51
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Chang Q, Zhang L, He C, Zhang B, Zhang J, Liu B, Zeng N, Zhu Z. HOXB9 induction of mesenchymal-to-epithelial transition in gastric carcinoma is negatively regulated by its hexapeptide motif. Oncotarget 2016; 6:42838-53. [PMID: 26536658 PMCID: PMC4767475 DOI: 10.18632/oncotarget.5814] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 10/13/2015] [Indexed: 01/03/2023] Open
Abstract
HOXB9, a transcription factor, plays an important role in development. While HOXB9 has been implicated in tumorigenesis and metastasis, its mechanisms are variable and its role in gastric carcinoma (GC) remains unclear. In the present study, we demonstrated that the expression of HOXB9 decreased in gastric carcinoma and was associated with malignancy and metastasis. Re-expression of HOXB9 in gastric cell lines resulted in the suppression of cell proliferation, migration, and invasion, which was accompanied by the induction of mesenchymal-to-epithelial transition (MET). Comparative sequence analysis and examination of a HOXB9 structural model indicated that three sites might possibly be involved in MET regulation. The in vitro study of HOXB9 mutants showed that these were unable to inhibit MET induction. However, when overexpressing a HOXB9 mutant lacking the hexapeptide motif, a more potent MET induction and tumor suppression was observed compared to that of the wild-type, indicating that the presence of the hexapeptide motif reduced HOXB9 MET induction and tumor suppression activity. Therefore, the results of the present study suggested that HOXB9 is a tumor suppressor in gastric carcinoma, and its activity was controlled by different regulatory mechanisms such as the hexapeptide motif as a "brake" in this case. The results of these regulatory effects could lead to either oncogenic or tumor suppressive roles of HOXB9, depending on the context of the particular type of cancer involved.
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Affiliation(s)
- Qing Chang
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Clinical Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Zhang
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Current Address: Department of Gastrointestinal Surgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Changyu He
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baogui Zhang
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zhang
- Department of Clinical Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingya Liu
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Naiyan Zeng
- Department of Pathology and Pathophysiology, Key laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenggang Zhu
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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52
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Mathiasen L, Valentini E, Boivin S, Cattaneo A, Blasi F, Svergun DI, Bruckmann C. The flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding. FEBS J 2016; 283:3134-54. [PMID: 27390177 DOI: 10.1111/febs.13801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/20/2016] [Accepted: 07/06/2016] [Indexed: 12/27/2022]
Abstract
UNLABELLED Transcription factors are known to modify the DNA that they bind. However, DNA can also serve as an allosteric ligand whose binding modifies the conformation of transcriptional regulators. Here, we describe how heterodimer PBX1:PREP1, formed by proteins playing major roles in embryonic development and tumorigenesis, undergoes an allosteric transition upon DNA binding. We demonstrate through a number of biochemical and biophysical methods that PBX1:PREP1 exhibits a structural change upon DNA binding. Small-angle X-ray scattering (SAXS), circular dichroism (CD), isothermal titration calorimetry (ITC), and limited proteolysis demonstrate a different shape, α-helical content, thermodynamic behavior, and solution environment of the holo-complex (with DNA) compared to the apo-complex (without DNA). Given that PBX1 as such does not have a defined DNA selectivity, structural changes upon DNA binding become major factors in the function of the PBX1:PREP1 complex. The observed changes are mapped at both the amino- and carboxy-terminal regions of the two proteins thereby providing important insights to determine how PBX1:PREP1 dimer functions. DATABASE Small-angle scattering data are available in SASBDB under accession numbers SASDAP7, SASDAQ7, and SASDAR7.
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Affiliation(s)
- Lisa Mathiasen
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | | | | | - Angela Cattaneo
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Francesco Blasi
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | | | - Chiara Bruckmann
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
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53
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Jagot-Lacoussiere L, Kotula E, Villoutreix BO, Bruzzoni-Giovanelli H, Poyet JL. A Cell-Penetrating Peptide Targeting AAC-11 Specifically Induces Cancer Cells Death. Cancer Res 2016; 76:5479-90. [DOI: 10.1158/0008-5472.can-16-0302] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/24/2016] [Indexed: 11/16/2022]
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54
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Abstract
Metazoans encode clusters of paralogous Hox genes that are critical for proper development of the body plan. However, there are a number of unresolved issues regarding how paralogous Hox factors achieve specificity to control distinct cell fates. First, how do Hox paralogs, which have very similar DNA binding preferences in vitro, drive different transcriptional programs in vivo? Second, the number of potential Hox binding sites within the genome is vast compared to the number of sites bound. Hence, what determines where in the genome Hox factors bind? Third, what determines whether a Hox factor will activate or repress a specific target gene? Here, we review the current evidence that is beginning to shed light onto these questions. In particular, we highlight how cooperative interactions with other transcription factors (especially PBC and HMP proteins) and the sequences of cis-regulatory modules provide a basis for the mechanisms of Hox specificity. We conclude by integrating a number of the concepts described throughout the review in a case study of a highly interrogated Drosophila cis-regulatory module named “The Distal-less Conserved Regulatory Element” (DCRE).
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Affiliation(s)
- Arya Zandvakili
- Molecular and Developmental Biology Graduate Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Correspondence: ; Tel.: +1-513-636-3366
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55
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Kachhap S, Priyadarshini P, Singh B. Molecular dynamics simulations show altered secondary structure of clawless in binary complex with DNA providing insights into aristaless-clawless-DNA ternary complex formation. J Biomol Struct Dyn 2016; 35:1153-1167. [PMID: 27058822 DOI: 10.1080/07391102.2016.1175967] [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: 10/22/2022]
Abstract
Aristaless (Al) and clawless (Cll) homeodomains that are involved in leg development in Drosophila melanogaster are known to bind cooperatively to 5'-(T/C)TAATTAA(T/A)(T/A)G-3' DNA sequence, but the mechanism of their binding to DNA is unknown. Molecular dynamics (MD) studies have been carried out on binary, ternary, and reconstructed protein-DNA complexes involving Al, Cll, and DNA along with binding free energy analysis of these complexes. Analysis of MD trajectories of Cll-3A01, binary complex reveals that C-terminal end of helixIII of Cll, unwind in the absence of Al and remains so in reconstructed ternary complex, Cll-3A01-Al. In addition, this change in secondary structure of Cll does not allow it to form protein-protein interactions with Al in the ternary reconstructed complex. However, secondary structure of Cll and its interactions are maintained in other reconstructed ternary complex, Al-3A01-Cll where Cll binds to Al-3A01, binary complex to form ternary complex. These interactions as observed during MD simulations compare well with those observed in ternary crystal structure. Thus, this study highlights the role of helixIII of Cll and protein-protein interactions while proposing likely mechanism of recognition in ternary complex, Al-Cll-DNA.
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Affiliation(s)
- Sangita Kachhap
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
| | - Pragya Priyadarshini
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
| | - Balvinder Singh
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
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56
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy provides a unique toolbox of experimental probes for studying dynamic processes on a wide range of timescales, ranging from picoseconds to milliseconds and beyond. Along with NMR hardware developments, recent methodological advancements have enabled the characterization of allosteric proteins at unprecedented detail, revealing intriguing aspects of allosteric mechanisms and increasing the proportion of the conformational ensemble that can be observed by experiment. Here, we present an overview of NMR spectroscopic methods for characterizing equilibrium fluctuations in free and bound states of allosteric proteins that have been most influential in the field. By combining NMR experimental approaches with molecular simulations, atomistic-level descriptions of the mechanisms by which allosteric phenomena take place are now within reach.
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Affiliation(s)
- Sarina Grutsch
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Sven Brüschweiler
- Department of Computational & Structural Biology, Max F. Perutz Laboratories, Campus Vienna Biocenter 5, Vienna, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
- * E-mail:
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57
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Rezsohazy R, Saurin AJ, Maurel-Zaffran C, Graba Y. Cellular and molecular insights into Hox protein action. Development 2016; 142:1212-27. [PMID: 25804734 DOI: 10.1242/dev.109785] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hox genes encode homeodomain transcription factors that control morphogenesis and have established functions in development and evolution. Hox proteins have remained enigmatic with regard to the molecular mechanisms that endow them with specific and diverse functions, and to the cellular functions that they control. Here, we review recent examples of Hox-controlled cellular functions that highlight their versatile and highly context-dependent activity. This provides the setting to discuss how Hox proteins control morphogenesis and organogenesis. We then summarise the molecular modalities underlying Hox protein function, in particular in light of current models of transcription factor function. Finally, we discuss how functional divergence between Hox proteins might be achieved to give rise to the many facets of their action.
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Affiliation(s)
- René Rezsohazy
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve B-1348, Belgium
| | - Andrew J Saurin
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille 13288, Cedex 09, France
| | | | - Yacine Graba
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille 13288, Cedex 09, France
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58
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Linares AJ, Lin CH, Damianov A, Adams KL, Novitch BG, Black DL. The splicing regulator PTBP1 controls the activity of the transcription factor Pbx1 during neuronal differentiation. eLife 2015; 4:e09268. [PMID: 26705333 PMCID: PMC4755740 DOI: 10.7554/elife.09268] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 12/22/2015] [Indexed: 12/13/2022] Open
Abstract
The RNA-binding proteins PTBP1 and PTBP2 control programs of alternative splicing during neuronal development. PTBP2 was found to maintain embryonic splicing patterns of many synaptic and cytoskeletal proteins during differentiation of neuronal progenitor cells (NPCs) into early neurons. However, the role of the earlier PTBP1 program in embryonic stem cells (ESCs) and NPCs was not clear. We show that PTBP1 controls a program of neuronal gene expression that includes the transcription factor Pbx1. We identify exons specifically regulated by PTBP1 and not PTBP2 as mouse ESCs differentiate into NPCs. We find that PTBP1 represses Pbx1 exon 7 and the expression of the neuronal Pbx1a isoform in ESCs. Using CRISPR-Cas9 to delete regulatory elements for exon 7, we induce Pbx1a expression in ESCs, finding that this activates transcription of neuronal genes. Thus, PTBP1 controls the activity of Pbx1 to suppress its neuronal transcriptional program prior to induction of NPC development. DOI:http://dx.doi.org/10.7554/eLife.09268.001 The neurons that transmit information around the nervous system develop in several stages. Embryonic stem cells specialize to form neuronal progenitor cells, which then develop into neurons. These cell types have different characteristics, in part because they make different proteins or different versions of the same proteins. To make a protein, the DNA sequence of a gene is used to build a molecule of ribonucleic acid (RNA) that acts as a template for the protein. However, not all of this sequence codes for the protein. The non-coding regions must be removed from the RNA, and the remaining “exons” joined together to form the final “mRNA” template. Not all of the exons are necessarily included in the final mRNA molecule. By joining together different combinations of exons, several different versions of a protein can be produced from a single gene. This process is known as alternative splicing. One way that alternative splicing is controlled is through proteins that bind to RNA and determine which exons are included or excluded from the final mRNA molecule. PTBP1 is an RNA-binding protein that controls alternative splicing in embryonic stem cells and neuronal progenitor cells. Embryonic stem cells have the ability to develop into all the cells of the body. In contrast, neuronal progenitor cells are restricted in their development and only give rise to specialized cells of the nervous system. The role of PTBP1 in these properties was not clear. Linares et al. have now used a range of techniques to study the RNA molecules produced in these two cell types and how these RNAs change when PTBP1 is removed. This identified many RNAs whose splicing is regulated by PTBP1, including mRNAs of the gene that produces a protein called Pbx1, which is an important regulator of neuronal development. Further investigation revealed that PTBP1 prevents a particular exon being included in the mRNA template for Pbx1. This creates an embryonic stem cell form of Pbx1 that does not affect neuronal genes. Removal of PTBP1 allows splicing of the Pbx1 exon and produces a version of Pbx1 that is found in neuronal progenitor cells and which turns on neuronal genes. Thus, through its action on Pbx1, one role of PTBP1 is to enable stem cells to maintain their non-neuronal properties and prevent their premature development into neuronal progenitor cells. The gene for Pbx1 is only one of many genes controlled by PTBP1 at the level of splicing. One challenge for the future will be to understand how these genes work together in a common program that determines the properties of stem cells. Another question regards how the different Pbx1 proteins in stem cells and in neuronal progenitors can exert different effects in the cells where they are made. DOI:http://dx.doi.org/10.7554/eLife.09268.002
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Affiliation(s)
- Anthony J Linares
- Molecular Biology Institute Graduate Program, University of California, Los Angeles, Los Angeles, United States
| | - Chia-Ho Lin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Andrey Damianov
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Katrina L Adams
- Molecular Biology Institute Graduate Program, University of California, Los Angeles, Los Angeles, United States.,Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Bennett G Novitch
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States
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59
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Foos N, Maurel-Zaffran C, Maté MJ, Vincentelli R, Hainaut M, Berenger H, Pradel J, Saurin AJ, Ortiz-Lombardía M, Graba Y. A flexible extension of the Drosophila ultrabithorax homeodomain defines a novel Hox/PBC interaction mode. Structure 2015; 23:270-9. [PMID: 25651060 DOI: 10.1016/j.str.2014.12.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/05/2014] [Accepted: 12/06/2014] [Indexed: 11/17/2022]
Abstract
The patterning function of Hox proteins relies on assembling protein complexes with PBC proteins, which often involves a protein motif found in most Hox proteins, the so-called Hexapeptide (HX). Hox/PBC complexes likely gained functional diversity by acquiring additional modes of interaction. Here, we structurally characterize the first HX alternative interaction mode based on the paralogue-specific UbdA motif and further functionally validate structure-based predictions. The UbdA motif folds as a flexible extension of the homeodomain recognition helix and defines Hox/PBC contacts that occur, compared with those mediated by the HX motif, on the opposing side of the DNA double helix. This provides a new molecular facet to Hox/PBC complex assembly and suggests possible mechanisms for the diversification of Hox protein function.
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Affiliation(s)
- Nicolas Foos
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Corinne Maurel-Zaffran
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France
| | - María Jesús Maté
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Renaud Vincentelli
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Matthieu Hainaut
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France
| | - Hélène Berenger
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France
| | - Jacques Pradel
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France
| | - Andrew J Saurin
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France
| | - Miguel Ortiz-Lombardía
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France.
| | - Yacine Graba
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7288, IBDM, Parc Scientifique de Luminy, Case 907, 13288 Marseille Cedex 09, France.
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60
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Turner M, Zhang Y, Carlson HL, Stadler HS, Ames JB. Chemical shift assignments of mouse HOXD13 DNA binding domain bound to duplex DNA. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:267-270. [PMID: 25491407 PMCID: PMC4465062 DOI: 10.1007/s12104-014-9589-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/03/2014] [Indexed: 06/04/2023]
Abstract
The homeobox gene (Hoxd13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of proteins that control embryonic morphogenesis. We report NMR chemical shift assignments of mouse Hoxd13 DNA binding domain bound to an 11-residue DNA duplex (BMRB No. 25133).
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Affiliation(s)
- Matthew Turner
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Yonghong Zhang
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Hanqian L Carlson
- Shriners Hospital for Children Research Department, 3101 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - H Scott Stadler
- Shriners Hospital for Children Research Department, 3101 SW Sam Jackson Park Road, Portland, OR, 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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61
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Yoshioka K, Oda A, Notsu C, Ohtsuka T, Kawai Y, Suzuki S, Nakamura T, Mabuchi Y, Matsuzaki Y, Goitsuka R. Loss of the Homeodomain Transcription Factor Prep1 Perturbs Adult Hematopoiesis in the Bone Marrow. PLoS One 2015; 10:e0136107. [PMID: 26285139 PMCID: PMC4540428 DOI: 10.1371/journal.pone.0136107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/29/2015] [Indexed: 11/18/2022] Open
Abstract
Prep1, a TALE-family homeodomain transcription factor, has been demonstrated to play a critical role in embryonic hematopoiesis, as its insufficiency caused late embryonic lethality associated with defective hematopoiesis and angiogenesis. In the present study, we generated hematopoietic- and endothelial cell-specific Prep1-deficient mice and demonstrated that expression of Prep1 in the hematopoietic cell compartment is not essential for either embryonic or adult hematopoiesis, although its absence causes significant hematopoietic abnormalities in the adult bone marrow. Loss of Prep1 promotes cell cycling of hematopoietic stem/progenitor cells (HSPC), leading to the expansion of the HSPC pool. Prep1 deficiency also results in the accumulation of lineage-committed progenitors, increased monocyte/macrophage differentiation and arrested erythroid maturation. Maturation of T cells and B cells is also perturbed in Prep-deficient mice. These findings provide novel insight into the pleiotropic roles of Prep1 in adult hematopoiesis that were unrecognized in previous studies using germline Prep1 hypomorphic mice.
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Affiliation(s)
- Kentaro Yoshioka
- Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Akihisa Oda
- Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Chihiro Notsu
- Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Takafumi Ohtsuka
- Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Yasuhiro Kawai
- Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Sadafumi Suzuki
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Takuro Nakamura
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Yo Mabuchi
- Department of Biochemistry and Biophysics, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Yumi Matsuzaki
- Department of Cancer Biology, Faculty of Medicine, Shimane University, Izumo-shi, Shimane, Japan
| | - Ryo Goitsuka
- Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
- * E-mail:
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62
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Merabet S, Galliot B. The TALE face of Hox proteins in animal evolution. Front Genet 2015; 6:267. [PMID: 26347770 PMCID: PMC4539518 DOI: 10.3389/fgene.2015.00267] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 07/31/2015] [Indexed: 01/22/2023] Open
Abstract
Hox genes are major regulators of embryonic development. One of their most conserved functions is to coordinate the formation of specific body structures along the anterior-posterior (AP) axis in Bilateria. This architectural role was at the basis of several morphological innovations across bilaterian evolution. In this review, we traced the origin of the Hox patterning system by considering the partnership with PBC and Meis proteins. PBC and Meis belong to the TALE-class of homeodomain-containing transcription factors and act as generic cofactors of Hox proteins for AP axis patterning in Bilateria. Recent data indicate that Hox proteins acquired the ability to interact with their TALE partners in the last common ancestor of Bilateria and Cnidaria. These interactions relied initially on a short peptide motif called hexapeptide (HX), which is present in Hox and non-Hox protein families. Remarkably, Hox proteins can also recruit the TALE cofactors by using specific PBC Interaction Motifs (SPIMs). We describe how a functional Hox/TALE patterning system emerged in eumetazoans through the acquisition of SPIMs. We anticipate that interaction flexibility could be found in other patterning systems, being at the heart of the astonishing morphological diversity observed in the animal kingdom.
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Affiliation(s)
- Samir Merabet
- Centre National de Recherche Scientifique, Institut de Génomique Fonctionnelle de Lyon Lyon, France ; Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon Lyon, France
| | - Brigitte Galliot
- Department of Genetics and Evolution, Faculty of Science, Institute of Genetics and Genomics in Geneva, University of Geneva Geneva, Switzerland
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63
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A new hereditary congenital facial palsy case supports arg5 in HOX-DNA binding domain as possible hot spot for mutations. Eur J Med Genet 2015; 58:358-63. [PMID: 26007620 DOI: 10.1016/j.ejmg.2015.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/18/2015] [Indexed: 11/22/2022]
Abstract
Moebius syndrome (MBS) is a rare congenital disorder characterized by rhombencephalic mal development, mainly presenting with facial palsy with limited gaze abduction. Most cases are sporadic, possibly caused by a combination of environmental and genetic factors; however, no proven specific associations have been yet established. Hereditary congenital facial palsy (HCFP) is an autosomal dominant congenital dysinnervation syndrome, recognizable by the isolated dysfunction of the seventh cranial nerve. Mutant mice for Hoxb1 were reported to present with facial weakness, resembling MBS. Recently a homozygous mutation altering arg5 residue of HOXB1 homeodomain into cys5 was identified in two families with HCFP. We screened 95 sporadic patients diagnosed as MBS or HCFP for mutations in HOXB1. A novel homozygous alteration was identified in one HCFP case, affecting the same residue, resulting to his5. In silico protein analysis predicted stronger HOXB1-DNA binding properties for his5 than cys5 that resulted to milder phenotype. It should be noted that, inclusive of the previous report, only two mutations revealed in HOXB1 associated with HCFP involved the same amino acid arg5 in HOXB1 residing in HOXB1-DNA-PBX1 ternary complex.
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Mathiasen L, Bruckmann C, Pasqualato S, Blasi F. Purification and characterization of a DNA-binding recombinant PREP1:PBX1 complex. PLoS One 2015; 10:e0125789. [PMID: 25856340 PMCID: PMC4391845 DOI: 10.1371/journal.pone.0125789] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/10/2015] [Indexed: 11/30/2022] Open
Abstract
Human PREP1 and PBX1 are homeodomain transcriptional factors, whose biochemical and structural characterization has not yet been fully described. Expression of full-length recombinant PREP1 (47.6 kDa) and PBX1 (46.6 kDa) in E. coli is difficult because of poor yield, high instability and insufficient purity, in particular for structural studies. We cloned the cDNA of both proteins into a dicistronic vector containing an N-terminal glutathione S-transferase (GST) tag and co-expressed and co-purified a stable PBX1:PREP1 complex. For structural studies, we produced two C-terminally truncated complexes that retain their ability to bind DNA and are more stable than the full-length proteins through various purification steps. Here we report the production of large amounts of soluble and pure recombinant human PBX1:PREP1 complex in an active form capable of binding DNA.
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Affiliation(s)
- Lisa Mathiasen
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), via Adamello 16, 20139, Milan, Italy
| | - Chiara Bruckmann
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), via Adamello 16, 20139, Milan, Italy
| | - Sebastiano Pasqualato
- Crystallography Unit, Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan, 20139, Italy
| | - Francesco Blasi
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), via Adamello 16, 20139, Milan, Italy
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65
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Farber PJ, Mittermaier A. Relaxation dispersion NMR spectroscopy for the study of protein allostery. Biophys Rev 2015; 7:191-200. [PMID: 28510170 DOI: 10.1007/s12551-015-0166-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/03/2015] [Indexed: 02/04/2023] Open
Abstract
Allosteric transmission of information between distant sites in biological macromolecules often involves collective transitions between active and inactive conformations. Nuclear magnetic resonance (NMR) spectroscopy can yield detailed information on these dynamics. In particular, relaxation dispersion techniques provide structural, dynamic, and mechanistic information on conformational transitions occurring on the millisecond to microsecond timescales. In this review, we provide an overview of the theory and analysis of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments and briefly describe their application to the study of allosteric dynamics in the homeodomain from the PBX transcription factor (PBX-HD). CPMG NMR data show that local folding (helix/coil) transitions in one part of PBX-HD help to communicate information between two distant binding sites. Furthermore, the combination of CPMG and other spin relaxation data show that this region can also undergo local misfolding, reminiscent of conformational ensemble models of allostery.
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Affiliation(s)
- Patrick J Farber
- Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Anthony Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W. room 322, Montreal, Quebec, Canada, H3A 0B8.
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Wegert J, Ishaque N, Vardapour R, Geörg C, Gu Z, Bieg M, Ziegler B, Bausenwein S, Nourkami N, Ludwig N, Keller A, Grimm C, Kneitz S, Williams RD, Chagtai T, Pritchard-Jones K, van Sluis P, Volckmann R, Koster J, Versteeg R, Acha T, O'Sullivan MJ, Bode PK, Niggli F, Tytgat GA, van Tinteren H, van den Heuvel-Eibrink MM, Meese E, Vokuhl C, Leuschner I, Graf N, Eils R, Pfister SM, Kool M, Gessler M. Mutations in the SIX1/2 pathway and the DROSHA/DGCR8 miRNA microprocessor complex underlie high-risk blastemal type Wilms tumors. Cancer Cell 2015; 27:298-311. [PMID: 25670083 DOI: 10.1016/j.ccell.2015.01.002] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/24/2014] [Accepted: 01/09/2015] [Indexed: 10/24/2022]
Abstract
Blastemal histology in chemotherapy-treated pediatric Wilms tumors (nephroblastoma) is associated with adverse prognosis. To uncover the underlying tumor biology and find therapeutic leads for this subgroup, we analyzed 58 blastemal type Wilms tumors by exome and transcriptome sequencing and validated our findings in a large replication cohort. Recurrent mutations included a hotspot mutation (Q177R) in the homeo-domain of SIX1 and SIX2 in tumors with high proliferative potential (18.1% of blastemal cases); mutations in the DROSHA/DGCR8 microprocessor genes (18.2% of blastemal cases); mutations in DICER1 and DIS3L2; and alterations in IGF2, MYCN, and TP53, the latter being strongly associated with dismal outcome. DROSHA and DGCR8 mutations strongly altered miRNA expression patterns in tumors, which was functionally validated in cell lines expressing mutant DROSHA.
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Affiliation(s)
- Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Wuerzburg University, 97074 Wuerzburg, Germany
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Heidelberg Center for Personalised Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Romina Vardapour
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Wuerzburg University, 97074 Wuerzburg, Germany
| | - Christina Geörg
- Heidelberg Center for Personalised Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Heidelberg Center for Personalised Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Matthias Bieg
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Heidelberg Center for Personalised Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Barbara Ziegler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Wuerzburg University, 97074 Wuerzburg, Germany
| | - Sabrina Bausenwein
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Wuerzburg University, 97074 Wuerzburg, Germany
| | - Nasenien Nourkami
- Department of Pediatric Oncology and Hematology, Saarland University Hospital, 66421 Homburg, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Clemens Grimm
- Theodor-Boveri-Institute/Biocenter, Biochemistry, Wuerzburg University, 97074 Wuerzburg, Germany
| | - Susanne Kneitz
- Theodor-Boveri-Institute/Biocenter, Physiological Chemistry, Wuerzburg University, 97074 Wuerzburg, Germany
| | | | - Tas Chagtai
- UCL Institute of Child Health, London WC1N 1EH, UK
| | | | - Peter van Sluis
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, 1007 MB Amsterdam, the Netherlands
| | - Richard Volckmann
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, 1007 MB Amsterdam, the Netherlands
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, 1007 MB Amsterdam, the Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, 1007 MB Amsterdam, the Netherlands
| | - Tomas Acha
- Unidad de Oncología Pediátrica, Hospital Materno-Infantil de Málaga, 29011 Malaga, Spain
| | - Maureen J O'Sullivan
- National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, and Trinity College, Dublin 12, Ireland
| | - Peter K Bode
- Department of Pediatric Hematology and Oncology, Children's University Hospital, 8032 Zurich, Switzerland
| | - Felix Niggli
- Department of Pediatric Hematology and Oncology, Children's University Hospital, 8032 Zurich, Switzerland
| | - Godelieve A Tytgat
- Department of Pediatric Oncology, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, 1007 MB Amsterdam, the Netherlands
| | - Harm van Tinteren
- Department of Pediatric Oncology, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, 1007 MB Amsterdam, the Netherlands
| | | | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Christian Vokuhl
- Kiel Paediatric Cancer Registry, Christian Albrechts University, 24105 Kiel, Germany
| | - Ivo Leuschner
- Kiel Paediatric Cancer Registry, Christian Albrechts University, 24105 Kiel, Germany
| | - Norbert Graf
- Department of Pediatric Oncology and Hematology, Saarland University Hospital, 66421 Homburg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Heidelberg Center for Personalised Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, 69121 Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Wuerzburg University, 97074 Wuerzburg, Germany.
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Li R, Wu F, Ruonala R, Sapkota D, Hu Z, Mu X. Isl1 and Pou4f2 form a complex to regulate target genes in developing retinal ganglion cells. PLoS One 2014; 9:e92105. [PMID: 24643061 PMCID: PMC3958441 DOI: 10.1371/journal.pone.0092105] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/17/2014] [Indexed: 02/01/2023] Open
Abstract
Precise regulation of gene expression during biological processes, including development, is often achieved by combinatorial action of multiple transcription factors. The mechanisms by which these factors collaborate are largely not known. We have shown previously that Isl1, a Lim-Homeodomain transcription factor, and Pou4f2, a class IV POU domain transcription factor, co-regulate a set of genes required for retinal ganglion cell (RGC) differentiation. Here we further explore how these two factors interact to precisely regulate gene expression during RGC development. By GST pulldown assays, co-immunoprecipitation, and electrophoretic mobility shift assays, we show that Isl1 and Pou4f2 form a complex in vitro and in vivo, and identify the domains within these two proteins that are responsible for this interaction. By luciferase assay, in situ hybridization, and RNA-seq, we further demonstrate that the two factors contribute quantitatively to gene expression in the developing RGCs. Although each factor alone can activate gene expression, both factors are required to achieve optimal expression levels. Finally, we discover that Isl1 and Pou4f2 can interact with other POU and Lim-Homeodomain factors respectively, indicating the interactions between these two classes of transcription factors are prevalent in development and other biological processes.
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Affiliation(s)
- Renzhong Li
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
| | - Raili Ruonala
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
| | - Darshan Sapkota
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Department of Biochemistry, University of Buffalo, Buffalo, New York, United States of America
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
| | - Zihua Hu
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Department of Biostatistics, University of Buffalo, Buffalo, New York, United States of America
- Department of Medicine, University of Buffalo, Buffalo, New York, United States of America
- Center of Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Department of Biochemistry, University of Buffalo, Buffalo, New York, United States of America
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- CCSG Cancer Genetics Program, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- * E-mail:
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69
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Longobardi E, Penkov D, Mateos D, De Florian G, Torres M, Blasi F. Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates. Dev Dyn 2014; 243:59-75. [PMID: 23873833 PMCID: PMC4232920 DOI: 10.1002/dvdy.24016] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 06/19/2013] [Accepted: 07/05/2013] [Indexed: 12/22/2022] Open
Abstract
TALE (three amino acids loop extension) homeodomain transcription factors are required in various steps of embryo development, in many adult physiological functions, and are involved in important pathologies. This review focuses on the PREP, MEIS, and PBX sub-families of TALE factors and aims at giving information on their biochemical properties, i.e., structure, interactors, and interaction surfaces. Members of the three sets of protein form dimers in which the common partner is PBX but they can also directly interact with other proteins forming higher-order complexes, in particular HOX. Finally, recent advances in determining the genome-wide DNA-binding sites of PREP1, MEIS1, and PBX1, and their partial correspondence with the binding sites of some HOX proteins, are reviewed. These studies have generated a few general rules that can be applied to all members of the three gene families. PREP and MEIS recognize slightly different consensus sequences: PREP prefers to bind to promoters and to have PBX as a DNA-binding partner; MEIS prefers HOX as partner, and both PREP and MEIS drive PBX to their own binding sites. This outlines the clear individuality of the PREP and MEIS proteins, the former mostly devoted to basic cellular functions, the latter more to developmental functions.
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Affiliation(s)
- E Longobardi
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Milano, Italy
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70
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Genetic organization of two types of flounder warm-temperature acclimation-associated 65-kDa protein and their gene expression profiles. Biosci Biotechnol Biochem 2013; 77:2065-72. [PMID: 24096660 DOI: 10.1271/bbb.130263] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We isolated and characterized two cDNA clone encoding warm-temperature acclimation-associated 65-kDa proteins (PoWap65-1 and PoWap65-2) from the olive flounder, Paralichthys olivaceus. The deduced amino acid sequences of PoWap65s showed overall identities of 33-73% with other fish Wap65 and mammalian hemopexin-like proteins. The 5'-flanking regions of both PoWap65-encoding genes contained various putative transcriptional elements. While PoWap65-1 and PoWap65-2 were structurally similar, they exhibited highly differential patterns of expression. PoWap65-1 was expressed only in the liver, whereas PoWap65-2 transcripts were detected in a wide range of tissues. The accumulation of PoWap65s mRNA was expressed differentially during development. Expression of them in warm temperatures also differed in flounder embryonic cells. PoWap65-1 was upregulated by temperature stimulation whereas PoWap65-2 was not detected. PoWap65s were highly regulated by Edwardsiella tarda infection and hypoxia. Pathogen challenge induced PoWap65-2 expression in the liver whereas PoWap65-1 was downregulated. Hypoxia induced the expression of both PoWap65s in the liver of juvenile fish.
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71
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Structure of novel enzyme in mannan biodegradation process 4-O-β-D-mannosyl-D-glucose phosphorylase MGP. J Mol Biol 2013; 425:4468-78. [PMID: 23954514 DOI: 10.1016/j.jmb.2013.08.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/01/2013] [Accepted: 08/05/2013] [Indexed: 11/20/2022]
Abstract
The crystal structure of a novel component of the mannan biodegradation system, 4-O-β-D-mannosyl-D-glucose phosphorylase (MGP), was determined to a 1.68-Å resolution. The structure of the enzyme revealed a unique homohexameric structure, which was formed by using two helices attached to the N-terminus and C-terminus as a tab for sticking between subunits. The structures of MGP complexes with genuine substrates, 4-O-β-D-mannosyl-D-glucose and phosphate, and the product D-mannose-1-phosphate were also determined. The complex structures revealed that the invariant residue Asp131, which is supposed to be the general acid/base, did not exist close to the glycosidic Glc-O4 atom, which should be protonated in the catalytic reaction. Also, no solvent molecule that might mediate a proton transfer from Asp131 was observed in the substrate complex structure, suggesting that the catalytic mechanism of MGP is different from those of known disaccharide phosphorylases.
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72
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Babin V, Wang D, Rose RB, Sagui C. Binding polymorphism in the DNA bound state of the Pdx1 homeodomain. PLoS Comput Biol 2013; 9:e1003160. [PMID: 23950697 PMCID: PMC3738460 DOI: 10.1371/journal.pcbi.1003160] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/13/2013] [Indexed: 11/18/2022] Open
Abstract
The subtle effects of DNA-protein recognition are illustrated in the homeodomain fold. This is one of several small DNA binding motifs that, in spite of limited DNA binding specificity, adopts crucial, specific roles when incorporated in a transcription factor. The homeodomain is composed of a 3-helix domain and a mobile N-terminal arm. Helix 3 (the recognition helix) interacts with the DNA bases through the major groove, while the N-terminal arm becomes ordered upon binding a specific sequence through the minor groove. Although many structural studies have characterized the DNA binding properties of homeodomains, the factors behind the binding specificity are still difficult to elucidate. A crystal structure of the Pdx1 homeodomain bound to DNA (PDB 2H1K) obtained previously in our lab shows two complexes with differences in the conformation of the N-terminal arm, major groove contacts, and backbone contacts, raising new questions about the DNA recognition process by homeodomains. Here, we carry out fully atomistic Molecular Dynamics simulations both in crystal and aqueous environments in order to elucidate the nature of the difference in binding contacts. The crystal simulations reproduce the X-ray experimental structures well. In the absence of crystal packing constraints, the differences between the two complexes increase during the solution simulations. Thus, the conformational differences are not an artifact of crystal packing. In solution, the homeodomain with a disordered N-terminal arm repositions to a partially specific orientation. Both the crystal and aqueous simulations support the existence of different stable binding conformers identified in the original crystallographic data with different degrees of specificity. We propose that protein-protein and protein-DNA interactions favor a subset of the possible conformations. This flexibility in DNA binding may facilitate multiple functions for the same transcription factor.
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Affiliation(s)
- Volodymyr Babin
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California, United States of America
| | - Dongli Wang
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert B. Rose
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (RBR); (CS)
| | - Celeste Sagui
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (RBR); (CS)
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73
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Ladam F, Sagerström CG. Hox regulation of transcription: more complex(es). Dev Dyn 2013; 243:4-15. [PMID: 23765878 DOI: 10.1002/dvdy.23997] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 05/31/2013] [Accepted: 06/03/2013] [Indexed: 11/10/2022] Open
Abstract
Hox genes encode transcription factors with important roles during embryogenesis and tissue differentiation. Genetic analyses initially demonstrated that interfering with Hox genes has profound effects on the specification of cell identity, suggesting that Hox proteins regulate very specific sets of target genes. However, subsequent biochemical analyses revealed that Hox proteins bind DNA with relatively low affinity and specificity. Furthermore, it became clear that a given Hox protein could activate or repress transcription, depending on the context. A resolution to these paradoxes presented itself with the discovery that Hox proteins do not function in isolation, but interact with other factors in complexes. The first such "cofactors" were members of the Extradenticle/Pbx and Homothorax/Meis/Prep families. However, the list of Hox-interacting proteins has continued to grow, suggesting that Hox complexes contain many more components than initially thought. Additionally, the activities of the various components and the exact mechanisms whereby they modulate the activity of the complex remain puzzling. Here, we review the various proteins known to participate in Hox complexes and discuss their likely functions. We also consider that Hox complexes of different compositions may have different activities and discuss mechanisms whereby Hox complexes may be switched between active and inactive states.
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Affiliation(s)
- Franck Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
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Penkov D, Mateos San Martín D, Fernandez-Díaz LC, Rosselló CA, Torroja C, Sánchez-Cabo F, Warnatz HJ, Sultan M, Yaspo ML, Gabrieli A, Tkachuk V, Brendolan A, Blasi F, Torres M. Analysis of the DNA-binding profile and function of TALE homeoproteins reveals their specialization and specific interactions with Hox genes/proteins. Cell Rep 2013; 3:1321-33. [PMID: 23602564 DOI: 10.1016/j.celrep.2013.03.029] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 02/19/2013] [Accepted: 03/20/2013] [Indexed: 11/28/2022] Open
Abstract
The interactions of Meis, Prep, and Pbx1 TALE homeoproteins with Hox proteins are essential for development and disease. Although Meis and Prep behave similarly in vitro, their in vivo activities remain largely unexplored. We show that Prep and Meis interact with largely independent sets of genomic sites and select different DNA-binding sequences, Prep associating mostly with promoters and housekeeping genes and Meis with promoter-remote regions and developmental genes. Hox target sequences associate strongly with Meis but not with Prep binding sites, while Pbx1 cooperates with both Prep and Meis. Accordingly, Meis1 shows strong genetic interaction with Pbx1 but not with Prep1. Meis1 and Prep1 nonetheless coregulate a subset of genes, predominantly through opposing effects. Notably, the TALE homeoprotein binding profile subdivides Hox clusters into two domains differentially regulated by Meis1 and Prep1. During evolution, Meis and Prep thus specialized their interactions but maintained significant regulatory coordination.
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Affiliation(s)
- Dmitry Penkov
- Foundation FIRC Institute of Molecular Oncology at the IFOM-IEO Campus, via Adamello 16, 20139 Milan, Italy
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Sambrani N, Hudry B, Maurel-Zaffran C, Zouaz A, Mishra R, Merabet S, Graba Y. Distinct molecular strategies for Hox-mediated limb suppression in Drosophila: from cooperativity to dispensability/antagonism in TALE partnership. PLoS Genet 2013; 9:e1003307. [PMID: 23505377 PMCID: PMC3591290 DOI: 10.1371/journal.pgen.1003307] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/18/2012] [Indexed: 11/19/2022] Open
Abstract
The emergence following gene duplication of a large repertoire of Hox paralogue proteins underlies the importance taken by Hox proteins in controlling animal body plans in development and evolution. Sequence divergence of paralogous proteins accounts for functional specialization, promoting axial morphological diversification in bilaterian animals. Yet functionally specialized paralogous Hox proteins also continue performing ancient common functions. In this study, we investigate how highly divergent Hox proteins perform an identical function. This was achieved by comparing in Drosophila the mode of limb suppression by the central (Ultrabithorax and AbdominalA) and posterior class (AbdominalB) Hox proteins. Results highlight that Hox-mediated limb suppression relies on distinct modes of DNA binding and a distinct use of TALE cofactors. Control of common functions by divergent Hox proteins, at least in the case studied, relies on evolving novel molecular properties. Thus, changes in protein sequences not only provide the driving force for functional specialization of Hox paralogue proteins, but also provide means to perform common ancient functions in distinct ways.
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Affiliation(s)
- Nagraj Sambrani
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
| | - Bruno Hudry
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
| | - Corinne Maurel-Zaffran
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
| | - Amel Zouaz
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
| | - Rakesh Mishra
- Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Samir Merabet
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
| | - Yacine Graba
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
- * E-mail:
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76
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Zhang P, Cao G, Sheng J, Xue R, Gong C. BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis. PLoS One 2012; 7:e47861. [PMID: 23152760 PMCID: PMC3494694 DOI: 10.1371/journal.pone.0047861] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 09/20/2012] [Indexed: 11/19/2022] Open
Abstract
TG-interacting factor (TGIF) in Drosophila consists of two tandemly-repeated genes, achintya (Dmachi) and vismay (Dmvis), which act as transcriptional activators in Drosophila spermatogenesis. In contrast, TGIF in humans is a transcriptional repressor that binds directly to DNA or interacts with corepressors to repress the transcription of target genes. In this study, we investigated the characteristics and functions of BmTGIF, a Bombyx mori homolog of DmTGIF. Like DmTGIF, BmTGIF is predominantly expressed in the testes and ovaries. Four alternatively spliced isoforms could be isolated from testes, and two isoforms from ovaries. Quantitative polymerase chain reaction indicated BmTGIF was abundantly expressed in the testis of 3rd instar larvae, when the testis is almost full of primary spermatocytes. The results of luciferase assays indicated that BmTGIF contains two adjacent acidic domains that activate the transcription of reporter genes. Immunofluorescence assay in BmN cells showed that the BmTGIF protein was located mainly in the nucleus, and paraffin sections of testis showed BmTGIF was grossly expressed in primary spermatocytes and mature sperms. Consistent with the role of DmVis in Drosophila development, BmTGIF significantly affected spermatid differentiation, as indicated by hematoxylin-eosin staining of paraffin sections of testis from BmTGIF-small interfering RNA (siRNA)-injected male silkworms. Co-immunoprecipitation experiments suggested that BmTGIF interacted with BmAly, and that they may recruit other factors to form a complex to regulate the genes required for meiotic divisions and spermatid differentiation. The results of this analysis of BmTGIF will improve our understanding of the mechanism of spermatid differentiation in B. mori, with potential applications for pest control.
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Affiliation(s)
- Pengjie Zhang
- School of Biology and Basic Medical Science, Soochow University, Suzhou, People’s Republic of China
| | - Guangli Cao
- School of Biology and Basic Medical Science, Soochow University, Suzhou, People’s Republic of China
- National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, People’s Republic of China
| | - Jie Sheng
- School of Biology and Basic Medical Science, Soochow University, Suzhou, People’s Republic of China
| | - Renyu Xue
- School of Biology and Basic Medical Science, Soochow University, Suzhou, People’s Republic of China
- National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, People’s Republic of China
| | - Chengliang Gong
- School of Biology and Basic Medical Science, Soochow University, Suzhou, People’s Republic of China
- National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, People’s Republic of China
- * E-mail:
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77
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Morgan R, Boxall A, Harrington KJ, Simpson GR, Gillett C, Michael A, Pandha HS. Targeting the HOX/PBX dimer in breast cancer. Breast Cancer Res Treat 2012; 136:389-98. [PMID: 23053648 DOI: 10.1007/s10549-012-2259-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 09/15/2012] [Indexed: 12/21/2022]
Abstract
The HOX genes are a family of closely related transcription factors that help to define the identity of cells and tissues during embryonic development and which are also frequently deregulated in a number of malignancies, including breast cancer. While relatively little is known about the roles that individual HOX genes play in cancer, it is however clear that these roles can be both contradictory, with some members acting as oncogenes and some as tumor suppressors, and also redundant, with several genes essentially having the same function. Here, we have attempted to address this complexity using the HXR9 peptide to target the interaction between HOX proteins and PBX, a second transcription factor that serves as a common co-factor for many HOX proteins. We show that HXR9 causes apoptosis in a number of breast cancer-derived cell lines and that sensitivity to HXR9 is directly related to the averaged expression of HOX genes HOXB1 through to HOXB9, providing a potential biomarker to predict the sensitivity of breast tumors to HXR9 or its derivatives. Measuring the expression of HOX genes HOXB1-HOXB9 in primary tumors revealed that a subset of tumors show highly elevated expression indicating that these might be potentially very sensitive to killing by HXR9. Furthermore, we show that while HXR9 blocks the oncogenic activity of HOX genes, it does not affect the known tumor-suppressor properties of a subset of HOX genes in breast cancer.
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Affiliation(s)
- Richard Morgan
- Oncology, Institute of Bioscience and Medicine, Faculty of Health and Medical Sciences, Leggett Building, University of Surrey, Surrey, GU2 7WG, UK.
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78
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Zou C, Levine EM. Vsx2 controls eye organogenesis and retinal progenitor identity via homeodomain and non-homeodomain residues required for high affinity DNA binding. PLoS Genet 2012; 8:e1002924. [PMID: 23028343 PMCID: PMC3447932 DOI: 10.1371/journal.pgen.1002924] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/05/2012] [Indexed: 12/26/2022] Open
Abstract
The homeodomain and adjacent CVC domain in the visual system homeobox (VSX) proteins are conserved from nematodes to humans. Humans with missense mutations in these regions of VSX2 have microphthalmia, suggesting both regions are critical for function. To assess this, we generated the corresponding mutations in mouse Vsx2. The homeodomain mutant protein lacked DNA binding activity and the knock-in mutant phenocopied the null mutant, ocular retardation J. The CVC mutant protein exhibited weakened DNA binding; and, although the corresponding knock-in allele was recessive, it unexpectedly caused the strongest phenotype, as indicated by severe microphthalmia and hyperpigmentation of the neural retina. This occurred through a cryptic transcriptional feedback loop involving the transcription factors Mitf and Otx1 and the Cdk inhibitor p27Kip1. Our data suggest that the phenotypic severity of the CVC mutant depends on the weakened DNA binding activity elicited by the CVC mutation and a previously unknown protein interaction between Vsx2 and its regulatory target Mitf. Our data also suggest that an essential function of the CVC domain is to assist the homeodomain in high-affinity DNA binding, which is required for eye organogenesis and unhindered execution of the retinal progenitor program in mammals. Finally, the genetic and phenotypic behaviors of the CVC mutation suggest it has the characteristics of a recessive neomorph, a rare type of genetic allele. Problems with the early development of the mammalian retina can cause congenital eye defects such as microphthalmia, in which the eye is dramatically smaller and functionally compromised. Severe microphthalmia is associated with mutations in the retinal-expressed visual system homeobox 2 (Vsx2) gene, but how Vsx2 controls retinal development, and ultimately eye formation, has remained unclear. We assessed the impact of two missense mutations, discovered in humans, on Vsx2 function and eye development in mice. One mutation altered a highly conserved residue of the homeodomain, and the other altered a highly conserved residue in the CVC domain, a region of unresolved function. Both mutations impacted the DNA binding properties of the protein, although to differing extents. Likewise, both mutations caused microphthalmia and disruptions in retinal development, also to differing extents and by distinct mechanisms. Our data suggest that Vsx2 acts as a gatekeeper of the retinal gene expression program by preventing the activation of interfering or competing gene expression programs. We propose that the evolutionary stable association between the VSX-class homeodomain and CVC domain set the stage for Vsx2 or its archetype to assume a gatekeeper function for retinal development and ultimately eye organogenesis.
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Affiliation(s)
- Changjiang Zou
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
| | - Edward M. Levine
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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79
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Webb B, Shaaban S, Gaspar H, Cunha L, Schubert C, Hao K, Robson C, Chan WM, Andrews C, MacKinnon S, Oystreck D, Hunter D, Iacovelli A, Ye X, Camminady A, Engle E, Jabs E. HOXB1 founder mutation in humans recapitulates the phenotype of Hoxb1-/- mice. Am J Hum Genet 2012; 91:171-9. [PMID: 22770981 DOI: 10.1016/j.ajhg.2012.05.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 04/30/2012] [Accepted: 05/11/2012] [Indexed: 10/28/2022] Open
Abstract
Members of the highly conserved homeobox (HOX) gene family encode transcription factors that confer cellular and tissue identities along the antero-posterior axis of mice and humans. We have identified a founder homozygous missense mutation in HOXB1 in two families from a conservative German American population. The resulting phenotype includes bilateral facial palsy, hearing loss, and strabismus and correlates extensively with the previously reported Hoxb1(-/-) mouse phenotype. The missense variant is predicted to result in the substitution of a cysteine for an arginine at amino acid residue 207 (Arg207Cys), which corresponds to the highly conserved Arg5 of the homeodomain. Arg5 interacts with thymine in the minor groove of DNA through hydrogen bonding and electrostatic attraction. Molecular modeling and an in vitro DNA-protein binding assay predict that the mutation would disrupt these interactions, destabilize the HOXB1:PBX1:DNA complex, and alter HOXB1 transcriptional activity.
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80
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A novel non-synonymous mutation in the homeodomain of HOXD13 causes synpolydactyly in a Chinese family. Clin Chim Acta 2012; 413:1049-52. [DOI: 10.1016/j.cca.2012.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 02/16/2012] [Accepted: 02/16/2012] [Indexed: 11/21/2022]
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81
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Hudry B, Remacle S, Delfini MC, Rezsohazy R, Graba Y, Merabet S. Hox proteins display a common and ancestral ability to diversify their interaction mode with the PBC class cofactors. PLoS Biol 2012; 10:e1001351. [PMID: 22745600 PMCID: PMC3383740 DOI: 10.1371/journal.pbio.1001351] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 05/10/2012] [Indexed: 02/02/2023] Open
Abstract
Hox protein function during development and evolution relies on conserved multiple interaction modes with cofactors of the PBC and Meis families. Hox transcription factors control a number of developmental processes with the help of the PBC class proteins. In vitro analyses have established that the formation of Hox/PBC complexes relies on a short conserved Hox protein motif called the hexapeptide (HX). This paradigm is at the basis of the vast majority of experimental approaches dedicated to the study of Hox protein function. Here we questioned the unique and general use of the HX for PBC recruitment by using the Bimolecular Fluorescence Complementation (BiFC) assay. This method allows analyzing Hox-PBC interactions in vivo and at a genome-wide scale. We found that the HX is dispensable for PBC recruitment in the majority of investigated Drosophila and mouse Hox proteins. We showed that HX-independent interaction modes are uncovered by the presence of Meis class cofactors, a property which was also observed with Hox proteins of the cnidarian sea anemone Nematostella vectensis. Finally, we revealed that paralog-specific motifs convey major PBC-recruiting functions in Drosophila Hox proteins. Altogether, our results highlight that flexibility in Hox-PBC interactions is an ancestral and evolutionary conserved character, which has strong implications for the understanding of Hox protein functions during normal development and pathologic processes. Hox proteins are key transcriptional regulators of animal development, famously helping to determine identity along the anterior-posterior body axis. Although their evolution and developmental roles are well established, the molecular mechanisms underlying their specific functions remain poorly characterized. The current dominant view is that interaction with different members of the PBC family of transcription factors confers specific DNA-binding properties on different Hox proteins. However, this idea conflicts with in vitro evidence that a short “hexapeptide” (HX) motif shared by most Hox proteins is solely responsible for generic PBC recruitment. Here we have used the BiFC (bimolecular fluorescence complementation) method to address the global importance of the HX motif for Hox-PBC interactions in living cells and living animals including fruit flies and chick embryos. We observe that most interactions between Hox and PBC proteins do not depend on HX, and that alternative protein motifs are widely used for PBC recruitment in vivo. We also show that DNA binding by a second family of cofactors, the Meis proteins, unmasks these alternative interaction modes and that this property is conserved not only across Bilateria, but also in the basal animal phylum Cnidaria. Taken together, our results demonstrate that Hox-PBC partnership relies on multiple interaction modes, which can be influenced by additional transcriptional partners. We propose that this ancestral feature has been essential for ensuring Hox functional plasticity during development and evolution.
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Affiliation(s)
- Bruno Hudry
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR7288, CNRS, AMU, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - Sophie Remacle
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Marie-Claire Delfini
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR7288, CNRS, AMU, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - René Rezsohazy
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Yacine Graba
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR7288, CNRS, AMU, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - Samir Merabet
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR7288, CNRS, AMU, Parc Scientifique de Luminy, Case 907, Marseille, France
- * E-mail:
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82
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Structural basis for homeodomain recognition by the cell-cycle regulator Geminin. Proc Natl Acad Sci U S A 2012; 109:8931-6. [PMID: 22615398 DOI: 10.1073/pnas.1200874109] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Homeodomain-containing transcription factors play a fundamental role in the regulation of numerous developmental and cellular processes. Their multiple regulatory functions are accomplished through context-dependent inputs of target DNA sequences and collaborating protein partners. Previous studies have well established the sequence-specific DNA binding to homeodomains; however, little is known about how protein partners regulate their functions through targeting homeodomains. Here we report the solution structure of the Hox homeodomain in complex with the cell-cycle regulator, Geminin, which inhibits Hox transcriptional activity and enrolls Hox in cell proliferative control. Side-chain carboxylates of glutamates and aspartates in the C terminus of Geminin generate an overall charge pattern resembling the DNA phosphate backbone. These residues provide electrostatic interactions with homeodomain, which combine with the van der Waals contacts to form the stereospecific complex. We further showed that the interaction with Geminin is homeodomain subclass-selective and Hox paralog-specific, which relies on the stapling role of residues R43 and M54 in helix III and the basic amino acid cluster in the N terminus. Interestingly, we found that the C-terminal residue Ser184 of Geminin could be phosphorylated by Casein kinase II, resulting in the enhanced binding to Hox and more potent inhibitory effect on Hox transcriptional activity, indicating an additional layer of regulation. This structure provides insight into the molecular mechanism underlying homeodomain-protein recognition and may serve as a paradigm for interactions between homeodomains and DNA-competitive peptide inhibitors.
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83
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Thiaville MM, Stoeck A, Chen L, Wu RC, Magnani L, Oidtman J, Shih IM, Lupien M, Wang TL. Identification of PBX1 target genes in cancer cells by global mapping of PBX1 binding sites. PLoS One 2012; 7:e36054. [PMID: 22567123 PMCID: PMC3342315 DOI: 10.1371/journal.pone.0036054] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/26/2012] [Indexed: 11/18/2022] Open
Abstract
PBX1 is a TALE homeodomain transcription factor involved in organogenesis and tumorigenesis. Although it has been shown that ovarian, breast, and melanoma cancer cells depend on PBX1 for cell growth and survival, the molecular mechanism of how PBX1 promotes tumorigenesis remains unclear. Here, we applied an integrated approach by overlapping PBX1 ChIP-chip targets with the PBX1-regulated transcriptome in ovarian cancer cells to identify genes whose transcription was directly regulated by PBX1. We further determined if PBX1 target genes identified in ovarian cancer cells were co-overexpressed with PBX1 in carcinoma tissues. By analyzing TCGA gene expression microarray datasets from ovarian serous carcinomas, we found co-upregulation of PBX1 and a significant number of its direct target genes. Among the PBX1 target genes, a homeodomain protein MEOX1 whose DNA binding motif was enriched in PBX1-immunoprecipicated DNA sequences was selected for functional analysis. We demonstrated that MEOX1 protein interacts with PBX1 protein and inhibition of MEOX1 yields a similar growth inhibitory phenotype as PBX1 suppression. Furthermore, ectopically expressed MEOX1 functionally rescued the PBX1-withdrawn effect, suggesting MEOX1 mediates the cellular growth signal of PBX1. These results demonstrate that MEOX1 is a critical target gene and cofactor of PBX1 in ovarian cancers.
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Affiliation(s)
- Michelle M. Thiaville
- Departments of Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Alexander Stoeck
- Departments of Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Li Chen
- Departments of Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia, United States of America
| | - Ren-Chin Wu
- Departments of Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Luca Magnani
- Institute of Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire, United States of America
| | - Jessica Oidtman
- Departments of Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Ie-Ming Shih
- Departments of Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Mathieu Lupien
- Institute of Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire, United States of America
| | - Tian-Li Wang
- Departments of Pathology and Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
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84
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Chu SW, Noyes MB, Christensen RG, Pierce BG, Zhu LJ, Weng Z, Stormo GD, Wolfe SA. Exploring the DNA-recognition potential of homeodomains. Genome Res 2012; 22:1889-98. [PMID: 22539651 PMCID: PMC3460184 DOI: 10.1101/gr.139014.112] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The recognition potential of most families of DNA-binding domains (DBDs) remains relatively unexplored. Homeodomains (HDs), like many other families of DBDs, display limited diversity in their preferred recognition sequences. To explore the recognition potential of HDs, we utilized a bacterial selection system to isolate HD variants, from a randomized library, that are compatible with each of the 64 possible 3' triplet sites (i.e., TAANNN). The majority of these selections yielded sets of HDs with overrepresented residues at specific recognition positions, implying the selection of specific binders. The DNA-binding specificity of 151 representative HD variants was subsequently characterized, identifying HDs that preferentially recognize 44 of these target sites. Many of these variants contain novel combinations of specificity determinants that are uncommon or absent in extant HDs. These novel determinants, when grafted into different HD backbones, produce a corresponding alteration in specificity. This information was used to create more explicit HD recognition models, which can inform the prediction of transcriptional regulatory networks for extant HDs or the engineering of HDs with novel DNA-recognition potential. The diversity of recovered HD recognition sequences raises important questions about the fitness barrier that restricts the evolution of alternate recognition modalities in natural systems.
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Affiliation(s)
- Stephanie W Chu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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85
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Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 2012; 147:1270-82. [PMID: 22153072 DOI: 10.1016/j.cell.2011.10.053] [Citation(s) in RCA: 371] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 08/19/2011] [Accepted: 10/06/2011] [Indexed: 11/30/2022]
Abstract
Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo. Transcription factors often bind DNA as multiprotein complexes, raising the possibility that complex formation might modify their DNA binding specificities. To test this hypothesis, we developed an experimental and computational platform, SELEX-seq, that can be used to determine the relative affinities to any DNA sequence for any transcription factor complex. Applying this method to all eight Drosophila Hox proteins, we show that they obtain novel recognition properties when they bind DNA with the dimeric cofactor Extradenticle-Homothorax (Exd). Exd-Hox specificities group into three main classes that obey Hox gene collinearity rules and DNA structure predictions suggest that anterior and posterior Hox proteins prefer DNA sequences with distinct minor groove topographies. Together, these data suggest that emergent DNA recognition properties revealed by interactions with cofactors contribute to transcription factor specificities in vivo.
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Affiliation(s)
- Matthew Slattery
- Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168(th) Street, HHSC 1104, New York, NY 10032, USA
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86
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Doerdelmann T, Kojetin DJ, Baird-Titus JM, Solt LA, Burris TP, Rance M. Structural and biophysical insights into the ligand-free Pitx2 homeodomain and a ring dermoid of the cornea inducing homeodomain mutant. Biochemistry 2012; 51:665-76. [PMID: 22224469 PMCID: PMC3264736 DOI: 10.1021/bi201639x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The homeodomain-containing transcription factor Pitx2 (pituitary homeobox protein 2) is present in many developing embryonic tissues, including the heart. Its homeodomain is responsible for the recognition and binding to target DNA sequences and thus constitutes a major functional unit in the Pitx2 protein. Nuclear magnetic resonance techniques were employed to determine the solution structure of the native Pitx2 homeodomain and a R24H mutant that causes autosomal dominantly inherited ring dermoid of the cornea syndrome. The structures reveal that both isoforms possess the canonical homeodomain fold. However, the R24H mutation results in a 2-fold increase in DNA binding affinity and a 5 °C decrease in thermal stability, while changing the dynamic environment of the homeodomain only locally. When introduced into full-length Pitx2c, the mutation results in an only 25% loss of transactivation activity. Our data correlate well with clinical observations suggesting a milder deficiency for the R24H mutation compared to those of other Pitx2 homeodomain mutations.
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Affiliation(s)
- Thomas Doerdelmann
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
| | - Douglas J. Kojetin
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jamie M. Baird-Titus
- College of Mount St. Joseph, Department of Chemistry, 5701 Delhi Road, Cincinnati, OH 45233, USA
| | - Laura A. Solt
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Thomas P. Burris
- The Scripps Research Institute, Scripps Florida, Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Mark Rance
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
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87
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Manley G, Loria JP. NMR insights into protein allostery. Arch Biochem Biophys 2011; 519:223-31. [PMID: 22198279 DOI: 10.1016/j.abb.2011.10.023] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 10/06/2011] [Accepted: 10/10/2011] [Indexed: 11/19/2022]
Abstract
Allosterism is one of nature's principal methods for regulating protein function. Allosterism utilizes ligand binding at one site to regulate the function of the protein by modulating the structure and dynamics of a distant binding site. In this review, we first survey solution NMR techniques and how they may be applied to the study of allostery. Subsequently, we describe several examples of application of NMR to protein allostery and highlight the unique insight provided by this experimental technique.
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Affiliation(s)
- Gregory Manley
- Department of Chemistry, Yale University, 225 Prospect Street, P.O. Box 208107, New Haven, CT 06520-8107, USA
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88
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Augustyniak R, Balayssac S, Ferrage F, Bodenhausen G, Lequin O. 1H, 13C and 15N resonance assignment of a 114-residue fragment of Engrailed 2 homeoprotein, a partially disordered protein. BIOMOLECULAR NMR ASSIGNMENTS 2011; 5:229-231. [PMID: 21516336 DOI: 10.1007/s12104-011-9306-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 04/14/2011] [Indexed: 05/30/2023]
Abstract
Engrailed 2 is a transcription factor belonging to the class of homeoproteins. These proteins possess a 60-residue DNA binding globular domain and play an important role in the early stages of development. We expressed and purified a 13.4 kDa fragment of Engrailed 2, which comprises a 54-residue N-terminal extension in addition to the homeodomain region. Almost all backbone and side-chain resonances have been assigned. The weak dispersion in the proton dimension of the (1)H-(15)N HSQC spectrum indicates the presence of disordered regions that do not belong to the homeodomain. This work is a first step toward the NMR investigation of the structure and dynamics of Engrailed 2 protein that contains a well-structured globular domain and partially disordered regions.
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89
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Delval S, Taminiau A, Lamy J, Lallemand C, Gilles C, Noël A, Rezsohazy R. The Pbx interaction motif of Hoxa1 is essential for its oncogenic activity. PLoS One 2011; 6:e25247. [PMID: 21957483 PMCID: PMC3177904 DOI: 10.1371/journal.pone.0025247] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 08/30/2011] [Indexed: 01/21/2023] Open
Abstract
Hoxa1 belongs to the Hox family of homeodomain transcription factors involved in patterning embryonic territories and governing organogenetic processes. In addition to its developmental functions, Hoxa1 has been shown to be an oncogene and to be overexpressed in the mammary gland in response to a deregulation of the autocrine growth hormone. It has therefore been suggested that Hoxa1 plays a pivotal role in the process linking autocrine growth hormone misregulation and mammary carcinogenesis. Like most Hox proteins, Hoxa1 can interact with Pbx proteins. This interaction relies on a Hox hexapeptidic sequence centred on conserved Tryptophan and Methionine residues. To address the importance of the Hox-Pbx interaction for the oncogenic activity of Hoxa1, we characterized here the properties of a Hoxa1 variant with substituted residues in the hexapeptide and demonstrate that the Hoxa1 mutant lost its ability to stimulate cell proliferation, anchorage-independent cell growth, and loss of contact inhibition. Therefore, the hexapeptide motif of Hoxa1 is required to confer its oncogenic activity, supporting the view that this activity relies on the ability of Hoxa1 to interact with Pbx.
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Affiliation(s)
- Stéphanie Delval
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute (ISV), Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Arnaud Taminiau
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute (ISV), Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Juliette Lamy
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute (ISV), Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Cécile Lallemand
- Laboratory of Biology of Tumors and Development, GIGA-Cancer, University of Liège and Centre Hospitalier Universitaire, Liège, Belgium
| | - Christine Gilles
- Laboratory of Biology of Tumors and Development, GIGA-Cancer, University of Liège and Centre Hospitalier Universitaire, Liège, Belgium
| | - Agnès Noël
- Laboratory of Biology of Tumors and Development, GIGA-Cancer, University of Liège and Centre Hospitalier Universitaire, Liège, Belgium
| | - René Rezsohazy
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute (ISV), Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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90
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Bjerke GA, Hyman-Walsh C, Wotton D. Cooperative transcriptional activation by Klf4, Meis2, and Pbx1. Mol Cell Biol 2011; 31:3723-33. [PMID: 21746878 PMCID: PMC3165729 DOI: 10.1128/mcb.01456-10] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 06/30/2011] [Indexed: 11/20/2022] Open
Abstract
The Kruppel-like factor Klf4 is implicated in tumorigenesis and maintaining stem cell pluripotency, and Klf4 can both activate and repress gene expression. We show that the Pbx1 and Meis2 homeodomain proteins interact with Klf4 and can be recruited to DNA elements comprising a Klf4 site or GC box, with adjacent Meis and Pbx sites. Meis2d and Pbx1a activate expression of p15(Ink4a) and E-cadherin, dependent on the Meis2d transcriptional activation domain. In HepG2 cells, reducing expression of endogenous Meis2 or Pbx1 decreases p15 gene expression and increases the number of cells entering S phase. Although DNA binding by all three proteins contributes to full cooperative activation, the sequence requirements for binding by Meis2 and Pbx1 are variable. In the E-cadherin promoter, a Pbx-like site is required for full activation, whereas in the p15 promoter, the Klf4 site appears to play the major role. Through a bioinformatics search we identified additional genes with conserved binding sites for Klf4, Meis2, and Pbx1 and show that at least some of these genes can be activated cooperatively by Klf4 and Meis2/Pbx1. We suggest a model in which genes with Klf4 sites can be cooperatively activated by Meis2/Pbx1 and Klf4, dependent primarily on recruitment by Klf4. This provides a mechanism to modulate transcriptional regulation by the multifunctional Klf4 transcription factor.
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Affiliation(s)
- Glen A. Bjerke
- Department of Biochemistry and Molecular Genetics and Center for Cell Signaling, University of Virginia, Charlottesville, Virginia
| | - Cathy Hyman-Walsh
- Department of Biochemistry and Molecular Genetics and Center for Cell Signaling, University of Virginia, Charlottesville, Virginia
| | - David Wotton
- Department of Biochemistry and Molecular Genetics and Center for Cell Signaling, University of Virginia, Charlottesville, Virginia
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91
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Zhang Y, Larsen CA, Stadler HS, Ames JB. Structural basis for sequence specific DNA binding and protein dimerization of HOXA13. PLoS One 2011; 6:e23069. [PMID: 21829694 PMCID: PMC3148250 DOI: 10.1371/journal.pone.0023069] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 07/12/2011] [Indexed: 11/18/2022] Open
Abstract
The homeobox gene (HOXA13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of genes during embryonic morphogenesis. Here we present the NMR structure of HOXA13 homeodomain (A13DBD) bound to an 11-mer DNA duplex. A13DBD forms a dimer that binds to DNA with a dissociation constant of 7.5 nM. The A13DBD/DNA complex has a molar mass of 35 kDa consistent with two molecules of DNA bound at both ends of the A13DBD dimer. A13DBD contains an N-terminal arm (residues 324 – 329) that binds in the DNA minor groove, and a C-terminal helix (residues 362 – 382) that contacts the ATAA nucleotide sequence in the major groove. The N370 side-chain forms hydrogen bonds with the purine base of A5* (base paired with T5). Side-chain methyl groups of V373 form hydrophobic contacts with the pyrimidine methyl groups of T5, T6* and T7*, responsible for recognition of TAA in the DNA core. I366 makes similar methyl contacts with T3* and T4*. Mutants (I366A, N370A and V373G) all have decreased DNA binding and transcriptional activity. Exposed protein residues (R337, K343, and F344) make intermolecular contacts at the protein dimer interface. The mutation F344A weakens protein dimerization and lowers transcriptional activity by 76%. We conclude that the non-conserved residue, V373 is critical for structurally recognizing TAA in the major groove, and that HOXA13 dimerization is required to activate transcription of target genes.
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Affiliation(s)
- Yonghong Zhang
- Department of Chemistry, University of California Davis, Davis, California, United States of America
| | - Christine A. Larsen
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States of America
- Shriners Hospital for Children Research Department, Portland, Oregon, United States of America
| | - H. Scott Stadler
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States of America
- Shriners Hospital for Children Research Department, Portland, Oregon, United States of America
| | - James B. Ames
- Department of Chemistry, University of California Davis, Davis, California, United States of America
- * E-mail:
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92
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Functional synthetic Antennapedia genes and the dual roles of YPWM motif and linker size in transcriptional activation and repression. Proc Natl Acad Sci U S A 2011; 108:11959-64. [PMID: 21712439 DOI: 10.1073/pnas.1108686108] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Segmental identity along the anteroposterior axis of bilateral animals is specified by Hox genes. These genes encode transcription factors, harboring the conserved homeodomain and, generally, a YPWM motif, which binds Hox cofactors and increases Hox transcriptional specificity in vivo. Here we derive synthetic Drosophila Antennapedia genes, consisting only of the YPWM motif and homeodomain, and investigate their functional role throughout development. Synthetic peptides and full-length Antennapedia proteins cause head-to-thorax transformations in the embryo, as well as antenna-to-tarsus and eye-to-wing transformations in the adult, thus converting the entire head to a mesothorax. This conversion is achieved by repression of genes required for head and antennal development and ectopic activation of genes promoting thoracic and tarsal fates, respectively. Synthetic Antennapedia peptides bind DNA specifically and interact with Extradenticle and Bric-à-brac interacting protein 2 cofactors in vitro and ex vivo. Substitution of the YPWM motif by alanines abolishes Antennapedia homeotic function, whereas substitution of YPWM by the WRPW repressor motif, which binds the transcriptional corepressor Groucho, allows all proteins to act as repressors only. Finally, naturally occurring variations in the size of the linker between the homeodomain and YPWM motif enhance Antennapedia repressive or activating efficiency, emphasizing the importance of linker size, rather than sequence, for specificity. Our results clearly show that synthetic Antennapedia genes are functional in vivo and therefore provide powerful tools for synthetic biology. Moreover, the YPWM motif is necessary--whereas the entire N terminus of the protein is dispensable--for Antennapedia homeotic function, indicating its dual role in transcriptional activation and repression by recruiting either coactivators or corepressors.
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93
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Seldeen KL, Deegan BJ, Bhat V, Mikles DC, McDonald CB, Farooq A. Energetic coupling along an allosteric communication channel drives the binding of Jun-Fos heterodimeric transcription factor to DNA. FEBS J 2011; 278:2090-104. [PMID: 21496208 DOI: 10.1111/j.1742-4658.2011.08124.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Although allostery plays a central role in driving protein-DNA interactions, the physical basis of such cooperative behavior remains poorly understood. In the present study, using isothermal titration calorimetry in conjunction with site-directed mutagenesis, we provide evidence that an intricate network of energetically-coupled residues within the basic regions of the Jun-Fos heterodimeric transcription factor accounts for its allosteric binding to DNA. Remarkably, energetic coupling is prevalent in residues that are both close in space, as well as residues distant in space, implicating the role of both short- and long-range cooperative interactions in driving the assembly of this key protein-DNA interaction. Unexpectedly, many of the energetically-coupled residues involved in orchestrating such a cooperative network of interactions are poorly conserved across other members of the basic zipper family, emphasizing the importance of basic residues in dictating the specificity of basic zipper-DNA interactions. Collectively, our thermodynamic analysis maps an allosteric communication channel driving a key protein-DNA interaction central to cellular functions in health and disease.
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Affiliation(s)
- Kenneth L Seldeen
- Department of Biochemistry & Molecular Biology and USylvester Braman Family Breast Cancer Institute, Leonard Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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94
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Merabet S, Hudry B. On the border of the homeotic function: Re-evaluating the controversial role of cofactor-recruiting motifs. Bioessays 2011; 33:499-507. [DOI: 10.1002/bies.201100019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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95
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Choo SW, White R, Russell S. Genome-wide analysis of the binding of the Hox protein Ultrabithorax and the Hox cofactor Homothorax in Drosophila. PLoS One 2011; 6:e14778. [PMID: 21483667 PMCID: PMC3071696 DOI: 10.1371/journal.pone.0014778] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 02/15/2011] [Indexed: 12/15/2022] Open
Abstract
Hox genes encode a family of transcription factors that are key developmental regulators with a highly conserved role in specifying segmental diversity along the metazoan body axis. Although they have been shown to regulate a wide variety of downstream processes, direct transcriptional targets have been difficult to identify and this has been a major obstacle to our understanding of Hox gene function. We report the identification of genome-wide binding sites for the Hox protein Ultrabithorax (Ubx) using a YFP-tagged Drosophila protein-trap line together with chromatin immunoprecipitation and microarray analysis. We identify 1,147 genes bound by Ubx at high confidence in chromatin from the haltere imaginal disc, a prominent site of Ubx function where it specifies haltere versus wing development. The functional relevance of these genes is supported by their overlap with genes differentially expressed between wing and haltere imaginal discs. The Ubx-bound gene set is highly enriched in genes involved in developmental processes and contains both high-level regulators as well as genes involved in more basic cellular functions. Several signalling pathways are highly enriched in the Ubx target gene set and our analysis supports the view that Hox genes regulate many levels of developmental pathways and have targets distributed throughout the gene network. We also performed genome-wide analysis of the binding sites for the Hox cofactor Homothorax (Hth), revealing a striking similarity with the Ubx binding profile. We suggest that these binding profiles may be strongly influenced by chromatin accessibility and provide evidence of a link between Ubx/Hth binding and chromatin state at genes regulated by Polycomb silencing. Overall, we define a set of direct Ubx targets in the haltere imaginal disc and suggest that chromatin accessibility has important implications for Hox target selection and for transcription factor binding in general.
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Affiliation(s)
- Siew Woh Choo
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
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96
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In der Rieden PMJ, Jansen HJ, Durston AJ. XMeis3 is necessary for mesodermal Hox gene expression and function. PLoS One 2011; 6:e18010. [PMID: 21464931 PMCID: PMC3065463 DOI: 10.1371/journal.pone.0018010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 02/21/2011] [Indexed: 12/13/2022] Open
Abstract
Hox transcription factors provide positional information during patterning of the anteroposterior axis. Hox transcription factors can co-operatively bind with PBC-class co-factors, enhancing specificity and affinity for their appropriate binding sites. The nuclear localisation of these co-factors is regulated by the Meis-class of homeodomain proteins. During development of the zebrafish hindbrain, Meis3 has previously been shown to synergise with Hoxb1 in the autoregulation of Hoxb1. In Xenopus XMeis3 posteriorises the embryo upon ectopic expression. Recently, an early temporally collinear expression sequence of Hox genes was detected in Xenopus gastrula mesoderm (see intro. P3). There is evidence that this sequence sets up the embryo's later axial Hox expression pattern by time-space translation. We investigated whether XMeis3 is involved in regulation of this early mesodermal Hox gene expression. Here, we present evidence that XMeis3 is necessary for expression of Hoxd1, Hoxb4 and Hoxc6 in mesoderm during gastrulation. In addition, we show that XMeis3 function is necessary for the progression of gastrulation. Finally, we present evidence for synergy between XMeis3 and Hoxd1 in Hoxd1 autoregulation in mesoderm during gastrulation.
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97
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Capellini TD, Zappavigna V, Selleri L. Pbx homeodomain proteins: TALEnted regulators of limb patterning and outgrowth. Dev Dyn 2011; 240:1063-86. [PMID: 21416555 DOI: 10.1002/dvdy.22605] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2011] [Indexed: 12/14/2022] Open
Abstract
Limb development has long provided an excellent model for understanding the genetic principles driving embryogenesis. Studies utilizing chick and mouse have led to new insights into limb patterning and morphogenesis. Recent research has centered on the regulatory networks underlying limb development. Here, we discuss the hierarchical, overlapping, and iterative roles of Pbx family members in appendicular development that have emerged from genetic analyses in the mouse. Pbx genes are essential in determining limb bud positioning, early bud formation, limb axes establishment and coordination, and patterning and morphogenesis of most elements of the limb and girdle. Pbx proteins directly regulate critical effectors of limb and girdle development, including morphogen-encoding genes like Shh in limb posterior mesoderm, and transcription factor-encoding genes like Alx1 in pre-scapular domains. Interestingly, at least in limb buds, Pbx appear to act not only as Hox cofactors, but also in the upstream control of 5' HoxA/D gene expression.
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Affiliation(s)
- Terence D Capellini
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, USA
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98
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Selection of distinct Hox-Extradenticle interaction modes fine-tunes Hox protein activity. Proc Natl Acad Sci U S A 2011; 108:2276-81. [PMID: 21262810 DOI: 10.1073/pnas.1006964108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hox genes encode transcription factors widely used for diversifying animal body plans in development and evolution. To achieve functional specificity, Hox proteins associate with PBC class proteins, Pre-B cell leukemia homeobox (Pbx) in vertebrates, and Extradenticle (Exd) in Drosophila, and were thought to use a unique hexapeptide-dependent generic mode of interaction. Recent findings, however, revealed the existence of an alternative, UbdA-dependent paralog-specific interaction mode providing diversity in Hox-PBC interactions. In this study, we investigated the basis for the selection of one of these two Hox-PBC interaction modes. Using naturally occurring variations and mutations in the Drosophila Ultrabithorax protein, we found that the linker region, a short domain separating the hexapeptide from the homeodomain, promotes an interaction mediated by the UbdA domain in a context-dependent manner. While using a UbdA-dependent interaction for the repression of the limb-promoting gene Distalless, interaction with Exd during segment-identity specification still relies on the hexapeptide motif. We further show that distinctly assembled Hox-PBC complexes display subtle but distinct repressive activities. These findings identify Hox-PBC interaction as a template for subtle regulation of Hox protein activity that may have played a major role in the diversification of Hox protein function in development and evolution.
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99
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Farber PJ, Mittermaier A. Concerted dynamics link allosteric sites in the PBX homeodomain. J Mol Biol 2011; 405:819-30. [PMID: 21087615 DOI: 10.1016/j.jmb.2010.11.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 10/08/2010] [Accepted: 11/09/2010] [Indexed: 11/18/2022]
Abstract
The PBX1 homeodomain (PBX-HD) cooperatively binds DNA with Hox transcription factors and helps to regulate gene expression during vertebrate development. Allostery plays an important role in these interactions. DNA binding on one surface of PBX-HD enhances interactions with Hox proteins at a different interface. In addition, DNA binding causes a 15-residue extension at the C-terminus of PBX-HD to undergo a disorder-to-helix transition, although this region does not directly contact the DNA. Deletion of the C-terminal extension reduces both the DNA affinity of PBX-HD and the cooperativity of forming the DNA/Hox/PBX-HD ternary complex. To better understand the mechanism underlying these allosteric interactions, we used NMR relaxation dispersion dynamics experiments to characterize millisecond-timescale motions in PBX-HD over a range of temperatures. The data show that the C-terminal extension folds to form a fourth α-helix to a level of 5-10%, even in the absence of binding partners. This suggests that PBX-HD transiently preorganizes prior to binding DNA, reminiscent of the "conformational selection" model of molecular recognition. Folding of the C-terminal extension in the unbound protein is accompanied by structural rearrangements in both the DNA binding site and the Hox binding site, suggesting a possible role for these dynamics in the allosteric mechanism of PBX-HD.
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Affiliation(s)
- Patrick J Farber
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 2K6
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100
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Abstract
The homeodomain is a protein domain of about 60 amino acids that is encoded by homeobox genes. The homeodomain is a DNA binding domain, and hence homeodomain proteins are essentially transcription factors (TFs). They have been shown to play major roles in many developmental processes of animals, as well as fungi and plants. A primary function of homeodomain proteins is to regulate the expression of other genes in development and differentiation. Thousands of homeobox genes have been identified, and they can be grouped into many different classes. Often other conserved protein domains are found linked to a homeodomain. Several particular types of homeobox genes are organized into chromosomal clusters. The best-known cluster, the HOX cluster, is found in all bilaterian animals. Tetrapods contain four HOX clusters that arose through duplication in early vertebrate evolution. The genes in these clusters are called Hox genes. Lower chordates, insects and nematodes tend to have only one HOX cluster. Of particular interest is that many of the HOX cluster genes function in the process of pattern formation along the anterior-posterior body axis. Many other types of homeodomain proteins play roles in the determination of cell fates and cell differentiation. Homeobox genes thus perform key roles for all aspects of the development of an organism.
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Affiliation(s)
- Thomas R Bürglin
- Department of Biosciences and Nutrition, and Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE 141 83, Huddinge, Sweden,
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