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Caengprasath N, Theerapanon T, Porntaveetus T, Shotelersuk V. MBTPS2, a membrane bound protease, underlying several distinct skin and bone disorders. J Transl Med 2021; 19:114. [PMID: 33743732 PMCID: PMC7981912 DOI: 10.1186/s12967-021-02779-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/08/2021] [Indexed: 12/27/2022] Open
Abstract
The MBTPS2 gene on the X-chromosome encodes the membrane-bound transcription factor protease, site-2 (MBTPS2) or site-2 protease (S2P) which cleaves and activates several signaling and regulatory proteins from the membrane. The MBTPS2 is critical for a myriad of cellular processes, ranging from the regulation of cholesterol homeostasis to unfolded protein responses. While its functional role has become much clearer in the recent years, how mutations in the MBTPS2 gene lead to several human disorders with different phenotypes including Ichthyosis Follicularis, Atrichia and Photophobia syndrome (IFAP) with or without BRESHECK syndrome, Keratosis Follicularis Spinulosa Decalvans (KFSD), Olmsted syndrome, and Osteogenesis Imperfecta type XIX remains obscure. This review presents the biological role of MBTPS2 in development, summarizes its mutations and implicated disorders, and discusses outstanding unanswered questions.
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Affiliation(s)
- Natarin Caengprasath
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Thanakorn Theerapanon
- Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thantrira Porntaveetus
- Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
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2
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Luman/CREB3 knock-down inhibit hCG induced MLTC-1 apoptosis. Theriogenology 2020; 161:140-150. [PMID: 33310232 DOI: 10.1016/j.theriogenology.2020.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/20/2020] [Accepted: 11/17/2020] [Indexed: 12/25/2022]
Abstract
Luman has been reported to be involved in the formation of COP II-mediated transport vesicles that affect protein transportation and secretion. Western blotting, immunohistochemistry, immunofluorescence, and RT-qPCR indicated that Luman is widely expressed in the male mouse reproductive system. In sperm, Luman was mainly located in the sperm tail, and the expression level increased with sperm maturity. In the testis, Luman was located in Leydig cells. In MLTC-1, a high-concentration hCG treatment significantly increased GRP78, ATF6, p-IRE1, and p-EIF2S1 expression but had no effect on Luman expression. To investigate the role of Luman in hCG-induced ER stress (ERS), experiments were conducted to examine the consequences of short hairpin RNA (shRNA)-mediated Luman knockdown in MLTC-1 cells. Luman knockdown decreased the percentage of S phase cells and up-regulated Cyclin A1, Cyclin B1, and Cyclin D2 expression. ELISA and WB results showed that with Luman knockdown, Cyp11a1, p-IRE1, and p-EIF2S1 expression and testosterone secretion were significantly increased, while GRP78 and CHOP expression were decreased. Flow cytometry results showed that Luman knockdown reduced MLTC-1 cell apoptosis. RT-qPCR and WB results showed that Luman knockdown significantly up-regulated BCL-2 expression and decreased Caspase-3 and BAX expression. These data suggest that Luman is widely expressed in the male mouse reproductive system. In MLTC-1 cells, Luman knockdown up-regulated p-IRE1, p-EIF2S1, and BCL-2 expression and decreased GRP78, CHOP, BAX, and Caspase-3 expression. We propose that Luman knockdown reduces cell apoptosis through the ERS pathway, thereby promoting cell survival and testosterone secretion. These findings provide new insights into the role of Luman in hCG-induced ERS.
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Wang L, Lu M, Zhang R, Guo W, Lin P, Yang D, Chen H, Tang K, Zhou D, Wang A, Jin Y. Inhibition of Luman/CREB3 expression leads to the upregulation of testosterone synthesis in mouse Leydig cells. J Cell Physiol 2019; 234:15257-15269. [PMID: 30673139 DOI: 10.1002/jcp.28171] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Luman, also known as cAMP-response element-binding protein 3, is an endoplasmic reticulum stress-related protein that has been identified as a novel transcriptional coregulator of a variety of nuclear receptors. Herein, immunohistochemistry results showed that Luman was specifically expressed in mouse Leydig cells in an age-dependent increase manner, from prepuberty to sexual maturation. Luman was not detected in Sertoli cells within the seminiferous tubules at any developmental period. The immunofluorescent experiment indicated that Luman was mainly located within the cytoplasm of murine Leydig tumor cells (MLTC-1) and primary Leydig cells (PLCs). To investigate the physiological function of Luman, experiments were conducted to examine the consequences of short hairpin RNA- and small interfering RNA-mediated Luman knock-down in MLTC-1 and PLCs, respectively. Luman knock-down significantly upregulated the expression of steroidogenic acute regulatory, cytochrome P450 cholesterol side-chain cleavage enzymes, 3β-hydroxysteroid dehydrogenase, and 17-α-hydroxylase/C17-20 lyase in MLTC-1 cells and PLCs. Luman knock-down caused an increase in human chorionic gonadotropin-stimulated testosterone production in vitro and in vivo. The nuclear receptors SF-1 and Nur-77 were significantly increased upon Luman knock-down in MLTC-1. By contrast, the level of the nuclear receptor SHP decreased. Luciferase reporter assay results demonstrated that Luman knock-down upregulated the activity of SF-1 and Nur-77 promoters. These data suggested that Luman expressed in mouse Leydig cells in an age-dependent increase manner. Luman knock-down upregulated the activity of SF-1 and Nur-77 promoters, which lead to the increase of testosterone synthesis and steroidogenesis genes expression. In conclusion, these findings provide us with new insights into the role Luman played in male reproduction.
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Affiliation(s)
- Lei Wang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Minjie Lu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruixue Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenwen Guo
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Pengfei Lin
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Diqi Yang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Huatao Chen
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Keqiong Tang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Dong Zhou
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Aihua Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China.,Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yaping Jin
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
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Sampieri L, Di Giusto P, Alvarez C. CREB3 Transcription Factors: ER-Golgi Stress Transducers as Hubs for Cellular Homeostasis. Front Cell Dev Biol 2019; 7:123. [PMID: 31334233 PMCID: PMC6616197 DOI: 10.3389/fcell.2019.00123] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/17/2019] [Indexed: 12/21/2022] Open
Abstract
CREB3 family of transcription factors are ER localized proteins that belong to the bZIP family. They are transported from the ER to the Golgi, cleaved by S1P and S2P proteases and the released N-terminal domains act as transcription factors. CREB3 family members regulate the expression of a large variety of genes and according to their tissue-specific expression profiles they play, among others, roles in acute phase response, lipid metabolism, development, survival, differentiation, organelle autoregulation, and protein secretion. They have been implicated in the ER and Golgi stress responses as regulators of the cell secretory capacity and cell specific cargos. In this review we provide an overview of the diverse functions of each member of the family (CREB3, CREB3L1, CREB3L2, CREB3L3, CREB3L4) with special focus on their role in the central nervous system.
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Affiliation(s)
- Luciana Sampieri
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Córdoba, Argentina.,Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Pablo Di Giusto
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Córdoba, Argentina.,Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Cecilia Alvarez
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Córdoba, Argentina.,Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
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Sabaratnam K, Renner M, Paesen G, Harlos K, Nair V, Owens RJ, Grimes JM. Insights from the crystal structure of the chicken CREB3 bZIP suggest that members of the CREB3 subfamily transcription factors may be activated in response to oxidative stress. Protein Sci 2019; 28:779-787. [PMID: 30653278 PMCID: PMC6423718 DOI: 10.1002/pro.3573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/14/2019] [Indexed: 12/23/2022]
Abstract
cAMP response element binding Protein 3 (CREB3) is an endoplasmic reticulum (ER) membrane‐bound transcription factor, which belongs to the basic leucine zipper (bZIP) superfamily of eukaryotic transcription factors. CREB3 plays a role in the ER‐stress induced unfolded protein response (UPR) and is a multifunctional cellular factor implicated in a number of biological processes including cell proliferation and migration, tumor suppression, and immune‐related gene expression. To gain structural insights into the transcription factor, we determined the crystal structure of the conserved bZIP domain of chicken CREB3 (chCREB3) to a resolution of 3.95 Å. The X‐ray structure provides evidence that chCREB3 can form a stable homodimer. The chCREB3 bZIP has a structured, pre‐formed DNA binding region, even in the absence of DNA, a feature that could potentially enhance both the DNA binding specificity and affinity of chCREB3. Significantly, the homodimeric bZIP possesses an intermolecular disulfide bond that connects equivalent cysteine residues of the parallel helices in the leucine zipper region. This disulfide bond in the hydrophobic core of the bZIP may increase the stability of the homodimer under oxidizing conditions. Moreover, sequence alignment of bZIP sequences from chicken, human, and mouse reveals that only members of the CREB3 subfamily contain this cysteine residue, indicating that it could act as a redox‐sensor. Taken together, these results suggest that the activity of these transcription factors may be redox‐regulated and they may be activated in response to oxidative stress. PDB Code(s): 6IAK
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Affiliation(s)
- Keshalini Sabaratnam
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom.,The Pirbright Institute, Woking, Guildford, Surrey, GU24 0NF, United Kingdom
| | - Max Renner
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Guido Paesen
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Karl Harlos
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute, Woking, Guildford, Surrey, GU24 0NF, United Kingdom
| | - Raymond J Owens
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom.,The Research Complex at Harwell, Oxfordshire, OX11 0FA, United Kingdom
| | - Jonathan M Grimes
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom.,Diamond Light Source Limited, Oxfordshire, OX11 0DE, United Kingdom
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6
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Pharmacologic inhibition of AKT leads to cell death in relapsed multiple myeloma. Cancer Lett 2018; 432:205-215. [DOI: 10.1016/j.canlet.2018.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/14/2018] [Accepted: 06/14/2018] [Indexed: 11/18/2022]
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7
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Torres-Odio S, Key J, Hoepken HH, Canet-Pons J, Valek L, Roller B, Walter M, Morales-Gordo B, Meierhofer D, Harter PN, Mittelbronn M, Tegeder I, Gispert S, Auburger G. Progression of pathology in PINK1-deficient mouse brain from splicing via ubiquitination, ER stress, and mitophagy changes to neuroinflammation. J Neuroinflammation 2017; 14:154. [PMID: 28768533 PMCID: PMC5541666 DOI: 10.1186/s12974-017-0928-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 07/26/2017] [Indexed: 12/18/2022] Open
Abstract
Background PINK1 deficiency causes the autosomal recessive PARK6 variant of Parkinson’s disease. PINK1 activates ubiquitin by phosphorylation and cooperates with the downstream ubiquitin ligase PARKIN, to exert quality control and control autophagic degradation of mitochondria and of misfolded proteins in all cell types. Methods Global transcriptome profiling of mouse brain and neuron cultures were assessed in protein-protein interaction diagrams and by pathway enrichment algorithms. Validation by quantitative reverse transcriptase polymerase chain reaction and immunoblots was performed, including human neuroblastoma cells and patient primary skin fibroblasts. Results In a first approach, we documented Pink1-deleted mice across the lifespan regarding brain mRNAs. The expression changes were always subtle, consistently affecting “intracellular membrane-bounded organelles”. Significant anomalies involved about 250 factors at age 6 weeks, 1300 at 6 months, and more than 3500 at age 18 months in the cerebellar tissue, including Srsf10, Ube3a, Mapk8, Creb3, and Nfkbia. Initially, mildly significant pathway enrichment for the spliceosome was apparent. Later, highly significant networks of ubiquitin-mediated proteolysis and endoplasmic reticulum protein processing occurred. Finally, an enrichment of neuroinflammation factors appeared, together with profiles of bacterial invasion and MAPK signaling changes—while mitophagy had minor significance. Immunohistochemistry showed pronounced cellular response of Iba1-positive microglia and GFAP-positive astrocytes; brain lipidomics observed increases of ceramides as neuroinflammatory signs at old age. In a second approach, we assessed PINK1 deficiency in the presence of a stressor. Marked dysregulations of microbial defense factors Ifit3 and Rsad2 were consistently observed upon five analyses: (1) Pink1−/− primary neurons in the first weeks after brain dissociation, (2) aged Pink1−/− midbrain with transgenic A53T-alpha-synuclein overexpression, (3) human neuroblastoma cells with PINK1-knockdown and murine Pink1−/− embryonal fibroblasts undergoing acute starvation, (4) triggering mitophagy in these cells with trifluoromethoxy carbonylcyanide phenylhydrazone (FCCP), and (5) subjecting them to pathogenic RNA-analogue poly(I:C). The stress regulation of MAVS, RSAD2, DDX58, IFIT3, IFIT1, and LRRK2 was PINK1 dependent. Dysregulation of some innate immunity genes was also found in skin fibroblast cells from PARK6 patients. Conclusions Thus, an individual biomarker with expression correlating to progression was not identified. Instead, more advanced disease stages involved additional pathways. Hence, our results identify PINK1 deficiency as an early modulator of innate immunity in neurons, which precedes late stages of neuroinflammation during alpha-synuclein spreading. Electronic supplementary material The online version of this article (doi:10.1186/s12974-017-0928-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sylvia Torres-Odio
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Jana Key
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Hans-Hermann Hoepken
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Júlia Canet-Pons
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Lucie Valek
- Institute of Clinical Pharmacology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Bastian Roller
- Edinger-Institute (Institute of Neurology), Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Michael Walter
- Institute for Medical Genetics, Eberhard-Karls-University of Tuebingen, 72076, Tuebingen, Germany
| | - Blas Morales-Gordo
- Department of Neurology, University Hospital San Cecilio, 18012, Granada, Spain
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Patrick N Harter
- Edinger-Institute (Institute of Neurology), Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Michel Mittelbronn
- Edinger-Institute (Institute of Neurology), Goethe University Medical School, 60590, Frankfurt am Main, Germany.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg, Luxembourg.,Department of Pathology, Laboratoire National de Santé, Dudelange, Luxembourg.,Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg, Luxembourg.,Department of Oncology, Luxembourg Institute of Health, NORLUX Neuro-Oncology Laboratory, Luxembourg, Luxembourg
| | - Irmgard Tegeder
- Institute of Clinical Pharmacology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Suzana Gispert
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany.
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Park OH, Park J, Yu M, An HT, Ko J, Kim YK. Identification and molecular characterization of cellular factors required for glucocorticoid receptor-mediated mRNA decay. Genes Dev 2017; 30:2093-2105. [PMID: 27798850 PMCID: PMC5066615 DOI: 10.1101/gad.286484.116] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/08/2016] [Indexed: 11/24/2022]
Abstract
In this study, Park et al. investigated the molecular mechanisms regulating glucocorticoid receptor-mediated mRNA decay (GMD). The authors characterize the molecular details of GMD, identify specific factors required for efficient GMD, and perform RNA sequencing, identifying many endogenous GMD substrates. Glucocorticoid (GC) receptor (GR) has been shown recently to bind a subset of mRNAs and elicit rapid mRNA degradation. However, the molecular details of GR-mediated mRNA decay (GMD) remain unclear. Here, we demonstrate that GMD triggers rapid degradation of target mRNAs in a translation-independent and exon junction complex-independent manner, confirming that GMD is mechanistically distinct from nonsense-mediated mRNA decay (NMD). Efficient GMD requires PNRC2 (proline-rich nuclear receptor coregulatory protein 2) binding, helicase ability, and ATM-mediated phosphorylation of UPF1 (upstream frameshift 1). We also identify two GMD-specific factors: an RNA-binding protein, YBX1 (Y-box-binding protein 1), and an endoribonuclease, HRSP12 (heat-responsive protein 12). In particular, using HRSP12 variants, which are known to disrupt trimerization of HRSP12, we show that HRSP12 plays an essential role in the formation of a functionally active GMD complex. Moreover, we determine the hierarchical recruitment of GMD factors to target mRNAs. Finally, our genome-wide analysis shows that GMD targets a variety of transcripts, implicating roles in a wide range of cellular processes, including immune responses.
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Affiliation(s)
- Ok Hyun Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Mira Yu
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyoung-Tae An
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jesang Ko
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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Zhao F, Wang N, Yi Y, Lin P, Tang K, Wang A, Jin Y. Knockdown of CREB3/Luman by shRNA in Mouse Granulosa Cells Results in Decreased Estradiol and Progesterone Synthesis and Promotes Cell Proliferation. PLoS One 2016; 11:e0168246. [PMID: 27973579 PMCID: PMC5156397 DOI: 10.1371/journal.pone.0168246] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/28/2016] [Indexed: 11/30/2022] Open
Abstract
Luman (also known as LZIP or CREB3) is a transcription factor and a member of the cAMP responsive element-binding (CREB) family proteins. Although Luman has been detected in apoptotic granulosa cells and disorganized atretic bodies, the physiological function of Luman in follicular development has not been reported. Our objective is to determine the role of Luman in folliculogenesis by knocking down Luman expression in mouse GCs (granulosa cells) using shRNA. Luman expression was successfully knocked down in mouse GCs at the mRNA and protein level, as confirmed by real-time quantitative PCR, western blot and immunofluorescence staining, respectively. Knockdown of Luman significantly decreased the concentrations of estradiol (E2) and progesterone (P4) in cell culture medium. Furthermore, Luman knockdown promoted cell proliferation but had no effect on cell apoptosis. To elucidate the regulatory mechanism underlying the effects of Luman knockdown on steroid synthesis and cell cycle, we measured the mRNA and protein expression levels of several related genes. The expression of Star, Cyp19a1, and Cyp1b1, which encode steroidogenic enzymes, was down-regulated, while that of Cyp11a1 and Runx2, which also encode steroidogenic enzymes, was up-regulated. The expression of the cell cycle factors Cyclin A1, Cyclin B1, Cyclin D2, and Cyclin E was significantly up-regulated. Among apoptosis-related genes, only Bcl-2 was down-regulated, while Caspase 3, Bax and p53 were not significantly affected, suggesting that Luman knockdown may regulate cell cycle activity and hormone secretion at the transcriptional and translational level in mouse GCs. The expression of two important genes associated with folliculogenesis in mouse GCs, Has2 and Ptgs2, were also significantly altered by Luman knockdown. In conclusion, the findings of this study indicate that Luman regulates mouse GCs modulation of steroid synthesis, cell cycle activity and other regulators of folliculogenesis.
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Affiliation(s)
- Fan Zhao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Nan Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanglei Yi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Pengfei Lin
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Keqiong Tang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Aihua Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yaping Jin
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail:
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10
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Kim J, Ko J. Human sLZIP promotes atherosclerosis via MMP-9 transcription and vascular smooth muscle cell migration. FASEB J 2014; 28:5010-21. [PMID: 25077563 DOI: 10.1096/fj.14-259218] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Atherosclerosis is a chronic inflammatory response of the vascular wall, and immune responses are involved in every phase of atherosclerosis, from initiation, to progression, and finally to plaque rupture. Cytokines are the major atherogenic mediators that promote plaque formation and progression by activation of inflammatory cells. They induce expressions of matrix metalloproteinases (MMPs), leading to vascular smooth muscle cell (VSMC) migration in atherosclerotic lesions. Although chronic inflammatory mediators, including tumor necrosis factor α (TNF-α) and MMPs, exacerbate atherosclerosis, the molecular mechanism of atherogenesis remains unclear. In this study we investigated the role of a novel transcription factor the human small leucine zipper protein (sLZIP) in TNF-α-induced MMP expression, VSMC migration, and atherosclerosis progression. The proinflammatory cytokine TNF-α enhanced sLZIP expression by 3-fold via activation of NF-κB signaling. sLZIP induced MMP-9 transcription and the proteolytic activity of MMP-9 by 2.8- and 3.2-fold (P< 0.05), respectively, in macrophages, leading to enhancement of VSMC migration by 2.7-fold (P<0.005). sLZIP(OE/+) (sLZIP transgenic); LDLR(-/-) mice fed a high-cholesterol diet exhibited enhanced arterial plaque formation and increased VSMC migration from the media into the intima by 2.8- and 2.6-fold (P<0.01), respectively, compared with atherosclerosis-prone LDLR(-/-) mice. These results indicate that human sLZIP plays a critical role in development of atherosclerosis and can be used as a therapeutic target molecule for treatment of atherosclerosis.
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Affiliation(s)
- Jeonghan Kim
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Jesang Ko
- Division of Life Sciences, Korea University, Seoul, South Korea
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Ying Z, Zhang R, Verge VMK, Misra V. Cloning and characterization of rat Luman/CREB3, a transcription factor highly expressed in nervous system tissue. J Mol Neurosci 2014; 55:347-54. [PMID: 24894591 DOI: 10.1007/s12031-014-0330-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/12/2014] [Indexed: 11/24/2022]
Abstract
Human Luman/CREB3 is a basic leucine zipper transcription factor involved in regulation of the unfolded protein response, dendritic cell maturation, and cell migration. But despite reported expression in primary sensory neurons, little is known about its role in the nervous system. To begin investigations into its role in the adult rat nervous system, the rat Luman/CREB3 coding sequence was isolated so its expression within the nervous system could be determined. The rat Luman/CREB3 clone contains a full-length open reading frame encoding 387 amino acids. The recombinant protein generated from this clone activated transcription in a manner equivalent to human Luman/CREB3 from a CAT reporter plasmid construct containing the unfolded protein response element. Quantitative RT-PCR revealed that rat Luman/CREB3 transcripts in a variety of rat tissues with the highest levels in nervous system tissue. In situ hybridization performed on tissue sections confirmed the findings and demonstrated that the Luman/CREB3 mRNA hybridization signal localizes to neurons and satellite glial cells in dorsal root ganglia, the cytoplasm of hepatocytes in liver, and the hippocampal pyramidal cell layers of CA1 and CA3 and the granular cell layer of the dentate gyrus. Collectively, these findings support a role for Luman/CREB3 in the regulation of nervous system function.
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Affiliation(s)
- Zhengxin Ying
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
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12
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Penzo M, Habiel DM, Ramadass M, Kew RR, Marcu KB. Cell migration to CXCL12 requires simultaneous IKKα and IKKβ-dependent NF-κB signaling. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1796-1804. [PMID: 24747690 DOI: 10.1016/j.bbamcr.2014.04.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 04/08/2014] [Accepted: 04/10/2014] [Indexed: 12/30/2022]
Abstract
CXCL12 and its unique receptor CXCR4, is critical for the homing of a variety of cell lineages during both development and tissue repair. CXCL12 is particularly important for the recruitment of hemato/lymphopoietic cells to their target organs. In conjunction with the damage-associated alarmin molecule HMGB1, CXCL12 mediates immune effector and stem/progenitor cell migration towards damaged tissues for subsequent repair. Previously, we showed that cell migration to HMGB1 simultaneously requires both IKKβ and IKKα-dependent NF-κB activation. IKKβ-mediated activation maintains sufficient expression of HMGB1's receptor RAGE, while IKKα-dependent NF-κB activation ensures continuous production of CXCL12, which complexes with HMGB1 to engage CXCR4. Here using fibroblasts and primary mature macrophages, we show that IKKβ and IKKα are simultaneously essential for cell migration in response to CXCL12 alone. Non-canonical NF-κB pathway subunits RelB and p52 are also both essential for cell migration towards CXCL12, suggesting that IKKα is required to drive non-canonical NF-κB signaling. Flow cytometric analyses of CXCR4 expression show that IKKβ, but not IKKα, is required to maintain a critical threshold level of this CXCL12 receptor. Time-lapse video microscopy experiments in primary MEFs reveal that IKKα is required both for polarization of cells towards a CXCL12 gradient and to establish a basal level of velocity towards CXCL12. In addition, CXCL12 modestly up-regulates IKKα-dependent p52 nuclear translocation and IKKα-dependent expression of the CXCL12 gene. On the basis of our collective results we posit that IKKα is needed to maintain the basal expression of a critical protein co-factor required for cell migration to CXCL12.
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Affiliation(s)
- Marianna Penzo
- CRBA Laboratory and Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
- Biochemistry and Cell Biology Dept., Stony Brook University, Stony Brook, New York 11794-5215, USA
| | - David M Habiel
- Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, NY, 11794 USA
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, New York 11794, USA
| | - Mahalakshmi Ramadass
- Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, NY, 11794 USA
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, New York 11794, USA
| | - Richard R Kew
- Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, NY, 11794 USA
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, New York 11794, USA
| | - Kenneth B Marcu
- Biochemistry and Cell Biology Dept., Stony Brook University, Stony Brook, New York 11794-5215, USA
- Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, NY, 11794 USA
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, New York 11794, USA
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13
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DenBoer LM, Iyer A, McCluggage ARR, Li Y, Martyn AC, Lu R. JAB1/CSN5 inhibits the activity of Luman/CREB3 by promoting its degradation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:921-9. [PMID: 23583719 DOI: 10.1016/j.bbagrm.2013.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 04/01/2013] [Accepted: 04/03/2013] [Indexed: 12/26/2022]
Abstract
Luman/CREB3 (also called LZIP) is an endoplasmic reticulum (ER)-bound transcription factor that has been implicated in the ER stress response. In this study, we used the region of Luman containing the basic DNA-binding domain as bait in a yeast two-hybrid screen and identified the Jun activation domain-binding protein 1 (JAB1) or the COP9 signalosome complex unit 5 (CSN5) as an interacting protein. We confirmed their direct binding by glutathione S-transferase pull-down assays, and verified the existence of such interaction in the cellular environment by mammalian two-hybrid and co-immunoprecipitation assays. Deletion mapping studies revealed that the MPN domain in JAB1 was essential and sufficient for the binding. JAB1 also colocalized with Luman in transfected cells. More interestingly, the nuclear form of Luman was shown to promote the translocation of JAB1 into the nucleus. We found that overexpression of JAB1 shortened the half-life of Luman by 67%, and repressed its transactivation function on GAL4 and unfolded protein response element (UPRE)-containing promoters. We therefore propose that JAB1 is a novel binding partner of Luman, which negatively regulates the activity of Luman by promoting its degradation.
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Affiliation(s)
- Lisa M DenBoer
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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14
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Yang Y, Jin Y, Martyn AC, Lin P, Song Y, Chen F, Hu L, Cui C, Li X, Li Q, Lu R, Wang A. Expression pattern implicates a potential role for luman recruitment factor in the process of implantation in uteri and development of preimplantation embryos in mice. J Reprod Dev 2013; 59:245-51. [PMID: 23400243 PMCID: PMC3934142 DOI: 10.1262/jrd.2012-137] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Luman/CREB3 recruitment factor (LRF or CREBRF) was identified as a regulator of Luman
(or CREB3) that is involved in the unfolded protein response during endoplasmic reticulum
stress. Luman is implicated in a multitude of functions ranging from viral infection and
immunity to cancer. The biological function of LRF, however, is unknown. In this paper, we
report that uteri of pregnant mice and embryos displayed enhanced LRF expression at all
stages, and the expressed LRF was found to be localized specifically at implantation
sites. On the other hand, uteri of mice induced for delayed implantation or pseudopregnant
mice showed low levels of LRF expression, suggesting that LRF mediates uterine receptivity
during implantation. Further, expression of LRF was found to be modulated by steroid
hormones such as progesterone and estradiol. This study thereby identifies a potential
role for LRF in the process of implantation in uteri and development of preimplantation
embryos in mice.
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Affiliation(s)
- Yanzhou Yang
- Key Open Laboratory of Animal Biotechnology, Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling Shaanxi 712100, PR China
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15
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Chan CP, Kok KH, Jin DY. CREB3 subfamily transcription factors are not created equal: Recent insights from global analyses and animal models. Cell Biosci 2011; 1:6. [PMID: 21711675 PMCID: PMC3116243 DOI: 10.1186/2045-3701-1-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 02/17/2011] [Indexed: 01/07/2023] Open
Abstract
The CREB3 subfamily of membrane-bound bZIP transcription factors has five members in mammals known as CREB3 and CREB3L1-L4. One current model suggests that CREB3 subfamily transcription factors are similar to ATF6 in regulated intramembrane proteolysis and transcriptional activation. Particularly, they were all thought to be proteolytically activated in response to endoplasmic reticulum (ER) stress to stimulate genes that are involved in unfolded protein response (UPR). Although the physiological inducers of their proteolytic activation remain to be identified, recent findings from microarray analyses, RNAi screens and gene knockouts not only demonstrated their critical roles in regulating development, metabolism, secretion, survival and tumorigenesis, but also revealed cell type-specific patterns in the activation of their target genes. Members of the CREB3 subfamily show differential activity despite their structural similarity. The spectrum of their biological function expands beyond ER stress and UPR. Further analyses are required to elucidate the mechanism of their proteolytic activation and the molecular basis of their target recognition.
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Affiliation(s)
- Chi-Ping Chan
- Department of Biochemistry and State Key Laboratory for Liver Research, LKS Faculty of Medicine, The University of Hong Kong.
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16
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Kim HC, Choi KC, Choi HK, Kang HB, Kim MJ, Lee YH, Lee OH, Lee J, Kim YJ, Jun W, Jeong JW, Yoon HG. HDAC3 selectively represses CREB3-mediated transcription and migration of metastatic breast cancer cells. Cell Mol Life Sci 2010; 67:3499-510. [PMID: 20473547 PMCID: PMC11115716 DOI: 10.1007/s00018-010-0388-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 04/19/2010] [Accepted: 04/23/2010] [Indexed: 12/19/2022]
Abstract
We identified CREB3 as a novel HDAC3-interacting protein in a yeast two-hybrid screen for HDAC3-interacting proteins. Among all class I HDACs, CREB3 specifically interacts with HDAC3, in vitro and in vivo. HDAC3 efficiently inhibited CREB3-enhanced NF-κB activation, whereas the other class I HDACs did not alter NF-κB-dependent promoter activities or the expression of NF-κB target genes. Importantly, both knock-down of CREB3 and overexpression of HDAC3 suppressed the transcriptional activation of the novel CREB3-regulated gene, CXCR4. Furthermore, CREB3 was shown to bind to the CRE element in the CXCR4 promoter and to activate the transcription of the CXCR4 gene by causing dissociation of HDAC3 and subsequently increasing histone acetylation. Importantly, both the depletion of HDAC3 and the overexpression of CREB3 substantially increased the migration of MDA-MB-231 metastatic breast cancer cells. Taken together, these findings suggest that HDAC3 selectively represses CREB3-mediated transcriptional activation and chemotactic signalling in human metastatic breast cancer cells.
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Affiliation(s)
- Han-Cheon Kim
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung-Chul Choi
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Hyo-Kyoung Choi
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Hee-Bum Kang
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Mi-Jeong Kim
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Yoo-Hyun Lee
- Department of Food and Nutrition, The University of Suwon, Suwon, Korea
| | - Ok-Hee Lee
- Severance Hospital Integrative Research Institute for Cerebral and Cardiovascular Disease, Yonsei University Health System, Seoul, Korea
| | - Jeongmin Lee
- Department of Medical Nutrition, Kyung Hee University, Yongin-si, Kyunggi-do 446-701 South Korea
| | - Young Jun Kim
- Department of Food and Biotechnology, Korea University, Jochiwon-eup, Yeongi-gun, Chungnam Korea
| | - Woojin Jun
- Department of Food and Nutrition, Chonnam National University, Gwangju, Korea
| | - Jae-Wook Jeong
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Ho-Geun Yoon
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
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Kang H, Kim YS, Ko J. A novel isoform of human LZIP negatively regulates the transactivation of the glucocorticoid receptor. Mol Endocrinol 2009; 23:1746-57. [PMID: 19779205 DOI: 10.1210/me.2009-0009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The human leucine zipper protein (LZIP) is a basic leucine zipper transcription factor that is involved in leukocyte migration, tumor suppression, and endoplasmic reticulum stress-associated protein degradation. Although evidence suggests a diversity of roles for LZIP, its function is not fully understood, and the subcellular localization of LZIP is still controversial. We identified a novel isoform of LZIP and characterized its function in ligand-induced transactivation of the glucocorticoid receptor (GR) in COS-7 and HeLa cells. A novel isoform of human LZIP designated as "sLZIP" contains a deleted putative transmembrane domain (amino acids 229-245) of LZIP and consists of 345 amino acids. LZIP and sLZIP were ubiquitously expressed in a variety of cell lines and tissues, with LZIP being much more common. sLZIP was mainly localized in the nucleus, whereas LZIP was located in the cytoplasm. Unlike LZIP, sLZIP was not involved in the chemokine-mediated signal pathway. sLZIP recruited histone deacetylases (HDACs) to the promoter region of the mouse mammary tumor virus luciferase reporter gene and enhanced the activities of HDACs, resulting in suppression of expression of the GR target genes. Our findings suggest that sLZIP functions as a negative regulator in glucocorticoid-induced transcriptional activation of GR by recruitment and activation of HDACs.
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Affiliation(s)
- Hyereen Kang
- School of Life Sciences and Biotechnology, Korea University, 5-1 Anam-dong, Seongbuk-gu, Seoul 136-701, Korea
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18
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Lee MMK, Wong YH. CCR1-mediated activation of nuclear factor-κB in THP-1 monocytic cells involvespertussistoxin-insensitive Gα14and Gα16signaling cascades. J Leukoc Biol 2009; 86:1319-29. [DOI: 10.1189/jlb.0209052] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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19
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Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM. OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif. BMC Bioinformatics 2009; 10:208. [PMID: 19583839 PMCID: PMC2718928 DOI: 10.1186/1471-2105-10-208] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 07/07/2009] [Indexed: 12/29/2022] Open
Abstract
Background DNA sequence binding motifs for several important transcription factors happen to be self-overlapping. Many of the current regulatory site identification methods do not explicitly take into account the overlapping sites. Moreover, most methods use arbitrary thresholds and fail to provide a biophysical interpretation of statistical quantities. In addition, commonly used approaches do not include the location of a site with respect to the transcription start site (TSS) in an integrated probabilistic framework while identifying sites. Ignoring these features can lead to inaccurate predictions as well as incorrect design and interpretation of experimental results. Results We have developed a tool based on a Hidden Markov Model (HMM) that identifies binding location of transcription factors with preference for self-overlapping DNA motifs by combining the effects of their alternative binding modes. Interpreting HMM parameters as biophysical quantities, this method uses the occupancy probability of a transcription factor on a DNA sequence as the discriminant function, earning the algorithm the name OHMM: Occupancy via Hidden Markov Model. OHMM learns the classification threshold by training emission probabilities using unaligned sequences containing known sites and estimating transition probabilities to reflect site density in all promoters in a genome. While identifying sites, it adjusts parameters to model site density changing with the distance from the transcription start site. Moreover, it provides guidance for designing padding sequences in gel shift experiments. In the context of binding sites to transcription factor NF-κB, we find that the occupancy probability predicted by OHMM correlates well with the binding affinity in gel shift experiments. High evolutionary conservation scores and enrichment in experimentally verified regulated genes suggest that NF-κB binding sites predicted by our method are likely to be functional. Conclusion Our method deals specifically with identifying locations with multiple overlapping binding sites by computing the local occupancy of the transcription factor. Moreover, considering OHMM as a biophysical model allows us to learn the classification threshold in a principled manner. Another feature of OHMM is that we allow transition probabilities to change with location relative to the TSS. OHMM could be used to predict physical occupancy, and provides guidance for proper design of gel-shift experiments. Based upon our predictions, new insights into NF-κB function and regulation and possible new biological roles of NF-κB were uncovered.
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Affiliation(s)
- Amar Drawid
- BioMAPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ, USA.
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Sung HJ, Kim YS, Kang H, Ko J. Human LZIP induces monocyte CC chemokine receptor 2 expression leading to enhancement of monocyte chemoattractant protein 1/CCL2-induced cell migration. Exp Mol Med 2009; 40:332-8. [PMID: 18587271 DOI: 10.3858/emm.2008.40.3.332] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Chemokines and chemokine receptors play a role in migration of circulating leukocytes to the region of inflammation. Human LZIP is an uncharacterized transcription factor and is known to participate in leukotactin (Lkn)-1/CCL15-induced cell migration. We investigated the role of human LZIP in expression of CC chemokine receptors (CCRs) and its involvement in monocyte migration. RNase protection analysis showed that LZIP increased mRNA expression of CCR2 and CCR1 in THP-1 cells. Surface expressions of both CCR2 and CCR1 were also increased by LZIP. Results from an electrophoretic mobility shift assay showed that LZIP binds to the C/EBP element in the CCR2 promoter. LZIP also enhanced the chemotactic activities of monocyte chemoattractant protein-1/CCL2 and Lkn-1. These results suggest that LZIP regulates expression of chemokine receptors that are involved in monocyte migration.
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Affiliation(s)
- Ho Joong Sung
- School of Life Sciences and Biotechnology, Korea University, Seoul, Korea
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21
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A novel protein, Luman/CREB3 recruitment factor, inhibits Luman activation of the unfolded protein response. Mol Cell Biol 2008; 28:3952-66. [PMID: 18391022 DOI: 10.1128/mcb.01439-07] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Luman/CREB3 (also called LZIP) is an endoplasmic reticulum (ER)-bound cellular transcription factor. It has been implicated in the mammalian unfolded protein response (UPR), as well as herpes simplex virus reactivation from latency in sensory neurons. Here, we report the identification of a novel Luman recruitment factor (LRF). Like Luman, LRF is a UPR-responsive basic-region leucine zipper protein that is prone to proteasomal degradation. Being a highly unstable protein, LRF interacts with Luman through the leucine zipper region and promotes Luman degradation. LRF was found to recruit the nuclear form of Luman to discrete nuclear foci, which overlap with the nuclear receptor coactivator GRIP1 bodies, and repress the transactivation activity of Luman. Compared to LRF+/+ mouse embryonic fibroblast (MEF) cells, the levels of CHOP, EDEM, and Herp were elevated in LRF-/- MEF cells. We propose that LRF is a negative regulator of the UPR. For Luman, it may represent another level of regulation following Luman proteolytic cleavage on the ER and nuclear translocation. In addition to inducing rapid Luman turnover, LRF may repress the transactivation potential of Luman by sequestering it in the LRF nuclear bodies away from key cofactors (such as HCF-1) that are required for transcriptional activation.
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Palumbo R, Galvez BG, Pusterla T, De Marchis F, Cossu G, Marcu KB, Bianchi ME. Cells migrating to sites of tissue damage in response to the danger signal HMGB1 require NF-kappaB activation. ACTA ACUST UNITED AC 2008; 179:33-40. [PMID: 17923528 PMCID: PMC2064729 DOI: 10.1083/jcb.200704015] [Citation(s) in RCA: 214] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Tissue damage is usually followed by healing, as both differentiated and stem cells migrate to replace dead or damaged cells. Mesoangioblasts (vessel-associated stem cells that can repair muscles) and fibroblasts migrate toward soluble factors released by damaged tissue. Two such factors are high mobility group box 1 (HMGB1), a nuclear protein that is released by cells undergoing unscheduled death (necrosis) but not by apoptotic cells, and stromal derived factor (SDF)–1/CXCL12. We find that HMGB1 activates the canonical nuclear factor κB (NF-κB) pathway via extracellular signal-regulated kinase phosphorylation. NF-κB signaling is necessary for chemotaxis toward HMGB1 and SDF-1/CXCL12, but not toward growth factor platelet-derived growth factor, formyl-met-leu-phe (a peptide that mimics bacterial invasion), or the archetypal NF-κB–activating signal tumor necrosis factor α. In dystrophic mice, mesoangioblasts injected into the general circulation ingress inefficiently into muscles if their NF-κB signaling pathway is disabled. These findings suggest that NF-κB signaling controls tissue regeneration in addition to early events in inflammation.
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Affiliation(s)
- Roberta Palumbo
- Chromatin Dynamics Unit, Stem Cell Research Institute, Istituto Scientifico San Raffaele, 20132 Milan, Italy
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