1
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Yang K, Feng Z, Pastor-Pareja JC. p24-Tango1 interactions ensure ER-Golgi interface stability and efficient transport. J Cell Biol 2024; 223:e202309045. [PMID: 38470362 PMCID: PMC10932740 DOI: 10.1083/jcb.202309045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/07/2024] [Accepted: 02/05/2024] [Indexed: 03/13/2024] Open
Abstract
The eukaryotic p24 family, consisting of α-, β-, γ- and δ-p24 subfamilies, has long been known to be involved in regulating secretion. Despite increasing interest in these proteins, fundamental questions remain about their role. Here, we systematically investigated Drosophila p24 proteins. We discovered that members of all four p24 subfamilies are required for general secretion and that their localizations between ER exit site (ERES) and Golgi are interdependent in an α→βδ→γ sequence. We also found that localization of p24 proteins and ERES determinant Tango1 requires interaction through their respective GOLD and SH3 lumenal domains, with Tango1 loss sending p24 proteins to the plasma membrane and vice versa. Finally, we show that p24 loss expands the COPII zone at ERES and increases the number of ER-Golgi vesicles, supporting a restrictive role of p24 proteins on vesicle budding for efficient transport. Our results reveal Tango1-p24 interplay as central to the generation of a stable ER-Golgi interface.
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Affiliation(s)
- Ke Yang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhi Feng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - José Carlos Pastor-Pareja
- School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Institute of Neurosciences, Consejo Superior de Investigaciones Científicas-Universidad Miguel Hernández, San Juan de Alicante, Spain
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2
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Wang C, Hu Z, Guo Y, Xiao W, Zhang Y, Zhou A, Chen P. The Role of BmTMED6 in Female Reproduction in Silkworm, Bombyx mori. INSECTS 2024; 15:103. [PMID: 38392522 PMCID: PMC10889480 DOI: 10.3390/insects15020103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 02/24/2024]
Abstract
Transmembrane emp24 domain (TMED) proteins have been extensively studied in mammalian embryonic development, immune regulation, and signal transduction. However, their role in insects, apart from Drosophila melanogaster, remains largely unexplored. Our previous study demonstrated the abundant expression of BmTMED6 across all stages and tissues of the silkworm. In this study, we investigate the function of BmTMED6 in reproduction. We observe significant differences in the expression of BmTMED6 between male and female silkworms, particularly in the head and fatboby, during the larval stage. Furthermore, qRT-PCR and WB analysis reveal substantial variation in BmTMED6 levels in the ovaries during pupal development, suggesting a potential association with silkworm female reproduction. We find that reducing TMED6 expression significantly decreases the number of eggs laid by female moths, leading to an accumulation of unlaid eggs in the abdomen. Moreover, downregulation of BmTMED6 leads to a decrease in the expression of BmDop2R1 and BmDop2R2, while overexpression of BmTMED6 in vitro has the opposite effect. These indicate that BmTMED6 plays a role in oviposition in female moths, potentially through the dopamine signaling pathway. This study provides a new regulatory mechanism for female reproduction in insects.
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Affiliation(s)
- Chunyang Wang
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Zunmei Hu
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yu Guo
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Wenfu Xiao
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Youhong Zhang
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Anlian Zhou
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Ping Chen
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
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3
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Li X, Li M, Xue X, Wang X. Proteomic analysis reveals oxidative stress-induced activation of Hippo signaling in thiamethoxam-exposed Drosophila. CHEMOSPHERE 2023; 338:139448. [PMID: 37437626 DOI: 10.1016/j.chemosphere.2023.139448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/12/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Thiamethoxam (THIA) is a widely used neonicotinoid insecticide. However, the toxicity and defense mechanisms activated in THIA-exposed insects are unclear. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) proteomics technology to identify changes in protein expression in THIA-exposed Drosophila. We found that the antioxidant proteins Cyp6a23 and Dys were upregulated, whereas vir-1 was downregulated, which may have been detoxification in response to THIA exposure. Prx5 downregulation promoted the generation of reactive oxygen species. Furthermore, the accumulation of reactive oxygen species led to the induction of antioxidant defenses in THIA-exposed Drosophila, thereby enhancing the levels of oxidative stress markers (e.g., superoxide dismutase, glutathione S-transferase, and glutathione) and reducing catalase expression. Furthermore, the Hippo signaling transcription coactivator Yki was inactivated by THIA. Our results suggesting that Hippo signaling may be necessary to promote insect survival in response to neonicotinoid insecticide toxicity.
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Affiliation(s)
- Xiaoqin Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, 100193, China
| | - Mingquan Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, 100193, China
| | - Xianle Xue
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China
| | - Xing Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, 100193, China.
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4
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Navarro KG, Chamberlin HM. Genetic characterization of C. elegans TMED genes. Dev Dyn 2023; 252:1149-1161. [PMID: 37204056 PMCID: PMC10524739 DOI: 10.1002/dvdy.601] [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: 11/02/2022] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND p24/transmembrane Emp24 domain (TMED) proteins are a set of evolutionarily conserved, single pass transmembrane proteins that have been shown to facilitate protein secretion and selection of cargo proteins to transport vesicles in the cellular secretion pathway. However, their functions in animal development are incompletely understood. RESULTS The C. elegans genome encodes eight identified TMED genes, with at least one member from each defined subfamily (α, β, γ, δ). TMED gene mutants exhibit a shared set of defects in embryonic viability, animal movement, and vulval morphology. Two γ subfamily genes, tmed-1 and tmed-3, exhibit the ability to compensate for each other, as defects in movement and vulva morphology are only apparent in double mutants. TMED mutants also exhibit a delay in breakdown of basement membrane during vulva development. CONCLUSIONS The results establish a genetic and experimental framework for the study of TMED gene function in C. elegans, and argue that a functional protein from each subfamily is important for a shared set of developmental processes. A specific function for TMED genes is to facilitate breakdown of the basement membrane between the somatic gonad and vulval epithelial cells, suggesting a role for TMED proteins in tissue reorganization during animal development.
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5
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Zhao T, Xiao Y, Huang B, Ran MJ, Duan X, Wang YF, Lu Y, Yu XQ. A dual role of lola in Drosophila ovary development: regulating stem cell niche establishment and repressing apoptosis. Cell Death Dis 2022; 13:756. [PMID: 36056003 PMCID: PMC9440207 DOI: 10.1038/s41419-022-05195-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/13/2022] [Accepted: 08/17/2022] [Indexed: 01/21/2023]
Abstract
In Drosophila ovary, niche is composed of somatic cells, including terminal filament cells (TFCs), cap cells (CCs) and escort cells (ECs), which provide extrinsic signals to maintain stem cell renewal or initiate cell differentiation. Niche establishment begins in larval stages when terminal filaments (TFs) are formed, but the underlying mechanism for the development of TFs remains largely unknown. Here we report that transcription factor longitudinals lacking (Lola) is essential for ovary morphogenesis. We showed that Lola protein was expressed abundantly in TFCs and CCs, although also in other cells, and lola was required for the establishment of niche during larval stage. Importantly, we found that knockdown expression of lola induced apoptosis in adult ovary, and that lola affected adult ovary morphogenesis by suppressing expression of Regulator of cullins 1b (Roc1b), an apoptosis-related gene that regulates caspase activation during spermatogenesis. These findings significantly expand our understanding of the mechanisms controlling niche establishment and adult oogenesis in Drosophila.
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Affiliation(s)
- Ting Zhao
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, PR China
| | - Yanhong Xiao
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, South China Normal University, Guangzhou, PR China
| | - Bo Huang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, PR China
| | - Mao-Jiu Ran
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, PR China
| | - Xin Duan
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, PR China
| | - Yu-Feng Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, PR China
| | - Yuzhen Lu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, South China Normal University, Guangzhou, PR China.
| | - Xiao-Qiang Yu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, South China Normal University, Guangzhou, PR China.
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6
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Mota DCAM, Cardoso IA, Mori RM, Batista MRB, Basso LGM, Nonato MC, Costa-Filho AJ, Mendes LFS. Structural and thermodynamic analyses of human TMED1 (p24γ1) Golgi dynamics. Biochimie 2021; 192:72-82. [PMID: 34634369 DOI: 10.1016/j.biochi.2021.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/29/2021] [Accepted: 10/03/2021] [Indexed: 12/11/2022]
Abstract
The transmembrane emp24 domain-containing (TMED) proteins, also called p24 proteins, are members of a family of sorting receptors present in all representatives of the Eukarya and abundantly present in all subcompartments of the early secretory pathway, namely the endoplasmic reticulum (ER), the Golgi, and the intermediate compartment. Although essential during the bidirectional transport between the ER and the Golgi, there is still a lack of information regarding the TMED's structure across different subfamilies. Besides, although the presence of a TMED homo-oligomerization was suggested previously based on crystallographic contacts observed for the isolated Golgi Dynamics (GOLD) domain, no further analyses of its presence in solution were done. Here, we describe the first high-resolution structure of a TMED1 GOLD representative and its biophysical characterization in solution. The crystal structure showed a dimer formation that is also present in solution in a salt-dependent manner, suggesting that the GOLD domain can form homodimers in solution even in the absence of the TMED1 coiled-coil region. A molecular dynamics description of the dimer stabilization, with a phylogenetic analysis of the residues important for the oligomerization and a model for the orientation towards the lipid membrane, are also presented.
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Affiliation(s)
- Danielly C A M Mota
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Iara A Cardoso
- Laboratório de Cristalografia de Proteínas, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Renan M Mori
- Laboratório de Cristalografia de Proteínas, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Mariana R B Batista
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Luis G M Basso
- Laboratório de Ciências Físicas, Centro de Ciência e Tecnologia, Universidade Estadual do Norte Fluminense Darcy, Campos dos Goytacazes, RJ, Brazil
| | - M Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Luis F S Mendes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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7
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Xia S, Ventura IM, Blaha A, Sgromo A, Han S, Izaurralde E, Long M. Rapid Gene evolution in an ancient post-transcriptional and translational regulatory system compensates for meiotic X chromosomal inactivation. Mol Biol Evol 2021; 39:6385248. [PMID: 34626117 PMCID: PMC8763131 DOI: 10.1093/molbev/msab296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
It is conventionally assumed that conserved pathways evolve slowly with little participation of gene evolution. Nevertheless, it has been recently observed that young genes can take over fundamental functions in essential biological processes, for example, development and reproduction. It is unclear how newly duplicated genes are integrated into ancestral networks and reshape the conserved pathways of important functions. Here, we investigated origination and function of two autosomal genes that evolved recently in Drosophila: Poseidon and Zeus, which were created by RNA-based duplications from the X-linked CAF40, a subunit of the conserved CCR4–NOT deadenylase complex involved in posttranscriptional and translational regulation. Knockdown and knockout assays show that the two genes quickly evolved critically important functions in viability and male fertility. Moreover, our transcriptome analysis demonstrates that the three genes have a broad and distinct effect in the expression of hundreds of genes, with almost half of the differentially expressed genes being perturbed exclusively by one paralog, but not the others. Co-immunoprecipitation and tethering assays show that the CAF40 paralog Poseidon maintains the ability to interact with the CCR4–NOT deadenylase complex and might act in posttranscriptional mRNA regulation. The rapid gene evolution in the ancient posttranscriptional and translational regulatory system may be driven by evolution of sex chromosomes to compensate for the meiotic X chromosomal inactivation (MXCI) in Drosophila.
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Affiliation(s)
- Shengqian Xia
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Iuri M Ventura
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA.,CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, 70040-020, Brazil
| | - Andreas Blaha
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Annamaria Sgromo
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shuaibo Han
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Manyuan Long
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA
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8
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Nihei CI, Nakanishi M. Cargo selection in the early secretory pathway of African trypanosomes. Parasitol Int 2021; 84:102379. [PMID: 34000424 DOI: 10.1016/j.parint.2021.102379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/30/2021] [Accepted: 05/06/2021] [Indexed: 11/25/2022]
Abstract
Membrane and secretory proteins are synthesized by ribosomes and then enter the endoplasmic reticulum (ER) where they undergo glycosylation and quality control for proper folding. Subsequently, proteins are transported to the Golgi apparatus and then sorted to the plasma membrane or intracellular organelles. Transport vesicles are formed at ER-exit sites (ERES) on the ER with several coat protein complexes. Cargo proteins loaded into the vesicles are selected by specific interactions with cargo receptors and/or adaptors during vesicle formation. p24 family and intracellular lectin ERGIC-53-membrane proteins are the known cargo receptors acting in the early secretory pathway (ER-Golgi). Oligomerization of the cargo receptors have been suggested to play an important role in cargo selection and sorting via posttranslational modifications in fungi and metazoans. On the other hand, the mechanisms involved in the early secretory pathway in protozoa remain unclear. In this review, we focus on Trypanosoma brucei as a representative of protozoan and discuss differences and commonalities in the molecular mechanisms of its early secretory pathway compared with other organisms.
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Affiliation(s)
- Coh-Ichi Nihei
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation (BIKAKEN), 3-14-23, Kamiosaki, Shinagawa-ku, Tokyo 141-0023, Japan.
| | - Masayuki Nakanishi
- Laboratory of Biochemistry, College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.
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9
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Abstract
Regulated transport through the secretory pathway is essential for embryonic development and homeostasis. Disruptions in this process impact cell fate, differentiation and survival, often resulting in abnormalities in morphogenesis and in disease. Several congenital malformations are caused by mutations in genes coding for proteins that regulate cargo protein transport in the secretory pathway. The severity of mutant phenotypes and the unclear aetiology of transport protein-associated pathologies have motivated research on the regulation and mechanisms through which these proteins contribute to morphogenesis. This review focuses on the role of the p24/transmembrane emp24 domain (TMED) family of cargo receptors in development and disease.
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10
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Divergence in Transcriptional and Regulatory Responses to Mating in Male and Female Fruitflies. Sci Rep 2019; 9:16100. [PMID: 31695054 PMCID: PMC6834580 DOI: 10.1038/s41598-019-51141-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/24/2019] [Indexed: 11/21/2022] Open
Abstract
Mating induces extensive physiological, biochemical and behavioural changes in female animals of many taxa. In contrast, the overall phenotypic and transcriptomic consequences of mating for males, hence how they might differ from those of females, are poorly described. Post mating responses in each sex are rapidly initiated, predicting the existence of regulatory mechanisms in addition to transcriptional responses involving de novo gene expression. That post mating responses appear different for each sex also predicts that the genome-wide signatures of mating should show evidence of sex-specific specialisation. In this study, we used high resolution RNA sequencing to provide the first direct comparisons of the transcriptomic responses of male and female Drosophila to mating, and the first comparison of mating-responsive miRNAs in both sexes in any species. As predicted, the results revealed the existence of sex- and body part-specific mRNA and miRNA expression profiles. More genes were differentially expressed in the female head-thorax than the abdomen following mating, whereas the opposite was true in males. Indeed, the transcriptional profile of male head-thorax tissue was largely unaffected by mating, and no differentially expressed genes were detected at the most stringent significance threshold. A subset of ribosomal genes in females were differentially expressed in both body parts, but in opposite directions, consistent with the existence of body part-specific resource allocation switching. Novel, mating-responsive miRNAs in each sex were also identified, and a miRNA-mRNA interactions analysis revealed putative targets among mating-responsive genes. We show that the structure of genome-wide responses by each sex to mating is strongly divergent, and provide new insights into how shared genomes can achieve characteristic distinctiveness.
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11
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Moskalev AA, Shaposhnikov MV, Zemskaya NV, Koval LА, Schegoleva EV, Guvatova ZG, Krasnov GS, Solovev IA, Sheptyakov MA, Zhavoronkov A, Kudryavtseva AV. Transcriptome Analysis of Long-lived Drosophila melanogaster E(z) Mutants Sheds Light on the Molecular Mechanisms of Longevity. Sci Rep 2019; 9:9151. [PMID: 31235842 PMCID: PMC6591219 DOI: 10.1038/s41598-019-45714-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
The E(z) histone methyltransferase heterozygous mutation in Drosophila is known to increase lifespan and stress resistance. However, the longevity mechanisms of E(z) mutants have not been revealed. Using genome-wide transcriptome analysis, we demonstrated that lifespan extension, increase of resistance to hyperthermia, oxidative stress and endoplasmic reticulum stress, and fecundity enhancement in E(z) heterozygous mutants are accompanied by changes in the expression level of 239 genes (p < 0.05). Our results demonstrated sex-specific effects of E(z) mutation on gene expression, which, however, did not lead to differences in lifespan extension in both sexes. We observed that a mutation in an E(z) gene leads to perturbations in gene expression, most of which participates in metabolism, such as Carbohydrate metabolism, Lipid metabolism, Drug metabolism, Nucleotide metabolism. Age-dependent changes in the expression of genes involved in pathways related to immune response, cell cycle, and ribosome biogenesis were found.
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Affiliation(s)
- Alexey A Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia. .,Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia. .,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | | | - Nadezhda V Zemskaya
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia
| | - Liubov А Koval
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia
| | - Eugenia V Schegoleva
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia
| | - Zulfiya G Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya A Solovev
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia
| | | | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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12
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Zheng Y, Bi J, Hou MY, Shen W, Zhang W, Ai H, Yu XQ, Wang YF. Ocnus is essential for male germ cell development in Drosophila melanogaster. INSECT MOLECULAR BIOLOGY 2018; 27:545-555. [PMID: 29732657 DOI: 10.1111/imb.12393] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The ocnus (ocn) gene encodes a protein abundant in the testes, implying its role in testis development. When Drosophila melanogaster is infected with the endosymbiont wMel Wolbachia, which affects the spermatogenesis of its hosts, ocn is downregulated in the third-instar larval testes, suggesting a role of ocn in spermatogenesis. In this study, we knocked down ocn in the testes and found that the hatch rates of embryos derived from ocn-knockdown males were significantly decreased, and 84.38% of the testes were much smaller in comparison to controls. Analysis of the smaller testes showed no germ cells but they had an extended hub. Using RNA-sequencing (RNA-Seq), we identified 69 genes with at least a twofold change (q-value < 5%) in their expression after ocn knockdown; of these, eight testes-specific and three reproduction-related genes were verified to be significantly downregulated using quantitative reverse transcription-PCR. Three genes (orientation disruptor, p24-2 and CG13541) were also significantly downregulated in the presence of Wolbachia. Furthermore, 98 genes were not expressed when ocn was knocked down in testes. These results suggest that ocn plays a crucial role in male germ cell development in Drosophila, possibly by regulating the expression of multiple spermatogenesis-related genes. Our data provide important information to help understand the molecular regulatory mechanisms underlying spermatogenesis.
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Affiliation(s)
- Y Zheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - J Bi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - M-Y Hou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - W Shen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - W Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - H Ai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - X-Q Yu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Y-F Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
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13
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Chakraborty M, VanKuren NW, Zhao R, Zhang X, Kalsow S, Emerson JJ. Hidden genetic variation shapes the structure of functional elements in Drosophila. Nat Genet 2018; 50:20-25. [PMID: 29255259 PMCID: PMC5742068 DOI: 10.1038/s41588-017-0010-y] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022]
Abstract
Mutations that add, subtract, rearrange, or otherwise refashion genome structure often affect phenotypes, although the fragmented nature of most contemporary assemblies obscures them. To discover such mutations, we assembled the first new reference-quality genome of Drosophila melanogaster since its initial sequencing. By comparing this new genome to the existing D. melanogaster assembly, we created a structural variant map of unprecedented resolution and identified extensive genetic variation that has remained hidden until now. Many of these variants constitute candidates underlying phenotypic variation, including tandem duplications and a transposable element insertion that amplifies the expression of detoxification-related genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high-quality reference genomes are to deciphering phenotypes.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
| | - Nicholas W VanKuren
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Roy Zhao
- Graduate Program in Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Xinwen Zhang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
- Graduate Program in Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
| | - Shannon Kalsow
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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14
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Manning L, Sheth J, Bridges S, Saadin A, Odinammadu K, Andrew D, Spencer S, Montell D, Starz-Gaiano M. A hormonal cue promotes timely follicle cell migration by modulating transcription profiles. Mech Dev 2017; 148:56-68. [PMID: 28610887 PMCID: PMC5758037 DOI: 10.1016/j.mod.2017.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/30/2017] [Accepted: 06/09/2017] [Indexed: 12/12/2022]
Abstract
Cell migration is essential during animal development. In the Drosophila ovary, the steroid hormone ecdysone coordinates nutrient sensing, growth, and the timing of morphogenesis events including border cell migration. To identify downstream effectors of ecdysone signaling, we profiled gene expression in wild-type follicle cells compared to cells expressing a dominant negative Ecdysone receptor or its coactivator Taiman. Of approximately 400 genes that showed differences in expression, we validated 16 candidate genes for expression in border and centripetal cells, and demonstrated that seven responded to ectopic ecdysone activation by changing their transcriptional levels. We found a requirement for seven putative targets in effective cell migration, including two other nuclear hormone receptors, a calcyphosine-encoding gene, and a prolyl hydroxylase. Thus, we identified multiple new genetic regulators modulated at the level of transcription that allow cells to interpret information from the environment and coordinate cell migration in vivo.
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Affiliation(s)
- Lathiena Manning
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States; UNC Chapel Hill, NC, United States
| | - Jinal Sheth
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Stacey Bridges
- University of Maryland School of Medicine, Baltimore, MD, United States
| | - Afsoon Saadin
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Kamsi Odinammadu
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Deborah Andrew
- Johns Hopkins School of Medicine, Baltimore, MD, United States
| | | | - Denise Montell
- University of Santa Barbara, Santa Barbara, CA, United States.
| | - Michelle Starz-Gaiano
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States.
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15
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Pastor-Cantizano N, Montesinos JC, Bernat-Silvestre C, Marcote MJ, Aniento F. p24 family proteins: key players in the regulation of trafficking along the secretory pathway. PROTOPLASMA 2016; 253:967-985. [PMID: 26224213 DOI: 10.1007/s00709-015-0858-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 07/13/2015] [Indexed: 05/20/2023]
Abstract
p24 family proteins have been known for a long time, but their functions have remained elusive. However, they are emerging as essential regulators of protein trafficking along the secretory pathway, influencing the composition, structure, and function of different organelles in the pathway, especially the ER and the Golgi apparatus. In addition, they appear to modulate the transport of specific cargos, including GPI-anchored proteins, G-protein-coupled receptors, or K/HDEL ligands. As a consequence, they have been shown to play specific roles in signaling, development, insulin secretion, and the pathogenesis of Alzheimer's disease. The search of new putative ligands may open the way to discover new functions for this fascinating family of proteins.
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Affiliation(s)
- Noelia Pastor-Cantizano
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de València, Avenida Vicente Andrés Estellés, s/n, E-46100, Burjassot, Valencia, Spain
| | - Juan Carlos Montesinos
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de València, Avenida Vicente Andrés Estellés, s/n, E-46100, Burjassot, Valencia, Spain
| | - César Bernat-Silvestre
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de València, Avenida Vicente Andrés Estellés, s/n, E-46100, Burjassot, Valencia, Spain
| | - María Jesús Marcote
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de València, Avenida Vicente Andrés Estellés, s/n, E-46100, Burjassot, Valencia, Spain
| | - Fernando Aniento
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de València, Avenida Vicente Andrés Estellés, s/n, E-46100, Burjassot, Valencia, Spain.
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16
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Buffering of Genetic Regulatory Networks in Drosophila melanogaster. Genetics 2016; 203:1177-90. [PMID: 27194752 DOI: 10.1534/genetics.116.188797] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/17/2016] [Indexed: 01/01/2023] Open
Abstract
Regulatory variation in gene expression can be described by cis- and trans-genetic components. Here we used RNA-seq data from a population panel of Drosophila melanogaster test crosses to compare allelic imbalance (AI) in female head tissue between mated and virgin flies, an environmental change known to affect transcription. Indeed, 3048 exons (1610 genes) are differentially expressed in this study. A Bayesian model for AI, with an intersection test, controls type I error. There are ∼200 genes with AI exclusively in mated or virgin flies, indicating an environmental component of expression regulation. On average 34% of genes within a cross and 54% of all genes show evidence for genetic regulation of transcription. Nearly all differentially regulated genes are affected in cis, with an average of 63% of expression variation explained by the cis-effects. Trans-effects explain 8% of the variance in AI on average and the interaction between cis and trans explains an average of 11% of the total variance in AI. In both environments cis- and trans-effects are compensatory in their overall effect, with a negative association between cis- and trans-effects in 85% of the exons examined. We hypothesize that the gene expression level perturbed by cis-regulatory mutations is compensated through trans-regulatory mechanisms, e.g., trans and cis by trans-factors buffering cis-mutations. In addition, when AI is detected in both environments, cis-mated, cis-virgin, and trans-mated-trans-virgin estimates are highly concordant with 99% of all exons positively correlated with a median correlation of 0.83 for cis and 0.95 for trans We conclude that the gene regulatory networks (GRNs) are robust and that trans-buffering explains robustness.
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17
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Chen L, Tang L, Xiang H, Jin L, Li Q, Dong Y, Wang W, Zhang G. Advances in genome editing technology and its promising application in evolutionary and ecological studies. Gigascience 2014; 3:24. [PMID: 25414792 PMCID: PMC4238018 DOI: 10.1186/2047-217x-3-24] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 10/04/2014] [Indexed: 12/26/2022] Open
Abstract
Genetic modification has long provided an approach for “reverse genetics”, analyzing gene function and linking DNA sequence to phenotype. However, traditional genome editing technologies have not kept pace with the soaring progress of the genome sequencing era, as a result of their inefficiency, time-consuming and labor-intensive methods. Recently, invented genome modification technologies, such as ZFN (Zinc Finger Nuclease), TALEN (Transcription Activator-Like Effector Nuclease), and CRISPR/Cas9 nuclease (Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 nuclease) can initiate genome editing easily, precisely and with no limitations by organism. These new tools have also offered intriguing possibilities for conducting functional large-scale experiments. In this review, we begin with a brief introduction of ZFN, TALEN, and CRISPR/Cas9 technologies, then generate an extensive prediction of effective TALEN and CRISPR/Cas9 target sites in the genomes of a broad range of taxonomic species. Based on the evidence, we highlight the potential and practicalities of TALEN and CRISPR/Cas9 editing in non-model organisms, and also compare the technologies and test interesting issues such as the functions of candidate domesticated, as well as candidate genes in life-environment interactions. When accompanied with a high-throughput sequencing platform, we forecast their potential revolutionary impacts on evolutionary and ecological research, which may offer an exciting prospect for connecting the gap between DNA sequence and phenotype in the near future.
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Affiliation(s)
- Lei Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
| | - Linyi Tang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hui Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
| | - Lijun Jin
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiye Li
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Yang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650223, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223, China ; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
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18
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Abstract
During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution.
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19
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Control of male and female fertility by the netrin axon guidance genes. PLoS One 2013; 8:e72524. [PMID: 23977313 PMCID: PMC3744485 DOI: 10.1371/journal.pone.0072524] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/17/2013] [Indexed: 01/29/2023] Open
Abstract
The netrin axon guidance genes have previously been implicated in fertility in C. elegans and in vertebrates. Here we show that adult Drosophila lacking both netrin genes, NetA and NetB, have fertility defects in both sexes together with an inability to fly and reduced viability. NetAB females produce fertilized eggs at a much lower rate than wild type. Oocyte development and ovarian innervation are unaffected in NetAB females, and the reproductive tract appears normal. A small gene, hog, that resides in an intron of NetB does not contribute to the NetAB phenotype. Restoring endogenous NetB expression rescues egg-laying, but additional genetic manipulations, such as restoration of netrin midline expression and inhibition of cell death have no effect on fertility. NetAB males induce reduced egg-laying in wild type females and display mirror movements of their wings during courtship. Measurement of courtship parameters revealed no difference compared to wild type males. Transgenic manipulations failed to rescue male fertility and mirror movements. Additional genetic manipulations, such as removal of the enabled gene, a known suppressor of the NetAB embryonic CNS phenotype, did not improve the behavioral defects. The ability to fly was rescued by inhibition of neuronal cell death and pan-neural NetA expression. Based on our results we hypothesize that the adult fertility defects of NetAB mutants are due to ovulation defects in females and a failure to properly transfer sperm proteins in males, and are likely to involve multiple neural circuits.
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