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Zhu L, Du Z, Kong Y, Wang X, Li H, Hou L, Kong X. The identification, evolutionary analysis, and immune roles of Rab family members in red swamp crayfish, Procambarus clarkii. Int J Biol Macromol 2024; 276:133606. [PMID: 38972658 DOI: 10.1016/j.ijbiomac.2024.133606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/23/2024] [Accepted: 06/30/2024] [Indexed: 07/09/2024]
Abstract
The Rab GTPase constitutes the largest family of small GTPases that regulate intracellular trafficking. Different eukaryotes possess varying numbers of Rab paralogs. However, limited knowledge exists regarding the evolutionary pattern of Rab family in most major eukaryotic supergroups. This study cloned 24 Rab genes from transcriptome data of Procambarus clarkii haemocytes. The multiple sequence alignment and phylogenetic tree analysis revealed a relatively high degree of conservation for PcRab. Furthermore, PcRab exhibited similarities in motif composition with all members showing presence of G, PM, RabF, and RabSF motifs. The tertiary structure indicated that PcRab proteins mainly consisted of α-helices and β-strands, and most PcRab proteins shared similar tertiary structures, and it was indicated that they have similar protein characteristics. Protein-protein interaction prediction identified a total of 20 interacting proteins involved in vesicle trafficking, phagocytosis, and signal transduction with 193 interactions. Expression analysis showed wide expression patterns for PcRab in P. clarkii organs. Upon infection by white spot syndrome virus and Aeromonas veronii, significant induction was observed for PcRab gene expression levels, indicating their involvement in pathogen response mechanisms. The present study represents the pioneering effort in comprehensively identifying and cloning the Rab family genes in crustacean, followed by a systematic investigation into their evolutionary patterns and immune response upon pathogen infection. The results provided valuable insights for further investigation into the molecular mechanism underlying the response of P. clarkii to pathogen infection.
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Affiliation(s)
- Lei Zhu
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Observation and Research Station on Water Ecosystem in Danjiangkou Reservoir of Henan Province, College of Fisheries, Henan Normal University, Xinxiang 453007, China.
| | - Zhengyan Du
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Observation and Research Station on Water Ecosystem in Danjiangkou Reservoir of Henan Province, College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Yiming Kong
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Observation and Research Station on Water Ecosystem in Danjiangkou Reservoir of Henan Province, College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Xinru Wang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Observation and Research Station on Water Ecosystem in Danjiangkou Reservoir of Henan Province, College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Hao Li
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Observation and Research Station on Water Ecosystem in Danjiangkou Reservoir of Henan Province, College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Libo Hou
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Observation and Research Station on Water Ecosystem in Danjiangkou Reservoir of Henan Province, College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Xianghui Kong
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Observation and Research Station on Water Ecosystem in Danjiangkou Reservoir of Henan Province, College of Fisheries, Henan Normal University, Xinxiang 453007, China
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Khan YA, Ian White K, Pfuetzner RA, Singal B, Esquivies L, Mckenzie G, Liu F, DeLong K, Choi UB, Montabana E, Mclaughlin T, Wickner WT, Brunger AT. Sec18 side-loading is essential for universal SNARE recycling across cellular contexts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.30.610324. [PMID: 39257774 PMCID: PMC11384006 DOI: 10.1101/2024.08.30.610324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
SNARE proteins drive membrane fusion as their core domains zipper into a parallel four-helix bundle1,2. After fusion, these bundles are disassembled by the AAA+ protein Sec18/NSF and its adaptor Sec17/ α-SNAP3,4 to make them available for subsequent rounds of membrane fusion. SNARE domains are often flanked by C-terminal transmembrane or N-terminal domains5. Previous structures of the NSF-α-SNAP-SNARE complex revealed SNARE domain threaded through the D1 ATPase ring6, posing a topological constraint as SNARE transmembrane domains would prevent complete substrate threading as suggested for other AAA+ systems7. Here, in vivo mass-spectrometry reveals N-terminal SNARE domain interactions with Sec18, exacerbating this topological issue. Cryo-EM structures of a yeast SNARE complex, Sec18, and Sec17 in a non-hydrolyzing condition shows SNARE Sso1 threaded through the D1 and D2 ATPase rings of Sec18, with its folded, N-terminal Habc domain interacting with the D2 ring. This domain does not unfold during Sec18/NSF activity. Cryo-EM structures under hydrolyzing conditions revealed substrate-released and substrate-free states of Sec18 with a coordinated opening in the side of the ATPase rings. Thus, Sec18/NSF operates by substrate side-loading and unloading topologically constrained SNARE substrates.
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Affiliation(s)
- Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
| | - K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Richard A Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Bharti Singal
- Stanford Cryo-EM microscopy center, Stanford University, Palo Alto, CA, USA
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Garvey Mckenzie
- Stanford University Mass Spectrometry, Stanford University, Palo Alto, CA, USA
| | - Fang Liu
- Stanford University Mass Spectrometry, Stanford University, Palo Alto, CA, USA
| | - Katherine DeLong
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Uchoer B Choi
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | | | - Theresa Mclaughlin
- Stanford University Mass Spectrometry, Stanford University, Palo Alto, CA, USA
| | - William T Wickner
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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Zuriegat Q, Abubakar YS, Wang Z, Chen M, Zhang J. Emerging Roles of Exocyst Complex in Fungi: A Review. J Fungi (Basel) 2024; 10:614. [PMID: 39330374 PMCID: PMC11433146 DOI: 10.3390/jof10090614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/19/2024] [Accepted: 08/21/2024] [Indexed: 09/28/2024] Open
Abstract
The exocyst complex, an evolutionarily conserved octameric protein assembly, plays a central role in the targeted binding and fusion of vesicles at the plasma membrane. In fungal cells, this transport system is essential for polarized growth, morphogenesis, cell wall maintenance and virulence. Recent advances have greatly improved our understanding of the role and regulation of the exocyst complex in fungi. This review synthesizes these developments and focuses on the intricate interplay between the exocyst complex, specific fungal cargos and regulatory proteins. Insights into thestructure of the exocyst and its functional dynamics have revealed new dimensions of its architecture and its interactions with the cellular environment. Furthermore, the regulation of exocyst activity involves complex signaling pathways and interactions with cytoskeletal elements that are crucial for its role in vesicle trafficking. By exploring these emerging themes, this review provides a comprehensive overview of the multifaceted functions of the exocyst complex in fungal biology. Understanding these mechanisms offers potential avenues for novel therapeutic strategies against fungal pathogens and insights into the general principles of vesicle trafficking in eukaryotic cells. The review therefore highlights the importance of the exocyst complex in maintaining cellular functions and its broader implications in fungal pathogenicity and cell biology.
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Affiliation(s)
- Qussai Zuriegat
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.S.A.); (Z.W.)
| | - Yakubu Saddeeq Abubakar
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.S.A.); (Z.W.)
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.S.A.); (Z.W.)
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, China
| | - Meilian Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, China
| | - Jun Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (Y.S.A.); (Z.W.)
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Wu H, Nguyen H, Hashim PH, Fogelgren B, Duncan FE, Ward WS. Oocyte-specific EXOC5 expression is required for mouse oogenesis and folliculogenesis. Mol Hum Reprod 2024; 30:gaae026. [PMID: 39037927 PMCID: PMC11299862 DOI: 10.1093/molehr/gaae026] [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: 05/10/2024] [Revised: 07/11/2024] [Indexed: 07/24/2024] Open
Abstract
EXOC5 is a crucial component of a large multi-subunit tethering complex, the exocyst complex, that is required for fusion of secretory vesicles with the plasma membrane. Exoc5 deleted mice die as early embryos. Therefore, to determine the role of EXOC5 in follicular and oocyte development, it was necessary to produce a conditional knockout (cKO), Zp3-Exoc5-cKO, in which Exoc5 was deleted only in oocytes. The first wave of folliculogenesis appeared histologically normal and progressed to the antral stage. However, after IVF with normal sperm, oocytes collected from the first wave (superovulated 21-day-old cKO mice) were shown to be developmentally incompetent. Adult follicular waves did not progress beyond the secondary follicle stage where they underwent apoptosis. Female cKO mice were infertile. Overall, these data suggest that the first wave of folliculogenesis is less sensitive to oocyte-specific loss of Exoc5, but the resulting gametes have reduced developmental competence. In contrast, subsequent waves of folliculogenesis require oocyte-specific Exoc5 for development past the preantral follicle stage. The Zp3-Exoc5-cKO mouse provides a model for disrupting folliculogenesis that also enables the separation between the first and subsequent waves of folliculogenesis.
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Affiliation(s)
- Hongwen Wu
- Department of Anatomy, Biochemistry & Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
- Department of Obstetrics, Gynecology & Women’s Health, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Hieu Nguyen
- Department of Anatomy, Biochemistry & Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
- Department of Obstetrics, Gynecology & Women’s Health, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Prianka H Hashim
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ben Fogelgren
- Department of Anatomy, Biochemistry & Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
- Department of Obstetrics, Gynecology & Women’s Health, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Francesca E Duncan
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - W Steven Ward
- Department of Anatomy, Biochemistry & Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
- Department of Obstetrics, Gynecology & Women’s Health, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
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Abstract
While the involvement of actin polymerization in cell migration is well-established, much less is known about the role of transmembrane water flow in cell motility. Here, we investigate the role of water influx in a prototypical migrating cell, the neutrophil, which undergoes rapid, directed movement to sites of injury, and infection. Chemoattractant exposure both increases cell volume and potentiates migration, but the causal link between these processes are not known. We combine single-cell volume measurements and a genome-wide CRISPR screen to identify the regulators of chemoattractant-induced neutrophil swelling, including NHE1, AE2, PI3K-gamma, and CA2. Through NHE1 inhibition in primary human neutrophils, we show that cell swelling is both necessary and sufficient for the potentiation of migration following chemoattractant stimulation. Our data demonstrate that chemoattractant-driven cell swelling complements cytoskeletal rearrangements to enhance migration speed.
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Affiliation(s)
- Tamas L Nagy
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Cardiovascular Research Institute, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Strickland
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Cardiovascular Research Institute, University of California, San FranciscoSan FranciscoUnited States
| | - Orion D Weiner
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Cardiovascular Research Institute, University of California, San FranciscoSan FranciscoUnited States
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Zuo X, Winkler B, Lerner K, Ilatovskaya DV, Zamaro AS, Dang Y, Su Y, Deng P, Fitzgibbon W, Hartman J, Park KM, Lipschutz JH. Cilia-deficient renal tubule cells are primed for injury with mitochondrial defects and aberrant tryptophan metabolism. Am J Physiol Renal Physiol 2024; 327:F61-F76. [PMID: 38721661 PMCID: PMC11390130 DOI: 10.1152/ajprenal.00225.2023] [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: 08/01/2023] [Revised: 04/11/2024] [Accepted: 04/24/2024] [Indexed: 06/21/2024] Open
Abstract
The exocyst and Ift88 are necessary for primary ciliogenesis. Overexpression of Exoc5 (OE), a central exocyst component, resulted in longer cilia and enhanced injury recovery. Mitochondria are involved in acute kidney injury (AKI). To investigate cilia and mitochondria, basal respiration and mitochondrial maximal and spare respiratory capacity were measured in Exoc5 OE, Exoc5 knockdown (KD), Exoc5 ciliary targeting sequence mutant (CTS-mut), control Madin-Darby canine kidney (MDCK), Ift88 knockout (KO), and Ift88 rescue cells. In Exoc5 KD, Exoc5 CTS-mut, and Ift88 KO cells, these parameters were decreased. In Exoc5 OE and Ift88 rescue cells they were increased. Reactive oxygen species were higher in Exoc5 KD, Exoc5 CTS-mut, and Ift88 KO cells compared with Exoc5 OE, control, and Ift88 rescue cells. By electron microscopy, mitochondria appeared abnormal in Exoc5 KD, Exoc5 CTS-mut, and Ift88 KO cells. A metabolomics screen of control, Exoc5 KD, Exoc5 CTS-mut, Exoc5 OE, Ift88 KO, and Ift88 rescue cells showed a marked increase in tryptophan levels in Exoc5 CTS-mut (113-fold) and Exoc5 KD (58-fold) compared with control cells. A 21% increase was seen in Ift88 KO compared with rescue cells. In Exoc5 OE compared with control cells, tryptophan was decreased 59%. To determine the effects of ciliary loss on AKI, we generated proximal tubule-specific Exoc5 and Ift88 KO mice. These mice had loss of primary cilia, decreased mitochondrial ATP synthase, and increased tryptophan in proximal tubules with greater injury following ischemia-reperfusion. These data indicate that cilia-deficient renal tubule cells are primed for injury with mitochondrial defects in tryptophan metabolism.NEW & NOTEWORTHY Mitochondria are centrally involved in acute kidney injury (AKI). Here, we show that cilia-deficient renal tubule cells both in vitro in cell culture and in vivo in mice are primed for injury with mitochondrial defects and aberrant tryptophan metabolism. These data suggest therapeutic strategies such as enhancing ciliogenesis or improving mitochondrial function to protect patients at risk for AKI.
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Affiliation(s)
- Xiaofeng Zuo
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Brennan Winkler
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Kasey Lerner
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Daria V Ilatovskaya
- Department of Physiology, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - Aleksandra S Zamaro
- Department of Physiology, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - Yujing Dang
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Yanhui Su
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Peifeng Deng
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Wayne Fitzgibbon
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Jessica Hartman
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Kwon Moo Park
- Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Joshua H Lipschutz
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
- Department of Medicine, Ralph H. Johnson Veterans Affairs Health Care System, Charleston, South Carolina, United States
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7
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Allen H, Zhu X, Li S, Gu Y. The TRAPPIII subunit, Trs85, has a dual role in the trafficking of cellulose synthase complexes in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1475-1485. [PMID: 38402593 DOI: 10.1111/tpj.16688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/27/2024]
Abstract
Plant cell walls are essential for defining plant growth and development, providing structural support to the main body and responding to abiotic and biotic cues. Cellulose, the main structural polymer of plant cell walls, is synthesized at the plasma membrane by cellulose synthase complexes (CSCs). The construction and transport of CSCs to and from the plasma membrane is poorly understood but is known to rely on the coordinated activity of cellulose synthase-interactive protein 1 (CSI1), a key regulator of CSC trafficking. In this study, we found that Trs85, a TRAPPIII complex subunit, interacted with CSI1 in vitro. Using functional genetics and live-cell imaging, we have shown that trs85-1 mutants have reduced cellulose content, stimulated CSC delivery, an increased population of static CSCs and deficient clathrin-mediated endocytosis in the primary cell wall. Overall, our findings suggest that Trs85 has a dual role in the trafficking of CSCs, by negatively regulating the exocytosis and clathrin-mediated endocytosis of CSCs.
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Affiliation(s)
- Holly Allen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Xiaoyu Zhu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Shundai Li
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Ying Gu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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Zeng BZ, Zhou XT, Gou HM, Che LL, Lu SX, Yang JB, Cheng YJ, Liang GP, Mao J. Molecular Evolution of SNAREs in Vitis vinifera and Expression Analysis under Phytohormones and Abiotic Stress. Int J Mol Sci 2024; 25:5984. [PMID: 38892171 PMCID: PMC11173047 DOI: 10.3390/ijms25115984] [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: 04/21/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
SNARE proteins (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) play a key role in mediating a variety of plant biological processes. Currently, the function of the SNARE gene family in phytohormonal and abiotic stress treatments in grapevine is currently unknown, making it worthwhile to characterize and analyze the function and expression of this family in grapevine. In the present study, 52 VvSNARE genes were identified and predominantly distributed on 18 chromosomes. Secondary structures showed that the VvSNARE genes family irregular random coils and α-helices. The promoter regions of the VvSNARE genes were enriched for light-, abiotic-stress-, and hormone-responsive elements. Intraspecific collinearity analysis identified 10 pairs collinear genes within the VvSNARE family and unveiled a greater number of collinear genes between grapevine and apple, as well as Arabidopsis thaliana, but less associations with Oryza sativa. Quantitative real-time PCR (qRT-PCR) analyses showed that the VvSNARE genes have response to treatments with ABA, NaCl, PEG, and 4 °C. Notably, VvSNARE2, VvSNARE14, VvSNARE15, and VvSNARE17 showed up-regulation in response to ABA treatment. VvSNARE2, VvSNARE15, VvSNARE18, VvSNARE19, VvSNARE20, VvSNARE24, VvSNARE25, and VvSNARE29 exhibited significant up-regulation when exposed to NaCl treatment. The PEG treatment led to significant down-regulation of VvSNARE1, VvSNARE8, VvSNARE23, VvSNARE25, VvSNARE26, VvSNARE31, and VvSNARE49 gene expression. The expression levels of VvSNARE37, VvSNARE44, and VvSNARE46 were significantly enhanced after exposure to 4 °C treatment. Furthermore, subcellular localization assays certified that VvSNARE37, VvSNARE44, and VvSNARE46 were specifically localized at the cell membrane. Overall, this study showed the critical role of the VvSNARE genes family in the abiotic stress response of grapevines, thereby providing novel candidate genes such as VvSNARE37, VvSNARE44, and VvSNARE46 for further exploration in grapevine stress tolerance research.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (B.-z.Z.); (X.-t.Z.); (H.-m.G.); (L.-l.C.); (S.-x.L.); (J.-b.Y.); (Y.-j.C.); (G.-p.L.)
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9
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Tang VT, Xiang J, Chen Z, McCormick J, Abbineni PS, Chen XW, Hoenerhoff M, Emmer BT, Khoriaty R, Lin JD, Ginsburg D. Functional overlap between the mammalian Sar1a and Sar1b paralogs in vivo. Proc Natl Acad Sci U S A 2024; 121:e2322164121. [PMID: 38687799 PMCID: PMC11087783 DOI: 10.1073/pnas.2322164121] [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: 12/20/2023] [Accepted: 03/29/2024] [Indexed: 05/02/2024] Open
Abstract
Proteins carrying a signal peptide and/or a transmembrane domain enter the intracellular secretory pathway at the endoplasmic reticulum (ER) and are transported to the Golgi apparatus via COPII vesicles or tubules. SAR1 initiates COPII coat assembly by recruiting other coat proteins to the ER membrane. Mammalian genomes encode two SAR1 paralogs, SAR1A and SAR1B. While these paralogs exhibit ~90% amino acid sequence identity, it is unknown whether they perform distinct or overlapping functions in vivo. We now report that genetic inactivation of Sar1a in mice results in lethality during midembryogenesis. We also confirm previous reports that complete deficiency of murine Sar1b results in perinatal lethality. In contrast, we demonstrate that deletion of Sar1b restricted to hepatocytes is compatible with survival, though resulting in hypocholesterolemia that can be rescued by adenovirus-mediated overexpression of either SAR1A or SAR1B. To further examine the in vivo function of these two paralogs, we genetically engineered mice with the Sar1a coding sequence replacing that of Sar1b at the endogenous Sar1b locus. Mice homozygous for this allele survive to adulthood and are phenotypically normal, demonstrating complete or near-complete overlap in function between the two SAR1 protein paralogs in mice. These data also suggest upregulation of SAR1A gene expression as a potential approach for the treatment of SAR1B deficiency (chylomicron retention disease) in humans.
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Affiliation(s)
- Vi T. Tang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI48109
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
| | - Jie Xiang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
| | - Zhimin Chen
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
| | - Joseph McCormick
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
| | - Prabhodh S. Abbineni
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL60153
| | - Xiao-Wei Chen
- State Key Laboratory of Membrane Biology, Peking University, Beijing100871, China
| | - Mark Hoenerhoff
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI48109
| | - Brian T. Emmer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI48109
| | - Rami Khoriaty
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI48109
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI48109
| | - Jiandie D. Lin
- Department of Human Genetics, University of Michigan, Ann Arbor, MI48109
| | - David Ginsburg
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI48109
- Department of Human Genetics, University of Michigan, Ann Arbor, MI48109
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI48109
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10
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Orr A, Wickner W. Sec18 binds the tethering/SM complex HOPS to engage the Qc-SNARE for membrane fusion. Mol Biol Cell 2024; 35:ar71. [PMID: 38536444 PMCID: PMC11151092 DOI: 10.1091/mbc.e24-02-0060] [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: 02/06/2024] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/18/2024] Open
Abstract
Membrane fusion is regulated by Rab GTPases, their tethering effectors such as HOPS, SNARE proteins on each fusion partner, SM proteins to catalyze SNARE assembly, Sec17 (SNAP), and Sec18 (NSF). Though concentrated HOPS can support fusion without Sec18, we now report that fusion falls off sharply at lower HOPS levels, where direct Sec18 binding to HOPS restores fusion. This Sec18-dependent fusion needs adenine nucleotide but neither ATP hydrolysis nor Sec17. Sec18 enhances HOPS recognition of the Qc-SNARE. With high levels of HOPS, Qc has a Km for fusion of a few nM. Either lower HOPS levels, or substitution of a synthetic tether for HOPS, strikingly increases the Km for Qc to several hundred nM. With dilute HOPS, Sec18 returns the Km for Qc to low nM. In contrast, HOPS concentration and Sec18 have no effect on Qb-SNARE recognition. Just as Qc is required for fusion but not for the initial assembly of SNAREs in trans, impaired Qc recognition by limiting HOPS without Sec18 still allows substantial trans-SNARE assembly. Thus, in addition to the known Sec18 functions of disassembling SNARE complexes, oligomerizing Sec17 for membrane association, and allowing Sec17 to drive fusion without complete SNARE zippering, we report a fourth Sec18 function, the Sec17-independent binding of Sec18 to HOPS to enhance functional Qc-SNARE engagement.
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Affiliation(s)
- Amy Orr
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755-3844
| | - William Wickner
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755-3844
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11
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Nagy TL, Strickland E, Weiner OD. Neutrophils actively swell to potentiate rapid migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.15.540704. [PMID: 37292824 PMCID: PMC10245588 DOI: 10.1101/2023.05.15.540704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
While the involvement of actin polymerization in cell migration is well-established, much less is known about the role of transmembrane water flow in cell motility. Here, we investigate the role of water influx in a prototypical migrating cell, the neutrophil, which undergoes rapid, directed movement to sites of injury and infection. Chemoattractant exposure both increases cell volume and potentiates migration, but the causal link between these processes is not known. We combine single cell volume measurements and a genome-wide CRISPR screen to identify the regulators of chemoattractant-induced neutrophil swelling, including NHE1, AE2, PI3K-gamma, and CA2. Through NHE1 inhibition in primary human neutrophils, we show that cell swelling is both necessary and sufficient for the potentiation of migration following chemoattractant stimulation. Our data demonstrate that chemoattractant-driven cell swelling complements cytoskeletal rearrangements to enhance migration speed.
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Affiliation(s)
- Tamas L Nagy
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Evelyn Strickland
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Orion D Weiner
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
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12
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Yang Y, Liu Z, Lu Y, Yu X, Zhu R, Cai X, Lin J, Wang Z, Zha D. Rab3a attenuates spinal cord injury by mediating vesicle release. Brain Res Bull 2024; 208:110884. [PMID: 38253132 DOI: 10.1016/j.brainresbull.2024.110884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 01/24/2024]
Abstract
BACKGROUND Rab3a regulates vesicle secretion and transport. Emerging evidences have shown that extracellular vesicles (EVs) can reach target lesions of injured spinal cords and exert a positive effect on these lesions. However, the molecular mechanism by which Rab3a regulates vesicle secretion to ameliorate spinal cord injury (SCI) is not fully understood. METHODS An SCI rat model was established which was used to examine the pathological changes and Rab3a expression in spinal cord tissue. Rab3a was overexpressed in the model rats to demonstrate its effect on SCI repair. Rab3a was also knocked down in neuronal cells to verify its role in vesicle secretion and neuronal cells. The binding protein of Rab3a was identified by Co-IP and mass spectrometry. RESULTS Rab3a was significantly downregulated in SCI rats and Rab3a overexpression promoted SCI repair. Rab3a knockdown inhibited the secretion of neuronal cell-derived EVs. Compared to the EVs from the equal number of control neuronal cells, EVs from Rab3a-knockdown neuronal cells promoted M1 macrophage polarization, which in turn, promoted neuronal cell apoptosis. Mechanistically, STXBP1 was identified as a binding protein of Rab3a, and their interaction promoted the secretion of neuronal cell-derived EVs. Furthermore, METTL2b was significantly downregulated in SCI rats, and METTL2b knockdown significantly reduced Rab3a protein expression. CONCLUSION These results suggest that Rab3a promotes the secretion of neuronal cell-derived EVs by interacting with its binding protein STXBP1. Neuronal cells-derived EVs inhibited the polarization of M1 macrophages in the spinal cord microenvironment, thereby promoting SCI repair. Our findings provide a theoretical basis for the clinical treatment of SCI.
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Affiliation(s)
- Yuhao Yang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, China
| | - Ziqiao Liu
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, China
| | - Yang Lu
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan University, Key Laboratory of Regenerative Medicine, Ministry of Education, Guangzhou, Guangdong 510630, China
| | - Xincheng Yu
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, China
| | - Rui Zhu
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, China
| | - Xingda Cai
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, China
| | - Jinghua Lin
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, China
| | - Zemin Wang
- Department of Orthopaedics, Chashan Hospital, Dongguan, Guangdong 523000, China
| | - Dingsheng Zha
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, China; Department of Orthopedics, The Affiliated Shunde Hospital of Jinan University, Foshan, Guangdong 528303, China.
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13
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Kang CJ, Guzmán-Clavel LE, Lei K, Koo M, To S, Roche JP. The exocyst subunit Sec15 is critical for proper synaptic development and function at the Drosophila NMJ. Mol Cell Neurosci 2024; 128:103914. [PMID: 38086519 DOI: 10.1016/j.mcn.2023.103914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
The exocyst protein complex is important for targeted vesicle fusion in a variety of cell types, however, its function in neurons is still not entirely known. We found that presynaptic knockdown (KD) of the exocyst component sec15 by transgenic RNAi expression caused a number of unexpected morphological and physiological defects in the synapse. These include the development of active zones (AZ) devoid of essential presynaptic proteins, an increase in the branching of the presynaptic arbor, the appearance of satellite boutons, and a decrease in the amplitude of stimulated postsynaptic currents as well as a decrease in the frequency of spontaneous synaptic vesicle release. We also found the release of extracellular vesicles from the presynaptic neuron was greatly diminished in the Sec15 KDs. These effects were mimicked by presynaptic knockdown of Rab11, a protein known to interact with the exocyst. sec15 RNAi expression caused an increase in phosphorylated Mothers against decapentaplegic (pMad) in the presynaptic terminal, an indication of enhanced bone morphogenic protein (BMP) signaling. Some morphological phenotypes caused by Sec15 knockdown were reduced by attenuation of BMP signaling through knockdown of wishful thinking (Wit), while other phenotypes were unaffected. Individual knockdown of multiple proteins of the exocyst complex also displayed a morphological phenotype similar to Sec15 KD. We conclude that Sec15, functioning as part of the exocyst complex, is critically important for proper formation and function of neuronal synapses. We propose a model in which Sec15 is involved in the trafficking of vesicles from the recycling endosome to the cell membrane as well as possibly trafficking extracellular vesicles for presynaptic release and these processes are necessary for the correct structure and function of the synapse.
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Affiliation(s)
- Chris J Kang
- Neuroscience Program, Amherst College, Amherst, MA 01002, United States of America
| | - Luis E Guzmán-Clavel
- Neuroscience Program, Amherst College, Amherst, MA 01002, United States of America
| | - Katherine Lei
- Neuroscience Program, Amherst College, Amherst, MA 01002, United States of America
| | - Martin Koo
- Neuroscience Program, Amherst College, Amherst, MA 01002, United States of America
| | - Steven To
- Neuroscience Program, Amherst College, Amherst, MA 01002, United States of America
| | - John P Roche
- Neuroscience Program, Amherst College, Amherst, MA 01002, United States of America; Department of Biology, Amherst College, Amherst, MA 01002, United States of America.
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14
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Tang VT, Xiang J, Chen Z, McCormick J, Abbineni PS, Chen XW, Hoenerhoff M, Emmer BT, Khoriaty R, Lin JD, Ginsburg D. Functional overlap between the mammalian Sar1a and Sar1b paralogs in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582310. [PMID: 38463989 PMCID: PMC10925261 DOI: 10.1101/2024.02.27.582310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Proteins carrying a signal peptide and/or a transmembrane domain enter the intracellular secretory pathway at the endoplasmic reticulum (ER) and are transported to the Golgi apparatus via COPII vesicles or tubules. SAR1 initiates COPII coat assembly by recruiting other coat proteins to the ER membrane. Mammalian genomes encode two SAR1 paralogs, SAR1A and SAR1B. While these paralogs exhibit ~90% amino acid sequence identity, it is unknown whether they perform distinct or overlapping functions in vivo. We now report that genetic inactivation of Sar1a in mice results in lethality during mid-embryogenesis. We also confirm previous reports that complete deficiency of murine Sar1b results in perinatal lethality. In contrast, we demonstrate that deletion of Sar1b restricted to hepatocytes is compatible with survival, though resulting in hypocholesterolemia that can be rescued by adenovirus-mediated overexpression of either SAR1A or SAR1B. To further examine the in vivo function of these 2 paralogs, we genetically engineered mice with the Sar1a coding sequence replacing that of Sar1b at the endogenous Sar1b locus. Mice homozygous for this allele survive to adulthood and are phenotypically normal, demonstrating complete or near-complete overlap in function between the two SAR1 protein paralogs in mice. These data also suggest upregulation of SAR1A gene expression as a potential approach for the treatment of SAR1B deficiency (chylomicron retention disease) in humans.
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Affiliation(s)
- Vi T. Tang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Jie Xiang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Zhimin Chen
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Joseph McCormick
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Prabhodh S. Abbineni
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60153
| | - Xiao-Wei Chen
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Mark Hoenerhoff
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Brian T. Emmer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Rami Khoriaty
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Jiandie D. Lin
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - David Ginsburg
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109
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15
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Dorantes-Torres C, Carrera-Reyna M, Santos W, Sánchez-López R, Merino E. PhyloString: A web server designed to identify, visualize, and evaluate functional relationships between orthologous protein groups across different phylogenetic lineages. PLoS One 2024; 19:e0297010. [PMID: 38277370 PMCID: PMC10817156 DOI: 10.1371/journal.pone.0297010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/27/2023] [Indexed: 01/28/2024] Open
Abstract
Proteins are biological units whose essence is defined by their functional relationships with other proteins or biomolecules such as RNA, DNA, lipids, or carbohydrates. These functions encompass enzymatic, structural, regulatory, or physical interaction roles. The STRING database (Nucleic Acids Research, 8 Jan 2021;49(D1): D605-12) provides an index that defines the functional interaction networks between proteins in model organisms. To facilitate the identification, visualization, and evaluation of potential functional networks across organisms from different phylogenetic lineages, we have developed PhyloString (https://biocomputo.ibt.unam.mx/phylostring/), a web server that utilizes the indices of the STRING database. PhyloString decomposes these functional networks into modules, representing cohesive units of proteins grouped based on their similarity of STRING values and the phylogenetic origins of their respective organisms. This study presents and thoroughly discusses examples of such functional networks and their modules identified using PhyloString.
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Affiliation(s)
- Claudia Dorantes-Torres
- Department of Molecular Microbiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Maricela Carrera-Reyna
- Department of Molecular Microbiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Walter Santos
- Department of Molecular Microbiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rosana Sánchez-López
- Department of Plant Molecular Biology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Enrique Merino
- Department of Molecular Microbiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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16
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Robinson CM, Duggan A, Forrester A. ER exit in physiology and disease. Front Mol Biosci 2024; 11:1352970. [PMID: 38314136 PMCID: PMC10835805 DOI: 10.3389/fmolb.2024.1352970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024] Open
Abstract
The biosynthetic secretory pathway is comprised of multiple steps, modifications and interactions that form a highly precise pathway of protein trafficking and secretion, that is essential for eukaryotic life. The general outline of this pathway is understood, however the specific mechanisms are still unclear. In the last 15 years there have been vast advancements in technology that enable us to advance our understanding of this complex and subtle pathway. Therefore, based on the strong foundation of work performed over the last 40 years, we can now build another level of understanding, using the new technologies available. The biosynthetic secretory pathway is a high precision process, that involves a number of tightly regulated steps: Protein folding and quality control, cargo selection for Endoplasmic Reticulum (ER) exit, Golgi trafficking, sorting and secretion. When deregulated it causes severe diseases that here we categorise into three main groups of aberrant secretion: decreased, excess and altered secretion. Each of these categories disrupts organ homeostasis differently, effecting extracellular matrix composition, changing signalling events, or damaging the secretory cells due to aberrant intracellular accumulation of secretory proteins. Diseases of aberrant secretion are very common, but despite this, there are few effective therapies. Here we describe ER exit sites (ERES) as key hubs for regulation of the secretory pathway, protein quality control and an integratory hub for signalling within the cell. This review also describes the challenges that will be faced in developing effective therapies, due to the specificity required of potential drug candidates and the crucial need to respect the fine equilibrium of the pathway. The development of novel tools is moving forward, and we can also use these tools to build our understanding of the acute regulation of ERES and protein trafficking. Here we review ERES regulation in context as a therapeutic strategy.
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Affiliation(s)
- Claire M Robinson
- School of Medicine, Health Sciences Centre, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Aislinn Duggan
- School of Medicine, Health Sciences Centre, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Alison Forrester
- Research Unit of Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
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17
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Ohya Y, Ghanegolmohammadi F, Itto-Nakama K. Application of unimodal probability distribution models for morphological phenotyping of budding yeast. FEMS Yeast Res 2024; 24:foad056. [PMID: 38169030 PMCID: PMC10804223 DOI: 10.1093/femsyr/foad056] [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: 06/28/2023] [Revised: 09/28/2023] [Accepted: 12/30/2023] [Indexed: 01/05/2024] Open
Abstract
Morphological phenotyping of the budding yeast Saccharomyces cerevisiae has helped to greatly clarify the functions of genes and increase our understanding of cellular functional networks. It is necessary to understand cell morphology and perform quantitative morphological analysis (QMA) but assigning precise values to morphological phenotypes has been challenging. We recently developed the Unimodal Morphological Data image analysis pipeline for this purpose. All true values can be estimated theoretically by applying an appropriate probability distribution if the distribution of experimental values follows a unimodal pattern. This reliable pipeline allows several downstream analyses, including detection of subtle morphological differences, selection of mutant strains with similar morphology, clustering based on morphology, and study of morphological diversity. In addition to basic research, morphological analyses of yeast cells can also be used in applied research to monitor breeding and fermentation processes and control the fermentation activity of yeast cells.
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Affiliation(s)
- Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
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18
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Gallo R, Rai AK, McIntyre ABR, Meyer K, Pelkmans L. DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites. Dev Cell 2023; 58:1880-1897.e11. [PMID: 37643612 DOI: 10.1016/j.devcel.2023.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/16/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
The dual-specificity kinase DYRK3 controls the formation and dissolution of multiple biomolecular condensates, regulating processes including stress recovery and mitotic progression. Here, we report that DYRK3 functionally interacts with proteins associated with endoplasmic reticulum (ER) exit sites (ERESs) and that inhibition of DYRK3 perturbs the organization of the ERES-Golgi interface and secretory trafficking. DYRK3-mediated regulation of ERES depends on the N-terminal intrinsically disordered region (IDR) of the peripheral membrane protein SEC16A, which co-phase separates with ERES components to form liquid-like condensates on the surface of the ER. By modulating the liquid-like properties of ERES, we show that their physical state is essential for functional cargo trafficking through the early secretory pathway. Our findings support a mechanism whereby phosphorylation by DYRK3 and its reversal by serine-threonine phosphatases regulate the material properties of ERES to create a favorable physicochemical environment for directional membrane traffic in eukaryotic cells.
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Affiliation(s)
- Raffaella Gallo
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Arpan Kumar Rai
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
| | - Alexa B R McIntyre
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Katrina Meyer
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
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19
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Nenciarini S, Cavalieri D. Immunomodulatory Potential of Fungal Extracellular Vesicles: Insights for Therapeutic Applications. Biomolecules 2023; 13:1487. [PMID: 37892168 PMCID: PMC10605264 DOI: 10.3390/biom13101487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Extracellular vesicles (EVs) are membranous vesicular organelles that perform a variety of biological functions including cell communication across different biological kingdoms. EVs of mammals and, to a lesser extent, bacteria have been deeply studied over the years, whereas investigations of fungal EVs are still in their infancy. Fungi, encompassing both yeast and filamentous forms, are increasingly recognized for their production of extracellular vesicles (EVs) containing a wealth of proteins, lipids, and nucleic acids. These EVs play pivotal roles in orchestrating fungal communities, bolstering pathogenicity, and mediating interactions with the environment. Fungal EVs have emerged as promising candidates for innovative applications, not only in the management of mycoses but also as carriers for therapeutic molecules. Yet, numerous questions persist regarding fungal EVs, including their mechanisms of generation, release, cargo regulation, and discharge. This comprehensive review delves into the present state of knowledge regarding fungal EVs and provides fresh insights into the most recent hypotheses on the mechanisms driving their immunomodulatory properties. Furthermore, we explore the considerable potential of fungal EVs in the realms of medicine and biotechnology. In the foreseeable future, engineered fungal cells may serve as vehicles for tailoring cargo- and antigen-specific EVs, positioning them as invaluable biotechnological tools for diverse medical applications, such as vaccines and drug delivery.
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Affiliation(s)
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy;
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20
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Quint M, Delker C, Balasubramanian S, Balcerowicz M, Casal JJ, Castroverde CDM, Chen M, Chen X, De Smet I, Fankhauser C, Franklin KA, Halliday KJ, Hayes S, Jiang D, Jung JH, Kaiserli E, Kumar SV, Maag D, Oh E, Park CM, Penfield S, Perrella G, Prat S, Reis RS, Wigge PA, Willige BC, van Zanten M. 25 Years of thermomorphogenesis research: milestones and perspectives. TRENDS IN PLANT SCIENCE 2023; 28:1098-1100. [PMID: 37574427 DOI: 10.1016/j.tplants.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Abstract
In 1998, Bill Gray and colleagues showed that warm temperatures trigger arabidopsis hypocotyl elongation in an auxin-dependent manner. This laid the foundation for a vibrant research discipline. With several active members of the 'thermomorphogenesis' community, we here reflect on 25 years of elevated ambient temperature research and look to the future.
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Affiliation(s)
- Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany.
| | - Carolin Delker
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | | | - Martin Balcerowicz
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, UK
| | - Jorge J Casal
- IFEVA, Universidad de Buenos Aires and CONICET, 1417 Buenos Aires, Argentina; Fundación Instituto Leloir, C1405 BWE, Buenos Aires, Argentina
| | | | - Meng Chen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Xuemei Chen
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Christian Fankhauser
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Karen J Halliday
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh 3H9 3BF, UK
| | - Scott Hayes
- Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Danhua Jiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jae-Hoon Jung
- Department of Biological Sciences, Sungkyunkwan University, 16419 Suwon, South Korea
| | - Eirini Kaiserli
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - S Vinod Kumar
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Daniel Maag
- Department of Pharmaceutical Biology, Julius von Sachs Institute of Biosciences, University of Würzburg, 97082 Würzburg, Germany
| | - Eunkyoo Oh
- Department of Life Sciences, Korea University, 02841 Seoul, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, 08826 Seoul, Korea; Plant Genomics and Breeding Institute, Seoul National University, 08826 Seoul, Korea
| | - Steven Penfield
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, UK
| | - Giorgio Perrella
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Salomé Prat
- Department of Plant Responses to Stress, Centre for Research in Agricultural Genomics (CRAG), Campus UAB, 08193 Cerdanyola, Barcelona, Spain
| | - Rodrigo S Reis
- Institute of Plant Sciences, University of Bern, 3013 Bern, Switzerland
| | - Philip A Wigge
- Leibniz Institut für Gemüse und Zierpflanzenbau, 14979 Großbeeren, Germany; Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Björn C Willige
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Martijn van Zanten
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands.
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21
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Heckle LA, Kozminski KG. Osh-dependent and -independent Regulation of PI4P Levels During Polarized Growth of Saccharomyces cerevisiae. Mol Biol Cell 2023; 34:ar104. [PMID: 37556206 PMCID: PMC10559303 DOI: 10.1091/mbc.e23-03-0089] [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: 03/10/2023] [Revised: 07/03/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
Polarized secretion facilitates polarized cell growth. For a secretory vesicle to dock at the plasma membrane, it must mature with a progressive association or dissociation of molecules that are, respectively, necessary for or inhibitory to vesicle docking, including an exchange of Rab GTPases. In current models, oxysterol-binding protein homologue 4 (Osh4p) establishes a phosphatidylinositol 4-phosphate (PI4P) gradient along the secretory trafficking pathway such that vesicles have higher PI4P levels after budding from the trans-Golgi relative to when vesicles arrive at the plasma membrane. In this study, using the lipid-binding domain P4M and live-cell imaging, we show that secretory vesicle-associated PI4P levels remain constant when vesicles traffic from the trans-Golgi to the plasma membrane. We also show that deletion of OSH4 does not alter vesicle-associated PI4P levels, though loss of any individual member of the OSH family or complete loss of OSH family function alters the intracellular distribution of PI4P. We propose a model in which the Rab GTPases Ypt32p and Sec4p remain associated with a secretory vesicle during trafficking, independent of PI4P levels and Osh4p. Together these data indicate the necessity of experiments revealing the location and timing of events required for vesicle maturation.
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Affiliation(s)
- Lindsay A. Heckle
- Department of Biology, University of Virginia, Charlottesville, VA 22904
| | - Keith G. Kozminski
- Department of Biology, University of Virginia, Charlottesville, VA 22904
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
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22
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Logue MJE, Farquhar RE, Eckhoff-Björngard Y, Cheung TT, Devor DC, McDonald FJ, Hamilton KL. The exocyst complex is required for the trafficking and delivery of KCa3.1 to the basolateral membrane of polarized epithelia. Am J Physiol Cell Physiol 2023; 324:C1249-C1262. [PMID: 37125772 PMCID: PMC10243536 DOI: 10.1152/ajpcell.00374.2022] [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: 08/17/2022] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
Control of the movement of ions and water across epithelia is essential for homeostasis. Changing the number or activity of ion channels at the plasma membrane is a significant regulator of epithelial transport. In polarized epithelia, the intermediate-conductance calcium-activated potassium channel, KCa3.1 is delivered to the basolateral membrane where it generates and maintains the electrochemical gradients required for epithelial transport. The mechanisms that control the delivery of KCa3.1 to the basolateral membrane are still emerging. Herein, we investigated the role of the highly conserved tethering complex exocyst. In epithelia, exocyst is involved in the tethering of post-Golgi secretory vesicles with the basolateral membrane, which is required before membrane fusion. In our Fisher rat thyroid cell line that stably expresses KCa3.1, siRNA knockdown of either of the exocyst subunits Sec3, Sec6, or Sec8 significantly decreased KCa3.1-specific current. In addition, knockdown of exocyst complex subunits significantly reduced the basolateral membrane protein level of KCa3.1. Finally, co-immunoprecipitation experiments suggest associations between Sec6 and KCa3.1, but not between Sec8 and KCa3.1. Collectively, based on these data and our previous studies, we suggest that components of exocyst complex are crucially important in the tethering of KCa3.1 to the basolateral membrane. After which, Soluble N-ethylmaleimide-sensitive factor (SNF) Attachment Receptors (SNARE) proteins aid in the insertion of KCa3.1-containing vesicles into the basolateral membrane of polarized epithelia.NEW & NOTEWORTHY Our Ussing chamber and immunoblot experiments demonstrate that when subunits of the exocyst complex were transiently knocked down, this significantly reduced the basolateral population and functional expression of KCa3.1. These data suggest, combined with our protein association experiments, that the exocyst complex regulates the tethering of KCa3.1-containing vesicles to the basolateral membrane prior to the SNARE-dependent insertion of channels into the basolateral membrane of epithelial cells.
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Affiliation(s)
- Matthew J E Logue
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Rachel E Farquhar
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Yoakim Eckhoff-Björngard
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Tanya T Cheung
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Daniel C Devor
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Fiona J McDonald
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Kirk L Hamilton
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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23
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Park M, Mayer U, Richter S, Jürgens G. NSF/αSNAP2-mediated cis-SNARE complex disassembly precedes vesicle fusion in Arabidopsis cytokinesis. NATURE PLANTS 2023; 9:889-897. [PMID: 37264150 DOI: 10.1038/s41477-023-01427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/04/2023] [Indexed: 06/03/2023]
Abstract
Eukaryotic membrane fusion requires trans-SNARE complexes bridging the gap between adjacent membranes1. Fusion between a transport vesicle and its target membrane transforms the trans- into a cis-SNARE complex. The latter interacts with the hexameric AAA+-ATPase N-ethylmaleimide-sensitive factor (NSF) and its co-factor alpha-soluble NSF attachment protein (αSNAP), forming a 20S complex2,3. ATPase activity disassembles the SNAP receptor (SNARE) complex into Qa-SNARE, which folds back onto itself, and its partners4,5. The fusion of identical membranes has a different sequence of events6. The fusion partners each have cis-SNARE complexes to be broken up by NSF and αSNAP. The Qa-SNARE monomers are then stabilized by interaction with Sec1/Munc18-type regulators (SM proteins) to form trans-SNARE complexes, as shown for the yeast vacuole7. Membrane fusion in Arabidopsis cytokinesis is formally akin to vacuolar fusion8. Membrane vesicles fuse with one another to form the partitioning membrane known as the cell plate. Cis-SNARE complexes of cytokinesis-specific Qa-SNARE KNOLLE and its SNARE partners are assembled at the endoplasmic reticulum and delivered by traffic via the Golgi/trans-Golgi network to the cell division plane9. The SM protein KEULE is required for the formation of trans-SNARE complexes between adjacent membrane vesicles10. Here we identify NSF and its adaptor αSNAP2 as necessary for the disassembly of KNOLLE cis-SNARE complexes, which is a prerequisite for KNOLLE-KEULE interaction in cytokinesis. In addition, we show that NSF is required for other trafficking pathways and interacts with the respective Q-SNAREs. The SNARE complex disassembly machinery is conserved in plants and plays a unique essential role in cytokinesis.
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Affiliation(s)
- Misoon Park
- ZMBP, Developmental Genetics, University of Tübingen, Tübingen, Germany
| | - Ulrike Mayer
- ZMBP, Developmental Genetics, University of Tübingen, Tübingen, Germany
| | - Sandra Richter
- ZMBP, Microscopy, University of Tübingen, Tübingen, Germany
| | - Gerd Jürgens
- ZMBP, Developmental Genetics, University of Tübingen, Tübingen, Germany.
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24
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Montag K, Ivanov R, Bauer P. Role of SEC14-like phosphatidylinositol transfer proteins in membrane identity and dynamics. FRONTIERS IN PLANT SCIENCE 2023; 14:1181031. [PMID: 37255567 PMCID: PMC10225987 DOI: 10.3389/fpls.2023.1181031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/05/2023] [Indexed: 06/01/2023]
Abstract
Membrane identity and dynamic processes, that act at membrane sites, provide important cues for regulating transport, signal transduction and communication across membranes. There are still numerous open questions as to how membrane identity changes and the dynamic processes acting at the surface of membranes are regulated in diverse eukaryotes in particular plants and which roles are being played by protein interaction complexes composed of peripheral and integral membrane proteins. One class of peripheral membrane proteins conserved across eukaryotes comprises the SEC14-like phosphatidylinositol transfer proteins (SEC14L-PITPs). These proteins share a SEC14 domain that contributes to membrane identity and fulfills regulatory functions in membrane trafficking by its ability to sense, bind, transport and exchange lipophilic substances between membranes, such as phosphoinositides and diverse other lipophilic substances. SEC14L-PITPs can occur as single-domain SEC14-only proteins in all investigated organisms or with a modular domain structure as multi-domain proteins in animals and streptophytes (comprising charales and land plants). Here, we present an overview on the functional roles of SEC14L-PITPs, with a special focus on the multi-domain SEC14L-PITPs of the SEC14-nodulin and SEC14-GOLD group (PATELLINs, PATLs in plants). This indicates that SEC14L-PITPs play diverse roles from membrane trafficking to organism fitness in plants. We concentrate on the structure of SEC14L-PITPs, their ability to not only bind phospholipids but also other lipophilic ligands, and their ability to regulate complex cellular responses through interacting with proteins at membrane sites.
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Affiliation(s)
- Karolin Montag
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
- Center of Excellence on Plant Sciences (CEPLAS), Germany
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25
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Hornbergs J, Montag K, Loschwitz J, Mohr I, Poschmann G, Schnake A, Gratz R, Brumbarova T, Eutebach M, Angrand K, Fink-Straube C, Stühler K, Zeier J, Hartmann L, Strodel B, Ivanov R, Bauer P. SEC14-GOLD protein PATELLIN2 binds IRON-REGULATED TRANSPORTER1 linking root iron uptake to vitamin E. PLANT PHYSIOLOGY 2023; 192:504-526. [PMID: 36493393 PMCID: PMC10152663 DOI: 10.1093/plphys/kiac563] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/23/2022] [Accepted: 12/07/2022] [Indexed: 05/03/2023]
Abstract
Organisms require micronutrients, and Arabidopsis (Arabidopsis thaliana) IRON-REGULATED TRANSPORTER1 (IRT1) is essential for iron (Fe2+) acquisition into root cells. Uptake of reactive Fe2+ exposes cells to the risk of membrane lipid peroxidation. Surprisingly little is known about how this is avoided. IRT1 activity is controlled by an intracellular variable region (IRT1vr) that acts as a regulatory protein interaction platform. Here, we describe that IRT1vr interacted with peripheral plasma membrane SEC14-Golgi dynamics (SEC14-GOLD) protein PATELLIN2 (PATL2). SEC14 proteins bind lipophilic substrates and transport or present them at the membrane. To date, no direct roles have been attributed to SEC14 proteins in Fe import. PATL2 affected root Fe acquisition responses, interacted with ROS response proteins in roots, and alleviated root lipid peroxidation. PATL2 had high affinity in vitro for the major lipophilic antioxidant vitamin E compound α-tocopherol. Molecular dynamics simulations provided insight into energetic constraints and the orientation and stability of the PATL2-ligand interaction in atomic detail. Hence, this work highlights a compelling mechanism connecting vitamin E with root metal ion transport at the plasma membrane with the participation of an IRT1-interacting and α-tocopherol-binding SEC14 protein.
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Affiliation(s)
- Jannik Hornbergs
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Karolin Montag
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Jennifer Loschwitz
- Institute of Theoretical Chemistry and Computer Chemistry, Heinrich Heine University, Düsseldorf 40225, Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Inga Mohr
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Anika Schnake
- Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Regina Gratz
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | | | - Monique Eutebach
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Kalina Angrand
- Department of Biosciences-Plant Biology, Saarland University, Campus A2.4, D-66123 Saarbrücken, Germany
| | | | - Kai Stühler
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Molecular Proteomics Laboratory, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Jürgen Zeier
- Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf 40225, Germany
| | - Laura Hartmann
- Institute of Macromolecular Chemistry, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Birgit Strodel
- Institute of Theoretical Chemistry and Computer Chemistry, Heinrich Heine University, Düsseldorf 40225, Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf 40225, Germany
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26
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Pereira C, Stalder D, Anderson GS, Shun-Shion AS, Houghton J, Antrobus R, Chapman MA, Fazakerley DJ, Gershlick DC. The exocyst complex is an essential component of the mammalian constitutive secretory pathway. J Cell Biol 2023; 222:e202205137. [PMID: 36920342 PMCID: PMC10041652 DOI: 10.1083/jcb.202205137] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/11/2022] [Accepted: 02/01/2023] [Indexed: 03/16/2023] Open
Abstract
Secreted proteins fulfill a vast array of functions, including immunity, signaling, and extracellular matrix remodeling. In the trans-Golgi network, proteins destined for constitutive secretion are sorted into post-Golgi carriers which fuse with the plasma membrane. The molecular machinery involved is poorly understood. Here, we have used kinetic trafficking assays and transient CRISPR-KO to study biosynthetic sorting from the Golgi to the plasma membrane. Depletion of all canonical exocyst subunits causes cargo accumulation in post-Golgi carriers. Exocyst subunits are recruited to and co-localize with carriers. Exocyst abrogation followed by kinetic trafficking assays of soluble cargoes results in intracellular cargo accumulation. Unbiased secretomics reveals impairment of soluble protein secretion after exocyst subunit knockout. Importantly, in specialized cell types, the loss of exocyst prevents constitutive secretion of antibodies in lymphocytes and of leptin in adipocytes. These data identify exocyst as the functional tether of secretory post-Golgi carriers at the plasma membrane and an essential component of the mammalian constitutive secretory pathway.
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Affiliation(s)
- Conceição Pereira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Danièle Stalder
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Amber S. Shun-Shion
- Metabolic Research Laboratory, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Jack Houghton
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Daniel J. Fazakerley
- Metabolic Research Laboratory, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - David C. Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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27
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Liu RJY, Al-Molieh Y, Chen SZ, Drobac M, Urban D, Chen CH, Yao HHY, Geng RSQ, Li L, Pluthero FG, Benlekbir S, Rubinstein JL, Kahr WHA. The Sec1/Munc18 protein VPS33B forms a uniquely bidirectional complex with VPS16B. J Biol Chem 2023; 299:104718. [PMID: 37062417 DOI: 10.1016/j.jbc.2023.104718] [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: 01/08/2023] [Revised: 03/03/2023] [Accepted: 04/07/2023] [Indexed: 04/18/2023] Open
Abstract
Loss of function variants of VPS33B and VIPAS39 (encoding VPS16B) are causative for arthrogryposis, renal dysfunction and cholestasis (ARC) syndrome, where early lethality of patients indicates that VPS33B and VPS16B play essential cellular roles. VPS33B is a member of the Sec1/Munc18 (SM) protein family, and thus thought to facilitate vesicular fusion via interaction with SNARE complexes, as does its paralog VPS33A in the homotypic fusion and vacuole sorting (HOPS) complex. VPS33B and VPS16B have been shown to associate, but little is known about the composition, structure or function of the VPS33B/VPS16B complex. We show here that human VPS33B/VPS16B is a high molecular weight complex, which we expressed in yeast to obtain material for structural, composition and stability analysis. Circular dichroism data indicate VPS33B/VPS16B has a well-folded α-helical secondary structure, for which size exclusion chromatography-multi angle light scattering revealed a MW of ∼315 kDa. Quantitative immunoblotting indicated the complex has a VPS33B:VPS16B ratio of 2:3. Expression of ARC syndrome-causing VPS33B missense variants showed that L30P disrupts complex formation, but not S243F or H344D. Truncated VPS16B containing amino acids 143-316 was sufficient to form a complex with VPS33B. Small angle X-ray scattering and negative staining electron microscopy revealed a two-lobed shape for VPS33B/VPS16B. Avidin tagging indicated that each lobe contains a VPS33B molecule, and they are oriented in opposite directions. From this we propose a structure for VPS33B/VPS16B that allows the copies of VPS33B at each end to interact with separate SNARE bundles and/or SNAREpins, plus their associated membrane components. Thus our observations reveal the only known potentially bidirectional SM protein complex.
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Affiliation(s)
- Richard J Y Liu
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Yusef Al-Molieh
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Shao Z Chen
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Marko Drobac
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Denisa Urban
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Chang H Chen
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Helen H Y Yao
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Ryan S Q Geng
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Ling Li
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Fred G Pluthero
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Samir Benlekbir
- Molecular Medicine Program, Research Institute, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - John L Rubinstein
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada; Molecular Medicine Program, Research Institute, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Walter H A Kahr
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada; Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada; Division of Haematology/Oncology, Department of Paediatrics, University of Toronto and The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
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28
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Safavian D, Kim MS, Xie H, El-Zeiry M, Palander O, Dai L, Collins RF, Froese C, Shannon R, Nagata KI, Trimble WS. Septin-mediated RhoA activation engages the exocyst complex to recruit the cilium transition zone. J Cell Biol 2023; 222:e201911062. [PMID: 36912772 PMCID: PMC10039714 DOI: 10.1083/jcb.201911062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/25/2022] [Accepted: 01/05/2023] [Indexed: 03/14/2023] Open
Abstract
Septins are filamentous GTPases that play important but poorly characterized roles in ciliogenesis. Here, we show that SEPTIN9 regulates RhoA signaling at the base of cilia by binding and activating the RhoA guanine nucleotide exchange factor, ARHGEF18. GTP-RhoA is known to activate the membrane targeting exocyst complex, and suppression of SEPTIN9 causes disruption of ciliogenesis and mislocalization of an exocyst subunit, SEC8. Using basal body-targeted proteins, we show that upregulating RhoA signaling at the cilium can rescue ciliary defects and mislocalization of SEC8 caused by global SEPTIN9 depletion. Moreover, we demonstrate that the transition zone components, RPGRIP1L and TCTN2, fail to accumulate at the transition zone in cells lacking SEPTIN9 or depleted of the exocyst complex. Thus, SEPTIN9 regulates the recruitment of transition zone proteins on Golgi-derived vesicles by activating the exocyst via RhoA to allow the formation of primary cilia.
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Affiliation(s)
- Darya Safavian
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Moshe S. Kim
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hong Xie
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maha El-Zeiry
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Oliva Palander
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Lu Dai
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Richard F. Collins
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Carol Froese
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rachel Shannon
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Koh-ichi Nagata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Aichi, Japan
| | - William S. Trimble
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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29
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Xia X, Peng CW, Ye QT, Bing XL, Hong XY. Rop plays conserved roles in the reproductive and digestive processes of spider mites. INSECT SCIENCE 2023; 30:351-364. [PMID: 35980307 DOI: 10.1111/1744-7917.13103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/19/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Ras opposite (Rop) is known to play an essential role in regulating vesicle trafficking, including synaptic transmission and general secretion. The fundamental roles of Rop have been confirmed by the observation that null mutations in many organisms generate lethal phenotypes during embryogenesis. However, the effects of Rop during the postembryonic stages, especially in non-model organisms, remain largely unknown. Here, we provide new data that enhance our understanding of Rop's roles in the adults of multiple species of Tetranychus spider mites (Acari: Tetranychidae), a class of notorious agricultural pests. Our in silico and experimental evidence demonstrated that Rop is under purifying selection and is highly conserved in Tetranychus spp. RNA interference experiments showed that Rop is required for maintaining normal fecundity but has no significant effect on survival. We further demonstrate that knockdown of Rop darkens the body color of spider mites and blocks the excretion of fecal pellets, which is likely to be related to an abnormality in the excretion of food waste in the digestive system. Overall, our findings clarify novel functions of a vesicle trafficking-related gene in the adult stage of multiple Tetranychus species and highlight the need to evaluate the roles of essential genes in various organisms.
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Affiliation(s)
- Xue Xia
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Chang-Wu Peng
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Qing-Tong Ye
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Li Bing
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
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30
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Shi R, Lu W, Tian Y, Wang B. Intestinal SEC16B modulates obesity by regulating chylomicron metabolism. Mol Metab 2023; 70:101693. [PMID: 36796587 PMCID: PMC9976576 DOI: 10.1016/j.molmet.2023.101693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/30/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
OBJECTIVE Genome-wide association studies (GWAS) have identified genetic variants in SEC16 homolog B (SEC16B) locus to be associated with obesity and body mass index (BMI) in various populations. SEC16B encodes a scaffold protein located at endoplasmic reticulum (ER) exit sites that is implicated to participate in the trafficking of COPII vesicles in mammalian cells. However, the function of SEC16B in vivo, especially in lipid metabolism, has not been investigated. METHODS We generated Sec16b intestinal knockout (IKO) mice and assessed the impact of its deficiency on high-fat diet (HFD) induced obesity and lipid absorption in both male and female mice. We examined lipid absorption in vivo by acute oil challenge and fasting/HFD refeeding. Biochemical analyses and imaging studies were performed to understand the underlying mechanisms. RESULTS Our results showed that Sec16b intestinal knockout (IKO) mice, especially female mice, were protected from HFD-induced obesity. Loss of Sec16b in intestine dramatically reduced postprandial serum triglyceride output upon intragastric lipid load or during overnight fasting and HFD refeeding. Further studies showed that intestinal Sec16b deficiency impaired apoB lipidation and chylomicron secretion. CONCLUSIONS Our studies demonstrated that intestinal SEC16B is required for dietary lipid absorption in mice. These results revealed that SEC16B plays important roles in chylomicron metabolism, which may shed light on the association between variants in SEC16B and obesity in human.
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Affiliation(s)
- Ruicheng Shi
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wei Lu
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ye Tian
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bo Wang
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Division of Nutritional Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Kashikuma R, Nagano M, Shimamura H, Nukaga K, Katsumata I, Y. Toshima J, Toshima J. Role of phosphatidylserine in the localization of cell surface membrane proteins in yeast. Cell Struct Funct 2023; 48:19-30. [PMID: 36517018 PMCID: PMC10725852 DOI: 10.1247/csf.22081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Phosphatidylserine (PS) is a constituent of the cell membrane, being especially abundant in the cytoplasmic leaflet, and plays important roles in a number of cellular functions, including the formation of cell polarity and intracellular vesicle transport. Several studies in mammalian cells have suggested the role of PS in retrograde membrane traffic through endosomes, but in yeast, where PS is localized primarily at the plasma membrane (PM), the role in intracellular organelles remains unclear. Additionally, it is reported that polarized endocytic site formation is defective in PS-depleted yeast cells, but the role in the endocytic machinery has not been well understood. In this study, to clarify the role of PS in the endocytic pathway, we analyzed the effect of PS depletion on endocytic internalization and post-endocytic transport. We demonstrated that in cell lacking the PS synthase Cho1p (cho1Δ cell), binding and internalization of mating pheromone α-factor into the cell was severely impaired. Interestingly, the processes of endocytosis were mostly unaffected, but protein transport from the trans-Golgi network (TGN) to the PM was defective and localization of cell surface proteins was severely impaired in cho1Δ cells. We also showed that PS accumulated in intracellular compartments in cells lacking Rcy1p and Vps52p, both of which are implicated in endosome-to-PM transport via the TGN, and that the number of Snx4p-residing endosomes was increased in cho1Δ cells. These results suggest that PS plays a crucial role in the transport and localization of cell surface membrane proteins.Key words: phosphatidylserine, endocytosis, recycling, vesicle transport.
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Affiliation(s)
- Ryutaro Kashikuma
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijyuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Makoto Nagano
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijyuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Hiroki Shimamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijyuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Kouya Nukaga
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijyuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Ikumi Katsumata
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijyuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Junko Y. Toshima
- School of Health Science, Tokyo University of Technology, 5-23-22 Nishikamata, Ota-ku, Tokyo 144-8535, Japan
| | - Jiro Toshima
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijyuku, Katsushika-ku, Tokyo 125-8585, Japan
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Qian H, Sun L, Wu M, Zhao W, Liu M, Liang S, Zhu X, Li L, Su Z, Lu J, Lin F, Liu X. The COPII subunit MoSec24B is involved in development, pathogenicity and autophagy in the rice blast fungus. FRONTIERS IN PLANT SCIENCE 2023; 13:1074107. [PMID: 36699840 PMCID: PMC9868959 DOI: 10.3389/fpls.2022.1074107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
The endoplasmic reticulum (ER) acts as the starting point of the secretory pathway, where approximately one-third of the proteins are correctly folded and modified, loaded into vesicles, and transported to the Golgi for further processing and modification. In this process, COPII vesicles are responsible for transporting cargo proteins from the ER to the Golgi. Here, we identified the inner shell subunit of COPII vesicles (MoSec24B) and explored the importance of MoSec24B in the rice blast fungus. The targeted disruption of MoSec24B led to decreased growth, reduced conidiation, restricted glycogen and lipids utilization, sensitivity to the cell wall and hypertonic stress, the failure of septin-mediated repolarization of appressorium, impaired appressorium turgor pressure, and decreased ability to infect, which resulted in reduced pathogenicity to the host plant. Furthermore, MoSec24B functions in the three mitogen-activated protein kinase (MAPK) signaling pathways by acting with MoMst50. Deletion of MoSec24B caused reduced lipidation of MoAtg8, accelerated degradation of exogenously introduced GFP-MoAtg8, and increased lipidation of MoAtg8 upon treatment with a late inhibitor of autophagy (BafA1), suggesting that MoSec24B regulates the fusion of late autophagosomes with vacuoles. Together, these results suggest that MoSec24B exerts a significant role in fungal development, the pathogenesis of filamentous fungi and autophagy.
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Affiliation(s)
- Hui Qian
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Lixiao Sun
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Minghua Wu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Wenhui Zhao
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengyu Liu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuang Liang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lin Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenzhu Su
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jianping Lu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Fucheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohong Liu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Tang VT, Ginsburg D. Cargo selection in endoplasmic reticulum-to-Golgi transport and relevant diseases. J Clin Invest 2023; 133:163838. [PMID: 36594468 PMCID: PMC9797344 DOI: 10.1172/jci163838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Most proteins destined for the extracellular space or various intracellular compartments must traverse the intracellular secretory pathway. The first step is the recruitment and transport of cargoes from the endoplasmic reticulum (ER) lumen to the Golgi apparatus by coat protein complex II (COPII), consisting of five core proteins. Additional ER transmembrane proteins that aid cargo recruitment are referred to as cargo receptors. Gene duplication events have resulted in multiple COPII paralogs present in the mammalian genome. Here, we review the functions of each COPII protein, human disorders associated with each paralog, and evidence for functional conservation between paralogs. We also provide a summary of current knowledge regarding two prototypical cargo receptors in mammals, LMAN1 and SURF4, and their roles in human health and disease.
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Affiliation(s)
- Vi T. Tang
- Department of Molecular and Integrative Physiology,,Life Sciences Institute
| | - David Ginsburg
- Life Sciences Institute,,Department of Internal Medicine,,Department of Human Genetics,,Department of Pediatrics and Communicable Diseases, and,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA
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Tran ML, Kim Y, von Blume J. Quantification of Protein Exit at the Trans-Golgi Network. Methods Mol Biol 2023; 2557:583-594. [PMID: 36512239 DOI: 10.1007/978-1-0716-2639-9_35] [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] [Indexed: 12/15/2022]
Abstract
With one-third of all newly synthesized proteins entering the secretory pathway, correct protein sorting is essential for cellular homeostasis. In the last three decades, researchers have developed numerous biochemical, genetic, and cell biological approaches to study protein export and sorting from the trans-Golgi network (TGN). However, accurately quantifying protein transport from one compartment to the next in the secretory pathway has been challenging. The Retention Using Selective Hooks (RUSH) system is a method that allows monitoring trafficking of a protein of interest in real time, similar to a pulse-chase experiment but without the need of radiolabeling. Accurate calculations, however, are necessary and currently lacking. Here, we combine the RUSH system with live cell imaging to quantify and calculate half lives. We exemplify our approach using a soluble secreted protein (LyzC). This system will benefit membrane trafficking researchers by adding numbers to protein export and comparing the export kinetics of different cargoes and variating conditions.
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Affiliation(s)
- Mai Ly Tran
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Yeongho Kim
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Julia von Blume
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
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Palfreyman MT, West SE, Jorgensen EM. SNARE Proteins in Synaptic Vesicle Fusion. ADVANCES IN NEUROBIOLOGY 2023; 33:63-118. [PMID: 37615864 DOI: 10.1007/978-3-031-34229-5_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Neurotransmitters are stored in small membrane-bound vesicles at synapses; a subset of synaptic vesicles is docked at release sites. Fusion of docked vesicles with the plasma membrane releases neurotransmitters. Membrane fusion at synapses, as well as all trafficking steps of the secretory pathway, is mediated by SNARE proteins. The SNAREs are the minimal fusion machinery. They zipper from N-termini to membrane-anchored C-termini to form a 4-helix bundle that forces the apposed membranes to fuse. At synapses, the SNAREs comprise a single helix from syntaxin and synaptobrevin; SNAP-25 contributes the other two helices to complete the bundle. Unc13 mediates synaptic vesicle docking and converts syntaxin into the permissive "open" configuration. The SM protein, Unc18, is required to initiate and proofread SNARE assembly. The SNAREs are then held in a half-zippered state by synaptotagmin and complexin. Calcium removes the synaptotagmin and complexin block, and the SNAREs drive vesicle fusion. After fusion, NSF and alpha-SNAP unwind the SNAREs and thereby recharge the system for further rounds of fusion. In this chapter, we will describe the discovery of the SNAREs, their relevant structural features, models for their function, and the central role of Unc18. In addition, we will touch upon the regulation of SNARE complex formation by Unc13, complexin, and synaptotagmin.
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Affiliation(s)
- Mark T Palfreyman
- School of Biological Sciences, and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Sam E West
- School of Biological Sciences, and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Erik M Jorgensen
- School of Biological Sciences, and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA.
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Swope RD, Hertzler JI, Stone MC, Kothe GO, Rolls MM. The exocyst complex is required for developmental and regenerative neurite growth in vivo. Dev Biol 2022; 492:1-13. [PMID: 36162553 PMCID: PMC10228574 DOI: 10.1016/j.ydbio.2022.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022]
Abstract
The exocyst complex is an important regulator of intracellular trafficking and tethers secretory vesicles to the plasma membrane. Understanding of its role in neuron outgrowth remains incomplete, and previous studies have come to different conclusions about its importance for axon and dendrite growth, particularly in vivo. To investigate exocyst function in vivo we used Drosophila sensory neurons as a model system. To bypass early developmental requirements in other cell types, we used neuron-specific RNAi to target seven exocyst subunits. Initial neuronal development proceeded normally in these backgrounds, however, we considered this could be due to residual exocyst function. To probe neuronal growth capacity at later times after RNAi initiation, we used laser microsurgery to remove axons or dendrites and prompt regrowth. Exocyst subunit RNAi reduced axon regeneration, although new axons could be specified. In control neurons, a vesicle trafficking marker often concentrated in the new axon, but this pattern was disrupted in Sec6 RNAi neurons. Dendrite regeneration was also severely reduced by exocyst RNAi, even though the trafficking marker did not accumulate in a strongly polarized manner during normal dendrite regeneration. The requirement for the exocyst was not limited to injury contexts as exocyst subunit RNAi eliminated dendrite regrowth after developmental pruning. We conclude that the exocyst is required for injury-induced and developmental neurite outgrowth, but that residual protein function can easily mask this requirement.
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Affiliation(s)
- Rachel D Swope
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA
| | - J Ian Hertzler
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA
| | - Michelle C Stone
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA
| | - Gregory O Kothe
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA
| | - Melissa M Rolls
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, University Park, PA, 16802, USA.
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Gao YQ, Chao DY. Localization and circulation: vesicle trafficking in regulating plant nutrient homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1350-1363. [PMID: 36321185 DOI: 10.1111/tpj.16020] [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: 07/23/2022] [Revised: 10/11/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Nutrient homeostasis is essential for plant growth and reproduction. Plants, therefore, have evolved tightly regulated mechanisms for the uptake, translocation, distribution, and storage of mineral nutrients. Considering that inorganic nutrient transport relies on membrane-based transporters and channels, vesicle trafficking, one of the fundamental cell biological processes, has become a hotspot of plant nutrition studies. In this review, we summarize recent advances in the study of how vesicle trafficking regulates nutrient homeostasis to contribute to the adaptation of plants to heterogeneous environments. We also discuss new perspectives on future studies, which may inspire researchers to investigate new approaches to improve the human diet and health by changing the nutrient quality of crops.
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Affiliation(s)
- Yi-Qun Gao
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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Simsek-Kiper PO, Jacob P, Upadhyai P, Taşkıran ZE, Guleria VS, Karaosmanoglu B, Imren G, Gocmen R, Bhavani GS, Kausthubham N, Shah H, Utine GE, Boduroglu K, Girisha KM. Biallelic loss-of-function variants in EXOC6B are associated with impaired primary ciliogenesis and cause spondylo-epi-metaphyseal dysplasia with joint laxity type 3. Hum Mutat 2022; 43:2116-2129. [PMID: 36150098 PMCID: PMC7615863 DOI: 10.1002/humu.24478] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/30/2022] [Accepted: 09/21/2022] [Indexed: 01/25/2023]
Abstract
Spondylo-epi-metaphyseal dysplasias with joint laxity, type 3 (SEMDJL3) is a genetic skeletal disorder characterized by multiple joint dislocations, caused by biallelic pathogenic variants in the EXOC6B gene. Only four individuals from two families have been reported to have this condition to date. The molecular pathogenesis related to primary ciliogenesis has not been enumerated in subjects with SEMDJL3. In this study, we report two additional affected individuals from unrelated families with biallelic pathogenic variants, c.2122+15447_2197-59588del and c.401T>G in EXOC6B identified by exome sequencing. One of the affected individuals had an intellectual disability and central nervous system anomalies, including hydrocephalus, hypoplastic mesencephalon, and thin corpus callosum. Using the fibroblast cell lines, we demonstrate the primary evidence for the abrogation of exocytosis in an individual with SEMDLJ3 leading to impaired primary ciliogenesis. Osteogenesis differentiation and pathways related to the extracellular matrix were also found to be reduced. Additionally, we provide a review of the clinical and molecular profile of all the mutation-proven patients reported hitherto, thereby further characterizing SEMDJL3. SEMDJL3 with biallelic pathogenic variants in EXOC6B might represent yet another ciliopathy with central nervous system involvement and joint dislocations.
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Affiliation(s)
| | - Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Zihni Ekim Taşkıran
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Vishal S. Guleria
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Beren Karaosmanoglu
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Gozde Imren
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Gandham S. Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hitesh Shah
- Department of Pediatric Orthopaedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gulen Eda Utine
- Department of Pediatric Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Koray Boduroglu
- Department of Pediatric Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Katta M. Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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Gingras RM, Sulpizio AM, Park J, Bretscher A. High-resolution secretory timeline from vesicle formation at the Golgi to fusion at the plasma membrane in S. cerevisiae. eLife 2022; 11:e78750. [PMID: 36331188 PMCID: PMC9671497 DOI: 10.7554/elife.78750] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022] Open
Abstract
Most of the components in the yeast secretory pathway have been studied, yet a high-resolution temporal timeline of their participation is lacking. Here, we define the order of acquisition, lifetime, and release of critical components involved in late secretion from the Golgi to the plasma membrane. Of particular interest is the timing of the many reported effectors of the secretory vesicle Rab protein Sec4, including the myosin-V Myo2, the exocyst complex, the lgl homolog Sro7, and the small yeast-specific protein Mso1. At the trans-Golgi network (TGN) Sec4's GEF, Sec2, is recruited to Ypt31-positive compartments, quickly followed by Sec4 and Myo2 and vesicle formation. While transported to the bud tip, the entire exocyst complex, including Sec3, is assembled on to the vesicle. Before fusion, vesicles tether for 5 s, during which the vesicle retains the exocyst complex and stimulates lateral recruitment of Rho3 on the plasma membrane. Sec2 and Myo2 are rapidly lost, followed by recruitment of cytosolic Sro7, and finally the SM protein Sec1, which appears for just 2 s prior to fusion. Perturbation experiments reveal an ordered and robust series of events during tethering that provide insights into the function of Sec4 and effector exchange.
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Affiliation(s)
- Robert M Gingras
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Abigail M Sulpizio
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Joelle Park
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Anthony Bretscher
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
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40
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Zhou L, Xue X, Yang K, Feng Z, Liu M, Pastor-Pareja JC. Convergence of secretory, endosomal, and autophagic routes in trans-Golgi-associated lysosomes. J Cell Biol 2022; 222:213547. [PMID: 36239631 PMCID: PMC9577102 DOI: 10.1083/jcb.202203045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 08/17/2022] [Accepted: 09/23/2022] [Indexed: 12/15/2022] Open
Abstract
At the trans-Golgi, complex traffic connections exist to the endolysosomal system additional to the main Golgi-to-plasma membrane secretory route. Here, we investigated three hits in a Drosophila screen displaying secretory cargo accumulation in autophagic vesicles: ESCRT-III component Vps20, SNARE-binding Rop, and lysosomal pump subunit VhaPPA1-1. We found that Vps20, Rop, and lysosomal markers localize near the trans-Golgi. Furthermore, we document that the vicinity of the trans-Golgi is the main cellular location for lysosomes and that early, late, and recycling endosomes associate as well with a trans-Golgi-associated degradative compartment where basal microautophagy of secretory cargo and other materials occurs. Disruption of this compartment causes cargo accumulation in our hits, including Munc18 homolog Rop, required with Syx1 and Syx4 for Rab11-mediated endosomal recycling. Finally, besides basal microautophagy, we show that the trans-Golgi-associated degradative compartment contributes to the growth of autophagic vesicles in developmental and starvation-induced macroautophagy. Our results argue that the fly trans-Golgi is the gravitational center of the whole endomembrane system.
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Affiliation(s)
- Lingjian Zhou
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xutong Xue
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Ke Yang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhi Feng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Min Liu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - José C. 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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41
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Bieniawski MA, Stevens KLP, Witham CM, Steuart RFL, Bankaitis VA, Mousley CJ. Diverse Sphingolipid Species Harbor Different Effects on Ire1 Clustering. Int J Mol Sci 2022; 23:ijms232012130. [PMID: 36293008 PMCID: PMC9602660 DOI: 10.3390/ijms232012130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
Endoplasmic reticulum (ER) function is dedicated to multiple essential processes in eukaryotes, including the processing of secretory proteins and the biogenesis of most membrane lipids. These roles implicate a heavy burden to the organelle, and it is thus prone to fluctuations in the homeostasis of molecules which govern these processes. The unfolded protein response (UPR) is a general ER stress response tasked with maintaining the ER for optimal function, mediated by the master activator Ire1. Ire1 is an ER transmembrane protein that initiates the UPR, forming characteristic oligomers in response to irregularities in luminal protein folding and in the membrane lipid environment. The role of lipids in regulating the UPR remains relatively obscure; however, recent research has revealed a potent role for sphingolipids in its activity. Here, we identify a major role for the oxysterol-binding protein Kes1, whose activity is of consequence to the sphingolipid profile in cells resulting in an inhibition of UPR activity. Using an mCherry-tagged derivative of Ire1, we observe that this occurs due to inhibition of Ire1 to form oligomers. Furthermore, we identify that a sphingolipid presence is required for Ire1 activity, and that specific sphingolipid profiles are of major consequence to Ire1 function. In addition, we highlight cases where Ire1 oligomerization is absent despite an active UPR, revealing a potential mechanism for UPR induction where Ire1 oligomerization is not necessary. This work provides a basis for the role of sphingolipids in controlling the UPR, where their metabolism harbors a crucial role in regulating its onset.
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Affiliation(s)
- Mark A. Bieniawski
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Kofi L. P. Stevens
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Christopher M. Witham
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Robert F. L. Steuart
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Vytas A. Bankaitis
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843-1114, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-1114, USA
- Department of Chemistry, Texas A&M University, College Station, TX 77843-1114, USA
| | - Carl J. Mousley
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Bentley, WA 6102, Australia
- Correspondence:
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Vanderwaeren L, Dok R, Voordeckers K, Nuyts S, Verstrepen KJ. Saccharomyces cerevisiae as a Model System for Eukaryotic Cell Biology, from Cell Cycle Control to DNA Damage Response. Int J Mol Sci 2022; 23:11665. [PMID: 36232965 PMCID: PMC9570374 DOI: 10.3390/ijms231911665] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has been used for bread making and beer brewing for thousands of years. In addition, its ease of manipulation, well-annotated genome, expansive molecular toolbox, and its strong conservation of basic eukaryotic biology also make it a prime model for eukaryotic cell biology and genetics. In this review, we discuss the characteristics that made yeast such an extensively used model organism and specifically focus on the DNA damage response pathway as a prime example of how research in S. cerevisiae helped elucidate a highly conserved biological process. In addition, we also highlight differences in the DNA damage response of S. cerevisiae and humans and discuss the challenges of using S. cerevisiae as a model system.
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Affiliation(s)
- Laura Vanderwaeren
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, Department M2S, KU Leuven, 3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium
| | - Rüveyda Dok
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Karin Voordeckers
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, Department M2S, KU Leuven, 3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium
| | - Sandra Nuyts
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
- Department of Radiation Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, Department M2S, KU Leuven, 3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3001 Leuven, Belgium
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Cui L, Li H, Xi Y, Hu Q, Liu H, Fan J, Xiang Y, Zhang X, Shui W, Lai Y. Vesicle trafficking and vesicle fusion: mechanisms, biological functions, and their implications for potential disease therapy. MOLECULAR BIOMEDICINE 2022; 3:29. [PMID: 36129576 PMCID: PMC9492833 DOI: 10.1186/s43556-022-00090-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Intracellular vesicle trafficking is the fundamental process to maintain the homeostasis of membrane-enclosed organelles in eukaryotic cells. These organelles transport cargo from the donor membrane to the target membrane through the cargo containing vesicles. Vesicle trafficking pathway includes vesicle formation from the donor membrane, vesicle transport, and vesicle fusion with the target membrane. Coat protein mediated vesicle formation is a delicate membrane budding process for cargo molecules selection and package into vesicle carriers. Vesicle transport is a dynamic and specific process for the cargo containing vesicles translocation from the donor membrane to the target membrane. This process requires a group of conserved proteins such as Rab GTPases, motor adaptors, and motor proteins to ensure vesicle transport along cytoskeletal track. Soluble N-ethyl-maleimide-sensitive factor (NSF) attachment protein receptors (SNARE)-mediated vesicle fusion is the final process for vesicle unloading the cargo molecules at the target membrane. To ensure vesicle fusion occurring at a defined position and time pattern in eukaryotic cell, multiple fusogenic proteins, such as synaptotagmin (Syt), complexin (Cpx), Munc13, Munc18 and other tethering factors, cooperate together to precisely regulate the process of vesicle fusion. Dysfunctions of the fusogenic proteins in SNARE-mediated vesicle fusion are closely related to many diseases. Recent studies have suggested that stimulated membrane fusion can be manipulated pharmacologically via disruption the interface between the SNARE complex and Ca2+ sensor protein. Here, we summarize recent insights into the molecular mechanisms of vesicle trafficking, and implications for the development of new therapeutics based on the manipulation of vesicle fusion.
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Chen M, Zhang Y, Jiang K, Wang W, Feng H, Zhen R, Moo C, Zhang Z, Shi J, Chen C. Grab regulates transferrin receptor recycling and iron uptake in developing erythroblasts. Blood 2022; 140:1145-1155. [PMID: 35820059 DOI: 10.1182/blood.2021015189] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/25/2022] [Indexed: 11/20/2022] Open
Abstract
Developing erythroblasts acquire massive amounts of iron through the transferrin (Tf) cycle, which involves endocytosis, sorting, and recycling of the Tf-Tf receptor (Tfrc) complex. Previous studies on the hemoglobin-deficit (hbd) mouse have shown that the exocyst complex is indispensable for the Tfrc recycling; however, the precise mechanism underlying the efficient exocytosis and recycling of Tfrc in erythroblasts remains unclear. Here, we identify the guanine nucleotide exchange factor Grab as a critical regulator of the Tf cycle and iron metabolism during erythropoiesis. Grab is highly expressed in differentiating erythroblasts. Loss of Grab diminishes the Tfrc recycling and iron uptake, leading to hemoglobinization defects in mouse primary erythroblasts, mammalian erythroleukemia cells, and zebrafish embryos. These defects can be alleviated by supplementing iron together with hinokitiol, a small-molecule natural compound that can mediate iron transport independent of the Tf cycle. Mechanistically, Grab regulates the exocytosis of Tfrc-associated vesicles by activating the GTPase Rab8, which subsequently promotes the recruitment of the exocyst complex and vesicle exocytosis. Our results reveal a critical role for Grab in regulating the Tf cycle and provide new insights into iron homeostasis and erythropoiesis.
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Affiliation(s)
- Mengying Chen
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuhan Zhang
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kailun Jiang
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Weixi Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - He Feng
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ru Zhen
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chingyee Moo
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Zhuonan Zhang
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jiahai Shi
- Synthetic Biology Translational Research Programs, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; and
| | - Caiyong Chen
- Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection, Institute of Cell and Developmental Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
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Small GTPase FoSec4-Mediated Protein Secretion Is Important for Polarized Growth, Reproduction and Pathogenicity in the Banana Fusarium Wilt Fungus Fusarium odoratissimum. J Fungi (Basel) 2022; 8:jof8080880. [PMID: 36012867 PMCID: PMC9410047 DOI: 10.3390/jof8080880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
Apical secretion at hyphal tips is important for the growth and development of filamentous fungi. In this study, we analyzed the role of the Rab GTPases FoSec4 involved in the secretion of the banana wilt fungal pathogen Fusarium odoratissimum. We found that the deletion of FoSEC4 affects the activity of extracellular hydrolases and protein secretion, indicating that FoSec4 plays an important role in the regulation of protein secretion in F. odoratissimum. As a typical Rab GTPase, Sec4 participates in the Rab cycle through the conversion between the active GTP-bound state and the inactive GDP-bound state, which is regulated by guanine nucleate exchange factors (GEFs) and GTPase-activating proteins (GAPs). We further found that FoSec2 can interact with dominant-negative FoSec4 (GDP-bound and nucleotide-free form, FoSec4DN), and that FoGyp5 can interact with dominant active FoSec4 (GTP-bound and constitutively active form, FoSec4CA). We evaluated the biofunctions of FoSec4, FoSec2 and FoGyp5, and found that FoSec4 is involved in the regulation of vegetative growth, reproduction, pathogenicity and the environmental stress response of F. odoratissimum, and that FocSec2 and FoGyp5 perform biofunctions consistent with FoSec4, indicating that FoSec2 and FoGyp5 may work as the GEF and the GAP, respectively, of FoSec4 in F. odoratissimum. We further found that the amino-terminal region and Sec2 domain are essential for the biological functions of FoSec2, while the carboxyl-terminal region and Tre-2/Bub2/Cdc16 (TBC) domain are essential for the biological functions of FoGyp5. In addition, FoSec4 mainly accumulated at the hyphal tips and partially colocalized with Spitzenkörper; however, FoGyp5 accumulated at the periphery of Spitzenkörper, suggesting that FoGyp5 may recognize and inactivate FoSec4 at a specific location in hyphal tips.
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Malis Y, Hirschberg K, Kaether C. Hanging the coat on a collar: Same function but different localization and mechanism for COPII. Bioessays 2022; 44:e2200064. [DOI: 10.1002/bies.202200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Yehonathan Malis
- Department of Pathology, Sackler School of Medicine Tel‐Aviv University Tel Aviv Israel
| | - Koret Hirschberg
- Department of Pathology, Sackler School of Medicine Tel‐Aviv University Tel Aviv Israel
| | - Christoph Kaether
- Leibniz Institute for Age Research – Fritz Lipmann Institute Jena Germany
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Peer M, Yuan H, Zhang Y, Korbula K, Novick P, Dong G. Double NPY motifs at the N-terminus of the yeast t-SNARE Sso2 synergistically bind Sec3 to promote membrane fusion. eLife 2022; 11:82041. [PMID: 35979953 PMCID: PMC9427108 DOI: 10.7554/elife.82041] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 11/29/2022] Open
Abstract
Exocytosis is an active vesicle trafficking process by which eukaryotes secrete materials to the extracellular environment and insert membrane proteins into the plasma membrane. The final step of exocytosis in yeast involves the assembly of two t-SNAREs, Sso1/2 and Sec9, with the v-SNARE, Snc1/2, on secretory vesicles. The rate-limiting step in this process is the formation of a binary complex of the two t-SNAREs. Despite a previous report of acceleration of binary complex assembly by Sec3, it remains unknown how Sso2 is efficiently recruited to the vesicle-docking site marked by Sec3. Here, we report a crystal structure of the pleckstrin homology (PH) domain of Sec3 in complex with a nearly full-length version of Sso2 lacking only its C-terminal transmembrane helix. The structure shows a previously uncharacterized binding site for Sec3 at the N-terminus of Sso2, consisting of two highly conserved triple residue motifs (NPY: Asn-Pro-Tyr). We further reveal that the two NPY motifs bind Sec3 synergistically, which together with the previously reported binding interface constitute dual-site interactions between Sso2 and Sec3 to drive the fusion of secretory vesicles at target sites on the plasma membrane.
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Affiliation(s)
- Maximilian Peer
- Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | - Hua Yuan
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States
| | - Yubo Zhang
- Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | | | - Peter Novick
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States
| | - Gang Dong
- Medical Unviersity of Vienna, Vienna, Austria
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Lavasanifar A, Taylor LS. Shedding Light on the Elephant in a Dark Room in the Discovery of New Medicine: Highlighting Molecular Pharmaceutics within ACS Bio & Med Chem Au. ACS BIO & MED CHEM AU 2022; 2:313-315. [PMID: 37102168 PMCID: PMC10114712 DOI: 10.1021/acsbiomedchemau.2c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Afsaneh Lavasanifar
- Faculty of Pharmacy & Pharmaceutical Sciences, University of Alberta, 2142F Katz Group Centre for Research, 11315-87 Ave NW, Edmonton T6G 2H5, Canada
| | - Lynne S. Taylor
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
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Synaptic Secretion and Beyond: Targeting Synapse and Neurotransmitters to Treat Neurodegenerative Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9176923. [PMID: 35923862 PMCID: PMC9343216 DOI: 10.1155/2022/9176923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/16/2022] [Accepted: 06/04/2022] [Indexed: 11/17/2022]
Abstract
The nervous system is important, because it regulates the physiological function of the body. Neurons are the most basic structural and functional unit of the nervous system. The synapse is an asymmetric structure that is important for neuronal function. The chemical transmission mode of the synapse is realized through neurotransmitters and electrical processes. Based on vesicle transport, the abnormal information transmission process in the synapse can lead to a series of neurorelated diseases. Numerous proteins and complexes that regulate the process of vesicle transport, such as SNARE proteins, Munc18-1, and Synaptotagmin-1, have been identified. Their regulation of synaptic vesicle secretion is complicated and delicate, and their defects can lead to a series of neurodegenerative diseases. This review will discuss the structure and functions of vesicle-based synapses and their roles in neurons. Furthermore, we will analyze neurotransmitter and synaptic functions in neurodegenerative diseases and discuss the potential of using related drugs in their treatment.
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Moon S, Kim YJ, Park HE, Kim J, Gho YS, Hong WJ, Kim EJ, Lee SK, Suh BC, An G, Jung KH. OsSNDP3 Functions for the Polar Tip Growth in Rice Pollen Together with OsSNDP2, a Paralog of OsSNDP3. RICE (NEW YORK, N.Y.) 2022; 15:39. [PMID: 35859217 PMCID: PMC9300783 DOI: 10.1186/s12284-022-00586-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/09/2022] [Indexed: 06/02/2023]
Abstract
Understanding pollen tube growth is critical for crop yield maintenance. The pollen tube provides a path for sperm cells for fertilization with egg cells. Cells must be subdivided into functionally and structurally distinct compartments for polar tip growth, and phosphoinositides are thought to be one of the facilitators for polarization during pollen tube growth. OsSNDP3 encodes Sec14-nodulin domain-containing protein and localizes in the nucleus and the microdomains of the plasma membrane in tobacco leaf epidermis cells. OsSNDP3 is thought to bind with phosphatidylinositol 4,5-bisphosphate based on the data including the information of basic amino acids in the C-terminal and colocalization with 2X Pleckstrin homology domain of Phospholipase C delta-1. OsSNDP3 interacts with a protein that contains a class I nodulin domain. We discovered that OsSNDP3 plays a significant role in pollen tube germination using CRISPR/Cas9 systems, whereas another pollen-preferential Sec14-nodulin domain-containing protein, OsSNDP2, additively functions with OsSNDP3 during pollen tube germination. Gene Ontology analysis using downregulated genes in ossndp3 indicated that the expression of genes involved in the phosphatidylinositol metabolic process and tip growth was significantly altered in ossndp3. OsSNDP3 aids pollen polar tip growth by binding with phosphatidylinositol 4,5-bisphosphate. We can better understand the roles of phosphoinositides during pollen tube growth by studying the functions of OsSNDP3 and OsSNDP2. And downregulated genes in ossndp3 might be useful targets for future research on polar tip growth.
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Affiliation(s)
- Sunok Moon
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, and Life and Industry Convergence Research Institute, Pusan National University, Miryang-si, 50463, Korea
| | - Ha Eun Park
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Junhyup Kim
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yun Shil Gho
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Woo-Jong Hong
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Eui-Jung Kim
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Su Kyoung Lee
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Gynheung An
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Ki-Hong Jung
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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