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Gou Y, Jing Y, Song J, Nagdy MM, Peng C, Zeng L, Chen M, Lan X, Htun ZLL, Liao Z, Li Y. A novel bHLH gene responsive to low nitrogen positively regulates the biosynthesis of medicinal tropane alkaloids in Atropa belladonna. Int J Biol Macromol 2024; 266:131012. [PMID: 38522709 DOI: 10.1016/j.ijbiomac.2024.131012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Medicinal tropane alkaloids (TAs), including hyoscyamine, anisodamine and scopolamine, are essential anticholinergic drugs specifically produced in several solanaceous plants. Atropa belladonna is one of the most important medicinal plants that produces TAs. Therefore, it is necessary to cultivate new A. belladonna germplasm with the high content of TAs. Here, we found that the levels of TAs were elevated under low nitrogen (LN) condition, and identified a LN-responsive bHLH transcription factor (TF) of A. belladonna (named LNIR) regulating the biosynthesis of TAs. The expression level of LNIR was highest in secondary roots where TAs are synthesized specifically, and was significantly induced by LN. Further research revealed that LNIR directly activated the transcription of hyoscyamine 6β-hydroxylase gene (H6H) by binding to its promoter, which converts hyoscyamine into anisodamine and subsequently epoxidizes anisodamine to form scopolamine. Overexpression of LNIR upregulated the expression levels of TA biosynthesis genes and consequently led to the increased production of TAs. In summary, we functionally identified a LN-responsive bHLH gene that facilitated the development of A. belladonna with high-yield TAs under the decreased usage of nitrogen fertilizer.
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Affiliation(s)
- Yuqin Gou
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yanming Jing
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiaxin Song
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Mohammad Mahmoud Nagdy
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; Department of Medicinal and Aromatic Plants Research, National Research Centre, 12311 Dokki, Cairo, Egypt
| | - Chao Peng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Lingjiang Zeng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Min Chen
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Centre, The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Xizang Characteristic Agricultural and Animal Husbandry Resources, Tibet Agriculture and Animal Husbandry College, Nyingchi of Xizang 860000, China
| | - Zun Lai Lai Htun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China; Department of Botany, University of Magway, Magway 04012, Myanmar
| | - Zhihua Liao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Yan Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City State Key Laboratory of Silkworm Genome Biology, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Yadav Y, Subbaroyan A, Martin OC, Samal A. Relative importance of composition structures and biologically meaningful logics in bipartite Boolean models of gene regulation. Sci Rep 2022; 12:18156. [PMID: 36307465 PMCID: PMC9616893 DOI: 10.1038/s41598-022-22654-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/18/2022] [Indexed: 12/31/2022] Open
Abstract
Boolean networks have been widely used to model gene networks. However, such models are coarse-grained to an extent that they abstract away molecular specificities of gene regulation. Alternatively, bipartite Boolean network models of gene regulation explicitly distinguish genes from transcription factors (TFs). In such bipartite models, multiple TFs may simultaneously contribute to gene regulation by forming heteromeric complexes, thus giving rise to composition structures. Since bipartite Boolean models are relatively recent, an empirical investigation of their biological plausibility is lacking. Here, we estimate the prevalence of composition structures arising through heteromeric complexes. Moreover, we present an additional mechanism where composition structures may arise as a result of multiple TFs binding to cis-regulatory regions and provide empirical support for this mechanism. Next, we compare the restriction in BFs imposed by composition structures and by biologically meaningful properties. We find that though composition structures can severely restrict the number of Boolean functions (BFs) driving a gene, the two types of minimally complex BFs, namely nested canalyzing functions (NCFs) and read-once functions (RoFs), are comparatively more restrictive. Finally, we find that composition structures are highly enriched in real networks, but this enrichment most likely comes from NCFs and RoFs.
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Affiliation(s)
- Yasharth Yadav
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
| | - Ajay Subbaroyan
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | - Olivier C Martin
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France.
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif sur Yvette, France.
| | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India.
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India.
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Wang J, Zhang S, Qiao H, Wang J. UMAP-DBP: An Improved DNA-Binding Proteins Prediction Method Based on Uniform Manifold Approximation and Projection. Protein J 2021; 40:562-75. [PMID: 34176069 DOI: 10.1007/s10930-021-10011-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 10/21/2022]
Abstract
DNA-binding proteins play a vital role in cellular processes. It is an extremely urgent to develop a high-throughput method for efficiently identifying DNA-binding proteins. According to the current research situation, some methods in machine learning and deep learning show excellent computational speed and accuracy, which are worthy of application. In this work, a novel predictor was proposed to predict DNA binding proteins called UMAP-DBP. Firstly, the feature extraction of primary protein sequence was realized based on physicochemical distance transformation, Profile-based auto-cross covariance and General series correlation pseudo amino acid composition. Secondly, uniform manifold approximation and projection (UMAP) and feature importance score methods were used for feature selection; there is a progressive relationship between them. Finally, the Adaboost operation engine with jackknife test were adopted for predicting DNA-binding proteins. For the jackknife test on the BP1075 and BP594, we obtained an overall accuracy of 82.97% and 82.14%, Cohen's kappa (CK) of 0.66 and 0.64, respectively. The results illustrate that a feasible method has been developed for predicting DNA-binding proteins by UMAP and Adaboost. This is the first study in which UMAP has been successfully applied to identify DNA-binding proteins. All the datasets and codes are accessible at https://github.com/Wang-Jinyue/UMAP-DBP .
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Horne CR, Venugopal H, Panjikar S, Wood DM, Henrickson A, Brookes E, North RA, Murphy JM, Friemann R, Griffin MDW, Ramm G, Demeler B, Dobson RCJ. Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism. Nat Commun 2021; 12:1988. [PMID: 33790291 PMCID: PMC8012715 DOI: 10.1038/s41467-021-22253-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 03/03/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism. The GntR superfamily is one of the largest families of transcription factors in prokaryotes. Here the authors combine biophysical analysis and structural biology to dissect the mechanism by which NanR — a GntR-family regulator — binds to its promoter to repress the transcription of genes necessary for sialic acid metabolism.
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Affiliation(s)
- Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Hariprasad Venugopal
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - David M Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Emre Brookes
- Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Michael D W Griffin
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Georg Ramm
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. .,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia.
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5
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Hennigs JK, Cao A, Li CG, Shi M, Mienert J, Miyagawa K, Körbelin J, Marciano DP, Chen PI, Roughley M, Elliott MV, Harper RL, Bill M, Chappell J, Moonen JR, Diebold I, Wang L, Snyder MP, Rabinovitch M. PPARγ-p53-Mediated Vasculoregenerative Program to Reverse Pulmonary Hypertension. Circ Res 2021; 128:401-418. [PMID: 33322916 PMCID: PMC7908816 DOI: 10.1161/circresaha.119.316339] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RATIONALE In pulmonary arterial hypertension (PAH), endothelial dysfunction and obliterative vascular disease are associated with DNA damage and impaired signaling of BMPR2 (bone morphogenetic protein type 2 receptor) via two downstream transcription factors, PPARγ (peroxisome proliferator-activated receptor gamma), and p53. OBJECTIVE We investigated the vasculoprotective and regenerative potential of a newly identified PPARγ-p53 transcription factor complex in the pulmonary endothelium. METHODS AND RESULTS In this study, we identified a pharmacologically inducible vasculoprotective mechanism in pulmonary arterial and lung MV (microvascular) endothelial cells in response to DNA damage and oxidant stress regulated in part by a BMPR2 dependent transcription factor complex between PPARγ and p53. Chromatin immunoprecipitation sequencing and RNA-sequencing established an inducible PPARγ-p53 mediated regenerative program regulating 19 genes involved in lung endothelial cell survival, angiogenesis and DNA repair including, EPHA2 (ephrin type-A receptor 2), FHL2 (four and a half LIM domains protein 2), JAG1 (jagged 1), SULF2 (extracellular sulfatase Sulf-2), and TIGAR (TP53-inducible glycolysis and apoptosis regulator). Expression of these genes was partially impaired when the PPARγ-p53 complex was pharmacologically disrupted or when BMPR2 was reduced in pulmonary artery endothelial cells (PAECs) subjected to oxidative stress. In endothelial cell-specific Bmpr2-knockout mice unable to stabilize p53 in endothelial cells under oxidative stress, Nutlin-3 rescued endothelial p53 and PPARγ-p53 complex formation and induced target genes, such as APLN (apelin) and JAG1, to regenerate pulmonary microvessels and reverse pulmonary hypertension. In PAECs from BMPR2 mutant PAH patients, pharmacological induction of p53 and PPARγ-p53 genes repaired damaged DNA utilizing genes from the nucleotide excision repair pathway without provoking PAEC apoptosis. CONCLUSIONS We identified a novel therapeutic strategy that activates a vasculoprotective gene regulation program in PAECs downstream of dysfunctional BMPR2 to rehabilitate PAH PAECs, regenerate pulmonary microvessels, and reverse disease. Our studies pave the way for p53-based vasculoregenerative therapies for PAH by extending the therapeutic focus to PAEC dysfunction and to DNA damage associated with PAH progression.
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Affiliation(s)
- Jan K. Hennigs
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pneumology & Center for Pulmonary Arterial Hypertension Hamburg
- II. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Aiqin Cao
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caiyun G. Li
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Minyi Shi
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julia Mienert
- Department of Pneumology & Center for Pulmonary Arterial Hypertension Hamburg
- II. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kazuya Miyagawa
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jakob Körbelin
- Department of Pneumology & Center for Pulmonary Arterial Hypertension Hamburg
- II. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - David P. Marciano
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pin-I Chen
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Roughley
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew V. Elliott
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rebecca L. Harper
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Bill
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James Chappell
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jan-Renier Moonen
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Isabel Diebold
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lingli Wang
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marlene Rabinovitch
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
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Rajeev L, Garber ME, Mukhopadhyay A. Tools to map target genes of bacterial two-component system response regulators. Environ Microbiol Rep 2020; 12:267-276. [PMID: 32212247 PMCID: PMC7318608 DOI: 10.1111/1758-2229.12838] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 05/05/2023]
Abstract
Studies on bacterial physiology are incomplete without knowledge of the signalling and regulatory systems that a bacterium uses to sense and respond to its environment. Two-component systems (TCSs) are among the most prevalent bacterial signalling systems, and they control essential and secondary physiological processes; however, even in model organisms, we lack a complete understanding of the signals sensed, the phosphotransfer partners and the functions regulated by these systems. In this review, we discuss several tools to map the genes targeted by transcriptionally acting TCSs. Many of these tools have been used for studying individual TCSs across diverse species, but systematic approaches to delineate entire signalling networks have been very few. Since genome sequences and high-throughput technologies are now readily available, the methods presented here can be applied to characterize the entire DNA-binding TCS signalling network in any bacterial species and are especially useful for non-model environmental bacteria.
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Affiliation(s)
- Lara Rajeev
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Megan E. Garber
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Department of Comparative BiochemistryUniversity of CaliforniaBerkeleyCA94720USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Department of Comparative BiochemistryUniversity of CaliforniaBerkeleyCA94720USA
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
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7
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Srivastava D, Mahony S. Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns. Biochim Biophys Acta Gene Regul Mech 2020; 1863:194443. [PMID: 31639474 PMCID: PMC7166147 DOI: 10.1016/j.bbagrm.2019.194443] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/21/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022]
Abstract
Transcription factors (TFs) selectively bind distinct sets of sites in different cell types. Such cell type-specific binding specificity is expected to result from interplay between the TF's intrinsic sequence preferences, cooperative interactions with other regulatory proteins, and cell type-specific chromatin landscapes. Cell type-specific TF binding events are highly correlated with patterns of chromatin accessibility and active histone modifications in the same cell type. However, since concurrent chromatin may itself be a consequence of TF binding, chromatin landscapes measured prior to TF activation provide more useful insights into how cell type-specific TF binding events became established in the first place. Here, we review the various sequence and chromatin determinants of cell type-specific TF binding specificity. We identify the current challenges and opportunities associated with computational approaches to characterizing, imputing, and predicting cell type-specific TF binding patterns. We further focus on studies that characterize TF binding in dynamic regulatory settings, and we discuss how these studies are leading to a more complex and nuanced understanding of dynamic protein-DNA binding activities. We propose that TF binding activities at individual sites can be viewed along a two-dimensional continuum of local sequence and chromatin context. Under this view, cell type-specific TF binding activities may result from either strongly favorable sequence features or strongly favorable chromatin context.
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Affiliation(s)
- Divyanshi Srivastava
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America.
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8
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Bischof LF, Haurat MF, Albers SV. Two membrane-bound transcription factors regulate expression of various type-IV-pili surface structures in Sulfolobus acidocaldarius. PeerJ 2019; 7:e6459. [PMID: 30828487 PMCID: PMC6396743 DOI: 10.7717/peerj.6459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/15/2019] [Indexed: 11/20/2022] Open
Abstract
In Archaea and Bacteria, gene expression is tightly regulated in response to environmental stimuli. In the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius nutrient limitation induces expression of the archaellum, the archaeal motility structure. This expression is orchestrated by a complex hierarchical network of positive and negative regulators-the archaellum regulatory network (arn). The membrane-bound one-component system ArnR and its paralog ArnR1 were recently described as main activators of archaellum expression in S. acidocaldarius. They regulate gene expression of the archaellum operon by targeting the promoter of flaB, encoding the archaellum filament protein. Here we describe a strategy for the isolation and biochemical characterization of these two archaellum regulators. Both regulators are capable of forming oligomers and are phosphorylated by the Ser/Thr kinase ArnC. Apart from binding to pflaB, ArnR but not ArnR1 bound to promoter sequences of aapF and upsX, which encode components of the archaeal adhesive pilus and UV-inducible pili system, demonstrating a regulatory connection between different surface appendages of S. acidocaldarius.
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Affiliation(s)
- Lisa Franziska Bischof
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), Freiburg, Germany
| | - Maria Florencia Haurat
- Department of Molecular Microbiology, Washington University, School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
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Abstract
Biological systems reach hierarchical complexity that has no counterpart outside the realm of biology. Undoubtedly, biological entities obey the fundamental physical laws. Can today's physics provide an explanatory framework for understanding the evolution of biological complexity? We argue that the physical foundation for understanding the origin and evolution of complexity can be gleaned at the interface between the theory of frustrated states resulting in pattern formation in glass-like media and the theory of self-organized criticality (SOC). On the one hand, SOC has been shown to emerge in spin-glass systems of high dimensionality. On the other hand, SOC is often viewed as the most appropriate physical description of evolutionary transitions in biology. We unify these two faces of SOC by showing that emergence of complex features in biological evolution typically, if not always, is triggered by frustration that is caused by competing interactions at different organizational levels. Such competing interactions lead to SOC, which represents the optimal conditions for the emergence of complexity. Competing interactions and frustrated states permeate biology at all organizational levels and are tightly linked to the ubiquitous competition for limiting resources. This perspective extends from the comparatively simple phenomena occurring in glasses to large-scale events of biological evolution, such as major evolutionary transitions. Frustration caused by competing interactions in multidimensional systems could be the general driving force behind the emergence of complexity, within and beyond the domain of biology.
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10
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Kemme CA, Marquez R, Luu RH, Iwahara J. Potential role of DNA methylation as a facilitator of target search processes for transcription factors through interplay with methyl-CpG-binding proteins. Nucleic Acids Res 2017; 45:7751-7759. [PMID: 28486614 PMCID: PMC5569922 DOI: 10.1093/nar/gkx387] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/06/2017] [Indexed: 11/12/2022] Open
Abstract
Eukaryotic genomes contain numerous non-functional high-affinity sequences for transcription factors. These sequences potentially serve as natural decoys that sequester transcription factors. We have previously shown that the presence of sequences similar to the target sequence could substantially impede association of the transcription factor Egr-1 with its targets. In this study, using a stopped-flow fluorescence method, we examined the kinetic impact of DNA methylation of decoys on the search process of the Egr-1 zinc-finger protein. We analyzed its association with an unmethylated target site on fluorescence-labeled DNA in the presence of competitor DNA duplexes, including Egr-1 decoys. DNA methylation of decoys alone did not affect target search kinetics. In the presence of the MeCP2 methyl-CpG-binding domain (MBD), however, DNA methylation of decoys substantially (∼10-30-fold) accelerated the target search process of the Egr-1 zinc-finger protein. This acceleration did not occur when the target was also methylated. These results suggest that when decoys are methylated, MBD proteins can block them and thereby allow Egr-1 to avoid sequestration in non-functional locations. This effect may occur in vivo for DNA methylation outside CpG islands (CGIs) and could facilitate localization of some transcription factors within regulatory CGIs, where DNA methylation is rare.
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Affiliation(s)
- Catherine A Kemme
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Rolando Marquez
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Ross H Luu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
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11
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Yesudhas D, Batool M, Anwar MA, Panneerselvam S, Choi S. Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Genes (Basel) 2017; 8:genes8080192. [PMID: 28763006 PMCID: PMC5575656 DOI: 10.3390/genes8080192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Muhammad Ayaz Anwar
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Suresh Panneerselvam
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
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12
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Nagy YI, Hussein MMM, Ragab YM, Attia AS. Isogenic mutations in the Moraxella catarrhalis CydDC system display pleiotropic phenotypes and reveal the role of a palindrome sequence in its transcriptional regulation. Microbiol Res 2017. [PMID: 28647125 DOI: 10.1016/j.micres.2017.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Moraxella catarrhalis is becoming an important human respiratory tract pathogen affecting significant proportions from the population. However, still little is known about its physiology and molecular regulation. To this end, the CydDC, which is a heterodimeric ATP binding cassette transporter that has been shown to contribute to the maintenance of the redox homeostasis across the periplasm in other Gram-negative bacteria, is studied here. Amino acids multiple sequence alignments indicated that M. catarrhalis CydC is different from the CydC proteins of the bacterial species in which this system has been previously studied. These findings prompted further interest in studying this system in M. catarrhalis. Isogenic mutant in the CydDC system showed suppression in growth rate, hypersensitivity to oxidative and reductive stress and increased accumulation of intracellular cysteine levels. In addition, the growth of cydC- mutant exhibited hypersensitivity to exogenous cysteine; however, it did not display a significant difference from its wild-type counterpart in the murine pulmonary clearance model. Moreover, a palindrome was detected 94bp upstream of the cydD ORF suggesting it might act as a potential regulatory element. Real-time reverse transcription-PCR analysis showed that deletion/change in the palindrome resulted into alterations in the transcription levels of cydC. A better understanding of such system and its regulation helps in developing better ways to combat M. catarrhalis infections.
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Affiliation(s)
- Yosra I Nagy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Manal M M Hussein
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Yasser M Ragab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Ahmed S Attia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
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13
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Yang CC, Chen MH, Lin SY, Andrews EH, Cheng C, Liu CC, Chen JJW. Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data. BMC Genomics 2017; 18:61. [PMID: 28068916 PMCID: PMC5223348 DOI: 10.1186/s12864-016-3450-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/21/2016] [Indexed: 01/18/2023] Open
Abstract
Background Transcription factors (TFs) often interact with one another to form TF complexes that bind DNA and regulate gene expression. Many databases are created to describe known TF complexes identified by either mammalian two-hybrid experiments or data mining. Lately, a wealth of ChIP-seq data on human TFs under different experiment conditions are available, making it possible to investigate condition-specific (cell type and/or physiologic state) TF complexes and their target genes. Results Here, we developed a systematic pipeline to infer Condition-Specific Targets of human TF-TF complexes (called the CST pipeline) by integrating ChIP-seq data and TF motifs. In total, we predicted 2,392 TF complexes and 13,504 high-confidence or 127,994 low-confidence regulatory interactions amongst TF complexes and their target genes. We validated our predictions by (i) comparing predicted TF complexes to external TF complex databases, (ii) validating selected target genes of TF complexes using ChIP-qPCR and RT-PCR experiments, and (iii) analysing target genes of select TF complexes using gene ontology enrichment to demonstrate the accuracy of our work. Finally, the predicted results above were integrated and employed to construct a CST database. Conclusions We built up a methodology to construct the CST database, which contributes to the analysis of transcriptional regulation and the identification of novel TF-TF complex formation in a certain condition. This database also allows users to visualize condition-specific TF regulatory networks through a user-friendly web interface. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3450-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chia-Chun Yang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, No. 250, Kuo-Kuang Rd., 40227, Taichung, Taiwan
| | - Min-Hsuan Chen
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Sheng-Yi Lin
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, No. 250, Kuo-Kuang Rd., 40227, Taichung, Taiwan
| | - Erik H Andrews
- Department of Genetics, Geisel School of Medicine at Dartmouth, 03755, Hanover, NH, USA
| | - Chao Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth, 03755, Hanover, NH, USA. .,Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, 03766, Lebanon, NH, USA.
| | - Chun-Chi Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan. .,Institute of Biomedical Sciences, National Chung Hsing University, No. 250, Kuo-Kuang Rd., 40227, Taichung, Taiwan. .,Agricultural Biotechnology Centre, National Chung Hsing University, Taichung, Taiwan.
| | - Jeremy J W Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan. .,Institute of Biomedical Sciences, National Chung Hsing University, No. 250, Kuo-Kuang Rd., 40227, Taichung, Taiwan. .,Agricultural Biotechnology Centre, National Chung Hsing University, Taichung, Taiwan.
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14
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Ramalingam A, Kudapa H, Pazhamala LT, Garg V, Varshney RK. Gene Expression and Yeast Two-Hybrid Studies of 1R-MYB Transcription Factor Mediating Drought Stress Response in Chickpea (Cicer arietinum L.). Front Plant Sci 2015; 6:1117. [PMID: 26734027 PMCID: PMC4689849 DOI: 10.3389/fpls.2015.01117] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/25/2015] [Indexed: 05/26/2023]
Abstract
Drought stress has been one of the serious constraints affecting chickpea productivity to a great extent. Genomics-assisted breeding has a potential to accelerate breeding precisely and efficiently. In order to do so, understanding the molecular mechanisms for drought tolerance and identification of candidate genes are crucial. Transcription factors (TFs) have important roles in the regulation of plant stress related genes. In this context, quantitative real time-PCR (qRT-PCR) was used to study the differential gene expression of selected TFs, identified from large-scale expressed sequence tags (ESTs) analysis, in contrasting drought responsive genotypes. Root tissues of ICC 4958 (tolerant), ICC 1882 (sensitive), JG 11 (elite), and JG 11+ (introgression line) were used for the study. Subsequently, a candidate single repeat MYB (1R-MYB) transcript that was remarkably induced in the drought tolerant genotypes under drought stress was cloned (coding sequence region for the 1R-MYB protein) and subjected to yeast two-hybrid (Y2H) analysis. The screening of a root cDNA library with Y2H using the 1R-MYB bait protein, identified three CDS encoding peptides namely, galactinol-sucrose galactosyltransferase 2, CBL (Calcineurin B-like)-interacting serine/threonine-protein kinase 25, and ABA responsive 17-like, which were confirmed by co-transformation in yeast. These findings provide preliminary insights into the ability of this 1R-MYB transcription factor to co-regulate drought tolerance mechanism in chickpea.
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Affiliation(s)
- Abirami Ramalingam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Lekha T. Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
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15
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Sundaresan S, Philosoph-Hadas S, Riov J, Mugasimangalam R, Kuravadi NA, Kochanek B, Salim S, Tucker ML, Meir S. De novo Transcriptome Sequencing and Development of Abscission Zone-Specific Microarray as a New Molecular Tool for Analysis of Tomato Organ Abscission. Front Plant Sci 2015; 6:1258. [PMID: 26834766 PMCID: PMC4712312 DOI: 10.3389/fpls.2015.01258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/24/2015] [Indexed: 05/19/2023]
Abstract
Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum) can be induced by flower removal or leaf deblading, respectively, which leads to auxin depletion, resulting in increased sensitivity of the abscission zone (AZ) to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq) to obtain a comprehensive transcriptome of tomato flower AZ (FAZ) and leaf AZ (LAZ) during abscission. RNA-Seq was performed on a pool of total RNA extracted from tomato FAZ and LAZ, at different abscission stages, followed by de novo assembly. The assembled clusters contained transcripts that are already known in the Solanaceae (SOL) genomics and NCBI databases, and over 8823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing the novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehensive set of transcripts, and for mining for naturally occurring antisense transcripts. We focused on comparing the global transcriptomes generated from the FAZ and the LAZ to establish the divergences and similarities in their transcriptional networks, and particularly to characterize the processes and transcriptional regulators enriched in gene clusters that are differentially regulated in these two AZs. This study is the first attempt to analyze the global gene expression in different AZs in tomato by combining the RNA-Seq technique with oligonucleotide microarrays. Our AZ-specific microarray chip provides a cost-effective approach for expression profiling and robust analysis of multiple samples in a rapid succession.
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Affiliation(s)
- Srivignesh Sundaresan
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Sonia Philosoph-Hadas
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
| | - Joseph Riov
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Raja Mugasimangalam
- Department of Bioinformatics, QTLomics Technologies Pvt. LtdBangalore, India
| | - Nagesh A. Kuravadi
- Department of Bioinformatics, QTLomics Technologies Pvt. LtdBangalore, India
| | - Bettina Kochanek
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
| | - Shoshana Salim
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
| | - Mark L. Tucker
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
| | - Shimon Meir
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani CenterBet-Dagan, Israel
- *Correspondence: Shimon Meir
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16
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Andrilenas KK, Penvose A, Siggers T. Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes. Brief Funct Genomics 2014; 14:17-29. [PMID: 25431149 DOI: 10.1093/bfgp/elu046] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Protein-DNA binding is central to specificity in gene regulation, and methods for characterizing transcription factor (TF)-DNA binding remain crucial to studies of regulatory specificity. High-throughput (HT) technologies have revolutionized our ability to characterize protein-DNA binding by significantly increasing the number of binding measurements that can be performed. Protein-binding microarrays (PBMs) are a robust and powerful HT platform for studying DNA-binding specificity of TFs. Analysis of PBM-determined DNA-binding profiles has provided new insight into the scope and mechanisms of TF binding diversity. In this review, we focus specifically on the PBM technique and discuss its application to the study of TF specificity, in particular, the binding diversity of TF homologs and multi-protein complexes.
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17
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Abstract
![]()
The study of high-affinity
protein interactions with equilibrium
dissociation constants (KD) in the picomolar
range is of significant interest in many fields, but the characterization
of stoichiometry and free energy of such high-affinity binding can
be far from trivial. Analytical ultracentrifugation has long been
considered a gold standard in the study of protein interactions but
is typically applied to systems with micromolar KD. Here we present a new approach for the study of high-affinity
interactions using fluorescence detected sedimentation velocity analytical
ultracentrifugation (FDS-SV). Taking full advantage of the large data
sets in FDS-SV by direct boundary modeling with sedimentation coefficient
distributions c(s), we demonstrate detection and
hydrodynamic resolution of protein complexes at low picomolar concentrations.
We show how this permits the characterization of the antibody–antigen
interactions with low picomolar binding constants, 2 orders of magnitude
lower than previously achieved. The strongly size-dependent separation
and quantitation by concentration, size, and shape of free and complex
species in free solution by FDS-SV has significant potential for studying
high-affinity multistep and multicomponent protein assemblies.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda, Maryland 20892, United States
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18
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Parra R, Paredes MA, Sanchez-Calle IM, Gomez-Jimenez MC. Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation. BMC Genomics 2013; 14:866. [PMID: 24320622 PMCID: PMC4046656 DOI: 10.1186/1471-2164-14-866] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 12/02/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In fleshy fruit, abscission of fully ripe fruit is a process intimately linked to the ripening process. In many fruit-tree species, such as olive (Olea europaea L. cv. Picual), there is a coupling of the full ripening and the activation of the abscission-zone (AZ). Although fully ripe fruit have marked physiological differences with respect to their AZs, dissimilarities in gene expression have not been thoroughly investigated. The present study examines the transcriptome of olive fruit and their AZ tissues at the last stage of ripening, monitored using mRNA-Seq. RESULTS Roche-454 massive parallel pyrosequencing enabled us to generate 397,457 high-quality EST sequences, among which 199,075 were from ripe-fruit pericarp and 198,382 from AZ tissues. We assembled these sequences into 19,062 contigs, grouped as 17,048 isotigs. Using the read amounts for each annotated isotig (from a total of 15,671), we identified 7,756 transcripts. A comparative analysis of the transcription profiles conducted in ripe-fruit pericarp and AZ evidenced that 4,391 genes were differentially expressed genes (DEGs) in fruit and AZ. Functional categorization of the DEGs revealed that AZ tissue has an apparently higher response to external stimuli than does that of ripe fruit, revealing a higher expression of auxin-signaling genes, as well as lignin catabolic and biosynthetic pathway, aromatic amino acid biosynthetic pathway, isoprenoid biosynthetic pathway, protein amino acid dephosphorylation, amino acid transport, and photosynthesis. By contrast, fruit-enriched transcripts are involved in ATP synthesis coupled proton transport, glycolysis, and cell-wall organization. Furthermore, over 150 transcripts encoding putative transcription-factors (TFs) were identified (37 fruit TFs and 113 AZ TFs), of which we randomly selected eight genes and we confirmed their expression patterns using quantitative RT-PCR. CONCLUSION We generated a set of EST sequences from olive fruit at full ripening, and DEGs between two different olive tissues, ripe fruit and their AZ, were also identified. Regarding the cross-talk between fruit and AZ, using qRT-PCR, we confirmed a set of TF genes that were differentially expressed, revealing profiles of expression that have not previously been reported, this offering a promising beginning for studies on the different transcription regulation in such tissues.
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Affiliation(s)
| | | | | | - Maria C Gomez-Jimenez
- Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz 06006, Spain.
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19
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Abstract
Binding of proteins to particular DNA sites across the genome is a primary determinant of specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded at multiple levels, from the detailed biophysical interactions between proteins and DNA, to the assembly of multi-protein complexes. At each level, variation in the mechanisms used to achieve specificity has led to difficulties in constructing and applying simple models of DNA binding. We review the complexities in protein–DNA binding found at multiple levels and discuss how they confound the idea of simple recognition codes. We discuss the impact of new high-throughput technologies for the characterization of protein–DNA binding, and how these technologies are uncovering new complexities in protein–DNA recognition. Finally, we review the concept of multi-protein recognition codes in which new DNA-binding specificities are achieved by the assembly of multi-protein complexes.
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Affiliation(s)
- Trevor Siggers
- Department of Biology, Boston University, Boston, MA 02215, USA, Departments of Biostatistics and Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
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20
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Li Y, Xu F, Liu C, Xu Y, Feng X, Liu BF. A novel microfluidic mixer based on dual-hydrodynamic focusing for interrogating the kinetics of DNA-protein interaction. Analyst 2013; 138:4475-82. [PMID: 23785706 DOI: 10.1039/c3an00521f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Kinetic measurement of biomacromolecular interaction plays a significant role in revealing the underlying mechanisms of cellular activities. Due to the small diffusion coefficient of biomacromolecules, it is difficult to resolve the rapid kinetic process with traditional analytical methods such as stopped-flow or laminar mixers. Here, we demonstrated a unique continuous-flow laminar mixer based on microfluidic dual-hydrodynamic focusing to characterize the kinetics of DNA-protein interactions. The time window of this mixer for kinetics observation could cover from sub-milliseconds to seconds, which made it possible to capture the folding process with a wide dynamic range. Moreover, the sample consumption was remarkably reduced to <0.55 μL min⁻¹, over 1000-fold saving in comparison to those reported previously. We further interrogated the interaction kinetics of G-quadruplex and the single-stranded DNA binding protein, indicating that this novel micromixer would be a useful approach for analyzing the interaction kinetics of biomacromolecules.
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Affiliation(s)
- Ying Li
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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21
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Bhargava A, Ahad A, Wang S, Mansfield SD, Haughn GW, Douglas CJ, Ellis BE. The interacting MYB75 and KNAT7 transcription factors modulate secondary cell wall deposition both in stems and seed coat in Arabidopsis. Planta 2013; 237:1199-211. [PMID: 23328896 DOI: 10.1007/s00425-012-1821-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/20/2012] [Indexed: 05/18/2023]
Abstract
The Arabidopsis thaliana KNAT7 (KNOX family) and MYB75 (MYB family) transcription factors were each shown earlier to interact in yeast two-hybrid assays, and to modulate secondary cell wall formation in inflorescence stems. We demonstrate here that their interaction also occurs in vivo, and that specific domains of each protein mediate this process. The participation of these interacting transcription factors in secondary cell wall formation was then extended to the developing seed coat through the use of targeted transcript analysis and SEM in single loss-of-function mutants. Novel genetic and protein-protein interactions of MYB75 and KNAT7 with other transcription factors known to be involved in seed coat regulation were also identified. We propose that a MYB75-associated protein complex is likely to be involved in modulating secondary cell wall biosynthesis in both the Arabidopsis inflorescence stem and seed coat, and that at least some parts of the transcriptional regulatory network in the two tissues are functionally conserved.
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Affiliation(s)
- Apurva Bhargava
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
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22
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Abstract
RNA editing is one of the post-transcriptional RNA processes. RNA editing generates RNA and protein diversity in eukaryotes and results in specific amino acid substitutions, deletions, and changes in gene expression levels. Adenosine-to-inosine RNA editing represents the most important class of editing in human and affects function of many genes. The importance of balancing RNA modification levels across time and space is becoming increasingly evident. In this review, we overview the biological significance of RNA editing including RNA editing in tumorigenesis, RNA editing in neuronal tissues, RNA editing as a regulator of gene expression, and RNA editing in dsRNA-mediated gene silencing, which may increase our understanding of RNA biology.
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23
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Abstract
Protein dimers and multimers are often employed by nature for DNA and RNA handling and formation of specific, high-affinity protein-oligonucleotide complexes. The repeating structure of dsDNA lends itself to recognition by multimeric protein complexes that can assemble about the helical structure. In the cases of both DNA and RNA, specific recognition of nucleotide sequences can be achieved by multidomain proteins or protein multimers. Furthermore large multimeric assemblies are utilised for the stable formation of structures such as rings and filaments. Also, the assembly of multimeric structures by interchangeable subunits can add layers of regulation and increase functional complexity. Thus there appear to be many advantages to oligonucleotide interactions that are conferred by dimerisation or multimerisation.
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Affiliation(s)
- Jackie Wilce
- Department of Biochemistry and Molecular Biology, and School of Biomedical Sciences, Monash Univerity, Melbourne, Victoria, Australia.
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Guo Y, Mahony S, Gifford DK. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput Biol 2012; 8:e1002638. [PMID: 22912568 PMCID: PMC3415389 DOI: 10.1371/journal.pcbi.1002638] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 06/15/2012] [Indexed: 12/27/2022] Open
Abstract
An essential component of genome function is the syntax of genomic regulatory elements that determine how diverse transcription factors interact to orchestrate a program of regulatory control. A precise characterization of in vivo spacing constraints between key transcription factors would reveal key aspects of this genomic regulatory language. To discover novel transcription factor spatial binding constraints in vivo, we developed a new integrative computational method, genome wide event finding and motif discovery (GEM). GEM resolves ChIP data into explanatory motifs and binding events at high spatial resolution by linking binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence. GEM analysis of 63 transcription factors in 214 ENCODE human ChIP-Seq experiments recovers more known factor motifs than other contemporary methods, and discovers six new motifs for factors with unknown binding specificity. GEM's adaptive learning of binding-event read distributions allows it to further improve upon previous methods for processing ChIP-Seq and ChIP-exo data to yield unsurpassed spatial resolution and discovery of closely spaced binding events of the same factor. In a systematic analysis of in vivo sequence-specific transcription factor binding using GEM, we have found hundreds of spatial binding constraints between factors. GEM found 37 examples of factor binding constraints in mouse ES cells, including strong distance-specific constraints between Klf4 and other key regulatory factors. In human ENCODE data, GEM found 390 examples of spatially constrained pair-wise binding, including such novel pairs as c-Fos:c-Jun/USF1, CTCF/Egr1, and HNF4A/FOXA1. The discovery of new factor-factor spatial constraints in ChIP data is significant because it proposes testable models for regulatory factor interactions that will help elucidate genome function and the implementation of combinatorial control. The letters in our genome spell words and phrases that control when each gene is activated. To understand how these words and phrases function in health and disease, we have developed a new computational method to determine what word positions in our genomic text are used by each genome regulatory protein, and how these active words are spaced relative to one another. Our method achieves exceptional spatial accuracy by integrating experimental data with the text of our genome to find the precise words that are regulated by each protein factor. Using this analysis we have discovered novel word spacings in the experimental data that suggest novel genome grammatical control constructs.
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Affiliation(s)
- Yuchun Guo
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Shaun Mahony
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (SM); (DKG)
| | - David K. Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (SM); (DKG)
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Takayama Y, Clore GM. Impact of protein/protein interactions on global intermolecular translocation rates of the transcription factors Sox2 and Oct1 between DNA cognate sites analyzed by z-exchange NMR spectroscopy. J Biol Chem 2012; 287:26962-70. [PMID: 22718759 DOI: 10.1074/jbc.m112.382960] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oct1 and Sox2 synergistically regulate developmental genes by binding to adjacent sites within promoters. We have investigated the kinetics of global intermolecular translocation of Sox2 and Oct1 between cognate sites located on different DNA molecules by z-exchange NMR spectroscopy. In the Hoxb1 promoter, the Sox2 and Oct1 sites are immediately adjacent to one another, and the intermolecular translocation rates are too slow to be measured by z-exchange spectroscopy. By introducing a 3-bp insertion between the Sox2 and Oct1 sites to mimic the spacing in the FGF4 enhancer, the interprotein contact surface is reduced, and the translocation rates are increased. Interaction between Sox2 and the POU-specific domain (POU(S)) of Oct1 does not affect the translocation mechanism but modulates the rates. Translocation involves only jumping (dissociation and reassociation) for Sox2, but both jumping and direct intersegment transfer (no dissociation into free solution) for Oct1. The dissociation (k(off) ∼1.5 s(-1)) and association (k(on) ∼5.1 × 10(9) m(-1)s(-1)) rate constants for Sox2 are reduced 4-fold and increased 5-fold, respectively, in the presence of Oct1. k(off) (∼3.5 s(-1)) for Oct1 is unaffected by Sox2, whereas k(on) (∼1.3 × 10(9) m(-1)s(-1)) is increased ∼13-fold. The direct intermolecular translocation rate (k(inter) ∼1.8 × 10(4) m(-1)s(-1)) for the POU(S) domain of Oct1 is reduced 2-fold by Sox2, whereas that for the POU homeodomain (POU(HD)) of Oct1 (k(inter) ∼ 1.7 × 10(4) m(-1)s(-1)) remains unaltered, consistent with the absence of contacts between Sox2 and POU(HD). The data suggest a model for the sequence of binding events involved in synergistic gene regulation by Sox2 and Oct1.
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Affiliation(s)
- Yuki Takayama
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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Funnell APW, Crossley M. Homo- and Heterodimerization in Transcriptional Regulation. Advances in Experimental Medicine and Biology 2012; 747:105-21. [DOI: 10.1007/978-1-4614-3229-6_7] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Shi Z, Trenholm S, Zhu M, Buddingh S, Star EN, Awatramani GB, Chow RL. Vsx1 regulates terminal differentiation of type 7 ON bipolar cells. J Neurosci 2011; 31:13118-27. [PMID: 21917795 DOI: 10.1523/JNEUROSCI.2331-11.2011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although retinal bipolar cells represent a morphologically well defined population of retinal interneurons, very little is known about the developmental mechanisms that regulate their processing. Furthermore, the identity of specific bipolar cell types that function in distinct visual circuits remains poorly understood. Here, we show that the homeobox gene Vsx1 is expressed in Type 7 ON bipolar cells. In the absence of Vsx1, Type 7 bipolar cells exhibit proper morphological specification but show defects in terminal gene expression. Vsx1 is required for the repression of bipolar cell-specific markers, including Calcium-binding protein 5 and Chx10. This contrasts its genetic requirement as an activator of gene expression in OFF bipolar cells. To assess possible ON signaling defects in Vsx1-null mice, we recorded specifically from ON-OFF directionally selective ganglion cells (DSGCs), which cofasciculate with Type 7 bipolar cell terminals. Vsx1-null ON-OFF DSGCs received more sustained excitatory synaptic input, possibly due to Type 7 bipolar cell defects. Interestingly, in Vsx1-null mice, the directionally selective circuit is functional but compromised. Together, these findings indicate that Vsx1 regulates terminal gene expression in Type 7 bipolar cells and is necessary for proper ON visual signaling within a directionally selective circuit.
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Abstract
The factors that influence preadipocyte determination remain poorly understood. In the present paper, we report that CREBL2 [CREB (cAMP-response-element-binding protein)-like 2], a novel bZIP_1 protein, is up-regulated during MDI-induced preadipocyte differentiation. During both overexpression and under physiological conditions, CREBL2 interacted and was entirely co-localized with CREB. Overexpression of CREBL2 was sufficient to promote adipogenesis via up-regulating the expression of PPARγ (peroxisome-proliferator-activated receptor γ) and C/EBPα (CCAAT/enhancer-binding protein α) and accelerate lipogenesis accompanied with increased GLUT (glucose transporter) 1 and GLUT4. CREBL2 knockdown restrained adipogenic conversion and lipogenesis. Additionally, depletion of CREB could completely block the effects of overexpressed CREBL2, whereas an increase in CREB could not drive adipogenesis in the absence of CREBL2, indicating that the roles for CREBL2 on adipogenesis were CREB-dependent. Furthermore, siCREBL2 [siRNA (short interfering RNA) against CREBL2] could down-regulate CREB transcriptional activity and suppress CREB phosphorylation. CREB knockdown decreased the CREBL2 protein levels and vice versa. Collectively, the results of the present study indicate that CREBL2 plays a critical role in adipogenesis and lipogenesis via interaction with CREB.
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Abstract
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) allows researchers to determine the genome-wide binding locations of individual transcription factors (TFs) at high resolution. This information can be interrogated to study various aspects of TF behaviour, including the mechanisms that control TF binding. Physical interaction between TFs comprises one important aspect of TF binding in eukaryotes, mediating tissue-specific gene expression. We have developed an algorithm, spaced motif analysis (SpaMo), which is able to infer physical interactions between the given TF and TFs bound at neighbouring sites at the DNA interface. The algorithm predicts TF interactions in half of the ChIP-seq data sets we test, with the majority of these predictions supported by direct evidence from the literature or evidence of homodimerization. High resolution motif spacing information obtained by this method can facilitate an improved understanding of individual TF complex structures. SpaMo can assist researchers in extracting maximum information relating to binding mechanisms from their TF ChIP-seq data. SpaMo is available for download and interactive use as part of the MEME Suite (http://meme.nbcr.net).
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Affiliation(s)
- Tom Whitington
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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Abstract
A global regulatory complex made up of two unconventional transcriptional factors, CarD and CarG, is implicated in the control of various processes in Myxococcus xanthus, a Gram-negative bacterium that serves as a prokaryotic model system for multicellular development and the response to blue light. CarD has a unique two-domain architecture composed of: (1) a C-terminal DNA-binding domain that resembles eukaryotic high mobility group A (HMGA) proteins, which are relatively abundant, nonhistone components of chromatin that remodel DNA and prime it for the assembly of multiprotein-DNA complexes essential for various DNA transactions, and (2) an N-terminal domain involved in interactions with CarG and RNA polymerase, which is also the founding member of the large CarD_TRCF family of bacterial proteins. CarG, which does not bind DNA directly, has a zinc-binding motif of the type found in the archaemetzincin class of metalloproteases that, in CarG, appears to play a purely structural role. This review aims to provide an overview of the known molecular details and insights emerging from the study of the singular CarD-CarG prokaryotic regulatory complex and its parallels with enhanceosomes, the higher order, nucleoprotein transcription complexes in eukaryotes.
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Affiliation(s)
- Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Area de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
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Abstract
Large volumes of protein sequence and structure data acquired by proteomic studies led to the development of computational bioinformatic techniques that made possible the functional annotation and structural characterization of proteins based on their primary structure. It has become evident from genome-wide analyses that many proteins in eukaryotic cells are either completely disordered or contain long unstructured regions that are crucial for their biological functions. The content of disorder increases with evolution indicating a possibly important role of disorder in the regulation of cellular systems. Transcription factors are no exception and several proteins of this class have recently been characterized as premolten/molten globules. Yet, mammalian cells rely on these proteins to control expression of their 30,000 or so genes. Basic region:leucine zipper (bZIP) DNA-binding proteins constitute a major class of eukaryotic transcriptional regulators. This review discusses how conformational flexibility "built" into the amino acid sequence allows bZIP proteins to interact with a large number of diverse molecular partners and to accomplish their manifold cellular tasks in a strictly regulated and coordinated manner.
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Affiliation(s)
- Maria Miller
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA.
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van Hijum SAFT, Medema MH, Kuipers OP. Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev 2009; 73:481-509, Table of Contents. [PMID: 19721087 PMCID: PMC2738135 DOI: 10.1128/mmbr.00037-08] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A major part of organismal complexity and versatility of prokaryotes resides in their ability to fine-tune gene expression to adequately respond to internal and external stimuli. Evolution has been very innovative in creating intricate mechanisms by which different regulatory signals operate and interact at promoters to drive gene expression. The regulation of target gene expression by transcription factors (TFs) is governed by control logic brought about by the interaction of regulators with TF binding sites (TFBSs) in cis-regulatory regions. A factor that in large part determines the strength of the response of a target to a given TF is motif stringency, the extent to which the TFBS fits the optimal TFBS sequence for a given TF. Advances in high-throughput technologies and computational genomics allow reconstruction of transcriptional regulatory networks in silico. To optimize the prediction of transcriptional regulatory networks, i.e., to separate direct regulation from indirect regulation, a thorough understanding of the control logic underlying the regulation of gene expression is required. This review summarizes the state of the art of the elements that determine the functionality of TFBSs by focusing on the molecular biological mechanisms and evolutionary origins of cis-regulatory regions.
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Affiliation(s)
- Sacha A F T van Hijum
- Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.
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Marcovitz A, Levy Y. Arc-repressor dimerization on DNA: folding rate enhancement by colocalization. Biophys J 2009; 96:4212-20. [PMID: 19450491 DOI: 10.1016/j.bpj.2009.01.057] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 01/13/2009] [Accepted: 01/15/2009] [Indexed: 02/04/2023] Open
Abstract
Multimeric proteins are ubiquitous in many cellular processes that require high levels of regulation. Eukaryotic gene expression is often regulated by a mechanism of combinatorial control that involves the binding of dimeric transcription factors to DNA together with the coordinated activity of additional proteins. In this study, we investigated the dimerization of the Arc-repressor on DNA with the aim of achieving microscopic insight into the possible advantages of interacting with DNA as a complex rather than as a monomeric single-domain protein. We used a computational coarse-grained model in which the protein dynamics was governed by native interactions and protein-DNA interactions were dictated by electrostatic forces. Inspired by previous experimental work that showed an enhanced refolding rate for the Arc-repressor in the presence of DNA and other polyanions, we focused on the mechanism and kinetics of the assembly of Arc monomers in the presence of single- (ssDNA) and double-stranded DNA (dsDNA) molecules in a low-salt concentration environment. The electrostatic interactions that attract the protein to the dsDNA were shown to be fundamental in colocalizing the unfolded Arc chains and in accelerating refolding. Arc monomers bind the dsDNA efficiently and nonspecifically, and search for each other via one-dimensional diffusion. The fastest folding of Arc is observed for DNA of 30 bp. Longer DNA is significantly less efficient in accelerating the Arc refolding rate, since the two subunits search distinct regions of the one-dimensional DNA and are therefore much less colocalized. The probability that the two unfolded chains will meet on 200 bp DNA is similar to that in the bulk. The colocalization of Arc subunits on ssDNA results in much faster folding compared to that obtained on dsDNA of the same length. Differences in the rate of Arc refolding, cooperativity, and the structure of its transition state ensemble introduced by ssDNA and dsDNA molecules demonstrate the important role of colocalization in biological self-assembly processes.
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Boogerd CJJ, Moorman AFM, Barnett P. Protein interactions at the heart of cardiac chamber formation. Ann Anat 2009; 191:505-17. [PMID: 19647421 DOI: 10.1016/j.aanat.2009.06.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 06/12/2009] [Indexed: 10/20/2022]
Abstract
The vertebrate heart is a muscular pump that contracts in a rhythmic fashion to propel the blood through the body. During evolution, the morphologically complex four-chambered heart of birds and mammals has evolved from a single-layered tube with peristaltic contractility. The heart of Drosophila, referred to as the dorsal vessel, is a blind sac composed of myogenic cells that contract rhythmically. The fish heart is composed of a single atrial chamber connected to a single ventricular chamber. The evolutionary development of fast-contracting chambers allowed the heart to build up high blood pressures. In amphibians two atrial chambers exist, separated by a septum, connecting to a single ventricle. The division of a common atrium and ventricle into right and left-sided chambers represents an evolutionary milestone in the development of the four-chambered heart and is necessary for separation of oxygenated and deoxygenated blood. In amphibians and reptiles, pulmonary and systemic circulations are incompletely separated allowing adaptable blood flows to both circulations. In contrast, the hearts of birds and mammals, in which septa completely separate the pulmonary and systemic circulations, both circulations have similar flows, but blood pressures can be regulated separately. In this review we focus, in a morphologically integrated fashion, on the molecular interactions that govern the intricate cardiac design.
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Affiliation(s)
- Cornelis J J Boogerd
- Heart Failure Research Center, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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Abstract
We explore how the genotype-phenotype map determines convergent evolution in a simple model of spatial gene regulation during development. Evolution is simulated via a Monte Carlo scheme that incorporates mutation, selection, and genetic drift, by using a bottom-up model of gene regulation with a fitness function that is optimized by a switch-like response to a morphogen gradient. We find that even for very simple regulation, the genotype-phenotype map gives rise to an emergent fitness landscape of remarkable complexity. This leads to a richness of evolutionary behavior as population size is increased that parallels the thermodynamics of physical systems as temperature decreases. Convergence is controlled by the existence of sufficiently dominant global optima in "free fitness," which is a quantity that is the balance of mutational entropy and fitness. In independent simulations at low population sizes, we find convergence to a phenotype of suboptimal fitness due to the multiplicity or entropy of solutions. This contrasts with convergence to the optimal fitness phenotype at high population size. However, at sufficiently large population sizes, we find convergence in only the phenotypes with greatest effect on fitness, whereas noncritical phenotypes exhibit divergence due to quenched disorder on a locally rough landscape. Our results predict that for large populations, the evolution of even simple gene regulatory circuits may be glassy-like, such that, counter to the commonly accepted view that conservation implies function, many conserved phenotypes are simply frozen accidents of little consequence to the fitness of the organism.
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Affiliation(s)
- Bhavin S Khatri
- Department of Physics, University of Surrey, Guildford GU2 7XH, United Kingdom.
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Kobayashi F, Maeta E, Terashima A, Kawaura K, Ogihara Y, Takumi S. Development of abiotic stress tolerance via bZIP-type transcription factor LIP19 in common wheat. J Exp Bot 2008; 59:891-905. [PMID: 18326864 DOI: 10.1093/jxb/ern014] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cereal lip19 genes encoding bZIP-type transcription factors are assumed to play a regulatory role in gene expression during the cold acclimation process. However, no direct evidence shows an association of LIP19-type bZIPs with stress tolerance or activation of stress-responsive Cor/Lea genes. To understand the molecular basis of development of abiotic stress tolerance through the LIP19 transcription factor, a wheat lip19 homologue, Wlip19, was isolated and characterized. Wlip19 expression was activated by low temperature in seedlings and was higher in a freezing-tolerant cultivar than in a freezing-sensitive one. Wlip19 also responded to drought and exogenous ABA treatment. Wlip19-expressing transgenic tobacco showed a significant increase in abiotic stress tolerance, especially freezing tolerance. Expression of a GUS reporter gene under the control of promoter sequences of four wheat Cor/Lea genes, Wdhn13, Wrab17, Wrab18, and Wrab19, was enhanced by Wlip19 expression in wheat callus and tobacco plants. These results indicate that WLIP19 acts as a transcriptional regulator of Cor/Lea genes in the development of abiotic stress tolerance. Moreover, direct protein-protein interaction between WLIP19 and a wheat OBF1 homologue TaOBF1, another bZIP-type transcription factor, was observed, suggesting that this interaction is conserved in cereals.
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Affiliation(s)
- Fuminori Kobayashi
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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Gelato KA, Martin SS, Liu PH, Saunders AA, Baldwin EP. Spatially directed assembly of a heterotetrameric Cre-Lox synapse restricts recombination specificity. J Mol Biol 2008; 378:653-65. [PMID: 18374357 DOI: 10.1016/j.jmb.2008.02.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 02/13/2008] [Accepted: 02/25/2008] [Indexed: 12/21/2022]
Abstract
The pseudo-fourfold homotetrameric synapse formed by Cre protein and target DNA restricts site-specific recombination to sequences containing dyad-symmetric Cre-binding repeats. Mixtures of engineered altered-specificity Cre monomers can form heterotetramers that recombine nonidentical asymmetric sequences, allowing greater flexibility for target site selection in the genome of interest. However, the variety of tetramers allowed by random subunit association increases the chances of unintended reactivity at nontarget sites. This problem can be circumvented by specifying a unique spatial arrangement of heterotetramer subunits. By reconfiguring intersubunit protein-protein contacts, we directed the assembly of two different Cre monomers, each having a distinct DNA sequence specificity, in an alternating (ABAB) configuration. This designed heterotetramer preferentially recombined a particular pair of asymmetric Lox sites over other pairs, whereas a mixture of freely associating subunits showed little bias. Alone, the engineered monomers had reduced reactivity towards both dyad-symmetric and asymmetric sites. Specificity arose because the organization of Cre-binding repeats of the preferred substrate matched the programmed arrangement of the subunits in the heterotetrameric synapse. When this "spatial matching" principle is applied, Cre-mediated recombination can be directed to asymmetric DNA sequences with greater fidelity.
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Affiliation(s)
- Kathy A Gelato
- Biochemistry and Molecular Biology Graduate Group, University of California, Davis, CA 95616, USA
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Abstract
Now that numerous high-quality complete genome sequences are available, many efforts are focusing on the "second genomic code", namely the code that determines how the precise temporal and spatial expression of each gene in the genome is achieved. In this regard, the elucidation of transcription regulatory networks that describe combined transcriptional circuits for an organism of interest has become valuable to our understanding of gene expression at a systems level. Such networks describe physical and regulatory interactions between transcription factors (TFs) and the target genes they regulate under different developmental, physiological, or pathological conditions. The mapping of high-quality transcription regulatory networks depends not only on the accuracy of the experimental or computational method chosen, but also relies on the quality of TF predictions. Moreover, the total repertoire of TFs is not only determined by the protein-coding capacity of the genome, but also by different protein properties, including dimerization, co-factor interactions and post-translational modifications. Here, we discuss the factors that influence TF functionality and, hence, the functionality of the networks in which they operate.
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Affiliation(s)
- Christian A Grove
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
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Abstract
Two fundamental principles can account for how regulated networks of interacting proteins originated in cells. These are the law of mass action, which holds that the binding of one molecule to another increases with concentration, and the fact that the colocalization of molecules vastly increases their local concentrations. It follows that colocalization can amplify the effect on one protein of random mutations in another protein and can therefore, through natural selection, lead to interactions between proteins and to a startling variety of complex allosteric controls. It also follows that allostery is common and that homologous proteins can have different allosteric mechanisms. Thus, the regulated protein networks of organisms seem to be the inevitable consequence of natural selection operating under physical laws.
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Affiliation(s)
- John Kuriyan
- Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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Abstract
A protein-DNA dimerizer constructed from a DNA-binding pyrrole-imidazole polyamide and the peptide FYPWMK facilitates binding of the natural transcription factor Exd to an adjacent DNA site. Previous dimerizers have been constructed with the peptide attached to an internal pyrrole monomer in an overall branched oligomer. Linear oligomers constructed by attaching the peptide to the polyamide C-terminus expand the range of protein-DNA dimerization to six additional DNA sites. Replacing the FYPWMK hexapeptide with a WM dipeptide, which was previously functional in branched compounds, does not lead to a functional linear dimerizer. Instead, inserting an additional lysine generates a minimal, linear WMK tripeptide conjugate that maintains the activity of the larger FYPWMK dimerizers in a single DNA-binding site orientation. These studies provide insight into the importance of linker length and composition, binding site spacing and orientation, and the protein-binding domain content that are important for the optimization of protein-DNA dimerizers suitable for biological experiments.
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Affiliation(s)
- Ryan L Stafford
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
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Abstract
In general, double-stranded RNA (dsRNA)-binding proteins (dsRBPs) are not sequence-specific. A dsRNA molecule in a cell will interact with any dsRBP it comes in contact with, suggesting that different dsRNA-mediated pathways intersect and affect each other. This paper analyzes evidence that the ADAR RNA editing enzymes, which act on dsRNA, affect dsRNA-mediated gene silencing pathways. Examples of how ADARs alter gene silencing pathways such as RNA interference, as well as mechanisms that allow the pathways to coexist and maintain their unique functions, are discussed.
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Affiliation(s)
- B L Bass
- Department of Biochemistry and Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah 84112, USA
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Abstract
Signal transduction cascades ultimately trigger transcriptional programs that are executed by transcription factors interacting with coactivator or corepressor proteins in large multi-protein complexes. Despite the difficulties associated with discovering and verifying potent antagonists (or agonists) of protein-protein interaction events, several small molecules have been identified within the last few years that modulate transcription by directly interacting with transcriptional proteins. Some of these small molecules display surprising selectivity and some even show efficacy in vivo. This review summarizes the current status in this developing field to illustrate the emerging opportunities in the chemical biology of transcription.
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Affiliation(s)
- Hans-Dieter Arndt
- Universität Dortmund, Fachbereich Chemie, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany.
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Fiala-Beer E, Lee AC, Murray M. Regulation of the rat CYP4A2 gene promoter by c-Jun and octamer binding protein-1. Int J Biochem Cell Biol 2007; 39:1235-47. [PMID: 17481938 DOI: 10.1016/j.biocel.2007.03.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 03/23/2007] [Accepted: 03/28/2007] [Indexed: 11/26/2022]
Abstract
The physiologically important cytochrome P450 (CYP) 4A2 arachidonic acid omega-hydroxylase gene is widely expressed in rat tissues. Although the induction of CYPs 4A by peroxisome proliferators and dietary lipids is established there is minimal information on the factors that control constitutive expression. To address this issue we cloned 1.4 kb of the CYP4A2 5'-upstream region and identified several DNA elements that resembled the activator protein-1 (AP-1) consensus sequence. Using a series of 5'-truncated reporter constructs a 42 bp region was detected that was responsive to the AP-1 factor c-Jun, which is important in basal gene regulation. The roles of two putative AP-1 elements at -47/-41 and -31/-25 were tested, with the former emerging from studies with mutagenised constructs as the functionally important site. These findings were supported by electromobility shift assay (EMSA) studies that indicated the interaction of the -47/-41 element with c-Jun. The -31/-25 element mediated the suppression of CYP4A2 transactivation by octamer binding protein-1 (oct-1). Thus, mutagenesis of this element relieved the modulatory effect of oct-1 on c-Jun-mediated transactivation. In EMSAs, the binding of nuclear proteins to the -31/-25 element was competed by an oct-1 consensus sequence and supershifted by an anti-oct-1 antibody. Overexpression of c-Jun in rat liver-derived H4IIE cells increased CYP4A2 mRNA to approximately 2-fold of control, but oct-1 overexpression was without significant effect. From chromatin immunoprecipitation assays both c-Jun and oct-1 bound to the CYP4A2 5'-upstream sequence in H4IIE cells. These findings implicate c-Jun and oct-1 as potentially important constitutive factors that modulate the transactivation of the CYP4A2 gene promoter.
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Affiliation(s)
- Eva Fiala-Beer
- Pharmacogenomics and Drug Development Group, Faculty of Pharmacy, University of Sydney, NSW 2006, Australia
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Nam Y, Sliz P, Pear WS, Aster JC, Blacklow SC. Cooperative assembly of higher-order Notch complexes functions as a switch to induce transcription. Proc Natl Acad Sci U S A 2007; 104:2103-8. [PMID: 17284587 PMCID: PMC1892977 DOI: 10.1073/pnas.0611092104] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Notch receptors control differentiation and contribute to pathologic states such as cancer by interacting directly with a transcription factor called CSL (for CBF-1/Suppressor of Hairless/Lag-1) to induce expression of target genes. A number of Notch-regulated targets, including genes of the hairy/enhancer-of-split family in organisms ranging from Drosophila to humans, are characterized by paired CSL-binding sites in a characteristic head-to-head arrangement. Using a combination of structural and molecular approaches, we establish here that cooperative formation of dimeric Notch transcription complexes on promoters with paired sites is required to activate transcription. Our findings identify a mechanistic step that can account for the exquisite sensitivity of Notch target genes to variation in signal strength and developmental context, enable new strategies for sensitive and reliable identification of Notch target genes, and lay the groundwork for the development of Notch pathway inhibitors that are active on target genes containing paired sites.
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Affiliation(s)
- Yunsun Nam
- *Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA 02115
| | - Piotr Sliz
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA 02115; and
| | - Warren S. Pear
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Jon C. Aster
- *Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA 02115
| | - Stephen C. Blacklow
- *Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA 02115
- To whom correspondence should be addressed. E-mail:
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Peñalver-Mellado M, García-Heras F, Padmanabhan S, García-Moreno D, Murillo FJ, Elías-Arnanz M. Recruitment of a novel zinc-bound transcriptional factor by a bacterial HMGA-type protein is required for regulating multiple processes in Myxococcus xanthus. Mol Microbiol 2006; 61:910-26. [PMID: 16879646 DOI: 10.1111/j.1365-2958.2006.05289.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enhanceosome assembly in eukaryotes often requires high mobility group A (HMGA) proteins. In prokaryotes, the only known transcriptional regulator with HMGA-like physical, structural and DNA-binding properties is Myxococcus xanthus CarD. Here, we report that every CarD-regulated process analysed also requires the product of gene carG, located immediately downstream of and transcriptionally coupled to carD. CarG has the zinc-binding H/C-rich metallopeptidase motif found in archaemetzincins, but with Q replacing a catalytically essential E. CarG, a monomer, binds two zinc atoms, shows no apparent metallopeptidase activity, and its stability in vivo absolutely requires the cysteines. This indicates a strictly structural role for zinc-binding. In vivo CarG localizes to the nucleoid but only if CarD is also present. In vitro CarG shows no DNA-binding but physically interacts with CarD via its N-terminal and not HMGA domain. CarD and CarG thus work as a single, physically linked, transcriptional regulatory unit, and if one exists in a bacterium so does the other. Like zinc-associated eukaryotic transcriptional adaptors in enhanceosome assembly, CarG regulates by interacting not with DNA but with another transcriptional factor.
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Affiliation(s)
- Marcos Peñalver-Mellado
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
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Abstract
Protein-protein interactions are fundamental to virtually every aspect of cellular functions. With the development of high-throughput technologies of both the yeast two-hybrid system and tandem mass spectrometry, genome-wide protein-linkage mapping has become a major objective in post-genomic research. While at least partial "interactome" networks of several model organisms are already available, in the plant field, progress in this respect is slow. However, even with comprehensive protein interaction data still missing, substantial recent advance in the graph-theoretical functional interpretation of complex network architectures might pave the way for novel approaches in plant research. This article reviews current progress and discussions in network biology. Emphasis is put on the question of what can be learned about protein functions and cellular processes by studying the topology of complex protein interaction networks and the evolutionary mechanisms underlying their development. Particularly the intermediate and local levels of network organization--the modules, motifs and cliques--are increasingly recognized as the operational units of biological functions. As demonstrated by some recent results from systematic analyses of plant protein families, protein interaction networks promise to be a valuable tool for a molecular understanding of functional specificities and for identifying novel regulatory components and pathways.
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Affiliation(s)
- Joachim F Uhrig
- Botanisches Institut III, Universität zu Köln, Gyrhof Strasse 15, 50931 Koln, Germany.
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Mandaokar A, Thines B, Shin B, Lange BM, Choi G, Koo YJ, Yoo YJ, Choi YD, Choi G, Browse J. Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling. Plant J 2006; 46:984-1008. [PMID: 16805732 DOI: 10.1111/j.1365-313x.2006.02756.x] [Citation(s) in RCA: 225] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In Arabidopsis, jasmonate is required for stamen and pollen maturation. Mutants deficient in jasmonate synthesis, such as opr3, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in opr3 stamens for 22 h following jasmonate treatment. In these experiments, a total of 821 genes were specifically induced by jasmonate and 480 genes were repressed. Comparisons with data from previous studies indicate that these genes constitute a stamen-specific jasmonate transcriptome, with a large proportion (70%) of the genes expressed in the sporophytic tissue but not in the pollen. Bioinformatics tools allowed us to associate many of the induced genes with metabolic pathways that are probably upregulated during jasmonate-induced maturation. Our pathway analysis led to the identification of specific genes within larger families of homologues that apparently encode stamen-specific isozymes. Extensive additional analysis of our dataset identified 13 transcription factors that may be key regulators of the stamen maturation processes triggered by jasmonate. Two of these transcription factors, MYB21 and MYB24, are the only members of subgroup 19 of the R2R3 family of MYB proteins. A myb21 mutant obtained by reverse genetics exhibited shorter anther filaments, delayed anther dehiscence and greatly reduced male fertility. A myb24 mutant was phenotypically wild-type, but production of a myb21myb24 double mutant indicated that introduction of the myb24 mutation exacerbated all three aspects of the myb21 phenotype. Exogenous jasmonate could not restore fertility to myb21 or myb21myb24 mutant plants. Together with the data from transcriptional profiling, these results indicate that MYB21 and MYB24 are induced by jasmonate and mediate important aspects of the jasmonate response during stamen development.
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Affiliation(s)
- Ajin Mandaokar
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
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Zimmermann IM, Heim MA, Weisshaar B, Uhrig JF. Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins. Plant J 2004; 40:22-34. [PMID: 15361138 DOI: 10.1111/j.1365-313x.2004.02183.x] [Citation(s) in RCA: 548] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In-depth analysis of protein-protein interaction specificities of the MYB protein family of Arabidopsis thaliana revealed a conserved amino acid signature ([DE]Lx(2)[RK]x(3)Lx(6)Lx(3)R) as the structural basis for interaction between MYB and R/B-like BHLH proteins. The motif has successfully been used to predict new MYB/BHLH interactions for A. thaliana proteins, it allows to discriminate between even closely related MYB proteins and it is conserved amongst higher plants. In A. thaliana, the motif is shared by fourteen R2R3 MYB proteins and six 1R MYB proteins. It is located on helices 1 and 2 of the R3 repeat and forms a characteristic surface-exposed pattern of hydrophobic and charged residues. Single-site mutation of any amino acid of the signature impairs the interaction. Two particular amino acids have been determined to account for most of the interaction stability. Functional specificity of MYB/BHLH complexes was investigated in vivo by a transient DFR promoter activation assay. Residues stabilizing the MYB/BHLH interaction were shown to be critical for promoter activation. By virtue of proved and predicted interaction specificities, this study provides a comprehensive survey of the MYB proteins that interact with R/B-like BHLH proteins potentially involved in the TTG1-dependent regulatory interaction network. The results are discussed with respect to multi-functionality, specificity and redundancy of MYB and BHLH protein function.
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Affiliation(s)
- Ilona M Zimmermann
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Koeln, Germany
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