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Farooq MA, Ayyaz A, Zou HX, Zhou W, Hannan F, Yan X. Jasmonic acid mediates Ca 2+ dependent signal transduction and plant immunity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 348:112239. [PMID: 39197534 DOI: 10.1016/j.plantsci.2024.112239] [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: 06/02/2024] [Revised: 08/18/2024] [Accepted: 08/23/2024] [Indexed: 09/01/2024]
Abstract
Pathogen attacks can cause significant damage to plants, posing a threaten to global food production. Plants have developed exquisite methods to rapidly store a key defensive hormone jasmonate (JA), which stimulates their entire evolutionary adaptive response to pathogen attack. However, understanding how plants initiate JA biosynthesis in response to pathogen attacks has remained elusive. In this review, we discuss the newly discovered JAV1-JAZ8-WRKY51 (JJW) complex, which plays a crucial role in regulating JA production to deter insect attacks. The JJW complex inhibits JA production in plants, maintaining a low baseline level of JA that promotes optimal plant development. However, when plants are attacked by insects, a rapid influx of calcium stimulates the JAV1 calcium-dependent protein phosphate, leading to the breakdown of the JJW complex and the activation of JA production. This surge in JA levels, initiates plant defense mechanisms against the invading insects. These findings shed light on the intricate defense system that plants have evolved to combat diseases.
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Affiliation(s)
- Muhammad Ahsan Farooq
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China
| | - Ahsan Ayyaz
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Hui-Xi Zou
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Fakhir Hannan
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
| | - Xiufeng Yan
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China.
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Symonds K, Smith MA, Esme O, Plaxton WC, Snedden WA. Characterization of Arabidopsis aldolases AtFBA4, AtFBA5, and their inhibition by morin and interaction with calmodulin. FEBS Lett 2024; 598:1864-1876. [PMID: 38997224 DOI: 10.1002/1873-3468.14979] [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: 03/23/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 07/14/2024]
Abstract
Fructose bisphosphate aldolases (FBAs) catalyze the reversible cleavage of fructose 1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. We analyzed two previously uncharacterized cytosolic Arabidopsis FBAs, AtFBA4 and AtFBA5. Based on a recent report, we examined the interaction of AtFBA4 with calmodulin (CaM)-like protein 11 (AtCML11). AtFBA4 did not bind AtCML11; however, we found that CaM bound AtFBA5 in a Ca2+-dependent manner with high specificity and affinity (KD ~ 190 nm) and enhanced its stability. AtFBA4 and AtFBA5 exhibited Michaelis-Menten kinetics with Km and Vmax values of 180 μm and 4.9 U·mg-1 for AtFBA4, and 6.0 μm and 0.30 U·mg-1 for AtFBA5, respectively. The flavonoid morin inhibited both isozymes. Our study suggests that Ca2+ signaling and flavanols may influence plant glycolysis/gluconeogenesis.
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Affiliation(s)
- Kyle Symonds
- Department of Biology, Queen's University, Kingston, Canada
| | - Milena A Smith
- Department of Biology, Queen's University, Kingston, Canada
| | - Oona Esme
- Department of Biology, Queen's University, Kingston, Canada
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3
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Thawornkuno C, Srisuksai K, Simanon N, Adisakwattana P, Ampawong S, Boonyuen U, Limpanont Y, Chusongsang P, Chusongsang Y, Kiangkoo N, Reamtong O. A reanalysis and integration of transcriptomics and proteomics datasets unveil novel drug targets for Mekong schistosomiasis. Sci Rep 2024; 14:12969. [PMID: 38839835 PMCID: PMC11153569 DOI: 10.1038/s41598-024-63869-0] [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: 04/22/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024] Open
Abstract
Schistosomiasis, caused by Schistosoma trematodes, is a significant global health concern, particularly affecting millions in Africa and Southeast Asia. Despite efforts to combat it, the rise of praziquantel (PZQ) resistance underscores the need for new treatment options. Protein kinases (PKs) are vital in cellular signaling and offer potential as drug targets. This study focused on focal adhesion kinase (FAK) as a candidate for anti-schistosomal therapy. Transcriptomic and proteomic analyses of adult S. mekongi worms identified FAK as a promising target due to its upregulation and essential role in cellular processes. Molecular docking simulations assessed the binding energy of FAK inhibitors to Schistosoma FAK versus human FAK. FAK inhibitor 14 and PF-03814735 exhibited strong binding to Schistosoma FAK with minimal binding for human FAK. In vitro assays confirmed significant anti-parasitic activity against S. mekongi, S. mansoni, and S. japonicum, comparable to PZQ, with low toxicity in human cells, indicating potential safety. These findings highlight FAK as a promising target for novel anti-schistosomal therapies. However, further research, including in vivo studies, is necessary to validate efficacy and safety before clinical use. This study offers a hopeful strategy to combat schistosomiasis and reduce its global impact.
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Affiliation(s)
- Charin Thawornkuno
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Krittika Srisuksai
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nattapon Simanon
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sumate Ampawong
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Usa Boonyuen
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yanin Limpanont
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Phiraphol Chusongsang
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yupa Chusongsang
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nuttapohn Kiangkoo
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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4
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Thines L, Jang H, Li Z, Sayedyahossein S, Maloney R, Nussinov R, Sacks DB. Disruption of Ca 2+/calmodulin:KSR1 interaction lowers ERK activation. Protein Sci 2024; 33:e4982. [PMID: 38591710 PMCID: PMC11002989 DOI: 10.1002/pro.4982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/22/2024] [Accepted: 03/16/2024] [Indexed: 04/10/2024]
Abstract
KSR1, a key scaffold protein for the MAPK pathway, facilitates ERK activation upon growth factor stimulation. We recently demonstrated that KSR1 binds the Ca2+-binding protein calmodulin (CaM), thereby providing an intersection between KSR1-mediated and Ca2+ signaling. In this study, we set out to generate a KSR1 point mutant with reduced Ca2+/CaM binding in order to unravel the functional implications of their interaction. To do so, we solved the structural determinants of complex formation. Using purified fragments of KSR1, we showed that Ca2+/CaM binds to the CA3 domain of KSR1. We then used in silico molecular modeling to predict contact residues for binding. This approach identified two possible modes of interaction: (1) binding of extended Ca2+/CaM to a globular conformation of KSR1-CA3 via electrostatic interactions or (2) binding of collapsed Ca2+/CaM to α-helical KSR1-CA3 via hydrophobic interactions. Experimentally, site-directed mutagenesis of the predicted contact residues for the two binding models favored that where collapsed Ca2+/CaM binds to the α-helical conformation of KSR1-CA3. Importantly, replacing KSR1-Phe355 with Asp reduces Ca2+/CaM binding by 76%. The KSR1-F355D mutation also significantly impairs the ability of EGF to activate ERK, which reveals that Ca2+/CaM binding promotes KSR1-mediated MAPK signaling. This work, by uncovering structural insight into the binding of KSR1 to Ca2+/CaM, identifies a KSR1 single-point mutant as a bioreagent to selectively study the crosstalk between Ca2+ and KSR1-mediated signaling.
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Affiliation(s)
- Louise Thines
- Department of Laboratory MedicineNational Institutes of HealthBethesdaMarylandUSA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation LaboratoryNational Cancer InstituteFrederickMarylandUSA
| | - Zhigang Li
- Department of Laboratory MedicineNational Institutes of HealthBethesdaMarylandUSA
| | - Samar Sayedyahossein
- Department of Laboratory MedicineNational Institutes of HealthBethesdaMarylandUSA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation LaboratoryNational Cancer InstituteFrederickMarylandUSA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation LaboratoryNational Cancer InstituteFrederickMarylandUSA
- Department of Human Molecular Genetics and BiochemistrySackler School of Medicine, Tel Aviv UniversityTel AvivIsrael
| | - David B. Sacks
- Department of Laboratory MedicineNational Institutes of HealthBethesdaMarylandUSA
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Halder R, Warshel A. Energetic and structural insights behind calcium induced conformational transition in calmodulin. Proteins 2024; 92:384-394. [PMID: 37915244 PMCID: PMC10872638 DOI: 10.1002/prot.26620] [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: 08/13/2023] [Revised: 10/01/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023]
Abstract
Calmodulin (CaM) is a key signaling protein that triggers several cellular and physiological processes inside the cell. Upon binding with calcium ion, CaM undergoes large scale conformational transition from a closed state to an open state that facilitates its interaction with various target protein and regulates their activity. This work explores the origin of the energetic and structural variation of the wild type and mutated CaM and explores the molecular origin for the structural differences between them. We first calculated the sequential calcium binding energy to CaM using the PDLD/S-LRA/β approach. This study shows a very good correlation with experimental calcium binding energies. Next we calculated the calcium binding energies to the wild type CaM and several mutated CaM systems which were reported experimentally. On the structural aspect, it has been reported experimentally that certain mutation (Q41L-K75I) in calcium bound CaM leads to complete conformational transition from an open to a closed state. By using equilibrium molecular dynamics simulation, free energy calculation and contact frequency map analysis, we have shown that the formation of a cluster of long-range hydrophobic contacts, initiated by the Q41L-K75I CaM variant is the driving force behind its closing motion. This study unravels the energetics and structural aspects behind calcium ion induced conformational changes in wild type CaM and its variant.
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Affiliation(s)
- Ritaban Halder
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
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Hau B, Symonds K, Teresinski H, Janssen A, Duff L, Smith M, Benidickson K, Plaxton W, Snedden WA. Arabidopsis Calmodulin-like Proteins CML13 and CML14 Interact with Calmodulin-Binding Transcriptional Activators and Function in Salinity Stress Response. PLANT & CELL PHYSIOLOGY 2024; 65:282-300. [PMID: 38036467 DOI: 10.1093/pcp/pcad152] [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: 09/05/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 12/02/2023]
Abstract
Eukaryotic cells use calcium ions (Ca2+) as second messengers, particularly in response to abiotic and biotic stresses. These signals are detected by Ca2+ sensor proteins, such as calmodulin (CaM), which regulate the downstream target proteins. Plants also possess many CaM-like proteins (CMLs), most of which remain unstudied. We recently demonstrated that Arabidopsis CML13 and CML14 interact with proteins containing isoleucine/glutamine (IQ) domains, including CaM-binding transcriptional activators (CAMTAs). Here, we show that CaM, CML13 and CML14 bind all six members of the Arabidopsis CAMTA family. Using a combination of in planta and in vitro protein-interaction assays, we tested 11 members of the CaM/CML family and demonstrated that only CaM, CML13 and CML14 bind to CAMTA IQ domains. CaM, CML13 and CML14 showed Ca2+-independent binding to the IQ region of CAMTA6 and CAMTA3, and CAMTA6 in vitro exhibited some specificity toward individual IQ domains within CAMTA6 in split-luciferase in planta assays. We show that cml13 mutants exhibited enhanced salinity tolerance during germination compared to wild-type plants, a phenotype similar to camta6 mutants. In contrast, plants overexpressing CML13-GFP or CML14-GFP in the wild-type background showed increased NaCl sensitivity. Under mannitol stress, cml13 mutants were more susceptible than camta6 mutants or wild-type plants. The phenotype of cml13 mutants could be rescued with the wild-type CML13 gene. Several salinity-marker genes under CAMTA6 control were similarly misregulated in both camta6 and cml13 mutants, further supporting a role for CML13 in CAMTA6 function. Collectively, our data suggest that CML13 and CML14 participate in abiotic stress signaling as CAMTA effectors.
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Affiliation(s)
- Bryan Hau
- Department of Biology, Queen's University, Kingston, ON K7L 4L8, Canada
| | - Kyle Symonds
- Department of Biology, Queen's University, Kingston, ON K7L 4L8, Canada
| | - Howard Teresinski
- Department of Biology, Queen's University, Kingston, ON K7L 4L8, Canada
| | - Abby Janssen
- Department of Biology, Queen's University, Kingston, ON K7L 4L8, Canada
| | - Liam Duff
- Department of Biology, Queen's University, Kingston, ON K7L 4L8, Canada
| | - Milena Smith
- Department of Biology, Queen's University, Kingston, ON K7L 4L8, Canada
| | | | - William Plaxton
- Department of Biology, Queen's University, Kingston, ON K7L 4L8, Canada
| | - Wayne A Snedden
- Department of Biology, Queen's University, Kingston, ON K7L 4L8, Canada
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7
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Tikunova SB, Thuma J, Davis JP. Mouse Models of Cardiomyopathies Caused by Mutations in Troponin C. Int J Mol Sci 2023; 24:12349. [PMID: 37569724 PMCID: PMC10419064 DOI: 10.3390/ijms241512349] [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: 07/01/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Cardiac muscle contraction is regulated via Ca2+ exchange with the hetero-trimeric troponin complex located on the thin filament. Binding of Ca2+ to cardiac troponin C, a Ca2+ sensing subunit within the troponin complex, results in a series of conformational re-arrangements among the thin filament components, leading to an increase in the formation of actomyosin cross-bridges and muscle contraction. Ultimately, a decline in intracellular Ca2+ leads to the dissociation of Ca2+ from troponin C, inhibiting cross-bridge cycling and initiating muscle relaxation. Therefore, troponin C plays a crucial role in the regulation of cardiac muscle contraction and relaxation. Naturally occurring and engineered mutations in troponin C can lead to altered interactions among components of the thin filament and to aberrant Ca2+ binding and exchange with the thin filament. Mutations in troponin C have been associated with various forms of cardiac disease, including hypertrophic, restrictive, dilated, and left ventricular noncompaction cardiomyopathies. Despite progress made to date, more information from human studies, biophysical characterizations, and animal models is required for a clearer understanding of disease drivers that lead to cardiomyopathies. The unique use of engineered cardiac troponin C with the L48Q mutation that had been thoroughly characterized and genetically introduced into mouse myocardium clearly demonstrates that Ca2+ sensitization in and of itself should not necessarily be considered a disease driver. This opens the door for small molecule and protein engineering strategies to help boost impaired systolic function. On the other hand, the engineered troponin C mutants (I61Q and D73N), genetically introduced into mouse myocardium, demonstrate that Ca2+ desensitization under basal conditions may be a driving factor for dilated cardiomyopathy. In addition to enhancing our knowledge of molecular mechanisms that trigger hypertrophy, dilation, morbidity, and mortality, these cardiomyopathy mouse models could be used to test novel treatment strategies for cardiovascular diseases. In this review, we will discuss (1) the various ways mutations in cardiac troponin C might lead to disease; (2) relevant data on mutations in cardiac troponin C linked to human disease, and (3) all currently existing mouse models containing cardiac troponin C mutations (disease-associated and engineered).
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Affiliation(s)
- Svetlana B. Tikunova
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University, Columbus, OH 43210, USA (J.P.D.)
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Li S, Lin S, Jiang P, Feng Q, Bao Z, Huang Y, Sun N. Discovery of Potential Protein Markers Associated with Quality Characteristics of Antarctic Krill ( Euphausia superba) Surimi Gel. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37478023 DOI: 10.1021/acs.jafc.3c02860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Antarctic krill are a consumption resource with great exploitation potential. However, the poor gel properties of Antarctic krill meat seriously limit its high-value application. In the present study, the quality characteristics and proteome changes of the κ-/ι-carrageenan-Antarctic krill surimi gel were systematically analyzed and compared. In addition, the transcriptome sequencing of Antarctic krill was carried out, which filled the gap in the Antarctic krill database. Higher molecular forces (disulfide bond and hydrophobic interaction) and the degree of network cross-linking significantly promoted the formation of κ/ι-carrageenan-Antarctic krill surimi compared to that of Antarctic krill surimi. This is the first study to investigate and map potential protein markers for quality characteristics of Antarctic krill surimi based on mass spectrometry-based label-free quantitative proteomics. The results could provide a theoretical reference for the quality control of Antarctic krill during application.
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Affiliation(s)
- Shuang Li
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Songyi Lin
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Pengfei Jiang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Qi Feng
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Zhijie Bao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Yihan Huang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Na Sun
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, P. R. China
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Lai P, Yang X, Li YH, Yin YL, Yao Q, Huang S, Fan YY, Song JK, Zhao GH. Characterization of CpCaM, a protein potentially involved in the growth of Cryptosporidium parvum. Parasitol Res 2023; 122:989-996. [PMID: 36879147 DOI: 10.1007/s00436-023-07803-9] [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: 09/27/2022] [Accepted: 02/24/2023] [Indexed: 03/08/2023]
Abstract
Cryptosporidium parvum is an important apicomplexan parasite causing severe diarrhea in both humans and animals. Calmodulin (CaM), a multifunctional and universal calcium-binding protein, contributes to the growth and development of apicomplexan parasites, but the role of CaM in C. parvum remains unknown. In this study, the CaM of C. parvum encoded by the cgd2_810 gene was expressed in Escherichia coli, and the biological functions of CpCaM were preliminarily investigated. The transcriptional level of the cgd2_810 gene peaked at 36 h post infection (pi), and the CpCaM protein was mainly located around the nucleus of the whole oocysts, in the middle of sporozoites and around the nucleus of merozoites. Anti-CpCaM antibody reduced the invasion of C. parvum sporozoites by 30.69%. The present study indicates that CpCaM is potentially involved in the growth of C. parvum. Results of the study expand our knowledge on the interaction between host and Cryptosporidium.
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Affiliation(s)
- Peng Lai
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Xin Yang
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Yun-Hui Li
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Yan-Ling Yin
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Qian Yao
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Shuang Huang
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Ying-Ying Fan
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Jun-Ke Song
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China.
| | - Guang-Hui Zhao
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China.
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Ulengin-Talkish I, Cyert MS. A cellular atlas of calcineurin signaling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119366. [PMID: 36191737 PMCID: PMC9948804 DOI: 10.1016/j.bbamcr.2022.119366] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Intracellular Ca2+ signals are temporally controlled and spatially restricted. Signaling occurs adjacent to sites of Ca2+ entry and/or release, where Ca2+-dependent effectors and their substrates co-localize to form signaling microdomains. Here we review signaling by calcineurin, the Ca2+/calmodulin regulated protein phosphatase and target of immunosuppressant drugs, Cyclosporin A and FK506. Although well known for its activation of the adaptive immune response via NFAT dephosphorylation, systematic mapping of human calcineurin substrates and regulators reveals unexpected roles for this versatile phosphatase throughout the cell. We discuss calcineurin function, with an emphasis on where signaling occurs and mechanisms that target calcineurin and its substrates to signaling microdomains, especially binding of cognate short linear peptide motifs (SLiMs). Calcineurin is ubiquitously expressed and regulates events at the plasma membrane, other intracellular membranes, mitochondria, the nuclear pore complex and centrosomes/cilia. Based on our expanding knowledge of localized CN actions, we describe a cellular atlas of Ca2+/calcineurin signaling.
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Affiliation(s)
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA 94035, United States.
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11
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Al-Khannaq M, Lytton J. Regulation of K +-Dependent Na +/Ca 2+-Exchangers (NCKX). Int J Mol Sci 2022; 24:ijms24010598. [PMID: 36614039 PMCID: PMC9820825 DOI: 10.3390/ijms24010598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022] Open
Abstract
Potassium-dependent sodium-calcium exchangers (NCKX) have emerged as key determinants of calcium (Ca2+) signaling and homeostasis, especially in environments where ion concentrations undergo large changes, such as excitatory cells and transport epithelia. The regulation of NCKX transporters enables them to respond to the changing cellular environment thereby helping to shape the extent and kinetics of Ca2+ signals. This review examines the current knowledge of the different ways in which NCKX activity can be modulated. These include (i) cellular and dynamic subcellular location (ii); changes in protein expression mediated at the gene, transcript, or protein level (iii); genetic changes resulting in altered protein structure or expression (iv); regulation via changes in substrate concentration (v); and post-translational modification, partner protein interactions, and allosteric regulation. Detailed mechanistic understanding of NCKX regulation is an emerging area of research with the potential to provide important new insights into transporter function, the control of Ca2+ signals, and possible interventions for dysregulated Ca2+ homeostasis.
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12
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Li X, Li B, Li J, Yang M, Bai Y, Chen K, Chen Z, Mao N. Mechanistic insights into the role of calcium in the allosteric regulation of the calmodulin-regulated death-associated protein kinase. Front Mol Biosci 2022; 9:1104942. [PMID: 36601586 PMCID: PMC9806222 DOI: 10.3389/fmolb.2022.1104942] [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: 11/22/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Calcium (Ca2+) signaling plays an important role in the regulation of many cellular functions. Ca2+-binding protein calmodulin (CaM) serves as a primary effector of calcium function. Ca2+/CaM binds to the death-associated protein kinase 1 (DAPK1) to regulate intracellular signaling pathways. However, the mechanism underlying the influence of Ca2+ on the conformational dynamics of the DAPK1-CaM interactions is still unclear. Here, we performed large-scale molecular dynamics (MD) simulations of the DAPK1-CaM complex in the Ca2+-bound and-unbound states to reveal the importance of Ca2+. MD simulations revealed that removal of Ca2+ increased the anti-correlated inter-domain motions between DAPK1 and CaM, which weakened the DAPK1-CaM interactions. Binding free energy calculations validated the decreased DAPK1-CaM interactions in the Ca2+-unbound state. Structural analysis further revealed that Ca2+ removal caused the significant conformational changes at the DAPK1-CaM interface, especially the helices α1, α2, α4, α6, and α7 from the CaM and the basic loop and the phosphate-binding loop from the DAPK1. These results may be useful to understand the biological role of Ca2+ in physiological processes.
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Affiliation(s)
- Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Bo Li
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jun Li
- Department of Orthopedics, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Mingyuan Yang
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yushu Bai
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
| | - Kai Chen
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
| | - Ningfang Mao
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
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13
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Tang N, Tian W, Ma GY, Xiao X, Zhou L, Li ZZ, Liu XX, Li CY, Wu KH, Liu W, Wang XY, Gao YY, Yang X, Qi J, Li D, Liu Y, Chen WS, Gao J, Li XQ, Cao W. TRPC channels blockade abolishes endotoxemic cardiac dysfunction by hampering intracellular inflammation and Ca 2+ leakage. Nat Commun 2022; 13:7455. [PMID: 36460692 PMCID: PMC9718841 DOI: 10.1038/s41467-022-35242-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 11/23/2022] [Indexed: 12/04/2022] Open
Abstract
Intracellular Ca2+ dysregulation is a key marker in septic cardiac dysfunction; however, regulation of the classic Ca2+ regulatory modules cannot successfully abolish this symptom. Here we show that the knockout of transient receptor potential canonical (TRPC) channel isoforms TRPC1 and TRPC6 can ameliorate LPS-challenged heart failure and prolong survival in mice. The LPS-triggered Ca2+ release from the endoplasmic reticulum both in cardiomyocytes and macrophages is significantly inhibited by Trpc1 or Trpc6 knockout. Meanwhile, TRPC's molecular partner - calmodulin - is uncoupled during Trpc1 or Trpc6 deficiency and binds to TLR4's Pococurante site and atypical isoleucine-glutamine-like motif to block the inflammation cascade. Blocking the C-terminal CaM/IP3R binding domain in TRPC with chemical inhibitor could obstruct the Ca2+ leak and TLR4-mediated inflammation burst, demonstrating a cardioprotective effect in endotoxemia and polymicrobial sepsis. Our findings provide insight into the pathogenesis of endotoxemic cardiac dysfunction and suggest a novel approach for its treatment.
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Affiliation(s)
- Na Tang
- grid.144022.10000 0004 1760 4150Department of Pharmacy, School of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi China ,grid.144022.10000 0004 1760 4150Shaanxi Key Laboratory of Natural Products & Chemical Biology, Northwest A&F University, Yangling, Shaanxi China
| | - Wen Tian
- grid.233520.50000 0004 1761 4404Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, Shaanxi China ,grid.233520.50000 0004 1761 4404Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Fourth Military Medical University, Xi’an, Shaanxi China
| | - Guang-Yuan Ma
- grid.144022.10000 0004 1760 4150Department of Pharmacy, School of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi China ,grid.144022.10000 0004 1760 4150Shaanxi Key Laboratory of Natural Products & Chemical Biology, Northwest A&F University, Yangling, Shaanxi China
| | - Xiong Xiao
- grid.233520.50000 0004 1761 4404Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, Shaanxi China ,grid.233520.50000 0004 1761 4404Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Fourth Military Medical University, Xi’an, Shaanxi China
| | - Lei Zhou
- grid.144022.10000 0004 1760 4150Department of Pharmacy, School of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi China ,grid.144022.10000 0004 1760 4150Shaanxi Key Laboratory of Natural Products & Chemical Biology, Northwest A&F University, Yangling, Shaanxi China
| | - Ze-Zhi Li
- grid.144022.10000 0004 1760 4150Department of Pharmacy, School of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi China ,grid.144022.10000 0004 1760 4150Shaanxi Key Laboratory of Natural Products & Chemical Biology, Northwest A&F University, Yangling, Shaanxi China
| | - Xiao-Xiao Liu
- grid.233520.50000 0004 1761 4404Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, Shaanxi China ,grid.233520.50000 0004 1761 4404Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Fourth Military Medical University, Xi’an, Shaanxi China
| | - Chong-Yao Li
- grid.412262.10000 0004 1761 5538Department of Pharmacy, Xi’an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi’an, Shaanxi China
| | - Ke-Han Wu
- grid.144022.10000 0004 1760 4150Department of Pharmacy, School of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi China ,grid.144022.10000 0004 1760 4150Shaanxi Key Laboratory of Natural Products & Chemical Biology, Northwest A&F University, Yangling, Shaanxi China
| | - Wenjuan Liu
- grid.144022.10000 0004 1760 4150Department of Pharmacy, School of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi China
| | - Xue-Ying Wang
- grid.233520.50000 0004 1761 4404Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, Shaanxi China ,grid.233520.50000 0004 1761 4404Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Fourth Military Medical University, Xi’an, Shaanxi China
| | - Yuan-Yuan Gao
- grid.233520.50000 0004 1761 4404Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, Shaanxi China ,grid.233520.50000 0004 1761 4404Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Fourth Military Medical University, Xi’an, Shaanxi China
| | - Xin Yang
- grid.144022.10000 0004 1760 4150Department of Pharmacy, School of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi China ,grid.144022.10000 0004 1760 4150Shaanxi Key Laboratory of Natural Products & Chemical Biology, Northwest A&F University, Yangling, Shaanxi China
| | - Jianzhao Qi
- grid.144022.10000 0004 1760 4150Shaanxi Key Laboratory of Natural Products & Chemical Biology, Northwest A&F University, Yangling, Shaanxi China
| | - Ding Li
- grid.144022.10000 0004 1760 4150Shaanxi Key Laboratory of Natural Products & Chemical Biology, Northwest A&F University, Yangling, Shaanxi China
| | - Yang Liu
- grid.233520.50000 0004 1761 4404Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi China
| | - Wen-Sheng Chen
- grid.233520.50000 0004 1761 4404Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi China ,Department of Cardiovascular Surgery, Xi’an Gaoxin Hospital, Xi’an, Shaanxi China
| | - Jinming Gao
- grid.144022.10000 0004 1760 4150Department of Pharmacy, School of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi China ,grid.144022.10000 0004 1760 4150Shaanxi Key Laboratory of Natural Products & Chemical Biology, Northwest A&F University, Yangling, Shaanxi China
| | - Xiao-Qiang Li
- grid.233520.50000 0004 1761 4404Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, Shaanxi China ,grid.233520.50000 0004 1761 4404Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medica of the State Administration of Traditional Chinese Medicine, Fourth Military Medical University, Xi’an, Shaanxi China
| | - Wei Cao
- grid.144022.10000 0004 1760 4150Department of Pharmacy, School of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi China ,grid.144022.10000 0004 1760 4150Shaanxi Key Laboratory of Natural Products & Chemical Biology, Northwest A&F University, Yangling, Shaanxi China
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14
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O’Day DH. Calmodulin Binding Domains in Critical Risk Proteins Involved in Neurodegeneration. Curr Issues Mol Biol 2022; 44:5802-5814. [PMID: 36421678 PMCID: PMC9689381 DOI: 10.3390/cimb44110394] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 08/26/2023] Open
Abstract
Neurodegeneration leads to multiple early changes in cognitive, emotional, and social behaviours and ultimately progresses to dementia. The dysregulation of calcium is one of the earliest potentially initiating events in the development of neurodegenerative diseases. A primary neuronal target of calcium is the small sensor and effector protein calmodulin that, in response to calcium levels, binds to and regulates hundreds of calmodulin binding proteins. The intimate and entangled relationship between calmodulin binding proteins and all phases of Alzheimer's disease has been established, but the relationship to other neurodegenerative diseases is just beginning to be evaluated. Risk factors and hallmark proteins from Parkinson's disease (PD; SNCA, Parkin, PINK1, LRRK2, PARK7), Huntington's disease (HD; Htt, TGM1, TGM2), Lewy Body disease (LBD; TMEM175, GBA), and amyotrophic lateral sclerosis/frontotemporal disease (ALS/FTD; VCP, FUS, TDP-43, TBK1, C90rf72, SQSTM1, CHCHD10, SOD1) were scanned for the presence of calmodulin binding domains and, within them, appropriate binding motifs. Binding domains and motifs were identified in multiple risk proteins, some of which are involved in multiple neurodegenerative diseases. The potential calmodulin binding profiles for risk proteins involved in HD, PD, LBD, and ALS/FTD coupled with other studies on proven binding proteins supports the central and potentially critical role for calmodulin in neurodegenerative events.
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Affiliation(s)
- Danton H. O’Day
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada;
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
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15
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Christoffer C, Kihara D. Domain-Based Protein Docking with Extremely Large Conformational Changes. J Mol Biol 2022; 434:167820. [PMID: 36089054 PMCID: PMC9992458 DOI: 10.1016/j.jmb.2022.167820] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 11/17/2022]
Abstract
Proteins are key components in many processes in living cells, and physical interactions with other proteins and nucleic acids often form key parts of their functions. In many cases, large flexibility of proteins as they interact is key to their function. To understand the mechanisms of these processes, it is necessary to consider the 3D structures of such protein complexes. When such structures are not yet experimentally determined, protein docking has long been present to computationally generate useful structure models. However, protein docking has long had the limitation that the consideration of flexibility is usually limited to very small movements or very small structures. Methods have been developed which handle minor flexibility via normal mode or other structure sampling, but new methods are required to model ordered proteins which undergo large-scale conformational changes to elucidate their function at the molecular level. Here, we present Flex-LZerD, a framework for docking such complexes. Via partial assembly multidomain docking and an iterative normal mode analysis admitting curvilinear motions, we demonstrate the ability to model the assembly of a variety of protein-protein and protein-nucleic acid complexes.
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Affiliation(s)
- Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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16
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Keppner A, Correia M, Santambrogio S, Koay TW, Maric D, Osterhof C, Winter DV, Clerc A, Stumpe M, Chalmel F, Dewilde S, Odermatt A, Kressler D, Hankeln T, Wenger RH, Hoogewijs D. Androglobin, a chimeric mammalian globin, is required for male fertility. eLife 2022; 11:72374. [PMID: 35700329 PMCID: PMC9249397 DOI: 10.7554/elife.72374] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Spermatogenesis is a highly specialized differentiation process driven by a dynamic gene expression program and ending with the production of mature spermatozoa. Whereas hundreds of genes are known to be essential for male germline proliferation and differentiation, the contribution of several genes remains uncharacterized. The predominant expression of the latest globin family member, androglobin (Adgb), in mammalian testis tissue prompted us to assess its physiological function in spermatogenesis. Adgb knockout mice display male infertility, reduced testis weight, impaired maturation of elongating spermatids, abnormal sperm shape, and ultrastructural defects in microtubule and mitochondrial organization. Epididymal sperm from Adgb knockout animals display multiple flagellar malformations including coiled, bifid or shortened flagella, and erratic acrosomal development. Following immunoprecipitation and mass spectrometry, we could identify septin 10 (Sept10) as interactor of Adgb. The Sept10-Adgb interaction was confirmed both in vivo using testis lysates and in vitro by reciprocal co-immunoprecipitation experiments. Furthermore, the absence of Adgb leads to mislocalization of Sept10 in sperm, indicating defective manchette and sperm annulus formation. Finally, in vitro data suggest that Adgb contributes to Sept10 proteolysis in a calmodulin-dependent manner. Collectively, our results provide evidence that Adgb is essential for murine spermatogenesis and further suggest that Adgb is required for sperm head shaping via the manchette and proper flagellum formation.
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Affiliation(s)
- Anna Keppner
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Miguel Correia
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | | | - Teng Wei Koay
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Darko Maric
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Carina Osterhof
- Institute for Organismic and Molecular Evolutionary Biology, University of Mainz, Mainz, Germany
| | - Denise V Winter
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Angèle Clerc
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Michael Stumpe
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Alex Odermatt
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Dieter Kressler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Thomas Hankeln
- Institute for Organismic and Molecular Evolutionary Biology, University of Mainz, Mainz, Germany
| | - Roland H Wenger
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - David Hoogewijs
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
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17
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Alam MS, Azam S, Pham K, Leyva D, Fouque KJD, Fernandez-Lima F, Miksovska J. Nanomolar affinity of EF-hands in neuronal calcium sensor 1 for bivalent cations Pb2+, Mn2+ and Hg2. Metallomics 2022; 14:6601456. [PMID: 35657675 DOI: 10.1093/mtomcs/mfac039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022]
Abstract
Abiogenic metals Pb and Hg are highly toxic since chronic and/or acute exposure often leads to severe neuropathologies. Mn2+ is an essential metal ion but in excess can impair neuronal function. In this study, we address in vitro the interactions between neuronal calcium sensor 1 (NCS1) and divalent cations. Results showed that non-physiological ions (Pb2+, Mn2+ and Hg2+) bind to EF-hands in NCS1 with nanomolar affinity and lower equilibrium dissociation constant than the physiological Ca2+ ion. (Kd,Pb2+ = 7.0±1.0 nM; Kd,Mn2+ = 34.0±6.0 nM; Kd, Hg2+ = 0.5±0.1 nM and 27.0±13.0 nM and Kd,Ca2+ = 96.0±48.0 nM). Native ultra-high resolution mass spectrometry (FT-ICR MS) and trapped ion mobility spectrometry - mass spectrometry (nESI-TIMS-MS) studies provided the NCS1-metal complex compositions - up to four Ca2+ or Mn2+ ions and three Pb2+ ions (M⋅Pb1-3Ca1-3, M⋅Mn1-4Ca1-2, and M⋅Ca1-4) were observed in complex - and similarity across the mobility profiles suggests that the overall native structure is preserved regardless of the number and type of cations. However, the non-physiological metal ions (Pb2+, Mn2+, and Hg2+) binding to NCS1 leads to more efficient quenching of Trp emission and a decrease in W30 and W103 solvent exposure compared to the apo and Ca2+ bound form, although the secondary structural rearrangement and exposure of hydrophobic sites are analogous to those for Ca2+ bound protein. Only Pb2+ and Hg2+ binding to EF-hands leads to the NCS1 dimerization whereas Mn2+ bound NCS1 remains in the monomeric form, suggesting that other factors in addition to metal ion coordination, are required for protein dimerization.
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Affiliation(s)
- Md Shofiul Alam
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA
| | - Samiol Azam
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA
| | - Khoa Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA
| | - Dennys Leyva
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA.,Biomolecular Sciences Institute, Florida International University, Miami, 33199USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA.,Biomolecular Sciences Institute, Florida International University, Miami, 33199USA
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA.,Biomolecular Sciences Institute, Florida International University, Miami, 33199USA
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18
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Puente-Santamaría L, Sanchez-Gonzalez L, Ramos-Ruiz R, del Peso L. Hypoxia classifier for transcriptome datasets. BMC Bioinformatics 2022; 23:204. [PMID: 35641902 PMCID: PMC9153107 DOI: 10.1186/s12859-022-04741-8] [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] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/17/2022] [Indexed: 12/02/2022] Open
Abstract
Molecular gene signatures are useful tools to characterize the physiological state of cell populations, but most have developed under a narrow range of conditions and cell types and are often restricted to a set of gene identities. Focusing on the transcriptional response to hypoxia, we aimed to generate widely applicable classifiers sourced from the results of a meta-analysis of 69 differential expression datasets which included 425 individual RNA-seq experiments from 33 different human cell types exposed to different degrees of hypoxia (0.1-5%[Formula: see text]) for 2-48 h. The resulting decision trees include both gene identities and quantitative boundaries, allowing for easy classification of individual samples without control or normoxic reference. Each tree is composed of 3-5 genes mostly drawn from a small set of just 8 genes (EGLN1, MIR210HG, NDRG1, ANKRD37, TCAF2, PFKFB3, BHLHE40, and MAFF). In spite of their simplicity, these classifiers achieve over 95% accuracy in cross validation and over 80% accuracy when applied to additional challenging datasets. Our results indicate that the classifiers are able to identify hypoxic tumor samples from bulk RNAseq and hypoxic regions within tumor from spatially resolved transcriptomics datasets. Moreover, application of the classifiers to histological sections from normal tissues suggest the presence of a hypoxic gene expression pattern in the kidney cortex not observed in other normoxic organs. Finally, tree classifiers described herein outperform traditional hypoxic gene signatures when compared against a wide range of datasets. This work describes a set of hypoxic gene signatures, structured as simple decision tress, that identify hypoxic samples and regions with high accuracy and can be applied to a broad variety of gene expression datasets and formats.
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Affiliation(s)
- Laura Puente-Santamaría
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), 28029 Madrid, Spain
- Genomics Unit Cantoblanco, Fundación Parque Científico de Madrid, C/ Faraday 7, 28049 Madrid, Spain
| | | | - Ricardo Ramos-Ruiz
- Genomics Unit Cantoblanco, Fundación Parque Científico de Madrid, C/ Faraday 7, 28049 Madrid, Spain
| | - Luis del Peso
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Unidad Asociada de Biomedicina CSIC-UCLM, 02006 Albacete, Spain
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19
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Advances of microRNAs in regulating mitochondrial function: new potential application in NAFLD treatment. Mol Biol Rep 2022; 49:9841-9853. [PMID: 35612781 DOI: 10.1007/s11033-022-07503-0] [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: 01/17/2022] [Accepted: 04/22/2022] [Indexed: 11/09/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is one of the most common metabolic diseases and closely associated with lipid disorder. Mitochondrion has been recognized to play a key role in lipid metabolism as the main site of energy metabolism in cells, and its dysfunction is involved in the progression of NAFLD. MicroRNAs (miRNAs), one of regulators in the pathogenesis of NAFLD, are discovered to modulate mitochondrial function by targeting mitochondrial proteins or mitochondrial-related factors, thereby improving or deteriorating NAFLD-associated pathologies. This review summarizes the differentially expressed miRNAs from clinical and experimental models of NAFLD with abilities in regulating mitochondrial function, expounds their underlying molecular mechanism and discusses their prospect and future research direction.
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20
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Liu Y, Fan H, Dong J, Chen J, Xu H, Zhou X. Phosphoproteomics of cold stress-responsive mechanisms in Rhododendron chrysanthum. Mol Biol Rep 2021; 49:303-312. [PMID: 34743272 DOI: 10.1007/s11033-021-06874-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/20/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND As an alpine plant, Rhododendron chrysanthum (R. chrysanthum) has evolved cold resistance mechanisms and become a valuable plant resource with the responsive mechanism of cold stress. METHODS AND RESULTS We adopt the phosphoproteomic and proteomic analysis combining with physiological measurement to illustrate the responsive mechanism of R. chrysanthum seedling under cold (4 °C) stress. After chilling for 12 h, 350 significantly changed proteins and 274 significantly changed phosphoproteins were detected. Clusters of Orthologous Groups (COG) analysis showed that significantly changed phosphoproteins and proteins indicated cold changed energy production and conversion and signal transduction. CONCLUSIONS The results indicated photosynthesis was inhibited under cold stress, but cold induced calcium-mediated signaling, reactive oxygen species (ROS) homeostasis and other transcription regulation factors could protect plants from the destruction caused by cold stress. These data provide the insight to the cold stress response and defense mechanisms of R. chrysanthum leaves at the phosphoproteome level.
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Affiliation(s)
- Yunbo Liu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China
| | - Hang Fan
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China
| | - Jiawei Dong
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China
| | - Jianyu Chen
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China
| | - Hongwei Xu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China.
| | - Xiaofu Zhou
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China.
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21
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Zhu X, Yuan H, Ningjuan O, Trotman CA, Van Dyke TE, Chen JJ, Shen G. 6-Shogaol promotes bone resorption and accelerates orthodontic tooth movement through the JNK-NFATc1 signaling axis. J Bone Miner Metab 2021; 39:962-973. [PMID: 34191125 PMCID: PMC8595588 DOI: 10.1007/s00774-021-01245-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Corticotomy is widely used in clinical practice to accelerate tooth movement and shorten the duration of orthodontic treatment. It is effective, but an invasive surgery is needed to induce alveolar bone osteopenia that enable rapid tooth movement. In this study, we discovered the potential of 6-shogaol as a more patient-friendly non-invasive alternative to induce transient osteopenia and accelerate tooth movement. MATERIALS AND METHODS The effects of 6-shogaol on the bone marrow macrophages (BMM) proliferation and osteoclast differentiation, and bone resorption were determined in vitro. Sprague-Dawley rats were distributed into three groups: CON, IPinj or Localinj and euthanized at day 28. Micro-CT, histology, immunohistological, and TUNEL analysis were performed to evaluate the tooth movement acceleration effect of 6-shogaol. RESULTS In vitro, 6-shogaol promotes osteoclast differentiation and functional demineralization of alveolar bone. RANKL-induced mRNA expression of osteoclastic-specific genes was significantly higher in the presence of 6-shogaol. A dose-dependent increase in the area of TRAP-positive cells was observed with 6-shogaol treatment. F-actin ring formation and increased bone resorption confirmed that osteoclasts treated with 6-shogaol were mature and functional. 6-shogaol stimulated JNK activation and NFATc1 expression during osteoclast differentiation. In vivo, 6-shogaol promotes alveolar bone transient osteopenia and accelerates orthodontic tooth movement. Alveolar bone mass was reduced, more osteoclasts were observed in bone resorption lacunae on the compression side, and the expression of RANKL and sclerostin were higher than the control group. In conclusion, our results suggest that 6-shogoal accelerates tooth movement by inducing osteopenia by a mechanism similar to surgically induced bone injury.
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Affiliation(s)
- Xiaofang Zhu
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
| | - Hao Yuan
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ouyang Ningjuan
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Carroll Ann Trotman
- Department of Orthodontics, Tufts University School of Dental Medicine, Boston, MA, USA
| | | | - Jake Jinkun Chen
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA.
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
| | - Guofang Shen
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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22
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Dudev T, Grauffel C, Lim C. Calcium in Signaling: Its Specificity and Vulnerabilities toward Biogenic and Abiogenic Metal Ions. J Phys Chem B 2021; 125:10419-10431. [PMID: 34515482 DOI: 10.1021/acs.jpcb.1c05154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Divalent calcium ion (Ca2+) plays an indispensable role as a second messenger in a myriad of signal transduction processes. Of utmost importance for the faultless functioning of calcium-modulated signaling proteins is their binding selectivity of the native metal cation over rival biogenic/abiogenic metal ion contenders in the intra/extracellular fluids. In this Perspective, we summarize recent findings on the competition between the cognate Ca2+ and other biogenic or abiogenic divalent cations for binding to Ca2+-signaling proteins or organic cofactors. We describe the competition between the two most abundant intracellular biogenic metal ions (Mg2+ and Ca2+) for Ca2+-binding sites in signaling proteins, followed by the rivalry between native Ca2+ and "therapeutic" Li+ as well as "toxic" Pb2+. We delineate the key factors governing the rivalry between the native and non-native cations in proteins and highlight key implications for the biological performance of the respective proteins/organic cofactors.
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Affiliation(s)
- Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University, Sofia 1164, Bulgaria
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300 Taiwan
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