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Abstract
Metabolic state is a potent modulator of sleep and circadian behavior, and animals acutely modulate their sleep in accordance with internal energy stores and food availability. Across phyla, hormones secreted from adipose tissue act in the brain to control neural physiology and behavior to modulate sleep and metabolic state. Growing evidence suggests the fat body is a critical regulator of complex behaviors, but little is known about the genes that function within the fat body to regulate sleep. To identify molecular factors functioning in non-neuronal tissues to regulate sleep, we performed an RNAi screen selectively knocking down genes in the fat body. We found that knockdown of Phosphoribosylformylglycinamidine synthase/Pfas (Ade2), a highly conserved gene involved the biosynthesis of purines, sleep regulation and energy stores. Flies heterozygous for multiple Ade2 mutations are also short sleepers and this effect is partially rescued by restoring Ade2 to the Drosophila fat body. Targeted knockdown of Ade2 in the fat body does not alter arousal threshold or the homeostatic response to sleep deprivation, suggesting a specific role in modulating baseline sleep duration. Together, these findings suggest Ade2 functions within the fat body to promote both sleep and energy storage, providing a functional link between these processes.
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2
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Tue NT, Yoshioka Y, Mizoguchi M, Yoshida H, Zurita M, Yamaguchi M. DREF plays multiple roles during Drosophila development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:705-712. [PMID: 28363744 DOI: 10.1016/j.bbagrm.2017.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 12/31/2022]
Abstract
DREF was originally identified as a transcription factor that coordinately regulates the expression of DNA replication- and proliferation-related genes in Drosophila. Subsequent studies demonstrated that DREF is involved in tumor suppressor pathways including p53 and Hippo signaling. DREF also regulates the expression of genes encoding components of the JNK and EGFR pathways during Drosophila development. DREF itself is under the control of the TOR pathway during cell and tissue growth responding to nutrition. Recent studies revealed that DREF plays a role in chromatin organization including insulator function, chromatin remodeling, and telomere maintenance. DREF is also involved in the regulation of genes related to mitochondrial biogenesis, linking it to cellular proliferation. Thus, DREF is now emerging as not only a transcription factor, but also a multi-functional protein. In this review, we summarize current advances in studies on the novel functions of Drosophila DREF.
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Affiliation(s)
- Nguyen Trong Tue
- Gene-Protein Research Center, Hanoi Medical University, Hanoi, Vietnam
| | - Yasuhide Yoshioka
- Faculty of Science and Engineering, Setsunan University, Osaka, Japan
| | - Megumi Mizoguchi
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hideki Yoshida
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; The Center for Advanced Insect Research, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Mario Zurita
- Departamento de Genética del Desarrollo Y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62250 Cuernavaca, Mor., Mexico
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; The Center for Advanced Insect Research, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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3
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The Hippo pathway as a target of the Drosophila DRE/DREF transcriptional regulatory pathway. Sci Rep 2014; 4:7196. [PMID: 25424907 PMCID: PMC4244634 DOI: 10.1038/srep07196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/04/2014] [Indexed: 01/08/2023] Open
Abstract
The DRE/DREF transcriptional regulatory system has been demonstrated to activate a wide variety of genes with various functions. In Drosophila, the Hippo pathway is known to suppress cell proliferation by inducing apoptosis and cell cycle arrest through inactivation of Yorkie, a transcription co-activator. In the present study, we found that half dose reduction of the hippo (hpo) gene induces ectopic DNA synthesis in eye discs that is suppressed by overexpression of DREF. Half reduction of the hpo gene dose reduced apoptosis in DREF-overexpressing flies. Consistent with these observations, overexpression of DREF increased the levels of hpo and phosphorylated Yorkie in eye discs. Interestingly, the diap1-lacZ reporter was seen to be significantly decreased by overexpression of DREF. Luciferase reporter assays in cultured S2 cells revealed that one of two DREs identified in the hpo gene promoter region was responsible for promoter activity in S2 cells. Furthermore, endogenous hpo mRNA was reduced in DREF knockdown S2 cells, and chromatin immnunoprecipitation assays with anti-DREF antibodies proved that DREF binds specifically to the hpo gene promoter region containing DREs in vivo. Together, these results indicate that the DRE/DREF pathway is required for transcriptional activation of the hpo gene to positively control Hippo pathways.
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4
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Yanai H, Yoshioka Y, Yoshida H, Nakao Y, Plessis A, Yamaguchi M. Drosophila myeloid leukemia factor acts with DREF to activate the JNK signaling pathway. Oncogenesis 2014; 3:e98. [PMID: 24752236 PMCID: PMC4007195 DOI: 10.1038/oncsis.2014.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/27/2014] [Accepted: 03/03/2014] [Indexed: 12/29/2022] Open
Abstract
Drosophila myelodysplasia/myeloid leukemia factor (dMLF), a homolog of human MLF1, oncogene was first identified by yeast two-hybrid screen using the DNA replication-related element-binding factor (DREF) as bait. DREF is a transcription factor that regulates proliferation-related genes in Drosophila. It is known that overexpression of dMLF in the wing imaginal discs through the engrailed-GAL4 driver causes an atrophied wing phenotype associated with the induction of apoptosis. However, the precise mechanisms involved have yet to be clarified. Here, we found the atrophied phenotype to be suppressed by loss-of-function mutation of Drosophila Jun N-terminal kinase (JNK), basket (bsk). Overexpression of dMLF induced ectopic JNK activation in the wing disc monitored with the puckered-lacZ reporter line, resulting in induction of apoptosis. The DREF-binding consensus DRE sequence could be shown to exist in the bsk promoter. Chromatin immunoprecipitation assays in S2 cells with anti-dMLF IgG and quantitative real-time PCR revealed that dMLF binds specifically to the bsk promoter region containing the DRE sequence. Furthermore, using a transient luciferase expression assay, we provide evidence that knockdown of dMLF reduced bsk gene promoter activity in S2 cells. Finally, we show that dMLF interacts with DREF in vivo. Altogether, these data indicate that dMLF acts with DREF to stimulate the bsk promoter and consequently activates the JNK pathway to promote apoptosis.
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Affiliation(s)
- H Yanai
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | - Y Yoshioka
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | - H Yoshida
- 1] Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan [2] Insect Biomedical Research Center, Kyoto Institute of Technology, Kyoto, Japan
| | - Y Nakao
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | - A Plessis
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - M Yamaguchi
- 1] Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan [2] Insect Biomedical Research Center, Kyoto Institute of Technology, Kyoto, Japan
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5
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Kawamori A, Shimaji K, Yamaguchi M. Control of e2f1 and PCNA by Drosophila transcription factor DREF. Genesis 2013; 51:741-50. [PMID: 23907762 DOI: 10.1002/dvg.22419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 07/19/2013] [Accepted: 07/24/2013] [Indexed: 12/26/2022]
Abstract
DREF (DNA replication-related element-binding factor), a zinc finger type transcription factor required for proper cell cycle progression in both mitotic and endocycling cells, is a positive regulator of E2F1, an important transcription factor which regulates genes related to the S-phase of the cell cycle. DREF and E2F1 regulate similar sets of replication-related genes, including proliferating cell nuclear antigen (PCNA), and play roles in the G1 to S phase transition. However, the relationships between dref and e2f1 or PCNA during development are poorly understood. Here, we provided evidence for novel control of e2f1 and PCNA involving DREF in endocycling cells. Somatic clone analysis demonstrated that dref knockdown stabilized E2F1 expression at posttranscriptional levels in endocycling salivary gland cells. Similarly, PCNA expression was up-regulated in the endocycling salivary gland cells. Genetic interaction analysis indicated that the endoreplication defects are partly caused via possible enhancement of E2F1 activity. From these results and previous reports, we conclude that regulation of e2f1 and PCNA by DREF in vivo is complex and the regulation mechanism may differ with the tissue and/or positions in the tissue.
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Affiliation(s)
- Akihito Kawamori
- Department of Applied Biology and Insect Biomedical Research Center, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan
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6
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Transcriptional regulation of the purine de novo synthesis gene Prat in Drosophila melanogaster. Gene 2013; 518:280-6. [DOI: 10.1016/j.gene.2013.01.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 11/18/2022]
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7
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Abstract
The regulation of organ size is a long-standing problem in animal development. Studies in this area have shown that organ-intrinsic patterning morphogens influence organ size, guiding growth in accordance with positional information. However, organ-extrinsic humoral factors such as insulin also affect organ size, synchronizing growth with nutrient levels. Proliferating cells must integrate instructions from morphogens with those from nutrition so that growth proceeds as a function of both inputs. Coordinating cell proliferation with morphogens and nutrients ensures organs scale appropriately with body size, but the basis of this coordination is unclear. Here, the problem is illustrated using the Drosophila wing--a paradigm for organ growth and size control--and a potential solution suggested.
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Affiliation(s)
- Joseph Parker
- Department of Genetics and Development, Columbia University College of Physicians and Surgeons, 701 West 168th Street, New York, NY 10032, USA.
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8
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O'Keefe DD, Edgar BA, Saucedo LJ. EndoGI modulates Notch signaling and axon guidance in Drosophila. Mech Dev 2010; 128:59-70. [PMID: 21055464 DOI: 10.1016/j.mod.2010.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 10/22/2010] [Accepted: 10/28/2010] [Indexed: 11/29/2022]
Abstract
Signaling through the Notch receptor has dramatically different effects depending on cell type and developmental timing. While a myriad of biological systems affected by Notch have been described, the molecular mechanisms by which a generic Notch signal is translated into a cell-type-specific output are less clear. Canonically, the Notch intracellular domain (NICD) translocates into the nucleus upon ligand binding to transcriptionally regulate target genes. In order to generate specificity, therefore, additional factors must exist that modulate NICD activity. Here we describe a novel regulator of the Notch pathway, Endonuclease GI (EndoGI). EndoGI localizes to the nucleus of most cells and activates Notch signaling when overexpressed. In the absence of endoGI, mutant animals are viable, but uncoordinated as motor neurons fail to innervate their appropriate muscle targets. Our data is therefore consistent with EndoGI functioning as a positive regulator of the Notch signaling pathway, playing a critical role during axon guidance of motor neurons.
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Affiliation(s)
- David D O'Keefe
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Av., N. Seattle, WA 98109, USA
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9
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Park JS, Kim YS, Kim JG, Lee SH, Park SY, Yamaguchi M, Yoo MA. Regulation of the Drosophila p38b gene by transcription factor DREF in the adult midgut. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:510-9. [PMID: 20346429 DOI: 10.1016/j.bbagrm.2010.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 03/17/2010] [Accepted: 03/18/2010] [Indexed: 01/14/2023]
Abstract
The Drosophila midgut is an excellent model for evaluation of gene networks that regulate adult stem cell proliferation and differentiation. The Drosophila p38b (D-p38b) gene has been shown to be involved in intestinal stem cell (ISC) proliferation and differentiation in the adult midgut. Here, we report that D-p38b gene expression is regulated by DREF (DNA replication-related element binding factor) in the adult midgut. We have identified a DRE in the 5'-flanking region of the D-p38b gene and showed that DREF could bind to this DRE via a gel mobility shift assay and a ChIP assay. Base-substitution mutations of the D-p38b promoter DRE and analyses of transformants carrying D-p38b-lacZ or D-p38b-DREmut-lacZ indicated that this DRE is required for the activity of the D-p38b gene promoter. Furthermore, by using the GAL4-UAS system, we showed that DREF regulates the activity of the D-p38b gene promoter in adult ISCs and progenitors. In addition, the D-p38b knockdown phenotypes in the midgut were rescued by DREF overexpression, suggesting a functional link between these two factors. Our results suggest that the D-p38b gene is regulated by the DREF pathway and that DREF is involved in the regulation of proliferation and differentiation of Drosophila ISCs and progenitors.
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Affiliation(s)
- Joung-Sun Park
- Department of Molecular Biology, Pusan National University, Busan 609-735, Korea
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10
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C. elegans BED domain transcription factor BED-3 controls lineage-specific cell proliferation during organogenesis. Dev Biol 2009; 338:226-36. [PMID: 20005870 PMCID: PMC2862168 DOI: 10.1016/j.ydbio.2009.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 11/09/2009] [Accepted: 12/04/2009] [Indexed: 11/23/2022]
Abstract
The control of cell division is critical to organogenesis, but how this control is achieved is not fully understood. We found that mutations in bed-3, encoding a BED Zn-finger domain transcription factor, confer a phenotype where a specific set of cell divisions during vulval organogenesis is lost. Unlike general cell cycle regulators in Caenorhabditis elegans, the function of bed-3 is restricted to specific lineages. Transcriptional reporters suggest that bed-3 is expressed in a limited number of cell types including vulval cells whose divisions are affected in bed-3 mutants. A bed-3 mutation also affects the expression pattern of the cdh-3 cadherin gene in the vulva. The phenotype of bed-3 mutants is similar to the phenotype caused by mutations in cog-1 (Nkx6), a component of a gene regulatory network controlling cell type specific gene expression in the vulval lineage. These results suggest that bed-3 is a key component linking the gene regulatory network controlling cell-type specification to control of cell division during vulval organogenesis.
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11
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miR-9a prevents apoptosis during wing development by repressing Drosophila LIM-only. Dev Biol 2009; 338:63-73. [PMID: 19944676 DOI: 10.1016/j.ydbio.2009.11.025] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 11/16/2009] [Accepted: 11/19/2009] [Indexed: 12/19/2022]
Abstract
Loss of Drosophila mir-9a induces a subtle increase in sensory bristles, but a substantial loss of wing tissue. Here, we establish that the latter phenotype is largely due to ectopic apoptosis in the dorsal wing primordium, and we could rescue wing development in the absence of this microRNA by dorsal-specific inhibition of apoptosis. Such apoptosis was a consequence of de-repressing Drosophila LIM-only (dLMO), which encodes a transcriptional regulator of wing and neural development. We observed cell-autonomous elevation of endogenous dLMO and a GFP-dLMO 3'UTR sensor in mir-9a mutant wing clones, and heterozygosity for dLMO rescued the apoptosis and wing defects of mir-9a mutants. We also provide evidence that dLMO, in addition to senseless, contributes to the bristle defects of the mir-9a mutant. Unexpectedly, the upregulation of dLMO, loss of Cut, and adult wing margin defects seen with mir-9a mutant clones were not recapitulated by clonal loss of the miRNA biogenesis factors Dicer-1 or Pasha, even though these mutant conditions similarly de-repressed miR-9a and dLMO sensor transgenes. Therefore, the failure to observe a phenotype upon conditional knockout of a miRNA processing factor does not reliably indicate the lack of critical roles of miRNAs in a given setting.
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12
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Emberly E, Blattes R, Schuettengruber B, Hennion M, Jiang N, Hart CM, Käs E, Cuvier O. BEAF regulates cell-cycle genes through the controlled deposition of H3K9 methylation marks into its conserved dual-core binding sites. PLoS Biol 2009; 6:2896-910. [PMID: 19108610 PMCID: PMC2605929 DOI: 10.1371/journal.pbio.0060327] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 11/11/2008] [Indexed: 12/25/2022] Open
Abstract
Chromatin insulators/boundary elements share the ability to insulate a transgene from its chromosomal context by blocking promiscuous enhancer–promoter interactions and heterochromatin spreading. Several insulating factors target different DNA consensus sequences, defining distinct subfamilies of insulators. Whether each of these families and factors might possess unique cellular functions is of particular interest. Here, we combined chromatin immunoprecipitations and computational approaches to break down the binding signature of the Drosophila boundary element–associated factor (BEAF) subfamily. We identify a dual-core BEAF binding signature at 1,720 sites genome-wide, defined by five to six BEAF binding motifs bracketing 200 bp AT-rich nuclease-resistant spacers. Dual-cores are tightly linked to hundreds of genes highly enriched in cell-cycle and chromosome organization/segregation annotations. siRNA depletion of BEAF from cells leads to cell-cycle and chromosome segregation defects. Quantitative RT-PCR analyses in BEAF-depleted cells show that BEAF controls the expression of dual core–associated genes, including key cell-cycle and chromosome segregation regulators. beaf mutants that impair its insulating function by preventing proper interactions of BEAF complexes with the dual-cores produce similar effects in embryos. Chromatin immunoprecipitations show that BEAF regulates transcriptional activity by restricting the deposition of methylated histone H3K9 marks in dual-cores. Our results reveal a novel role for BEAF chromatin dual-cores in regulating a distinct set of genes involved in chromosome organization/segregation and the cell cycle. The genome of eukaryotes is packaged in chromatin, which consists of DNA, histones, and accessory proteins. This leads to a general repression of genes, particularly for those exposed to mostly condensed, heterochromatin regions. DNA sequences called chromatin insulators/boundary elements are able to insulate a gene from its chromosomal context by blocking promiscuous heterochromatin spreading. No common feature has been identified among the insulators/boundary elements known so far. Rather, distinct subfamilies of insulators harbor different DNA consensus sequences targeted by different DNA-binding factors, which confer their insulating activity. Determining whether distinct subfamilies possess distinct cellular functions is important for understanding genome regulation. Here, using Drosophila, we have combined computational and experimental approaches to address the function of the boundary element-associated factor (BEAF) subfamily of insulators. We identify hundreds of BEAF dual-cores that are defined by a particular arrangement of DNA sequence motifs bracketing nucleosome binding sequences, and that mark the genomic BEAF binding sites. BEAF dual-cores are close to hundreds of genes that regulate chromosome organization/segregation and the cell cycle. Since BEAF acts by restricting the deposition of repressing epigenetic histone marks, which affects the accessibility of chromatin, its depletion affects the expression of cell-cycle genes. Our data reveal a new role for BEAF in regulating the cell cycle through its binding to highly conserved chromatin dual-cores. Chromatin Dual-Cores define new potent nucleosome-associatedcis-regulatory elements that regulate the accessibility of promoters of genes controlling chromosome organization/segregation and the cell cycle.
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Affiliation(s)
- Eldon Emberly
- Physics Department, Simon Fraser University, Burnaby, British Columbia, Canada
- * To whom correspondence should be addressed. E-mail: (EE); (OC)
| | - Roxane Blattes
- CNRS, Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, UPS, France
| | - Bernd Schuettengruber
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana, United States of America
| | - Magali Hennion
- CNRS, Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, UPS, France
- Institut de Genetique Humaine, Department of Genome Dynamics, CNRS, Montpelier, France
| | - Nan Jiang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana, United States of America
| | - Craig M Hart
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana, United States of America
| | - Emmanuel Käs
- CNRS, Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, UPS, France
| | - Olivier Cuvier
- Institut de Genetique Humaine, Department of Genome Dynamics, CNRS, Montpelier, France
- * To whom correspondence should be addressed. E-mail: (EE); (OC)
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Park JS, Kim SR, Park SY, Yang DJ, Lee SH, Choi YJ, Bae MK, Yamaguchi M, Kim YS, Yoo MA. Big brain, a Drosophila homologue of mammalian aquaporin, is regulated by the DRE/DREF system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1779:789-96. [DOI: 10.1016/j.bbagrm.2008.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 07/19/2008] [Accepted: 07/28/2008] [Indexed: 11/28/2022]
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The DRE/DREF transcriptional regulatory system: a master key for cell proliferation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2007; 1779:81-9. [PMID: 18155677 DOI: 10.1016/j.bbagrm.2007.11.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Revised: 11/27/2007] [Accepted: 11/27/2007] [Indexed: 11/23/2022]
Abstract
The coordinate expression of many cell proliferation-related genes is required for the cellular shift from the resting state into the proliferating state. One regulatory factor involved in this process, the transcription regulatory factor named DREF (DNA replication-related element-binding factor) was discovered in Drosophila and later found to have orthologues in other species including human. Drosophila DREF is a homo-dimer of a polypeptide of 709 amino acid residues, and shares about 22% identity in its amino acid sequence with the human homolog of 694 amino acid residues. The Drosophila DREF homo-dimer binds specifically to the DRE sequence (5'-TATCGATA) in the promoters of many DNA replication/ cell proliferation-related genes to activate their transcription, and the N-terminal region of DREF carries a domain for specific DRE-binding and homo-dimer formation. Ectopic expression of DREF in eye imaginal discs induces abnormal DNA synthesis, apoptosis and failure to differentiate. Conversely, expression of the dominant negative N-terminal region in larval salivary glands reduces endo-replication. Furthermore, RNA interference-mediated knockdown of DREF in vivo demonstrated its requirement for normal progression through the cell cycle and consequently for growth of imaginal discs and the endoreplicating organs. Both Drosophila and human DREF's interact genetically and physically with regulatory factors related to chromatin structures, suggesting that DREF activates the expression of proliferation-related genes through modification of the 3-D conformation of DNA. A search of the Drosophila genome database identified about 150 genes carrying DRE sequences in their promoter regions, many of which are related to reactions required for cell proliferation such as DNA replication, transcriptional regulation, cell cycle regulation, growth signal transduction and protein metabolism. Thus, DREF appears to be a master key-like factor for cell proliferation. Several differentiation-related transcription factors containing homeodomains down-regulate the function or expression of DREF by distinct mechanisms, suggesting a differentiation-coupled repression of cell proliferation via the DRE/DREF system.
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15
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Kim YS, Shin MJ, Yang DJ, Yamaguchi M, Park SY, Yoo MA. Transcriptional regulation of the Drosophila ANT gene by the DRE/DREF system. Genes Cells 2007; 12:569-79. [PMID: 17535248 DOI: 10.1111/j.1365-2443.2007.01075.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenine nucleotide translocase (ANT) is a crucial component in the maintenance of cellular energy homeostasis, as well as in the formation of the mitochondrial permeability transition pores. However, the molecular mechanisms regulating the expression of the ANT gene are poorly understood. In this study, we have identified three DNA replication-related elements (DRE; 5'-TATCGATA) in the 5'-flanking region of the Drosophila ANT (dANT) gene. Gel-mobility shift analyses revealed that all three of the DREs were recognized by the DRE-binding factor (DREF). The site-directed mutagenesis of these DRE sites induces a considerable reduction in the activity of the dANT gene promoter in vitro. Analyses with transgenic flies harboring a dANT-lacZ fusion gene bearing the wild-type or mutant DRE sites showed that the DRE sites were required for the expression of dANT in vivo. We determined that the over-expression or knockdown of DREF exerts a regulatory effect on the activity of the dANT promoter. In addition, we observed the collapse of mitochondrial membrane potential in the eye imaginal discs in which DREF was over-expressed. These results show that DRE/DREF is a crucial regulator of dANT gene expression, and also suggest the possibility that cross-talk may occur between the DRE/DREF system and mitochondrial functioning.
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Affiliation(s)
- Young Shin Kim
- Research Institute of Genetic Engineering, Pusan National University, Busan 609-735, Korea
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16
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Anuradha A, Annadurai RS, Shashidhara LS. Actin cytoskeleton as a putative target of the neem limonoid Azadirachtin A. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2007; 37:627-34. [PMID: 17517339 DOI: 10.1016/j.ibmb.2007.03.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 02/28/2007] [Accepted: 03/08/2007] [Indexed: 05/15/2023]
Abstract
Limonoids isolated from the Indian neem tree (Azadirachta indica) have been gaining global acceptance in agricultural applications and in contemporary medicine for their myriad but discrete properties. However, their mode of action is still not very well understood. We have studied the mode of action of Azadirachtin A, the major limonoid of neem seed extracts, using Drosophila melanogaster as the model system. Azadirachtin A induces moderate-to-severe phenotypes in different tissues in a dose-dependent manner. At the cellular level, Azadirachtin A induces depolymerization of Actin leading to arrest of cells and subsequently apoptosis in a caspase-independent manner. Azadirachtin A-induced phenotypes were rescued by the over-expression of Cyclin E in a tissue-dependent manner. Cyclin E, which caused global rescue of Azadirachtin A-induced phenotypes, also effected rearrangement of the actin filaments. These results suggest that probably actin is a target of Azadirachtin A activity.
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Yamashita D, Sano Y, Adachi Y, Okamoto Y, Osada H, Takahashi T, Yamaguchi T, Osumi T, Hirose F. hDREF regulates cell proliferation and expression of ribosomal protein genes. Mol Cell Biol 2007; 27:2003-13. [PMID: 17220279 PMCID: PMC1820502 DOI: 10.1128/mcb.01462-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although ribosomal proteins (RPs) are essential cellular constituents in all living organisms, mechanisms underlying regulation of their gene expression in mammals remain unclear. We have established that 22 out of 79 human RP genes contain sequences similar to the human DREF (DNA replication-related element-binding factor; hDREF) binding sequence (hDRE) within 200-bp regions upstream of their transcriptional start sites. Electrophoretic gel mobility shift assays and chromatin immunoprecipitation analysis indicated that hDREF binds to hDRE-like sequences in the RP genes both in vitro and in vivo. In addition, transient luciferase assays revealed that hDRE-like sequences act as positive elements for RP gene transcription and cotransfection of an hDREF-expressing plasmid was found to stimulate RP gene promoter activity. Like that of hDREF, expression of RP genes is increased during the late G(1) to S phases, and depletion of hDREF using short hairpin RNA-mediated knockdown decreased RP gene expression and cell proliferation in normal human fibroblasts. Knockdown of the RPS6 gene also resulted in impairment of cell proliferation. These data suggest that hDREF is an important transcription factor for cell proliferation which plays roles in cell cycle-dependent regulation of a number of RP genes.
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Affiliation(s)
- Daisuke Yamashita
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
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Yamashita D, Komori H, Higuchi Y, Yamaguchi T, Osumi T, Hirose F. Human DNA replication-related element binding factor (hDREF) self-association via hATC domain is necessary for its nuclear accumulation and DNA binding. J Biol Chem 2007; 282:7563-75. [PMID: 17209048 DOI: 10.1074/jbc.m607180200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We previously demonstrated that hDREF, a human homologue of Drosophila DNA replication-related element binding factor (dDREF), is a DNA-binding protein predominantly distributed with granular structures in the nucleus. Here, glutathione S-transferase pulldown and chemical cross-linking assays showed that the carboxyl-terminal hATC domain of hDREF, highly conserved among hAT transposase family members, possesses self-association activity. Immunoprecipitation analyses demonstrated that hDREF self-associates in vivo, dependent on hATC domain. Moreover, analyses using a series of hDREF mutants carrying amino acid substitutions in the hATC domain revealed that conserved hydrophobic amino acids are essential for self-association. Immunofluorescence studies further showed that all hDREF mutants lacking self-association activity failed to accumulate in the nucleus. Self-association-defective hDREF mutants also lost association with endogenous importin beta1. Moreover, electrophoretic gel-mobility shift assays revealed that the mutations completely abolished the DNA binding activity of hDREF. These results suggest that self-association of hDREF via the hATC domain is necessary for its nuclear accumulation and DNA binding. We also found that ZBED4/KIAA0637, another member of the human hAT family, also self-associates, again dependent on the hATC domain, with deletion resulting in loss of efficient nuclear accumulation. Thus, hATC domains of human hAT family members appear to have conserved functions in self-association that are required for nuclear accumulation.
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Affiliation(s)
- Daisuke Yamashita
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678-1297, Japan
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Martin-Lannerée S, Lasbleiz C, Sanial M, Fouix S, Besse F, Tricoire H, Plessis A. Characterization of the Drosophila myeloid leukemia factor. Genes Cells 2006; 11:1317-35. [PMID: 17121541 DOI: 10.1111/j.1365-2443.2006.01023.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In human, the myeloid leukemia factor 1 (hMLF1) has been shown to be involved in acute leukemia, and mlf related genes are present in many animals. Despite their extensive representation and their good conservation, very little is understood about their function. In Drosophila, dMLF physically interacts with both the transcription regulatory factor DREF and an antagonist of the Hedgehog pathway, Suppressor of Fused, whose over-expression in the fly suppresses the toxicity induced by polyglutamine. No connection between these data has, however, been established. Here, we show that dmlf is widely and dynamically expressed during fly development. We isolated and analyzed the first dmlf mutants: embryos lacking maternal dmlf product have a low viability with no specific defect, and dmlf(-)- adults display weak phenotypes. We monitored dMLF subcellular localization in the fly and cultured cells. We were able to show that, although generally nuclear, dMLF can also be cytoplasmic, depending on the developmental context. Furthermore, two differently spliced variants of dMLF display differential subcellular localization, allowing the identification of regions of dMLF potentially important for its localization. Finally, we demonstrate that dMLF can act developmentally and postdevelopmentally to suppress neurodegeneration and premature aging in a cerebellar ataxia model.
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Affiliation(s)
- Séverine Martin-Lannerée
- Laboratoire de Génétique du Développement et Evolution, Institut Jacques Monod, UMR 7592 CNRS Université Paris 6 et Paris 7, 2 place Jussieu, 75 251 Paris Cedex 05, France
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Hyun J, Jasper H, Bohmann D. DREF is required for efficient growth and cell cycle progression in Drosophila imaginal discs. Mol Cell Biol 2005; 25:5590-8. [PMID: 15964814 PMCID: PMC1157005 DOI: 10.1128/mcb.25.13.5590-5598.2005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Based on overexpression studies and target gene analyses, the transcription factor DNA replication-related element factor (DREF) has been proposed to regulate growth and replication in Drosophila melanogaster. Here we present loss-of-function experiments to analyze the contribution of DREF to these processes. RNA interference-mediated extinction of DREF function in vivo demonstrates a requirement for the protein for normal progression through the cell cycle and consequently for growth of imaginal discs and the derived adult organs. We show that DREF regulates the expression of genes that are required for the transition of imaginal disc cells through S phase. In conditions of suppressed apoptosis, DREF activation can cause overgrowth of developing organs. These data establish DREF as a global regulator of transcriptional programs that mediate cell proliferation and organ growth during animal development.
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Affiliation(s)
- Joogyung Hyun
- Department of Biomedical Genetics, The Aab Institute of Biomedical Sciences, University of Rochester Medical Center, 601 Elmwood Avenue, Box 633, Rochester, NY 14642, USA
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21
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Casso DJ, Tanda S, Biehs B, Martoglio B, Kornberg TB. Drosophila signal peptide peptidase is an essential protease for larval development. Genetics 2005; 170:139-48. [PMID: 15716490 PMCID: PMC1449732 DOI: 10.1534/genetics.104.039933] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Accepted: 01/26/2005] [Indexed: 11/18/2022] Open
Abstract
We identified the Drosophila melanogaster Signal peptide peptidase gene (Spp) that encodes a multipass transmembrane aspartyl protease. Drosophila SPP is homologous to the human signal peptide peptidase (SPP) and is distantly related to the presenilins. We show that, like human SPP, Drosophila SPP can proteolyze a model signal peptide and is sensitive to an SPP protease inhibitor and that it localizes to the endoplasmic reticulum. Expression of Drosophila SPP was first apparent at germ band extension, and in late embryos it was robust in the salivary glands, proventriculus, and tracheae. Flies bearing mutations in conserved residues or carrying deficiencies for the Spp gene had defective tracheae and died as larvae.
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Affiliation(s)
- David J Casso
- Department of Biochemistry and Biophysics, University of California, San Francisco, 94143, USA
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Yoshida H, Kwon E, Hirose F, Otsuki K, Yamada M, Yamaguchi M. DREF is required for EGFR signalling during Drosophila wing vein development. Genes Cells 2005; 9:935-44. [PMID: 15461664 DOI: 10.1111/j.1365-2443.2004.00775.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The DNA replication-related element binding factor (DREF) has been suggested as being involved in regulation of DNA replication- and proliferation-related genes in Drosophila. Recently, by searching the Drosophila genome database, we also found DRE-like sequences in the 5'-flanking regions of many genes with other functions. In addition, immunostaining of polytene chromosomes with an anti-DREF monoclonal antibody revealed that DREF can bind to a hundred regions of polytene chromosomes, suggesting regulation of multiple genes and multiple roles in vivo. When we over-expressed DREF protein or inverted repeat RNA of the DREF gene in wing imaginal discs using the GAL4-UAS targeted expression system in Drosophila, the results were veins of increased width and a loss of veins, respectively. With DREF over-expression, Rolled, a Drosophila MAPK homologue, was ectopically activated. Furthermore, half reduction of the D-raf gene dose suppressed this DREF-induced vein of increased width phenotype. In addition, when DREF transcripts were reduced by introducing double-stranded RNA of the DREF gene into S2 cells, the D-raf gene promoter activity was diminished to 4%. These data indicate that DREF is involved in regulation of vein formation through the activation of EGFR signalling in the Drosophila wing imaginal discs.
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Affiliation(s)
- Hideki Yoshida
- Venture Laboratory, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan
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Choi TY, Park SY, Kang HS, Cheong JH, Kim HD, Lee BL, Hirose F, Yamaguchi M, Yoo MA. Redox regulation of DNA binding activity of DREF (DNA replication-related element binding factor) in Drosophila. Biochem J 2004; 378:833-8. [PMID: 14651474 PMCID: PMC1224010 DOI: 10.1042/bj20031601] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Accepted: 12/02/2003] [Indexed: 11/17/2022]
Abstract
DREF [DRE (DNA replication-related element) binding factor] is an 80 kDa polypeptide homodimer which plays an important role in regulating cell proliferation-related genes. Both DNA binding and dimer formation activities are associated with residues 16-115 of the N-terminal region. However, the mechanisms by which DREF dimerization and DNA binding are regulated remain unknown. Here, we report that the DNA binding activity of DREF is regulated by a redox mechanism, and that the cysteine residues are involved in this regulation. Electrophoretic mobility shift analysis using Drosophila Kc cell extracts or recombinant DREF proteins indicated that the DNA binding domain is sufficient for redox regulation. Site-directed mutagenesis and transient transfection assays showed that Cys59 and/or Cys62 are critical both for DNA binding and for redox regulation, whereas Cys91 is dispensable. In addition, experiments using Kc cells indicated that the DNA binding activity and function of DREF are affected by the intracellular redox state. These findings give insight into the exact nature of DREF function in the regulation of target genes by the intracellular redox state.
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Affiliation(s)
- Tae-Yeong Choi
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 609-735, Korea
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Fouix S, Martin-Lannerée S, Sanial M, Morla L, Lamour-Isnard C, Plessis A. Over-expression of a novel nuclear interactor of Suppressor of fused, theDrosophilamyelodysplasia/myeloid leukaemia factor, induces abnormal morphogenesis associated with increased apoptosis and DNA synthesis. Genes Cells 2003; 8:897-911. [PMID: 14622141 DOI: 10.1046/j.1365-2443.2003.00685.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND In Drosophila and vertebrates, suppressor of fused (Su(fu)) proteins act as negative regulators of the Gli/Ci transcription factors, which mediate the transcriptional effects of Hh signalling. RESULTS We sought for novel partners of Su(fu) in fly using the two-hybrid method. Most of the Su(fu) interactors thus identified are (or are likely to be) able to enter the nucleus. We focused on one of these putative partners, dMLF, which resembles vertebrate myelodysplasia/myeloid leukaemia factors 1 and 2. We demonstrate that dMLF binds specifically to Su(fu) in vitro and in vivo. Using a novel anti-dMLF antibody, we showed, that dMLF is a nuclear, chromosome-associated protein. We over-expressed a dMLF transgene in fly using an inducible expression system and showed that dMLF over-expression disrupts normal development, leading to either a lethal phenotype or adult structural defects associated with apoptosis and increased DNA synthesis. Furthermore, the dMLF-induced eye phenotype is enhanced by the loss of Su(fu) function, suggesting a genetic interaction between Su(fu) and dMLF. CONCLUSION We propose that dSu(fu) and dMLF act together at the transcriptional level to coordinate patterning and proliferation during development.
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Affiliation(s)
- Sylvaine Fouix
- Laboratoire de génétique du développement et évolution, Institut Jacques Monod, 2 Place Jussieu 75251 Paris, France
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