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Luo Q, Zhang M, Lyu M, Ke C, Gao X. Structure and function of vasa gene in gonadal gametogenesis of Pacific abalone. Int J Biol Macromol 2024; 277:134449. [PMID: 39098680 DOI: 10.1016/j.ijbiomac.2024.134449] [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: 03/23/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/06/2024]
Abstract
Pacific abalone (Haliotis discus hannai) is a marine gastropod mollusc with significant economic importance in both global fisheries and aquaculture. However, studies exploring the gonadal development and regulatory mechanisms of Haliotis discus hannai are limited. This study aimed to explore whether the vasa gene acted as a molecular marker for germ cells. Initially, the vasa gene was successfully cloned using the cDNA-end rapid amplification technique. The cloned gene had a 2478-bp-long open reading frame and encoded 825 amino acids. Then, a recombinant expression vector was constructed based on the Vasa protein, and an 87-kDa recombinant protein was prepared. Subsequently, a polyclonal antibody was prepared using the purified recombinant protein. The enzyme-linked immunosorbent assay (ELISA) confirmed the titer of the antibody to be ≥512 K. The immunohistochemical analysis revealed that Vasa was widely expressed in oogonia, Stage I oocytes, spermatogonia, and primary spermatocytes. The specific expression of Vasa in the hermaphroditic gonads of abalone was assessed using western blotting to investigate the effects of different photoperiods (12 L:12D, 24 L:0D, 18 L:6D, and 6 L:18D) on the gonadal development of abalone (P < 0.05), with higher expression levels observed in the ovarian proliferative and spermary maturing stages compared with other developmental stages (P < 0.05). Additionally, Vasa exhibited the highest expression in the spermary and ovary under a photoperiod of 18 L:6D (P < 0.05). These data demonstrated the key role of Vasa in developing germ cells in abalone. They shed light upon the molecular mechanism through which the photoperiod influenced Vasa expression and regulated gonadal development in abalone. The findings might provide theoretical references for analyzing the differentiation pattern of abalone germ cells and the genetic improvement and conservation of germplasm resources.
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Affiliation(s)
- Qi Luo
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Mo Zhang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Mingxin Lyu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Caihuan Ke
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaolong Gao
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
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2
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Ma QL, Zhang CX, Chen JP, Li JM, Zhang Y. Three RNA helicase DDX genes are essential for the development and oocyte maturation in Laodelphax striatellus. PEST MANAGEMENT SCIENCE 2024. [PMID: 39248013 DOI: 10.1002/ps.8396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/02/2024] [Accepted: 08/19/2024] [Indexed: 09/10/2024]
Abstract
BACKGROUND DEAD-box protein (DDX) is a member of the DDX RNA helicase family that exerts multiple functions in RNA metabolism, cell cycle, tumorigenesis, signal pathway, and fertility, particularly in mammals. Nevertheless, the biological functions of DDXs in insects have not been fully resolved and attracted increasing attention these years. Laodelphax striatellus (Hemiptera) is a notorious rice pest through feeding on rice sap and transmitting plant viruses. In this study, we aim to elucidate the functional characterization of DDXs in L. striatellus, and to exploit potential target genes for the development of pest control strategies. RESULTS In this study, we characterized the expression patterns of LsDDX6, LsDDX47, and LsDDX51 in planthoppers and analyzed their conserved motifs. These genes were found to be expressed in all tissues and developmental stages examined, with significantly higher transcript levels observed in the ovary. Knockdown of LsDDX6, LsDDX47, and LsDDX51 resulted in an obvious lethal phenotype in nymphs and abnormal ovarian development in adults. Furthermore, a total of 27 DDXs were identified in L. striatellus, and most DDXs were highly expressed in ovary and structure analysis result revealed that all of the DDXs possessed nine motifs that were unique to the DDX family. CONCLUSION The three DDX RNA helicases (LsDDX6, LsDDX47, and LsDDX51) are essential for both survivorship and reproduction in L. striatellus. Considering a total number of 27 DDXs identified in L. striatellus, they might serve as promising candidates for application in RNAi-based control of this destructive pest. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Qing-Lu Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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Tapescu I, Cherry S. DDX RNA helicases: key players in cellular homeostasis and innate antiviral immunity. J Virol 2024:e0004024. [PMID: 39212449 DOI: 10.1128/jvi.00040-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
RNA helicases are integral in RNA metabolism, performing important roles in cellular homeostasis and stress responses. In particular, the DExD/H-box (DDX) helicase family possesses a conserved catalytic core that binds structural features rather than specific sequences in RNA targets. DDXs have critical roles in all aspects of RNA metabolism including ribosome biogenesis, translation, RNA export, and RNA stability. Importantly, functional specialization within this family arises from divergent N and C termini and is driven at least in part by gene duplications with 18 of the 42 human helicases having paralogs. In addition to their key roles in the homeostatic control of cellular RNA, these factors have critical roles in RNA virus infection. The canonical RIG-I-like receptors (RLRs) play pivotal roles in cytoplasmic sensing of viral RNA structures, inducing antiviral gene expression. Additional RNA helicases function as viral sensors or regulators, further diversifying the innate immune defense arsenal. Moreover, some of these helicases have been coopted by viruses to facilitate their replication. Altogether, DDX helicases exhibit functional specificity, playing intricate roles in RNA metabolism and host defense. This review will discuss the mechanisms by which these RNA helicases recognize diverse RNA structures in cellular and viral RNAs, and how this impacts RNA processing and innate immune responses.
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Affiliation(s)
- Iulia Tapescu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Biochemistry and Biophysics Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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4
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Rao R, Huang X, Wang X, Li X, Liao H, Abuduwaili N, Wei X, Li D, Huang G. Genome-wide identification and analysis of DEAD-box RNA helicases in Gossypium hirsutum. Gene 2024; 920:148495. [PMID: 38663690 DOI: 10.1016/j.gene.2024.148495] [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: 11/25/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
DEAD-box RNA helicases, a prominent subfamily within the RNA helicase superfamily 2 (SF2), play crucial roles in the growth, development, and abiotic stress responses of plants. This study identifies 146 DEAD-box RNA helicase genes (GhDEADs) and categorizes them into four Clades (Clade A-D) through phylogenetic analysis. Promoter analysis reveals cis-acting elements linked to plant responses to light, methyl jasmonate (MeJA), abscisic acid (ABA), low temperature, and drought. RNA-seq data demonstrate that Clade C GhDEADs exhibit elevated and ubiquitous expression across different tissues, validating their connection to leaf development through real-time quantitative polymerase chain reaction (RT-qPCR) analysis. Notably, over half of GhDEADs display up-regulation in the leaves of virus-induced gene silencing (VIGS) plants of GhVIR-A/D (members of m6A methyltransferase complex, which regulate leaf morphogenesis). In conclusion, this study offers a comprehensive insight into GhDEADs, emphasizing their potential involvement in leaf development.
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Affiliation(s)
- Ruotong Rao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China.
| | - Xiaoyu Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Xinting Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Xuelong Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Huiping Liao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Nigara Abuduwaili
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi 830017, Xinjiang Autonomous Region, China
| | - Xiuzhen Wei
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi 830017, Xinjiang Autonomous Region, China
| | - Dengdi Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China.
| | - Gengqing Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China; Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi 830017, Xinjiang Autonomous Region, China.
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5
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Hausmann S, Geiser J, Allen G, Geslain S, Valentini M. Intrinsically disordered regions regulate RhlE RNA helicase functions in bacteria. Nucleic Acids Res 2024; 52:7809-7824. [PMID: 38874491 PMCID: PMC11260450 DOI: 10.1093/nar/gkae511] [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: 01/12/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024] Open
Abstract
RNA helicases-central enzymes in RNA metabolism-often feature intrinsically disordered regions (IDRs) that enable phase separation and complex molecular interactions. In the bacterial pathogen Pseudomonas aeruginosa, the non-redundant RhlE1 and RhlE2 RNA helicases share a conserved REC catalytic core but differ in C-terminal IDRs. Here, we show how the IDR diversity defines RhlE RNA helicase specificity of function. Both IDRs facilitate RNA binding and phase separation, localizing proteins in cytoplasmic clusters. However, RhlE2 IDR is more efficient in enhancing REC core RNA unwinding, exhibits a greater tendency for phase separation, and interacts with the RNase E endonuclease, a crucial player in mRNA degradation. Swapping IDRs results in chimeric proteins that are biochemically active but functionally distinct as compared to their native counterparts. The RECRhlE1-IDRRhlE2 chimera improves cold growth of a rhlE1 mutant, gains interaction with RNase E and affects a subset of both RhlE1 and RhlE2 RNA targets. The RECRhlE2-IDRRhlE1 chimera instead hampers bacterial growth at low temperatures in the absence of RhlE1, with its detrimental effect linked to aberrant RNA droplets. By showing that IDRs modulate both protein core activities and subcellular localization, our study defines the impact of IDR diversity on the functional differentiation of RNA helicases.
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Affiliation(s)
- Stéphane Hausmann
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Johan Geiser
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - George Edward Allen
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sandra Amandine Marie Geslain
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Martina Valentini
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Martin HJ, Hossain MA, Wellnitz J, Kelestemur E, Hochuli JE, Parveen S, Arrowsmith C, Willson TM, Muratov E, Tropsha A. Heli-SMACC: Helicase-targeting SMAll Molecule Compound Collection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.04.602122. [PMID: 39026851 PMCID: PMC11257486 DOI: 10.1101/2024.07.04.602122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Helicases have emerged as promising targets for the development of antiviral drugs; however, the family remains largely undrugged. To support the focused development of viral helicase inhibitors we identified, collected, and integrated all chemogenomics data for all available helicases from the ChEMBL database. After thoroughly curating and enriching the data with relevant annotations we have created a derivative database of helicase inhibitors which we dubbed Heli-SMACC (Helicase-targeting SMAll Molecule Compound Collection). The current version of Heli-SMACC contains 20,432 bioactivity entries for viral, human, and bacterial helicases. We have selected 30 compounds with promising viral helicase activity and tested them in a SARS-CoV-2 NSP13 ATPase assay. Twelve compounds demonstrated ATPase inhibition and a consistent dose-response curve. The Heli-SMACC database may serve as a reference for virologists and medicinal chemists working on the development of novel helicase inhibitors. Heli-SMACC is publicly available at https://smacc.mml.unc.edu.
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Affiliation(s)
- Holli-Joi Martin
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Mohammad A. Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - James Wellnitz
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Enes Kelestemur
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Joshua E. Hochuli
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Sumera Parveen
- The Structural Genomics Consortium, University of Toronto, Canada
| | | | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Eugene Muratov
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Alexander Tropsha
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
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7
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Hussain A. DEAD Box RNA Helicases: Biochemical Properties, Role in RNA Processing and Ribosome Biogenesis. Cell Biochem Biophys 2024; 82:427-434. [PMID: 38430409 DOI: 10.1007/s12013-024-01240-w] [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: 12/12/2022] [Accepted: 02/20/2024] [Indexed: 03/03/2024]
Abstract
DEAD box RNA helicases are a versatile group of ATP dependent enzymes that play an essential role in cellular processes like transcription, RNA processing, ribosome biogenesis and translation. These enzymes perform structural rearrangement of complex RNA molecules and enhance the productive folding of RNA and organization of macromolecular complexes. In this review article besides providing the outline about structural organization of helicases, an in-depth discussion will be done on the biochemical properties of RNA helicases like their substrate binding, binding and hydrolysis of ATP and related conformational changes that are important for functioning of the RNA helicase enzymes. I will extensively discuss the physiological role of RNA helicases in RNA processing and ribosome biogenesis.
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Affiliation(s)
- Ashaq Hussain
- Centre for Cellular and Molecular Biology, Hyderabad, India.
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8
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da Silva RH, Silva MDD, Ferreira-Neto JRC, Souza BDB, de Araújo FN, Oliveira EJDS, Benko-Iseppon AM, da Costa AF, Kido ÉA. DEAD-Box RNA Helicase Family in Physic Nut ( Jatropha curcas L.): Structural Characterization and Response to Salinity. PLANTS (BASEL, SWITZERLAND) 2024; 13:905. [PMID: 38592921 PMCID: PMC10974417 DOI: 10.3390/plants13060905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Helicases, motor proteins present in both prokaryotes and eukaryotes, play a direct role in various steps of RNA metabolism. Specifically, SF2 RNA helicases, a subset of the DEAD-box family, are essential players in plant developmental processes and responses to biotic and abiotic stresses. Despite this, information on this family in the physic nut (Jatropha curcas L.) remains limited, spanning from structural patterns to stress responses. We identified 79 genes encoding DEAD-box RNA helicases (JcDHX) in the J. curcas genome. These genes were further categorized into three subfamilies: DEAD (42 genes), DEAH (30 genes), and DExH/D (seven genes). Characterization of the encoded proteins revealed a remarkable diversity, with observed patterns in domains, motifs, and exon-intron structures suggesting that the DEAH and DExH/D subfamilies in J. curcas likely contribute to the overall versatility of the family. Three-dimensional modeling of the candidates showed characteristic hallmarks, highlighting the expected functional performance of these enzymes. The promoter regions of the JcDHX genes revealed potential cis-elements such as Dof-type, BBR-BPC, and AP2-ERF, indicating their potential involvement in the response to abiotic stresses. Analysis of RNA-Seq data from the roots of physic nut accessions exposed to 150 mM of NaCl for 3 h showed most of the JcDHX candidates repressed. The protein-protein interaction network indicated that JcDHX proteins occupy central positions, connecting events associated with RNA metabolism. Quantitative PCR analysis validated the expression of nine DEAD-box RNA helicase transcripts, showing significant associations with key components of the stress response, including RNA turnover, ribosome biogenesis, DNA repair, clathrin-mediated vesicular transport, phosphatidyl 3,5-inositol synthesis, and mitochondrial translation. Furthermore, the induced expression of one transcript (JcDHX44) was confirmed, suggesting that it is a potential candidate for future functional analyses to better understand its role in salinity stress tolerance. This study represents the first global report on the DEAD-box family of RNA helicases in physic nuts and displays structural characteristics compatible with their functions, likely serving as a critical component of the plant's response pathways.
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Affiliation(s)
- Rahisa Helena da Silva
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - Manassés Daniel da Silva
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - José Ribamar Costa Ferreira-Neto
- Plant Genetics and Biotechnology Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - Bruna de Brito Souza
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - Francielly Negreiros de Araújo
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - Elvia Jéssica da Silva Oliveira
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | - Ana Maria Benko-Iseppon
- Plant Genetics and Biotechnology Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
| | | | - Éderson Akio Kido
- Plant Molecular Genetics Laboratory, Genetics Department, Center of Biosciences, Federal University of Pernambuco, Recife CEP 50670-901, PE, Brazil
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Lawal MM, Roy P, McCullagh M. Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13. J Phys Chem B 2024; 128:492-503. [PMID: 38175211 PMCID: PMC11256563 DOI: 10.1021/acs.jpcb.3c06714] [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] [Indexed: 01/05/2024]
Abstract
In response to the emergence of COVID-19, caused by SARS-CoV-2, there has been a growing interest in understanding the functional mechanisms of the viral proteins to aid in the development of new therapeutics. Nonstructural protein 13 (nsp13) helicase is an attractive target for antivirals because it is essential for viral replication and has a low mutation rate, yet the structural mechanisms by which this enzyme binds and hydrolyzes ATP to cause unidirectional RNA translocation remain elusive. Using Gaussian accelerated molecular dynamics (GaMD), we generated comprehensive conformational ensembles of all substrate states along the ATP-dependent cycle. Shape-GMM clustering of the protein yields four protein conformations that describe an opening and closing of both the ATP pocket and the RNA cleft that is achieved through a combination of conformational selection and induction along the ATP hydrolysis cycle. Furthermore, three protein-RNA conformations are observed that implicate motifs Ia, IV, and V as playing a pivotal role in an ATP-dependent inchworm translocation mechanism. Finally, based on a linear discriminant analysis of protein conformations, we identify L405 as a pivotal residue for the opening and closing mechanism and propose a L405D mutation as a way to disrupt translocation. This research enhances our understanding of nsp13's role in viral replication and could contribute to the development of antiviral strategies.
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Affiliation(s)
- Monsurat M. Lawal
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74074, USA
- These authors contributed equally to this work
| | - Priti Roy
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74074, USA
- These authors contributed equally to this work
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74074, USA
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Moore AFT, Berhie Y, Weislow IS, Koculi E. Substrate Specificities of DDX1: A Human DEAD-box protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.573566. [PMID: 38260591 PMCID: PMC10802426 DOI: 10.1101/2024.01.09.573566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
DDX1 is a human protein which belongs to the DEAD-box protein family of enzymes and is involved in various stages of RNA metabolism from transcription to decay. Many members of the DEAD-box family of enzymes use the energy of ATP binding and hydrolysis to perform their cellular functions. On the other hand, a few members of the DEAD-box family of enzymes bind and/or hydrolyze other nucleotides in addition to ATP. Furthermore, the ATPase activity of DEAD-box family members is stimulated differently by nucleic acids of various structures. The identity of the nucleotides that the DDX1 hydrolyzes and the structure of the nucleic acids upon which it acts in the cell remain largely unknown. Identifying the DDX1 protein's in vitro substrates is important for deciphering the molecular roles of DDX1 in cells. Here we identify the nucleic acid sequences and structures supporting the nucleotide hydrolysis activity of DDX1 and its nucleotide specificity. Our data demonstrate that the DDX1 protein hydrolyzes only ATP and deoxy-ATP in the presence of RNA. The ATP hydrolysis activity of DDX1 is stimulated by multiple molecules: single-stranded RNA molecules as short as ten nucleotides, a blunt-ended double-stranded RNA molecule, a hybrid of a double-stranded DNA-RNA molecule, and a single-stranded DNA molecule. Under our experimental conditions, the single-stranded DNA molecule stimulates the ATPase activity of DDX1 at a significantly reduced extent when compared to the other investigated RNA constructs or the hybrid double-stranded DNA/RNA molecule.
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Affiliation(s)
- Anthony F. T. Moore
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Physical Sciences, Orlando, FL 32816-2366
| | - Yepeth Berhie
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Physical Sciences, Orlando, FL 32816-2366
| | - Isaac S. Weislow
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 W University Ave, Chemistry and Computer Science, El Paso, TX, 79902-5802
| | - Eda Koculi
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 W University Ave, Chemistry and Computer Science, El Paso, TX, 79902-5802
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11
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Zaib S, Rana N, Ali HS, Ur Rehman M, Awwad NS, Ibrahium HA, Khan I. Identification of potential inhibitors targeting yellow fever virus helicase through ligand and structure-based computational studies. J Biomol Struct Dyn 2023:1-18. [PMID: 38109183 DOI: 10.1080/07391102.2023.2294839] [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: 08/14/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
Yellow fever is a flavivirus having plus-sensed RNA which encodes a single polyprotein. Host proteases cut this polyprotein into seven nonstructural proteins including a vital NS3 protein. The present study aims to identify the most effective inhibitor against the helicase (NS3) using different advanced ligand and structure-based computational studies. A set of 300 ligands was selected against helicase by chemical structural similarity model, which are similar to S-adenosyl-l-cysteine using infiniSee. This tool screens billions of compounds through a similarity search from in-built chemical spaces (CHEMriya, Galaxi, KnowledgeSpace and REALSpace). The pharmacophore was designed from ligands in the library that showed same features. According to the sequence of ligands, six compounds (29, 87, 99, 116, 148, and 208) were taken for pharmacophore designing against helicase protein. Subsequently, compounds from the library which showed the best pharmacophore shared-features were docked using FlexX functionality of SeeSAR and their optibrium properties were analyzed. Afterward, their ADME was improved by replacing the unfavorable fragments, which resulted in the generation of new compounds. The selected best compounds (301, 302, 303 and 304) were docked using SeeSAR and their pharmacokinetics and toxicological properties were evaluated using SwissADME. The optimal inhibitor for yellow fever helicase was 2-amino-N-(4-(dimethylamino)thiazol-2-yl)-4-methyloxazole-5-carboxamide (302), which exhibits promising potential for drug development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Nehal Rana
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Hafiz Saqib Ali
- Chemistry Research Laboratory, Department of Chemistry and the INEOS Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Mujeeb Ur Rehman
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Nasser S Awwad
- Department of Chemistry, King Khalid University, Abha, Saudi Arabia
| | - Hala A Ibrahium
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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12
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Fang T, Wang X, Huangfu N. Superfamily II helicases: the potential therapeutic target for cardiovascular diseases. Front Cardiovasc Med 2023; 10:1309491. [PMID: 38152606 PMCID: PMC10752008 DOI: 10.3389/fcvm.2023.1309491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023] Open
Abstract
Cardiovascular diseases (CVDs) still maintain high morbidity and mortality globally. Helicases, a unique class of enzymes, are extensively implicated in the processes of nucleic acid (NA) metabolism across various organisms. They play a pivotal role in gene expression, inflammatory response, lipid metabolism, and so forth. However, abnormal helicase expression has been associated with immune response, cancer, and intellectual disability in humans. Superfamily II (SFII) is one of the largest and most diverse of the helicase superfamilies. Increasing evidence has implicated SFⅡ helicases in the pathogenesis of multiple CVDs. In this review, we comprehensively review the regulation mechanism of SFⅡ helicases in CVDs including atherosclerosis, myocardial infarction, cardiomyopathies, and heart failure, which will contribute to the investigation of ideal therapeutic targets for CVDs.
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Affiliation(s)
- Tianxiang Fang
- Health Science Center, Ningbo University, Ningbo, China
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, China
- Department of Cardiology, Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, China
- Clinical Medicine Research Centre for Cardiovascular Disease of Ningbo, Ningbo, China
| | - Xizhi Wang
- Department of Cardiology, Lihuili Hospital Affiliated to Ningbo University, Ningbo, China
| | - Ning Huangfu
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, China
- Department of Cardiology, Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, China
- Clinical Medicine Research Centre for Cardiovascular Disease of Ningbo, Ningbo, China
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13
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Tang N, Wen W, Liu Z, Xiong X, Wu Y. HELQ as a DNA helicase: Its novel role in normal cell function and tumorigenesis (Review). Oncol Rep 2023; 50:220. [PMID: 37921071 PMCID: PMC10652244 DOI: 10.3892/or.2023.8657] [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: 02/22/2023] [Accepted: 08/08/2023] [Indexed: 11/04/2023] Open
Abstract
Helicase POLQ‑like (HELQ or Hel308), is a highly conserved, 3'‑5' superfamily II DNA helicase that contributes to diverse DNA processes, including DNA repair, unwinding, and strand annealing. HELQ deficiency leads to subfertility, due to its critical role in germ cell stability. In addition, the abnormal expression of HELQ has been observed in multiple tumors and a number of molecular pathways, including the nucleotide excision repair, checkpoint kinase 1‑DNA repair protein RAD51 homolog 1 and ATM/ATR pathways, have been shown to be involved in HELQ. In the present review, the structure and characteristics of HELQ, as well as its major functions in DNA processing, were described. Molecular mechanisms involving HELQ in the context of tumorigenesis were also described. It was deduced that HELQ biology warrants investigation, and that its critical roles in the regulation of various DNA processes and participation in tumorigenesis are clinically relevant.
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Affiliation(s)
- Nan Tang
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital of Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Weilun Wen
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital of Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Zhihe Liu
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital of Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Xifeng Xiong
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital of Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Yanhua Wu
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital of Jinan University, Guangzhou, Guangdong 510220, P.R. China
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14
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Park S, Yang JB, Park YH, Kim YK, Jeoung D, Kim HY, Jung HS. Structural insight into crystal structure of helicase domain of DDX53. Biochem Biophys Res Commun 2023; 677:190-195. [PMID: 37603933 DOI: 10.1016/j.bbrc.2023.08.022] [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: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/23/2023]
Abstract
DEAD box helicase proteins are a family of RNA helicases that participate in various RNA metabolisms such as RNA unwinding, RNA processing, and RNPase activities. A particular DEAD box protein, the DDX53 protein, is primarily expressed in cancer cells and plays a crucial role in tumorigenesis. Numerous studies have revealed that DDX53 interacts with various microRNA and Histone deacetylases. However, its molecular structure and the detailed binding interaction between DDX53 and microRNA or HDAC is still unclear. In this study, we used X-ray crystallography to investigate the 3D structure of the hlicase C-terminal domain of DDX53, and successfully determined its crystal structure at a resolution of 1.97 Å. Subsequently, a functional analysis of RNA was conducted by examining the binding properties thereof with DDX53 by transmission electron microscopy and computing-based molecular docking simulation. The defined 3D model of DDX53 not only provides a structural basis for the fundamental understanding of DDX53 but is also expected to contribute to the field of anti-cancer drug discovery such as structure-based drug discovery and computer-aided drug design.
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Affiliation(s)
- Suncheol Park
- Research Center for Bioconvergence Analysis, Division of Analytical Science Research, Korea Basic Science Institute, Cheongju, Chungbuk, 28119, Republic of Korea
| | - Jeong Bin Yang
- Division of Chemistry & Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea
| | - Yoon Ho Park
- Division of Chemistry & Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea
| | - Young Kwan Kim
- Panolos Bioscience Inc., Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Dooil Jeoung
- Division of Chemistry & Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea
| | - Hye-Yeon Kim
- Research Center for Bioconvergence Analysis, Division of Analytical Science Research, Korea Basic Science Institute, Cheongju, Chungbuk, 28119, Republic of Korea.
| | - Hyun Suk Jung
- Division of Chemistry & Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea.
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15
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Lawal MM, Roy P, McCullagh M. The Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560057. [PMID: 37808802 PMCID: PMC10557736 DOI: 10.1101/2023.09.28.560057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
In response to the emergence of COVID-19, caused by SARS-CoV-2, there has been a growing interest in understanding the functional mechanisms of the viral proteins to aid in the development of new therapeutics. Non-structural protein 13 (Nsp13) helicase is an attractive target for antivirals because it is essential for viral replication and has a low mutation rate; yet, the structural mechanisms by which this enzyme binds and hydrolyzes ATP to cause unidirectional RNA translocation remain elusive. Using Gaussian accelerated molecular dynamics (GaMD), we generated a comprehensive conformational ensemble of all substrate states along the ATP-dependent cycle. ShapeGMM clustering of the protein yields four protein conformations that describe an opening and closing of both the ATP pocket and RNA cleft. This opening and closing is achieved through a combination of conformational selection and induction along the ATP cycle. Furthermore, three protein-RNA conformations are observed that implicate motifs Ia, IV, and V as playing a pivotal role in an ATP-dependent inchworm translocation mechanism. Finally, based on a linear discriminant analysis of protein conformations, we identify L405 as a pivotal residue for the opening and closing mechanism and propose a L405D mutation as a way of testing our proposed mechanism. This research enhances our understanding of nsp13's role in viral replication and could contribute to the development of antiviral strategies.
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Affiliation(s)
- Monsurat M. Lawal
- Department of Chemistry, Oklahoma State University, Stillwater OK
- These authors contributed equally to this work
| | - Priti Roy
- Department of Chemistry, Oklahoma State University, Stillwater OK
- These authors contributed equally to this work
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater OK
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16
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Luo P, Shi C, Zhou Y, Zhou J, Zhang X, Wang Y, Yang Y, Peng X, Xie T, Tang X. The nuclear-localized RNA helicase 13 is essential for chloroplast development in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5057-5071. [PMID: 37310806 DOI: 10.1093/jxb/erad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023]
Abstract
The chloroplast is a semi-autonomous organelle with a double membrane structure, and its structural stability is a prerequisite for its correct function. Chloroplast development is regulated by known nuclear-encoded chloroplast proteins or proteins encoded within the chloroplast itself. However, the mechanism of chloroplast development regulated by other organelles remains largely unknown. Here, we report that the nuclear-localized DEAD-box RNA helicase 13 (RH13) is essential for chloroplast development in Arabidopsis thaliana. RH13 is widely expressed in tissues and localized to the nucleolus. A homozygous rh13 mutant shows abnormal chloroplast structure and leaf morphogenesis. Proteomic analysis showed that the expression levels of photosynthesis-related proteins in chloroplasts were reduced due to loss of RH13. Furthermore, RNA-sequencing and proteomics data revealed decreases in the expression levels of these chloroplast-related genes, which undergo alternative splicing events in the rh13 mutant. Taken together, we propose that nucleolus-localized RH13 is critical for chloroplast development in Arabidopsis.
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Affiliation(s)
- Pan Luo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan 430062, China
| | - Ce Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yi Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan 430062, China
| | - Jiao Zhou
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xuecheng Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yukun Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yong Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan 430062, China
| | - Xiongbo Peng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Tingting Xie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingchun Tang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan 430062, China
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17
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Wang H, Zhai L, Wang S, Zheng B, Hu H, Li X, Bian S. Identification of R2R3-MYB family in blueberry and its potential involvement of anthocyanin biosynthesis in fruits. BMC Genomics 2023; 24:505. [PMID: 37648968 PMCID: PMC10466896 DOI: 10.1186/s12864-023-09605-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Blueberries (Vaccinium corymbosum) are regarded as "superfoods" attributed to large amounts of anthocyanins, a group of flavonoid metabolites, which provide pigmentation in plant and beneficial effects for human health. MYB transcription factor is one of vital components in the regulation of plant secondary metabolism, which occupies a dominant position in the regulatory network of anthocyanin biosynthesis. However, the role of MYB family in blueberry responding to anthocyanin biosynthesis remains elusive. RESULTS In this study, we conducted a comprehensive analysis of VcMYBs in blueberry based on the genome data, including phylogenetic relationship, conserved motifs, identification of differentially expressed MYB genes during fruit development and their expression profiling, etc. A total of 437 unique MYB sequences with two SANT domains were identified in blueberry, which were divided into 3 phylogenetic trees. Noticeably, there are many trigenic and tetragenic VcMYBs pairs with more than 95% identity to each other. Meanwhile, the transcript accumulations of VcMYBs were surveyed underlying blueberry fruit development, and they showed diverse expression patterns, suggesting various functional roles in fruit ripening. More importantly, distinct transcript profiles between skin and pulp of ripe fruit were observed for several VcMYBs, such as VcMYB437, implying the potential roles in anthocyanin biosynthesis. CONCLUSIONS Totally, 437 VcMYBs were identified and characterized. Subsequently, their transcriptional patterns were explored during fruit development and fruit tissues (skin and pulp) closely related to anthocyanin biosynthesis. These genome-wide data and findings will contribute to demonstrating the functional roles of VcMYBs and their regulatory mechanisms for anthocyanins production and accumulation in blueberry in the future study.
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Affiliation(s)
- Haiyang Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun, China
| | - Shouwen Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Botian Zheng
- College of Plant Science, Jilin University, Changchun, China
| | - Honglu Hu
- College of Plant Science, Jilin University, Changchun, China
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun, China.
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, China.
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18
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Rauthan K, Joshi S, Kumar L, Goel D, Kumar S. Functional annotation of uncharacterized proteins from Fusobacterium nucleatum: identification of virulence factors. Genomics Inform 2023; 21:e21. [PMID: 37415454 PMCID: PMC10326533 DOI: 10.5808/gi.22065] [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: 09/29/2022] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 07/08/2023] Open
Abstract
Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as "Uncharacterized." Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.
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Affiliation(s)
- Kanchan Rauthan
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Saranya Joshi
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Lokesh Kumar
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Divya Goel
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Sudhir Kumar
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
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19
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Naineni SK, Cencic R, Robert F, Brown LE, Haque M, Scott-Talib J, Sénéchal P, Schmeing TM, Porco JA, Pelletier J. Exploring the targeting spectrum of rocaglates among eIF4A homologs. RNA (NEW YORK, N.Y.) 2023; 29:826-835. [PMID: 36882295 PMCID: PMC10187672 DOI: 10.1261/rna.079318.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/16/2023] [Indexed: 05/18/2023]
Abstract
Inhibition of eukaryotic translation initiation through unscheduled RNA clamping of the DEAD-box (DDX) RNA helicases eIF4A1 and eIF4A2 has been documented for pateamine A (PatA) and rocaglates-two structurally different classes of compounds that share overlapping binding sites on eIF4A. Clamping of eIF4A to RNA causes steric blocks that interfere with ribosome binding and scanning, rationalizing the potency of these molecules since not all eIF4A molecules need to be engaged to elicit a biological effect. In addition to targeting translation, PatA and analogs have also been shown to target the eIF4A homolog, eIF4A3-a helicase necessary for exon junction complex (EJC) formation. EJCs are deposited on mRNAs upstream of exon-exon junctions and, when present downstream from premature termination codons (PTCs), participate in nonsense-mediated decay (NMD), a quality control mechanism aimed at preventing the production of dominant-negative or gain-of-function polypeptides from faulty mRNA transcripts. We find that rocaglates can also interact with eIF4A3 to induce RNA clamping. Rocaglates also inhibit EJC-dependent NMD in mammalian cells, but this does not appear to be due to induced eIF4A3-RNA clamping, but rather a secondary consequence of translation inhibition incurred by clamping eIF4A1 and eIF4A2 to mRNA.
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Affiliation(s)
- Sai Kiran Naineni
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
| | - Regina Cencic
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
| | - Francis Robert
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
| | - Lauren E Brown
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Massachusetts 02215, USA
| | - Minza Haque
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
| | | | - Patrick Sénéchal
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Quebec, H3G 0B1 Canada
| | - John A Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Massachusetts 02215, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Quebec, H3G 0B1 Canada
- McGill Research Center on Complex Traits, McGill University, Quebec, H3G 0B1 Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Quebec, H3A 1A3 Canada
- Department of Oncology, McGill University, Quebec, H4A 3T2 Canada
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20
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Yamazaki H, Namba Y, Kuriyama S, Nishida KM, Kajiya A, Siomi MC. Bombyx Vasa sequesters transposon mRNAs in nuage via phase separation requiring RNA binding and self-association. Nat Commun 2023; 14:1942. [PMID: 37029111 PMCID: PMC10081994 DOI: 10.1038/s41467-023-37634-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/24/2023] [Indexed: 04/09/2023] Open
Abstract
Bombyx Vasa (BmVasa) assembles non-membranous organelle, nuage or Vasa bodies, in germ cells, known as the center for Siwi-dependent transposon silencing and concomitant Ago3-piRISC biogenesis. However, details of the body assembly remain unclear. Here, we show that the N-terminal intrinsically disordered region (N-IDR) and RNA helicase domain of BmVasa are responsible for self-association and RNA binding, respectively, but N-IDR is also required for full RNA-binding activity. Both domains are essential for Vasa body assembly in vivo and droplet formation in vitro via phase separation. FAST-iCLIP reveals that BmVasa preferentially binds transposon mRNAs. Loss of Siwi function derepresses transposons but has marginal effects on BmVasa-RNA binding. This study shows that BmVasa assembles nuage by phase separation via its ability to self-associate and bind newly exported transposon mRNAs. This unique property of BmVasa allows transposon mRNAs to be sequestered and enriched in nuage, resulting in effective Siwi-dependent transposon repression and Ago3-piRISC biogenesis.
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Affiliation(s)
- Hiroya Yamazaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yurika Namba
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Shogo Kuriyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Kazumichi M Nishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Asako Kajiya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0032, Japan
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0032, Japan.
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21
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Sather LM, Zamani M, Muhammed Z, Kearsley JVS, Fisher GT, Jones KM, Finan TM. A broadly distributed predicted helicase/nuclease confers phage resistance via abortive infection. Cell Host Microbe 2023; 31:343-355.e5. [PMID: 36893733 DOI: 10.1016/j.chom.2023.01.010] [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: 08/31/2022] [Revised: 11/16/2022] [Accepted: 01/11/2023] [Indexed: 03/11/2023]
Abstract
There is strong selection for the evolution of systems that protect bacterial populations from viral attack. We report a single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti, a nitrogen-fixing alpha-proteobacterium. Homologs of Hna are distributed widely across bacterial lineages, and a homologous protein from Escherichia coli also confers phage defense. Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense. Hna variably impacts phage DNA replication but consistently triggers an abortive infection response in which infected cells carrying the system die but do not release phage progeny. A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB), independent of phage infection. Thus, we conclude that Hna limits phage spread by initiating abortive infection in response to a phage protein.
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Affiliation(s)
- Leah M Sather
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Maryam Zamani
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Zahed Muhammed
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Jason V S Kearsley
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Gabrielle T Fisher
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Kathryn M Jones
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Turlough M Finan
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada.
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22
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Ju X, Dong L, Ding Q. Hepatitis E Virus Life Cycle. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1417:141-157. [PMID: 37223864 DOI: 10.1007/978-981-99-1304-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Hepatitis E virus (HEV) infects over 20 million people worldwide per year, leading to 30,000-40,000 deaths. In most cases HEV infection in a self-limited, acute illness. However, chronic infections could occur in immunocompromised individuals. Due to scarcity of robust cell culture models in vitro and genetic tractable animal models in vivo, the details of HEV life cycle, as well as its interaction with host cells still remain elusive, which dampens antivirals discovery. In this chapter, we present an update in the HEV infectious cycle steps: entry, genome replication/subgenomic RNA transcription, assembly, and release. Moreover, we discussed the future prospective on HEV research and illustrates important questions urgently to be addressed.
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Affiliation(s)
- Xiaohui Ju
- School of Medicine, Tsinghua University, Beijing, China
| | - Lin Dong
- School of Medicine, Tsinghua University, Beijing, China
| | - Qiang Ding
- School of Medicine, Tsinghua University, Beijing, China.
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23
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Wang L, Guzmán M, Sola I, Enjuanes L, Zuñiga S. Cytoplasmic ribonucleoprotein complexes, RNA helicases and coronavirus infection. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.1078454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA metabolism in the eukaryotic cell includes the formation of ribonucleoprotein complexes (RNPs) that, depending on their protein components, have a different function. Cytoplasmic RNPs, such as stress granules (SGs) or P-bodies (PBs) are quite relevant during infections modulating viral and cellular RNA expression and as key players in the host cell antiviral response. RNA helicases are abundant components of RNPs and could have a significant effect on viral infection. This review focuses in the role that RNPs and RNA helicases have during coronavirus (CoVs) infection. CoVs are emerging highly pathogenic viruses with a large single-stranded RNA genome. During CoV infection, a complex network of RNA-protein interactions in different RNP structures is established. In general, RNA helicases and RNPs have an antiviral function, but there is limited knowledge on whether the viral protein interactions with cell components are mediators of this antiviral effect or are part of the CoV antiviral counteraction mechanism. Additional data is needed to elucidate the role of these RNA-protein interactions during CoV infection and their potential contribution to viral replication or pathogenesis.
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24
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The Discovery of Novel Ferulic Acid Derivatives Incorporating Substituted Isopropanolamine Moieties as Potential Tobacco Mosaic Virus Helicase Inhibitors. Int J Mol Sci 2022; 23:ijms232213991. [PMID: 36430473 PMCID: PMC9698358 DOI: 10.3390/ijms232213991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
Target-based drug design, a high-efficiency strategy used to guide the development of novel pesticide candidates, has attracted widespread attention. Herein, various natural-derived ferulic acid derivatives incorporating substituted isopropanolamine moieties were designed to target the tobacco mosaic virus (TMV) helicase. Bioassays demonstrating the optimized A19, A20, A29, and A31 displayed excellent in vivo antiviral curative abilities, affording corresponding EC50 values of 251.1, 336.2, 347.1, and 385.5 μg/mL, which visibly surpassed those of commercial ribavirin (655.0 μg/mL). Moreover, configurational analysis shows that the R-forms of target compounds were more beneficial to aggrandize antiviral profiles. Mechanism studies indicate that R-A19 had a strong affinity (Kd = 5.4 μM) to the TMV helicase and inhibited its ability to hydrolyze ATP (50.61% at 200 μM). Meanwhile, A19 could down-regulate the expression of the TMV helicase gene in the host to attenuate viral replication. These results illustrate the excellent inhibitory activity of A19 towards the TMV helicase. Additionally, docking simulations uncovered that R-A19 formed more hydrogen bonds with the TMV helicase in the binding pocket. Recent studies have unambiguously manifested that these designed derivatives could be considered as promising potential helicase-based inhibitors for plant disease control.
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Hurst-Hess KR, Saxena A, Rudra P, Yang Y, Ghosh P. Mycobacterium abscessus HelR interacts with RNA polymerase to confer intrinsic rifamycin resistance. Mol Cell 2022; 82:3166-3177.e5. [PMID: 35905736 PMCID: PMC9444957 DOI: 10.1016/j.molcel.2022.06.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 02/08/2022] [Accepted: 06/28/2022] [Indexed: 10/16/2022]
Abstract
Rifampicin (RIF), the frontline drug against M. tuberculosis, is completely ineffective against M. abscessus, partially due to the presence of an ADP-ribosyltransferase (Arr) that inactivates RIF. Using RNA-seq, we show that exposure of M. abscessus to sublethal doses of RIF and Rifabutin (RBT), a close analog of RIF, results in an ∼25-fold upregulation of Mab_helR in laboratory and clinical isolates. An isogenic deletion in Mab_helR results in RIF/RBT hypersensitivity, and overexpression of Mab_helR confers RIF tolerance in M. tuberculosis. We demonstrate an increased HelR-RNAP association in RIF-exposed bacteria and a MabHelR-mediated dissociation of RNAP from stalled initiation complexes in vitro. Finally, we show that the tip of the PCh-loop of Mab_helR, present in proximity to RIF, is critical for conferring RIF resistance but dispensable for dissociation of stalled RNAP complexes, suggesting that HelR-mediated RIF resistance requires a step in addition to displacement of RIF-stalled RNAP.
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Affiliation(s)
- Kelley R Hurst-Hess
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Aavrati Saxena
- School of Public Health, University at Albany, Albany, NY 12208, USA
| | - Paulami Rudra
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Yong Yang
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Pallavi Ghosh
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; School of Public Health, University at Albany, Albany, NY 12208, USA.
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Tumor-Promoting ATAD2 and Its Preclinical Challenges. Biomolecules 2022; 12:biom12081040. [PMID: 36008934 PMCID: PMC9405547 DOI: 10.3390/biom12081040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
ATAD2 has received extensive attention in recent years as one prospective oncogene with tumor-promoting features in many malignancies. ATAD2 is a highly conserved bromodomain family protein that exerts its biological functions by mainly AAA ATPase and bromodomain. ATAD2 acts as an epigenetic decoder and transcription factor or co-activator, which is engaged in cellular activities, such as transcriptional regulation, DNA replication, and protein modification. ATAD2 has been reported to be highly expressed in a variety of human malignancies, including gastrointestinal malignancies, reproductive malignancies, urological malignancies, lung cancer, and other types of malignancies. ATAD2 is involved in the activation of multiple oncogenic signaling pathways and is closely associated with tumorigenesis, progression, chemoresistance, and poor prognosis, but the oncogenic mechanisms vary in different cancer types. Moreover, the direct targeting of ATAD2’s bromodomain may be a very challenging task. In this review, we summarized the role of ATAD2 in various types of malignancies and pointed out the pharmacological direction.
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Pitsillou E, Liang J, Hung A, Karagiannis TC. The SARS-CoV-2 helicase as a target for antiviral therapy: Identification of potential small molecule inhibitors by in silico modelling. J Mol Graph Model 2022; 114:108193. [PMID: 35462185 PMCID: PMC9014761 DOI: 10.1016/j.jmgm.2022.108193] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/18/2022]
Abstract
Although vaccines that provide protection against severe illness from coronavirus disease (COVID-19) have been made available, emerging variant strains of severe acute respiratory syndrome 2 coronavirus 2 (SARS-CoV-2) are of concern. A different research direction involves investigation of antiviral therapeutics. In addition to structural proteins, the SARS-CoV-2 non-structural proteins are of interest and this includes the helicase (nsp13). In this study, an initial screen of 300 ligands was performed to identify potential inhibitors of the SARS-CoV-2 nsp13 examining the nucleoside triphosphatase site (NTPase activity) as the target region. The antiviral activity of polyphenols has been previously reported in the literature and as a result, the phenolic compounds and fatty acids from the OliveNet™ library were utilised. Synthetic compounds with antimicrobial and anti-inflammatory properties were also selected. The structures of the SARS-CoV and MERS-CoV helicases, as well as the human RECQ-like DNA helicase, DHX9 helicase, PcrA helicase, hepatitis C NS3 helicase, and mouse Dna2 nuclease-helicase were used for comparison. As expected, sequence and structural homology between the various species was evident. A number of broad-spectrum and well-known inhibitors interacted with the NTPase active site highlighting the need to potentially identify more specific inhibitors for SARS-CoV-2. Acetylcysteine, clavulanic acid and homovanillic acid were identified as potential lead compounds for the SARS-CoV-2 helicase. Molecular dynamics simulations were performed with the leads bound to the SARS-CoV-2 helicase for 200 ns in triplicate, with favourable binding free energies to the NTPase site. Given their availability, further exploration of their potential inhibitory activity could be considered.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3052, Australia.
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Li J, Ma J, Kumar V, Fu H, Xu C, Wang S, Jia Q, Fan Q, Xi X, Li M, Liu H, Lu Y. Identification of flexible Pif1-DNA interactions and their impacts on enzymatic activities. Nucleic Acids Res 2022; 50:7002-7012. [PMID: 35748877 PMCID: PMC9262596 DOI: 10.1093/nar/gkac529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022] Open
Abstract
Flexible regions in biomolecular complexes, although crucial to understanding structure-function relationships, are often unclear in high-resolution crystal structures. In this study, we showed that single-molecule techniques, in combination with computational modeling, can characterize dynamic conformations not resolved by high-resolution structure determination methods. Taking two Pif1 helicases (ScPif1 and BsPif1) as model systems, we found that, besides a few tightly bound nucleotides, adjacent solvent-exposed nucleotides interact dynamically with the helicase surfaces. The whole nucleotide segment possessed curved conformations and covered the two RecA-like domains of the helicases, which are essential for the inch-worm mechanism. The synergetic approach reveals that the interactions between the exposed nucleotides and the helicases could be reduced by large stretching forces or electrostatically shielded with high-concentration salt, subsequently resulting in reduced translocation rates of the helicases. The dynamic interactions between the exposed nucleotides and the helicases underlay the force- and salt-dependences of their enzymatic activities. The present single-molecule based approach complements high-resolution structural methods in deciphering the molecular mechanisms of the helicases.
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Affiliation(s)
| | | | | | - Hang Fu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China,School of Physics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuang Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qi Jia
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Qinkai Fan
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China,School of Physics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuguang Xi
- Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette F-91190, France
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China,School of Physics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiguang Liu
- Correspondence may also be addressed to Haiguang Liu. Tel: +86 10 56981816;
| | - Ying Lu
- To whom correspondence should be addressed. Tel: +86 10 82648122;
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Vasconcellos AF, Melo RM, Mandacaru SC, de Oliveira LS, de Oliveira AS, Moraes ECDS, Trugilho MRDO, Ricart CAO, Báo SN, Resende RO, Charneau S. Aedes aegypti Aag-2 Cell Proteome Modulation in Response to Chikungunya Virus Infection. Front Cell Infect Microbiol 2022; 12:920425. [PMID: 35782121 PMCID: PMC9240781 DOI: 10.3389/fcimb.2022.920425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/18/2022] [Indexed: 01/16/2023] Open
Abstract
Chikungunya virus (CHIKV) is a single-stranded positive RNA virus that belongs to the genus Alphavirus and is transmitted to humans by infected Aedes aegypti and Aedes albopictus bites. In humans, CHIKV usually causes painful symptoms during acute and chronic stages of infection. Conversely, virus–vector interaction does not disturb the mosquito’s fitness, allowing a persistent infection. Herein, we studied CHIKV infection of Ae. aegypti Aag-2 cells (multiplicity of infection (MOI) of 0.1) for 48 h through label-free quantitative proteomic analysis and transmission electron microscopy (TEM). TEM images showed a high load of intracellular viral cargo at 48 h postinfection (hpi), as well as an unusual elongated mitochondria morphology that might indicate a mitochondrial imbalance. Proteome analysis revealed 196 regulated protein groups upon infection, which are related to protein synthesis, energy metabolism, signaling pathways, and apoptosis. These Aag-2 proteins regulated during CHIKV infection might have roles in antiviral and/or proviral mechanisms and the balance between viral propagation and the survival of host cells, possibly leading to the persistent infection.
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Affiliation(s)
- Anna Fernanda Vasconcellos
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
- Laboratory of Virology, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Reynaldo Magalhães Melo
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Samuel Coelho Mandacaru
- Laboratory of Toxinology and Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Lucas Silva de Oliveira
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Athos Silva de Oliveira
- Laboratory of Virology, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | | | | | - Carlos André Ornelas Ricart
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Sônia Nair Báo
- Laboratory of Microscopy and Microanalysis, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Renato Oliveira Resende
- Laboratory of Virology, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
- *Correspondence: Sébastien Charneau, ; Renato Oliveira Resende,
| | - Sébastien Charneau
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
- *Correspondence: Sébastien Charneau, ; Renato Oliveira Resende,
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30
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Rao S, Mahmoudi T. DEAD-ly Affairs: The Roles of DEAD-Box Proteins on HIV-1 Viral RNA Metabolism. Front Cell Dev Biol 2022; 10:917599. [PMID: 35769258 PMCID: PMC9234453 DOI: 10.3389/fcell.2022.917599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
In order to ensure viral gene expression, Human Immunodeficiency virus type-1 (HIV-1) recruits numerous host proteins that promote optimal RNA metabolism of the HIV-1 viral RNAs (vRNAs), such as the proteins of the DEAD-box family. The DEAD-box family of RNA helicases regulates multiple steps of RNA metabolism and processing, including transcription, splicing, nucleocytoplasmic export, trafficking, translation and turnover, mediated by their ATP-dependent RNA unwinding ability. In this review, we provide an overview of the functions and role of all DEAD-box family protein members thus far described to influence various aspects of HIV-1 vRNA metabolism. We describe the molecular mechanisms by which HIV-1 hijacks these host proteins to promote its gene expression and we discuss the implications of these interactions during viral infection, their possible roles in the maintenance of viral latency and in inducing cell death. We also speculate on the emerging potential of pharmacological inhibitors of DEAD-box proteins as novel therapeutics to control the HIV-1 pandemic.
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Affiliation(s)
- Shringar Rao
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Centre, Rotterdam, Netherlands
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31
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Chen Z, Xiong X, Li Y, Huang M, Ren Y, Wu D, Qiu Y, Chen M, Shu T, Zhou X. The nonstructural protein 2C of Coxsackie B virus has RNA helicase and chaperoning activities. Virol Sin 2022; 37:656-663. [PMID: 35589079 PMCID: PMC9583185 DOI: 10.1016/j.virs.2022.05.004] [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: 03/30/2022] [Accepted: 05/10/2022] [Indexed: 11/24/2022] Open
Abstract
RNA-remodeling proteins, including RNA helicases and chaperones, play vital roles in the remodeling of structured RNAs. During viral replication, viruses require RNA-remodeling proteins to facilitate proper folding and/or re-folding the viral RNA elements. Coxsackieviruses B3 (CVB3) and Coxsackieviruses B5 (CVB5), belonging to the genus Enterovirus in the family Picornaviridae, have been reported to cause various infectious diseases such as hand-foot-and-mouth disease, aseptic meningitis, and viral myocarditis. However, little is known about whether CVB3 and CVB5 encode any RNA remodeling proteins. In this study, we showed that 2C proteins of CVB3 and CVB5 contained the conserved SF3 helicase A, B, and C motifs, and functioned not only as RNA helicase that unwound RNA helix bidirectionally in an NTP-dependent manner, but also as RNA chaperone that remodeled structured RNAs and facilitated RNA strand annealing independently of NTP. In addition, we determined that the NTPase activity and RNA helicase activity of 2C proteins of CVB3 and CVB5 were dependent on the presence of divalent metallic ions. Our findings demonstrate that 2C proteins of CVBs possess RNA-remodeling activity and underline the functional importance of 2C protein in the life cycle of CVBs. 2C proteins of CVB3 and CVB5 function as RNA helicase in an NTP-dependent manner. 2C proteins of CVB3 and CVB5 possess RNA-remodeling activity independently of NTP. 2C proteins may have functional significance in the life cycle of CVBs.
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Affiliation(s)
- Ziyu Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xiaobei Xiong
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yiyang Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100081, China
| | - Muhan Huang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yujie Ren
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Di Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yang Qiu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100081, China
| | - Mingzhou Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Ting Shu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Xi Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100081, China.
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32
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Osorio Garcia MA, Satyshur KA, Cox MM, Keck JL. X-ray crystal structure of the Escherichia coli RadD DNA repair protein bound to ADP reveals a novel zinc ribbon domain. PLoS One 2022; 17:e0266031. [PMID: 35482735 PMCID: PMC9049331 DOI: 10.1371/journal.pone.0266031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/11/2022] [Indexed: 11/19/2022] Open
Abstract
Genome maintenance is an essential process in all cells. In prokaryotes, the RadD protein is important for survival under conditions that include DNA-damaging radiation. Precisely how RadD participates in genome maintenance remains unclear. Here we present a high-resolution X-ray crystal structure of ADP-bound Escherichia coli RadD, revealing a zinc-ribbon element that was not modelled in a previous RadD crystal structure. Insights into the mode of nucleotide binding and additional structure refinement afforded by the new RadD model will help to drive investigations into the activity of RadD as a genome stability and repair factor.
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Affiliation(s)
- Miguel A. Osorio Garcia
- Department of Biochemistry, University of Wisconsin, Madison, Madison, WI, United States of America
- * E-mail: (MMC); (JLK); (MAOG)
| | - Kenneth A. Satyshur
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin, Madison, Madison, WI, United States of America
- * E-mail: (MMC); (JLK); (MAOG)
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
- * E-mail: (MMC); (JLK); (MAOG)
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Du Pont KE, McCullagh M, Geiss BJ. Conserved motifs in the flavivirus NS3 RNA helicase enzyme. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1688. [PMID: 34472205 PMCID: PMC8888775 DOI: 10.1002/wrna.1688] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023]
Abstract
Flaviviruses are a major health concern because over half of the world population is at risk of infection and there are very few antiviral therapeutics to treat diseases resulting from infection. Replication is an essential part of the flavivirus survival. One of the viral proteins, NS3 helicase, is critical for unwinding the double stranded RNA intermediate during flaviviral replication. The helicase performs the unwinding of the viral RNA intermediate structure in an ATP-dependent manner. NS3 helicase is a member of the Viral/DEAH-like subfamily of the superfamily 2 helicase containing eight highly conserved structural motifs (I, Ia, II, III, IV, IVa, V, and VI) localized between the ATP-binding and RNA-binding pockets. Of these structural motifs only three are well characterized for function in flaviviruses (I, II, and VI). The roles of the other structural motifs are not well understood for NS3 helicase function, but comparison of NS3 with other superfamily 2 helicases within the viral/DEAH-like, DEAH/RHA, and DEAD-box subfamilies can be used to elucidate the roles of these structural motifs in the flavivirus NS3 helicase. This review aims to summarize the role of each conserved structural motif within flavivirus NS3 in RNA helicase function. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Kelly E. Du Pont
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, USA
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Brian J. Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
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Weis K, Hondele M. The Role of DEAD-Box ATPases in Gene Expression and the Regulation of RNA-Protein Condensates. Annu Rev Biochem 2022; 91:197-219. [PMID: 35303788 DOI: 10.1146/annurev-biochem-032620-105429] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DEAD-box ATPases constitute a very large protein family present in all cells, often in great abundance. From bacteria to humans, they play critical roles in many aspects of RNA metabolism, and due to their widespread importance in RNA biology, they have been characterized in great detail at both the structural and biochemical levels. DEAD-box proteins function as RNA-dependent ATPases that can unwind short duplexes of RNA, remodel ribonucleoprotein (RNP) complexes, or act as clamps to promote RNP assembly. Yet, it often remains enigmatic how individual DEAD-box proteins mechanistically contribute to specific RNA-processing steps. Here, we review the role of DEAD-box ATPases in the regulation of gene expression and propose that one common function of these enzymes is in the regulation of liquid-liquid phase separation of RNP condensates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Karsten Weis
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland;
| | - Maria Hondele
- Biozentrum, University of Basel, Basel, Switzerland;
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35
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Perez-Lemus GR, Menéndez CA, Alvarado W, Byléhn F, de Pablo JJ. Toward wide-spectrum antivirals against coronaviruses: Molecular characterization of SARS-CoV-2 NSP13 helicase inhibitors. SCIENCE ADVANCES 2022; 8:eabj4526. [PMID: 34995115 PMCID: PMC8741187 DOI: 10.1126/sciadv.abj4526] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/17/2021] [Indexed: 05/31/2023]
Abstract
To date, effective therapeutic treatments that confer strong attenuation against coronaviruses (CoVs) remain elusive. Among potential drug targets, the helicase of CoVs is attractive due to its sequence conservation and indispensability. We rely on atomistic molecular dynamics simulations to explore the structural coordination and dynamics associated with the SARS-CoV-2 Nsp13 apo enzyme, as well as their complexes with natural ligands. A complex communication network is revealed among the five domains of Nsp13, which is differentially activated because of the presence of the ligands, as shown by shear strain analysis, principal components analysis, dynamical cross-correlation matrix analysis, and water transport analysis. The binding free energy and the corresponding mechanism of action are presented for three small molecules that were shown to be efficient inhibitors of the previous SARS-CoV Nsp13 enzyme. Together, our findings provide critical fresh insights for rational design of broad-spectrum antivirals against CoVs.
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Affiliation(s)
| | - Cintia A. Menéndez
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Walter Alvarado
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Fabian Byléhn
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Juan J. de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Argonne National Laboratory, 9700 Cass Ave, Lemont, IL 60439 USA
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Bi L, Qin Z, Hou XM, Modesti M, Sun B. Simultaneous Mechanical and Fluorescence Detection of Helicase-Catalyzed DNA Unwinding. Methods Mol Biol 2022; 2478:329-347. [PMID: 36063326 DOI: 10.1007/978-1-0716-2229-2_12] [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] [Indexed: 06/15/2023]
Abstract
Helicases are ubiquitous molecular motor proteins that utilize the energy derived from the hydrolysis of nucleoside triphosphates (NTPs) to transiently convert the duplex form of nucleic acids to single-stranded intermediates for many biological processes. These enzymes play vital roles in nearly all aspects of nucleic acid metabolism, such as DNA repair and RNA splicing. Understanding helicase's functional roles requires methods to dissect the mechanisms of motor proteins at the molecular level. In the past three decades, there has been a large increase in the application of single-molecule approaches to investigate helicases. These techniques, such as optical tweezers and single-molecule fluorescence, offer capabilities to monitor helicase motions with unprecedented spatiotemporal resolution, to apply quantitative forces to probe the chemo-mechanical activities of these motors and to resolve helicase heterogeneity at the single-molecule level. In this chapter, we describe a single-molecule method that combines optical tweezers with confocal fluorescence microscopy to study helicase-catalyzed DNA unwinding. Using Bloom syndrome protein (BLM), a multifunctional helicase that maintains genome stability, as an example, we show that this method allows for the simultaneous detection of displacement, force and fluorescence signals of a single DNA molecule during unwinding in real time, leading to the discovery of a distinct bidirectional unwinding mode of BLM that is activated by a single-stranded DNA binding protein called replication protein A (RPA). We provide detailed instructions on how to prepare two DNA templates to be used in the assays, purify the BLM and RPA proteins, perform single-molecule experiments, and acquire and analyse the data.
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Affiliation(s)
- Lulu Bi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhenheng Qin
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Mauro Modesti
- Cancer Research Center of Marseille, Marseille, France
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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De Colibus L, Stunnenberg M, Geijtenbeek TB. DDX3X structural analysis: Implications in the pharmacology and innate immunity. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:100-109. [PMID: 35647523 PMCID: PMC9133689 DOI: 10.1016/j.crimmu.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/01/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
The human DEAD-Box Helicase 3 X-Linked (DDX3X) is an ATP-dependent RNA helicase involved in virtually every step of RNA metabolism, ranging from transcription regulation in the nucleus to translation initiation and stress granule (SG) formation, and plays crucial roles in innate immunity, as well as tumorigenesis and viral infections. This review discusses latest advances in DDX3X biology and structure-function relationship, including the implications of the recent DDX3X crystal structure in complex with double stranded RNA for RNA metabolism, DDX3X involvement in the cross-talk between innate immune responses and cell stress adaptation, and the roles of DDX3X in controlling cell fate. The human DDX3X, an ATP-dependent RNA helicase, plays a central role in a variety of cellular processes involving RNA. DDX3X is implicated in antiviral signalling pathways. DDX3X interacts with full-length NLRP3 and its NACHT domain. The recent crystal structure of DDX3X in complex with dsRNA offers a model for understanding its binding to the HIV-1 TAR hairpin sequence.
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DEAD/H-box helicases:Anti-viral and pro-viral roles during infections. Virus Res 2021; 309:198658. [PMID: 34929216 DOI: 10.1016/j.virusres.2021.198658] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/26/2021] [Accepted: 12/14/2021] [Indexed: 02/08/2023]
Abstract
DEAD/H-box RNA helicases make the prominent family of helicases super family-2 which take part in almost all RNA-related processes, from initiation of transcription to RNA decay pathways. In addition to these RNA-related activities, in recent years a certain number of these helicases are reported to play important roles in anti-viral immunity through various ways. Along with RLHs, endosomal TLRs, and cytosolic DNA receptors, many RNA helicases including DDX3, DHX9, DDX6, DDX41, DHX33, DDX60, DHX36 and DDX1-DDX21-DHX36 complex act as viral nucleic acid sensors or co-sensors. These helicases mostly follow RLHs-MAVS and STING mediated signaling cascades to trigger induction of type-I interferons and pro-inflammatory cytokines. Many of them also function as downstream adaptor molecules (DDX3), segments of stress and processing bodies (DDX3 and DDX6) or negative regulators (DDX19, DDX24, DDX25, DDX39A and DDX46). On the contrary, many studies indicated that several DEAD/H-box helicases such as DDX1, DDX3, DDX6, DDX24, and DHX9 could be exploited by viruses to evade innate immune responses, suggesting that these helicases seem to have a dual function as anti-viral innate immune mediators and viral replication cofactors. In this review, we summarized the current knowledge on several representative DEAD/H-box helicases, with an emphasis on their functions in innate immunity responses, involved in their anti-viral and pro-viral roles.
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Su C, Tang YD, Zheng C. DExD/H-box helicases: multifunctional regulators in antiviral innate immunity. Cell Mol Life Sci 2021; 79:2. [PMID: 34910251 PMCID: PMC8671602 DOI: 10.1007/s00018-021-04072-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023]
Abstract
DExD/H-box helicases play critical roles in multiple cellular processes, including transcription, cellular RNA metabolism, translation, and infections. Several seminal studies over the past decades have delineated the distinct functions of DExD/H-box helicases in regulating antiviral innate immune signaling pathways, including Toll-like receptors, retinoic acid-inducible gene I-like receptors, cyclic GMP-AMP synthase-the stimulator of interferon gene, and NOD-like receptors signaling pathways. Besides the prominent regulatory roles, there is increasing attention on their functions as nucleic acid sensors involved in antiviral innate immunity. Here we summarize the complex regulatory roles of DExD/H-box helicases in antiviral innate immunity. A better understanding of the underlying molecular mechanisms of DExD/H-box helicases' regulatory roles is vital for developing new therapeutics targeting DExD/H-box helicases and their mediated signaling transduction in viral infectious diseases.
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Affiliation(s)
- Chenhe Su
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- The Wistar Institute, Philadelphia, PA, USA
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
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40
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Ru JN, Hou ZH, Zheng L, Zhao Q, Wang FZ, Chen J, Zhou YB, Chen M, Ma YZ, Xi YJ, Xu ZS. Genome-Wide Analysis of DEAD-box RNA Helicase Family in Wheat ( Triticum aestivum) and Functional Identification of TaDEAD-box57 in Abiotic Stress Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:797276. [PMID: 34956297 PMCID: PMC8699334 DOI: 10.3389/fpls.2021.797276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/01/2021] [Indexed: 05/29/2023]
Abstract
DEAD-box RNA helicases constitute the largest subfamily of RNA helicase superfamily 2 (SF2), and play crucial roles in plant growth, development, and abiotic stress responses. Wheat is one of the most important cereal crops in worldwide, and abiotic stresses greatly restrict its production. So far, the DEAD-box RNA helicase family has yet to be characterized in wheat. Here, we performed a comprehensive genome-wide analysis of the DEAD-box RNA helicase family in wheat, including phylogenetic relationships, chromosomal distribution, duplication events, and protein motifs. A total of 141 TaDEAD-box genes were identified and found to be unevenly distributed across all 21 chromosomes. Whole genome/segmental duplication was identified as the likely main driving factor for expansion of the TaDEAD-box family. Expression patterns of the 141 TaDEAD-box genes were compared across different tissues and under abiotic stresses to identify genes to be important in growth or stress responses. TaDEAD-box57-3B was significantly up-regulated under multiple abiotic stresses, and was therefore selected for further analysis. TaDEAD-box57-3B was localized to the cytoplasm and plasma membrane. Ectopic expression of TaDEAD-box57-3B in Arabidopsis improved tolerance to drought and salt stress as measured by germination rates, root lengths, fresh weights, and survival rates. Transgenic lines also showed higher levels of proline and chlorophyll and lower levels of malonaldehyde (MDA) than WT plants in response to drought or salt stress. In response to cold stress, the transgenic lines showed significantly better growth and higher survival rates than WT plants. These results indicate that TaDEAD-box57-3B may increase tolerance to drought, salt, and cold stress in transgenic plants through regulating the degree of membrane lipid peroxidation. This study provides new insights for understanding evolution and function in the TaDEAD-box gene family.
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Affiliation(s)
- Jing-Na Ru
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ze-Hao Hou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Lei Zheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Qi Zhao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Feng-Zhi Wang
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement/Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Jun Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yong-Bin Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ya-Jun Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
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Meir A, Greene EC. Srs2 and Pif1 as Model Systems for Understanding Sf1a and Sf1b Helicase Structure and Function. Genes (Basel) 2021; 12:1319. [PMID: 34573298 PMCID: PMC8469786 DOI: 10.3390/genes12091319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 01/19/2023] Open
Abstract
Helicases are enzymes that convert the chemical energy stored in ATP into mechanical work, allowing them to move along and manipulate nucleic acids. The helicase superfamily 1 (Sf1) is one of the largest subgroups of helicases and they are required for a range of cellular activities across all domains of life. Sf1 helicases can be further subdivided into two classes called the Sf1a and Sf1b helicases, which move in opposite directions on nucleic acids. The results of this movement can range from the separation of strands within duplex nucleic acids to the physical remodeling or removal of nucleoprotein complexes. Here, we describe the characteristics of the Sf1a helicase Srs2 and the Sf1b helicase Pif1, both from the model organism Saccharomyces cerevisiae, focusing on the roles that they play in homologous recombination, a DNA repair pathway that is necessary for maintaining genome integrity.
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Affiliation(s)
| | - Eric C. Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA;
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Proteomic Analysis Reveals Growth Inhibition of Coriolus versicolor by Methanol Extracts of Cinnamomum camphora Xylem. INT J POLYM SCI 2021. [DOI: 10.1155/2021/6337906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The extracts of decay-resistant tree species are important research objects for the future development of wood preservatives. To understand the antifungal mechanisms of Coriolus versicolor inhibition with methanol extracts of C. camphora xylem, the protein profiles of C. versicolor were analyzed using 2-DE followed by MALDI-TOF/MS and bioinformatic analyses. The results showed that 41 protein spots were obviously changed among the 366-385 protein spots of C. versicolor treated with methanol extracts of C. camphora xylem. Twenty-one protein spots were upregulated, and 20 protein spots were downregulated. Cellular localization was performed to identify these differential proteins, and biological process and functional analysis found that 9 of these proteins were in the cytoplasm, 6 were intracellular, and 5 were in the mitochondrion. A total of 18.8% were mapped to small-molecule metabolic processes, 12.5% to cellular amino acid metabolic processes, and 10.9% to cellular nitrogen compound metabolic processes. Twenty-five percent of the differential proteins were associated with ion bonding, 15% with oxidoreductase activity, and 15% with ATPase activity and transmembrane transport activity. Downregulated expression of aspartate aminotransferase, ATP synthase alpha chain, DEAD/DEAH-box helicase, and phosphoglycerate kinase showed that the methanol extracts of C. camphora xylem disrupted functional aspects such as nitrogen and carbon metabolism, energy metabolism, hormone signal response, and glucose metabolism, eventually leading to C. versicolor inhibition.
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43
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Nawaz A, Shilikbay T, Skariah G, Ceman S. Unwinding the roles of RNA helicase MOV10. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1682. [PMID: 34327836 PMCID: PMC8799784 DOI: 10.1002/wrna.1682] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022]
Abstract
MOV10 is an RNA helicase that associates with the RNA‐induced silencing complex component Argonaute (AGO), likely resolving RNA secondary structures. MOV10 also binds the Fragile X mental retardation protein to block AGO2 binding at some sites and associates with UPF1, a principal component of the nonsense‐mediated RNA decay pathway. MOV10 is widely expressed and has a key role in the cellular response to viral infection and in suppressing retrotransposition. Posttranslational modifications of MOV10 include ubiquitination, which leads to stimulation‐dependent degradation, and phosphorylation, which has an unknown function. MOV10 localizes to the nucleus and/or cytoplasm in a cell type‐specific and developmental stage‐specific manner. Knockout of Mov10 leads to embryonic lethality, underscoring an important role in development where it is required for the completion of gastrulation. MOV10 is expressed throughout the organism; however, most studies have focused on germline cells and neurons. In the testes, the knockdown of Mov10 disrupts proliferation of spermatogonial progenitor cells. In brain, MOV10 is significantly elevated postnatally and binds mRNAs encoding cytoskeleton and neuron projection proteins, suggesting an important role in neuronal architecture. Heterozygous Mov10 mutant mice are hyperactive and anxious and their cultured hippocampal neurons have reduced dendritic arborization. Zygotic knockdown of Mov10 in Xenopus laevis causes abnormal head and eye development and mislocalization of neuronal precursors in the brain. Thus, MOV10 plays a vital role during development, defense against viral infection and in neuronal development and function: its many roles and regulation are only beginning to be unraveled. This article is categorized under:RNA Interactions with Proteins and Other Molecules > RNA‐Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications
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Affiliation(s)
- Aatiqa Nawaz
- Department of Cell and Developmental Biology, University of Illinois-Urbana Champaign, Champaign, Illinois, USA
| | - Temirlan Shilikbay
- Department of Cell and Developmental Biology, University of Illinois-Urbana Champaign, Champaign, Illinois, USA
| | - Geena Skariah
- Neuroscience Program, University of Illinois-Urbana Champaign, Champaign, Illinois, USA.,Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephanie Ceman
- Department of Cell and Developmental Biology, Neuroscience Program, University of Illinois-Urbana Champaign, Champaign, Illinois, USA
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Zhang G, Li S, Cheng KW, Chou TF. AAA ATPases as therapeutic targets: Structure, functions, and small-molecule inhibitors. Eur J Med Chem 2021; 219:113446. [PMID: 33873056 PMCID: PMC8165034 DOI: 10.1016/j.ejmech.2021.113446] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/21/2021] [Accepted: 03/30/2021] [Indexed: 01/07/2023]
Abstract
ATPases Associated with Diverse Cellular Activity (AAA ATPase) are essential enzymes found in all organisms. They are involved in various processes such as DNA replication, protein degradation, membrane fusion, microtubule serving, peroxisome biogenesis, signal transduction, and the regulation of gene expression. Due to the importance of AAA ATPases, several researchers identified and developed small-molecule inhibitors against these enzymes. We discuss six AAA ATPases that are potential drug targets and have well-developed inhibitors. We compare available structures that suggest significant differences of the ATP binding pockets among the AAA ATPases with or without ligand. The distances from ADP to the His20 in the His-Ser-His motif and the Arg finger (Arg353 or Arg378) in both RUVBL1/2 complex structures bound with or without ADP have significant differences, suggesting dramatically different interactions of the binding site with ADP. Taken together, the inhibitors of six well-studied AAA ATPases and their structural information suggest further development of specific AAA ATPase inhibitors due to difference in their structures. Future chemical biology coupled with proteomic approaches could be employed to develop variant specific, complex specific, and pathway specific inhibitors or activators for AAA ATPase proteins.
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Affiliation(s)
- Gang Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
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45
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Han P, Hu Y, An X, Song L, Fan H, Tong Y. Biochemical and genomic characterization of a novel bacteriophage BUCT555 lysing Stenotrophomonas maltophilia. Virus Res 2021; 301:198465. [PMID: 34052250 DOI: 10.1016/j.virusres.2021.198465] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/25/2022]
Abstract
Stenotrophomonas maltophilia is a common conditional pathogen, and it is naturally resistant to most commonly used clinical antibiotics. The bacteriophage is considered to be a potential antibiotic alternative for treating multi-drug-resistant bacteria. In this study, a bacteriophage BUCT555 was isolated from hospital sewage for lysing the clinical multi-drug resistant Stenotrophomonas maltophilia. Electron microscopy studies revealed this phage belongs to the Podoviridae family. The double-stranded DNA genome of bacteriophage BUCT555 is composed of 39,440 bp with a GC content of 61.43%. The genome contains 57 open reading frames, 14 of which had assigned functions, while no virulence related genes, antibiotic resistance genes or tRNA were identified. The burst size of BUCT555 was 204 pfu per infected cell. Structure proteins of bacteriophage BUCT555 generated by SDS-PAGE and HPLC-MS revealed that it contains seven proteins with molecular weight ranging from 19 to 89 kDa. BLASTn analysis showed that phage BUCT555 has 2% homology with other phages in NCBI database, suggesting BUCT555 is a new phage genus of Podoviridae that infects Stenotrophomonas maltophilia. Characterization of the bacteriophage BUCT555 enriches our knowledge about the diversity of Stenotrophomonas maltophilia bacteriophages.
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Affiliation(s)
- Pengjun Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yunjia Hu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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46
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Mannucci I, Dang NDP, Huber H, Murry JB, Abramson J, Althoff T, Banka S, Baynam G, Bearden D, Beleza-Meireles A, Benke PJ, Berland S, Bierhals T, Bilan F, Bindoff LA, Braathen GJ, Busk ØL, Chenbhanich J, Denecke J, Escobar LF, Estes C, Fleischer J, Groepper D, Haaxma CA, Hempel M, Holler-Managan Y, Houge G, Jackson A, Kellogg L, Keren B, Kiraly-Borri C, Kraus C, Kubisch C, Le Guyader G, Ljungblad UW, Brenman LM, Martinez-Agosto JA, Might M, Miller DT, Minks KQ, Moghaddam B, Nava C, Nelson SF, Parant JM, Prescott T, Rajabi F, Randrianaivo H, Reiter SF, Schuurs-Hoeijmakers J, Shieh PB, Slavotinek A, Smithson S, Stegmann APA, Tomczak K, Tveten K, Wang J, Whitlock JH, Zweier C, McWalter K, Juusola J, Quintero-Rivera F, Fischer U, Yeo NC, Kreienkamp HJ, Lessel D. Genotype-phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders. Genome Med 2021; 13:90. [PMID: 34020708 PMCID: PMC8140440 DOI: 10.1186/s13073-021-00900-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/28/2021] [Indexed: 12/27/2022] Open
Abstract
Background We aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder. Methods Clinical and genetic data from affected individuals were collected through Facebook-based family support group, GeneMatcher, and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays. Results We identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment, and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual harboring a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location, and type we establish two distinct clinical subtypes. DHX30 loss-of-function variants cause a milder phenotype whereas a severe phenotype is caused by HCM missense variants that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of-function with respect to SG formation. Behavioral characterization of dhx30-deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype. Conclusions Our study highlights the usefulness of social media to define novel Mendelian disorders and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories, and research laboratories. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00900-3.
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Affiliation(s)
- Ilaria Mannucci
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Nghi D P Dang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Hannes Huber
- Department of Biochemistry, Theodor Boveri Institute, Biocenter of the University of Würzburg, 97070, Würzburg, Germany
| | - Jaclyn B Murry
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Jeff Abramson
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Thorsten Althoff
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.,Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gareth Baynam
- Faculty of Medicine and Health Sciences, University of Western Australia, Perth, WA, Australia.,Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, Australia.,Telethon Kids Institute, Perth, Australia
| | - David Bearden
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | - Ana Beleza-Meireles
- Clinical Genetics Department, University Hospitals Bristol and Weston, Bristol, UK
| | - Paul J Benke
- Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Frederic Bilan
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Cliniques et Expérimentales-INSERM U1084, Université de Poitiers, Poitiers, France
| | - Laurence A Bindoff
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway.,Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | | | - Øyvind L Busk
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Jirat Chenbhanich
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, 20246, Hamburg, Germany
| | - Luis F Escobar
- Peyton Manning Children's Hospital, Ascension Health, Indianapolis, IN, USA
| | - Caroline Estes
- Peyton Manning Children's Hospital, Ascension Health, Indianapolis, IN, USA
| | - Julie Fleischer
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA
| | - Daniel Groepper
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Yolanda Holler-Managan
- Division of Neurology, Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.,Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Boris Keren
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Cornelia Kraus
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Gwenael Le Guyader
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Cliniques et Expérimentales-INSERM U1084, Université de Poitiers, Poitiers, France
| | - Ulf W Ljungblad
- Department of Pediatrics, Vestfold Hospital, 3116, Tønsberg, Norway
| | | | - Julian A Martinez-Agosto
- UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Semel Institute of Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pediatrics, Division of Medical Genetics at David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics at David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew Might
- Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL, 35210, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Kelly Q Minks
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | | | - Caroline Nava
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Stanley F Nelson
- UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics at David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA, USA.,Center for Duchenne Muscular Dystrophy, University of California Los Angeles, Los Angeles, CA, USA
| | - John M Parant
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Hanitra Randrianaivo
- UF de Génétique Médicale, GHSR, CHU de La Réunion, Saint Pierre, La Réunion, France
| | - Simone F Reiter
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | | | - Perry B Shieh
- Department of Neurology at David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah Smithson
- Clinical Genetics Department, University Hospitals Bristol and Weston, Bristol, UK
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, the Netherlands.,Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kinga Tomczak
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Jordan H Whitlock
- Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL, 35210, USA
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany.,Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | | | | | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, Biocenter of the University of Würzburg, 97070, Würzburg, Germany
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA.
| | - Hans-Jürgen Kreienkamp
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
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47
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Abidi SH, Almansour NM, Amerzhanov D, Allemailem KS, Rafaqat W, Ibrahim MAA, la Fleur P, Lukac M, Ali S. Repurposing potential of posaconazole and grazoprevir as inhibitors of SARS-CoV-2 helicase. Sci Rep 2021; 11:10290. [PMID: 33986405 PMCID: PMC8119689 DOI: 10.1038/s41598-021-89724-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/13/2021] [Indexed: 01/08/2023] Open
Abstract
As the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic engulfs millions worldwide, the quest for vaccines or drugs against the virus continues. The helicase protein of SARS-CoV-2 represents an attractive target for drug discovery since inhibition of helicase activity can suppress viral replication. Using in silico approaches, we have identified drugs that interact with SARS-CoV-2 helicase based on the presence of amino acid arrangements matching binding sites of drugs in previously annotated protein structures. The drugs exhibiting an RMSD of ≤ 3.0 Å were further analyzed using molecular docking, molecular dynamics (MD) simulation, and post-MD analyses. Using these approaches, we found 12 drugs that showed strong interactions with SARS-CoV-2 helicase amino acids. The analyses were performed using the recently available SARS-CoV-2 helicase structure (PDB ID: 5RL6). Based on the MM-GBSA approach, out of the 12 drugs, two drugs, namely posaconazole and grazoprevir, showed the most favorable binding energy, - 54.8 and - 49.1 kcal/mol, respectively. Furthermore, of the amino acids found conserved among all human coronaviruses, 10/11 and 10/12 were targeted by, respectively, grazoprevir and posaconazole. These residues are part of the crucial DEAD-like helicase C and DEXXQc_Upf1-like/ DEAD-like helicase domains. Strong interactions of posaconazole and grazoprevir with conserved amino acids indicate that the drugs can be potent against SARS-CoV-2. Since the amino acids are conserved among the human coronaviruses, the virus is unlikely to develop resistance mutations against these drugs. Since these drugs are already in use, they may be immediately repurposed for SARS-CoV-2 therapy.
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Affiliation(s)
- Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Daulet Amerzhanov
- Nazarbayev University School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | | | - Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Philip la Fleur
- Nazarbayev University School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Martin Lukac
- Department of Computer Science, School of Engineering and Digital Sciences, Nazarbayev University, Astana, Kazakhstan
| | - Syed Ali
- Nazarbayev University School of Medicine, Nazarbayev University, Astana, Kazakhstan.
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48
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Wei Q, Geng J, Chen Y, Lin H, Wang J, Fang Z, Wang F, Zhang Z. Structure and function of DEAH-box helicase 32 and its role in cancer. Oncol Lett 2021; 21:382. [PMID: 33777205 PMCID: PMC7988694 DOI: 10.3892/ol.2021.12643] [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: 08/16/2020] [Accepted: 12/23/2020] [Indexed: 11/06/2022] Open
Abstract
DEAH-box helicase 32 (DHX32) is an RNA helicase with unique structural characteristics that is involved in numerous biological processes associated with RNA, including ribosome biosynthesis, transcription, mRNA splicing and translation. Increasing evidence suggests that abnormal DHX32 expression contributes to cancer initiation and development, due to dysregulated cell proliferation, differentiation, apoptosis and other processes. In the current review, the discovery, structure and function of DHX32, as well as the association between abnormal DHX32 expression and tumors are discussed. DHX32 expression is downregulated in acute lymphoblastic leukemia, but upregulated in solid tumors, including colorectal and breast cancer. Furthermore, DHX32 expression levels are associated with the pathological and clinical features of the cancer. Therefore, DHX32 may serve as a novel liquid biopsy marker for auxiliary diagnosis and prognosis screening, as well as a possible target for cancer therapy. The molecular mechanism underlying the contribution of DHX32 towards the initiation and development of cancer requires further investigation for the development of anticancer treatments based on manipulating DHX32 expression and function.
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Affiliation(s)
- Qingchun Wei
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Jinting Geng
- Xiamen Key Laboratory of Biomarker Translational Medicine, Center of Medical Laboratory of Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Yongquan Chen
- Xiamen Key Laboratory of Biomarker Translational Medicine, Center of Medical Laboratory of Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Huayue Lin
- Center of Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, Fujian 361104, P.R. China
| | - Jiajia Wang
- Center of Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, Fujian 361104, P.R. China
| | - Zanxi Fang
- Center of Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, Fujian 361104, P.R. China
| | - Fen Wang
- Center for Cancer and Stem Cell Biology, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
| | - Zhongying Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
- Xiamen Key Laboratory of Biomarker Translational Medicine, Center of Medical Laboratory of Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
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49
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Sergeeva O, Zatsepin T. RNA Helicases as Shadow Modulators of Cell Cycle Progression. Int J Mol Sci 2021; 22:2984. [PMID: 33804185 PMCID: PMC8001981 DOI: 10.3390/ijms22062984] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/06/2021] [Accepted: 03/10/2021] [Indexed: 02/07/2023] Open
Abstract
The progress of the cell cycle is directly regulated by modulation of cyclins and cyclin-dependent kinases. However, many proteins that control DNA replication, RNA transcription and the synthesis and degradation of proteins can manage the activity or levels of master cell cycle regulators. Among them, RNA helicases are key participants in RNA metabolism involved in the global or specific tuning of cell cycle regulators at the level of transcription and translation. Several RNA helicases have been recently evaluated as promising therapeutic targets, including eIF4A, DDX3 and DDX5. However, targeting RNA helicases can result in side effects due to the influence on the cell cycle. In this review, we discuss direct and indirect participation of RNA helicases in the regulation of the cell cycle in order to draw attention to downstream events that may occur after suppression or inhibition of RNA helicases.
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Affiliation(s)
- Olga Sergeeva
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30b1, 121205 Moscow, Russia;
| | - Timofei Zatsepin
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30b1, 121205 Moscow, Russia;
- Department of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
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50
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Xiong X, Lai X, Li A, Liu Z, Ma N. Diversity roles of CHD1L in normal cell function and tumorigenesis. Biomark Res 2021; 9:16. [PMID: 33663617 PMCID: PMC7934534 DOI: 10.1186/s40364-021-00269-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/16/2021] [Indexed: 12/14/2022] Open
Abstract
Chromodomain helicase/ATPase DNA binding protein 1-like gene (CHD1L) is a multifunctional protein participated in diverse cellular processes, including chromosome remodeling, cell differentiation and development. CHD1L is a regulator of chromosomal integrity maintenance, DNA repair and transcriptional regulation through its bindings to DNA. By regulating kinds of complex networks, CHD1L has been identified as a potent anti-apoptotic and pro-proliferative factor. CHD1L is also an oncoprotein since its overexpression leads to dysregulation of related downstream targets in various cancers. The latest advances in the functional molecular basis of CHD1L in normal cells will be described in this review. As the same time, we will describe the current understanding of CHD1L in terms of structure, characteristics, function and the molecular mechanisms underlying CHD1L in tumorigenesis. We inference that the role of CHD1L which involve in multiple cellular processes and oncogenesis is well worth further studying in basic biology and clinical relevance.
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Affiliation(s)
- Xifeng Xiong
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, 510220, China
| | - Xudong Lai
- Departement of infectious disease, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, 510220, China
| | - Aiguo Li
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, 510220, China.
| | - Zhihe Liu
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, 510220, China.
| | - Ningfang Ma
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China. .,Department of Histology and Embryology, Guangzhou Medical University, Xinzao Town, Panyu District, Guangzhou, 511436, China.
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