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Sun Z, Xia W, Lyu Y, Song Y, Wang M, Zhang R, Sui G, Li Z, Song L, Wu C, Liew CC, Yu L, Cheng G, Cheng C. Immune-related gene expression signatures in colorectal cancer. Oncol Lett 2021; 22:543. [PMID: 34079596 PMCID: PMC8157333 DOI: 10.3892/ol.2021.12804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/11/2021] [Indexed: 12/24/2022] Open
Abstract
The immune system is crucial in regulating colorectal cancer (CRC) tumorigenesis. Identification of immune-related transcriptomic signatures derived from the peripheral blood of patients with CRC would provide insights into CRC pathogenesis, and suggest novel clues to potential immunotherapy strategies for the disease. The present study collected blood samples from 59 patients with CRC and 62 healthy control patients and performed whole blood gene expression profiling using microarray hybridization. Immune-related gene expression signatures for CRC were identified from immune gene datasets, and an algorithmic predictive model was constructed for distinguishing CRC from controls. Model performance was characterized using an area under the receiver operating characteristic curve (ROC AUC). Functional categories for CRC-specific gene expression signatures were determined using gene set enrichment analyses. A Kaplan-Meier plotter survival analysis was also performed for CRC-specific immune genes in order to characterize the association between gene expression and CRC prognosis. The present study identified five CRC-specific immune genes [protein phosphatase 3 regulatory subunit Bα (PPP3R1), amyloid β precursor protein, cathepsin H, proteasome activator subunit 4 and DEAD-Box Helicase 3 X-Linked]. A predictive model based on this five-gene panel showed good discriminatory power (independent test set sensitivity, 83.3%; specificity, 94.7%, accuracy, 89.2%; ROC AUC, 0.96). The candidate genes were involved in pathways associated with ‘adaptive immune responses’, ‘innate immune responses’ and ‘cytokine signaling’. The survival analysis found that a high level of PPP3R1 expression was associated with a poor CRC prognosis. The present study identified five CRC-specific immune genes that were potential diagnostic biomarkers for CRC. The biological function analysis indicated a close association between CRC pathogenesis and the immune system, and may reveal more information about the immunogenic and pathogenic mechanisms driving CRC in the future. Overall, the association between PPP3R1 expression and survival of patients with CRC revealed potential new targets for CRC immunotherapy.
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Affiliation(s)
- Zhenqing Sun
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Wei Xia
- Department of Nuclear Medicine, The Seventh People's Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Yali Lyu
- R&D Department, Huaxia Bangfu Technology Incorporated, Beijing 100000, P.R. China
| | - Yanan Song
- Department of Nuclear Medicine, The Seventh People's Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Min Wang
- R&D Department, Huaxia Bangfu Technology Incorporated, Beijing 100000, P.R. China
| | - Ruirui Zhang
- R&D Department, Huaxia Bangfu Technology Incorporated, Beijing 100000, P.R. China
| | - Guode Sui
- Department of General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Zhenlu Li
- Department of General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Li Song
- Department of General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Changliang Wu
- Department of General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Choong-Chin Liew
- Golden Health Diagnostics Inc., Yan Cheng, Jiangsu 224000, P.R. China.,Department of Clinical Pathology and Laboratory Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lei Yu
- R&D Department, Huaxia Bangfu Technology Incorporated, Beijing 100000, P.R. China
| | - Guang Cheng
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Changming Cheng
- R&D Department, Huaxia Bangfu Technology Incorporated, Beijing 100000, P.R. China
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Tang L, Levy T, Guillory S, Halpern D, Zweifach J, Giserman-Kiss I, Foss-Feig JH, Frank Y, Lozano R, Belani P, Layton C, Lerman B, Frowner E, Breen MS, De Rubeis S, Kostic A, Kolevzon A, Buxbaum JD, Siper PM, Grice DE. Prospective and detailed behavioral phenotyping in DDX3X syndrome. Mol Autism 2021; 12:36. [PMID: 33993884 PMCID: PMC8127248 DOI: 10.1186/s13229-021-00431-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/01/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND DDX3X syndrome is a recently identified genetic disorder that accounts for 1-3% of cases of unexplained developmental delay and/or intellectual disability (ID) in females, and is associated with motor and language delays, and autism spectrum disorder (ASD). To date, the published phenotypic characterization of this syndrome has primarily relied on medical record review; in addition, the behavioral dimensions of the syndrome have not been fully explored. METHODS We carried out multi-day, prospective, detailed phenotyping of DDX3X syndrome in 14 females and 1 male, focusing on behavioral, psychological, and neurological measures. Three participants in this cohort were previously reported with limited phenotype information and were re-evaluated for this study. We compared results against population norms and contrasted phenotypes between individuals harboring either (1) protein-truncating variants or (2) missense variants or in-frame deletions. RESULTS Eighty percent (80%) of individuals met criteria for ID, 60% for ASD and 53% for attention-deficit/hyperactivity disorder (ADHD). Motor and language delays were common as were sensory processing abnormalities. The cohort included 5 missense, 3 intronic/splice-site, 2 nonsense, 2 frameshift, 2 in-frame deletions, and one initiation codon variant. Genotype-phenotype correlations indicated that, on average, missense variants/in-frame deletions were associated with more severe language, motor, and adaptive deficits in comparison to protein-truncating variants. LIMITATIONS Sample size is modest, however, DDX3X syndrome is a rare and underdiagnosed disorder. CONCLUSION This study, representing a first, prospective, detailed characterization of DDX3X syndrome, extends our understanding of the neurobehavioral phenotype. Gold-standard diagnostic approaches demonstrated high rates of ID, ASD, and ADHD. In addition, sensory deficits were observed to be a key part of the syndrome. Even with a modest sample, we observe evidence for genotype-phenotype correlations with missense variants/in-frame deletions generally associated with more severe phenotypes.
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Affiliation(s)
- Lara Tang
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Tess Levy
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Sylvia Guillory
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Danielle Halpern
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Jessica Zweifach
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Ivy Giserman-Kiss
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Jennifer H. Foss-Feig
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Yitzchak Frank
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Reymundo Lozano
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Puneet Belani
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Christina Layton
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Bonnie Lerman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Emanuel Frowner
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Michael S. Breen
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ana Kostic
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Alexander Kolevzon
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Paige M. Siper
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Dorothy E. Grice
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1230, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Division of Tics, OCD, and Related Disorders, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
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Deogharkar A, Singh SV, Bharambe HS, Paul R, Moiyadi A, Goel A, Shetty P, Sridhar E, Gupta T, Jalali R, Goel N, Gadewal N, Muthukumar S, Shirsat NV. Downregulation of ARID1B, a tumor-suppressor in the WNT subgroup medulloblastoma, activates multiple oncogenic signaling pathways. Hum Mol Genet 2021; 30:1721-1733. [PMID: 33949667 DOI: 10.1093/hmg/ddab134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 12/22/2022] Open
Abstract
Medulloblastoma, a common pediatric malignant brain tumor, consists of four distinct molecular subgroups WNT, SHH, Group 3, and Group 4. Exome sequencing of 11 WNT subgroup medulloblastomas from an Indian cohort identified mutations in several chromatin modifier genes, including genes of the mammalian SWI/SNF complex. The genome of WNT subgroup tumors is known to be stable except for monosomy 6. Two tumors, having monosomy 6, carried a loss of function mutation in the ARID1B gene located on chromosome 6. ARID1B expression is also lower in the WNT subgroup tumors compared to other subgroups and normal cerebellar tissues that could result in haploinsufficiency. The shRNA-mediated knockdown of ARID1B expression resulted in a significant increase in the malignant potential of medulloblastoma cells. Transcriptome sequencing identified upregulation of several genes encoding cell adhesion proteins, matrix metalloproteases indicating the epithelial-mesenchymal transition. The ARID1B knockdown also upregulated ERK1/ERK2 and PI3K/AKT signaling with a decrease in the expression of several negative regulators of these pathways. The expression of negative regulators of the WNT signaling like TLE1, MDFI, GPX3, ALX4, DLC1, MEST decreased upon ARID1B knockdown resulting in the activation of the canonical WNT signaling pathway. Synthetic lethality has been reported between SWI-SNF complex mutations and EZH2 inhibition, suggesting EZH2 inhibition as a possible therapeutic modality for WNT subgroup medulloblastomas. Thus, the identification of ARID1B as a tumor suppressor and its downregulation resulting in the activation of multiple signaling pathways opens up opportunities for novel therapeutic modalities for the treatment of WNT subgroup medulloblastoma.
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Affiliation(s)
- Akash Deogharkar
- Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210
| | - Satishkumar Vishram Singh
- Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210
| | - Harish Shrikrishna Bharambe
- Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210
| | - Raikamal Paul
- Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210
| | | | | | | | | | - Tejpal Gupta
- Department of Radiation Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai 400012
| | - Rakesh Jalali
- Department of Radiation Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai 400012
| | - Naina Goel
- Department of Pathology, Seth G. S. Medical College, Parel, Mumbai 400012
| | - Nikhil Gadewal
- Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210
| | - Sahana Muthukumar
- Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210
| | - Neelam Vishwanath Shirsat
- Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210
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dos Santos Vasconcelos CR, Rezende AM. Systematic in silico Evaluation of Leishmania spp. Proteomes for Drug Discovery. Front Chem 2021; 9:607139. [PMID: 33987166 PMCID: PMC8111926 DOI: 10.3389/fchem.2021.607139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/24/2021] [Indexed: 11/18/2022] Open
Abstract
Leishmaniasis is a group of neglected infectious diseases, with approximately 1. 3 million new cases each year, for which the available therapies have serious limitations. Therefore, it is extremely important to apply efficient and low-cost methods capable of selecting the best therapeutic targets to speed up the development of new therapies against those diseases. Thus, we propose the use of integrated computational methods capable of evaluating the druggability of the predicted proteomes of Leishmania braziliensis and Leishmania infantum, species responsible for the different clinical manifestations of leishmaniasis in Brazil. The protein members of those proteomes were assessed based on their structural, chemical, and functional contexts applying methods that integrate data on molecular function, biological processes, subcellular localization, drug binding sites, druggability, and gene expression. These data were compared to those extracted from already known drug targets (BindingDB targets), which made it possible to evaluate Leishmania proteomes for their biological relevance and treatability. Through this methodology, we identified more than 100 proteins of each Leishmania species with druggability characteristics, and potential interaction with available drugs. Among those, 31 and 37 proteins of L. braziliensis and L. infantum, respectively, have never been tested as drug targets, and they have shown evidence of gene expression in the evolutionary stage of pharmacological interest. Also, some of those Leishmania targets showed an alignment similarity of <50% when compared to the human proteome, making these proteins pharmacologically attractive, as they present a reduced risk of side effects. The methodology used in this study also allowed the evaluation of opportunities for the repurposing of compounds as anti-leishmaniasis drugs, inferring potential interaction between Leishmania proteins and ~1,000 compounds, of which only 15 have already been tested as a treatment for leishmaniasis. Besides, a list of potential Leishmania targets to be tested using drugs described at BindingDB, such as the potential interaction of the DEAD box RNA helicase, TRYR, and PEPCK proteins with the Staurosporine compound, was made available to the public.
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Affiliation(s)
- Crhisllane Rafaele dos Santos Vasconcelos
- Bioinformatics Plataform, Microbiology Department, Instituto Aggeu Magalhães, Recife, Brazil
- Posgraduate Program in Genetics, Genetics Department, Universidade Federal de Pernambuco, Recife, Brazil
| | - Antonio Mauro Rezende
- Bioinformatics Plataform, Microbiology Department, Instituto Aggeu Magalhães, Recife, Brazil
- Posgraduate Program in Genetics, Genetics Department, Universidade Federal de Pernambuco, Recife, Brazil
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Wurm JP. Assignment of the Ile, Leu, Val, Met and Ala methyl group resonances of the DEAD-box RNA helicase DbpA from E. coli. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:121-128. [PMID: 33277687 PMCID: PMC7973409 DOI: 10.1007/s12104-020-09994-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
ATP-dependent DEAD-box helicases constitute one of the largest families of RNA helicases and are important regulators of most RNA-dependent cellular processes. The functional core of these enzymes consists of two RecA-like domains. Changes in the interdomain orientation of these domains upon ATP and RNA binding result in the unwinding of double-stranded RNA. The DEAD-box helicase DbpA from E. coli is involved in ribosome maturation. It possesses a C-terminal RNA recognition motif (RRM) in addition to the canonical RecA-like domains. The RRM recruits DbpA to nascent ribosomes by binding to hairpin 92 of the 23S rRNA. To follow the conformational changes of Dbpa during the catalytic cycle we initiated solution state NMR studies. We use a divide and conquer approach to obtain an almost complete resonance assignment of the isoleucine, leucine, valine, methionine and alanine methyl group signals of full length DbpA (49 kDa). In addition, we also report the backbone resonance assignments of two fragments of DbpA that were used in the course of the methyl group assignment. These assignments are the first step towards a better understanding of the molecular mechanism behind the ATP-dependent RNA unwinding process catalyzed by DEAD-box helicases.
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Affiliation(s)
- Jan Philip Wurm
- Department of Biophysics I, University of Regensburg, 93053, Regensburg, Germany.
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Wang J, Li T, Deng S, Ma E, Zhang J, Xing S. The RNA helicase DDX3 is required for ovarian development and oocyte maturation in Locusta migratoria. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 106:e21775. [PMID: 33644918 DOI: 10.1002/arch.21775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
DDX3 represents a well-defined subfamily of DEAD-box RNA helicase and exerts multiple functions in RNA metabolism, cell cycle, tumorigenesis, signal pathway, and fertility. Our previous study has shown that LmDDX3, the ortholog of DDX3 in Locusta migratoria, is ubiquitously expressed, and with a high abundance in testis and ovary. Knockdown of LmDDX3 results in a lethal phenotype in nymph, but it still remains unclear for its role in reproductive process. In this study, we therefore characterized LmDDX3 expression in female adult locust and analyzed its function in oocyte development. LmDDX3 was expressed in all tissues examined with significant more transcripts in ovary and hindgut. In ovary, a strong expression level was detected at the day just after adult eclosion, and a dramatic reduction then occurred during the oocyte development. LmDDX3 RNAi led to a reduced vitellogenin (Vg) expression in fat body via partially at least, the JH signaling pathway, and caused an upregulation of vitellogenin receptor (VgR) in ovary, and thus blocked the ovarian development and oocyte maturation. Sequence and phylogenetic analysis indicated that LmDDX3 was closely related to termite DDX3. Taken together, these data reveal a critical role for LmDDX3 in regulating the transcription of Vg and VgR, two major factors in vitellogenesis that is a key process required for ovary development and oocyte maturation in locust, and contribute thereof a new putative target for locust biological control.
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Affiliation(s)
- Junxiu Wang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Tingting Li
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Sufang Deng
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Enbo Ma
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
- Shanxi Provincial Key Laboratory of Agricultural Integrated Pest Management, Taiyuan, Shanxi, China
| | - Jianzhen Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
- Shanxi Provincial Key Laboratory of Agricultural Integrated Pest Management, Taiyuan, Shanxi, China
| | - Shuping Xing
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
- Shanxi Provincial Key Laboratory of Agricultural Integrated Pest Management, Taiyuan, Shanxi, China
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Abstract
The DEAD-box helicase family member DDX3X (DBX, DDX3) functions in nearly all stages of RNA metabolism and participates in the progression of many diseases, including virus infection, inflammation, intellectual disabilities and cancer. Over two decades, many studies have gradually unveiled the role of DDX3X in tumorigenesis and tumour progression. In fact, DDX3X possesses numerous functions in cancer biology and is closely related to many well-known molecules. In this review, we describe the function of DDX3X in RNA metabolism, cellular stress response, innate immune response, metabolic stress response in pancreatic β cells and embryo development. Then, we focused on the role of DDX3X in cancer biology and systematically demonstrated its functions in various aspects of tumorigenesis and development. To provide a more intuitive understanding of the role of DDX3X in cancer, we summarized its functions and specific mechanisms in various types of cancer and presented its involvement in cancer-related signalling pathways.
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Mutations in genes encoding regulators of mRNA decapping and translation initiation: links to intellectual disability. Biochem Soc Trans 2021; 48:1199-1211. [PMID: 32412080 PMCID: PMC7329352 DOI: 10.1042/bst20200109] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022]
Abstract
Intellectual disability (ID) affects at least 1% of the population, and typically presents in the first few years of life. ID is characterized by impairments in cognition and adaptive behavior and is often accompanied by further delays in language and motor skills, as seen in many neurodevelopmental disorders (NDD). Recent widespread high-throughput approaches that utilize whole-exome sequencing or whole-genome sequencing have allowed for a considerable increase in the identification of these pathogenic variants in monogenic forms of ID. Notwithstanding this progress, the molecular and cellular consequences of the identified mutations remain mostly unknown. This is particularly important as the associated protein dysfunctions are the prerequisite to the identification of targets for novel drugs of these rare disorders. Recent Next-Generation sequencing-based studies have further established that mutations in genes encoding proteins involved in RNA metabolism are a major cause of NDD. Here, we review recent studies linking germline mutations in genes encoding factors mediating mRNA decay and regulators of translation, namely DCPS, EDC3, DDX6 helicase and ID. These RNA-binding proteins have well-established roles in mRNA decapping and/or translational repression, and the mutations abrogate their ability to remove 5′ caps from mRNA, diminish their interactions with cofactors and stabilize sub-sets of transcripts. Additional genes encoding RNA helicases with roles in translation including DDX3X and DHX30 have also been linked to NDD. Given the speed in the acquisition, analysis and sharing of sequencing data, and the importance of post-transcriptional regulation for brain development, we anticipate mutations in more such factors being identified and functionally characterized.
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The methyltransferase PRMT1 regulates γ-globin translation. J Biol Chem 2021; 296:100417. [PMID: 33587951 PMCID: PMC7966866 DOI: 10.1016/j.jbc.2021.100417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/03/2021] [Accepted: 02/10/2021] [Indexed: 12/30/2022] Open
Abstract
Induction of fetal hemoglobin to overcome adult β-globin gene deficiency is an effective therapeutic strategy to ameliorate human β-hemoglobinopathies. Previous work has revealed that fetal γ-globin can be translationally induced via integrated stress signaling, but other studies have indicated that activating stress may eventually suppress γ-globin expression transcriptionally. The mechanism by which γ-globin expression is regulated at the translational level remains largely unknown, limiting our ability to determine whether activating stress is a realistic therapeutic option for these disorders. In this study, we performed a functional CRISPR screen targeting protein arginine methyltransferases (PRMTs) to look for changes in γ-globin expression in K562 cells. We not only discovered that several specific PRMTs may block γ-globin transcription, but also revealed PRMT1 as a unique family member that is able to suppress γ-globin synthesis specifically at the translational level. We further identified that a non-AUG uORF within the 5' untranslated region of γ-globin serves as a barrier for translation, which is bypassed upon PRMT1 deficiency. Finally, we found that this novel mechanism of γ-globin suppression could be pharmacologically targeted by the PRMT1 inhibitor, furamidine dihydrochloride. These data raise new questions regarding methyltransferase function and may offer a new therapeutic direction for β-hemoglobinopathies.
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60
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Hao L, Zhang Q, Qiao HY, Zhao FY, Jiang JY, Huyan LY, Liu BQ, Yan J, Li C, Wang HQ. TRIM29 alters bioenergetics of pancreatic cancer cells via cooperation of miR-2355-3p and DDX3X recruitment to AK4 transcript. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 24:579-590. [PMID: 33898107 PMCID: PMC8054099 DOI: 10.1016/j.omtn.2021.01.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/22/2021] [Indexed: 12/28/2022]
Abstract
TRIM29 is dysregulated in pancreatic cancer and implicated in maintenance of stem-cell-like characters of pancreatic cancer cells. However, the exact mechanisms underlying oncogenic function of TRIM29 in pancreatic cancer cells remain largely unclarified. Using a global screening procedure, the current study found that adenylate kinase 4 (AK4) was profoundly reduced by TRIM29 knockdown. In addition, our data demonstrated that TRIM29 knockdown altered bioenergetics and suppressed proliferation and invasion of pancreatic cancer cells via downregulation of AK4 at the posttranscriptional level. The current study demonstrated that upregulation of microRNA-2355-3p (miR-2355-3p) upregulated AK4 expression via facilitating DDX3X recruitment to the AK4 transcript, and TRIM29 knockdown thereby destabilized the AK4 transcript via miR-2355-3p downregulation. Collectively, our study uncovers posttranscriptional stabilization of the AK4 transcript by miR-2355-3p interaction to facilitate DDX3X recruitment. Regulation of AK4 by TRIM29 via miR-2355-3p thereby provides additional information for further identification of attractive targets for therapy with pancreatic cancer.
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Affiliation(s)
- Liang Hao
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110026, China.,Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110026, China.,Department of Chemistry, China Medical University, Shenyang 110126, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110026, China.,Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110026, China.,Criminal Investigation Police University of China, Shenyang 110854, China
| | - Huai-Yu Qiao
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110026, China
| | - Fu-Ying Zhao
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110026, China
| | - Jing-Yi Jiang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110026, China
| | - Ling-Yue Huyan
- 5+3 integrated clinical medicine 103K, China Medical University, Shenyang 110026, China
| | - Bao-Qin Liu
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110026, China
| | - Jing Yan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110026, China
| | - Chao Li
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110026, China
| | - Hua-Qin Wang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110026, China.,Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110026, China
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61
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Mokdadi M, Abdelkrim YZ, Banroques J, Huvelle E, Oualha R, Yeter-Alat H, Guizani I, Barhoumi M, Tanner NK. The In Silico Identification of Potential Members of the Ded1/DDX3 Subfamily of DEAD-Box RNA Helicases from the Protozoan Parasite Leishmania infantum and Their Analyses in Yeast. Genes (Basel) 2021; 12:212. [PMID: 33535521 PMCID: PMC7912733 DOI: 10.3390/genes12020212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
DEAD-box RNA helicases are ubiquitous proteins found in all kingdoms of life and that are associated with all processes involving RNA. Their central roles in biology make these proteins potential targets for therapeutic or prophylactic drugs. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest because of their important role(s) in translation. In this paper, we identified and aligned the protein sequences of 28 different DEAD-box proteins from the kinetoplast-protozoan parasite Leishmania infantum, which is the cause of the visceral form of leishmaniasis that is often lethal if left untreated, and compared them with the consensus sequence derived from DEAD-box proteins in general, and from the Ded1/DDX3 subfamily in particular, from a wide variety of other organisms. We identified three potential homologs of the Ded1/DDX3 subfamily and the equivalent proteins from the related protozoan parasite Trypanosoma brucei, which is the causative agent of sleeping sickness. We subsequently tested these proteins for their ability to complement a yeast strain deleted for the essential DED1 gene. We found that the DEAD-box proteins from Trypanosomatids are highly divergent from other eukaryotes, and consequently they are suitable targets for protein-specific drugs.
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Affiliation(s)
- Molka Mokdadi
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
- Institut National des Sciences Appliquées et Technologies, Université de Carthage, CEDEX, Tunis 1080, Tunisia
| | - Yosser Zina Abdelkrim
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Josette Banroques
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Emmeline Huvelle
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Rafeh Oualha
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Hilal Yeter-Alat
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Mourad Barhoumi
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - N. Kyle Tanner
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
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Perfetto M, Xu X, Lu C, Shi Y, Yousaf N, Li J, Yien YY, Wei S. The RNA helicase DDX3 induces neural crest by promoting AKT activity. Development 2021; 148:dev.184341. [PMID: 33318149 DOI: 10.1242/dev.184341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/02/2020] [Indexed: 01/02/2023]
Abstract
Mutations in the RNA helicase DDX3 have emerged as a frequent cause of intellectual disability in humans. Because many individuals carrying DDX3 mutations have additional defects in craniofacial structures and other tissues containing neural crest (NC)-derived cells, we hypothesized that DDX3 is also important for NC development. Using Xenopus tropicalis as a model, we show that DDX3 is required for normal NC induction and craniofacial morphogenesis by regulating AKT kinase activity. Depletion of DDX3 decreases AKT activity and AKT-dependent inhibitory phosphorylation of GSK3β, leading to reduced levels of β-catenin and Snai1: two GSK3β substrates that are crucial for NC induction. DDX3 function in regulating these downstream signaling events during NC induction is likely mediated by RAC1, a small GTPase whose translation depends on the RNA helicase activity of DDX3. These results suggest an evolutionarily conserved role of DDX3 in NC development by promoting AKT activity, and provide a potential mechanism for the NC-related birth defects displayed by individuals harboring mutations in DDX3 and its downstream effectors in this signaling cascade.
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Affiliation(s)
- Mark Perfetto
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA.,Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Xiaolu Xu
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Congyu Lu
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Yu Shi
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Natasha Yousaf
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Jiejing Li
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA.,Department of Clinical Laboratory, The Affiliated Hospital of KMUST, Medical School, Kunming University of Science and Technology, Kunming 650032, China
| | - Yvette Y Yien
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shuo Wei
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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63
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Hua Q, Liu Y, Li M, Chen Y, Diao Q, Zeng H, Jiang Y. Tobacco-Related Exposure Upregulates Circ_0035266 to Exacerbate Inflammatory Responses in Human Bronchial Epithelial Cells. Toxicol Sci 2021; 179:70-83. [PMID: 33107911 DOI: 10.1093/toxsci/kfaa163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
One of the most carcinogenic chemicals found in cigarette tobacco smoke is 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), which has been confirmed to be associated with the etiology of diverse cancers. Lipopolysaccharide (LPS), another biologically active component of cigarette smoke, is a risk factor which enhances NNK-induced lung tumorigenesis due to chronic lung inflammation. Although inflammatory responses play critical roles in the initiation of many tumors, our knowledge about the mechanisms of NNK+LPS on inflammation is currently limited. Here, we investigated the inflammatory effects of NNK+LPS in human bronchial epithelial cells (BEAS-2B) and explored the underlying mechanisms mediated by circular RNAs (circRNAs). We identified a novel circRNA, circ_0035266, which was strongly upregulated in NNK+LPS-induced BEAS-2B cells and enhanced the inflammatory responses to NNK+LPS by regulating the secretion of pro-inflammatory cytokines interleukin (IL)-6 and IL-8. Specifically, circ_0035266 knockdown alleviated NNK+LPS-induced inflammatory responses, whereas overexpression of circ_0035266 had the opposite effect. Moreover, dual-luciferase reporter and fluorescence in situ hybridization (FISH) assays verified that circ_0035266 bound to miR-181d-5p directly in the cytoplasm. qRT-PCR, dual-luciferase reporter assays, and Western blot analyses showed that DDX3X (DDX3) was the downstream target of miR-181d-5p and that DDX3X expression levels were modulated by circ_0035266. These results suggested that circ_0035266 served as a competitive endogenous RNA for miR-181d-5p to regulate DDX3X expression, which is involved in the modulation of NNK+LPS-induced inflammatory responses in BEAS-2B cells.
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Affiliation(s)
- Qiuhan Hua
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Yufei Liu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Meizhen Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Yingnan Chen
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Qinqin Diao
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Huixian Zeng
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Yiguo Jiang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, P.R. China
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64
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Saito M, Iestamantavicius V, Hess D, Matthias P. Monitoring Acetylation of the RNA Helicase DDX3X, a Protein Critical for Formation of Stress Granules. Methods Mol Biol 2021; 2209:217-234. [PMID: 33201472 DOI: 10.1007/978-1-0716-0935-4_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Stress granules are dynamic structures that assemble in response to various forms of stress, such as heat shock or oxidative stress, among others. We had previously shown that the lysine deacetylase HDAC6 is required for the formation of stress granules, but the substrate important for this function was not known. We recently found that the RNA helicase DDX3X is a novel HDAC6 substrate, which is critical for the formation of stress granules. Through a series of detailed experiments, we showed that, upon stress, DDX3X becomes acetylated in an intrinsically disordered region; this alters its propensity to undergo phase separation and inhibits growth of the stress granules. HDAC6, by deacetylating DDX3X, allows maturation of the stress granules. This work identified acetylation of an RNA helicase as a critical regulator of the stress response. Here, we present methods to analyze the acetylation of DDX3X; these methods can be easily adapted to study the acetylation of other helicases, or other proteins.
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Affiliation(s)
- Makoto Saito
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Sciences, University of Basel, Basel, Switzerland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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65
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Brown NP, Vergara AM, Whelan AB, Guerra P, Bolger TA. Medulloblastoma-associated mutations in the DEAD-box RNA helicase DDX3X/DED1 cause specific defects in translation. J Biol Chem 2021; 296:100296. [PMID: 33460649 PMCID: PMC7949108 DOI: 10.1016/j.jbc.2021.100296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/05/2021] [Accepted: 01/12/2021] [Indexed: 01/22/2023] Open
Abstract
Medulloblastoma is the most common pediatric brain cancer, and sequencing studies identified frequent mutations in DDX3X, a DEAD-box RNA helicase primarily implicated in translation. Forty-two different sites were identified, suggesting that the functional effects of the mutations are complex. To investigate how these mutations are affecting DDX3X cellular function, we constructed a full set of equivalent mutant alleles in DED1, the Saccharomyces cerevisiae ortholog of DDX3X, and characterized their effects in vivo and in vitro. Most of the medulloblastoma-associated mutants in DDX3X/DED1 (ded1-mam) showed substantial growth defects, indicating that functional effects are conserved in yeast. Further, while translation was affected in some mutants, translation defects affecting bulk mRNA were neither consistent nor correlated with the growth phenotypes. Likewise, increased formation of stress granules in ded1-mam mutants was common but did not correspond to the severity of the mutants' growth defects. In contrast, defects in translating mRNAs containing secondary structure in their 5' untranslated regions (UTRs) were found in almost all ded1-mam mutants and correlated well with growth phenotypes. We thus conclude that these specific translation defects, rather than generalized effects on translation, are responsible for the observed cellular phenotypes and likely contribute to DDX3X-mutant medulloblastoma. Examination of ATPase activity and RNA binding of recombinant mutant proteins also did not reveal a consistent defect, indicating that the translation defects are derived from multiple enzymatic deficiencies. This work suggests that future studies into medulloblastoma pathology should focus on this specific translation defect, while taking into account the wide spectrum of DDX3X mutations.
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Affiliation(s)
- Nicolette P Brown
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Ashley M Vergara
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Alisha B Whelan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Paolo Guerra
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Timothy A Bolger
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA.
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66
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Russon MP, Westerhouse KM, Tran EJ. Transcription, translation, and DNA repair: new insights from emerging noncanonical substrates of RNA helicases. Biol Chem 2020; 402:637-644. [PMID: 33857360 DOI: 10.1515/hsz-2020-0333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/23/2020] [Indexed: 11/15/2022]
Abstract
RNA helicases are enzymes that exist in all domains of life whose canonical functions include ATP-dependent remodeling of RNA structures and displacement of proteins from ribonucleoprotein complexes (RNPs). These enzymes play roles in virtually all processes of RNA metabolism, including pre-mRNA splicing, rRNA processing, nuclear mRNA export, translation and RNA decay. Here we review emerging noncanonical substrates of RNA helicases including RNA-DNA hybrids (R-loops) and RNA and DNA G-quadruplexes and discuss their biological significance.
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Affiliation(s)
- Matthew P Russon
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN, 47907, USA
| | - Kirsten M Westerhouse
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN, 47907, USA
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN, 47907, USA.,Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN, 47907, USA
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67
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Jarmoskaite I, Tijerina P, Russell R. ATP utilization by a DEAD-box protein during refolding of a misfolded group I intron ribozyme. J Biol Chem 2020; 296:100132. [PMID: 33262215 PMCID: PMC7948464 DOI: 10.1074/jbc.ra120.015029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/17/2020] [Accepted: 12/01/2020] [Indexed: 12/31/2022] Open
Abstract
DEAD-box helicase proteins perform ATP-dependent rearrangements of structured RNAs throughout RNA biology. Short RNA helices are unwound in a single ATPase cycle, but the ATP requirement for more complex RNA structural rearrangements is unknown. Here we measure the amount of ATP used for native refolding of a misfolded group I intron ribozyme by CYT-19, a Neurospora crassa DEAD-box protein that functions as a general chaperone for mitochondrial group I introns. By comparing the rates of ATP hydrolysis and ribozyme refolding, we find that several hundred ATP molecules are hydrolyzed during refolding of each ribozyme molecule. After subtracting nonproductive ATP hydrolysis that occurs in the absence of ribozyme refolding, we find that approximately 100 ATPs are hydrolyzed per refolded RNA as a consequence of interactions specific to the misfolded ribozyme. This value is insensitive to changes in ATP and CYT-19 concentration and decreases with decreasing ribozyme stability. Because of earlier findings that ∼90% of global ribozyme unfolding cycles lead back to the kinetically preferred misfolded conformation and are not observed, we estimate that each global unfolding cycle consumes ∼10 ATPs. Our results indicate that CYT-19 functions as a general RNA chaperone by using a stochastic, energy-intensive mechanism to promote RNA unfolding and refolding, suggesting an evolutionary convergence with protein chaperones.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Pilar Tijerina
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.
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68
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Mason AC, Wente SR. Functions of Gle1 are governed by two distinct modes of self-association. J Biol Chem 2020; 295:16813-16825. [PMID: 32981894 PMCID: PMC7864074 DOI: 10.1074/jbc.ra120.015715] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/23/2020] [Indexed: 11/08/2022] Open
Abstract
Gle1 is a conserved, essential regulator of DEAD-box RNA helicases, with critical roles defined in mRNA export, translation initiation, translation termination, and stress granule formation. Mechanisms that specify which, where, and when DDXs are targeted by Gle1 are critical to understand. In addition to roles for stress-induced phosphorylation and inositol hexakisphosphate binding in specifying Gle1 function, Gle1 oligomerizes via its N-terminal domain in a phosphorylation-dependent manner. However, a thorough analysis of the role for Gle1 self-association is lacking. Here, we find that Gle1 self-association is driven by two distinct regions: a coiled-coil domain and a novel 10-amino acid aggregation-prone region, both of which are necessary for proper Gle1 oligomerization. By exogenous expression in HeLa cells, we tested the function of a series of mutations that impact the oligomerization domains of the Gle1A and Gle1B isoforms. Gle1 oligomerization is necessary for many, but not all aspects of Gle1A and Gle1B function, and the requirements for each interaction domain differ. Whereas the coiled-coil domain and aggregation-prone region additively contribute to competent mRNA export and stress granule formation, both self-association domains are independently required for regulation of translation under cellular stress. In contrast, Gle1 self-association is dispensable for phosphorylation and nonstressed translation initiation. Collectively, we reveal self-association functions as an additional mode of Gle1 regulation to ensure proper mRNA export and translation. This work also provides further insight into the mechanisms underlying human gle1 disease mutants found in prenatally lethal forms of arthrogryposis.
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Affiliation(s)
- Aaron C Mason
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Susan R Wente
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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69
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Deschepper CF. Regulatory effects of the Uty/Ddx3y locus on neighboring chromosome Y genes and autosomal mRNA transcripts in adult mouse non-reproductive cells. Sci Rep 2020; 10:14900. [PMID: 32913328 PMCID: PMC7484786 DOI: 10.1038/s41598-020-71447-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/13/2020] [Indexed: 12/22/2022] Open
Abstract
In addition to sperm-related genes, the male-specific chromosome Y (chrY) contains a class of ubiquitously expressed and evolutionary conserved dosage-sensitive regulator genes that include the neighboring Uty, Ddx3y and (in mice) Eif2s3y genes. However, no study to date has investigated the functional impact of targeted mutations of any of these genes within adult non-reproductive somatic cells. We thus compared adult male mice carrying a gene trap within their Uty gene (UtyGT) to their wild-type (WT) isogenic controls, and performed deep sequencing of RNA and genome-wide profiling of chromatin features in extracts from either cardiac tissue, cardiomyocyte-specific nuclei or purified cardiomyocytes. The apparent impact of UtyGT on gene transcription concentrated mostly on chrY genes surrounding the locus of insertion, i.e. Uty, Ddx3y, long non-coding RNAs (lncRNAs) contained within their introns and Eif2s3y, in addition to possible effects on the autosomal Malat1 lncRNA. Notwithstanding, UtyGT also caused coordinate changes in the abundance of hundreds of mRNA transcripts related to coherent cell functions, including RNA processing and translation. The results altogether indicated that tightly co-regulated chrY genes had nonetheless more widespread effects on the autosomal transcriptome in adult somatic cells, most likely due to mechanisms other than just transcriptional regulation of corresponding protein-coding genes.
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Affiliation(s)
- Christian F Deschepper
- Cardiovascular Biology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM) and Université de Montréal, 100 Pine Ave West, Montréal, QC, H2W 1R7, Canada.
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70
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Akirtava C, McManus CJ. Control of translation by eukaryotic mRNA transcript leaders-Insights from high-throughput assays and computational modeling. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1623. [PMID: 32869519 DOI: 10.1002/wrna.1623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/23/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022]
Abstract
Eukaryotic gene expression is tightly regulated during translation of mRNA to protein. Mis-regulation of translation can lead to aberrant proteins which accumulate in cancers and cause neurodegenerative diseases. Foundational studies on model genes established fundamental roles for mRNA 5' transcript leader (TL) sequences in controlling ribosome recruitment, scanning, and initiation. TL cis-regulatory elements and their corresponding trans-acting factors control cap-dependent initiation under unstressed conditions. Under stress, cap-dependent initiation is suppressed, and specific mRNA structures and sequences promote translation of stress-responsive transcripts to remodel the proteome. In this review, we summarize current knowledge of TL functions in translation initiation. We focus on insights from high-throughput analyses of ribosome occupancy, mRNA structure, RNA Binding Protein occupancy, and massively parallel reporter assays. These data-driven approaches, coupled with computational analyses and modeling, have paved the way for a comprehensive understanding of TL functions. Finally, we will discuss areas of future research on the roles of mRNA sequences and structures in translation. This article is categorized under: Translation > Translation Mechanisms RNA Evolution and Genomics > Computational Analyses of RNA RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Christina Akirtava
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Charles Joel McManus
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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71
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Nagy PD. Host protein chaperones, RNA helicases and the ubiquitin network highlight the arms race for resources between tombusviruses and their hosts. Adv Virus Res 2020; 107:133-158. [PMID: 32711728 PMCID: PMC7342006 DOI: 10.1016/bs.aivir.2020.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Positive-strand RNA viruses need to arrogate many cellular resources to support their replication and infection cycles. These viruses co-opt host factors, lipids and subcellular membranes and exploit cellular metabolites to built viral replication organelles in infected cells. However, the host cells have their defensive arsenal of factors to protect themselves from easy exploitation by viruses. In this review, the author discusses an emerging arms race for cellular resources between viruses and hosts, which occur during the early events of virus-host interactions. Recent findings with tomato bushy stunt virus and its hosts revealed that the need of the virus to exploit and co-opt given members of protein families provides an opportunity for the host to deploy additional members of the same or associated protein family to interfere with virus replication. Three examples with well-established heat shock protein 70 and RNA helicase protein families and the ubiquitin network will be described to illustrate this model on the early arms race for cellular resources between tombusviruses and their hosts. We predict that arms race for resources with additional cellular protein families will be discovered with tombusviruses. These advances will fortify research on interactions among other plant and animal viruses and their hosts.
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Affiliation(s)
- Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States.
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72
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Abstract
The stage at which ribosomes are recruited to messenger RNAs (mRNAs) is an elaborate and highly regulated phase of protein synthesis. Upon completion of this step, a ribosome is positioned at an appropriate initiation codon and primed to synthesize the encoded polypeptide product. In most circumstances, this step commits the ribosome to translate the mRNA. We summarize the knowledge regarding the initiation factors implicated in this activity as well as review different mechanisms by which this process is conducted.
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Affiliation(s)
- Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada; , .,Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Oncology, McGill University, Montreal, Quebec H4A 3T2, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada; , .,Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada
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73
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General and Target-Specific DExD/H RNA Helicases in Eukaryotic Translation Initiation. Int J Mol Sci 2020; 21:ijms21124402. [PMID: 32575790 PMCID: PMC7352612 DOI: 10.3390/ijms21124402] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
DExD (DDX)- and DExH (DHX)-box RNA helicases, named after their Asp-Glu-x-Asp/His motifs, are integral to almost all RNA metabolic processes in eukaryotic cells. They play myriad roles in processes ranging from transcription and mRNA-protein complex remodeling, to RNA decay and translation. This last facet, translation, is an intricate process that involves DDX/DHX helicases and presents a regulatory node that is highly targetable. Studies aimed at better understanding this family of conserved proteins have revealed insights into their structures, catalytic mechanisms, and biological roles. They have also led to the development of chemical modulators that seek to exploit their essential roles in diseases. Herein, we review the most recent insights on several general and target-specific DDX/DHX helicases in eukaryotic translation initiation.
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74
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Gulay S, Gupta N, Lorsch JR, Hinnebusch AG. Distinct interactions of eIF4A and eIF4E with RNA helicase Ded1 stimulate translation in vivo. eLife 2020; 9:58243. [PMID: 32469309 PMCID: PMC7343385 DOI: 10.7554/elife.58243] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022] Open
Abstract
Yeast DEAD-box helicase Ded1 stimulates translation initiation, particularly of mRNAs with structured 5'UTRs. Interactions of the Ded1 N-terminal domain (NTD) with eIF4A, and Ded1-CTD with eIF4G, subunits of eIF4F, enhance Ded1 unwinding activity and stimulation of preinitiation complex (PIC) assembly in vitro. However, the importance of these interactions, and of Ded1-eIF4E association, in vivo were poorly understood. We identified separate amino acid clusters in the Ded1-NTD required for binding to eIF4A or eIF4E in vitro. Disrupting each cluster selectively impairs native Ded1 association with eIF4A or eIF4E, and reduces cell growth, polysome assembly, and translation of reporter mRNAs with structured 5'UTRs. It also impairs Ded1 stimulation of PIC assembly on a structured mRNA in vitro. Ablating Ded1 interactions with eIF4A/eIF4E unveiled a requirement for the Ded1-CTD for robust initiation. Thus, Ded1 function in vivo is stimulated by independent interactions of its NTD with eIF4E and eIF4A, and its CTD with eIF4G.
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Affiliation(s)
- Suna Gulay
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Neha Gupta
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Jon R Lorsch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
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75
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Lennox AL, Hoye ML, Jiang R, Johnson-Kerner BL, Suit LA, Venkataramanan S, Sheehan CJ, Alsina FC, Fregeau B, Aldinger KA, Moey C, Lobach I, Afenjar A, Babovic-Vuksanovic D, Bézieau S, Blackburn PR, Bunt J, Burglen L, Campeau PM, Charles P, Chung BHY, Cogné B, Curry C, D'Agostino MD, Di Donato N, Faivre L, Héron D, Innes AM, Isidor B, Keren B, Kimball A, Klee EW, Kuentz P, Küry S, Martin-Coignard D, Mirzaa G, Mignot C, Miyake N, Matsumoto N, Fujita A, Nava C, Nizon M, Rodriguez D, Blok LS, Thauvin-Robinet C, Thevenon J, Vincent M, Ziegler A, Dobyns W, Richards LJ, Barkovich AJ, Floor SN, Silver DL, Sherr EH. Pathogenic DDX3X Mutations Impair RNA Metabolism and Neurogenesis during Fetal Cortical Development. Neuron 2020; 106:404-420.e8. [PMID: 32135084 PMCID: PMC7331285 DOI: 10.1016/j.neuron.2020.01.042] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 11/05/2019] [Accepted: 01/29/2020] [Indexed: 12/16/2022]
Abstract
De novo germline mutations in the RNA helicase DDX3X account for 1%-3% of unexplained intellectual disability (ID) cases in females and are associated with autism, brain malformations, and epilepsy. Yet, the developmental and molecular mechanisms by which DDX3X mutations impair brain function are unknown. Here, we use human and mouse genetics and cell biological and biochemical approaches to elucidate mechanisms by which pathogenic DDX3X variants disrupt brain development. We report the largest clinical cohort to date with DDX3X mutations (n = 107), demonstrating a striking correlation between recurrent dominant missense mutations, polymicrogyria, and the most severe clinical outcomes. We show that Ddx3x controls cortical development by regulating neuron generation. Severe DDX3X missense mutations profoundly disrupt RNA helicase activity, induce ectopic RNA-protein granules in neural progenitors and neurons, and impair translation. Together, these results uncover key mechanisms underlying DDX3X syndrome and highlight aberrant RNA metabolism in the pathogenesis of neurodevelopmental disease.
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Affiliation(s)
- Ashley L Lennox
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ruiji Jiang
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Lindsey A Suit
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Srivats Venkataramanan
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Charles J Sheehan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Fernando C Alsina
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Brieana Fregeau
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Ching Moey
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Iryna Lobach
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alexandra Afenjar
- Centre de référence des malformations et maladies congénitales du cervelet et Département de génétique et embryologie médicale, APHP, Sorbonne Université, Hôpital Armand Trousseau, 75012 Paris, France
| | - Dusica Babovic-Vuksanovic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA; Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | - Patrick R Blackburn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jens Bunt
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Lydie Burglen
- Centre de référence des malformations et maladies congénitales du cervelet et Département de génétique et embryologie médicale, APHP, Sorbonne Université, Hôpital Armand Trousseau, 75012 Paris, France
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal and CHU Sainte-Justine, Montreal, QC, Canada
| | - Perrine Charles
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié Salpêtrière et Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | - Cynthia Curry
- Genetic Medicine, University of California San Francisco/Fresno, Fresno, CA 93701, USA
| | - Maria Daniela D'Agostino
- Division of Medical Genetics, Departments of Specialized Medicine and Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Laurence Faivre
- Centre de référence Anomalies du Développement et Syndromes Malformatifs, INSERM UMR 1231 GAD, CHU de Dijon et Université de Bourgogne, Dijon, France
| | - Delphine Héron
- APHP, Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | - Boris Keren
- APHP, Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Amy Kimball
- Harvey Institute of Human Genetics, Greater Baltimore Medical Center, Baltimore, MD, USA
| | - Eric W Klee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Paul Kuentz
- UMR-INSERM 1231 GAD, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | | | - Ghayda Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
| | - Cyril Mignot
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié Salpêtrière et Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Caroline Nava
- APHP, Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | - Diana Rodriguez
- Centre de Référence Neurogénétique & Service de Neurologie Pédiatrique, APHP, Sorbonne Université, Hôpital Armand Trousseau, 75012 Paris, France
| | - Lot Snijders Blok
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Christel Thauvin-Robinet
- Centre de référence Déficience Intellectuelle, INSERM UMR 1231 GAD, CHU de Dijon et Université de Bourgogne, Dijon, France
| | - Julien Thevenon
- Centre de référence Anomalies du Développement et Syndromes Malformatifs, INSERM UMR 1231 GAD, CHU de Dijon et Université de Bourgogne, Dijon, France
| | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | | | - William Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Departments of Pediatrics and Neurology, University of Washington, Seattle, WA 98101, USA
| | - Linda J Richards
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia; The University of Queensland, School of Biomedical Sciences, Brisbane 4072, QLD, Australia
| | - A James Barkovich
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Duke Institute for Brain Sciences, Duke University, Durham, NC 27710, USA.
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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76
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Kamjula V, Kanneganti A, Metla R, Nidamanuri K, Idupulapati S, Runthala A. Decoding the vital segments in human ATP-dependent RNA helicase. Bioinformation 2020; 16:160-170. [PMID: 32405168 PMCID: PMC7196165 DOI: 10.6026/97320630016160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 02/20/2020] [Indexed: 12/28/2022] Open
Abstract
An analysis of the ATP-dependent RNA helicase using known functionally close analogs helps disclose the structural and functional information of the enzyme. The enzyme plays several interlinked biological functions and there is an urgent need to interpret its key active-site residues to infer function and establish role. The human protein q96c10.1 is annotated using tools such as interpro, go and cdd. The physicochemical properties are estimated using the tool protparam. We describe the enzyme protein model developed using modeller to identify active site residues. We used consurf to estimate the structural conservation and is evolutionary relationship is inferred using known close sequence homologs. The active site is predicted using castp and its topological flexibility is estimated through cabs-flex. The protein is annotated as a hydrolase using available data and ddx58 is found as its top-ranked interacting protein partner. We show that about 124 residues are found to be highly conserved among 259 homologs, clustered in 7 clades with the active-site showing low sequence conservation. It is further shown that only 9 loci among the 42 active-site residues are conserved with limited structural fluctuation from the wild type structure. Thus, we document various useful information linked to function, sequence similarity and phylogeny of the enzyme for annotation as potential helicase as designated by uniprot. Data shows limited degree of conserved sequence segments with topological flexibility unlike in other subfamily members of the protein.
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Affiliation(s)
- Vandana Kamjula
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Ananya Kanneganti
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Rohan Metla
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Kusuma Nidamanuri
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Sudarshan Idupulapati
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Ashish Runthala
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
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77
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Sulkowska A, Auber A, Sikorski PJ, Silhavy DN, Auth M, Sitkiewicz E, Jean V, Merret RM, Bousquet-Antonelli CC, Kufel J. RNA Helicases from the DEA(D/H)-Box Family Contribute to Plant NMD Efficiency. PLANT & CELL PHYSIOLOGY 2020; 61:144-157. [PMID: 31560399 DOI: 10.1093/pcp/pcz186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic RNA surveillance mechanism that degrades aberrant mRNAs comprising a premature translation termination codon. The adenosine triphosphate (ATP)-dependent RNA helicase up-frameshift 1 (UPF1) is a major NMD factor in all studied organisms; however, the complexity of this mechanism has not been fully characterized in plants. To identify plant NMD factors, we analyzed UPF1-interacting proteins using tandem affinity purification coupled to mass spectrometry. Canonical members of the NMD pathway were found along with numerous NMD candidate factors, including conserved DEA(D/H)-box RNA helicase homologs of human DDX3, DDX5 and DDX6, translation initiation factors, ribosomal proteins and transport factors. Our functional studies revealed that depletion of DDX3 helicases enhances the accumulation of NMD target reporter mRNAs but does not result in increased protein levels. In contrast, silencing of DDX6 group leads to decreased accumulation of the NMD substrate. The inhibitory effect of DDX6-like helicases on NMD was confirmed by transient overexpression of RH12 helicase. These results indicate that DDX3 and DDX6 helicases in plants have a direct and opposing contribution to NMD and act as functional NMD factors.
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Affiliation(s)
- Aleksandra Sulkowska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andor Auber
- Agricultural Biotechnology Institute, Szent-Gy�rgyi 4, H-2100 G�d�llő, Hungary
| | - Pawel J Sikorski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Dï Niel Silhavy
- Agricultural Biotechnology Institute, Szent-Gy�rgyi 4, H-2100 G�d�llő, Hungary
| | - Mariann Auth
- Agricultural Biotechnology Institute, Szent-Gy�rgyi 4, H-2100 G�d�llő, Hungary
| | - Ewa Sitkiewicz
- Proteomics Laboratory, Biophysics Department, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Viviane Jean
- UMR5096 LGDP, Universit� de Perpignan Via Domitia, UMR5096 LGDP58, Avenue Paul Alduy, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, Perpignan Cedex, France
| | - Rï My Merret
- UMR5096 LGDP, Universit� de Perpignan Via Domitia, UMR5096 LGDP58, Avenue Paul Alduy, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, Perpignan Cedex, France
| | - Cï Cile Bousquet-Antonelli
- UMR5096 LGDP, Universit� de Perpignan Via Domitia, UMR5096 LGDP58, Avenue Paul Alduy, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, Perpignan Cedex, France
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
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78
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Sen ND, Gupta N, K Archer S, Preiss T, Lorsch JR, Hinnebusch AG. Functional interplay between DEAD-box RNA helicases Ded1 and Dbp1 in preinitiation complex attachment and scanning on structured mRNAs in vivo. Nucleic Acids Res 2019; 47:8785-8806. [PMID: 31299079 DOI: 10.1093/nar/gkz595] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 01/03/2023] Open
Abstract
RNA structures that impede ribosome binding or subsequent scanning of the 5'-untranslated region (5'-UTR) for the AUG initiation codon reduce translation efficiency. Yeast DEAD-box RNA helicase Ded1 appears to promote translation by resolving 5'-UTR structures, but whether its paralog, Dbp1, performs similar functions is unknown. Furthermore, direct in vivo evidence was lacking that Ded1 or Dbp1 resolves 5'-UTR structures that impede attachment of the 43S preinitiation complex (PIC) or scanning. Here, profiling of translating 80S ribosomes reveals that the translational efficiencies of many more mRNAs are reduced in a ded1-ts dbp1Δ double mutant versus either single mutant, becoming highly dependent on Dbp1 or Ded1 only when the other helicase is impaired. Such 'conditionally hyperdependent' mRNAs contain unusually long 5'-UTRs with heightened propensity for secondary structure and longer transcript lengths. Consistently, overexpressing Dbp1 in ded1 cells improves the translation of many such Ded1-hyperdependent mRNAs. Importantly, Dbp1 mimics Ded1 in conferring greater acceleration of 48S PIC assembly in a purified system on mRNAs harboring structured 5'-UTRs. Profiling 40S initiation complexes in ded1 and dbp1 mutants provides direct evidence that Ded1 and Dbp1 cooperate to stimulate both PIC attachment and scanning on many Ded1/Dbp1-hyperdependent mRNAs in vivo.
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Affiliation(s)
- Neelam Dabas Sen
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neha Gupta
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stuart K Archer
- Monash Bioinformatics Platform, Monash University, Clayton, VIC 3800, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.,Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Jon R Lorsch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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79
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Raj S, Bagchi D, Orero JV, Banroques J, Tanner NK, Croquette V. Mechanistic characterization of the DEAD-box RNA helicase Ded1 from yeast as revealed by a novel technique using single-molecule magnetic tweezers. Nucleic Acids Res 2019; 47:3699-3710. [PMID: 30993346 PMCID: PMC6468243 DOI: 10.1093/nar/gkz057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/21/2019] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
DEAD-box helicases are involved in all steps of RNA metabolism. They are ATP-dependent RNA binding proteins and RNA-dependent ATPases. They can displace short duplexes, but they lack processivity. Their mechanism and functioning are not clearly understood; classical or bulk biochemical assays are not sufficient to answer these questions. Single-molecule techniques provide useful tools, but they are limited in cases where the proteins are nonprocessive and give weak signals. We present here a new, magnetic-tweezers-based, single-molecule assay that is simple and that can sensitively measure the displacement time of a small, hybridized, RNA oligonucleotide. Tens of molecules can be analyzed at the same time. Comparing the displacement times with and without a helicase gives insights into the enzymatic activity of the protein. We used this assay to study yeast Ded1, which is orthologous to human DDX3. Although Ded1 acts on a variety of substrates, we find that Ded1 requires an RNA substrate for its ATP-dependent unwinding activity and that ATP hydrolysis is needed to see this activity. Further, we find that only intramolecular single-stranded RNA extensions enhance this activity. We propose a model where ATP-bound Ded1 stabilizes partially unwound duplexes and where multiple binding events may be needed to see displacement.
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Affiliation(s)
- Saurabh Raj
- Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Debjani Bagchi
- Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Jessica Valle Orero
- Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Josette Banroques
- Laboratoire d'Expression Génétique Microbienne, CNRS UMR8261/Université Paris 7-Diderot, Sorbonne Paris Cité Universités, 13 rue Pierre et Marie Curie, Paris, France.,Institut de Biologie Physico-Chimique, PSL Research University, 75005 Paris, France
| | - N Kyle Tanner
- Laboratoire d'Expression Génétique Microbienne, CNRS UMR8261/Université Paris 7-Diderot, Sorbonne Paris Cité Universités, 13 rue Pierre et Marie Curie, Paris, France.,Institut de Biologie Physico-Chimique, PSL Research University, 75005 Paris, France
| | - Vincent Croquette
- Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France.,ESPCI Paris, PSL University, 10 rue Vauquelin, 75005 Paris, France
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80
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Cheng W, Wang S, Zhang Z, Morgens DW, Hayes LR, Lee S, Portz B, Xie Y, Nguyen BV, Haney MS, Yan S, Dong D, Coyne AN, Yang J, Xian F, Cleveland DW, Qiu Z, Rothstein JD, Shorter J, Gao FB, Bassik MC, Sun S. CRISPR-Cas9 Screens Identify the RNA Helicase DDX3X as a Repressor of C9ORF72 (GGGGCC)n Repeat-Associated Non-AUG Translation. Neuron 2019; 104:885-898.e8. [PMID: 31587919 DOI: 10.1016/j.neuron.2019.09.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/16/2019] [Accepted: 09/04/2019] [Indexed: 12/14/2022]
Abstract
Hexanucleotide GGGGCC repeat expansion in C9ORF72 is the most prevalent genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). One pathogenic mechanism is the aberrant accumulation of dipeptide repeat (DPR) proteins produced by the unconventional translation of expanded RNA repeats. Here, we performed genome-wide CRISPR-Cas9 screens for modifiers of DPR protein production in human cells. We found that DDX3X, an RNA helicase, suppresses the repeat-associated non-AUG translation of GGGGCC repeats. DDX3X directly binds to (GGGGCC)n RNAs but not antisense (CCCCGG)n RNAs. Its helicase activity is essential for the translation repression. Reduction of DDX3X increases DPR levels in C9ORF72-ALS/FTD patient cells and enhances (GGGGCC)n-mediated toxicity in Drosophila. Elevating DDX3X expression is sufficient to decrease DPR levels, rescue nucleocytoplasmic transport abnormalities, and improve survival of patient iPSC-differentiated neurons. This work identifies genetic modifiers of DPR protein production and provides potential therapeutic targets for C9ORF72-ALS/FTD.
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Affiliation(s)
- Weiwei Cheng
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaopeng Wang
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhe Zhang
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David W Morgens
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lindsey R Hayes
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Soojin Lee
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yongzhi Xie
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Baotram V Nguyen
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael S Haney
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirui Yan
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daoyuan Dong
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alyssa N Coyne
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Junhua Yang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fengfan Xian
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Don W Cleveland
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Zhaozhu Qiu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeffrey D Rothstein
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shuying Sun
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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81
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de Bisschop G, Ameur M, Ulryck N, Benattia F, Ponchon L, Sargueil B, Chamond N. HIV-1 gRNA, a biological substrate, uncovers the potency of DDX3X biochemical activity. Biochimie 2019; 164:83-94. [PMID: 30910425 DOI: 10.1016/j.biochi.2019.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/12/2019] [Indexed: 11/30/2022]
Abstract
DEAD-box helicases play central roles in the metabolism of many RNAs and ribonucleoproteins by assisting their synthesis, folding, function and even their degradation or disassembly. They have been implicated in various phenomena, and it is often difficult to rationalize their molecular roles from in vivo studies. Once purified in vitro, most of them only exhibit a marginal activity and poor specificity. The current model is that they gain specificity and activity through interaction of their intrinsically disordered domains with specific RNA or proteins. DDX3 is a DEAD-box cellular helicase that has been involved in several steps of the HIV viral cycle, including transcription, RNA export to the cytoplasm and translation. In this study, we investigated DDX3 biochemical properties in the context of a biological substrate. DDX3 was overexpressed, purified and its enzymatic activities as well as its RNA binding properties were characterized using both model substrates and a biological substrate, HIV-1 gRNA. Biochemical characterization of DDX3 in the context of a biological substrate identifies HIV-1 gRNA as a rare example of specific substrate and unravels the extent of DDX3 ATPase activity. Analysis of DDX3 binding capacity indicates an unexpected dissociation between its binding capacity and its biochemical activity. We further demonstrate that interaction of DDX3 with HIV-1 gRNA relies both on specific RNA determinants and on the disordered N- and C-terminal regions of the protein. These findings shed a new light regarding the potentiality of DDX3 biochemical activity supporting its multiple cellular functions.
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Affiliation(s)
| | - Mélissa Ameur
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France
| | - Nathalie Ulryck
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France
| | - Fatima Benattia
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France
| | - Luc Ponchon
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France
| | - Bruno Sargueil
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France.
| | - Nathalie Chamond
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France.
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82
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Janapala Y, Preiss T, Shirokikh NE. Control of Translation at the Initiation Phase During Glucose Starvation in Yeast. Int J Mol Sci 2019; 20:E4043. [PMID: 31430885 PMCID: PMC6720308 DOI: 10.3390/ijms20164043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/10/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Glucose is one of the most important sources of carbon across all life. Glucose starvation is a key stress relevant to all eukaryotic cells. Glucose starvation responses have important implications in diseases, such as diabetes and cancer. In yeast, glucose starvation causes rapid and dramatic effects on the synthesis of proteins (mRNA translation). Response to glucose deficiency targets the initiation phase of translation by different mechanisms and with diverse dynamics. Concomitantly, translationally repressed mRNAs and components of the protein synthesis machinery may enter a variety of cytoplasmic foci, which also form with variable kinetics and may store or degrade mRNA. Much progress has been made in understanding these processes in the last decade, including with the use of high-throughput/omics methods of RNA and RNA:protein detection. This review dissects the current knowledge of yeast reactions to glucose starvation systematized by the stage of translation initiation, with the focus on rapid responses. We provide parallels to mechanisms found in higher eukaryotes, such as metazoans, for the most critical responses, and point out major remaining gaps in knowledge and possible future directions of research on translational responses to glucose starvation.
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Affiliation(s)
- Yoshika Janapala
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.
| | - Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
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83
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Song H, Ji X. The mechanism of RNA duplex recognition and unwinding by DEAD-box helicase DDX3X. Nat Commun 2019; 10:3085. [PMID: 31300642 PMCID: PMC6626043 DOI: 10.1038/s41467-019-11083-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 06/16/2019] [Indexed: 12/02/2022] Open
Abstract
DEAD-box helicases (DDXs) regulate RNA processing and metabolism by unwinding short double-stranded (ds) RNAs. Sharing a helicase core composed of two RecA-like domains (D1D2), DDXs function in an ATP-dependent, non-processive manner. As an attractive target for cancer and AIDS treatment, DDX3X and its orthologs are extensively studied, yielding a wealth of biochemical and biophysical data, including structures of apo-D1D2 and post-unwound D1D2:single-stranded RNA complex, and the structure of a D2:dsRNA complex that is thought to represent a pre-unwound state. However, the structure of a pre-unwound D1D2:dsRNA complex remains elusive, and thus, the mechanism of DDX action is not fully understood. Here, we describe the structure of a D1D2 core in complex with a 23-base pair dsRNA at pre-unwound state, revealing that two DDXs recognize a 2-turn dsRNA, each DDX mainly recognizes a single RNA strand, and conformational changes induced by ATP binding unwinds the RNA duplex in a cooperative manner.
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Affiliation(s)
- He Song
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
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84
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Aryanpur PP, Renner DM, Rodela E, Mittelmeier TM, Byrd A, Bolger TA. The DEAD-box RNA helicase Ded1 has a role in the translational response to TORC1 inhibition. Mol Biol Cell 2019; 30:2171-2184. [PMID: 31141444 PMCID: PMC6743465 DOI: 10.1091/mbc.e18-11-0702] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Ded1 is a DEAD-box RNA helicase with essential roles in translation initiation. It binds to the eukaryotic initiation factor 4F (eIF4F) complex and promotes 48S preinitiation complex assembly and start-site scanning of 5′ untranslated regions of mRNAs. Most prior studies of Ded1 cellular function were conducted in steady-state conditions during nutrient-rich growth. In this work, however, we examine its role in the translational response during target of rapamycin (TOR)C1 inhibition and identify a novel function of Ded1 as a translation repressor. We show that C-terminal mutants of DED1 are defective in down-regulating translation following TORC1 inhibition using rapamycin. Furthermore, following TORC1 inhibition, eIF4G1 normally dissociates from translation complexes and is degraded, and this process is attenuated in mutant cells. Mapping of the functional requirements for Ded1 in this translational response indicates that Ded1 enzymatic activity and interaction with eIF4G1 are required, while homo-oligomerization may be dispensable. Our results are consistent with a model wherein Ded1 stalls translation and specifically removes eIF4G1 from translation preinitiation complexes, thus removing eIF4G1 from the translating mRNA pool and leading to the codegradation of both proteins. Shared features among DED1 orthologues suggest that this role is conserved and may be implicated in pathologies such as oncogenesis.
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Affiliation(s)
- Peyman P Aryanpur
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Tucson, AZ 85721
| | - David M Renner
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Tucson, AZ 85721
| | - Emily Rodela
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Tucson, AZ 85721
| | - Telsa M Mittelmeier
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Tucson, AZ 85721
| | - Aaron Byrd
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Tucson, AZ 85721
| | - Timothy A Bolger
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Tucson, AZ 85721
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85
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From the magic bullet to the magic target: exploiting the diverse roles of DDX3X in viral infections and tumorigenesis. Future Med Chem 2019; 11:1357-1381. [PMID: 30816053 DOI: 10.4155/fmc-2018-0451] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
DDX3X is an ATPase/RNA helicase of the DEAD-box family and one of the most multifaceted helicases known up to date, acting in RNA metabolism, cell cycle control, apoptosis, stress response and innate immunity. Depending on the virus or the viral cycle stage, DDX3X can act either in a proviral fashion or as an antiviral factor. Similarly, in different cancer types, it can act either as an oncogene or a tumor-suppressor gene. Accumulating evidence indicated that DDX3X can be considered a promising target for anticancer and antiviral chemotherapy, but also that its exploitation requires a deeper understanding of the molecular mechanisms underlying its dual role in cancer and viral infections. In this Review, we will summarize the known roles of DDX3X in different tumor types and viral infections, and the different inhibitors available, illustrating the possible advantages and potential caveats of their use as anticancer and antiviral drugs.
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86
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Perčulija V, Ouyang S. Diverse Roles of DEAD/DEAH-Box Helicases in Innate Immunity and Diseases. HELICASES FROM ALL DOMAINS OF LIFE 2019. [PMCID: PMC7158350 DOI: 10.1016/b978-0-12-814685-9.00009-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
DEAD/DEAH-box helicases are enzymes that belong to the DEAD/H-box family of SF2 helicase superfamily. These enzymes are essential in RNA metabolism, where they are involved in a number of processes that require manipulation of RNA structure. Recent studies have found that some DEAD/DEAH-box helicases play important roles in innate immunity, where they act as sensors of cytosolic DNA/RNA, as adaptor proteins, or as regulators of signaling and gene expression. In spite of their function in immunity, DEAD/DEAH-box helicases can also be hijacked and exploited by viruses to circumvent detection and aid in viral replication. These findings not only imply that DEAD/DEAH-box helicases have a broader function than previously thought, but also give us a much better understanding of immune mechanisms and diseases that arise due to the dysregulation or evasion thereof. In this chapter, we demonstrate the known scope of activities of human DEAD/DEAH-box helicases in innate immunity and interaction with viruses or other pathogens. Additionally, we give an outline of diseases in which they are, or may be, involved in the context of immunity.
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87
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DDX3 Participates in Translational Control of Inflammation Induced by Infections and Injuries. Mol Cell Biol 2018; 39:MCB.00285-18. [PMID: 30373933 DOI: 10.1128/mcb.00285-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/10/2018] [Indexed: 12/28/2022] Open
Abstract
Recent studies have suggested that DDX3 functions in antiviral innate immunity, but the underlying mechanism remains elusive. We previously identified target mRNAs whose translation is controlled by DDX3. Pathway enrichment analysis of these targets indicated that DDX3 is involved in various infections and inflammation. Using immunoblotting, we confirmed that PACT, STAT1, GNB2, Rac1, TAK1, and p38 mitogen-activated protein kinase (MAPK) proteins are downregulated by DDX3 knockdown in human monocytic THP-1 cells and epithelial HeLa cells. Polysome profiling revealed that DDX3 knockdown reduces the translational efficiency of target mRNAs. We further demonstrated DDX3-mediated translational control of target mRNAs by luciferase reporter assays. To examine the effects of DDX3 knockdown on macrophage migration and phagocytosis, we performed in vitro cell migration assay and flow cytometry analysis of the uptake of green fluorescent protein-expressing Escherichia coli in THP-1 cells. The DDX3 knockdown cells exhibited impaired macrophage migration and phagocytosis. Moreover, we used a human cytokine antibody array to identify the cytokines affected by DDX3 knockdown. Several chemokines were decreased considerably in DDX3 knockdown THP-1 cells after lipopolysaccharide or poly(I·C) stimulation. Lastly, we demonstrated that DDX3 is crucial for the recruitment of phagocytes to the site of inflammation in transgenic zebrafish.
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88
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Xing Z, Ma WK, Tran EJ. The DDX5/Dbp2 subfamily of DEAD-box RNA helicases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1519. [PMID: 30506978 DOI: 10.1002/wrna.1519] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/26/2018] [Accepted: 11/01/2018] [Indexed: 01/05/2023]
Abstract
The mammalian DEAD-box RNA helicase DDX5, its paralog DDX17, and their orthologs in Saccharomyces cerevisiae and Drosophila melanogaster, namely Dbp2 and Rm62, define a subfamily of DEAD-box proteins. Members from this subfamily share highly conserved protein sequences and cellular functions. They are involved in multiple steps of RNA metabolism including mRNA processing, microRNA processing, ribosome biogenesis, RNA decay, and regulation of long noncoding RNA activities. The DDX5/Dbp2 subfamily is also implicated in transcription regulation, cellular signaling pathways, and energy metabolism. One emerging theme underlying the diverse cellular functions is that the DDX5/Dbp2 subfamily of DEAD-box helicases act as chaperones for complexes formed by RNA molecules and proteins (RNP) in vivo. This RNP chaperone activity governs the functions of various RNA species through their lifetime. Importantly, mammalian DDX5 and DDX17 are involved in cancer progression when overexpressed through alteration of transcription and signaling pathways, meaning that they are possible targets for cancer therapy. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Zheng Xing
- Department of Biochemistry, Purdue University, West Lafayette, Indiana.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana
| | - Wai Kit Ma
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, West Lafayette, Indiana.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana
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89
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Jankowsky E, Guenther UP. A helicase links upstream ORFs and RNA structure. Curr Genet 2018; 65:453-456. [PMID: 30483885 DOI: 10.1007/s00294-018-0911-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 01/08/2023]
Abstract
Upstream open reading frames (uORFs) in 5' UTRs of eukaryotic mRNAs are increasingly recognized as important elements that regulate cellular protein synthesis. Since uORFs can start from non-AUG codons, an enormous number of potential uORF initiation sites exists in 5'UTRs. However, only a subset of these sites is used and it has been unclear how actual start sites are selected. Studies of the DEAD-box helicase Ded1p from S. cerevisiae show that translation of uORFs with non-AUG initiation codons occurs upstream of mRNA structures that emerge with defective Ded1p. The data designate mRNA structure as important determinant for non-AUG initiation sites of uORFs. Ded1p can control this RNA structure and thereby regulate uORF translation.
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Affiliation(s)
- Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Ulf-Peter Guenther
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,EMBL, Heidelberg, Germany
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90
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Abstract
Cap-dependent translation initiation begins by assembly of a pre-initiation ribosomal complex that scans the 5' Untranslated Region in order to localise the start codon. During this process, RNA secondary structures are melted by RNA helicases. Guenther et al reported that the yeast helicase Ded1, an orthologue of the mammalian DDX3 helicase, is responsible for this activity. When Ded1 is non-functional, RNA structures in the 5'UTR promote translation initiation on Alternative Translation Initiation Sites (ATIS) lead to uORF translation and consequently down-regulation of the main ORF. This mechanism is driven by the sole presence of RNA secondary structures located downstream of ATIS. Translation initiation mediated by RNA structures is found in other messenger RNAs. We propose to name this novel mechanism STructure-Assisted-RNA-Translation or START.
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Affiliation(s)
- Gilbert Eriani
- a Architecture et Réactivité de l'ARN UPR 9002, CNRS , Université de Strasbourg , Strasbourg , France
| | - Franck Martin
- a Architecture et Réactivité de l'ARN UPR 9002, CNRS , Université de Strasbourg , Strasbourg , France
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91
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Brennan R, Haap-Hoff A, Gu L, Gautier V, Long A, Schröder M. Investigating nucleo-cytoplasmic shuttling of the human DEAD-box helicase DDX3. Eur J Cell Biol 2018; 97:501-511. [PMID: 30131165 DOI: 10.1016/j.ejcb.2018.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 01/20/2023] Open
Abstract
The human DEAD-box helicase DDX3 is a multi-functional protein involved in the regulation of gene expression and additional non-conventional roles as signalling adaptor molecule that are independent of its enzymatic RNA remodeling activity. It is a nucleo-cytoplasmic shuttling protein and it has previously been suggested that dysregulation of its subcellular localization could contribute to tumourigenesis. Indeed, both tumour suppressor and oncogenic functions have been attributed to DDX3. In this study, we investigated the regulation of DDX3's nucleocytoplasmic shuttling. We confirmed that an N-terminal conserved Nuclear Export Signal (NES) is required for export of human DDX3 from the nucleus, and identified three regions within DDX3 that can independently facilitate its nuclear import. We also aimed to identify conditions that alter DDX3's subcellular localisation. Viral infection, cytokine treatment and DNA damage only induced minor changes in DDX3's subcellular distribution as determined by High Content Analysis. However, DDX3's nuclear localization increased in early mitotic cells (during prophase) concomitant with an increase in DDX3 expression levels. Our results are likely to have implications for the proposed use of (nuclear) DDX3 as a prognostic biomarker in cancer.
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Affiliation(s)
- Ruth Brennan
- Institute of Immunology, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Antje Haap-Hoff
- School of Medicine, Trinity College Dublin, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Dublin 2, Ireland
| | - Lili Gu
- Institute of Immunology, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Virginie Gautier
- School of Medicine, Centre for Research in Infectious Diseases (CRID), University College Dublin, Belfield, Dublin 4, Ireland
| | - Aideen Long
- School of Medicine, Trinity College Dublin, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Dublin 2, Ireland
| | - Martina Schröder
- Institute of Immunology, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland.
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92
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Cannizzaro E, Bannister AJ, Han N, Alendar A, Kouzarides T. DDX3X RNA helicase affects breast cancer cell cycle progression by regulating expression of KLF4. FEBS Lett 2018; 592:2308-2322. [PMID: 29782654 PMCID: PMC6100109 DOI: 10.1002/1873-3468.13106] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 12/13/2022]
Abstract
DDX3X is a multifunctional RNA helicase with documented roles in different cancer types. Here, we demonstrate that DDX3X plays an oncogenic role in breast cancer cells by modulating the cell cycle. Depletion of DDX3X in MCF7 cells slows cell proliferation by inducing a G1 phase arrest. Notably, DDX3X inhibits expression of Kruppel-like factor 4 (KLF4), a transcription factor and cell cycle repressor. Moreover, DDX3X directly interacts with KLF4 mRNA and regulates its splicing. We show that DDX3X-mediated repression of KLF4 promotes expression of S-phase inducing genes in MCF7 breast cancer cells. These findings provide evidence for a novel function of DDX3X in regulating expression and downstream functions of KLF4, a master negative regulator of the cell cycle.
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Affiliation(s)
- Ester Cannizzaro
- Department of Pathology and Gurdon InstituteUniversity of CambridgeCambridgeUK
| | | | - Namshik Han
- Department of Pathology and Gurdon InstituteUniversity of CambridgeCambridgeUK
| | - Andrej Alendar
- Department of Pathology and Gurdon InstituteUniversity of CambridgeCambridgeUK
| | - Tony Kouzarides
- Department of Pathology and Gurdon InstituteUniversity of CambridgeCambridgeUK
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93
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The helicase Ded1p controls use of near-cognate translation initiation codons in 5' UTRs. Nature 2018; 559:130-134. [PMID: 29950728 PMCID: PMC6226265 DOI: 10.1038/s41586-018-0258-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/08/2018] [Indexed: 12/21/2022]
Abstract
The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian orthologue DDX3 are critical for the initiation of translation1. Mutations in DDX3 are linked to tumorigenesis2-4 and intellectual disability5, and the enzyme is targeted by a range of viruses6. How Ded1p and its orthologues engage RNAs during the initiation of translation is unknown. Here we show, by integrating transcriptome-wide analyses of translation, RNA structure and Ded1p-RNA binding, that the effects of Ded1p on the initiation of translation are connected to near-cognate initiation codons in 5' untranslated regions. Ded1p associates with the translation pre-initiation complex at the mRNA entry channel and repressing the activity of Ded1p leads to the accumulation of RNA structure in 5' untranslated regions, the initiation of translation from near-cognate start codons immediately upstream of these structures and decreased protein synthesis from the corresponding main open reading frames. The data reveal a program for the regulation of translation that links Ded1p, the activation of near-cognate start codons and mRNA structure. This program has a role in meiosis, in which a marked decrease in the levels of Ded1p is accompanied by the activation of the alternative translation initiation sites that are seen when the activity of Ded1p is repressed. Our observations indicate that Ded1p affects translation initiation by controlling the use of near-cognate initiation codons that are proximal to mRNA structure in 5' untranslated regions.
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94
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Meier-Stephenson V, Mrozowich T, Pham M, Patel TR. DEAD-box helicases: the Yin and Yang roles in viral infections. Biotechnol Genet Eng Rev 2018; 34:3-32. [PMID: 29742983 DOI: 10.1080/02648725.2018.1467146] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Viruses hijack the host cell machinery and recruit host proteins to aid their replication. Several host proteins also play vital roles in inhibiting viral replication. Emerging class of host proteins central to both of these processes are the DEAD-box helicases: a highly conserved family of ATP-dependent RNA helicases, bearing a common D-E-A-D (Asp-Glu-Ala-Asp) motif. They play key roles in numerous cellular processes, including transcription, splicing, miRNA biogenesis and translation. Though their sequences are highly conserved, these helicases have quite diverse roles in the cell. Interestingly, often these helicases display contradictory actions in terms of the support and/or clearance of invading viruses. Increasing evidence highlights the importance of these enzymes, however, little is known about the structural basis of viral RNA recognition by the members of the DEAD-box family. This review summarizes the current knowledge in the field for selected DEAD-box helicases and highlights their diverse actions upon viral invasion of the host cell. We anticipate that through a better understanding of how these helicases are being utilized by viral RNAs and proteins to aid viral replication, it will be possible to address the urgent need to develop novel therapeutic approaches to combat viral infections.
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Affiliation(s)
- Vanessa Meier-Stephenson
- a Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute , University of Lethbridge , Lethbridge , Canada.,b Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine , University of Calgary , Calgary , Canada
| | - Tyler Mrozowich
- a Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute , University of Lethbridge , Lethbridge , Canada
| | - Mimi Pham
- a Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute , University of Lethbridge , Lethbridge , Canada
| | - Trushar R Patel
- a Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute , University of Lethbridge , Lethbridge , Canada.,b Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine , University of Calgary , Calgary , Canada.,c Faculty of Medicine & Dentistry, DiscoveryLab , University of Alberta , Edmonton , Canada
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95
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Kellaris G, Khan K, Baig SM, Tsai IC, Zamora FM, Ruggieri P, Natowicz MR, Katsanis N. A hypomorphic inherited pathogenic variant in DDX3X causes male intellectual disability with additional neurodevelopmental and neurodegenerative features. Hum Genomics 2018; 12:11. [PMID: 29490693 PMCID: PMC5831694 DOI: 10.1186/s40246-018-0141-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/15/2018] [Indexed: 12/19/2022] Open
Abstract
Background Intellectual disability (ID) is a common condition with a population prevalence frequency of 1–3% and an enrichment for males, driven in part by the contribution of mutant alleles on the X-chromosome. Among the more than 500 genes associated with ID, DDX3X represents an outlier in sex specificity. Nearly all reported pathogenic variants of DDX3X are de novo, affect mostly females, and appear to be loss of function variants, consistent with the hypothesis that haploinsufficiency at this locus on the X-chromosome is likely to be lethal in males. Results We evaluated two male siblings with syndromic features characterized by mild-to-moderate ID and progressive spasticity. Quad-based whole-exome sequencing revealed a maternally inherited missense variant encoding p.R79K in DDX3X in both siblings and no other apparent pathogenic variants. We assessed its possible relevance to their phenotype using an established functional assay for DDX3X activity in zebrafish embryos and found that this allele causes a partial loss of DDX3X function and thus represents a hypomorphic variant. Conclusions Our genetic and functional data suggest that partial loss of function of DDX3X can cause syndromic ID. The p.R79K allele affects a region of the protein outside the critical RNA helicase domain, offering a credible explanation for the observed retention of partial function, viability in hemizygous males, and lack of pathology in females. These findings expand the gender spectrum of pathology of this locus and suggest that analysis for DDX3X variants should be considered relevant for both males and females. Electronic supplementary material The online version of this article (10.1186/s40246-018-0141-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Georgios Kellaris
- Center for Human Disease Modeling, Duke University, 300 North Duke Street, Durham, NC, 27701, USA.,Department of Medical Genetics, University of Athens Medical School, Aghia Sophia Children's Hospital, 11527, Athens, Greece
| | - Kamal Khan
- Center for Human Disease Modeling, Duke University, 300 North Duke Street, Durham, NC, 27701, USA.,Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, 38000, Pakistan
| | - Shahid M Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, 38000, Pakistan
| | - I-Chun Tsai
- Center for Human Disease Modeling, Duke University, 300 North Duke Street, Durham, NC, 27701, USA
| | | | - Paul Ruggieri
- Imaging Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Marvin R Natowicz
- Pathology and Laboratory Medicine and Genomic Medicine Institutes, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, 300 North Duke Street, Durham, NC, 27701, USA. .,Imaging Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.
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96
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The DEAD-Box RNA Helicase DDX3 Interacts with m 6A RNA Demethylase ALKBH5. Stem Cells Int 2017; 2017:8596135. [PMID: 29333169 PMCID: PMC5733242 DOI: 10.1155/2017/8596135] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/27/2017] [Accepted: 08/17/2017] [Indexed: 02/06/2023] Open
Abstract
DDX3 is a member of the family of DEAD-box RNA helicases. DDX3 is a multifaceted helicase and plays essential roles in key biological processes such as cell cycle, stress response, apoptosis, and RNA metabolism. In this study, we found that DDX3 interacted with ALKBH5, an m6A RNA demethylase. The ATP domain of DDX3 and DSBH domain of ALKBH5 were indispensable to their interaction with each other. Furthermore, DDX3 could modulate the demethylation of mRNAs. We also showed that DDX3 regulated the methylation status of microRNAs and there was an interaction between DDX3 and AGO2. The dynamics of m6A RNA modification is still a field demanding further investigation, and here, we add a link by showing that RNA demethylation can be regulated by proteins such as DDX3.
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97
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Aryanpur PP, Regan CA, Collins JM, Mittelmeier TM, Renner DM, Vergara AM, Brown NP, Bolger TA. Gle1 Regulates RNA Binding of the DEAD-Box Helicase Ded1 in Its Complex Role in Translation Initiation. Mol Cell Biol 2017; 37:e00139-17. [PMID: 28784717 PMCID: PMC5640818 DOI: 10.1128/mcb.00139-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/05/2017] [Accepted: 07/21/2017] [Indexed: 02/07/2023] Open
Abstract
DEAD-box proteins (DBPs) are required in gene expression to facilitate changes to ribonucleoprotein complexes, but the cellular mechanisms and regulation of DBPs are not fully defined. Gle1 is a multifunctional regulator of DBPs with roles in mRNA export and translation. In translation, Gle1 modulates Ded1, a DBP required for initiation. However, DED1 overexpression causes defects, suggesting that Ded1 can promote or repress translation in different contexts. Here we show that GLE1 expression suppresses the repressive effects of DED1 in vivo and Gle1 counteracts Ded1 in translation assays in vitro Furthermore, both Ded1 and Gle1 affect the assembly of preinitiation complexes. Through mutation analysis and binding assays, we show that Gle1 inhibits Ded1 by reducing its affinity for RNA. Our results are consistent with a model wherein active Ded1 promotes translation but inactive or excess Ded1 leads to translation repression. Gle1 can inhibit either role of Ded1, positioning it as a gatekeeper to optimize Ded1 activity to the appropriate level for translation. This study suggests a paradigm for finely controlling the activity of DEAD-box proteins to optimize their function in RNA-based processes. It also positions the versatile regulator Gle1 as a potential node for the coordination of different steps of gene expression.
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Affiliation(s)
- Peyman P Aryanpur
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Chelsea A Regan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - John M Collins
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Telsa M Mittelmeier
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - David M Renner
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Ashley M Vergara
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Nicolette P Brown
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Timothy A Bolger
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
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98
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Adjibade P, Grenier St-Sauveur V, Bergeman J, Huot ME, Khandjian EW, Mazroui R. DDX3 regulates endoplasmic reticulum stress-induced ATF4 expression. Sci Rep 2017; 7:13832. [PMID: 29062139 PMCID: PMC5653821 DOI: 10.1038/s41598-017-14262-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 10/06/2017] [Indexed: 12/26/2022] Open
Abstract
Accumulation of unfolded and potentially toxic proteins in the endoplasmic reticulum (ER) activates a cell stress adaptive response, which involves a reprogramming of general gene expression. ATF4 is a master stress-induced transcription factor that orchestrates gene expression in cells treated with various ER stress inducers including those used to treat cancers. ER stress-induced ATF4 expression occurs mainly at the translational level involving the activity of the phosphorylated (P) translation initiation factor (eIF) eIF2α. While it is well established that under ER stress PeIF2α drives ATF4 expression through a specialised mode of translation re-initiation, factors (e.g. RNA-binding proteins and specific eIFs) involved in PeIF2α-mediated ATF4 translation remain unknown. Here we identified the RNA-binding protein named DDX3 as a promotor of ATF4 expression in cancer cells treated with sorafenib, an ER stress inducer used as a chemotherapeutic. Depletion experiments showed that DDX3 is required for PeIF2α-mediated ATF4 expression. Luciferase and polyribosomes assays showed that DDX3 drives ER stress-induced ATF4 mRNA expression at the translational level. Protein-interaction assays showed that DDX3 binds the eIF4F complex, which we found to be required for ER stress-induced ATF4 expression. This study thus showed that PeIF2α-mediated ATF4 mRNA translation requires DDX3 as a part of the eIF4F complex.
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Affiliation(s)
- Pauline Adjibade
- Centre de recherche en cancérologie. Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Université Laval, Québec, PQ, Canada
| | - Valérie Grenier St-Sauveur
- Centre de recherche en cancérologie. Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Université Laval, Québec, PQ, Canada.,Complexe de diagnostic et d'épidémiosurveillance vétérinaires du Québec (CDEVQ) Université de Montréal, Montréal, Canada
| | - Jonathan Bergeman
- Centre de recherche en cancérologie. Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Université Laval, Québec, PQ, Canada
| | - Marc-Etienne Huot
- Centre de recherche en cancérologie. Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Université Laval, Québec, PQ, Canada
| | - Edouard W Khandjian
- Centre de Recherche, Institut universitaire en santé mentale de Québec. Département de psychiatrie et de neurosciences, Faculté de médecine, Université Laval, Québec, PQ, Canada
| | - Rachid Mazroui
- Centre de recherche en cancérologie. Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, Université Laval, Québec, PQ, Canada.
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99
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Milani L, Pecci A, Cifaldi C, Maurizii MG. PL10 DEAD-Box Protein is Expressed during Germ Cell Differentiation in the Reptile Podarcis sicula (Family Lacertidae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:433-448. [PMID: 28656658 DOI: 10.1002/jez.b.22744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/15/2017] [Accepted: 04/05/2017] [Indexed: 11/09/2022]
Abstract
Among genes involved in the regulation of germ cell differentiation, those of DDX4/Vasa and the Ded1/DDX3 subfamilies encode for DEAD-box ATP-dependent RNA helicases, proteins involved in many mechanisms related to RNA processing. For the first time in reptiles, using specific antibodies at confocal microscopy, we analysed the localization pattern of a Ded1/DDX3 subfamily member in testis and ovary of Podarcis sicula (Ps-PL10) during the reproductive cycle. In testis, Ps-PL10 is expressed in the cytoplasm of spermatocytes and it is not detected in spermatogonia. Differently from Ps-VASA, in round spermatids, Ps-PL10 is not segregated in the chromatoid body but it accumulates in the cytoplasm of residual bodies, and mature spermatozoa are unstained. These observations suggest that in males, Ps-PL10 (1) is involved in spermatogenesis and (2) is then eliminated with residual bodies. In the ovary, Ps-PL10 is present with granules in the cytoplasm of early meiotic cells of the germinal bed (GB), while it is not present in oogonia and somatic cells of the GB stroma. In follicular cells of ovarian follicles, Ps-PL10 expression starts after their fusion with the oocyte. Numerous Ps-PL10 spots are visible in pyriform (nurse-like) cells concomitantly with the protein accumulation in the cytoplasm of differentiating oocyte. In pyriform cells, Ps-PL10 spots are present in the cytoplasm and nuclei, as observed for Ps-VASA, and in the nucleoli, suggesting for Ps-PL10 a role in rRNA processing and in the transport of molecules from the nucleus to cytoplasm and from nurse cells to the oocyte.
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Affiliation(s)
- Liliana Milani
- Department of Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Andrea Pecci
- Department of Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Carmine Cifaldi
- Department of Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Maria Gabriella Maurizii
- Department of Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
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100
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Biochemical Differences and Similarities between the DEAD-Box Helicase Orthologs DDX3X and Ded1p. J Mol Biol 2017; 429:3730-3742. [PMID: 29037760 DOI: 10.1016/j.jmb.2017.10.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 12/14/2022]
Abstract
DDX3X is a conserved DEAD-box RNA helicase involved in translation initiation and other processes of RNA metabolism. Mutations in human DDX3X and deregulation of its expression are linked to tumorigenesis and intellectual disability. The protein is also targeted by diverse viruses. Previous studies demonstrated helicase and NTPase activities for DDX3X, but important biochemical features of the enzyme remain unclear. Here, we systematically characterize enzymatic activities of human DDX3X and compare these to its closely related Saccharomyces cerevisiae ortholog Ded1p. We show that DDX3X, like Ded1p, utilizes exclusively adenosine triphosphates to unwind helices, oligomerizes to function as efficient RNA helicase, and does not unwind DNA duplexes. The ATPase activity of DDX3X is markedly stimulated by RNA and weaker by DNA, although DNA binds to the enzyme. For RNA unwinding, DDX3X shows a greater preference than Ded1p for substrates with unpaired regions 3' to the duplex over those with 5' unpaired regions. DDX3X separates longer RNA duplexes faster than Ded1p and is less potent than Ded1p in facilitating strand annealing. Our results reveal that the biochemical activities of human DDX3X are typical for DEAD-box RNA helicases, but diverge quantitatively from its highly similar S. cerevisiae ortholog Ded1p.
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