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Zhao D, Guan P, Wei L, Gao J, Guo L, Tian D, Li Q, Guo Z, Cui H, Li Y, Guo J. Comprehensive identification and expression analysis of FAR1/FHY3 genes under drought stress in maize ( Zea mays L.). PeerJ 2024; 12:e17684. [PMID: 38952979 PMCID: PMC11216215 DOI: 10.7717/peerj.17684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024] Open
Abstract
Background FAR1/FHY3 transcription factors are derived from transposase, which play important roles in light signal transduction, growth and development, and response to stress by regulating downstream gene expression. Although many FAR1/FHY3 members have been identified in various species, the FAR1/FHY3 genes in maize are not well characterized and their function in drought are unknown. Method The FAR1/FHY3 family in the maize genome was identified using PlantTFDB, Pfam, Smart, and NCBI-CDD websites. In order to investigate the evolution and functions of FAR1 genes in maize, the information of protein sequences, chromosome localization, subcellular localization, conserved motifs, evolutionary relationships and tissue expression patterns were analyzed by bioinformatics, and the expression patterns under drought stress were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Results A total of 24 ZmFAR members in maize genome, which can be divided into five subfamilies, with large differences in protein and gene structures among subfamilies. The promoter regions of ZmFARs contain abundant abiotic stress-responsive and hormone-respovensive cis-elements. Among them, drought-responsive cis-elements are quite abundant. ZmFARs were expressed in all tissues detected, but the expression level varies widely. The expression of ZmFARs were mostly down-regulated in primary roots, seminal roots, lateral roots, and mesocotyls under water deficit. Most ZmFARs were down-regulated in root after PEG-simulated drought stress. Conclusions We performed a genome-wide and systematic identification of FAR1/FHY3 genes in maize. And most ZmFARs were down-regulated in root after drought stress. These results indicate that FAR1/FHY3 transcription factors have important roles in drought stress response, which can lay a foundation for further analysis of the functions of ZmFARs in response to drought stress.
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Affiliation(s)
- Dongbo Zhao
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Peiyan Guan
- College of Life Science, Dezhou University, Dezhou, Shandong, China
| | - Longxue Wei
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Jiansheng Gao
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Lianghai Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Dianbin Tian
- Pingyuan County Rural Revitalization Service Center, Pingyuan, Shandong, China
| | - Qingfang Li
- Linyi County Agricultural and Rural Bureau, Linyi, Shandong, China
| | - Zhihui Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Huini Cui
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Yongjun Li
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Jianjun Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
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Gong K, Huang Y, Zheng Y, Hao W, Shi K. ZSWIM4 inhibition improves chemosensitivity in epithelial ovarian cancer cells by suppressing intracellular glycine biosynthesis. J Transl Med 2024; 22:192. [PMID: 38383406 PMCID: PMC10880229 DOI: 10.1186/s12967-024-04980-8] [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: 11/13/2023] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Zinc finger SWIM-type containing 4 (ZSWIM4) induces drug resistance in breast cancer cells. However, its role in epithelial ovarian cancer (EOC) remains unknown. In this study, we aimed to investigate the clinical significance of ZSWIM4 expression in EOC and develop new clinical therapeutic strategies for EOC. METHODS ZSWIM4 expression in control and EOC tumor tissues was examined using immunohistochemistry. Lentiviral transduction, Cell Counting Kit-8 assay, tumorsphere formation assay, flow cytometry, western blotting, and animal xenograft model were used to assess the role of ZSWIM4 in chemotherapy. Cleavage Under Targets and Tagmentation (CUT&Tag) assays, chromatin immunoprecipitation assays, and luciferase reporter assays were used to confirm FOXK1-mediated upregulation of ZSWIM4 expression. The mechanism by which ZSWIM4 inhibition improves chemosensitivity was evaluated using RNA-sequencing. A ZSWIM4-targeting inhibitor was explored by virtual screening and surface plasmon resonance analysis. Patient-derived organoid (PDO) models were constructed from EOC tumor tissues with ZSWIM4 expression. RESULTS ZSWIM4 was overexpressed in EOC tumor tissues and impaired patient prognoses. Its expression correlated positively with EOC recurrence. ZSWIM4 expression was upregulated following carboplatin treatment, which, in turn, contributed to chemoresistance. Silencing ZSWIM4 expression sensitized EOC cells to carboplatin treatment in vitro and in vivo. FOXK1 could bind to the GTAAACA sequence of the ZSWIM4 promoter region to upregulate ZSWIM4 transcriptional activity and FOXK1 expression increased following carboplatin treatment, leading to an increase in ZSWIM4 expression. Mechanistically, ZSWIM4 knockdown downregulated the expression of several rate-limiting enzymes involved in glycine synthesis, causing a decrease in intracellular glycine levels, thus enhancing intracellular reactive oxygen species production induced by carboplatin treatment. Compound IPN60090 directly bound to ZSWIM4 protein and exerted a significant chemosensitizing effect in both EOC cells and PDO models. CONCLUSIONS ZSWIM4 inhibition enhanced EOC cell chemosensitivity by ameliorating intracellular glycine metabolism reprogramming, thus providing a new potential therapeutic strategy for EOC.
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Affiliation(s)
- Kunxiang Gong
- Institute of Reproductive Health and Perinatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
- Department of Gynecology and Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Yinger Huang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yanqin Zheng
- Department of Gynecology and Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Wenbo Hao
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Kun Shi
- Institute of Reproductive Health and Perinatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
- Department of Gynecology and Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China.
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Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller P, Genikhovich G. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife 2024; 13:e80803. [PMID: 38323609 PMCID: PMC10849676 DOI: 10.7554/elife.80803] [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: 06/05/2022] [Accepted: 01/28/2024] [Indexed: 02/08/2024] Open
Abstract
BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is zswim4-6, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression.
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Affiliation(s)
- Paul Knabl
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of ViennaViennaAustria
| | - Alexandra Schauer
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
| | | | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
| | | | | | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
- University of KonstanzKonstanzGermany
| | - Grigory Genikhovich
- Department of Neurosciences and Developmental Biology, University of ViennaViennaAustria
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Wang C, Liu Z, Zeng Y, Zhou L, Long Q, Hassan IU, Zhang Y, Qi X, Cai D, Mao B, Lu G, Sun J, Yao Y, Deng Y, Zhao Q, Feng B, Zhou Q, Chan WY, Zhao H. ZSWIM4 regulates embryonic patterning and BMP signaling by promoting nuclear Smad1 degradation. EMBO Rep 2024; 25:646-671. [PMID: 38177922 PMCID: PMC10897318 DOI: 10.1038/s44319-023-00046-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: 02/23/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
The dorsoventral gradient of BMP signaling plays an essential role in embryonic patterning. Zinc Finger SWIM-Type Containing 4 (zswim4) is expressed in the Spemann-Mangold organizer at the onset of Xenopus gastrulation and is then enriched in the developing neuroectoderm at the mid-gastrula stages. Knockdown or knockout of zswim4 causes ventralization. Overexpression of zswim4 decreases, whereas knockdown of zswim4 increases the expression levels of ventrolateral mesoderm marker genes. Mechanistically, ZSWIM4 attenuates the BMP signal by reducing the protein stability of SMAD1 in the nucleus. Stable isotope labeling by amino acids in cell culture (SILAC) identifies Elongin B (ELOB) and Elongin C (ELOC) as the interaction partners of ZSWIM4. Accordingly, ZSWIM4 forms a complex with the Cul2-RING ubiquitin ligase and ELOB and ELOC, promoting the ubiquitination and degradation of SMAD1 in the nucleus. Our study identifies a novel mechanism that restricts BMP signaling in the nucleus.
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Affiliation(s)
- Chengdong Wang
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ziran Liu
- Qingdao Municipal Center for Disease Control and Prevention, 266033, Qingdao, Shandong, China
| | - Yelin Zeng
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Liangji Zhou
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qi Long
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Imtiaz Ul Hassan
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuanliang Zhang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Xufeng Qi
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, 510632, Guangzhou, Guangdong, China
| | - Dongqing Cai
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, 510632, Guangzhou, Guangdong, China
| | - Bingyu Mao
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China
- Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Chinese Academy of Sciences, Kunming, China
| | - Gang Lu
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jianmin Sun
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Ningxia Medical University, No. 1160 Shengli Street, 750004, Yinchuan, China
| | - Yonggang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, China
- Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Chinese Academy of Sciences, Kunming, China
| | - Yi Deng
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Bo Feng
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qin Zhou
- School of Basic Medical Sciences, Harbin Medical University, 150081, Harbin, China
| | - Wai Yee Chan
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hui Zhao
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Ji N, Liu Z, She H, Xu Z, Zhang H, Fang Z, Qian W. A Genome-Wide Association Study Reveals the Genetic Mechanisms of Nutrient Accumulation in Spinach. Genes (Basel) 2024; 15:172. [PMID: 38397162 PMCID: PMC10887921 DOI: 10.3390/genes15020172] [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: 12/21/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Spinach is a significant source of vitamins, minerals, and antioxidants. These nutrients make it delicious and beneficial for human health. However, the genetic mechanism underlying the accumulation of nutrients in spinach remains unclear. In this study, we analyzed the content of chlorophyll a, chlorophyll b, oxalate, nitrate, crude fiber, soluble sugars, manganese, copper, and iron in 62 different spinach accessions. Additionally, 3,356,182 high-quality, single-nucleotide polymorphisms were found using resequencing and used in a genome-wide association study. A total of 2077 loci were discovered that significantly correlated with the concentrations of the nutritional elements. Data mining identified key genes in these intervals for four traits: chlorophyll, oxalate, soluble sugar, and Fe. Our study provides insights into the genetic architecture of nutrient variation and facilitates spinach breeding for good nutrition.
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Affiliation(s)
- Ni Ji
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhengwu Fang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang 453000, China
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6
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Fu S, Wang K, Ma T, Liang Y, Ma Z, Wu J, Xu Y, Zhou X. An evolutionarily conserved C4HC3-type E3 ligase regulates plant broad-spectrum resistance against pathogens. THE PLANT CELL 2022; 34:1822-1843. [PMID: 35171277 PMCID: PMC9048923 DOI: 10.1093/plcell/koac055] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/11/2022] [Indexed: 05/27/2023]
Abstract
Deployment of broad-spectrum disease resistance against multiple pathogen species is an efficient way to control plant diseases. Here, we identify a Microtubule-associated C4HC3-type E3 Ligase (MEL) in both Nicotiana benthamiana and Oryza sativa, and show that it is able to integrate and initiate a series of host immune signaling, conferring broad-spectrum resistance to viral, fungal, and bacterial pathogens. We demonstrate that MEL forms homodimer through intermolecular disulfide bonds between its cysteine residues in the SWIM domain, and interacts with its substrate serine hydroxymethyltrasferase 1 (SHMT1) through the YφNL motif. Ubiquitin ligase activity, homodimerization and YφNL motif are indispensable for MEL to regulate plant immunity by mediating SHMT1 degradation through the 26S proteasome pathway. Our findings provide a fundamental basis for utilizing the MEL-SHMT1 module to generate broad-spectrum-resistant rice to global destructive pathogens including rice stripe virus, Magnaporthe oryzae, and Xanthomonas oryzae pv. oryzae.
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Affiliation(s)
| | | | - Tingting Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yan Liang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yi Xu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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ZSWIM8 is a myogenic protein that partly prevents C2C12 differentiation. Sci Rep 2021; 11:20880. [PMID: 34686700 PMCID: PMC8536758 DOI: 10.1038/s41598-021-00306-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/08/2021] [Indexed: 12/17/2022] Open
Abstract
Cell adhesion molecule-related/downregulated by oncogenes (Cdon) is a cell-surface receptor that mediates cell–cell interactions and positively regulates myogenesis. The cytoplasmic region of Cdon interacts with other proteins to form a Cdon/JLP/Bnip-2/CDC42 complex that activates p38 mitogen-activated protein kinase (MAPK) and induces myogenesis. However, Cdon complex may include other proteins during myogenesis. In this study, we found that Cullin 2-interacting protein zinc finger SWIM type containing 8 (ZSWIM8) ubiquitin ligase is induced during C2C12 differentiation and is included in the Cdon complex. We knocked-down Zswim8 in C2C12 cells to determine the effect of ZSWIM8 on differentiation. However, we detected neither ZSWIM8-dependent ubiquitination nor the degradation of Bnip2, Cdon, or JLP. In contrast, ZSWIM8 knockdown accelerated C2C12 differentiation. These results suggest that ZSWIM8 is a Cdon complex-included myogenic protein that prevents C2C12 differentiation without affecting the stability of Bnip2, Cdon, and JLP.
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8
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Gong K, Song K, Zhu Z, Xiang Q, Wang K, Shi J. SWIM domain protein ZSWIM4 is required for JAK2 inhibition resistance in breast cancer. Life Sci 2021; 279:119696. [PMID: 34102191 DOI: 10.1016/j.lfs.2021.119696] [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: 02/04/2021] [Revised: 05/24/2021] [Accepted: 06/02/2021] [Indexed: 11/24/2022]
Abstract
AIMS Janus kinase 2 (JAK2)/signal transducer and activator of transcription (STAT) signaling plays a critical role in the progression of breast cancer. However, a small part of tumor cells survived from the killing effect of JAK2 inhibitor. We aimed to find out the mechanism of drug resistance in breast cancer cells and develop new therapeutic strategies. MATERIALS AND METHODS The anti-tumor effect of TG101209 in breast cancer cells was confirmed by cell counting kit 8 and flow cytometry. Western blotting was used to determine the up-regulation of zinc finger SWIM-type containing 4 (ZSWIM4) induced by TG101209. In vitro and in vivo experiments were performed to evaluate the role of ZSWIM4 in the resistance of breast cancer cells to TG101209. Through the determination and analysis of 50% inhibiting concentration (IC50) curves, the effect of combination therapy was confirmed. KEY FINDINGS Our data indicate that the elevated expression of ZSWIM4 contributes to JAK2 inhibition resistance, as knockdown of ZSWIM4 significantly enhances the sensitivity of breast cancer cells to TG101209 and over-expression of this gene mitigates the killing effect. Furthermore, the expression of vitamin D receptor (VDR) and utilization of 1α,25-(OH)2VD3 is decreased in ZSWIM4-knockdown breast cancer cells. VDR-silencing or GW0742-mediated blockade of VDR activity can partially reverse the JAK2 inhibition resistance. SIGNIFICANCE Our data implicated that ZSWIM4 might be an inducible resistance gene of JAK2 inhibition in breast cancer cells. The combination of JAK2 inhibitor and VDR inhibitor may achieve better coordinated therapeutic effect in breast cancer.
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Affiliation(s)
- Kunxiang Gong
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China; Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Kai Song
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China; Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Zhenyun Zhu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China; Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Qin Xiang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China; Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Kun Wang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China; The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Jian Shi
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China; Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, Guangdong, China; Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou 510282, Guangdong, China.
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Chang CC, Kuo HY, Chen SY, Lin WT, Lu KM, Saito T, Liu FC. Developmental Characterization of Schizophrenia-Associated Gene Zswim6 in Mouse Forebrain. Front Neuroanat 2021; 15:669631. [PMID: 34054439 PMCID: PMC8161499 DOI: 10.3389/fnana.2021.669631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
Schizophrenia is a devastating neuropsychiatric disease with a globally 1% life-long prevalence. Clinical studies have linked Zswim6 mutations to developmental and neurological diseases, including schizophrenia. Zswim6’s function remains largely unknown. Given the involvement of Zswim6 in schizophrenia and schizophrenia as a neurodevelopmental disease, it is important to understand the spatiotemporal expression pattern of Zswim6 in the developing brain. Here, we performed a comprehensive analysis of the spatiotemporal expression pattern of Zswim6 in the mouse forebrain by in situ hybridization with radioactive and non-radioactive-labeled riboprobes. Zswim6 mRNA was detected as early as E11.5 in the ventral forebrain. At E11.5–E13.5, Zswim6 was highly expressed in the lateral ganglionic eminence (LGE). The LGE consisted of two progenitor populations. Dlx+;Er81+ cells in dorsal LGE comprised progenitors of olfactory bulb interneurons, whereas Dlx+;Isl1+ progenitors in ventral LGE gave rise to striatal projection neurons. Zswim6 was not colocalized with Er81 in the dorsal LGE. In the ventral LGE, Zswim6 was colocalized with striatal progenitor marker Nolz-1. Zswim6 was highly expressed in the subventricular zone (SVZ) of LGE in which progenitors undergo the transition from proliferation to differentiation. Double labeling showed that Zswim6 was not colocalized with proliferation marker Ki67 but was colocalized with differentiation marker Tuj1 in the SVZ, suggesting Zswim6 expression in early differentiating neurons. Zswim6 was also expressed in the adjacent structures of medial and caudal ganglionic eminences (MGE, CGE) that contained progenitors of cortical interneurons. At E15.5 and E17.5, Zswim6 was expressed in several key brain regions that were involved in the pathogenesis of schizophrenia, including the striatum, cerebral cortex, hippocampus, and medial habenular nucleus. Zswim6 was persistently expressed in the postnatal brain. Cell type analysis indicated that Zswim6 mRNA was colocalized with D1R-expressing striatonigral and D2R-expressing striatopallidal neurons of the adult striatum with a higher colocalization in striatopallidal neurons. These findings are of particular interest as striatal dopamine D2 receptors are known to be involved in the pathophysiology of schizophrenia. In summary, the comprehensive analysis provides an anatomical framework for the study of Zswim6 function and Zswim6-associated neurological disorders.
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Affiliation(s)
- Chuan-Chie Chang
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsiao-Ying Kuo
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shih-Yun Chen
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wan-Ting Lin
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Kuan-Ming Lu
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tetsuichiro Saito
- Department of Developmental Biology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Fu-Chin Liu
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
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Novel compound variants of the AR and MAP3K1 genes are related to the clinical heterogeneity of androgen insensitivity syndrome. Biosci Rep 2021; 40:222776. [PMID: 32338288 PMCID: PMC7953519 DOI: 10.1042/bsr20200616] [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: 03/02/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/13/2022] Open
Abstract
Androgen insensitivity syndrome (AIS; OMIM 300068) is the most frequent cause of 46, XY disorders of sex development (DSD). However, the correlation between genotype and phenotype has not been determined. We conducted a systematic analysis of the clinical characteristics, hormone levels, ultrasonography data and histopathology of a 46, XY Chinese patient with AIS. The family was followed up for nearly 8 years. We applied whole-exome sequencing (WES) for genetic analysis of the pedigree and performed bioinformatic analysis of the identified variants. Human embryonic kidney 293T/17 (HEK293T/17) cells were transiently transfected with wild-type or mutant AR and MAP3K1 plasmid. Cell lysates were used to analyze androgen receptor (AR) production. A novel hemizygous AR variant (c.2070C>A, p. His690Glu) and a rare heterozygous MAP3K1 variant (c.778C>T, p. Arg260Cys) were identified by WES in the proband and her mother. Bioinformatic analysis predicted these two variants to be pathogenic. Multiple amino acid sequence alignments showed that p. His690 and p. Arg260 are conserved among various species. His690Glu is a mutation that decreased the AR production, whereas the Arg260Cys mutation increased the AR production. The novel compound variants of the AR and MAP3K1 genes also increased the production of AR protein. Thus, the phenotype of the patient may be caused by defects in both the AR and MAP3K1 signaling pathways. Compound variants of the AR and MAP3K1 genes resulted in a specific phenotype in this patient with AIS. WES might reveal genetic variants that explain the heterogeneity of AIS.
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11
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Mestre MR, González-Delgado A, Gutiérrez-Rus LI, Martínez-Abarca F, Toro N. Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems. Nucleic Acids Res 2021; 48:12632-12647. [PMID: 33275130 PMCID: PMC7736814 DOI: 10.1093/nar/gkaa1149] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline for the systematic prediction of genes specifically associated with retron RTs based on a previously reported large dataset representative of the diversity of prokaryotic RTs. We found that retrons generally comprise a tripartite system composed of the ncRNA, the RT and an additional protein or RT-fused domain with diverse enzymatic functions. These retron systems are highly modular, and their components have coevolved to different extents. Based on the additional module, we classified retrons into 13 types, some of which include additional variants. Our findings provide a basis for future studies on the biological function of retrons and for expanding their biotechnological applications.
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Affiliation(s)
- Mario Rodríguez Mestre
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Alejandro González-Delgado
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Luis I Gutiérrez-Rus
- Departamento de Química Física. Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Francisco Martínez-Abarca
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
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12
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Shi CY, Kingston ER, Kleaveland B, Lin DH, Stubna MW, Bartel DP. The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation. Science 2020; 370:science.abc9359. [PMID: 33184237 DOI: 10.1126/science.abc9359] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/07/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to direct widespread posttranscriptional gene repression. Although association with AGO typically protects miRNAs from nucleases, extensive pairing to some unusual target RNAs can trigger miRNA degradation. We found that this target-directed miRNA degradation (TDMD) required the ZSWIM8 Cullin-RING E3 ubiquitin ligase. This and other findings support a mechanistic model of TDMD in which target-directed proteolysis of AGO by the ubiquitin-proteasome pathway exposes the miRNA for degradation. Moreover, loss-of-function studies indicated that the ZSWIM8 Cullin-RING ligase accelerates degradation of numerous miRNAs in cells of mammals, flies, and nematodes, thereby specifying the half-lives of most short-lived miRNAs. These results elucidate the mechanism of TDMD and expand its inferred role in shaping miRNA levels in bilaterian animals.
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Affiliation(s)
- Charlie Y Shi
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elena R Kingston
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benjamin Kleaveland
- Department of Pathology and Lab Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Daniel H Lin
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael W Stubna
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA. .,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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13
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Li HD, Chen X, Xu JJ, Du XS, Yang Y, Li JJ, Yang XJ, Huang HM, Li XF, Wu MF, Zhang C, Zhang C, Li Z, Wang H, Meng XM, Huang C, Li J. DNMT3b-mediated methylation of ZSWIM3 enhances inflammation in alcohol-induced liver injury via regulating TRAF2-mediated NF-κB pathway. Clin Sci (Lond) 2020. [DOI: https:/doi.org/10.1042/cs20200031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Abstract
The regulation of macrophages during inflammatory responses is a crucial process in alcoholic liver disease (ALD) and aberrant macrophage DNA methylation is associated with inflammation. Our preliminary screening results of macrophage methylation in the present study demonstrated the zinc finger SWI2/SNF2 and MuDR (SWIM)-domain containing 3 (ZSWIM3) were hypermethylated in the 5′ untranslated region (5′-UTR) region. ZSWIM3, a novel zinc finger-chelate domain of SWIM, is predicted to function in DNA-binding and protein-binding interactions. Its expression was found to be consistently decreased in macrophages isolated from livers of ethyl alcohol (EtOH)-fed mice and in EtOH+lipopolysaccharide (LPS)-induced RAW264.7 cells. Over-expression of ZSWIM3 was found to attenuate chronic+binge ethanol feeding-induced liver injury and inhibit inflammatory responses in vivo. Enforced expression of ZSWIM3 in vitro was also found to have anti-inflammatory effects. Aberrant expression of ZSWIM3 in alcohol-induced liver injury (ALI) was found to be associated with hypermethylation. Analysis of CpG prediction indicated the presence of two methylated sites in the ZSWIM3 promoter region and methylation inhibitor and DNA methyltransferases (DNMTs)-siRNA transfection were found to restore down-regulated ZSWIM3. Chromatin immunoprecipitation (ChIP) assay and molecular docking affirmed the role of DNMT 3b (DNMT3b) as a principal regulator of ZSWIM3 expression. Mechanistically, ZSWIM3 might affect inflammation by binding with tumor necrosis factor receptor-associated factor 2 (TRAF2), which further mediates the activation of the nuclear transcription factor κB (NF-κB) pathway. The present study, therefore, provides detailed insights into the possible structure and function of ZSWIM3 and thus, contributes new substantial research in the elucidation of the pathogenesis of ALI.
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Affiliation(s)
- Hai-Di Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xin Chen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Jie-Jie Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xiao-Sa Du
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Yang Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, U.S.A
| | - Juan-Juan Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xiao-Juan Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Hui-Min Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xiao-Feng Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Ming-Fei Wu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Chong Zhang
- Hepatobiliary surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Chao Zhang
- Hepatobiliary surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zeng Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Hua Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
- Hepatobiliary surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
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14
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Li HD, Chen X, Xu JJ, Du XS, Yang Y, Li JJ, Yang XJ, Huang HM, Li XF, Wu MF, Zhang C, Zhang C, Li Z, Wang H, Meng XM, Huang C, Li J. DNMT3b-mediated methylation of ZSWIM3 enhances inflammation in alcohol-induced liver injury via regulating TRAF2-mediated NF-κB pathway. Clin Sci (Lond) 2020; 134:1935-1956. [PMID: 32639005 DOI: 10.1042/cs20200031] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2023]
Abstract
The regulation of macrophages during inflammatory responses is a crucial process in alcoholic liver disease (ALD) and aberrant macrophage DNA methylation is associated with inflammation. Our preliminary screening results of macrophage methylation in the present study demonstrated the zinc finger SWI2/SNF2 and MuDR (SWIM)-domain containing 3 (ZSWIM3) were hypermethylated in the 5' untranslated region (5'-UTR) region. ZSWIM3, a novel zinc finger-chelate domain of SWIM, is predicted to function in DNA-binding and protein-binding interactions. Its expression was found to be consistently decreased in macrophages isolated from livers of ethyl alcohol (EtOH)-fed mice and in EtOH+lipopolysaccharide (LPS)-induced RAW264.7 cells. Over-expression of ZSWIM3 was found to attenuate chronic+binge ethanol feeding-induced liver injury and inhibit inflammatory responses in vivo. Enforced expression of ZSWIM3 in vitro was also found to have anti-inflammatory effects. Aberrant expression of ZSWIM3 in alcohol-induced liver injury (ALI) was found to be associated with hypermethylation. Analysis of CpG prediction indicated the presence of two methylated sites in the ZSWIM3 promoter region and methylation inhibitor and DNA methyltransferases (DNMTs)-siRNA transfection were found to restore down-regulated ZSWIM3. Chromatin immunoprecipitation (ChIP) assay and molecular docking affirmed the role of DNMT 3b (DNMT3b) as a principal regulator of ZSWIM3 expression. Mechanistically, ZSWIM3 might affect inflammation by binding with tumor necrosis factor receptor-associated factor 2 (TRAF2), which further mediates the activation of the nuclear transcription factor κB (NF-κB) pathway. The present study, therefore, provides detailed insights into the possible structure and function of ZSWIM3 and thus, contributes new substantial research in the elucidation of the pathogenesis of ALI.
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Affiliation(s)
- Hai-Di Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xin Chen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Jie-Jie Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xiao-Sa Du
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Yang Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, U.S.A
| | - Juan-Juan Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xiao-Juan Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Hui-Min Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xiao-Feng Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Ming-Fei Wu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Chong Zhang
- Hepatobiliary surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Chao Zhang
- Hepatobiliary surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zeng Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Hua Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
- Hepatobiliary surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
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15
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Li HD, Chen X, Xu JJ, Du XS, Yang Y, Li JJ, Yang XJ, Huang HM, Li XF, Wu MF, Zhang C, Zhang C, Li Z, Wang H, Meng XM, Huang C, Li J. DNMT3b-mediated methylation of ZSWIM3 enhances inflammation in alcohol-induced liver injury via regulating TRAF2-mediated NF-κB pathway. Clin Sci (Lond) 2020. [DOI: https://doi.org/10.1042/cs20200031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abstract
The regulation of macrophages during inflammatory responses is a crucial process in alcoholic liver disease (ALD) and aberrant macrophage DNA methylation is associated with inflammation. Our preliminary screening results of macrophage methylation in the present study demonstrated the zinc finger SWI2/SNF2 and MuDR (SWIM)-domain containing 3 (ZSWIM3) were hypermethylated in the 5′ untranslated region (5′-UTR) region. ZSWIM3, a novel zinc finger-chelate domain of SWIM, is predicted to function in DNA-binding and protein-binding interactions. Its expression was found to be consistently decreased in macrophages isolated from livers of ethyl alcohol (EtOH)-fed mice and in EtOH+lipopolysaccharide (LPS)-induced RAW264.7 cells. Over-expression of ZSWIM3 was found to attenuate chronic+binge ethanol feeding-induced liver injury and inhibit inflammatory responses in vivo. Enforced expression of ZSWIM3 in vitro was also found to have anti-inflammatory effects. Aberrant expression of ZSWIM3 in alcohol-induced liver injury (ALI) was found to be associated with hypermethylation. Analysis of CpG prediction indicated the presence of two methylated sites in the ZSWIM3 promoter region and methylation inhibitor and DNA methyltransferases (DNMTs)-siRNA transfection were found to restore down-regulated ZSWIM3. Chromatin immunoprecipitation (ChIP) assay and molecular docking affirmed the role of DNMT 3b (DNMT3b) as a principal regulator of ZSWIM3 expression. Mechanistically, ZSWIM3 might affect inflammation by binding with tumor necrosis factor receptor-associated factor 2 (TRAF2), which further mediates the activation of the nuclear transcription factor κB (NF-κB) pathway. The present study, therefore, provides detailed insights into the possible structure and function of ZSWIM3 and thus, contributes new substantial research in the elucidation of the pathogenesis of ALI.
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Affiliation(s)
- Hai-Di Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xin Chen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Jie-Jie Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xiao-Sa Du
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Yang Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, U.S.A
| | - Juan-Juan Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xiao-Juan Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Hui-Min Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Xiao-Feng Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Ming-Fei Wu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Chong Zhang
- Hepatobiliary surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Chao Zhang
- Hepatobiliary surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zeng Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Hua Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
- Hepatobiliary surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
- The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei, China
- Institute for Liver Diseases of Anhui Medical University, Hefei, China
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China
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16
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Molin WT, Yaguchi A, Blenner M, Saski CA. The EccDNA Replicon: A Heritable, Extranuclear Vehicle That Enables Gene Amplification and Glyphosate Resistance in Amaranthus palmeri. THE PLANT CELL 2020; 32:2132-2140. [PMID: 32327538 PMCID: PMC7346551 DOI: 10.1105/tpc.20.00099] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/09/2020] [Accepted: 04/21/2020] [Indexed: 05/10/2023]
Abstract
Gene copy number variation is a predominant mechanism used by organisms to respond to selective pressures from the environment. This often results in unbalanced structural variations that perpetuate as adaptations to sustain life. However, the underlying mechanisms that give rise to gene proliferation are poorly understood. Here, we show a unique result of genomic plasticity in Amaranthus palmeri: a massive, ∼400-kb extrachromosomal circular DNA (eccDNA) that harbors the 5-ENOYLPYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE (EPSPS) gene and 58 other genes whose encoded functions traverse detoxification, replication, recombination, transposition, tethering, and transport. Gene expression analysis under glyphosate stress showed transcription of 41 of these 59 genes, with high expression of EPSPS, as well as genes coding for aminotransferases, zinc finger proteins, and several uncharacterized proteins. The genomic architecture of the eccDNA replicon is composed of a complex arrangement of repeat sequences and mobile genetic elements interspersed among arrays of clustered palindromes that may be crucial for stability, DNA duplication and tethering, and/or a means of nuclear integration of the adjacent and intervening sequences. Comparative analysis of orthologous genes in grain amaranth (Amaranthus hypochondriacus) and waterhemp (Amaranthus tuberculatus) suggests that higher order chromatin interactions contribute to the genomic origins of the A. palmeri eccDNA replicon structure.
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Affiliation(s)
- William T Molin
- Crop Protection Systems Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Stoneville, Mississippi 38776
| | - Allison Yaguchi
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, South Carolina 29634
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17
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Chang CC, Kuo HY, Chen SY, Lin WT, Lu KM, Saito T, Liu FC. Developmental characterization of Zswim5 expression in the progenitor domains and tangential migration pathways of cortical interneurons in the mouse forebrain. J Comp Neurol 2020; 528:2404-2419. [PMID: 32144752 DOI: 10.1002/cne.24900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 12/18/2022]
Abstract
GABAergic interneurons play an essential role in modulating cortical networks. The progenitor domains of cortical interneurons are localized in developing ventral forebrain, including the medial ganglionic eminence (MGE), caudal ganglionic eminence (CGE), preoptic area (POA), and preoptic hypothalamic border domain (POH). Here, we characterized the expression pattern of Zswim5, an MGE-enriched gene in the mouse forebrain. At E11.5-E13.5, prominent Zswim5 expression was detected in the subventricular zone (SVZ) of MGE, POA, and POH, but not CGE of ventral telencephalon where progenitors of cortical interneurons resided. At E15.5 and E17.5, Zswim5 expression remained in the MGE/pallidum primordium and ventral germinal zone. Zswim5 mRNA was markedly decreased after birth and was absent in the adult forebrain. Interestingly, the Zswim5 expression pattern resembled the tangential migration pathways of cortical interneurons. Zswim5-positive cells in the MGE appeared to migrate from the MGE through the SVZ of LGE to overlying neocortex. Indeed, Zswim5 was co-localized with Nkx2.1 and Lhx6, markers of progenitors and migratory cortical interneurons. Double labeling showed that Ascl1/Mash1-positive cells co-expressed Zswim5. Zswim5 expressing cells contained none or at most low levels of Ki67 but co-expressed Tuj1 in the SVZ of MGE. These results suggest that Zswim5 is immediately upregulated as progenitors exiting cell cycle become postmitotic. Given that recent studies have elucidated that the cell fate of cortical interneurons is determined shortly after becoming postmitotic, the timing of Zswim5 expression in early postmitotic interneurons suggests a potential role of Zswim5 in regulation of neurogenesis and tangential migration of cortical interneurons.
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Affiliation(s)
- Chuan-Chie Chang
- Institute of Neuroscience, National Yang-Ming University, Taipei, Taiwan
| | - Hsiao-Ying Kuo
- Institute of Neuroscience, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Yun Chen
- Institute of Neuroscience, National Yang-Ming University, Taipei, Taiwan
| | - Wan-Ting Lin
- Institute of Neuroscience, National Yang-Ming University, Taipei, Taiwan
| | - Kuan-Ming Lu
- Institute of Neuroscience, National Yang-Ming University, Taipei, Taiwan
| | - Tetsuichiro Saito
- Department of Developmental Biology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Fu-Chin Liu
- Institute of Neuroscience, National Yang-Ming University, Taipei, Taiwan
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18
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Xu K, Liu B, Ma Y, Xu B, Xing X. A novel SWIM domain protein ZSWIM5 inhibits the malignant progression of non-small-cell lung cancer. Cancer Manag Res 2018; 10:3245-3254. [PMID: 30233241 PMCID: PMC6130280 DOI: 10.2147/cmar.s174355] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Purpose Zinc finger SWIM-type containing 5 (ZSWIM5) is a newly discovered protein, which contains a novel zinc-chelating domain SWIM (CxCxnCxH), and is predicted to interact with DNA or proteins. Currently, the knowledge of functions of ZSWIM5 remains limited. In this study, we aimed to elucidate the biological functions of ZSWIM5 and their mechanisms. Patients and methods We detected the expression of ZSWIM5 in samples from 139 cases of non-small-cell lung cancer (NSCLC) patients and six cell lines using immunohistochemistry and Western blot. Moreover, we explored the biological functions of ZSWIM5 in lung cancer cells by siRNA interference and cDNA transfection of ZSWIM5. Results The results showed that compared with adjacent non-tumor lung tissues, ZSWIM5 expression was significantly decreased in NSCLC tissues (P=0.0199) and that the ZSWIM5-positive rate in non-tumor tissues (76.67%) was notably higher than that in NSCLC tissues (40.29%). ZSWIM5 expression in human normal bronchial epithelial cells was also much higher than that in lung cancer lines (P<0.001). ZSWIM5-negative expression was significantly related to TNM stage (P<0.001), lymph node metastasis (P=0.002), and poor prognosis (P<0.001) of NSCLC patients. MTT and colony formation assays showed that ZSWIM5 could inhibit the proliferation and colony formation abilities of lung cancer cells. Meanwhile, the results of transwell and wound healing assays showed that ZSWIM5 could suppress the invasion and migration of lung cancer cells. Further investigation revealed that ZSWIM5 could downregulate cyclin D1, cyclin E, cyclin A2, MMP2, and MMP9 expression, which affected the proliferation, invasion, and migration abilities of lung cancer cells. Conclusion ZSWIM5 could inhibit the malignant progression of NSCLC by affecting the expression of cyclins and MMPs.
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Affiliation(s)
- Ke Xu
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Shenyang, Liaoning Province, People's Republic of China,
| | - Bin Liu
- Department of Medical Oncology, Cancer Hospital of China Medical University, Shenyang, Liaoning Province, People's Republic of China
| | - Yegang Ma
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Shenyang, Liaoning Province, People's Republic of China,
| | - Baojin Xu
- General Surgery Liaoning Cancer Hospital and Institute, Shenyang, Liaoning Province, People's Republic of China
| | - Xiaojing Xing
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Shenyang, Liaoning Province, People's Republic of China,
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19
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Zhang S, Wang L, Tao Y, Bai T, Lu R, Zhang T, Chen J, Ding J. Structural basis for the functional role of the Shu complex in homologous recombination. Nucleic Acids Res 2018; 45:13068-13079. [PMID: 29069504 PMCID: PMC5727457 DOI: 10.1093/nar/gkx992] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/11/2017] [Indexed: 12/11/2022] Open
Abstract
The Shu complex, a conserved regulator consisting of Csm2, Psy3, Shu1 and Shu2 in budding yeast, plays an important role in the assembly of the Rad51–ssDNA filament in homologous recombination. However, the molecular basis for the assembly of the Shu complex and its functional role in DNA repair is still elusive. Here, we report the crystal structure of the yeast Shu complex, revealing that Csm2, Psy3, Shu1 and Shu2 interact with each other in sequence to form a V-shape overall structure. Shu1 adopts a structure resembling the ATPase core domain of Rad51 and represents a new Rad51 paralog. Shu2 assumes a novel structural fold consisting of a conserved zinc-finger containing SWIM domain and a small insertion domain. The functional roles of the key residues are validated using mutagenesis and in vitro pull-down and in vivo yeast growth studies. Structural analysis together with available biological data identifies two potential DNA-binding sites, one of which might be responsible for binding the ssDNA region of the 3′-overhang DNA and the other for the dsDNA region. Collectively, these findings reveal the molecular basis for the assembly of the Shu complex and shed new insight on its functional role in homologous recombination.
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Affiliation(s)
- Shicheng Zhang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences; 333 Haike Road, Shanghai 201210, China
| | - Linlin Wang
- School of Life Sciences, Shanghai University, 333 Nanchen Road, Shanghai 200444, China
| | - Ye Tao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences; 333 Haike Road, Shanghai 201210, China
| | - Tuya Bai
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences; 333 Haike Road, Shanghai 201210, China
| | - Rong Lu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences; 333 Haike Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
| | - Tianlong Zhang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences; 333 Haike Road, Shanghai 201210, China
| | - Jiangye Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences; 333 Haike Road, Shanghai 201210, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences; 333 Haike Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
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20
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Ma L, Li G. FAR1-RELATED SEQUENCE (FRS) and FRS-RELATED FACTOR (FRF) Family Proteins in Arabidopsis Growth and Development. FRONTIERS IN PLANT SCIENCE 2018; 9:692. [PMID: 29930561 PMCID: PMC6000157 DOI: 10.3389/fpls.2018.00692] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/07/2018] [Indexed: 05/18/2023]
Abstract
Transposable elements make important contributions to adaptation and evolution of their host genomes. The well-characterized transposase-derived transcription factor FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and its homologue FAR-RED IMPAIRED RESPONSE1 (FAR1) have crucial functions in plant growth and development. In addition, FHY3 and FAR1 are the founding members of the FRS (FAR1-RELATED SEQUENCE) and FRF (FRS-RELATED FACTOR) families, which are conserved among land plants. Although the coding sequences of many putative FRS and FRF orthologs have been found in various clades of angiosperms, their physiological functions remain elusive. Here, we summarize recent progress toward characterizing the molecular mechanisms of FHY3 and FAR1, as well as other FRS-FRF family proteins, examining their roles in regulating plant growth and development. This review also suggests future directions for further functional characterization of other FRS-FRF family proteins in plants.
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Affiliation(s)
- Lin Ma
- School of Biological Science and Technology, University of Jinan, Jinan, China
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Gang Li,
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21
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Palmer EE, Kumar R, Gordon CT, Shaw M, Hubert L, Carroll R, Rio M, Murray L, Leffler M, Dudding-Byth T, Oufadem M, Lalani SR, Lewis AM, Xia F, Tam A, Webster R, Brammah S, Filippini F, Pollard J, Spies J, Minoche AE, Cowley MJ, Risen S, Powell-Hamilton NN, Tusi JE, Immken L, Nagakura H, Bole-Feysot C, Nitschké P, Garrigue A, de Saint Basile G, Kivuva E, Scott RH, Rendon A, Munnich A, Newman W, Kerr B, Besmond C, Rosenfeld JA, Amiel J, Field M, Gecz J, Gecz J. A Recurrent De Novo Nonsense Variant in ZSWIM6 Results in Severe Intellectual Disability without Frontonasal or Limb Malformations. Am J Hum Genet 2017; 101:995-1005. [PMID: 29198722 DOI: 10.1016/j.ajhg.2017.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 10/16/2017] [Indexed: 10/18/2022] Open
Abstract
A recurrent de novo missense variant within the C-terminal Sin3-like domain of ZSWIM6 was previously reported to cause acromelic frontonasal dysostosis (AFND), an autosomal-dominant severe frontonasal and limb malformation syndrome, associated with neurocognitive and motor delay, via a proposed gain-of-function effect. We present detailed phenotypic information on seven unrelated individuals with a recurrent de novo nonsense variant (c.2737C>T [p.Arg913Ter]) in the penultimate exon of ZSWIM6 who have severe-profound intellectual disability and additional central and peripheral nervous system symptoms but an absence of frontonasal or limb malformations. We show that the c.2737C>T variant does not trigger nonsense-mediated decay of the ZSWIM6 mRNA in affected individual-derived cells. This finding supports the existence of a truncated ZSWIM6 protein lacking the Sin3-like domain, which could have a dominant-negative effect. This study builds support for a key role for ZSWIM6 in neuronal development and function, in addition to its putative roles in limb and craniofacial development, and provides a striking example of different variants in the same gene leading to distinct phenotypes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jozef Gecz
- School of Medicine, The Robinson Research Institute, The University of Adelaide, North Adelaide, SA 5005, Australia; Healthy Mothers and Babies, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia.
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22
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Kalyandurg P, Gil JF, Lukhovitskaya NI, Flores B, Müller G, Chuquillanqui C, Palomino L, Monjane A, Barker I, Kreuze J, Savenkov EI. Molecular and pathobiological characterization of 61 Potato mop-top virus full-length cDNAs reveals great variability of the virus in the centre of potato domestication, novel genotypes and evidence for recombination. MOLECULAR PLANT PATHOLOGY 2017; 18:864-877. [PMID: 28390168 PMCID: PMC6638219 DOI: 10.1111/mpp.12552] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/17/2017] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
The evolutionary divergence of Potato mop-top virus (PMTV), a tri-partite, single-stranded RNA virus, is exceptionally low, based on the analysis of sequences obtained from isolates from Europe, Asia and North America. In general, RNA viruses exist as dynamic populations of closely related and recombinant genomes that are subjected to continuous genetic variation. The reason behind the low genetic variation of PMTV remains unclear. The question remains as to whether the low variability is a shared property of all PMTV isolates or is a result of the limited number of isolates characterized so far. We hypothesized that higher divergence of the virus might exist in the Andean regions of South America, the centre of potato domestication. Here, we report high variability of PMTV isolates collected from 12 fields in three locations in the Andean region of Peru. To evaluate PMTV genetic variation in Peru, we generated full-length cDNA clones, which allowed reliable comparative molecular and pathobiological characterization of individual isolates. We found significant divergence of the CP-RT and 8K sequences. The 8K cistron, which encodes a viral suppressor of RNA silencing, was found to be under diversifying selection. Phylogenetic analysis determined that, based on the CP-RT sequence, all PMTV isolates could be categorized into three separate lineages (clades). Moreover, we found evidence for recombination between two clades. Using infectious cDNA clones of the representatives of these two clades, as well as reassortants for the RNA-CP genomic component, we determined the pathobiological differences between the lineages, which we coined as S (for severe) and M (for mild) types. Interestingly, all isolates characterized previously (from Europe, Asia and North America) fall into the S-type clade, whereas most of the Peruvian isolates belong to the M-type. Taken together, our results support the notion of the single introduction of PMTV from the centre of potato origin to Europe, and subsequent spread of the S-type into Asia and USA. This is also supported by the suggested novel classification of isolates based on genetic constellations.
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Affiliation(s)
- Pruthvi Kalyandurg
- Department of Plant Biology, Uppsala BioCenter SLUSwedish University of Agricultural Sciences, Linnean Center for Plant BiologyUppsala75007Sweden
| | - Jose Fernando Gil
- Department of Plant Biology, Uppsala BioCenter SLUSwedish University of Agricultural Sciences, Linnean Center for Plant BiologyUppsala75007Sweden
| | - Nina I. Lukhovitskaya
- Department of Plant Biology, Uppsala BioCenter SLUSwedish University of Agricultural Sciences, Linnean Center for Plant BiologyUppsala75007Sweden
- Present address:
Division of Virology, Department of PathologyUniversity of CambridgeHills RoadCambridgeCB2 0QQUK
| | - Betty Flores
- International Potato Center (CIP)Apartado 1558Lima12Peru
| | | | | | - Ladislao Palomino
- Instituto Nacional de Innovación Agraria (INIA)EEA – Andenes04540CuzcoPeru
| | - Aderito Monjane
- Department of Plant Biology, Uppsala BioCenter SLUSwedish University of Agricultural Sciences, Linnean Center for Plant BiologyUppsala75007Sweden
- Present address:
Norwegian Veterinary Institute0106OsloNorway
| | - Ian Barker
- International Potato Center (CIP)Apartado 1558Lima12Peru
- Present address:
Syngenta Foundation for Sustainable Agriculture4002BaselSwitzerland
| | - Jan Kreuze
- International Potato Center (CIP)Apartado 1558Lima12Peru
| | - Eugene I. Savenkov
- Department of Plant Biology, Uppsala BioCenter SLUSwedish University of Agricultural Sciences, Linnean Center for Plant BiologyUppsala75007Sweden
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23
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Tischfield DJ, Saraswat DK, Furash A, Fowler SC, Fuccillo MV, Anderson SA. Loss of the neurodevelopmental gene Zswim6 alters striatal morphology and motor regulation. Neurobiol Dis 2017; 103:174-183. [PMID: 28433741 PMCID: PMC5703052 DOI: 10.1016/j.nbd.2017.04.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 04/08/2017] [Accepted: 04/15/2017] [Indexed: 01/06/2023] Open
Abstract
The zinc-finger SWIM domain-containing protein 6 (ZSWIM6) is a protein of unknown function that has been associated with schizophrenia and limited educational attainment by three independent genome-wide association studies. Additionally, a putatively causal point mutation in ZSWIM6 has been identified in several cases of acromelic frontonasal dysostosis with severe intellectual disability. Despite the growing number of studies implicating ZSWIM6 as an important regulator of brain development, its role in this process has never been examined. Here, we report the generation of Zswim6 knockout mice and provide a detailed anatomical and behavioral characterization of the resulting phenotype. We show that Zswim6 is initially expressed widely during embryonic brain development but becomes restricted to the striatum postnatally. Loss of Zswim6 causes a reduction in striatal volume and changes in medium spiny neuron morphology. These changes are associated with alterations in motor control, including hyperactivity, impaired rotarod performance, repetitive movements, and behavioral hyperresponsiveness to amphetamine. Together, our results show that Zswim6 is indispensable to normal brain function and support the notion that Zswim6 might serve as an important contributor to the pathogenesis of schizophrenia and other neurodevelopmental disorders.
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Affiliation(s)
- David J Tischfield
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6085, USA; Department of Psychiatry, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine ARC 517, Philadelphia, PA 19104-5127, USA
| | - Dave K Saraswat
- Department of Psychiatry, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine ARC 517, Philadelphia, PA 19104-5127, USA
| | - Andrew Furash
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6085, USA
| | - Stephen C Fowler
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS 66045, USA
| | - Marc V Fuccillo
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6085, USA
| | - Stewart A Anderson
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6085, USA; Department of Psychiatry, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine ARC 517, Philadelphia, PA 19104-5127, USA.
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Farlie PG, Baker NL, Yap P, Tan TY. Frontonasal Dysplasia: Towards an Understanding of Molecular and Developmental Aetiology. Mol Syndromol 2016; 7:312-321. [PMID: 27920634 DOI: 10.1159/000450533] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2016] [Indexed: 01/09/2023] Open
Abstract
The complex anatomy of the skull and face arises from the requirement to support multiple sensory and structural functions. During embryonic development, the diverse component elements of the neuro- and viscerocranium must be generated independently and subsequently united in a manner that sustains and promotes the growth of the brain and sensory organs, while achieving a level of structural integrity necessary for the individual to become a free-living organism. While each of these individual craniofacial components is essential, the cranial and facial midline lies at a structural nexus that unites these disparately derived elements, fusing them into a whole. Defects of the craniofacial midline can have a profound impact on both form and function, manifesting in a diverse array of phenotypes and clinical entities that can be broadly defined as frontonasal dysplasias (FNDs). Recent advances in the identification of the genetic basis of FNDs along with the analysis of developmental mechanisms impacted by these mutations have dramatically altered our understanding of this complex group of conditions.
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Affiliation(s)
- Peter G Farlie
- Murdoch Childrens Research Institute, University of Melbourne, Parkville, Vic., Australia; Department of Paediatrics, University of Melbourne, Parkville, Vic., Australia
| | - Naomi L Baker
- Murdoch Childrens Research Institute, University of Melbourne, Parkville, Vic., Australia; Department of Paediatrics, University of Melbourne, Parkville, Vic., Australia
| | - Patrick Yap
- Victorian Clinical Genetics Service, Royal Children's Hospital, University of Melbourne, Parkville, Vic., Australia; Genetic Health Service New Zealand (Northern Hub), Auckland City Hospital, Auckland, New Zealand
| | - Tiong Y Tan
- Victorian Clinical Genetics Service, Royal Children's Hospital, University of Melbourne, Parkville, Vic., Australia; Department of Paediatrics, University of Melbourne, Parkville, Vic., Australia
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25
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Martino J, Bernstein KA. The Shu complex is a conserved regulator of homologous recombination. FEMS Yeast Res 2016; 16:fow073. [PMID: 27589940 DOI: 10.1093/femsyr/fow073] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2016] [Indexed: 02/06/2023] Open
Abstract
Homologous recombination (HR) is an error-free DNA repair mechanism that maintains genome integrity by repairing double-strand breaks (DSBs). Defects in HR lead to genomic instability and are associated with cancer predisposition. A key step in HR is the formation of Rad51 nucleoprotein filaments which are responsible for the homology search and strand invasion steps that define HR. Recently, the budding yeast Shu complex has emerged as an important regulator of Rad51 along with the other Rad51 mediators including Rad52 and the Rad51 paralogs, Rad55-Rad57. The Shu complex is a heterotetramer consisting of two novel Rad51 paralogs, Psy3 and Csm2, along with Shu1 and a SWIM domain-containing protein, Shu2. Studies done primarily in yeast have provided evidence that the Shu complex regulates HR at several types of DNA DSBs (i.e. replication-associated and meiotic DSBs) and that its role in HR is highly conserved across eukaryotic lineages. This review highlights the main findings of these studies and discusses the proposed specific roles of the Shu complex in many aspects of recombination-mediated DNA repair.
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Affiliation(s)
- Julieta Martino
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
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26
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VEX1 controls the allelic exclusion required for antigenic variation in trypanosomes. Proc Natl Acad Sci U S A 2016; 113:7225-30. [PMID: 27226299 DOI: 10.1073/pnas.1600344113] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Allelic exclusion underpins antigenic variation and immune evasion in African trypanosomes. These bloodstream parasites use RNA polymerase-I (pol-I) to transcribe just one telomeric variant surface glycoprotein (VSG) gene at a time, producing superabundant and switchable VSG coats. We identified trypanosome VSG exclusion-1 (VEX1) using a genetic screen for defects in telomere-exclusive expression. VEX1 was sequestered by the active VSG and silencing of other VSGs failed when VEX1 was either ectopically expressed or depleted, indicating positive and negative regulation, respectively. Positive regulation affected VSGs and nontelomeric pol-I-transcribed genes, whereas negative regulation primarily affected VSGs. Negative regulation by VEX1 also affected telomeric pol-I-transcribed reporter constructs, but only when they contained blocks of sequence sharing homology with a pol-I-transcribed locus. We conclude that restricted positive regulation due to VEX1 sequestration, combined with VEX1-dependent, possibly homology-dependent silencing, drives a "winner-takes-all" mechanism of allelic exclusion.
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27
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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28
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Promotion of Homologous Recombination by SWS-1 in Complex with RAD-51 Paralogs in Caenorhabditis elegans. Genetics 2016; 203:133-45. [PMID: 26936927 DOI: 10.1534/genetics.115.185827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/19/2016] [Indexed: 11/18/2022] Open
Abstract
Homologous recombination (HR) repairs cytotoxic DNA double-strand breaks (DSBs) with high fidelity. Deficiencies in HR result in genome instability. A key early step in HR is the search for and invasion of a homologous DNA template by a single-stranded RAD-51 nucleoprotein filament. The Shu complex, composed of a SWIM domain-containing protein and its interacting RAD51 paralogs, promotes HR by regulating RAD51 filament dynamics. Despite Shu complex orthologs throughout eukaryotes, our understanding of its function has been most extensively characterized in budding yeast. Evolutionary analysis of the SWIM domain identified Caenorhabditis elegans sws-1 as a putative homolog of the yeast Shu complex member Shu2. Using a CRISPR-induced nonsense allele of sws-1, we show that sws-1 promotes HR in mitotic and meiotic nuclei. sws-1 mutants exhibit sensitivity to DSB-inducing agents and fail to form mitotic RAD-51 foci following treatment with camptothecin. Phenotypic similarities between sws-1 and the two RAD-51 paralogs rfs-1 and rip-1 suggest that they function together. Indeed, we detect direct interaction between SWS-1 and RIP-1 by yeast two-hybrid assay that is mediated by the SWIM domain in SWS-1 and the Walker B motif in RIP-1 Furthermore, RIP-1 bridges an interaction between SWS-1 and RFS-1, suggesting that RIP-1 facilitates complex formation with SWS-1 and RFS-1 We propose that SWS-1, RIP-1, and RFS-1 compose a C. elegans Shu complex. Our work provides a new model for studying Shu complex disruption in the context of a multicellular organism that has important implications as to why mutations in the human RAD51 paralogs are associated with genome instability.
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29
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Twigg SRF, Ousager LB, Miller KA, Zhou Y, Elalaoui SC, Sefiani A, Bak GS, Hove H, Hansen LK, Fagerberg CR, Tajir M, Wilkie AOM. Acromelic frontonasal dysostosis and ZSWIM6 mutation: phenotypic spectrum and mosaicism. Clin Genet 2016; 90:270-5. [PMID: 26706854 PMCID: PMC5025718 DOI: 10.1111/cge.12721] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 11/24/2022]
Abstract
Acromelic frontonasal dysostosis (AFND) is a distinctive and rare frontonasal malformation that presents in combination with brain and limb abnormalities. A single recurrent heterozygous missense substitution in ZSWIM6, encoding a protein of unknown function, was previously shown to underlie this disorder in four unrelated cases. Here we describe four additional individuals from three families, comprising two sporadic subjects (one of whom had no limb malformation) and a mildly affected female with a severely affected son. In the latter family we demonstrate parental mosaicism through deep sequencing of DNA isolated from a variety of tissues, which each contain different levels of mutation. This has important implications for genetic counselling.
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Affiliation(s)
- S R F Twigg
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - L B Ousager
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - K A Miller
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Y Zhou
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - S C Elalaoui
- Human Genomics Center, Faculty of Medicine and Pharmacy of Rabat, Rabat, Morocco.,Department of Medical Genetics, National Institute of Health, Rabat, Morocco
| | - A Sefiani
- Human Genomics Center, Faculty of Medicine and Pharmacy of Rabat, Rabat, Morocco.,Department of Medical Genetics, National Institute of Health, Rabat, Morocco
| | - G S Bak
- Department of Obstetrics and Gynecology, Odense University Hospital, Odense, Denmark
| | - H Hove
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - L K Hansen
- Department of Paediatrics, Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | - C R Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - M Tajir
- Human Genomics Center, Faculty of Medicine and Pharmacy of Rabat, Rabat, Morocco.,Department of Medical Genetics, National Institute of Health, Rabat, Morocco
| | - A O M Wilkie
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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30
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Dispensability of zinc and the putative zinc-binding domain in bacterial glutamyl-tRNA synthetase. Biosci Rep 2015; 35:BSR20150005. [PMID: 25686371 PMCID: PMC4381286 DOI: 10.1042/bsr20150005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The putative zinc-binding domain (pZBD) in Escherichia coli glutamyl-tRNA synthetase (GluRS) is known to correctly position the tRNA acceptor arm and modulate the amino acid-binding site. However, its functional role in other bacterial species is not clear since many bacterial GluRSs lack a zinc-binding motif in the pZBD. From experimental studies on pZBD-swapped E. coli GluRS, with Thermosynechoccus elongatus GluRS, Burkholderia thailandensis GluRS and E. coli glutamyl-queuosine-tRNAAsp synthetase (Glu-Q-RS), we show that E. coli GluRS, containing the zinc-free pZBD of B. thailandensis, is as functional as the zinc-bound wild-type E. coli GluRS, whereas the other constructs, all zinc-bound, show impaired function. A pZBD-tinkered version of E. coli GluRS that still retained Zn-binding capacity, also showed reduced activity. This suggests that zinc is not essential for the pZBD to be functional. From extensive structural and sequence analyses from whole genome database of bacterial GluRS, we further show that in addition to many bacterial GluRS lacking a zinc-binding motif, the pZBD is actually deleted in some bacteria, all containing either glutaminyl-tRNA synthetase (GlnRS) or a second copy of GluRS (GluRS2). Correlation between the absence of pZBD and the occurrence of glutamine amidotransferase CAB (GatCAB) in the genome suggests that the primordial role of the pZBD was to facilitate transamidation of misacylated Glu-tRNAGln via interaction with GatCAB, whereas its role in tRNAGlu interaction may be a consequence of the presence of pZBD. Zinc is functionally important in glutamylation of tRNAGlu in Escherichia coli, yet, it is absent from many bacterial glutamyl-tRNA synthetases (GluRSs). We demonstrate and rationalize why zinc or the putative zinc-binding domain (pZBD) is not indispensable in all bacterial GluRSs.
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31
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Evolutionary and functional analysis of the invariant SWIM domain in the conserved Shu2/SWS1 protein family from Saccharomyces cerevisiae to Homo sapiens. Genetics 2015; 199:1023-33. [PMID: 25659377 DOI: 10.1534/genetics.114.173518] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/02/2015] [Indexed: 11/18/2022] Open
Abstract
The Saccharomyces cerevisiae Shu2 protein is an important regulator of Rad51, which promotes homologous recombination (HR). Shu2 functions in the Shu complex with Shu1 and the Rad51 paralogs Csm2 and Psy3. Shu2 belongs to the SWS1 protein family, which is characterized by its SWIM domain (CXC...Xn...CXH), a zinc-binding motif. In humans, SWS1 interacts with the Rad51 paralog SWSAP1. Using genetic and evolutionary analyses, we examined the role of the Shu complex in mitotic and meiotic processes across eukaryotic lineages. We provide evidence that the SWS1 protein family contains orthologous genes in early-branching eukaryote lineages (e.g., Giardia lamblia), as well as in multicellular eukaryotes including Caenorhabditis elegans and Drosophila melanogaster. Using sequence analysis, we expanded the SWIM domain to include an invariant alanine three residues after the terminal CXH motif (CXC…Xn…CXHXXA). We found that the SWIM domain is conserved in all eukaryotic orthologs, and accordingly, in vivo disruption of the invariant residues within the canonical SWIM domain inhibits DNA damage tolerance in yeast and protein-protein interactions in yeast and humans. Furthermore, using evolutionary analyses, we found that yeast and Drosophila Shu2 exhibit strong coevolutionary signatures with meiotic proteins, and in yeast, its disruption leads to decreased meiotic progeny. Together our data indicate that the SWS1 family is an ancient and highly conserved eukaryotic regulator of meiotic and mitotic HR.
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32
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Smith J, Hing A, Clarke C, Johnson N, Perez F, Park S, Horst J, Mecham B, Maves L, Nickerson D, Cunningham M, Cunningham ML. Exome sequencing identifies a recurrent de novo ZSWIM6 mutation associated with acromelic frontonasal dysostosis. Am J Hum Genet 2014; 95:235-40. [PMID: 25105228 DOI: 10.1016/j.ajhg.2014.07.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 07/15/2014] [Indexed: 10/24/2022] Open
Abstract
Acromelic frontonasal dysostosis (AFND) is a rare disorder characterized by distinct craniofacial, brain, and limb malformations, including frontonasal dysplasia, interhemispheric lipoma, agenesis of the corpus callosum, tibial hemimelia, preaxial polydactyly of the feet, and intellectual disability. Exome sequencing of one trio and two unrelated probands revealed the same heterozygous variant (c.3487C>T [p. Arg1163Trp]) in a highly conserved protein domain of ZSWIM6; this variant has not been seen in the 1000 Genomes data, dbSNP, or the Exome Sequencing Project. Sanger validation of the three trios confirmed that the variant was de novo and was also present in a fourth isolated proband. In situ hybridization of early zebrafish embryos at 24 hr postfertilization (hpf) demonstrated telencephalic expression of zswim6 and onset of midbrain, hindbrain, and retinal expression at 48 hpf. Immunohistochemistry of later-stage mouse embryos demonstrated tissue-specific expression in the derivatives of all three germ layers. qRT-PCR expression analysis of osteoblast and fibroblast cell lines available from two probands was suggestive of Hedgehog pathway activation, indicating that the ZSWIM6 mutation associated with AFND may lead to the craniofacial, brain and limb malformations through the disruption of Hedgehog signaling.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Michael L Cunningham
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Craniofacial Center, Seattle Children's Hospital, Seattle, WA 98105, USA.
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33
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Ko KK, Powell MS, Hogarth PM. ZSWIM1: A novel biomarker in T helper cell differentiation. Immunol Lett 2014; 160:133-8. [DOI: 10.1016/j.imlet.2014.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/23/2014] [Accepted: 01/28/2014] [Indexed: 10/25/2022]
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34
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Pham TT, Angus SP, Johnson GL. MAP3K1: Genomic Alterations in Cancer and Function in Promoting Cell Survival or Apoptosis. Genes Cancer 2014; 4:419-26. [PMID: 24386504 DOI: 10.1177/1947601913513950] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 11/02/2013] [Indexed: 12/15/2022] Open
Abstract
MAP3K1 is a member of the mitogen-activated protein kinase kinase kinase (MAP3K) family of serine/threonine kinases. MAP3K1 regulates JNK activation and is unique among human kinases in that it also encodes an E3 ligase domain that ubiquitylates c-Jun and ERK1/2. Full length MAP3K1 regulates cell migration and contributes to pro-survival signaling while its caspase 3-mediated cleavage generates a C-terminal kinase domain that promotes apoptosis. The critical function of MAP3K1 in cell fate decisions suggests that it may be a target for deregulation in cancer. Recent large-scale genomic studies have revealed that MAP3K1 copy number loss and somatic missense or nonsense mutations are observed in a significant number of different cancers, being most prominent in luminal breast cancer. The alteration of MAP3K1 in diverse cancer types demonstrates the importance of defining phenotypes for possible therapeutic targeting of tumor cell vulnerabilities created when MAP3K1 function is lost or gained.
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Affiliation(s)
- Trang T Pham
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Steven P Angus
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Gary L Johnson
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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35
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Hayes ML, Giang K, Berhane B, Mulligan RM. Identification of two pentatricopeptide repeat genes required for RNA editing and zinc binding by C-terminal cytidine deaminase-like domains. J Biol Chem 2013; 288:36519-29. [PMID: 24194514 DOI: 10.1074/jbc.m113.485755] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Many transcripts expressed from plant organelle genomes are modified by C-to-U RNA editing. Nuclear encoded pentatricopeptide repeat (PPR) proteins are required as RNA binding specificity determinants in the RNA editing mechanism. Bioinformatic analysis has shown that most of the Arabidopsis PPR proteins necessary for RNA editing events include a C-terminal portion that shares structural characteristics with a superfamily of deaminases. The DYW deaminase domain includes a highly conserved zinc binding motif that shares characteristics with cytidine deaminases. The Arabidopsis PPR genes, ELI1 and DOT4, both have DYW deaminase domains and are required for single RNA editing events in chloroplasts. The ELI1 DYW deaminase domain was expressed as a recombinant protein in Escherichia coli and was shown to bind two zinc atoms per polypeptide. Thus, the DYW deaminase domain binds a zinc metal ion, as expected for a cytidine deaminase, and is potentially the catalytic component of an editing complex. Genetic complementation experiments demonstrate that large portions of the DYW deaminase domain of ELI1 may be eliminated, but the truncated genes retain the ability to restore editing site conversion in a mutant plant. These results suggest that the catalytic activity can be supplied in trans by uncharacterized protein(s) of the editosome.
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36
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Wang Z, Hou Y, Guo X, van der Voet M, Boxem M, Dixon JE, Chisholm AD, Jin Y. The EBAX-type Cullin-RING E3 ligase and Hsp90 guard the protein quality of the SAX-3/Robo receptor in developing neurons. Neuron 2013; 79:903-16. [PMID: 24012004 PMCID: PMC3779136 DOI: 10.1016/j.neuron.2013.06.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2013] [Indexed: 12/14/2022]
Abstract
Although protein quality control (PQC) is generally perceived as important for the development of the nervous system, the specific mechanisms of neuronal PQC have remained poorly understood. Here, we report that C. elegans Elongin BC-binding axon regulator (EBAX-1), a conserved BC-box protein, regulates axon guidance through PQC of the SAX-3/Robo receptor. EBAX-1 buffers guidance errors against temperature variations. As a substrate-recognition subunit in the Elongin BC-containing Cullin-RING ubiquitin ligase (CRL), EBAX-1 also binds to DAF-21, a cytosolic Hsp90 chaperone. The EBAX-type CRL and DAF-21 collaboratively regulate SAX-3-mediated axon pathfinding. Biochemical and imaging assays indicate that EBAX-1 specifically recognizes misfolded SAX-3 and promotes its degradation in vitro and in vivo. Importantly, vertebrate EBAX also shows substrate preference toward aberrant Robo3 implicated in horizontal gaze palsy with progressive scoliosis (HGPPS). Together, our findings demonstrate a triage PQC mechanism mediated by the EBAX-type CRL and DAF-21/Hsp90 that maintains the accuracy of neuronal wiring.
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Affiliation(s)
- Zhiping Wang
- Neurobiology Section, Division of Biological Sciences, UC San Diego, La Jolla, CA 92093
| | - Yanli Hou
- Department of Molecular, Cell, and Developmental Biology, UC Santa Cruz, CA 95064
| | - Xing Guo
- Department of Pharmacology, School of Medicine, UC San Diego, La Jolla, CA 92093
| | | | - Mike Boxem
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Jack E. Dixon
- Department of Pharmacology, School of Medicine, UC San Diego, La Jolla, CA 92093
- Howard Hughes Medical Institute
| | - Andrew D. Chisholm
- Neurobiology Section, Division of Biological Sciences, UC San Diego, La Jolla, CA 92093
| | - Yishi Jin
- Neurobiology Section, Division of Biological Sciences, UC San Diego, La Jolla, CA 92093
- Howard Hughes Medical Institute
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37
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Henry LG, Aruni W, Sandberg L, Fletcher HM. Protective role of the PG1036-PG1037-PG1038 operon in oxidative stress in Porphyromonas gingivalis W83. PLoS One 2013; 8:e69645. [PMID: 23990885 PMCID: PMC3747172 DOI: 10.1371/journal.pone.0069645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/13/2013] [Indexed: 12/15/2022] Open
Abstract
As an anaerobe, Porphyromonas gingivalis is significantly affected by the harsh inflammatory environment of the periodontal pocket during initial colonization and active periodontal disease. We reported previously that the repair of oxidative stress-induced DNA damage involving 8-oxo-7,8-dihydroguanine (8-oxoG) may occur by an undescribed mechanism in P. gingivalis. DNA affinity fractionation identified PG1037, a conserved hypothetical protein, among other proteins, that were bound to the 8-oxoG lesion. PG1037 is part of the uvrA-PG1037-pcrA operon in P. gingivalis which is known to be upregulated under H2O2 induced stress. A PCR-based linear transformation method was used to inactivate the uvrA and pcrA genes by allelic exchange mutagenesis. Several attempts to inactivate PG1037 were unsuccessful. Similar to the wild-type when plated on Brucella blood agar, the uvrA and pcrA-defective mutants were black-pigmented and beta-hemolytic. These isogenic mutants also had reduced gingipain activities and were more sensitive to H2O2 and UV irradiation compared to the parent strain. Additionally, glycosylase assays revealed that 8-oxoG repair activities were similar in both wild-type and mutant P. gingivalis strains. Several proteins, some of which are known to have oxidoreducatse activity, were shown to interact with PG1037. The purified recombinant PG1037 protein could protect DNA from H2O2-induced damage. Collectively, these findings suggest that the uvrA-PG1037-pcrA operon may play an important role in hydrogen peroxide stress-induced resistance in P. gingivalis.
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Affiliation(s)
- Leroy G. Henry
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, United States of America
| | - Wilson Aruni
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, United States of America
| | - Lawrence Sandberg
- Division of Biochemistry, School of Medicine, Loma Linda University, Loma Linda, California, United States of America
| | - Hansel M. Fletcher
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, United States of America
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38
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Abstract
Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation.Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g.,in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (e.g.,the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS).Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation,and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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39
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Abstract
MEKK1 [MAPK (mitogen-activated protein kinase)/ERK (extracellular-signal-regulated kinase) kinase kinase 1] is a MAP3K (MAPK kinase kinase) that regulates MAPK activation, and is the only known mammalian kinase that is also a ubiquitin ligase. MEKK1 contains a RING domain within its N-terminal regulatory region, and MEKK1 has been shown to ubiquitylate the AP-1 (activator protein 1) transcription factor protein c-Jun, but the mechanism by which MEKK1 interacts with c-Jun to induce ubiquitylation has not been defined. Proximal to the RING domain is a SWIM (SWI2/SNF2 and MuDR) domain of undetermined function. In the present study, we demonstrate that the MEKK1 SWIM domain, but not the RING domain, directly associates with the c-Jun DNA-binding domain, and that the SWIM domain is required for MEKK1-dependent c-Jun ubiquitylation. We further show that this MEKK1 SWIM-Jun interaction is specific, as SWIM domains from other proteins failed to bind c-Jun. We reveal that, although the Jun and Fos DNA-binding domains are highly conserved, the MEKK1 SWIM domain does not bind Fos. Finally, we identify the sequence unique to Jun proteins required for specific interaction with the MEKK1 SWIM domain. Therefore we propose that the MEKK1 SWIM domain represents a novel substrate-binding domain necessary for direct interaction between c-Jun and MEKK1 that promotes MEKK1-dependent c-Jun ubiquitylation.
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40
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She Z, Gao ZQ, Liu Y, Wang WJ, Liu GF, Shtykova EV, Xu JH, Dong YH. Structural and SAXS analysis of the budding yeast SHU-complex proteins. FEBS Lett 2012; 586:2306-12. [PMID: 22749910 DOI: 10.1016/j.febslet.2012.06.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/08/2012] [Accepted: 06/14/2012] [Indexed: 11/25/2022]
Abstract
In Saccharomyces cerevisiae, four proteins, Shu1, Shu2, Psy3 and Csm2, form a stable SHU-complex both in vivo and in vitro. These proteins are involved in the early stages of the homologous recombination DNA damage repair process. In this paper, the crystal structure of the Psy3-Csm2 sub-complex is presented at 1.8Å resolution and successfully fitted into our small angle X-ray scattering (SAXS) data of the SHU-complex. Taken together with our electrophoretic mobility shift assay (EMSA) results, a model is proposed for the SHU-protein complex coupled with DNA.
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Affiliation(s)
- Zhun She
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
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41
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Zhou Q. A swimy locus on Y chromosome of the platyfish (Xiphophorus maculatus) is derived from a novel DNA transposon Zisupton. Gene 2012; 503:254-9. [PMID: 22579468 DOI: 10.1016/j.gene.2012.04.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 03/09/2012] [Accepted: 04/18/2012] [Indexed: 12/13/2022]
Abstract
A swimy locus derived from a novel DNA transposon Zisupton was located on the sex determination region (SD) of Xiphophorus maculatus. The analysis of expression pattern showed that swimy was exclusively expressed in adult testis in X. maculatus. The putative 939 aa sequence contains four Zn-finger domains, such as two C2H2 type, one NFX type and one SWIM type Zn-finger domain, and one SAP DNA-binding domain. Swimy has about 7 copies per haploid X. maculatus genome with Y-specific copies located in the SD region, and become the second new W-linked marker of platyfish. Analysis of the structure and distribution of this sex-linked marker is benefit to shed new light on the evolutionary dynamics of sex chromosomes in fish.
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Affiliation(s)
- Qingchun Zhou
- Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg 97074, Germany.
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42
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Maple J, Winge P, Tveitaskog AE, Gargano D, Bones AM, Møller SG. Genome-wide gene expression profiles in response to plastid division perturbations. PLANTA 2011; 234:1055-1063. [PMID: 21713643 DOI: 10.1007/s00425-011-1459-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 06/06/2011] [Indexed: 05/31/2023]
Abstract
Plastids are vital organelles involved in important metabolic functions that directly affect plant growth and development. Plastids divide by binary fission involving the coordination of numerous protein components. A tight control of the plastid division process ensures that: there is a full plastid complement during and after cell division, specialized cell types have optimal plastid numbers; the division rate is modulated in response to stress, metabolic fluxes and developmental status. However, how this control is exerted by the host nucleus is unclear. Here, we report a genome-wide microarray analysis of three accumulation and replication of chloroplasts (arc) mutants that show a spectrum of altered plastid division characteristics. To ensure a comprehensive data set, we selected arc3, arc5 and arc11 because they harbour mutations in protein components of both the stromal and cytosolic division machinery, are of different evolutionary origin and display different phenotypic severities in terms of chloroplast number, size and volume. We show that a surprisingly low number of genes are affected by altered plastid division status, but that the affected genes encode proteins important for a variety of fundamental plant processes.
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Affiliation(s)
- Jodi Maple
- Faculty of Science and Technology, Centre for Organelle Research, University of Stavanger, 4068, Stavanger, Norway
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43
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Bohne A, Zhou Q, Darras A, Schmidt C, Schartl M, Galiana-Arnoux D, Volff JN. Zisupton--A Novel Superfamily of DNA Transposable Elements Recently Active in Fish. Mol Biol Evol 2011; 29:631-45. [DOI: 10.1093/molbev/msr208] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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44
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Song J, Durrant WE, Wang S, Yan S, Tan EH, Dong X. DNA repair proteins are directly involved in regulation of gene expression during plant immune response. Cell Host Microbe 2011; 9:115-24. [PMID: 21320694 DOI: 10.1016/j.chom.2011.01.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Revised: 11/29/2010] [Accepted: 01/24/2011] [Indexed: 12/13/2022]
Abstract
Systemic acquired resistance (SAR), an inducible plant-defense response to local infection, requires the signaling molecule salicylic acid (SA) and the transcriptional coactivator NPR1, with concerted activation of pathogenesis-related (PR) genes. Arabidopsis sni1 is an npr1 suppressor and derepression of defense genes in sni1 causes reduced growth and fertility and increased homologous recombination. Characterizing suppressors of sni1, we identify the DNA damage repair proteins SSN2 and RAD51D as genetic and physical interactors with SNI1. During plant defense, SSN2 and possibly RAD51D replace the transcription repressor SNI1 at pathogenesis-related gene promoters. In the presence of SNI1, NPR1 is also required for SSN2 binding. Thus, coordinated action of SNI1, SSN2-RAD51D, and NPR1 ensures the tight control of plant immune gene expression. Given that the SSN2-RAD51D complex is conserved in eukaryotes, their dual function in homologous recombination and transcription regulation of plant-defense genes suggests a general link between these two stress responses.
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Affiliation(s)
- Junqi Song
- Department of Biology, Duke University, Durham, NC 27708, USA
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45
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Bernstein KA, Reid RJD, Sunjevaric I, Demuth K, Burgess RC, Rothstein R. The Shu complex, which contains Rad51 paralogues, promotes DNA repair through inhibition of the Srs2 anti-recombinase. Mol Biol Cell 2011; 22:1599-607. [PMID: 21372173 PMCID: PMC3084681 DOI: 10.1091/mbc.e10-08-0691] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Shu complex, which contains RAD51 paralogues, is involved in the decision between homologous recombination and error-prone repair. We discovered a link to ribosomal DNA (rDNA) recombination when we found an interaction between one member of the Shu complex, SHU1, and UAF30, a component of the upstream activating factor complex (UAF), which regulates rDNA transcription. In the absence of Uaf30, rDNA copy number increases, and this increase depends on several functional subunits of the Shu complex. Furthermore, in the absence of Uaf30, we find that Shu1 and Srs2, an anti-recombinase DNA helicase with which the Shu complex physically interacts, act in the same pathway regulating rDNA recombination. In addition, Shu1 modulates Srs2 recruitment to both induced and spontaneous foci correlating with a decrease in Rad51 foci, demonstrating that the Shu complex is an important regulator of Srs2 activity. Last, we show that Shu1 regulation of Srs2 to double-strand breaks is not restricted to the rDNA, indicating a more general function for the Shu complex in the regulation of Srs2. We propose that the Shu complex shifts the balance of repair toward Rad51 filament stabilization by inhibiting the disassembly reaction of Srs2.
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Affiliation(s)
- Kara A Bernstein
- Department of Genetics & Development, Columbia University Medical Center, New York, NY 10032, USA
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46
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Hua-Van A, Capy P. Analysis of the DDE motif in the Mutator superfamily. J Mol Evol 2009; 67:670-81. [PMID: 19018586 DOI: 10.1007/s00239-008-9178-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 10/16/2008] [Indexed: 01/29/2023]
Abstract
The eukaryotic Mutator family of transposable elements is widespread in plants. Active or potentially active copies are also found in fungi and protozoans, and sequences related to this family have been detected in metazoans as well. Members of this family are called Mutator-like elements (MULEs). They encode transposases, which contain a region conserved with transposases of the IS256 prokaryotic family, known to harbor a DDE catalytic domain. Different DDE or D34E motifs have been proposed in some groups of eukaryotic MULEs based on primary sequence conservation. On a large number of protein sequences related to, and representative of, all MULE families, we analyzed global conservation, the close environment of different acidic residues and the secondary structure. This allowed us to identify a potential DDE motif that is likely to be homologous to the one in IS256-like transposases. The characteristics of this motif are depicted in each known family of MULEs. Different hypotheses about the evolution of this triad are discussed.
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Affiliation(s)
- Aurélie Hua-Van
- Laboratoire Evolution, Génomes et Spéciation UPR9034, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, France.
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Molecular specification and patterning of progenitor cells in the lateral and medial ganglionic eminences. J Neurosci 2008; 28:9504-18. [PMID: 18799682 DOI: 10.1523/jneurosci.2341-08.2008] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We characterized intrinsic and extrinsic specification of progenitors in the lateral and medial ganglionic eminences (LGE and MGE). We identified seven genes whose expression is enriched or restricted in either the LGE [biregional cell adhesion molecule-related/downregulated by oncogenes binding protein (Boc), Frizzled homolog 8 (Fzd8), Ankrd43 (ankyrin repeat domain-containing protein 43), and Ikzf1 (Ikaros family zinc finger 1)] or MGE [Map3k12 binding inhibitory protein 1 (Mbip); zinc-finger, SWIM domain containing 5 (Zswim5); and Adamts5 [a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 5]]. Boc, Fzd8, Mbip, and Zswim5 are apparently expressed in LGE or MGE progenitors, whereas the remaining three are seen in the postmitotic mantle zone. Relative expression levels are altered and regional distinctions are lost for each gene in LGE or MGE cells propagated as neurospheres, indicating that these newly identified molecular characteristics of LGE or MGE progenitors depend on forebrain signals not available in the neurosphere assay. Analyses of Pax6(Sey/Sey), Shh(-/-), and Gli3(XtJ/XtJ) mutants suggests that LGE and MGE progenitor identity does not rely exclusively on previously established forebrain-intrinsic patterning mechanisms. Among a limited number of additional potential patterning mechanisms, we found that extrinsic signals from the frontonasal mesenchyme are essential for Shh- and Fgf8-dependent regulation of LGE and MGE genes. Thus, extrinsic and intrinsic forebrain patterning mechanisms cooperate to establish LGE and MGE progenitor identity, and presumably their capacities to generate distinct classes of neuronal progeny.
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48
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Lin R, Teng Y, Park HJ, Ding L, Black C, Fang P, Wang H. Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction. PLANT PHYSIOLOGY 2008; 148:981-92. [PMID: 18715961 PMCID: PMC2556831 DOI: 10.1104/pp.108.120436] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 08/15/2008] [Indexed: 05/20/2023]
Abstract
Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. We recently showed that Arabidopsis (Arabidopsis thaliana) FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), a pair of homologous proteins sharing significant sequence homology to Mutator-like transposases, act as novel transcription factors essential for activating the expression of FHY1 and FHL (for FHY1-like), whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses. FHY3, FAR1, and Mutator-like transposases also share a similar domain structure, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). In this study, we performed a promoter-swapping analysis of FHY3 and FAR1. Our results suggest that the partially overlapping functions of FHY3 and FAR1 entail divergence of their promoter activities and protein subfunctionalization. To gain a better understanding of the molecular mode of FHY3 function, we performed a structure-function analysis, using site-directed mutagenesis and transgenic approaches. We show that the conserved N-terminal C2H2 zinc finger domain is essential for direct DNA binding and biological function of FHY3 in mediating light signaling, whereas the central core transposase domain and C-terminal SWIM domain are essential for the transcriptional regulatory activity of FHY3 and its homodimerization or heterodimerization with FAR1. Furthermore, the ability to form homodimers or heterodimers largely correlates with the transcriptional regulatory activity of FHY3 in plant cells. Together, our results reveal discrete roles of the multiple domains of FHY3 and provide functional support for the proposition that FHY3 and FAR1 represent transcription factors derived from a Mutator-like transposase(s).
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Affiliation(s)
- Rongcheng Lin
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
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49
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Abstract
The control and coordination of eukaryotic gene expression rely on transcriptional and post-transcriptional regulatory networks. Although progress has been made in mapping the components and deciphering the function of these networks, the mechanisms by which such intricate circuits originate and evolve remain poorly understood. Here I revisit and expand earlier models and propose that genomic repeats, and in particular transposable elements, have been a rich source of material for the assembly and tinkering of eukaryotic gene regulatory systems.
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Affiliation(s)
- Cédric Feschotte
- Department of Biology, Life Science Building, BOX 19498, University of Texas, Arlington, Texas 76019, USA.
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50
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Mahrour N, Redwine WB, Florens L, Swanson SK, Martin-Brown S, Bradford WD, Staehling-Hampton K, Washburn MP, Conaway RC, Conaway JW. Characterization of Cullin-box Sequences That Direct Recruitment of Cul2-Rbx1 and Cul5-Rbx2 Modules to Elongin BC-based Ubiquitin Ligases. J Biol Chem 2008; 283:8005-13. [DOI: 10.1074/jbc.m706987200] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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