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Kotha SR, Staller MV. Clusters of acidic and hydrophobic residues can predict acidic transcriptional activation domains from protein sequence. Genetics 2023; 225:iyad131. [PMID: 37462277 PMCID: PMC10550315 DOI: 10.1093/genetics/iyad131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/03/2023] [Indexed: 10/06/2023] Open
Abstract
Transcription factors activate gene expression in development, homeostasis, and stress with DNA binding domains and activation domains. Although there exist excellent computational models for predicting DNA binding domains from protein sequence, models for predicting activation domains from protein sequence have lagged, particularly in metazoans. We recently developed a simple and accurate predictor of acidic activation domains on human transcription factors. Here, we show how the accuracy of this human predictor arises from the clustering of aromatic, leucine, and acidic residues, which together are necessary for acidic activation domain function. When we combine our predictor with the predictions of convolutional neural network (CNN) models trained in yeast, the intersection is more accurate than individual models, emphasizing that each approach carries orthogonal information. We synthesize these findings into a new set of activation domain predictions on human transcription factors.
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Affiliation(s)
- Sanjana R Kotha
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
| | - Max Valentín Staller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
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2
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Tran H, Walczak AM, Dostatni N. Constraints and limitations on the transcriptional response downstream of the Bicoid morphogen gradient. Curr Top Dev Biol 2020; 137:119-142. [PMID: 32143741 DOI: 10.1016/bs.ctdb.2019.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The regulation of the hunchback promoter expression by the maternal Bicoid gradient has been studied as a model system in development for many years. Yet, at the level of quantitative agreement between data and theoretical models, even the first step of this regulation, transcription, continues to be challenging. This situation is slowly progressing, thanks to quantitative live-imaging techniques coupled to advanced statistical data analysis and modeling. Here, we outline the current state of our knowledge of this apparently "simple" step, highlighting the newly appreciated role of bursty transcription dynamics and its regulation.
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Affiliation(s)
- Huy Tran
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics, Paris, France; Ecole Normale Supérieure, PSL Research University, CNRS, Sorbonne Université, Laboratoire de Physique, Paris, France
| | - Aleksandra M Walczak
- Ecole Normale Supérieure, PSL Research University, CNRS, Sorbonne Université, Laboratoire de Physique, Paris, France.
| | - Nathalie Dostatni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics, Paris, France.
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3
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Mannervik M. Control of Drosophila embryo patterning by transcriptional co-regulators. Exp Cell Res 2013; 321:47-57. [PMID: 24157250 DOI: 10.1016/j.yexcr.2013.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 12/29/2022]
Abstract
A combination of broadly expressed transcriptional activators and spatially restricted repressors are used to pattern embryos into cells of different fate. Transcriptional co-regulators are essential mediators of transcription factor function, and contribute to selective transcriptional responses in embryo development. A two step mechanism of transcriptional regulation is discussed, where remodeling of chromatin is initially required, followed by stimulation of recruitment or release of RNA polymerase from the promoter. Transcriptional co-regulators are essential for both of these steps. In particular, most co-activators are associated with histone acetylation and co-repressors with histone deacetylation. In the early Drosophila embryo, genome-wide studies have shown that the CBP co-activator has a preference for associating with some transcription factors and regulatory regions. The Groucho, CtBP, Ebi, Atrophin and Brakeless co-repressors are selectively used to limit zygotic gene expression. New findings are summarized which show that different co-repressors are often utilized by a single repressor, that the context in which a co-repressor is recruited to DNA can affect its activity, and that co-regulators may switch from co-repressors to co-activators and vice versa. The possibility that co-regulator activity is regulated and plays an instructive role in development is discussed as well. This review highlights how findings in Drosophila embryos have contributed to the understanding of transcriptional regulation in eukaryotes as well as to mechanisms of animal embryo patterning.
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Affiliation(s)
- Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Arrheniuslaboratories E3, SE-106 91 Stockholm, Sweden.
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4
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TNFα induced FOXP3–NFκB interaction dampens the tumor suppressor role of FOXP3 in gastric cancer cells. Biochem Biophys Res Commun 2013. [DOI: 10.1016/j.bbrc.2012.11.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Liu J, Ma J. Dampened regulates the activating potency of Bicoid and the embryonic patterning outcome in Drosophila. Nat Commun 2013; 4:2968. [PMID: 24336107 PMCID: PMC3902774 DOI: 10.1038/ncomms3968] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 11/18/2013] [Indexed: 01/26/2023] Open
Abstract
The Drosophila morphogen gradient of Bicoid (Bcd) initiates anterior-posterior (AP) patterning; however, it is poorly understood how its ability to activate a target gene may have an impact on this process. Here we report an F-box protein, Dampened (Dmpd) as a nuclear cofactor of Bcd that can enhance its activating potency. We establish a quantitative platform to specifically investigate two parameters of a Bcd target gene response, expression amplitude and boundary position. We show that embryos lacking Dmpd have a reduced amplitude of Bcd-activated hunchback (hb) expression at a critical time of development. This is because of a reduced Bcd-dependent transcribing probability. This defect is faithfully propagated further downstream of the AP-patterning network to alter the spatial characteristics of even-skipped (eve) stripes. Thus, unlike another Bcd-interacting F-box protein Fate-shifted (Fsd), which controls AP patterning through regulating the Bcd gradient profile, Dmpd achieves its patterning role through regulating the activating potency of Bcd.
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Affiliation(s)
- Junbo Liu
- Division of Biomedical Informatics Cincinnati Children's Research Foundation 3333 Burnet Avenue Cincinnati, Ohio United States of America
| | - Jun Ma
- Division of Biomedical Informatics Cincinnati Children's Research Foundation 3333 Burnet Avenue Cincinnati, Ohio United States of America
- Division of Developmental Biology Cincinnati Children's Research Foundation 3333 Burnet Avenue Cincinnati, Ohio United States of America
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6
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Fates-shifted is an F-box protein that targets Bicoid for degradation and regulates developmental fate determination in Drosophila embryos. Nat Cell Biol 2010; 13:22-9. [PMID: 21170036 PMCID: PMC3074934 DOI: 10.1038/ncb2141] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 11/17/2010] [Indexed: 12/31/2022]
Abstract
Bicoid (Bcd) is a morphogenetic protein that instructs patterning along the anterior-posterior (A-P) axis in Drosophila embryos. Despite extensive studies, what controls the formation of a normal concentration gradient of Bcd remains an unresolved and controversial question. In this report we show that Bcd protein degradation is mediated by the ubiquitin-proteasome pathway. We identify a novel F-box protein, encoded by fates-shifted (fsd), that plays an important role in Bcd protein degradation by targeting it for ubiquitination. Embryos from females lacking fsd have an altered Bcd gradient profile, resulting in a shift of the fatemap along the A-P axis. Our study represents a first experimental demonstration that, contrary to an alternative hypothesis, Bcd protein degradation is required for normal gradient formation and developmental fate determination.
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7
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Lemke S, Busch SE, Antonopoulos DA, Meyer F, Domanus MH, Schmidt-Ott U. Maternal activation of gap genes in the hover fly Episyrphus. Development 2010; 137:1709-19. [DOI: 10.1242/dev.046649] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The metameric organization of the insect body plan is initiated with the activation of gap genes, a set of transcription-factor-encoding genes that are zygotically expressed in broad and partially overlapping domains along the anteroposterior (AP) axis of the early embryo. The spatial pattern of gap gene expression domains along the AP axis is generally conserved, but the maternal genes that regulate their expression are not. Building on the comprehensive knowledge of maternal gap gene activation in Drosophila, we used loss- and gain-of-function experiments in the hover fly Episyrphus balteatus (Syrphidae) to address the question of how the maternal regulation of gap genes evolved. We find that, in Episyrphus, a highly diverged bicoid ortholog is solely responsible for the AP polarity of the embryo. Episyrphus bicoid represses anterior zygotic expression of caudal and activates the anterior and central gap genes orthodenticle, hunchback and Krüppel. In bicoid-deficient Episyrphus embryos, nanos is insufficient to generate morphological asymmetry along the AP axis. Furthermore, we find that torso transiently regulates anterior repression of caudal and is required for the activation of orthodenticle, whereas all posterior gap gene domains of knirps, giant, hunchback, tailless and huckebein depend on caudal. We conclude that all maternal coordinate genes have altered their specific functions during the radiation of higher flies (Cyclorrhapha).
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Affiliation(s)
- Steffen Lemke
- University of Chicago, Department of Organismal Biology and Anatomy, CLSC 921B, 920 E. 58th Street, Chicago, IL 60637, USA
| | - Stephanie E. Busch
- University of Chicago, Department of Organismal Biology and Anatomy, CLSC 921B, 920 E. 58th Street, Chicago, IL 60637, USA
| | - Dionysios A. Antonopoulos
- Argonne National Laboratory, Institute for Genomics & Systems Biology, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Folker Meyer
- Argonne National Laboratory, Institute for Genomics & Systems Biology, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Marc H. Domanus
- Argonne National Laboratory, Institute for Genomics & Systems Biology, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Urs Schmidt-Ott
- University of Chicago, Department of Organismal Biology and Anatomy, CLSC 921B, 920 E. 58th Street, Chicago, IL 60637, USA
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8
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Gregor T, McGregor AP, Wieschaus EF. Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos. Dev Biol 2008; 316:350-8. [PMID: 18328473 DOI: 10.1016/j.ydbio.2008.01.039] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 01/21/2008] [Accepted: 01/23/2008] [Indexed: 12/19/2022]
Abstract
The Bicoid morphogen evolved approximately 150 MYA from a Hox3 duplication and is only found in higher dipterans. A major difference between dipteran species, however, is the size of the embryo, which varies up to 5-fold. Although the expression of developmental factors scale with egg length, it remains unknown how this scaling is achieved. To test whether scaling is accounted for by the properties of Bicoid, we expressed eGFP fused to the coding region of bicoid from three dipteran species in transgenic Drosophila embryos using the Drosophila bicoid cis-regulatory and mRNA localization sequences. In such embryos, we find that Lucilia sericata and Calliphora vicina Bicoid produce gradients very similar to the endogenous Drosophila gradient and much shorter than what they would have produced in their own respective species. The common shape of the Drosophila, Lucilia and Calliphora Bicoid gradients appears to be a conserved feature of the Bicoid protein. Surprisingly, despite their similar distributions, we find that Bicoid from Lucilia and Calliphora do not rescue Drosophila bicoid mutants, suggesting that that Bicoid proteins have evolved species-specific functional amino acid differences. We also found that maternal expression and anteriorly localization of proteins other than Bcd does not necessarily give rise to a gradient; eGFP produced a uniform protein distribution. However, a shallow gradient was observed using eGFP-NLS, suggesting nuclear localization may be necessary but not sufficient for gradient formation.
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Affiliation(s)
- Thomas Gregor
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
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9
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Crauk O, Dostatni N. Bicoid Determines Sharp and Precise Target Gene Expression in the Drosophila Embryo. Curr Biol 2005; 15:1888-98. [PMID: 16271865 DOI: 10.1016/j.cub.2005.09.046] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 09/20/2005] [Accepted: 09/21/2005] [Indexed: 10/25/2022]
Abstract
BACKGROUND The activity of the Bicoid (Bcd) transcription factor is a useful example of how quantitative information contained in a smooth morphogen gradient is transformed into discrete and precise patterns of target gene expression. There are two distinct and important aspects to this process: the "sharpening" of the posterior borders of the expression domains and the "precision" of where the target genes are expressed along the length of the embryo as the syncytial embryo begins to cellularize. Although the sharpening phenomenon was observed over a decade ago, it is still poorly understood. RESULTS Here, we show that a Bcd reporter gene containing binding sites only for Bcd is expressed, like natural targets of Bcd, in a precise domain with a sharp boundary. Analysis of embryos expressing deleted forms of Bcd indicates that the sharpness of the Bcd target gene hunchback's expression involves the glutamine-rich and C-terminal activation domains of Bcd. Furthermore, several artificial Gal4-derived transcription factors expressed as gradients in the embryo share Bcd's ability to drive precise target gene expression with sharp boundaries. CONCLUSION Thus, contrary to recent reports proposing that the Bcd gradient is not sufficient to establish precise positional information, we show that Bcd drives precise and sharp expression of its target genes through a process that depends exclusively on its ability to activate transcription.
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Affiliation(s)
- Olivier Crauk
- Laboratory of Nuclear Dynamics and Genome Plasticity, CNRS/UMR 218, Institut Curie, Paris, France
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10
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Fu D, Ma J. Interplay between positive and negative activities that influence the role of Bicoid in transcription. Nucleic Acids Res 2005; 33:3985-93. [PMID: 16030350 PMCID: PMC1178001 DOI: 10.1093/nar/gki691] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 05/20/2005] [Accepted: 06/16/2005] [Indexed: 11/13/2022] Open
Abstract
The Drosophila mophogenetic protein Bicoid (Bcd) can activate transcription in a concentration-dependent manner in embryos. It contains a self-inhibitory domain that can interact with the co-repressor Sin3A. In this report, we study a Bcd mutant, Bcd(A57-61), which has a strengthened self-inhibitory function and is unable to activate the hb-CAT reporter in Drosophila cells, to analyze the role of co-factors in regulating Bcd function. We show that increased concentrations of the co-activator dCBP in cells can switch this protein from its inactive state to an active state on the hb-CAT reporter. The C-terminal portion of Bcd(A57-61) is required to mediate such activity-rescuing function of dCBP. Although capable of binding to DNA in vitro, Bcd(A57-61) is unable to access the hb enhancer element in cells, suggesting that its DNA binding defect is only manifested in a cellular context. Increased concentrations of dCBP restore not only the ability of Bcd(A57-61) to access the hb enhancer element in cells but also the occupancy of the general transcription factors TBP and TFIIB at the reporter promoter. These and other results suggest that an activator can undergo switches between its active and inactive states through sensing the opposing actions of positive and negative co-factors.
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Affiliation(s)
- Dechen Fu
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, Graduate Program in Molecular and Developmental Biology, University of Cincinnati College of Medicine3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Jun Ma
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, Graduate Program in Molecular and Developmental Biology, University of Cincinnati College of Medicine3333 Burnet Avenue Cincinnati, OH 45229, USA
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11
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Abstract
In Drosophila, a Bcd protein gradient orchestrates patterning along the anteroposterior embryonic axis. However, studies of basal flies and other insects have revealed that bcd is a derived Hox3 gene found only in higher dipterans. To understand how bcd acquired its role in flies and how anteroposterior patterning mechanisms have evolved, I first review key features of bcd function in Drosophila: anterior localization and transcriptional and translation control of gene expression. I then discuss investigations of bcd in other higher dipterans that have provided insight into the evolution of regulatory interactions and the Bcd gradient. Finally, I review studies of Drosophila and other insects that address the evolution of bcd function and integration of bcd into ancestral regulatory mechanisms. I suggest further comparative studies may allow us to identify the intermediate steps in bcd evolution. This will make bcd a paradigm for the origin and evolution of genes and regulatory networks.
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Affiliation(s)
- Alistair P McGregor
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey 08540, USA.
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12
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Fu D, Wen Y, Ma J. The co-activator CREB-binding protein participates in enhancer-dependent activities of bicoid. J Biol Chem 2004; 279:48725-33. [PMID: 15358774 DOI: 10.1074/jbc.m407066200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bicoid (Bcd) is a transcriptional activator required for early embryonic patterning in Drosophila. Despite extensive studies, it currently remains unclear how Bcd activates transcription and what proteins participate in its activation process. In this report, we describe experiments to analyze the role of the Drosophila co-activator dCBP in Bcd-mediated activation. In Drosophila S2 cells, the Bcd activity is increased by the co-transfection of plasmids expressing dCBP and reduced by double-stranded RNA-mediated interference against dCBP. We further show that Bcd and dCBP can interact with each other and that Bcd-interacting domains of dCBP can cause dominant negative effects on Bcd activity in S2 cells. Our comparison of two Bcd-responsive enhancers, hunchback (hb) and knirps (kni), reveals a differential role of dCBP in facilitating Bcd activation. A dCBP mutant defective in its histone acetyltransferase activity exhibits a reduced, but not abolished, co-activator function for Bcd. Our chromatin immunoprecipitation experiments show that dCBP can increase not only the occupancy of Bcd itself at the enhancers but also the recruitment of general transcription factors to the promoter. Together, these experiments suggest that dCBP is an enhancer-dependent co-activator of Bcd, facilitating its activation through multiple mechanisms.
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Affiliation(s)
- Dechen Fu
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, Graduate Program in Molecular and Developmental Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
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13
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Niessing D, Blanke S, Jäckle H. Bicoid associates with the 5'-cap-bound complex of caudal mRNA and represses translation. Genes Dev 2002; 16:2576-82. [PMID: 12368268 PMCID: PMC187448 DOI: 10.1101/gad.240002] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Translational control plays a key role in many biological processes including pattern formation during early Drosophila embryogenesis. In this process, the anterior determinant Bicoid (BCD) acts not only as a transcriptional activator of segmentation genes but also causes specific translational repression of ubiquitously distributed caudal (cad) mRNA in the anterior region of the embryo. We show that translational repression of cad mRNA is dependent on a functional eIF4E-binding motif. The results suggest a novel mode of translational repression, which combines the strategy of target-specific binding to 3'-untranslated sequences and interference with 5'-cap-dependent translation initiation in one protein.
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Affiliation(s)
- Dierk Niessing
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Molekulare Entwicklungsbiologie, 37077 Göttingen, Germany
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Melamed P, Koh M, Preklathan P, Bei L, Hew C. Multiple mechanisms for Pitx-1 transactivation of a luteinizing hormone beta subunit gene. J Biol Chem 2002; 277:26200-7. [PMID: 12011080 DOI: 10.1074/jbc.m201605200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pituitary homeobox factor-1 (Pitx-1) transactivates a number of pituitary-specific genes through direct interaction with other specific transcription factors. We demonstrate here that Pitx-1 plays a crucial role in the regulation of the Chinook salmon luteinizing hormone beta gene promoter through a number of novel mechanisms. On the proximal promoter its action involves a synergistic effect with steroidogenic factor-1 (SF-1) alone or in combination with the estrogen receptor; promoter activity being induced by 9- or 35-fold over controls, respectively. Further upstream, a series of four Pitx-1 response elements (located between 1366 and 1506 bp from the transcriptional start site) is also involved in regulating the promoter activity. The two distal sequences have the greatest effect on the basal activity and are also essential for the gonadotropin-releasing hormone (GnRH) response. Mammalian two-hybrid assays revealed that Pitx-1 can homodimerize. Moreover, circular permutation assays indicate that binding of Pitx-1 to more than one response element induces conformational changes of the target DNA. This constitutes an additional mechanism through which Pitx-1 can mediate transactivation of this gene, allowing the demonstrated interaction of proximal response elements and distal enhancers, thus facilitating the maximal GnRH response that was seen in the longer promoter constructs. Our research also indicates that Pitx-1 is phosphorylated on three residues when bound to the DNA.
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Affiliation(s)
- Philippa Melamed
- Functional Genomics Laboratories, Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117542 Singapore.
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15
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Shaw PJ, Wratten NS, McGregor AP, Dover GA. Coevolution in bicoid-dependent promoters and the inception of regulatory incompatibilities among species of higher Diptera. Evol Dev 2002; 4:265-77. [PMID: 12168619 DOI: 10.1046/j.1525-142x.2002.02016.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To what extent and in what way do gene promoters and their transacting regulatory proteins coevolve? In this and in earlier publications we show that the Bicoid-dependent promoters of the segmentation genes hunchback and tailless in species of higher Diptera (Drosophila, Musca, Calliphora, and Lucilia) are different with respect to the copy number, spacing, sequence, and orientation of Bicoid binding sites. At the same time there are significant amino acid differences in the Bicoid homeodomain. To test these interspecific differences, we used a series of functional assays, starting with the analysis of Bicoid binding affinities of individual sites, through to transgene rescue experiments, to compare within-species with between-species mixtures of Bicoid homeodomains and hunchback or tailless promoters. We observed that components taken from different species interact with less efficiency compared with those taken from within the same species. Our interpretation is that such interspecific incompatibilities are a consequence of interactive genetic elements coevolving one with another, hence maintaining functional compatibility within each species. At the same time such a process allows differences to accumulate between species regarding the precise molecular basis whereby the common function is effected.
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Affiliation(s)
- P J Shaw
- Department of Genetics, University of Leicester, UK.
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16
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Zhao C, York A, Yang F, Forsthoefel DJ, Dave V, Fu D, Zhang D, Corado MS, Small S, Seeger MA, Ma J. The activity of the Drosophila morphogenetic protein Bicoid is inhibited by a domain located outside its homeodomain. Development 2002; 129:1669-80. [PMID: 11923203 DOI: 10.1242/dev.129.7.1669] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Drosophila morphogenetic protein Bicoid (Bcd) is a homeodomain-containing activator that stimulates the expression of target genes during early embryonic development. We demonstrate that a small domain of Bcd located immediately N-terminally of the homeodomain represses its own activity in Drosophila cells. This domain, referred to as a self-inhibitory domain, works as an independent module that does not rely on any other sequences of Bcd and can repress the activity of heterologous activators. We further show that this domain of Bcd does not affect its properties of DNA binding or subcellular distribution. A Bcd derivative with point mutations in the self-inhibitory domain severely affects pattern formation and target gene expression in Drosophila embryos. We also provide evidence to suggest that the action of the self-inhibitory domain requires a Drosophila co-factor(s), other than CtBP or dSAP18. Our results suggest that proper action of Bcd as a transcriptional activator and molecular morphogen during embryonic development is dependent on the downregulation of its own activity through an interaction with a novel co-repressor(s) or complex(es).
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Affiliation(s)
- Chen Zhao
- Division of Developmental Biology, Children's Hospital Research Foundation, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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17
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Shaw PJ, Salameh A, McGregor AP, Bala S, Dover GA. Divergent structure and function of the bicoid gene in Muscoidea fly species. Evol Dev 2001; 3:251-62. [PMID: 11478522 DOI: 10.1046/j.1525-142x.2001.003004251.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have investigated the evolution of the bicoid (bcd) gene in fly species of the Muscoidea Superfamily. We obtained the complete bcd sequence from the housefly Musca domestica and found polymorphism in the coding region among Musca strains. In addition to Musca, we cloned most of the bcd coding sequences from two blowfly species Calliphora vicina and Lucilia sericata. The 5' and 3' regulatory regions flanking the Musca bcd gene are widely diverged in sequence from Drosophila; however, some important sequence motifs identified in Drosophila bcd are present. The predicted RNA secondary structures of the 3' UTRs are similar, despite sequence divergence. Comparison of Bicoid (Bcd) proteins shows a serine-rich domain of unknown function is present in the Muscoidea species, but is absent in other species. The in vivo function of bcd in Musca was tested by RNAi to mimic loss of function phenotype. We obtained a head defect phenotype similar to weak bcd alleles of Drosophila. Although our comparisons initially suggest functional conservation between species, closer inspection reveals significant differences. Divergence of structural motifs, such as regulatory elements in flanking regions and conservation of protein domains in some species but not in others, points to functional divergence between species. We suggest that the larger embryonic size in Muscoidea species restricts the morphogenetic activity of a weak Bcd activator, which has evolved a more specialized role in head determination and lost some functions in thoracic development.
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Affiliation(s)
- P J Shaw
- Department of Genetics, University of Leicester, UK.
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18
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Janody F, Sturny R, Schaeffer V, Azou Y, Dostatni N. Two distinct domains of Bicoid mediate its transcriptional downregulation by the Torso pathway. Development 2001; 128:2281-90. [PMID: 11493547 DOI: 10.1242/dev.128.12.2281] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The transcriptional activity of the Bicoid morphogen is directly downregulated by the Torso signal transduction cascade at the anterior pole of the Drosophila embryo. This regulation does not involve the homeodomain or direct phosphorylation of Bicoid. We analyse the transcriptional regulation of Bicoid in response to the Torso pathway, using Bicoid variants and fusion proteins between the Bicoid domains and the Gal4 DNA-binding domain. We show that Bicoid possesses three autonomous activation domains. Two of these domains, the serine/threonine-rich and the acidic domains, are downregulated by Torso, whereas the third activation domain, which is rich in glutamine, is not. The alanine-rich domain, previously described as an activation domain in vitro, has a repressive activity that is independent of Torso. Thus, Bicoid downregulation by Torso results from a competition between the glutamine-rich domain that is insensitive to Torso and the serine/threonine-rich and acidic activation domains downregulated by Torso. The alanine-rich domain contributes to this process indirectly by reducing the global activity of the protein and in particular the activity of the glutamine-rich domain that might otherwise prevent downregulation by Torso.
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Affiliation(s)
- F Janody
- Developmental Biology Institute of Marseille, Laboratoire de Génétique et Physiologie du Développement, Université de la Méditerrannée, Luminy, Case 907, 13288 Marseille Cedex 09, France
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19
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Giani L, Bucci S, Ragghianti M, Mancino G. Expression of TAFII70 RNA and protein during oogenesis and development of the amphibian Pleurodeles waltl. Mech Dev 2000; 99:191-4. [PMID: 11091092 DOI: 10.1016/s0925-4773(00)00482-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
TAFs are thought to play an essential role in eukaryotic RNA polymerase II transcription by mediating the expression of distinct subsets of genes. TAFII60/70 was studied in yeast, Drosophila and humans: in the present work, we analyzed the homologue PwTAFII70 in Pleurodeles. The gene is expressed in ovarian oocytes and throughout development, and the level of expression decreases in late embryos. The transcripts are localized in the animal hemisphere of the fertilized eggs and in the animal blastomeres of embryos at cleavage; later PwTAFII70 mRNA is expressed in the neural plate and folds. TAFII70 protein, which is present in fertilized eggs and throughout development, progressively shows a lower level of expression starting from the neurula stage.
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Affiliation(s)
- L Giani
- Dipartimento di Fisiologia e Biochimica, Laboratorio di Biologia cellulare e dello sviluppo, Università degli Studi di Pisa, Pisa, Italy
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20
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Schaeffer V, Killian D, Desplan C, Wimmer EA. High bicoid levels render the terminal system dispensable for Drosophila head development. Development 2000; 127:3993-9. [PMID: 10952897 DOI: 10.1242/dev.127.18.3993] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Drosophila, the gradient of the Bicoid (Bcd) morphogen organizes the anteroposterior axis while the ends of the embryo are patterned by the maternal terminal system. At the posterior pole, expression of terminal gap genes is mediated by the local activation of the Torso receptor tyrosine kinase (Tor). At the anterior, terminal gap genes are also activated by the Tor pathway but Bcd contributes to their activation. Here we present evidence that Tor and Bcd act independently on common target genes in an additive manner. Furthermore, we show that the terminal maternal system is not required for proper head development, since high levels of Bcd activity can functionally rescue the lack of terminal system activity at the anterior pole. This observation is consistent with a recent evolution of an anterior morphogenetic center consisting of Bcd and anterior Tor function.
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Affiliation(s)
- V Schaeffer
- Department of Biology, New York University, New York NY 10003 USA
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21
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Chen Z, Manley JL. Robust mRNA transcription in chicken DT40 cells depleted of TAF(II)31 suggests both functional degeneracy and evolutionary divergence. Mol Cell Biol 2000; 20:5064-76. [PMID: 10866663 PMCID: PMC85956 DOI: 10.1128/mcb.20.14.5064-5076.2000] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have employed gene targeting coupled with conditional expression to construct a chicken DT40 cell line in which a tetracycline (Tet)-repressible promoter is exclusively responsible for expression of cTAF(II)31, a histone-like TAF(II) residing in both the transcription factor TFIID and the histone acetylase complex PCAF/SAGA. Tet addition resulted in rapid loss of cTAF(II)31 mRNA and protein, eventually leading to apoptotic cell death. Significantly, five of six other TAF(II)s tested were also rapidly depleted, but levels of the TATA binding protein and subunits of PCAF/SAGA were at most modestly compromised. Strikingly, pulse-labeling experiments indicate that total poly(A)(+) mRNA transcription was not significantly reduced after cTAF(II)31 depletion, and steady-state levels of several specific transcripts remained the same or decreased only mildly. Moreover, activation of c-fos transcription following serum starvation occurred efficiently in the absence of cTAF(II)31. These data, which contrast with comparable studies in yeast, strongly suggest that cTAF(II)31 and perhaps other TAF(II)s are not essential for general mRNA transcription in DT40 cells. We propose that this is due to extensive functional degeneracy in the highly complex metazoan transcriptional machinery.
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Affiliation(s)
- Z Chen
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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22
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Torigoi E, Bennani-Baiti IM, Rosen C, Gonzalez K, Morcillo P, Ptashne M, Dorsett D. Chip interacts with diverse homeodomain proteins and potentiates bicoid activity in vivo. Proc Natl Acad Sci U S A 2000; 97:2686-91. [PMID: 10688916 PMCID: PMC15990 DOI: 10.1073/pnas.050586397] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Drosophila protein Chip potentiates activation by several enhancers and is required for embryonic segmentation. Chip and its mammalian homologs interact with and promote dimerization of nuclear LIM proteins. No known Drosophila LIM proteins, however, are required for segmentation, nor for expression of most genes known to be regulated by Chip. Here we show that Chip also interacts with diverse homeodomain proteins using residues distinct from those that interact with LIM proteins, and that Chip potentiates activity of one of these homeodomain proteins in Drosophila embryos and in yeast. These and other observations help explain the roles of Chip in segmentation and suggest a model to explain how Chip potentiates activation by diverse enhancers.
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Affiliation(s)
- E Torigoi
- Molecular Biology Program, Sloan-Kettering Division of the Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
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23
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Janody F, Sturny R, Catala F, Desplan C, Dostatni N. Phosphorylation of bicoid on MAP-kinase sites: contribution to its interaction with the torso pathway. Development 2000; 127:279-89. [PMID: 10603346 DOI: 10.1242/dev.127.2.279] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Torso signal transduction pathway exhibits two opposite effects on the activity of the Bicoid (Bcd) morphogen: (i) Bcd function is repressed by Torso (Tor) at the anterior pole of the embryo leading to a retraction of the expression of many Bcd targets from the most anterior region of the embryo, where the Tor tyrosine kinase receptor is activated, and (ii) Bcd function is strengthened by Tor in a broader anterior region, as indicated by a shift of the posterior border of Bcd targets towards the anterior pole in embryos deprived from Tor activity. Anterior repression of Bcd targets was not observed in embryos lacking maternal contribution of D-sor, which acts downstream of Tor and encodes a MAP-kinase kinase. This indicates that the Ras signalling cascade is directly involved in this process, although the known transcriptional effectors of the Tor pathway, tll and hkb, are not (Ronchi, E., Treisman, J., Dostatni, N., Struhl, G. and Desplan, C. (1993) Cell 74, 347–355). Bcd is a good in vitro substrate for phosphorylation by MAP-kinase and phosphorylation of the protein occur in vivo on MAP-kinase sites. In the presence of a Bcd mutant that could no longer be phosphorylated by MAP-kinase, expression of Bcd targets remained repressed by Tor at the pole while strengthening of Bcd activity was reduced. These experiments indicate that phosphorylation of Bcd by MAP-kinase is likely to be required for the Tor pathway to induce its full positive effect on Bcd. This suggests that Tor signalling acts at a distance from the anterior pole by direct modification of the diffusing Bcd morphogen.
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Affiliation(s)
- F Janody
- LGPD, Institut de Biologie du Développement de Marseille, Parc Scientifique de Luminy, Case 907, France
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