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Villarreal-Puente A, Altamirano-Torres C, Jiménez-Mejía G, Hernández-Bautista C, Montalvo-Méndez R, Vázquez M, Zurita M, Reséndez-Pérez D. Novel Antennapedia and Ultrabithorax trimeric complexes with TBP and Exd regulate transcription. Hereditas 2024; 161:25. [PMID: 39080786 PMCID: PMC11290222 DOI: 10.1186/s41065-024-00327-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Hox proteins interact with DNA and many other proteins, co-factors, transcriptional factors, chromatin remodeling components, non-coding RNAs and even the extracellular matrix that assembles the Hox complexes. The number of interacting partners continues to grow with diverse components and more transcriptional factors than initially thought. Hox complexes present many activities, but their molecular mechanisms to modulate their target genes remain unsolved. RESULTS In this paper we showed the protein-protein interaction of Antp with Ubx through the homeodomain using BiFC in Drosophila. Analysis of Antp-deletional mutants showed that AntpHD helixes 1 and 2 are required for the interaction with Ubx. Also, we found a novel interaction of Ubx with TBP, in which the PolyQ domain of TBP is required for the interaction. Moreover, we also detected the formation of two new trimeric complexes of Antp with Ubx, TBP and Exd using BiFC-FRET; these proteins, however, do not form a trimeric interaction with BIP2 or TFIIEβ. The novel trimeric complexes reduced Antp transcriptional activity, indicating that they could confer specificity for repression. CONCLUSIONS Our results increase the number of transcriptional factors in the Antp and Ubx interactomes that form two novel trimeric complexes with TBP and Exd. We also report a new Ubx interaction with TBP. These novel interactions provide important clues of the dynamics of Hox-interacting complexes involved in transcriptional regulation, contributing to better understand Hox function.
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Affiliation(s)
- Alely Villarreal-Puente
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Claudia Altamirano-Torres
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Gustavo Jiménez-Mejía
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Carolina Hernández-Bautista
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Rubén Montalvo-Méndez
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Martha Vázquez
- Instituto de Biotecnología, Departamento de Fisiología Molecular y Genética del Desarrollo, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mario Zurita
- Instituto de Biotecnología, Departamento de Fisiología Molecular y Genética del Desarrollo, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Diana Reséndez-Pérez
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México.
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México.
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Du J, Yin H, Li J, Zhang W, Ding G, Zhou D, Sun Y, Shen B. Transcription factor B-H2 regulates CYP9J34 expression conveying deltamethrin resistance in Culex pipiens pallens. PEST MANAGEMENT SCIENCE 2024; 80:1991-2000. [PMID: 38092527 DOI: 10.1002/ps.7934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Mosquitoes are vectors of various diseases, posing significant health threats worldwide. Chemical pesticides, particularly pyrethroids like deltamethrin, are commonly used for mosquito control, but the emergence of resistant mosquito populations has become a concern. In the deltamethrin-resistant (DR) strain of Culex pipiens pallens, the highly expressed cytochrome P450 9 J34 (CYP9J34) gene is believed to play a role in resistance, yet the underlying mechanism remains unclear. RESULTS Quantitative polymerase chain reaction with reverse transcription (qRT-PCR) analysis revealed that the expression of CYP9J34 was 14.6-fold higher in DR strains than in deltamethrin-susceptible (DS) strains. The recombinant production of CYP9J34 protein of Cx. pipiens pallens showed that the protein could directly metabolize deltamethrin, yielding the major metabolite 4'-OH deltamethrin. Through dual luciferase reporter assays and RNA interference, the transcription factor homeobox protein B-H2-like (B-H2) was identified to modulate the expression of the CYP9J34 gene, contributing to mosquito resistance to deltamethrin. CONCLUSIONS Our findings demonstrate that the CYP9J34 protein could directly degrade deltamethrin, and the transcription factor B-H2 could regulate CYP9J34 expression, influencing the resistance of mosquitoes to deltamethrin. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Jiajia Du
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Haitao Yin
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Jinze Li
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Wenxing Zhang
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Guangshuo Ding
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Dan Zhou
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Yan Sun
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Bo Shen
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
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Le MH, Morgan B, Lu MY, Moctezuma V, Burgos O, Huang JP. The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests. Mol Ecol Resour 2024; 24:e13908. [PMID: 38063363 DOI: 10.1111/1755-0998.13908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/14/2023] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations in loci of adaptive significance. We sequenced and assembled high-quality chromosome-level genomes of four Hercules beetles which exhibit divergence in male horn size and shape and body colouration. The four Hercules beetle genomes were assembled to 11 pseudo-chromosomes, where the three genomes assembled using Nanopore data (Dynastes grantii, D. hyllus and D. tityus) were mapped to the genome assembled using PacBio + Hi-C data (D. maya). We demonstrated a striking similarity in genome structure among the four species. This conservative genome structure may be attributed to our use of the D. maya assembly as the reference; however, it is worth noting that such a conservative genome structure is a recurring phenomenon among scarab beetles. We further identified homologues of nine and three candidate-gene families that may be associated with the evolution of horn structure and body colouration respectively. Structural variations in Scr and Ebony2 were detected and discussed for their putative impacts on generating morphological diversity in beetles. We also reconstructed the demographic histories of the four Hercules beetles using heterozygosity information from the diploid genomes. We found that the demographic histories of the beetles closely recapitulated historical changes in suitable forest habitats driven by climate shifts.
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Affiliation(s)
- My-Hanh Le
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Brett Morgan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Mei-Yeh Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Victor Moctezuma
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, Mexico
| | - Oscar Burgos
- Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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4
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Kalis AK, Sterrett MC, Armstrong C, Ballmer A, Burkstrand K, Chilson E, Emlen E, Ferrer E, Loeb S, Olin T, Tran K, Wheeler A, Ross Wolff J. Hox proteins interact to pattern neuronal subtypes in Caenorhabditis elegans males. Genetics 2022; 220:iyac010. [PMID: 35137058 PMCID: PMC8982040 DOI: 10.1093/genetics/iyac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/10/2022] [Indexed: 11/14/2022] Open
Abstract
Hox transcription factors are conserved regulators of neuronal subtype specification on the anteroposterior axis in animals, with disruption of Hox gene expression leading to homeotic transformations of neuronal identities. We have taken advantage of an unusual mutation in the Caenorhabditis elegans Hox gene lin-39, lin-39(ccc16), which transforms neuronal fates in the C. elegans male ventral nerve cord in a manner that depends on a second Hox gene, mab-5. We have performed a genetic analysis centered around this homeotic allele of lin-39 in conjunction with reporters for neuronal target genes and protein interaction assays to explore how LIN-39 and MAB-5 exert both flexibility and specificity in target regulation. We identify cis-regulatory modules in neuronal reporters that are both region-specific and Hox-responsive. Using these reporters of neuronal subtype, we also find that the lin-39(ccc16) mutation disrupts neuronal fates specifically in the region where lin-39 and mab-5 are coexpressed, and that the protein encoded by lin-39(ccc16) is active only in the absence of mab-5. Moreover, the fates of neurons typical to the region of lin-39-mab-5 coexpression depend on both Hox genes. Our genetic analysis, along with evidence from Bimolecular Fluorescence Complementation protein interaction assays, supports a model in which LIN-39 and MAB-5 act at an array of cis-regulatory modules to cooperatively activate and to individually activate or repress neuronal gene expression, resulting in regionally specific neuronal fates.
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Affiliation(s)
- Andrea K Kalis
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | - Maria C Sterrett
- Department of Biology, Carleton College, Northfield, MN 55057, USA
| | - Cecily Armstrong
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | | | - Kylie Burkstrand
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | - Elizabeth Chilson
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | - Estee Emlen
- Department of Biology, Carleton College, Northfield, MN 55057, USA
| | - Emma Ferrer
- Department of Biology, Carleton College, Northfield, MN 55057, USA
| | - Seanna Loeb
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | - Taylor Olin
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | - Kevin Tran
- Department of Biology, Carleton College, Northfield, MN 55057, USA
| | - Andrew Wheeler
- Department of Biology, Carleton College, Northfield, MN 55057, USA
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Guo Z, Qin J, Zhou X, Zhang Y. Insect Transcription Factors: A Landscape of Their Structures and Biological Functions in Drosophila and beyond. Int J Mol Sci 2018; 19:ijms19113691. [PMID: 30469390 PMCID: PMC6274879 DOI: 10.3390/ijms19113691] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 12/17/2022] Open
Abstract
Transcription factors (TFs) play essential roles in the transcriptional regulation of functional genes, and are involved in diverse physiological processes in living organisms. The fruit fly Drosophila melanogaster, a simple and easily manipulated organismal model, has been extensively applied to study the biological functions of TFs and their related transcriptional regulation mechanisms. It is noteworthy that with the development of genetic tools such as CRISPR/Cas9 and the next-generation genome sequencing techniques in recent years, identification and dissection the complex genetic regulatory networks of TFs have also made great progress in other insects beyond Drosophila. However, unfortunately, there is no comprehensive review that systematically summarizes the structures and biological functions of TFs in both model and non-model insects. Here, we spend extensive effort in collecting vast related studies, and attempt to provide an impartial overview of the progress of the structure and biological functions of current documented TFs in insects, as well as the classical and emerging research methods for studying their regulatory functions. Consequently, considering the importance of versatile TFs in orchestrating diverse insect physiological processes, this review will assist a growing number of entomologists to interrogate this understudied field, and to propel the progress of their contributions to pest control and even human health.
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Affiliation(s)
- Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianying Qin
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China.
| | - Xiaomao Zhou
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China.
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Altamirano-Torres C, Salinas-Hernández JE, Cárdenas-Chávez DL, Rodríguez-Padilla C, Reséndez-Pérez D. Transcription factor TFIIEβ interacts with two exposed positions in helix 2 of the Antennapedia homeodomain to control homeotic function in Drosophila. PLoS One 2018; 13:e0205905. [PMID: 30321227 PMCID: PMC6188894 DOI: 10.1371/journal.pone.0205905] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/03/2018] [Indexed: 01/02/2023] Open
Abstract
Homeoproteins contain the conserved homeodomain (HD) and have an important role determining embryo body plan during development. HDs increase their DNA-binding specificity by interacting with additional cofactors outlining a Hox interactome with a multiplicity of protein-protein interactions. In Drosophila, the first link of functional contact with a general transcription factor (GTF) was found between Antennapedia (Antp) and BIP2 (TFIID complex). Hox proteins also interact with other components of Pol II machinery such as the subunit Med19 from Mediator (MED) complex, TFIIEβ and transcription-pausing factor M1BP. All these interactions clearly demonstrate Hox-driven transcriptional regulation, but the precise molecular mechanism remains unclear. In this paper, we focused on the Antp-TFIIEβ protein-protein interface to establish the specific contacts as well as its functional role. Using Bimolecular Fluorescence Complementation (BiFC) in cell culture and in vivo we found that TFIIEβ interacts with Antp through the HD independently of the YPWM motif and the direct physical interaction is at helix 2, specifically aminoacidic positions I32 and H36 of Antp. We also found, through ectopic assays, that these two positions in helix 2 are crucial for Antp homeotic function in head involution, and thoracic and antenna-to tarsus transformations. Interestingly, overexpression of Antp and TFIIEβ in the antennal disc showed that this interaction is required for the antenna-to-tarsus transformation. In conclusion, interaction of Antp with TFIIEβ is important for the functional specificity of Antennapedia, and amino acids 32 and 36 in Antp HD helix 2 are key for this interaction. Our results open the possibility to more broadly analyze Antp-TFIIEβ interaction on the transcriptional control for the activation and/or repression of target genes in the Hox interactome during Drosophila development.
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Affiliation(s)
- Claudia Altamirano-Torres
- Department of Immunology and Virology, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Department of Cell Biology and Genetics, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Jannet E. Salinas-Hernández
- Department of Immunology and Virology, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Diana L. Cárdenas-Chávez
- Department of Immunology and Virology, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Cristina Rodríguez-Padilla
- Department of Immunology and Virology, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Diana Reséndez-Pérez
- Department of Immunology and Virology, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Department of Cell Biology and Genetics, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- * E-mail:
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7
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Deng H, Kerppola TK. Visualization of the Genomic Loci That Are Bound by Specific Multiprotein Complexes by Bimolecular Fluorescence Complementation Analysis on Drosophila Polytene Chromosomes. Methods Enzymol 2017; 589:429-455. [PMID: 28336073 DOI: 10.1016/bs.mie.2017.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
We have developed a procedure that enables visualization of the genomic loci that are bound by complexes formed by a specific combination of chromatin-binding proteins. This procedure is based on imaging bimolecular fluorescence complementation (BiFC) complexes on Drosophila polytene chromosomes. BiFC complexes are formed by the facilitated association of two fluorescent protein fragments that are fused to proteins that interact with, or are in close proximity to, each other. The intensity of BiFC complex fluorescence at individual genomic loci is greatly enhanced by the parallel alignment of hundreds of chromatids within the polytene chromosomes. The loci that are bound by the complexes are mapped by comparing the locations of BiFC complex fluorescence with the stereotypical banding patterns of the chromosomes. We describe strategies for the design, expression, and validation of fusion proteins for the analysis of BiFC complex binding on polytene chromosomes. We detail protocols for the preparation of polytene chromosome spreads that have been optimized for the purpose of BiFC complex visualization. Finally, we provide guidance for the interpretation of results from studies of BiFC complex binding on polytene chromosomes and for comparison of the genomic loci that are bound by BiFC complexes with those that are bound by subunits of the corresponding endogenous complexes. The visualization of BiFC complex binding on polytene chromosomes provides a unique method to visualize multiprotein complex binding at specific loci, throughout the genome, in individual cells.
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Affiliation(s)
- Huai Deng
- University of Michigan, Ann Arbor, MI, United States
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8
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Jiang Y, Liu C, Yan D, Wen X, Liu Y, Wang H, Dai J, Zhang Y, Liu Y, Zhou B, Ren X. MdHB1 down-regulation activates anthocyanin biosynthesis in the white-fleshed apple cultivar 'Granny Smith'. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1055-1069. [PMID: 28338881 DOI: 10.1093/jxb/erx029] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Coloration in apple (Malus×domestica) flesh is mainly caused by the accumulation of anthocyanin. Anthocyanin is biosynthesized through the flavonoid pathway and regulated by MYB, bHLH, and WD40 transcription factors (TFs). Here, we report that the HD-Zip I TF MdHB1 was also involved in the regulation of anthocyanin accumulation. MdHB1 silencing caused the accumulation of anthocyanin in 'Granny Smith' flesh, whereas its overexpression reduced the flesh content of anthocyanin in 'Ballerina' (red-fleshed apple). Moreover, flowers of transgenic tobacco (Nicotiana tabacum 'NC89') overexpressing MdHB1 showed a remarkable reduction in pigmentation. Transient promoter activation assays and yeast one-hybrid results indicated that MdHB1 indirectly inhibited expression of the anthocyanin biosynthetic genes encoding dihydroflavonol-4-reductase (DFR) and UDP-glucose:flavonoid 3-O-glycosyltransferase (UFGT). Yeast two-hybrid and bimolecular fluorescence complementation determined that MdHB1 acted as a homodimer and could interact with MYB, bHLH, and WD40 in the cytoplasm, consistent with its cytoplasmic localization by green fluorescent protein fluorescence observations. Together, these results suggest that MdHB1 constrains MdMYB10, MdbHLH3, and MdTTG1 to the cytoplasm, and then represses the transcription of MdDFR and MdUFGT indirectly. When MdHB1 is silenced, these TFs are released to activate the expression of MdDFR and MdUFGT and also anthocyanin biosynthesis, resulting in red flesh in 'Granny Smith'.
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Affiliation(s)
- Yonghua Jiang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cuihua Liu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dan Yan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaohong Wen
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanli Liu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haojie Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jieyu Dai
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yujie Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanfei Liu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bin Zhou
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaolin Ren
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Bobola N, Merabet S. Homeodomain proteins in action: similar DNA binding preferences, highly variable connectivity. Curr Opin Genet Dev 2016; 43:1-8. [PMID: 27768937 DOI: 10.1016/j.gde.2016.09.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 09/28/2016] [Indexed: 12/18/2022]
Abstract
Homeodomain proteins are evolutionary conserved proteins present in the entire eukaryote kingdom. They execute functions that are essential for life, both in developing and adult organisms. Most homeodomain proteins act as transcription factors and bind DNA to control the activity of other genes. In contrast to their similar DNA binding specificity, homeodomain proteins execute highly diverse and context-dependent functions. Several factors, including genome accessibility, DNA shape, combinatorial binding and the ability to interact with many transcriptional partners, diversify the activity of homeodomain proteins and culminate in the activation of highly dynamic, context-specific transcriptional programs. Clarifying how homeodomain transcription factors work is central to our understanding of development, disease and evolution.
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Affiliation(s)
- Nicoletta Bobola
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, Centre National de Recherche Scientifique, Ecole Normale Supérieure de Lyon, France.
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10
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Bürglin TR, Affolter M. Homeodomain proteins: an update. Chromosoma 2015; 125:497-521. [PMID: 26464018 PMCID: PMC4901127 DOI: 10.1007/s00412-015-0543-8] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/20/2015] [Accepted: 09/21/2015] [Indexed: 12/17/2022]
Abstract
Here, we provide an update of our review on homeobox genes that we wrote together with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have become possible due to genome sequencing projects. Using the 103 Drosophila homeobox genes as example, we present an updated classification. In animals, there are 16 major classes, ANTP, PRD, PRD-LIKE, POU, HNF, CUT (with four subclasses: ONECUT, CUX, SATB, and CMP), LIM, ZF, CERS, PROS, SIX/SO, plus the TALE superclass with the classes IRO, MKX, TGIF, PBC, and MEIS. In plants, there are 11 major classes, i.e., HD-ZIP (with four subclasses: I to IV), WOX, NDX, PHD, PLINC, LD, DDT, SAWADEE, PINTOX, and the two TALE classes KNOX and BEL. Most of these classes encode additional domains apart from the homeodomain. Numerous insights have been obtained in the last two decades into how homeodomain proteins bind to DNA and increase their specificity by interacting with other proteins to regulate cell- and tissue-specific gene expression. Not only protein-DNA base pair contacts are important for proper target selection; recent experiments also reveal that the shape of the DNA plays a role in specificity. Using selected examples, we highlight different mechanisms of homeodomain protein-DNA interaction. The PRD class of homeobox genes was of special interest to Walter Gehring in the last two decades. The PRD class comprises six families in Bilateria, and tinkers with four different motifs, i.e., the PAIRED domain, the Groucho-interacting motif EH1 (aka Octapeptide or TN), the homeodomain, and the OAR motif. Homologs of the co-repressor protein Groucho are also present in plants (TOPLESS), where they have been shown to interact with small amphipathic motives (EAR), and in yeast (TUP1), where we find an EH1-like motif in MATα2.
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Affiliation(s)
- Thomas R. Bürglin
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
- />Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Markus Affolter
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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Papadopoulos DK, Krmpot AJ, Nikolić SN, Krautz R, Terenius L, Tomancak P, Rigler R, Gehring WJ, Vukojević V. Probing the kinetic landscape of Hox transcription factor-DNA binding in live cells by massively parallel Fluorescence Correlation Spectroscopy. Mech Dev 2015; 138 Pt 2:218-225. [PMID: 26428533 DOI: 10.1016/j.mod.2015.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 11/25/2022]
Abstract
Hox genes encode transcription factors that control the formation of body structures, segment-specifically along the anterior-posterior axis of metazoans. Hox transcription factors bind nuclear DNA pervasively and regulate a plethora of target genes, deploying various molecular mechanisms that depend on the developmental and cellular context. To analyze quantitatively the dynamics of their DNA-binding behavior we have used confocal laser scanning microscopy (CLSM), single-point fluorescence correlation spectroscopy (FCS), fluorescence cross-correlation spectroscopy (FCCS) and bimolecular fluorescence complementation (BiFC). We show that the Hox transcription factor Sex combs reduced (Scr) forms dimers that strongly associate with its specific fork head binding site (fkh250) in live salivary gland cell nuclei. In contrast, dimers of a constitutively inactive, phospho-mimicking variant of Scr show weak, non-specific DNA-binding. Our studies reveal that nuclear dynamics of Scr is complex, exhibiting a changing landscape of interactions that is difficult to characterize by probing one point at a time. Therefore, we also provide mechanistic evidence using massively parallel FCS (mpFCS). We found that Scr dimers are predominantly formed on the DNA and are equally abundant at the chromosomes and an introduced multimeric fkh250 binding-site, indicating different mobilities, presumably reflecting transient binding with different affinities on the DNA. Our proof-of-principle results emphasize the advantages of mpFCS for quantitative characterization of fast dynamic processes in live cells.
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Affiliation(s)
| | - Aleksandar J Krmpot
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden; Institute of Physics, University of Belgrade, 11080 Belgrade, Serbia
| | - Stanko N Nikolić
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden; Institute of Physics, University of Belgrade, 11080 Belgrade, Serbia
| | - Robert Krautz
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Lars Terenius
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden
| | - Pavel Tomancak
- Max-Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Rudolf Rigler
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Laboratory of Biomedical Optics, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Walter J Gehring
- Department of Cell Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Vladana Vukojević
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden.
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12
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Meng M, Cheng DJ, Peng J, Qian WL, Li JR, Dai DD, Zhang TL, Xia QY. The homeodomain transcription factors antennapedia and POU-M2 regulate the transcription of the steroidogenic enzyme gene Phantom in the silkworm. J Biol Chem 2015; 290:24438-52. [PMID: 26253172 DOI: 10.1074/jbc.m115.651810] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 12/22/2022] Open
Abstract
The steroid hormone ecdysone, which controls insect molting and metamorphosis, is synthesized in the prothoracic gland (PG), and several steroidogenic enzymes that are expressed specifically in the PG are involved in ecdysteroidogenesis. In this study, we identified new regulators that are involved in the transcriptional control of the silkworm steroidogenic enzyme genes. In silico analysis predicted several potential cis-regulatory elements (CREs) for the homeodomain transcription factors Antennapedia (Antp) and POU-M2 in the proximal promoters of steroidogenic enzyme genes. Antp and POU-M2 are expressed dynamically in the PG during larval development, and their overexpression in silkworm embryo-derived (BmE) cells induced the expression of steroidogenic enzyme genes. Importantly, luciferase reporter analyses, electrophoretic mobility shift assays, and chromatin immunoprecipitation assays revealed that Antp and POU-M2 promote the transcription of the silkworm steroidogenic enzyme gene Phantom (Phm) by binding directly to specific motifs within overlapping CREs in the Phm promoter. Mutations of these CREs in the Phm promoter suppressed the transcriptional activities of both Antp and POU-M2 in BmE cells and decreased the activities of mutated Phm promoters in the silkworm PG. In addition, pulldown and co-immunoprecipitation assays demonstrated that Antp can interact with POU-M2. Moreover, RNA interference-mediated down-regulation of either Antp or POU-M2 during silkworm wandering not only decreased the ecdysone titer but also led to the failure of metamorphosis. In summary, our results suggest that Antp and POU-M2 coordinate the transcription of the silkworm Phm gene directly, indicating new roles for homeodomain proteins in regulating insect ecdysteroidogenesis.
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Affiliation(s)
- Meng Meng
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Dao-Jun Cheng
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Jian Peng
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Wen-Liang Qian
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Jia-Rui Li
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Dan-Dan Dai
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Tian-Lei Zhang
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Qing-You Xia
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
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13
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Saadaoui M, Litim-Mecheri I, Macchi M, Graba Y, Maurel-Zaffran C. A survey of conservation of sea spider and Drosophila Hox protein activities. Mech Dev 2015; 138 Pt 2:73-86. [PMID: 26238019 DOI: 10.1016/j.mod.2015.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/24/2015] [Accepted: 07/25/2015] [Indexed: 01/29/2023]
Abstract
Hox proteins have well-established functions in development and evolution, controlling the final morphology of bilaterian animals. The common phylogenetic origin of Hox proteins and the associated evolutionary diversification of protein sequences provide a unique framework to explore the relationship between changes in protein sequence and function. In this study, we aimed at questioning how sequence variation within arthropod Hox proteins influences function. This was achieved by exploring the functional impact of sequence conservation/divergence of the Hox genes, labial, Sex comb reduced, Deformed, Ultrabithorax and abdominalA from two distant arthropods, the sea spider and the well-studied Drosophila. Results highlight a correlation between sequence conservation within the homeodomain and the degree of functional conservation, and identify a novel functional domain in the Labial protein.
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Affiliation(s)
- Mehdi Saadaoui
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France; Institut de Biologie de l'ENS, 46, rue d'Ulm, 75005 Paris, France
| | - Isma Litim-Mecheri
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France; IGBMC, INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Meiggie Macchi
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
| | - Yacine Graba
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
| | - Corinne Maurel-Zaffran
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
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14
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Role of HOXA9 in leukemia: dysregulation, cofactors and essential targets. Oncogene 2015; 35:1090-8. [PMID: 26028034 DOI: 10.1038/onc.2015.174] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/24/2015] [Accepted: 04/14/2015] [Indexed: 02/08/2023]
Abstract
HOXA9 is a homeodomain-containing transcription factor that has an important role in hematopoietic stem cell expansion and is commonly deregulated in acute leukemias. A variety of upstream genetic alterations in acute myeloid leukemia lead to overexpression of HOXA9, which is a strong predictor of poor prognosis. In many cases, HOXA9 has been shown to be necessary for maintaining leukemic transformation; however, the molecular mechanisms through which it promotes leukemogenesis remain elusive. Recent work has established that HOXA9 regulates downstream gene expression through binding at promoter distal enhancers along with a subset of cell-specific cofactor and collaborator proteins. Increasing efforts are being made to identify both the critical cofactors and target genes required for maintaining transformation in HOXA9-overexpressing leukemias. With continued advances in understanding HOXA9-mediated transformation, there is a wealth of opportunity for developing novel therapeutics that would be applicable for greater than 50% of AML with overexpression of HOXA9.
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15
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Drewell RA, Nevarez MJ, Kurata JS, Winkler LN, Li L, Dresch JM. Deciphering the combinatorial architecture of a Drosophila homeotic gene enhancer. Mech Dev 2014; 131:68-77. [PMID: 24514265 DOI: 10.1016/j.mod.2013.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 10/07/2013] [Accepted: 10/08/2013] [Indexed: 01/20/2023]
Abstract
In Drosophila, the 330 kb bithorax complex regulates cellular differentiation along the anterior–posterior axis during development in the thorax and abdomen and is comprised of three homeotic genes: Ultrabithorax, abdominal-A, and Abdominal-B. The expression of each of these genes is in turn controlled through interactions between transcription factors and a number of cis-regulatory modules in the neighboring intergenic regions. In this study, we examine how the sequence architecture of transcription factor binding sites mediates the functional activity of one of these cis-regulatory modules. Using computational, mathematical modeling and experimental molecular genetic approaches we investigate the IAB7b enhancer, which regulates Abdominal-B expression specifically in the presumptive seventh and ninth abdominal segments of the early embryo. A cross-species comparison of the IAB7b enhancer reveals an evolutionarily conserved signature motif containing two FUSHI-TARAZU activator transcription factor binding sites. We find that the transcriptional repressors KNIRPS, KRUPPEL and GIANT are able to restrict reporter gene expression to the posterior abdominal segments, using different molecular mechanisms including short-range repression and competitive binding. Additionally, we show the functional importance of the spacing between the two FUSHI-TARAZU binding sites and discuss the potential importance of cooperativity for transcriptional activation. Our results demonstrate that the transcriptional output of the IAB7b cis-regulatory module relies on a complex set of combinatorial inputs mediated by specific transcription factor binding and that the sequence architecture at this enhancer is critical to maintain robust regulatory function.
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16
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Deng H, Kerppola TK. Visualization of the Drosophila dKeap1-CncC interaction on chromatin illumines cooperative, xenobiotic-specific gene activation. Development 2014; 141:3277-88. [PMID: 25063457 DOI: 10.1242/dev.110528] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Interactions among transcription factors control their physiological functions by regulating their binding specificities and transcriptional activities. We implement a strategy to visualize directly the genomic loci that are bound by multi-protein complexes in single cells in Drosophila. This method is based on bimolecular fluorescence complementation (BiFC) analysis of protein interactions on polytene chromosomes. Drosophila Keap1 (dKeap1)-CncC complexes localized to the nucleus and bound chromatin loci that were not bound preferentially by dKeap1 or CncC when they were expressed separately. dKeap1 and CncC binding at these loci was enhanced by phenobarbital, but not by tert-butylhydroquinone (tBHQ) or paraquat. Endogenous dKeap1 and CncC activated transcription of the Jheh (Jheh1, Jheh2, Jheh3) and dKeap1 genes at these loci, whereas CncC alone activated other xenobiotic response genes. Ectopic dKeap1 expression increased CncC binding at the Jheh and dKeap1 gene loci and activated their transcription, whereas dKeap1 inhibited CncC binding at other xenobiotic response gene loci and suppressed their transcription. The combinatorial chromatin-binding specificities and transcriptional activities of dKeap1-CncC complexes mediated the selective activation of different sets of genes by different xenobiotic compounds, in part through feed-forward activation of dKeap1 transcription.
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Affiliation(s)
- Huai Deng
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-0650, USA
| | - Tom K Kerppola
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-0650, USA
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17
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Refki PN, Armisén D, Crumière AJJ, Viala S, Khila A. Emergence of tissue sensitivity to Hox protein levels underlies the evolution of an adaptive morphological trait. Dev Biol 2014; 392:441-53. [PMID: 24886828 PMCID: PMC4111901 DOI: 10.1016/j.ydbio.2014.05.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 05/20/2014] [Accepted: 05/24/2014] [Indexed: 11/16/2022]
Abstract
Growth control scales morphological attributes and, therefore, provides a critical contribution to the evolution of adaptive traits. Yet, the genetic mechanisms underlying growth in the context of specific ecological adaptations are poorly understood. In water striders, adaptation to locomotion on the water surface is associated with allometric and functional changes in thoracic appendages, such that T2-legs, used as propelling oars, are longer than T3-legs, used as steering rudders. The Hox gene Ubx establishes this derived morphology by elongating T2-legs but shortening T3-legs. Using gene expression assays, RNAi knockdown, and comparative transcriptomics, we demonstrate that the evolution of water surface rowing as a novel means of locomotion is associated with the evolution of a dose-dependent promoting-repressing effect of Ubx on leg growth. In the water strider Limnoporus dissortis, T3-legs express six to seven times higher levels of Ubx compared to T2-legs. Ubx RNAi shortens T2-legs and the severity of this phenotype increases with increased depletion of Ubx protein. Conversely, Ubx RNAi lengthens T3-legs but this phenotype is partially rescued when Ubx protein is further depleted. This dose-dependent effect of Ubx on leg growth is absent in non-rowing relatives that retain the ancestral relative leg length. We also show that the spatial patterns of expression of dpp, wg, hh, egfr, dll, exd, hth, and dac are unchanged in Ubx RNAi treatments. This indicates that the dose-dependent opposite effect of Ubx on T2- and T3-legs operates without any apparent effect on the spatial expression of major leg patterning genes. Our data suggest that scaling of adaptive allometries can evolve through changes in the levels of expression of Hox proteins early during ontogeny, and in the sensitivity of the tissues that express them, without any major effects on pattern formation. Ubx is generally expressed at higher levels in T3- relative to T2-legs in semi-aquatic insects. It is only in the derived Gerridae where the high levels of Ubx result in reduced T3-leg length. In the Gerridae, the response of leg tissues to Ubx levels is bimodal. Changes in Ubx regulation and function have evolved in Limnoporus without disrupting patterning hierarchies. Changes in Hox protein levels and emergence of tissue sensitivity to these levels can shape adaptive morphological traits.
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Affiliation(s)
- Peter Nagui Refki
- Institut de Génomique Fonctionnelle de Lyon, CNRS-UMR5242, Ecole Normale Supérieure de Lyon, 46 Allée d׳Italie, 69364 Lyon Cedex 07, France; Université Claude Bernard Lyon 1, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, CNRS-UMR5242, Ecole Normale Supérieure de Lyon, 46 Allée d׳Italie, 69364 Lyon Cedex 07, France
| | - Antonin Jean Johan Crumière
- Institut de Génomique Fonctionnelle de Lyon, CNRS-UMR5242, Ecole Normale Supérieure de Lyon, 46 Allée d׳Italie, 69364 Lyon Cedex 07, France; Université Claude Bernard Lyon 1, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - Séverine Viala
- Institut de Génomique Fonctionnelle de Lyon, CNRS-UMR5242, Ecole Normale Supérieure de Lyon, 46 Allée d׳Italie, 69364 Lyon Cedex 07, France
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, CNRS-UMR5242, Ecole Normale Supérieure de Lyon, 46 Allée d׳Italie, 69364 Lyon Cedex 07, France.
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18
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Chuang HN, Hsiao KM, Chang HY, Wu CC, Pan H. The homeobox transcription factor Irxl1 negatively regulates MyoD expression and myoblast differentiation. FEBS J 2014; 281:2990-3003. [PMID: 24814716 DOI: 10.1111/febs.12837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/07/2014] [Accepted: 04/30/2014] [Indexed: 11/29/2022]
Abstract
Irxl1/Mkx (Iroquois homeobox-like 1/Mohawk) encodes a member of the TALE subfamily of homeodomain proteins. It is expressed in multiple mesoderm-derived tissues and has recently been shown to regulate tendon differentiation during mouse embryonic development. Previously we showed that knockdown of Irxl1 in zebrafish caused a deficit in neural crest cells which consequently resulted in deformation of craniofacial muscles and arch cartilages. Here, we further demonstrate that loss of Irxl1 function results in deformed somites with disordered muscle fibers and myotendinous junctions. Because expression of myoD is increased in the somites of Irxl1 knockdown morphants, we test whether Irxl1 negatively regulates myoD expression. When stable C2C12 myoblasts overexpressing Irxl1/Mkx were induced to differentiate, myotube formation was inhibited and protein levels of myoD and myosin heavy chain were decreased accordingly. A series of deletion constructs of myoD promoter fragments were tested by luciferase reporter assays, which identified a promoter fragment that is necessary and sufficient for Irxl1-mediated repression. Direct interaction of Irxl1 and myoD promoter was subsequently elucidated by yeast one-hybrid assays, electrophoretic mobility shift assays and chromatin immunoprecipitation analysis. Furthermore, mouse Mkx also binds to and represses myoD promoter. These results indicate that Irxl1/Mkx can repress myoD expression through direct binding to its promoter and may thus play a negative regulatory role in muscle differentiation.
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Affiliation(s)
- Han-Ni Chuang
- Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, Taiwan; Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
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19
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Acquisition of a leucine zipper motif as a mechanism of antimorphy for an allele of the Drosophila Hox gene Sex combs reduced. G3-GENES GENOMES GENETICS 2014; 4:829-38. [PMID: 24622333 PMCID: PMC4025482 DOI: 10.1534/g3.114.010769] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In 1932, Müller first used the term "antimorphic" to describe mutant alleles that have an effect that is antagonistic to that of the wild-type allele from which they were derived. In a previous characterization of mutant alleles of the Drosophila melanogaster Hox gene, Sex combs reduced (Scr), we identified the missense, antimorphic allele Scr14, which is a Ser10-to-Leu change in the N-terminally located, bilateran-specific octapeptide motif. Here we propose that the cause of Scr14 antimorphy is the acquisition of a leucine zipper oligomerization motif spanning the octapeptide motif and adjacently located protostome-specific LASCY motif. Analysis of the primary and predicted secondary structures of the SCR N-terminus suggests that while the SCR+ encodes a short, α-helical region containing one putative heptad repeat, the same region in SCR14 encodes a longer, α-helical region containing two putative heptad repeats. In addition, in vitro cross-linking assays demonstrated strong oligomerization of SCR14 but not SCR+. For in vivo sex comb formation, we observed reciprocal inhibition of endogenous SCR+ and SCR14 activity by ectopic expression of truncated SCR14 and SCR+ peptides, respectively. The acquisition of an oligomerization domain in SCR14 presents a novel mechanism of antimorphy relative to the dominant negative mechanism, which maintains oligomerization between the wild-type and mutant protein subunits.
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20
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Wang W, Tindell N, Yan S, Yoder JH. Homeotic functions of the Teashirt transcription factor during adult Drosophila development. Biol Open 2012; 2:18-29. [PMID: 23336073 PMCID: PMC3545265 DOI: 10.1242/bio.20122915] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 09/24/2012] [Indexed: 12/31/2022] Open
Abstract
During Drosophila development region-specific regulation of target genes by Hox proteins is modulated by genetic interactions with various cofactors and genetic collaborators. During embryogenesis one such modulator of Hox target specificity is the zinc-finger transcription factor Teashirt (Tsh) that is expressed in the developing trunk and cooperatively functions with trunk-specific Hox proteins to promote appropriate segment fate. This embryonic function of Tsh is characterized as homeotic since loss of embryonic Tsh activity leads to transformation of trunk segments toward head identity. In addition to this embryonic homeotic role, Tsh also performs vital Hox-independent functions through patterning numerous embryonic, larval and adult structures. Here we address whether the homeotic function of Tsh is maintained throughout development by investigating its contribution to patterning the adult abdomen. We show that Tsh is expressed throughout the developing abdomen and that this expression is dependent on the three Bithorax Hox proteins Ultrabithorax, Abdominal-A and Abdominal-B. Conditional reduction of Tsh activity during pupation reveals broad homeotic roles for this transcription factor throughout the adult abdomen. Additionally we show that, as during embryogenesis, the tsh paralog tiptop (tio) plays a partially redundant role in this homeotic activity.
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Affiliation(s)
- Wei Wang
- Department of Biological Sciences, Box 870344, University of Alabama , Tuscaloosa, AL 35487 , USA
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