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Lee KE, Cho JH, Song HO. Calumenin, a Ca 2+ Binding Protein, Is Required for Dauer Formation in Caenorhabditis elegans. BIOLOGY 2023; 12:biology12030464. [PMID: 36979156 PMCID: PMC10044922 DOI: 10.3390/biology12030464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023]
Abstract
Caenorhabditis elegans can adapt and survive in dynamically changing environments by the smart and delicate switching of molecular plasticity. C. elegans dauer diapause is a form of phenotypic and developmental plasticity that induces reversible developmental arrest upon environmental cues. An ER (endoplasmic reticulum)-resident Ca2+ binding protein, calumenin has been reported to function in a variety of malignant diseases in vertebrates and in the process of muscle contraction-relaxation. In C. elegans, CALU-1 is known to function in Ca2+-regulated behaviors (pharyngeal pumping and defecation) and cuticle formation. The cuticles of dauer larvae are morphologically distinct from those of larvae that develop in favorable conditions. The structure of the dauer cuticle is thicker and more highly reinforced than that of other larval stages to protect dauer larvae from various environmental insults. Since the calu-1(tm1783) mutant exhibited abnormal cuticle structures such as highly deformed annuli and alae, we investigated whether CALU-1 is involved in dauer formation or not. Ascaroside pheromone (ascr#2) and crude daumone were used under starvation conditions to analyze the rate of dauer formation in the calu-1(tm1783) mutant. Surprisingly, the dauer ratio of the calu-1(tm1783) mutant was extremely low compared to that of the wild type. In fact, the calu-1(tm1783) mutants were mostly unable to enter diapause. We also found that calu-1 is expressed in body-wall muscle and AIA interneurons at the dauer stage. Taken together, our results suggest that CALU-1 is required for normal entry into diapause in C. elegans.
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Affiliation(s)
- Kyung Eun Lee
- Department of Infection Biology, Wonkwang University School of Medicine, Iksan 54538, Republic of Korea
| | - Jeong Hoon Cho
- Department of Biology Education, College of Education, Chosun University, Gwangju 61452, Republic of Korea
| | - Hyun-Ok Song
- Department of Infection Biology, Wonkwang University School of Medicine, Iksan 54538, Republic of Korea
- Department of Biomedical Science, Graduate School, Wonkwang University, Iksan 54538, Republic of Korea
- Institute of Wonkwang Medical Science, Wonkwang University, Iksan 54538, Republic of Korea
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2
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Tian X, Zheng P, Zhou C, Wang X, Ma H, Ma W, Zhou X, Teng J, Chen J. DIPK2A promotes STX17- and VAMP7-mediated autophagosome-lysosome fusion by binding to VAMP7B. Autophagy 2019; 16:797-810. [PMID: 31251111 DOI: 10.1080/15548627.2019.1637199] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Autophagosome and lysosome fusion is an important macroautophagy/autophagy process for cargo degradation, and SNARE proteins, including STX17, SNAP29, VAMP7 and VAMP8, are key players in this process. However, the manner in which this process is precisely regulated is poorly understood. Here, we show that VAMP7B, a SNARE domain-disrupted isoform of R-SNARE protein VAMP7, competes with SNARE domain functional isoform VAMP7A to bind to STX17 and inhibits autophagosome-lysosome fusion. Moreover, we show that DIPK2A, a late endosome- and lysosome-localized protein, binds to VAMP7B, which inhibits the interaction of VAMP7B with STX17 and enhances the binding of STX17 to VAMP7A, thus enhancing autophagosome-lysosome fusion. Furthermore, DIPK2A participates in autophagic degradation of mitochondria proteins and alleviates apoptosis. Thus, we reveal a new aspect of autophagosome-lysosome fusion in which different isoforms of VAMP7 compete with STX17 and their regulation by DIPK2A.Abbreviations: DIPK2A: divergent protein kinase domain 2A; EEA1: early endosome antigen 1; GOLGA2: golgin A2; LAMP1: lysosomal associated membrane protein 1; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MFN2: mitofusin 2; MT-CO2: mitochondrially encoded cytochrome c oxidase II; PARP1: poly(ADP-ribose) polymerase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; RAB5A: RAB5A, member RAS oncogene family; RAB7A: RAB7A, member RAS oncogene family; REEP: receptor accessory protein; RTN4: reticulon 4; SNARE: SNAP receptor; SQSTM1/p62: sequestosome 1; STX17: syntaxin 17; TOMM20: translocase of outer mitochondrial membrane 20; VAMP7: vesicle associated membrane protein 7; VAMP8: vesicle associated membrane protein 8.
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Affiliation(s)
- Xiaoyu Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Pengli Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Chenqian Zhou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Xurui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Hua Ma
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Wei Ma
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xiaokai Zhou
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Junlin Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Jianguo Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
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Chen Q, Xiao Y, Chai P, Zheng P, Teng J, Chen J. ATL3 Is a Tubular ER-Phagy Receptor for GABARAP-Mediated Selective Autophagy. Curr Biol 2019; 29:846-855.e6. [PMID: 30773365 DOI: 10.1016/j.cub.2019.01.041] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 12/06/2018] [Accepted: 01/15/2019] [Indexed: 12/30/2022]
Abstract
The endoplasmic reticulum (ER) consists of the nuclear envelope and both peripheral ER sheets and a peripheral tubular network [1, 2]. In response to physiological or pathological conditions, receptor-mediated selective ER-phagy, engulfing specific ER subdomains or components, is essential for ER turnover and homeostasis [3-6]. Four mammalian receptors for ER-phagy have been reported: FAM134B [7], reticulon 3 (RTN3) [8], SEC62 [9], and CCPG1 [10]. However, these ER-phagy receptors function in subcellular- and tissue- or physiological- and pathological-condition-specific manners, so the diversity of ER-phagy receptors and underlying mechanisms remain largely unknown [3, 4]. Atlastins (ATL1, ATL2, and ATL3), in mammals, are a class of membrane-bound, dynamin-like GTPases that function in ER fusion [11, 12]. ATL1 is expressed mainly in the central nervous system, while ATL2 and ATL3 are more ubiquitously distributed [13]. Recent studies showed that ATL2 mainly affects ER morphology by promoting ER fusion, whereas alterations in ER morphology are hardly detectable after ATL3 depletion [14, 15]. Here, we show that ATL3 functions as a receptor for ER-phagy, promoting tubular ER degradation upon starvation. ATL3 specifically binds to GABARAP, but not LC3, subfamily proteins via 2 GABARAP interaction motifs (GIMs). ATL3-GABARAP interaction is essential for ATL3 to function in ER-phagy. Moreover, hereditary sensory and autonomic neuropathy type I (HSAN I)-associated ATL3 mutations (Y192C and P338R) disrupt ATL3's association with GABARAP and impair ATL3's function in ER-phagy, suggesting that defective ER-phagy is involved in HSAN I. Therefore, we reveal a new ATL3 function for GABARAP-mediated ER-phagy in the degradation of tubular ER.
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Affiliation(s)
- Qingzhou Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Ya Xiao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Peiyuan Chai
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Pengli Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Junlin Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China.
| | - Jianguo Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China; Center for Quantitative Biology, Peking University, Beijing 100871, China.
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DNA damage triggers tubular endoplasmic reticulum extension to promote apoptosis by facilitating ER-mitochondria signaling. Cell Res 2018; 28:833-854. [PMID: 30030520 PMCID: PMC6063967 DOI: 10.1038/s41422-018-0065-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 05/23/2018] [Accepted: 06/13/2018] [Indexed: 12/11/2022] Open
Abstract
The endoplasmic reticulum (ER) is composed of the nuclear envelope, perinuclear sheets and a peripheral tubular network. The peripheral ER and mitochondria form tight contacts at specific subdomains, which coordinate the functions of the two organelles and are required for multiple cellular processes such as Ca2+ transfer and apoptosis. However, it is largely unknown how ER morphology and ER-mitochondria signaling are dynamically regulated under different physiological or pathological conditions such as DNA damage. Here we show that the peripheral, tubular ER undergoes significant extension in response to DNA damage, and that this process is dependent on p53-mediated transcriptional activation of the ER-shaping proteins REEP1, REEP2 and EI24 (alias PIG8). This promotes the formation of ER-mitochondria contacts through EI24 and the mitochondrial outer membrane protein VDAC2, facilitates Ca2+ transfer from ER to mitochondria and promotes DNA damage-induced apoptosis. Thus, we identify a unique DNA damage response pathway involving alterations in ER morphology, ER-mitochondria signaling, and apoptosis.
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Xu S, Xu Y, Chen L, Fang Q, Song S, Chen J, Teng J. RCN1 suppresses ER stress-induced apoptosis via calcium homeostasis and PERK-CHOP signaling. Oncogenesis 2017; 6:e304. [PMID: 28319095 PMCID: PMC5533947 DOI: 10.1038/oncsis.2017.6] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/07/2016] [Accepted: 01/03/2017] [Indexed: 02/07/2023] Open
Abstract
Endoplasmic reticulum (ER) stress is caused by the disturbance of ER homeostasis and leads to the activation of the unfolded protein response (UPR), which alleviates stress at an early stage and triggers apoptosis if homeostasis fails over a prolonged timeframe. Here, we report that reticulocalbin 1 (RCN1), a member of the CREC family, is transactivated by nuclear factor kappa B (NF-κB) during ER stress and inhibits ER stress-induced apoptosis. The depletion of RCN1 increases the UPR during drug-induced ER stress by activating PRKR-like ER kinase–CCAAT/enhancer-binding protein-homologous protein (PERK–CHOP) signaling, thus inducing apoptosis. Furthermore, we found that the first two EF-hand calcium-binding motifs of RCN1 specifically interact with inositol 1,4,5-trisphosphate (IP3) receptor type 1 (IP3R1) on loop 3 of its ER luminal domain and inhibit ER calcium release and apoptosis. Together, these data indicate that RCN1, a target of NF-κB, suppresses ER calcium release by binding to IP3R1 and decreases the UPR, thereby inhibiting ER stress-induced apoptosis.
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Affiliation(s)
- S Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
| | - Y Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
| | - L Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
| | - Q Fang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
| | - S Song
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
| | - J Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
| | - J Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
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Aune Westergaard Hansen G, Ludvigsen M, Jacobsen C, Cangemi C, Melholt Rasmussen L, Vorum H, Honoré B. Fibulin-1C, C1 Esterase Inhibitor and Glucose Regulated Protein 75 Interact with the CREC Proteins, Calumenin and Reticulocalbin. PLoS One 2015; 10:e0132283. [PMID: 26161649 PMCID: PMC4498735 DOI: 10.1371/journal.pone.0132283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 06/11/2015] [Indexed: 01/12/2023] Open
Abstract
Affinity purification, immunoprecipitation, gel electrophoresis and mass spectrometry were used to identify fibulin-1C, C1 esterase inhibitor and glucose regulated protein 75, grp75, as binding partners of the CREC proteins, calumenin and reticulocalbin. Surface plasmon resonance was used to verify the interaction of all three proteins with each of the CREC proteins. Fibulin-1C interacts with calumenin and reticulocalbin with an estimated dissociation constant around 50-60 nM. The interaction, at least for reticulocalbin, was not dependent upon the presence of Ca2+. C1 esterase inhibitor interacted with both proteins with an estimated dissociation constant at 1 μM for reticulocalbin and 150 nM for calumenin. The interaction, at least for calumenin, was dependent upon the presence of Ca2+ with strong interaction at 3.5 mM while no detectable interaction could be found at 0.1 mM. Grp75 binds with an affinity of approximately 3-7 nM with reticulocalbin as well as with calumenin. These interactions suggest functional participation of the CREC proteins in chaperone activity, cell proliferation and transformation, cellular aging, haemostasis and thrombosis as well as modulation of the complement system in fighting bacterial infection.
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Affiliation(s)
| | - Maja Ludvigsen
- Department of Biomedicine, Ole Worms Allé 3, Building 1182, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Christian Jacobsen
- Department of Biomedicine, Ole Worms Allé 3, Building 1182, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Claudia Cangemi
- Department of Clinical Biochemistry and Pharmacology, Center for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Sdr. Boulevard 29, DK-5000 Odense C, Denmark
| | - Lars Melholt Rasmussen
- Department of Clinical Biochemistry and Pharmacology, Center for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Sdr. Boulevard 29, DK-5000 Odense C, Denmark
| | - Henrik Vorum
- Department of Ophthalmology, Aalborg University Hospital, Hobrovej 18–22, 9100 Aalborg, Denmark
| | - Bent Honoré
- Department of Biomedicine, Ole Worms Allé 3, Building 1182, Aarhus University, DK-8000 Aarhus C, Denmark
- * E-mail:
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7
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Zhou MT, Qin Y, Li M, Chen C, Chen X, Shu HB, Guo L. Quantitative Proteomics Reveals the Roles of Peroxisome-associated Proteins in Antiviral Innate Immune Responses. Mol Cell Proteomics 2015; 14:2535-49. [PMID: 26124285 DOI: 10.1074/mcp.m115.048413] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Indexed: 11/06/2022] Open
Abstract
Compared with whole-cell proteomic analysis, subcellular proteomic analysis is advantageous not only for the increased coverage of low abundance proteins but also for generating organelle-specific data containing information regarding dynamic protein movement. In the present study, peroxisome-enriched fractions from Sendai virus (SeV)-infected or uninfected HepG2 cells were obtained and subjected to quantitative proteomics analysis. We identified 311 proteins that were significantly changed by SeV infection. Among these altered proteins, 25 are immune response-related proteins. Further bioinformatic analysis indicated that SeV infection inhibits cell cycle-related proteins and membrane attack complex-related proteins, all of which are beneficial for the survival and replication of SeV within host cells. Using Luciferase reporter assays on several innate immune-related reporters, we performed functional analysis on 11 candidate proteins. We identified LGALS3BP and CALU as potential negative regulators of the virus-induced activation of the type I interferons.
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Affiliation(s)
- Mao-Tian Zhou
- From the ‡State Key Laboratory of Virology, College of Life Sciences
| | - Yue Qin
- From the ‡State Key Laboratory of Virology, College of Life Sciences; §Medical Research Institute, Wuhan University
| | - Mi Li
- From the ‡State Key Laboratory of Virology, College of Life Sciences; §Medical Research Institute, Wuhan University
| | - Chen Chen
- From the ‡State Key Laboratory of Virology, College of Life Sciences
| | - Xi Chen
- ¶Wuhan Institute of Biotechnology, Wuhan, China
| | - Hong-Bing Shu
- From the ‡State Key Laboratory of Virology, College of Life Sciences; §Medical Research Institute, Wuhan University;
| | - Lin Guo
- From the ‡State Key Laboratory of Virology, College of Life Sciences;
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8
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Calumenin and fibulin-1 on tumor metastasis: Implications for pharmacology. Pharmacol Res 2015; 99:11-5. [PMID: 25976680 DOI: 10.1016/j.phrs.2015.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 05/01/2015] [Accepted: 05/01/2015] [Indexed: 01/08/2023]
Abstract
Tumor metastasis is a key cause of cancer mortality, and inhibiting migration of cancer cells is one of the major directions of anti-metastatic drug development. Calumenin and fibulin-1 are two extracellular proteins that synergistically inhibit cell migration and tumor metastasis, and could potentially be served as targets for pharmacological research of anti-metastatic drugs. This review briefly introduces the multi-function of these two proteins, and discusses the mechanism of how they regulate cell migration and tumor metastasis.
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Jover E, Marín F, Quintana M, Pérez-Andreu J, Hurtado JA, Rodríguez C, Martínez-González J, González-Conejero R, Valdés M, Hernández-Romero D. CALU polymorphism A29809G affects calumenin availability involving vascular calcification. J Mol Cell Cardiol 2015; 82:218-27. [PMID: 25823396 DOI: 10.1016/j.yjmcc.2015.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/09/2015] [Accepted: 03/24/2015] [Indexed: 01/07/2023]
Abstract
Calumenin inhibits gamma-carboxylation of matrix-Gla-protein preventing BMP2-dependent calcification. Our aim was to explore the clinical relevance and functionality of the CALU polymorphism rs1043550, and the relationship of calumenin time-dependent expression profile with the active calcification of human vascular smooth muscle cells (hVSMC). Coronary artery calcium score and lesion severity were assessed by cardiac computed tomography in 139 consecutive low-risk patients genotyped for rs1043550. Polymorphic (G) allele carriage was associated with lower calcium (OR: 6.19, p=0.042). Calcified arteries from CALU 'A' allele carriers undergoing cardiovascular surgery exhibited higher residual calcification, higher calumenin immunostaining and lower matrix-Gla-protein, contrary to 'G' allele carriers. In a luciferase reporter system in vascular cells, polymorphic 'G' allele reduced the mRNA stability by 30% (p < 0.05). Osteogenic high-phosphate media induced active differentiation of hVSMC onto functional osteoblast-like cells as demonstrated by extracellular matrix mineralization and osteoblast markers expression. Calumenin was early over-expressed at day 3 (p < 0.05), but decreased thereafter (mRNA and protein) with implications on gamma-carboxylation system. Calumenin was found released and co-localizing with extracellular matrix calcifications. The CALU polymorphism rs1043550 affects mRNA stability and tissue availability of calumenin thus supporting the protective clinical significance. Calumenin shows a time-dependent profile during induced calcification. These data demonstrate a novel association of vascular calcification with the VSMC phenotypic transition into osteoblast-like cells. Moreover, hyperphosphatemic stimuli render calumenin accumulation in the mineralized extracellular matrix.
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MESH Headings
- Alleles
- Calcium/metabolism
- Calcium-Binding Proteins/genetics
- Calcium-Binding Proteins/metabolism
- Cell Culture Techniques
- Cell Differentiation
- Cells, Cultured
- Coronary Vessels/metabolism
- Coronary Vessels/pathology
- Extracellular Matrix/metabolism
- Extracellular Matrix Proteins/metabolism
- Humans
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/cytology
- Myocytes, Smooth Muscle/metabolism
- Osteoblasts/cytology
- Osteoblasts/metabolism
- Polymorphism, Single Nucleotide
- RNA Stability/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Vascular Calcification/genetics
- Vascular Calcification/metabolism
- Matrix Gla Protein
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Affiliation(s)
- Eva Jover
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Francisco Marín
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain.
| | - Míriam Quintana
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Joaquín Pérez-Andreu
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - José Antonio Hurtado
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Cristina Rodríguez
- Centro de Investigación Cardiovascular, CSIC-ICCC, Instituto de Investigación Biomédica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - José Martínez-González
- Centro de Investigación Cardiovascular, CSIC-ICCC, Instituto de Investigación Biomédica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | | | - Mariano Valdés
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Diana Hernández-Romero
- Hospital Clínico Universitario Virgen de la Arrixaca, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
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Abascal F, Tress ML, Valencia A. The evolutionary fate of alternatively spliced homologous exons after gene duplication. Genome Biol Evol 2015; 7:1392-403. [PMID: 25931610 PMCID: PMC4494069 DOI: 10.1093/gbe/evv076] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly understood. Here, we have carried out a study of the evolution of alternatively spliced exons after gene duplication to better understand the interaction between the two processes. We created a manually curated set of 97 human genes with mutually exclusively spliced homologous exons and analyzed the evolution of these exons across five distantly related vertebrates (lamprey, spotted gar, zebrafish, fugu, and coelacanth). Most of these exons had an ancient origin (more than 400 Ma). We found examples supporting two extreme evolutionary models for the behaviour of homologous axons after gene duplication. We observed 11 events in which gene duplication was accompanied by splice isoform separation, that is, each paralog specifically conserved just one distinct ancestral homologous exon. At other extreme, we identified genes in which the homologous exons were always conserved within paralogs, suggesting that the alternative splicing event cannot easily be separated from the function in these genes. That many homologous exons fall in between these two extremes highlights the diversity of biological systems and suggests that the subtle balance between alternative splicing and gene duplication is adjusted to the specific cellular context of each gene.
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Affiliation(s)
- Federico Abascal
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Michael L Tress
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Alfonso Valencia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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Tripathi R, Benz N, Culleton B, Trouvé P, Férec C. Biophysical characterisation of calumenin as a charged F508del-CFTR folding modulator. PLoS One 2014; 9:e104970. [PMID: 25120007 PMCID: PMC4132023 DOI: 10.1371/journal.pone.0104970] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/16/2014] [Indexed: 11/19/2022] Open
Abstract
The cystic fibrosis transmembrane regulator (CFTR) is a cyclic-AMP dependent chloride channel expressed at the apical surface of epithelial cells lining various organs such as the respiratory tract. Defective processing and functioning of this protein caused by mutations in the CFTR gene results in loss of ionic balance, defective mucus clearance, increased proliferation of biofilms and inflammation of human airways observed in cystic fibrosis (CF) patients. The process by which CFTR folds and matures under the influence of various chaperones in the secretory pathway remains incompletely understood. Recently, calumenin, a secretory protein, belonging to the CREC family of low affinity calcium binding proteins has been identified as a putative CFTR chaperone whose biophysical properties and functions remain uncharacterized. We compared hydropathy, instability, charge, unfoldability, disorder and aggregation propensity of calumenin and other CREC family members with CFTR associated chaperones and calcium binding proteins, wild-type and mutant CFTR proteins and intrinsically disordered proteins (IDPs). We observed that calumenin, along with other CREC proteins, was significantly more charged and less folded compared to CFTR associated chaperones. Moreover like IDPs, calumenin and other CREC proteins were found to be less hydrophobic and aggregation prone. Phylogenetic analysis revealed a close link between calumenin and other CREC proteins indicating how evolution might have shaped their similar biophysical properties. Experimentally, calumenin was observed to significantly reduce F508del-CFTR aggregation in a manner similar to AavLEA1, a well-characterized IDP. Fluorescence microscopy based imaging analysis also revealed altered trafficking of calumenin in bronchial cells expressing F508del-CFTR, indicating its direct role in the pathophysiology of CF. In conclusion, calumenin is characterized as a charged protein exhibiting close similarity with IDPs and is hypothesized to regulate F508del-CFTR folding by electrostatic effects. This work provides useful insights for designing optimized synthetic structural correctors of CFTR mutant proteins in the future.
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Affiliation(s)
- Rashmi Tripathi
- INSERM UMR1078, Brest, France
- Université de Bretagne Occidentale, Faculté de Medecine et des sciences de la santé, Brest, France
- * E-mail:
| | - Nathalie Benz
- INSERM UMR1078, Brest, France
- Association Gaétan Saleün, Brest, France
| | - Bridget Culleton
- Hôpital Morvan, Laboratoire de Génétique Moléculaire et d‘Histocompatibilité, Brest, France
| | | | - Claude Férec
- INSERM UMR1078, Brest, France
- Université de Bretagne Occidentale, Faculté de Medecine et des sciences de la santé, Brest, France
- Hôpital Morvan, Laboratoire de Génétique Moléculaire et d‘Histocompatibilité, Brest, France
- Etablissement Français du Sang-Bretagne, Brest, France
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12
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Chen L, Xu S, Liu L, Wen X, Xu Y, Chen J, Teng J. Cab45S inhibits the ER stress-induced IRE1-JNK pathway and apoptosis via GRP78/BiP. Cell Death Dis 2014; 5:e1219. [PMID: 24810055 PMCID: PMC4047922 DOI: 10.1038/cddis.2014.193] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/19/2014] [Accepted: 04/01/2014] [Indexed: 01/07/2023]
Abstract
Disturbance of endoplasmic reticulum (ER) homeostasis causes ER stress and leads to activation of the unfolded protein response, which reduces the stress and promotes cell survival at the early stage of stress, or triggers cell death and apoptosis when homeostasis is not restored under prolonged ER stress. Here, we report that Cab45S, a member of the CREC family, inhibits ER stress-induced apoptosis. Depletion of Cab45S increases inositol-requiring kinase 1 (IRE1) activity, thus producing more spliced forms of X-box-binding protein 1 mRNA at the early stage of stress and leads to phosphorylation of c-Jun N-terminal kinase, which finally induces apoptosis. Furthermore, we find that Cab45S specifically interacts with 78-kDa glucose-regulated protein/immunoglobulin heavy chain binding protein (GRP78/BiP) on its nucleotide-binding domain. Cab45S enhances GRP78/BiP protein level and stabilizes the interaction of GRP78/BiP with IRE1 to inhibit ER stress-induced IRE1 activation and apoptosis. Together, Cab45S, a novel regulator of GRP78/BiP, suppresses ER stress-induced IRE1 activation and apoptosis by binding to and elevating GRP78/BiP, and has a role in the inhibition of ER stress-induced apoptosis.
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Affiliation(s)
- L Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
| | - S Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
| | - L Liu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
| | - X Wen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
| | - Y Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
| | - J Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
- Center for Quantitative Biology, Peking University, Beijing, China
| | - J Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Bio-membrane and Membrane Bio-engineering, College of Life Sciences, Peking University, Beijing, China
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13
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Webb SE, Miller AL. Calcium signaling in extraembryonic domains during early teleost development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 304:369-418. [PMID: 23809440 DOI: 10.1016/b978-0-12-407696-9.00007-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
It is becoming recognized that the extraembryonic domains of developing vertebrates, that is, those that make no cellular contribution to the embryo proper, act as important signaling centers that induce and pattern the germ layers and help establish the key embryonic axes. In the embryos of teleost fish, in particular, significant progress has been made in understanding how signaling activity in extraembryonic domains, such as the enveloping layer, the yolk syncytial layer, and the yolk cell, might help regulate development via a combination of inductive interactions, cellular dynamics, and localized gene expression. Ca(2+) signaling in a variety of forms that include propagating waves and standing gradients is a feature found in all three teleostean extraembryonic domains. This leads us to propose that in addition to their other well-characterized signaling activities, extraembryonic domains are well suited (due to their relative stability and continuity) to act as Ca(2+) signaling centers and conduits.
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Affiliation(s)
- Sarah E Webb
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
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14
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Wang Q, Shen B, Chen L, Zheng P, Feng H, Hao Q, Liu X, Liu L, Xu S, Chen J, Teng J. Extracellular calumenin suppresses ERK1/2 signaling and cell migration by protecting fibulin-1 from MMP-13-mediated proteolysis. Oncogene 2014; 34:1006-18. [DOI: 10.1038/onc.2014.52] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/06/2014] [Accepted: 01/20/2014] [Indexed: 01/04/2023]
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15
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Feng H, Chen L, Wang Q, Shen B, Liu L, Zheng P, Xu S, Liu X, Chen J, Teng J. Calumenin-15 facilitates filopodia formation by promoting TGF-β superfamily cytokine GDF-15 transcription. Cell Death Dis 2013; 4:e870. [PMID: 24136234 PMCID: PMC3920949 DOI: 10.1038/cddis.2013.403] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/04/2013] [Accepted: 09/11/2013] [Indexed: 12/12/2022]
Abstract
Filopodia, which are actin-rich finger-like membrane protrusions, have an important role in cell migration and tumor metastasis. Here we identify 13 novel calumenin (Calu) isoforms (Calu 3-15) produced by alternative splicing, and find that Calu-15 promotes filopodia formation and cell migration. Calu-15 shuttles between the nucleus and cytoplasm through interacting with importin α, Ran GTPase, and Crm1. The phosphorylation of the threonine at position 73 (Thr-73) by casein kinase 2 (CK2) is essential for the nuclear import of Calu-15, and either Thr-73 mutation or inhibition of CK2 interrupts its nuclear localization. In the nucleus, Calu-15 increases the transcription of growth differentiation factor-15 (GDF-15), a member of the transforming growth factor-β (TGF-β) superfamily, via binding to its promoter region. Furthermore, Calu-15 induces filopodia formation mediated by GDF-15. Together, we identify that Calu-15, a novel isoform of Calu with phosphorylation-dependent nuclear localization, has a critical role in promoting filopodia formation and cell migration by upregulating the GDF-15 transcription.
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Affiliation(s)
- H Feng
- State Key Laboratory of Bio-membrane and Membrane Bio-engineering, Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - L Chen
- State Key Laboratory of Bio-membrane and Membrane Bio-engineering, Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Q Wang
- State Key Laboratory of Bio-membrane and Membrane Bio-engineering, Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - B Shen
- State Key Laboratory of Bio-membrane and Membrane Bio-engineering, Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - L Liu
- State Key Laboratory of Bio-membrane and Membrane Bio-engineering, Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - P Zheng
- State Key Laboratory of Bio-membrane and Membrane Bio-engineering, Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - S Xu
- State Key Laboratory of Bio-membrane and Membrane Bio-engineering, Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - X Liu
- State Key Laboratory of Bio-membrane and Membrane Bio-engineering, Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - J Chen
- State Key Laboratory of Bio-membrane and Membrane Bio-engineering, Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
- Center for Quantitative Biology, Peking University, Beijing, China
| | - J Teng
- State Key Laboratory of Bio-membrane and Membrane Bio-engineering, Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
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16
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Wang Q, Shen B, Zheng P, Feng H, Guo Y, Cao W, Chen L, Liu X, Zhao G, Xu S, Shen W, Chen J, Teng J. BmCREC is an endoplasmic reticulum (ER) resident protein and required for ER/Golgi morphology. J Biol Chem 2013; 288:26649-57. [PMID: 23921381 DOI: 10.1074/jbc.m113.463018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Silkworm posterior silkgland is a model for studying intracellular trafficking. Here, using this model, we identify several potential cargo proteins of BmKinesin-1 and focus on one candidate, BmCREC. BmCREC (also known as Bombyx mori DNA supercoiling factor, BmSCF) was previously proposed to supercoil DNA in the nucleus. However, we show here that BmCREC is localized in the ER lumen. Its C-terminal tetrapeptide HDEF is recognized by the KDEL receptor, and subsequently it is retrogradely transported by coat protein I (COPI) vesicles to the ER. Lacking the HDEF tetrapeptide of BmCREC or knocking down COPI subunits results in decreased ER retention and simultaneously increased secretion of BmCREC. Furthermore, we find that BmCREC knockdown markedly disrupts the morphology of the ER and Golgi apparatus and leads to a defect of posterior silkgland tube expansion. Together, our results clarify the ER retention mechanism of BmCREC and reveal that BmCREC is indispensable for maintaining ER/Golgi morphology.
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Affiliation(s)
- Qiao Wang
- From the Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Biomembrane and Membrane Bioengineering, College of Life Sciences, Peking University, Beijing 100871, China
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