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Gan Z, Yuan J, Liu X, Dong D, Li F, Li X. Comparative transcriptomic analysis of deep- and shallow-water barnacle species (Cirripedia, Poecilasmatidae) provides insights into deep-sea adaptation of sessile crustaceans. BMC Genomics 2020; 21:240. [PMID: 32183697 PMCID: PMC7077169 DOI: 10.1186/s12864-020-6642-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/03/2020] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Barnacles are specialized marine organisms that differ from other crustaceans in possession of a calcareous shell, which is attached to submerged surfaces. Barnacles have a wide distribution, mostly in the intertidal zone and shallow waters, but a few species inhabit the deep-sea floor. It is of interest to investigate how such sessile crustaceans became adapted to extreme deep-sea environments. We sequenced the transcriptomes of a deep-sea barnacle, Glyptelasma gigas collected at a depth of 731 m from the northern area of the Zhongjiannan Basin, and a shallow-water coordinal relative, Octolasmis warwicki. The purpose of this study was to provide genetic resources for investigating adaptation mechanisms of deep-sea barnacles. RESULTS Totals of 62,470 and 51,585 unigenes were assembled for G. gigas and O. warwicki, respectively, and functional annotation of these unigenes was made using public databases. Comparison of the protein-coding genes between the deep- and shallow-water barnacles, and with those of four other shallow-water crustaceans, revealed 26 gene families that had experienced significant expansion in G. gigas. Functional annotation showed that these expanded genes were predominately related to DNA repair, signal transduction and carbohydrate metabolism. Base substitution analysis on the 11,611 single-copy orthologs between G. gigas and O. warwicki indicated that 25 of them were distinctly positive selected in the deep-sea barnacle, including genes related to transcription, DNA repair, ligand binding, ion channels and energy metabolism, potentially indicating their importance for survival of G. gigas in the deep-sea environment. CONCLUSIONS The barnacle G. gigas has adopted strategies of expansion of specific gene families and of positive selection of key genes to counteract the negative effects of high hydrostatic pressure, hypoxia, low temperature and food limitation on the deep-sea floor. These expanded gene families and genes under positive selection would tend to enhance the capacities of G. gigas for signal transduction, genetic information processing and energy metabolism, and facilitate networks for perceiving and responding physiologically to the environmental conditions in deep-sea habitats. In short, our results provide genomic evidence relating to deep-sea adaptation of G. gigas, which provide a basis for further biological studies of sessile crustaceans in the deep sea.
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Affiliation(s)
- Zhibin Gan
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jianbo Yuan
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xinming Liu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Dong Dong
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fuhua Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
| | - Xinzheng Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
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Endoplasmic reticulum-plasma membrane contacts: Principals of phosphoinositide and calcium signaling. Curr Opin Cell Biol 2020; 63:125-134. [PMID: 32088611 DOI: 10.1016/j.ceb.2020.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 12/29/2022]
Abstract
The endoplasmic reticulum (ER) forms an extensive network of membrane contact sites with intra-cellular organelles and the plasma membrane (PM). Interorganelle contacts have vital roles in membrane lipid and ion dynamics. In particular, ER-PM contacts are integral to numerous inter-cellular and intra-cellular signaling pathways including phosphoinositide lipid and calcium signaling, mechanotransduction, metabolic regulation, and cell stress responses. Accordingly, ER-PM contacts serve important signaling functions in excitable cells including neurons and muscle and endocrine cells. This review highlights recent advances in our understanding of the vital roles for ER-PM contacts in phosphoinositide and calcium signaling and how signaling pathways in turn regulate proteins that form and function at ER-PM contacts.
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Cabrita I, Benedetto R, Schreiber R, Kunzelmann K. Niclosamide repurposed for the treatment of inflammatory airway disease. JCI Insight 2019; 4:128414. [PMID: 31391337 DOI: 10.1172/jci.insight.128414] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022] Open
Abstract
Inflammatory airway diseases, such as asthma, cystic fibrosis (CF), and chronic obstructive pulmonary disease (COPD), are characterized by mucus hypersecretion and airway plugging. In both CF and asthma, enhanced expression of the Ca2+-activated Cl- channel TMEM16A is detected in mucus-producing club/goblet cells and airway smooth muscle. TMEM16A contributes to mucus hypersecretion and bronchoconstriction, which are both inhibited by blockers of TMEM16A, such as niflumic acid. Here we demonstrate that the FDA-approved drug niclosamide, a potent inhibitor of TMEM16A identified by high-throughput screening, is an inhibitor of both TMEM16A and TMEM16F. In asthmatic mice, niclosamide reduced mucus production and secretion, as well as bronchoconstriction, and showed additional antiinflammatory effects. Using transgenic asthmatic mice, we found evidence that TMEM16A and TMEM16F are required for normal mucus production/secretion, which may be due to their effects on intracellular Ca2+ signaling. TMEM16A and TMEM16F support exocytic release of mucus and inflammatory mediators, both of which are blocked by niclosamide. Thus, inhibition of mucus and cytokine release, bronchorelaxation, and reported antibacterial effects make niclosamide a potentially suitable drug for the treatment of inflammatory airway diseases, such as CF, asthma, and COPD.
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Chandra G, Defour A, Mamchoui K, Pandey K, Mishra S, Mouly V, Sreetama S, Mahad Ahmad M, Mahjneh I, Morizono H, Pattabiraman N, Menon AK, Jaiswal JK. Dysregulated calcium homeostasis prevents plasma membrane repair in Anoctamin 5/TMEM16E-deficient patient muscle cells. Cell Death Discov 2019; 5:118. [PMID: 31341644 PMCID: PMC6639303 DOI: 10.1038/s41420-019-0197-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/10/2019] [Accepted: 06/13/2019] [Indexed: 01/30/2023] Open
Abstract
Autosomal recessive mutations in Anoctamin 5 (ANO5/TMEM16E), a member of the transmembrane 16 (TMEM16) family of Ca2+-activated ion channels and phospholipid scramblases, cause adult-onset muscular dystrophies (limb girdle muscular dystrophy 2L (LGMD2L) and Miyoshi Muscular Dystrophy (MMD3). However, the molecular role of ANO5 is unclear and ANO5 knockout mouse models show conflicting requirements of ANO5 in muscle. To study the role of ANO5 in human muscle cells we generated a myoblast line from a MMD3-patient carrying the c.2272C>T mutation, which we find causes the mutant protein to be degraded. The patient myoblasts exhibit normal myogenesis, but are compromised in their plasma membrane repair (PMR) ability. The repair deficit is linked to the poor ability of the endoplasmic reticulum (ER) to clear cytosolic Ca2+ increase caused by focal plasma membrane injury. Expression of wild-type ANO5 or pharmacological prevention of injury-triggered cytosolic Ca2+ overload enable injured patient muscle cells to repair. A homology model of ANO5 shows that several of the known LGMD2L/MMD3 patient mutations line the transmembrane region of the protein implicated in its channel activity. These results point to a role of cytosolic Ca2+ homeostasis in PMR, indicate a role for ANO5 in ER-mediated cytosolic Ca2+ uptake and identify normalization of cytosolic Ca2+ homeostasis as a potential therapeutic approach to treat muscular dystrophies caused by ANO5 deficit.
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Affiliation(s)
- Goutam Chandra
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA
| | - Aurelia Defour
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA.,7Present Address: Aix Marseille Université, UMR_S 910, Génétique Médicale et Génomique Fonctionnelle, 13385 Marseille, France
| | - Kamel Mamchoui
- 2Center for Research in Myology, Sorbonne Universités, UPMC Université Paris 06, INSERM UMRS974, 47 Boulevard de l'hôpital, 75013 Paris, France
| | - Kalpana Pandey
- 3Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 USA
| | - Soumya Mishra
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA
| | - Vincent Mouly
- 2Center for Research in Myology, Sorbonne Universités, UPMC Université Paris 06, INSERM UMRS974, 47 Boulevard de l'hôpital, 75013 Paris, France
| | - SenChandra Sreetama
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA
| | - Mohammad Mahad Ahmad
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA
| | - Ibrahim Mahjneh
- 4Department of Neurology, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Hiroki Morizono
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA.,5Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20037 USA
| | | | - Anant K Menon
- 3Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 USA
| | - Jyoti K Jaiswal
- 1Center of Genetic Medicine Research, Children's National Health System, 111 Michigan Avenue, NW, Washington, DC 20010 USA.,5Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20037 USA
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