Department of Neurology, Perth Children’s Hospital, Perth, WA 6009, Australia
- Department of Metabolic Medicine and Rheumatology, Perth Children’s Hospital, Perth, WA 6009, Australia
| | - Shanti Balasubramaniam
- Department of Metabolic Medicine and Rheumatology, Perth Children’s Hospital, Perth, WA 6009, Australia
- Genetic Metabolic Disorders Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2145, Australia
| | - David J. Amor
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - Miriam Fanjul-Fernandez
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - Mark J. Cowley
- Precision Medicine Theme, Children’s Cancer Institute, Kensington, NSW 2750, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute, University of New South Wales, Randwick, NSW 2010, Australia
- School of Women’s and Children’s Health, University of New South Wales, Randwick, NSW 2031, Australia
| | - Michael C. Fahey
- Department of Paediatrics, Monash University, Melbourne, VIC 3168, Australia
| | - Mary K. Koenig
- The University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Gregory M. Enns
- Department of Pediatrics, Division of Medical Genetics, Stanford University, Stanford, CA 94305, USA
| | - Simon Sadedin
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - Meredith J. Wilson
- Department of Clinical Genetics, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Discipline of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Tiong Y. Tan
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - David R. Thorburn
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - John Christodoulou
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2050, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
- Correspondence: ; Tel.: +613-9936-6353
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12
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Chu LY, Agrawal S, Chen YP, Yang WZ, Yuan HS. Structural insights into nanoRNA degradation by human Rexo2. RNA (NEW YORK, N.Y.) 2019; 25:737-746. [PMID: 30926754 PMCID: PMC6521605 DOI: 10.1261/rna.070557.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
Human RNA exoribonuclease 2 (Rexo2) is an evolutionarily conserved 3'-to-5' DEDDh-family exonuclease located primarily in mitochondria. Rexo2 degrades small RNA oligonucleotides of <5 nucleotides (nanoRNA) in a way similar to Escherichia coli Oligoribonuclease (ORN), suggesting that it plays a role in RNA turnover in mitochondria. However, how Rexo2 preferentially binds and degrades nanoRNA remains elusive. Here, we show that Rexo2 binds small RNA and DNA oligonucleotides with the highest affinity, and it is most robust in degrading small nanoRNA into mononucleotides in the presence of magnesium ions. We further determined three crystal structures of Rexo2 in complex with single-stranded RNA or DNA at resolutions of 1.8-2.2 Å. Rexo2 forms a homodimer and interacts mainly with the last two 3'-end nucleobases of substrates by hydrophobic and π-π stacking interactions via Leu53, Trp96, and Tyr164, signifying its preference in binding and degrading short oligonucleotides without sequence specificity. Crystal structure of Rexo2 is highly similar to that of the RNA-degrading enzyme ORN, revealing a two-magnesium-ion-dependent hydrolysis mechanism. This study thus provides the molecular basis for human Rexo2, showing how it binds and degrades nanoRNA into nucleoside monophosphates and plays a crucial role in RNA salvage pathways in mammalian mitochondria.
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MESH Headings
- 14-3-3 Proteins/chemistry
- 14-3-3 Proteins/genetics
- 14-3-3 Proteins/metabolism
- Binding Sites
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cations, Divalent
- Cloning, Molecular
- Crystallography, X-Ray
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Exoribonucleases/chemistry
- Exoribonucleases/genetics
- Exoribonucleases/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Humans
- Hydrolysis
- Hydrophobic and Hydrophilic Interactions
- Magnesium/chemistry
- Magnesium/metabolism
- Mitochondria/chemistry
- Mitochondria/metabolism
- Mitochondrial Proteins/chemistry
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Models, Molecular
- Oligoribonucleotides/chemistry
- Oligoribonucleotides/genetics
- Oligoribonucleotides/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Multimerization
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
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Affiliation(s)
- Lee-Ya Chu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin Chu, Taiwan 30013, Republic of China
| | - Sashank Agrawal
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 11490, Republic of China
| | - Yi-Ping Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
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13
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Jeandard D, Smirnova A, Tarassov I, Barrey E, Smirnov A, Entelis N. Import of Non-Coding RNAs into Human Mitochondria: A Critical Review and Emerging Approaches. Cells 2019; 8:E286. [PMID: 30917553 PMCID: PMC6468882 DOI: 10.3390/cells8030286] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/19/2019] [Accepted: 03/23/2019] [Indexed: 01/26/2023] Open
Abstract
Mitochondria harbor their own genetic system, yet critically depend on the import of a number of nuclear-encoded macromolecules to ensure their expression. In all eukaryotes, selected non-coding RNAs produced from the nuclear genome are partially redirected into the mitochondria, where they participate in gene expression. Therefore, the mitochondrial RNome represents an intricate mixture of the intrinsic transcriptome and the extrinsic RNA importome. In this review, we summarize and critically analyze data on the nuclear-encoded transcripts detected in human mitochondria and outline the proposed molecular mechanisms of their mitochondrial import. Special attention is given to the various experimental approaches used to study the mitochondrial RNome, including some recently developed genome-wide and in situ techniques.
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Affiliation(s)
- Damien Jeandard
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Anna Smirnova
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Ivan Tarassov
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Eric Barrey
- GABI-UMR1313, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | | | - Nina Entelis
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
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