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Zhou C, Yang G, Meng P, Qin W, Li Y, Lin Z, Hui W, Zhang H, Lu F. Identification and engineering of the aprE regulatory region and relevant regulatory proteins in Bacillus licheniformis 2709. Enzyme Microb Technol 2024; 172:110310. [PMID: 37925770 DOI: 10.1016/j.enzmictec.2023.110310] [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: 05/10/2023] [Revised: 08/01/2023] [Accepted: 08/27/2023] [Indexed: 11/07/2023]
Abstract
Bacillus licheniformis 2709 is the main industrial producer of alkaline protease (AprE), but its biosynthesis is strictly controlled by a highly sophisticated transcriptional network. In this study, the UP elements of aprE located 74-98, 98-119 and 140-340 bp upstream of the transcriptional start site (TSS) were identified, which presented obvious effects on the transcription of aprE. To further analyze the transcriptional mechanism, the specific proteins binding to the approximately 500-bp DNA sequences were subsequently captured by reverse-chromatin immunoprecipitation (reverse-ChIP) and DNA pull-down (DPD) assays, which captured the transcriptional factors CggR, FruR, and YhcZ. The study demonstrated that CggR, FruR and YhcZ had no significant effect on cell growth and aprE expression. Then, aprE expression was significantly enhanced by deleting a potential negative regulatory factor binding site in the genome. The AprE enzyme activity in shake flasks of the genomic mutant BL ∆1 was 47% higher than in the original strain, while the aprE transcription level increased 3.16 times. The protocol established in this study provides a valuable reference for the high-level production of proteins in other Bacillus species. At the same time, it will help reveal the molecular mechanism of the transcriptional regulatory network of aprE and provide important theoretical guidance for further enhancing the yield of AprE.
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Affiliation(s)
- Cuixia Zhou
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China; Key laboratory of industrial fermentation microbiology, Ministry of education, College of biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Guangcheng Yang
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China.
| | - Panpan Meng
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China
| | - Weishuai Qin
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China
| | - Yanyan Li
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China
| | - Zhenxian Lin
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China
| | - Wei Hui
- Key laboratory of industrial fermentation microbiology, Ministry of education, College of biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Huitu Zhang
- Key laboratory of industrial fermentation microbiology, Ministry of education, College of biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Fuping Lu
- Key laboratory of industrial fermentation microbiology, Ministry of education, College of biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China.
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Dejosez M, Dall'Agnese A, Ramamoorthy M, Platt J, Yin X, Hogan M, Brosh R, Weintraub AS, Hnisz D, Abraham BJ, Young RA, Zwaka TP. Regulatory architecture of housekeeping genes is driven by promoter assemblies. Cell Rep 2023; 42:112505. [PMID: 37182209 PMCID: PMC10329844 DOI: 10.1016/j.celrep.2023.112505] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/22/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Genes that are key to cell identity are generally regulated by cell-type-specific enhancer elements bound by transcription factors, some of which facilitate looping to distant gene promoters. In contrast, genes that encode housekeeping functions, whose regulation is essential for normal cell metabolism and growth, generally lack interactions with distal enhancers. We find that Ronin (Thap11) assembles multiple promoters of housekeeping and metabolic genes to regulate gene expression. This behavior is analogous to how enhancers are brought together with promoters to regulate cell identity genes. Thus, Ronin-dependent promoter assemblies provide a mechanism to explain why housekeeping genes can forgo distal enhancer elements and why Ronin is important for cellular metabolism and growth control. We propose that clustering of regulatory elements is a mechanism common to cell identity and housekeeping genes but is accomplished by different factors binding distinct control elements to establish enhancer-promoter or promoter-promoter interactions, respectively.
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Affiliation(s)
- Marion Dejosez
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Alessandra Dall'Agnese
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mahesh Ramamoorthy
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Jesse Platt
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Xing Yin
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Megan Hogan
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Ran Brosh
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brian J Abraham
- St. Jude Research Children's Hospital, Memphis, TN 38105, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Thomas P Zwaka
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA.
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4
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Luo X, Xia Y, Li XD, Wang JY. The effect of AP-2δ on transcription of the Prestin gene in HEI-OC1 cells upon oxidative stress. Cell Mol Biol Lett 2019; 24:45. [PMID: 31297132 PMCID: PMC6595603 DOI: 10.1186/s11658-019-0170-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/07/2019] [Indexed: 12/18/2022] Open
Abstract
Background The study aimed to investigate the effect of oxidative stress on Prestin expression, and explore the transcription factors (TFs) that are involved in regulating the expression of Prestin in House Ear Institute-Organ of Corti 1 (HEI-OC1) cells upon oxidative stress. Methods Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were used to detect the expression level of Prestin. Reverse chromatin immunoprecipitation (reverse ChIP) assay was performed to identify proteins that could bind to the Prestin gene. Small interfering RNA (siRNA) and chromatin immunoprecipitation (ChIP) experiments were used to further verify the results. HEI-OC1 cells were incubated with four different concentrations of tert-butyl hydroperoxide (t-BHP) for 24 h or 48 h to construct the oxidative stress model. Results Oxidative stress induced Prestin increase at the mRNA level but with a concomitant decrease at the protein level. TF activating enhancer binding protein-2δ (AP-2δ) screened by reverse ChIP assay was demonstrated to bind to transcriptional start site 1441 of the Prestin promoter region and negatively regulate the expression of Prestin by siRNA and ChIP experiments. Furthermore, AP-2δ was down-regulated under oxidative stress. Conclusions In conclusion, oxidative stress inhibits the expression of Prestin protein, and the transcription mechanism is triggered to compensate for the loss of Prestin protein. AP-2δ is one of the important TFs that suppresses transcription of the Prestin gene, and AP-2δ suppression further boosted Prestin mRNA activation under oxidative stress. Electronic supplementary material The online version of this article (10.1186/s11658-019-0170-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xuan Luo
- 1Department of Labor Health and Environmental Hygiene, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510310 China
| | - Yun Xia
- 2Department of Labor Health and Environmental Hygiene, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510310 China
| | - Xu-Dong Li
- Key Laboratory, Occupational Disease Prevention and Control of Hospital of Guangdong Province, Guangzhou, 510300 China
| | - Jun-Yi Wang
- 1Department of Labor Health and Environmental Hygiene, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510310 China
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5
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Köger N, Brieger A, Hinrichsen IM, Zeuzem S, Plotz G. Analysis of MUTYH alternative transcript expression, promoter function, and the effect of human genetic variants. Hum Mutat 2019; 40:472-482. [PMID: 30653782 DOI: 10.1002/humu.23709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 12/14/2018] [Accepted: 01/14/2019] [Indexed: 01/07/2023]
Abstract
The human DNA repair gene MUTYH, whose mutational loss causes a colorectal polyposis and cancer predisposition, contains three alternative first exons. In order to analyze alternative transcription and the effect of genetic alterations found in humans, we established a cell-based minigene experimental model supporting transcription and splicing and thoroughly verified its functionality. We identified highly conserved promoter areas and inactivated them in the minigene, and also introduced six human variants. Moreover, the potential contribution of CpG island methylation and specific transcription factors on MUTYH transcription was addressed. The findings allowed to attribute regulatory roles to three conserved motifs in the promoter: an M4 motif, a transcription factor IIB recognition element, and a GC box. Moreover, the data showed that three patient variants compromised MUTYH expression and therefore have the potential to cause pathogenic effects. We did not find evidence for a biologically relevant contribution of CpG island methylation or a direct transcriptional activation by DNA damage. Besides insight into the regulation of MUTYH transcription, the work therefore provides a functional MUTYH minigene experimental system suitable as a diagnostic tool for analyzing patient variants, and a functional map of the promotor that also can facilitate pathogenicity classifications of human variants.
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Affiliation(s)
- Nicole Köger
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinikum, Frankfurt, Germany
| | - Angela Brieger
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinikum, Frankfurt, Germany
| | - Inga M Hinrichsen
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinikum, Frankfurt, Germany
| | - Stefan Zeuzem
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinikum, Frankfurt, Germany
| | - Guido Plotz
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinikum, Frankfurt, Germany
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Boutboul D, Kuehn HS, Van de Wyngaert Z, Niemela JE, Callebaut I, Stoddard J, Lenoir C, Barlogis V, Farnarier C, Vely F, Yoshida N, Kojima S, Kanegane H, Hoshino A, Hauck F, Lhermitte L, Asnafi V, Roehrs P, Chen S, Verbsky JW, Calvo KR, Husami A, Zhang K, Roberts J, Amrol D, Sleaseman J, Hsu AP, Holland SM, Marsh R, Fischer A, Fleisher TA, Picard C, Latour S, Rosenzweig SD. Dominant-negative IKZF1 mutations cause a T, B, and myeloid cell combined immunodeficiency. J Clin Invest 2018; 128:3071-3087. [PMID: 29889099 DOI: 10.1172/jci98164] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 04/17/2018] [Indexed: 01/20/2023] Open
Abstract
Ikaros/IKZF1 is an essential transcription factor expressed throughout hematopoiesis. IKZF1 is implicated in lymphocyte and myeloid differentiation and negative regulation of cell proliferation. In humans, somatic mutations in IKZF1 have been linked to the development of B cell acute lymphoblastic leukemia (ALL) in children and adults. Recently, heterozygous germline IKZF1 mutations have been identified in patients with a B cell immune deficiency mimicking common variable immunodeficiency. These mutations demonstrated incomplete penetrance and led to haploinsufficiency. Herein, we report 7 unrelated patients with a novel early-onset combined immunodeficiency associated with de novo germline IKZF1 heterozygous mutations affecting amino acid N159 located in the DNA-binding domain of IKZF1. Different bacterial and viral infections were diagnosed, but Pneumocystis jirovecii pneumonia was reported in all patients. One patient developed a T cell ALL. This immunodeficiency was characterized by innate and adaptive immune defects, including low numbers of B cells, neutrophils, eosinophils, and myeloid dendritic cells, as well as T cell and monocyte dysfunctions. Notably, most T cells exhibited a naive phenotype and were unable to evolve into effector memory cells. Functional studies indicated these mutations act as dominant negative. This defect expands the clinical spectrum of human IKZF1-associated diseases from somatic to germline, from haploinsufficient to dominant negative.
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Affiliation(s)
- David Boutboul
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Paris, France
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Zoé Van de Wyngaert
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Paris, France.,University Paris Descartes Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Julie E Niemela
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Isabelle Callebaut
- Centre National de la Recherche Scientifique UMR 7590, Sorbonne Universities, University Pierre et Marie Curie-Paris 6-MNHN-IRD-IUC, Paris, France
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Christelle Lenoir
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Paris, France
| | - Vincent Barlogis
- Department of Paediatric Haematology-Oncology, La Timone Hospital, Marseille, France
| | - Catherine Farnarier
- Assistance Publique - Hôpitaux de Marseille (APHM) Hôpital Timone Enfants, Service d'Immunologie - Marseille Immunopôle, Marseille, France
| | - Frédéric Vely
- Aix Marseille University, APHM, CNRS, Inserm, Centre d'Immunologie de Marseille-Luminy (CIML), Hôpital Timone Enfants, Service d'Immunologie - Marseille Immunopôle, Marseille, France
| | - Nao Yoshida
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hirokazu Kanegane
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akihiro Hoshino
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fabian Hauck
- Department of Pediatric Immunology and Rheumatology, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Ludovic Lhermitte
- University Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Inserm 1151 and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (APHP), Necker-Enfants Malades Hospital, Paris, France
| | - Vahid Asnafi
- University Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Inserm 1151 and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (APHP), Necker-Enfants Malades Hospital, Paris, France
| | - Philip Roehrs
- Levine Children's Hospital, Carolinas Healthcare System, Charlotte, North Carolina, USA
| | - Shaoying Chen
- Department of Pediatrics, Division of Rheumatology, Medical College of Wisconsin, Madison, Wisconsin, USA
| | - James W Verbsky
- Department of Pediatrics, Division of Rheumatology, Medical College of Wisconsin, Madison, Wisconsin, USA
| | - Katherine R Calvo
- Hematology section, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Ammar Husami
- Division of Human Genetics and Division of Immune Deficiency and Bone Marrow Transplant, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Kejian Zhang
- Division of Human Genetics and Division of Immune Deficiency and Bone Marrow Transplant, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Joseph Roberts
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - David Amrol
- University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - John Sleaseman
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Amy P Hsu
- Laboratory of Clinical Infectious Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Steven M Holland
- Laboratory of Clinical Infectious Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Rebecca Marsh
- Division of Human Genetics and Division of Immune Deficiency and Bone Marrow Transplant, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Alain Fischer
- University Paris Descartes Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, APHP, Paris, France.,Collège de France, Paris, France
| | - Thomas A Fleisher
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Capucine Picard
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Paris, France.,Centre d'Etude des Déficits Immunitaires, Necker-Enfants Malades Hospital, APHP, Paris, France
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Inserm UMR 1163, Paris, France
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
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