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McKowen JK, Dassanayake M, Hart CM. The Tofu mutation restores female fertility to Drosophila with a null BEAF mutation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580197. [PMID: 38405992 PMCID: PMC10888741 DOI: 10.1101/2024.02.13.580197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Compensatory mutations offer clues to deciphering the role of a particular protein in cellular processes. Here we investigate an unknown compensatory mutation, present in the BEAFNP6377 fly line, that provides sufficient rescue of the defective ovary phenotype caused by null BEAF alleles to allow maintenance of fly stocks lacking the chromatin domain insulator proteins Boundary Element-Associated Factors BEAF-32A and BEAF-32B. We call this mutation Tofu. We employ both classical genetics and genomic sequencing to attempt to identify the mutation. We find evidence that points to a mutation in a predicted Polycomb response element upstream of the ribbon gene, which may lead to aberrant rib expression.
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Affiliation(s)
- J. Keller McKowen
- Louisiana State University Department of Biological Sciences, Baton Rouge, Louisiana, 70803
| | - Maheshi Dassanayake
- Louisiana State University Department of Biological Sciences, Baton Rouge, Louisiana, 70803
| | - Craig M. Hart
- Louisiana State University Department of Biological Sciences, Baton Rouge, Louisiana, 70803
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Peng D, Jackson D, Palicha B, Kernfeld E, Laughner N, Shoemaker A, Celniker SE, Loganathan R, Cahan P, Andrew DJ. Organogenetic transcriptomes of the Drosophila embryo at single cell resolution. Development 2024; 151:dev202097. [PMID: 38174902 PMCID: PMC10820837 DOI: 10.1242/dev.202097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
To gain insight into the transcription programs activated during the formation of Drosophila larval structures, we carried out single cell RNA sequencing during two periods of Drosophila embryogenesis: stages 10-12, when most organs are first specified and initiate morphological and physiological specialization; and stages 13-16, when organs achieve their final mature architectures and begin to function. Our data confirm previous findings with regards to functional specialization of some organs - the salivary gland and trachea - and clarify the embryonic functions of another - the plasmatocytes. We also identify two early developmental trajectories in germ cells and uncover a potential role for proteolysis during germline stem cell specialization. We identify the likely cell type of origin for key components of the Drosophila matrisome and several commonly used Drosophila embryonic cell culture lines. Finally, we compare our findings with other recent related studies and with other modalities for identifying tissue-specific gene expression patterns. These data provide a useful community resource for identifying many new players in tissue-specific morphogenesis and functional specialization of developing organs.
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Affiliation(s)
- Da Peng
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dorian Jackson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bianca Palicha
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric Kernfeld
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nathaniel Laughner
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ashleigh Shoemaker
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rajprasad Loganathan
- Department of Biological Sciences, Wichita State University, Wichita, KS 67260, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Deborah J. Andrew
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Loganathan R, Levings DC, Kim JH, Wells MB, Chiu H, Wu Y, Slattery M, Andrew DJ. Ribbon boosts ribosomal protein gene expression to coordinate organ form and function. J Cell Biol 2022; 221:213030. [PMID: 35195669 PMCID: PMC9237840 DOI: 10.1083/jcb.202110073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/19/2021] [Accepted: 01/24/2022] [Indexed: 11/22/2022] Open
Abstract
Cell growth is well defined for late (postembryonic) stages of development, but evidence for early (embryonic) cell growth during postmitotic morphogenesis is limited. Here, we report early cell growth as a key characteristic of tubulogenesis in the Drosophila embryonic salivary gland (SG) and trachea. A BTB/POZ domain nuclear factor, Ribbon (Rib), mediates this early cell growth. Rib binds the transcription start site of nearly every SG-expressed ribosomal protein gene (RPG) and is required for full expression of all RPGs tested. Rib binding to RPG promoters in vitro is weak and not sequence specific, suggesting that specificity is achieved through cofactor interactions. Accordingly, we demonstrate Rib’s ability to physically interact with each of the three known regulators of RPG transcription. Surprisingly, Rib-dependent early cell growth in another tubular organ, the embryonic trachea, is not mediated by direct RPG transcription. These findings support a model of early cell growth customized by transcriptional regulatory networks to coordinate organ form and function.
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Affiliation(s)
| | - Daniel C Levings
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN
| | - Ji Hoon Kim
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD
| | - Michael B Wells
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD
| | - Hannah Chiu
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD
| | - Yifan Wu
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN
| | - Deborah J Andrew
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD
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Johnson DM, Wells MB, Fox R, Lee JS, Loganathan R, Levings D, Bastien A, Slattery M, Andrew DJ. CrebA increases secretory capacity through direct transcriptional regulation of the secretory machinery, a subset of secretory cargo, and other key regulators. Traffic 2021; 21:560-577. [PMID: 32613751 DOI: 10.1111/tra.12753] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 12/27/2022]
Abstract
Specialization of many cells, including the acinar cells of the salivary glands and pancreas, milk-producing cells of mammary glands, mucus-secreting goblet cells, antibody-producing plasma cells, and cells that generate the dense extracellular matrices of bone and cartilage, requires scaling up both secretory machinery and cell-type specific secretory cargo. Using tissue-specific genome-scale analyses, we determine how increases in secretory capacity are coordinated with increases in secretory load in the Drosophila salivary gland (SG), an ideal model for gaining mechanistic insight into the functional specialization of secretory organs. Our findings show that CrebA, a bZIP transcription factor, directly binds genes encoding the core secretory machinery, including protein components of the signal recognition particle and receptor, ER cargo translocators, Cop I and Cop II vesicles, as well as the structural proteins and enzymes of these organelles. CrebA directly binds a subset of SG cargo genes and CrebA binds and boosts expression of Sage, a SG-specific transcription factor essential for cargo expression. To further enhance secretory output, CrebA binds and activates Xbp1 and Tudor-SN. Thus, CrebA directly upregulates the machinery of secretion and additional factors to increase overall secretory capacity in professional secretory cells; concomitant increases in cargo are achieved both directly and indirectly.
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Affiliation(s)
- Dorothy M Johnson
- The Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael B Wells
- The Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rebecca Fox
- The Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joslynn S Lee
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, Minnesota, USA
| | - Rajprasad Loganathan
- The Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel Levings
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, Minnesota, USA
| | - Abigail Bastien
- The Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, Minnesota, USA
| | - Deborah J Andrew
- The Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Silva D, Olsen KW, Bednarz MN, Droste A, Lenkeit CP, Chaharbakhshi E, Temple-Wood ER, Jemc JC. Regulation of Gonad Morphogenesis in Drosophila melanogaster by BTB Family Transcription Factors. PLoS One 2016; 11:e0167283. [PMID: 27898696 PMCID: PMC5127561 DOI: 10.1371/journal.pone.0167283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/07/2016] [Indexed: 02/06/2023] Open
Abstract
During embryogenesis, primordial germ cells (PGCs) and somatic gonadal precursor cells (SGPs) migrate and coalesce to form the early gonad. A failure of the PGCs and SGPs to form a gonad with the proper architecture not only affects germ cell development, but can also lead to infertility. Therefore, it is critical to identify the molecular mechanisms that function within both the PGCs and SGPs to promote gonad morphogenesis. We have characterized the phenotypes of two genes, longitudinals lacking (lola) and ribbon (rib), that are required for the coalescence and compaction of the embryonic gonad in Drosophila melanogaster. rib and lola are expressed in the SGPs of the developing gonad, and genetic interaction analysis suggests these proteins cooperate to regulate gonad development. Both genes encode proteins with DNA binding motifs and a conserved protein-protein interaction domain, known as the Broad complex, Tramtrack, Bric-à-brac (BTB) domain. Through molecular modeling and yeast-two hybrid studies, we demonstrate that Rib and Lola homo- and heterodimerize via their BTB domains. In addition, analysis of the colocalization of Rib and Lola with marks of transcriptional activation and repression on polytene chromosomes reveals that Rib and Lola colocalize with both repressive and activating marks and with each other. While previous studies have identified Rib and Lola targets in other tissues, we find that Rib and Lola are likely to function via different downstream targets in the gonad. These results suggest that Rib and Lola act as dual-function transcription factors to cooperatively regulate embryonic gonad morphogenesis.
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Affiliation(s)
- Diane Silva
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Kenneth W. Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States of America
| | - Magdalena N. Bednarz
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Andrew Droste
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | | | - Edwin Chaharbakhshi
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Emily R. Temple-Wood
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Jennifer C. Jemc
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- * E-mail:
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Chaharbakhshi E, Jemc JC. Broad-complex, tramtrack, and bric-à-brac (BTB) proteins: Critical regulators of development. Genesis 2016; 54:505-518. [DOI: 10.1002/dvg.22964] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Edwin Chaharbakhshi
- Department of Biology; Loyola University Chicago; Chicago IL
- Stritch School of Medicine; Loyola University Chicago; Maywood IL
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