1
|
He Y, Shi Q, Ling Y, Guo H, Fei Y, Wu R, Tang C, Zhang X, Yao L. ABLIM1, a novel ubiquitin E3 ligase, promotes growth and metastasis of colorectal cancer through targeting IĸBα ubiquitination and activating NF-ĸB signaling. Cell Death Differ 2024; 31:203-216. [PMID: 38228802 PMCID: PMC10850134 DOI: 10.1038/s41418-024-01256-y] [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: 06/29/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
Actin-binding LIM protein 1 (ABLIM1), a member of the LIM-domain protein family, has been reported as a suppressor in several tumors whereas its role in colorectal cancer (CRC) remains unknown. In this study, we find that ABLIM1 is up-regulated in CRC patients and high levels of ABLIM1 predict short disease-free survival time. Knock-down of ABLIM1 in CRC cell lines by lenti-virus leads to inhibited cell proliferation, migration, and invasion capabilities in vitro and impaired growth of tumor xenografts and liver metastasis lesions in vivo, while ABLIM1 overexpression accelerates tumor growth and invasion in vitro. Mechanistically, we uncover that ABLIM1 activates the NF-ĸB/CCL-20 signaling through modulating IĸBα ubiquitination and proteasomal-mediated degradation. Further co-immunoprecipitation, in vivo and in vitro ubiquitination assays reveal ABLIM1 as a novel ubiquitin E3 ligase binding to IĸBα. Interestingly, The E3 ligase catalysis activity of ABLIM1 depends on its 402-778aa rather than its LIM domains and its interaction with IĸBα relies on the HP domain. Our findings delineate the oncogenic role of ABLIM1 in CRC progression and reveal it as a novel E3 ligase targeting IĸBα, providing new insights into the regulation of NF-ĸB signaling in tumors.
Collapse
Affiliation(s)
- Ying He
- Central Laboratory, First Affiliated Hospital of Huzhou University, Huzhou, 313000, Zhejiang, China
- Huzhou Key Laboratory of Translational Medicine, First People's Hospital of Huzhou, Huzhou, 313000, Zhejiang, China
| | - Qian Shi
- Central Laboratory, First Affiliated Hospital of Huzhou University, Huzhou, 313000, Zhejiang, China
- Huzhou Key Laboratory of Translational Medicine, First People's Hospital of Huzhou, Huzhou, 313000, Zhejiang, China
| | - Yuhang Ling
- Central Laboratory, First Affiliated Hospital of Huzhou University, Huzhou, 313000, Zhejiang, China
- Huzhou Key Laboratory of Translational Medicine, First People's Hospital of Huzhou, Huzhou, 313000, Zhejiang, China
| | - Huihui Guo
- Central Laboratory, First Affiliated Hospital of Huzhou University, Huzhou, 313000, Zhejiang, China
- Huzhou Key Laboratory of Translational Medicine, First People's Hospital of Huzhou, Huzhou, 313000, Zhejiang, China
| | - Yi Fei
- Department of Colorectal Surgery, First Affiliated Hospital of Huzhou University, Huzhou, 313000, Zhejiang, China
| | - Ruoyu Wu
- Department of Gastroenterology, First Affiliated Hospital of Huzhou University, Huzhou, 313000, Zhejiang, China
| | - Chengwu Tang
- Central Laboratory, First Affiliated Hospital of Huzhou University, Huzhou, 313000, Zhejiang, China.
- Huzhou Key Laboratory of Translational Medicine, First People's Hospital of Huzhou, Huzhou, 313000, Zhejiang, China.
| | - Xilin Zhang
- Central Laboratory, First Affiliated Hospital of Huzhou University, Huzhou, 313000, Zhejiang, China.
- Huzhou Key Laboratory of Translational Medicine, First People's Hospital of Huzhou, Huzhou, 313000, Zhejiang, China.
| | - Linhua Yao
- Huzhou Key Laboratory of Translational Medicine, First People's Hospital of Huzhou, Huzhou, 313000, Zhejiang, China.
- Department of Gastroenterology, First Affiliated Hospital of Huzhou University, Huzhou, 313000, Zhejiang, China.
| |
Collapse
|
2
|
Wen J, Deng M, Zhao K, Zhou H, Wu R, Li M, Cheng H, Li P, Zhang R, Lv J. Characterization of Plant Homeodomain Transcription Factor Genes Involved in Flower Development and Multiple Abiotic Stress Response in Pepper. Genes (Basel) 2023; 14:1737. [PMID: 37761877 PMCID: PMC10531376 DOI: 10.3390/genes14091737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Plant homeodomain (PHD) transcription factor genes are involved in plant development and in a plant's response to stress. However, there are few reports about this gene family in peppers (Capsicum annuum L.). In this study, the pepper inbred line "Zunla-1" was used as the reference genome, and a total of 43 PHD genes were identified, and systematic analysis was performed to study the chromosomal location, evolutionary relationship, gene structure, domains, and upstream cis-regulatory elements of the CaPHD genes. The fewest CaPHD genes were located on chromosome 4, while the most were on chromosome 3. Genes with similar gene structures and domains were clustered together. Expression analysis showed that the expression of CaPHD genes was quite different in different tissues and in response to various stress treatments. The expression of CaPHD17 was different in the early stage of flower bud development in the near-isogenic cytoplasmic male-sterile inbred and the maintainer inbred lines. It is speculated that this gene is involved in the development of male sterility in pepper. CaPHD37 was significantly upregulated in leaves and roots after heat stress, and it is speculated that CaPHD37 plays an important role in tolerating heat stress in pepper; in addition, CaPHD9, CaPHD10, CaPHD11, CaPHD17, CaPHD19, CaPHD20, and CaPHD43 were not sensitive to abiotic stress or hormonal factors. This study will provide the basis for further research into the function of CaPHD genes in plant development and responses to abiotic stresses and hormones.
Collapse
Affiliation(s)
- Jinfen Wen
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650500, China;
| | - Minghua Deng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Kai Zhao
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Huidan Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Rui Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Mengjuan Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Hong Cheng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Pingping Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Ruihao Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Junheng Lv
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| |
Collapse
|
3
|
Yu Y, He J, Liu W, Li Z, Weng S, He J, Guo C. Molecular Characterization and Functional Analysis of Hypoxia-Responsive Factor Prolyl Hydroxylase Domain 2 in Mandarin Fish ( Siniperca chuatsi). Animals (Basel) 2023; 13:ani13091556. [PMID: 37174593 PMCID: PMC10177477 DOI: 10.3390/ani13091556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/18/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
With increased breeding density, the phenomenon of hypoxia gradually increases in aquaculture. Hypoxia is primarily mediated by the hypoxia-inducible factor 1 (HIF-1) signaling pathway. Prolyl hydroxylase domain proteins (PHD) are cellular oxygen-sensing molecules that regulate the stability of HIF-1α through hydroxylation. In this study, the characterization of the PHD2 from mandarin fish Siniperca chuatsi (scPHD2) and its roles in the HIF-1 signaling pathway were investigated. Bioinformation analysis showed that scPHD2 had the conserved prolyl 4-hydroxylase alpha subunit homolog domains at its C-terminal and was more closely related to other Perciformes PHD2 than other PHD2. Tissue-distribution results revealed that scphd2 gene was expressed in all tissues tested and more highly expressed in blood and liver than in other tested tissues. Dual-luciferase reporter gene and RT-qPCR assays showed that scPHD2 overexpression could significantly inhibit the HIF-1 signaling pathway. Co-immunoprecipitation analysis showed that scPHD2 could interact with scHIF-1α. Protein degradation experiment results suggested that scPHD2 could promote scHIF-1α degradation through the proteasome degradation pathway. This study advances our understanding of how the HIF-1 signaling pathway is regulated by scPHD2 and will help in understanding the molecular mechanisms underlying hypoxia adaptation in teleost fish.
Collapse
Affiliation(s)
- Yang Yu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China
| | - Jian He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China
| | - Wenhui Liu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China
| | - Zhimin Li
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China
| | - Shaoping Weng
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China
| | - Changjun Guo
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China
| |
Collapse
|
4
|
Rajan S, Terman JR, Reisler E. MICAL-mediated oxidation of actin and its effects on cytoskeletal and cellular dynamics. Front Cell Dev Biol 2023; 11:1124202. [PMID: 36875759 PMCID: PMC9982024 DOI: 10.3389/fcell.2023.1124202] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Actin and its dynamic structural remodelings are involved in multiple cellular functions, including maintaining cell shape and integrity, cytokinesis, motility, navigation, and muscle contraction. Many actin-binding proteins regulate the cytoskeleton to facilitate these functions. Recently, actin's post-translational modifications (PTMs) and their importance to actin functions have gained increasing recognition. The MICAL family of proteins has emerged as important actin regulatory oxidation-reduction (Redox) enzymes, influencing actin's properties both in vitro and in vivo. MICALs specifically bind to actin filaments and selectively oxidize actin's methionine residues 44 and 47, which perturbs filaments' structure and leads to their disassembly. This review provides an overview of the MICALs and the impact of MICAL-mediated oxidation on actin's properties, including its assembly and disassembly, effects on other actin-binding proteins, and on cells and tissue systems.
Collapse
Affiliation(s)
- Sudeepa Rajan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jonathan R. Terman
- Departments of Neuroscience and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
5
|
Zhou X, Speer RM, Volk L, Hudson LG, Liu KJ. Arsenic co-carcinogenesis: Inhibition of DNA repair and interaction with zinc finger proteins. Semin Cancer Biol 2021; 76:86-98. [PMID: 33984503 PMCID: PMC8578584 DOI: 10.1016/j.semcancer.2021.05.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/17/2022]
Abstract
Arsenic is widely present in the environment and is associated with various population health risks including cancers. Arsenic exposure at environmentally relevant levels enhances the mutagenic effect of other carcinogens such as ultraviolet radiation. Investigation on the molecular mechanisms could inform the prevention and intervention strategies of arsenic carcinogenesis and co-carcinogenesis. Arsenic inhibition of DNA repair has been demonstrated to be an important mechanism, and certain DNA repair proteins have been identified to be extremely sensitive to arsenic exposure. This review will summarize the recent advances in understanding the mechanisms of arsenic carcinogenesis and co-carcinogenesis, including DNA damage induction and ROS generation, particularly how arsenic inhibits DNA repair through an integrated molecular mechanism which includes its interactions with sensitive zinc finger DNA repair proteins.
Collapse
Affiliation(s)
- Xixi Zhou
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Rachel M Speer
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Lindsay Volk
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Laurie G Hudson
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
| | - Ke Jian Liu
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
| |
Collapse
|
6
|
Guo ZS, Qu Z. PDLIM2: Signaling pathways and functions in cancer suppression and host immunity. Biochim Biophys Acta Rev Cancer 2021; 1876:188630. [PMID: 34571051 DOI: 10.1016/j.bbcan.2021.188630] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/30/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022]
Abstract
PDZ and LIM domains-containing proteins play pivotal functions in cell cytoskeleton organization, cell polarization and differentiation. As a key member of the family, PDLIM2 regulates stability and activity of transcription factors such as NF-κB, STATs and β-catenin, and thus exert it functions in inflammation, immunity, and cancer. PDLIM2 functions as a tumor suppressor in multiple tissues and it is often genetically mutated or epigenetically silenced in human cancers derived from lung, breast, ovarian and other histologies. However, in certain types of cancers, PDLIM2 may promote cancer cell proliferation and metastases. Therefore, PDLIM2 is added to a long list of genes that can function as tumor suppressor or oncogenic protein. During tumorigenesis induced by oncogenic viruses, PDLIM2 is a key target. Through promotion of NF-κB/RelA and STAT3 degradation, PDLIM2 enhances expression of proteins involved in antigen presentation and promotes T-cell activation while repressing multidrug resistance genes, thereby rendering mutated cells susceptible to immune surveillance and cytotoxicity mediated by immune cells and chemotherapeutic drugs. Intriguingly, PDLIM2 in alveolar macrophages (AMs) plays key roles in monitoring lung tumorigenesis, as its selective genetic deletion leads to constitutive activation of STAT3, driving monocyte differentiation to AMs with pro-tumorigenic polarization and activation. PDLIM2 has also been explored as a therapeutic target for cancer therapy. At the end of this review, we provide perspectives on this important molecule and discuss the future directions of both basic and translational studies.
Collapse
Affiliation(s)
- Zong Sheng Guo
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Zhaoxia Qu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| |
Collapse
|
7
|
Singh S, Chopperla R, Shingote P, Chhapekar SS, Deshmukh R, Khan S, Padaria JC, Sharma TR, Solanke AU. Overexpression of EcDREB2A transcription factor from finger millet in tobacco enhances tolerance to heat stress through ROS scavenging. J Biotechnol 2021; 336:10-24. [PMID: 34116128 DOI: 10.1016/j.jbiotec.2021.06.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 03/04/2021] [Accepted: 06/04/2021] [Indexed: 01/04/2023]
Abstract
An extreme temperature regime beyond desired level imposes significant stress in crop plants. The low and high temperature stresses are one of the primary constraints for plant development and yield. Finger millet, being a climate resilient crop, is a potential source of novel stress tolerant genes. In this study, functional characterization of finger millet DREB2A gene in different abiotic stress conditions was done. This novel EcDREB2A transcription factor isolated from finger millet is a truncated version of DREB2A gene compared to previously reported DREB genes from other plant species. The overexpression of EcDREB2A in transgenic tobacco exhibits improved tolerance against heat stress 42 °C for up to 7 days, by altering physiology and biochemical means. However, same transgenic lines were unable to provide tolerance to 200 mM NaCl and 200 mM Mannitol stress. Under heat stress conditions, increased seed germination with improved lateral roots, fresh and dry weight relative to wild type (WT) was observed. The EcDREB2A transgenics exposed to heat stress showed improved rate of stomatal conductance, chlorophyll and carotenoids contents, and other photosynthesis parameters compared to WT plants. EcDREB2A overexpression also resulted in increased antioxidant enzyme activity (SOD, CAT, GR, POD and, APX) with decreased electrolyte leakage (EL), H2O2, and malondialdehyde (MDA) content than WT plants under heat stress. Quantitative real time expression analysis demonstrated that all eight downstream genes were significantly upregulated in transgenic plants only after heat stress. Our data provide a clear demonstration of the positive impact of overexpression of EcDREB2A providing heat stress tolerance to plants.
Collapse
Affiliation(s)
- Sonam Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | | | - Prashant Shingote
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | | | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Suphiya Khan
- Banasthali University, Banasthali, 304022, India
| | - Jasdeep C Padaria
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Tilak Raj Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; Indian Council of Agricultural Research, New Delhi, 110001, India
| | | |
Collapse
|
8
|
Yusuf AP, Abubakar MB, Malami I, Ibrahim KG, Abubakar B, Bello MB, Qusty N, Elazab ST, Imam MU, Alexiou A, Batiha GES. Zinc Metalloproteins in Epigenetics and Their Crosstalk. Life (Basel) 2021; 11:life11030186. [PMID: 33652690 PMCID: PMC7996840 DOI: 10.3390/life11030186] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
More than half a century ago, zinc was established as an essential micronutrient for normal human physiology. In silico data suggest that about 10% of the human proteome potentially binds zinc. Many proteins with zinc-binding domains (ZBDs) are involved in epigenetic modifications such as DNA methylation and histone modifications, which regulate transcription in physiological and pathological conditions. Zinc metalloproteins in epigenetics are mainly zinc metalloenzymes and zinc finger proteins (ZFPs), which are classified into writers, erasers, readers, editors, and feeders. Altogether, these classes of proteins engage in crosstalk that fundamentally maintains the epigenome's modus operandi. Changes in the expression or function of these proteins induced by zinc deficiency or loss of function mutations in their ZBDs may lead to aberrant epigenetic reprogramming, which may worsen the risk of non-communicable chronic diseases. This review attempts to address zinc's role and its proteins in natural epigenetic programming and artificial reprogramming and briefly discusses how the ZBDs in these proteins interact with the chromatin.
Collapse
Affiliation(s)
- Abdurrahman Pharmacy Yusuf
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
| | - Murtala Bello Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
- Correspondence: (M.B.A.); (A.A.); (G.E.-S.B.)
| | - Ibrahim Malami
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Kasimu Ghandi Ibrahim
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Bilyaminu Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Naeem Qusty
- Medical Laboratories Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Mecca 21955, Saudi Arabia;
| | - Sara T. Elazab
- Department of Pharmacology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Dakahlia 35516, Egypt;
| | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
- AFNP Med, Haidingergasse 29, 1030 Vienna, Austria
- Correspondence: (M.B.A.); (A.A.); (G.E.-S.B.)
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, AlBeheira 22511, Egypt
- Correspondence: (M.B.A.); (A.A.); (G.E.-S.B.)
| |
Collapse
|
9
|
Zhou C, Zhu J, Qian N, Guo J, Yan C. Bacillus subtilis SL18r Induces Tomato Resistance Against Botrytis cinerea, Involving Activation of Long Non-coding RNA, MSTRG18363, to Decoy miR1918. FRONTIERS IN PLANT SCIENCE 2021; 11:634819. [PMID: 33613592 PMCID: PMC7887324 DOI: 10.3389/fpls.2020.634819] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Mounting evidence has indicated that beneficial rhizobacteria can suppress foliar pathogen invasion via elicitation of induced systemic resistance (ISR). However, it remains elusive whether long non-coding RNAs (lncRNAs) are involved in the mediation of the rhizobacteria-primed ISR processes in plants. Herein, we demonstrated the ability of the rhizobacterial strain Bacillus subtilis SL18r to trigger ISR in tomato plants against the foliar pathogen Botrytis cinerea. Comparative transcriptome analysis was conducted to screen differentially expressed lncRNAs (DELs) between the non-inoculated and SL18r-inoculated plants. Among these DELs, four variants of MSTRG18363 possessed conserved binding sites for miR1918, which negatively regulates immune systems in tomato plants. The expression of MSTRG18363 in tomato leaves was significantly induced by SL18r inoculation. The transcription of MSTRG18363 was negatively correlated with the expression of miR1918, but displayed a positive correlation with the transcription of the RING-H2 finger gene SlATL20 (a target gene of miR1918). Moreover, MSTRG18363-overexpressing plants exhibited the enhanced disease resistance, reduction of miR1918 transcripts, and marked increases of SlATL20 expression. However, the SL18r-induced disease resistance was largely impaired in the MSTRG18363-silenced plants. VIGS-mediated SlATL20 silencing also greatly weakened the SL18r-induced disease resistance. Collectively, our results suggested that induction of MSTRG18363 expression in tomato plants by SL18r was conducive to promoting the decoy of miR1918 and regulating the expression of SlATL20, thereby provoking the ISR responses against foliar pathogen infection.
Collapse
Affiliation(s)
- Cheng Zhou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural Affairs, Anhui Science and Technology University, Bengbu, China
| | - Jingjing Zhu
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural Affairs, Anhui Science and Technology University, Bengbu, China
| | - Nana Qian
- Key Lab of Bio-Organic Fertilizer Creation, Ministry of Agriculture and Rural Affairs, Anhui Science and Technology University, Bengbu, China
| | - Jiansheng Guo
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Congsheng Yan
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, China
| |
Collapse
|
10
|
Landry-Voyer AM, Bergeron D, Yague-Sanz C, Baker B, Bachand F. PDCD2 functions as an evolutionarily conserved chaperone dedicated for the 40S ribosomal protein uS5 (RPS2). Nucleic Acids Res 2020; 48:12900-12916. [PMID: 33245768 PMCID: PMC7736825 DOI: 10.1093/nar/gkaa1108] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Accepted: 10/28/2020] [Indexed: 11/12/2022] Open
Abstract
PDCD2 is an evolutionarily conserved protein with previously characterized homologs in Drosophila (zfrp8) and budding yeast (Tsr4). Although mammalian PDCD2 is essential for cell proliferation and embryonic development, the function of PDCD2 that underlies its fundamental cellular role has remained unclear. Here, we used quantitative proteomics approaches to define the protein-protein interaction network of human PDCD2. Our data revealed that PDCD2 specifically interacts with the 40S ribosomal protein uS5 (RPS2) and that the PDCD2-uS5 complex is assembled co-translationally. Loss of PDCD2 expression leads to defects in the synthesis of the small ribosomal subunit that phenocopy a uS5 deficiency. Notably, we show that PDCD2 is important for the accumulation of soluble uS5 protein as well as its incorporation into 40S ribosomal subunit. Our findings support that the essential molecular function of PDCD2 is to act as a dedicated ribosomal protein chaperone that recognizes uS5 co-translationally in the cytoplasm and accompanies uS5 to ribosome assembly sites in the nucleus. As most dedicated ribosomal protein chaperones have been identified in yeast, our study reveals that similar mechanisms exist in human cells to assist ribosomal proteins coordinate their folding, nuclear import and assembly in pre-ribosomal particles.
Collapse
Affiliation(s)
- Anne-Marie Landry-Voyer
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Danny Bergeron
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Carlo Yague-Sanz
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Breac Baker
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Francois Bachand
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| |
Collapse
|
11
|
Oh S, Boo K, Kim J, Baek SA, Jeon Y, You J, Lee H, Choi HJ, Park D, Lee JM, Baek SH. The chromatin-binding protein PHF6 functions as an E3 ubiquitin ligase of H2BK120 via H2BK12Ac recognition for activation of trophectodermal genes. Nucleic Acids Res 2020; 48:9037-9052. [PMID: 32735658 PMCID: PMC7498345 DOI: 10.1093/nar/gkaa626] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Epigenetic regulation is important for establishing lineage-specific gene expression during early development. Although signaling pathways have been well-studied for regulation of trophectoderm reprogramming, epigenetic regulation of trophectodermal genes with histone modification dynamics have been poorly understood. Here, we identify that plant homeodomain finger protein 6 (PHF6) is a key epigenetic regulator for activation of trophectodermal genes using RNA-sequencing and ChIP assays. PHF6 acts as an E3 ubiquitin ligase for ubiquitination of H2BK120 (H2BK120ub) via its extended plant homeodomain 1 (PHD1), while the extended PHD2 of PHF6 recognizes acetylation of H2BK12 (H2BK12Ac). Intriguingly, the recognition of H2BK12Ac by PHF6 is important for exerting its E3 ubiquitin ligase activity for H2BK120ub. Together, our data provide evidence that PHF6 is crucial for epigenetic regulation of trophectodermal gene expression by linking H2BK12Ac to H2BK120ub modification.
Collapse
Affiliation(s)
- Sungryong Oh
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Kyungjin Boo
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jaebeom Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Seon Ah Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Yoon Jeon
- Graduate School of Cancer Science and Policy, Research Institute, National Cancer Center, Goyang 10408, South Korea
| | - Junghyun You
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, Research Institute, National Cancer Center, Goyang 10408, South Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Daechan Park
- Department of Biological Sciences, College of Natural Sciences, Ajou University, Suwon 16499, South Korea
| | - Ji Min Lee
- Department of Molecular Bioscience, College of Biomedical Sciences, Kangwon National University, Chuncheon 24341, South Korea
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| |
Collapse
|
12
|
Maares M, Haase H. A Guide to Human Zinc Absorption: General Overview and Recent Advances of In Vitro Intestinal Models. Nutrients 2020; 12:E762. [PMID: 32183116 PMCID: PMC7146416 DOI: 10.3390/nu12030762] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/23/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022] Open
Abstract
Zinc absorption in the small intestine is one of the main mechanisms regulating the systemic homeostasis of this essential trace element. This review summarizes the key aspects of human zinc homeostasis and distribution. In particular, current knowledge on human intestinal zinc absorption and the influence of diet-derived factors on bioaccessibility and bioavailability as well as intrinsic luminal and basolateral factors with an impact on zinc uptake are discussed. Their investigation is increasingly performed using in vitro cellular intestinal models, which are continually being refined and keep gaining importance for studying zinc uptake and transport via the human intestinal epithelium. The vast majority of these models is based on the human intestinal cell line Caco-2 in combination with other relevant components of the intestinal epithelium, such as mucin-secreting goblet cells and in vitro digestion models, and applying improved compositions of apical and basolateral media to mimic the in vivo situation as closely as possible. Particular emphasis is placed on summarizing previous applications as well as key results of these models, comparing their results to data obtained in humans, and discussing their advantages and limitations.
Collapse
Affiliation(s)
- Maria Maares
- Technische Universität Berlin, Chair of Food Chemistry and Toxicology, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Hajo Haase
- Technische Universität Berlin, Chair of Food Chemistry and Toxicology, Straße des 17. Juni 135, 10623 Berlin, Germany
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, D-13353 Potsdam-Berlin-Jena, Germany
| |
Collapse
|
13
|
Abbas MN, Liang H, Kausar S, Dong Z, Cui H. Zinc finger protein RP-8, the Bombyx mori ortholog of programmed cell death 2, regulates cell proliferation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 104:103542. [PMID: 31730828 DOI: 10.1016/j.dci.2019.103542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/11/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Programmed cell death 2 (PDCD2) is a highly conserved eukaryotic protein indispensable for various physiological processes such as cell proliferation, development, and apoptosis. In the present study, we identified a Zinc finger protein RP-8 from the silkworm, Bombyx mori (BmZfrp8), the ortholog of PDCD2 protein. The quantitative real-time PCR analysis revealed the ubiquitous distribution of BmZfrp8 in the different tissues; however, the gene's transcription level was highest in those of the silk gland, testis, and ovary. Additionally, the expression levels of BmZfrp8 were unequal on different days of embryonic development, and it reached the highest level on the 5th day of early development. The challenge with pathogens influenced the expression level of BmZfrp8 in both hemocyte and fat body when compared with the control. Administration of 20-hydroxyecdysone significantly enhanced the BmZfrp8 expression in hemocyte. The knock-down of BmZfrp8 by double-stranded RNA suppressed the expression of developmental pathway associated genes as well as cell cycle-associated genes. Furthermore, the RNAi treated cells also showed cell cycle arrest compared to the control group. Taken together, BmZfrp8 may have a critical biological role in of B. mori, since it regulates the expression of the developmental pathway and cell cycle-associated genes.
Collapse
Affiliation(s)
- Muhammad Nadeem Abbas
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing, 400715, China.
| | - Hanghua Liang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing, 400715, China.
| | - Saima Kausar
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing, 400715, China.
| | - Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing, 400715, China.
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing, 400715, China.
| |
Collapse
|
14
|
Binder MS, Brown E, Aversano T, Wagner KR, Calkins H, Barth AS. Novel FHL1 Mutation Associated With Hypertrophic Cardiomyopathy, Sudden Cardiac Death, and Myopathy. JACC Case Rep 2020; 2:372-377. [PMID: 34317245 PMCID: PMC8311586 DOI: 10.1016/j.jaccas.2019.11.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 11/23/2022]
Abstract
A 24-year-old man with muscle cramps and a family history of sudden death presented with palpitations. Electrocardiography showed signs of left ventricular hypertrophy and nonsustained ventricular tachycardia, and imaging studies confirmed hypertrophic cardiomyopathy. Genetic testing revealed a novel FHL1 mutation associated with Emery-Dreifuss muscular dystrophy. An implantable cardioverter-defibrillator was placed. (Level of Difficulty: Advanced.)
Collapse
|
15
|
Zhou J, Xu Y, Lin S, Guo Y, Deng W, Zhang Y, Guo A, Xue Y. iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations. Nucleic Acids Res 2019; 46:D447-D453. [PMID: 29106644 PMCID: PMC5753239 DOI: 10.1093/nar/gkx1041] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/18/2017] [Indexed: 01/01/2023] Open
Abstract
Here, we described the updated database iUUCD 2.0 (http://iuucd.biocuckoo.org/) for ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), ubiquitin-protein ligases (E3s), deubiquitinating enzymes (DUBs), ubiquitin/ubiquitin-like binding domains (UBDs) and ubiquitin-like domains (ULDs), which act as key regulators in modulating ubiquitin and ubiquitin-like (UB/UBL) conjugations. In total, iUUCD 2.0 contained 136 512 UB/UBL regulators, including 1230 E1s, 5636 E2s, 93 343 E3s, 9548 DUBs, 30 173 UBDs and 11 099 ULDs in 148 eukaryotic species. In particular, we provided rich annotations for regulators of eight model organisms, especially in humans, by compiling and integrating the knowledge from nearly 70 widely used public databases that cover cancer mutations, single nucleotide polymorphisms (SNPs), mRNA expression, DNA and RNA elements, protein–protein interactions, protein 3D structures, disease-associated information, drug-target relations, post-translational modifications, DNA methylation and protein expression/proteomics. Compared with our previously developed UUCD 1.0 (∼0.41 GB), iUUCD 2.0 has a size of ∼32.1 GB of data with a >75-fold increase in data volume. We anticipate that iUUCD 2.0 can be a more useful resource for further study of UB/UBL conjugations.
Collapse
Affiliation(s)
- Jiaqi Zhou
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yang Xu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shaofeng Lin
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yaping Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wankun Deng
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Anyuan Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| |
Collapse
|
16
|
Zheng Y, Xue Y, Ren X, Liu M, Li X, Jia Y, Niu Y, Ni JQ, Zhang Y, Ji JY. The Lysine Demethylase dKDM2 Is Non-essential for Viability, but Regulates Circadian Rhythms in Drosophila. Front Genet 2018; 9:354. [PMID: 30233643 PMCID: PMC6131532 DOI: 10.3389/fgene.2018.00354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/15/2018] [Indexed: 12/29/2022] Open
Abstract
Post-translational modification of histones, such as histone methylation controlled by specific methyltransferases and demethylases, play critical roles in modulating chromatin dynamics and transcription in eukaryotes. Misregulation of histone methylation can lead to aberrant gene expression, thereby contributing to abnormal development and diseases such as cancer. As such, the mammalian lysine-specific demethylase 2 (KDM2) homologs, KDM2A and KDM2B, are either oncogenic or tumor suppressive depending on specific pathological contexts. However, the role of KDM2 proteins during development remains poorly understood. Unlike vertebrates, Drosophila has only one KDM2 homolog (dKDM2), but its functions in vivo remain elusive due to the complexities of the existing mutant alleles. To address this problem, we have generated two dKdm2 null alleles using the CRISPR/Cas9 technique. These dKdm2 homozygous mutants are fully viable and fertile, with no developmental defects observed under laboratory conditions. However, the dKdm2 null mutant adults display defects in circadian rhythms. Most of the dKdm2 mutants become arrhythmic under constant darkness, while the circadian period of the rhythmic mutant flies is approximately 1 h shorter than the control. Interestingly, lengthened circadian periods are observed when dKDM2 is overexpressed in circadian pacemaker neurons. Taken together, these results demonstrate that dKdm2 is not essential for viability; instead, dKDM2 protein plays important roles in regulating circadian rhythms in Drosophila. Further analyses of the molecular mechanisms of dKDM2 and its orthologs in vertebrates regarding the regulation of circadian rhythms will advance our understanding of the epigenetic regulations of circadian clocks.
Collapse
Affiliation(s)
- Yani Zheng
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX, United States
| | - Yongbo Xue
- Department of Biology, University of Nevada, Reno, Reno, NV, United States
| | - Xingjie Ren
- Gene Regulatory Laboratory, School of Medicine, Tsinghua University, Beijing, China
| | - Mengmeng Liu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX, United States
| | - Xiao Li
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX, United States
| | - Yu Jia
- Gene Regulatory Laboratory, School of Medicine, Tsinghua University, Beijing, China
| | - Ye Niu
- Department of Biology, University of Nevada, Reno, Reno, NV, United States
| | - Jian-Quan Ni
- Gene Regulatory Laboratory, School of Medicine, Tsinghua University, Beijing, China
| | - Yong Zhang
- Department of Biology, University of Nevada, Reno, Reno, NV, United States
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX, United States
| |
Collapse
|
17
|
Loss-of-function zinc finger mutation in the EGLN1 gene associated with erythrocytosis. Blood 2018; 132:1455-1458. [PMID: 30111608 DOI: 10.1182/blood-2018-06-854711] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/09/2018] [Indexed: 12/13/2022] Open
|
18
|
Xiao D, Wang H, Hao L, Guo X, Ma X, Qian Y, Chen H, Ma J, Zhang J, Sheng W, Shou W, Huang G, Ma D. The roles of SMYD4 in epigenetic regulation of cardiac development in zebrafish. PLoS Genet 2018; 14:e1007578. [PMID: 30110327 PMCID: PMC6110521 DOI: 10.1371/journal.pgen.1007578] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 08/27/2018] [Accepted: 07/20/2018] [Indexed: 12/15/2022] Open
Abstract
SMYD4 belongs to a family of lysine methyltransferases. We analyzed the role of smyd4 in zebrafish development by generating a smyd4 mutant zebrafish line (smyd4L544Efs*1) using the CRISPR/Cas9 technology. The maternal and zygotic smyd4L544Efs*1 mutants demonstrated severe cardiac malformations, including defects in left-right patterning and looping and hypoplastic ventricles, suggesting that smyd4 was critical for heart development. Importantly, we identified two rare SMYD4 genetic variants in a 208-patient cohort with congenital heart defects. Both biochemical and functional analyses indicated that SMYD4(G345D) was pathogenic. Our data suggested that smyd4 functions as a histone methyltransferase and, by interacting with HDAC1, also serves as a potential modulator for histone acetylation. Transcriptome and bioinformatics analyses of smyd4L544Efs*1 and wild-type developing hearts suggested that smyd4 is a key epigenetic regulator involved in regulating endoplasmic reticulum-mediated protein processing and several important metabolic pathways in developing zebrafish hearts. SMYD4 belongs to a SET and MYND domain-containing lysine methyltransferase. In zebrafish, smyd4 is ubiquitously expressed in early embryos and becomes enriched in the developing heart at 48 hours post-fertilization (hpf). We generated a smyd4 mutant zebrafish line (smyd4L544Efs*1) using the CRISPR/Cas9 technology. The maternal and zygotic smyd4L544Efs*1 mutants demonstrated a strong defect in cardiomyocyte proliferation, which led to a severe cardiac malformation, including left-right looping defects and hypoplastic ventricles. More importantly, two rare genetic variants of SMYD4 were enriched in a 208-patient cohort with congenital heart defects. Both biochemical and functional analyses indicated that SMYD4(G345D) was highly pathogenic. Using mass spectrometric analysis, SMYD4 was shown to specifically interact with histone deacetylase 1 (HDAC1) via its MYND domain. Altered di- and tri-methylation of histone 3 lysine 4 (H3K4me2 and H3K4me3) and acetylation of histone 3 in smyd4L544Efs*1 mutants suggested that smyd4 plays an important role in epigenetic regulation. Transcriptome and pathway analyses demonstrated that the expression levels of 3,856 genes were significantly altered, which included cardiac contractile genes, key signaling pathways in cardiac development, the endoplasmic reticulum-mediated protein processing pathway, and several important metabolic pathways. Taken together, our data suggests that smyd4 is a key epigenetic regulator of cardiac development.
Collapse
Affiliation(s)
- Deyong Xiao
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Collaborative Innovation Center of Genetics and Development, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Huijun Wang
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
| | - Lili Hao
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Collaborative Innovation Center of Genetics and Development, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiao Guo
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
| | - Xiaojing Ma
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
- Pediatric Heart Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Yanyan Qian
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
| | - Hongbo Chen
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
| | - Jing Ma
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
- Pediatric Heart Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Collaborative Innovation Center of Genetics and Development, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wei Sheng
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
- Pediatric Heart Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Weinian Shou
- Cardiovascular Developmental Biology Group, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States of America
- * E-mail: (WS); (GH); (DM)
| | - Guoying Huang
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
- Pediatric Heart Center, Children’s Hospital of Fudan University, Shanghai, China
- * E-mail: (WS); (GH); (DM)
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Collaborative Innovation Center of Genetics and Development, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children’s Hospital of Fudan University, Shanghai, China
- * E-mail: (WS); (GH); (DM)
| |
Collapse
|
19
|
Cho SJ, Yoon C, Lee JH, Chang KK, Lin JX, Kim YH, Kook MC, Aksoy BA, Park DJ, Ashktorab H, Smoot DT, Schultz N, Yoon SS. KMT2C Mutations in Diffuse-Type Gastric Adenocarcinoma Promote Epithelial-to-Mesenchymal Transition. Clin Cancer Res 2018; 24:6556-6569. [PMID: 30108106 DOI: 10.1158/1078-0432.ccr-17-1679] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/13/2017] [Accepted: 08/09/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE Lauren diffuse-type gastric adenocarcinomas (DGAs) are generally genomically stable. We identified lysine (K)-specific methyltransferase 2C (KMT2C) as a frequently mutated gene and examined its role in DGA progression. EXPERIMENTAL DESIGN We performed whole exome sequencing on tumor samples of 27 patients with DGA who underwent gastrectomy. Lysine (K)-specific methyltransferase 2C (KMT2C) was analyzed in DGA cell lines and in patient tumors. RESULTS KMT2C was the most frequently mutated gene (11 of 27 tumors [41%]). KMT2C expression by immunohistochemistry in tumors from 135 patients with DGA undergoing gastrectomy inversely correlated with more advanced tumor stage (P = 0.023) and worse overall survival (P = 0.017). KMT2C shRNA knockdown in non-transformed HFE-145 gastric epithelial cells promoted epithelial-to-mesenchymal transition (EMT) as demonstrated by increased expression of EMT-related proteins N-cadherin and Slug. Migration and invasion in gastric epithelial cells following KMT2C knockdown increased by 47- to 88-fold. In the DGA cell lines MKN-45 and SNU-668, which have lost KMT2C expression, KMT2C re-expression decreased expression of EMT-related proteins, reduced cell migration by 52% to 60%, and reduced cell invasion by 50% to 74%. Flank xenografts derived from KMT2C-expressing DGA organoids, compared with wild-type organoids, grew more slowly and lost their infiltrative leading edge. EMT can lead to the acquisition of cancer stem cell (CSC) phenotypes. KMT2C re-expression in DGA cell lines reduced spheroid formation by 77% to 78% and reversed CSC resistance to chemotherapy via promotion of DNA damage and apoptosis. CONCLUSIONS KMT2C is frequently mutated in certain populations with DGA. KMT2C loss in DGA promotes EMT and is associated with worse overall survival.
Collapse
Affiliation(s)
- Soo-Jeong Cho
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
- Center for Gastric Cancer, National Cancer Center, Goyang, South Korea
| | - Changhwan Yoon
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Jun Ho Lee
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Kevin K Chang
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Jian-Xian Lin
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Young-Ho Kim
- Division of Clinical Research, Rare Cancer Branch, National Cancer Center, Goyang, South Korea
| | - Myeong-Cherl Kook
- Center for Gastric Cancer, National Cancer Center, Goyang, South Korea
| | - Bülent Arman Aksoy
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Do Joong Park
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | | | - Duane T Smoot
- Department of Internal Medicine, Meharry Medical College, Nashville, Tennessee
| | - Nikolaus Schultz
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Sam S Yoon
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York.
| |
Collapse
|
20
|
Sala S, Ampe C. An emerging link between LIM domain proteins and nuclear receptors. Cell Mol Life Sci 2018; 75:1959-1971. [PMID: 29428964 PMCID: PMC11105726 DOI: 10.1007/s00018-018-2774-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 02/01/2018] [Accepted: 02/06/2018] [Indexed: 12/13/2022]
Abstract
Nuclear receptors are ligand-activated transcription factors that partake in several biological processes including development, reproduction and metabolism. Over the last decade, evidence has accumulated that group 2, 3 and 4 LIM domain proteins, primarily known for their roles in actin cytoskeleton organization, also partake in gene transcription regulation. They shuttle between the cytoplasm and the nucleus, amongst other as a consequence of triggering cells with ligands of nuclear receptors. LIM domain proteins act as important coregulators of nuclear receptor-mediated gene transcription, in which they can either function as coactivators or corepressors. In establishing interactions with nuclear receptors, the LIM domains are important, yet pleiotropy of LIM domain proteins and nuclear receptors frequently occurs. LIM domain protein-nuclear receptor complexes function in diverse physiological processes. Their association is, however, often linked to diseases including cancer.
Collapse
Affiliation(s)
- Stefano Sala
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Christophe Ampe
- Department of Biochemistry, Ghent University, Ghent, Belgium.
| |
Collapse
|
21
|
He L, Zhu J, Han F, Tang Y, Zhou C, Dai J, Wang Y, Zhou H, He J, Wu H. LMO1 Gene Polymorphisms Reduce Neuroblastoma Risk in Eastern Chinese Children: A Three-Center Case-Control Study. Front Oncol 2018; 8:468. [PMID: 30406033 PMCID: PMC6206234 DOI: 10.3389/fonc.2018.00468] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/04/2018] [Indexed: 02/05/2023] Open
Abstract
Background: Neuroblastoma, a neuroendocrine tumor, stems from the developing sympathetic nervous system. Previous genome-wide association studies (GWASs) have discovered a number of neuroblastoma susceptibility genes in Caucasians including LIM domain only 1 (LMO1). Objective: We conducted a three-center case-control study including 313 cases and 716 controls with the purpose to evaluate the association between five GWAS-identified LMO1 variants (rs110419 A>G, rs4758051 G>A, rs10840002 A>G, rs204938 A>G, and rs2168101 G>T) and neuroblastoma susceptibility in eastern Chinese children. Methods: Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to evaluate the strength of the associations. False positive report possibility (FPRP) analysis was performed to check whether significant results were noteworthy. Results: Significant associations with neuroblastoma risk were found for four (rs110419, rs4758051, rs10840002, and rs2168101) out of the five polymorphisms. Combined analysis demonstrated that carriers of 4-5 protective genotypes had a significantly decreased risk of neuroblastoma in comparison those with 0-3 protective genotypes (adjusted OR = 0.51, 95% CI = 0.39-0.68, P < 0.0001). Haplotype analysis of the five SNPs yield four significant haplotypes associated with neuroblastoma susceptibility. Conclusion: In conclusion, we confirmed LMO1 polymorphisms may reduce neuroblastoma risk in eastern Chinese populations.
Collapse
Affiliation(s)
- Lili He
- Department of Pathology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jinhong Zhu
- Department of Clinical Laboratory, Molecular Epidemiology Laboratory, Harbin Medical University Cancer Hospital, Harbin, China
| | - Fei Han
- Department of Pathology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yingzi Tang
- Department of Pathology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chunlei Zhou
- Department of Pathology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jincheng Dai
- Department of Pathology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yizhen Wang
- Department of Pathology, Anhui Provincial Children's Hospital, Hefei, China
| | - Haixia Zhou
- Department of Hematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Jing He
| | - Haiyan Wu
- Department of Pathology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Haiyan Wu
| |
Collapse
|
22
|
Huang Y, Chen DH, Liu BY, Shen WH, Ruan Y. Conservation and diversification of polycomb repressive complex 2 (PRC2) proteins in the green lineage. Brief Funct Genomics 2017; 16:106-119. [PMID: 27032420 DOI: 10.1093/bfgp/elw007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The polycomb group (PcG) proteins are key epigenetic regulators of gene expression in animals and plants. They act in multiprotein complexes, of which the best characterized is the polycomb repressive complex 2 (PRC2), which catalyses the trimethylation of histone H3 at lysine 27 (H3K27me3) at chromatin targets. In Arabidopsis thaliana, PRC2 proteins are involved in the regulation of diverse developmental processes, including cell fate determination, vegetative growth and development, flowering time control and embryogenesis. Here, we systematically analysed the evolutionary conservation and diversification of PRC2 components in lower and higher plants. We searched for and identified PRC2 homologues from the sequenced genomes of several green lineage species, from the unicellular green alga Ostreococcus lucimarinus to more complicated angiosperms. We found that some PRC2 core components, e.g. E(z), ESC/FIE and MSI/p55, are ancient and have multiplied coincidently with multicellular evolution. For one component, some members are newly formed, especially in the Cruciferae. During evolution, higher plants underwent copy number multiplication of various PRC2 components, which occurred independently for each component, without any obvious co-amplification of PRC2 members. Among the amplified members, usually one was well-conserved and the others were more diversified. Gene amplification occurred at different times for different PcG members during green lineage evolution. Certain PRC2 core components or members of them were highly conserved. Our study provides an insight into the evolutionary conservation and diversification of PcG proteins and may guide future functional characterization of these important epigenetic regulators in plants other than Arabidopsis.
Collapse
Affiliation(s)
- Yong Huang
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China
| | - Dong-Hong Chen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China
| | - Bo-Yu Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, China
| | - Wen-Hui Shen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Institut de Biologie Moléculaire Des Plantes Du CNRS, Université de Strasbourg, 12 Rue Du Général Zimmer, Strasbourg Cedex, France
| | - Ying Ruan
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, Changsha, China.,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China.,Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, China
| |
Collapse
|
23
|
Cassandri M, Smirnov A, Novelli F, Pitolli C, Agostini M, Malewicz M, Melino G, Raschellà G. Zinc-finger proteins in health and disease. Cell Death Discov 2017; 3:17071. [PMID: 29152378 PMCID: PMC5683310 DOI: 10.1038/cddiscovery.2017.71] [Citation(s) in RCA: 406] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 02/07/2023] Open
Abstract
Zinc-finger proteins (ZNFs) are one of the most abundant groups of proteins and have a wide range of molecular functions. Given the wide variety of zinc-finger domains, ZNFs are able to interact with DNA, RNA, PAR (poly-ADP-ribose) and other proteins. Thus, ZNFs are involved in the regulation of several cellular processes. In fact, ZNFs are implicated in transcriptional regulation, ubiquitin-mediated protein degradation, signal transduction, actin targeting, DNA repair, cell migration, and numerous other processes. The aim of this review is to provide a comprehensive summary of the current state of knowledge of this class of proteins. Firstly, we describe the actual classification of ZNFs, their structure and functions. Secondly, we focus on the biological role of ZNFs in the development of organisms under normal physiological and pathological conditions.
Collapse
Affiliation(s)
- Matteo Cassandri
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Artem Smirnov
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Flavia Novelli
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Consuelo Pitolli
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Massimiliano Agostini
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Michal Malewicz
- Medical Research Council, Toxicology Unit, Leicester University, Leicester LE1 9HN, UK
| | - Gerry Melino
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy.,Medical Research Council, Toxicology Unit, Leicester University, Leicester LE1 9HN, UK
| | - Giuseppe Raschellà
- ENEA Research Center Casaccia, Laboratory of Biosafety and Risk Assessment, Via Anguillarese, Rome, Italy
| |
Collapse
|
24
|
Ramzan K, Bin-Abbas B, Al-Jomaa L, Allam R, Al-Owain M, Imtiaz F. Two novel LHX3 mutations in patients with combined pituitary hormone deficiency including cervical rigidity and sensorineural hearing loss. BMC Endocr Disord 2017; 17:17. [PMID: 28302169 PMCID: PMC5356396 DOI: 10.1186/s12902-017-0164-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/22/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Congenital combined pituitary hormone deficiency (CPHD) is a rare heterogeneous group of conditions. CPHD-type 3 (CPHD3; MIM# 221750) is caused by recessive mutations in LHX3, a LIM-homeodomain transcription factor gene. The isoforms of LHX3 are critical for pituitary gland formation and specification of the anterior pituitary hormone-secreting cell types. They also play distinct roles in the development of neuroendocrine and auditory systems. CASE PRESENTATION Here, we summarize the clinical, endocrinological, radiological and molecular features of three patients from two unrelated families. Clinical evaluation revealed severe CPHD coupled with cervical vertebral malformations (rigid neck, scoliosis), mild developmental delay and moderate sensorineural hearing loss (SNHL). The patients were diagnosed with CPHD3 based on the array of hormone deficiencies and other associated syndromic symptoms, suggestive of targeted LHX3 gene sequencing. A novel missense mutation c.437G > T (p. Cys146Phe) and a novel nonsense mutation c.466C > T (p. Arg156Ter), both in homozygous forms, were found. The altered Cys146 resides in the LIM2 domain of the encoded protein and is a phylogenetically conserved residue, which mediates LHX3 transcription factor binding with a zinc cation. The p. Arg156Ter is predicted to result in a severely truncated protein, lacking the DNA binding homeodomain. CONCLUSIONS Considering genotype/phenotype correlation, we suggest that the presence of SNHL and limited neck rotation should be considered in the differential diagnosis of CPHD3 to facilitate molecular diagnosis. This report describes the first LHX3 mutations from Saudi patients and highlights the importance of combining molecular diagnosis with the clinical findings. In addition, it also expands the knowledge of LHX3-related CPHD3 phenotype and the allelic spectrum for this gene.
Collapse
Affiliation(s)
- Khushnooda Ramzan
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, P.O.Box 3354, Riyadh, 11211 Saudi Arabia
| | - Bassam Bin-Abbas
- Department of Pediatrics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Lolwa Al-Jomaa
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, P.O.Box 3354, Riyadh, 11211 Saudi Arabia
| | - Rabab Allam
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, P.O.Box 3354, Riyadh, 11211 Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Faiqa Imtiaz
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, P.O.Box 3354, Riyadh, 11211 Saudi Arabia
| |
Collapse
|
25
|
Chou WL, Chung YL, Fang JC, Lu CA. Novel interaction between CCR4 and CAF1 in rice CCR4-NOT deadenylase complex. PLANT MOLECULAR BIOLOGY 2017; 93:79-96. [PMID: 27714489 DOI: 10.1007/s11103-016-0548-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/28/2016] [Indexed: 06/06/2023]
Abstract
Rice is an important crop in the world. However, little is known about rice mRNA deadenylation, which is an important regulation step of gene expression at the post-transcriptional level. The CCR4-NOT1 complex contains two key components, CCR4 and CAF1, which are the main cytoplasmic deadenylases in eukaryotic cells. In yeast and humans, CCR4 can interact with CAF1 via its N-terminal LRR domain. However, no CCR4 protein containing N-terminal LRR motifs have been found in plants. In this manuscript, we demonstrate a novel pattern of interaction between OsCCR4 and OsCAF1 in the rice CCR4-NOT complex, and that OsCAF1 acts as a bridge between OsCCR4 and OsNOT1 in this complex. Our results revealed that the Mynd-like domain at the N-terminus of rice CCR4 proteins and the PXLXP motif at the rice CAF1 N-terminus play critical roles in OsCCR4-OsCAF1 interaction. Deadenylation, also called poly(A) tail shortening, is the first rate-limiting step in general cytoplasmic mRNA degradation in eukaryotic cells. Carbon catabolite repressor (CCR)4 and CCR4-associated factor (CAF)1 in the CCR4-NOT complex function in mRNA poly(A) tail shortening. CCR4s contain N-terminal leucine-rich repeat (LRR) motifs that interact with CAF1s in yeast, fruit fly and mammals. In silico analysis has not identified any plant CCR4 proteins that contain LRR motifs. Here, two rice CCR4 homologous genes, OsCCR4a and OsCCR4b, were identified. The isolated recombinant exonuclease-endonuclease-phosphatase domain of OsCCR4a and OsCCR4b exhibited 3'-5' exonuclease activity in vitro, and point mutation of a catalytic residue in this domain disrupted the deadenylase activity. Both OsCCR4a and OsCCR4b fluorescent fusion proteins were localized in the rice cytoplasm and nucleus, and both associated with processing bodies via their N-terminus. Binding analyses showed that OsCCR4a and OsCCR4b directly interacted with three rice CAF1 family members: OsCAF1A, OsCAF1G and OsCAF1H. The zf-MYND-like domain at the N terminus of rice CCR4 and the PXLXP motif of rice CAF1 play critical roles in OsCCR4-OsCAF1 interaction. OsCAF1 proteins, but not OsCCR4 proteins, can interact with the MIG4G domain of rice OsNOT1. Our studies thus reveal a hitherto undiscovered novel interaction pattern that connects OsCCR4 and OsCAF1 in the rice CCR4-NOT complex.
Collapse
Affiliation(s)
- Wei-Lun Chou
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Yue-Lin Chung
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Jhen-Cheng Fang
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Chung-An Lu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC.
| |
Collapse
|
26
|
Luan Y, Cui J, Wang W, Meng J. MiR1918 enhances tomato sensitivity to Phytophthora infestans infection. Sci Rep 2016; 6:35858. [PMID: 27779242 PMCID: PMC5078808 DOI: 10.1038/srep35858] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 10/06/2016] [Indexed: 12/03/2022] Open
Abstract
Late blight of tomato is caused by the oomycete pathogen Phytophthora infestans. In our previous work, we identified and characterized a miR1918 in P. infestans (pi-miR1918), and showed that its sequence is similar to the sequence of tomato miR1918 (sly-miR1918). In this study, we used Arabidopsis thaliana pre-miR159a as a backbone to synthesize pi-miR1918 via PCR and mutagenesis. The artificial pi-miR1918 was used to investigate the role of miR1918 in tomato-P. infestans interaction. Trangenic tomato plants that overexpressed the artificial pi-miR1918 displayed more serious disease symptoms than wild-type tomato plants after infection with P. infestans, as shown by increased number of necrotic cells, lesion sizes and number of sporangia per leaf. The target genes of pi-miR1918 and sly-miR1918 were also predicted for tomato and P. infestans, respectively. qPCR analysis of these targets also performed during tomato-P. infestans interaction. The expression of target gene, RING finger were negatively correlated with miR1918 in the all Lines of transgenic tomato plants. In addition, we used the 5′ RACE to determine the cleavage site of miR1918 to RING finger. These results suggested that miR1918 might be involved in the silencing of target genes, thereby enhancing the susceptibility of tomato to P. infestans infection.
Collapse
Affiliation(s)
- Yushi Luan
- School of Life science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Jun Cui
- School of Life science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Weichen Wang
- School of Life science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| |
Collapse
|
27
|
The Zinc Finger of Prolyl Hydroxylase Domain Protein 2 Is Essential for Efficient Hydroxylation of Hypoxia-Inducible Factor α. Mol Cell Biol 2016; 36:2328-43. [PMID: 27325674 DOI: 10.1128/mcb.00090-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/12/2016] [Indexed: 12/21/2022] Open
Abstract
Prolyl hydroxylase domain protein 2 (PHD2) (also known as EGLN1) is a key oxygen sensor in mammals that posttranslationally modifies hypoxia-inducible factor α (HIF-α) and targets it for degradation. In addition to its catalytic domain, PHD2 contains an evolutionarily conserved zinc finger domain, which we have previously proposed recruits PHD2 to the HSP90 pathway to promote HIF-α hydroxylation. Here, we provide evidence that this recruitment is critical both in vitro and in vivo We show that in vitro, the zinc finger can function as an autonomous recruitment domain to facilitate interaction with HIF-α. In vivo, ablation of zinc finger function by a C36S/C42S Egln1 knock-in mutation results in upregulation of the erythropoietin gene, erythrocytosis, and augmented hypoxic ventilatory response, all hallmarks of Egln1 loss of function and HIF stabilization. Hence, the zinc finger ordinarily performs a critical positive regulatory function. Intriguingly, the function of this zinc finger is impaired in high-altitude-adapted Tibetans, suggesting that their adaptation to high altitude may, in part, be due to a loss-of-function EGLN1 allele. Thus, these findings have important implications for understanding both the molecular mechanism of the hypoxic response and human adaptation to high altitude.
Collapse
|
28
|
Panchenko MV. Structure, function and regulation of jade family PHD finger 1 (JADE1). Gene 2016; 589:1-11. [PMID: 27155521 DOI: 10.1016/j.gene.2016.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/28/2016] [Accepted: 05/01/2016] [Indexed: 12/24/2022]
Abstract
The family of JADE proteins includes three paralogues encoded by individual genes and designated PHF17 (JADE1), PHF16 (JADE2), and PHF15 (JADE3). All three JADE proteins bear in tandem two Plant Homeo-domains (PHD) which are zinc finger domains. This review focuses on one member of the JADE family, JADE1. Studies addressing the biochemical, cellular and biological role of JADE1 are discussed. Recent discoveries of JADE1 function in the regulation of the epithelial cell cycle with potential relevance to disease are presented. Unresolved questions and future directions are formulated.
Collapse
Affiliation(s)
- Maria V Panchenko
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, United States.
| |
Collapse
|
29
|
Harter MR, Liu CD, Shen CL, Gonzalez-Hurtado E, Zhang ZM, Xu M, Martinez E, Peng CW, Song J. BS69/ZMYND11 C-Terminal Domains Bind and Inhibit EBNA2. PLoS Pathog 2016; 12:e1005414. [PMID: 26845565 PMCID: PMC4742278 DOI: 10.1371/journal.ppat.1005414] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/04/2016] [Indexed: 12/20/2022] Open
Abstract
Epstein-Barr virus (EBV) nuclear antigen 2 (EBNA2) plays an important role in driving immortalization of EBV-infected B cells through regulating the expression of many viral and cellular genes. We report a structural study of the tumor suppressor BS69/ZMYND11 C-terminal region, comprised of tandem coiled-coil-MYND domains (BS69CC-MYND), in complex with an EBNA2 peptide containing a PXLXP motif. The coiled-coil domain of BS69 self-associates to bring two separate MYND domains in close proximity, thereby enhancing the BS69 MYND-EBNA2 interaction. ITC analysis of BS69CC-MYND with a C-terminal fragment of EBNA2 further suggests that the BS69CC-MYND homodimer synergistically binds to the two EBNA2 PXLXP motifs that are respectively located in the conserved regions CR7 and CR8. Furthermore, we showed that EBNA2 interacts with BS69 and down-regulates its expression at both mRNA and protein levels in EBV-infected B cells. Ectopic BS69CC-MYND is recruited to viral target promoters through interactions with EBNA2, inhibits EBNA2-mediated transcription activation, and impairs proliferation of lymphoblastoid cell lines (LCLs). Substitution of critical residues in the MYND domain impairs the BS69-EBNA2 interaction and abolishes the BS69 inhibition of the EBNA2-mediated transactivation and LCL proliferation. This study identifies the BS69 C-terminal domains as an inhibitor of EBNA2, which may have important implications in development of novel therapeutic strategies against EBV infection. Since the discovery of Epstein-Barr virus (EBV) 50 years ago, the etiologic links between EBV and a variety of human cancers have gained wide recognition. It is estimated that >90% of the worldwide population carry this virus, which causes over 200,000 cancers across the world every year. One of the key proteins in driving immortalization of EBV-infected B cells is Epstein-Barr virus nuclear antigen 2 (EBNA2), which regulates the expression of many cellular and viral genes. However, the molecular mechanism underlying the interactions between EBNA2 and cellular transcriptional regulators remains enigmatic. Here, we determined the crystal structure of the coiled-coil and MYND tandem domains of BS69/ZMYND11, a candidate tumor suppressor, in complex with an EBNA2 peptide containing a PXLXP motif. We found that the coiled-coil and MYND domains of BS69 cooperate in binding to EBNA2. We also showed that EBNA2 interacts with BS69 and down-regulates its expression at both mRNA and protein levels in EBV-associated B cells. Ectopic BS69 coiled-coil-MYND dual domain is recruited to viral target promoters through interaction with EBNA2, inhibits EBNA2-mediated transcription activation, and impairs proliferation of lymphoblastoid cell lines (LCLs). Together, this study identifies the BS69 C-terminal domains as an inhibitor of EBNA2.
Collapse
Affiliation(s)
- Matthew R. Harter
- Department of Biochemistry, University of California, Riverside, Riverside, California, United States of America
| | - Cheng-Der Liu
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
| | - Chih-Lung Shen
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
| | - Elsie Gonzalez-Hurtado
- Department of Biochemistry, University of California, Riverside, Riverside, California, United States of America
- MARC U-STAR Program, University of California, Riverside, Riverside, California, United States of America
| | - Zhi-Min Zhang
- Department of Biochemistry, University of California, Riverside, Riverside, California, United States of America
| | - Muyu Xu
- Department of Biochemistry, University of California, Riverside, Riverside, California, United States of America
| | - Ernest Martinez
- Department of Biochemistry, University of California, Riverside, Riverside, California, United States of America
- MARC U-STAR Program, University of California, Riverside, Riverside, California, United States of America
| | - Chih-Wen Peng
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
- * E-mail: (CWP); (JS)
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, Riverside, California, United States of America
- * E-mail: (CWP); (JS)
| |
Collapse
|
30
|
Barrière Y, Courtial A, Chateigner-Boutin AL, Denoue D, Grima-Pettenati J. Breeding maize for silage and biofuel production, an illustration of a step forward with the genome sequence. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:310-329. [PMID: 26566848 DOI: 10.1016/j.plantsci.2015.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 08/04/2015] [Accepted: 08/13/2015] [Indexed: 05/21/2023]
Abstract
The knowledge of the gene families mostly impacting cell wall digestibility variations would significantly increase the efficiency of marker-assisted selection when breeding maize and grass varieties with improved silage feeding value and/or with better straw fermentability into alcohol or methane. The maize genome sequence of the B73 inbred line was released at the end of 2009, opening up new avenues to identify the genetic determinants of quantitative traits. Colocalizations between a large set of candidate genes putatively involved in secondary cell wall assembly and QTLs for cell wall digestibility (IVNDFD) were then investigated, considering physical positions of both genes and QTLs. Based on available data from six RIL progenies, 59 QTLs corresponding to 38 non-overlapping positions were matched up with a list of 442 genes distributed all over the genome. Altogether, 176 genes colocalized with IVNDFD QTLs and most often, several candidate genes colocalized at each QTL position. Frequent QTL colocalizations were found firstly with genes encoding ZmMYB and ZmNAC transcription factors, and secondly with genes encoding zinc finger, bHLH, and xylogen regulation factors. In contrast, close colocalizations were less frequent with genes involved in monolignol biosynthesis, and found only with the C4H2, CCoAOMT5, and CCR1 genes. Close colocalizations were also infrequent with genes involved in cell wall feruloylation and cross-linkages. Altogether, investigated colocalizations between candidate genes and cell wall digestibility QTLs suggested a prevalent role of regulation factors over constitutive cell wall genes on digestibility variations.
Collapse
Affiliation(s)
- Yves Barrière
- INRA, UR889, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France.
| | - Audrey Courtial
- LRSV, Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Paul Sabatier Toulouse III / CNRS, Auzeville, BP 42617, 31326 Castanet-Tolosan, France; INRA, US1258, Centre National de Ressources Génomiques Végétales, CS 52627, 31326 Castanet-Tolosan, France
| | | | - Dominique Denoue
- INRA, UR889, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France
| | - Jacqueline Grima-Pettenati
- LRSV, Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Paul Sabatier Toulouse III / CNRS, Auzeville, BP 42617, 31326 Castanet-Tolosan, France
| |
Collapse
|
31
|
Radó-Trilla N, Arató K, Pegueroles C, Raya A, de la Luna S, Albà MM. Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors. Mol Biol Evol 2015; 32:2263-72. [PMID: 25931513 PMCID: PMC4540963 DOI: 10.1093/molbev/msv103] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The high regulatory complexity of vertebrates has been related to two rounds of whole genome duplication (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families originated during the 2R-WGD contains LCRs. The number of gene duplicates with LCRs is 155 out of 550 analyzed (28%), about twice as many as the number of single copy genes with LCRs (15 out of 115, 13%). In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.
Collapse
Affiliation(s)
- Núria Radó-Trilla
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Krisztina Arató
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Cinta Pegueroles
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Alicia Raya
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Susana de la Luna
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| |
Collapse
|
32
|
Kaur G, Subramanian S. The UBR-box and its relationship to binuclear RING-like treble clef zinc fingers. Biol Direct 2015; 10:36. [PMID: 26185100 PMCID: PMC4506424 DOI: 10.1186/s13062-015-0066-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/02/2015] [Indexed: 11/30/2022] Open
Abstract
Background The N-end rule pathway is a part of the ubiquitin–dependent proteolytic system wherein N-recognin proteins recognize the amino terminal degradation signals (N-degrons) of the substrate. The type 1 N-degron recognizing UBR-box domain of the eukaryotic Arg/N-end rule pathway is known to possess a novel three-zinc-stabilized heart-shaped fold. Results Using sequence and structure analysis we argue that the UBR-box fold emerged from a binuclear RING-like treble clef zinc finger. The RING-like core is preserved in the UBR-box and the metal-chelating motifs display significant sequence and structural similarity to B-box and ZZ domains. UBR-box domains retrieved in our analysis co-occur with a variety of other protein domains, suggestive of its involvement in diverse biological roles. The UBR-box is a unique family of RING-like treble clefs as it displays a distinct circular permutation at the zinc-knuckle of the first zinc-binding site unlike other documented permutations of the RING-like domains which occur at the second zinc-binding site. The circular permutation of the RING-like treble clef scaffold has possibly aided the gain of a novel and relatively deep cleft suited for binding N-degrons. The N- and C-terminal extensions to the circularly permuted RING-like region bind a third zinc ion, which likely provides additional stability to the domain by keeping the two halves of the permuted zinc-knuckle together. Conclusions Structural modifications and extensions to the RING-like core have resulted in a novel UBR-box fold, which can recognize and target the type 1 N-degron containing proteins for ubiquitin-mediated proteolysis. The UBR-box appears to have emerged during the expansion of ubiquitin system pathway-related functions in eukaryotes, but is also likely to have other non-N-recognin functions as well. Reviewers This article was reviewed by Eugene Koonin, Balaji Santhanam, Kira S. Makarova. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0066-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gurmeet Kaur
- CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, 160036, India.
| | - Srikrishna Subramanian
- CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, 160036, India.
| |
Collapse
|
33
|
Du SJ, Tan X, Zhang J. SMYD proteins: key regulators in skeletal and cardiac muscle development and function. Anat Rec (Hoboken) 2015; 297:1650-62. [PMID: 25125178 DOI: 10.1002/ar.22972] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 04/28/2014] [Accepted: 04/28/2014] [Indexed: 11/07/2022]
Abstract
Muscle fibers are composed of myofibrils, one of the most highly ordered macromolecular assemblies in cells. Recent studies demonstrate that members of the Smyd family play critical roles in myofibril assembly of skeletal and cardiac muscle during development. The Smyd family consists of five members including Smyd1, Smyd2, Smyd3, Smyd4, and Smyd5. They share two highly conserved structural and functional domains, namely the SET and MYND domains involved in lysine methylation and protein-protein interaction, respectively. Smyd1 is specifically expressed in muscle cells under the regulation of myogenic transcriptional factors of the MyoD and Mef2 families and the serum responsive factor. Loss of function studies reveal that Smyd1 is required for cardiomyogenesis and sarcomere assembly in skeletal and cardiac muscles. Smyd2, on another hand, is dispensable for heart development in mice. However, Smyd2 appears to play a role in myofilament organization in both skeletal and cardiac muscles via Hsp90 methylation. A Drosophila Smyd4 homologue is a muscle-specific transcriptional modulator involved in the development or function of adult muscle. The molecular mechanisms by which Smyd family proteins function in muscle cells are not well understood. It has been suggested that members of the Smyd family may use multiple mechanisms to control muscle development and cell differentiation, including transcriptional regulation, epigenetic regulation via histone methylation, and methylation of proteins other than histones, such as molecular chaperone Hsp90.
Collapse
Affiliation(s)
- Shao Jun Du
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland
| | | | | |
Collapse
|
34
|
Kochańczyk T, Drozd A, Krężel A. Relationship between the architecture of zinc coordination and zinc binding affinity in proteins – insights into zinc regulation. Metallomics 2015; 7:244-57. [DOI: 10.1039/c4mt00094c] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Relationship between the architecture and stability of zinc proteins.
Collapse
Affiliation(s)
- Tomasz Kochańczyk
- Laboratory of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław, Poland
| | - Agnieszka Drozd
- Laboratory of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław, Poland
| | - Artur Krężel
- Laboratory of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław, Poland
| |
Collapse
|
35
|
Burroughs AM, Aravind L. Analysis of two domains with novel RNA-processing activities throws light on the complex evolution of ribosomal RNA biogenesis. Front Genet 2014; 5:424. [PMID: 25566315 PMCID: PMC4275035 DOI: 10.3389/fgene.2014.00424] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/19/2014] [Indexed: 11/13/2022] Open
Abstract
Ribosomal biogenesis has been extensively investigated, especially to identify the elusive nucleases and cofactors involved in the complex rRNA processing events in eukaryotes. Large-scale screens in yeast identified two biochemically uncharacterized proteins, TSR3 and TSR4, as being key players required for rRNA maturation. Using multiple computational approaches we identify the conserved domains comprising these proteins and establish sequence and structural features providing novel insights regarding their roles. TSR3 is unified with the DTW domain into a novel superfamily of predicted enzymatic domains, with the balance of the available evidence pointing toward an RNase role with the archaeo-eukaryotic TSR3 proteins processing rRNA and the bacterial versions potentially processing tRNA. TSR4, its other eukaryotic homologs PDCD2/rp-8, PDCD2L, Zfrp8, and trus, the predominantly bacterial DUF1963 proteins, and other uncharacterized proteins are unified into a new domain superfamily, which arose from an ancient duplication event of a strand-swapped, dimer-forming all-beta unit. We identify conserved features mediating protein-protein interactions (PPIs) and propose a potential chaperone-like function. While contextual evidence supports a conserved role in ribosome biogenesis for the eukaryotic TSR4-related proteins, there is no evidence for such a role for the bacterial versions. Whereas TSR3-related proteins can be traced to the last universal common ancestor (LUCA) with a well-supported archaeo-eukaryotic branch, TSR4-related proteins of eukaryotes are derived from within the bacterial radiation of this superfamily, with archaea entirely lacking them. This provides evidence for “systems admixture,” which followed the early endosymbiotic event, playing a key role in the emergence of the uniquely eukaryotic ribosome biogenesis process.
Collapse
Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD, USA
| |
Collapse
|
36
|
Abstract
Humans have adapted to the chronic hypoxia of high altitude in several locations, and recent genome-wide studies have indicated a genetic basis. In some populations, genetic signatures have been identified in the hypoxia-inducible factor (HIF) pathway, which orchestrates the transcriptional response to hypoxia. In Tibetans, they have been found in the HIF2A (EPAS1) gene, which encodes for HIF-2α, and the prolyl hydroxylase domain protein 2 (PHD2, also known as EGLN1) gene, which encodes for one of its key regulators, PHD2. High-altitude adaptation may be due to multiple genes that act in concert with one another. Unraveling their mechanism of action can offer new therapeutic approaches toward treating common human diseases characterized by chronic hypoxia.
Collapse
Affiliation(s)
- Abigail W Bigham
- Department of Anthropology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Frank S Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
37
|
Hu GW, Yan XW, Qin YJ, Nie HT. Molecular cloning and expression analysis of inhibitor of growth protein 3 (ING3) in the Manila clam, Ruditapes philippinarum. Mol Biol Rep 2014; 41:3583-90. [PMID: 24566680 DOI: 10.1007/s11033-014-3221-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 01/28/2014] [Indexed: 11/27/2022]
Abstract
Inhibitor of growth protein 3 (ING3), a new member of ING family, is involved in the regulation of various processes. In this study, a full-length cDNA of ING3 (named as RpING3) was cloned from the gill of Ruditapes philippinarum by rapid amplification of cDNA ends method for the first time. The cDNA obtained was 1442 bp exclusive of poly (A) residues with a 1248 bp open reading frame encoding 415 amino acids. The RpING3 protein has a calculated molecular weight of 46.59 kDa and isoelectric point of 6.62. Two conserved motif and some functional sites were found. Tissue distribution analysis of the RpING3 mRNA revealed that the RpING3 expression level was much higher in gill and digestive gland while lower in mantle, foot and adductor muscle. The temporal expression of RpING3 in digestive gland after lead exposure was recorded by quantitative real-time PCR. The result showed that RpING3 was rapidly up-regulated at 6 h post-exposure and reached tenfold of the control group. These results suggest that RpING3 dependent signaling pathway is present in Manila clam and RpING3 may play important roles in protecting cells from heavy metal damage in R. philippinarum.
Collapse
Affiliation(s)
- Guang-Wei Hu
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | | | | | | |
Collapse
|
38
|
Minakhina S, Changela N, Steward R. Zfrp8/PDCD2 is required in ovarian stem cells and interacts with the piRNA pathway machinery. Development 2014; 141:259-68. [PMID: 24381196 DOI: 10.1242/dev.101410] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The maintenance of stem cells is central to generating diverse cell populations in many tissues throughout the life of an animal. Elucidating the mechanisms involved in how stem cells are formed and maintained is crucial to understanding both normal developmental processes and the growth of many cancers. Previously, we showed that Zfrp8/PDCD2 is essential for the maintenance of Drosophila hematopoietic stem cells. Here, we show that Zfrp8/PDCD2 is also required in both germline and follicle stem cells in the Drosophila ovary. Expression of human PDCD2 fully rescues the Zfrp8 phenotype, underlining the functional conservation of Zfrp8/PDCD2. The piRNA pathway is essential in early oogenesis, and we find that nuclear localization of Zfrp8 in germline stem cells and their offspring is regulated by some piRNA pathway genes. We also show that Zfrp8 forms a complex with the piRNA pathway protein Maelstrom and controls the accumulation of Maelstrom in the nuage. Furthermore, Zfrp8 regulates the activity of specific transposable elements also controlled by Maelstrom and Piwi. Our results suggest that Zfrp8/PDCD2 is not an integral member of the piRNA pathway, but has an overlapping function, possibly competing with Maelstrom and Piwi.
Collapse
Affiliation(s)
- Svetlana Minakhina
- Rutgers University, Department of Molecular Biology, Waksman Institute, Cancer Institute of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | | | | |
Collapse
|
39
|
Fedoreyeva LI, Smirnova TA, Kolomijtseva GY, Khavinson VK, Vanyushin BF. Interaction of short peptides with FITC-labeled wheat histones and their complexes with deoxyribooligonucleotides. BIOCHEMISTRY (MOSCOW) 2013; 78:166-75. [PMID: 23581987 DOI: 10.1134/s0006297913020053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Judging from fluorescence modulation (quenching), short peptides (Ala-Glu-Asp-Gly, Glu-Asp-Arg, Ala-Glu-Asp-Leu, Lys-Glu-Asp-Gly, Ala-Glu-Asp-Arg, and Lys-Glu-Asp-Trp) bind with FITC-labeled wheat histones H1, H2B, H3, and H4. This results from the interaction of the peptides with the N-terminal histone regions that contain respective and seemingly homologous peptide-binding motifs. Because homologous amino acid sequences in wheat core histones were not found, the peptides seem to bind with some core histone regions having specific conformational structure. Peptide binding with histones and histone-deoxyribooligonucleotide complexes depends on the nature of the histone and the primary structures of the peptides and oligonucleotides; thus, it is site specific. Histones H1 bind preferentially with single-stranded oligonucleotides by homologous sites in the C-terminal region of the protein. Unlike histone H1, the core histones bind predominantly with double-stranded methylated oligonucleotides and methylated DNA. Stern-Volmer constants of interaction of histone H1 and core histones with double-stranded hemimethylated oligonucleotides are higher compared with that of binding with unmethylated ones. DNA or deoxyribooligonucleotides in a complex with histones can enhance or inhibit peptide binding. It is suggested that site-specific interactions of short biologically active peptides with histone tails can serve in chromatin as control epigenetic mechanisms of regulation of gene activity and cellular differentiation.
Collapse
Affiliation(s)
- L I Fedoreyeva
- All Russia Research Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, 127550 Moscow, Russia
| | | | | | | | | |
Collapse
|
40
|
Song Y, Gao J, Yang F, Kua CS, Liu J, Cannon CH. Molecular evolutionary analysis of the Alfin-like protein family in Arabidopsis lyrata, Arabidopsis thaliana, and Thellungiella halophila. PLoS One 2013; 8:e66838. [PMID: 23840867 PMCID: PMC3698079 DOI: 10.1371/journal.pone.0066838] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 05/10/2013] [Indexed: 01/07/2023] Open
Abstract
In previous studies, the Alfin1 gene, a transcription factor, enhanced salt tolerance in alfalfa, primarily through altering gene expression levels in the root. Here, we examined the molecular evolution of the Alfin-like (AL) proteins in two Arabidopsis species (A. lyrata and A. thaliana) and a salt-tolerant close relative Thellungiella halophila. These AL-like proteins could be divided into four groups and the two known DUF3594 and PHD-finger domains had co-evolved within each group of genes, irrespective of species, due to gene duplication events in the common ancestor of all three species while gene loss was observed only in T. halophila. To detect whether natural selection acted in the evolution of AL genes, we calculated synonymous substitution ratios (dn/ds) and codon usage statistics, finding positive selection operated on four branches and significant differences in biased codon usage in the AL family between T. halophila and A. lyrata or A. thaliana. Distinctively, only the AL7 branch was under positive selection on the PHD-finger domain and the three members on the branch showed the smallest difference when codon bias was evaluated among the seven clusters. Functional analysis based on transgenic overexpression lines and T-DNA insertion mutants indicated that salt-stress-induced AtAL7 could play a negative role in salt tolerance of A. thaliana, suggesting that adaptive evolution occurred in the members of AL gene family.
Collapse
Affiliation(s)
- Yu Song
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Graduate School of the Chinese Academy of Sciences, Beijing People’s Republic of China
| | - Jie Gao
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
| | - Fengxi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Chai-Shian Kua
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Graduate School of the Chinese Academy of Sciences, Beijing People’s Republic of China
| | - Jingxin Liu
- Institute of Plant Production and Agroecology in the Tropics and Subtropics (380), Agroecology Section, University of Hohenheim Stuttgart, Germany
| | - Charles H. Cannon
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| |
Collapse
|
41
|
Song D, Li LS, Heaton-Johnson KJ, Arsenault PR, Master SR, Lee FS. Prolyl hydroxylase domain protein 2 (PHD2) binds a Pro-Xaa-Leu-Glu motif, linking it to the heat shock protein 90 pathway. J Biol Chem 2013; 288:9662-9674. [PMID: 23413029 DOI: 10.1074/jbc.m112.440552] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Prolyl hydroxylase domain protein 2 (PHD2, also known as Egg Laying Defective Nine homolog 1) is a key oxygen-sensing protein in metazoans. In an oxygen-dependent manner, PHD2 site-specifically prolyl hydroxylates the master transcription factor of the hypoxic response, hypoxia-inducible factor-α (HIF-α), thereby targeting HIF-α for degradation. In this report we show that the heat shock protein 90 (HSP90) co-chaperones p23 and FKBP38 interact via a conserved Pro-Xaa-Leu-Glu motif (where Xaa = any amino acid) in these proteins with the N-terminal Myeloid Nervy and DEAF-1 (MYND)-type zinc finger of PHD2. Knockdown of p23 augments hypoxia-induced HIF-1α protein levels and HIF target genes. We propose that p23 recruits PHD2 to the HSP90 machinery to facilitate HIF-1α hydroxylation. These findings identify a link between two ancient pathways, the PHD:HIF and the HSP90 pathways, and suggest that this link was established concurrent with the emergence of the PHD:HIF pathway in evolution.
Collapse
Affiliation(s)
- Daisheng Song
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Lin-Sheng Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Katherine J Heaton-Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Patrick R Arsenault
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Stephen R Master
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Frank S Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
| |
Collapse
|
42
|
Abstract
LIM-domain proteins are a large family of proteins that are emerging as key molecules in a wide variety of human cancers. In particular, all members of the human LIM-domain-only (LMO) proteins, LMO1-4, which are required for many developmental processes, are implicated in the onset or the progression of several cancers, including T cell leukaemia, breast cancer and neuroblastoma. These small proteins contain two protein-interacting LIM domains but little additional sequence, and they seem to function by nucleating the formation of new transcriptional complexes and/or by disrupting existing transcriptional complexes to modulate gene expression programmes. Through these activities, the LMO proteins have important cellular roles in processes that are relevant to cancer such as self-renewal, cell cycle regulation and metastasis. These functions highlight the therapeutic potential of targeting these proteins in cancer.
Collapse
Affiliation(s)
- Jacqueline M Matthews
- School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia. jacqui.matthews@ sydney.edu.au
| | | | | | | |
Collapse
|
43
|
Stokes PH, Liew CW, Kwan AH, Foo P, Barker HE, Djamirze A, O'Reilly V, Visvader JE, Mackay JP, Matthews JM. Structural basis of the interaction of the breast cancer oncogene LMO4 with the tumour suppressor CtIP/RBBP8. J Mol Biol 2013; 425:1101-10. [PMID: 23353824 DOI: 10.1016/j.jmb.2013.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/12/2013] [Accepted: 01/15/2013] [Indexed: 12/14/2022]
Abstract
LIM-only protein 4 (LMO4) is strongly linked to the progression of breast cancer. Although the mechanisms underlying this phenomenon are not well understood, a role is emerging for LMO4 in regulation of the cell cycle. We determined the solution structure of LMO4 in complex with CtIP (C-terminal binding protein interacting protein)/RBBP8, a tumour suppressor protein that is involved in cell cycle progression, DNA repair and transcriptional regulation. Our data reveal that CtIP and the essential LMO cofactor LDB1 (LIM-domain binding protein 1) bind to the same face on LMO4 and cannot simultaneously bind to LMO4. We hypothesise that overexpression of LMO4 may disrupt some of the normal tumour suppressor activities of CtIP, thereby contributing to breast cancer progression.
Collapse
Affiliation(s)
- P H Stokes
- School of Molecular Bioscience, University of Sydney, NSW 2006, Australia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Matthews JM, Potts JR. The tandem β-zipper: Modular binding of tandem domains and linear motifs. FEBS Lett 2013; 587:1164-71. [DOI: 10.1016/j.febslet.2013.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/07/2013] [Accepted: 01/07/2013] [Indexed: 11/17/2022]
|
45
|
Cbl-c ubiquitin ligase activity is increased via the interaction of its RING finger domain with a LIM domain of the paxillin homolog, Hic 5. PLoS One 2012; 7:e49428. [PMID: 23145173 PMCID: PMC3492284 DOI: 10.1371/journal.pone.0049428] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 10/08/2012] [Indexed: 12/31/2022] Open
Abstract
Cbl proteins (Cbl, Cbl-b and Cbl-c) are ubiquitin ligases that are critical regulators of tyrosine kinase signaling. In this study we identify a new Cbl-c interacting protein, Hydrogen peroxide Induced Construct 5 (Hic-5). The two proteins interact through a novel interaction mediated by the RING finger of Cbl-c and the LIM2 domain of Hic-5. Further, this interaction is mediated and dependent on specific zinc coordinating complexes within the RING finger and LIM domain. Binding of Hic-5 to Cbl-c leads to an increase in the ubiquitin ligase activity of Cbl-c once Cbl-c has been activated by Src phosphorylation or through an activating phosphomimetic mutation. In addition, co-transfection of Hic-5 with Cbl-c leads to an increase in Cbl-c mediated ubiquitination of the EGFR. These data suggest that Hic-5 enhances Cbl-c ubiquitin ligase activity once Cbl-c has been phosphorylated and activated. Interactions between heterologous RING fingers have been shown to activate E3s. This is the first demonstration of enhancement of ubiquitin ligase activity of a RING finger ubiquitin ligase by the direct interaction of a LIM zinc coordinating domain.
Collapse
|
46
|
Dastmalchi S, Wilkinson-White L, Kwan AH, Gamsjaeger R, Mackay JP, Matthews JM. Solution structure of a tethered Lmo2(LIM2) /Ldb1(LID) complex. Protein Sci 2012; 21:1768-74. [PMID: 22936624 PMCID: PMC3527713 DOI: 10.1002/pro.2153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/21/2012] [Accepted: 08/24/2012] [Indexed: 11/05/2022]
Abstract
LIM-only protein 2, Lmo2, is a regulatory protein that is essential for hematopoietic development and inappropriate overexpression of Lmo2 in T-cells contributes to T-cell leukemia. It exerts its functions by mediating protein-protein interactions and nucleating multicomponent transcriptional complexes. Lmo2 interacts with LIM domain binding protein 1 (Ldb1) through the tandem LIM domains of Lmo2 and the LIM interaction domain (LID) of Ldb1. Here, we present the solution structure of the LIM2 domain of Lmo2 bound to Ldb1(LID) . The ordered regions of Ldb1 in this complex correspond well with binding hotspots previously defined by mutagenic studies. Comparisons of this Lmo2(LIM2) -Ldb1(LID) structure with previously determined structures of the Lmo2/Ldb1(LID) complexes lead to the conclusion that modular binding of tandem LIM domains in Lmo2 to tandem linear motifs in Ldb1 is accompanied by several disorder-to-order transitions and/or conformational changes in both proteins.
Collapse
Affiliation(s)
- Siavoush Dastmalchi
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
- Biotechnology Research Centre and School of Pharmacy, Tabriz University of Medical SciencesTabriz, Iran
| | - Lorna Wilkinson-White
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
| | - Ann H Kwan
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
| | - Roland Gamsjaeger
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
- School of Science and Health, University of Western SydneyPenrith, New South Wales 2751, Australia
| | - Joel P Mackay
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
| | - Jacqueline M Matthews
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
| |
Collapse
|
47
|
|
48
|
Chung CW. Small molecule bromodomain inhibitors: extending the druggable genome. PROGRESS IN MEDICINAL CHEMISTRY 2012; 51:1-55. [PMID: 22520470 DOI: 10.1016/b978-0-12-396493-9.00001-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chun-Wa Chung
- Computational and Structural Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
| |
Collapse
|
49
|
Bhati M, Lee C, Gadd MS, Jeffries CM, Kwan A, Whitten AE, Trewhella J, Mackay JP, Matthews JM. Solution structure of the LIM-homeodomain transcription factor complex Lhx3/Ldb1 and the effects of a pituitary mutation on key Lhx3 interactions. PLoS One 2012; 7:e40719. [PMID: 22848397 PMCID: PMC3405102 DOI: 10.1371/journal.pone.0040719] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 06/12/2012] [Indexed: 01/01/2023] Open
Abstract
Lhx3 is a LIM-homeodomain (LIM-HD) transcription factor that regulates neural cell subtype specification and pituitary development in vertebrates, and mutations in this protein cause combined pituitary hormone deficiency syndrome (CPHDS). The recently published structures of Lhx3 in complex with each of two key protein partners, Isl1 and Ldb1, provide an opportunity to understand the effect of mutations and posttranslational modifications on key protein-protein interactions. Here, we use small-angle X-ray scattering of an Ldb1-Lhx3 complex to confirm that in solution the protein is well represented by our previously determined NMR structure as an ensemble of conformers each comprising two well-defined halves (each made up of LIM domain from Lhx3 and the corresponding binding motif in Ldb1) with some flexibility between the two halves. NMR analysis of an Lhx3 mutant that causes CPHDS, Lhx3(Y114C), shows that the mutation does not alter the zinc-ligation properties of Lhx3, but appears to cause a structural rearrangement of the hydrophobic core of the LIM2 domain of Lhx3 that destabilises the domain and/or reduces the affinity of Lhx3 for both Ldb1 and Isl1. Thus the mutation would affect the formation of Lhx3-containing transcription factor complexes, particularly in the pituitary gland where these complexes are required for the production of multiple pituitary cell types and hormones.
Collapse
Affiliation(s)
- Mugdha Bhati
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Christopher Lee
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Morgan S. Gadd
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Cy M. Jeffries
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Ann Kwan
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Andrew E. Whitten
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Jill Trewhella
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P. Mackay
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Jacqueline M. Matthews
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
| |
Collapse
|
50
|
Janzer A, Stamm K, Becker A, Zimmer A, Buettner R, Kirfel J. The H3K4me3 histone demethylase Fbxl10 is a regulator of chemokine expression, cellular morphology, and the metabolome of fibroblasts. J Biol Chem 2012; 287:30984-92. [PMID: 22825849 DOI: 10.1074/jbc.m112.341040] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Fbxl10 (Jhdm1b/Kdm2b) is a conserved and ubiquitously expressed member of the JHDM (JmjC domain-containing histone demethylase) family. Fbxl10 was implicated in the demethylation of H3K4me3 or H3K36me2 thereby removing active chromatin marks and inhibiting gene transcription. Apart from the JmjC domain, Fbxl10 consists of a CxxC domain, a PHD domain, and an Fbox domain. By purifying the JmjC and the PHD domain of Fbxl10 and using different approaches we were able to characterize the properties of these domains in vitro. Our results suggest that Fbxl10 is rather a H3K4me3 than a H3K36me2 histone demethylase. The PHD domain exerts a dual function in binding H3K4me3 and H3K36me2 and exhibiting E3 ubiquitin ligase activity. We generated mouse embryonic fibroblasts stably overexpressing Fbxl10. These cells reveal an increase in cell size but no changes in proliferation, mitosis, or apoptosis. Using a microarray approach we were able to identify potentially new target genes for Fbxl10 including chemokines, the noncoding RNA Xist, and proteins involved in metabolic processes. Additionally, we found that Fbxl10 is recruited to the promoters of Ccl7, Xist, Crabp2, and RipK3. Promoter occupancy by Fbxl10 was accompanied by reduced levels of H3K4me3 but unchanged levels of H3K36me2. Furthermore, knockdown of Fbxl10 using small interfering RNA approaches showed inverse regulation of Fbxl10 target genes. In summary, our data reveal a regulatory role of Fbxl10 in cell morphology, chemokine expression, and the metabolic control of fibroblasts.
Collapse
Affiliation(s)
- Andreas Janzer
- Institute of Pathology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | | | | | | | | | | |
Collapse
|