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Troutman TD, Bennett H, Sakai M, Seidman JS, Heinz S, Glass CK. Purification of mouse hepatic non-parenchymal cells or nuclei for use in ChIP-seq and other next-generation sequencing approaches. STAR Protoc 2021; 2:100363. [PMID: 33748781 PMCID: PMC7960533 DOI: 10.1016/j.xpro.2021.100363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Significant advancements in understanding disease mechanisms can occur through combined analysis of next-generation sequencing datasets generated using purified cell populations. Here, we detail our optimized protocol for purification of mouse hepatic macrophages (or other liver non-parenchymal populations) suitable for use in various next-generation sequencing protocols. An alternative framework is described for sorting pre-fixed hepatic nuclei populations. This strategy has the advantage of rapidly preserving the nuclei and can facilitate success with ChIP-seq for more challenging molecules. For complete details on the use and execution of these protocols, please refer to Muse et al. (2018), Sakai et al. (2019), and Seidman et al. (2020).
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Affiliation(s)
- Ty D. Troutman
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hunter Bennett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Biochemistry & Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
| | - Jason S. Seidman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sven Heinz
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christopher K. Glass
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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2
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Bartlett SL, Diel DG, Wang L, Zec S, Laverack M, Martins M, Caserta LC, Killian ML, Terio K, Olmstead C, Delaney MA, Stokol T, Ivančić M, Jenkins-Moore M, Ingerman K, Teegan T, McCann C, Thomas P, McAloose D, Sykes JM, Calle PP. SARS-COV-2 INFECTION AND LONGITUDINAL FECAL SCREENING IN MALAYAN TIGERS ( PANTHERA TIGRIS JACKSONI), AMUR TIGERS ( PANTHERA TIGRIS ALTAICA ), AND AFRICAN LIONS ( PANTHERA LEO KRUGERI) AT THE BRONX ZOO, NEW YORK, USA. J Zoo Wildl Med 2021; 51:733-744. [PMID: 33480553 DOI: 10.1638/2020-0171] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged as the cause of a global pandemic in 2019-2020. In March 2020, New York City became the epicenter in the United States for the pandemic. On 27 March 2020, a Malayan tiger (Panthera tigris jacksoni) at the Bronx Zoo in New York City developed a cough and wheezing with subsequent inappetence. Over the next week, an additional Malayan tiger and two Amur tigers (Panthera tigris altaica) in the same building and three lions (Panthera leo krugeri) in a separate building also became ill. The index case was anesthetized for diagnostic workup. Physical examination and bloodwork results were unremarkable. Thoracic radiography and ultrasonography revealed a bronchial pattern with peribronchial cuffing and mild lung consolidation with alveolar-interstitial syndrome, respectively. SARS-CoV-2 RNA was identified by real-time, reverse transcriptase PCR (rRT-PCR) on oropharyngeal and nasal swabs and tracheal wash fluid. Cytologic examination of tracheal wash fluid revealed necrosis, and viral RNA was detected in necrotic cells by in situ hybridization, confirming virus-associated tissue damage. SARS-CoV-2 was isolated from the tracheal wash fluid of the index case, as well as the feces from one Amur tiger and one lion. Fecal viral RNA shedding was confirmed in all seven clinical cases and an asymptomatic Amur tiger. Respiratory signs abated within 1-5 days for most animals, although they persisted intermittently for 16 days in the index case. Fecal RNA shedding persisted for as long as 35 days beyond cessation of respiratory signs. This case series describes the clinical presentation, diagnostic evaluation, and management of tigers and lions infected with SARS-CoV-2 and describes the duration of viral RNA fecal shedding in these cases. This report documents the first known natural transmission of SARS-CoV-2 from humans to nondomestic felids.
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Affiliation(s)
| | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | | | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Mathias Martins
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Leonardo Cardia Caserta
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Veterinary Services, United States Department of Agriculture, Ames, IA 50010, USA
| | - Karen Terio
- Zoological Pathology Program, College of Veterinary Medicine, University of Illinois, Brookfield, IL 60513, USA
| | - Colleen Olmstead
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | - Martha A Delaney
- Zoological Pathology Program, College of Veterinary Medicine, University of Illinois, Brookfield, IL 60513, USA
| | - Tracy Stokol
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Melinda Jenkins-Moore
- National Veterinary Services Laboratories, Veterinary Services, United States Department of Agriculture, Ames, IA 50010, USA
| | | | - Taryn Teegan
- Wildlife Conservation Society, Bronx, NY 10460, USA
| | | | | | | | - John M Sykes
- Wildlife Conservation Society, Bronx, NY 10460, USA
| | - Paul P Calle
- Wildlife Conservation Society, Bronx, NY 10460, USA
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Luo Q, Liu R, Zeng L, Wu Y, Jiang Y, Yang Q, Nie Q. Isolation and molecular characterization of NtMYB4a, a putative transcription activation factor involved in anthocyanin synthesis in tobacco. Gene 2020; 760:144990. [PMID: 32721476 DOI: 10.1016/j.gene.2020.144990] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 02/08/2023]
Abstract
The MYB transcription factors are involved in the regulation of plant secondary metabolism, cell development and morphogenesis, and stress response. Here, a full-length, 816-bp NtMYB4a cDNA, which encodes a protein comprising 271 amino acids, was isolated from tobacco leaves. Phylogenetic analysis revealed that NtMYB4a is most similar to Nicotiana. attenuata MYB4, followed by Eriobotrya japonica MYB4, and NtMYB4a clustered with transcriptional activators rather than repressors. Subcellular localization assays showed that NtMYB4 localized in the nucleus, membrane, and cytoplasm. Expression analyses revealed differential expression of NtMYB4a among different tissues and organs and between different developmental stages, with most expression occurring in the stems and leaves during the full-bloom stage. Moreover, NtMYB4a expression was induced by cold, NaCl, PEG, abscisic acid, methyl jasmonate, and dark stressors, and the expression patterns and maximum expression levels varied with the type of stress. Overexpression of NtMYB4a upregulated NtPAL, Nt4CL, NtCHS, NtCHI, NtF3H, NtDFR, NtANS, and NtUFGT, which resulted in increased anthocyanin content in the tobacco corolla and darker colors. However, CRISPR/Cas9-mediated knockout of NtMYB4a downregulated NtPAL, NtC4H, Nt4CL, NtCHS, NtCHI, NtF3H, NtANS, and NtUFGT, which resulted in reduced anthocyanin content, and lighter corolla colors. These results indicated that NtMYB4a positively regulates anthocyanin biosynthesis and is involved in abiotic stress responses in tobacco plants.
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Affiliation(s)
- Qian Luo
- Key Laboratory of Tobacco Quality in Guizhou Province, College of Tobacco, Guizhou University, Guiyang 550025, China
| | - Renxiang Liu
- Key Laboratory of Tobacco Quality in Guizhou Province, College of Tobacco, Guizhou University, Guiyang 550025, China
| | - Lugui Zeng
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Yuyao Wu
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Yue Jiang
- Key Laboratory of Tobacco Quality in Guizhou Province, College of Tobacco, Guizhou University, Guiyang 550025, China
| | - Qin Yang
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Qiong Nie
- Key Laboratory of Tobacco Quality in Guizhou Province, College of Tobacco, Guizhou University, Guiyang 550025, China; College of Agriculture, Guizhou University, Guiyang 550025, China.
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Hong Y, Wang Z, Shi H, Yao J, Liu X, Wang F, Zeng L, Xie Z, Zhu JK. Reciprocal regulation between nicotinamide adenine dinucleotide metabolism and abscisic acid and stress response pathways in Arabidopsis. PLoS Genet 2020; 16:e1008892. [PMID: 32569316 PMCID: PMC7332101 DOI: 10.1371/journal.pgen.1008892] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/02/2020] [Accepted: 05/27/2020] [Indexed: 12/28/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) is an essential coenzyme that has emerged as a central hub linking redox equilibrium and signal transduction in living organisms. The homeostasis of NAD is required for plant growth, development, and adaption to environmental cues. In this study, we isolated a chilling hypersensitive Arabidopsis thaliana mutant named qs-2 and identified the causal mutation in the gene encoding quinolinate synthase (QS) critical for NAD biosynthesis. The qs-2 mutant is also hypersensitive to salt stress and abscisic acid (ABA) but resistant to drought stress. The qs-2 mutant accumulates a reduced level of NAD and over-accumulates reactive oxygen species (ROS). The ABA-hypersensitivity of qs-2 can be rescued by supplementation of NAD precursors and by mutations in the ABA signaling components SnRK2s or RBOHF. Furthermore, ABA-induced over-accumulation of ROS in the qs-2 mutant is dependent on the SnRK2s and RBOHF. The expression of QS gene is repressed directly by ABI4, a transcription factor in the ABA response pathway. Together, our findings reveal an unexpected interplay between NAD biosynthesis and ABA and stress signaling, which is critical for our understanding of the regulation of plant growth and stress responses.
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Affiliation(s)
- Yechun Hong
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, P.R. China
| | - Zhen Wang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (ZW); (JKZ)
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, United States of America
| | - Juanjuan Yao
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, P.R. China
| | - Xue Liu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fuxing Wang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, P.R. China
| | - Liang Zeng
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhi Xie
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, P.R. China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail: (ZW); (JKZ)
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Bianchessi D, Ibba MC, Saletti V, Blasa S, Langella T, Paterra R, Cagnoli GA, Melloni G, Scuvera G, Natacci F, Cesaretti C, Finocchiaro G, Eoli M. Simultaneous Detection of NF1, SPRED1, LZTR1, and NF2 Gene Mutations by Targeted NGS in an Italian Cohort of Suspected NF1 Patients. Genes (Basel) 2020; 11:genes11060671. [PMID: 32575496 PMCID: PMC7349720 DOI: 10.3390/genes11060671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 12/30/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) displays overlapping phenotypes with other neurocutaneous diseases such as Legius Syndrome. Here, we present results obtained using a next generation sequencing (NGS) panel including NF1, NF2, SPRED1, SMARCB1, and LZTR1 genes on Ion Torrent. Together with NGS, the Multiplex Ligation-Dependent Probe Amplification Analysis (MLPA) method was performed to rule out large deletions/duplications in NF1 gene; we validated the MLPA/NGS approach using Sanger sequencing on DNA or RNA of both positive and negative samples. In our cohort, a pathogenic variant was found in 175 patients; the pathogenic variant was observed in NF1 gene in 168 cases. A SPRED1 pathogenic variant was also found in one child and in a one year old boy, both NF2 and LZTR1 pathogenic variants were observed; in addition, we identified five LZTR1 pathogenic variants in three children and two adults. Six NF1 pathogenic variants, that the NGS analysis failed to identify, were detected on RNA by Sanger. NGS allows the identification of novel mutations in five genes in the same sequencing run, permitting unambiguous recognition of disorders with overlapping phenotypes with NF1 and facilitating genetic counseling and a personalized follow-up.
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Affiliation(s)
- Donatella Bianchessi
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Maria Cristina Ibba
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (V.S.); (G.M.)
| | - Stefania Blasa
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza dell’Ateneo Nuovo, 1, 20126 Milan, Italy
| | - Tiziana Langella
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian, 20133 Milan, Italy
| | - Rosina Paterra
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Giulia Anna Cagnoli
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy; (G.A.C.); (F.N.); (C.C.)
| | - Giulia Melloni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (V.S.); (G.M.)
| | - Giulietta Scuvera
- Pediatric Highly Intensive Care Unit, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy;
| | - Federica Natacci
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy; (G.A.C.); (F.N.); (C.C.)
| | - Claudia Cesaretti
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, via Francesco Sforza 28, 20122 Milan, Italy; (G.A.C.); (F.N.); (C.C.)
| | - Gaetano Finocchiaro
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
| | - Marica Eoli
- Molecular Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Celoria 11, 20133 Milan, Italy; (D.B.); (M.C.I.); (S.B.); (T.L.); (R.P.); (G.F.)
- Correspondence:
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Sega P, Kruszka K, Szewc Ł, Szweykowska-Kulińska Z, Pacak A. Identification of transcription factors that bind to the 5'-UTR of the barley PHO2 gene. Plant Mol Biol 2020; 102:73-88. [PMID: 31745747 DOI: 10.1007/s11103-019-00932-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
In barley and other higher plants, phosphate homeostasis is maintained by a regulatory network involving the PHO2 (PHOSPHATE2) encoding ubiquitin-conjugating (UBC) E2 enzyme, the PHR1 (PHOSPHATE STARVATION RESPONSE 1) transcription factor (TF), IPS1 (INDUCED BYPHOSPHATESTARVATION1) RNA, and miR399. During phosphate ion (Pi) deprivation, PHR1 positively regulates MIR399 expression, after transcription and processing mature miR399 guides the Ago protein to the 5'-UTR of PHO2 transcripts. Non-coding IPS1 RNA is highly expressed during Pi starvation, and the sequestration of miR399 molecules protects PHO2 mRNA from complete degradation. Here, we reveal new cis- and trans-regulatory elements that are crucial for efficient PHO2 gene expression in barley. We found that the 5'-UTR of PHO2 contains two PHR1 binding sites (P1BSs) and one Pi-responsive PHO element. Using a yeast one-hybrid (Y1H) assay, we identified two candidate proteins that might mediate this transcriptional regulation: a barley PHR1 ortholog and a TF containing an uncharacterized MYB domain. Additional results classified this new potential TF as belonging to the APL (ALTERED PHLOEM DEVELOPMENT) protein family, and we observed its nuclear localization in barley protoplasts. Pi starvation induced the accumulation of barley APL transcripts in both the shoots and roots. Interestingly, the deletion of the P1BS motif from the first intron of the barley 5'-UTR led to a significant increase in the transcription of a downstream β-glucuronidase (GUS) reporter gene in tobacco leaves. Our work extends the current knowledge about putative cis- and trans-regulatory elements that may affect the expression of the barley PHO2 gene.
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Affiliation(s)
- Paweł Sega
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Łukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Zofia Szweykowska-Kulińska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
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Shao J, Xu Y, Fang M. BRG1 deficiency in endothelial cells alleviates thioacetamide induced liver fibrosis in mice. Biochem Biophys Res Commun 2019; 521:212-219. [PMID: 31635808 DOI: 10.1016/j.bbrc.2019.10.109] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/12/2019] [Indexed: 12/11/2022]
Abstract
Liver sinusoidal endothelial cells play a key role maintaining the hepatic homeostasis, the disruption of which is associated with such end-stage liver diseases as hepatocellular carcinoma and cirrhosis. In the present study we investigated the role of brahma-related gene 1 (BRG1), a chromatin remodeling protein, in regulating endothelial transcription and the implication in liver fibrosis. We report that endothelial-specific deletion of BRG1 in mice attenuated liver fibrosis induced by injection with thioacetamide (TAA). Coincidently, alleviation of liver fibrosis as a result of endothelial BRG1 deletion was accompanied by an up-regulation of eNOS activity and NO bioavailability. In cultured endothelial cells, exposure to lipopolysaccharide (LPS) suppressed eNOS activity whereas BRG1 depletion with small interfering RNA restored eNOS-dependent NO production. Further analysis revealed that BRG1 was recruited to the caveolin-1 (CAV1) promoter by Sp1 and activated transcription of CAV1, which in turn inhibited eNOS activity. Mechanistically, BRG1 interacted with the H3K4 trimethyltransferase MLL1 to modulate H3K4 trimethylation surrounding the CAV1 promoter thereby contributing to LPS-induced CAV1 activation. In conclusion, our data unveil a novel role for BRG1 in the regulation of endothelial function and liver fibrosis.
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Affiliation(s)
- Jing Shao
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yong Xu
- Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Mingming Fang
- Department of Clinical Medicine and Center for Experimental Medicine, Jiangsu Health Vocational College, Nanjing, China; Institute of Biomedical Research, Liaocheng University, Liaocheng, China.
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Kalkreuter E, Keeler AM, Malico AA, Bingham KS, Gayen AK, Williams GJ. Development of a Genetically Encoded Biosensor for Detection of Polyketide Synthase Extender Units in Escherichia coli. ACS Synth Biol 2019; 8:1391-1400. [PMID: 31134799 PMCID: PMC6915837 DOI: 10.1021/acssynbio.9b00078] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The scaffolds of polyketides are constructed via assembly of extender units based on malonyl-CoA and its derivatives that are substituted at the C2-position with diverse chemical functionality. Subsequently, a transcription-factor-based biosensor for malonyl-CoA has proven to be a powerful tool for detecting malonyl-CoA, facilitating the dynamic regulation of malonyl-CoA biosynthesis and guiding high-throughput engineering of malonyl-CoA-dependent processes. Yet, a biosensor for the detection of malonyl-CoA derivatives has yet to be reported, severely restricting the application of high-throughput synthetic biology approaches to engineering extender unit biosynthesis and limiting the ability to dynamically regulate the biosynthesis of polyketide products that are dependent on such α-carboxyacyl-CoAs. Herein, the FapR biosensor was re-engineered and optimized for a range of mCoA concentrations across a panel of E. coli strains. The effector specificity of FapR was probed by cell-free transcription-translation, revealing that a variety of non-native and non-natural acyl-thioesters are FapR effectors. This FapR promiscuity proved sufficient for the detection of the polyketide extender unit methylmalonyl-CoA in E. coli, providing the first reported genetically encoded biosensor for this important metabolite. As such, the previously unknown broad effector promiscuity of FapR provides a platform to develop new tools and approaches that can be leveraged to overcome limitations of pathways that construct diverse α-carboxyacyl-CoAs and those that are dependent on them, including biofuels, antibiotics, anticancer drugs, and other value-added products.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
- Comparative Medicine Institute, NC State University, Raleigh, North Carolina 27695, United States
- Present address: Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Aaron M. Keeler
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
| | - Alexandra A. Malico
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
| | - Kyle S. Bingham
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
- Present address: UNC Chapel Hill School of Medicine, Chapel Hill, North Carolina 27516, United States
| | - Anuran K. Gayen
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
| | - Gavin J. Williams
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
- Comparative Medicine Institute, NC State University, Raleigh, North Carolina 27695, United States
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Chowdhury M, Zhang J, Xu XX, He Z, Lu Y, Liu XS, Wang YF, Yu XQ. An in vitro study of NF-κB factors cooperatively in regulation of Drosophila melanogaster antimicrobial peptide genes. Dev Comp Immunol 2019; 95:50-58. [PMID: 30735676 DOI: 10.1016/j.dci.2019.01.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
An important innate immune response in Drosophila melanogaster is the production of antimicrobial peptides (AMPs). Expression of AMP genes is mediated by the Toll and immune deficiency (IMD) pathways via NF-κB transcription factors Dorsal, DIF and Relish. Dorsal and DIF act downstream of the Toll pathway, whereas Relish acts in the IMD pathway. Dorsal and DIF are held inactive in the cytoplasm by the IκB protein Cactus, while Relish contains an IκB-like inhibitory domain at the C-terminus. NF-κB factors normally form homodimers and heterodimers to regulate gene expression, but formation of heterodimers between Relish and DIF or Dorsal and the specificity and activity of the three NF-κB homodimers and heterodimers are not well understood. In this study, we compared the activity of Rel homology domains (RHDs) of Dorsal, DIF and Relish in activation of Drosophila AMP gene promoters, demonstrated that Relish-RHD (Rel-RHD) interacted with both Dorsal-RHD and DIF-RHD, Relish-N interacted with DIF and Dorsal, and overexpression of individual RHD and co-expression of any two RHDs activated the activity of AMP gene promoters to various levels, suggesting formation of homodimers and heterodimers among Dorsal, DIF and Relish. Rel-RHD homodimers were stronger activators than heterodimers of Rel-RHD with either DIF-RHD or Dorsal-RHD, while DIF-RHD-Dorsal-RHD heterodimers were stronger activators than either DIF-RHD or Dorsal-RHD homodimers in activation of AMP gene promoters. We also identified the nucleotides at the 6th and 8th positions of the 3' half-sites of the κB motifs that are important for the specificity and activity of NF-κB transcription factors.
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Affiliation(s)
- Munmun Chowdhury
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri - Kansas City, Kansas City, MO, 64110, USA
| | - Jie Zhang
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri - Kansas City, Kansas City, MO, 64110, USA
| | - Xiao-Xia Xu
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri - Kansas City, Kansas City, MO, 64110, USA; College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhen He
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri - Kansas City, Kansas City, MO, 64110, USA; School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yuzhen Lu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xu-Sheng Liu
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yu-Feng Wang
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Xiao-Qiang Yu
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri - Kansas City, Kansas City, MO, 64110, USA; School of Life Sciences, Central China Normal University, Wuhan, 430079, China; Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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10
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Zhang Y, Ji A, Xu Z, Luo H, Song J. The AP2/ERF transcription factor SmERF128 positively regulates diterpenoid biosynthesis in Salvia miltiorrhiza. Plant Mol Biol 2019; 100:83-93. [PMID: 30847712 DOI: 10.1007/s11103-019-00845-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 02/18/2019] [Indexed: 05/02/2023]
Abstract
The novel AP2/ERF transcription factor SmERF128 positively regulates diterpenoid tanshinone biosynthesis by activating the expression of SmCPS1, SmKSL1, and SmCYP76AH1 in Salvia miltiorrhiza. Certain members of the APETALA2/ethylene-responsive factor (AP2/ERF) family regulate plant secondary metabolism. Although it is clearly documented that AP2/ERF transcription factors (TFs) are involved in sesquiterpenoid biosynthesis, the regulation of diterpenoid biosynthesis by AP2/ERF TFs remains elusive. Here, we report that the novel AP2/ERF TF SmERF128 positively regulates diterpenoid tanshinone biosynthesis in Salvia miltiorrhiza. Overexpression of SmERF128 increased the expression levels of copalyl diphosphate synthase 1 (SmCPS1), kaurene synthase-like 1 (SmKSL1) and cytochrome P450 monooxygenase 76AH1 (SmCYP76AH1), whereas their expression levels were decreased when SmERF128 was silenced. Accordingly, the content of tanshinone was reduced in SmERF128 RNA interference (RNAi) hairy roots and dramatically increased in SmERF128 overexpression hairy roots, as demonstrated through Ultra Performance Liquid Chromatography (UPLC) and Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis. Furthermore, SmERF128 activated the expression of SmCPS1, SmKSL1, and SmCYP76AH1 by binding to the GCC box, and to the CRTDREHVCBF2 (CBF2) and RAV1AAT (RAA) motifs within their promoters during in vivo and in vitro assays. Our findings not only reveal the molecular basis of how the AP2/ERF transcription factor SmERF128 regulates diterpenoid biosynthesis, but also provide useful information for improving tanshinone production through genetic engineering.
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Affiliation(s)
- Yu Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- College of Chinese Materia Medica, Shanxi University of Chinese Medicine, Jinzhong, 030619, China
| | - Aijia Ji
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Hongmei Luo
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, 100193, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, 666100, China.
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, 100193, China.
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11
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Coulombe B, Killeen M, Liljelund P, Honda B, Xiao H, Ingles CJ, Greenblatt J. Identification of three mammalian proteins that bind to the yeast TATA box protein TFIID. Gene Expr 2018; 2:99-110. [PMID: 1633441 PMCID: PMC6057387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The TATA box binding transcription factor TFIID of S. cerevisiae was used as a ligand for affinity chromatography. Polypeptides that bind specifically to yeast TFIID (TFIID-associated proteins, DAPs) were purified from human HeLa (heDAPs) and calf thymus (ctDAPs) whole cell extracts. Both heDAP and ctDAP fractions altered the binding of TFIID to the TATA element, and substituted for the TFIIA transcription activity in a reconstituted in vitro system. The heDAP fraction also behaved like TFIIA in its ability to form a promoter-TFIID-TFIIA complex and to recruit TFIIB to such a complex. The interaction of DAPs with TFIID can confer heat-resistance (47 degrees C) on recombinant yeast or human TFIID. SDS-PAGE analysis revealed that three polypeptides from HeLa extracts specifically bound to yTFIID columns (heDAP35, heDAP21, and heDAP12). These data suggest that a multi-subunit transcription factor with the properties of TFIIA can bind to TFIID in the absence of DNA.
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Affiliation(s)
- B Coulombe
- Banting and Best Department of Medical Research, University of Toronto, Ontario
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12
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Carrasco-Orellana C, Stappung Y, Mendez-Yañez A, Allan AC, Espley RV, Plunkett BJ, Moya-Leon MA, Herrera R. Characterization of a ripening-related transcription factor FcNAC1 from Fragaria chiloensis fruit. Sci Rep 2018; 8:10524. [PMID: 30002382 PMCID: PMC6043618 DOI: 10.1038/s41598-018-28226-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/19/2018] [Indexed: 11/15/2022] Open
Abstract
Fragaria chiloensis is a strawberry endemic from Chile with attractive white-pink fruit, pleasant aroma and taste. However, this fruit has a limited post-harvest period due to fast softening. Several transcription factors (TFs) are involved in the regulation of fruit ripening, and members of the NAC family have been implicated in cell wall remodeling. FcNAC1 was isolated from F. chiloensis fruit, coding a protein of 332 amino acid residues and displaying a characteristic NAC domain at the N terminus. FcNAC1 protein showed nuclear localization. An increase in transcript level was observed during ripening. A sequence of 1488 bp of FcNAC1 promoter was obtained. In silico analysis identified cis elements able to respond to some hormones and Secondary wall NAC binding elements (SNBE), and responding to auxin and ABA. A structural model of FcNAC1 provided evidence for interaction with DNA sequences containing SNBE, while a dual luciferase assay confirmed the transcriptional activation by FcNAC1 of the promoter of FcPL, a gene involved in cell wall remodeling in F. chiloensis fruit. The results suggest the participation of FcNAC1 during ripening development of strawberry fruit, by regulating pectin metabolism during softening.
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Affiliation(s)
- C Carrasco-Orellana
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Y Stappung
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - A Mendez-Yañez
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - A C Allan
- New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, 1025, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - R V Espley
- New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, 1025, New Zealand
| | - B J Plunkett
- New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, 1025, New Zealand
| | - M A Moya-Leon
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - R Herrera
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile.
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13
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Hannon C, Cruz-Migoni A, Platonova O, Owen RL, Nettleship JE, Miller A, Carr SB, Harris G, Rabbitts TH, Phillips SEV. Cloning, purification and structure determination of the HIV integrase-binding domain of lens epithelium-derived growth factor. Acta Crystallogr F Struct Biol Commun 2018; 74:143-149. [PMID: 29497017 PMCID: PMC5947699 DOI: 10.1107/s2053230x18001553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 01/23/2018] [Indexed: 12/04/2022] Open
Abstract
Lens epithelium-derived growth factor (LEDGF)/p75 is the dominant binding partner of HIV-1 integrase in human cells. The crystal structure of the HIV integrase-binding domain (IBD) of LEDGF has been determined in the absence of ligand. IBD was overexpressed in Escherichia coli, purified and crystallized by sitting-drop vapour diffusion. X-ray diffraction data were collected at Diamond Light Source to a resolution of 2.05 Å. The crystals belonged to space group P21, with eight polypeptide chains in the asymmetric unit arranged as an unusual octamer composed of four domain-swapped IBD dimers. IBD exists as a mixture of monomers and dimers in concentrated solutions, but the dimers are unlikely to be biologically relevant.
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Affiliation(s)
- Clare Hannon
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, England
- West Suffolk Hospital, Hardwick Lane, Bury St Edmunds IP33 2QZ, England
| | - Abimael Cruz-Migoni
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, England
| | - Olga Platonova
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, England
| | - Robin L. Owen
- Diamond Light Source, Rutherford Appleton Laboratory, Didcot OX11 0DE, England
| | - Joanne E. Nettleship
- Oxford Protein Production Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Ami Miller
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, England
| | - Stephen B. Carr
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - Gemma Harris
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - Terence H. Rabbitts
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, England
| | - Simon E. V. Phillips
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
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14
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O’Brien LL, Guo Q, Bahrami-Samani E, Park JS, Hasso SM, Lee YJ, Fang A, Kim AD, Guo J, Hong TM, Peterson KA, Lozanoff S, Raviram R, Ren B, Fogelgren B, Smith AD, Valouev A, McMahon AP. Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies. PLoS Genet 2018; 14:e1007181. [PMID: 29377931 PMCID: PMC5805373 DOI: 10.1371/journal.pgen.1007181] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/08/2018] [Accepted: 01/01/2018] [Indexed: 12/12/2022] Open
Abstract
Nephron progenitor number determines nephron endowment; a reduced nephron count is linked to the onset of kidney disease. Several transcriptional regulators including Six2, Wt1, Osr1, Sall1, Eya1, Pax2, and Hox11 paralogues are required for specification and/or maintenance of nephron progenitors. However, little is known about the regulatory intersection of these players. Here, we have mapped nephron progenitor-specific transcriptional networks of Six2, Hoxd11, Osr1, and Wt1. We identified 373 multi-factor associated 'regulatory hotspots' around genes closely associated with progenitor programs. To examine their functional significance, we deleted 'hotspot' enhancer elements for Six2 and Wnt4. Removal of the distal enhancer for Six2 leads to a ~40% reduction in Six2 expression. When combined with a Six2 null allele, progeny display a premature depletion of nephron progenitors. Loss of the Wnt4 enhancer led to a significant reduction of Wnt4 expression in renal vesicles and a mildly hypoplastic kidney, a phenotype also enhanced in combination with a Wnt4 null mutation. To explore the regulatory landscape that supports proper target gene expression, we performed CTCF ChIP-seq to identify insulator-boundary regions. One such putative boundary lies between the Six2 and Six3 loci. Evidence for the functional significance of this boundary was obtained by deep sequencing of the radiation-induced Brachyrrhine (Br) mutant allele. We identified an inversion of the Six2/Six3 locus around the CTCF-bound boundary, removing Six2 from its distal enhancer regulation, but placed next to Six3 enhancer elements which support ectopic Six2 expression in the lens where Six3 is normally expressed. Six3 is now predicted to fall under control of the Six2 distal enhancer. Consistent with this view, we observed ectopic Six3 in nephron progenitors. 4C-seq supports the model for Six2 distal enhancer interactions in wild-type and Br/+ mouse kidneys. Together, these data expand our view of the regulatory genome and regulatory landscape underpinning mammalian nephrogenesis.
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Affiliation(s)
- Lori L. O’Brien
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Preventative Medicine, Division of Bioinformatics, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Emad Bahrami-Samani
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Joo-Seop Park
- Division of Pediatric Urology and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Sean M. Hasso
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Young-Jin Lee
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Alan Fang
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Albert D. Kim
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Trudy M. Hong
- Department of Anatomy, Biochemistry, and Physiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | | | - Scott Lozanoff
- Department of Anatomy, Biochemistry, and Physiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Ramya Raviram
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, University of California San Diego La Jolla, California, United States of America
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, University of California San Diego La Jolla, California, United States of America
| | - Ben Fogelgren
- Department of Anatomy, Biochemistry, and Physiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Andrew D. Smith
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Anton Valouev
- Department of Preventative Medicine, Division of Bioinformatics, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
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15
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Wu W, Zhen X, Shi N. DNA-binding domain of myelin-gene regulatory factor: purification, crystallization and X-ray analysis. Acta Crystallogr F Struct Biol Commun 2017; 73:393-397. [PMID: 28695847 PMCID: PMC5505243 DOI: 10.1107/s2053230x17007828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 05/26/2017] [Indexed: 11/10/2022] Open
Abstract
The myelin sheath, which envelops axons in the vertebrate central nervous system, is crucial for the rapid conduction of action potentials. Myelin-gene regulatory factor (MRF) is a recently identified transcription factor that is required for myelin-sheath formation. Loss of MRF leads to demyelinating diseases and motor learning deficiency. MRF is a membrane-bound transcription factor that undergoes autocleavage from the endoplasmic reticulum membrane. The N-terminus of MRF contains a DNA-binding domain (DBD) that functions as a homotrimer. In this study, the MRF DBD was cloned, purified and crystallized in order to understand the molecular mechanism that regulates the transcription of myelin genes. Selenomethionine was subsequently introduced into the crystals to obtain the phases for the MRF DBD structure. The native and selenomethionine-labelled crystals exhibited diffraction to 2.50 and 2.51 Å resolution, respectively. The crystals belonged to space group P321 and the selenomethionine-labelled crystals had unit-cell parameters a = 104.0, b = 104.0, c = 46.7 Å, α = 90, β = 90, γ = 120°. The calculated Matthews coefficient was 3.04 Å3 Da-1 and the solvent content was 59.5%, indicating the presence of one MRF DBD molecule in the asymmetric unit.
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Affiliation(s)
- WenYu Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao Road West, Fuzhou, Fujian 350002, People’s Republic of China
| | - Xiangkai Zhen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao Road West, Fuzhou, Fujian 350002, People’s Republic of China
| | - Ning Shi
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao Road West, Fuzhou, Fujian 350002, People’s Republic of China
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16
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Shestakova EA, Boutin M, Bourassa S, Bonneil E, Bijl JJ. [Identification of proteins associated with transcription factors HOXA9 and E2A-PBX1 by tandem affinity purification]. Mol Biol (Mosk) 2017; 51:490-501. [PMID: 28707666 DOI: 10.7868/s0026898417030132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/20/2016] [Indexed: 11/23/2022]
Abstract
Chimeric transcription factor E2A-PBX1 induces the development of acute lymphoblastic B-cell leukemia in children. Using a transgenic mouse model, we previously demonstrated that homeobox (HOX) gene HOXA9 genetically interact with E2A-PBX1 gene in the development of B-cell leukemia in mice. HOXA9 itself is a potent oncogene resulting in myeloid leukemia when overexpressed, which is strongly accelerated by its collaborator Meis1. HOX, PBX1 and MEIS1 proteins have been shown to form hetero dimeric or trimeric complexes in different combinations. Cooperative interaction between PBX1 and HOX proteins enhances their DNA binding specificity, essential for HOX dependent developmental programs. PBX1 is retained in E2A-PBX1, and thus the strong transcriptional activator properties of E2A-PBX1 may lead to aberrant activation of normally repressed targets of HOX-PBX complexes. However, although there is evidence that E2A-PBX1 could bind to HOX and MEIS1 proteins it is still unclear whether such complexes are actually required for leukemic transformation or whether E2A-PBX1 and HOXA9 are each part of larger protein complexes acting in independent complementing oncogenic pathways. In this study we aim to search for other HOXA9 and E2A-PBX1 interacting proteins. To identify novel proteins interacting with human E2A-PBX1 or HOXA9 we used tandem affinity purification (TAP) of protein complexes from 697 pre-B leukemic and HeLa cell lines transduced to express E2A-PBX1 or HOXA9, respectively, with covalently attached FLAG/HA peptides. The protein composition of each complex was determined using tandem mass-spectrometry. In the E2A-PBX1 containing complex we identified lymphoid transcription factor IKAROS, chromatin remodeling factors of SWI/SNF family while multiple subunits of translation initiation factor eIF3, E3 ubiquitin ligase UBR5 emerged from the HOXA9 complex as potential critical protein partners. This is the first time the protein partners of either E2A-PBX1 or HOXA9 oncoproteins were identified using an unbiased biochemical approach. The identification of translation initiation factors associated with HOXA9 might indicate a novel function for HOX proteins independent of their transcriptional activity.
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Affiliation(s)
- E A Shestakova
- HMR Research Center, University of Montreal, Montreal, QC, Canada
- Blokhin Russian Cancer Research Center, Moscow, 115478 Russia
| | - M Boutin
- Proteomic Platform CHU de Quebec Research Center, Quebec, QC, Canada
| | - S Bourassa
- Proteomic Platform CHU de Quebec Research Center, Quebec, QC, Canada
| | - E Bonneil
- Proteomic Platform, IRIC University of Montreal, Montreal, QC, Canada
| | - J J Bijl
- HMR Research Center, University of Montreal, Montreal, QC, Canada
- Department of Medicine University of Montreal, Montreal, QC Canada
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17
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Kuang JF, Chen JY, Liu XC, Han YC, Xiao YY, Shan W, Tang Y, Wu KQ, He JX, Lu WJ. The transcriptional regulatory network mediated by banana (Musa acuminata) dehydration-responsive element binding (MaDREB) transcription factors in fruit ripening. New Phytol 2017; 214:762-781. [PMID: 28044313 DOI: 10.1111/nph.14389] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 11/16/2016] [Indexed: 05/24/2023]
Abstract
Fruit ripening is a complex, genetically programmed process involving the action of critical transcription factors (TFs). Despite the established significance of dehydration-responsive element binding (DREB) TFs in plant abiotic stress responses, the involvement of DREBs in fruit ripening is yet to be determined. Here, we identified four genes encoding ripening-regulated DREB TFs in banana (Musa acuminata), MaDREB1, MaDREB2, MaDREB3, and MaDREB4, and demonstrated that they play regulatory roles in fruit ripening. We showed that MaDREB1-MaDREB4 are nucleus-localized, induced by ethylene and encompass transcriptional activation activities. We performed a genome-wide chromatin immunoprecipitation and high-throughput sequencing (ChIP-Seq) experiment for MaDREB2 and identified 697 genomic regions as potential targets of MaDREB2. MaDREB2 binds to hundreds of loci with diverse functions and its binding sites are distributed in the promoter regions proximal to the transcriptional start site (TSS). Most of the MaDREB2-binding targets contain the conserved (A/G)CC(G/C)AC motif and MaDREB2 appears to directly regulate the expression of a number of genes involved in fruit ripening. In combination with transcriptome profiling (RNA sequencing) data, our results indicate that MaDREB2 may serve as both transcriptional activator and repressor during banana fruit ripening. In conclusion, our study suggests a hierarchical regulatory model of fruit ripening in banana and that the MaDREB TFs may act as transcriptional regulators in the regulatory network.
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Affiliation(s)
- Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xun-Cheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yan-Chao Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yun-Yi Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Ke-Qiang Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jun-Xian He
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
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Schmidt K, Steiner K, Petrov B, Georgiev O, Schaffner W. Short-lived mammals (shrew, mouse) have a less robust metal-responsive transcription factor than humans and bats. Biometals 2016; 29:423-32. [PMID: 27067444 PMCID: PMC4879176 DOI: 10.1007/s10534-016-9926-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 11/30/2022]
Abstract
Non-essential "heavy" metals such as cadmium tend to accumulate in an organism and thus are a particular threat for long-lived animals. Here we show that two unrelated, short-lived groups of mammals (rodents and shrews, separated by 100 Mio years of evolution) each have independently acquired mutations in their metal-responsive transcription factor (MTF-1) in a domain relevant for robust transcriptional induction by zinc and cadmium. While key amino acids are mutated in rodents, in shrews an entire exon is skipped. Rodents and especially shrews are unique regarding the alterations of this region. To investigate the biological relevance of these alterations, MTF-1s from the common shrew (Sorex araneus), the mouse, humans and a bat (Myotis blythii), were tested by cotransfection with a reporter gene into cells lacking MTF-1. Whereas shrews only live for 1.5-2.5 years, bats, although living on a very similar insect diet, have a lifespan of several decades. We find that bat MTF-1 is similarly metal-responsive as its human counterpart, while shrew MTF-1 is less responsive, similar to mouse MTF-1. We propose that in comparison to most other mammals, the short-lived shrews and rodents can afford a "lower-quality" system for heavy metal homeostasis and detoxification.
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Affiliation(s)
- Katharina Schmidt
- Institute of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
| | - Kurt Steiner
- Institute of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
| | - Boyan Petrov
- National Museum of Natural History, 1000, Sofia, Bulgaria
| | - Oleg Georgiev
- Institute of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.
| | - Walter Schaffner
- Institute of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.
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Schweingruber C, Soffientini P, Ruepp MD, Bachi A, Mühlemann O. Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID). PLoS One 2016; 11:e0150239. [PMID: 26934103 PMCID: PMC4774922 DOI: 10.1371/journal.pone.0150239] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/02/2016] [Indexed: 01/09/2023] Open
Abstract
Proximity-dependent trans-biotinylation by the Escherichia coli biotin ligase BirA mutant R118G (BirA*) allows stringent streptavidin affinity purification of proximal proteins. This so-called BioID method provides an alternative to the widely used co-immunoprecipitation (co-IP) to identify protein-protein interactions. Here, we used BioID, on its own and combined with co-IP, to identify proteins involved in nonsense-mediated mRNA decay (NMD), a post-transcriptional mRNA turnover pathway that targets mRNAs that fail to terminate translation properly. In particular, we expressed BirA* fused to the well characterized NMD factors UPF1, UPF2 and SMG5 and detected by liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) the streptavidin-purified biotinylated proteins. While the identified already known interactors confirmed the usefulness of BioID, we also found new potentially important interactors that have escaped previous detection by co-IP, presumably because they associate only weakly and/or very transiently with the NMD machinery. Our results suggest that SMG5 only transiently contacts the UPF1-UPF2-UPF3 complex and that it provides a physical link to the decapping complex. In addition, BioID revealed among others CRKL and EIF4A2 as putative novel transient interactors with NMD factors, but whether or not they have a function in NMD remains to be elucidated.
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Affiliation(s)
- Christoph Schweingruber
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Angela Bachi
- IFOM-FIRC Institute of Molecular Oncology, Milan, Italy
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
- * E-mail:
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20
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Zhai R, Wang Z, Zhang S, Meng G, Song L, Wang Z, Li P, Ma F, Xu L. Two MYB transcription factors regulate flavonoid biosynthesis in pear fruit (Pyrus bretschneideri Rehd.). J Exp Bot 2016; 67:1275-84. [PMID: 26687179 DOI: 10.1093/jxb/erv524] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Flavonoid compounds play important roles in the modern diet, and pear fruits are an excellent dietary source of these metabolites. However, information on the regulatory network of flavonoid biosynthesis in pear fruits is rare. In this work, 18 putative flavonoid-related MYB transcription factors (TFs) were screened by phylogenetic analysis and four of them were correlated with flavonoid biosynthesis patterns in pear fruits. Among these MYB-like genes, the specific functions of two novel MYB TFs, designated as PbMYB10b and PbMYB9, were further verified by both overexpression and RNAi transient assays. PbMYB10b, a PAP-type MYB TF with atypical motifs in its conserved region, regulated the anthocyanin and proanthocyanidin pathways by inducing the expression of PbDFR, but its function could be complemented by other MYB TFs. PbMYB9, a TT2-type MYB, not only acted as the specific activator of the proanthocyanidin pathway by activating the PbANR promoter, but also induced the synthesis of anthocyanins and flavonols by binding the PbUFGT1 promoter in pear fruits. The MYBCORE-like element has been identified in both the PbUFGT1 promoter and ANR promoters in most species, but it was not found in UFGT promoters isolated from other species. This finding was also supported by a yeast one-hybrid assay and thus enhanced the likelihood of the interaction between PbMYB9 and the PbUFGT1 promoter.
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Affiliation(s)
- Rui Zhai
- College of Horticulture, Northwest A&F University, Taicheng Road NO.3, Yangling, Shaanxi Province, China
| | - Zhimin Wang
- College of Horticulture, Northwest A&F University, Taicheng Road NO.3, Yangling, Shaanxi Province, China
| | - Shiwei Zhang
- College of Horticulture, Northwest A&F University, Taicheng Road NO.3, Yangling, Shaanxi Province, China
| | - Geng Meng
- College of Horticulture, Northwest A&F University, Taicheng Road NO.3, Yangling, Shaanxi Province, China
| | - Linyan Song
- College of Horticulture, Northwest A&F University, Taicheng Road NO.3, Yangling, Shaanxi Province, China
| | - Zhigang Wang
- College of Horticulture, Northwest A&F University, Taicheng Road NO.3, Yangling, Shaanxi Province, China
| | - Pengmin Li
- College of Horticulture, Northwest A&F University, Taicheng Road NO.3, Yangling, Shaanxi Province, China
| | - Fengwang Ma
- College of Horticulture, Northwest A&F University, Taicheng Road NO.3, Yangling, Shaanxi Province, China
| | - Lingfei Xu
- College of Horticulture, Northwest A&F University, Taicheng Road NO.3, Yangling, Shaanxi Province, China
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21
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Babitha KC, Vemanna RS, Nataraja KN, Udayakumar M. Overexpression of EcbHLH57 Transcription Factor from Eleusine coracana L. in Tobacco Confers Tolerance to Salt, Oxidative and Drought Stress. PLoS One 2015; 10:e0137098. [PMID: 26366726 PMCID: PMC4569372 DOI: 10.1371/journal.pone.0137098] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 08/12/2015] [Indexed: 02/01/2023] Open
Abstract
Basic helix-loop-helix (bHLH) transcription factors constitute one of the largest families in plants and are known to be involved in various developmental processes and stress tolerance. We report the characterization of a stress responsive bHLH transcription factor from stress adapted species finger millet which is homologous to OsbHLH57 and designated as EcbHLH57. The full length sequence of EcbHLH57 consisted of 256 amino acids with a conserved bHLH domain followed by leucine repeats. In finger millet, EcbHLH57 transcripts were induced by ABA, NaCl, PEG, methyl viologen (MV) treatments and drought stress. Overexpression of EcbHLH57 in tobacco significantly increased the tolerance to salinity and drought stress with improved root growth. Transgenic plants showed higher photosynthetic rate and stomatal conductance under drought stress that resulted in higher biomass. Under long-term salinity stress, the transgenic plants accumulated higher seed weight/pod and pod number. The transgenic plants were also tolerant to oxidative stress and showed less accumulation of H202 and MDA levels. The overexpression of EcbHLH57 enhanced the expression of stress responsive genes such as LEA14, rd29A, rd29B, SOD, APX, ADH1, HSP70 and also PP2C and hence improved tolerance to diverse stresses.
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Affiliation(s)
- K. C. Babitha
- Department of Crop Physiology, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - Ramu S. Vemanna
- Department of Crop Physiology, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - Karaba N. Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - M. Udayakumar
- Department of Crop Physiology, University of Agricultural Sciences, Bangalore, Karnataka, India
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22
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DuMond JF, He Y, Burg MB, Ferraris JD. Expression, fermentation and purification of a predicted intrinsically disordered region of the transcription factor, NFAT5. Protein Expr Purif 2015; 115:141-5. [PMID: 26256058 DOI: 10.1016/j.pep.2015.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/29/2015] [Accepted: 08/04/2015] [Indexed: 11/17/2022]
Abstract
Hypertonicity stimulates Nuclear Factor of Activated T-cells 5 (NFAT5) nuclear localization and transactivating activity. Many transcription factors are known to contain intrinsically disordered regions (IDRs) which become more structured with local environmental changes such as osmolality, temperature and tonicity. The transactivating domain of NFAT5 is predicted to be intrinsically disordered under normal tonicity, and under high NaCl, the activity of this domain is increased. To study the binding of co-regulatory proteins at IDRs a cDNA construct expressing the NFAT5 TAD was created and transformed into Escherichia coli cells. Transformed E. coli cells were mass produced by fermentation and extracted by cell lysis to release the NFAT5 TAD. The NFAT5 TAD was subsequently purified using a His-tag column, cation exchange chromatography as well as hydrophobic interaction chromatography and then characterized by mass spectrometry (MS).
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Affiliation(s)
- Jenna F DuMond
- National Institutes of Health, National Heart, Lung and Blood Institute, Systems Biology Center, Bethesda, MD 20892, United States.
| | - Yi He
- National Institutes of Health, National Heart, Lung and Blood Institute, Biochemistry and Biophysics Center, Bethesda, MD 20892, United States.
| | - Maurice B Burg
- National Institutes of Health, National Heart, Lung and Blood Institute, Systems Biology Center, Bethesda, MD 20892, United States.
| | - Joan D Ferraris
- National Institutes of Health, National Heart, Lung and Blood Institute, Systems Biology Center, Bethesda, MD 20892, United States.
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23
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Santiago AS, Santos CA, Mendes JS, Toledo MAS, Beloti LL, Souza AA, Souza AP. Characterization of the LysR-type transcriptional regulator YcjZ-like from Xylella fastidiosa overexpressed in Escherichia coli. Protein Expr Purif 2015; 113:72-8. [PMID: 25979465 DOI: 10.1016/j.pep.2015.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 11/20/2022]
Abstract
The Xylella fastidiosa 9a5c strain is a xylem-limited phytopathogen that is the causal agent of citrus variegated chlorosis (CVC). This bacterium is able to form a biofilm and occlude the xylem vessels of susceptible plants, which leads to significant agricultural and economic losses. Biofilms are associated with bacterial pathogenicity because they are very resistant to antibiotics and other metal-based chemicals that are used in agriculture. The X. fastidiosa YcjZ-like (XfYcjZ-like) protein belongs to the LysR-type transcriptional regulator (LTTR) family and is involved in various cellular functions that range from quorum sensing to bacterial survival. In the present study, we report the cloning, expression and purification of XfYcjZ-like, which was overexpressed in Escherichia coli. The secondary folding of the recombinant and purified protein was assessed by circular dichroism, which revealed that XfYcjZ-like contains a typical α/β fold. An initial hydrodynamic characterization showed that XfYcjZ-like is a globular tetramer in solution. In addition, using a polyclonal antibody against XfYcjZ-like, we assessed the expression profile of this protein during the different developmental phases of X. fastidiosa in in vitro cultivated biofilm cells and demonstrated that XfYcjZ-like is upregulated in planktonic cells in response to a copper shock treatment. Finally, the ability of XfYcjZ-like to interact with its own predicted promoter was confirmed in vitro, which is a typical feature of LysR. Taken together, our findings indicated that the XfYcjZ-like protein is involved in both the organization of the architecture and the maturation of the bacterial biofilm and that it is responsive to oxidative stress.
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Affiliation(s)
- André S Santiago
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Clelton A Santos
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Juliano S Mendes
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo A S Toledo
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Lilian L Beloti
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Alessandra A Souza
- Centro APTA Citros Sylvio Moreira/IAC, Rodovia Anhanguera Km 158, Cordeirópolis, SP, Brazil
| | - Anete P Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil; Departamento de Biologia Vegetal, Instituto de Biologia (IB), Universidade Estadual de Campinas, Campinas, SP, Brazil.
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24
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Hsu CC, Chen YY, Tsai WC, Chen WH, Chen HH. Three R2R3-MYB transcription factors regulate distinct floral pigmentation patterning in Phalaenopsis spp. Plant Physiol 2015; 168:175-91. [PMID: 25739699 PMCID: PMC4424010 DOI: 10.1104/pp.114.254599] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 02/27/2015] [Indexed: 05/19/2023]
Abstract
Orchidaceae are well known for their fascinating floral morphologic features, specialized pollination, and distinctive ecological strategies. With their long-lasting flowers of various colors and pigmentation patterning, Phalaenopsis spp. have become important ornamental plants worldwide. In this study, we identified three R2R3-MYB transcription factors PeMYB2, PeMYB11, and PeMYB12. Their expression profiles were concomitant with red color formation in Phalaenopsis spp. flowers. Transient assay of overexpression of three PeMYBs verified that PeMYB2 resulted in anthocyanin accumulation, and these PeMYBs could activate the expression of three downstream structural genes Phalaenopsis spp. Flavanone 3-hydroxylase5, Phalaenopsis spp. Dihydroflavonol 4-reductase1, and Phalaenopsis spp. Anthocyanidin synthase3. In addition, these three PeMYBs participated in the distinct pigmentation patterning in a single flower, which was revealed by virus-induced gene silencing. In the sepals/petals, silencing of PeMYB2, PeMYB11, and PeMYB12 resulted in the loss of the full-red pigmentation, red spots, and venation patterns, respectively. Moreover, different pigmentation patterning was regulated by PeMYBs in the sepals/petals and lip. PeMYB11 was responsive to the red spots in the callus of the lip, and PeMYB12 participated in the full pigmentation in the central lobe of the lip. The differential pigmentation patterning was validated by RNA in situ hybridization. Additional assessment was performed in six Phalaenopsis spp. cultivars with different color patterns. The combined expression of these three PeMYBs in different ratios leads to a wealth of complicated floral pigmentation patterning in Phalaenopsis spp.
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Affiliation(s)
- Chia-Chi Hsu
- Department of Life Sciences (C.-C.H., Y.-Y.C., H.-H.C.),Institute of Tropical Plant Sciences (W.-C.T.), andOrchid Research and Development Center (W.-C.T., W.-H.C., H.-H.C.), National Cheng Kung University, Tainan 701, Taiwan
| | - You-Yi Chen
- Department of Life Sciences (C.-C.H., Y.-Y.C., H.-H.C.),Institute of Tropical Plant Sciences (W.-C.T.), andOrchid Research and Development Center (W.-C.T., W.-H.C., H.-H.C.), National Cheng Kung University, Tainan 701, Taiwan
| | - Wen-Chieh Tsai
- Department of Life Sciences (C.-C.H., Y.-Y.C., H.-H.C.),Institute of Tropical Plant Sciences (W.-C.T.), andOrchid Research and Development Center (W.-C.T., W.-H.C., H.-H.C.), National Cheng Kung University, Tainan 701, Taiwan
| | - Wen-Huei Chen
- Department of Life Sciences (C.-C.H., Y.-Y.C., H.-H.C.),Institute of Tropical Plant Sciences (W.-C.T.), andOrchid Research and Development Center (W.-C.T., W.-H.C., H.-H.C.), National Cheng Kung University, Tainan 701, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences (C.-C.H., Y.-Y.C., H.-H.C.),Institute of Tropical Plant Sciences (W.-C.T.), andOrchid Research and Development Center (W.-C.T., W.-H.C., H.-H.C.), National Cheng Kung University, Tainan 701, Taiwan
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25
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Jia Y, Jarrett HW. Method for trapping affinity chromatography of transcription factors using aldehyde-hydrazide coupling to agarose. Anal Biochem 2015; 482:1-6. [PMID: 25935261 DOI: 10.1016/j.ab.2015.04.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 11/17/2022]
Abstract
The use of a method of coupling DNA was investigated for trapping and purifying transcription factors. Using the GFP-C/EBP (CAAT/enhancer binding protein) fusion protein as a model, trapping gives higher purity and comparable yield to conventional affinity chromatography. The chemistry used is mild and was shown to have no detrimental effect on GFP fluorescence or GFP-C/EBP DNA binding. The method involves introducing a ribose nucleotide to the 3' end of a DNA sequence. Reaction with mM NaIO4 (sodium metaperiodate) produces a dialdehyde of ribose that couples to hydrazide-agarose. The DNA is combined at nM concentration with a nuclear extract or other protein mixture, and DNA-protein complexes form. The complex is then coupled to hydrazide-agarose for trapping the DNA-protein complex and the protein eluted by increasing NaCl concentration. Using a different oligonucleotide with the proximal E-box sequence from the human telomerase promoter, USF-2 transcription factor was purified by trapping, again with higher purity than results from conventional affinity chromatography and similar yield. Other transcription factors binding E-boxes, including E2A, c-Myc, and Myo-D, were also purified, but myogenin and NFκB were not. Therefore, this approach proved to be valuable for both affinity chromatography and the trapping approach.
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Affiliation(s)
- Yinshan Jia
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Harry W Jarrett
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA.
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26
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Dulermo R, Onodera T, Coste G, Passot F, Dutertre M, Porteron M, Confalonieri F, Sommer S, Pasternak C. Identification of new genes contributing to the extreme radioresistance of Deinococcus radiodurans using a Tn5-based transposon mutant library. PLoS One 2015; 10:e0124358. [PMID: 25884619 PMCID: PMC4401554 DOI: 10.1371/journal.pone.0124358] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/02/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we have developed an extremely efficient in vivo Tn5-based mutagenesis procedure to construct a Deinococcus radiodurans insertion mutant library subsequently screened for sensitivity to genotoxic agents such as γ and UV radiations or mitomycin C. The genes inactivated in radiosensitive mutants belong to various functional categories, including DNA repair functions, stress responses, signal transduction, membrane transport, several metabolic pathways, and genes of unknown function. Interestingly, preliminary characterization of previously undescribed radiosensitive mutants suggests the contribution of cyclic di-AMP signaling in the recovery of D. radiodurans cells from genotoxic stresses, probably by modulating several pathways involved in the overall cell response. Our analyses also point out a new transcriptional regulator belonging to the GntR family, encoded by DR0265, and a predicted RNase belonging to the newly described Y family, both contributing to the extreme radioresistance of D. radiodurans. Altogether, this work has revealed new cell responses involved either directly or indirectly in repair of various cell damage and confirmed that D. radiodurans extreme radiation resistance is determined by a multiplicity of pathways acting as a complex network.
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Affiliation(s)
- Rémi Dulermo
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Takefumi Onodera
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Geneviève Coste
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Fanny Passot
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Murielle Dutertre
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Martine Porteron
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Fabrice Confalonieri
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Suzanne Sommer
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Cécile Pasternak
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
- * E-mail:
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27
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Buck M, Engl C, Joly N, Jovanovic G, Jovanovic M, Lawton E, McDonald C, Schumacher J, Waite C, Zhang N. In vitro and in vivo methodologies for studying the Sigma 54-dependent transcription. Methods Mol Biol 2015; 1276:53-79. [PMID: 25665558 DOI: 10.1007/978-1-4939-2392-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Here we describe approaches and methods to assaying in vitro the major variant bacterial sigma factor, Sigma 54 (σ(54)), in a purified system. We include the complete transcription system, binding interactions between σ54 and its activators, as well as the self-assembly and the critical ATPase activity of the cognate activators which serve to remodel the closed promoter complexes. We also present in vivo methodologies that are used to study the impact of physiological processes, metabolic states, global signalling networks, and cellular architecture on the control of σ(54)-dependent gene expression.
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Affiliation(s)
- Martin Buck
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK,
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Brdlik CM, Niu W, Snyder M. Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans. Methods Enzymol 2014; 539:89-111. [PMID: 24581441 DOI: 10.1016/b978-0-12-420120-0.00007-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The global identification of transcription factor (TF) binding sites is a critical step in the elucidation of the functional elements of the genome. Several methods have been developed that map TF binding in human cells, yeast, and other model organisms. These methods make use of chromatin immunoprecipitation, or ChIP, and take advantage of the fact that formaldehyde fixation of living cells can be used to cross-link DNA sequences to the TFs that bind them in vivo. In ChIP, the cross-linked TF-DNA complexes are sheared by sonication, size fractionated, and incubated with antibody specific to the TF of interest to generate a library of TF-bound DNA sequences. ChIP-chip was the first technology developed to globally identify TF-bound DNA sequences and involves subsequent hybridization of the ChIP DNA to oligonucleotide microarrays. However, ChIP-chip proved to be costly, labor-intensive, and limited by the fixed number of probes available on the microarray chip. ChIP-Seq combines ChIP with massively parallel high-throughput sequencing (see Explanatory Chapter: Next Generation Sequencing) and has demonstrated vast improvement over ChIP-chip with respect to time and cost, signal-to-noise ratio, and resolution. In particular, multiplex sequencing can be used to achieve a higher throughput in ChIP-Seq analyses involving organisms with genomes of lower complexity than that of human (Lefrançois et al., 2009) and thereby reduce the cost and amount of time needed for each result. The multiplex ChIP-Seq method described in this section has been developed for Caenorhabditis elegans, but is easily adaptable for other organisms.
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Affiliation(s)
| | - Wei Niu
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA.
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Sadhukhan A, Kobayashi Y, Kobayashi Y, Tokizawa M, Yamamoto YY, Iuchi S, Koyama H, Panda SK, Sahoo L. VuDREB2A, a novel DREB2-type transcription factor in the drought-tolerant legume cowpea, mediates DRE-dependent expression of stress-responsive genes and confers enhanced drought resistance in transgenic Arabidopsis. Planta 2014; 240:645-664. [PMID: 25030652 DOI: 10.1007/s00425-014-2111-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/17/2014] [Indexed: 06/03/2023]
Abstract
VuDREB2A exists in cowpea as a canonical DREB2-type transcription factor, having the ability to bind dehydration-responsive elements in vitro and confer enhanced drought resistance in transgenic Arabidopsis. Cowpea (Vigna unguiculata L. Walp) is an important cultivated legume that can survive better in arid conditions than other crops. But the molecular mechanisms involved in the drought tolerance of this species remain elusive with very few reported candidate genes. The Dehydration-Responsive Element-Binding Protein2 (DREB2) group of transcription factors plays key roles in plant responses to drought. However, no DREB2 ortholog has been reported from cowpea so far. In this study, we isolated and characterized a gene from cowpea, namely VuDREB2A, encoding a protein of 377 amino acids exhibiting features of reported DREB2-type proteins. In cowpea, VuDREB2A transcript accumulation was highly induced by desiccation, heat and salt, but slightly by exogenous abscisic acid (ABA) treatment. We also isolated the VuDREB2A promoter and predicted stress-responsive cis-elements in it using Arabidopsis microarray data. The E. coli-expressed VuDREB2A protein showed binding to synthetic oligonucleotides with Dehydration-Responsive Elements (DREs) from Arabidopsis, in electrophoretic mobility shift assays. Heterologous expression of VuDREB2A in Arabidopsis significantly improved plant survival under drought. In addition, overexpression of a truncated version of VuDREB2A, after removal of a putative negative regulatory domain (between amino acids 132-182) led to a dwarf phenotype in the transgenic plants. Microarray and quantitative PCR analyses of VuDREB2A overexpressing Arabidopsis revealed up-regulation of stress-responsive genes having DRE overrepresented in their promoters. In summary, our results indicate that VuDREB2A conserves the basic functionality and mode of regulation of DREB2A in Arabidopsis and could be a potent candidate gene for the genetic improvement of drought resistance in cowpea.
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Affiliation(s)
- Ayan Sadhukhan
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
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Hu X, Zhang Y, Huang Q, Wang L, Yang R, Li X, Zhou D, Zhong Q. [Purification and DNA-binding of ToxR truncated protein of Vibrio parahaemolyticus]. Wei Sheng Wu Xue Bao 2014; 54:956-961. [PMID: 25345029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
OBJECTIVE The DNA-binding domain of ToxR protein of Vibrio parahaemolyticus was expressed using the Escherichia coli BL21lambdaDE3 protein expression system, and its DNA-binding activity was characterized. METHODS The fragment of DNA-binding domain at N-terminal of ToxR (ToxR-N) was amplified by PCR from V. parahaemolyticus strain RIMD2210633, and then cloned into the BamHI and Hind III sites of the vector pET28a. The recombinant plasmid pET28a was transformed into BL21lambdaDE3. Over-expression of His-ToxR-N in the LB medium was induced by adding 1 mmol/L IPTG (isopropyl-b-D-thiogalactoside). The over-expressed protein was purified under native conditions with nickel loaded HiTrap Chelating Sepharose columns (Amersham), and then the His-tag was removed by using restricted thrombin. The electrophoretic mobility shift assay was used to analyze the DNA-binding activity of ToxR-N to the promoter-proximal DNA regions of calR and VP1687, respectively. The promoter-proximal regions of calR and VP1687 were separately cloned into the pHRP309 vector containing a promoterless lacZ gene. Then, each of the two recombinant LacZ reporter plasmids was transformed into the wide-type strain (WT) and the toxR null mutant strain (DeltatoxR), respectively, to measure the promoter activity (the beta-Galactosidase activity) of the target genes in WT and DeltatoxR by using the beta-Galactosidase Enzyme Assay System. RESULTS The purified ToxR-N protein had the ability to bind to the upstream DNA regions of calR but not VP1687. The LacZ fusion results showed that the transcription of calR and VP1687 was positively and negatively regulated by ToxR in V. parahaemolyticus, respectively. CONCLUSION The recombinant ToxR-N protein could be used for studying the transcriptional regulation mechanism in V. parahaemolyticus. ToxR fulfills a mechanism of negative regulation of T3SS1 genes by activating the expression of calR through protein-proximal promoter DNA association.
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McCarthy RR, Mooij MJ, Reen FJ, Lesouhaitier O, O'Gara F. A new regulator of pathogenicity (bvlR) is required for full virulence and tight microcolony formation in Pseudomonas aeruginosa. Microbiology (Reading) 2014; 160:1488-1500. [PMID: 24829363 DOI: 10.1099/mic.0.075291-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
LysR-type transcriptional regulators (LTTRs) are the most common family of transcriptional regulators found in the opportunistic pathogen Pseudomonas aeruginosa. They are known to regulate a wide variety of virulence determinants and have emerged recently as positive global regulators of pathogenicity in a broad spectrum of important bacterial pathogens. However, in spite of their key role in modulating expression of key virulence determinants underpinning pathogenic traits associated with the process of infection, surprisingly few are found to be transcriptionally altered by contact with host cells. BvlR (PA14_26880) an LTTR of previously unknown function, has been shown to be induced in response to host cell contact, and was therefore investigated for its potential role in virulence. BvlR expression was found to play a pivotal role in the regulation of acute virulence determinants such as type III secretion system and exotoxin A production. BvlR also played a key role in P. aeruginosa pathogenicity within the Caenorhabditis elegans acute model of infection. Loss of BvlR led to an inability to form tight microcolonies, a key step in biofilm formation in the cystic fibrosis lung, although surface attachment was increased. Unusually for LTTRs, BvlR was shown to exert its influence through the transcriptional repression of many genes, including the virulence-associated cupA and alg genes. This highlights the importance of BvlR as a new virulence regulator in P. aeruginosa with a central role in modulating key events in the pathogen-host interactome.
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Affiliation(s)
- Ronan R McCarthy
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Marlies J Mooij
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - F Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen, 55 rue Saint Germain, 27000 Evreux, France
| | - Fergal O'Gara
- Curtin University, School of Biomedical Sciences, Perth, WA, Australia
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
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Nam SW, Park KC, Choi HS, Lee B, Kim SW. Identification of Zinc Finger, MYM-type 2 (ZMYM2) as a regulator of sorafenib resistance in hepatocellular carcinoma cell lines. J Gastroenterol Hepatol 2014; 29:633-9. [PMID: 24716227 DOI: 10.1111/jgh.12414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND AND AIM Hepatocellular carcinoma (HCC) is an aggressive malignancy with a very complex molecular process. There is no successful therapy for advanced HCC at present. Recently, sorafenib has been used as a systemic therapy to improve survival in patients with advanced HCC, but increasing reports of recurrence or non-responsiveness indicate the limitations of sorafenib as a therapeutic agent. Therefore, identification of genes involved in sorafenib resistance is important to effectively treat advanced HCC. METHODS We performed a genomic screening with a short-hairpin RNA library cassette on HCC cell lines to find genes relating resistance to sorafenib. RESULTS Zinc finger, MYM type 2 (ZMYM2) was sequenced after three successive screens in vitro as a challengeable target. The inhibition of ZMYM2 resulted in sorafenib-resistance in formerly sensitive HCC cell lines. Immunohistochemical comparison of tumor and non-tumor regions showed stronger ZMYM2 staining intensities in non-tumor regions than in tumor regions. CONCLUSION ZMYM2 may play an important role in sorafenib resistance.
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Zhang P, Yang P, Zhang Z, Han B, Wang W, Wang Y, Cao Y, Hu T. Isolation and characterization of a buffalograss (Buchloe dactyloides) dehydration responsive element binding transcription factor, BdDREB2. Gene 2014; 536:123-8. [PMID: 24333268 DOI: 10.1016/j.gene.2013.11.060] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 11/15/2013] [Accepted: 11/27/2013] [Indexed: 11/23/2022]
Abstract
Dehydration responsive element binding (DREB) transcription factors play an important role in the regulation of stress-related genes. These factors contribute to resistance to different abiotic stresses. In the present study, a novel DREB transcription factor, BdDREB2, isolated from Buchloe dactyloides, was cloned and characterized. The BdDREB2 protein was estimated to have a molecular weight of 28.36kDa, a pI of 5.53 and a typical AP2/ERF domain. The expression of BdDREB2 was involved in responses to drought and salt stresses. Overexpression of BdDREB2 in tobacco showed higher relative water and proline content, and was associated with lower MDA content under drought stress, suggesting that the transgenic tobacco may tolerate drought stress better. Results demonstrate that BdDREB2 may play an important role in the regulation of abiotic stress responses, and mediate many physiological pathways that enhance stress tolerance in plants.
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Affiliation(s)
- Pan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Peizhi Yang
- Department of Grassland Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Zhiqiang Zhang
- Department of Grassland Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Bo Han
- Department of Grassland Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Weidong Wang
- Department of Grassland Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Yafang Wang
- Department of Grassland Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Yuman Cao
- Department of Grassland Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Tianming Hu
- Department of Grassland Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Abstract
BACKGROUND Studies of gene regulation often utilize genome-wide predictions of transcription factor (TF) binding sites. Most existing prediction methods are based on sequence information alone, ignoring biological contexts such as developmental stages and tissue types. Experimental methods to study in vivo binding, including ChIP-chip and ChIP-seq, can only study one transcription factor in a single cell type and under a specific condition in each experiment, and therefore cannot scale to determine the full set of regulatory interactions in mammalian transcriptional regulatory networks. RESULTS We developed a new computational approach, PIPES, for predicting tissue-specific TF binding. PIPES integrates in vitro protein binding microarrays (PBMs), sequence conservation and tissue-specific epigenetic (DNase I hypersensitivity) information. We demonstrate that PIPES improves over existing methods on distinguishing between in vivo bound and unbound sequences using ChIP-seq data for 11 mouse TFs. In addition, our predictions are in good agreement with current knowledge of tissue-specific TF regulation. CONCLUSIONS We provide a systematic map of computationally predicted tissue-specific binding targets for 284 mouse TFs across 55 tissue/cell types. Such comprehensive resource is useful for researchers studying gene regulation.
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Affiliation(s)
| | | | - Ziv Bar-Joseph
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
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Abstract
Serratia marcescens has been known as a temperature-dependent producer of two chemically different exolipids (red pigment prodigiosin and biosurfactant serrawettin W1) in parallel. During genetic investigation of such control mechanisms, mini-Tn 5 insertional mutant Tan1 overproducing these exolipids was isolated. The gene concerning such disregulation was identified as hexS by DNA cloning followed by sequencing and homology analysis of the presumed product with 314 amino-acids. The product HexS was the homologue of HexA of Erwinia carotovora ssp. carotovora and classified as a transcriptional regulator belonging to LysR family. By RT-PCR analysis, the hexS mutant was shown to over-transcribe the pigA gene (the first gene of the pig cluster involved in prodigiosin synthesis) and the swrW gene encoding serrawettin W1 synthetase belonging to the nonribosomal peptide synthetase family. In contrast, transcription of the pswP gene encoding phosphopantetheinyl transferase in Tan1 was in the level of parent strain 274. Purified protein encoded in his(6)-hexS demonstrated binding activity to DNA fragments of the upstream region of pigA and swrW genes and not to that of the pswP gene. S. marcescens strain 274 transformed with a low-copy plasmid carrying hexS demonstrated reduced production of prodigiosin and serrawettin W1, and reduced activity of exoenzymes (protease, chitinase, and DNase) except phospholipase C. Possible generation of virulent S. marcescens by derepression or mutation of the hexS gene in infected tissues or ex vivo environments was suggested.
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Affiliation(s)
- Taichiro Tanikawa
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
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Yang T, Meng L, Wang X, Wang L, Jiao K. Direct electrochemical DNA detection originated from the self-redox signal of sulfonated polyaniline enhanced by graphene oxide in neutral solution. ACS Appl Mater Interfaces 2013; 5:10889-10894. [PMID: 24088603 DOI: 10.1021/am403090y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this paper, a type of direct DNA impedance detection using the self-redox signal change of sulfonated polyaniline (SPAN) enhanced by graphene oxide (GNO) was reported, here SPAN is a copolymer obtained from aniline and m-aminobenzenesulfonic acid. The resulting nanocomposite was characterized by scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, cyclic voltammetry, and electrochemical impedance spectroscopy. The π-π planar structure of GNO and the carboxyl groups on the surface of GNO ensured it could act as an excellent substrate for adsorption and polymerization of aniline monomer. Because of the existence of GNO, the electrochemical activities of SPAN were enhanced obviously. Because of abundant sulfonic acid groups, the resulting nanocomposite showed obvious self-redox signal even at physiological pH, which is beneficial for biosensing field. DNA probes with amine groups could be covalently attached to the modified electrode surface through the acyl chloride cross-linking reaction of sulfonic groups and amines. When the flexible probe DNA was successfully grafted, the electrode was coated and electron transfer between electrode and buffer was restrained. Thus, the inner impedance value of SPAN (rather than using outer classic EIS probe, [Fe(CN)6](3-/4-)) increased significantly. After hybridization, the rigid helix opened the electron channel, which induced impedance value decreased dramatically. As an initial application of this system, the PML/RARA fusion gene sequence formed from promyelocytic leukemia (PML) and retinoic acid receptor alpha (RARA) was successfully detected.
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Affiliation(s)
- Tao Yang
- Key Laboratory of Eco-chemical Engineering (Ministry of Education), College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao 266042, China
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Shapyrina EV, Shadrin AM, Solonin AS. [Purification of recombinant Bacillus cereus ResD-ResE proteins expressed in Escherichia coli strains]. Prikl Biokhim Mikrobiol 2013; 49:547-553. [PMID: 25434178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recombinant E. coli strains expressing the Bacillus cereus ATCC 14579T resD and resEgenes fused with the ubiquitin gene were constructed, and purification of the ResD and ResE proteins was performed. The approach used in the study allowed us to increase the protein yield of the electrophoretic homogeneous ResD andResE proteins without denaturation steps up to 150 mg per gram of wet cell weight.
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Nagore LI, Nadeau RJ, Guo Q, Jadhav YLA, Jarrett HW, Haskins WE. Purification and characterization of transcription factors. Mass Spectrom Rev 2013; 32:386-398. [PMID: 23832591 PMCID: PMC3758410 DOI: 10.1002/mas.21369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 11/19/2012] [Accepted: 11/19/2012] [Indexed: 06/02/2023]
Abstract
Transcription factors (TFs) are essential for the expression of all proteins, including those involved in human health and disease. However, TFs are resistant to proteomic characterization because they are frequently masked by more abundant proteins due to the limited dynamic range of capillary liquid chromatography-tandem mass spectrometry and protein database searching. Purification methods, particularly strategies that exploit the high affinity of TFs for DNA response elements (REs) on gene promoters, can enrich TFs prior to proteomic analysis to improve dynamic range and penetrance of the TF proteome. For example, trapping of TF complexes specific for particular REs has been achieved by recovering the element DNA-protein complex on solid supports. Additional methods for improving dynamic range include two- and three-dimensional gel electrophoresis incorporating electrophoretic mobility shift assays and Southwestern blotting for detection. Here we review methods for TF purification and characterization. We fully expect that future investigations will apply these and other methods to illuminate this important but challenging proteome.
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Affiliation(s)
- LI Nagore
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
| | - RJ Nadeau
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - Q Guo
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - YLA Jadhav
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - HW Jarrett
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
| | - WE Haskins
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Departments of Biology, University of Texas at San Antonio, San Antonio, TX, 78249
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
- Departments of Medicine, Division of Hematology & Medical Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229
- Cancer Therapy & Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229
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Min X, Zhong W, Zhao S, Dong J, Dong S, Zhou A, Yan W, Wang D. [Studies on expression, purification, crystal growth and optimization of putative transcription factor LytR from Streptococcus pneumoniae]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2013; 30:812-821. [PMID: 24059062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The aim of the present study was to obtain the crystal of transcription factor LytR of streptococcus pneumoniae for X-ray crystal structure and function analysis. The LytR gene of D39 strains from Streptococcus pneumoniae (S. pn) was cloned into the prokaryotic expression vector pET32a(+), then overexpression was obtained in the E. coli BL21 (DE3) through transformation of the recombinant plasmid that had been verified by colony PCR and sequencing. Soluble fusion protein with His-tag highly expressed by the induction of 0.5 mmol/L IPTG and was purified by a three step procedure, the purity of the purified LytR recombinant protein was over 90%. Preliminary screening of crystallization conditions was performed using the hanging-drop vapour-diffusing method with Hampton Crystal screen and PEG screen kits. The protein crystals X-ray diffraction data were collected from a single crystal and more stick crystals whose X-ray diffraction reached 4.0 A were obtained. These works laid the foundation for further research on the 3D structure of putative transcription factor LytR and its biological aspects.
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Affiliation(s)
- Xun Min
- Department of Medicine Laboratory, Affliated Hospital of Zunyi Medical College, Zunyi 563003, China
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Qiu J, Liu Y, Yu M, Pang Z, Chen W, Xu Z. Identification and functional characterization of MRE-binding transcription factor (MTF) in Crassostrea gigas and its conserved role in metal-induced response. Mol Biol Rep 2013; 40:3321-31. [PMID: 23271123 DOI: 10.1007/s11033-012-2407-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 12/18/2012] [Indexed: 10/27/2022]
Abstract
The full-length cDNA that encodes the MRE-binding transcription factor (MTF) was cloned from the Pacific oyster (Crassostrea gigas) using reverse transcription polymerase chain reaction and the rapid amplification of cDNA ends. The cgMTF cDNA sequence is 2892 bp long, with a 2508 bp open reading frame that encodes an 835-amino acid polypeptide. Multiple alignment revealed that cgMTF has four putative zinc finger-like regions in cgMTF with three C2C2-type zinc fingers and one C2H2-type zinc finger. After 12 h of exposure to Cd(2+), the cgMTF mRNA level was increased in a dose-dependent manner, which then subsided with time. cgMTF stimulates the cgMT promoter reporter in the HEK293 cell line in a dose-dependent manner. When either of the metal-responsive elements (MRE1 or MRE2) of the cgMT promoter was mutated, the cgMT promoter reporter activity was significantly reduced. After the two MREs were mutated simultaneously, the promoter activity was completely abolished. In conclusion, we identified an MTF in C. gigas and revealed the presence of an evolutionarily conserved molecular mechanism for coping with environmental metal stress.
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Affiliation(s)
- Jinrong Qiu
- South China Institute of Environmental Sciences, MEP, Guangzhou 510655, China
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Deindl S, Hwang WL, Hota SK, Blosser TR, Prasad P, Bartholomew B, Zhuang X. ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps. Cell 2013; 152:442-52. [PMID: 23374341 DOI: 10.1016/j.cell.2012.12.040] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 10/16/2012] [Accepted: 12/17/2012] [Indexed: 12/27/2022]
Abstract
ISWI-family enzymes remodel chromatin by sliding nucleosomes along DNA, but the nucleosome translocation mechanism remains unclear. Here we use single-molecule FRET to probe nucleosome translocation by ISWI-family remodelers. Distinct ISWI-family members translocate nucleosomes with a similar stepping pattern maintained by the catalytic subunit of the enzyme. Nucleosome remodeling begins with a 7 bp step of DNA translocation followed by 3 bp subsequent steps toward the exit side of nucleosomes. These multi-bp, compound steps are comprised of 1 bp substeps. DNA movement on the entry side of the nucleosome occurs only after 7 bp of exit-side translocation, and each entry-side step draws in a 3 bp equivalent of DNA that allows three additional base pairs to be moved to the exit side. Our results suggest a remodeling mechanism with well-defined coordination at different nucleosomal sites featuring DNA translocation toward the exit side in 1 bp steps preceding multi-bp steps of DNA movement on the entry side.
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Affiliation(s)
- Sebastian Deindl
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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Riske F, Berard N, Albee K, Pan P, Henderson M, Adams K, Godwin S, Spear S. Development of a platform process for adenovirus purification that removes human SET and nucleolin and provides high purity vector for gene delivery. Biotechnol Bioeng 2013; 110:848-56. [PMID: 23042531 DOI: 10.1002/bit.24742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 08/23/2012] [Accepted: 09/26/2012] [Indexed: 12/16/2023]
Abstract
The manufacturing of virus occurs at a modest scale in comparison to many therapeutic proteins mainly because a gene therapy dose is typically only µg of vector. Although modest in scale the generation of high purity virus is challenging due to low viral expression levels and the difficulties in adequately characterizing such a large and complex molecule. A 100 L bioreactor might produce only 100 mg of virus that must be separated from host and process impurities that are typically greater by several orders of magnitude. Furthermore, in the later purification stages the main milieu component is often virus at low concentration (µg/mL) which may non-specifically adsorb to purification surfaces resulting in a lowered virus recovery. This study describes our approach to develop a scalable, manufacturable robust process for an Adenovirus (Ad) gene therapy vector. A number of analytical tools were developed to guide the purification design. During process development, two human proteins, SET and nucleolin, were identified in viral preparations. To our knowledge, this is the first time that SET and nucleolin have been described in Ad. In this report we detail a process for their removal and the robust removal of all process, product and host cell impurities.
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Affiliation(s)
- Frank Riske
- Department of Purification Development, Genzyme a Sanofi Company, Framingham, Massachusetts 01710, USA.
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Omer S, Kumar S, Khan BM. Over-expression of a subgroup 4 R2R3 type MYB transcription factor gene from Leucaena leucocephala reduces lignin content in transgenic tobacco. Plant Cell Rep 2013; 32:161-71. [PMID: 23052594 DOI: 10.1007/s00299-012-1350-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 09/18/2012] [Accepted: 09/19/2012] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE : LlMYB1 , a subgroup 4 R2R3-type MYB transcription factor gene from Leucaena leucocephala appears to be a repressor of lignin biosynthesis pathway by regulating the transcription of general phenylpropanoid pathway genes. R2R3MYB transcription factors are known to play a wide role in regulating the phenylpropanoid pathway in plants. In this study, we report isolation, cloning and characterization of an R2R3MYB transcription factor gene (LlMYB1) from an economically important tree species, Leucaena leucocephala. LlMYB1 consists of 705 bp coding sequence corresponding to 235 amino acids. Sequence alignment revealed that the N-terminal (MYB) domain of the gene shares up to 95 % similarity with subgroup 4 (Sg4) members of R2R3Myb gene family functionally known to be lignin repressors. Highly divergent C-terminal region of the gene carried an ERF-associated amphiphilic repression (EAR) motif, another characteristic of the Sg4. The gene was phylogenetically grouped closest with AmMYB308, a known repressor of monolignol biosynthetic pathway genes. Spatio-temporal expression studies at different ages of seedlings using quantitative real-time PCR (QRT-PCR) showed highest transcript level of the gene in 10 day old stem tissues. Over-expression of the gene in transgenic tobacco showed statistically significant decline in the transcript levels of the general phenylpropanoid pathway genes and reduction in lignin content. Our study suggests that LlMYB1 might be playing the role of a repressor of lignin biosynthesis in L. leucocephala.
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Affiliation(s)
- Sumita Omer
- Plant Tissue Culture Division, CSIR-National Chemical Laboratory, Pune 411008, India
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Abstract
Co-immunoprecipitation (Co-IP) (followed by immunoblotting) is a technique widely used to characterize specific protein-protein interactions. Investigating interactions of proteins containing "sticky" polyalanine (PolyA) tracts encounters difficulties using conventional Co-IP procedures. Here, we present strategies to specifically capture proteins containing these difficult PolyA tracts, enabling subsequent robust detection of interacting proteins by Co-IP.
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Affiliation(s)
- T R Mattiske
- Department of Paediatrics, University of Adelaide, Adelaide, SA, Australia
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Tanaka Y, Ehira S, Teramoto H, Inui M, Yukawa H. Coordinated regulation of gnd, which encodes 6-phosphogluconate dehydrogenase, by the two transcriptional regulators GntR1 and RamA in Corynebacterium glutamicum. J Bacteriol 2012; 194:6527-36. [PMID: 23024346 PMCID: PMC3497509 DOI: 10.1128/jb.01635-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 09/21/2012] [Indexed: 11/20/2022] Open
Abstract
The transcriptional regulation of Corynebacterium glutamicum gnd, encoding 6-phosphogluconate dehydrogenase, was investigated. Two transcriptional regulators, GntR1 and RamA, were isolated by affinity purification using gnd promoter DNA. GntR1 was previously identified as a repressor of gluconate utilization genes, including gnd. Involvement of RamA in gnd expression had not been investigated to date. The level of gnd mRNA was barely affected by the single deletion of ramA. However, gnd expression was downregulated in the ramA gntR1 double mutant compared to that of the gntR1 single mutant, suggesting that RamA activates gnd expression. Two RamA binding sites are found in the 5' upstream region of gnd. Mutation proximal to the transcriptional start site diminished the gluconate-dependent induction of gnd-lacZ. DNase I footprinting assay revealed two GntR1 binding sites, with one corresponding to a previously proposed site that overlaps with the -10 region. The other site overlaps the RamA binding site. GntR1 binding to this newly identified site inhibits DNA binding of RamA. Therefore, it is likely that GntR1 represses gnd expression by preventing both RNA polymerase and RamA binding to the promoter. In addition, DNA binding activity of RamA was reduced by high concentrations of NAD(P)H but not by NAD(P), implying that RamA senses the redox perturbation of the cell.
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Affiliation(s)
- Yuya Tanaka
- Research Institute of Innovative Technology for the Earth, Kizugawadai, Kizugawa, Kyoto, Japan
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Bouaziz D, Pirrello J, Ben Amor H, Hammami A, Charfeddine M, Dhieb A, Bouzayen M, Gargouri-Bouzid R. Ectopic expression of dehydration responsive element binding proteins (StDREB2) confers higher tolerance to salt stress in potato. Plant Physiol Biochem 2012; 60:98-108. [PMID: 22922109 DOI: 10.1016/j.plaphy.2012.07.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 07/26/2012] [Indexed: 05/24/2023]
Abstract
Dehydration responsive element binding proteins (DREB) are members of a larger family of transcription factors, many of which have been reported to contribute to plant responses to abiotic stresses in several species. While, little is known about their role in potato (Solanum tuberosum). This report describes the cloning and characterization of a DREB transcription factor cDNA, StDREB2, isolated from potato (cv Nicola) plants submitted to salt treatment. Based on a multiple sequence alignment, this protein was classified into the A-5 group of DREB subfamily. Expression studies revealed that StDREB2 was induced in leaves, roots and stems upon various abiotic stresses and in response to exogenous treatment with abscisic acid (ABA). In agreement with this expression pattern, over-expression of StDREB2 in transgenic potato plants resulted in enhanced tolerance to salt stress. These data suggest that the isolated StDREB2 encodes a functional protein involved in plant response to different abiotic stresses. An electrophoretic mobility shift assay (EMSA) indicated that the StDREB2 protein bound specifically to the DRE core element (ACCGAGA) in vitro. Moreover, Semi quantitative RT-PCR analysis revealed that the transcript level of a putative target gene i.e. δ(1)-pyrroline-5-carboxylate synthase (P5CS) was up-regulated in transgenic plants submitted to salt stress conditions. A concomitant increase in proline accumulation was also observed under these conditions. Taking together, all these data suggest that StDREB2 takes part in the processes underlying plant responses to abiotic stresses probably via the regulation of ABA hormone signaling and through a mechanism allowing proline synthesis.
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Affiliation(s)
- Donia Bouaziz
- Laboratoire des Biotechnologies Végétales Appliquées à l'Amélioration des Cultures, Ecole Nationale d'Ingénieurs de Sfax, Route Soukra Km 4, BP 1173, 3038 Sfax, Tunisia.
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Bai H, Lan JP, Gan Q, Wang XY, Hou MM, Cao YH, Li LY, Liu LJ, Hao YJ, Yin CC, Wu L, Zhu LH, Liu GZ. Identification and expression analysis of components involved in rice Xa21-mediated disease resistance signalling. Plant Biol (Stuttg) 2012; 14:914-922. [PMID: 22672582 DOI: 10.1111/j.1438-8677.2012.00585.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Rice Xa21 gene encodes a receptor-like kinase that confers broad-spectrum resistance against Xanthomonas oryzae pv. oryzae (Xoo). Recently, a number of genes involved in the Xa21-mediated disease resistance pathway have been identified. Based on our previous data and the literature, we chose 16 candidate proteins and made corresponding antibodies. Using Western blotting, we systematically investigated the expression profile of the proteins in Xa21-mediated disease resistance response. We found nine proteins with altered expression. We further compared their expression in resistance, susceptible and mock responses, and found that GST expression was up-regulated during the resistance process, indicating GST is a positive regulator in resistance responses. ATPsB expression was down-regulated during both the resistance and susceptible response processes, although it was higher in the resistance response than that in the susceptible response. The total amount of MYB, GAPDH, CatB, Trx and NB-ARC proteins was lower in the resistance than in the susceptible response, but their abundance per unit bacteria in the resistance response was still higher than in the susceptible response, suggesting that these proteins might be positive regulators in the resistance response. In addition, expression of another ERF was induced by inoculation with bacterial blight pathogen, and expression of Zf-LSD1 was activated by wounding stress alone. Interestingly, most proteins showed similar altered expression patterns in the resistance and susceptible responses, but differed to some extents, implying that both responses might share common molecular mechanisms. This study revealed evidence of resistance-related protein expression, providing a foundation for better understanding of their functions.
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Affiliation(s)
- H Bai
- Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
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Abstract
Human nonintegrin laminin receptor is a multifunctional protein acting as an integral component of the ribosome and a cell surface receptor for laminin-1. The laminin receptor is overexpressed in several human cancers and is also the cell surface receptor for several viruses and pathogenic prion proteins, making it a pathologically significant protein. This study focused on the proteomic characterization of laminin receptor interacting proteins from Mus musculus. The use of affinity chromatography with immobilized recombinant laminin receptor coupled with mass spectrometry analysis identified 45 proteins with high confidence. Following validation through coimmunoprecipitation, the proteins were classified based on predicted function into ribosomal, RNA processing, signal transduction/metabolism, protein processing, cytoskeleton/cell anchorage, DNA/chromatin, and unknown functions. A significant portion of the identified proteins is related to functions or localizations previously described for laminin receptor. This work represents a comprehensive proteomic approach to studying laminin receptor and provides an essential stepping stone to a better mechanistic understanding of this protein's diverse functions.
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Affiliation(s)
- Lisa Venticinque
- Gene Therapy Center, Cancer Institute and Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016
| | - Daniel Meruelo
- Gene Therapy Center, Cancer Institute and Department of Pathology, New York University School of Medicine, 550 First Avenue, New York, NY 10016
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Chen YH, Zhao L, Pang LR, Li XY, Weng SP, He JG. Identification and characterization of Inositol-requiring enzyme-1 and X-box binding protein 1, two proteins involved in the unfolded protein response of Litopenaeus vannamei. Dev Comp Immunol 2012; 38:66-77. [PMID: 22554476 DOI: 10.1016/j.dci.2012.04.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 04/13/2012] [Accepted: 04/16/2012] [Indexed: 05/31/2023]
Abstract
The inositol-requiring enzyme-1 (IRE1)-X-box binding protein 1 (IRE1-XBP1) pathway is the key branch of the unfolded protein response (UPR). To investigate the role of the IRE1-XBP1 pathway in reducing environmental stress and increasing anti-viral immunity in Litopenaeus vannamei, homologues of IRE1 (designated as LvIRE1) and XBP1 (designated as LvXBP1) were identified and characterized. The full-length cDNA of LvIRE1 is 4908bp long, with an open reading frame (ORF) that encodies a putative 1174 amino acid protein. The full-length cDNA of LvXBP1 is 1746bp long. It contains two ORFs that encode putative 278 amino acid and 157 amino acid proteins, respectively. LvXBP1 mRNA has the predicted IRE1 splicing motifs CNG'CNGN located within the loop regions of two short hairpins. Sequencing of the splicing fragment induced by endoplasmic reticulum (ER)-stress showed a 3bp or 4bp frame shift from the predicted sites. The spliced form LvXBP1 (LvXBP1s) contained an ORF encodes a putative 463 amino acid protein. The reporter gene assays indicated that LvXBP1s activates the promoter of L. vannamei immunoglobulin heavy chain binding protein (LvBip), an important UPR effector. RT-PCR showed that LvXBP1 was spliced during the experiments. For heat shock treatment, the total LvXBP1 expression was increased and peaked at about 36h, whereas the percentages of the two isoforms were relatively stable. For the WSSV challenge, LvXBP1 was upregulated during the experiment and the percentage of the spliced form continuously declined after 18h of infection. Knock-down of LvXBP1 by RNA interference resulted in a lower cumulative mortality of L. vannamei under WSSV infection. Furthermore, the expression profiles of LvIRE1 and LvXBP1 in the gills, hemocytes, intestines, and hepatopancreas of the WSSV-challenged shrimp were detected using real-time RT-PCR. Taken together, these results confirm that the IRE1-XBP1 pathway is important for L. vannamei environmental stress resistance, suggest that L. vannamei IRE1-XBP1 may activated by WSSV and be annexed to serve the virus.
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Affiliation(s)
- Yi-Hong Chen
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, PR China
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50
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Huyck RW, Keightley A, Laity JH. Expression and purification of full length mouse metal response element binding transcription factor-1 using Pichia pastoris. Protein Expr Purif 2012; 85:86-93. [PMID: 22780964 DOI: 10.1016/j.pep.2012.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/31/2012] [Accepted: 06/28/2012] [Indexed: 12/01/2022]
Abstract
The metal response element binding transcription factor-1 (MTF-1) is an important stress response, heavy metal detoxification, and zinc homeostasis factor in eukaryotic organisms from Drosophila to humans. MTF-1 transcriptional regulation is primarily mediated by elevated levels of labile zinc, which direct MTF-1 to bind the metal response element (MRE). This process involves direct zinc binding to the MTF-1 zinc fingers, and zinc dependent interaction of the MTF-1 acidic region with the p300 coactivator protein. Here, the first recombinant expression system for mutant and wild type (WT) mouse MTF-1 (mMTF-1) suitable for biochemical and biophysical studies in vitro is reported. Using the methyltropic yeast Pichia pastoris, nearly half-milligram recombinant WT and mutant mMTF-1 were produced per liter of P. pastoris cell culture, and purified by a FLAG-tag epitope. Using a first pass ammonium sulfate purification, followed by anti-FLAG affinity resin, mMTF-1 was purified to >95% purity. This recombinant mMTF-1 was then assayed for direct protein-protein interactions with p300 by co-immunoprecipitation. Surface plasmon resonance studies on mMTF-1 provided the first quantitative DNA binding affinity measurements to the MRE promotor element (K(d)=5±3 nM). Both assays demonstrated the functional activity of the recombinant mMTF-1, while elucidating the molecular basis for mMTF-1-p300 functional synergy, and provided new insights into the mMTF-1 domain specific roles in DNA binding. Overall, this production system provides accessibility for the first time to a multitude of in vitro studies using recombinant mutant and WT mMTF-1, which greatly facilitates new approaches to understanding the complex and varied functions of this protein.
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Affiliation(s)
- Ryan W Huyck
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110-2499, United States.
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