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Qi Z, Jung C, Bandilla P, Ludwig C, Heron M, Sophie Kiesel A, Museridze M, Philippou‐Massier J, Nikolov M, Renna Max Schnepf A, Unnerstall U, Ceolin S, Mühlig B, Gompel N, Soeding J, Gaul U. Large-scale analysis of Drosophila core promoter function using synthetic promoters. Mol Syst Biol 2022; 18:e9816. [PMID: 35156763 PMCID: PMC8842121 DOI: 10.15252/msb.20209816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 02/02/2023] Open
Abstract
The core promoter plays a central role in setting metazoan gene expression levels, but how exactly it "computes" expression remains poorly understood. To dissect its function, we carried out a comprehensive structure-function analysis in Drosophila. First, we performed a genome-wide bioinformatic analysis, providing an improved picture of the sequence motifs architecture. We then measured synthetic promoters' activities of ~3,000 mutational variants with and without an external stimulus (hormonal activation), at large scale and with high accuracy using robotics and a dual luciferase reporter assay. We observed a strong impact on activity of the different types of mutations, including knockout of individual sequence motifs and motif combinations, variations of motif strength, nucleosome positioning, and flanking sequences. A linear combination of the individual motif features largely accounts for the combinatorial effects on core promoter activity. These findings shed new light on the quantitative assessment of gene expression in metazoans.
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Affiliation(s)
- Zhan Qi
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Christophe Jung
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Peter Bandilla
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Claudia Ludwig
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Mark Heron
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Anja Sophie Kiesel
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Mariam Museridze
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Julia Philippou‐Massier
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Miroslav Nikolov
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Alessio Renna Max Schnepf
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Ulrich Unnerstall
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Stefano Ceolin
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Bettina Mühlig
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Nicolas Gompel
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Johannes Soeding
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
- Max Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Ulrike Gaul
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
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Vellichirammal NN, Gupta P, Hall TA, Brisson JA. Ecdysone signaling underlies the pea aphid transgenerational wing polyphenism. Proc Natl Acad Sci U S A 2017; 114:1419-1423. [PMID: 28115695 PMCID: PMC5307454 DOI: 10.1073/pnas.1617640114] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The wing polyphenism of pea aphids is a compelling laboratory model with which to study the molecular mechanisms underlying phenotypic plasticity. In this polyphenism, environmental stressors such as high aphid density cause asexual, viviparous adult female aphids to alter the developmental fate of their embryos from wingless to winged morphs. This polyphenism is transgenerational, in that the pea aphid mother experiences the environmental signals, but it is her offspring that are affected. Previous research suggested that the steroid hormone ecdysone may play a role in this polyphenism. Here, we analyzed ecdysone-related gene expression patterns and found that they were consistent with a down-regulation of the ecdysone pathway being involved in the production of winged offspring. We therefore predicted that reduced ecdysone signaling would result in more winged offspring. Experimental injections of ecdysone or its analog resulted in a decreased production of winged offspring. Conversely, interfering with ecdysone signaling using an ecdysone receptor antagonist or knocking down the ecdysone receptor gene with RNAi resulted in an increased production of winged offspring. Our results are therefore consistent with the idea that ecdysone plays a causative role in the regulation of the proportion of winged offspring produced in response to crowding in this polyphenism. Our results also show that an environmentally regulated maternal hormone can mediate phenotype production in the next generation, as well as provide significant insight into the molecular mechanisms underlying the functioning of transgenerational phenotypic plasticity.
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Affiliation(s)
| | - Purba Gupta
- Department of Biology, University of Rochester, Rochester, NY 14627
| | - Tannice A Hall
- Department of Life Sciences, University of the West Indies, Mona, Kingston 7, Jamaica
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López-Vidal J, Gómez-Sebastián S, Sánchez-Ramos I, Escribano JM. Characterization of a Trichoplusia ni hexamerin-derived promoter in the AcMNPV baculovirus vector. J Biotechnol 2013; 165:201-8. [PMID: 23578810 DOI: 10.1016/j.jbiotec.2013.03.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/18/2013] [Accepted: 03/21/2013] [Indexed: 12/24/2022]
Abstract
The promoter sequences of the encoding genes for the three most abundant hexamerins of the Lepidoptera Trichoplusia ni were isolated and cloned into the Autographa californica multiple nucleopolyhedrovirus (AcMNPV)-derived baculovirus expression vector. From the sequences analyzed, the DNA region driving the expression of the Basic juvenile hormone-suppressible protein 2 (BJHSP-2), denominated pB2, presented the highest promoter strength in the context of the baculovirus vector in Sf21 insect cells. This promoter activity occurred earlier in baculovirus-infected cells than that achieved by a conventional polyhedrin promoter (polh), but surprisingly stopped at 48h post-infection. A mapping of pB2 essential promoter elements determined that a region of about 400bp, denominated pB29, retained and even increased the transcriptional activity with respect to the parental full-length sequence. Finally, several chimeric combinations of the insect-derived pB2 with the virus-derived conventional polh or p10 promoters were constructed and incorporated into an AcMNPV baculovirus vector. The pB2-p10 combination showed increased recombinant protein expression at early times post-infection and similar expression levels at very late times post-infection in Sf21 cells with respect to conventional late promoters. To the best of our knowledge, pB2 is the first promoter isolated from the Lepidoptera T. ni, the natural host of AcMNPV, to be assayed in a baculovirus expression vector.
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Affiliation(s)
- Javier López-Vidal
- Alternative Gene Expression S.L. (ALGENEX), Centro Empresarial, Parque Científico y Tecnológico de la Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
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Jones G, Teal P, Henrich VC, Krzywonos A, Sapa A, Wozniak M, Smolka J, Jones D. Ligand binding pocket function of Drosophila USP is necessary for metamorphosis. Gen Comp Endocrinol 2013; 182:73-82. [PMID: 23211750 DOI: 10.1016/j.ygcen.2012.11.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/22/2012] [Accepted: 11/05/2012] [Indexed: 10/27/2022]
Abstract
The widely accepted paradigm that epoxidized methyl farnesoates ("juvenile hormones," JHs) are the principal sesquiterpenoid hormones regulating insect metamorphosis was assessed in Drosophila melanogaster. GC-MS analysis of circulating methyl farnesoids during the mid to late 3rd instar showed that methyl farnesoate is predominant over methyl epoxyfarnesoate (=JH III). The circulating concentration of methyl farnesoate (reaching nearly 500 nM), was easily high enough on a kinetic basis to load the Drosophila ortholog of the nuclear hormone receptor RXR (also known as "ultraspiracle," USP), whereas the circulating concentrations of JH III and methyl bisepoxyfarnesoate (bisepoxyJH III) were not. The hypothesis that the ligand pocket of USP necessarily binds an endogenous ligand for differentiation of the immature to the adult was tested with USP mutated at residue that normally extends a side chain into the ligand binding pocket. An equilibrium binding assay confirmed that the mutation (Q288A) strongly altered methyl farnesoate interaction with USP, while a heterologous cell-line transfection assay confirmed that the mutation did not allosterically alter the transcriptional response of the ultraspiracle/ecdysone receptor heterodimer to ecdysteroid signaling. Transgenic wildtype USP driven by the cognate natural promoter rescued null animals to develop to the adult inside a normally formed puparium, while in contrast animals transgenically expressing instead the ligand pocket mutant exhibited developmental derangement at the larval to pupal transition, including failure to form a properly shaped or sclerotized puparium. Other point mutations to the pocket strongly reducing affinity for methyl farnesoate similarly disrupted the larval to pupal metamorphosis. These results suggest that normal larval to pupal maturation in this mecopteran model insect requires the involvement of a distinct endocrine axis of USP binding to its own endogenous terpenoid ligand.
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Affiliation(s)
- Grace Jones
- Department of Biology, University of Kentucky, Lexington, KY 40504, USA.
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Riddiford LM. How does juvenile hormone control insect metamorphosis and reproduction? Gen Comp Endocrinol 2012; 179:477-84. [PMID: 22728566 DOI: 10.1016/j.ygcen.2012.06.001] [Citation(s) in RCA: 216] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/22/2012] [Accepted: 06/01/2012] [Indexed: 01/08/2023]
Abstract
In insects juvenile hormone (JH) regulates both metamorphosis and reproduction. This lecture focuses on our current understanding of JH action at the molecular level in both of these processes based primarily on studies in the tobacco hornworm Manduca sexta, the flour beetle Tribolium castaneum, the mosquito Aedes aegypti, and the fruit fly Drosophila melanogaster. The roles of the JH receptor complex and the transcription factors that it regulates during larval molting and metamorphosis are summarized. Also highlighted are the intriguing interactions of the JH and insulin signaling pathways in both imaginal disc development and vitellogenesis. Critical actions of JH and its receptor in the timing of maturation of the adult optic lobe and of female receptivity in Drosophila are also discussed.
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Affiliation(s)
- Lynn M Riddiford
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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Jindra M, Palli SR, Riddiford LM. The juvenile hormone signaling pathway in insect development. ANNUAL REVIEW OF ENTOMOLOGY 2012; 58:181-204. [PMID: 22994547 DOI: 10.1146/annurev-ento-120811-153700] [Citation(s) in RCA: 564] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The molecular action of juvenile hormone (JH), a regulator of vital importance to insects, was until recently regarded as a mystery. The past few years have seen an explosion of studies of JH signaling, sparked by a finding that a JH-resistance gene, Methoprene-tolerant (Met), plays a critical role in insect metamorphosis. Here, we summarize the recently acquired knowledge on the capacity of Met to bind JH, which has been mapped to a particular ligand-binding domain, thus establishing this bHLH-PAS protein as a novel type of an intracellular hormone receptor. Next, we consider the significance of JH-dependent interactions of Met with other transcription factors and signaling pathways. We examine the regulation and biological roles of genes acting downstream of JH and Met in insect metamorphosis. Finally, we discuss the current gaps in our understanding of JH action and outline directions for future research.
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Affiliation(s)
- Marek Jindra
- Biology Center, Academy of Sciences of the Czech Republic, 37005 Ceske Budejovice, Czech Republic
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Bernardo TJ, Dubrovsky EB. Molecular Mechanisms of Transcription Activation by Juvenile Hormone: A Critical Role for bHLH-PAS and Nuclear Receptor Proteins. INSECTS 2012; 3:324-38. [PMID: 26467963 PMCID: PMC4553631 DOI: 10.3390/insects3010324] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 03/15/2012] [Accepted: 03/16/2012] [Indexed: 11/16/2022]
Abstract
Juvenile hormone (JH) is responsible for controlling many biological processes. In several insect species JH has been implicated as a key regulator of developmental timing, preventing the premature onset of metamorphosis during larval growth periods. However, the molecular basis of JH action is not well-understood. In this review, we highlight recent advances which demonstrate the importance of transcription factors from the bHLH-PAS and nuclear receptor families in mediating the response to JH.
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Affiliation(s)
| | - Edward B Dubrovsky
- Department of Biology, Fordham University, Bronx, NY 10458, USA.
- Center for Cancer, Genetic Diseases, and Gene Regulation, Fordham University, Bronx, NY 10458, USA.
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