1
|
Yuan P, Cai Q, Hu Z. Arabidopsis DEAD-box RNA helicase 12 is required for salt tolerance during seed germination. Biochem Biophys Res Commun 2024; 725:150228. [PMID: 38936167 DOI: 10.1016/j.bbrc.2024.150228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
The DEAD-box family is the largest family of RNA helicases (RHs), playing crucial roles in RNA metabolism and plant stress resistance. In this study, we report that an RNA helicase, RH12, positively regulates plant salt tolerance, as rh12 knockout mutants exhibit heightened sensitivity to salt stress. Further analysis indicates that RH12 is involved in the abscisic acid (ABA) response, as rh12 knockout mutants show increased sensitivity to ABA. Examination of reactive oxygen species (ROS) revealed that RH12 helps inhibit ROS accumulation under salt stress during seed germination. Additionally, RH12 accelerates the degradation of specific germination-related transcripts. In conclusion, our results demonstrate that RH12 plays multiple roles in the salt stress response in Arabidopsis.
Collapse
Affiliation(s)
- Penglai Yuan
- College of Life Sciences, Nanjing Agricultural University, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Qingsheng Cai
- College of Life Sciences, Nanjing Agricultural University, China.
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Liu WJ, Chen Y, Liu Y, Chang MX. The dexd/H-box helicase DHX40 is a novel negative regulator during GCRV infection via targeting the host RLR helicases and viral nonstructural protein NS38. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109730. [PMID: 38942250 DOI: 10.1016/j.fsi.2024.109730] [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: 05/03/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
RLR helicases RIG-I and MDA5, which are known as pattern recognition receptors to sense cytoplasmic viral RNAs and trigger antiviral immune responses, are DExD/H-box helicases. In teleost, whether and how non-RLR helicases regulate RLR helicases to affect viral infection remains unclear. Here, we report that the non-RLR helicase DHX40 from grass carp (namely gcDHX40) is a negative regulator of grass carp reovirus (GCRV) infection and RLR-mediated type I IFN production. GcDHX40 was a cytoplasmic protein. Ectopic expression of gcDHX40 facilitated GCRV replication and suppressed type I IFN production induced by GCRV infection and by those genes involved the RLR antiviral signaling pathway. Mechanistically, gcDHX40 promoted the generation of viral inclusion bodies (VIBs) by interacting with the NS38 protein of GCRV. Additionally, gcDHX40 interacted with RLR helicase, and impaired the formation of RLR-MAVS functional complexes. Taken together, our results indicate that gcDHX40 is a novel important proviral host factor involving in promoting the generation of GCRV VIBs and inhibiting the production of RLR-mediated type I IFNs.
Collapse
Affiliation(s)
- Wen Jin Liu
- College of life sciences, Jiangxi Normal university, Nanchang, Jiangxi, China; Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yang Chen
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Liu
- College of life sciences, Jiangxi Normal university, Nanchang, Jiangxi, China.
| | - Ming Xian Chang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
4
|
Taniguchi I, Hirose T, Ohno M. The RNA helicase DDX39 contributes to the nuclear export of spliceosomal U snRNA by loading of PHAX onto RNA. Nucleic Acids Res 2024:gkae622. [PMID: 39011894 DOI: 10.1093/nar/gkae622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 07/01/2024] [Accepted: 07/04/2024] [Indexed: 07/17/2024] Open
Abstract
RNA helicases are involved in RNA metabolism in an ATP-dependent manner. Although many RNA helicases unwind the RNA structure and/or remove proteins from the RNA, some can load their interacting proteins onto RNAs. Here, we developed an in vitro strategy to identify the ATP-dependent factors involved in spliceosomal uridine-rich small nuclear RNA (U snRNA) export. We identified the RNA helicase UAP56/DDX39B, a component of the mRNA export complex named the transcription-export (TREX) complex, and its closely related RNA helicase URH49/DDX39A as the factors that stimulated RNA binding of PHAX, an adapter protein for U snRNA export. ALYREF, another TREX component, acted as a bridge between PHAX and UAP56/DDX39B. We also showed that UAP56/DDX39B and ALYREF participate in U snRNA export through a mechanism distinct from that of mRNA export. This study describes a novel aspect of the TREX components for U snRNP biogenesis and highlights the loading activity of RNA helicases.
Collapse
Affiliation(s)
- Ichiro Taniguchi
- Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan
| | - Mutsuhito Ohno
- Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| |
Collapse
|
5
|
Firdous Z, Kalra S, Chattopadhyay R, Bari VK. Current insight into the role of mRNA decay pathways in fungal pathogenesis. Microbiol Res 2024; 283:127671. [PMID: 38479232 DOI: 10.1016/j.micres.2024.127671] [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: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
Pathogenic fungal species can cause superficial and mucosal infections, to potentially fatal systemic or invasive infections in humans. These infections are more common in immunocompromised or critically ill patients and have a significant morbidity and fatality rate. Fungal pathogens utilize several strategies to adapt the host environment resulting in efficient and comprehensive alterations in their cellular metabolism. Fungal virulence is regulated by several factors and post-transcriptional regulation mechanisms involving mRNA molecules are one of them. Post-transcriptional controls have emerged as critical regulatory mechanisms involved in the pathogenesis of fungal species. The untranslated upstream and downstream regions of the mRNA, as well as RNA-binding proteins, regulate morphogenesis and virulence by controlling mRNA degradation and stability. The limited number of available therapeutic drugs, the emergence of multidrug resistance, and high death rates associated with systemic fungal illnesses pose a serious risk to human health. Therefore, new antifungal treatments that specifically target mRNA pathway components can decrease fungal pathogenicity and when combined increase the effectiveness of currently available antifungal drugs. This review summarizes the mRNA degradation pathways and their role in fungal pathogenesis.
Collapse
Affiliation(s)
- Zulikha Firdous
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Sapna Kalra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Rituja Chattopadhyay
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Vinay Kumar Bari
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India.
| |
Collapse
|
6
|
Mizrahi R, Ostersetzer-Biran O. Mitochondrial RNA Helicases: Key Players in the Regulation of Plant Organellar RNA Splicing and Gene Expression. Int J Mol Sci 2024; 25:5502. [PMID: 38791540 PMCID: PMC11122041 DOI: 10.3390/ijms25105502] [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: 03/12/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial genomes of land plants are large and exhibit a complex mode of gene organization and expression, particularly at the post-transcriptional level. The primary organellar transcripts in plants undergo extensive maturation steps, including endo- and/or exo-nucleolytic cleavage, RNA-base modifications (mostly C-to-U deaminations) and both 'cis'- and 'trans'-splicing events. These essential processing steps rely on the activities of a large set of nuclear-encoded factors. RNA helicases serve as key players in RNA metabolism, participating in the regulation of transcription, mRNA processing and translation. They unwind RNA secondary structures and facilitate the formation of ribonucleoprotein complexes crucial for various stages of gene expression. Furthermore, RNA helicases are involved in RNA metabolism by modulating pre-mRNA maturation, transport and degradation processes. These enzymes are, therefore, pivotal in RNA quality-control mechanisms, ensuring the fidelity and efficiency of RNA processing and turnover in plant mitochondria. This review summarizes the significant roles played by helicases in regulating the highly dynamic processes of mitochondrial transcription, RNA processing and translation in plants. We further discuss recent advancements in understanding how dysregulation of mitochondrial RNA helicases affects the splicing of organellar genes, leading to respiratory dysfunctions, and consequently, altered growth, development and physiology of land plants.
Collapse
Affiliation(s)
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus—Givat Ram, Jerusalem 9190401, Israel
| |
Collapse
|
7
|
Jablonka S, Yildirim E. Disease Mechanisms and Therapeutic Approaches in SMARD1-Insights from Animal Models and Cell Models. Biomedicines 2024; 12:845. [PMID: 38672198 PMCID: PMC11048220 DOI: 10.3390/biomedicines12040845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/04/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Spinal muscular atrophy with respiratory distress type 1 (SMARD1) is a fatal childhood motoneuron disease caused by mutations in the IGHMBP2 gene. It is characterized by muscle weakness, initially affecting the distal extremities due to the degeneration of spinal α-motoneurons, and respiratory distress, due to the paralysis of the diaphragm. Infantile forms with a severe course of the disease can be distinguished from juvenile forms with a milder course. Mutations in the IGHMBP2 gene have also been found in patients with peripheral neuropathy Charcot-Marie-Tooth type 2S (CMT2S). IGHMBP2 is an ATP-dependent 5'→3' RNA helicase thought to be involved in translational mechanisms. In recent years, several animal models representing both SMARD1 forms and CMT2S have been generated to initially study disease mechanisms. Later, the models showed very well that both stem cell therapies and the delivery of the human IGHMBP2 cDNA by AAV9 approaches (AAV9-IGHMBP2) can lead to significant improvements in disease symptoms. Therefore, the SMARD1 animal models, in addition to the cellular models, provide an inexhaustible source for obtaining knowledge of disease mechanisms, disease progression at the cellular level, and deeper insights into the development of therapies against SMARD1.
Collapse
Affiliation(s)
- Sibylle Jablonka
- Institute of Clinical Neurobiology, University Hospital Würzburg, Versbacher Strasse 5, 97078 Würzburg, Germany;
| | | |
Collapse
|
8
|
Fatahi B, Sorkheh K, Sofo A. Deciphering the possible role of RNA-helicase genes mechanism in response to abiotic stresses in rapeseed (Brassica napus L.). BMC PLANT BIOLOGY 2024; 24:206. [PMID: 38509484 PMCID: PMC10953219 DOI: 10.1186/s12870-024-04893-0] [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: 08/05/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND Plants mediate several defense mechanisms to withstand abiotic stresses. Several gene families respond to stress as well as multiple transcription factors to minimize abiotic stresses without minimizing their effects on performance potential. RNA helicase (RH) is one of the foremost critical gene families that can play an influential role in tolerating abiotic stresses in plants. However, little knowledge is present about this protein family in rapeseed (canola). Here, we performed a comprehensive survey analysis of the RH protein family in rapeseed (Brassica napus L.). RESULTS A total of 133 BnRHs genes have been discovered in this study. By phylogenetic analysis, RHs genes were divided into one main group and a subgroup. Examination of the chromosomal position of the identified genes showed that most of the genes (27%) were located on chromosome 3. All 133 identified sequences contained the main DEXDC domain, the HELICC domain, and a number of sub-domains. The results of biological process studies showed that about 17% of the proteins acted as RHs, 22% as ATP binding, and 14% as mRNA binding. Each part of the conserved motifs, communication network, and three-dimensional structure of the proteins were examined separately. The results showed that the RWC in leaf tissue decreased with higher levels of drought stress and in both root and leaf tissues sodium concentration was increased upon increased levels of salt stress treatments. The proline content were found to be increased in leaf and root with the increased level of stress treatment. Finally, the expression patterns of eight selected RHs genes that have been exposed to drought, salinity, cold, heat and cadmium stresses were investigated by qPCR. The results showed the effect of genes under stress. Examination of gene expression in the Hayola #4815 cultivar showed that all primers except primer #79 had less expression in both leaves and roots than the control level. CONCLUSIONS New finding from the study have been presented new insights for better understanding the function and possible mechanism of RH in response to abiotic stress in rapeseed.
Collapse
Affiliation(s)
- Bahareh Fatahi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box 61355/144, Ahvaz, Iran
| | - Karim Sorkheh
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box 61355/144, Ahvaz, Iran.
| | - Adriano Sofo
- Department of European and Mediterranean Cultures, Architecture, Environment, Cultural Heritage (DiCEM), Università degli Studi della Basilicata, Via Lanera 20, 75100, Matera, MT, Italy
| |
Collapse
|
9
|
Gan H, Cai J, Li L, Zheng X, Yan L, Hu X, Zhao N, Li B, He J, Wang D, Pang P. Endothelium-targeted Ddx24 conditional knockout exacerbates ConA-induced hepatitis in mice due to vascular hyper-permeability. Int Immunopharmacol 2024; 129:111618. [PMID: 38354508 DOI: 10.1016/j.intimp.2024.111618] [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: 10/24/2023] [Revised: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Acute hepatitis is a progressive inflammatory disorder that can lead to liver failure. Endothelial permeability is the vital pathophysiological change involved in infiltrating inflammatory factors. DDX24 has been implicated in immune signaling. However, the precise role of DDX24 in immune-mediated hepatitis remains unclear. Here, we investigate the phenotype of endothelium-targeted Ddx24 conditional knockout mice with Concanavalin A (ConA)-induced hepatitis. METHODS Mice with homozygous endothelium-targeted Ddx24 conditional knockout (Ddx24flox/flox; Cdh5-Cre+) were established using the CRISPR/Cas9 mediated Cre-loxP system. We investigated the biological functions of endothelial cells derived from transgenic mice and explored the effects of Ddx24 in mice with ConA-induced hepatitis in vivo. The mass spectrometry was performed to identify the differentially expressed proteins in liver tissues of transgenic mice. RESULT We successfully established mice with endothelium-targeted Ddx24 conditional knockout. The results showed migration and tube formation potentials of murine aortic endothelial cells with DDX24 silencing were significantly promoted. No differences were observed between Ddx24flox/flox; Cdh5-Cre+ and control regarding body weight and length, pathological tissue change and embryogenesis. We demonstrated Ddx24flox/flox; Cdh5-Cre+ exhibited exacerbation of ConA-induced hepatitis by up-regulating TNF-α and IFN-γ. Furthermore, endothelium-targeted Ddx24 conditional knockout caused vascular hyper-permeability in ConA-injected mice by down-regulating vascular integrity-associated proteins. Mechanistically, we identified Ddx24 might regulate immune-mediated hepatitis by inflammation-related permeable barrier pathways. CONCLUSION These findings prove that endothelium-targeted Ddx24 conditional knockout exacerbates ConA-induced hepatitis in mice because of vascular hyper-permeability. The findings indicate a crucial role of DDX24 in regulating immune-mediated hepatitis, suggesting DDX24 as a potential therapeutic target in the disorder.
Collapse
Affiliation(s)
- Hairun Gan
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Jianxun Cai
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Luting Li
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Xiaodi Zheng
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Leye Yan
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Xinyan Hu
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Ni Zhao
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Bing Li
- Department of Ophthalmology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China.
| | - Jianan He
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China.
| | - Dashuai Wang
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China.
| | - Pengfei Pang
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China.
| |
Collapse
|
10
|
Patrick EM, Yadav R, Senanayake K, Cotter K, Putnam AA, Jankowsky E, Comstock MJ. High-resolution fleezers reveal duplex opening and stepwise assembly by an oligomer of the DEAD-box helicase Ded1p. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582829. [PMID: 38496418 PMCID: PMC10942383 DOI: 10.1101/2024.02.29.582829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
DEAD-box RNA helicases are ubiquitous in all domains of life where they bind and remodel RNA and RNA-protein complexes. DEAD-box helicases unwind RNA duplexes by local opening of helical regions without directional movement through the duplexes and some of these enzymes, including Ded1p from Saccharomyces cerevisiae, oligomerize to effectively unwind RNA duplexes. Whether and how DEAD-box helicases coordinate oligomerization and unwinding is not known and it is unclear how many base pairs are actively opened. Using high-resolution optical tweezers and fluorescence, we reveal a highly dynamic and stochastic process of multiple Ded1p protomers assembling on and unwinding an RNA duplex. One Ded1p protomer binds to a duplex-adjacent ssRNA tail and promotes binding and subsequent unwinding of the duplex by additional Ded1p protomers in 4-6 bp steps. The data also reveal rapid duplex unwinding and rezipping linked with binding and dissociation of individual protomers and coordinated with the ATP hydrolysis cycle.
Collapse
|
11
|
Nie G, Chen S, Song Q, Zou D, Li M, Tang X, Deng Y, Huang B, Yang M, Lv G, Zhang Y. DHX33 mediates p53 to regulate mevalonate pathway gene transcription in human cancers. Biochim Biophys Acta Gen Subj 2024; 1868:130547. [PMID: 38143011 DOI: 10.1016/j.bbagen.2023.130547] [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: 08/06/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Tumor suppressor p53 is frequently null or mutated in human cancers. Here in this study, DHX33 protein was found to be induced in p53 null cells in vitro, and in p53 mutant lung tumorigenesis in vivo. Cholesterol metabolism through mevalonate pathway is pivotal for cell proliferation and is frequently altered in human cancers. Mice carrying mutant p53 and KrasG12D alleles showed upregulation of mevalonate pathway gene expression. However upon DHX33 loss, their upregulation was significantly debilitated. Additionally, in many human cancer cells, DHX33 knockdown caused inhibition of mavelonate pathway gene transcription. We propose DHX33 locates downstream of mutant p53 and Ras to regulate mevalonate pathway gene transcription and thereby supports cancer development in vivo.
Collapse
Affiliation(s)
- Guangli Nie
- Shenzhen KeYe Life Technologies Co., Ltd, Shenzhen, Guangdong 518000, China
| | - Shiyun Chen
- Shenzhen KeYe Life Technologies Co., Ltd, Shenzhen, Guangdong 518000, China; Southern University of Science and Technology, Shenzhen, China
| | - Qingzhi Song
- Department of Gastrointestinal Surgery, Peking University Shenzhen Hospital, China
| | - Dongxu Zou
- Shenzhen KeYe Life Technologies Co., Ltd, Shenzhen, Guangdong 518000, China
| | - Maggie Li
- Shenzhen College of International Education, Shenzhen, China
| | - Xiyu Tang
- Shenzhen KeYe Life Technologies Co., Ltd, Shenzhen, Guangdong 518000, China
| | - Yuanlian Deng
- Shenzhen KeYe Life Technologies Co., Ltd, Shenzhen, Guangdong 518000, China
| | - Bizhou Huang
- Shenzhen KeYe Life Technologies Co., Ltd, Shenzhen, Guangdong 518000, China
| | - Mengxia Yang
- Shenzhen KeYe Life Technologies Co., Ltd, Shenzhen, Guangdong 518000, China
| | - Guoqing Lv
- Shenzhen College of International Education, Shenzhen, China.
| | - Yandong Zhang
- Shenzhen KeYe Life Technologies Co., Ltd, Shenzhen, Guangdong 518000, China; Southern University of Science and Technology, Shenzhen, China.
| |
Collapse
|
12
|
Winstone L, Jung Y, Wu Y. DDX41: exploring the roles of a versatile helicase. Biochem Soc Trans 2024; 52:395-405. [PMID: 38348889 PMCID: PMC10903454 DOI: 10.1042/bst20230725] [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: 10/23/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/29/2024]
Abstract
DDX41 is a DEAD-box helicase and is conserved across species. Mutations in DDX41 have been associated with myeloid neoplasms, including myelodysplastic syndrome and acute myeloid leukemia. Though its pathogenesis is not completely known, DDX41 has been shown to have many cellular roles, including in pre-mRNA splicing, innate immune sensing, ribosome biogenesis, translational regulation, and R-loop metabolism. In this review, we will summarize the latest understandings regarding the various roles of DDX41, as well as highlight challenges associated with drug development to target DDX41. Overall, understanding the molecular and cellular mechanisms of DDX41 could help develop novel therapeutic options for DDX41 mutation-related hematologic malignancies.
Collapse
Affiliation(s)
- Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Yohan Jung
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| |
Collapse
|
13
|
Arul Nambi Rajan A, Asada R, Montpetit B. Gle1 is required for tRNA to stimulate Dbp5 ATPase activity in vitro and promote Dbp5-mediated tRNA export in vivo in Saccharomyces cerevisiae. eLife 2024; 12:RP89835. [PMID: 38189406 PMCID: PMC10945473 DOI: 10.7554/elife.89835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
Cells must maintain a pool of processed and charged transfer RNAs (tRNA) to sustain translation capacity and efficiency. Numerous parallel pathways support the processing and directional movement of tRNA in and out of the nucleus to meet this cellular demand. Recently, several proteins known to control messenger RNA (mRNA) transport were implicated in tRNA export. The DEAD-box Protein 5, Dbp5, is one such example. In this study, genetic and molecular evidence demonstrates that Dbp5 functions parallel to the canonical tRNA export factor Los1. In vivo co-immunoprecipitation data further shows Dbp5 is recruited to tRNA independent of Los1, Msn5 (another tRNA export factor), or Mex67 (mRNA export adaptor), which contrasts with Dbp5 recruitment to mRNA that is abolished upon loss of Mex67 function. However, as with mRNA export, overexpression of Dbp5 dominant-negative mutants indicates a functional ATPase cycle and that binding of Dbp5 to Gle1 is required by Dbp5 to direct tRNA export. Biochemical characterization of the Dbp5 catalytic cycle demonstrates the direct interaction of Dbp5 with tRNA (or double-stranded RNA) does not activate Dbp5 ATPase activity, rather tRNA acts synergistically with Gle1 to fully activate Dbp5. These data suggest a model where Dbp5 directly binds tRNA to mediate export, which is spatially regulated via Dbp5 ATPase activation at nuclear pore complexes by Gle1.
Collapse
Affiliation(s)
- Arvind Arul Nambi Rajan
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, DavisDavisUnited States
| | - Ryuta Asada
- Department of Viticulture and Enology, University of California, DavisDavisUnited States
| | - Ben Montpetit
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, DavisDavisUnited States
- Department of Viticulture and Enology, University of California, DavisDavisUnited States
| |
Collapse
|
14
|
Scala M, Bradley CA, Howe JL, Trost B, Salazar NB, Shum C, Reuter MS, MacDonald JR, Ko SY, Frankland PW, Granger L, Anadiotis G, Pullano V, Brusco A, Keller R, Parisotto S, Pedro HF, Lusk L, McDonnell PP, Helbig I, Mullegama SV, Douine ED, Russell BE, Nelson SF, Zara F, Scherer SW. Genetic variants in DDX53 contribute to Autism Spectrum Disorder associated with the Xp22.11 locus. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.21.23300383. [PMID: 38234782 PMCID: PMC10793518 DOI: 10.1101/2023.12.21.23300383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Autism Spectrum Disorder (ASD) exhibits an ~4:1 male-to-female sex bias and is characterized by early-onset impairment of social/communication skills, restricted interests, and stereotyped behaviors. Disruption of the Xp22.11 locus has been associated with ASD in males. This locus includes the three-exon PTCHD1 gene, an adjacent multi-isoform long noncoding RNA (lncRNA) named PTCHD1-AS (spanning ~1Mb), and a poorly characterized single-exon RNA helicase named DDX53 that is intronic to PTCHD1-AS. While the relationship between PTCHD1/PTCHD1-AS and ASD is being studied, the role of DDX53 has not been examined, in part because there is no apparent functional murine orthologue. Through clinical testing, here, we identified 6 males and 1 female with ASD from 6 unrelated families carrying rare, predicted-damaging or loss-of-function variants in DDX53. Then, we examined databases, including the Autism Speaks MSSNG and Simons Foundation Autism Research Initiative, as well as population controls. We identified 24 additional individuals with ASD harboring rare, damaging DDX53 variations, including the same variants detected in two families from the original clinical analysis. In this extended cohort of 31 participants with ASD (28 male, 3 female), we identified 25 mostly maternally-inherited variations in DDX53, including 18 missense changes, 2 truncating variants, 2 in-frame variants, 2 deletions in the 3' UTR and 1 copy number deletion. Our findings in humans support a direct link between DDX53 and ASD, which will be important in clinical genetic testing. These same autism-related findings, coupled with the observation that a functional orthologous gene is not found in mouse, may also influence the design and interpretation of murine-modelling of ASD.
Collapse
Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Clarrisa A. Bradley
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer L. Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nelson Bautista Salazar
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Carole Shum
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Miriam S. Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeffrey R. MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sangyoon Y. Ko
- Program in Neurosciences and Mental Health, The Hospital for Sick Children and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Paul W. Frankland
- Program in Neurosciences and Mental Health, The Hospital for Sick Children and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Psychology and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Leslie Granger
- Department of Genetics and Metabolism, Randall Children’s Hospital, Portland, OR 97227, USA
| | - George Anadiotis
- Department of Genetics and Metabolism, Randall Children’s Hospital, Portland, OR 97227, USA
| | - Verdiana Pullano
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Alfredo Brusco
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | - Roberto Keller
- Adult Autism Centre DSM ASL Città di Torino, 10138 Turin, Italy
| | - Sarah Parisotto
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Helio F. Pedro
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Laina Lusk
- Epilepsy Neurogenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pamela Pojomovsky McDonnell
- Epilepsy Neurogenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ingo Helbig
- Epilepsy Neurogenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Emilie D. Douine
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Bianca E. Russell
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- McLaughlin Centre, Toronto, ON M5G 0A4, Canada
| |
Collapse
|
15
|
Jagtap PKA, Müller M, Kiss AE, Thomae AW, Lapouge K, Beck M, Becker PB, Hennig J. Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless. Mol Cell 2023; 83:4318-4333.e10. [PMID: 37989319 DOI: 10.1016/j.molcel.2023.10.026] [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: 11/12/2022] [Revised: 07/27/2023] [Accepted: 10/18/2023] [Indexed: 11/23/2023]
Abstract
RNA unwinding by DExH-type helicases underlies most RNA metabolism and function. It remains unresolved if and how the basic unwinding reaction of helicases is regulated by auxiliary domains. We explored the interplay between the RecA and auxiliary domains of the RNA helicase maleless (MLE) from Drosophila using structural and functional studies. We discovered that MLE exists in a dsRNA-bound open conformation and that the auxiliary dsRBD2 domain aligns the substrate RNA with the accessible helicase tunnel. In an ATP-dependent manner, dsRBD2 associates with the helicase module, leading to tunnel closure around ssRNA. Furthermore, our structures provide a rationale for blunt-ended dsRNA unwinding and 3'-5' translocation by MLE. Structure-based MLE mutations confirm the functional relevance of our model for RNA unwinding. Our findings contribute to our understanding of the fundamental mechanics of auxiliary domains in DExH helicase MLE, which serves as a model for its human ortholog and potential therapeutic target, DHX9/RHA.
Collapse
Affiliation(s)
- Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany.
| | - Marisa Müller
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Anna E Kiss
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Andreas W Thomae
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany; Core Facility Bioimaging at the Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany.
| |
Collapse
|
16
|
Gotur D, Case A, Liu J, Sickmier EA, Holt N, Knockenhauer KE, Yao S, Lee YT, Copeland RA, Buker SM, Boriack-Sjodin PA. Development of assays to support identification and characterization of modulators of DExH-box helicase DHX9. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:376-384. [PMID: 37625785 DOI: 10.1016/j.slasd.2023.08.006] [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: 06/06/2023] [Revised: 08/02/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
DHX9 is a DExH-box RNA helicase that utilizes hydrolysis of all four nucleotide triphosphates (NTPs) to power cycles of 3' to 5' directional movement to resolve and/or unwind double stranded RNA, DNA, and RNA/DNA hybrids, R-loops, triplex-DNA and G-quadraplexes. DHX9 activity is important for both viral amplification and maintaining genomic stability in cancer cells; therefore, it is a therapeutic target of interest for drug discovery efforts. Biochemical assays measuring ATP hydrolysis and oligonucleotide unwinding for DHX9 have been developed and characterized, and these assays can support high-throughput compound screening efforts under balanced conditions. Assay development efforts revealed DHX9 can use double stranded RNA with 18-mer poly(U) 3' overhangs and as well as significantly shorter overhangs at the 5' or 3' end as substrates. The enzymatic assays are augmented by a robust SPR assay for compound validation. A mechanism-derived inhibitor, GTPγS, was characterized as part of the validation of these assays and a crystal structure of GDP bound to cat DHX9 has been solved. In addition to enabling drug discovery efforts for DHX9, these assays may be extrapolated to other RNA helicases providing a valuable toolkit for this important target class.
Collapse
Affiliation(s)
- Deepali Gotur
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - April Case
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - Julie Liu
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - E Allen Sickmier
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - Nicholas Holt
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | | | - Shihua Yao
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - Young-Tae Lee
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | | | - Shane M Buker
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | | |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Zhang XD, Han Y, Yang ZM, Sun D. DEAD-box RNA helicase 6 regulates drought and abscisic acid stress responses in rapeseed (Brassica napus). Gene 2023; 886:147717. [PMID: 37595852 DOI: 10.1016/j.gene.2023.147717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/05/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
DEAD-box RNA helicase is a major subfamily of RNA helicases with vital roles played in plant growth, development, and plant-environment interactions. RNA helicase 6 in rapeseed (Brassica napus) (BnRH6) is a member of DEAD-box RNA helicase. While previous research has demonstrated the role of BnRH6 in salt stress regulation, the involvement of BnRH6 in drought stress adaptation remains unknown. This report described a function of BnRH6 in drought stress response. BnRH6 was sufficiently induced by osmotic stress. Transgenic Brassica napus and Arabidopsis thaliana (Arabidopsis) overexpressing BnRH6 (OE) showed a drought tolerance phenotype, characterized by improved plant growth, increased survival rates, reduced water loss, leaf chlorosis and oxidative stress. Furthermore, BnRH6 was also induced by exogenous abscisic acid (ABA). BnRH6 overexpression plants exhibited ABA hypersensitivity with lagging seed germination, growth stunt and diminished stomatal opening in the presence of ABA, suggesting the involvement of ABA signal. Assessment of several well-identified drought stress responsive genes such as Calcium-dependent Protein Kinase 14 (BnCDPK14), Enhanced Response to ABA1 (BnERA1) and ABA Insensitive 1 (BnABI1) revealed that their expressions were accordingly changed in BnOE plants, possibly with interplays between BnRH6 and those genes. Our data highlighted the functional role of BnRH6, which plays a positive role in active regulation of drought stress response likely through an ABA-dependent manner in rapeseed plants.
Collapse
Affiliation(s)
- Xian Duo Zhang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuxiang Han
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Di Sun
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
19
|
Tapescu I, Taschuk F, Pokharel SM, Zginnyk O, Ferretti M, Bailer PF, Whig K, Madden EA, Heise MT, Schultz DC, Cherry S. The RNA helicase DDX39A binds a conserved structure in chikungunya virus RNA to control infection. Mol Cell 2023; 83:4174-4189.e7. [PMID: 37949067 PMCID: PMC10722560 DOI: 10.1016/j.molcel.2023.10.008] [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: 10/17/2022] [Revised: 04/25/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Alphaviruses are a large group of re-emerging arthropod-borne RNA viruses. The compact viral RNA genomes harbor diverse structures that facilitate replication. These structures can be recognized by antiviral cellular RNA-binding proteins, including DExD-box (DDX) helicases, that bind viral RNAs to control infection. The full spectrum of antiviral DDXs and the structures that are recognized remain unclear. Genetic screening identified DDX39A as antiviral against the alphavirus chikungunya virus (CHIKV) and other medically relevant alphaviruses. Upon infection, the predominantly nuclear DDX39A accumulates in the cytoplasm inhibiting alphavirus replication, independent of the canonical interferon pathway. Biochemically, DDX39A binds to CHIKV genomic RNA, interacting with the 5' conserved sequence element (5'CSE), which is essential for the antiviral activity of DDX39A. Altogether, DDX39A relocalization and binding to a conserved structural element in the alphavirus genomic RNA attenuates infection, revealing a previously unknown layer to the cellular control of infection.
Collapse
Affiliation(s)
- Iulia Tapescu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Biochemistry and Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Frances Taschuk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Swechha M Pokharel
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oleksandr Zginnyk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Max Ferretti
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter F Bailer
- Biochemistry and Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Kanupryia Whig
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily A Madden
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, NC, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC, USA
| | - David C Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
20
|
Wang Y, Nie G, Wang X, Ge W, Zhang Y. Development of small molecule inhibitors targeting RNA helicase DHX33 as anti-cancer agents. Bioorg Med Chem Lett 2023; 96:129505. [PMID: 37838340 DOI: 10.1016/j.bmcl.2023.129505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/19/2023] [Accepted: 10/07/2023] [Indexed: 10/16/2023]
Abstract
RNA helicase DHX33 has been identified to be a critical factor in promoting cancer development. Genetic deletion of DHX33 significantly blocks tumorigenesis. Importantly, its helicase activity was found to be pivotal for exerting cellular functions. Herein we used a helicase-based high throughput screening (HTS) to discover DHX33 inhibitors from Chembridge chemical library containing 15,000 small molecules. We identified a hit compound containing benzimidazole ring that demonstrated activity against DHX33 with certain selectivity. Further structural optimization led to the design and synthesis of a series of analog inhibitors. Considering the potential role of DHX33 in cancer development, the compounds were evaluated based on the cytotoxicity activity in U251-MG cancer cells in vitro. Among them, compound IVa (KY386) was identified to be a selective inhibitor for DHX33 helicase with potent anti-cancer activity and moderate metabolic stability. These results support the promising role of DHX33 inhibitors for development of novel anti-cancer drugs.
Collapse
Affiliation(s)
- Yingcai Wang
- Shenzhen KeYe Life Technologies Co., Ltd, Shenzhen, Guangdong 518000, China; Acme Bioscience, Inc, Palo Alto, CA 94303, USA
| | - Guangli Nie
- Shenzhen KeYe Life Technologies Co., Ltd, Shenzhen, Guangdong 518000, China
| | - Xingshun Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei Ge
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Yandong Zhang
- Shenzhen KeYe Life Technologies Co., Ltd, Shenzhen, Guangdong 518000, China.
| |
Collapse
|
21
|
Rajan AAN, Asada R, Montpetit B. Gle1 is required for tRNA to stimulate Dbp5 ATPase activity in vitro and to promote Dbp5 mediated tRNA export in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547072. [PMID: 37425677 PMCID: PMC10327206 DOI: 10.1101/2023.06.29.547072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cells must maintain a pool of processed and charged transfer RNAs (tRNA) to sustain translation capacity and efficiency. Numerous parallel pathways support the processing and directional movement of tRNA in and out of the nucleus to meet this cellular demand. Recently, several proteins known to control messenger RNA (mRNA) transport were implicated in tRNA export. The DEAD-box Protein 5, Dbp5, is one such example. In this study, genetic and molecular evidence demonstrates that Dbp5 functions parallel to the canonical tRNA export factor Los1. In vivo co-immunoprecipitation data further shows Dbp5 is recruited to tRNA independent of Los1, Msn5 (another tRNA export factor), or Mex67 (mRNA export adaptor), which contrasts with Dbp5 recruitment to mRNA that is abolished upon loss of Mex67 function. However, as with mRNA export, overexpression of Dbp5 dominant-negative mutants indicates a functional ATPase cycle and that binding of Dbp5 to Gle1 is required by Dbp5 to direct tRNA export. Biochemical characterization of the Dbp5 catalytic cycle demonstrates the direct interaction of Dbp5 with tRNA (or double stranded RNA) does not activate Dbp5 ATPase activity, rather tRNA acts synergistically with Gle1 to fully activate Dbp5. These data suggest a model where Dbp5 directly binds tRNA to mediate export, which is spatially regulated via Dbp5 ATPase activation at nuclear pore complexes by Gle1.
Collapse
Affiliation(s)
- Arvind Arul Nambi Rajan
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis, Davis, CA, USA
| | - Ryuta Asada
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Ben Montpetit
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis, Davis, CA, USA
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| |
Collapse
|
22
|
Yang S, Winstone L, Mondal S, Wu Y. Helicases in R-loop Formation and Resolution. J Biol Chem 2023; 299:105307. [PMID: 37778731 PMCID: PMC10641170 DOI: 10.1016/j.jbc.2023.105307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023] Open
Abstract
With the development and wide usage of CRISPR technology, the presence of R-loop structures, which consist of an RNA-DNA hybrid and a displaced single-strand (ss) DNA, has become well accepted. R-loop structures have been implicated in a variety of circumstances and play critical roles in the metabolism of nucleic acid and relevant biological processes, including transcription, DNA repair, and telomere maintenance. Helicases are enzymes that use an ATP-driven motor force to unwind double-strand (ds) DNA, dsRNA, or RNA-DNA hybrids. Additionally, certain helicases have strand-annealing activity. Thus, helicases possess unique positions for R-loop biogenesis: they utilize their strand-annealing activity to promote the hybridization of RNA to DNA, leading to the formation of R-loops; conversely, they utilize their unwinding activity to separate RNA-DNA hybrids and resolve R-loops. Indeed, numerous helicases such as senataxin (SETX), Aquarius (AQR), WRN, BLM, RTEL1, PIF1, FANCM, ATRX (alpha-thalassemia/mental retardation, X-linked), CasDinG, and several DEAD/H-box proteins are reported to resolve R-loops; while other helicases, such as Cas3 and UPF1, are reported to stimulate R-loop formation. Moreover, helicases like DDX1, DDX17, and DHX9 have been identified in both R-loop formation and resolution. In this review, we will summarize the latest understandings regarding the roles of helicases in R-loop metabolism. Additionally, we will highlight challenges associated with drug discovery in the context of targeting these R-loop helicases.
Collapse
Affiliation(s)
- Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sohaumn Mondal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
| |
Collapse
|
23
|
Gambelli A, Ferrando A, Boncristiani C, Schoeftner S. Regulation and function of R-loops at repetitive elements. Biochimie 2023; 214:141-155. [PMID: 37619810 DOI: 10.1016/j.biochi.2023.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the human genome, including repetitive regions, hold transcriptional activity. This anticipates that R-loops management plays a central role for the regulation and integrity of genomes. This function is expected to have a particular relevance for repetitive sequences that make up to 75% of the human genome. Here, we review the impact of R-loops on the function and stability of repetitive regions such as centromeres, telomeres, rDNA arrays, transposable elements and triplet repeat expansions and discuss their relevance for associated pathological conditions.
Collapse
Affiliation(s)
- Alice Gambelli
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Alessandro Ferrando
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Chiara Boncristiani
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Stefan Schoeftner
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy.
| |
Collapse
|
24
|
Lee YT, Sickmier EA, Grigoriu S, Castro J, Boriack-Sjodin PA. Crystal structures of the DExH-box RNA helicase DHX9. Acta Crystallogr D Struct Biol 2023; 79:980-991. [PMID: 37860960 PMCID: PMC10619421 DOI: 10.1107/s2059798323007611] [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: 06/06/2023] [Accepted: 08/31/2023] [Indexed: 10/21/2023] Open
Abstract
DHX9 is a DExH-box RNA helicase with versatile functions in transcription, translation, RNA processing and regulation of DNA replication. DHX9 has recently emerged as a promising target for oncology, but to date no mammalian structures have been published. Here, crystal structures of human, dog and cat DHX9 bound to ADP are reported. The three mammalian DHX9 structures share identical structural folds. Additionally, the overall architecture and the individual domain structures of DHX9 are highly conserved with those of MLE, the Drosophila orthologue of DHX9 previously solved in complex with RNA and a transition-state analogue of ATP. Due to differences in the bound substrates and global domain orientations, the localized loop conformations and occupancy of dsRNA-binding domain 2 (dsRBD2) differ between the mammalian DHX9 and MLE structures. The combined effects of the structural changes considerably alter the RNA-binding channel, providing an opportunity to compare active and inactive states of the helicase. Finally, the mammalian DHX9 structures provide a potential tool for structure-based drug-design efforts.
Collapse
Affiliation(s)
- Young-Tae Lee
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | | | - Simina Grigoriu
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - Jennifer Castro
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | | |
Collapse
|
25
|
Ding J, Wang S, Liu Q, Duan Y, Cheng T, Ye Z, Cui Z, Zhang A, Liu Q, Zhang Z, Zhang N, Liu Q, An N, Zhao J, Yi D, Li Q, Wang J, Zhang Y, Ma L, Guo S, Wang J, Liang C, Zhou J, Cen S, Li X. Schlafen-5 inhibits LINE-1 retrotransposition. iScience 2023; 26:107968. [PMID: 37810251 PMCID: PMC10551903 DOI: 10.1016/j.isci.2023.107968] [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: 11/18/2022] [Revised: 07/20/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Abstract
Long interspersed element 1 (LINE-1) is the only currently known active autonomous transposon in humans, and its retrotransposition may cause deleterious effects on the structure and function of host cell genomes and result in sporadic genetic diseases. Host cells therefore developed defense strategies to restrict LINE-1 mobilization. In this study, we demonstrated that IFN-inducible Schlafen5 (SLFN5) inhibits LINE-1 retrotransposition. Mechanistic studies revealed that SLFN5 interrupts LINE-1 ribonucleoprotein particle (RNP) formation, thus diminishing nuclear entry of the LINE-1 RNA template and subsequent LINE-1 cDNA production. The ability of SLFN5 to bind to LINE-1 RNA and the involvement of the helicase domain of SLFN5 in its inhibitory activity suggest a mechanism that SLFN5 binds to LINE-1 RNA followed by dissociation of ORF1p through its helicase activity, resulting in impaired RNP formation. These data highlight a new mechanism of host cells to restrict LINE-1 mobilization.
Collapse
Affiliation(s)
- Jiwei Ding
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shujie Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qipeng Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yuqing Duan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tingting Cheng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhongjie Ye
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhanding Cui
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qiuyu Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zixiong Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qian Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ni An
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dongrong Yi
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yongxin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Saisai Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jinhui Wang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chen Liang
- The Lady Davis Institute-Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
26
|
Banu MSA, Huda KMK, Harun-Ur-Rashid M, Parveen S, Shahinul Islam SM, Tuteja N. Phenotypic and microarray analysis reveals salinity stress-induced oxidative tolerance in transgenic rice expressing a DEAD-box RNA helicase, OsDB10. PLANT MOLECULAR BIOLOGY 2023; 113:19-32. [PMID: 37523054 DOI: 10.1007/s11103-023-01372-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023]
Abstract
Helicases are the motor proteins not only involved in the process of mRNA metabolism but also played a significant role in providing abiotic stresses tolerance. In this study, a DEAD-box RNA helicase OsDB10 was cloned and functionally characterized. The transcript levels of OsDB10 were increased both in shoot and root upon salt, heat, cold, and ABA application and was more prominent in shoot compared to root. Genomic integration of OsDB10 in transgenic rice was confirmed by PCR, Southern blot and qRT-PCR analysis. The transgenic plants showed quicker seed germination, reduced necrosis, higher chlorophyll, more survival rate, better seedling growth, and produced more grain yield under salinity stress. Furthermore, transgenic lines also accumulated less Na+ and high K+ ions and salinity tolerance of the transgenic were also assayed by measuring different bio-physiological indices. Moreover, the OsDB10 transgenic plants showed enhanced tolerance to salinity-induced oxidative stress by scavenging ROS and increased activity of antioxidants enzymes. Microarray analysis showed upregulation of transcriptional regulations and metabolic reprogramming as OsDB10 overexpression modulates the expression of many other genes. Altogether, our results confirmed that OsDB10 is a functional DEAD-box RNA helicase and played vital roles in plant defence response against salinity stress.
Collapse
Affiliation(s)
- Mst Sufara Akhter Banu
- Bangladesh Agricultural Research Council (BARC), Dhaka, 1215, Bangladesh
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Kazi Md Kamrul Huda
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh.
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India.
| | - Md Harun-Ur-Rashid
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh
| | - Shahanaz Parveen
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh
| | - S M Shahinul Islam
- Institute of Biological Sciences, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| |
Collapse
|
27
|
Venus S, Tandjigora K, Jankowsky E. The Viral Protein K7 Inhibits Biochemical Activities and Condensate Formation by the DEAD-box Helicase DDX3X. J Mol Biol 2023; 435:168217. [PMID: 37517790 PMCID: PMC10528715 DOI: 10.1016/j.jmb.2023.168217] [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: 03/10/2023] [Revised: 06/17/2023] [Accepted: 07/24/2023] [Indexed: 08/01/2023]
Abstract
The DEAD-box RNA helicase DDX3X promotes translation initiation and associates with stress granules. A range of diverse viruses produce proteins that target DDX3X, including hepatitis C, dengue, vaccinia, and influenza A. The interaction of some of these viral proteins with DDX3X has been shown to affect antiviral intracellular signaling, but it is unknown whether and how viral proteins impact the biochemical activities of DDX3X and its physical roles in cells. Here we show that the protein K7 from vaccinia virus, which binds to an intrinsically disordered region in the N-terminus of DDX3X, inhibits RNA helicase and RNA-stimulated ATPase activities, as well as liquid-liquid phase separation of DDX3X in vitro. We demonstrate in HCT 116 cells that K7 inhibits association of DDX3X with stress granules, as well as the formation of aberrant granules induced by expression of DDX3X with a point mutation linked to medulloblastoma and DDX3X syndrome. The results show that targeting of the intrinsically disordered N-terminus is an effective viral strategy to modulate the biochemical functions and subcellular localization of DDX3X. Our findings also have potential therapeutic implications for diseases linked to aberrant DDX3X granule formation.
Collapse
Affiliation(s)
- Sarah Venus
- Center for RNA Science and Therapeutics, Department of Biochemistry, Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44016, United States
| | - Kaba Tandjigora
- Center for RNA Science and Therapeutics, Department of Biochemistry, Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44016, United States
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, Department of Biochemistry, Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44016, United States.
| |
Collapse
|
28
|
Bohnsack KE, Yi S, Venus S, Jankowsky E, Bohnsack MT. Cellular functions of eukaryotic RNA helicases and their links to human diseases. Nat Rev Mol Cell Biol 2023; 24:749-769. [PMID: 37474727 DOI: 10.1038/s41580-023-00628-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
RNA helicases are highly conserved proteins that use nucleoside triphosphates to bind or remodel RNA, RNA-protein complexes or both. RNA helicases are classified into the DEAD-box, DEAH/RHA, Ski2-like, Upf1-like and RIG-I families, and are the largest class of enzymes active in eukaryotic RNA metabolism - virtually all aspects of gene expression and its regulation involve RNA helicases. Mutation and dysregulation of these enzymes have been linked to a multitude of diseases, including cancer and neurological disorders. In this Review, we discuss the regulation and functional mechanisms of RNA helicases and their roles in eukaryotic RNA metabolism, including in transcription regulation, pre-mRNA splicing, ribosome assembly, translation and RNA decay. We highlight intriguing models that link helicase structure, mechanisms of function (such as local strand unwinding, translocation, winching, RNA clamping and displacing RNA-binding proteins) and biological roles, including emerging connections between RNA helicases and cellular condensates formed through liquid-liquid phase separation. We also discuss associations of RNA helicases with human diseases and recent efforts towards the design of small-molecule inhibitors of these pivotal regulators of eukaryotic gene expression.
Collapse
Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna, Cambridge, MA, USA.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| |
Collapse
|
29
|
Wang X, Chen S, Wen F, Zeng Y, Zhang Y. RNA helicase DHX33 regulates HMGB family genes in human cancer cells. Cell Signal 2023; 110:110832. [PMID: 37543097 DOI: 10.1016/j.cellsig.2023.110832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/07/2023]
Abstract
RNA helicase DHX33 has been shown to be aberrantly expressed in various human cancers, however, its role in tumorigenesis remains incompletely understood. In this report, we uncovered that a family of DNA architecture proteins, HMGBs, can be regulated by DHX33 in cancer cells but not in normal cells. Specifically, DHX33 knockdown caused the downregulation of HMGBs at the levels of both gene transcription and protein expression. Notably, in RAS driven lung tumorigenesis, nuclear HMGBs proteins can be induced via DHX33. When DHX33 was knocked out, HMGBs overexpression was debilitated. Mechanistically, DHX33 was found to bind to the promoters of HMGB family genes and regulated their transcription through demethylation on gene promoters. Our study reveals a novel mechanism for DHX33 to promote tumorigenesis and highlights its therapeutic value in human cancers.
Collapse
Affiliation(s)
- Xingshun Wang
- The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan 653199, China
| | - Shiyun Chen
- Shenzhen KeYe Life Technologies, Co., Ltd, Shenzhen, Guangdong 518122, China; Southern University of Science and Technology, Shenzhen, China
| | - Fuyu Wen
- Shenzhen KeYe Life Technologies, Co., Ltd, Shenzhen, Guangdong 518122, China
| | - Yong Zeng
- The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan 653199, China.
| | - Yandong Zhang
- Shenzhen KeYe Life Technologies, Co., Ltd, Shenzhen, Guangdong 518122, China.
| |
Collapse
|
30
|
Incicco JJ, Cababie LA, Sarto C, Adler NS, Amrein F, Mikkelsen E, Arrar M, Kaufman SB. Thermodynamic and mechanistic analysis of the functional properties of dengue virus NS3 helicase. Biophys Rev 2023; 15:591-600. [PMID: 37681085 PMCID: PMC10480135 DOI: 10.1007/s12551-023-01101-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/17/2023] [Indexed: 09/09/2023] Open
Abstract
The Dengue Virus (DENV) non-structural protein 3 (NS3) is a multi-functional protein critical in the viral life cycle. The DENV NS3 is comprised of a serine protease domain and a helicase domain. The helicase domain itself acts as a molecular motor, either translocating in a unidirectional manner along single-stranded RNA or unwinding double-stranded RNA, processes fueled by the hydrolysis of nucleoside triphosphates. In this brief review, we summarize our contributions and ongoing efforts to uncover the thermodynamic and mechanistic functional properties of the DENV NS3 as an NTPase and helicase.
Collapse
Affiliation(s)
- J. Jeremías Incicco
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, CONICET, Junín 956, Caba, 1113 Argentina
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Caba, 1113 Argentina
| | - Leila A. Cababie
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, CONICET, Junín 956, Caba, 1113 Argentina
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Caba, 1113 Argentina
| | - Carolina Sarto
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires. CONICET, Intendente Güiraldes 2160, Caba, 1428 Argentina
| | - Natalia S. Adler
- CONICET. Centro de Investigaciones en Bionanociencias (CIBION), Godoy Cruz 2390, Caba, 1425 Argentina
| | - Fernando Amrein
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, CONICET, Junín 956, Caba, 1113 Argentina
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Caba, 1113 Argentina
| | - Evelyn Mikkelsen
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, CONICET, Junín 956, Caba, 1113 Argentina
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Caba, 1113 Argentina
| | - Mehrnoosh Arrar
- Instituto de Cálculo, Universidad de Buenos Aires. CONICET, Intendente Güiraldes 2160, Caba, 1428 Argentina
| | - Sergio B. Kaufman
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, CONICET, Junín 956, Caba, 1113 Argentina
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Caba, 1113 Argentina
| |
Collapse
|
31
|
Kito Y, Matsumoto A, Ichihara K, Shiraishi C, Tang R, Hatano A, Matsumoto M, Han P, Iwasaki S, Nakayama KI. The ASC-1 complex promotes translation initiation by scanning ribosomes. EMBO J 2023; 42:e112869. [PMID: 37092320 PMCID: PMC10267693 DOI: 10.15252/embj.2022112869] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/18/2023] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Translation initiates when the eIF4F complex binds the 5' mRNA cap, followed by 5' untranslated region scanning for the start codon by scanning ribosomes. Here, we demonstrate that the ASC-1 complex (ASCC), which was previously shown to promote the dissociation of colliding 80S ribosomes, associates with scanning ribosomes to regulate translation initiation. Selective translation complex profiling (TCP-seq) analysis revealed that ASCC3, a helicase domain-containing subunit of ASCC, localizes predominantly to the 5' untranslated region of mRNAs. Ribo-seq, TCP-seq, and luciferase reporter analyses showed that ASCC3 knockdown impairs 43S preinitiation complex loading and scanning dynamics, thereby reducing translation efficiency. Whereas eIF4A, an RNA helicase in the eIF4F complex, is important for global translation, ASCC was found to regulate the scanning process for a specific subset of transcripts. Our results have thus revealed that ASCC is required not only for dissociation of colliding 80S ribosomes but also for efficient translation initiation by scanning ribosomes at a subset of transcripts.
Collapse
Affiliation(s)
- Yuki Kito
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Akinobu Matsumoto
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Kazuya Ichihara
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Chisa Shiraishi
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Ronghao Tang
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Atsushi Hatano
- Department of Omics and Systems BiologyGraduate School of Medical and Dental Sciences, Niigata UniversityNiigataJapan
| | - Masaki Matsumoto
- Department of Omics and Systems BiologyGraduate School of Medical and Dental Sciences, Niigata UniversityNiigataJapan
| | - Peixun Han
- RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchWakoJapan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchWakoJapan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
| | - Keiichi I Nakayama
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Liu Y, Zhou G, Song L, Wen Q, Xie S, Chen L, Wang L, Xie X, Chen X, Pu Y, Chen G. DEAD-Box Helicase 17 Promotes Amyloidogenesis by Regulating BACE1 Translation. Brain Sci 2023; 13:brainsci13050745. [PMID: 37239217 DOI: 10.3390/brainsci13050745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/17/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Amyloidogenesis is one of the key pathophysiological changes in Alzheimer's disease (AD). Accumulation of the toxic Aβ results from the catalytic processing of β-amyloid precursor protein (APP) associated β-amyloid converting enzyme 1 (BACE1) activity. It is reported that dead-box helicase 17 (DDX17) controls RNA metabolism and is involved in the development of multiple diseases. However, whether DDX17 might play a role in amyloidogenesis has not been documented. In the present study, we found that DDX17 protein level was significantly increased in HEK and SH-SY5Y cells that stably express full-length APP (HEK-APP and Y5Y-APP) and in the brain of APP/PS1 mice, an animal model of AD. DDX17 knockdown, as opposed to DDX17 overexpression, markedly reduced the protein levels of BACE1 and the β-amyloid peptide (Aβ) in Y5Y-APP cells. We further found that DDX17-mediated enhancement of BACE1 was selectively attenuated by translation inhibitors. Specifically, DDX17 selectively interacted with the 5' untranslated region (5'UTR) of BACE1 mRNA, and deletion of the 5'UTR abolished the effect of DDX17 on luciferase activity or protein level of BACE1. Here, we show that the enhanced expression of DDX17 in AD was associated with amyloidogenesis; through the 5'UTR-dependent BACE1 translation, DDX17 might serve as an important mediator contributing to the progression of AD.
Collapse
Affiliation(s)
- Yue Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Guifeng Zhou
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Li Song
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Qixin Wen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Shiqi Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Long Chen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Lu Wang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Xiaoyong Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Xue Chen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Yalan Pu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| | - Guojun Chen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
| |
Collapse
|
34
|
Smirnova EV, Rakitina TV, Ziganshin RH, Saratov GA, Arapidi GP, Belogurov AA, Kudriaeva AA. Identification of Myelin Basic Protein Proximity Interactome Using TurboID Labeling Proteomics. Cells 2023; 12:cells12060944. [PMID: 36980286 PMCID: PMC10047773 DOI: 10.3390/cells12060944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Myelin basic protein (MBP) is one of the key structural elements of the myelin sheath and has autoantigenic properties in multiple sclerosis (MS). Its intracellular interaction network is still partially deconvoluted due to the unfolded structure, abnormally basic charge, and specific cellular localization. Here we used the fusion protein of MBP with TurboID, an engineered biotin ligase that uses ATP to convert biotin to reactive biotin-AMP that covalently attaches to nearby proteins, to determine MBP interactome. Despite evident benefits, the proximity labeling proteomics technique generates high background noise, especially in the case of proteins tending to semi-specific interactions. In order to recognize unique MBP partners, we additionally mapped protein interaction networks for deaminated MBP variant and cyclin-dependent kinase inhibitor 1 (p21), mimicking MBP in terms of natively unfolded state, size and basic amino acid clusters. We found that in the plasma membrane region, MBP is colocalized with adhesion proteins occludin and myelin protein zero-like protein 1, solute carrier family transporters ZIP6 and SNAT1, Eph receptors ligand Ephrin-B1, and structural components of the vesicle transport machinery-synaptosomal-associated protein 23 (SNAP23), vesicle-associated membrane protein 3 (VAMP3), protein transport protein hSec23B and cytoplasmic dynein 1 heavy chain 1. We also detected that MBP potentially interacts with proteins involved in Fe2+ and lipid metabolism, namely, ganglioside GM2 activator protein, long-chain-fatty-acid-CoA ligase 4 (ACSL4), NADH-cytochrome b5 reductase 1 (CYB5R1) and metalloreductase STEAP3. Assuming the emerging role of ferroptosis and vesicle cargo docking in the development of autoimmune neurodegeneration, MBP may recruit and regulate the activity of these processes, thus, having a more inclusive role in the integrity of the myelin sheath.
Collapse
Affiliation(s)
- Evgeniya V Smirnova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana V Rakitina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Rustam H Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - George A Saratov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
| | - Georgij P Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Alexey A Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Department of Biological Chemistry, Evdokimov Moscow State University of Medicine and Dentistry, Ministry of Health of Russian Federation, 127473 Moscow, Russia
| | - Anna A Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| |
Collapse
|
35
|
Piljukov VJ, Sillamaa S, Sedman T, Garber N, Rätsep M, Freiberg A, Sedman J. Mitochondrial Irc3 helicase of the thermotolerant yeast Ogataea polymorpha displays dual DNA- and RNA-stimulated ATPase activity. Mitochondrion 2023; 69:130-139. [PMID: 36764503 DOI: 10.1016/j.mito.2023.02.004] [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: 08/22/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
Irc3 is one of the six mitochondrial helicases described in Saccharomyces cerevisiae. Physiological functions of Irc3 are not completely understood as both DNA metabolic processes and mRNA translation have been suggested to be direct targets of the helicase. In vitro analysis of Irc3 has been hampered by the modest thermostability of the S. cerevisiae protein. Here, we purified a homologous helicase (Irc3op) of the thermotolerant yeast Ogataea polymorpha that retains structural integrity and catalytic activity at temperatures above 40 °C. Irc3op can complement the respiratory deficiency phenotype of a S. cerevisiae irc3Δ mutant, indicating conservation of biochemical functions. The ATPase activity of Irc3op is best stimulated by branched and double- stranded DNA cofactors. Single-stranded DNA binds Irc3op tightly but is a weak activator of the ATPase activity. We could also detect a lower level stimulation with RNA, especially with molecules possessing a compact three-dimensional structure. These results support the idea that that Irc3 might have dual specificity and remodel both DNA and RNA molecules in vivo. Furthermore, our analysis of kinetic parameters predicts that Irc3 could have a regulatory function via sensing changes of the mitochondrial ATP pool or respond to the accumulation of single-stranded DNA.
Collapse
Affiliation(s)
- Vlad-Julian Piljukov
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, 51010 Tartu, Estonia
| | - Sirelin Sillamaa
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, 51010 Tartu, Estonia
| | - Tiina Sedman
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, 51010 Tartu, Estonia
| | - Natalja Garber
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, 51010 Tartu, Estonia
| | - Margus Rätsep
- Laboratory of Biophysics, Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
| | - Arvi Freiberg
- Laboratory of Biophysics, Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
| | - Juhan Sedman
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, 51010 Tartu, Estonia.
| |
Collapse
|
36
|
Gao S, Han B, Xu B, Wang N, Zhang Y, Liu X, Zhang M, Wang G, Guan X, Huang J, Liu M, Shi W. SAV Nsp2 regulates NF-κB signaling to induce inflammatory responses by targeting host DDX3. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 140:104612. [PMID: 36473548 DOI: 10.1016/j.dci.2022.104612] [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: 10/11/2022] [Revised: 12/02/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Salmon alphavirus (SAV) infection leads to severe pancreas disease (PD) with typical inflammatory responses in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Nsp2, an important nonstructural protein of SAV, can activate NF-κB signaling pathway to reduce inflammatory responses. However, the molecular mechanism remains unclear. In this study, the ML (279-421aa) of Nsp2 was revealed to be the key domain for activating NF-κB. We focused on a host protein, DEAD-box RNA helicase 3 (DDX3), that may interact with Nsp2 to regulate NF-κB-induced inflammatory. The interaction between DDX3 and Nsp2 was confirmed in vitro. Overexpression of DDX3 inhibited the activation of NF-κB by Nsp2. SAV Nsp2 relieves the inhibitory effect of DDX3 on NF-κB, thereby initiating the innate immune response. This study revealed the molecular mechanism of Nsp2-induced inflammatory response by targeting DDX3 to activate NF-κB, providing a theoretical basis for revealing the underlying infection mechanism and pathogenesis of SAV.
Collapse
Affiliation(s)
- Shuai Gao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Bing Han
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Baoxing Xu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Na Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yanru Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Xuefei Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Mengmeng Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Guanbo Wang
- Wellcome-Wolfson Institute for Exprerimental Medicine Queen's University Belfast, 97 Lisburn Rd, Belfast, BT9 7BL, UK
| | - Xueting Guan
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Jinshan Huang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China
| | - Min Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China.
| | - Wen Shi
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, PR China.
| |
Collapse
|
37
|
Yao J, Cai Y, Chen Z, Wang X, Lai X, Pan L, Li Y, Wang S. Dhx15 regulates zebrafish intestinal development through the Wnt signaling pathway. Genomics 2023; 115:110578. [PMID: 36775210 DOI: 10.1016/j.ygeno.2023.110578] [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: 08/08/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
DEAH-box helicase 15 (DHX15) is ATP-dependent RNA helicase which is known for its role in RNA metabolism. Recent studies reported DHX15 involves in the intestinal immunity. However, the role of DHX15 (or RNA helicase) in intestinal development is poorly understood. Here, we revealed an unidentified role for dhx15 in regulating zebrafish intestinal development. We found the profound intestinal defects in dhx15 knockout zebrafish. Decreased proliferation and increased apoptosis of the intestine cells were observed when dhx15 were deleted. Further RNA genome wide analysis and qRT-PCR analysis showed the Wnt signaling pathway is down-regulated in the dhx15 knockout zebrafish. Thus, we concluded that dhx15 regulates zebrafish intestinal development through the Wnt signaling pathway. Here, we provided new insights into the role of dhx15 in intestinal development beyond its well-characterized role in intestinal immunity.
Collapse
Affiliation(s)
- Jinpeng Yao
- Union Clinical Medical Colleges, Fujian Medical University, Fuzhou, China
| | - Yuanhua Cai
- Union Clinical Medical Colleges, Fujian Medical University, Fuzhou, China; Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zhixiang Chen
- Union Clinical Medical Colleges, Fujian Medical University, Fuzhou, China
| | - Xuechun Wang
- Union Clinical Medical Colleges, Fujian Medical University, Fuzhou, China
| | - Xiaolin Lai
- Union Clinical Medical Colleges, Fujian Medical University, Fuzhou, China; Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Lili Pan
- Union Clinical Medical Colleges, Fujian Medical University, Fuzhou, China; Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yang Li
- Union Clinical Medical Colleges, Fujian Medical University, Fuzhou, China; Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shaoyuan Wang
- Union Clinical Medical Colleges, Fujian Medical University, Fuzhou, China; Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, China.
| |
Collapse
|
38
|
Naineni SK, Robert F, Nagar B, Pelletier J. Targeting DEAD-box RNA helicases: The emergence of molecular staples. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1738. [PMID: 35581936 DOI: 10.1002/wrna.1738] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 12/29/2022]
Abstract
RNA helicases constitute a large family of proteins that play critical roles in mediating RNA function. They have been implicated in all facets of gene expression pathways involving RNA, from transcription to processing, transport and translation, and storage and decay. There is significant interest in developing small molecule inhibitors to RNA helicases as some family members have been documented to be dysregulated in neurological and neurodevelopment disorders, as well as in cancers. Although different functional properties of RNA helicases offer multiple opportunities for small molecule development, molecular staples have recently come to the forefront. These bifunctional molecules interact with both protein and RNA components to lock them together, thereby imparting novel gain-of-function properties to their targets. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Sai Kiran Naineni
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Francis Robert
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Bhushan Nagar
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
39
|
The Terminal Extensions of Dbp7 Influence Growth and 60S Ribosomal Subunit Biogenesis in Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24043460. [PMID: 36834876 PMCID: PMC9960301 DOI: 10.3390/ijms24043460] [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: 01/19/2023] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Ribosome synthesis is a complex process that involves a large set of protein trans-acting factors, among them DEx(D/H)-box helicases. These are enzymes that carry out remodelling activities onto RNAs by hydrolysing ATP. The nucleolar DEGD-box protein Dbp7 is required for the biogenesis of large 60S ribosomal subunits. Recently, we have shown that Dbp7 is an RNA helicase that regulates the dynamic base-pairing between the snR190 small nucleolar RNA and the precursors of the ribosomal RNA within early pre-60S ribosomal particles. As the rest of DEx(D/H)-box proteins, Dbp7 has a modular organization formed by a helicase core region, which contains conserved motifs, and variable, non-conserved N- and C-terminal extensions. The role of these extensions remains unknown. Herein, we show that the N-terminal domain of Dbp7 is necessary for efficient nuclear import of the protein. Indeed, a basic bipartite nuclear localization signal (NLS) could be identified in its N-terminal domain. Removal of this putative NLS impairs, but does not abolish, Dbp7 nuclear import. Both N- and C-terminal domains are required for normal growth and 60S ribosomal subunit synthesis. Furthermore, we have studied the role of these domains in the association of Dbp7 with pre-ribosomal particles. Altogether, our results show that the N- and C-terminal domains of Dbp7 are important for the optimal function of this protein during ribosome biogenesis.
Collapse
|
40
|
Calvo PA, Mateo-Cáceres V, Díaz-Arco S, Redrejo-Rodríguez M, de Vega M. The enterohemorrhagic Escherichia coli insertion sequence-excision enhancer protein is a DNA polymerase with microhomology-mediated end-joining activity. Nucleic Acids Res 2023; 51:1189-1207. [PMID: 36715333 PMCID: PMC9943667 DOI: 10.1093/nar/gkad017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/31/2023] Open
Abstract
Bacterial genomes contain an abundance of transposable insertion sequence (IS) elements that are essential for genome evolution and fitness. Among them, IS629 is present in most strains of enterohemorrhagic Escherichia coli O157 and accounts for many polymorphisms associated with gene inactivation and/or genomic deletions. The excision of IS629 from the genome is promoted by IS-excision enhancer (IEE) protein. Despite IEE has been identified in the most pathogenic serotypes of E. coli, its biochemical features that could explain its role in IS excision are not yet understood. We show that IEE is present in >30% of all available E. coli genome assemblies, and is highly conserved and very abundant within enterohemorrhagic, enteropathogenic and enterotoxigenic genomes. In vitro analysis of the recombinant protein from E. coli O157:H7 revealed the presence of a Mn2+-dependent error-prone DNA polymerase activity in its N-terminal archaeo-eukaryotic primase (AEP) domain able to promote dislocations of the primer and template strands. Importantly, IEE could efficiently perform in vitro an end-joining reaction of 3'-single-strand DNA overhangs with ≥4 bp of homology requiring both the N-terminal AEP and C-terminal helicase domains. The proposed role for IEE in the novel IS excision mechanism is discussed.
Collapse
Affiliation(s)
- Patricia A Calvo
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Nicolás Cabrera 1, Madrid 28049, Spain
| | - Víctor Mateo-Cáceres
- Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas Alberto Sols (Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Silvia Díaz-Arco
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Nicolás Cabrera 1, Madrid 28049, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas Alberto Sols (Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Miguel de Vega
- To whom correspondence should be addressed. Tel: +34 911964717; Fax: +34 911964420;
| |
Collapse
|
41
|
Arna AB, Patel H, Singh RS, Vizeacoumar FS, Kusalik A, Freywald A, Vizeacoumar FJ, Wu Y. Synthetic lethal interactions of DEAD/H-box helicases as targets for cancer therapy. Front Oncol 2023; 12:1087989. [PMID: 36761420 PMCID: PMC9905851 DOI: 10.3389/fonc.2022.1087989] [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: 11/02/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023] Open
Abstract
DEAD/H-box helicases are implicated in virtually every aspect of RNA metabolism, including transcription, pre-mRNA splicing, ribosomes biogenesis, nuclear export, translation initiation, RNA degradation, and mRNA editing. Most of these helicases are upregulated in various cancers and mutations in some of them are associated with several malignancies. Lately, synthetic lethality (SL) and synthetic dosage lethality (SDL) approaches, where genetic interactions of cancer-related genes are exploited as therapeutic targets, are emerging as a leading area of cancer research. Several DEAD/H-box helicases, including DDX3, DDX9 (Dbp9), DDX10 (Dbp4), DDX11 (ChlR1), and DDX41 (Sacy-1), have been subjected to SL analyses in humans and different model organisms. It remains to be explored whether SDL can be utilized to identity druggable targets in DEAD/H-box helicase overexpressing cancers. In this review, we analyze gene expression data of a subset of DEAD/H-box helicases in multiple cancer types and discuss how their SL/SDL interactions can be used for therapeutic purposes. We also summarize the latest developments in clinical applications, apart from discussing some of the challenges in drug discovery in the context of targeting DEAD/H-box helicases.
Collapse
Affiliation(s)
- Ananna Bhadra Arna
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hardikkumar Patel
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Franco J. Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan and Saskatchewan Cancer Agency, Saskatoon, SK, Canada,*Correspondence: Yuliang Wu, ; Franco J. Vizeacoumar,
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada,*Correspondence: Yuliang Wu, ; Franco J. Vizeacoumar,
| |
Collapse
|
42
|
Gan H, Li L, Hu X, Cai J, Hu X, Zhang H, Zhao N, Xu X, Guo H, Pang P. DDX24 regulates the chemosensitivity of hepatocellular carcinoma to sorafenib via mediating the expression of SNORA18. Cancer Biol Ther 2022; 23:1-14. [PMID: 36310384 PMCID: PMC9629112 DOI: 10.1080/15384047.2022.2135960] [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] [Indexed: 01/31/2023] Open
Abstract
Sorafenib (SFN) is a multi-kinase inhibitor drug for the treatment of advanced hepatocellular carcinoma (HCC), but its limited efficacy is a major obstacle to the clinical outcomes of patients with HCC. We aimed to explore a novel molecular mechanism underlying the chemosensitivity of HCC to SFN, and to identify a promising therapeutic target for HCC treatment. In this study, bioinformatic analysis revealed that DDX24 was associated with poor survival in HCC cases, and significantly related to the pathways modulating tumor development. DDX24 regulated HCC cell proliferation and migration potentials. Moreover, reduction of DDX24 promoted the sorafenib-mediated inhibition of HCC cell growth and migration, the elevation of sorafenib-induced HCC cell apoptosis. DDX24 overexpression suppressed the inhibitory effect of SFN on cell proliferation and migration and reduced the apoptosis induced by SFN. Further, DDX24, combined with SFN treatment, presented a synergistic enhancement of the sensitivity of SFN to the growth and migration of HCC cells via AKT/ERK and the epithelial-mesenchymal transition (EMT) pathways, and that it modulated apoptosis via the caspase/PARP pathway. Mechanistically, SNORA18 served as a target gene for DDX24, regulating the chemosensitivity of sorafenib-treated HCC cells. Furthermore, SNORA18 knockdown or overexpression could partially reverse the inhibition or elevation of cell viability, colony formation and migration induced by DDX24 in sorafenib-treated HCC cells, respectively. Collectively, our results suggest that DDX24 regulates the chemosensitivity of HCC to SFN by mediating the expression of SNORA18, which may act as an effective therapeutic target for improving SFN efficiency in HCC treatment.
Collapse
Affiliation(s)
- Hairun Gan
- Center for Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,CONTACT Hairun Gan Center for Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, 519000, China
| | - Luting Li
- Center for Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Xinyan Hu
- Center for Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Jianxun Cai
- Center for Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Xiaojun Hu
- Center for Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Haopei Zhang
- Center for Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Ni Zhao
- Center for Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Xiwei Xu
- The Cancer Center of the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Hui Guo
- Center for Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Pengfei Pang
- Center for Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China,Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| |
Collapse
|
43
|
Cruz VE, Sekulski K, Peddada N, Sailer C, Balasubramanian S, Weirich CS, Stengel F, Erzberger JP. Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. Nat Struct Mol Biol 2022; 29:1228-1238. [PMID: 36482249 PMCID: PMC10680166 DOI: 10.1038/s41594-022-00874-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/14/2022] [Indexed: 12/13/2022]
Abstract
DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly.
Collapse
Affiliation(s)
- Victor Emmanuel Cruz
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, Dallas, TX, USA
| | - Kamil Sekulski
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, Dallas, TX, USA
| | - Nagesh Peddada
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, Dallas, TX, USA
| | - Carolin Sailer
- Department of Biology, University of Konstanz, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
- Department of Biomedical Sciences, University of Copenhagen, København, Denmark
| | - Sahana Balasubramanian
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, Dallas, TX, USA
- Cell Biology & Molecular Physiology Department, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christine S Weirich
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, Dallas, TX, USA
| | - Florian Stengel
- Department of Biology, University of Konstanz, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Jan P Erzberger
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, Dallas, TX, USA.
| |
Collapse
|
44
|
Hussain A, Ray MK. DEAD box RNA helicases protect Antarctic Pseudomonas syringae Lz4W against oxidative stress. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 106:105382. [PMID: 36336276 DOI: 10.1016/j.meegid.2022.105382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
Abstract
DEAD box RNA helicases are involved in important cellular processes like RNA metabolism (Processing and Degradation), ribosome biogenesis and translation. Besides being crucial to the formation of cold adapted degradosomes, RNA helicases have been implicated in structural rearrangement of RNA, implying a role in alleviation of RNA secondary structure stabilization at low temperature. This study depicts the results of experiments on protective role played by DEAD box RNA helicases against nucleic acid damaging agents. RNA helicase mutants ΔrhlE, ΔsrmB, ΔcsdA, ΔdbpA and ΔrhlB cells were exposed to various DNA damaging agents (UV, Paraquat, Mitomycin C, Hydroxyurea and Hydrogen peroxide) and assessed for sensitivity to them. Our results illustrate that ∆csdA displayed sensitivity to paraquat (that causes oxidative damage) and UV radiation induced DNA damage. On the other hand, ∆srmB displays sensitivity to hydroxyurea that causes damage to the replication forks (RFs) by inhibiting ribonucleotide reductase and depleting the dNTP pool of cells. However, all five RNA helicase mutants were resistant to H2O2 mediated oxidative stress and mitomycin C induced DNA cross-links.
Collapse
Affiliation(s)
- Ashaq Hussain
- Centre for Cellular and Molecular Biology, Hyderabad, India.
| | - Malay Kumar Ray
- Centre for Cellular and Molecular Biology, Hyderabad, India.
| |
Collapse
|
45
|
Dhamodharan A, Okada H, Muraoka M, Wright D, Okubo A, Saga Y. P-body dynamics revealed by DDX6 protein knockdown via the auxin-inducible degron system. Dev Growth Differ 2022; 64:537-547. [PMID: 36353942 DOI: 10.1111/dgd.12821] [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: 06/14/2022] [Revised: 10/02/2022] [Accepted: 10/21/2022] [Indexed: 11/12/2022]
Abstract
The transcriptome dynamically changes via several transcriptional and post-transcriptional mechanisms. RNA-binding proteins contribute to such mechanisms to regulate the cellular status. DDX6 is one such protein and a core component of processing bodies (P-bodies), membrane-less cytosolic substructures where RNA and proteins localize and are functionally regulated. Despite the importance of DDX6, owing to the lack of tightly controlled methods for protein knockdown, it was difficult to assess in high time resolution how its depletion exactly affects the P-body assembly structure. Therefore, we adopted an advanced protein degradation method, the auxin-induced degron (AID) system, to degrade DDX6 acutely in ES cells. By introducing AID-tagged DDX6 and the E3 ligase subunit of OsTIR1 into ES cells, we successfully degraded DDX6 following auxin analog (indole-3-acetic acid, IAA) treatment. The degradation rate of DDX6 was slower than that of the cytosolic reporter protein EGFP but was enhanced by increasing the OsTIR1 dosage. Lastly, we confirmed that a substantial portion of P-bodies disappears around the time of 1 hr after IAA addition consistent with DDX6 depletion detected by western blot. In accordance with this, we detected transcriptome changes by 6 hr after IAA treatment. Therefore, we demonstrated the applicability of the AID method to gain insight into the function of P-bodies and their protein components.
Collapse
Affiliation(s)
- Adithya Dhamodharan
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Hajime Okada
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Masafumi Muraoka
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Danelle Wright
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Akemi Okubo
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Yumiko Saga
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
46
|
Sadic M, Schneider WM, Katsara O, Medina GN, Fisher A, Mogulothu A, Yu Y, Gu M, de los Santos T, Schneider RJ, Dittmann M. DDX60 selectively reduces translation off viral type II internal ribosome entry sites. EMBO Rep 2022; 23:e55218. [PMID: 36256515 PMCID: PMC9724679 DOI: 10.15252/embr.202255218] [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: 04/11/2022] [Revised: 09/07/2022] [Accepted: 09/15/2022] [Indexed: 11/05/2022] Open
Abstract
Co-opting host cell protein synthesis is a hallmark of many virus infections. In response, certain host defense proteins limit mRNA translation globally, albeit at the cost of the host cell's own protein synthesis. Here, we describe an interferon-stimulated helicase, DDX60, that decreases translation from viral internal ribosome entry sites (IRESs). DDX60 acts selectively on type II IRESs of encephalomyocarditis virus (EMCV) and foot and mouth disease virus (FMDV), but not by other IRES types or by 5' cap. Correspondingly, DDX60 reduces EMCV and FMDV (type II IRES) replication, but not that of poliovirus or bovine enterovirus 1 (BEV-1; type I IRES). Furthermore, replacing the IRES of poliovirus with a type II IRES is sufficient for DDX60 to inhibit viral replication. Finally, DDX60 selectively modulates the amount of translating ribosomes on viral and in vitro transcribed type II IRES mRNAs, but not 5' capped mRNA. Our study identifies a novel facet in the repertoire of interferon-stimulated effector genes, the selective downregulation of translation from viral type II IRES elements.
Collapse
Affiliation(s)
| | | | | | - Gisselle N Medina
- Plum Island Animal Disease Center, ARSUSDAGreenportNYUSA,National Bio and Agro‐Defense Facility (NBAF), ARSUSDAManhattanKSUSA
| | | | - Aishwarya Mogulothu
- Plum Island Animal Disease Center, ARSUSDAGreenportNYUSA,Department of Pathobiology and Veterinary ScienceUniversity of ConnecticutStorrsCTUSA
| | - Yingpu Yu
- The Rockefeller UniversityNew YorkNYUSA
| | | | | | | | | |
Collapse
|
47
|
Kim J, Muraoka M, Okada H, Toyoda A, Ajima R, Saga Y. The RNA helicase DDX6 controls early mouse embryogenesis by repressing aberrant inhibition of BMP signaling through miRNA-mediated gene silencing. PLoS Genet 2022; 18:e1009967. [PMID: 36197846 PMCID: PMC9534413 DOI: 10.1371/journal.pgen.1009967] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
The evolutionarily conserved RNA helicase DDX6 is a central player in post-transcriptional regulation, but its role during embryogenesis remains elusive. We here show that DDX6 enables proper cell lineage specification from pluripotent cells by analyzing Ddx6 knockout (KO) mouse embryos and employing an in vitro epiblast-like cell (EpiLC) induction system. Our study unveils that DDX6 is an important BMP signaling regulator. Deletion of Ddx6 causes the aberrant upregulation of the negative regulators of BMP signaling, which is accompanied by enhanced expression of Nodal and related genes. Ddx6 KO pluripotent cells acquire higher pluripotency with a strong inclination toward neural lineage commitment. During gastrulation, abnormally expanded Nodal and Eomes expression in the primitive streak likely promotes endoderm cell fate specification while inhibiting mesoderm differentiation. We also genetically dissected major DDX6 pathways by generating Dgcr8, Dcp2, and Eif4enif1 KO models in addition to Ddx6 KO. We found that the miRNA pathway mutant Dgcr8 KO phenocopies Ddx6 KO, indicating that DDX6 mostly works along with the miRNA pathway during early development, whereas its P-body-related functions are dispensable. Therefore, we conclude that DDX6 prevents aberrant upregulation of BMP signaling inhibitors by participating in miRNA-mediated gene silencing processes. Overall, this study delineates how DDX6 affects the development of the three primary germ layers during early mouse embryogenesis and the underlying mechanism of DDX6 function.
Collapse
Affiliation(s)
- Jessica Kim
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masafumi Muraoka
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Hajime Okada
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Rieko Ajima
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
- * E-mail: (RA); (YS)
| | - Yumiko Saga
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
- * E-mail: (RA); (YS)
| |
Collapse
|
48
|
Bohnsack KE, Kanwal N, Bohnsack MT. Prp43/DHX15 exemplify RNA helicase multifunctionality in the gene expression network. Nucleic Acids Res 2022; 50:9012-9022. [PMID: 35993807 PMCID: PMC9458436 DOI: 10.1093/nar/gkac687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Dynamic regulation of RNA folding and structure is critical for the biogenesis and function of RNAs and ribonucleoprotein (RNP) complexes. Through their nucleotide triphosphate-dependent remodelling functions, RNA helicases are key modulators of RNA/RNP structure. While some RNA helicases are dedicated to a specific target RNA, others are multifunctional and engage numerous substrate RNAs in different aspects of RNA metabolism. The discovery of such multitasking RNA helicases raises the intriguing question of how these enzymes can act on diverse RNAs but also maintain specificity for their particular targets within the RNA-dense cellular environment. Furthermore, the identification of RNA helicases that sit at the nexus between different aspects of RNA metabolism raises the possibility that they mediate cross-regulation of different cellular processes. Prominent and extensively characterized multifunctional DEAH/RHA-box RNA helicases are DHX15 and its Saccharomyces cerevisiae (yeast) homologue Prp43. Due to their central roles in key cellular processes, these enzymes have also served as prototypes for mechanistic studies elucidating the mode of action of this type of enzyme. Here, we summarize the current knowledge on the structure, regulation and cellular functions of Prp43/DHX15, and discuss the general concept and implications of RNA helicase multifunctionality.
Collapse
Affiliation(s)
- Katherine E Bohnsack
- Correspondence may also be addressed to Katherine E. Bohnsack. Tel: +49 551 3969305; Fax: +49 551 395960;
| | - Nidhi Kanwal
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- To whom correspondence should be addressed. Tel: +49 551 395968; Fax: +49 551 395960;
| |
Collapse
|
49
|
Bonczek O, Wang L, Gnanasundram SV, Chen S, Haronikova L, Zavadil-Kokas F, Vojtesek B. DNA and RNA Binding Proteins: From Motifs to Roles in Cancer. Int J Mol Sci 2022; 23:ijms23169329. [PMID: 36012592 PMCID: PMC9408909 DOI: 10.3390/ijms23169329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
DNA and RNA binding proteins (DRBPs) are a broad class of molecules that regulate numerous cellular processes across all living organisms, creating intricate dynamic multilevel networks to control nucleotide metabolism and gene expression. These interactions are highly regulated, and dysregulation contributes to the development of a variety of diseases, including cancer. An increasing number of proteins with DNA and/or RNA binding activities have been identified in recent years, and it is important to understand how their activities are related to the molecular mechanisms of cancer. In addition, many of these proteins have overlapping functions, and it is therefore essential to analyze not only the loss of function of individual factors, but also to group abnormalities into specific types of activities in regard to particular cancer types. In this review, we summarize the classes of DNA-binding, RNA-binding, and DRBPs, drawing particular attention to the similarities and differences between these protein classes. We also perform a cross-search analysis of relevant protein databases, together with our own pipeline, to identify DRBPs involved in cancer. We discuss the most common DRBPs and how they are related to specific cancers, reviewing their biochemical, molecular biological, and cellular properties to highlight their functions and potential as targets for treatment.
Collapse
Affiliation(s)
- Ondrej Bonczek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
- Correspondence: (O.B.); (B.V.)
| | - Lixiao Wang
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | - Lucia Haronikova
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Filip Zavadil-Kokas
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Borivoj Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Correspondence: (O.B.); (B.V.)
| |
Collapse
|
50
|
Jia R, Lin J, You J, Li S, Shan G, Huang C. The DEAD-box helicase Hlc regulates basal transcription and chromatin opening of stress-responsive genes. Nucleic Acids Res 2022; 50:9175-9189. [PMID: 35950495 PMCID: PMC9458421 DOI: 10.1093/nar/gkac684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/17/2022] [Accepted: 07/28/2022] [Indexed: 12/24/2022] Open
Abstract
Stress-responsive genes are lowly transcribed under normal conditions and robustly induced in response to stress. The significant difference between basal and induced transcription indicates that the general transcriptional machinery requires a mechanism to distinguish each transcription state. However, what factors specifically function in basal transcription remains poorly understood. Using a classic model stress-responsive gene (Drosophila MtnA), we found that knockdown of the DEAD-box helicase Hlc resulted in a significant transcription attenuation of MtnA under normal, but not stressed, conditions. Mechanistically, Hlc directly binds to the MtnA locus to maintain the accessibility of chromatin near the transcriptional start site, which allows the recruitment of RNA polymerase II and subsequent MtnA transcription. Using RNA-seq, we then identified plenty of additional stress-responsive genes whose basal transcription was reduced upon knockdown of Hlc. Taken together, these data suggest that Hlc-mediated basal transcription regulation is an essential and widespread mechanism for precise control of stress-responsive genes.
Collapse
Affiliation(s)
| | | | | | - Shi Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- To whom correspondence should be addressed. Tel: +86 19956025374;
| |
Collapse
|