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von Ehr J, Oberstrass L, Yazgan E, Schnaubelt LI, Blümel N, McNicoll F, Weigand JE, Zarnack K, Müller-McNicoll M, Korn SM, Schlundt A. Arid5a uses disordered extensions of its core ARID domain for distinct DNA- and RNA-recognition and gene regulation. J Biol Chem 2024; 300:107457. [PMID: 38866324 DOI: 10.1016/j.jbc.2024.107457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/23/2024] [Accepted: 06/01/2024] [Indexed: 06/14/2024] Open
Abstract
AT-rich interacting domain (ARID)-containing proteins, Arids, are a heterogeneous DNA-binding protein family involved in transcription regulation and chromatin processing. For the member Arid5a, no exact DNA-binding preference has been experimentally defined so far. Additionally, the protein binds to mRNA motifs for transcript stabilization, supposedly through the DNA-binding ARID domain. To date, however, no unbiased RNA motif definition and clear dissection of nucleic acid-binding through the ARID domain have been undertaken. Using NMR-centered biochemistry, we here define the Arid5a DNA preference. Further, high-throughput in vitro binding reveals a consensus RNA-binding motif engaged by the core ARID domain. Finally, transcriptome-wide binding (iCLIP2) reveals that Arid5a has a weak preference for (A)U-rich regions in pre-mRNA transcripts of factors related to RNA processing. We find that the intrinsically disordered regions flanking the ARID domain modulate the specificity and affinity of DNA binding, while they appear crucial for RNA interactions. Ultimately, our data suggest that Arid5a uses its extended ARID domain for bifunctional gene regulation and that the involvement of IDR extensions is a more general feature of Arids in interacting with different nucleic acids at the chromatin-mRNA interface.
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Affiliation(s)
- Julian von Ehr
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany; IMPRS on Cellular Biophysics, Frankfurt, Germany
| | - Lasse Oberstrass
- University of Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marburg, Germany
| | - Ege Yazgan
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Lara Ina Schnaubelt
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany
| | - Nicole Blümel
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Francois McNicoll
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Julia E Weigand
- University of Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marburg, Germany
| | - Kathi Zarnack
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Michaela Müller-McNicoll
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany; Max-Planck Institute for Biophysics, Frankfurt, Germany
| | - Sophie Marianne Korn
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Frankfurt, Germany; University of Greifswald, Institute of Biochemistry, Greifswald, Germany.
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Barua D, Płecha M, Muszewska A. A minimal Fanconi Anemia complex in early diverging fungi. Sci Rep 2024; 14:9922. [PMID: 38688950 PMCID: PMC11061109 DOI: 10.1038/s41598-024-60318-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
Fanconi Anemia (FA) pathway resolves DNA interstrand cross links (ICL). The FA pathway was initially recognized in vertebrates, but was later confirmed in other animals and speculated in fungi. FA proteins FANCM, FANCL and FANCJ are present in Saccharomyces cerevisiae but, their mechanism of interaction to resolve ICL is still unclear. Unlike Dikarya, early diverging fungi (EDF) possess more traits shared with animals. We traced the evolutionary history of the FA pathway across Opisthokonta. We scanned complete proteomes for FA-related homologs to establish their taxonomic distribution and analyzed their phylogenetic trees. We checked transcription profiles of FA genes to test if they respond to environmental conditions and their genomic localizations for potential co-localization. We identified fungal homologs of the activation and ID complexes, 5 out of 8 core proteins, all of the endonucleases, and deubiquitination proteins. All fungi lack FANCC, FANCF and FANCG proteins responsible for post-replication repair and chromosome stability in animals. The observed taxonomic distribution can be attributed to a gradual degradation of the FA pathway from EDF to Dikarya. One of the key differences is that EDF have the ID complex recruiting endonucleases to the site of ICL. Moreover, 21 out of 32 identified FA genes are upregulated in response to different growth conditions. Several FA genes are co-localized in fungal genomes which also could facilitate co-expression. Our results indicate that a minimal FA pathway might still be functional in Mucoromycota with a gradual loss of components in Dikarya ancestors.
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Affiliation(s)
- Drishtee Barua
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Magdalena Płecha
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland.
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3
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Ong SC, Luo HW, Cheng WH, Ku FM, Tsai CY, Huang PJ, Lee CC, Yeh YM, Lin R, Chiu CH, Tang P. The core exosome proteome of Trichomonas vaginalis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024; 57:246-256. [PMID: 38383245 DOI: 10.1016/j.jmii.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/15/2024] [Accepted: 02/13/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Trichomonas vaginalis is parasitic protozoan that causes human urogenital infections. Accumulated reports indicated that exosomes released by this parasite play a crucial role in transmitting information and substances between cells during host-parasite interactions. Current knowledge on the protein contents in T. vaginalis exosome is mainly generated from three previous studies that used different T. vaginalis isolates as an experimental model. Whether T. vaginalis exosomes comprise a common set of proteins (core exosome proteome) is still unclear. METHODS To explore the core exosome proteome in T. vaginalis, we used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify the contents of sucrose ultracentrifugation-enriched exosome and supernatant fractions isolated from six isolates. RESULTS Transmission electron microscopy (TEM) confirmed the presence of exosomes in the enriched fraction. Proteomic analysis identified a total of 1870 proteins from exosomal extracts. There were 1207 exosomal-specific proteins after excluding 436 'non-core exosomal proteins'. Among these, 72 common exosomal-specific proteins were expressed in all six isolates. Compared with three published T. vaginalis exosome proteome datasets, we identified 16 core exosomal-specific proteins. These core exosomal-specific proteins included tetraspanin (TvTSP1), the classical exosome marker, and proteins mainly involved in catalytic activity and binding such as ribosomal proteins, ras-associated binding (Rab) proteins, and heterotrimeric G proteins. CONCLUSIONS Our study highlighted the importance of using supernatant fraction from exosomal extract as a control to eliminate 'non-core exosomal proteins'. We compiled a reference core exosome proteome of T. vaginalis, which is essential for developing a fundamental understanding of exosome-mediated cell communication and host-parasite interaction.
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Affiliation(s)
- Seow-Chin Ong
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Hong-Wei Luo
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Wei-Hung Cheng
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan City, Taiwan.
| | - Fu-Man Ku
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Chih-Yu Tsai
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan; Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Department of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Rose Lin
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan.
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Petrus Tang
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan District, Taoyuan City, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
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Moore AFT, Berhie Y, Weislow IS, Koculi E. Substrate Specificities of DDX1: A Human DEAD-box protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.573566. [PMID: 38260591 PMCID: PMC10802426 DOI: 10.1101/2024.01.09.573566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
DDX1 is a human protein which belongs to the DEAD-box protein family of enzymes and is involved in various stages of RNA metabolism from transcription to decay. Many members of the DEAD-box family of enzymes use the energy of ATP binding and hydrolysis to perform their cellular functions. On the other hand, a few members of the DEAD-box family of enzymes bind and/or hydrolyze other nucleotides in addition to ATP. Furthermore, the ATPase activity of DEAD-box family members is stimulated differently by nucleic acids of various structures. The identity of the nucleotides that the DDX1 hydrolyzes and the structure of the nucleic acids upon which it acts in the cell remain largely unknown. Identifying the DDX1 protein's in vitro substrates is important for deciphering the molecular roles of DDX1 in cells. Here we identify the nucleic acid sequences and structures supporting the nucleotide hydrolysis activity of DDX1 and its nucleotide specificity. Our data demonstrate that the DDX1 protein hydrolyzes only ATP and deoxy-ATP in the presence of RNA. The ATP hydrolysis activity of DDX1 is stimulated by multiple molecules: single-stranded RNA molecules as short as ten nucleotides, a blunt-ended double-stranded RNA molecule, a hybrid of a double-stranded DNA-RNA molecule, and a single-stranded DNA molecule. Under our experimental conditions, the single-stranded DNA molecule stimulates the ATPase activity of DDX1 at a significantly reduced extent when compared to the other investigated RNA constructs or the hybrid double-stranded DNA/RNA molecule.
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Affiliation(s)
- Anthony F. T. Moore
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Physical Sciences, Orlando, FL 32816-2366
| | - Yepeth Berhie
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Physical Sciences, Orlando, FL 32816-2366
| | - Isaac S. Weislow
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 W University Ave, Chemistry and Computer Science, El Paso, TX, 79902-5802
| | - Eda Koculi
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 W University Ave, Chemistry and Computer Science, El Paso, TX, 79902-5802
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Tan H, Wang W, Zhou C, Wang Y, Zhang S, Yang P, Guo R, Chen W, Zhang J, Ye L, Cui Y, Ni T, Zheng K. Single-cell RNA-seq uncovers dynamic processes orchestrated by RNA-binding protein DDX43 in chromatin remodeling during spermiogenesis. Nat Commun 2023; 14:2499. [PMID: 37120627 DOI: 10.1038/s41467-023-38199-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 04/20/2023] [Indexed: 05/01/2023] Open
Abstract
Mammalian spermatogenesis shows prominent chromatin and transcriptomic switches in germ cells, but it is unclear how such dynamics are controlled. Here we identify RNA helicase DDX43 as an essential regulator of the chromatin remodeling process during spermiogenesis. Testis-specific Ddx43 knockout mice show male infertility with defective histone-to-protamine replacement and post-meiotic chromatin condensation defects. The loss of its ATP hydrolysis activity by a missense mutation replicates the infertility phenotype in global Ddx43 knockout mice. Single-cell RNA sequencing analyses of germ cells depleted of Ddx43 or expressing the Ddx43 ATPase-dead mutant reveals that DDX43 regulates dynamic RNA regulatory processes that underlie spermatid chromatin remodeling and differentiation. Transcriptomic profiling focusing on early-stage spermatids combined with enhanced crosslinking immunoprecipitation and sequencing further identifies Elfn2 as DDX43-targeted hub gene. These findings illustrate an essential role for DDX43 in spermiogenesis and highlight the single-cell-based strategy to dissect cell-state-specific regulation of male germline development.
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Affiliation(s)
- Huanhuan Tan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
- Reproductive Medicine Center, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, 400016, Chongqing, Yuzhong District, China
| | - Weixu Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences and Huashan Hospital, Fudan University, 200438, Shanghai, China
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Congjin Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Yanfeng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Shu Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Pinglan Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Rui Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Wei Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences and Huashan Hospital, Fudan University, 200438, Shanghai, China
| | - Jinwen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Yiqiang Cui
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China.
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences and Huashan Hospital, Fudan University, 200438, Shanghai, China.
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China.
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6
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Amer NN, Khairat R, Hammad AM, Kamel MM. DDX43 mRNA expression and protein levels in relation to clinicopathological profile of breast cancer. PLoS One 2023; 18:e0284455. [PMID: 37200388 DOI: 10.1371/journal.pone.0284455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 04/01/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Breast cancer (BC) is the most often diagnosed cancer in women globally. Cancer cells appear to rely heavily on RNA helicases. DDX43 is one of DEAD- box RNA helicase family members. But, the relationship between clinicopathological, prognostic significance in different BC subtypes and DDX43 expression remains unclear. Therefore, the purpose of this study was to assess the clinicopathological significance of DDX43 protein and mRNA expression in different BC subtypes. MATERIALS AND METHODS A total of 80 females newly diagnosed with BC and 20 control females that were age-matched were recruited for this study. DDX43 protein levels were measured by ELISA technique. We used a real-time polymerase chain reaction quantification (real-time PCR) to measure the levels of DDX43 mRNA expression. Levels of DDX43 protein and mRNA expression within BC patients had been compared to those of control subjects and correlated with clinicopathological data. RESULTS The mean normalized serum levels of DDX43 protein were slightly higher in control than in both benign and malignant groups, but this result was non-significant. The mean normalized level of DDX43 mRNA expression was higher in the control than in both benign and malignant cases, although the results were not statistically significant and marginally significant, respectively. Moreover, the mean normalized level of DDX43 mRNA expression was significantly higher in benign than in malignant cases. In malignant cases, low DDX43 protein expression was linked to higher nuclear grade and invasive duct carcinoma (IDC), whereas high mRNA expression was linked to the aggressive types of breast cancer such as TNBC, higher tumor and nuclear grades. CONCLUSION This study explored the potential of using blood DDX43 mRNA expression or protein levels, or both in clinical settings as a marker of disease progression in human breast cancer. DDX43 mRNA expression proposes a less invasive method for discriminating benign from malignant BC.
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Affiliation(s)
- Noha N Amer
- Faculty of Pharmacy (Girls), Department of Biochemistry and Molecular Biology, Al-Azhar University, Cairo, Egypt
| | - Rabab Khairat
- Medical Molecular Genetics Department, Human Genetics and Genomic Research Division, National Research Center, Cairo, Egypt
| | - Amal M Hammad
- Faculty of medicine, Department of Medical Biochemistry, Al-Azhar University, Damietta, Egypt
| | - Mahmoud M Kamel
- Clinical Pathology Department, National Cancer Institute, Cairo, Egypt
- Baheya Centre for Early Detection and Treatment of Breast Cancer, Giza, Egypt
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Singh RS, Vidhyasagar V, Yang S, Arna AB, Yadav M, Aggarwal A, Aguilera AN, Shinriki S, Bhanumathy KK, Pandey K, Xu A, Rapin N, Bosch M, DeCoteau J, Xiang J, Vizeacoumar FJ, Zhou Y, Misra V, Matsui H, Ross SR, Wu Y. DDX41 is required for cGAS-STING activation against DNA virus infection. Cell Rep 2022; 39:110856. [PMID: 35613581 PMCID: PMC9205463 DOI: 10.1016/j.celrep.2022.110856] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 04/07/2022] [Accepted: 05/02/2022] [Indexed: 12/27/2022] Open
Abstract
Upon binding double-stranded DNA (dsDNA), cyclic GMP-AMP synthase (cGAS) is activated and initiates the cGAS-stimulator of IFN genes (STING)-type I interferon pathway. DEAD-box helicase 41 (DDX41) is a DEAD-box helicase, and mutations in DDX41 cause myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). Here, we show that DDX41-knockout (KO) cells have reduced type I interferon production after DNA virus infection. Unexpectedly, activations of cGAS and STING are affected in DDX41 KO cells, suggesting that DDX41 functions upstream of cGAS. The recombinant DDX41 protein exhibits ATP-dependent DNA-unwinding activity and ATP-independent strand-annealing activity. The MDS/AML-derived mutant R525H has reduced unwinding activity but retains normal strand-annealing activity and stimulates greater cGAS dinucleotide-synthesis activity than wild-type DDX41. Overexpression of R525H in either DDX41-deficient or -proficient cells results in higher type I interferon production. Our results have led to the hypothesis that DDX41 utilizes its unwinding and annealing activities to regulate the homeostasis of dsDNA and single-stranded DNA (ssDNA), which, in turn, regulates cGAS-STING activation. cGAS is activated by dsDNA. Singh et al. find DDX41 regulates cGAS activation through unwinding and annealing activities on dsDNA and ssDNA, respectively, and MDS/AML patient mutant R525H causes overactivation of innate immune response due to its unbalanced activities. This DDX41-cGAS-STING pathway may be related to molecular pathogenesis of MDS/AML.
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Affiliation(s)
- Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | | | - Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Ananna Bhadra Arna
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Manisha Yadav
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Aanchal Aggarwal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Alexya N Aguilera
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Satoru Shinriki
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | | | - Kannupriya Pandey
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Aizhang Xu
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - Noreen Rapin
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Mark Bosch
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - John DeCoteau
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Jim Xiang
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - Franco J Vizeacoumar
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada; Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Vikram Misra
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Susan R Ross
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada.
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8
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Shankar Singh R, Bhadra Arna A, Dong H, Yadav M, Aggarwal A, Wu Y. Structure-function analysis of DEAD-box helicase DDX43. Methods 2022; 204:286-299. [DOI: 10.1016/j.ymeth.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/15/2022] [Accepted: 03/02/2022] [Indexed: 01/21/2023] Open
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Saito T, Whatmore P, Taylor JF, Fernandes JMO, Adam AC, Tocher DR, Espe M, Skjærven KH. Micronutrient supplementation affects DNA methylation in male gonads with potential intergenerational epigenetic inheritance involving the embryonic development through glutamate receptor-associated genes. BMC Genomics 2022; 23:115. [PMID: 35144563 PMCID: PMC8832813 DOI: 10.1186/s12864-022-08348-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 01/28/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND DNA methylation has an important role in intergenerational inheritance. An increasing number of studies have reported evidence of germline inheritance of DNA methylation induced by nutritional signals in mammals. Vitamins and minerals as micronutrients contribute to growth performance in vertebrates, including Atlantic salmon (Salmo salar), and also have a role in epigenetics as environmental factors that alter DNA methylation status. It is important to understand whether micronutrients in the paternal diet can influence the offspring through alterations of DNA methylation signatures in male germ cells. RESULTS Here, we show the effect of micronutrient supplementation on DNA methylation profiles in the male gonad through a whole life cycle feeding trial of Atlantic salmon fed three graded levels of micronutrient components. Our results strongly indicate that micronutrient supplementation affects the DNA methylation status of genes associated with cell signalling, synaptic signalling, and embryonic development. In particular, it substantially affects DNA methylation status in the promoter region of a glutamate receptor gene, glutamate receptor ionotropic, NMDA 3A-like (grin3a-like), when the fish are fed both medium and high doses of micronutrients. Furthermore, two transcription factors, histone deacetylase 2 (hdac2) and a zinc finger protein, bind to the hyper-methylated site in the grin3a-like promoter. An estimated function of hdac2 together with a zinc finger indicates that grin3a-like has a potential role in intergenerational epigenetic inheritance and the regulation of embryonic development affected by paternal diet. CONCLUSIONS The present study demonstrates alterations of gene expression patterns and DNA methylation signatures in the male gonad when Atlantic salmon are fed different levels of micronutrients. Alterations of gene expression patterns are of great interest because the gonads are supposed to have limited metabolic activities compared to other organs, whereas alterations of DNA methylation signatures are of great importance in the field of nutritional epigenetics because the signatures affected by nutrition could be transferred to the next generation. We provide extensive data resources for future work in the context of potential intergenerational inheritance through the male germline.
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Affiliation(s)
| | | | - John F Taylor
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Scotland, UK
| | | | | | - Douglas R Tocher
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Scotland, UK
| | - Marit Espe
- Institute of Marine Research, Bergen, Norway
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10
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Natural transformation protein ComFA exhibits single-stranded DNA translocase activity. J Bacteriol 2022; 204:e0051821. [PMID: 35041498 DOI: 10.1128/jb.00518-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Natural transformation is one of the major mechanisms of horizontal gene transfer in bacterial populations and has been demonstrated in numerous species of bacteria. Despite the prevalence of natural transformation, much of the molecular mechanism remains unexplored. One major outstanding question is how the cell powers DNA import, which is rapid and highly processive. ComFA is one of a handful of proteins required for natural transformation in gram-positive bacteria. Its structural resemblance to the DEAD-box helicase family has led to a long-held hypothesis that ComFA acts as a motor to help drive DNA import into the cytosol. Here, we explored the helicase and translocase activity of ComFA to address this hypothesis. We followed the DNA-dependent ATPase activity of ComFA and, combined with mathematical modeling, demonstrated that ComFA likely translocates on single-stranded DNA from 5' to 3'. However, this translocase activity does not lead to DNA unwinding in the conditions we tested. Further, we analyzed the ATPase cycle of ComFA and found that ATP hydrolysis stimulates the release of DNA, providing a potential mechanism for translocation. These findings help define the molecular contribution of ComFA to natural transformation and support the conclusion that ComFA plays a key role in powering DNA uptake. Importance Competence, or the ability of bacteria to take up and incorporate foreign DNA in a process called natural transformation, is common in the bacterial kingdom. Research in several bacterial species suggests that long, contiguous stretches of DNA are imported into cells in a processive manner, but how bacteria power transformation remains unclear. Our finding that ComFA, a DEAD-box helicase required for competence in gram-positive bacteria, translocates on single-stranded DNA from 5' to 3', supports the long held hypothesis that ComFA may be the motor powering DNA transport during natural transformation. Moreover, ComFA may be a previously unidentified type of DEAD-box helicase-one with the capability of extended translocation on single-stranded DNA.
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11
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Zhou X, Gao F, Lu M, Liu Z, Wang M, Cao J, Ke X, Yi M. DDX43 recruits TRIF or IPS-1 as an adaptor and activates the IFN-β pathway in Nile tilapia (Oreochromis niloticus). Mol Immunol 2022; 143:7-16. [PMID: 34990938 DOI: 10.1016/j.molimm.2021.12.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/13/2023]
Abstract
DDX43 is one of the members of the DExD/H-box protein family, and emerging data suggest that it may play an important role in antiviral immunity across mammals. However, little is known about DDX43 in the fish immune response. In this study, we isolated the cDNA sequence of ddx43 in Nile tilapia (Oreochromis niloticus). The ddx43 gene was 2338 bp in length, contained an open reading frame (ORF) of 2064 bp and encoded a polypeptide of 687 amino acids. The predicted protein of OnDDX43 has three conserved domains, including the RNA binding domain KH, DEAD-like helicase superfamily DEXDc and C-terminal HELICc domain. In healthy Nile tilapia, the Onddx43 transcript was broadly expressed in all examined tissues, with the highest expression levels in the muscle and brain and the lowest in the liver. After challenge with Streptococcus agalactiae, lipopolysaccharides (LPS) and polyinosinic polycytidylic acid (Poly I:C), the expression level of Onddx43 mRNA was upregulated or downregulated in all of the tissues tested. Overexpression of OnDDX43 in 293 T cells showed that it has a positive regulatory effect on IFN-β. The subcellular localization showed that OnDDX43 was expressed in the cytoplasm. We performed further pull-down assays and found that OnDDX43 interacted with both interferon-β promoter stimulator1 (IPS-1) and TIR domain-containing adaptor inducing interferon-β (TRIF).
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Affiliation(s)
- Xin Zhou
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Fengying Gao
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China; Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510380, China.
| | - Maixin Lu
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China; Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510380, China.
| | - Zhigang Liu
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China; Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510380, China
| | - Miao Wang
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China; Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510380, China
| | - Jianmeng Cao
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China; Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510380, China
| | - Xiaoli Ke
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China; Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510380, China
| | - Mengmeng Yi
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China; Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510380, China
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12
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Su C, Tang YD, Zheng C. DExD/H-box helicases: multifunctional regulators in antiviral innate immunity. Cell Mol Life Sci 2021; 79:2. [PMID: 34910251 PMCID: PMC8671602 DOI: 10.1007/s00018-021-04072-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023]
Abstract
DExD/H-box helicases play critical roles in multiple cellular processes, including transcription, cellular RNA metabolism, translation, and infections. Several seminal studies over the past decades have delineated the distinct functions of DExD/H-box helicases in regulating antiviral innate immune signaling pathways, including Toll-like receptors, retinoic acid-inducible gene I-like receptors, cyclic GMP-AMP synthase-the stimulator of interferon gene, and NOD-like receptors signaling pathways. Besides the prominent regulatory roles, there is increasing attention on their functions as nucleic acid sensors involved in antiviral innate immunity. Here we summarize the complex regulatory roles of DExD/H-box helicases in antiviral innate immunity. A better understanding of the underlying molecular mechanisms of DExD/H-box helicases' regulatory roles is vital for developing new therapeutics targeting DExD/H-box helicases and their mediated signaling transduction in viral infectious diseases.
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Affiliation(s)
- Chenhe Su
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- The Wistar Institute, Philadelphia, PA, USA
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
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13
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Liu Y, Zhu X, Wang K, Zhang B, Qiu S. The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans. Front Mol Biosci 2021; 8:783889. [PMID: 34912850 PMCID: PMC8667583 DOI: 10.3389/fmolb.2021.783889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/02/2021] [Indexed: 01/19/2023] Open
Abstract
G-quadruplexes (G4s) are stable non-canonical secondary structures formed by G-rich DNA or RNA sequences. They play various regulatory roles in many biological processes. It is commonly agreed that G4 unwinding helicases play key roles in G4 metabolism and function, and these processes are closely related to physiological and pathological processes. In recent years, more and more functional and mechanistic details of G4 helicases have been discovered; therefore, it is necessary to carefully sort out the current research efforts. Here, we provide a systematic summary of G4 unwinding helicases from the perspective of functions and molecular mechanisms. First, we provide a general introduction about helicases and G4s. Next, we comprehensively summarize G4 unfolding helicases in humans and their proposed cellular functions. Then, we review their study methods and molecular mechanisms. Finally, we share our perspective on further prospects. We believe this review will provide opportunities for researchers to reach the frontiers in the functions and molecular mechanisms of human G4 unwinding helicases.
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Affiliation(s)
- Yang Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Xinting Zhu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Shuyi Qiu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
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14
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Lalonde M, Trauner M, Werner M, Hamperl S. Consequences and Resolution of Transcription-Replication Conflicts. Life (Basel) 2021; 11:life11070637. [PMID: 34209204 PMCID: PMC8303131 DOI: 10.3390/life11070637] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/17/2022] Open
Abstract
Transcription–replication conflicts occur when the two critical cellular machineries responsible for gene expression and genome duplication collide with each other on the same genomic location. Although both prokaryotic and eukaryotic cells have evolved multiple mechanisms to coordinate these processes on individual chromosomes, it is now clear that conflicts can arise due to aberrant transcription regulation and premature proliferation, leading to DNA replication stress and genomic instability. As both are considered hallmarks of aging and human diseases such as cancer, understanding the cellular consequences of conflicts is of paramount importance. In this article, we summarize our current knowledge on where and when collisions occur and how these encounters affect the genome and chromatin landscape of cells. Finally, we conclude with the different cellular pathways and multiple mechanisms that cells have put in place at conflict sites to ensure the resolution of conflicts and accurate genome duplication.
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15
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Murakami R, Sumiyoshi T, Negishi L, Siomi MC. DEAD-box polypeptide 43 facilitates piRNA amplification by actively liberating RNA from Ago3-piRISC. EMBO Rep 2021; 22:e51313. [PMID: 33555135 PMCID: PMC8025031 DOI: 10.15252/embr.202051313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/28/2020] [Accepted: 01/08/2021] [Indexed: 12/25/2022] Open
Abstract
The piRNA amplification pathway in Bombyx is operated by Ago3 and Siwi in their piRISC form. The DEAD‐box protein, Vasa, facilitates Ago3‐piRISC production by liberating cleaved RNAs from Siwi‐piRISC in an ATP hydrolysis‐dependent manner. However, the Vasa‐like factor facilitating Siwi‐piRISC production along this pathway remains unknown. Here, we identify DEAD‐box polypeptide 43 (DDX43) as the Vasa‐like protein functioning in Siwi‐piRISC production. DDX43 belongs to the helicase superfamily II along with Vasa, and it contains a similar helicase core. DDX43 also contains a K‐homology (KH) domain, a prevalent RNA‐binding domain, within its N‐terminal region. Biochemical analyses show that the helicase core is responsible for Ago3‐piRISC interaction and ATP hydrolysis, while the KH domain enhances the ATPase activity of the helicase core. This enhancement is independent of the RNA‐binding activity of the KH domain. For maximal DDX43 RNA‐binding activity, both the KH domain and helicase core are required. This study not only provides new insight into the piRNA amplification mechanism but also reveals unique collaborations between the two domains supporting DDX43 function within the pathway.
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Affiliation(s)
- Ryo Murakami
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tetsutaro Sumiyoshi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Lumi Negishi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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16
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Yadav M, Singh RS, Hogan D, Vidhyasagar V, Yang S, Chung IYW, Kusalik A, Dmitriev OY, Cygler M, Wu Y. The KH domain facilitates the substrate specificity and unwinding processivity of DDX43 helicase. J Biol Chem 2021; 296:100085. [PMID: 33199368 PMCID: PMC7949032 DOI: 10.1074/jbc.ra120.015824] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/03/2020] [Accepted: 11/16/2020] [Indexed: 01/21/2023] Open
Abstract
The K-homology (KH) domain is a nucleic acid-binding domain present in many proteins. Recently, we found that the DEAD-box helicase DDX43 contains a KH domain in its N-terminus; however, its function remains unknown. Here, we purified recombinant DDX43 KH domain protein and found that it prefers binding ssDNA and ssRNA. Electrophoretic mobility shift assay and NMR revealed that the KH domain favors pyrimidines over purines. Mutational analysis showed that the GXXG loop in the KH domain is involved in pyrimidine binding. Moreover, we found that an alanine residue adjacent to the GXXG loop is critical for binding. Systematic evolution of ligands by exponential enrichment, chromatin immunoprecipitation-seq, and cross-linking immunoprecipitation-seq showed that the KH domain binds C-/T-rich DNA and U-rich RNA. Bioinformatics analysis suggested that the KH domain prefers to bind promoters. Using 15N-heteronuclear single quantum coherence NMR, the optimal binding sequence was identified as TTGT. Finally, we found that the full-length DDX43 helicase prefers DNA or RNA substrates with TTGT or UUGU single-stranded tails and that the KH domain is critically important for sequence specificity and unwinding processivity. Collectively, our results demonstrated that the KH domain facilitates the substrate specificity and processivity of the DDX43 helicase.
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Affiliation(s)
- Manisha Yadav
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Daniel Hogan
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ivy Yeuk Wah Chung
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Oleg Y Dmitriev
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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17
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Kim S, Kang N, Park SH, Wells J, Hwang T, Ryu E, Kim BG, Hwang S, Kim SJ, Kang S, Lee S, Stirling P, Myung K, Lee KY. ATAD5 restricts R-loop formation through PCNA unloading and RNA helicase maintenance at the replication fork. Nucleic Acids Res 2020; 48:7218-7238. [PMID: 32542338 PMCID: PMC7367208 DOI: 10.1093/nar/gkaa501] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/27/2022] Open
Abstract
R-loops are formed when replicative forks collide with the transcriptional machinery and can cause genomic instability. However, it is unclear how R-loops are regulated at transcription-replication conflict (TRC) sites and how replisome proteins are regulated to prevent R-loop formation or mediate R-loop tolerance. Here, we report that ATAD5, a PCNA unloader, plays dual functions to reduce R-loops both under normal and replication stress conditions. ATAD5 interacts with RNA helicases such as DDX1, DDX5, DDX21 and DHX9 and increases the abundance of these helicases at replication forks to facilitate R-loop resolution. Depletion of ATAD5 or ATAD5-interacting RNA helicases consistently increases R-loops during the S phase and reduces the replication rate, both of which are enhanced by replication stress. In addition to R-loop resolution, ATAD5 prevents the generation of new R-loops behind the replication forks by unloading PCNA which, otherwise, accumulates and persists on DNA, causing a collision with the transcription machinery. Depletion of ATAD5 reduces transcription rates due to PCNA accumulation. Consistent with the role of ATAD5 and RNA helicases in maintaining genomic integrity by regulating R-loops, the corresponding genes were mutated or downregulated in several human tumors.
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Affiliation(s)
- Sangin Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Nalae Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - James Wells
- Terry Fox laboratory, BC Cancer Agency, Vancouver, Canada
| | - Taejoo Hwang
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Seong-Jung Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Semin Lee
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Peter Stirling
- Terry Fox laboratory, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
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18
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Li M, Klungland A. Modifications and interactions at the R-loop. DNA Repair (Amst) 2020; 96:102958. [PMID: 32961406 DOI: 10.1016/j.dnarep.2020.102958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 10/23/2022]
Abstract
R-loops are tripartite structures consisting of an RNA:DNA hybrid and a displaced single-stranded DNA [1]. They are widespread and occupy up to 5 % of the mammalian genomes [2]. R-loops have a key role in genome stability, and known functions associated with gene regulation, DNA replication, chromatin patterning, immunoglobuline gene recombination and DNA Double-strand break repair [3-7]. Novel methodology, including the application of the S9.6 antibody, have more recently led to detailed knowledge on the genome-wide distribution of the R-loops as well as the identification of the R-loop interactome [8-10]. The regulation of R-loops was recently shown to also depend on dynamic RNA-methylation, including METTL3/14 dependent 6-methylAdenines (m6As) and METTL8 dependent 3-methylCytosines (m3Cs) [11-13].
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Affiliation(s)
- Miaomiao Li
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway; Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, NO-0317, Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway; Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, NO-0317, Oslo, Norway.
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19
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DEAD-Box Helicases: Sensors, Regulators, and Effectors for Antiviral Defense. Viruses 2020; 12:v12020181. [PMID: 32033386 PMCID: PMC7077277 DOI: 10.3390/v12020181] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
DEAD-box helicases are a large family of conserved RNA-binding proteins that belong to the broader group of cellular DExD/H helicases. Members of the DEAD-box helicase family have roles throughout cellular RNA metabolism from biogenesis to decay. Moreover, there is emerging evidence that cellular RNA helicases, including DEAD-box helicases, play roles in the recognition of foreign nucleic acids and the modulation of viral infection. As intracellular parasites, viruses must evade detection by innate immune sensing mechanisms and degradation by cellular machinery while also manipulating host cell processes to facilitate replication. The ability of DEAD-box helicases to recognize RNA in a sequence-independent manner, as well as the breadth of cellular functions carried out by members of this family, lead them to influence innate recognition and viral infections in multiple ways. Indeed, DEAD-box helicases have been shown to contribute to intracellular immune sensing, act as antiviral effectors, and even to be coopted by viruses to promote their replication. However, our understanding of the mechanisms underlying these interactions, as well as the cellular roles of DEAD-box helicases themselves, is limited in many cases. We will discuss the diverse roles that members of the DEAD-box helicase family play during viral infections.
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20
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DDX43 prefers single strand substrate and its full binding activity requires physical connection of all domains. Biochem Biophys Res Commun 2019; 520:594-599. [PMID: 31623828 DOI: 10.1016/j.bbrc.2019.09.114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 09/26/2019] [Indexed: 11/22/2022]
Abstract
DDX43 is a cancer/testis antigen and is thought to stimulate oncogenic pathways in cell proliferation, while its specific function in cancer development is largely unexplored. DDX43 is the member of RNA helicase in DEAD-box family, consists of conserved helicase core and a single K-homology (KH) domain in its N-terminus. In this paper, we expressed and purified human DDX43 protein in E. coli and demonstrated that this protein is a homogeneous monomer. To understand the role and explore the substrates preference of DDX43 in vitro, we systematically studied its binding properties. We found that DDX43 prefers single-strand DNA or RNA with length longer than 12 nt and much prefers guanosine than the other three nucleotides. Achievement of the full binding affinity of protein to substrate needs the existence of all domains, and they must be connected. The absence of either of them or the disjunction can result in a decreased binding affinity to substrates, approximately reduced 10-fold. We also found that the unwinding ability of DDX43 in vitro was neither efficient nor sustainable.
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21
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Plasmodium falciparum specific helicase 2 is a dual, bipolar helicase and is crucial for parasite growth. Sci Rep 2019; 9:1519. [PMID: 30728406 PMCID: PMC6365506 DOI: 10.1038/s41598-018-38032-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022] Open
Abstract
Human malaria infection is a major challenge across the globe and is responsible for millions of deaths annually. Rapidly emerging drug resistant strains against the new class of anti-malarial drugs are major threat to control the disease burden worldwide. Helicases are present in every organism and have important role in various nucleic acid metabolic processes. Previously we have reported the presence of three parasite specific helicases (PSH) in Plasmodium falciparum 3D7 strain. Here we present the detailed biochemical characterization of PfPSH2. PfPSH2 is DNA and RNA stimulated ATPase and is able to unwind partially duplex DNA and RNA substrates. It can translocate in both 3' to 5' and 5' to 3' directions. PfPSH2 is expressed in all the stages of intraerythrocytic development and it is localized in cytoplasm in P. falciparum 3D7 strain. The dsRNA mediated inhibition study suggests that PfPSH2 is important for the growth and survival of the parasite. This study presents the detailed characterization of PfPSH2 and lays the foundation for future development of PfPSH2 as drug target.
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22
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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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23
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Wang X, Ge W, Zhang Y. Recombinant DHX33 Protein Possesses Dual DNA/RNA Helicase Activity. Biochemistry 2018; 58:250-258. [PMID: 29870660 DOI: 10.1021/acs.biochem.8b00166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA helicase DHX33 has been shown to participate in a variety of cellular activities, including ribosome biogenesis, protein translation, and gene transcription. We and others further discovered that DHX33 is strongly expressed in several types of human cancers and plays important roles in promoting cancer cell proliferation. To better understand the molecular mechanism for DHX33 in exerting its biological functions, we purified recombinant DHX33 and performed biochemical studies in vitro. DHX33 protein was found to have ATPase activity that is dependent on DNA or RNA duplexes. The ATPase activity of DHX33 is coupled with its RNA/DNA unwinding activity. If a key residue in the ATP binding site were mutated, the mutant DHX33 could not unwind DNA/RNA duplexes. Furthermore, a deletion mutant of a RKK motif previously identified to be involved in ribosome DNA binding could still unwind DNA duplexes, albeit with reduced efficiency. In summary, our study reveals that purified DHX33 protein possesses unwinding activity toward DNA and RNA duplexes.
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Affiliation(s)
- Xingshun Wang
- Department of Biology , Southern University of Science and Technology , Shenzhen , Guangdong 518055 , P. R. China.,Faculty of Health Sciences , University of Macau , Macau , China
| | - Wei Ge
- Faculty of Health Sciences , University of Macau , Macau , China
| | - Yandong Zhang
- Department of Biology , Southern University of Science and Technology , Shenzhen , Guangdong 518055 , P. R. China
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Distinct RNA-unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs. Biochem Soc Trans 2017; 45:1313-1321. [PMID: 29150525 DOI: 10.1042/bst20170095] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 01/03/2023]
Abstract
Structured RNAs and RNA-protein complexes (RNPs) fold through complex pathways that are replete with misfolded traps, and many RNAs and RNPs undergo extensive conformational changes during their functional cycles. These folding steps and conformational transitions are frequently promoted by RNA chaperone proteins, notably by superfamily 2 (SF2) RNA helicase proteins. The two largest families of SF2 helicases, DEAD-box and DEAH-box proteins, share evolutionarily conserved helicase cores, but unwind RNA helices through distinct mechanisms. Recent studies have advanced our understanding of how their distinct mechanisms enable DEAD-box proteins to disrupt RNA base pairs on the surfaces of structured RNAs and RNPs, while some DEAH-box proteins are adept at disrupting base pairs in the interior of RNPs. Proteins from these families use these mechanisms to chaperone folding and promote rearrangements of structured RNAs and RNPs, including the spliceosome, and may use related mechanisms to maintain cellular messenger RNAs in unfolded or partially unfolded conformations.
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