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Huntzinger E, Sinteff J, Morlet B, Séraphin B. HELZ2: a new, interferon-regulated, human 3'-5' exoribonuclease of the RNB family is expressed from a non-canonical initiation codon. Nucleic Acids Res 2023; 51:9279-9293. [PMID: 37602378 PMCID: PMC10516660 DOI: 10.1093/nar/gkad673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/27/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023] Open
Abstract
Proteins containing a RNB domain, originally identified in Escherichia coli RNase II, are widely present throughout the tree of life. Many RNB proteins have 3'-5' exoribonucleolytic activity but some have lost catalytic activity during evolution. Database searches identified a new RNB domain-containing protein in human: HELZ2. Analysis of genomic and expression data combined with evolutionary information suggested that the human HELZ2 protein is produced from an unforeseen non-canonical initiation codon in Hominidae. This unusual property was confirmed experimentally, extending the human protein by 247 residues. Human HELZ2 was further shown to be an active ribonuclease despite the substitution of a key residue in its catalytic center. HELZ2 RNase activity is lost in cells from some cancer patients as a result of somatic mutations. HELZ2 harbors also two RNA helicase domains and several zinc fingers and its expression is induced by interferon treatment. We demonstrate that HELZ2 is able to degrade structured RNAs through the coordinated ATP-dependent displacement of duplex RNA mediated by its RNA helicase domains and its 3'-5' ribonucleolytic action. The expression characteristics and biochemical properties of HELZ2 support a role for this factor in response to viruses and/or mobile elements.
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Affiliation(s)
- Eric Huntzinger
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Jordan Sinteff
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
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Forbes Beadle L, Love JC, Shapovalova Y, Artemev A, Rattray M, Ashe HL. Combined modelling of mRNA decay dynamics and single-molecule imaging in the Drosophila embryo uncovers a role for P-bodies in 5' to 3' degradation. PLoS Biol 2023; 21:e3001956. [PMID: 36649329 PMCID: PMC9882958 DOI: 10.1371/journal.pbio.3001956] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 01/27/2023] [Accepted: 12/13/2022] [Indexed: 01/18/2023] Open
Abstract
Regulation of mRNA degradation is critical for a diverse array of cellular processes and developmental cell fate decisions. Many methods for determining mRNA half-lives rely on transcriptional inhibition or metabolic labelling. Here, we use a non-invasive method for estimating half-lives for hundreds of mRNAs in the early Drosophila embryo. This approach uses the intronic and exonic reads from a total RNA-seq time series and Gaussian process regression to model the dynamics of premature and mature mRNAs. We show how regulation of mRNA stability is used to establish a range of mature mRNA dynamics during embryogenesis, despite shared transcription profiles. Using single-molecule imaging, we provide evidence that, for the mRNAs tested, there is a correlation between short half-life and mRNA association with P-bodies. Moreover, we detect an enrichment of mRNA 3' ends in P-bodies in the early embryo, consistent with 5' to 3' degradation occurring in P-bodies for at least a subset of mRNAs. We discuss our findings in relation to recently published data suggesting that the primary function of P-bodies in other biological contexts is mRNA storage.
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Affiliation(s)
- Lauren Forbes Beadle
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Jennifer C. Love
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Yuliya Shapovalova
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Artem Artemev
- Department of Computing, Imperial College London, London, United Kingdom
| | - Magnus Rattray
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- * E-mail: (MR); (HLA)
| | - Hilary L. Ashe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- * E-mail: (MR); (HLA)
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Costa SM, Saramago M, Matos RG, Arraiano CM, Viegas SC. How hydrolytic exoribonucleases impact human disease: Two sides of the same story. FEBS Open Bio 2022. [PMID: 35247037 DOI: 10.1002/2211-5463.13392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/05/2022] Open
Abstract
RNAs are extremely important molecules inside the cell which perform many different functions. For example, messenger RNAs, transfer RNAs, and ribosomal RNAs are involved in protein synthesis, whereas non-coding RNAs have numerous regulatory roles. Ribonucleases are the enzymes responsible for the processing and degradation of all types of RNAs, having multiple roles in every aspect of RNA metabolism. However, the involvement of RNases in disease is still not well understood. This review focuses on the involvement of the RNase II/RNB family of 3'-5' exoribonucleases in human disease. This can be attributed to direct effects, whereby mutations in the eukaryotic enzymes of this family (Dis3 (or Rrp44), Dis3L1 (or Dis3L), and Dis3L2) are associated with a disease, or indirect effects, whereby mutations in the prokaryotic counterparts of RNase II/RNB family (RNase II and/or RNase R) affect the physiology and virulence of several human pathogens. In this review, we will compare the structural and biochemical characteristics of the members of the RNase II/RNB family of enzymes. The outcomes of mutations impacting enzymatic function will be revisited, in terms of both the direct and indirect effects on disease. Furthermore, we also describe the SARS-CoV-2 viral exoribonuclease and its importance to combat COVID-19 pandemic. As a result, RNases may be a good therapeutic target to reduce bacterial and viral pathogenicity. These are the two perspectives on RNase II/RNB family enzymes that will be presented in this review.
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Affiliation(s)
- Susana M Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
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Abula A, Li X, Quan X, Yang T, Liu Y, Guo H, Li T, Ji X. Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation. Nucleic Acids Res 2021; 49:4738-4749. [PMID: 33788943 PMCID: PMC8096214 DOI: 10.1093/nar/gkab202] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/09/2021] [Accepted: 03/13/2021] [Indexed: 02/01/2023] Open
Abstract
RNA 2′-O-methylation is widely distributed and plays important roles in various cellular processes. Mycoplasma genitalium RNase R (MgR), a prokaryotic member of the RNase II/RNB family, is a 3′-5′ exoribonuclease and is particularly sensitive to RNA 2′-O-methylation. However, how RNase R interacts with various RNA species and exhibits remarkable sensitivity to substrate 2′-O-methyl modifications remains elusive. Here we report high-resolution crystal structures of MgR in apo form and in complex with various RNA substrates. The structural data together with extensive biochemical analysis quantitively illustrate MgR’s ribonuclease activity and significant sensitivity to RNA 2′-O-methylation. Comparison to its related homologs reveals an exquisite mechanism for the recognition and degradation of RNA substrates. Through structural and mutagenesis studies, we identified proline 277 to be responsible for the significant sensitivity of MgR to RNA 2′-O-methylation within the RNase II/RNB family. We also generated several MgR variants with modulated activities. Our work provides a mechanistic understanding of MgR activity that can be harnessed as a powerful RNA analytical tool that will open up a new venue for RNA 2′-O-methylations research in biological and clinical samples.
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Affiliation(s)
- Abudureyimu Abula
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaona Li
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xing Quan
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tingting Yang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yue Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Hangtian Guo
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tinghan Li
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China.,Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, China
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Gowans LJJ, Al Dhaheri N, Li M, Busch T, Obiri-Yeboah S, Oti AA, Sabbah DK, Arthur FKN, Awotoye WO, Alade AA, Twumasi P, Agbenorku P, Plange-Rhule G, Naicker T, Donkor P, Murray JC, Sobreira NLM, Butali A. Co-occurrence of orofacial clefts and clubfoot phenotypes in a sub-Saharan African cohort: Whole-exome sequencing implicates multiple syndromes and genes. Mol Genet Genomic Med 2021; 9:e1655. [PMID: 33719213 PMCID: PMC8123728 DOI: 10.1002/mgg3.1655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
Background Orofacial clefts (OFCs) are congenital malformations of the face and palate, with an incidence of 1 per 700 live births. Clubfoot or congenital talipes equinovarus (CTEV) is a three‐dimensional abnormality of the leg, ankle, and feet that leads to the anomalous positioning of foot and ankle joints and has an incidence of 1 per 1000 live births. OFCs and CTEV may occur together or separately in certain genetic syndromes in addition to other congenital abnormalities. Here, we sought to decipher the genetic etiology of OFC and CTEV that occurred together in six probands. Methods At the time of recruitment, the most clinically obvious congenital anomalies in these individuals were the OFC and CTEV. We carried out whole‐exome sequencing (WES) on DNA samples from probands and available parents employing the Agilent SureSelect XT kit and Illumina HiSeq2500 platform, followed by bioinformatics analyses. WES variants were validated by clinical Sanger Sequencing. Results Of the six probands, we observed probable pathogenic genetic variants in four. In three probands with probable pathogenic genetic variants, each individual had variants in three different genes, whereas one proband had probable pathogenic variant in just one gene. In one proband, we observed variants in DIS3L2, a gene associated with Perlman syndrome. A second proband had variants in EPG5 (associated with Vici Syndrome), BARX1 and MKI67, while another proband had potentially etiologic variants in FRAS1 (associated with Fraser Syndrome 1), TCOF1 (associated with Treacher Collins Syndrome 1) and MKI67. The last proband had variants in FRAS1, PRDM16 (associated with Cardiomyopathy, dilated, 1LL/Left ventricular noncompaction 8) and CHD7 (associated with CHARGE syndrome/Hypogonadotropic hypogonadism 5 with or without anosmia). Conclusion Our results suggest that clubfoot and OFCs are two congenital abnormalities that can co‐occur in certain individuals with varying genetic causes and expressivity, warranting the need for deep phenotyping.
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Affiliation(s)
- Lord J J Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Oral and Maxillofacial Sciences, Dental School, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - Noura Al Dhaheri
- Department of Medical Genetics, John Hopkins University, Baltimore, MD, USA
| | - Mary Li
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - Tamara Busch
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - Solomon Obiri-Yeboah
- Department of Oral and Maxillofacial Sciences, Dental School, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander A Oti
- Department of Oral and Maxillofacial Sciences, Dental School, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniel K Sabbah
- Department of Orthodontics and Child Oral Health, Dental School, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Fareed K N Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Waheed O Awotoye
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - Azeez A Alade
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - Peter Twumasi
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Pius Agbenorku
- Department of Surgery, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gyikua Plange-Rhule
- Department of Child Health, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Thirona Naicker
- Department of Pediatrics, University of KwaZulu-Natal, South Africa
| | - Peter Donkor
- Department of Oral and Maxillofacial Sciences, Dental School, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Surgery, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Nara L M Sobreira
- Department of Medical Genetics, John Hopkins University, Baltimore, MD, USA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
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