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Bader S, Tuller T. Advanced computational predictive models of miRNA-mRNA interaction efficiency. Comput Struct Biotechnol J 2024; 23:1740-1754. [PMID: 38689718 PMCID: PMC11058727 DOI: 10.1016/j.csbj.2024.04.015] [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: 01/10/2024] [Revised: 04/06/2024] [Accepted: 04/07/2024] [Indexed: 05/02/2024] Open
Abstract
The modeling of miRNA-mRNA interactions holds significant implications for synthetic biology and human health. However, this research area presents specific challenges due to the multifaceted nature of mRNA downregulation by miRNAs, influenced by numerous factors including competition or synergism among miRNAs and mRNAs. In this study, we present an improved computational model for predicting miRNA-mRNA interactions, addressing aspects not previously modeled. Firstly, we integrated a novel set of features that significantly enhanced the predictor's performance. Secondly, we demonstrated the cell-specific nature of certain aspects of miRNA-mRNA interactions, highlighting the importance of designing models tailored to specific cell types for improved accuracy. Moreover, we introduce a miRNA binding site interaction model (miBSIM) that, for the first time, accounts for both the distribution of miRNA binding sites along the mRNA and their respective strengths in regulating mRNA stability. Our analysis suggests that distant miRNA sites often compete with each other, revealing the intricate interplay of binding site interactions. Overall, our new predictive model shows a significant improvement of up to 6.43% over previous models in the field. The code of our model is available at https://www.cs.tau.ac.il/~tamirtul/miBSIM.
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Affiliation(s)
- Sharon Bader
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
- The Segol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
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52
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Su HL, Lai SJ, Tsai KC, Fung KM, Lung TL, Hsu HM, Wu YC, Liu CH, Lai HX, Lin JH, Tseng TS. Structure-guided identification and characterization of potent inhibitors targeting PhoP and MtrA to combat mycobacteria. Comput Struct Biotechnol J 2024; 23:1477-1488. [PMID: 38623562 PMCID: PMC11016868 DOI: 10.1016/j.csbj.2024.04.005] [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: 12/24/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Mycobacteria are causative agents of tuberculosis (TB), which is a global health concern. Drug-resistant TB strains are rapidly emerging, thereby necessitating the urgent development of new drugs. Two-component signal transduction systems (TCSs) are signaling pathways involved in the regulation of various bacterial behaviors and responses to environmental stimuli. Applying specific inhibitors of TCSs can disrupt bacterial signaling, growth, and virulence, and can help combat drug-resistant TB. We conducted a comprehensive pharmacophore-based inhibitor screening and biochemical and biophysical examinations to identify, characterize, and validate potential inhibitors targeting the response regulators PhoP and MtrA of mycobacteria. The constructed pharmacophore model Phar-PR-n4 identified effective inhibitors of formation of the PhoP-DNA complex: ST132 (IC50 = 29 ± 1.6 µM) and ST166 (IC50 = 18 ± 1.3 µM). ST166 (KD = 18.4 ± 4.3 μM) and ST132 (KD = 14.5 ± 0.1 μM) strongly targeted PhoP in a slow-on, slow-off manner. The inhibitory potency and binding affinity of ST166 and ST132 for MtrAC were comparable to those of PhoP. Structural analyses and molecular dynamics simulations revealed that ST166 and ST132 mainly interact with the α8-helix and C-terminal β-hairpin of PhoP, with functionally essential residue hotspots for structure-based inhibitor optimization. Moreover, ST166 has in vitro antibacterial activity against Macrobacterium marinum. Thus, ST166, with its characteristic 1,2,5,6-tetrathiocane and terminal sulphonic groups, has excellent potential as a candidate for the development of novel antimicrobial agents to combat pathogenic mycobacteria.
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Affiliation(s)
- Han-Li Su
- Department of Emergency Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City 600, Taiwan
| | - Shu-Jung Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Kit-Man Fung
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei 11529, Taiwan
| | - Tse-Lin Lung
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Hsing-Mien Hsu
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Yi-Chen Wu
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Ching-Hui Liu
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Hui-Xiang Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Jiun-Han Lin
- Department of Industrial Technology, Ministry of Economic Affairs, Taipei, Taiwan
- Food Industry Research and Development Institute, Hsinchu City, Taiwan
| | - Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
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Sun Y, Zhu Y, Zhang P, Sheng S, Guan Z, Cong Y. Hemagglutinin glycosylation pattern-specific effects: implications for the fitness of H9.4.2.5-branched H9N2 avian influenza viruses. Emerg Microbes Infect 2024; 13:2364736. [PMID: 38847071 PMCID: PMC11182062 DOI: 10.1080/22221751.2024.2364736] [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: 03/27/2024] [Accepted: 06/02/2024] [Indexed: 06/16/2024]
Abstract
Since 2007, h9.4.2.5 has emerged as the most predominant branch of H9N2 avian influenza viruses (AIVs) that affects the majority of the global poultry population. The spread of this viral branch in vaccinated chicken flocks has not been considerably curbed despite numerous efforts. The evolutionary fitness of h9.4.2.5-branched AIVs must consequently be taken into consideration. The glycosylation modifications of hemagglutinin (HA) play a pivotal role in regulating the balance between receptor affinity and immune evasion for influenza viruses. Sequence alignment showed that five major HA glycosylation patterns have evolved over time in h9.4.2.5-branched AIVs. Here, we compared the adaptive phenotypes of five virus mutants with different HA glycosylation patterns. According to the results, the mutant with 6 N-linked glycans displayed the best acid and thermal stability and a better capacity for multiplication, although having a relatively lower receptor affinity than 7 glycans. The antigenic profile between the five mutants revealed a distinct antigenic distance, indicating that variations in glycosylation level have an impact on antigenic drift. These findings suggest that changes in the number of glycans on HA can not only modulate the receptor affinity and antigenicity of H9N2 AIVs, but also affect their stability and multiplication. These adaptive phenotypes may underlie the biological basis for the dominant strain switchover of h9.4.2.5-branched AIVs. Overall, our study provides a systematic insight into how changes in HA glycosylation patterns regulate the evolutionary fitness and epidemiological dominance drift of h9.4.2.5-branched H9N2 AIVs, which will be of great benefit for the glycosylation-dependent vaccine design.
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Affiliation(s)
- Yixue Sun
- Department of Policies and Regulations, Changchun University, Changchun, People’s Republic of China
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yanting Zhu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Pengju Zhang
- Institute of Animal Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, People’s Republic of China
| | - Shouzhi Sheng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhenhong Guan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yanlong Cong
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
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54
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Wu H, Liu Y, Liu C. The interregulatory circuit between non-coding RNA and apoptotic signaling in diabetic cardiomyopathy. Noncoding RNA Res 2024; 9:1080-1097. [PMID: 39022683 PMCID: PMC11254508 DOI: 10.1016/j.ncrna.2024.06.011] [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: 03/07/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
Diabetes mellitus has surged in prevalence, emerging as a prominent epidemic and assuming a foremost position among prevalent medical disorders. Diabetes constitutes a pivotal risk element for cardiovascular maladies, with diabetic cardiomyopathy (DCM) standing out as a substantial complication encountered by individuals with diabetes. Apoptosis represents a physiological phenomenon observed throughout the aging and developmental stages, giving rise to the programmed cell death, which is implicated in DCM. Non-coding RNAs assume significant functions in modulation of gene expression. Their deviant expression of ncRNAs is implicated in overseeing diverse cellular attributes such as proliferation, apoptosis, and has been postulated to play a role in the progression of DCM. Notably, ncRNAs and the process of apoptosis can mutually influence and cooperate in shaping the destiny of human cardiac tissues. Therefore, the exploration of the interplay between apoptosis and non-coding RNAs holds paramount importance in the formulation of efficacious therapeutic and preventive approaches for managing DCM. In this review, we provide a comprehensive overview of the apoptotic signaling pathways relevant to DCM and subsequently delve into the reciprocal regulation between apoptosis and ncRNAs in DCM. These insights contribute to an enhanced comprehension of DCM and the development of therapeutic strategies.
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Affiliation(s)
- Hao Wu
- Public Health Clinical Center Affiliated to Shandong University, Jinan, 250100, China
| | - Yan Liu
- Public Health Clinical Center Affiliated to Shandong University, Jinan, 250100, China
| | - Chunli Liu
- Public Health Clinical Center Affiliated to Shandong University, Jinan, 250100, China
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55
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Elbahnsi A, Dudas B, Cisternino S, Declèves X, Miteva MA. Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations. Comput Struct Biotechnol J 2024; 23:2548-2564. [PMID: 38989058 PMCID: PMC11233806 DOI: 10.1016/j.csbj.2024.06.010] [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: 05/02/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024] Open
Abstract
P-glycoprotein (P-gp) plays a crucial role in cellular detoxification and drug efflux processes, transitioning between inward-facing (IF) open, occluded, and outward-facing (OF) states to facilitate substrate transport. Its role is critical in cancer therapy, where P-gp contributes to the multidrug resistance phenotype. In our study, classical and enhanced molecular dynamics (MD) simulations were conducted to dissect the structural and functional features of the P-gp conformational states. Our advanced MD simulations, including kinetically excited targeted MD (ketMD) and adiabatic biasing MD (ABMD), provided deeper insights into state transition and translocation mechanisms. Our findings suggest that the unkinking of TM4 and TM10 helices is a prerequisite for correctly achieving the outward conformation. Simulations of the IF-occluded conformations, characterized by kinked TM4 and TM10 helices, consistently demonstrated altered communication between the transmembrane domains (TMDs) and nucleotide binding domain 2 (NBD2), suggesting the implication of this interface in inhibiting P-gp's efflux function. A particular emphasis was placed on the unstructured linker segment connecting the NBD1 to TMD2 and its role in the transporter's dynamics. With the linker present, we specifically noticed a potential entrance of cholesterol (CHOL) through the TM4-TM6 portal, shedding light on crucial residues involved in accommodating CHOL. We therefore suggest that this entry mechanism could be employed for some P-gp substrates or inhibitors. Our results provide critical data for understanding P-gp functioning and developing new P-gp inhibitors for establishing more effective strategies against multidrug resistance.
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Affiliation(s)
- Ahmad Elbahnsi
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Balint Dudas
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Salvatore Cisternino
- Université Paris Cité, Inserm UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Paris, France
| | - Xavier Declèves
- Université Paris Cité, Inserm UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Paris, France
| | - Maria A. Miteva
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
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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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57
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Srivastava LK, Ehrlicher AJ. Sensing the squeeze: nuclear mechanotransduction in health and disease. Nucleus 2024; 15:2374854. [PMID: 38951951 PMCID: PMC11221475 DOI: 10.1080/19491034.2024.2374854] [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: 02/23/2024] [Accepted: 06/26/2024] [Indexed: 07/03/2024] Open
Abstract
The nucleus not only is a repository for DNA but also a center of cellular and nuclear mechanotransduction. From nuclear deformation to the interplay between mechanosensing components and genetic control, the nucleus is poised at the nexus of mechanical forces and cellular function. Understanding the stresses acting on the nucleus, its mechanical properties, and their effects on gene expression is therefore crucial to appreciate its mechanosensitive function. In this review, we examine many elements of nuclear mechanotransduction, and discuss the repercussions on the health of cells and states of illness. By describing the processes that underlie nuclear mechanosensation and analyzing its effects on gene regulation, the review endeavors to open new avenues for studying nuclear mechanics in physiology and diseases.
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Affiliation(s)
| | - Allen J. Ehrlicher
- Department of Bioengineering, McGill University, Montreal, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
- Centre for Structural Biology, McGill University, Montreal, Canada
- Department of Mechanical Engineering, McGill University, Montreal, Canada
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Canada
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Li H, E W, Zhao D, Liu H, Pei J, Du B, Liu K, Zhu X, Wang C. Response of Paenibacillus polymyxa SC2 to the stress of polymyxin B and a key ABC transporter YwjA involved. Appl Microbiol Biotechnol 2024; 108:17. [PMID: 38170316 DOI: 10.1007/s00253-023-12916-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/24/2023] [Accepted: 10/04/2023] [Indexed: 01/05/2024]
Abstract
Polymyxins are cationic peptide antibiotics and regarded as the "final line of defense" against multidrug-resistant bacterial infections. Meanwhile, some polymyxin-resistant strains and the corresponding resistance mechanisms have also been reported. However, the response of the polymyxin-producing strain Paenibacillus polymyxa to polymyxin stress remains unclear. The purpose of this study was to investigate the stress response of gram-positive P. polymyxa SC2 to polymyxin B and to identify functional genes involved in the stress response process. Polymyxin B treatment upregulated the expression of genes related to basal metabolism, transcriptional regulation, transport, and flagella formation and increased intracellular ROS levels, flagellar motility, and biofilm formation in P. polymyxa SC2. Adding magnesium, calcium, and iron alleviated the stress of polymyxin B on P. polymyxa SC2, furthermore, magnesium and calcium could improve the resistance of P. polymyxa SC2 to polymyxin B by promoting biofilm formation. Meanwhile, functional identification of differentially expressed genes indicated that an ABC superfamily transporter YwjA was involved in the stress response to polymyxin B of P. polymyxa SC2. This study provides an important reference for improving the resistance of P. polymyxa to polymyxins and increasing the yield of polymyxins. KEY POINTS: • Phenotypic responses of P. polymyxa to polymyxin B was performed and indicated by RNA-seq • Forming biofilm was a key strategy of P. polymyxa to alleviate polymyxin stress • ABC transporter YwjA was involved in the stress resistance of P. polymyxa to polymyxin B.
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Affiliation(s)
- Hui Li
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Wenhui E
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Dongying Zhao
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Haiyang Liu
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Jian Pei
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Binghai Du
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Kai Liu
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Chengqiang Wang
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China.
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59
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Liu HL, Nan H, Zhao WW, Wan XB, Fan XJ. Phase separation in DNA double-strand break response. Nucleus 2024; 15:2296243. [PMID: 38146123 PMCID: PMC10761171 DOI: 10.1080/19491034.2023.2296243] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 12/12/2023] [Indexed: 12/27/2023] Open
Abstract
DNA double-strand break (DSB) is the most dangerous type of DNA damage, which may lead to cell death or oncogenic mutations. Homologous recombination (HR) and nonhomologous end-joining (NHEJ) are two typical DSB repair mechanisms. Recently, many studies have revealed that liquid-liquid phase separation (LLPS) plays a pivotal role in DSB repair and response. Through LLPS, the crucial biomolecules are quickly recruited to damaged sites with a high concentration to ensure DNA repair is conducted quickly and efficiently, which facilitates DSB repair factors activating downstream proteins or transmitting signals. In addition, the dysregulation of the DSB repair factor's phase separation has been reported to promote the development of a variety of diseases. This review not only provides a comprehensive overview of the emerging roles of LLPS in the repair of DSB but also sheds light on the regulatory patterns of phase separation in relation to the DNA damage response (DDR).
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Affiliation(s)
- Huan-Lei Liu
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, P.R. China
- College of Life Sciences, Northwest AF University, Yangling, Shaanxi, China
| | - Hao Nan
- College of Life Sciences, Northwest AF University, Yangling, Shaanxi, China
| | - Wan-Wen Zhao
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, P.R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
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60
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Sánchez-Hernández R, Benítez-Angeles M, Hernández-Vega AM, Rosenbaum T. Recent advances on the structure and the function relationships of the TRPV4 ion channel. Channels (Austin) 2024; 18:2313323. [PMID: 38354101 PMCID: PMC10868539 DOI: 10.1080/19336950.2024.2313323] [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: 12/01/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
The members of the superfamily of Transient Receptor Potential (TRP) ion channels are physiologically important molecules that have been studied for many years and are still being intensively researched. Among the vanilloid TRP subfamily, the TRPV4 ion channel is an interesting protein due to its involvement in several essential physiological processes and in the development of various diseases. As in other proteins, changes in its function that lead to the development of pathological states, have been closely associated with modification of its regulation by different molecules, but also by the appearance of mutations which affect the structure and gating of the channel. In the last few years, some structures for the TRPV4 channel have been solved. Due to the importance of this protein in physiology, here we discuss the recent progress in determining the structure of the TRPV4 channel, which has been achieved in three species of animals (Xenopus tropicalis, Mus musculus, and Homo sapiens), highlighting conserved features as well as key differences among them and emphasizing the binding sites for some ligands that play crucial roles in its regulation.
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Affiliation(s)
- Raúl Sánchez-Hernández
- Departamento de Neurociencia Cognitiva, División Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - Miguel Benítez-Angeles
- Departamento de Neurociencia Cognitiva, División Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - Ana M. Hernández-Vega
- Departamento de Neurociencia Cognitiva, División Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - Tamara Rosenbaum
- Departamento de Neurociencia Cognitiva, División Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico, Mexico
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Walsh ME, King GA, Ünal E. Not just binary: embracing the complexity of nuclear division dynamics. Nucleus 2024; 15:2360601. [PMID: 38842147 PMCID: PMC11164224 DOI: 10.1080/19491034.2024.2360601] [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: 02/09/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024] Open
Abstract
Cell division presents a challenge for eukaryotic cells: how can chromosomes effectively segregate within the confines of a membranous nuclear compartment? Different organisms have evolved diverse solutions by modulating the degree of nuclear compartmentalization, ranging from complete nuclear envelope breakdown to complete maintenance of nuclear compartmentalization via nuclear envelope expansion. Many intermediate forms exist between these extremes, suggesting that nuclear dynamics during cell division are surprisingly plastic. In this review, we highlight the evolutionary diversity of nuclear divisions, focusing on two defining characteristics: (1) chromosome compartmentalization and (2) nucleocytoplasmic transport. Further, we highlight recent evidence that nuclear behavior during division can vary within different cellular contexts in the same organism. The variation observed within and between organisms underscores the dynamic evolution of nuclear divisions tailored to specific contexts and cellular requirements. In-depth investigation of diverse nuclear divisions will enhance our understanding of the nucleus, both in physiological and pathological states.
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Affiliation(s)
- Madison E. Walsh
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA
| | - Grant A. King
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA
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Nickerson JA, Momen-Heravi F. Long non-coding RNAs: roles in cellular stress responses and epigenetic mechanisms regulating chromatin. Nucleus 2024; 15:2350180. [PMID: 38773934 PMCID: PMC11123517 DOI: 10.1080/19491034.2024.2350180] [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: 01/18/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Most of the genome is transcribed into RNA but only 2% of the sequence codes for proteins. Non-coding RNA transcripts include a very large number of long noncoding RNAs (lncRNAs). A growing number of identified lncRNAs operate in cellular stress responses, for example in response to hypoxia, genotoxic stress, and oxidative stress. Additionally, lncRNA plays important roles in epigenetic mechanisms operating at chromatin and in maintaining chromatin architecture. Here, we address three lncRNA topics that have had significant recent advances. The first is an emerging role for many lncRNAs in cellular stress responses. The second is the development of high throughput screening assays to develop causal relationships between lncRNAs across the genome with cellular functions. Finally, we turn to recent advances in understanding the role of lncRNAs in regulating chromatin architecture and epigenetics, advances that build on some of the earliest work linking RNA to chromatin architecture.
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Affiliation(s)
- Jeffrey A Nickerson
- Division of Genes & Development, Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Fatemeh Momen-Heravi
- College of Dental Medicine, Columbia University Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
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Wei J, Luo J, Yang F, Dai W, Huang Z, Yan Y, Luo M. Comparative genomic and metabolomic analysis reveals the potential of a newly isolated Enterococcus faecium B6 involved in lipogenic effects. Gene 2024; 927:148668. [PMID: 38852695 DOI: 10.1016/j.gene.2024.148668] [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: 02/12/2024] [Revised: 06/01/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Evidence has indicated that Enterococcus plays a vital role in non-alcoholic fatty liver disease (NAFLD) development. However, the microbial genetic basis and metabolic potential in the disease are yet unknown. We previously isolated a bacteria Enterococcus faecium B6 (E. faecium B6) from children with NAFLD for the first time. Here, we aim to systematically investigate the potential of strain B6 in lipogenic effects. The lipogenic effects of strain B6 were explored in vitro and in vivo. The genomic and functional characterizations were investigated by whole-genome sequencing and comparative genomic analysis. Moreover, the metabolite profiles were unraveled by an untargeted metabolomic analysis. We demonstrated that strain B6 could effectively induce lipogenic effects in the liver of mice. Strain B6 contained a circular chromosome and two circular plasmids and posed various functions. Compared to the other two probiotic strains of E. faecium, strain B6 exhibited unique functions in pathways of ABC transporters, phosphotransferase system, and amino sugar and nucleotide sugar metabolism. Moreover, strain B6 produced several metabolites, mainly enriched in the protein digestion and absorption pathway. The unique potential of strain B6 in lipogenic effects was probably associated with glycolysis, fatty acid synthesis, and glutamine and choline transport. This study pioneeringly revealed the metabolic characteristics and specific detrimental traits of strain B6. The findings provided new insights into the underlying mechanisms of E. faecium in lipogenic effects, and laid essential foundations for further understanding of E. faecium-related disease.
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Affiliation(s)
- Jia Wei
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Jiayou Luo
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Fei Yang
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang 421001, Hunan, China
| | - Wen Dai
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Zhihang Huang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Yulin Yan
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Miyang Luo
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China.
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64
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Chan S, Liu Z, Chen Y, Chen S, Liang Y, Yang Z, Zhang Z, Li M, Zhang X, Liu X. The JAK-STAT signaling-related signature serves as a prognostic and predictive biomarker for renal cell carcinoma immunotherapy. Gene 2024; 927:148719. [PMID: 38917875 DOI: 10.1016/j.gene.2024.148719] [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: 12/13/2023] [Revised: 05/19/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024]
Abstract
Renal cell carcinoma (RCC) represents a significant portion of genitourinary cancers, marked by challenging prognosis and high metastasis rates. Immunotherapy has been applied in managing advanced renal cell carcinoma, but the therapeutic outcomes are unsatisfactory. In this study, we order to construct a Janus kinase/signal transduction and activator transcriptional (JAK/STAT)-related signature linked to kidney patient outcomes for better predicting the efficacy to immune checkpoint inhibitors (ICIs) and to provide guidance for effective combination therapy. We screened 25 differentially expressed genes (DEGs) that exhibited high expression in RCC samples and were enriched in the JAK-STAT signaling pathway. Among these genes, 11 key genes were identified and correlated with the expectation of Kidney Clear Cell Carcinoma (KIRC) patients and all these genes was significantly elevated in RCC tumor tissues and cancer cells compared to para-cancer tissues and normal renal cells. Utilizing these 11 genes, we divided RCC patients into high-risk and low-risk groups. We found a clear correlation between the clinicopathologic factors of KIRC patients and the JAK-STAT-related risk score. And the IHC results shown that the JAK3 and STAT4 expression of tumor was significantly higher than normal tissue in RCC patients, the level of JAK3 and STAT4 was positively related to the T stage of RCC patients. In addition, high-risk patients had a poorer prognosis and greater protumor immune cell infiltration, and benefitted less from immunotherapy than did low-risk patients. Furthermore, the JAK-STAT-related risk score can predict disease-free survival (DFS) in RCC patients according to the nomogram, which constructed in combination with other clinical features such as age, TNM-staging and stage. Our study demonstrated the JAK-STAT signaling pathway's important regulatory function in RCC tumor immunity. This insight not only enhances our ability to accurately predict the survival rate of RCC patients, but also underscores a potential therapeutic alternative for RCC, involving the combined targeting of the JAK-STAT pathway and immune checkpoints.
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Affiliation(s)
- Szehoi Chan
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Zixuan Liu
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Yingying Chen
- College of Stomatology, Jinan University, Guangzhou 510632, China
| | - Shuna Chen
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Yuelan Liang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Ziyi Yang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Zixuan Zhang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Miao Li
- Department of Dermatovenereology, The Seveneth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518106, China.
| | - Xingding Zhang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China.
| | - Xueqi Liu
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China.
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Yacoub HA, Mahmoud MM, Al-Hejin AM, Abujamel TS, Tabrez S, Abd-Elmaksoud S. Effect of Nk-lysin peptides on bacterial growth, MIC, antimicrobial resistance, and viral activities. Anim Biotechnol 2024; 35:2290520. [PMID: 38100547 DOI: 10.1080/10495398.2023.2290520] [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] [Indexed: 12/17/2023]
Abstract
NK-lysins from chicken, bovine and human are used as antiviral and antibacterial agents. Gram-negative and gram-positive microorganisms, including Streptococcus pyogenes, Streptococcus mutans, Escherichia coli, Pseudomonas aeruginosa, Klebsiella oxytoca, Shigella sonnei, Klebsiella pneumoniae and Salmonella typhimurium, are susceptible to NK-lysin treatment. The presence of dominant TEM-1 gene was noted in all untreated and treated bacteria, while TOHO-1 gene was absent in all bacteria. Importantly, β-lactamase genes CTX-M-1, CTX-M-8, and CTX-M-9 genes were detected in untreated bacterial strains; however, none of these were found in any bacterial strains following treatment with NK-lysin peptides. NK-lysin peptides are also used to test for inhibition of infectivity, which ranged from 50 to 90% depending on NK-lysin species. Chicken, bo vine and human NK-lysin peptides are demonstrated herein to have antibacterial activity and antiviral activity against Rotavirus (strain SA-11). On the basis of the comparison between these peptides, potent antiviral activity of bovine NK-lysin against Rotavirus (strain SA-11) is particularly evident, inhibiting infection by up to 90%. However, growth was also significantly inhibited by chicken and human NK-lysin peptides, restricted by 80 and 50%, respectively. This study provided a novel treatment using NK-lysin peptides to inhibit expression of β-lactamase genes in β-lactam antibiotic-resistant bacterial infections.
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Affiliation(s)
- Haitham A Yacoub
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Cairo, Egypt
| | - Maged Mostafa Mahmoud
- Regerenative Medicine Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia (SA)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia (SA)
| | - Ahmed M Al-Hejin
- Biological Sciences Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Turki S Abujamel
- Regerenative Medicine Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia (SA)
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shams Tabrez
- Regerenative Medicine Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia (SA)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia (SA)
| | - Sherif Abd-Elmaksoud
- Environmental Virology Laboratory, Water Pollution Research Department, Environmental Research Institute, National Research Centre, Cairo, Egypt
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66
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Osborne M, Fubara A, Ó Cinnéide E, Coughlan AY, Wolfe KH. WHO elements - A new category of selfish genetic elements at the borderline between homing elements and transposable elements. Semin Cell Dev Biol 2024; 163:2-13. [PMID: 38664119 DOI: 10.1016/j.semcdb.2024.04.001] [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: 11/21/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
Homing genetic elements are a form of selfish DNA that inserts into a specific target site in the genome and spreads through the population by a process of biased inheritance. Two well-known types of homing element, called inteins and homing introns, were discovered decades ago. In this review we describe WHO elements, a newly discovered type of homing element that constitutes a distinct third category but is rare, having been found only in a few yeast species so far. WHO elements are inferred to spread using the same molecular homing mechanism as inteins and introns: they encode a site-specific endonuclease that cleaves the genome at the target site, making a DNA break that is subsequently repaired by copying the element. For most WHO elements, the target site is in the glycolytic gene FBA1. WHO elements differ from inteins and homing introns in two fundamental ways: they do not interrupt their host gene (FBA1), and they occur in clusters. The clusters were formed by successive integrations of different WHO elements into the FBA1 locus, the result of an 'arms race' between the endonuclease and its target site. We also describe one family of WHO elements (WHO10) that is no longer specifically associated with the FBA1 locus and instead appears to have become transposable, inserting at random genomic sites in Torulaspora globosa with up to 26 copies per strain. The WHO family of elements is therefore at the borderline between homing genetic elements and transposable elements.
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Affiliation(s)
- Matthieu Osborne
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Athaliah Fubara
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Eoin Ó Cinnéide
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Aisling Y Coughlan
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Kenneth H Wolfe
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland.
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67
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Zhang B, Zhou F, Yu X, Zhang P, Sun X, Su J, Fan C, Shu W, Dong Q, Zeng C. An enantioselective fluorescent probe for detecting arginine and glutamic acids. Food Chem 2024; 455:139976. [PMID: 38850978 DOI: 10.1016/j.foodchem.2024.139976] [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: 03/13/2024] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
Amino acids are important chiral compounds in the human body, and are important basic components that make up the human body and play an important role in the human body. Among them, different enantiomers of an amino acid may have different roles, and different types of amino acids can be interconverted. However, the content of D-amino acids is much lower than that of L-amino acids, which is difficult to be detected. At present, many of the potential roles of D-amino acids, such as the conversion of D-amino acids to each other, have not yet been fully revealed. Hence, we synthesized fluorescent probe (R)-5 by condensation of 1,1'-Bi-2-naphthol (BINOL) and 2-(Aminomethyl)pyridine with Schiff base, which can recognize both D-arginine and D-glutamic acid at low concentrations. Meanwhile, (R)-5 can be applied to paper-based sensors for the detection of arginine and glutamate in living cells and for food amino acid detection.
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Affiliation(s)
- Binjie Zhang
- School of Chemistry and Chemical Engineering, Key Laboratory of Ministry of Education for Advanced Materials in Tropical Island Resources, Collaborative Innovation Center of Ecological Civilization, Hainan University, No 58, Renmin Avenue, Haikou 570228, China
| | - Feng Zhou
- School of Chemistry and Chemical Engineering, Key Laboratory of Ministry of Education for Advanced Materials in Tropical Island Resources, Collaborative Innovation Center of Ecological Civilization, Hainan University, No 58, Renmin Avenue, Haikou 570228, China
| | - Xianzhe Yu
- School of Chemistry and Chemical Engineering, Key Laboratory of Ministry of Education for Advanced Materials in Tropical Island Resources, Collaborative Innovation Center of Ecological Civilization, Hainan University, No 58, Renmin Avenue, Haikou 570228, China
| | - Peng Zhang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Xiaoqian Sun
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Jiali Su
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Cailing Fan
- School of Chemistry and Chemical Engineering, Key Laboratory of Ministry of Education for Advanced Materials in Tropical Island Resources, Collaborative Innovation Center of Ecological Civilization, Hainan University, No 58, Renmin Avenue, Haikou 570228, China.
| | - Wei Shu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, China.
| | - Qinxi Dong
- School of Chemistry and Chemical Engineering, Key Laboratory of Ministry of Education for Advanced Materials in Tropical Island Resources, Collaborative Innovation Center of Ecological Civilization, Hainan University, No 58, Renmin Avenue, Haikou 570228, China
| | - Chaoyuan Zeng
- School of Chemistry and Chemical Engineering, Key Laboratory of Ministry of Education for Advanced Materials in Tropical Island Resources, Collaborative Innovation Center of Ecological Civilization, Hainan University, No 58, Renmin Avenue, Haikou 570228, China.
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68
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Lembo A, Molinaro A, De Castro C, Berti F, Biagini M. Impact of glycosylation on viral vaccines. Carbohydr Polym 2024; 342:122402. [PMID: 39048237 DOI: 10.1016/j.carbpol.2024.122402] [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: 02/26/2024] [Revised: 05/24/2024] [Accepted: 06/11/2024] [Indexed: 07/27/2024]
Abstract
Glycosylation is the most prominent modification important for vaccines and its specific pattern depends on several factors that need to be considered when developing a new biopharmaceutical. Tailor-made glycosylation can be exploited to develop more effective and safer vaccines; for this reason, a deep understanding of both glycoengineering strategies and glycans structures and functions is required. In this review we discuss the recent advances concerning glycoprotein expression systems and the explanation of glycans immunomodulation mechanisms. Furthermore, we highlight how glycans tune the immunological properties among different vaccines platforms (whole virus, recombinant protein, nucleic acid), also comparing commercially available formulations and describing the state-of-the-art analytical technologies for glycosylation analysis. The whole review stresses the aspect of glycoprotein glycans as a potential tool to overcome nowadays medical needs in vaccine field.
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Affiliation(s)
- Antonio Lembo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy; GSK, Siena, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Cristina De Castro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.
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69
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Yang Z, Jiang Q, Zhong T, Hu X, Cao B, Han Z, Zhao S, Qin J. Large stokes shift and near-infrared fluorescent probe for bioimaging and evaluating the HClO in an rheumatoid arthritis mouse model. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124547. [PMID: 38823237 DOI: 10.1016/j.saa.2024.124547] [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: 01/19/2024] [Revised: 05/20/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024]
Abstract
It is crucial to identify aberrant HClO levels in living things since they pose a major health risk and are a frequent reactive oxygen species (ROS) in living organisms. In order to detect HClO in various biological systems, we created and synthesized a near-infrared fluorescent probe with an oxime group (-C = N-OH) as a recognition unit. The probe DCMP1 has the advantages of fast response (10 min), near-infrared emission (660 nm), large Stokes shift (170 nm) and high selectivity. This probe DCMP1 not only detects endogenous HClO in living cells, but also enables further fluorescence detection of HClO in living zebrafish. More importantly, it can also be used for fluorescence imaging of HClO in an rheumatoid arthritis mouse model. This fluorescent probe DCMP1 is anticipated to be an effective tool for researching HClO.
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Affiliation(s)
- Zhengmin Yang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, PR China; Qiannan Medical College for Nationalities, Duyun 558003, PR China
| | - Qingke Jiang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, PR China
| | - Tiantian Zhong
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, PR China
| | - Xianyun Hu
- Qiannan Medical College for Nationalities, Duyun 558003, PR China
| | - Bingying Cao
- Qiannan Medical College for Nationalities, Duyun 558003, PR China
| | - Zhongyao Han
- Qiannan Medical College for Nationalities, Duyun 558003, PR China
| | - Shulin Zhao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, PR China
| | - Jiangke Qin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, PR China.
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70
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Vu JT, Tavasoli KU, Sheedy CJ, Chowdhury SP, Mandjikian L, Bacal J, Morrissey MA, Richardson CD, Gardner BM. A genome-wide screen links peroxisome regulation with Wnt signaling through RNF146 and TNKS/2. J Cell Biol 2024; 223:e202312069. [PMID: 38967608 PMCID: PMC11223164 DOI: 10.1083/jcb.202312069] [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: 12/20/2023] [Revised: 05/22/2024] [Accepted: 06/07/2024] [Indexed: 07/06/2024] Open
Abstract
Peroxisomes are membrane-bound organelles harboring metabolic enzymes. In humans, peroxisomes are required for normal development, yet the genes regulating peroxisome function remain unclear. We performed a genome-wide CRISPRi screen to identify novel factors involved in peroxisomal homeostasis. We found that inhibition of RNF146, an E3 ligase activated by poly(ADP-ribose), reduced the import of proteins into peroxisomes. RNF146-mediated loss of peroxisome import depended on the stabilization and activity of the poly(ADP-ribose) polymerases TNKS and TNKS2, which bind the peroxisomal membrane protein PEX14. We propose that RNF146 and TNKS/2 regulate peroxisome import efficiency by PARsylation of proteins at the peroxisome membrane. Interestingly, we found that the loss of peroxisomes increased TNKS/2 and RNF146-dependent degradation of non-peroxisomal substrates, including the β-catenin destruction complex component AXIN1, which was sufficient to alter the amplitude of β-catenin transcription. Together, these observations not only suggest previously undescribed roles for RNF146 in peroxisomal regulation but also a novel role in bridging peroxisome function with Wnt/β-catenin signaling during development.
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Affiliation(s)
- Jonathan T. Vu
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Katherine U. Tavasoli
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Connor J. Sheedy
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Soham P. Chowdhury
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Lori Mandjikian
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Julien Bacal
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Meghan A. Morrissey
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Chris D. Richardson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Brooke M. Gardner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
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Ferdoush J, Kadir RA, Ogle M, Saha A. Regulation of eukaryotic transcription initiation in response to cellular stress. Gene 2024; 924:148616. [PMID: 38795856 DOI: 10.1016/j.gene.2024.148616] [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: 11/22/2023] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
Transcription initiation is a vital step in the regulation of eukaryotic gene expression. It can be dysregulated in response to various cellular stressors which is associated with numerous human diseases including cancer. Transcription initiation is facilitated via many gene-specific trans-regulatory elements such as transcription factors, activators, and coactivators through their interactions with transcription pre-initiation complex (PIC). These trans-regulatory elements can uniquely facilitate PIC formation (hence, transcription initiation) in response to cellular nutrient stress. Cellular nutrient stress also regulates the activity of other pathways such as target of rapamycin (TOR) pathway. TOR pathway exhibits distinct regulatory mechanisms of transcriptional activation in response to stress. Like TOR pathway, the cell cycle regulatory pathway is also found to be linked to transcriptional regulation in response to cellular stress. Several transcription factors such as p53, C/EBP Homologous Protein (CHOP), activating transcription factor 6 (ATF6α), E2F, transforming growth factor (TGF)-β, Adenomatous polyposis coli (APC), SMAD, and MYC have been implicated in regulation of transcription of target genes involved in cell cycle progression, apoptosis, and DNA damage repair pathways. Additionally, cellular metabolic and oxidative stressors have been found to regulate the activity of long non-coding RNAs (lncRNA). LncRNA regulates transcription by upregulating or downregulating the transcription regulatory proteins involved in metabolic and cell signaling pathways. Numerous human diseases, triggered by chronic cellular stressors, are associated with abnormal regulation of transcription. Hence, understanding these mechanisms would help unravel the molecular regulatory insights with potential therapeutic interventions. Therefore, here we emphasize the recent advances of regulation of eukaryotic transcription initiation in response to cellular stress.
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Affiliation(s)
- Jannatul Ferdoush
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA.
| | - Rizwaan Abdul Kadir
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Matthew Ogle
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Ayan Saha
- Department of Bioinformatics and Biotechnology, Asian University for Women, Chattogram, Bangladesh
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72
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Li D, Jia J, Zeng H, Zhong X, Chen H, Yi C. Efficacy of exercise rehabilitation for managing patients with Alzheimer's disease. Neural Regen Res 2024; 19:2175-2188. [PMID: 38488551 PMCID: PMC11034587 DOI: 10.4103/1673-5374.391308] [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: 06/26/2023] [Revised: 10/16/2023] [Accepted: 11/25/2023] [Indexed: 04/24/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive and degenerative neurological disease characterized by the deterioration of cognitive functions. While a definitive cure and optimal medication to impede disease progression are currently unavailable, a plethora of studies have highlighted the potential advantages of exercise rehabilitation for managing this condition. Those studies show that exercise rehabilitation can enhance cognitive function and improve the quality of life for individuals affected by AD. Therefore, exercise rehabilitation has been regarded as one of the most important strategies for managing patients with AD. Herein, we provide a comprehensive analysis of the currently available findings on exercise rehabilitation in patients with AD, with a focus on the exercise types which have shown efficacy when implemented alone or combined with other treatment methods, as well as the potential mechanisms underlying these positive effects. Specifically, we explain how exercise may improve the brain microenvironment and neuronal plasticity. In conclusion, exercise is a cost-effective intervention to enhance cognitive performance and improve quality of life in patients with mild to moderate cognitive dysfunction. Therefore, it can potentially become both a physical activity and a tailored intervention. This review may aid the development of more effective and individualized treatment strategies to address the challenges imposed by this debilitating disease, especially in low- and middle-income countries.
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Affiliation(s)
- Dan Li
- Department of Pathology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, China
| | - Jinning Jia
- Department of Pathology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, China
| | - Haibo Zeng
- Department of Pathology, Huichang County People’s Hospital, Ganzhou, Jiangxi Province, China
| | - Xiaoyan Zhong
- Department of Pathology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, China
| | - Hui Chen
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Chenju Yi
- Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong Province, China
- Shenzhen Key Laboratory of Chinese Medicine Active Substance Screening and Translational Research, Shenzhen, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong Province, China
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73
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Amo-Aparicio J, Dinarello CA, Lopez-Vales R. Metabolic reprogramming of the inflammatory response in the nervous system: the crossover between inflammation and metabolism. Neural Regen Res 2024; 19:2189-2201. [PMID: 38488552 PMCID: PMC11034585 DOI: 10.4103/1673-5374.391330] [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: 08/24/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 04/24/2024] Open
Abstract
Metabolism is a fundamental process by which biochemicals are broken down to produce energy (catabolism) or used to build macromolecules (anabolism). Metabolism has received renewed attention as a mechanism that generates molecules that modulate multiple cellular responses. This was first identified in cancer cells as the Warburg effect, but it is also present in immunocompetent cells. Studies have revealed a bidirectional influence of cellular metabolism and immune cell function, highlighting the significance of metabolic reprogramming in immune cell activation and effector functions. Metabolic processes such as glycolysis, oxidative phosphorylation, and fatty acid oxidation have been shown to undergo dynamic changes during immune cell response, facilitating the energetic and biosynthetic demands. This review aims to provide a better understanding of the metabolic reprogramming that occurs in different immune cells upon activation, with a special focus on central nervous system disorders. Understanding the metabolic changes of the immune response not only provides insights into the fundamental mechanisms that regulate immune cell function but also opens new approaches for therapeutic strategies aimed at manipulating the immune system.
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Affiliation(s)
| | | | - Ruben Lopez-Vales
- Institute of Neurosciences, and Department Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Spain
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74
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Jiang D, Chen R, Wang L, Xu G. Screening, expression and anti-tumor functional identification of anti-LAG-3 nanobodies. Protein Expr Purif 2024; 222:106522. [PMID: 38851552 DOI: 10.1016/j.pep.2024.106522] [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: 04/22/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024]
Abstract
OBJECTIVE To screen and obtain specific anti-lymphocyte activation gene-3 (LAG3) nanobody sequences, purify and express recombinant anti-LAG3 nanobody, and verify its effect on promoting T cells to kill tumor cells. METHODS Based on the camel derived natural nanobody phage display library constructed by the research group, the biotinylated LAG3 antigen was used as the target, and the anti-LAG3 nanobody sequences were screened by biotin-streptavidin liquid phase screening, phage-ELISA and sequencing. The sequence-conjμgated human IgG1 Fc fragment was obtained, the recombinant anti-LAG3 nanobody expression vector was constructed, the expression of the recombinant anti-LAG3 nanobody was induced by IPTG and purified, and the characteristics and functions of the recombinant anti-LAG3 nanobody were verified by SDS-PAGE, Western blot, cytotoxicity assay, etc. RESULTS: One anti-LAG3 nanobody sequence was successfully screened, and the corresponding recombinant anti-LAG3 nanobody-expressing bacteria were constructed. The results of SDS-PAGE, Western blot and cytotoxicity assay showed that the recombinant anti-LAG3 nanobody was successfully expressed, which was specific, and it could promote the killing ability of T cells against tumor cells, and the optimal concentration was 200 μg/mL. CONCLUSION The recombinant anti-LAG3 nanobody screened and expressed has specific and auxiliary anti-tumor cell effects, which lays a foundation for its subsequent application.
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Affiliation(s)
- Dan Jiang
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong, 523808, China
| | - Rui Chen
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong, 523808, China
| | - Liyan Wang
- Ningxia Chinese Medicine Research Centre, Yinchuan, Ningxia, 750000, China
| | - Guangxian Xu
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong, 523808, China.
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75
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Soleimani A, Alizadeh H. Unlocking the potential of Extensin Signal peptide and Elastin-like polypeptide tag fused to Shigella dysenteriae's IpaDSTxB to improve protein expression and purification in Nicotiana tabacum and Medicagosativa. Protein Expr Purif 2024; 222:106521. [PMID: 38852714 DOI: 10.1016/j.pep.2024.106521] [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: 04/29/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
Plants are often seen as a potent tool in the recombinant protein production industry. However, unlike bacterial expression, it is not a popular method due to the low yield and difficulty of protein extraction and purification. Therefore, developing a new high efficient and easy to purify platform is crucial. One of the best approaches to make extraction easier is to utilize the Extensin Signal peptide (EXT) to translocate the recombinant protein to the outside of the cell, along with incorporating an Elastin-like polypeptide tag (ELP) to enhance purification and accumulation rates. In this research, we transiently expressed Shigella dysenteriae's IpaDSTxB fused to both NtEXT and ELP in both Nicotiana tabacum and Medicago sativa. Our results demonstrated that N. tabacum, with an average yield of 6.39 ng/μg TSP, outperforms M. sativa, which had an average yield of 3.58 ng/μg TSP. On the other hand, analyzing NtEXT signal peptide indicated that merging EXT to the constructs facilitates translocation of IpaDSTxB to the apoplast by 78.4% and 65.9% in N. tabacum and M. sativa, respectively. Conversely, the mean level for constructs without EXT was below 25% for both plants. Furthermore, investigation into the orientation of ELP showed that merging it to the C-terminal of IpaDSTxB leads to a higher accumulation rate in both N. tabacum and M. sativa by 1.39 and 1.28 times, respectively. It also facilitates purification rate by over 70% in comparison to 20% of the 6His tag. The results show a highly efficient and easy to purify platform for the expression of heterologous proteins in plant.
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Affiliation(s)
- AmirMohammad Soleimani
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
| | - Houshang Alizadeh
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
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76
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Su Y, Xu T, Sun Y. Evolutionarily conserved Otub1 suppresses antiviral immune response by promoting Irf3 proteasomal degradation in miiuy croaker, Miichthys miiuy. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 159:105218. [PMID: 38914152 DOI: 10.1016/j.dci.2024.105218] [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: 03/18/2024] [Revised: 06/02/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Increasing evidence has been shown that OTUB1, a member of OTU deubiquitinases, is of importance in regulating the immune system. However, its molecular identification and functional characterization in teleosts are still rarely known. In this work, we cloned the otub1 of miiuy croaker (Miichthys miiuy), analyzed its sequence, structure, and evolution at genetic and protein levels, and determined its function in the antiviral immune response. The complete open reading frame (ORF) of miiuy croaker otub1 is 843 bp in length, encoding 280 amino acids. Miiuy croaker Otub1 has an OTU domain at the carboxyl terminus, which is a common functional domain that exists in OTU deubiquitinases. Molecular characteristics and evolution analysis results indicated that miiuy croaker Otub1, especially its functional domain, is highly conserved during evolution. The luciferase reporter assays showed that miiuy croaker Otub1 could significantly inhibit the poly(I:C) and Irf3-induced IFN1 and IFN-stimulated response element (ISRE) activation. Further experiments showed that miiuy croaker Otub1 decreases Irf3 protein abundance by promoting its proteasomal degradation. These data suggest that the evolutionarily conserved Otub1 acts as a suppressor in controlling antiviral immune response by promoting Irf3 proteasomal degradation in miiuy croaker.
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Affiliation(s)
- Yanli Su
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai, China.
| | - Yuena Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, China.
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77
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Li YR, Ling LB, Chao A, Fugmann SD, Yang SY. Transient chromatin decompaction at the start of D. melanogaster male embryonic germline development. Life Sci Alliance 2024; 7:e202302401. [PMID: 38991729 PMCID: PMC11239976 DOI: 10.26508/lsa.202302401] [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: 09/27/2023] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
Embryonic germ cells develop rapidly to establish the foundation for future developmental trajectories, and in this process, they make critical lineage choices including the configuration of their unique identity and a decision on sex. Here, we use single-cell genomics patterns for the entire embryonic germline in Drosophila melanogaster along with the somatic gonadal precursors after embryonic gonad coalescence to investigate molecular mechanisms involved in the setting up and regulation of the germline program. Profiling of the early germline chromatin landscape revealed sex- and stage-specific features. In the male germline immediately after zygotic activation, the chromatin structure underwent a brief remodeling phase during which nucleosome density was lower and deconcentrated from promoter regions. These findings echoed enrichment analysis results of our genomics data in which top candidates were factors with the ability to mediate large-scale chromatin reorganization. Together, they point to the importance of chromatin regulation in the early germline and raise the possibility of a conserved epigenetic reprogramming-like process required for proper initiation of germline development.
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Affiliation(s)
- Yi-Ru Li
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Li Bin Ling
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Angel Chao
- https://ror.org/02dnn6q67 Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sebastian D Fugmann
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/00d80zx46 Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/02dnn6q67 Department of Nephrology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shu Yuan Yang
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/00d80zx46 Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/02dnn6q67 Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
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78
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Kron NS, Fieber LA, Baker L, Campbell C, Schmale MC. Host response to Aplysia Abyssovirus 1 in nervous system and gill. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 159:105211. [PMID: 38885747 DOI: 10.1016/j.dci.2024.105211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
The California sea hare (Aplysia californica) is a model for age associated cognitive decline. Recent researched identified a novel nidovirus, Aplysia Abyssovirus 1, with broad tropism enriched in the Aplysia nervous system. This virus is ubiquitous in wild and maricultured, young and old animals without obvious pathology. Here we re-evaluated gene expression data from several previous studies to investigate differential expression in the nervous system and gill in response to virus and aging as well as the mutational spectrum observed in the viral sequences obtained from these datasets. Viral load and age were highly correlated, indicating persistent infection. Upregulated genes in response to virus were enriched for immune genes and signatures of ER and proteostatic stress, while downregulated genes were enriched for mitochondrial metabolism. Differential expression with respect to age suggested increased iron accumulation and decreased glycolysis, fatty acid metabolism, and proteasome function. Interaction of gene expression trends associated with viral infection and aging suggest that viral infection likely plays a role in aging in the Aplysia nervous system. Mutation analysis of viral RNA identified signatures suggesting ADAR and AID/APOBEC like deaminase act as part of Aplysia anti-viral defense.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA.
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
| | - Lydia Baker
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
| | | | - Michael C Schmale
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
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79
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Zhao H, Xu X, Yuan B, Qi B, Li Y. Fibrillation of soy protein isolate in the presence of metal ions: Structure and gelation behavior. Food Chem 2024; 453:139672. [PMID: 38805941 DOI: 10.1016/j.foodchem.2024.139672] [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: 03/01/2024] [Revised: 04/24/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024]
Abstract
The structure and functional properties of protein fibrils are closely related to environmental factors in fibrillation. Herein, soy protein isolate fibrils (SPIFs, 22 mg/mL) were prepared under acid-heating conditions in the presence of 100 mM metal ions (K+, Na+, Ca2+, Mg2+, and Fe3+). Except for Fe3+, fibrillation and subsequent larger fibril aggregates were promoted, ultimately leading to gel formation. Compared with K+ or Na+, the addition of Ca2+ or Mg2+ resulted in more organized SPIF structures with increased β-sheet contents and higher ThT fluorescence intensities. Furthermore, both of them resulted in longer fibrils with an average contour length of 700-800 nm, which significantly enhanced the storage modulus. However, the presence of Fe3+ accelerated protein hydrolysis and inhibited SPIF formation, resulting in samples consistently exhibited liquid behavior. These findings provide a foundation for understanding the influence of metal ions on regulating the fibrillation and gelling properties of SPIFs.
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Affiliation(s)
- Hekai Zhao
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xinru Xu
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Bingbing Yuan
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Baokun Qi
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
| | - Yang Li
- College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Chongnqing Research Institute, Harbin Institute of Technology, Chongqing 401135, China.
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80
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Wang XF, Li T, Yang M, Huang Y. Periorbital purpura can be the only initial symptom of primary light chain amyloidosis: A case report. World J Clin Cases 2024; 12:5946-5951. [DOI: 10.12998/wjcc.v12.i26.5946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Primary light chain amyloidosis is a rare and complex disease with complex clinical features and is highly susceptible to misdiagnosis and underdiagnosis in the early stages.
CASE SUMMARY We report a case of a 47-year-old female patient whose only initial symptom was periorbital purpura, which was not taken seriously enough. As the disease progressed, pleural effusion gradually appeared, and after systematic diagnosis and treatment, she was diagnosed with “primary light chain amyloidosis”. She achieved rapid hematological remission after treatment with a daratumumab + bortezomib + cyclophosphamide + dexamethasone regimen.
CONCLUSION Periorbital purpura can be the only initial symptom of primary light chain amyloidosis; we should pay attention to the cases where the initial clinical symptoms are only periorbital purpura.
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Affiliation(s)
- Xiu-Feng Wang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang 453100, Henan Province, China
| | - Ting Li
- Department of Blood Purification, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang 453100, Henan Province, China
| | - Man Yang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang 453100, Henan Province, China
| | - Yan Huang
- Department of Hematology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang 453100, Henan Province, China
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81
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Denizci E, Altun G, Kaplan S. Morphological evidence for the potential protective effects of curcumin and Garcinia kola against diabetes in the rat hippocampus. Brain Res 2024; 1839:149020. [PMID: 38788929 DOI: 10.1016/j.brainres.2024.149020] [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: 04/11/2024] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 05/26/2024]
Abstract
This research investigated the effects of sciatic nerve transection and diabetes on the hippocampus, and the protective effects of Garcinia kola and curcumin. Thirty-five adults male Wistar albino rats were divided into five groups: a control group (Cont), a transected group (Sham group), a transected + diabetes mellitus group (DM), a transected + diabetes mellitus + Garcinia kola group (DM + GK), and a transected + DM + curcumin group (DM + Cur), each containing seven animals. The experimental diabetes model was created with the intraperitoneal injection of a single dose of streptozotocin. No procedure was applied to the Cont group, while sciatic nerve transection was performed on the other groups. Garcinia kola was administered to the rats in DM + GK, and curcumin to those in DM + Cur. Cardiac perfusion was performed at the end of the experimental period. Brain tissues were dissected for stereological, histopathological, and immunohistochemical evaluations. The volume ratios of hippocampal layers to the entire hippocampus volume were compared between the groups. Anti-S100, anti-caspase 3, and anti-SOX 2 antibodies were used for immunohistochemical analysis. No statistically significant difference was observed in the volume ratios of the four hippocampal layers. However, the volume ratio of the stratum lucidum was higher in the Sham, DM, and DM + Cur groups compared to the Cont group. While curcumin exhibited a protective effect on hippocampal tissue following diabetes induction, Garcinia kola had only a weak protective effect. Increased cell density and nuclear deterioration due to diabetes and nerve transection can be partially ameliorated by treatment with Garcinia kola and curcumin.
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Affiliation(s)
- Eda Denizci
- Department of Histology and Embryology, Ondokuz Mayıs University, Samsun 55139, Turkey
| | - Gamze Altun
- Department of Histology and Embryology, Ondokuz Mayıs University, Samsun 55139, Turkey
| | - Süleyman Kaplan
- Department of Histology and Embryology, Ondokuz Mayıs University, Samsun 55139, Turkey; Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
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82
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Queirós V, Azeiteiro UM, Santos JL, Alonso E, Soares AMVM, Barata C, Freitas R. Unravelling biochemical responses in the species Mytilus galloprovincialis exposed to the antineoplastics ifosfamide and cisplatin under different temperature scenarios. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173668. [PMID: 38839013 DOI: 10.1016/j.scitotenv.2024.173668] [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: 04/26/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
This study investigates the chronic impact of two of the most widely consumed antineoplastic drugs, Ifosfamide (IF) and Cisplatin (CDDP), on the bivalve species Mytilus galloprovincialis under current (17 °C) and predicted warming conditions (21 °C). Accompanying the expected increase in worldwide cancer incidence, antineoplastics detection in the aquatic environment is also expected to rise. Mussels were exposed to varying concentrations of IF (10, 100, 500 ng/L) and CDDP (10, 100, 1000 ng/L) for 28 days. Biochemical analyses focused on metabolic, antioxidant and biotransformation capacities, cellular damage, and neurotoxicity. Results showed temperature-dependent variations in biochemical responses. Metabolic capacity remained stable in mussels exposed to IF, while CDDP exposure increased it at 1000 ng/L for both temperatures. Antioxidant enzyme activities were unaffected by IF, but CDDP activated them, particularly at 21 °C. Biotransformation capacity was unchanged by IF but enhanced by CDDP. Nevertheless, cellular damage occurred at CDDP concentrations above 100 ng/L, regardless of temperature. Integrated biomarker responses highlighted CDDP's greater impact, emphasizing the critical role of temperature in shaping organismal responses and underscoring the complexity of environmental stressor interactions.
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Affiliation(s)
- Vanessa Queirós
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ulisses M Azeiteiro
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Juan Luis Santos
- Departamento de Química Analítica, Escuela Politécnica Superior, Universidad de Sevilla, C/ Virgen de África 7, 41011 Sevilla, Spain
| | - Esteban Alonso
- Departamento de Química Analítica, Escuela Politécnica Superior, Universidad de Sevilla, C/ Virgen de África 7, 41011 Sevilla, Spain
| | - Amadeu M V M Soares
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carlos Barata
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, C/ Jordi Girona 18, 08034 Barcelona, Spain
| | - Rosa Freitas
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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83
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Budischowsky D, Sulaeva I, Støpamo FG, Lehrhofer AF, Hettegger H, Várnai A, Eijsink VGH, Rosenau T, Potthast A. Oxidized reducing ends in celluloses: Quantitative profiling relative to molar mass distribution by fluorescence labeling. Carbohydr Polym 2024; 340:122210. [PMID: 38858031 DOI: 10.1016/j.carbpol.2024.122210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 06/12/2024]
Abstract
Fluorescence labeling with N-(1-naphthyl)ethylenediamine is highly effective for quantifying oxidized reducing end groups (REGs) in cellulosic materials. When combined with size exclusion chromatography in DMAc/LiCl, along with fluorescence / multiple-angle laser light scattering / refractive index detection, a detailed profile of C1-oxidized REGs relative to the molecular weight distribution of the cellulosic material can be obtained. In this work, the derivatization process was extensively optimized, to be carried out heterogeneously in the solvent N-methyl-2-pyrrolidone. Furthermore, we show that to achieve high selectivity for carboxyl groups at the C1 position, keto and aldehyde groups need to be selectively reduced (e.g., by NaBH4), and carboxyl groups other than at C1 need to be blocked (e.g., by methylation with (trimethylsilyl)diazomethane) prior to fluorescence labeling of carboxyl groups at C1 position. Finally, we demonstrate the practical value of the analytical method by measuring the content of the C1-oxidized REGs in cellulose samples after chemical (by Pinnick oxidation) or enzymatic (by treatment with C1-oxidizing LPMO enzymes) oxidation of various pulp samples.
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Affiliation(s)
- David Budischowsky
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, A-1190 Vienna, Austria.
| | - Irina Sulaeva
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, A-1190 Vienna, Austria; Core Facility Analysis of Lignocellulosics (ALICE), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 24, A-3430 Tulln, Austria.
| | - Fredrik G Støpamo
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432 Ås, Norway.
| | - Anna F Lehrhofer
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, A-1190 Vienna, Austria.
| | - Hubert Hettegger
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, A-1190 Vienna, Austria; Christian Doppler Laboratory for Cellulose High-Tech Materials, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 24, A-3430 Tulln, Austria.
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432 Ås, Norway.
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432 Ås, Norway.
| | - Thomas Rosenau
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, A-1190 Vienna, Austria.
| | - Antje Potthast
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, A-1190 Vienna, Austria.
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84
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Navanukraw P, Chotimanukul S, Udomthanaisit L, Setthawong P, Saehlee S, Seetaha S, Choowongkomon K, Chatdarong K. Antibody fragments targeting the extracellular domain of follicular stimulating hormone receptor for contraception in male dogs and cats. Theriogenology 2024; 226:110-119. [PMID: 38875921 DOI: 10.1016/j.theriogenology.2024.06.005] [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: 05/05/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024]
Abstract
The increased LH levels resulting from the absence of negative feedback after castration has been linked to long-term health issues. A need exists for an alternative contraceptive agent that functions without interfering the LH pathways. This study aimed to develop antibody fragments against the follicular-stimulating hormone receptor (anti-FSHr) using phage-display technology and evaluate its effects on Sertoli cell functions. Phage clones against the extracellular domain of dog and cat FSHr selected from an antibody fragment phagemid library were analyzed for binding kinetics by surface plasmon resonance. Sertoli cells were isolated from testes of adult animals (five dogs and five cats). Efficacy test was performed by treating Sertoli cell cultures (SCCs) with anti-FSHr antibody fragments compared with untreated in triplicates. Expressions of androgen binding protein (ABP), inhibin subunit beta B (IHBB) and vascular endothelial growth factor A (VEGFA) mRNA in SCCs were quantified by RT-qPCR. The results demonstrated that the molecular weight of the purified dog and cat anti-FSHr antibody fragment was 25 kDa and 15 kDa, respectively. Based on protein molecular weight, the antibody fragment of dogs and cats was therefore, so-called single-chain variable fragments (scFv) and nanobody (nb), respectively. The binding affinity with dissociation constant (KD) was 2.32 × 10-7 M and 2.83 × 10-9 M for dog and cat anti-FSHr antibody fragments, respectively. The cross-binding kinetic interactions between the dog anti-FSHr scFv and the cat ECD of FSHr could not be fitted to the curves to determine the binding kinetics. However, the cross-binding affinity KD between the cat anti-FSHr nb and the dog ECD FSHr was 1.75 × 10-4 M. The mRNA expression of ABP, IHBB and VEGFA in SCCs was less (P < 0.05) in both dogs (12.26, 4.07 and 5.11 folds, respectively) and cats (39.53, 14.07 and 20.29 folds, respectively) treated with anti-FSHr antibody fragments, indicating the Sertoli cell functions were suppressed. In conclusion, this study demonstrated the establishment of species-specific antibody fragments against FSHr in SCCs for dogs and cats. The fragment proteins illustrate potential to be developed as non-surgical contraceptive agent targeting FSHr in companion animals.
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Affiliation(s)
- Pakpoom Navanukraw
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Sroisuda Chotimanukul
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Larindhorn Udomthanaisit
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Piyathip Setthawong
- Department of Physiology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Siriwan Saehlee
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Supaphorn Seetaha
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | - Kaywalee Chatdarong
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
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85
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Koll R, Theilen J, Hauten E, Woodhouse JN, Thiel R, Möllmann C, Fabrizius A. Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173656. [PMID: 38830414 DOI: 10.1016/j.scitotenv.2024.173656] [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: 03/04/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.
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Affiliation(s)
- Raphael Koll
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany.
| | - Jesse Theilen
- University of Hamburg, Department of Biology, Biodiversity Research, Germany
| | - Elena Hauten
- University of Hamburg, Institute of Marine Ecosystem and Fishery Science, Marine ecosystem dynamics, Germany
| | - Jason Nicholas Woodhouse
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Microbial and phytoplankton Ecology, Germany
| | - Ralf Thiel
- Leibniz Institute for the Analysis of Biodiversity Change (LIB) - Hamburg site, Centre for Taxonomy & Morphology, Zoological Museum, Germany; University of Hamburg, Department of Biology, Biodiversity Research, Germany
| | - Christian Möllmann
- University of Hamburg, Institute of Marine Ecosystem and Fishery Science, Marine ecosystem dynamics, Germany
| | - Andrej Fabrizius
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany
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86
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Zhai S, Tan Y, Zhu C, Zhang C, Gao Y, Mao Q, Zhang Y, Duan H, Yin Y. PepExplainer: An explainable deep learning model for selection-based macrocyclic peptide bioactivity prediction and optimization. Eur J Med Chem 2024; 275:116628. [PMID: 38944933 DOI: 10.1016/j.ejmech.2024.116628] [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: 04/17/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024]
Abstract
Macrocyclic peptides possess unique features, making them highly promising as a drug modality. However, evaluating their bioactivity through wet lab experiments is generally resource-intensive and time-consuming. Despite advancements in artificial intelligence (AI) for bioactivity prediction, challenges remain due to limited data availability and the interpretability issues in deep learning models, often leading to less-than-ideal predictions. To address these challenges, we developed PepExplainer, an explainable graph neural network based on substructure mask explanation (SME). This model excels at deciphering amino acid substructures, translating macrocyclic peptides into detailed molecular graphs at the atomic level, and efficiently handling non-canonical amino acids and complex macrocyclic peptide structures. PepExplainer's effectiveness is enhanced by utilizing the correlation between peptide enrichment data from selection-based focused library and bioactivity data, and employing transfer learning to improve bioactivity predictions of macrocyclic peptides against IL-17C/IL-17 RE interaction. Additionally, PepExplainer underwent further validation for bioactivity prediction using an additional set of thirteen newly synthesized macrocyclic peptides. Moreover, it enabled the optimization of the IC50 of a macrocyclic peptide, reducing it from 15 nM to 5.6 nM based on the contribution score provided by PepExplainer. This achievement underscores PepExplainer's skill in deciphering complex molecular patterns, highlighting its potential to accelerate the discovery and optimization of macrocyclic peptides.
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Affiliation(s)
- Silong Zhai
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yahong Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Cheng Zhu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Chengyun Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yan Gao
- Qilu Institute of Technology, Jinan, 250200, China
| | - Qingyi Mao
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Hongliang Duan
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, 999078, China.
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China; Shandong Research Institute of Industrial Technology, Jinan, 250101, China.
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87
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Arthur R, Jamwal S, Kumar P. A review on polyamines as promising next-generation neuroprotective and anti-aging therapy. Eur J Pharmacol 2024; 978:176804. [PMID: 38950837 DOI: 10.1016/j.ejphar.2024.176804] [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: 03/25/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Neurodegenerative disorders are diseases characterized by progressive degeneration of neurons and associated structures and are a major global issue growing more widespread as the global population's average age increases. Despite several investigations on their etiology, the specific cause of these disorders remains unknown. However, there are few symptomatic therapies to treat these disorders. Polyamines (PAs) (putrescine, spermidine, and spermine) are being studied for their role in neuroprotection, aging and cognitive impairment. They are ubiquitous polycations which have relatively higher concentrations in the brain and possess pleiotropic biochemical activities, including regulation of gene expression, ion channels, mitochondria Ca2+ transport, autophagy induction, programmed cell death, and many more. Their cellular content is tightly regulated, and substantial evidence indicates that their altered levels and metabolism are strongly implicated in aging, stress, cognitive dysfunction, and neurodegenerative disorders. In addition, dietary polyamine supplementation has been reported to induce anti-aging effects, anti-oxidant effects, and improve locomotor abnormalities, and cognitive dysfunction. Thus, restoring the polyamine level is considered a promising pharmacological strategy to counteract neurodegeneration. This review highlights PAs' physiological role and the molecular mechanism underpinning their proposed neuroprotective effect in aging and neurodegenerative disorders.
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Affiliation(s)
- Richmond Arthur
- Department of Pharmacology, Central University of Punjab, Bathinda, India
| | - Sumit Jamwal
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Bathinda, India.
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88
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Wang ZY, Gao ST, Gou XJ, Qiu FR, Feng Q. IL-1 receptor-associated kinase family proteins: An overview of their role in liver disease. Eur J Pharmacol 2024; 978:176773. [PMID: 38936453 DOI: 10.1016/j.ejphar.2024.176773] [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: 03/19/2024] [Revised: 06/16/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
The interleukin-1 receptor-associated kinase (IRAK) family is a group of serine-threonine kinases that regulates various cellular processes via toll-like receptor (TLR)/interleukin-1 receptor (IL1R)-mediated signaling. The IRAK family comprises four members, including IRAK1, IRAK2, IRAK3, and IRAK4, which play an important role in the expression of various inflammatory genes, thereby contributing to the inflammatory response. IRAKs are key proteins in chronic and acute liver diseases, and recent evidence has implicated IRAK family proteins (IRAK1, IRAK3, and IRAK4) in the progression of liver-related disorders, including alcoholic liver disease, non-alcoholic steatohepatitis, hepatitis virus infection, acute liver failure, liver ischemia-reperfusion injury, and hepatocellular carcinoma. In this article, we provide a comprehensive review of the role of IRAK family proteins and their associated inflammatory signaling pathways in the pathogenesis of liver diseases. The purpose of this study is to explore whether IRAK family proteins can serve as the main target for the treatment of liver related diseases.
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Affiliation(s)
- Zhuo-Yuan Wang
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Si-Ting Gao
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xiao-Jun Gou
- Central Laboratory, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine of Shanghai, Shanghai University of Traditional Chinese Medicine, Shanghai, 201999, China
| | - Fu-Rong Qiu
- Laboratory of Clinical Pharmacokinetics, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Qin Feng
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Central Laboratory, ShuGuang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, 201203, China; Key Laboratory of Liver and Kidney Diseases, Shanghai University of Traditional Chinese Medicine, Ministry of Education, Shanghai, 201203, China.
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89
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Li H, Liu BJ, Xu J, Song SS, Ba R, Zhang J, Huan XJ, Wang D, Miao ZH, Liu T, He JX, Xiong B. Design, synthesis, and biological evaluation of pyrido[2,3-d]pyrimidin-7(8H)-one derivatives as potent USP1 inhibitors. Eur J Med Chem 2024; 275:116568. [PMID: 38889606 DOI: 10.1016/j.ejmech.2024.116568] [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: 04/20/2024] [Revised: 05/24/2024] [Accepted: 06/02/2024] [Indexed: 06/20/2024]
Abstract
USP1 has emerged as a novel and potential target for drug discovery in single therapeutic agents or combination with chemotherapy and molecular targeted therapy. In this study, based on the disclosed structure of ML323 and KSQ-4279, we designed and synthesized a series of pyrido[2,3-d]pyrimidin-7(8H)-one derivatives as potent USP1 inhibitors by cyclization strategy and the systematic structure-activity relationship exploration was conducted. The representative compounds 1k, 1m and 2d displayed excellent USP1/UAF inhibition and exhibited strong antiproliferation effect in NCI-H1299 cells. Further flow cytometry analysis revealed that they could arrest breast cancer cells MDA-MB-436 in the S phase. Inhibition mechanism study of compound 1m indicated these derivatives acted as reversible and noncompetitive USP1 inhibitors. Of note, the combination of compound 1m with PARP inhibitor olaparib generated enhanced cell killing in olaparib-resistant MDA-MB-436/OP cells, and compound 1m exhibited excellent oral pharmacokinetic properties in mice. Overall, our efforts may provide a reliable basis for the development of novel USP1 inhibitor as a single therapeutic agent and in combination with PARP inhibitors.
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Affiliation(s)
- Hongrui Li
- Shenyang Pharmaceutical University, 103 Wenhua Rd, Shenyang, Liaoning, 110016, PR China; Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, PR China; State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China; Yangtze Delta Drug Advanced Research Institute, 100 Dongtinghu Road, Nantong, 226133, PR China
| | - Ben-Jin Liu
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, PR China; State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, PR China
| | - Jiahao Xu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, PR China; State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China; Yangtze Delta Drug Advanced Research Institute, 100 Dongtinghu Road, Nantong, 226133, PR China; School of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, PR China
| | - Shan-Shan Song
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, PR China
| | - Ruixian Ba
- Shenyang Pharmaceutical University, 103 Wenhua Rd, Shenyang, Liaoning, 110016, PR China; Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, PR China; State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China; Yangtze Delta Drug Advanced Research Institute, 100 Dongtinghu Road, Nantong, 226133, PR China
| | - Junjie Zhang
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, PR China; State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Xia-Juan Huan
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China; State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, PR China
| | - Dun Wang
- Shenyang Pharmaceutical University, 103 Wenhua Rd, Shenyang, Liaoning, 110016, PR China
| | - Ze-Hong Miao
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, PR China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China; State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, PR China
| | - Tongchao Liu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, PR China; State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China.
| | - Jin-Xue He
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China; State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, PR China.
| | - Bing Xiong
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, PR China; State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China; Yangtze Delta Drug Advanced Research Institute, 100 Dongtinghu Road, Nantong, 226133, PR China.
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90
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Chen J, Gao L. SLC7A11-mediated cystine import protects against NDUFS7 deficiency-induced cell death in HEK293T cells. Biochem Biophys Res Commun 2024; 723:150178. [PMID: 38823363 DOI: 10.1016/j.bbrc.2024.150178] [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: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
Cell models of mitochondrial complex Ⅰ (CⅠ) deficiency display significant elevations in reactive oxygen species (ROS) levels and an increase in cellular apoptosis. However, the underlying mechanisms governing anti-apoptotic processes in CⅠ-deficient cells remain elusive. Here, we introduced a mutation in NDUFS7, a crucial subunit of CI, in HEK293T cells and found that the absence of NDUFS7 resulted in reduced cell proliferation, elevated cell death, and increased susceptibility to oxidative stress. Mechanismly, we revealed that the upregulation of SLC7A11 played a crucial role in mitigating cell death resulting from NDUFS7 deficiency. Specifically, the increased expression of SLC7A11 enhanced cystine import, which subsequently reduced cell death by promoting the biosynthesis of reduced glutathione (GSH). Collectively, our findings suggest that SLC7A11-mediated cystine import, representing a novel pathway independent of NADPH production, plays a vital role in protection against NDUFS7 deficiency-induced cell death. This novel pathway provides potential insights into the understanding of pathogenic mechanisms and the therapeutic management of mitochondrial disorders associated with CⅠ deficiency.
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Affiliation(s)
- Jieli Chen
- Clinical Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Liuze Gao
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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91
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Sun QA, Grimmett ZW, Hess DT, Perez LG, Qian Z, Chaube R, Venetos NM, Plummer BN, Laurita KR, Premont RT, Stamler JS. Physiological role for S-nitrosylation of RyR1 in skeletal muscle function and development. Biochem Biophys Res Commun 2024; 723:150163. [PMID: 38820626 DOI: 10.1016/j.bbrc.2024.150163] [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: 04/17/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024]
Abstract
Excitation-contraction coupling in skeletal muscle myofibers depends upon Ca2+ release from the sarcoplasmic reticulum through the ryanodine receptor/Ca2+-release channel RyR1. The RyR1 contains ∼100 Cys thiols of which ∼30 comprise an allosteric network subject to posttranslational modification by S-nitrosylation, S-palmitoylation and S-oxidation. However, the role and function of these modifications is not understood. Although aberrant S-nitrosylation of multiple unidentified sites has been associated with dystrophic diseases, malignant hyperthermia and other myopathic syndromes, S-nitrosylation in physiological situations is reportedly specific to a single (1 of ∼100) Cys in RyR1, Cys3636 in a manner gated by pO2. Using mice expressing a form of RyR1 with a Cys3636→Ala point mutation to prevent S-nitrosylation at this site, we showed that Cys3636 was the principal target of endogenous S-nitrosylation during normal muscle function. The absence of Cys3636 S-nitrosylation suppressed stimulus-evoked Ca2+ release at physiological pO2 (at least in part by altering the regulation of RyR1 by Ca2+/calmodulin), eliminated pO2 coupling, and diminished skeletal myocyte contractility in vitro and measures of muscle strength in vivo. Furthermore, we found that abrogation of Cys3636 S-nitrosylation resulted in a developmental defect reflected in diminished myofiber diameter, altered fiber subtypes, and altered expression of genes implicated in muscle development and atrophy. Thus, our findings establish a physiological role for pO2-coupled S-nitrosylation of RyR1 in skeletal muscle contractility and development and provide foundation for future studies of RyR1 modifications in physiology and disease.
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Affiliation(s)
- Qi-An Sun
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
| | - Zachary W Grimmett
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
| | - Douglas T Hess
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
| | - Lautaro G Perez
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Zhaoxia Qian
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
| | - Ruchi Chaube
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
| | - Nicholas M Venetos
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
| | - Bradley N Plummer
- Heart and Vascular Research Center, MetroHealth Campus of Case Western Reserve University, Cleveland, OH, 44109, USA
| | - Kenneth R Laurita
- Heart and Vascular Research Center, MetroHealth Campus of Case Western Reserve University, Cleveland, OH, 44109, USA
| | - Richard T Premont
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
| | - Jonathan S Stamler
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA.
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92
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Yang H, Wu P, Wang T, Yu Y, Li J, Liu R, Ruan Q. Topical ophthalmic instillation of engineered hMSCs-derived exosomes: A novel non-invasive therapeutic strategy for ocular posterior-segment disorder. Biochem Biophys Res Commun 2024; 723:150212. [PMID: 38850812 DOI: 10.1016/j.bbrc.2024.150212] [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: 05/13/2024] [Revised: 05/16/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
Due to the presence of protective mechanisms and blood-ocular barriers in the eye, drugs aimed at treating posterior segment ophthalmic disorder have to be administrated mostly through periocular or intravitreal injection. In the current study, we sought to investigate whether topical ophthalmic instillation of human mesenchymal stem cells (hMSCs)-derived exosomes can prevent and treat experimental autoimmune uveitis (EAU), a posterior segment ophthalmic disease induced in animals and considered a model of human autoimmune diseases of the eye. Our studies reveal that topical ophthalmic instillation of hMSCs-derived exosomes can effectively ameliorate EAU. More importantly, we demonstrate that exosomes modified by trans-activator of transcription peptide (TAT) were more effective than naive exosomes in penetrating ocular barrier and preventing/treating EAU. Taken together, these results indicate that topical ophthalmic instillation of TAT-peptide modified exosomes represents a novel non-invasive therapeutic strategy for posterior-segment ophthalmic disorders.
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Affiliation(s)
- Huiying Yang
- Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, 250000, China; Eye Institute of Shandong First Medical University, State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Qingdao, 266071, China
| | - Peipei Wu
- Eye Institute of Shandong First Medical University, Qingdao Eye Hospital of Shandong First Medical University, Qingdao, 266071, China
| | - Ting Wang
- Eye Institute of Shandong First Medical University, Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), Jinan, 250021, China
| | - Yang Yu
- Eye Institute of Shandong First Medical University, State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Qingdao, 266071, China
| | - Jun Li
- Eye Institute of Shandong First Medical University, Qingdao Eye Hospital of Shandong First Medical University, Qingdao, 266071, China
| | - Ruiling Liu
- Eye Institute of Shandong First Medical University, State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Qingdao, 266071, China; Henan Key Laboratory of Engineering Antibody Medicine, Medical College of Henan University, Kaifeng, 475004, China.
| | - Qingguo Ruan
- Eye Institute of Shandong First Medical University, State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Qingdao, 266071, China; Henan Key Laboratory of Engineering Antibody Medicine, Medical College of Henan University, Kaifeng, 475004, China.
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93
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Casler JC, Harper CS, White AJ, Anderson HL, Lackner LL. Mitochondria-ER-PM contacts regulate mitochondrial division and PI(4)P distribution. J Cell Biol 2024; 223:e202308144. [PMID: 38781029 PMCID: PMC11116812 DOI: 10.1083/jcb.202308144] [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: 08/18/2023] [Revised: 12/13/2023] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
The mitochondria-ER-cortex anchor (MECA) forms a tripartite membrane contact site between mitochondria, the endoplasmic reticulum (ER), and the plasma membrane (PM). The core component of MECA, Num1, interacts with the PM and mitochondria via two distinct lipid-binding domains; however, the molecular mechanism by which Num1 interacts with the ER is unclear. Here, we demonstrate that Num1 contains a FFAT motif in its C-terminus that interacts with the integral ER membrane protein Scs2. While dispensable for Num1's functions in mitochondrial tethering and dynein anchoring, the FFAT motif is required for Num1's role in promoting mitochondrial division. Unexpectedly, we also reveal a novel function of MECA in regulating the distribution of phosphatidylinositol-4-phosphate (PI(4)P). Breaking Num1 association with any of the three membranes it tethers results in an accumulation of PI(4)P on the PM, likely via disrupting Sac1-mediated PI(4)P turnover. This work establishes MECA as an important regulatory hub that spatially organizes mitochondria, ER, and PM to coordinate crucial cellular functions.
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Affiliation(s)
- Jason C. Casler
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Clare S. Harper
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Antoineen J. White
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Heidi L. Anderson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Laura L. Lackner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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94
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Pimm ML, Haarer BK, Nobles AD, Haney LM, Marcin AG, Alcaide Eligio M, Henty-Ridilla JL. Coordination of actin plus-end dynamics by IQGAP1, formin, and capping protein. J Cell Biol 2024; 223:e202305065. [PMID: 38787349 PMCID: PMC11117073 DOI: 10.1083/jcb.202305065] [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: 05/16/2023] [Revised: 04/01/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Cell processes require precise regulation of actin polymerization that is mediated by plus-end regulatory proteins. Detailed mechanisms that explain plus-end dynamics involve regulators with opposing roles, including factors that enhance assembly, e.g., the formin mDia1, and others that stop growth (capping protein, CP). We explore IQGAP1's roles in regulating actin filament plus-ends and the consequences of perturbing its activity in cells. We confirm that IQGAP1 pauses elongation and interacts with plus ends through two residues (C756 and C781). We directly visualize the dynamic interplay between IQGAP1 and mDia1, revealing that IQGAP1 displaces the formin to influence actin assembly. Using four-color TIRF, we show that IQGAP1's displacement activity extends to formin-CP "decision complexes," promoting end-binding protein turnover at plus-ends. Loss of IQGAP1 or its plus-end activities disrupts morphology and migration, emphasizing its essential role. These results reveal a new role for IQGAP1 in promoting protein turnover on filament ends and provide new insights into how plus-end actin assembly is regulated in cells.
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Affiliation(s)
- Morgan L. Pimm
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Brian K. Haarer
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Alexander D. Nobles
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Laura M. Haney
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Alexandra G. Marcin
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Marcela Alcaide Eligio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Jessica L. Henty-Ridilla
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
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95
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Neahring L, Cho NH, He Y, Liu G, Fernandes J, Rux CJ, Nakos K, Subramanian R, Upadhyayula S, Yildiz A, Dumont S. Torques within and outside the human spindle balance twist at anaphase. J Cell Biol 2024; 223:e202312046. [PMID: 38869473 PMCID: PMC11176257 DOI: 10.1083/jcb.202312046] [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: 12/11/2023] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
At each cell division, nanometer-scale motors and microtubules give rise to the micron-scale spindle. Many mitotic motors step helically around microtubules in vitro, and most are predicted to twist the spindle in a left-handed direction. However, the human spindle exhibits only slight global twist, raising the question of how these molecular torques are balanced. Here, we find that anaphase spindles in the epithelial cell line MCF10A have a high baseline twist, and we identify factors that both increase and decrease this twist. The midzone motors KIF4A and MKLP1 are together required for left-handed twist at anaphase, and we show that KIF4A generates left-handed torque in vitro. The actin cytoskeleton also contributes to left-handed twist, but dynein and its cortical recruitment factor LGN counteract it. Together, our work demonstrates that force generators regulate twist in opposite directions from both within and outside the spindle, preventing strong spindle twist during chromosome segregation.
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Affiliation(s)
- Lila Neahring
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Nathan H. Cho
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Yifei He
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Gaoxiang Liu
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jonathan Fernandes
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Caleb J. Rux
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA
| | - Konstantinos Nakos
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Radhika Subramanian
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Srigokul Upadhyayula
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ahmet Yildiz
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Physics Department, University of California Berkeley, Berkeley, CA, USA
| | - Sophie Dumont
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA, USA
- UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
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96
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Lacombe A, Scorrano L. The interplay between mitochondrial dynamics and autophagy: From a key homeostatic mechanism to a driver of pathology. Semin Cell Dev Biol 2024; 161-162:1-19. [PMID: 38430721 DOI: 10.1016/j.semcdb.2024.02.001] [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: 11/06/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
The complex relationship between mitochondrial dynamics and autophagy illustrates how two cellular housekeeping processes are intimately linked, illuminating fundamental principles of cellular homeostasis and shedding light on disparate pathological conditions including several neurodegenerative disorders. Here we review the basic tenets of mitochondrial dynamics i.e., the concerted balance between fusion and fission of the organelle, and its interplay with macroautophagy and selective mitochondrial autophagy, also dubbed mitophagy, in the maintenance of mitochondrial quality control and ultimately in cell viability. We illustrate how conditions of altered mitochondrial dynamics reverberate on autophagy and vice versa. Finally, we illustrate how altered interplay between these two key cellular processes participates in the pathogenesis of human disorders affecting multiple organs and systems.
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Affiliation(s)
- Alice Lacombe
- Dept. of Biology, University of Padova, Padova, Italy
| | - Luca Scorrano
- Dept. of Biology, University of Padova, Padova, Italy; Veneto Institute of Molecular Medicine, Padova, Italy.
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97
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Wu Y, Li J, Zhu L, Wang D, Song J, Yu X, Li Y, Tang BZ. Photosensitive AIEgens sensitize bacteria to oxidative damage and modulate the inflammatory responses of macrophages to salvage the photodynamic therapy against MRSA. Biomaterials 2024; 309:122583. [PMID: 38692148 DOI: 10.1016/j.biomaterials.2024.122583] [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: 01/17/2024] [Revised: 04/07/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
The urgent need for antimicrobial agents to combat infections caused by multidrug-resistant bacteria facilitates the exploration of alternative strategies such as photosensitizer (PS)-mediated photoinactivation. However, increasing studies have discovered uncorrelated bactericidal activities among PSs possessing similar photodynamic and pathogen-targeted properties. To optimize the photodynamic therapy (PDT) against infections, we investigated three type-I PSs of D-π-A AIEgens TI, TBI, and TTI. The capacities of reactive oxygen species (ROS) generation of TI, TBI, and TTI did not align with their bactericidal activities. Despite exhibiting the lowest photodynamic efficiency, TI exhibited the highest activities against methicillin-resistant Staphylococcus aureus (MRSA) by impairing the anti-oxidative responses of bacteria. By comparison, TTI, characterized by the strongest ROS production, inactivated intracellular MRSA by potentiating the inflammatory response of macrophages. Unlike TI and TTI, TBI, despite possessing moderate photodynamic activities and inducing ROS accumulation in both MRSA and macrophages, did not exhibit any antibacterial activity. Therefore, relying on the disturbed anti-oxidative metabolism of pathogens or potentiated host immune responses, transient ROS bursts can effectively control bacterial infections. Our study reevaluates the contribution of photodynamic activities of PSs to bacterial elimination and provides new insights into discovering novel antibacterial targets and agents.
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Affiliation(s)
- Yifan Wu
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China; Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Jiangao Li
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China; Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Liwei Zhu
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Deliang Wang
- Department of Materials Chemistry, Huzhou University, Huzhou, Zhejiang, 313000, China
| | - Jiayi Song
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Xiyong Yu
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Ying Li
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China.
| | - Ben Zhong Tang
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Guangdong, 518172, China.
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98
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Liu D, Tian Z, Tusong K, Mamat H, Luo Y. Expression, purification and characterization of CTP synthase PyrG in Staphylococcusaureus. Protein Expr Purif 2024; 221:106520. [PMID: 38833752 DOI: 10.1016/j.pep.2024.106520] [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: 03/23/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/06/2024]
Abstract
Staphylococcus aureus (S. aureus) presents a significant challenge in both nosocomial and community settings due to its pathogenicity. The emergence of drug-resistant strains exacerbates S. aureus infections, leading to increased mortality rates. PyrG, a member of the cytidine triphosphate (CTP) synthase family, serves as a crucial therapeutic target against S. aureus due to the pivotal role of CTP in cellular metabolism. However, the structural and mechanistic details of S. aureus PyrG remains unknown. Here, we successfully expressed and purified monomeric PyrG. Mutational experiments were conducted based on the results of molecular docking. Based on the results of the molecular docking, we carried out mutation experiments and found that Q386A dramatically decreased the CTP synthase activity compared to the wild-type protein, while Y54A almost completely abolished the activity. Exposure of S. aureus to the kinase inhibitor crizotinib increased expression of gene pyrG. Our results identify the two key sites on PyrG for the CTP synthase activity, and present PyrG gene expression increased during the treatment of crizotinib, which may eventually provide valuable guidance for the development of new drugs against S. aureus infections.
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Affiliation(s)
- Dafeng Liu
- Xinjiang Key Laboratory of Lavender Conservation and Utilization, College of Biological Sciences and Technology, Yili Normal University, Yining, 835000, Xinjiang, China; School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Zhu Tian
- Xinjiang Key Laboratory of Lavender Conservation and Utilization, College of Biological Sciences and Technology, Yili Normal University, Yining, 835000, Xinjiang, China
| | - Kuerban Tusong
- Xinjiang Key Laboratory of Lavender Conservation and Utilization, College of Biological Sciences and Technology, Yili Normal University, Yining, 835000, Xinjiang, China
| | - Hayrinsa Mamat
- Xinjiang Key Laboratory of Lavender Conservation and Utilization, College of Biological Sciences and Technology, Yili Normal University, Yining, 835000, Xinjiang, China
| | - Yihan Luo
- Xinjiang Key Laboratory of Lavender Conservation and Utilization, College of Biological Sciences and Technology, Yili Normal University, Yining, 835000, Xinjiang, China
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99
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Li WJ, Li RY, Wang DY, Shen M, Liu HL. CXCR3 participates in asymmetric division of mouse oocytes by modulating actin dynamics. Theriogenology 2024; 225:43-54. [PMID: 38788628 DOI: 10.1016/j.theriogenology.2024.05.028] [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: 12/29/2023] [Revised: 04/24/2024] [Accepted: 05/18/2024] [Indexed: 05/26/2024]
Abstract
Extensive research has been conducted on the role of CXCR3 in immune responses and inflammation. However, the role of CXCR3 in the reproductive system, particularly in oocyte development, remains unknown. In this study, we present findings on the involvement of CXCR3 in the meiotic division process of mouse oocytes. We found CXCR3 was expressed consistently throughout the entire maturation process of mouse oocyte. Inhibition of CXCR3 impaired the asymmetric division of oocyte, while the injection of Cxcr3 mRNA was capable of restoring these defects. Further study showed that inhibition of CXCR3 perturbed spindle migration by affecting LIMK/cofilin pathway-mediated actin remodeling. Knockout of CXCR3 led to an upregulation of actin-binding protein and an increased ATP level in GV-stage oocytes, while maintaining normal actin dynamics during the process of meiosis. Additionally, we noticed the expression level of DYNLT1 is markedly elevated in CXCR3-null oocytes. DYNLT1 bound with the Arp2/3 complex, and knockdown of DYNLT1 in CXCR3-null oocytes impaired the organization of cytoplasmic actin, suggesting the regulatory role of DYNLT1 in actin organization, and the compensatory expression of DYNLT1 may contribute to maintain normal actin dynamics in CXCR3-knockout oocytes. In summary, our findings provide insights into the intricate network of actin dynamics associated with CXCR3 during oocyte meiosis.
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Affiliation(s)
- Wei-Jian Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
| | - Rong-Yang Li
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
| | - Da-Yu Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
| | - Ming Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
| | - Hong-Lin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
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100
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Mu J, Li X, Jia Q. Anchoring Au nanoclusters into coordination polymers: A novel approach toward ATP detection and its application. Talanta 2024; 277:126306. [PMID: 38795592 DOI: 10.1016/j.talanta.2024.126306] [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: 02/28/2024] [Revised: 05/09/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
Adenosine triphosphate (ATP) is the main source of energy required for all life activities and is used as a biomarker for diseases such as cancer. It is of great significance to design a novel fluorescent probe with favorable performance for monitoring the changes of ATP concentration. Herein, a fluorescence probe named ZnCPs@AuNCs for ATP sensing was designed and fabricated by integrating AuNCs into ZnCPs. The emission intensity of AuNCs was greatly enhanced upon the formation of the ZnCPs@AuNCs nanocomposites, which may be attributed to ZnCPs restricting the molecular motion of AuNCs. Upon the introduction of ATP, the fluorescence intensity at 564 nm of ZnCPs@AuNCs is quenched. According to this phenomenon, a sensitive and reliable ATP sensing platform was established. Moreover, ZnCPs@AuNCs were incorporated into a poly (vinyl alcohol) matrix for the fabrication of fluorescent film, which exhibited solid-state fluorescence. Inspired by the remarkable fluorescent properties of ZnCPs@AuNCs, the fluorescent hydrogel was prepared by mixing ZnCPs@AuNCs with κ-carrageenan, which demonstrated a response to ATP and favorable self-healing ability. This work presents a perspective of ZnCPs@AuNCs in multiple applications such as biosensing, fluorescent film, and hydrogel construction.
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Affiliation(s)
- Jin Mu
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Xiqian Li
- Obstetrics & Gynecology, China-Japan Union Hospital of Jilin University, Changchun, 130012, China
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun, 130012, China.
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