1
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Li X, Feng R, Luo P, Zhang Y, Lu L. Synergistic effects of putative Ca 2+-binding sites of calmodulin in fungal development, temperature stress and virulence of Aspergillus fumigatus. Virulence 2024; 15:2290757. [PMID: 38085844 PMCID: PMC10761034 DOI: 10.1080/21505594.2023.2290757] [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: 07/28/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
In pathogenic fungi, calcium-calmodulin-dependent serine-threonine-specific phosphatase calcineurin is involved in morphogenesis and virulence. Therefore, calcineurin and its tightly related protein complexes are attractive antifungal drug targets. However, there is limited knowledge available on the relationship between in vivo Ca2+-binding sites of calmodulin (CaM) and its functions in regulating stress responses, morphogenesis, and pathogenesis. In the current study, we demonstrated that calmodulin is required for hyphal growth, conidiation, and virulence in the human fungal pathogen, Aspergillus fumigatus. Site-directed mutations of calmodulin revealed that a single Ca2+-binding site mutation had no significant effect on A. fumigatus hyphal development, but multiple Ca2+-binding site mutations exhibited synergistic effects, especially when cultured at 42 °C, indicating that calmodulin function in response to temperature stress depends on its Ca2+-binding sites. Western blotting implied that mutations in Ca2+-binding sites caused highly degraded calmodulin fragments, suggesting that the loss of Ca2+-binding sites results in reduced protein stability. Moreover, normal intracellular calcium homeostasis and the nuclear translocation of the transcriptional factor CrzA are dependent on Ca2+-binding sites of AfCaM, demonstrating that Ca2+-binding sites of calmodulin are required for calcium signalling and its major transcription factor CrzA. Importantly, in situ mutations for four Ca2+-binding sites of calmodulin resulted in an almost complete loss of virulence in the Galleria mellonella wax moth model. This study shed more light on the functional characterization of putative calcium-binding sites of calmodulin in the morphogenesis and virulence of A. fumigatus, which enhances our understanding of calmodulin biological functions in cells of opportunistic fungal pathogens.
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Affiliation(s)
- Xingyue Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ruoyun Feng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Pan Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yuanwei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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2
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Li J, Meng S, Zhang Z, Wang Y, Li Z, Yan S, Shen J, Liu X, Zhang S. Nanoparticle-mediated calmodulin dsRNA and cyantraniliprole co-delivery system: High-efficient control of two key pear pests while ensuring safety for natural enemy insects. Int J Biol Macromol 2024; 277:134478. [PMID: 39102908 DOI: 10.1016/j.ijbiomac.2024.134478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/26/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
Currently, the predominant method for managing pests in orchards is chemical control. However, prolonged use of chemicals leads to resistance issues and raise ecological safety. A promising approach to tackle these challenges involves nanoparticles-mediated delivery system of dsRNA and pesticides. Despite its potential, this strategy has not been widely applied in controlling pests in pear orchards. In this study, we developed a nanoparticle-mediated ternary biopesticide to tackle resistance and safety concerns associated with calmodulin dsRNA and cyantraniliprole. Initially, we assessed the effectiveness of cyantraniliprole against two key pear pests, Grapholita molesta and Cacopsylla chinensis. Subsequently, we observed an upregualtion of genes CaM and CN following cyantraniliprole treatment. Furthermore, inhibiting or silencing GmCaM and CcGaM enhanced the sensitivity to cyantraniliprole more effectively. By introducing hairpin RNA into the pET30a-BL21 RNaseIII- system to silence GmCaM and CcCaM, we developed a nanoparticle-mediated co-delivery system that exhibited improved control over these two pests. Importantly, our research demonstrated that using reduced cyantraniliprole dosages through ternary biopesticides could help mitigate risks to natural enemies. Overall, our research emphasizes the enhanced effectiveness of ternary biopesticides in boosting the performance of dsRNA and pesticide against pear pests, while fostering environmental sustainability-a novel advancement in this field.
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Affiliation(s)
- Jianying Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shili Meng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhixian Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yilin Wang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhen Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shuo Yan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jie Shen
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaoxia Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China.
| | - Songdou Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China; Sanya Institute of China Agricultural University, 572025 Sanya City, Hainan Province, China.
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3
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McGruddy RA, Smeele ZE, Manley B, Masucci JD, Haywood J, Lester PJ. RNA interference as a next-generation control method for suppressing Varroa destructor reproduction in honey bee (Apis mellifera) hives. PEST MANAGEMENT SCIENCE 2024; 80:4770-4778. [PMID: 38801186 DOI: 10.1002/ps.8193] [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: 02/24/2024] [Revised: 04/10/2024] [Accepted: 05/12/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND The Varroa mite (Varroa destructor) is considered to be the greatest threat to apiculture worldwide. RNA interference (RNAi) using double-stranded RNA (dsRNA) as a gene silencing mechanism has emerged as a next-generation strategy for mite control. RESULTS We explored the impact of a dsRNA biopesticide, named vadescana, designed to silence the calmodulin gene in Varroa, on mite fitness in mini-hives housed in a laboratory. Two dosages were tested: 2 g/L dsRNA and 8 g/L dsRNA. Vadescana appeared to have no effect on mite survival, however, mite fertility was substantially reduced. The majority of foundress mites exposed to vadescana failed to produce any offspring. No dose-dependent effect of vadescana was observed, as both the low and high doses inhibited mite reproduction equally well in the mini-hives and neither dose impacted pupal survival of the honey bee. Approximately 95% of bee pupae were alive at uncapping across all treatment groups. CONCLUSION These findings suggest that vadescana has significant potential as an effective alternative to conventional methods for Varroa control, with broader implications for the utilization of RNAi as a next-generation tool in the management of pest species. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Rose A McGruddy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Zoe E Smeele
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Brian Manley
- GreenLight Biosciences, Research Triangle Park, Durham, NC, USA
| | - James D Masucci
- GreenLight Biosciences, Research Triangle Park, Durham, NC, USA
| | - John Haywood
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington, New Zealand
| | - Philip J Lester
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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4
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Cui Y, Wu K, Yao X. The CDPK-related protein kinase HvCRK2 and HvCRK4 interact with HvCML32 to negatively regulate drought tolerance in transgenic Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108909. [PMID: 38971089 DOI: 10.1016/j.plaphy.2024.108909] [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: 04/04/2024] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Calcium-dependent protein kinase (CDPK) as one of calcium sensors were play important roles in stress responses. CDPK-related protein kinase (CRK) was identified as subgroup III of CDPK has been characterized in many plants, but the members and functions of CRK genes in hulless barley (Hordeum vulgare L.) has not been clarified. Here, we identified four HvCRK genes and named HvCRK1-4 according to chromosomes localization. Moreover, the physiological function of highly induced genes of HvCRK2 and HvCRK4 were investigated in drought stress tolerance by examining their overexpression transgenic lines functions generated in Arabidopsis thaliana. Under drought stress, both overexpression HvCRK2 and HvCRK4 displayed reduced drought resistance, and accompanied by higher accumulation levels of ROS. Notably, overexpression of HvCRK2 and HvCRK4 reduced sensitivity to exogenous ABA, meanwhile the expression of ABA-responsive genes in transgenic plants were down-regulated compared to the wild type in response to drought stress. Furthermore, the physically interaction of HvCRK2 and HvCRK4 with calmodulin (CaM) and calmodulin-like (CML) proteins were determined in vivo, the further results showed that HvCML32 binds to HvCRK2/4 S_TKC structural domains and negatively regulates drought tolerance. In summary, this study identified HvCRK members and indicated that HvCRK2 and HvCRK4 genes play negative roles in drought tolerance, and provide insight into potential molecular mechanism of HvCRK2 and HvCRK4 in response to drought stress.
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Affiliation(s)
- Yongmei Cui
- Academy of Agricultural and Forestry Sciences, Qinghai University, 810016, Xining, China; Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, 810016, Xining, China; Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, 810016, Xining, China; Oinghai Hulless Barley Subcenter of National Triticeae Improvement Center, 810016, Xining, China
| | - Kunlun Wu
- Academy of Agricultural and Forestry Sciences, Qinghai University, 810016, Xining, China; Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, 810016, Xining, China; Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, 810016, Xining, China; Oinghai Hulless Barley Subcenter of National Triticeae Improvement Center, 810016, Xining, China.
| | - Xiaohua Yao
- Academy of Agricultural and Forestry Sciences, Qinghai University, 810016, Xining, China; Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, 810016, Xining, China; Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, 810016, Xining, China; Oinghai Hulless Barley Subcenter of National Triticeae Improvement Center, 810016, Xining, China.
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5
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Yang JL, Sun X, Shi JX, Cui QX, Cao XY, Wang KT, An MX, Wu SJ, Yang YL, Sun HZ, Zhao WD. Calmodulin Triggers Activity-Dependent rRNA Biogenesis via Interaction with DDX21. J Neurosci 2024; 44:e1841232024. [PMID: 39060175 PMCID: PMC11358605 DOI: 10.1523/jneurosci.1841-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 07/11/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Protein synthesis in response to neuronal activity, known as activity-dependent translation, is critical for synaptic plasticity and memory formation. However, the signaling cascades that couple neuronal activity to the translational events remain elusive. In this study, we identified the role of calmodulin (CaM), a conserved Ca2+-binding protein, in ribosomal RNA (rRNA) biogenesis in neurons. We found the CaM-regulated rRNA synthesis is Ca2+-dependent and necessary for nascent protein synthesis and axon growth in hippocampal neurons. Mechanistically, CaM interacts with nucleolar DEAD (Asp-Glu-Ala-Asp) box RNA helicase (DDX21) in a Ca2+-dependent manner to regulate nascent rRNA transcription within nucleoli. We further found CaM alters the conformation of DDX21 to liberate the DDX21-sequestered RPA194, the catalytic subunit of RNA polymerase I, to facilitate transcription of ribosomal DNA. Using high-throughput screening, we identified the small molecules batefenterol and indacaterol that attenuate the CaM-DDX21 interaction and suppress nascent rRNA synthesis and axon growth in hippocampal neurons. These results unveiled the previously unrecognized role of CaM as a messenger to link the activity-induced Ca2+ influx to the nucleolar events essential for protein synthesis. We thus identified the ability of CaM to transmit information to the nucleoli of neurons in response to stimulation.
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Affiliation(s)
- Jia-Lin Yang
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Xue Sun
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Jun-Xiu Shi
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Qing-Xu Cui
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Xin-Yu Cao
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Kai-Tuo Wang
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Ming-Xin An
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Si-Jin Wu
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Yong-Liang Yang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Hong-Zan Sun
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Wei-Dong Zhao
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
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6
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Chen Y, Chen J, Liang L, Dai W, Li N, Dong S, Zhan Y, Chen G, Yu Y. Compound heterozygous mutations of NTNG2 cause intellectual disability via inhibition of the CaMKII signaling. J Genet Genomics 2024:S1673-8527(24)00198-X. [PMID: 39151821 DOI: 10.1016/j.jgg.2024.08.001] [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: 05/22/2024] [Revised: 08/04/2024] [Accepted: 08/05/2024] [Indexed: 08/19/2024]
Abstract
Netrin-G2 is a membrane-anchored protein and is known to play critical roles in neuronal circuit development and synaptic organization. In this study, we identify compound heterozygous mutations of c.547delC, p.(Arg183Alafs*186) and c.605G>A, p.(Trp202*) in NTNG2 causing a syndrome exhibiting developmental delay, intellectual disability, hypotonia, and facial dysmorphism. To elucidate the underlying cellular and molecular mechanisms, CRISPR-Cas9 technology is employed to generate a knock-in mouse model expressing the R183Afs and W202X mutations. We report that the Ntng2R183Afs/W202X mice exhibit hypotonia and impaired learning and memory. We find that levels of CaMKII and p-GluA1Ser831 are decreased and excitatory postsynaptic transmission and long-term potentiation are impaired. To increase the activity of CaMKII, the mutant mice have received intraperitoneal injections of DCP-LA, a CaMKII agonist, and show improved cognitive function. Together, our findings reveal molecular mechanisms of how NTNG2 deficiency leads to impairments of cognitive ability and synaptic plasticity.
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Affiliation(s)
- Yaoting Chen
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Jiang Chen
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu 210008, China
| | - Lili Liang
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Weiqian Dai
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Nan Li
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Shuangshuang Dong
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Yongkun Zhan
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research, Shanghai 200092, China.
| | - Guiquan Chen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, Jiangsu 210061, China.
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research, Shanghai 200092, China.
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7
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Mom R, Mocquet V, Auguin D, Réty S. Aquaporin Modulation by Cations, a Review. Curr Issues Mol Biol 2024; 46:7955-7975. [PMID: 39194687 DOI: 10.3390/cimb46080470] [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: 07/05/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
Aquaporins (AQPs) are transmembrane channels initially discovered for their role in water flux facilitation through biological membranes. Over the years, a much more complex and subtle picture of these channels appeared, highlighting many other solutes accommodated by AQPs and a dense regulatory network finely tuning cell membranes' water permeability. At the intersection between several transduction pathways (e.g., cell volume regulation, calcium signaling, potassium cycling, etc.), this wide and ancient protein family is considered an important therapeutic target for cancer treatment and many other pathophysiologies. However, a precise and isoform-specific modulation of these channels function is still challenging. Among the modulators of AQPs functions, cations have been shown to play a significant contribution, starting with mercury being historically associated with the inhibition of AQPs since their discovery. While the comprehension of AQPs modulation by cations has improved, a unifying molecular mechanism integrating all current knowledge is still lacking. In an effort to extract general trends, we reviewed all known modulations of AQPs by cations to capture a first glimpse of this regulatory network. We paid particular attention to the associated molecular mechanisms and pinpointed the residues involved in cation binding and in conformational changes tied up to the modulation of the channel function.
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Affiliation(s)
- Robin Mom
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Vincent Mocquet
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Daniel Auguin
- Laboratoire de Physiologie, Ecologie et Environnement (P2E), UPRES EA 1207/USC INRAE-1328, UFR Sciences et Techniques, Université d'Orléans, F-45067 Orléans, France
| | - Stéphane Réty
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
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8
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Lombard V, Grudinin S, Laine E. Explaining Conformational Diversity in Protein Families through Molecular Motions. Sci Data 2024; 11:752. [PMID: 38987561 PMCID: PMC11237097 DOI: 10.1038/s41597-024-03524-5] [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: 01/31/2024] [Accepted: 06/14/2024] [Indexed: 07/12/2024] Open
Abstract
Proteins play a central role in biological processes, and understanding their conformational variability is crucial for unraveling their functional mechanisms. Recent advancements in high-throughput technologies have enhanced our knowledge of protein structures, yet predicting their multiple conformational states and motions remains challenging. This study introduces Dimensionality Analysis for protein Conformational Exploration (DANCE) for a systematic and comprehensive description of protein families conformational variability. DANCE accommodates both experimental and predicted structures. It is suitable for analysing anything from single proteins to superfamilies. Employing it, we clustered all experimentally resolved protein structures available in the Protein Data Bank into conformational collections and characterized them as sets of linear motions. The resource facilitates access and exploitation of the multiple states adopted by a protein and its homologs. Beyond descriptive analysis, we assessed classical dimensionality reduction techniques for sampling unseen states on a representative benchmark. This work improves our understanding of how proteins deform to perform their functions and opens ways to a standardised evaluation of methods designed to sample and generate protein conformations.
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Affiliation(s)
- Valentin Lombard
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005, Paris, France
| | - Sergei Grudinin
- Université Grenoble Alpes, CNRS, Grenoble INP, LJK, 38000, Grenoble, France.
| | - Elodie Laine
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005, Paris, France.
- Institut Universitaire de France (IUF), Paris, France.
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9
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Kim JW, Yong AJH, Aisenberg EE, Lobel JH, Wang W, Dawson TM, Dawson VL, Gao R, Jan YN, Bateup HS, Ingolia NT. Molecular recording of calcium signals via calcium-dependent proximity labeling. Nat Chem Biol 2024; 20:894-905. [PMID: 38658655 DOI: 10.1038/s41589-024-01603-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024]
Abstract
Calcium ions serve as key intracellular signals. Local, transient increases in calcium concentrations can activate calcium sensor proteins that in turn trigger downstream effectors. In neurons, calcium transients play a central role in regulating neurotransmitter release and synaptic plasticity. However, it is challenging to capture the molecular events associated with these localized and ephemeral calcium signals. Here we present an engineered biotin ligase that generates permanent molecular traces in a calcium-dependent manner. The enzyme, calcium-dependent BioID (Cal-ID), biotinylates nearby proteins within minutes in response to elevated local calcium levels. The biotinylated proteins can be identified via mass spectrometry and visualized using microscopy. In neurons, Cal-ID labeling is triggered by neuronal activity, leading to prominent protein biotinylation that enables transcription-independent activity labeling in the brain. In summary, Cal-ID produces a biochemical record of calcium signals and neuronal activity with high spatial resolution and molecular specificity.
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Affiliation(s)
- J Wren Kim
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
| | - Adeline J H Yong
- Department of Physiology at the University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA, USA
| | - Erin E Aisenberg
- Helen Wills Neuroscience Institute at the University of California, Berkeley, Berkeley, CA, USA
| | - Joseph H Lobel
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
| | - Wei Wang
- Department of Chemistry at the University of Illinois, Chicago, Chicago, IL, USA
| | - Ted M Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruixuan Gao
- Department of Chemistry at the University of Illinois, Chicago, Chicago, IL, USA
| | - Yuh Nung Jan
- Department of Physiology at the University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA, USA
| | - Helen S Bateup
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute at the University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA.
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10
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Greene D, Shiferaw Y. Identifying Key Binding Interactions Between the Cardiac L-Type Calcium Channel and Calmodulin Using Molecular Dynamics Simulations. J Phys Chem B 2024; 128:6097-6111. [PMID: 38870543 PMCID: PMC11215769 DOI: 10.1021/acs.jpcb.4c02251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024]
Abstract
Defects in the binding of the calcium sensing protein calmodulin (CaM) to the L-type calcium channel (CaV1.2) or to the ryanodine receptor type 2 (RyR2) can lead to dangerous cardiac arrhythmias with distinct phenotypes, such as long-QT syndrome (LQTS) and catecholaminergic ventricular tachycardia (CPVT). Certain CaM mutations lead to LQTS while other mutations lead to CPVT, but the mechanisms by which a specific mutation can lead to each disease phenotype are not well-understood. In this study, we use long, 2 μs molecular dynamics simulations and a multitrajectory approach to identify the key binding interactions between the IQ domain of CaV1.2 and CaM. Five key interactions are found between CaV1.2 and CaM in the C-lobe, 1 in the central linker, and 2 in the N-lobe. In addition, while 5 key interactions appear between residues 120-149 in the C-lobe of CaM when it interacts with CaV1.2, only 1 key interaction is found within this region of CaM when it interacts with the RyR2. We show that this difference in the distribution of key interactions correlates with the known distribution of CaM mutations that lead to LQTS or CPVT. This correlation suggests that a disruption of key binding interactions is a plausible mechanism that can lead to these two different disease phenotypes.
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Affiliation(s)
- D’Artagnan Greene
- Department of Physics and
Astronomy, California State University Northridge, 18111 Nordhoff Street, Northridge, California 91330-8268, United States of
America
| | - Yohannes Shiferaw
- Department of Physics and
Astronomy, California State University Northridge, 18111 Nordhoff Street, Northridge, California 91330-8268, United States of
America
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11
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Boto T, Tomchik SM. Functional Imaging of Learning-Induced Plasticity in the Central Nervous System with Genetically Encoded Reporters in Drosophila. Cold Spring Harb Protoc 2024; 2024:pdb.top107799. [PMID: 37197830 DOI: 10.1101/pdb.top107799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Learning and memory allow animals to adjust their behavior based on the predictive value of their past experiences. Memories often exist in complex representations, spread across numerous cells and synapses in the brain. Studying relatively simple forms of memory provides insights into the fundamental processes that underlie multiple forms of memory. Associative learning occurs when an animal learns the relationship between two previously unrelated sensory stimuli, such as when a hungry animal learns that a particular odor is followed by a tasty reward. Drosophila is a particularly powerful model to study how this type of memory works. The fundamental principles are widely shared among animals, and there is a wide range of genetic tools available to study circuit function in flies. In addition, the olfactory structures that mediate associative learning in flies, such as the mushroom body and its associated neurons, are anatomically organized, relatively well-characterized, and readily accessible to imaging. Here, we review the olfactory anatomy and physiology of the olfactory system, describe how plasticity in the olfactory pathway mediates learning and memory, and explain the general principles underlying calcium imaging approaches.
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Affiliation(s)
- Tamara Boto
- Department of Physiology, Trinity College Dublin, Dublin 2, Ireland
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Seth M Tomchik
- Neuroscience and Pharmacology, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
- Iowa Neuroscience Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
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12
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Rasaily M, Ngiimei D S, Thaosen RK, Gupta S, Deka S, Tamuli R. Methods for the detection of intracellular calcium in filamentous fungi. MethodsX 2024; 12:102570. [PMID: 38322134 PMCID: PMC10844858 DOI: 10.1016/j.mex.2024.102570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
Calcium (Ca2+), a critical secondary messenger, is also known as the molecule of life and death. The cell responds to a minute change in Ca2+ concentration and tightly maintains Ca2+ homeostasis. Therefore, determining the cell Ca2+ level is critical to understand Ca2+ distribution in the cell and various cell processes. Many techniques have been developed to measure Ca2+ in the cell. We review here different methods used to detect and measure Ca2+ in filamentous fungi. Ca2+-sensitive fluorescent chlortetracycline hydrochloride (CTC), Ca2+-selective microelectrode, Ca2+ isotopes, aequorins, and RGECOs are commonly used to measure the Ca2+ level in filamentous fungi. The use of CTC was one of the earliest methods, developed in 1988, to measure the Ca2+ gradient in the filamentous fungus Neurospora crassa. Subsequently, Ca2+-specific microelectrodes were developed later in the 1990s to identify Ca2+ ion flux variations, and to measure Ca2+ concentration. Another method for quantifying Ca2+ is by using radio-labeled Ca2+ as a tracer. The usage of 45Ca to measure Ca2+ in Saccharomyces cerevisiae was reported previously and the same methodology was also used to detect Ca2+ in N. crassa recently. Subsequently, genetically engineered Ca2+ indicators (GECIs) like aequorins and RGECOs have been developed as Ca2+ indicators to detect and visualize Ca2+ inside the cell. In this review, we summarize various methodologies used to detect and measure Ca2+ in filamentous fungi with their advantages and limitations. •Chlortetracycline (CTC) fluorescence assay is used for visualizing Ca2+ level, whereas microelectrodes technique is used to determine Ca2+ flux in the cell.•Radioactive 45Ca is useful for quantification of Ca2+ in the cellular compartments.•Genetically modified calcium indicators (GECIs) are used to study Ca2+ dynamics in the cell.
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Affiliation(s)
- Megha Rasaily
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Serena Ngiimei D
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Rahul Kumar Thaosen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Surabhi Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
| | - Sangeeta Deka
- Centre for the Environment, Indian Institute of Technology Guwahati, India
| | - Ranjan Tamuli
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India
- Centre for the Environment, Indian Institute of Technology Guwahati, India
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13
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Qu Y, Wang S, Jiang H, Wang Q, Liao Y, Qiu X, Tan L, Song C, Ding C, Sun Y, Yang Z. The Ca 2+-dependent phosphatase calcineurin dephosphorylates TBK1 to suppress antiviral innate immunity. J Virol 2024; 98:e0001624. [PMID: 38563732 PMCID: PMC11092360 DOI: 10.1128/jvi.00016-24] [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: 02/06/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
Tumor necrosis factor receptor-associated factor family member-associated NF-κB activator-binding kinase 1 (TBK1) plays a key role in the induction of the type 1 interferon (IFN-I) response, which is an important component of innate antiviral defense. Viruses target calcium (Ca2+) signaling networks, which participate in the regulation of the viral life cycle, as well as mediate the host antiviral response. Although many studies have focused on the role of Ca2+ signaling in the regulation of IFN-I, the relationship between Ca2+ and TBK1 in different infection models requires further elucidation. Here, we examined the effects of the Newcastle disease virus (NDV)-induced increase in intracellular Ca2+ levels on the suppression of host antiviral responses. We demonstrated that intracellular Ca2+ increased significantly during NDV infection, leading to impaired IFN-I production and antiviral immunity through the activation of calcineurin (CaN). Depletion of Ca²+ was found to lead to a significant increase in virus-induced IFN-I production resulting in the inhibition of viral replication. Mechanistically, the accumulation of Ca2+ in response to viral infection increases the phosphatase activity of CaN, which in turn dephosphorylates and inactivates TBK1 in a Ca2+-dependent manner. Furthermore, the inhibition of CaN on viral replication was counteracted in TBK1 knockout cells. Together, our data demonstrate that NDV hijacks Ca2+ signaling networks to negatively regulate innate immunity via the CaN-TBK1 signaling axis. Thus, our findings not only identify the mechanism by which viruses exploit Ca2+ signaling to evade the host antiviral response but also, more importantly, highlight the potential role of Ca2+ homeostasis in the viral innate immune response.IMPORTANCEViral infections disrupt intracellular Ca2+ homeostasis, which affects the regulation of various host processes to create conditions that are conducive for their own proliferation, including the host immune response. The mechanism by which viruses trigger TBK1 activation and IFN-I induction through viral pathogen-associated molecular patterns has been well defined. However, the effects of virus-mediated Ca2+ imbalance on the IFN-I pathway requires further elucidation, especially with respect to TBK1 activation. Herein, we report that NDV infection causes an increase in intracellular free Ca2+ that leads to activation of the serine/threonine phosphatase CaN, which subsequently dephosphorylates TBK1 and negatively regulates IFN-I production. Furthermore, depletion of Ca2+ or inhibition of CaN activity exerts antiviral effects by promoting the production of IFN-I and inhibiting viral replication. Thus, our results reveal the potential role of Ca2+ in the innate immune response to viruses and provide a theoretical reference for the treatment of viral infectious diseases.
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Affiliation(s)
- Yang Qu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Siyuan Wang
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hui Jiang
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Qingyi Wang
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ying Liao
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Lei Tan
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Cuiping Song
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Chan Ding
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yingjie Sun
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Zengqi Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
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14
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Yu S, Li S, Wang W, Tang D. OsCAMTA3 Negatively Regulates Disease Resistance to Magnaporthe oryzae by Associating with OsCAMTAPL in Rice. Int J Mol Sci 2024; 25:5049. [PMID: 38732268 PMCID: PMC11084498 DOI: 10.3390/ijms25095049] [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: 03/28/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Rice (Oryza sativa) is one of the most important staple foods worldwide. However, rice blast disease, caused by the ascomycete fungus Magnaporthe oryzae, seriously affects the yield and quality of rice. Calmodulin-binding transcriptional activators (CAMTAs) play vital roles in the response to biotic stresses. In this study, we showed that OsCAMTA3 and CAMTA PROTEIN LIKE (OsCAMTAPL), an OsCAMTA3 homolog that lacks the DNA-binding domain, functioned together in negatively regulating disease resistance in rice. OsCAMTA3 associated with OsCAMTAPL. The oscamta3 and oscamtapl mutants showed enhanced resistance compared to wild-type plants, and oscamta3/pl double mutants showed more robust resistance to M. oryzae than oscamta3 or oscamtapl. An RNA-Seq analysis revealed that 59 and 73 genes, respectively, were differentially expressed in wild-type plants and oscamta3 before and after inoculation with M. oryzae, including OsALDH2B1, an acetaldehyde dehydrogenase that negatively regulates plant immunity. OsCAMTA3 could directly bind to the promoter of OsALDH2B1, and OsALDH2B1 expression was decreased in oscamta3, oscamtapl, and oscamta3/pl mutants. In conclusion, OsCAMTA3 associates with OsCAMTAPL to regulate disease resistance by binding and activating the expression of OsALDH2B1 in rice, which reveals a strategy by which rice controls rice blast disease and provides important genes for resistance breeding holding a certain positive impact on ensuring food security.
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Affiliation(s)
| | | | - Wei Wang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Y.); (S.L.)
| | - Dingzhong Tang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Y.); (S.L.)
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15
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Mickus R, Raškevičius V, Sarapinienė I, Mikalayeva V, Prekeris R, Skeberdis VA. Phosphorylation-dependent allosteric regulation of Cx43 gap junction inhibitor potency. Biomed Pharmacother 2024; 174:116550. [PMID: 38593702 DOI: 10.1016/j.biopha.2024.116550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024] Open
Abstract
Physiological and pathological processes such as homeostasis, embryogenesis, development, tumorigenesis, and cell movement depend on the intercellular communication through gap junctions (GJIC). Connexin (Cx)-based GJ channels are formed of two apposing hemichannels in the contiguous cells and provide a direct pathway for electrical and metabolic intercellular communication. The main modulators of GJ conductance are transjunctional voltage, intracellular pH, Ca2+, Mg2+, and phosphorylation. Chemical modulators of GJIC are being used in cases of various intercellular communication-dependent diseases. In this study, we used molecular docking, dual whole-cell patch-clamp, and Western blotting to investigate the impact of connexin phosphorylation on GJ chemical gating by α-pinene and other GJ inhibitors (octanol, carbenoxolone, mefloquine, intracellular pH, glycyrrhetinic acid, and sevoflurane) in HeLa cells expressing exogenous Cx43 (full length and truncated at amino acid 258) and other connexins typical of heart and/or nervous system (Cx36, Cx40, Cx45, and Cx47), and in cells expressing endogenous Cx43 (Novikoff and U-87). We found that Ca2+-regulated kinases, such as Ca2+/calmodulin-dependent kinase II, atypical protein kinase C, cyclin-dependent kinase, and Pyk2 kinase may allosterically modulate the potency of α-pinene through phosphorylation of Cx43 C-terminus. The identified new phenomenon was Cx isoform-, inhibitor-, and cell type-dependent. Overall, these results suggest that compounds, the potency of which depends on receptor phosphorylation, might be of particular interest in developing targeted therapies for diseases accompanied by high kinase activity, such as cardiac arrhythmias, epilepsy, stroke, essential tremor, inflammation, and cancer.
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Affiliation(s)
- Rokas Mickus
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas LT-50162, Lithuania
| | - Vytautas Raškevičius
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas LT-50162, Lithuania
| | - Ieva Sarapinienė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas LT-50162, Lithuania
| | - Valeryia Mikalayeva
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas LT-50162, Lithuania
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80015, USA
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16
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Baltasar-Marchueta M, Llona L, M-Alicante S, Barbolla I, Ibarluzea MG, Ramis R, Salomon AM, Fundora B, Araujo A, Muguruza-Montero A, Nuñez E, Pérez-Olea S, Villanueva C, Leonardo A, Arrasate S, Sotomayor N, Villarroel A, Bergara A, Lete E, González-Díaz H. Identification of Riluzole derivatives as novel calmodulin inhibitors with neuroprotective activity by a joint synthesis, biosensor, and computational guided strategy. Biomed Pharmacother 2024; 174:116602. [PMID: 38636396 DOI: 10.1016/j.biopha.2024.116602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
The development of new molecules for the treatment of calmodulin related cardiovascular or neurodegenerative diseases is an interesting goal. In this work, we introduce a novel strategy with four main steps: (1) chemical synthesis of target molecules, (2) Förster Resonance Energy Transfer (FRET) biosensor development and in vitro biological assay of new derivatives, (3) Cheminformatics models development and in vivo activity prediction, and (4) Docking studies. This strategy is illustrated with a case study. Firstly, a series of 4-substituted Riluzole derivatives 1-3 were synthetized through a strategy that involves the construction of the 4-bromoriluzole framework and its further functionalization via palladium catalysis or organolithium chemistry. Next, a FRET biosensor for monitoring Ca2+-dependent CaM-ligands interactions has been developed and used for the in vitro assay of Riluzole derivatives. In particular, the best inhibition (80%) was observed for 4-methoxyphenylriluzole 2b. Besides, we trained and validated a new Networks Invariant, Information Fusion, Perturbation Theory, and Machine Learning (NIFPTML) model for predicting probability profiles of in vivo biological activity parameters in different regions of the brain. Next, we used this model to predict the in vivo activity of the compounds experimentally studied in vitro. Last, docking study conducted on Riluzole and its derivatives has provided valuable insights into their binding conformations with the target protein, involving calmodulin and the SK4 channel. This new combined strategy may be useful to reduce assay costs (animals, materials, time, and human resources) in the drug discovery process of calmodulin inhibitors.
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Affiliation(s)
- Maider Baltasar-Marchueta
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Leire Llona
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | | | - Iratxe Barbolla
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Markel Garcia Ibarluzea
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Rafael Ramis
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Ane Miren Salomon
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Brenda Fundora
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Ariane Araujo
- Biofisika Institute, CSIC-UPV/EHU, Leioa 48940, Spain
| | | | - Eider Nuñez
- Biofisika Institute, CSIC-UPV/EHU, Leioa 48940, Spain
| | - Scarlett Pérez-Olea
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Christian Villanueva
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Aritz Leonardo
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Sonia Arrasate
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Nuria Sotomayor
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | | | - Aitor Bergara
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain.
| | - Esther Lete
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain.
| | - Humberto González-Díaz
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain; Biofisika Institute, CSIC-UPV/EHU, Leioa 48940, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48011, Spain.
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17
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Song X, Li S, He S, Zheng H, Li R, Liu L, Geng T, Zhao M, Gong D. Integration of Whole-Genome Resequencing and Transcriptome Sequencing Reveals Candidate Genes in High Glossiness of Eggshell. Animals (Basel) 2024; 14:1141. [PMID: 38672292 PMCID: PMC11047648 DOI: 10.3390/ani14081141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Eggshell gloss is an important characteristic for the manifestation of eggshell appearance. However, no study has yet identified potential candidate genes for eggshell gloss between high-gloss (HG) and low-gloss (LG) chickens. The aim of this study was to perform a preliminary investigation into the formation mechanism of eggshell gloss and to identify potential genes. The eggshell gloss of 300-day-old Rhode Island Red hens was measured from three aspects. Uterine tissues of the selected HG and LG (n = 5) hens were collected for RNA-seq. Blood samples were also collected for whole-genome resequencing (WGRS). RNA-seq analysis showed that 150 differentially expressed genes (DEGs) were identified in the uterine tissues of HG and LG hens. These DEGs were mainly enriched in the calcium signaling pathway and the neuroactive ligand-receptor interaction pathway. Importantly, these two pathways were also significantly enriched in the WGRS analysis results. Further joint analysis of WGRS and RNA-seq data revealed that 5-hydroxytryptamine receptor 1F (HTR1F), zinc finger protein 536 (ZNF536), NEDD8 ubiquitin-like modifier (NEDD8), nerve growth factor (NGF) and calmodulin 1 (CALM1) are potential candidate genes for eggshell gloss. In summary, our research provides a reference for the study of eggshell gloss and lays a foundation for improving egg glossiness in layer breeding.
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Affiliation(s)
- Xiang Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Shuo Li
- Jiangsu Beinongda Agriculture and Animal Husbandry Technology Co., Ltd., Taizhou 225300, China
| | - Shixiong He
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Hongxiang Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Ruijie Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Tuoyu Geng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Minmeng Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
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18
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Ouyang M, Zhou B, Li C, Deng L. Characterization of PDGF-Induced Subcellular Calcium Regulation through Calcium Channels in Airway Smooth Muscle Cells by FRET Biosensors. BIOSENSORS 2024; 14:179. [PMID: 38667172 PMCID: PMC11048225 DOI: 10.3390/bios14040179] [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: 01/29/2024] [Revised: 03/21/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024]
Abstract
The homeostasis of cellular calcium is fundamental for many physiological processes, while the calcium levels remain inhomogeneous within cells. During the onset of asthma, epithelial and inflammatory cells secrete platelet-derived growth factor (PDGF), inducing the proliferation and migration of airway smooth muscle (ASM) to the epidermal layer, narrowing the airway. The regulation of ASM cells by PDGF is closely related to the conduction of calcium signals. In this work, we generated subcellular-targeted FRET biosensors to investigate calcium regulation in the different compartments of ASM cells. A PDGF-induced cytoplasmic calcium [Ca2+]C increase was attributed to both extracellular calcium influx and endoplasmic reticulum (ER) calcium [Ca2+]ER release, which was partially regulated by the PLC-IP3R pathway. Interestingly, the removal of the extracellular calcium influx led to inhibited ER calcium release, likely through inhibitory effects on the calcium-dependent activation of the ER ryanodine receptor. The inhibition of the L-type calcium channel on the plasma membrane or the SERCA pump on the ER resulted in both reduced [Ca2+]C and [Ca2+]ER from PDGF stimulation, while IP3R channel inhibition led to reduced [Ca2+]C only. The inhibited SERCA pump caused an immediate [Ca2+]C increase and [Ca2+]ER decrease, indicating active calcium exchange between the cytosol and ER storage in resting cells. PDGF-induced calcium at the outer mitochondrial membrane sub-region showed a similar regulatory response to cytosolic calcium, not influenced by the inhibition of the mitochondrial calcium uniporter channel. Therefore, our work identifies calcium flow pathways among the extracellular medium, cell cytosol, and ER via regulatory calcium channels. Specifically, extracellular calcium flow has an essential function in fully activating ER calcium release.
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Affiliation(s)
- Mingxing Ouyang
- Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou 213164, China
| | - Binqian Zhou
- Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou 213164, China
- School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Chunmei Li
- Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou 213164, China
| | - Linhong Deng
- Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou 213164, China
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19
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Díaz-Piña DA, Rivera-Ramírez N, García-López G, Díaz NF, Molina-Hernández A. Calcium and Neural Stem Cell Proliferation. Int J Mol Sci 2024; 25:4073. [PMID: 38612887 PMCID: PMC11012558 DOI: 10.3390/ijms25074073] [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: 02/08/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Intracellular calcium plays a pivotal role in central nervous system (CNS) development by regulating various processes such as cell proliferation, migration, differentiation, and maturation. However, understanding the involvement of calcium (Ca2+) in these processes during CNS development is challenging due to the dynamic nature of this cation and the evolving cell populations during development. While Ca2+ transient patterns have been observed in specific cell processes and molecules responsible for Ca2+ homeostasis have been identified in excitable and non-excitable cells, further research into Ca2+ dynamics and the underlying mechanisms in neural stem cells (NSCs) is required. This review focuses on molecules involved in Ca2+ entrance expressed in NSCs in vivo and in vitro, which are crucial for Ca2+ dynamics and signaling. It also discusses how these molecules might play a key role in balancing cell proliferation for self-renewal or promoting differentiation. These processes are finely regulated in a time-dependent manner throughout brain development, influenced by extrinsic and intrinsic factors that directly or indirectly modulate Ca2+ dynamics. Furthermore, this review addresses the potential implications of understanding Ca2+ dynamics in NSCs for treating neurological disorders. Despite significant progress in this field, unraveling the elements contributing to Ca2+ intracellular dynamics in cell proliferation remains a challenging puzzle that requires further investigation.
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Affiliation(s)
- Dafne Astrid Díaz-Piña
- Departamento de Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de México 11000, Mexico
- Facultad de Medicina, Circuito Exterior Universitario, Universidad Nacional Autónoma de México Universitario, Copilco Universidad, Coyoacán, Ciudad de México 04360, Mexico
| | - Nayeli Rivera-Ramírez
- Departamento de Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de México 11000, Mexico
| | - Guadalupe García-López
- Departamento de Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de México 11000, Mexico
| | - Néstor Fabián Díaz
- Departamento de Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de México 11000, Mexico
| | - Anayansi Molina-Hernández
- Departamento de Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de México 11000, Mexico
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20
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Kuwashima Y, Yanagawa M, Maekawa M, Abe M, Sako Y, Arita M. TRPV4-dependent Ca 2+ influx determines cholesterol dynamics at the plasma membrane. Biophys J 2024; 123:867-884. [PMID: 38433447 PMCID: PMC10995426 DOI: 10.1016/j.bpj.2024.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/01/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024] Open
Abstract
The activities of the transient receptor potential vanilloid 4 (TRPV4), a Ca2+-permeable nonselective cation channel, are controlled by its surrounding membrane lipids (e.g., cholesterol, phosphoinositides). The transmembrane region of TRPV4 contains a cholesterol recognition amino acid consensus (CRAC) motif and its inverted (CARC) motif located in the plasmalemmal cytosolic leaflet. TRPV4 localizes in caveolae, a bulb-shaped cholesterol-rich domain at the plasma membrane. Here, we visualized the spatiotemporal interactions between TRPV4 and cholesterol at the plasma membrane in living cells by dual-color single-molecule imaging using total internal reflection fluorescence microscopy. To this aim, we labeled cholesterol at the cytosolic leaflets of the plasma membrane using a cholesterol biosensor, D4H. Our single-molecule tracking analysis showed that the TRPV4 molecules colocalize with D4H-accessible cholesterol molecules mainly in the low fluidity membrane domains in which both molecules are highly clustered. Colocalization of TRPV4 and D4H-accessible cholesterol was observed both inside and outside of caveolae. Agonist-evoked TRPV4 activation remarkably decreased colocalization probability and association rate between TRPV4 and D4H-accessible cholesterol molecules. Interestingly, upon TRPV4 activation, the particle density of D4H-accessible cholesterol molecules was decreased and the D4H-accessible cholesterol molecules in the fast-diffusing state were increased at the plasma membrane. The introduction of skeletal dysplasia-associated R616Q mutation into the CRAC/CARC motif of TRPV4, which reduced the interaction with cholesterol clusters, could not alter the D4H-accessible cholesterol dynamics. Mechanistically, TRPV4-mediated Ca2+ influx and the C-terminal calmodulin-binding site of TRPV4 are essential for modulating the plasmalemmal D4H-accessible cholesterol dynamics. We propose that TRPV4 remodels its surrounding plasmalemmal environment by manipulating cholesterol dynamics through Ca2+ influx.
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Affiliation(s)
- Yutaro Kuwashima
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan; Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan
| | - Masataka Yanagawa
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan; Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Masashi Maekawa
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan; Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences (IMS), Kanagawa, Japan
| | - Mitsuhiro Abe
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan.
| | - Makoto Arita
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan; Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences (IMS), Kanagawa, Japan; Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan; Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, Japan.
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21
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Villalobos-Escobedo FS, Jijón-Lorenzo R, Avalos-Fuentes JA, Paz-Bermúdez F, Recillas-Morales S, Rojas IC, Leyva-Gómez G, Cortés H, Florán B. Dopamine D3 receptor modulates D2 receptor effects on cAMP and GABA release at striatopallidal terminals-Modulation by the Ca 2+-Calmodulin-CaMKII system. Eur J Neurosci 2024; 59:1441-1459. [PMID: 38151481 DOI: 10.1111/ejn.16237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 12/29/2023]
Abstract
Dopamine D2 receptor (D2R) is expressed in striatopallidal neurons and decreases forskolin-stimulated cyclic adenine monophosphate (cAMP) accumulation and gamma-aminobutyric acid (GABA) release. Dopamine D3 receptor (D3R) mRNA is expressed in a population of striatal D2R-expressing neurons. Also, D3R protein and binding have been reported in the neuropil of globus pallidus. We explore whether D2R and D3R colocalize in striatopallidal terminals and whether D3R modulates the D2R effect on forskolin-stimulated [3H]cAMP accumulation in pallidal synaptosomes and high K+ stimulated-[3H]GABA release in pallidal slices. Previous reports in heterologous systems indicate that calmodulin (CaM) and CaMKII modulate D2R and D3R functions; thus, we study whether this system regulates its functional interaction. D2R immunoprecipitates with CaM, and pretreatment with ophiobolin A or depolarization of synaptosomes with 15 mM of K+ decreases it. Both treatments increase the D2R inhibition of forskolin-stimulated [3H]cAMP accumulation when activated with quinpirole, indicating a negative modulation of CaM on D2R function. Quinpirole also activates D3R, potentiating D2R inhibition of cAMP accumulation in the ophiobolin A-treated synaptosomes. D2R and D3R immunoprecipitate in pallidal synaptosomes and decrease after the kainic acid striatal lesion, indicating the striatal origin of the presynaptic receptors. CaM-kinase II alfa (CaMKIIα) immunoprecipitates with D3R and increases after high K+ depolarization. In the presence of KN62, a CaMKIIα blocker, D3R potentiates D2R effects on cAMP accumulation in depolarized synaptosomes and GABA release in pallidal slices, indicating D3R function regulation by CaMKIIα. Our data indicate that D3R potentiates the D2R effect on cAMP accumulation and GABA release at pallidal terminals, an interaction regulated by the CaM-CaMKIIα system.
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Affiliation(s)
- Flor Selene Villalobos-Escobedo
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Rafael Jijón-Lorenzo
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - José Arturo Avalos-Fuentes
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Francisco Paz-Bermúdez
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | | | - Israel Conde Rojas
- Neurobiology of Eating, FES-Iztacala, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Gerardo Leyva-Gómez
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Hernán Cortés
- Laboratorio de Medicina Genómica, Departamento de Genómica, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Mexico City, Mexico
| | - Benjamín Florán
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
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22
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Guerrache A, Micheau O. TNF-Related Apoptosis-Inducing Ligand: Non-Apoptotic Signalling. Cells 2024; 13:521. [PMID: 38534365 DOI: 10.3390/cells13060521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/01/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
TNF-related apoptosis-inducing ligand (TRAIL or Apo2 or TNFSF10) belongs to the TNF superfamily. When bound to its agonistic receptors, TRAIL can induce apoptosis in tumour cells, while sparing healthy cells. Over the last three decades, this tumour selectivity has prompted many studies aiming at evaluating the anti-tumoral potential of TRAIL or its derivatives. Although most of these attempts have failed, so far, novel formulations are still being evaluated. However, emerging evidence indicates that TRAIL can also trigger a non-canonical signal transduction pathway that is likely to be detrimental for its use in oncology. Likewise, an increasing number of studies suggest that in some circumstances TRAIL can induce, via Death receptor 5 (DR5), tumour cell motility, potentially leading to and contributing to tumour metastasis. While the pro-apoptotic signal transduction machinery of TRAIL is well known from a mechanistic point of view, that of the non-canonical pathway is less understood. In this study, we the current state of knowledge of TRAIL non-canonical signalling.
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Affiliation(s)
- Abderrahmane Guerrache
- Université de Bourgogne, 21000 Dijon, France
- INSERM Research Center U1231, «Equipe DesCarTes», 21000 Dijon, France
| | - Olivier Micheau
- Université de Bourgogne, 21000 Dijon, France
- INSERM Research Center U1231, «Equipe DesCarTes», 21000 Dijon, France
- Laboratoire d'Excellence LipSTIC, 21000 Dijon, France
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23
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Zhang W, Chen S, Ma B, Ding Y, Liu X, He C, Wang B, Yuan M. Trifluoperazine regulates blood-brain barrier permeability via the MLCK/p-MLC pathway to promote ischemic stroke recovery. iScience 2024; 27:109156. [PMID: 38439960 PMCID: PMC10910233 DOI: 10.1016/j.isci.2024.109156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 03/06/2024] Open
Abstract
Blood-brain barrier (BBB) disruption following ischemic stroke (IS) can induce significant aftereffects. Elevated calmodulin (CaM) expression following stroke causes calcium overload-a key contributor to BBB collapse. Trifluoperazine (TFP), a CaM inhibitor, reduces CaM overexpression following IS. However, it remains unclear whether TFP participates in BBB repair after IS. We administered TFP to mice subjected to middle cerebral artery occlusion (MCAO) and bEnd.3 cells subjected to oxygen-glucose deprivation (OGD). TFP treatment in MCAO mice reduced cerebral CaM expression and infarct size and decreased BBB permeability. OGD-treated bEnd.3 cells showed significantly increased CaM protein levels and reduced tight junction (TJ) protein levels; these changes were reversed by TFP treatment. Our results found that TFP administration in mice inhibited actin contraction following cerebral ischemia-reperfusion by suppressing the MLCK/p-MLC pathway, thereby attenuating cell retraction, improving TJ protein integrity, and reducing BBB permeability. Consequently, this treatment may promote neurological function recovery after IS.
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Affiliation(s)
- Wentao Zhang
- The Second Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Sisi Chen
- The Second Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Bin Ma
- The Second Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Yingmei Ding
- The Second Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Xiaofen Liu
- The Second Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Caijun He
- The Second Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Biao Wang
- The Second Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Mei Yuan
- The Second Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Affiliated Nanhua Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
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24
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Zhang H, Hu S, Yang P, Long H, Ma Q, Yin D, Xu G. HDAC9-mediated calmodulin deacetylation induces memory impairment in Alzheimer's disease. CNS Neurosci Ther 2024; 30:e14573. [PMID: 38421101 PMCID: PMC10850929 DOI: 10.1111/cns.14573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/20/2023] [Accepted: 12/04/2023] [Indexed: 03/02/2024] Open
Abstract
AIMS Alzheimer's disease (AD) is a neurodegenerative disease characterized by progressive cognitive dysfunction and memory impairment. AD pathology involves protein acetylation. Previous studies have mainly focused on histone acetylation in AD, however, the roles of nonhistone acetylation in AD are less explored. METHODS The protein acetylation and expression levels were detected by western blotting and co-immunoprecipitation. The stoichiometry of acetylation was measured by home-made and site-specific antibodies against acetylated-CaM (Ac-CaM) at K22, K95, and K116. Hippocampus-dependent learning and memory were evaluated by using the Morris water maze, novel object recognition, and contextual fear conditioning tests. RESULTS We showed that calmodulin (CaM) acetylation is reduced in plasma of AD patients and mice. CaM acetylation and its target Ca2+ /CaM-dependent kinase II α (CaMKIIα) activity were severely impaired in AD mouse brain. The stoichiometry showed that Ac-K22, K95-CaM acetylation were decreased in AD patients and mice. Moreover, we screened and identified that lysine deacetylase 9 (HDAC9) was the main deacetylase for CaM. In addition, HDAC9 inhibition increased CaM acetylation and CaMKIIα activity, and hippocampus-dependent memory in AD mice. CONCLUSIONS HDAC9-mediated CaM deacetylation induces memory impairment in AD, HDAC9, or CaM acetylation may become potential therapeutic targets for AD.
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Affiliation(s)
- Hai‐Long Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Institute of NeuroscienceSuzhou Medical College of Soochow University, Medical Center of Soochow UniversitySuzhouChina
| | - Shufen Hu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Institute of NeuroscienceSuzhou Medical College of Soochow University, Medical Center of Soochow UniversitySuzhouChina
| | - Pin Yang
- Key Laboratory of Brain Functional Genomics, Ministry of Education and Shanghai, School of Life ScienceEast China Normal UniversityShanghaiChina
| | - Han‐Chun Long
- Department of NeurologyThe Affiliated Xingyi City Hospital of Guizhou Medical UniversityXingyiChina
| | - Quan‐Hong Ma
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Institute of NeuroscienceSuzhou Medical College of Soochow University, Medical Center of Soochow UniversitySuzhouChina
| | - Dong‐Min Yin
- Key Laboratory of Brain Functional Genomics, Ministry of Education and Shanghai, School of Life ScienceEast China Normal UniversityShanghaiChina
| | - Guang‐Yin Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Institute of NeuroscienceSuzhou Medical College of Soochow University, Medical Center of Soochow UniversitySuzhouChina
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25
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Ismatullah H, Jabeen I, Kiani YS. Structural and functional insight into a new emerging target IP 3R in cancer. J Biomol Struct Dyn 2024; 42:2170-2196. [PMID: 37070253 DOI: 10.1080/07391102.2023.2201332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Calcium signaling has been identified as an important phenomenon in a plethora of cellular processes. Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ER-residing intracellular calcium (Ca2+) release channels responsible for cell bioenergetics by transferring calcium from the ER to the mitochondria. The recent availability of full-length IP3R channel structure has enabled the researchers to design the IP3 competitive ligands and reveal the channel gating mechanism by elucidating the conformational changes induced by ligands. However, limited knowledge is available for IP3R antagonists and the exact mechanism of action of these antagonists within a tumorigenic environment of a cell. Here in this review a summarized information about the role of IP3R in cell proliferation and apoptosis has been discussed. Moreover, structure and gating mechanism of IP3R in the presence of antagonists have been provided in this review. Additionally, compelling information about ligand-based studies (both agonists and antagonists) has been discussed. The shortcomings of these studies and the challenges toward the design of potent IP3R modulators have also been provided in this review. However, the conformational changes induced by antagonists for channel gating mechanism still display some major drawbacks that need to be addressed. However, the design, synthesis and availability of isoform-specific antagonists is a rather challenging one due to intra-structural similarity within the binding domain of each isoform. HighlightsThe intricate complexity of IP3R's in cellular processes declares them an important target whereby, the recently solved structure depicts the receptor's potential involvement in a complex network of processes spanning from cell proliferation to cell death.Pharmacological inhibition of IP3R attenuates the proliferation or invasiveness of cancers, thus inducing necrotic cell death.Despite significant advancements, there is a tremendous need to design new potential hits to target IP3R, based upon 3D structural features and pharmacophoric patterns.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Humaira Ismatullah
- Department of Sciences, School of Interdisciplinary Engineering and Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Ishrat Jabeen
- Department of Sciences, School of Interdisciplinary Engineering and Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Yusra Sajid Kiani
- Department of Sciences, School of Interdisciplinary Engineering and Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
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26
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Xu M, Zhang Z, Ling C, Jiao Y, Zhang X. Genome-Wide Identification of the IQM Gene Family and Their Transcriptional Responses to Abiotic Stresses in Kiwifruit ( Actinidia eriantha). Genes (Basel) 2024; 15:147. [PMID: 38397137 PMCID: PMC10887524 DOI: 10.3390/genes15020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
IQM is a plant-specific calcium-binding protein that plays a pivotal role in various aspects of plant growth response to stressors. We investigated the IQM gene family and its expression patterns under diverse abiotic stresses and conducted a comprehensive analysis and characterization of the AeIQMs, including protein structure, genomic location, phylogenetic relationships, gene expression profiles, salt tolerance, and expression patterns of this gene family under different abiotic stresses. Based on phylogenetic analysis, these 10 AeIQMs were classified into three distinct subfamilies (I-III). Analysis of the protein motifs revealed a considerable level of conservation among these AeIQM proteins within their respective subfamilies in kiwifruit. The genomic distribution of the 10 AeIQM genes spanned across eight chromosomes, where four pairs of IQM gene duplicates were associated with segmental duplication events. qRT-PCR analysis revealed diverse expression patterns of these AeIQM genes under different hormone treatments, and most AeIQMs showed inducibility by salt stress. Further investigations indicated that overexpression of AeIQMs in yeast significantly enhanced salt tolerance. These findings suggest that AeIQM genes might be involved in hormonal signal transduction and response to abiotic stress in Actinidia eriantha. In summary, this study provides valuable insights into the physiological functions of IQMs in kiwifruit.
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Affiliation(s)
- Minyan Xu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Zhi Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Chengcheng Ling
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- College of Food and Bioengineering, Bengbu University, Bengbu 233030, China
| | - Yuhuan Jiao
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Xin Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
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27
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Rodrigues CHM, Portelli S, Ascher DB. Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges. Hum Genet 2024:10.1007/s00439-023-02623-4. [PMID: 38227011 DOI: 10.1007/s00439-023-02623-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/18/2023] [Indexed: 01/17/2024]
Abstract
Missense mutations are known contributors to diverse genetic disorders, due to their subtle, single amino acid changes imparted on the resultant protein. Because of this, understanding the impact of these mutations on protein stability and function is crucial for unravelling disease mechanisms and developing targeted therapies. The Critical Assessment of Genome Interpretation (CAGI) provides a valuable platform for benchmarking state-of-the-art computational methods in predicting the impact of disease-related mutations on protein thermodynamics. Here we report the performance of our comprehensive platform of structure-based computational approaches to evaluate mutations impacting protein structure and function on 3 challenges from CAGI6: Calmodulin, MAPK1 and MAPK3. Our stability predictors have achieved correlations of up to 0.74 and AUCs of 1 when predicting changes in ΔΔG for MAPK1 and MAPK3, respectively, and AUC of up to 0.75 in the Calmodulin challenge. Overall, our study highlights the importance of structure-based approaches in understanding the effects of missense mutations on protein thermodynamics. The results obtained from the CAGI6 challenges contribute to the ongoing efforts to enhance our understanding of disease mechanisms and facilitate the development of personalised medicine approaches.
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Affiliation(s)
- Carlos H M Rodrigues
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Stephanie Portelli
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia.
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28
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Li X, Guan H, Ma C, Dai Y, Su J, Chen X, Yuan Q, Wang J. Combination of bulk RNA sequencing and scRNA sequencing uncover the molecular characteristics of MAPK signaling in kidney renal clear cell carcinoma. Aging (Albany NY) 2024; 16:1414-1439. [PMID: 38217548 PMCID: PMC10866414 DOI: 10.18632/aging.205436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/01/2023] [Indexed: 01/15/2024]
Abstract
The MAPK signaling pathway significantly impacts cancer progression and resistance; however, its functions remain incompletely assessed across various cancers, particularly in kidney renal clear cell carcinoma (KIRC). Therefore, there is an urgent need for comprehensive pan-cancer investigations of MAPK signaling, particularly within the context of KIRC. In this research, we obtained TCGA pan-cancer multi-omics data and conducted a comprehensive analysis of the genomic and transcriptomic characteristics of the MAPK signaling pathway. For in-depth investigation in KIRC, status of MAPK pathway was quantitatively estimated by ssGSEA and Ward algorithm was utilized for cluster analysis. Molecular characteristics and clinical prognoses of KIRC patients with distinct MAPK activities were comprehensively explored using a series of bioinformatics algorithms. Subsequently, a combination of LASSO and COX regression analyses were utilized sequentially to construct a MAPK-related signature to help identify the risk level of each sample. Patients in the C1 subtype exhibited relatively higher levels of MAPK signaling activity, which were associated with abundant immune cell infiltration and favorable clinical outcomes. Single-cell RNA sequencing (scRNA-seq) analysis of KIRC samples identified seven distinct cell types, and endothelial cells in tumor tissues had obviously higher MAPK scores than normal tissues. The immunohistochemistry results indicated the reduced expression levels of PAPSS1, MAP3K11, and SPRED1 in KIRC samples. In conclusion, our study represents the first integration of bulk RNA sequencing and single-cell RNA sequencing to elucidate the molecular characteristics of MAPK signaling in KIRC, providing a solid foundation for precision oncology.
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Affiliation(s)
- Xiunan Li
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hewen Guan
- Department of Dermatology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Chuanyu Ma
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yunfei Dai
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Ji Su
- Department of Urology, Central Hospital of Benxi, Benxi, Liaoning, China
| | - Xu Chen
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qihang Yuan
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jianbo Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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29
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Saini G, Parasa MK, Clayton KN, Fraseur JG, Bolton SC, Lin KP, Wereley ST, Kinzer-Ursem TL. Immobilization of azide-functionalized proteins to micro- and nanoparticles directly from cell lysate. Mikrochim Acta 2023; 191:46. [PMID: 38129631 PMCID: PMC10739308 DOI: 10.1007/s00604-023-06068-4] [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: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/23/2023]
Abstract
Immobilization of proteins and enzymes on solid supports has been utilized in a variety of applications, from improved protein stability on supported catalysts in industrial processes to fabrication of biosensors, biochips, and microdevices. A critical requirement for these applications is facile yet stable covalent conjugation between the immobilized and fully active protein and the solid support to produce stable, highly bio-active conjugates. Here, we report functionalization of solid surfaces (gold nanoparticles and magnetic beads) with bio-active proteins using site-specific and biorthogonal labeling and azide-alkyne cycloaddition, a click chemistry. Specifically, we recombinantly express and selectively label calcium-dependent proteins, calmodulin and calcineurin, and cAMP-dependent protein kinase A (PKA) with N-terminal azide-tags for efficient conjugation to nanoparticles and magnetic beads. We successfully immobilized the proteins on to the solid supports directly from the cell lysate with click chemistry, forgoing the step of purification. This approach is optimized to yield low particle aggregation and high levels of protein activity post-conjugation. The entire process enables streamlined workflows for bioconjugation and highly active conjugated proteins.
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Affiliation(s)
- Gunjan Saini
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Mrugesh Krishna Parasa
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Katherine N Clayton
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Julia G Fraseur
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Scott C Bolton
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Kevin P Lin
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47906, USA
| | - Steven T Wereley
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA.
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30
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Gharios R, Francis RM, DeForest CA. Chemical and Biological Engineering Strategies to Make and Modify Next-Generation Hydrogel Biomaterials. MATTER 2023; 6:4195-4244. [PMID: 38313360 PMCID: PMC10836217 DOI: 10.1016/j.matt.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
There is a growing interest in the development of technologies to probe and direct in vitro cellular function for fundamental organoid and stem cell biology, functional tissue and metabolic engineering, and biotherapeutic formulation. Recapitulating many critical aspects of the native cellular niche, hydrogel biomaterials have proven to be a defining platform technology in this space, catapulting biological investigation from traditional two-dimensional (2D) culture into the 3D world. Seeking to better emulate the dynamic heterogeneity characteristic of all living tissues, global efforts over the last several years have centered around upgrading hydrogel design from relatively simple and static architectures into stimuli-responsive and spatiotemporally evolvable niches. Towards this end, advances from traditionally disparate fields including bioorthogonal click chemistry, chemoenzymatic synthesis, and DNA nanotechnology have been co-opted and integrated to construct 4D-tunable systems that undergo preprogrammed functional changes in response to user-defined inputs. In this Review, we highlight how advances in synthetic, semisynthetic, and bio-based chemistries have played a critical role in the triggered creation and customization of next-generation hydrogel biomaterials. We also chart how these advances stand to energize the translational pipeline of hydrogels from bench to market and close with an outlook on outstanding opportunities and challenges that lay ahead.
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Affiliation(s)
- Ryan Gharios
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Ryan M. Francis
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
| | - Cole A. DeForest
- Department of Chemical Engineering, University of Washington, Seattle WA 98105, USA
- Department of Bioengineering, University of Washington, Seattle WA 98105, USA
- Department of Chemistry, University of Washington, Seattle WA 98105, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle WA 98109, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle WA 98105, USA
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31
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Yang Y, Liu Y, Xia Y, Cheng J, Liu P. Tandem mass tag (TMT) quantitative proteomics and phosphoproteomic of Takifugu rubripes infected with Cryptocaryon irritans. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101124. [PMID: 37647835 DOI: 10.1016/j.cbd.2023.101124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
In this study, we identified the differentially expressed proteins in gills stimulated by infected ciliates and analyzed the immune mechanisms of T. rubripes infected with the ciliate Cryptocaryon irritans. Through liquid chromatography analysis, a total of 144 proteins were identified with significant differences, of which 58 were upregulated and 86 were downregulated. Among phosphorylated proteins, we identified a total of 167 significantly different phosphorylated proteins, of which 44 were upregulated, 123 were downregulated, 60 were upregulated, and 208 were downregulated. We analyzed the data of proteomics and Phosphorylated proteome quantification protein omics to finally identify three phosphorylated proteins (RPS27, eNOS and CaM) and two phosphorylated protein kinases(CaMKII and MAPK1) as potential biomarkers for T. rubripes immune responses. We finally identified three phosphorylated proteins (RPS27, eNOS and CaM) and two phosphorylated protein kinases (CaMKII and MAPK1) as potential biomarkers of immune response of T. rubripes. Our research findings provide new insights into the immune mechanism of T. rubripes, which may serve as an effective indicator of C. irritans infection in T. rubripes.
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Affiliation(s)
- Yi Yang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China
| | - Yanyun Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China
| | - Yuqing Xia
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jianxin Cheng
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Pengfei Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China.
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Baltrusaitis EE, Ravitch EE, Fenton AR, Perez TA, Holzbaur ELF, Dominguez R. Interaction between the mitochondrial adaptor MIRO and the motor adaptor TRAK. J Biol Chem 2023; 299:105441. [PMID: 37949220 PMCID: PMC10746525 DOI: 10.1016/j.jbc.2023.105441] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023] Open
Abstract
MIRO (mitochondrial Rho GTPase) consists of two GTPase domains flanking two Ca2+-binding EF-hand domains. A C-terminal transmembrane helix anchors MIRO to the outer mitochondrial membrane, where it functions as a general adaptor for the recruitment of cytoskeletal proteins that control mitochondrial dynamics. One protein recruited by MIRO is TRAK (trafficking kinesin-binding protein), which in turn recruits the microtubule-based motors kinesin-1 and dynein-dynactin. The mechanism by which MIRO interacts with TRAK is not well understood. Here, we map and quantitatively characterize the interaction of human MIRO1 and TRAK1 and test its potential regulation by Ca2+ and/or GTP binding. TRAK1 binds MIRO1 with low micromolar affinity. The interaction was mapped to a fragment comprising MIRO1's EF-hands and C-terminal GTPase domain and to a conserved sequence motif within TRAK1 residues 394 to 431, immediately C-terminal to the Spindly motif. This sequence is sufficient for MIRO1 binding in vitro and is necessary for MIRO1-dependent localization of TRAK1 to mitochondria in cells. MIRO1's EF-hands bind Ca2+ with dissociation constants (KD) of 3.9 μM and 300 nM. This suggests that under cellular conditions one EF-hand may be constitutively bound to Ca2+ whereas the other EF-hand binds Ca2+ in a regulated manner, depending on its local concentration. Yet, the MIRO1-TRAK1 interaction is independent of Ca2+ binding to the EF-hands and of the nucleotide state (GDP or GTP) of the C-terminal GTPase. The interaction is also independent of TRAK1 dimerization, such that a TRAK1 dimer can be expected to bind two MIRO1 molecules on the mitochondrial surface.
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Affiliation(s)
- Elana E Baltrusaitis
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erika E Ravitch
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adam R Fenton
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Tania A Perez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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Liu M, Xiao Y, Yang Y, Zhou S, Shen X, Zhang Y, Wang W. Carrier proteins boost expression of PR-39-derived peptide in Pichia pastoris. J Appl Microbiol 2023; 134:lxad297. [PMID: 38052427 DOI: 10.1093/jambio/lxad297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/16/2023] [Accepted: 12/04/2023] [Indexed: 12/07/2023]
Abstract
AIMS Multidrug resistance presents difficulties in preventing and treating bacterial infections. Proline-rich antimicrobial peptides (PrAMPs) inhibit bacterial growth by affecting the intracellular targets rather than by permeabilizing the membrane. The aim of this study was to develop a yeast-based fusion carrier system using calmodulin (CaM) and xylanase (XynCDBFV) as two carriers to express the model PrAMP PR-39-derived peptide (PR-39-DP) in Pichia pastoris. METHODS AND RESULTS Fusion protein secreted into the culture supernatant was purified in a one-step on-column digestion using human rhinovirus 3C protease, obtaining the target peptide PR-39-DP. The growth curves of Escherichia coli were monitored by recording the OD600 values of the bacteria. The antibacterial activity of PR-39-DP was evaluated in killing assays performed on E. coli. The yield of PR-39-DP was 1.0-1.2 mg l-1 in the CaM fusion carrier system, approximately three times that of the XynCDBFV fusion carrier system. The minimal inhibitory concentration of PR-39-DP was ∼10.5 µg ml-1. CONCLUSIONS CaM and XynCDBFV provide increased stability and promote the expression and secretion of active PR-39-DP.
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Affiliation(s)
- Minzhi Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the People's Republic of China, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yao Xiao
- Department of Pharmacy, The Fourth Affiliated Hospital of China Medical University, Shenyang 100032, China
| | - Yan Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the People's Republic of China, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Sihan Zhou
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the People's Republic of China, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xin Shen
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the People's Republic of China, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Youxi Zhang
- Department of Pharmacy, The Fourth Affiliated Hospital of China Medical University, Shenyang 100032, China
| | - Wei Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the People's Republic of China, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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34
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Mackiewicz J, Lisek M, Boczek T. Targeting CaN/NFAT in Alzheimer's brain degeneration. Front Immunol 2023; 14:1281882. [PMID: 38077352 PMCID: PMC10701682 DOI: 10.3389/fimmu.2023.1281882] [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: 08/23/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by a progressive loss of cognitive functions. While the exact causes of this debilitating disorder remain elusive, numerous investigations have characterized its two core pathologies: the presence of β-amyloid plaques and tau tangles. Additionally, multiple studies of postmortem brain tissue, as well as results from AD preclinical models, have consistently demonstrated the presence of a sustained inflammatory response. As the persistent immune response is associated with neurodegeneration, it became clear that it may also exacerbate other AD pathologies, providing a link between the initial deposition of β-amyloid plaques and the later development of neurofibrillary tangles. Initially discovered in T cells, the nuclear factor of activated T-cells (NFAT) is one of the main transcription factors driving the expression of inflammatory genes and thus regulating immune responses. NFAT-dependent production of inflammatory mediators is controlled by Ca2+-dependent protein phosphatase calcineurin (CaN), which dephosphorylates NFAT and promotes its transcriptional activity. A substantial body of evidence has demonstrated that aberrant CaN/NFAT signaling is linked to several pathologies observed in AD, including neuronal apoptosis, synaptic deficits, and glia activation. In view of this, the role of NFAT isoforms in AD has been linked to disease progression at different stages, some of which are paralleled to diminished cognitive status. The use of classical inhibitors of CaN/NFAT signaling, such as tacrolimus or cyclosporine, or adeno-associated viruses to specifically inhibit astrocytic NFAT activation, has alleviated some symptoms of AD by diminishing β-amyloid neurotoxicity and neuroinflammation. In this article, we discuss the recent findings related to the contribution of CaN/NFAT signaling to the progression of AD and highlight the possible benefits of targeting this pathway in AD treatment.
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Affiliation(s)
| | | | - Tomasz Boczek
- Department of Molecular Neurochemistry, Medical University of Lodz, Lodz, Poland
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35
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Biggs BW, de Paz AM, Bhan NJ, Cybulski TR, Church GM, Tyo KEJ. Engineering Ca 2+-Dependent DNA Polymerase Activity. ACS Synth Biol 2023; 12:3301-3311. [PMID: 37856140 DOI: 10.1021/acssynbio.3c00302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Advancements in synthetic biology have provided new opportunities in biosensing, with applications ranging from genetic programming to diagnostics. Next generation biosensors aim to expand the number of accessible environments for measurements, increase the number of measurable phenomena, and improve the quality of the measurement. To this end, an emerging area in the field has been the integration of DNA as an information storage medium within biosensor outputs, leveraging nucleic acids to record the biosensor state over time. However, slow signal transduction steps, due to the time scales of transcription and translation, bottleneck many sensing-DNA recording approaches. DNA polymerases (DNAPs) have been proposed as a solution to the signal transduction problem by operating as both the sensor and responder, but there is presently a lack of DNAPs with functional sensitivity to many desirable target ligands. Here, we engineer components of the Pol δ replicative polymerase complex of Saccharomyces cerevisiae to sense and respond to Ca2+, a metal cofactor relevant to numerous biological phenomena. Through domain insertion and binding site grafting to Pol δ subunits, we demonstrate functional allosteric sensitivity to Ca2+. Together, this work provides an important foundation for future efforts in the development of DNAP-based biosensors.
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Affiliation(s)
- Bradley W Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexandra M de Paz
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Namita J Bhan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Thaddeus R Cybulski
- Interdepartmental Neuroscience Program, Northwestern University, Chicago, Illinois 60611, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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36
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O’Day DH. Protein Biomarkers Shared by Multiple Neurodegenerative Diseases Are Calmodulin-Binding Proteins Offering Novel and Potentially Universal Therapeutic Targets. J Clin Med 2023; 12:7045. [PMID: 38002659 PMCID: PMC10672630 DOI: 10.3390/jcm12227045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Seven major neurodegenerative diseases and their variants share many overlapping biomarkers that are calmodulin-binding proteins: Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), frontotemporal lobar dementia (FTD), Huntington's disease (HD), Lewy body disease (LBD), multiple sclerosis (MS), and Parkinson's disease (PD). Calcium dysregulation is an early and persistent event in each of these diseases, with calmodulin serving as an initial and primary target of increased cytosolic calcium. Considering the central role of calcium dysregulation and its downstream impact on calcium signaling, calmodulin has gained interest as a major regulator of neurodegenerative events. Here, we show that calmodulin serves a critical role in neurodegenerative diseases via binding to and regulating an abundance of biomarkers, many of which are involved in multiple neurodegenerative diseases. Of special interest are the shared functions of calmodulin in the generation of protein biomarker aggregates in AD, HD, LBD, and PD, where calmodulin not only binds to amyloid beta, pTau, alpha-synuclein, and mutant huntingtin but also, via its regulation of transglutaminase 2, converts them into toxic protein aggregates. It is suggested that several calmodulin binding proteins could immediately serve as primary drug targets, while combinations of calmodulin binding proteins could provide simultaneous insight into the onset and progression of multiple neurodegenerative diseases.
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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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37
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Lučić I, Jiang P, Franz A, Bursztyn Y, Liu F, Plested AJR. Controlling the interaction between CaMKII and Calmodulin with a photocrosslinking unnatural amino acid. Protein Sci 2023; 32:e4798. [PMID: 37784242 PMCID: PMC10588329 DOI: 10.1002/pro.4798] [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: 11/29/2022] [Revised: 09/08/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Using unnatural amino acid mutagenesis, we made a mutant of CaMKII that forms a covalent linkage to Calmodulin upon illumination by UV light. Like wild-type CaMKII, the L308BzF mutant stoichiometrically binds to Calmodulin, in a calcium-dependent manner. Using this construct, we demonstrate that Calmodulin binding to CaMKII, even under these stochiometric conditions, does not perturb the CaMKII oligomeric state. Furthermore, we were able to achieve activation of CaMKII L308BzF by UV-induced binding of Calmodulin, which, once established, is further insensitive to calcium depletion. In addition to the canonical auto-inhibitory role of the regulatory segment, inter-subunit crosslinking in the absence of CaM indicates that kinase domains and regulatory segments are substantially mobile in basal conditions. Characterization of CaMKIIL308BzF in vitro, and its expression in mammalian cells, suggests it could be a promising candidate for control of CaMKII activity in mammalian cells with light.
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Affiliation(s)
- Iva Lučić
- Institute of Biology, Cellular BiophysicsHumboldt Universität zu BerlinBerlinGermany
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Pin‐Lian Jiang
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Andreas Franz
- Freie Universität Berlin, Institute of Chemistry and BiochemistryBerlinGermany
| | - Yuval Bursztyn
- Institute of Biology, Cellular BiophysicsHumboldt Universität zu BerlinBerlinGermany
| | - Fan Liu
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
- Charité‐Universitätsmedizin BerlinBerlinGermany
| | - Andrew J. R. Plested
- Institute of Biology, Cellular BiophysicsHumboldt Universität zu BerlinBerlinGermany
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
- NeuroCure, Charité UniversitätsmedizinBerlinGermany
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38
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Kaiser J, Nay K, Horne CR, McAloon LM, Fuller OK, Muller AG, Whyte DG, Means AR, Walder K, Berk M, Hannan AJ, Murphy JM, Febbraio MA, Gundlach AL, Scott JW. CaMKK2 as an emerging treatment target for bipolar disorder. Mol Psychiatry 2023; 28:4500-4511. [PMID: 37730845 PMCID: PMC10914626 DOI: 10.1038/s41380-023-02260-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 08/30/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023]
Abstract
Current pharmacological treatments for bipolar disorder are inadequate and based on serendipitously discovered drugs often with limited efficacy, burdensome side-effects, and unclear mechanisms of action. Advances in drug development for the treatment of bipolar disorder remain incremental and have come largely from repurposing drugs used for other psychiatric conditions, a strategy that has failed to find truly revolutionary therapies, as it does not target the mood instability that characterises the condition. The lack of therapeutic innovation in the bipolar disorder field is largely due to a poor understanding of the underlying disease mechanisms and the consequent absence of validated drug targets. A compelling new treatment target is the Ca2+-calmodulin dependent protein kinase kinase-2 (CaMKK2) enzyme. CaMKK2 is highly enriched in brain neurons and regulates energy metabolism and neuronal processes that underpin higher order functions such as long-term memory, mood, and other affective functions. Loss-of-function polymorphisms and a rare missense mutation in human CAMKK2 are associated with bipolar disorder, and genetic deletion of Camkk2 in mice causes bipolar-like behaviours similar to those in patients. Furthermore, these behaviours are ameliorated by lithium, which increases CaMKK2 activity. In this review, we discuss multiple convergent lines of evidence that support targeting of CaMKK2 as a new treatment strategy for bipolar disorder.
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Affiliation(s)
- Jacqueline Kaiser
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- School of Behavioural and Health Sciences, Australian Catholic University, Fitzroy, VIC, 3065, Australia
| | - Kevin Nay
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Luke M McAloon
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- School of Behavioural and Health Sciences, Australian Catholic University, Fitzroy, VIC, 3065, Australia
| | - Oliver K Fuller
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
| | - Abbey G Muller
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
| | - Douglas G Whyte
- School of Behavioural and Health Sciences, Australian Catholic University, Fitzroy, VIC, 3065, Australia
| | - Anthony R Means
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ken Walder
- The Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, 3220, Australia
| | - Michael Berk
- The Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, 3220, Australia
- Orygen, The National Centre of Excellence in Youth Mental Health, Parkville, VIC, 3052, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Anthony J Hannan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - James M Murphy
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Mark A Febbraio
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
| | - Andrew L Gundlach
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - John W Scott
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia.
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia.
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia.
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Aragona M, Briglia M, Porcino C, Mhalhel K, Cometa M, Germanà PG, Montalbano G, Levanti M, Laurà R, Abbate F, Germanà A, Guerrera MC. Localization of Calretinin, Parvalbumin, and S100 Protein in Nothobranchius guentheri Retina: A Suitable Model for the Retina Aging. Life (Basel) 2023; 13:2050. [PMID: 37895432 PMCID: PMC10608213 DOI: 10.3390/life13102050] [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: 06/28/2023] [Revised: 08/05/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Calcium-binding proteins (CaBPs) are members of a heterogeneous family of proteins able to buffer intracellular Ca2+ ion concentration. CaBPs are expressed in the central and peripheral nervous system, including a subpopulation of retinal neurons. Since neurons expressing different CaBPs show different susceptibility to degeneration, it could be hypothesized that they are not just markers of different neuronal subpopulations, but that they might be crucial in survival. CaBPs' ability to buffer Ca2+ cytoplasmatic concentration makes them able to defend against a toxic increase in intracellular calcium that can lead to neurodegenerative processes, including those related to aging. An emergent model for aging studies is the annual killifish belonging to the Nothobranchius genus, thanks to its short lifespan. Members of this genus, such as Nothobranchius guentheri, show a retinal stratigraphy similar to that of other actinopterygian fishes and humans. However, according to our knowledge, CaBPs' occurrence and distribution in the retina of N. guentheri have never been investigated before. Therefore, the present study aimed to localize Calretinin N-18, Parvalbumin, and S100 protein (S100p) in the N. guentheri retina with immunohistochemistry methods. The results of the present investigation demonstrate for the first time the occurrence of Calretinin N-18, Parvalbumin, and S100p in N. guentheri retina and, consequently, the potential key role of these CaBPs in the biology of the retinal cells. Hence, the suitability of N. guentheri as a model to study the changes in CaBPs' expression patterns during neurodegenerative processes affecting the retina related both to disease and aging can be assumed.
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Affiliation(s)
| | | | - Caterina Porcino
- Zebrafish Neuromorphology Lab, Department of Veterinary Sciences, University of Messina, 98168 Messina, Italy; (M.A.); (M.B.); (K.M.); (M.C.); (P.G.G.); (G.M.); (M.L.); (R.L.); (F.A.); (A.G.); (M.C.G.)
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Zhang D, Chen D, Wang K, Pan J, Tang J, Zhang H. Electrical stimulation of cochlear implant promotes activation of macrophages and fibroblasts under inflammation. Laryngoscope Investig Otolaryngol 2023; 8:1390-1400. [PMID: 37899874 PMCID: PMC10601573 DOI: 10.1002/lio2.1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 10/31/2023] Open
Abstract
Objectives The implanted electrodes deliver electric signals to spiral ganglion neurons, conferring restored hearing of cochlear implantation (CI) recipients. Postimplantation intracochlear fibrosis, which is observed in most CI recipients, disturbs the electrical signals and impairs the long-term outcome of CI. The macrophages and fibroblasts activation is critical for the development of intracochlear fibrosis. However, the effect of electric stimulation of cochlear implant (ESCI) on the activity of macrophages and fibroblasts was unclear. In the present study, a human cochlear implant was modified to stimulate cultured macrophages and fibroblasts. Methods By measuring cellular marker and the expression level of cytokine production, the polarization and activity of macrophages and fibroblasts were examined with or without ESCI. Results Our data showed that ESCI had little effects on the morphology, density, and distribution of culturing macrophages and fibroblasts. Furthermore, ESCI alone did not affect the polarization of macrophages or the function of fibroblasts without the treatment of inflammatory factors. However, in the presence of LPS or IL-4, ESCI further promoted the polarization of macrophages, and increased the expression of pro-inflammatory or anti-inflammatory factors, respectively. For fibroblasts, ESCI further increased the collagen I synthesis induced by TGF-β1 treatment. Nifedipine inhibited ESCI induced calcium influx, and hereby abolished the promoted polarization and activation of macrophages and fibroblasts. Conclusion Our results suggest that acute inflammation should be well inhibited before the activation of cochlear implants to control the postoperative intracochlear fibrosis. The voltage-gated calcium channels could be considered as the targets for reducing postimplantation inflammation and fibrosis. Level of Evidence NA.
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Affiliation(s)
- Dingling Zhang
- Department of Otolaryngology Head and Neck SurgeryZhujiang Hospital of Southern Medical UniversityGuangzhouChina
| | - Dongxiu Chen
- Department of Otolaryngology Head and Neck SurgeryZhujiang Hospital of Southern Medical UniversityGuangzhouChina
| | - Kaiye Wang
- Department of Otolaryngology Head and Neck SurgeryZhujiang Hospital of Southern Medical UniversityGuangzhouChina
| | - Jing Pan
- Department of Otolaryngology Head and Neck SurgeryZhujiang Hospital of Southern Medical UniversityGuangzhouChina
| | - Jie Tang
- Department of Otolaryngology Head and Neck SurgeryZhujiang Hospital of Southern Medical UniversityGuangzhouChina
- Department of PhysiologySouthern Medical University School of Basic Medical SciencesGuangzhouChina
- Key Laboratory of Mental Health of the Ministry of EducationSouthern Medical UniversityGuangzhouChina
- Hearing Research CenterSouthern Medical UniversityGuangzhouChina
| | - Hongzheng Zhang
- Department of Otolaryngology Head and Neck SurgeryZhujiang Hospital of Southern Medical UniversityGuangzhouChina
- Hearing Research CenterSouthern Medical UniversityGuangzhouChina
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41
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Ryder S, Pedigo J, Ojennus DD. Elucidating the Role of a Calcium-Binding Loop in an x-Prolyl Aminodipeptidase from Lb. helveticus. ACS OMEGA 2023; 8:35410-35416. [PMID: 37779945 PMCID: PMC10536834 DOI: 10.1021/acsomega.3c05639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023]
Abstract
Prolyl aminodipeptidase (PepX) is an α/β hydrolase that cleaves at penultimate N-terminal prolyl peptide bonds. The crystal structure of PepX from Lactobacillus helveticus exhibits a calcium-binding loop within the catalytic domain. The calcium-binding sequence of xDxDxDGxxD within this loop is highly conserved in PepX proteins among lactic acid bacteria, but its purpose remains unknown. Enzyme activity is not significantly affected in the presence of the metal chelator ethylenediaminetetraacetic acid (EDTA), nor in the presence of excess calcium ions. To eliminate calcium binding, D196A and D194A/D196A mutations were constructed within the conserved calcium-binding sequence motif. Enzyme activity and stability of the D196A mutant were comparable to the wild-type enzyme by colorimetric kinetic assays and protein thermal shift assays. However, the D194A/D196A mutant was inactive though it retained native-like structure and thermal stability, contradicting the EDTA and calcium titration results. This suggests calcium binding to PepX may be essential for activity.
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Affiliation(s)
- Stephanie Ryder
- Department of Chemistry, Whitworth
University, 300 W. Hawthorne Rd., Spokane, Washington 99251, United States
| | | | - Deanna Dahlke Ojennus
- Department of Chemistry, Whitworth
University, 300 W. Hawthorne Rd., Spokane, Washington 99251, United States
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Li Q, Gao L, Yu F, Lü S, Yang P. Evolution and diversification of CaM/CML gene family in green plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107922. [PMID: 37573794 DOI: 10.1016/j.plaphy.2023.107922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/18/2023] [Accepted: 07/29/2023] [Indexed: 08/15/2023]
Abstract
Calmodulin (CaM) and calmodulin-like (CML) proteins are crucial Ca2+ sensors, which are widely involved in different biological processes of plants, including their growth and development, and stress responses. However, the origin and evolution of the CaM/CML gene family in plants remain elusive. In this study, 2133 CaM and 23094 CML genes were identified from the 1000 plants project (1 KP) species and the sequenced plants, covering algae, mosses, monilophytes, lycophytes, flowering plants, and all other green plant branches. Analysis showed that the size of the CML subfamily was correlated with the genome size of corresponding plant species, as well as the total gene number in the genome. Moreover, with the evolution from algae to angiosperms, the number of CML genes in plants increased gradually which could have been driven mainly by genome-wide segmental duplication events, while the number of CaMs remained basically stable at 2-3. Phylogenetic analysis demonstrated that CaM first appeared in green algae, while CML appeared earlier and has already been presented in dinoflagellates. Further analysis showed that the number and sequence of EF-hand domain in CaMs are highly conserved, while those of CMLs are diverse among different plant taxa. Expression analysis revealed that the expression level of CaMs was generally higher than that of CMLs, indicating that the high-expression genes have essential functions, while the low-expression genes are the main reasons for the functional diversity of the CaM/CML gene family in plants. The results might contribute to understanding the evolution of CaM/CML genes as well as their molecular functions.
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Affiliation(s)
- Qinghua Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430026, China.
| | - Li Gao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430026, China.
| | - Feng Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430026, China.
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430026, China.
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430026, China.
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43
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Marak CNK, Tamuli R. Calmodulin, Calcium/Calmodulin-Dependent Kinases-1 and 2 Regulate Expression of the Heat Shock Proteins for Heat Shock Tolerance and Pheromone Signaling Genes for Sexual Development in Neurospora crassa. Indian J Microbiol 2023; 63:317-323. [PMID: 37781015 PMCID: PMC10533439 DOI: 10.1007/s12088-023-01091-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 08/05/2023] [Indexed: 10/03/2023] Open
Abstract
Calmodulin (CaM) is a primary Ca2+ sensor that binds and activates numerous target proteins and regulates several cellular processes in eukaryotes. CaM is essential in Neurospora crassa; therefore, we generated a CaM mutant using repeat-induced point (RIP) mutation and investigated the cmdRIP mutant phenotypes. We also studied knockout mutants of four Ca2+/CaM kinases (camk-1, 2, 3, and 4) for their role during stress conditions and sexual development. The cmdRIP, ∆camk-1, and ∆camk-2 mutants showed reduced survival and growth rates under heat stress, oxidative stress, pH, and ER stress conditions. In addition, under the heat stress conditions, expression of the heat shock protein genes hsp70 and hsp80 was reduced in the cmdRIP, ∆camk-1, and ∆camk-2 mutants. The cmdRIP mutant was also defective in cell fusion, its vegetative hyphae could not support the fertilized wild type perithecia graft, and female sterile. Furthermore, the expression of pheromone signaling genes pre-1, pre-2, ccg-4, mfa-1, and fmf-1 was reduced in the cmdRIP, ∆camk-1, and ∆camk-2 mutants. Therefore, CaM, Ca2+/CaMK-1 and 2 are involved in the tolerance to heat stress conditions and sexual development by regulating the heat shock and pheromone response pathways, respectively, in N. crassa. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01091-8.
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Affiliation(s)
- Christy Noche K. Marak
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781 039 India
| | - Ranjan Tamuli
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781 039 India
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Du Q, Zhu T, Wen G, Jin H, An J, Xu J, Xie R, Zhu J, Yang X, Zhang T, Liu Q, Yao S, Yang X, Tuo B, Ma X. The S100 calcium-binding protein A6 plays a crucial role in hepatic steatosis by mediating lipophagy. Hepatol Commun 2023; 7:e0232. [PMID: 37655980 PMCID: PMC10476764 DOI: 10.1097/hc9.0000000000000232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/10/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND S100 calcium-binding protein A6 (S100A6) is a calcium-binding protein that is involved in a variety of cellular processes, such as proliferation, apoptosis, and the cellular response to various stress stimuli. However, its role in NAFLD and associated metabolic diseases remains uncertain. METHODS AND RESULTS In this study, we revealed a new function and mechanism of S100A6 in NAFLD. S100A6 expression was upregulated in human and mouse livers with hepatic steatosis, and the depletion of hepatic S100A6 remarkably inhibited lipid accumulation, insulin resistance, inflammation, and obesity in a high-fat, high-cholesterol (HFHC) diet-induced murine hepatic steatosis model. In vitro mechanistic investigations showed that the depletion of S100A6 in hepatocytes restored lipophagy, suggesting S100A6 inhibition could alleviate HFHC-induced NAFLD. Moreover, S100A6 liver-specific ablation mediated by AAV9 alleviated NAFLD in obese mice. CONCLUSIONS Our study demonstrates that S100A6 functions as a positive regulator of NAFLD, targeting the S100A6-lipophagy axis may be a promising treatment option for NAFLD and associated metabolic diseases.
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Affiliation(s)
- Qian Du
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Tingting Zhu
- School of Medicine, Guizhou University, Guiyang, Guizhou, China
| | - Guorong Wen
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Hai Jin
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Jiaxing An
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Jingyu Xu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Rui Xie
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Jiaxing Zhu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Xiaoxu Yang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Ting Zhang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Qi Liu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Shun Yao
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Xingyue Yang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Biguang Tuo
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, China
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
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Brohus M, Busuioc AO, Wimmer R, Nyegaard M, Overgaard MT. Calmodulin mutations affecting Gly114 impair binding to the Na V1.5 IQ-domain. Front Pharmacol 2023; 14:1210140. [PMID: 37663247 PMCID: PMC10469309 DOI: 10.3389/fphar.2023.1210140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/25/2023] [Indexed: 09/05/2023] Open
Abstract
Missense variants in CALM genes encoding the Ca2+-binding protein calmodulin (CaM) cause severe cardiac arrhythmias. The disease mechanisms have been attributed to dysregulation of RyR2, for Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT) and/or CaV1.2, for Long-QT Syndrome (LQTS). Recently, a novel CALM2 variant, G114R, was identified in a mother and two of her four children, all of whom died suddenly while asleep at a young age. The G114R variant impairs closure of CaV1.2 and RyR2, consistent with a CPVT and/or mild LQTS phenotype. However, the children carrying the CALM2 G114R variant displayed a phenotype commonly observed with variants in NaV1.5, i.e., Brugada Syndrome (BrS) or LQT3, where death while asleep is a common feature. We therefore hypothesized that the G114R variant specifically would interfere with NaV1.5 binding. Here, we demonstrate that CaM binding to the NaV1.5 IQ-domain is severely impaired for two CaM variants G114R and G114W. The impact was most severe at low and intermediate Ca2+ concentrations (up to 4 µM) resulting in more than a 50-fold reduction in NaV1.5 binding affinity, and a smaller 1.5 to 11-fold reduction at high Ca2+ concentrations (25-400 µM). In contrast, the arrhythmogenic CaM-N98S variant only induced a 1.5-fold reduction in NaV1.5 binding and only at 4 µM Ca2+. A non-arrhythmogenic I10T variant in CaM did not impair NaV1.5 IQ binding. These data suggest that the interaction between NaV1.5 and CaM is decreased with certain CaM variants, which may alter the cardiac sodium current, INa. Overall, these results suggest that the phenotypic spectrum of calmodulinopathies may likely expand to include BrS- and/or LQT3-like traits.
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Affiliation(s)
- Malene Brohus
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Ana-Octavia Busuioc
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Gistrup, Denmark
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O’Day DH. Alzheimer's Disease beyond Calcium Dysregulation: The Complex Interplay between Calmodulin, Calmodulin-Binding Proteins and Amyloid Beta from Disease Onset through Progression. Curr Issues Mol Biol 2023; 45:6246-6261. [PMID: 37623212 PMCID: PMC10453589 DOI: 10.3390/cimb45080393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
A multifactorial syndrome, Alzheimer's disease is the main cause of dementia, but there is no existing therapy to prevent it or stop its progression. One of the earliest events of Alzheimer's disease is the disruption of calcium homeostasis but that is just a prelude to the disease's devastating impact. Calcium does not work alone but must interact with downstream cellular components of which the small regulatory protein calmodulin is central, if not primary. This review supports the idea that, due to calcium dyshomeostasis, calmodulin is a dominant regulatory protein that functions in all stages of Alzheimer's disease, and these regulatory events are impacted by amyloid beta. Amyloid beta not only binds to and regulates calmodulin but also multiple calmodulin-binding proteins involved in Alzheimer's. Together, they act on the regulation of calcium dyshomeostasis, neuroinflammation, amyloidogenesis, memory formation, neuronal plasticity and more. The complex interactions between calmodulin, its binding proteins and amyloid beta may explain why many therapies have failed or are doomed to failure unless they are considered.
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Affiliation(s)
- Danton H. O’Day
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada;
- Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
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Li T, Ci Liu T, Liu N, Zhang M. Changes in urinary exosomal protein CALM1 may serve as an early noninvasive biomarker for diagnosing diabetic kidney disease. Clin Chim Acta 2023; 547:117466. [PMID: 37406751 DOI: 10.1016/j.cca.2023.117466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND The risk of the development and progression of diabetic kidney disease (DKD) was increased by abnormal calcium release. However, it is still unknown whether calcium signal pathway-related proteins are changed in urinary exosomes. This study aims to explore the changes in urinary exosomal proteins, which may provide novel biomarkers for diagnosing DKD. METHODS Urinary exosomes were isolated from 132 participants by size exclusion chromatography method and 72 participants were tested by LC-MS/MS (Discovery phase). Correlation and multivariate logistics analysis were applied to evaluate selected urinary proteins. Western blot and ELISA were used to validate the selected protein (Validation phase: n = 60). The diagnostic performance of the selected biomarker was evaluated by receiver operating characteristic curve analyses between the discovery and validation phases. RESULTS Sixteen calcium signal pathway-related proteins were identified, however, only Calmodulin-1(CALM1) was continuously increased. Different expression of CALM1 was found in patients with different level of estimated glomerular filtration rate (eGFR) in two cohorts. The level of CALM1 was correlated with eGFR and serum creatinine levels in two cohorts. Multivariate analysis revealed that serum albumin (ALB) levels and CALM1 were independent risk factors for DKD. A diagnostic model based on CALM1 and serum ALB levels that could significantly distinguish DKD was established and validated. CONCLUSIONS Significant changes in calcium signal pathway-related urinary exosomal proteins were observed. The CALM1 may serve as an early noninvasive biomarker for diagnosing DKD.
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Affiliation(s)
- Tao Li
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing 100038, China
| | - Tian Ci Liu
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing 100038, China
| | - Na Liu
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing 100038, China
| | - Man Zhang
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing 100038, China; Institute of Regenerative Medicine and Laboratory Technology Innovation, Qingdao University, Qingdao 266071, China.
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Song J, Ham J, Park S, Park SJ, Kim HS, Song G, Lim W. Alpinumisoflavone Activates Disruption of Calcium Homeostasis, Mitochondria and Autophagosome to Suppress Development of Endometriosis. Antioxidants (Basel) 2023; 12:1324. [PMID: 37507864 PMCID: PMC10376749 DOI: 10.3390/antiox12071324] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/10/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Alpinumisoflavone is an isoflavonoid extracted from the Cudrania tricuspidate fruit and Genista pichisermolliana. It has various physiological functions, such as anti-inflammation, anti-proliferation, and apoptosis, in malignant tumors. However, the effect of alpinumisoflavone is still not known in chronic diseases and other benign reproductive diseases, such as endometriosis. In this study, we examined the cell death effects of alpinumisoflavone on the endometriosis cell lines, End1/E6E7 and VK2/E6E7. Results indicated that alpinumisoflavone inhibited cell migration and proliferation and led to cell cycle arrest, depolarization of mitochondria membrane potential, apoptosis, and disruption of calcium homeostasis in the endometriosis cell lines. However, the cellular proliferation of normal uterine epithelial cells was not changed by alpinumisoflavone. The alteration in Ca2+ levels was estimated in fluo-4 AM-stained End1/E6E7 and VK2/E6E7 cells after alpinumisoflavone treatment with or without calcium inhibitor, 2-aminoethoxydiphenyl borate (2-APB). The results indicated that a combination of alpinumisoflavone and a calcium inhibitor reduced the calcium accumulation in the cytosol of endometriosis cells. Additionally, alpinumisoflavone decreased oxidative phosphorylation (OXPHOS) in the endometriotic cells. Moreover, protein expression analysis revealed that alpinumisoflavone inactivated AKT signaling pathways, whereas it increased MAPK, ER stress, and autophagy regulatory proteins in End1/E6E7 and VK2/E6E7 cell lines. In summary, our results suggested that alpinumisoflavone could be a promising effective management agent or an adjuvant therapy for benign disease endometriosis.
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Affiliation(s)
- Jisoo Song
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jiyeon Ham
- Institute of Animal Molecular Biotechnology, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sunwoo Park
- Department of Plant & Biomaterials Science, Gyeongsang National University, Jinju-si 52725, Republic of Korea
- Department of GreenBio Science, Gyeongsang National University, Jinju-si 52725, Republic of Korea
| | - Soo Jin Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hee Seung Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Gwonhwa Song
- Institute of Animal Molecular Biotechnology, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Whasun Lim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
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Daronnat L, Holfeltz V, Boubals N, Dumas T, Guilbaud P, Martinez DM, Moisy P, Sauge-Merle S, Lemaire D, Solari PL, Berthon L, Berthomieu C. Investigation of the Plutonium(IV) Interactions with Two Variants of the EF-Hand Ca-Binding Site I of Calmodulin. Inorg Chem 2023; 62:8334-8346. [PMID: 37184364 DOI: 10.1021/acs.inorgchem.3c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Due to its presence in the nuclear industry and its strong radiotoxicity, plutonium is an actinide of major interest in the event of internal contamination. To improve the understanding of its mechanisms of transport and accumulation in the body, the complexation of Pu(IV) to the most common protein calcium-binding motif found in cells, the EF-hand motif of calmodulin, was investigated. Visible and X-ray absorption spectroscopies (XAS) in solution made it possible to investigate the speciation of plutonium at physiological pH (pH 7.4) and pH 6 in two variants of the calmodulin Ca-binding site I and using Pu(IV) in different media: carbonate, chloride, or nitrate solutions. Three different species of Pu were identified in the samples, with formation of 1:1 Pu(IV):calmodulin peptide complexes, Pu(IV) reduction, and formation of peptide-mediated Pu(IV) hexanuclear cluster.
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Affiliation(s)
- Loïc Daronnat
- CEA, DES, ISEC, DMRC, Univ Montpellier, Marcoule, Bagnols-sur-cèze 30200, France
| | - Vanessa Holfeltz
- CEA, DES, ISEC, DMRC, Univ Montpellier, Marcoule, Bagnols-sur-cèze 30200, France
| | - Nathalie Boubals
- CEA, DES, ISEC, DMRC, Univ Montpellier, Marcoule, Bagnols-sur-cèze 30200, France
| | - Thomas Dumas
- CEA, DES, ISEC, DMRC, Univ Montpellier, Marcoule, Bagnols-sur-cèze 30200, France
| | - Philippe Guilbaud
- CEA, DES, ISEC, DMRC, Univ Montpellier, Marcoule, Bagnols-sur-cèze 30200, France
| | | | - Philippe Moisy
- CEA, DES, ISEC, DMRC, Univ Montpellier, Marcoule, Bagnols-sur-cèze 30200, France
| | - Sandrine Sauge-Merle
- Aix Marseille Université, CEA, CNRS, BIAM, UMR7265, IPM, Saint Paul-Lez-Durance 13108, France
| | - David Lemaire
- Aix Marseille Université, CEA, CNRS, BIAM, UMR7265, IPM, Saint Paul-Lez-Durance 13108, France
| | - Pier Lorenzo Solari
- Synchrotron SOLEIL, L'Orme des Merisiers, Départementale 128, Saint Aubin 91190, France
| | - Laurence Berthon
- CEA, DES, ISEC, DMRC, Univ Montpellier, Marcoule, Bagnols-sur-cèze 30200, France
| | - Catherine Berthomieu
- Aix Marseille Université, CEA, CNRS, BIAM, UMR7265, IPM, Saint Paul-Lez-Durance 13108, France
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Xue N, Sun M, Gai Z, Bai M, Sun J, Sai S, Zhang L. Genome-Wide Identification and Expression Analysis of Calmodulin (CaM) and Calmodulin-Like (CML) Genes in the Brown Algae Saccharina japonica. PLANTS (BASEL, SWITZERLAND) 2023; 12:1934. [PMID: 37653850 PMCID: PMC10222329 DOI: 10.3390/plants12101934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 09/02/2023]
Abstract
Calmodulins (CaMs) and Calmodulin-like proteins (CMLs) are vital in plant growth, development, and stress responses. However, CaMs and CMLs have not been fully identified and characterized in brown algae, which has been evolving independently of the well-studied green plant lineage. In this study, whole-genome searches revealed one SjCaM and eight SjCMLs in Saccharina japonica, and one EsCaM and eleven EsCMLs in Ectocarpus sp. SjCaM and EsCaM encoded identical protein products and shared 88.59-89.93% amino acid identities with Arabidopsis thaliana AtCaMs, thereby indicating that brown algae CaMs retained a similar Ca2+ sensors function as in plants. The phylogenetic and gene structure analysis results showed that there was significant divergence in the gene sequences among brown algae CMLs. Furthermore, evolutionary analysis indicated that the function of brown alga CMLs was relatively conserved, which may be related to the fact that brown algae do not need to face complex environments like terrestrial plants. Regulatory elements prediction and the expression analysis revealed the probable functioning of SjCaM/CML genes in gametophyte development and the stress response in S. japonica. In addition, the SjCaM/SjCMLs interacting proteins and chemicals were preliminarily predicted, suggesting that SjCaM/SjCMLs might play putative roles in Ca2+/CaM-mediated growth and development processes and stimulus responses. Therefore, these results will facilitate our understanding of the evolution of brown algae CaMs/CMLs and the functional identification of SjCaM/SjCMLs.
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Affiliation(s)
- Nianchao Xue
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Minghui Sun
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Zihan Gai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Meihan Bai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Juan Sun
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Shandong Technology Innovation Center of Algae and Sea Cucumber, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai 264003, China
| | - Shan Sai
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Shandong Technology Innovation Center of Algae and Sea Cucumber, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai 264003, China
| | - Linan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
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