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Chowdhury MAR, Haq MM, Lee JH, Jeong S. Multi-faceted regulation of CREB family transcription factors. Front Mol Neurosci 2024; 17:1408949. [PMID: 39165717 PMCID: PMC11333461 DOI: 10.3389/fnmol.2024.1408949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/12/2024] [Indexed: 08/22/2024] Open
Abstract
cAMP response element-binding protein (CREB) is a ubiquitously expressed nuclear transcription factor, which can be constitutively activated regardless of external stimuli or be inducibly activated by external factors such as stressors, hormones, neurotransmitters, and growth factors. However, CREB controls diverse biological processes including cell growth, differentiation, proliferation, survival, apoptosis in a cell-type-specific manner. The diverse functions of CREB appear to be due to CREB-mediated differential gene expression that depends on cAMP response elements and multi-faceted regulation of CREB activity. Indeed, the transcriptional activity of CREB is controlled at several levels including alternative splicing, post-translational modification, dimerization, specific transcriptional co-activators, non-coding small RNAs, and epigenetic regulation. In this review, we present versatile regulatory modes of CREB family transcription factors and discuss their functional consequences.
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Affiliation(s)
- Md Arifur Rahman Chowdhury
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Molecular Biology, and Research Center of Bioactive Materials, Jeonbuk National University, Jeonju, Republic of Korea
| | - Md Mazedul Haq
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Molecular Biology, and Research Center of Bioactive Materials, Jeonbuk National University, Jeonju, Republic of Korea
| | - Jeong Hwan Lee
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Sangyun Jeong
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Molecular Biology, and Research Center of Bioactive Materials, Jeonbuk National University, Jeonju, Republic of Korea
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2
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Feng XA, Yamadi M, Fu Y, Ness KM, Liu C, Ahmed I, Bowman GD, Johnson ME, Ha T, Wu C. GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.14.549009. [PMID: 37502885 PMCID: PMC10369947 DOI: 10.1101/2023.07.14.549009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
To elucidate how eukaryotic sequence-specific transcription factors (TFs) search for gene targets on chromatin, we used multi-color smFRET and single-particle imaging to track the diffusion of purified GAGA-Associated Factor (GAF) on DNA and nucleosomes. Monomeric GAF DNA-binding domain (DBD) bearing one zinc finger finds its cognate site by 1D or 3D diffusion on bare DNA and rapidly slides back-and-forth between naturally clustered motifs for seconds before escape. Multimeric, full-length GAF also finds clustered motifs on DNA by 1D-3D diffusion, but remains locked on target for longer periods. Nucleosome architecture effectively blocks GAF-DBD 1D-sliding into the histone core but favors retention of GAF-DBD when targeting solvent-exposed sites by 3D-diffusion. Despite the occlusive power of nucleosomes, 1D-3D facilitated diffusion enables GAF to effectively search for clustered cognate motifs in chromatin, providing a mechanism for navigation to nucleosome and nucleosome-free sites by a member of the largest TF family.
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Affiliation(s)
- Xinyu A Feng
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maryam Yamadi
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yiben Fu
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kaitlin M Ness
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Celina Liu
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ishtiyaq Ahmed
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gregory D Bowman
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Margaret E Johnson
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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3
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Patra P, Gao YQ. Structural and dynamical aspect of DNA motif sequence specific binding of AP-1 transcription factor. J Chem Phys 2024; 160:115103. [PMID: 38506297 DOI: 10.1063/5.0196508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Activator protein-1 (AP-1) comprises one of the largest and most evolutionary conserved families of ubiquitous eukaryotic transcription factors that act as a pioneer factor. Diversity in DNA binding interaction of AP-1 through a conserved basic-zipper (bZIP) domain directs in-depth understanding of how AP-1 achieves its DNA binding selectivity and consequently gene regulation specificity. Here, we address the structural and dynamical aspects of the DNA target recognition process of AP-1 using microsecond-long atomistic simulations based on the structure of the human AP-1 FosB/JunD bZIP-DNA complex. Our results show the unique role of DNA shape features in selective base specific interactions, characteristic ion population, and solvation properties of DNA grooves to form the motif sequence specific AP-1-DNA complex. The TpG step at the two terminals of the AP-1 site plays an important role in the structural adjustment of DNA by modifying the helical twist in the AP-1 bound state. We addressed the role of intrinsic motion of the bZIP domain in terms of opening and closing gripper motions of DNA binding helices, in target site recognition and binding of AP-1 factors. Our observations suggest that binding to the cognate motif in DNA is mainly accompanied with the precise adjustment of closing gripper motion of DNA binding helices of the bZIP domain.
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Affiliation(s)
- Piya Patra
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518107 Shenzhen, China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518107 Shenzhen, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
- Biomedical Pioneering Innovation Center, Peking University, 100871 Beijing, China
- Changping Laboratory, Beijing 102200, China
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4
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Ahmad HMN, Andrade A, Song E. Continuous Real-Time Detection of Serotonin Using an Aptamer-Based Electrochemical Biosensor. BIOSENSORS 2023; 13:983. [PMID: 37998158 PMCID: PMC10669129 DOI: 10.3390/bios13110983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
Serotonin (5-HT) is a critical neurotransmitter involved in many neuronal functions, and 5-HT depletion has been linked to several mental diseases. The fast release and clearance of serotonin in the extracellular space, low analyte concentrations, and a multitude of interfering species make the detection of serotonin challenging. This work presents an electrochemical aptamer-based biosensing platform that can monitor 5-HT continuously with high sensitivity and selectivity. Our electrochemical sensor showed a response time of approximately 1 min to a step change in the serotonin concentration in continuous monitoring using a single-frequency EIS (electrochemical impedance spectroscopy) technique. The developed sensing platform was able to detect 5-HT in the range of 25-150 nM in the continuous sample fluid flow with a detection limit (LOD) of 5.6 nM. The electrochemical sensor showed promising selectivity against other species with similar chemical structures and redox potentials, including dopamine (DA), norepinephrine (NE), L-tryptophan (L-TP), 5-hydroxyindoleacetic acid (5-HIAA), and 5-hydroxytryptophan (5-HTP). The proposed sensing platform is able to achieve high selectivity in the nanomolar range continuously in real-time, demonstrating the potential for monitoring serotonin from neurons in organ-on-a-chip or brain-on-a-chip-based platforms.
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Affiliation(s)
- Habib M. N. Ahmad
- Department of Electrical & Computer Engineering, University of New Hampshire, Durham, NH 03824, USA;
| | - Arturo Andrade
- Robert J. & Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA;
- Department of Neuroscience, Brown University, Providence, RI 02912, USA
| | - Edward Song
- Department of Electrical & Computer Engineering, University of New Hampshire, Durham, NH 03824, USA;
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5
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Bravo M, Simón J, González-Recio I, Martinez-Cruz LA, Goikoetxea-Usandizaga N, Martínez-Chantar ML. Magnesium and Liver Metabolism Through the Lifespan. Adv Nutr 2023; 14:739-751. [PMID: 37207838 PMCID: PMC10334155 DOI: 10.1016/j.advnut.2023.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 05/21/2023] Open
Abstract
Within the organism, the liver is the main organ responsible for metabolic homeostasis and xenobiotic transformation. To maintain an adequate liver weight-to-bodyweight ratio, this organ has an extraordinary regenerative capacity and is able to respond to an acute insult or partial hepatectomy. Maintenance of hepatic homeostasis is crucial for the proper functioning of the liver, and in this context, adequate nutrition with macro- and micronutrient intake is mandatory. Among all known macro-minerals, magnesium has a key role in energy metabolism and in metabolic and signaling pathways that maintain liver function and physiology throughout its life span. In the present review, the cation is reported as a potential key molecule during embryogenesis, liver regeneration, and aging. The exact role of the cation during liver formation and regeneration is not fully understood due to its unclear role in the activation and inhibition of those processes, and further research in a developmental context is needed. As individuals age, they may develop hypomagnesemia, a condition that aggravates the characteristic alterations. Additionally, risk of developing liver pathologies increases with age, and hypomagnesemia may be a contributing factor. Therefore, magnesium loss must be prevented by adequate intake of magnesium-rich foods such as seeds, nuts, spinach, or rice to prevent age-related hepatic alterations and contribute to the maintenance of hepatic homeostasis. Since magnesium-rich sources include a variety of foods, a varied and balanced diet can meet both macronutrient and micronutrient needs.
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Affiliation(s)
- Miren Bravo
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio (Bizkaia), Spain
| | - Jorge Simón
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio (Bizkaia), Spain; Center for Biomedical Research in Liver and Digestive Diseases Network (CIBERehd), Bizkaia, Spain
| | - Irene González-Recio
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio (Bizkaia), Spain
| | - Luis Alfonso Martinez-Cruz
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio (Bizkaia), Spain
| | - Naroa Goikoetxea-Usandizaga
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio (Bizkaia), Spain; Center for Biomedical Research in Liver and Digestive Diseases Network (CIBERehd), Bizkaia, Spain.
| | - María Luz Martínez-Chantar
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio (Bizkaia), Spain; Center for Biomedical Research in Liver and Digestive Diseases Network (CIBERehd), Bizkaia, Spain.
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6
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Mohd Jaafar F, Monsion B, Mertens PPC, Attoui H. Identification of Orbivirus Non-Structural Protein 5 (NS5), Its Role and Interaction with RNA/DNA in Infected Cells. Int J Mol Sci 2023; 24:ijms24076845. [PMID: 37047816 PMCID: PMC10095184 DOI: 10.3390/ijms24076845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/31/2023] [Indexed: 04/09/2023] Open
Abstract
Bioinformatic analyses have predicted that orbiviruses encode an additional, small non-structural protein (NS5) from a secondary open reading frame on genome segment 10. However, this protein has not previously been detected in infected mammalian or insect cells. NS5-specific antibodies were generated in mice and were used to identify NS5 synthesised in orbivirus-infected BSR cells or cells transfected with NS5 expression plasmids. Confocal microscopy shows that although NS5 accumulates in the nucleus, particularly in the nucleolus, which becomes disrupted, it also appears in the cell cytoplasm, co-localising with mitochondria. NS5 helps to prevent the degradation of ribosomal RNAs during infection and reduces host-cell protein synthesis However, it helps to extend cell viability by supporting viral protein synthesis and virus replication. Pulldown studies showed that NS5 binds to ssRNAs and supercoiled DNAs and demonstrates interactions with ZBP1, suggesting that it modulates host-cell responses.
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Affiliation(s)
- Fauziah Mohd Jaafar
- UMR1161 VIROLOGIE, INRAE, Ecole Nationale Vétérinaire d’Alfort, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France
| | - Baptiste Monsion
- UMR1161 VIROLOGIE, INRAE, Ecole Nationale Vétérinaire d’Alfort, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France
| | - Peter P. C. Mertens
- One Virology, The Wolfson Centre for Global Virus Research, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
| | - Houssam Attoui
- UMR1161 VIROLOGIE, INRAE, Ecole Nationale Vétérinaire d’Alfort, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France
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7
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Bentley EP, Scholl D, Wright PE, Deniz AA. Coupling of binding and differential subdomain folding of the intrinsically disordered transcription factor CREB. FEBS Lett 2023; 597:917-932. [PMID: 36480418 PMCID: PMC10089947 DOI: 10.1002/1873-3468.14554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
The cyclic AMP response element binding protein (CREB) contains a basic leucine zipper motif (bZIP) that forms a coiled coil structure upon dimerization and specific DNA binding. Although this state is well characterized, key features of CREB bZIP binding and folding are not well understood. We used single-molecule Förster resonance energy transfer (smFRET) to probe conformations of CREB bZIP subdomains. We found differential folding of the basic region and leucine zipper in response to different binding partners; a strong and previously unreported DNA-independent dimerization affinity; folding upon binding to nonspecific DNA; and evidence of long-range interdomain interactions in full-length CREB that modulate DNA binding. These studies provide new insights into DNA binding and dimerization and have implications for CREB function.
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Affiliation(s)
- Emily P. Bentley
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Daniel Scholl
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
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8
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Tomaž Š, Petek M, Lukan T, Pogačar K, Stare K, Teixeira Prates E, Jacobson DA, Zrimec J, Bajc G, Butala M, Pompe Novak M, Dudley Q, Patron N, Taler-Verčič A, Usenik A, Turk D, Prat S, Coll A, Gruden K. A mini-TGA protein modulates gene expression through heterogeneous association with transcription factors. PLANT PHYSIOLOGY 2023; 191:1934-1952. [PMID: 36517238 PMCID: PMC10022624 DOI: 10.1093/plphys/kiac579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
TGA (TGACG-binding) transcription factors, which bind their target DNA through a conserved basic region leucine zipper (bZIP) domain, are vital regulators of gene expression in salicylic acid (SA)-mediated plant immunity. Here, we investigated the role of StTGA2.1, a potato (Solanum tuberosum) TGA lacking the full bZIP, which we named a mini-TGA. Such truncated proteins have been widely assigned as loss-of-function mutants. We, however, confirmed that StTGA2.1 overexpression compensates for SA-deficiency, indicating a distinct mechanism of action compared with model plant species. To understand the underlying mechanisms, we showed that StTGA2.1 can physically interact with StTGA2.2 and StTGA2.3, while its interaction with DNA was not detected. We investigated the changes in transcriptional regulation due to StTGA2.1 overexpression, identifying direct and indirect target genes. Using in planta transactivation assays, we confirmed that StTGA2.1 interacts with StTGA2.3 to activate StPRX07, a member of class III peroxidases (StPRX), which are known to play role in immune response. Finally, via structural modeling and molecular dynamics simulations, we hypothesized that the compact molecular architecture of StTGA2.1 distorts DNA conformation upon heterodimer binding to enable transcriptional activation. This study demonstrates how protein truncation can lead to distinct functions and that such events should be studied carefully in other protein families.
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Affiliation(s)
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Tjaša Lukan
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Karmen Pogačar
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Katja Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Erica Teixeira Prates
- Biosciences Division, Oak Ridge National Laboratory,, Oak Ridge, Tennessee 37831, USA
| | - Daniel A Jacobson
- Biosciences Division, Oak Ridge National Laboratory,, Oak Ridge, Tennessee 37831, USA
| | - Jan Zrimec
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Gregor Bajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maruša Pompe Novak
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
- School for Viticulture and Enology, University of Nova Gorica, 5271 Vipava, Slovenia
| | - Quentin Dudley
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Nicola Patron
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Ajda Taler-Verčič
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, 1000 Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, 1000 Ljubljana, Slovenia
| | - Salomé Prat
- Department of Plant Development and Signal Transduction, Centre for Research in Agricultural Genomics, 08193 Cerdanyola, Barcelona, Spain
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9
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Patra P, Gao YQ. Sequence-Specific Structural Features and Solvation Properties of Transcription Factor Binding DNA Motifs: Insights from Molecular Dynamics Simulation. J Phys Chem B 2022; 126:9187-9206. [PMID: 36322688 DOI: 10.1021/acs.jpcb.2c05749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sequence-specific recognition of transcription factor (TF) binding motifs in the target site of DNA over the vast amount of non-target DNA is of primary importance for the transcriptional regulation of gene expression by the TFs. Binding of TFs to the target site of DNA relies not only on the direct contact formation but also on the structural and conformational features of DNA. Recognition of DNA structural features or shape readout by proteins is an important factor in the context of TF-DNA interaction. Based on the atomistic molecular simulation, here we report the sequence-dependent unique structural features, solvation, and ion-binding properties of biologically relevant AT- and GC-rich human TF binding motifs in DNA. Counterion and water distribution around the motif is found to be sensitive to the motif sequence, which is accompanied with the DNA shape features. The motif sequence affects the electrostatic potential along the grooves, and cytosine methylation alters the DNA shape features. Characteristic solvation properties of TF binding motif DNA fragments infer that an ionic environment and hydration influences are essential to describe TF-DNA interactions.
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Affiliation(s)
- Piya Patra
- Shenzhen Bay Laboratory, Institute of Systems and Physical Biology, Shenzhen 518107, China
| | - Yi Qin Gao
- Shenzhen Bay Laboratory, Institute of Systems and Physical Biology, Shenzhen 518107, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China
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10
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Nishizaki SS, Boyle AP. SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions. BMC Bioinformatics 2022; 23:317. [PMID: 35927613 PMCID: PMC9351228 DOI: 10.1186/s12859-022-04865-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
MOTIVATION Aberrant DNA methylation in transcription factor binding sites has been shown to lead to anomalous gene regulation that is strongly associated with human disease. However, the majority of methylation-sensitive positions within transcription factor binding sites remain unknown. Here we introduce SEMplMe, a computational tool to generate predictions of the effect of methylation on transcription factor binding strength in every position within a transcription factor's motif. RESULTS SEMplMe uses ChIP-seq and whole genome bisulfite sequencing to predict effects of methylation within binding sites. SEMplMe validates known methylation sensitive and insensitive positions within a binding motif, identifies cell type specific transcription factor binding driven by methylation, and outperforms SELEX-based predictions for CTCF. These predictions can be used to identify aberrant sites of DNA methylation contributing to human disease. AVAILABILITY AND IMPLEMENTATION SEMplMe is available from https://github.com/Boyle-Lab/SEMplMe .
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Affiliation(s)
- Sierra S Nishizaki
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
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11
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Wang S, Xia D, Wang X, Cao H, Wu C, Sun Z, Zhang D, Liu H. C/EBPβ regulates the JAK/STAT signaling pathway in triple-negative breast cancer. FEBS Open Bio 2021; 11:1250-1258. [PMID: 33660927 PMCID: PMC8016132 DOI: 10.1002/2211-5463.13138] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/17/2020] [Accepted: 03/03/2021] [Indexed: 11/21/2022] Open
Abstract
C/EBPβ is a member of the CCAAT/enhancer‐binding protein (C/EBP) family, which consists of a number of b‐ZIP transcription factors. Although C/EBPβ has been implicated in the development of certain cancers, including breast cancer, it remains unknown whether dysregulation of C/EBPβ in breast cancer is subtype‐specific. Moreover, the underlying mechanisms by which C/EBPβ regulates breast cancer carcinogenesis are not fully understood. Here, we present evidence that C/EBPβ is specifically overexpressed in human TNBC samples, but not in non‐TNBC samples. C/EBPβ depletion dramatically suppressed TNBC cell growth, migration, invasion, and colony formation ability. A subsequent mechanistic study revealed that the JAK/STAT signaling pathway was upregulated in C/EBPβ_high TNBC samples compared with C/EBPβ_low TNBC samples. C/EBPβ ChIP‐seq and qPCR were performed to demonstrate that C/EBPβ directly binds to and regulates JAK/STAT signaling pathway genes in TNBC. Taken together, our data indicate the oncogenic role of C/EBPβ in human TNBC and reveal a novel mechanism by which C/EBPβ promotes TNBC carcinogenesis.
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Affiliation(s)
- Shu Wang
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, China
| | - Dian Xia
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, China
| | - Xianzhi Wang
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, China.,School of Pharmacy, Bengbu Medical College, China
| | - Haowei Cao
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, China
| | - Chaoshen Wu
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, China
| | - Zhaoran Sun
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, China
| | - Daoyong Zhang
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, China
| | - Hao Liu
- School of Pharmacy, Bengbu Medical College, China
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12
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Goett-Zink L, Klocke JL, Bögeholz LAK, Kottke T. In-cell infrared difference spectroscopy of LOV photoreceptors reveals structural responses to light altered in living cells. J Biol Chem 2020; 295:11729-11741. [PMID: 32580943 PMCID: PMC7450117 DOI: 10.1074/jbc.ra120.013091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/21/2020] [Indexed: 12/19/2022] Open
Abstract
Proteins are usually studied in well-defined buffer conditions, which differ substantially from those within a host cell. In some cases, the intracellular environment has an impact on the mechanism, which might be missed by in vitro experiments. IR difference spectroscopy previously has been applied to study the light-induced response of photoreceptors and photoenzymes in vitro Here, we established the in-cell IR difference (ICIRD) spectroscopy in the transmission and attenuated total reflection configuration to investigate the light-induced response of soluble proteins in living bacterial cells. ICIRD spectroscopy on the light, oxygen, or voltage (LOV) domains of the blue light receptors aureochrome and phototropin revealed a suppression of the response of specific secondary structure elements, indicating that the intracellular environment affects LOV photoreceptor mechanisms in general. Moreover, in-cell fluorescence spectroscopy disclosed that the intracellular environment slows down the recovery of the light-induced flavin adduct. Segment-resolved ICIRD spectroscopy on basic-region leucine zipper (bZIP)-LOV of aureochrome 1a from the diatom Phaeodactylum tricornutum indicated a signal progression from the LOV sensor to the bZIP effector independent of unfolding of the connecting A'α-helix, an observation that stood in contrast to in vitro results. This deviation was recapitulated in vitro by emulating the intracellular environment through the addition of the crowding agent BSA, but not by sucrose polymers. We conclude that ICIRD spectroscopy is a noninvasive, label-free approach for assessing conformational changes in receptors in living cells at ambient conditions. As demonstrated, these near-native responses may deviate from the mechanisms established under in vitro conditions.
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Affiliation(s)
- Lukas Goett-Zink
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Jessica L Klocke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Lena A K Bögeholz
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
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13
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Shimaoka T, Wang Y, Morishima M, Miyamoto S, Ono K. Magnesium Deficiency Causes Transcriptional Downregulation of Kir2.1 and Kv4.2 Channels in Cardiomyocytes Resulting in QT Interval Prolongation. Circ J 2020; 84:1244-1253. [DOI: 10.1253/circj.cj-20-0310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Toru Shimaoka
- Department of Pathophysiology, Oita University School of Medicine
- Department of Cardiovascular Surgery, Oita University School of Medicine
| | - Yan Wang
- Department of Pathophysiology, Oita University School of Medicine
| | - Masaki Morishima
- Department of Pathophysiology, Oita University School of Medicine
| | - Shinji Miyamoto
- Department of Cardiovascular Surgery, Oita University School of Medicine
| | - Katsushige Ono
- Department of Pathophysiology, Oita University School of Medicine
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14
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Cuculis L, Zhao C, Abil Z, Zhao H, Shukla D, Schroeder CM. Divalent cations promote TALE DNA-binding specificity. Nucleic Acids Res 2020; 48:1406-1422. [PMID: 31863586 PMCID: PMC7026652 DOI: 10.1093/nar/gkz1174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/18/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Recent advances in gene editing have been enabled by programmable nucleases such as transcription activator-like effector nucleases (TALENs) and CRISPR–Cas9. However, several open questions remain regarding the molecular machinery in these systems, including fundamental search and binding behavior as well as role of off-target binding and specificity. In order to achieve efficient and specific cleavage at target sites, a high degree of target site discrimination must be demonstrated for gene editing applications. In this work, we studied the binding affinity and specificity for a series of TALE proteins under a variety of solution conditions using in vitro fluorescence methods and molecular dynamics (MD) simulations. Remarkably, we identified that TALEs demonstrate high sequence specificity only upon addition of small amounts of certain divalent cations (Mg2+, Ca2+). However, under purely monovalent salt conditions (K+, Na+), TALEs bind to specific and non-specific DNA with nearly equal affinity. Divalent cations preferentially bind to DNA over monovalent cations, which attenuates non-specific interactions between TALEs and DNA and further stabilizes specific interactions. Overall, these results uncover new mechanistic insights into the binding action of TALEs and further provide potential avenues for engineering and application of TALE- or TALEN-based systems for genome editing and regulation.
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Affiliation(s)
| | - Chuankai Zhao
- Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA
| | - Zhanar Abil
- Department of Biochemistry, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemistry, Urbana, IL 61801, USA.,Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA.,Department of Biochemistry, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, Urbana, IL 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, Urbana, IL 61801, USA.,National Center for Supercomputing Applications, Urbana, IL 61801, USA.,NIH Center for Macromolecular Modeling and Bioinformatics, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Charles M Schroeder
- Department of Chemistry, Urbana, IL 61801, USA.,Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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15
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Purkait R, Sinha C. Solvent-tuned discriminant sensing of Al3+, Mg2+and HF2−by vanilinyl-picolinyl hydrazide Schiff base. NEW J CHEM 2019. [DOI: 10.1039/c9nj00325h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
X-ray structurally characterized solid-state emissive vanilinyl organic entity shows fluorescence sensitivity towards multi-analytes.
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Affiliation(s)
- Rakesh Purkait
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032
- India
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16
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Shnitkind S, Martinez-Yamout MA, Dyson HJ, Wright PE. Structural Basis for Graded Inhibition of CREB:DNA Interactions by Multisite Phosphorylation. Biochemistry 2018; 57:6964-6972. [PMID: 30507144 PMCID: PMC6474821 DOI: 10.1021/acs.biochem.8b01092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphorylation of the kinase inducible domain (KID) of the cyclic AMP response element binding transcription factor (CREB) regulates its function through several mechanisms. Transcriptional activation occurs following phosphorylation at serine 133, but multisite phosphorylation in a neighboring region termed the CK cassette, residues 108-117, results in inhibition of CREB-mediated transcription. A molecular-level understanding of the mechanism of these opposing reactions has been lacking, in part because of the difficulty of preparing multiply phosphorylated CREB in vitro. By substituting a single residue, we have generated an engineered mammalian CREB in which the CK cassette can be phosphorylated in vitro by casein kinases and have characterized its interactions with cyclic AMP response element DNA. Phosphorylation of the CK cassette promotes an intramolecular interaction between the KID domain and the site of DNA binding, the basic region of the C-terminal basic leucine zipper (bZip) domain. Competition between the phosphorylated KID domain and DNA for bZip binding results in a decreased affinity of CREB for DNA. The binding free energy calculated from the dissociation constant is directly proportional to the number of phosphate groups in the CK cassette, indicating that the DNA binding is regulated by a rheostat-like mechanism. The rheostat is modulated by variation of the concentration of cations such as Mg2+ and by alternative isoforms such as the natural CREB isoform that lacks residues 162-272. Multisite phosphorylation of CREB represents a versatile mechanism by which transcription can be tuned to meet the variable needs of the cell.
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Affiliation(s)
- Sergey Shnitkind
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla California 92037
| | - Maria A. Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla California 92037
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla California 92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla California 92037
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17
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Tateyama S, Kobayashi I, Hisatomi O. Target Sequence Recognition by a Light-Activatable Basic Leucine Zipper Factor, Photozipper. Biochemistry 2018; 57:6615-6623. [PMID: 30388362 DOI: 10.1021/acs.biochem.8b00995] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photozipper (PZ) is a light-activatable basic leucine zipper (bZIP) protein composed of a bZIP domain and a light-oxygen-voltage-sensing domain of aureochrome-1. Blue light induces dimerization and subsequently increases the affinity of PZ for the target DNA sequence. We prepared site-directed PZ mutants in which Asn131 (N131) in the basic region was substituted with Ala and Gln. N131 mutants showed spectroscopic and dimerization properties almost identical to those of wild-type PZ and an increase in helical content in the presence of the target sequence. Quantitative analyses by an electrophoretic mobility shift assay and quartz crystal microbalance (QCM) measurements demonstrated that the half-maximal effective concentrations of N131 mutants to bind to the target sequence were significantly higher than those of PZ. QCM data also revealed that N131 substitutions accelerated the dissociation without affecting the association, suggesting that a base-specific interaction of N131 occurred after the association between PZ and DNA. Activation of PZ by illumination decreased both the standard errors and the unstable period of QCM data. Optical control of transcription factors will provide new knowledge of the recognition of the target sequence.
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Affiliation(s)
- Samu Tateyama
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Toyonaka , Osaka 560-0043 , Japan
| | - Itsuki Kobayashi
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Toyonaka , Osaka 560-0043 , Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Toyonaka , Osaka 560-0043 , Japan
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18
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Nakatani Y, Hisatomi O. Quantitative analyses of the equilibria among DNA complexes of a blue-light-regulated bZIP module, Photozipper. Biophys Physicobiol 2018; 15:8-17. [PMID: 29450110 PMCID: PMC5812316 DOI: 10.2142/biophysico.15.0_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/21/2017] [Indexed: 01/28/2023] Open
Abstract
Aureochrome1 is a blue-light-receptor protein identified in a stramenopile alga, Vaucheria frigida. Photozipper (PZ) is an N-terminally truncated, monomeric, V. frigida aureochrome1 fragment containing a basic leucine zipper (bZIP) domain and a light–oxygen–voltage (LOV)-sensing domain. PZ dimerizes upon photoexcitation and consequently increases its affinity for the target sequence. In the present study, to understand the equilibria among DNA complexes of PZ, DNA binding by PZ and mutational variants was quantitatively investigated by electrophoretic-mobility-shift assay and fluorescence-correlation spectroscopy in the dark and light states. DNA binding by PZ was sequence-specific and light-dependent. The half-maximal effective concentration of PZ for binding to the target DNA sequence was ~40 nM in the light, which was >10-fold less than the value in the dark. By contrast, the dimeric PZ-S2C variant (with intermolecular disulfide bonds) had higher affinity for the target sequence, with dissociation constants of ~4 nM, irrespective of the light conditions. Substitutions of Glu159 and Lys164 in the leucine zipper region decreased the affinity of PZ for the target sequence, especially in the light, suggesting that these residues form inter-helical salt bridges between leucine zipper regions, stabilizing the dimer–DNA complex. Our quantitative analyses of the equilibria in PZ–DNA-complex formation suggest that the blue-light-induced dimerization of LOV domains and coiled-coil formation by leucine zipper regions are the primary determinants of the affinity of PZ for the target sequence.
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Affiliation(s)
- Yoichi Nakatani
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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19
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A-ZIP53, a dominant negative reveals the molecular mechanism of heterodimerization between bZIP53, bZIP10 and bZIP25 involved in Arabidopsis seed maturation. Sci Rep 2017; 7:14343. [PMID: 29084982 PMCID: PMC5662769 DOI: 10.1038/s41598-017-14167-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/05/2017] [Indexed: 12/31/2022] Open
Abstract
In Arabidopsis, maturation phase, an intricate process in seed formation is tightly regulated by the DNA binding activity of protagonist basic leucine zipper 53 (bZIP53) transcription factor and its heterodimerizing partners, bZIP10 and bZIP25. Structural determinants responsible for heterodimerization specificity of bZIP53 are poorly understood. Analysis of amino acid sequences of three bZIPs does not identify interactions that may favor heterodimerization. Here, we describe a designed dominant negative termed A-ZIP53 that has a glutamic acid-rich amphipathic peptide sequence attached to N-terminal of bZIP53 leucine zipper. Circular dichroism (CD) and mass spectrometry studies with equimolar mixture of three bZIP proteins in pairs showed no heterodimer formation whereas A-ZIP53 interacted and formed stable heterodimers with bZIP53, bZIP10, and bZIP25. A-ZIP53 electrostatically mimics DNA and can overcome repulsion between basic DNA binding regions of three bZIP proteins. Gel shift experiments showed that A-ZIP53 can inhibit the DNA binding of three proteins. CD studies demonstrated the specificity of A-ZIP53 as it did not interact with bZIP39 and bZIP72. Transient co-transfections in Arabidopsis protoplasts showed that A-ZIP53 inhibited three bZIPs and their putative heterodimers-mediated transactivation of GUS reporter gene. Furthermore, four newly designed acidic extensions were evaluated for their ability to interact with three bZIPs.
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20
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Syed KS, He X, Tillo D, Wang J, Durell SR, Vinson C. 5-Methylcytosine (5mC) and 5-Hydroxymethylcytosine (5hmC) Enhance the DNA Binding of CREB1 to the C/EBP Half-Site Tetranucleotide GCAA. Biochemistry 2016; 55:6940-6948. [PMID: 27951657 DOI: 10.1021/acs.biochem.6b00796] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In human and mouse stem cells and brain, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) can occur outside of CG dinucleotides. Using protein binding microarrays (PBMs) containing 60-mer DNA probes, we evaluated the effect of 5mC and 5hmC on one DNA strand on the double-stranded DNA binding of the mouse B-ZIP transcription factors (TFs) CREB1, ATF1, and JUND. 5mC inhibited binding of CREB1 to the canonical CRE half-site |GTCA but enhanced binding to the C/EBP half-site |GCAA. 5hmC inhibited binding of CREB1 to all 8-mers except TGAT|GCAA, where binding is enhanced. We observed similar DNA binding patterns with ATF1, a closely related B-ZIP domain. In contrast, both 5mC and 5hmC inhibited binding of JUND. These results identify new DNA sequences that are well-bound by CREB1 and ATF1 only when they contain 5mC or 5hmC. Analysis of two X-ray structures examines the consequences of 5mC and 5hmC on DNA binding by CREB and FOS|JUN.
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Affiliation(s)
- Khund Sayeed Syed
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
| | - Ximiao He
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
| | - Desiree Tillo
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
| | - Jun Wang
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
| | - Stewart R Durell
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
| | - Charles Vinson
- Laboratory of Metabolism and ‡Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health , Room 3128, Building 37, Bethesda, Maryland 20892, United States
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21
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Rossetti M, Ranallo S, Idili A, Palleschi G, Porchetta A, Ricci F. Allosteric DNA nanoswitches for controlled release of a molecular cargo triggered by biological inputs. Chem Sci 2016; 8:914-920. [PMID: 28572901 PMCID: PMC5452262 DOI: 10.1039/c6sc03404g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/03/2016] [Indexed: 12/14/2022] Open
Abstract
A rationally designed new class of DNA-based nanoswitches allosterically regulated by specific biological targets, antibodies and transcription factors, can load and release a molecular cargo in a controlled fashion.
Here we demonstrate the rational design of a new class of DNA-based nanoswitches which are allosterically regulated by specific biological targets, antibodies and transcription factors, and are able to load and release a molecular cargo (i.e. doxorubicin) in a controlled fashion. In our first model system we rationally designed a stem-loop DNA-nanoswitch that adopts two mutually exclusive conformations: a “Load” conformation containing a doxorubicin-intercalating domain and a “Release” conformation containing a duplex portion recognized by a specific transcription-factor (here Tata Binding Protein). The binding of the transcription factor pushes this conformational equilibrium towards the “Release” state thus leading to doxorubicin release from the nanoswitch. In our second model system we designed a similar stem-loop DNA-nanoswitch for which conformational change and subsequent doxorubicin release can be triggered by a specific antibody. Our approach augments the current tool kit of smart drug release mechanisms regulated by different biological inputs.
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Affiliation(s)
- Marianna Rossetti
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Simona Ranallo
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Andrea Idili
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Giuseppe Palleschi
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Alessandro Porchetta
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Francesco Ricci
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
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22
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Banerjee A, Herman E, Serif M, Maestre-Reyna M, Hepp S, Pokorny R, Kroth PG, Essen LO, Kottke T. Allosteric communication between DNA-binding and light-responsive domains of diatom class I aureochromes. Nucleic Acids Res 2016; 44:5957-70. [PMID: 27179025 PMCID: PMC4937327 DOI: 10.1093/nar/gkw420] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/04/2016] [Indexed: 12/20/2022] Open
Abstract
The modular architecture of aureochrome blue light receptors, found in several algal groups including diatoms, is unique by having the LOV-type photoreceptor domain fused to the C-terminus of its putative effector, an N-terminal DNA-binding bZIP module. The structural and functional understanding of aureochromes’ light-dependent signaling mechanism is limited, despite their promise as an optogenetic tool. We show that class I aureochromes 1a and 1c from the diatom Phaeodactylum tricornutum are regulated in a light-independent circadian rhythm. These aureochromes are capable to form functional homo- and heterodimers, which recognize the ACGT core sequence within the canonical ‘aureo box’, TGACGT, in a light-independent manner. The bZIP domain holds a more folded and less flexible but extended conformation in the duplex DNA-bound state. FT-IR spectroscopy in the absence and the presence of DNA shows light-dependent helix unfolding in the LOV domain, which leads to conformational changes in the bZIP region. The solution structure of DNA bound to aureochrome points to a tilted orientation that was further validated by molecular dynamics simulations. We propose that aureochrome signaling relies on an allosteric pathway from LOV to bZIP that results in conformational changes near the bZIP-DNA interface without major effects on the binding affinity.
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Affiliation(s)
- Ankan Banerjee
- Structural Biochemistry - Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Elena Herman
- Physical and Biophysical Chemistry - Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Manuel Serif
- Plant Ecophysiology - Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Sec. 2 Nankang, Taipei 11529, Taiwan
| | - Sebastian Hepp
- Structural Biochemistry - Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Richard Pokorny
- Faculty of Biology, Department of Plant Physiology and Photobiology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Peter G Kroth
- Plant Ecophysiology - Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Lars-Oliver Essen
- Structural Biochemistry - Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry - Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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23
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Heintz U, Schlichting I. Blue light-induced LOV domain dimerization enhances the affinity of Aureochrome 1a for its target DNA sequence. eLife 2016; 5:e11860. [PMID: 26754770 PMCID: PMC4721966 DOI: 10.7554/elife.11860] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/25/2015] [Indexed: 01/03/2023] Open
Abstract
The design of synthetic optogenetic tools that allow precise spatiotemporal control of biological processes previously inaccessible to optogenetic control has developed rapidly over the last years. Rational design of such tools requires detailed knowledge of allosteric light signaling in natural photoreceptors. To understand allosteric communication between sensor and effector domains, characterization of all relevant signaling states is required. Here, we describe the mechanism of light-dependent DNA binding of the light-oxygen-voltage (LOV) transcription factor Aureochrome 1a from Phaeodactylum tricornutum (PtAu1a) and present crystal structures of a dark state LOV monomer and a fully light-adapted LOV dimer. In combination with hydrogen/deuterium-exchange, solution scattering data and DNA-binding experiments, our studies reveal a light-sensitive interaction between the LOV and basic region leucine zipper DNA-binding domain that together with LOV dimerization results in modulation of the DNA affinity of PtAu1a. We discuss the implications of these results for the design of synthetic LOV-based photosensors with application in optogenetics.
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Affiliation(s)
- Udo Heintz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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24
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Quantitative imaging of magnesium distribution at single-cell resolution in brain tumors and infiltrating tumor cells with secondary ion mass spectrometry (SIMS). J Neurooncol 2015; 127:33-41. [PMID: 26703785 DOI: 10.1007/s11060-015-2022-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/18/2015] [Indexed: 02/07/2023]
Abstract
Glioblastoma multiforme (GBM) is one of the deadliest forms of human brain tumors. The infiltrative pattern of growth of these tumors includes the spread of individual and/or clusters of tumor cells at some distance from the main tumor mass in parts of the brain protected by an intact blood-brain-barrier. Pathophysiological studies of GBM could be greatly enhanced by analytical techniques capable of in situ single-cell resolution measurements of infiltrating tumor cells. Magnesium homeostasis is an area of active investigation in high grade gliomas. In the present study, we have used the F98 rat glioma as a model of human GBM and an elemental/isotopic imaging technique of secondary ion mass spectrometry, a CAMECA IMS-3f ion microscope, for studying Mg distribution with single-cell resolution in freeze-dried brain tissue cryosections. Quantitative observations were made on tumor cells in the main tumor mass, contiguous brain tissue, and infiltrating tumor cells in adjacent normal brain. The brain tissue contained a significantly lower total Mg concentration of 4.70 ± 0.93 mmol/kg wet weight (mean ± SD) in comparison to 11.64 ± 1.96 mmol/kg wet weight in tumor cells of the main tumor mass and 10.72 ± 1.76 mmol/kg wet weight in infiltrating tumor cells (p < 0.05). The nucleus of individual tumor cells contained elevated levels of bound Mg. These observations have established that there was enhanced influx and increased binding of Mg in tumor cells. They provide strong support for further investigation of altered Mg homeostasis and activation of Mg-transporting channels in GBMs as possible therapeutic targets.
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Yamanaka R, Shindo Y, Karube T, Hotta K, Suzuki K, Oka K. Neural depolarization triggers Mg2+ influx in rat hippocampal neurons. Neuroscience 2015; 310:731-41. [DOI: 10.1016/j.neuroscience.2015.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/26/2015] [Accepted: 10/02/2015] [Indexed: 12/14/2022]
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Cohen DM, Won KJ, Nguyen N, Lazar MA, Chen CS, Steger DJ. ATF4 licenses C/EBPβ activity in human mesenchymal stem cells primed for adipogenesis. eLife 2015; 4:e06821. [PMID: 26111340 PMCID: PMC4501333 DOI: 10.7554/elife.06821] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 06/25/2015] [Indexed: 12/24/2022] Open
Abstract
A well-established cascade of transcription factor (TF) activity orchestrates adipogenesis in response to chemical cues, yet how cell-intrinsic determinants of differentiation such as cell shape and/or seeding density inform this transcriptional program remain enigmatic. Here, we uncover a novel mechanism licensing transcription in human mesenchymal stem cells (hMSCs) adipogenically primed by confluence. Prior to adipogenesis, confluency promotes heterodimer recruitment of the bZip TFs C/EBPβ and ATF4 to a non-canonical C/EBP DNA sequence. ATF4 depletion decreases both cell-density-dependent transcription and adipocyte differentiation. Global profiling in hMSCs and a novel cell-free assay reveals that ATF4 requires C/EBPβ for genomic binding at a motif distinct from that bound by the C/EBPβ homodimer. Our observations demonstrate that C/EBPβ bridges the transcriptional programs in naïve, confluent cells and early differentiating pre-adipocytes. Moreover, they suggest that homo- and heterodimer formation poise C/EBPβ to execute diverse and stage-specific transcriptional programs by exploiting an expanded motif repertoire.
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Affiliation(s)
- Daniel M Cohen
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Kyoung-Jae Won
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Nha Nguyen
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Mitchell A Lazar
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Christopher S Chen
- Department of Biomedical Engineering, Boston University, Boston, United States
| | - David J Steger
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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Nerlich A, Ruangkiattikul N, Laarmann K, Janze N, Dittrich-Breiholz O, Kracht M, Goethe R. C/EBPβ is a transcriptional key regulator of IL-36α in murine macrophages. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:966-78. [PMID: 26066982 DOI: 10.1016/j.bbagrm.2015.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/15/2015] [Accepted: 06/01/2015] [Indexed: 12/25/2022]
Abstract
Interleukin (IL)-36α - one of the novel members of the IL-1 family of cytokines - is a potent regulator of dendritic and T cells and plays an important role in inflammatory processes like experimental skin inflammation in mice and in mouse models for human psoriasis. Here, we demonstrate that C/EBPβ, a transcription factor required for the selective expression of inflammatory genes, is a key activator of the Il36A gene in murine macrophages. RNAi-mediated suppression of C/EBPβ expression in macrophages (C/EBPβ(low) cells) significantly impaired Il36A gene induction following challenge with LPS. Despite the presence of five predicted C/EBP binding sites, luciferase reporter assays demonstrated that C/EBPβ confers responsiveness to LPS primarily through a half-CRE•C/EBP element in the proximal Il36A promoter. Electrophoretic mobility shift assays showed that C/EBPβ but not CREB proteins interact with this critical half-CRE•C/EBP element. In addition, overexpression of C/EBPβ in C/EBPβ(low) cells enhanced the expression of Il36A whereas CREB-1 had no effect. Finally, chromatin immunoprecipitation confirmed that C/EBPβ but neither CREB-1, ATF-2 nor ATF4 is directly recruited to the proximal promoter region of the Il36A gene. Together, these findings demonstrate an essential role of C/EBPβ in the regulation of the Il36A gene via the proximal half-CRE•C/EBP element in response to inflammatory stimuli.
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Affiliation(s)
- Andreas Nerlich
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany.
| | - Nanthapon Ruangkiattikul
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | - Kristin Laarmann
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | - Nina Janze
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | | | - Michael Kracht
- Rudolf -Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
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Wang M, Banerjee K, Baker H, Cave JW. Nucleotide sequence conservation of novel and established cis-regulatory sites within the tyrosine hydroxylase gene promoter. ACTA ACUST UNITED AC 2014; 10:74-90. [PMID: 25774193 DOI: 10.1007/s11515-014-1341-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Tyrosine hydroxylase (TH) is the rate-limiting enzyme in catecholamine biosynthesis and its gene proximal promoter ( < 1 kb upstream from the transcription start site) is essential for regulating transcription in both the developing and adult nervous systems. Several putative regulatory elements within the TH proximal promoter have been reported, but evolutionary conservation of these elements has not been thoroughly investigated. Since many vertebrate species are used to model development, function and disorders of human catecholaminergic neurons, identifying evolutionarily conserved transcription regulatory mechanisms is a high priority. In this study, we align TH proximal promoter nucleotide sequences from several vertebrate species to identify evolutionarily conserved motifs. This analysis identified three elements (a TATA box, cyclic AMP response element (CRE) and a 5'-GGTGG-3' site) that constitute the core of an ancient vertebrate TH promoter. Focusing on only eutherian mammals, two regions of high conservation within the proximal promoter were identified: a ∼250 bp region adjacent to the transcription start site and a ∼85 bp region located approximately 350 bp further upstream. Within both regions, conservation of previously reported cis-regulatory motifs and human single nucleotide variants was evaluated. Transcription reporter assays in a TH -expressing cell line demonstrated the functionality of highly conserved motifs in the proximal promoter regions and electromobility shift assays showed that brain-region specific complexes assemble on these motifs. These studies also identified a non-canonical CRE binding (CREB) protein recognition element in the proximal promoter. Together, these studies provide a detailed analysis of evolutionary conservation within the TH promoter and identify potential cis-regulatory motifs that underlie a core set of regulatory mechanisms in mammals.
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Affiliation(s)
- Meng Wang
- Burke Medical Research Institute, White Plains, NY 10605, USA
| | | | - Harriet Baker
- Burke Medical Research Institute, White Plains, NY 10605, USA ; Weill Cornell Medical College Brain and Mind Research Institute, NY 10065, USA
| | - John W Cave
- Burke Medical Research Institute, White Plains, NY 10605, USA ; Weill Cornell Medical College Brain and Mind Research Institute, NY 10065, USA
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Rastinejad F, Ollendorff V, Polikarpov I. Nuclear receptor full-length architectures: confronting myth and illusion with high resolution. Trends Biochem Sci 2014; 40:16-24. [PMID: 25435400 DOI: 10.1016/j.tibs.2014.10.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/29/2014] [Accepted: 10/30/2014] [Indexed: 12/31/2022]
Abstract
The crystal structures of three nuclear receptor (NR) complexes have emerged to reveal their multidomain architectures on DNA. These pictures provide unprecedented views of interfacial couplings between the DNA-binding domains (DBDs) and ligand-binding domains (LBDs). The detailed pictures contrast with previous interpretations of low-resolution electron microscopy (EM) and small angle X-ray scattering (SAXS) data, which had suggested a common architecture with noninteracting DBDs and LBDs. Revisiting both historical and recent interpretations of NR architecture, we invoke new principles underlying higher-order quaternary organization and the allosteric transmission of signals between domains. We also discuss how NR architectures are being probed in living cells to understand dimerization and DNA-binding events in real time.
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Affiliation(s)
- Fraydoon Rastinejad
- Sanford-Burnham Medical Research Institute, Metabolic Disease Program, 6400 Sanger Road, Lake Nona, FL 32827, USA.
| | - Vincent Ollendorff
- INRA, UMR866 Dynamique Musculaire et Métabolisme, F-34060 Montpellier Université Montpellier 1, F-34000 Montpellier - Université Montpellier 2, F-34000 Montpellier, France
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense, 400, São Carlos, SP, 13560-970, Brazil
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Hariharan P, Hari N, Anthony SP. Triphenylamine based new Schiff base ligand: Solvent dependent selective fluorescence sensing of Mg 2+ and Fe 3+ ions. INORG CHEM COMMUN 2014. [DOI: 10.1016/j.inoche.2014.08.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Analysis of RXR/THR and RXR/PPARG2 heterodimerization by bioluminescence resonance energy transfer (BRET). PLoS One 2013; 8:e84569. [PMID: 24391967 PMCID: PMC3877338 DOI: 10.1371/journal.pone.0084569] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/25/2013] [Indexed: 01/18/2023] Open
Abstract
Background Nuclear receptors (NR) regulate transcription of genes involved in many biological processes such as development, cell proliferation, differentiation and cell death. Amongst them, PPARG2 and THR control tissue glucose and lipid homeostasis which are deregulated in severe pathophysiological conditions such as metabolic syndromes. Methodology/Principal Findings Here, we describe a real time BRET approach to monitor heterodimerization between RXR and PPARG2 or THR in vitro or in living cells. The presence of a specific DNA target was required to induce in vitro a BRET shift reflecting heterodimerization of RXR/PPARG2 or RXR/THR. As in electrophoretic mobility shift assay (EMSA), the stringency and specificity of the BRET shift assay depended upon assay condition optimization including MgCl2 concentration. For the nuclear receptors, we found by mutagenesis analysis that each heterodimer partner must harbor an intact DNA binding domain to induce BRET and heterodimerization on a DNA target. Moreover the interaction between the PPARG2 ligand binding domain and the RXR DNA binding domain stabilized the heterodimer on its DNA target. BRET microscopy in living cells highlighted the heterodimerization of RXR/PPARG2 within the nucleus clustered in discrete foci that may represent active target gene transcription regulation regions. BRET imaging also suggested that heterodimerization between RXR and PPARG2 required the DNA binding of PPARG2. Conclusions/Significance The BRET approach described here allowed us to study the dynamic interactions which exist between NR in vitro or in living cells and can provide important information on heterodimerization modes, affinity with a given RE and subcellular localization of the heterodimers. This method could be used to study real time changes of NR heterodimers occurring on DNA depending upon cell activation, chromatin state and help to define the mechanisms of ligands or drug action designed to target NRs.
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Mann IK, Chatterjee R, Zhao J, He X, Weirauch MT, Hughes TR, Vinson C. CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo. Genome Res 2013; 23:988-97. [PMID: 23590861 PMCID: PMC3668366 DOI: 10.1101/gr.146654.112] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Two Agilent DNA array designs were used. One contained 40,000 features using de Bruijn sequences where each 8-mer occurs 32 times in various positions in the DNA sequence. The second contained 180,000 features with each CG containing 8-mer occurring three times. The first design was better for identification of binding motifs, while the second was better for quantification. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD, and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. The electrophoretic mobility shift assay (EMSA) confirmed these results. CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50× methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo. CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome. After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays. This methodology can be used to identify new methylated DNA sequences preferentially bound by TFs, which may be functional in vivo.
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Krasikova YS, Rechkunova NI, Maltseva EA, Craescu CT, Petruseva IO, Lavrik OI. Influence of centrin 2 on the interaction of nucleotide excision repair factors with damaged DNA. BIOCHEMISTRY (MOSCOW) 2012; 77:346-53. [PMID: 22809153 DOI: 10.1134/s0006297912040050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have examined the influence of centrin 2 (Cen2) on the interaction of nucleotide excision repair factors (XPC-HR23b, RPA, and XPA) with 48-mer DNA duplexes bearing the dUMP derivative 5-{3-[6-(carboxyamidofluoresceinyl)amidocapromoyl]allyl}-2'-deoxyuridine-5'-monophosphate. The fluorescein residue linked to the nucleotide base imitates a bulky lesion of DNA. Cen2 stimulated the binding and increased the yield of DNA adducts with XPC-HR23b, a protein recognizing bulky damages in DNA. Stimulation of the binding was most pronounced in the presence of Mg(2+) and demonstrated a bell-shaped dependence on Cen2 concentration. The addition of Cen2 changed the stoichiometry of RPA-DNA complexes and diminished the yield of RPA-DNA covalent crosslinks. We have shown that Cen2 influences the binding of RPA and XPA with DNA, which results in formation of additional DNA-protein complexes possibly including Cen2. We have also found some evidence of direct contacts between Cen2 and DNA. These results in concert with the literature data suggest that Cen2 can be a regulatory element in the nucleotide excision repair system.
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Affiliation(s)
- Y S Krasikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentieva 8, 630090 Novosibirsk, Russia
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Yamashima T. ‘PUFA–GPR40–CREB signaling’ hypothesis for the adult primate neurogenesis. Prog Lipid Res 2012; 51:221-31. [DOI: 10.1016/j.plipres.2012.02.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Dong Y, Li J, Jiang X, Song F, Cheng Y, Zhu C. Na+ Triggered Fluorescence Sensors for Mg2+ Detection Based on a Coumarin Salen Moiety. Org Lett 2011; 13:2252-5. [DOI: 10.1021/ol200530g] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yu Dong
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Junfeng Li
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Xiaoxiang Jiang
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Fengyan Song
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Yixiang Cheng
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Chengjian Zhu
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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Merz K, Herold S, Lie DC. CREB in adult neurogenesis - master and partner in the development of adult-born neurons? Eur J Neurosci 2011; 33:1078-86. [DOI: 10.1111/j.1460-9568.2011.07606.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Repression of transcriptional activity of C/EBPalpha by E2F-dimerization partner complexes. Mol Cell Biol 2010; 30:2293-304. [PMID: 20176812 DOI: 10.1128/mcb.01619-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The transcription factor CCAAT/enhancer-binding protein alpha (C/EBPalpha) coordinates proliferation arrest and the differentiation of myeloid progenitors, adipocytes, hepatocytes, keratinocytes, and cells of the lung and placenta. C/EBPalpha transactivates lineage-specific differentiation genes and inhibits proliferation by repressing E2F-regulated genes. The myeloproliferative C/EBPalpha BRM2 mutant serves as a paradigm for recurrent human C-terminal bZIP C/EBPalpha mutations that are involved in acute myeloid leukemogenesis. BRM2 fails to repress E2F and to induce adipogenesis and granulopoiesis. The data presented here show that, independently of pocket proteins, C/EBPalpha interacts with the dimerization partner (DP) of E2F and that C/EBPalpha-E2F/DP interaction prevents both binding of C/EBPalpha to its cognate sites on DNA and transactivation of C/EBP target genes. The BRM2 mutant, in addition, exhibits enhanced interaction with E2F-DP and reduced affinity toward DNA and yet retains transactivation potential and differentiation competence that becomes exposed when E2F/DP levels are low. Our data suggest a tripartite balance between C/EBPalpha, E2F/DP, and pocket proteins in the control of proliferation, differentiation, and tumorigenesis.
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Rishi V, Oh WJ, Heyerdahl SL, Zhao J, Scudiero D, Shoemaker RH, Vinson C. 12 Arylstibonic acids that inhibit the DNA binding of five B-ZIP dimers. J Struct Biol 2010; 170:216-25. [PMID: 20176111 DOI: 10.1016/j.jsb.2010.02.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 02/16/2010] [Accepted: 02/16/2010] [Indexed: 01/07/2023]
Abstract
Previously, we identified an arylstibonic acid, NSC13778 that specifically binds to the basic region of the C/EBPalpha B-ZIP domain and disrupts DNA binding. We now examine a panel of 14 additional arylstibonic acid derivatives of NSC13778 for their ability to inhibit the DNA binding of five B-ZIP dimers (c-Fos|JunD, VBP, C/EBPalpha, C/EBPbeta, and CREB). They show various specificities at inhibiting the DNA binding of five B-ZIP domains. NSC13746 inhibits the DNA binding of C/EBPbeta and CREB at 100nM and promiscuously inhibiting the DNA binding of all five proteins in the 1muM range. Dialysis experiments indicate that NSC 13746 binding to the B-ZIP domain is reversible. Thermal denaturation studies indicate that NSC13746 binds the B-ZIP domain. Some compounds specifically inhibit DNA binding, with VBP and c-Fos|JunD being most easily disrupted. These compounds inhibit, with similar specificities to the pure B-ZIP domains, the DNA binding of nuclear extract to the AP1 DNA sequence but no inhibition is observed to SP1 containing oligonucleotide. Transient transfection assays indicate that NSC13746 can inhibit the TPA induced activation of two B-ZIP dependent reporters. These experiments suggest that arylstibonic acids are promising leads for inhibiting the DNA binding of a group of B-ZIP proteins in cells.
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Affiliation(s)
- Vikas Rishi
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Building 37, Room 3128, Bethesda, MD 20892, USA
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Rozenberg J, Rishi V, Orosz A, Moitra J, Glick A, Vinson C. Inhibition of CREB function in mouse epidermis reduces papilloma formation. Mol Cancer Res 2009; 7:654-64. [PMID: 19435810 DOI: 10.1158/1541-7786.mcr-08-0011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We used a double transgenic tetracycline system to conditionally express A-CREB, a dominant negative protein that prevents the DNA binding and function of cAMP-responsive element binding protein (CREB) family members, in mouse basal epidermis using the keratin 5 promoter. There was no phenotype in the adult. However, following a 7,12-dimethylbenz(a)anthracene (DMBA)/phorbol-12-myristate-13-acetate two-stage skin carcinogenesis experiment, A-CREB-expressing epidermis develop 5-fold fewer papillomas than wild-type controls. However, A-CREB expression one month after DMBA treatment does not prevent papilloma formation, suggesting that CREB functions at an early stage of papilloma formation. Oncogenic H-Ras genes with A-->T mutations in codon 61 were found in wild-type skin but not in A-CREB-expressing skin 2 days after DMBA treatment, suggesting that A-CREB either prevents DMBA mutagenesis or kills oncogenic H-Ras cells. In primary keratinocyte cultures, A-CREB expression induced apoptosis of v-Ras(Ha)-infected cells and suppressed the expression of cell cycle proteins cyclin B1 and cyclin D1. These results suggest that inhibiting CREB function is a valuable cancer prevention strategy.
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Affiliation(s)
- Julian Rozenberg
- Laboratory of Metabolism, National Cancer Institute, NIH, 37 Convent Drive, Room 2D24, Bethesda, MD 20892, USA
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CCAAT/enhancer-binding protein beta: its role in breast cancer and associations with receptor tyrosine kinases. Expert Rev Mol Med 2009; 11:e12. [PMID: 19351437 DOI: 10.1017/s1462399409001033] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The CCAAT/enhancer-binding proteins (C/EBPs) are a family of leucine-zipper transcription factors that regulate gene expression to control cellular proliferation, differentiation, inflammation and metabolism. Encoded by an intronless gene, C/EBPbeta is expressed as several distinct protein isoforms (LAP1, LAP2, LIP) whose expression is regulated by the differential use of several in-frame translation start sites. LAP1 and LAP2 are transcriptional activators and are associated with differentiation, whereas LIP is frequently elevated in proliferative tissue and acts as a dominant-negative inhibitor of transcription. However, emerging evidence suggests that LIP can serve as a transcriptional activator in some cellular contexts, and that LAP1 and LAP2 might also have unique actions. The LIP:LAP ratio is crucial for the maintenance of normal growth and development, and increases in this ratio lead to aggressive forms of breast cancer. This review discusses the regulation of C/EBPbeta activity by post-translational modification, the individual actions of LAP1, LAP2 and LIP, and the functions and downstream targets that are unique to each isoform. The role of the C/EBPbeta isoforms in breast cancer is discussed and emphasis is placed on their interactions with receptor tyrosine kinases.
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Agarwal S, Kumar R, Gupta P, Dixit A. Identification and Characterization of a Positive Regulatory cis-element Within the Upstream Region of c-jun. J Biochem 2008; 144:741-52. [DOI: 10.1093/jb/mvn129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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Oh WJ, Rishi V, Orosz A, Gerdes MJ, Vinson C. Inhibition of CCAAT/enhancer binding protein family DNA binding in mouse epidermis prevents and regresses papillomas. Cancer Res 2007; 67:1867-76. [PMID: 17308129 DOI: 10.1158/0008-5472.can-06-2746] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The CCAAT/enhancer binding proteins (C/EBP) are a family of B-ZIP DNA binding proteins that act as transcription factors to regulate growth and differentiation of many cell types, including keratinocytes. To examine the consequences of inhibiting the C/EBP family of transcription factors in skin, we generated transgenic mice that use the tetracycline system to conditionally express A-C/EBP, a dominant negative that inhibits the DNA binding of C/EBP family members. We expressed A-C/EBP in the basal layer of the skin epidermis during a two-step skin carcinogenesis protocol. A-C/EBP expression caused hyperplasia of the basal epidermis and increased apoptosis in the suprabasal epidermis. The mice developed fewer papillomas and had systemic hair loss. A-C/EBP expression caused C/EBPbeta protein to disappear whereas C/EBPalpha, p53, Bax, and caspase-3 protein levels were dramatically up-regulated in the suprabasal layer. Primary keratinocytes recapitulate the A-C/EBP induction of cell growth and increase in p53 protein. A-C/EBP expression after papilloma development caused the papillomas to regress with an associated increase in apoptosis and up-regulation of p53 protein. Furthermore, A-C/EBP-expressing mice heterozygous for p53 were more susceptible to papilloma formation, suggesting that the suppression of papilloma formation has a p53-dependent mechanism. These results implicate DNA binding of C/EBP family members as a potential molecular therapeutic target.
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Affiliation(s)
- Won Jun Oh
- Laboratory of Metabolism, National Cancer Institute, Center for Cancer Research/NIH, Bethesda, MD 20892, USA
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Gerdes MJ, Myakishev M, Frost NA, Rishi V, Moitra J, Acharya A, Levy MR, Park SW, Glick A, Yuspa SH, Vinson C. Activator protein-1 activity regulates epithelial tumor cell identity. Cancer Res 2006; 66:7578-88. [PMID: 16885357 DOI: 10.1158/0008-5472.can-06-1247] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To examine the consequences of inhibiting activator protein-1 (AP-1) transcription factors in skin, transgenic mice were generated, which use the tetracycline system to conditionally express A-FOS, a dominant negative that inhibits AP-1 DNA binding. Older mice develop mild alopecia and hyperplasia of sebaceous glands, particularly around the eyes. When A-FOS was expressed during chemical-induced skin carcinogenesis, mice do not develop characteristic benign and malignant squamous lesions but instead develop benign sebaceous adenomas containing a signature mutation in the H-ras proto-oncogene. Inhibiting AP-1 activity after tumor formation caused squamous tumors to transdifferentiate into sebaceous tumors. Furthermore, reactivating AP-1 in sebaceous tumors results in a reciprocal transdifferentiation into squamous tumors. In both cases of transdifferentiation, individual cells express molecular markers for both cell types, indicating individual tumor cells have the capacity to express multiple lineages. Molecular characterization of cultured keratinocytes and tumor material indicates that AP-1 regulates the balance between the wnt/beta-catenin and hedgehog signaling pathways that determine squamous and sebaceous lineages, respectively. Chromatin immunoprecipitation analysis indicates that c-Jun binds several wnt promoters, which are misregulated by A-FOS expression, suggesting that members of the wnt pathway can be a primary targets of AP-1 transcriptional regulation. Thus, AP-1 activity regulates tumor cell lineage and is essential to maintain the squamous tumor cell identity.
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Affiliation(s)
- Michael J Gerdes
- Laboratory of Cellular Carcinogenesis and Tumor Promotion, National Cancer Institute, Center for Cancer Research, Bethesda, MD 20892, USA
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Amoutzias GD, Bornberg-Bauer E, Oliver SG, Robertson DL. Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network. BMC Genomics 2006; 7:107. [PMID: 16674813 PMCID: PMC1479340 DOI: 10.1186/1471-2164-7-107] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Accepted: 05/04/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND bZIPs are transcription factors that are found throughout the eukarya from fungi to flowering plants and mammals. They contain highly conserved basic region (BR) and leucine zipper (LZ) domains and often function as environmental sensors. Specifically, bZIPs frequently have a role in mediating the response to oxidative stress, a crucial environmental signal that needs to be transduced to the gene regulatory network. RESULTS Based on sequence comparisons and experimental data on a number of important bZIP transcription factors, we predict which bZIPs are under redox control and which are regulated via protein phosphorylation. By integrating genomic, phylogenetic and functional data from the literature, we then propose a link between oxidative stress and the choice of interaction partners for the bZIP proteins. CONCLUSION This integration permits the bZIP dimerization network to be interpreted in functional terms, especially in the context of the role of bZIP proteins in the response to environmental stress. This analysis demonstrates the importance of abiotic factors in shaping regulatory networks.
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Affiliation(s)
- Gregory D Amoutzias
- Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Erich Bornberg-Bauer
- Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- Bioinformatics Division, Institute of Botany, School of Biological Sciences, University of Münster, Schlossplatz 4, D4814P, Germany
| | - Stephen G Oliver
- Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - David L Robertson
- Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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Rishi V, Potter T, Laudeman J, Reinhart R, Silvers T, Selby M, Stevenson T, Krosky P, Stephen AG, Acharya A, Moll J, Oh WJ, Scudiero D, Shoemaker RH, Vinson C. A high-throughput fluorescence-anisotropy screen that identifies small molecule inhibitors of the DNA binding of B-ZIP transcription factors. Anal Biochem 2005; 340:259-71. [PMID: 15840499 DOI: 10.1016/j.ab.2005.02.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Indexed: 11/28/2022]
Abstract
We have developed a high-throughput fluorescence anisotropy screen, using a 384-well format, to identify small molecules that disrupt the DNA binding of B-ZIP proteins. Binding of a B-ZIP dimer to fluorescently labeled DNA can be monitored by fluorescence anisotropy. We screened the National Cancer Institute diversity set of 1990 compounds to identify small molecules that disrupt the B-ZIP|DNA complex of CREB, C/EBPbeta, VBP, and AP-1 (FOS|JUND) bound to their cognate DNA sequence. We identified 21 compounds that inhibited the DNA binding of at least one B-ZIP protein, and 12 representative compounds were grouped depending on whether they displaced ethidium bromide from DNA. Of the 6 compounds that did not displace ethidium bromide, 2 also inhibited B-ZIP binding to DNA in a secondary electrophoretic mobility shift assay screen with some specificity. Thermal stability monitored by circular dichroism spectroscopy demonstrated that both compounds bound the basic region of the B-ZIP motif. NSC13778 preferentially binds C/EBPalpha 1000-fold better than it binds C/EBPbeta. Chimeric proteins combining C/EBPalpha and C/EBPbeta mapped the binding of NSC13778 to three amino acids immediately N terminal of the leucine zipper of C/EBPalpha. These experiments suggest that the DNA binding of B-ZIP transcription factors is a potential target for clinical intervention.
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Affiliation(s)
- Vikas Rishi
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C. Clustering of DNA sequences in human promoters. Genome Res 2004; 14:1562-74. [PMID: 15256515 PMCID: PMC509265 DOI: 10.1101/gr.1953904] [Citation(s) in RCA: 174] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long (8-mer) in a set of 13,010 human genomic promoter sequences aligned relative to the putative transcription start site (TSS). A limited number of 8-mers have peaks in their distribution (cluster), and most cluster within 100 bp of the TSS. The 156 DNA sequences exhibiting the greatest statistically significant clustering near the TSS can be placed into nine groups of related sequences. Each group is defined by a consensus sequence, and seven of these consensus sequences are known binding sites for the transcription factors (TFs) SP1, NF-Y, ETS, CREB, TBP, USF, and NRF-1. One sequence, which we named Clus1, is not a known TF binding site. The ninth sequence group is composed of the strand-specific Kozak sequence that clusters downstream of the TSS. An examination of the co-occurrence of these TF consensus sequences indicates a positive correlation for most of them except for sequences bound by TBP (the TATA box). Human mRNA expression data from 29 tissues indicate that the ETS, NRF-1, and Clus1 sequences that cluster are predominantly found in the promoters of housekeeping genes (e.g., ribosomal genes). In contrast, TATA is more abundant in the promoters of tissue-specific genes. This analysis identified eight DNA sequences in 5082 promoters that we suggest are important for regulating gene expression.
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Affiliation(s)
- Peter C FitzGerald
- Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Rishi V, Gal J, Krylov D, Fridriksson J, Boysen MS, Mandrup S, Vinson C. SREBP-1 dimerization specificity maps to both the helix-loop-helix and leucine zipper domains: use of a dominant negative. J Biol Chem 2003; 279:11863-74. [PMID: 14702347 DOI: 10.1074/jbc.m308000200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian SREBP family contains two genes that code for B-HLH-ZIP proteins that bind sequence-specific DNA to regulate the expression of genes involved in lipid metabolism. We have designed a dominant negative (DN), termed A-SREBP-1, that inhibits the DNA binding of either SREBP protein. A-SREBP-1 consists of the dimerization domain of B-SREBP-1 and a polyglutamic acid sequence that replaces the basic region. A-SREBP-1 heterodimerizes with either B-SREBP-1 or B-SREBP-2, and both heterodimers are more stable than B-SREBP-1 bound to DNA. Circular dichroism thermal denaturation studies show that the B-SREBP-1.A-SREBP-1 heterodimer is -9.8 kcal mol(-1) dimer(-1) more stable than the B-SREBP-1 homodimer. EMSA assays demonstrate that A-SREBP-1 can inhibit the DNA binding of either B-SREBP-1 or B-SREBP-2 in an equimolar competition but does not inhibit the DNA binding of the three B-HLH-ZIP proteins MAX, USF, or MITF, even at 100 molar eq. Chimeric proteins containing the HLH domain of SREBP-1 and the leucine zipper from either MAX, USF, or MITF indicate that both the HLH and leucine zipper regions of SREBP-1 contribute to its dimerization specificity. Transient co-transfection studies demonstrate that A-SREBP-1 can inhibit the transactivation of SREBP-1 and SREBP-2 but not USF. A-SREBP-1 may be useful in metabolic diseases where SREBP family members are overexpressed.
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Affiliation(s)
- Vikas Rishi
- Laboratory of Metabolism, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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