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Chen T, Jia Y, Chen J, Qi G. Comparative transcriptome analysis of whiteflies raised on cotton leaf curl Multan virus-infected cotton plants. Front Vet Sci 2024; 11:1417590. [PMID: 39263677 PMCID: PMC11389618 DOI: 10.3389/fvets.2024.1417590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/29/2024] [Indexed: 09/13/2024] Open
Abstract
Cotton leaf curl Multan virus (CLCuMuV), a serious viral disease causative agent in cotton plants in South Asia, is transmitted by the Bemisia tabaci cryptic species complex in a persistent circulative manner. A previous study indicated that Asia II-7 whiteflies could transmit CLCuMuV, while Mediterranean (MED) whiteflies failed to transmit CLCuMuV. However, little is known about the genes involved in this process. In this study, Asia II-7 and MED B. tabaci were utilized to determine transcriptomic responses after 48 h of acquisition access periods (AAPs). Result of Illumina sequencing revealed that, 14,213 and 8,986 differentially expressed genes (DEGs) were identified. Furthermore, DEGs related to the immune system and metabolism of Asia II-7 and MED in response to CLCuMuV-infected plants were identified and analyzed using Gene Ontologies (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the number of related DEGs in MED was lower than that of Asia II-7. The most abundant groups of DEGs between both viruliferous and aviruliferous whitefly species were the zf-C2H2 family of transcription factors (TFs). Notably, in comparison to viruliferous MED, Asia II-7 exhibited more DEGs related to cathepsin biosynthesis. Overall, this study provides the basic information for investigating the molecular mechanism of how begomoviruses affect B. tabaci metabolism and immune response either as vector cryptic species or non-vector species.
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Affiliation(s)
- Ting Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection /Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yanbo Jia
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection /Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jie Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection /Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guojun Qi
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection /Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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2
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Hannon CE, Eisen MB. Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors. eLife 2024; 12:RP88221. [PMID: 38275292 PMCID: PMC10945700 DOI: 10.7554/elife.88221] [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] [Indexed: 01/27/2024] Open
Abstract
Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the early Drosophila embryo. A nearly ubiquitous feature of eukaryotic transcription factors is that they contain intrinsically disordered regions (IDRs) that often arise from low complexity amino acid sequences within the protein. It has been proposed that IDRs within transcription factors drive co-localization of transcriptional machinery and target genes into high-concentration clusters within nuclei. Here, we test that hypothesis directly, by conducting a broad survey of the subnuclear localization of IDRs derived from transcription factors. Using a novel algorithm to identify IDRs in the Drosophila proteome, we generated a library of IDRs from transcription factors expressed in the early Drosophila embryo. We used this library to perform a high-throughput imaging screen in Drosophila Schneider-2 (S2) cells. We found that while subnuclear clustering does not occur when the majority of IDRs are expressed alone, it is frequently seen in full-length transcription factors. These results are consistent in live Drosophila embryos, suggesting that IDRs are insufficient to drive the subnuclear clustering behavior of transcription factors. Furthermore, the clustering of transcription factors in living embryos was unaffected by the deletion of IDR sequences. Our results demonstrate that IDRs are unlikely to be the primary molecular drivers of the clustering observed during transcription, suggesting a more complex and nuanced role for these disordered protein sequences.
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Affiliation(s)
- Colleen E Hannon
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Michael B Eisen
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
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3
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Ghosh S, Srinivasan R, Ghanim M. A C2H2 zinc finger transcription factor of the whitefly Bemisia tabaci interacts with the capsid proteins of begomoviruses and inhibits virus retention. INSECT MOLECULAR BIOLOGY 2023; 32:240-250. [PMID: 36571165 DOI: 10.1111/imb.12827] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/19/2022] [Indexed: 05/15/2023]
Abstract
Begomoviruses are a group of ssDNA viruses exclusively transmitted by the whitefly Bemisia tabaci and constrain vegetable production in the old and new worlds. Although multiple molecular determinants governing the transmission of begomoviruses by whiteflies have been unravelled, factors critical for transmission majorly remain unknown. In this study, a whitefly C2H2 zinc finger (ZF) protein, 100% identical to the vascular endothelial ZF-like gene (vezf) protein was confirmed to interact with the CP of both old- and new-world begomoviruses. This was achieved by a yeast two-hybrid (Y2H) system screening of a whitefly cDNA library using capsid protein (CP) of TYLCV as a bait. In silico annotation of vezf protein revealed that it contains a N-terminal ZF-associated domain (ZAD) alongside multiple C2H2 ZF domains on the C-terminal end. ZAD-ZF proteins form the most abundant class of transcription factors within insects. Herein, we validated the interaction of vezf with four diverse begomoviruses and its functional role in begomovirus transmission. Silencing of the vezf gene of B. tabaci led to increased retention of three diverse begomoviruses tested. Vezf is the first insect transcription factor identified to interact with plant viruses and can be crucial to understand the possible mechanisms by which plant viruses modulate transcription of their insect vectors during transmission.
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Affiliation(s)
- Saptarshi Ghosh
- Department of Entomology, Volcani Center, Rishon Lezion, Israel
- Department of Entomology, University of Georgia, Griffin, Georgia, USA
| | | | - Murad Ghanim
- Department of Entomology, Volcani Center, Rishon Lezion, Israel
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4
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Li M, Kasan K, Saha Z, Yoon Y, Schmidt-Ott U. Twenty-seven ZAD-ZNF genes of Drosophila melanogaster are orthologous to the embryo polarity determining mosquito gene cucoid. PLoS One 2023; 18:e0274716. [PMID: 36595500 PMCID: PMC9810180 DOI: 10.1371/journal.pone.0274716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/16/2022] [Indexed: 01/04/2023] Open
Abstract
The C2H2 zinc finger gene cucoid establishes anterior-posterior (AP) polarity in the early embryo of culicine mosquitoes. This gene is unrelated to genes that establish embryo polarity in other fly species (Diptera), such as the homeobox gene bicoid, which serves this function in the traditional model organism Drosophila melanogaster. The cucoid gene is a conserved single copy gene across lower dipterans but nothing is known about its function in other species, and its evolution in higher dipterans, including Drosophila, is unresolved. We found that cucoid is a member of the ZAD-containing C2H2 zinc finger (ZAD-ZNF) gene family and is orthologous to 27 of the 91 members of this family in D. melanogaster, including M1BP, ranshi, ouib, nom, zaf1, odj, Nnk, trem, Zif, and eighteen uncharacterized genes. Available knowledge of the functions of cucoid orthologs in Drosophila melanogaster suggest that the progenitor of this lineage specific expansion may have played a role in regulating chromatin. We also describe many aspects of the gene duplication history of cucoid in the brachyceran lineage of D. melanogaster, thereby providing a framework for predicting potential redundancies among these genes in D. melanogaster.
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Affiliation(s)
- Muzi Li
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Koray Kasan
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Zinnia Saha
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Yoseop Yoon
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Urs Schmidt-Ott
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
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5
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Shapiro-Kulnane L, Bautista O, Salz HK. An RNA-interference screen in Drosophila to identify ZAD-containing C2H2 zinc finger genes that function in female germ cells. G3-GENES GENOMES GENETICS 2021; 11:6025177. [PMID: 33561227 PMCID: PMC8022714 DOI: 10.1093/g3journal/jkaa016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/14/2020] [Indexed: 11/24/2022]
Abstract
The zinc finger-associated domain (ZAD) is present in over 90 C2H2 zinc finger (ZNF) proteins. Despite their abundance, only a few ZAD-ZNF genes have been characterized to date. Here, we systematically analyze the function of 68 ZAD-ZNF genes in Drosophila female germ cells by performing an in vivo RNA-interference screen. We identified eight ZAD-ZNF genes required for oogenesis, and based on further characterization of the knockdown phenotypes, we uncovered defects broadly consistent with functions in germ cell specification and/or survival, early differentiation, and egg chamber maturation. These results provide a candidate pool for future studies aimed at functionalization of this large but poorly characterized gene family.
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Affiliation(s)
- Laura Shapiro-Kulnane
- Department of Genetics and Genome Sciences, Case Western Reserve University, School of Medicine, 10900 Euclid Ave. Cleveland, OH 44106, USA
| | - Oscar Bautista
- Department of Genetics and Genome Sciences, Case Western Reserve University, School of Medicine, 10900 Euclid Ave. Cleveland, OH 44106, USA
| | - Helen K Salz
- Department of Genetics and Genome Sciences, Case Western Reserve University, School of Medicine, 10900 Euclid Ave. Cleveland, OH 44106, USA
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6
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Peterson SC, Samuelson KB, Hanlon SL. Multi-Scale Organization of the Drosophila melanogaster Genome. Genes (Basel) 2021; 12:817. [PMID: 34071789 PMCID: PMC8228293 DOI: 10.3390/genes12060817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
Interphase chromatin, despite its appearance, is a highly organized framework of loops and bends. Chromosomes are folded into topologically associating domains, or TADs, and each chromosome and its homolog occupy a distinct territory within the nucleus. In Drosophila, genome organization is exceptional because homologous chromosome pairing is in both germline and somatic tissues, which promote interhomolog interactions such as transvection that can affect gene expression in trans. In this review, we focus on what is known about genome organization in Drosophila and discuss it from TADs to territory. We start by examining intrachromosomal organization at the sub-chromosome level into TADs, followed by a comprehensive analysis of the known proteins that play a key role in TAD formation and boundary establishment. We then zoom out to examine interhomolog interactions such as pairing and transvection that are abundant in Drosophila but rare in other model systems. Finally, we discuss chromosome territories that form within the nucleus, resulting in a complete picture of the multi-scale organization of the Drosophila genome.
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Affiliation(s)
| | | | - Stacey L. Hanlon
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (S.C.P.); (K.B.S.)
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7
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Kasinathan B, Colmenares SU, McConnell H, Young JM, Karpen GH, Malik HS. Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila. eLife 2020; 9:e63368. [PMID: 33169670 PMCID: PMC7655104 DOI: 10.7554/elife.63368] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
Contrary to dogma, evolutionarily young and dynamic genes can encode essential functions. We find that evolutionarily dynamic ZAD-ZNF genes, which encode the most abundant class of insect transcription factors, are more likely to encode essential functions in Drosophila melanogaster than ancient, conserved ZAD-ZNF genes. We focus on the Nicknack ZAD-ZNF gene, which is evolutionarily young, poorly retained in Drosophila species, and evolves under strong positive selection. Yet we find that it is necessary for larval development in D. melanogaster. We show that Nicknack encodes a heterochromatin-localizing protein like its paralog Oddjob, also an evolutionarily dynamic yet essential ZAD-ZNF gene. We find that the divergent D. simulans Nicknack protein can still localize to D. melanogaster heterochromatin and rescue viability of female but not male Nicknack-null D. melanogaster. Our findings suggest that innovation for rapidly changing heterochromatin functions might generally explain the essentiality of many evolutionarily dynamic ZAD-ZNF genes in insects.
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Affiliation(s)
- Bhavatharini Kasinathan
- Medical Scientist Training Program, University of Washington School of MedicineSeattleUnited States
- Molecular and Cellular Biology Graduate program, University of Washington School of MedicineSeattleUnited States
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Serafin U Colmenares
- Biological Systems and Engineering Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California at BerkeleyBerkeleyUnited States
- Innovative Genomics InstituteBerkeleyUnited States
| | - Hannah McConnell
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Gary H Karpen
- Biological Systems and Engineering Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California at BerkeleyBerkeleyUnited States
- Innovative Genomics InstituteBerkeleyUnited States
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research CenterSeattleUnited States
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8
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Li C, Zhang H, Gao R, Zuo W, Liu Y, Hu H, Luan Y, Lu C, Tong X, Dai F. Identification and effect of Zf-AD-containing C2H2 zinc finger genes on BmNPV replication in the silkworm (Bombyx mori). PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 170:104678. [PMID: 32980066 DOI: 10.1016/j.pestbp.2020.104678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/31/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Zf-AD-containing C2H2 zinc -finger genes (ZAD) are uniquely present and have lineage-specific expansion in arthropods. Arthropods are also the hosts of Baculoviruses. We studied the possible relationship between the lineage-specific expansion of ZAD genes and arthropod-Baculovirus co-evolution. We used the silkworm (Bombyx mori) as a model. We identified 73 ZAD genes (BmZAD) in the silkworm. Sequence-based similarity analysis showed that nine clusters involving 28 BmZADs may have undergone species-specific expansion in the silkworm. Expression pattern analysis showed that the BmZADs were divided into five groups. Group I comprised 10 genes with high expression in multiple tissues, suggesting that BmZADs may play roles in the development of various tissues. We identified six BmZADs that could be induced by the Nucleopolyhedrovirus (BmNPV). Among them, BmZAD69 expression is capable of responding to BmNPV infection, and the ZAD domain is indispensable for the function of BmZAD69 in BmNPV replication. We also detected a 3 bp deletion at 1.7 kb upstream of BmZAD69, which may make it more sensitive to BmNPV infection, and thus elevate the BmNPV resistance in Qiufeng_N, a strain with strong virus resistance. These data suggest that BmZADs may be involved in BmNPV infection and that ZAD genes may play a role in arthropod-Baculovirus co-evolution.
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Affiliation(s)
- Chunlin Li
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Hao Zhang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Rui Gao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Weidong Zuo
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Yanyu Liu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Hai Hu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Yue Luan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing 400715, China.
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing 400715, China.
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9
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Dong Y, Avva SVSP, Maharjan M, Jacobi J, Hart CM. Promoter-Proximal Chromatin Domain Insulator Protein BEAF Mediates Local and Long-Range Communication with a Transcription Factor and Directly Activates a Housekeeping Promoter in Drosophila. Genetics 2020; 215:89-101. [PMID: 32179582 PMCID: PMC7198264 DOI: 10.1534/genetics.120.303144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/12/2020] [Indexed: 12/23/2022] Open
Abstract
BEAF (Boundary Element-Associated Factor) was originally identified as a Drosophila melanogaster chromatin domain insulator-binding protein, suggesting a role in gene regulation through chromatin organization and dynamics. Genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, suggesting a role in promoter function. This would be a nontraditional role for an insulator-binding protein. To gain insight into molecular mechanisms of BEAF function, we identified interacting proteins using yeast two-hybrid assays. Here, we focus on the transcription factor Serendipity δ (Sry-δ). Interactions were confirmed in pull-down experiments using bacterially expressed proteins, by bimolecular fluorescence complementation, and in a genetic assay in transgenic flies. Sry-δ interacted with promoter-proximal BEAF both when bound to DNA adjacent to BEAF or > 2-kb upstream to activate a reporter gene in transient transfection experiments. The interaction between BEAF and Sry-δ was detected using both a minimal developmental promoter (y) and a housekeeping promoter (RpS12), while BEAF alone strongly activated the housekeeping promoter. These two functions for BEAF implicate it in playing a direct role in gene regulation at hundreds of BEAF-associated promoters.
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Affiliation(s)
- Yuankai Dong
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - S V Satya Prakash Avva
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Mukesh Maharjan
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Janice Jacobi
- Hayward Genetics Center, Tulane University, New Orleans, Louisiana 70112
| | - Craig M Hart
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
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10
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Nazario-Yepiz NO, Riesgo-Escovar JR. piragua encodes a zinc finger protein required for development in Drosophila. Mech Dev 2016; 144:171-181. [PMID: 28011160 DOI: 10.1016/j.mod.2016.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 11/07/2016] [Accepted: 12/19/2016] [Indexed: 02/06/2023]
Abstract
We isolated and characterized embryonic lethal mutations in piragua (prg). The prg locus encodes a protein with an amino terminus Zinc Finger-Associated-Domain (ZAD) and nine C2H2 zinc fingers (ZF). prg mRNA and protein expression during embryogenesis is dynamic with widespread maternal contribution, and subsequent expression in epithelial precursors. About a quarter of prg mutant embryos do not develop cuticle, and from those that do a small fraction have cuticular defects. Roughly half of prg mutants die during embryogenesis. prg mutants have an extended phenocritical period encompassing embryogenesis and first instar larval stage, since the other half of prg mutants die as first or second instar larvae. During dorsal closure, time-lapse high-resolution imaging shows defects arising out of sluggishness in closure, resolving at times in failures of closure. prg is expressed in imaginal discs, and is required for imaginal development. prg was identified in imaginal tissue in a cell super competition screen, together with other genes, like flower. We find that flower mutations are also embryonic lethal with a similar phenocritical period and strong embryonic mutant phenotypes (head involution defects, primarily). The two loci interact genetically in the embryo, as they increase embryonic mortality to close to 90% with the same embryonic phenotypes (dorsal closure and head involution defects, plus lack of cuticle). Mutant prg clones generated in developing dorsal thorax and eye imaginal tissue have strong developmental defects (lack of bristles and ommatidial malformations). prg is required in several developmental morphogenetic processes.
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Affiliation(s)
- Nestor O Nazario-Yepiz
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, UNAM, Campus UNAM Juriquilla, Boulevard Juriquilla 3001, Querétaro, Querétaro c.p. 76230, Mexico
| | - Juan R Riesgo-Escovar
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, UNAM, Campus UNAM Juriquilla, Boulevard Juriquilla 3001, Querétaro, Querétaro c.p. 76230, Mexico.
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11
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Zolotarev N, Fedotova A, Kyrchanova O, Bonchuk A, Penin AA, Lando AS, Eliseeva IA, Kulakovskiy IV, Maksimenko O, Georgiev P. Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila. Nucleic Acids Res 2016; 44:7228-41. [PMID: 27137890 PMCID: PMC5009728 DOI: 10.1093/nar/gkw371] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/23/2016] [Indexed: 12/18/2022] Open
Abstract
According to recent models, as yet poorly studied architectural proteins appear to be required for local regulation of enhancer-promoter interactions, as well as for global chromosome organization. Transcription factors ZIPIC, Pita and Zw5 belong to the class of chromatin insulator proteins and preferentially bind to promoters near the TSS and extensively colocalize with cohesin and condensin complexes. ZIPIC, Pita and Zw5 are structurally similar in containing the N-terminal zinc finger-associated domain (ZAD) and different numbers of C2H2-type zinc fingers at the C-terminus. Here we have shown that the ZAD domains of ZIPIC, Pita and Zw5 form homodimers. In Drosophila transgenic lines, these proteins are able to support long-distance interaction between GAL4 activator and the reporter gene promoter. However, no functional interaction between binding sites for different proteins has been revealed, suggesting that such interactions are highly specific. ZIPIC facilitates long-distance stimulation of the reporter gene by GAL4 activator in yeast model system. Many of the genomic binding sites of ZIPIC, Pita and Zw5 are located at the boundaries of topologically associated domains (TADs). Thus, ZAD-containing zinc-finger proteins can be attributed to the class of architectural proteins.
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Affiliation(s)
- Nikolay Zolotarev
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, Moscow 119334, Russia
| | - Anna Fedotova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, Moscow 119334, Russia
| | - Olga Kyrchanova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, Moscow 119334, Russia
| | - Artem Bonchuk
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, Moscow 119334, Russia
| | - Aleksey A Penin
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia; Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051 Russia; Department of Genetics, Faculty of Biology, Moscow State University, Moscow 119991, Russia
| | - Andrey S Lando
- Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, Moscow, GSP-1, 119991, Russia
| | - Irina A Eliseeva
- Group of Protein Biosynthesis Regulation, Institute of Protein Research, Institutskaya str. 4, Pushchino 142290, Russia
| | - Ivan V Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, Moscow, GSP-1, 119991, Russia Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova str. 32, Moscow, GSP-1, 119991, Russia
| | - Oksana Maksimenko
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, Moscow 119334, Russia
| | - Pavel Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, Moscow 119334, Russia
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12
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Komura-Kawa T, Hirota K, Shimada-Niwa Y, Yamauchi R, Shimell M, Shinoda T, Fukamizu A, O’Connor MB, Niwa R. The Drosophila Zinc Finger Transcription Factor Ouija Board Controls Ecdysteroid Biosynthesis through Specific Regulation of spookier. PLoS Genet 2015; 11:e1005712. [PMID: 26658797 PMCID: PMC4684333 DOI: 10.1371/journal.pgen.1005712] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 11/08/2015] [Indexed: 01/01/2023] Open
Abstract
Steroid hormones are crucial for many biological events in multicellular organisms. In insects, the principal steroid hormones are ecdysteroids, which play essential roles in regulating molting and metamorphosis. During larval and pupal development, ecdysteroids are synthesized in the prothoracic gland (PG) from dietary cholesterol via a series of hydroxylation and oxidation steps. The expression of all but one of the known ecdysteroid biosynthetic enzymes is restricted to the PG, but the transcriptional regulatory networks responsible for generating such exquisite tissue-specific regulation is only beginning to be elucidated. Here, we report identification and characterization of the C2H2-type zinc finger transcription factor Ouija board (Ouib) necessary for ecdysteroid production in the PG in the fruit fly Drosophila melanogaster. Expression of ouib is predominantly limited to the PG, and genetic null mutants of ouib result in larval developmental arrest that can be rescued by administrating an active ecdysteroid. Interestingly, ouib mutant animals exhibit a strong reduction in the expression of one ecdysteroid biosynthetic enzyme, spookier. Using a cell culture-based luciferase reporter assay, Ouib protein stimulates transcription of spok by binding to a specific ~15 bp response element in the spok PG enhancer element. Most remarkable, the developmental arrest phenotype of ouib mutants is rescued by over-expression of a functionally-equivalent paralog of spookier. These observations imply that the main biological function of Ouib is to specifically regulate spookier transcription during Drosophila development. Steroid hormones are crucial for development and reproduction in multicellular organisms. The spatially-restricted expression of almost all steroid biosynthesis genes is key to the specialization of steroid producing cells. In the last decade, insects have become the focus for research on the biosynthesis of the principal steroid hormones, ecdysteroids. However, the transcriptional regulatory mechanisms controlling the ecdysteroid biosynthesis genes are largely unknown. Here we show that a novel zinc finger transcription factor Ouija board (Ouib) is essential for activating the expression of one ecdysteroid biosynthesis gene, spookier, in the ecdysteroid producing cells. Ouib is the first invertebrate transcription factor that is predominantly expressed in the steroidogenic organs and essential for development via inducing expression of the steroidogenic gene. In addition, this is the first report showing the catalytic step-specific control of steroid hormone biosynthesis through transcriptional regulation.
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Affiliation(s)
- Tatsuya Komura-Kawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiko Hirota
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuko Shimada-Niwa
- Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Rieko Yamauchi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - MaryJane Shimell
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Tetsuro Shinoda
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Akiyoshi Fukamizu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Michael B. O’Connor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ryusuke Niwa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- * E-mail:
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