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Anglès F, Gupta V, Wang C, Balch WE. COPII cage assembly factor Sec13 integrates information flow regulating endomembrane function in response to human variation. Sci Rep 2024; 14:10160. [PMID: 38698045 PMCID: PMC11065896 DOI: 10.1038/s41598-024-60687-2] [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: 07/12/2023] [Accepted: 04/26/2024] [Indexed: 05/05/2024] Open
Abstract
How information flow is coordinated for managing transit of 1/3 of the genome through endomembrane pathways by the coat complex II (COPII) system in response to human variation remains an enigma. By examining the interactome of the COPII cage-assembly component Sec13, we show that it is simultaneously associated with multiple protein complexes that facilitate different features of a continuous program of chromatin organization, transcription, translation, trafficking, and degradation steps that are differentially sensitive to Sec13 levels. For the trafficking step, and unlike other COPII components, reduction of Sec13 expression decreased the ubiquitination and degradation of wild-type (WT) and F508del variant cargo protein cystic fibrosis transmembrane conductance regulator (CFTR) leading to a striking increase in fold stability suggesting that the events differentiating export from degradation are critically dependent on COPII cage assembly at the ER Golgi intermediate compartment (ERGIC) associated recycling and degradation step linked to COPI exchange. Given Sec13's multiple roles in protein complex assemblies that change in response to its expression, we suggest that Sec13 serves as an unanticipated master regulator coordinating information flow from the genome to the proteome to facilitate spatial covariant features initiating and maintaining design and function of membrane architecture in response to human variation.
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Affiliation(s)
- Frédéric Anglès
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Vijay Gupta
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Chao Wang
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - William E Balch
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA.
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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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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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Li H, Feng YH, Xia C, Chen Y, Lu XY, Wei Y, Qian LL, Zhu MY, Gao GY, Meng YF, You YL, Tian Q, Liang KQ, Li YT, Lv CT, Rui XY, Wei MY, Zhang B. Physiological and transcriptomic analysis dissects the molecular mechanism governing meat quality during postmortem aging in Hu sheep ( Ovis aries). Front Nutr 2024; 10:1321938. [PMID: 38249602 PMCID: PMC10799347 DOI: 10.3389/fnut.2023.1321938] [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: 10/15/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Hu sheep, known for its high quality and productivity, lack fundamental scientific research in China. Methods This study focused on the effects of 24 h postmortem aging on the meat physiological and transcriptomic alteration in Hu sheep. Results The results showed that the 24 h aging process exerts a substantial influence on the mutton color, texture, and water content as compared to untreated group. Transcriptomic analysis identified 1,668 differentially expressed genes. Functional enrichment analysis highlighted the importance of glycolysis metabolism, protein processing in endoplasmic reticulum, and the FcγR-mediated phagocytosis pathway in mediating meat quality modification following postmortem aging. Furthermore, protein-protein interaction analysis uncovered complex regulatory networks involving glycolysis, the MAPK signaling pathway, protein metabolism, and the immune response. Discussion Collectively, these findings offer valuable insights into the molecular mechanisms underlying meat quality changes during postmortem aging in Hu sheep, emphasizing the potential for improving quality control strategies in mutton production.
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Affiliation(s)
- Huan Li
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yan-Hui Feng
- College of Food Engineering, Anhui Science and Technology University, Chuzhou, Anhui, China
| | - Chao Xia
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yu Chen
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Xin-Yi Lu
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yue Wei
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Le-Le Qian
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Meng-Yao Zhu
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Guo-Yv Gao
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Ya-Fei Meng
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yv-Le You
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Qi Tian
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Kun-Qi Liang
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yun-Tao Li
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Chao-Tian Lv
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Xiang-Yun Rui
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Ming-Yue Wei
- School of Ecology, Resources and Environment, Dezhou University, Dezhou, Shandong, China
| | - Bin Zhang
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
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Kasberg W, Luong P, Swift KA, Audhya A. Nutrient deprivation alters the rate of COPII coat assembly to tune secretory protein transport. RESEARCH SQUARE 2023:rs.3.rs-2652351. [PMID: 36993182 PMCID: PMC10055522 DOI: 10.21203/rs.3.rs-2652351/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Co-assembly of the multilayered coat protein complex II (COPII) with the Sari GTPase at subdomains of the endoplasmic reticulum (ER) enables secretory cargoes to be concentrated efficiently within nascent transport intermediates, which subsequently deliver their contents to ER-Golgi intermediate compartments. Here, we define the spatiotemporal accumulation of native COPII subunits and secretory cargoes at ER subdomains under differing nutrient availability conditions using a combination of CRISPR/Cas9-mediated genome editing and live cell imaging. Our findings demonstrate that the rate of inner COPII coat assembly serves as a determinant for the pace of cargo export, irrespective of COPII subunit expression levels. Moreover, increasing inner COPII coat assembly kinetics is sufficient to rescue cargo trafficking deficits caused by acute nutrient limitation in a manner dependent on Sar1 GTPase activity. Our findings are consistent with a model in which the rate of inner COPII coat formation acts as an important control point to regulate cargo export from the ER.
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Affiliation(s)
- William Kasberg
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Peter Luong
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Kevin A. Swift
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, USA
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