1
|
Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Thomas H, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Eye proteome of Drosophila melanogaster. Proteomics 2024; 24:e2300330. [PMID: 37963819 DOI: 10.1002/pmic.202300330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
Drosophila melanogaster is a popular model organism to elucidate the molecular mechanisms that underlie the structure and function of the eye as well as the causes of retinopathies, aging, light-induced damage, or dietary deficiencies. Large-scale screens have isolated genes whose mutation causes morphological and functional ocular defects, which led to the discovery of key components of the phototransduction cascade. However, the proteome of the Drosophila eye is poorly characterized. Here, we used GeLC-MS/MS to quantify 3516 proteins, including the absolute (molar) quantities of 43 proteins in the eye of adult male Drosophila reared on standard laboratory food. This work provides a generic and expandable resource for further genetic, pharmacological, and dietary studies.
Collapse
Affiliation(s)
- Mukesh Kumar
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Canan Has
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Khanh Lam-Kamath
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Sophie Ayciriex
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Deepshe Dewett
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Mhamed Bashir
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Clara Poupault
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Henrik Thomas
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Jens Rister
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| |
Collapse
|
2
|
Zheng Y, Chen S. Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research. Front Cell Neurosci 2024; 18:1347436. [PMID: 38414750 PMCID: PMC10896975 DOI: 10.3389/fncel.2024.1347436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.
Collapse
Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
| | - Shiming Chen
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, Saint Louis, MO, United States
| |
Collapse
|
3
|
Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Eye proteome of Drosophila melanogaster. bioRxiv 2023:2023.03.04.531088. [PMID: 36945598 PMCID: PMC10028839 DOI: 10.1101/2023.03.04.531088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
The Drosophila melanogaster eye is a popular model to elucidate the molecular mechanisms that underlie the structure and function of the eye as well as the causes of retinopathies. For instance, the Drosophila eye has been used to investigate the impacts of ageing and environmental stresses such as light-induced damage or dietary deficiencies. Moreover, large-scale screens have isolated genes whose mutation causes morphological and functional ocular defects, which includes key components of the phototransduction cascade. However, the proteome of the Drosophila eye is poorly characterized. Here, we used GeLC-MS/MS to quantify 3516 proteins he adult Drosophila melanogaster eye and provide a generic and expandable resource for further genetic, pharmacological, and dietary studies.
Collapse
|
4
|
Bunker J, Bashir M, Bailey S, Boodram P, Perry A, Delaney R, Tsachaki M, Sprecher SG, Nelson E, Call GB, Rister J. Blimp-1/PRDM1 and Hr3/RORβ specify the blue-sensitive photoreceptor subtype in Drosophila by repressing the hippo pathway. Front Cell Dev Biol 2023; 11:1058961. [PMID: 36960411 PMCID: PMC10027706 DOI: 10.3389/fcell.2023.1058961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
During terminal differentiation of the mammalian retina, transcription factors control binary cell fate decisions that generate functionally distinct subtypes of photoreceptor neurons. For instance, Otx2 and RORβ activate the expression of the transcriptional repressor Blimp-1/PRDM1 that represses bipolar interneuron fate and promotes rod photoreceptor fate. Moreover, Otx2 and Crx promote expression of the nuclear receptor Nrl that promotes rod photoreceptor fate and represses cone photoreceptor fate. Mutations in these four transcription factors cause severe eye diseases such as retinitis pigmentosa. Here, we show that a post-mitotic binary fate decision in Drosophila color photoreceptor subtype specification requires ecdysone signaling and involves orthologs of these transcription factors: Drosophila Blimp-1/PRDM1 and Hr3/RORβ promote blue-sensitive (Rh5) photoreceptor fate and repress green-sensitive (Rh6) photoreceptor fate through the transcriptional repression of warts/LATS, the nexus of the phylogenetically conserved Hippo tumor suppressor pathway. Moreover, we identify a novel interaction between Blimp-1 and warts, whereby Blimp-1 represses a warts intronic enhancer in blue-sensitive photoreceptors and thereby gives rise to specific expression of warts in green-sensitive photoreceptors. Together, these results reveal that conserved transcriptional regulators play key roles in terminal cell fate decisions in both the Drosophila and the mammalian retina, and the mechanistic insights further deepen our understanding of how Hippo pathway signaling is repurposed to control photoreceptor fates for Drosophila color vision.
Collapse
Affiliation(s)
- Joseph Bunker
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Mhamed Bashir
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Sydney Bailey
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Pamela Boodram
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
- NYU Langone Medical Center, New York, NY, United States
| | - Alexis Perry
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Rory Delaney
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Maria Tsachaki
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Simon G. Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Erik Nelson
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, United States
| | - Gerald B. Call
- Department of Pharmacology, College of Graduate Studies, Midwestern University, Glendale, AZ, United States
| | - Jens Rister
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
- *Correspondence: Jens Rister,
| |
Collapse
|
5
|
McCulloch KJ, Macias-Muñoz A, Briscoe AD. Insect opsins and evo-devo: what have we learned in 25 years? Philos Trans R Soc Lond B Biol Sci 2022; 377:20210288. [PMID: 36058243 PMCID: PMC9441233 DOI: 10.1098/rstb.2021.0288] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/16/2022] [Indexed: 12/16/2022] Open
Abstract
The visual pigments known as opsins are the primary molecular basis for colour vision in animals. Insects are among the most diverse of animal groups and their visual systems reflect a variety of life histories. The study of insect opsins in the fruit fly Drosophila melanogaster has led to major advances in the fields of neuroscience, development and evolution. In the last 25 years, research in D. melanogaster has improved our understanding of opsin genotype-phenotype relationships while comparative work in other insects has expanded our understanding of the evolution of insect eyes via gene duplication, coexpression and homologue switching. Even so, until recently, technology and sampling have limited our understanding of the fundamental mechanisms that evolution uses to shape the diversity of insect eyes. With the advent of genome editing and in vitro expression assays, the study of insect opsins is poised to reveal new frontiers in evolutionary biology, visual neuroscience, and animal behaviour. This article is part of the theme issue 'Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods'.
Collapse
Affiliation(s)
- Kyle J. McCulloch
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Aide Macias-Muñoz
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Adriana D. Briscoe
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA 92697, USA
| |
Collapse
|
6
|
Datta RR, Rister J. The power of the (imperfect) palindrome: Sequence-specific roles of palindromic motifs in gene regulation. Bioessays 2022; 44:e2100191. [PMID: 35195290 PMCID: PMC8957550 DOI: 10.1002/bies.202100191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/22/2022]
Abstract
In human languages, a palindrome reads the same forward as backward (e.g., 'madam'). In regulatory DNA, a palindrome is an inverted sequence repeat that allows a transcription factor to bind as a homodimer or as a heterodimer with another type of transcription factor. Regulatory palindromes are typically imperfect, that is, the repeated sequences differ in at least one base pair, but the functional significance of this asymmetry remains poorly understood. Here, we review the use of imperfect palindromes in Drosophila photoreceptor differentiation and mammalian steroid receptor signaling. Moreover, we discuss mechanistic explanations for the predominance of imperfect palindromes over perfect palindromes in these two gene regulatory contexts. Lastly, we propose to elucidate whether specific imperfectly palindromic variants have specific regulatory functions in steroid receptor signaling and whether such variants can help predict transcriptional outcomes as well as the response of individual patients to drug treatments.
Collapse
Affiliation(s)
- Rhea R Datta
- Department of Biology, Hamilton College, Clinton, New York, USA
| | - Jens Rister
- Department of Biology, University of Massachusetts Boston, Integrated Sciences Complex, Boston, Massachusetts, USA
| |
Collapse
|