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Shen J, Liu F, Tang C. Scaling dictates the decoder structure. Sci Bull (Beijing) 2022; 67:1486-1495. [PMID: 36546192 DOI: 10.1016/j.scib.2022.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/06/2022] [Accepted: 06/13/2022] [Indexed: 01/07/2023]
Abstract
Despite fluctuations in embryo size within a species, the spatial gene expression pattern and hence the embryonic structure can nonetheless maintain the correct proportion to the embryo size. This is known as the scaling phenomenon. For morphogen-induced patterning of gene expression, the positional information encoded in the local morphogen concentrations is decoded by the downstream genetic network (the decoder). In this paper, we show that the requirement of scaling sets severe constraints on the geometric structure of such a local decoder, which in turn enables deduction of mutants' behavior and extraction of regulation information without going into any molecular details. We demonstrate that the Drosophila gap gene system achieves scaling in the way consistent with our theory-the decoder geometry required by scaling correctly accounts for the observed gap gene expression pattern in nearly all maternal morphogen mutants. Furthermore, the regulation logic and the coding/decoding strategy of the gap gene system can also be revealed from the decoder geometry. Our work provides a general theoretical framework for a large class of problems where scaling output is achieved by non-scaling inputs and a local decoder, as well as a unified understanding of scaling, mutants' behavior, and gene regulation for the Drosophila gap gene system.
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Affiliation(s)
- Jingxiang Shen
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Feng Liu
- Center for Quantitative Biology, Peking University, Beijing 100871, China; School of Physics, Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; School of Physics, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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Ohsako T, Shirakami M, Oiwa K, Ibaraki K, Karr TL, Tomaru M, Sanuki R, Takano-Shimizu-Kouno T. The Drosophila Neprilysin 4 gene is essential for sperm function following sperm transfer to females. Genes Genet Syst 2021; 96:177-186. [PMID: 34556622 DOI: 10.1266/ggs.21-00024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Sperm are modified substantially in passing through both the male and the female reproductive tracts, only thereafter becoming functionally competent to fertilize eggs. Drosophila sperm become motile in the seminal vesicle; after ejaculation, they interact with seminal fluid proteins and undergo biochemical changes on their surface while they are stored in the female sperm storage organs. However, the molecular mechanisms underlying these maturation processes remain largely unknown. Here, we focused on Drosophila Neprilysin genes, which are the fly orthologs of the mouse Membrane metallo-endopeptidase-like 1 (Mmel1) gene. While Mmel1 knockout male mice have reduced fertility without abnormality in either testis morphology or sperm motility, there are inconsistent results regarding the association of any Neprilysin gene with male fertility in Drosophila. We examined the association of the Nep1-5 genes with male fertility by RNAi and found that Nep4 gene function is specifically required in germline cells. To investigate this in more detail, we induced mutations in the Nep4 gene by the CRISPR/Cas9 system and isolated two mutants, both of which were viable and female fertile, but male sterile. The mutant males had normal-looking testes and sperm; during copulation, sperm were transferred to females and stored in the seminal receptacle and paired spermathecae. However, following sperm transfer and storage, three defects were observed for Nep4 mutant sperm. First, sperm were quickly discarded by the females; second, the proportion of eggs fertilized was significantly lower for mutant sperm than for control sperm; and third, most eggs laid did not initiate development after sperm entry. Taking these observations together, we conclude that the Nep4 gene is essential for sperm function following sperm transfer to females.
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Affiliation(s)
- Takashi Ohsako
- Advanced Technology Center, Kyoto Institute of Technology
| | - Machi Shirakami
- Graduate School of Science and Technology, Kyoto Institute of Technology
| | - Kazuharu Oiwa
- Graduate School of Science and Technology, Kyoto Institute of Technology
| | - Kimihide Ibaraki
- Graduate School of Science and Technology, Kyoto Institute of Technology
| | - Timothy L Karr
- Mass Spectroscopy Core Facility, Biodesign Institute, Arizona State University
| | - Masatoshi Tomaru
- Faculty of Applied Biology, Kyoto Institute of Technology.,Advanced Insect Research Promotion Center, Kyoto Institute of Technology
| | - Rikako Sanuki
- Faculty of Applied Biology, Kyoto Institute of Technology.,Advanced Insect Research Promotion Center, Kyoto Institute of Technology
| | - Toshiyuki Takano-Shimizu-Kouno
- Faculty of Applied Biology, Kyoto Institute of Technology.,Advanced Insect Research Promotion Center, Kyoto Institute of Technology
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Ibaraki K, Nakatsuka M, Ohsako T, Watanabe M, Miyazaki Y, Shirakami M, Karr TL, Sanuki R, Tomaru M, Takano-Shimizu-Kouno T. A cross-species approach for the identification of Drosophila male sterility genes. G3 GENES|GENOMES|GENETICS 2021; 11:6288452. [PMID: 34849808 PMCID: PMC8496277 DOI: 10.1093/g3journal/jkab183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/13/2021] [Indexed: 12/03/2022]
Abstract
Male reproduction encompasses many essential cellular processes and interactions. As a focal point for these events, sperm offer opportunities for advancing our understanding of sexual reproduction at multiple levels during development. Using male sterility genes identified in human, mouse, and fruit fly databases as a starting point, 103 Drosophila melanogaster genes were screened for their association with male sterility by tissue-specific RNAi knockdown and CRISPR/Cas9-mediated mutagenesis. This list included 56 genes associated with male infertility in the human databases, but not found in the Drosophila database, resulting in the discovery of 63 new genes associated with male fertility in Drosophila. The phenotypes identified were categorized into six distinct classes affecting sperm development. Interestingly, the second largest class (Class VI) caused sterility despite apparently normal testis and sperm morphology suggesting that these proteins may have functions in the mature sperm following spermatogenesis. We focused on one such gene, Rack 1, and found that it plays an important role in two developmental periods, in early germline cells or germline stem cells and in spermatogenic cells or sperm. Taken together, many genes are yet to be identified and their role in male reproduction, especially after ejaculation, remains to be elucidated in Drosophila, where a wealth of data from human and other model organisms would be useful.
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Affiliation(s)
- Kimihide Ibaraki
- Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Mihoko Nakatsuka
- Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Takashi Ohsako
- Advanced Technology Center, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Masahide Watanabe
- Department of Drosophila Genomics and Genetic Resources, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Kyoto 616-8354, Japan
| | - Yu Miyazaki
- Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Machi Shirakami
- Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Timothy L Karr
- Mass Spectroscopy Core Facility, Biodesign Institute, Arizona State University, Tempe, AZ 85257-7205, USA
| | - Rikako Sanuki
- Department of Drosophila Genomics and Genetic Resources, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Kyoto 616-8354, Japan
- Faculty of Applied Biology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Masatoshi Tomaru
- Department of Drosophila Genomics and Genetic Resources, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Kyoto 616-8354, Japan
- Faculty of Applied Biology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Toshiyuki Takano-Shimizu-Kouno
- Department of Drosophila Genomics and Genetic Resources, Advanced Insect Research Promotion Center, Kyoto Institute of Technology, Kyoto 616-8354, Japan
- Faculty of Applied Biology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
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Drosophila IRBP bZIP heterodimer binds P-element DNA and affects hybrid dysgenesis. Proc Natl Acad Sci U S A 2016; 113:13003-13008. [PMID: 27799520 DOI: 10.1073/pnas.1613508113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In Drosophila, P-element transposition causes mutagenesis and genome instability during hybrid dysgenesis. The P-element 31-bp terminal inverted repeats (TIRs) contain sequences essential for transposase cleavage and have been implicated in DNA repair via protein-DNA interactions with cellular proteins. The identity and function of these cellular proteins were unknown. Biochemical characterization of proteins that bind the TIRs identified a heterodimeric basic leucine zipper (bZIP) complex between an uncharacterized protein that we termed "Inverted Repeat Binding Protein (IRBP) 18" and its partner Xrp1. The reconstituted IRBP18/Xrp1 heterodimer binds sequence-specifically to its dsDNA-binding site within the P-element TIRs. Genetic analyses implicate both proteins as critical for repair of DNA breaks following transposase cleavage in vivo. These results identify a cellular protein complex that binds an active mobile element and plays a more general role in maintaining genome stability.
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