1
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Magkakis K, Orädd F, Ahn B, Da Silva V, Appio R, Plivelic TS, Andersson M. Real-time structural characterization of protein response to a caged compound by fast detector readout and high-brilliance synchrotron radiation. Structure 2024; 32:1519-1527.e3. [PMID: 38889721 DOI: 10.1016/j.str.2024.05.015] [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: 04/19/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024]
Abstract
Protein dynamics are essential to biological function, and methods to determine such structural rearrangements constitute a frontier in structural biology. Synchrotron radiation can track real-time protein dynamics, but accessibility to dedicated high-flux single X-ray pulse time-resolved beamlines is scarce and protein targets amendable to such characterization are limited. These limitations can be alleviated by triggering the reaction by laser-induced activation of a caged compound and probing the structural dynamics by fast-readout detectors. In this work, we established time-resolved X-ray solution scattering (TR-XSS) at the CoSAXS beamline at the MAX IV Laboratory synchrotron. Laser-induced activation of caged ATP initiated phosphoryl transfer in the adenylate kinase (AdK) enzyme, and the reaction was monitored up to 50 ms with a 2-ms temporal resolution achieved by the detector readout. The time-resolved structural signal of the protein showed minimal radiation damage effects and excellent agreement to data collected by a single X-ray pulse approach.
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Affiliation(s)
| | - Fredrik Orädd
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Byungnam Ahn
- MAX IV Laboratory, Lund University, Lund, Sweden
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2
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Rua AJ, Mitchell W, Claypool SM, Alder NN, Alexandrescu AT. Perturbations in mitochondrial metabolism associated with defective cardiolipin biosynthesis: An in-organello real-time NMR study. J Biol Chem 2024:107746. [PMID: 39236875 DOI: 10.1016/j.jbc.2024.107746] [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: 06/19/2024] [Revised: 08/20/2024] [Accepted: 08/27/2024] [Indexed: 09/07/2024] Open
Abstract
Mitochondria are central to cellular metabolism; hence, their dysfunction contributes to a wide array of human diseases. Cardiolipin, the signature phospholipid of the mitochondrion, affects proper cristae morphology, bioenergetic functions, and metabolic reactions carried out in mitochondrial membranes. To match tissue-specific metabolic demands, cardiolipin typically undergoes an acyl tail remodeling process with the final step carried out by the phospholipid-lysophospholipid transacylase tafazzin. Mutations in tafazzin are the primary cause of Barth syndrome. Here, we investigated how defects in cardiolipin biosynthesis and remodeling impacts metabolic flux through the TCA cycle and associated yeast pathways. Nuclear magnetic resonance was used to monitor in real-time the metabolic fate of 13C3-pyruvate in isolated mitochondria from three isogenic yeast strains. We compared mitochondria from a wild-type strain to mitochondria from a Δtaz1 strain that lacks tafazzin and contains lower amounts of unremodeled cardiolipin, and mitochondria from a Δcrd1 strain that lacks cardiolipin synthase and cannot synthesize cardiolipin. We found that the 13C-label from the pyruvate substrate was distributed through twelve metabolites. Several of the metabolites were specific to yeast pathways including branched chain amino acids and fusel alcohol synthesis. While most metabolites showed similar kinetics amongst the different strains, mevalonate concentrations were significantly increased in Δtaz1 mitochondria. Additionally, the kinetic profiles of α-ketoglutarate, as well as NAD+ and NADH measured in separate experiments, displayed significantly lower concentrations for Δtaz1 and Δcrd1 mitochondria at most time points. Taken together, the results show how cardiolipin remodeling influences pyruvate metabolism, tricarboxylic acid cycle flux, and the levels of mitochondrial nucleotides.
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Affiliation(s)
- Antonio J Rua
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Wayne Mitchell
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Steven M Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nathan N Alder
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - Andrei T Alexandrescu
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA.
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3
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Guan X, Tang QY, Ren W, Chen M, Wang W, Wolynes PG, Li W. Predicting protein conformational motions using energetic frustration analysis and AlphaFold2. Proc Natl Acad Sci U S A 2024; 121:e2410662121. [PMID: 39163334 PMCID: PMC11363347 DOI: 10.1073/pnas.2410662121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/16/2024] [Indexed: 08/22/2024] Open
Abstract
Proteins perform their biological functions through motion. Although high throughput prediction of the three-dimensional static structures of proteins has proved feasible using deep-learning-based methods, predicting the conformational motions remains a challenge. Purely data-driven machine learning methods encounter difficulty for addressing such motions because available laboratory data on conformational motions are still limited. In this work, we develop a method for generating protein allosteric motions by integrating physical energy landscape information into deep-learning-based methods. We show that local energetic frustration, which represents a quantification of the local features of the energy landscape governing protein allosteric dynamics, can be utilized to empower AlphaFold2 (AF2) to predict protein conformational motions. Starting from ground state static structures, this integrative method generates alternative structures as well as pathways of protein conformational motions, using a progressive enhancement of the energetic frustration features in the input multiple sequence alignment sequences. For a model protein adenylate kinase, we show that the generated conformational motions are consistent with available experimental and molecular dynamics simulation data. Applying the method to another two proteins KaiB and ribose-binding protein, which involve large-amplitude conformational changes, can also successfully generate the alternative conformations. We also show how to extract overall features of the AF2 energy landscape topography, which has been considered by many to be black box. Incorporating physical knowledge into deep-learning-based structure prediction algorithms provides a useful strategy to address the challenges of dynamic structure prediction of allosteric proteins.
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Affiliation(s)
- Xingyue Guan
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing210093, China
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang325000, China
| | - Qian-Yuan Tang
- Department of Physics, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region999077, China
| | - Weitong Ren
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang325000, China
| | | | - Wei Wang
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing210093, China
| | - Peter G. Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX77005
| | - Wenfei Li
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing210093, China
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang325000, China
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4
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Li J, Zhan Z, Li Y, Sun Y, Zhou T, Xu K. Chromosome-level genome assembly of a deep-sea Venus flytrap sea anemone sheds light upon adaptations to an extremely oligotrophic environment. Mol Ecol 2024:e17504. [PMID: 39166453 DOI: 10.1111/mec.17504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/29/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024]
Abstract
The Venus flytrap sea anemone Actinoscyphia liui inhabits the nutrient-limited deep ocean in the tropical western Pacific. Compared with most other sea anemones, it has undergone a distinct modification of body shape similar to that of the botanic flytrap. However, the molecular mechanism by which such a peculiar sea anemone adapts to a deep-sea oligotrophic environment is unknown. Here, we report the chromosomal-level genome of A. liui constructed from PacBio and Hi-C data. The assembled genome is 522 Mb in size and exhibits a continuous scaffold N50 of 58.4 Mb. Different from most other sea anemones, which typically possess 14-18 chromosomes per haplotype, A. liui has only 11. The reduced number of chromosomes is associated with chromosome fusion, which likely represents an adaptive strategy to economize energy in oligotrophic deep-sea environments. Comparative analysis with other deep-sea sea anemones revealed adaptive evolution in genes related to cellular autophagy (TMBIM6, SESN1, SCOCB and RPTOR) and mitochondrial energy metabolism (MDH1B and KAD2), which may aid in A. liui coping with severe food scarcity. Meanwhile, the genome has undergone at least two rounds of expansion in gene families associated with fast synaptic transmission, facilitating rapid responses to water currents and prey. Positive selection was detected on putative phosphorylation sites of muscle contraction-related proteins, possibly further improving feeding efficiency. Overall, the present study provides insights into the molecular adaptation to deep-sea oligotrophic environments and sheds light upon potential effects of a novel morphology on the evolution of Cnidaria.
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Affiliation(s)
- Junyuan Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Agriculture and Bioengineering, Taizhou Vocational College of Science and Technology, Taizhou, China
| | - Zifeng Zhan
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yang Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yanan Sun
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Tong Zhou
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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5
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Sobh A, Encinas E, Patel A, Surapaneni G, Bonilla E, Kaestner C, Poullard J, Clerio M, Vasan K, Freeman T, Lv D, Dupéré-Richer D, Riva A, Barwick BG, Zhou D, Boise LH, Mitsiades CS, Kim B, Bennett RL, Chandel NS, Licht JD. NSD2 drives t(4;14) myeloma cell dependence on adenylate kinase 2 by diverting one-carbon metabolism to the epigenome. Blood 2024; 144:283-295. [PMID: 38598835 DOI: 10.1182/blood.2023022859] [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: 01/29/2024] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
ABSTRACT Chromosomal translocation (4;14), an adverse prognostic factor in multiple myeloma (MM), drives overexpression of the histone methyltransferase nuclear receptor binding SET domain protein 2 (NSD2). A genome-wide CRISPR screen in MM cells identified adenylate kinase 2 (AK2), an enzyme critical for high-energy phosphate transfer from the mitochondria, as an NSD2-driven vulnerability. AK2 suppression in t(4;14) MM cells decreased nicotinamide adenine dinucleotide phosphate (NADP[H]) critical for conversion of ribonucleotides to deoxyribonucleosides, leading to replication stress, DNA damage, and apoptosis. Driving a large genome-wide increase in chromatin methylation, NSD2 overexpression depletes S-adenosylmethionine, compromising the synthesis of creatine from its precursor, guanidinoacetate. Creatine supplementation restored NADP(H) levels, reduced DNA damage, and rescued AK2-deficient t(4;14) MM cells. As the creatine phosphate shuttle constitutes an alternative means for mitochondrial high-energy phosphate transport, these results indicate that NSD2-driven creatine depletion underlies the hypersensitivity of t(4;14) MM cells to AK2 loss. Furthermore, AK2 depletion in t(4;14) cells impaired protein folding in the endoplasmic reticulum, consistent with impaired use of mitochondrial adenosine triphosphate (ATP). Accordingly, AK2 suppression increased the sensitivity of MM cells to proteasome inhibition. These findings delineate a novel mechanism in which aberrant transfer of carbon to the epigenome creates a metabolic vulnerability, with direct therapeutic implications for t(4;14) MM.
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Affiliation(s)
- Amin Sobh
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Elena Encinas
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Alisha Patel
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Greeshma Surapaneni
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Emilie Bonilla
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Charlotte Kaestner
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Janai Poullard
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Monica Clerio
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Karthik Vasan
- Department of Medicine, Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Tzipporah Freeman
- Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center San Antonio, San Antonio, TX
| | - Daphné Dupéré-Richer
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, The University of Florida, Gainesville, FL
| | - Benjamin G Barwick
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center San Antonio, San Antonio, TX
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Richard L Bennett
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Navdeep S Chandel
- Department of Medicine, Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
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6
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Lian P, Cai X, Wang C, Zhai H, Liu K, Yang X, Wu Y, Ma Z, Cao X, Xu Y. Identification and experimental validation of m7G-related molecular subtypes, immune signature, and feature genes in Alzheimer's disease. Heliyon 2024; 10:e33836. [PMID: 39027505 PMCID: PMC11255592 DOI: 10.1016/j.heliyon.2024.e33836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 06/01/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024] Open
Abstract
Background Studies has shown that N7-methylguanosine (m7G) modification plays a critical role in neurological diseases. However, the exact role and association of m7G with the immune microenvironment in Alzheimer's disease (AD) remain largely unknown and unexplored. Methods The study datasets comprised 667 AD samples and 503 control samples selected from eight datasets in the Gene Expression Omnibus database; m7G regulator genes were obtained from previous literature. The AD subtypes were identified by consensus clustering analysis according to m7G regulator genes. The clinical characteristics, immune infiltration, and biological functions of the AD subgroups were evaluated. A combination of different types of machine-learning algorithms were used for the identification of AD genes. We also assessed and validated the diagnostic performance of the identified genes via qRT-PCR, immunofluorescence, and immunohistochemical analyses. Results Two AD distinct subgroups, namely cluster A and cluster B, were identified. Cluster A had poor pathological progression and immune infiltration, representing a high-risk subgroup for AD. The differentially expressed genes of cluster A were enriched in immune and synapse-related pathways, suggesting that these genes probably contribute to AD progression by regulating immune-related pathways. Additionally, five feature genes (AEBP1, CARTPT, AK5, NPTX2, and COPG2IT1) were identified, which were used to construct a nomogram model with good ability to predict AD. The animal experiment analyses further confirmed that these feature genes were associated with AD development. Conclusion To the best of our knowledge, this is the first study to reveal close correlations among m7G RNA modification, the immune microenvironment, and the pathogenesis of AD. We also identified five feature genes associated with AD, further contributing to our understanding of the underlying mechanisms and potential therapeutic targets for AD.
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Affiliation(s)
- Piaopiao Lian
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xing Cai
- Department of Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cailin Wang
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Zhai
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoman Yang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yi Wu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhuoran Ma
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuebing Cao
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Xu
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Jin Y, Chen M, Chen F, Gao Z, Li X, Hu L, Cai D, Zhao S, Song Z. AK7-deficiency reversal inhibits ccRCC progression and boosts anti-PD1 immunotherapy sensitivity. Aging (Albany NY) 2024; 16:11072-11089. [PMID: 38970774 PMCID: PMC11272107 DOI: 10.18632/aging.206006] [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] [Accepted: 06/03/2024] [Indexed: 07/08/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common kidney cancer with subtle early symptoms, high recurrence rates, and low sensitivity to traditional treatments like radiotherapy and chemotherapy. Identifying novel therapeutic targets is critical. The expression level of adenylate kinases 7 (AK7) in ccRCC was examined by the TCGAportal and UALCAN databases. The effect of AK7 on proliferation, invasion and migration of ccRCC cell lines was evaluated by cell assay. The correlation between AK7 expression and prognosis, as well as its direct relationship with immunotherapy efficacy, was analyzed using CANCERTOOL and Kaplan-Meier plotter data. Moreover, the TISIDB database was used to study the relationship between AK7 and immune markers. The effect of overexpressed AK7 combined with PD1 monoclonal antibody on ccRCC was evaluated in animal experiments. The results showed that low level of AK7 expression was observed in ccRCC tissues. The expression of AK7 can regulate the proliferation, invasion, and migration of human ccRCC cell lines. The level of AK7 expression was associated with OS of ccRCC patients. This was potentially due to the negative connection between AK7 expression and CD8+ T cell depletion, indicating that immunotherapy might be less effective in individuals with low AK7 expression. Conversely, augmenting AK7 demonstrated an enhanced effectiveness of anti-PD1 therapy. The findings of our research strongly indicated that AK7 could serve as both a prognostic indicator and therapeutic target for patients with ccRCC. Moreover, the overexpression of AK7 combined with anti-PD1 held promising potential as a therapeutic approach for treating ccRCC.
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Affiliation(s)
- Yigang Jin
- Department of Urology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Minjie Chen
- Department of Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Fei Chen
- Department of Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Zhaofeng Gao
- Department of Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Xiaoping Li
- Department of Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Lingyu Hu
- Department of Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Dandan Cai
- Department of Urology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Siqi Zhao
- Department of Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Zhengwei Song
- Department of Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
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Schanda P, Haran G. NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function. Annu Rev Biophys 2024; 53:247-273. [PMID: 38346243 DOI: 10.1146/annurev-biophys-070323-022428] [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: 07/18/2024]
Abstract
Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.
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Affiliation(s)
- Paul Schanda
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria;
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel;
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9
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Rua AJ, Mitchell W, Claypool SM, Alder NN, Alexandrescu AT. Perturbations in mitochondrial metabolism associated with defective cardiolipin biosynthesis: An in-organello real-time NMR study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599628. [PMID: 38948727 PMCID: PMC11212973 DOI: 10.1101/2024.06.18.599628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Mitochondria are central to cellular metabolism; hence, their dysfunction contributes to a wide array of human diseases including cancer, cardiopathy, neurodegeneration, and heritable pathologies such as Barth syndrome. Cardiolipin, the signature phospholipid of the mitochondrion promotes proper cristae morphology, bioenergetic functions, and directly affects metabolic reactions carried out in mitochondrial membranes. To match tissue-specific metabolic demands, cardiolipin typically undergoes an acyl tail remodeling process with the final step carried out by the phospholipid-lysophospholipid transacylase tafazzin. Mutations in the tafazzin gene are the primary cause of Barth syndrome. Here, we investigated how defects in cardiolipin biosynthesis and remodeling impact metabolic flux through the tricarboxylic acid cycle and associated pathways in yeast. Nuclear magnetic resonance was used to monitor in real-time the metabolic fate of 13C3-pyruvate in isolated mitochondria from three isogenic yeast strains. We compared mitochondria from a wild-type strain to mitochondria from a Δtaz1 strain that lacks tafazzin and contains lower amounts of unremodeled cardiolipin, and mitochondria from a Δcrd1 strain that lacks cardiolipin synthase and cannot synthesize cardiolipin. We found that the 13C-label from the pyruvate substrate was distributed through about twelve metabolites. Several of the identified metabolites were specific to yeast pathways, including branched chain amino acids and fusel alcohol synthesis. Most metabolites showed similar kinetics amongst the different strains but mevalonate and α-ketoglutarate, as well as the NAD+/NADH couple measured in separate nuclear magnetic resonance experiments, showed pronounced differences. Taken together, the results show that cardiolipin remodeling influences pyruvate metabolism, tricarboxylic acid cycle flux, and the levels of mitochondrial nucleotides.
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Affiliation(s)
- Antonio J. Rua
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Wayne Mitchell
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Steven M. Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Mitochondrial Phospholipid Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nathan N. Alder
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Andrei T. Alexandrescu
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
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10
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Sodders MJ, Avila-Pacheco J, Okorie EC, Shen M, Kumari N, Marathi A, Lakhani M, Bullock K, Pierce K, Dennis C, Jeanfavre S, Sarkar S, Scherzer CR, Clish C, Olsen AL. Genetic screening and metabolomics identify glial adenosine metabolism as a therapeutic target in Parkinson's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594309. [PMID: 38798570 PMCID: PMC11118494 DOI: 10.1101/2024.05.15.594309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder and lacks disease-modifying therapies. We developed a Drosophila model for identifying novel glial-based therapeutic targets for PD. Human alpha-synuclein is expressed in neurons and individual genes are independently knocked down in glia. We performed a forward genetic screen, knocking down the entire Drosophila kinome in glia in alpha-synuclein expressing flies. Among the top hits were five genes (Ak1, Ak6, Adk1, Adk2, and awd) involved in adenosine metabolism. Knockdown of each gene improved locomotor dysfunction, rescued neurodegeneration, and increased brain adenosine levels. We determined that the mechanism of neuroprotection involves adenosine itself, as opposed to a downstream metabolite. We dove deeper into the mechanism for one gene, Ak1, finding rescue of dopaminergic neuron loss, alpha-synuclein aggregation, and bioenergetic dysfunction after glial Ak1 knockdown. We performed metabolomics in Drosophila and in human PD patients, allowing us to comprehensively characterize changes in purine metabolism and identify potential biomarkers of dysfunctional adenosine metabolism in people. These experiments support glial adenosine as a novel therapeutic target in PD.
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11
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Kozakiewicz-Piekarz A, Grzegórska M, Ziemkiewicz K, Grab K, Baranowski MR, Zapadka M, Karpiel M, Kupcewicz B, Kowalska J, Wujak M. Synthesis, kinetic studies, and QSAR of dinucleoside polyphosphate derivatives as human AK1 inhibitors. Bioorg Chem 2024; 148:107432. [PMID: 38744169 DOI: 10.1016/j.bioorg.2024.107432] [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: 03/15/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Adenylate kinase (AK) plays a crucial role in the metabolic monitoring of cellular adenine nucleotide homeostasis by catalyzing the reversible transfer of a phosphate group between ATP and AMP, yielding two ADP molecules. By regulating the nucleotide levels and energy metabolism, the enzyme is considered a disease modifier and potential therapeutic target for various human diseases, including malignancies and inflammatory and neurodegenerative disorders. However, lacking approved drugs targeting AK hinders broad studies on this enzyme's pathological importance and therapeutic potential. In this work, we determined the effect of a series of dinucleoside polyphosphate derivatives, commercially available (11 compounds) and newly synthesized (8 compounds), on the catalytic activity of human adenylate kinase isoenzyme 1 (hAK1). The tested compounds belonged to the following groups: (1) diadenosine polyphosphates with different phosphate chain lengths, (2) base-modified derivatives, and (3) phosphate-modified derivatives. We found that all the investigated compounds inhibited the catalytic activity of hAK1, yet with different efficiencies. Three dinucleoside polyphosphates showed IC50 values below 1 µM, and the most significant inhibitory effect was observed for P1-(5'-adenosyl) P5-(5'-adenosyl) pentaphosphate (Ap5A). To understand the observed differences in the inhibition efficiency of the tested dinucleoside polyphosphates, the molecular docking of these compounds to hAK1 was performed. Finally, we conducted a quantitative structure-activity relationship (QSAR) analysis to establish a computational prediction model for hAK1 modulators. Two PLS-regression-based models were built using kinetic data obtained from the AK1 activity analysis performed in both directions of the enzymatic reaction. Model 1 (AMP and ATP synthesis) had a good prediction power (R2 = 0.931, Q2 = 0.854, and MAE = 0.286), while Model 2 (ADP synthesis) exhibited a moderate quality (R2 = 0.913, Q2 = 0.848, and MAE = 0.370). These studies can help better understand the interactions between dinucleoside polyphosphates and adenylate kinase to attain more effective and selective inhibitors in the future.
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Affiliation(s)
| | - Magdalena Grzegórska
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7 87-100 Torun, Poland
| | - Kamil Ziemkiewicz
- Centre of New Technologies, University of Warsaw, Banacha 2C 02-097 Warsaw, Poland
| | - Katarzyna Grab
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 02-093 Warsaw, Poland
| | - Marek R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 02-093 Warsaw, Poland
| | - Mariusz Zapadka
- Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2 85-089 Bydgoszcz, Poland
| | - Marta Karpiel
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2 30-387 Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. S. Łojasiewicza 11 30-348 Krakow, Poland
| | - Bogumiła Kupcewicz
- Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2 85-089 Bydgoszcz, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 02-093 Warsaw, Poland
| | - Magdalena Wujak
- Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2 85-089 Bydgoszcz, Poland.
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12
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Chang T, Tang H, Zhou X, He J, Liu N, Li Y, Xiang W, Yao Z. A novel homozygous nonsense variant of AK7 is associated with multiple morphological abnormalities of the sperm flagella. Reprod Biomed Online 2024; 48:103765. [PMID: 38492416 DOI: 10.1016/j.rbmo.2023.103765] [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: 08/20/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 03/18/2024]
Abstract
RESEARCH QUESTION Is the novel homozygous nonsense variant of AK7 associated with multiple morphological abnormalities of the sperm flagella (MMAF), a specific type of oligoasthenoteratozoospermia leading to male infertility? DESIGN Whole-exome sequencing and Sanger sequencing were performed to identify potential gene variants. Immunoblotting and immunofluorescence were applied to confirm the relationship between mutated genes and disease phenotypes. The concentration of reactive oxygen species and the rate of apoptosis were measured to evaluate the mitochondrial function of spermatozoa. Transmission electron microscopy and scanning electron microscopy were employed to observe sperm ultrastructure. RESULTS A novel homozygous nonsense variant of AK7, c.1153A>T (p. Lys385*), was identified in two infertile siblings with asthenoteratozoospermia through whole-exome sequencing. Both immunoblotting and immunofluorescence assays showed practically complete absence of AK7 in the patient's spermatozoa. Additionally, the individual with the novel AK7 variant exhibited a phenotype characterized by severe oxidative stress and apoptosis caused by mitochondrial metabolic dysfunction of spermatozoa. Notably, remarkable flagellar defects with multiple axonemes in uniflagellate spermatozoa, accompanied by mitochondrial vacuolization, were observed; this has not been reported previously in patients with other AK7 variants. CONCLUSIONS This study found that a novel identified homozygous nonsense variant of AK7 may be associated with MMAF-related asthenoteratozoospermia. The observed functional associations between mitochondria and sperm flagellar assembly provide evidence for potential mutual regulation between AK7 and flagella-associated proteins during spermatogenesis.
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Affiliation(s)
- Tianli Chang
- Reproductive Medicine Centre, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongying Tang
- Reproductive Medicine Centre, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xu Zhou
- Reproductive Medicine Centre, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jingliang He
- Reproductive Medicine Centre, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Nenghui Liu
- Reproductive Medicine Centre, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yanping Li
- Reproductive Medicine Centre, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenpei Xiang
- Institute of Reproductive Health, Centre of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhongyuan Yao
- Reproductive Medicine Centre, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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13
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Lygate CA. Maintaining energy provision in the heart: the creatine kinase system in ischaemia-reperfusion injury and chronic heart failure. Clin Sci (Lond) 2024; 138:491-514. [PMID: 38639724 DOI: 10.1042/cs20230616] [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: 12/18/2023] [Revised: 03/25/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
The non-stop provision of chemical energy is of critical importance to normal cardiac function, requiring the rapid turnover of ATP to power both relaxation and contraction. Central to this is the creatine kinase (CK) phosphagen system, which buffers local ATP levels to optimise the energy available from ATP hydrolysis, to stimulate energy production via the mitochondria and to smooth out mismatches between energy supply and demand. In this review, we discuss the changes that occur in high-energy phosphate metabolism (i.e., in ATP and phosphocreatine) during ischaemia and reperfusion, which represents an acute crisis of energy provision. Evidence is presented from preclinical models that augmentation of the CK system can reduce ischaemia-reperfusion injury and improve functional recovery. Energetic impairment is also a hallmark of chronic heart failure, in particular, down-regulation of the CK system and loss of adenine nucleotides, which may contribute to pathophysiology by limiting ATP supply. Herein, we discuss the evidence for this hypothesis based on preclinical studies and in patients using magnetic resonance spectroscopy. We conclude that the correlative evidence linking impaired energetics to cardiac dysfunction is compelling; however, causal evidence from loss-of-function models remains equivocal. Nevertheless, proof-of-principle studies suggest that augmentation of CK activity is a therapeutic target to improve cardiac function and remodelling in the failing heart. Further work is necessary to translate these findings to the clinic, in particular, a better understanding of the mechanisms by which the CK system is regulated in disease.
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Affiliation(s)
- Craig A Lygate
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, United Kingdom
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14
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Yang S, Song C. Switching Go̅ -Martini for Investigating Protein Conformational Transitions and Associated Protein-Lipid Interactions. J Chem Theory Comput 2024; 20:2618-2629. [PMID: 38447049 DOI: 10.1021/acs.jctc.3c01222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Proteins are dynamic biomolecules that can transform between different conformational states when exerting physiological functions, which is difficult to simulate using all-atom methods. Coarse-grained (CG) Go̅-like models are widely used to investigate large-scale conformational transitions, which usually adopt implicit solvent models and therefore cannot explicitly capture the interaction between proteins and surrounding molecules, such as water and lipid molecules. Here, we present a new method, named Switching Go̅-Martini, to simulate large-scale protein conformational transitions between different states, based on the switching Go̅ method and the CG Martini 3 force field. The method is straightforward and efficient, as demonstrated by the benchmarking applications for multiple protein systems, including glutamine binding protein (GlnBP), adenylate kinase (AdK), and β2-adrenergic receptor (β2AR). Moreover, by employing the Switching Go̅-Martini method, we can not only unveil the conformational transition from the E2Pi-PL state to E1 state of the type 4 P-type ATPase (P4-ATPase) flippase ATP8A1-CDC50 but also provide insights into the intricate details of lipid transport.
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Affiliation(s)
- Song Yang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chen Song
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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15
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Bundhoo E, Ghoorah AW, Jaufeerally-Fakim Y. Large-scale Pan Genomic Analysis of Mycobacterium tuberculosis Reveals Key Insights Into Molecular Evolutionary Rate of Specific Processes and Functions. Evol Bioinform Online 2024; 20:11769343241239463. [PMID: 38532808 PMCID: PMC10964447 DOI: 10.1177/11769343241239463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), an infectious disease that is a major killer worldwide. Due to selection pressure caused by the use of antibacterial drugs, Mtb is characterised by mutational events that have given rise to multi drug resistant (MDR) and extensively drug resistant (XDR) phenotypes. The rate at which mutations occur is an important factor in the study of molecular evolution, and it helps understand gene evolution. Within the same species, different protein-coding genes evolve at different rates. To estimate the rates of molecular evolution of protein-coding genes, a commonly used parameter is the ratio dN/dS, where dN is the rate of non-synonymous substitutions and dS is the rate of synonymous substitutions. Here, we determined the estimated rates of molecular evolution of select biological processes and molecular functions across 264 strains of Mtb. We also investigated the molecular evolutionary rates of core genes of Mtb by computing the dN/dS values, and estimated the pan genome of the 264 strains of Mtb. Our results show that the cellular amino acid metabolic process and the kinase activity function evolve at a significantly higher rate, while the carbohydrate metabolic process evolves at a significantly lower rate for M. tuberculosis. These high rates of evolution correlate well with Mtb physiology and pathogenicity. We further propose that the core genome of M. tuberculosis likely experiences varying rates of molecular evolution which may drive an interplay between core genome and accessory genome during M. tuberculosis evolution.
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Affiliation(s)
- Eshan Bundhoo
- Department of Agricultural & Food Science, Faculty of Agriculture, University of Mauritius, Reduit, Mauritius
| | - Anisah W Ghoorah
- Department of Digital Technologies, Faculty of Information, Communication & Digital Technologies, University of Mauritius, Reduit, Mauritius
| | - Yasmina Jaufeerally-Fakim
- Department of Agricultural & Food Science, Faculty of Agriculture, University of Mauritius, Reduit, Mauritius
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16
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Ji S, Zhou Y, Chen J, Yang M, Li C, Liu M, Liu Y, Jiang L. An ATP "Synthase" Derived from a Single Structural Domain of Bacterial Histidine Kinase. Angew Chem Int Ed Engl 2024; 63:e202318503. [PMID: 38311597 DOI: 10.1002/anie.202318503] [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: 12/03/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/06/2024]
Abstract
ATP (adenosine triphosphate) is a vital energy source for living organisms, and its biosynthesis and precise concentration regulation often depend on macromolecular machinery composed of protein complexes or complicated multidomain proteins. We have identified a single-domain protein HK853CA derived from bacterial histidine kinases (HK) that can catalyze ATP synthesis efficiently. Here, we explored the reaction mechanism and multiple factors that influence this catalysis through a combination of experimental techniques and molecular simulations. Moreover, we optimized its enzymatic activity and applied it as an ATP replenishment machinery to other ATP-dependent systems. Our results broaden the understanding of ATP biosynthesis and show that the single CA domain can be applied as a new biomolecular catalyst used for ATP supply.
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Affiliation(s)
- Shixia Ji
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Magnetic Resonance in Biological System, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yuan Zhou
- Key Laboratory of Magnetic Resonance in Biological System, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jiawen Chen
- Key Laboratory of Magnetic Resonance in Biological System, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological System, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological System, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Maili Liu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Magnetic Resonance in Biological System, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yixiang Liu
- Key Laboratory of Magnetic Resonance in Biological System, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ling Jiang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Magnetic Resonance in Biological System, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430074, China
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17
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Coleman T, Shin J, Silberg JJ, Shamoo Y, Atkinson JT. The Biochemical Impact of Extracting an Embedded Adenylate Kinase Domain Using Circular Permutation. Biochemistry 2024; 63:599-609. [PMID: 38357768 DOI: 10.1021/acs.biochem.3c00605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Adenylate kinases (AKs) have evolved AMP-binding and lid domains that are encoded as continuous polypeptides embedded at different locations within the discontinuous polypeptide encoding the core domain. A prior study showed that AK homologues of different stabilities consistently retain cellular activity following circular permutation that splits a region with high energetic frustration within the AMP-binding domain into discontinuous fragments. Herein, we show that mesophilic and thermophilic AKs having this topological restructuring retain activity and substrate-binding characteristics of the parental AK. While permutation decreased the activity of both AK homologues at physiological temperatures, the catalytic activity of the thermophilic AK increased upon permutation when assayed >30 °C below the melting temperature of the native AK. The thermostabilities of the permuted AKs were uniformly lower than those of native AKs, and they exhibited multiphasic unfolding transitions, unlike the native AKs, which presented cooperative thermal unfolding. In addition, proteolytic digestion revealed that permutation destabilized each AK in differing manners, and mass spectrometry suggested that the new termini within the AMP-binding domain were responsible for the increased proteolysis sensitivity. These findings illustrate how changes in contact order can be used to tune enzyme activity and alter folding dynamics in multidomain enzymes.
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Affiliation(s)
- Tom Coleman
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - John Shin
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, MS-362, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, Texas 77005, United States
| | - Yousif Shamoo
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Joshua T Atkinson
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90007, United States
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey 08544, United States
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18
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Stepanova M, Aherne CM. Adenosine in Intestinal Epithelial Barrier Function. Cells 2024; 13:381. [PMID: 38474346 DOI: 10.3390/cells13050381] [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: 12/23/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
At the intestinal front, several lines of defense are in place to resist infection and injury, the mucus layer, gut microbiome and strong epithelial junctions, to name a few. Their collaboration creates a resilient barrier. In intestinal disorders, such as inflammatory bowel disease (IBD), barrier function is compromised, which results in rampant inflammation and tissue injury. In response to the destruction, the intestinal epithelium releases adenosine, a small but powerful nucleoside that functions as an alarm signal. Amidst the chaos of inflammation, adenosine aims to restore order. Within the scope of its effects is the ability to regulate intestinal epithelial barrier integrity. This review aims to define the contributions of adenosine to mucus production, microbiome-dependent barrier protection, tight junction dynamics, chloride secretion and acid-base balance to reinforce its importance in the intestinal epithelial barrier.
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Affiliation(s)
- Mariya Stepanova
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Carol M Aherne
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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19
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Miura T, Kouzu H, Tanno M, Tatekoshi Y, Kuno A. Role of AMP deaminase in diabetic cardiomyopathy. Mol Cell Biochem 2024:10.1007/s11010-024-04951-z. [PMID: 38386218 DOI: 10.1007/s11010-024-04951-z] [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: 12/19/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024]
Abstract
Diabetes mellitus is one of the major causes of ischemic and nonischemic heart failure. While hypertension and coronary artery disease are frequent comorbidities in patients with diabetes, cardiac contractile dysfunction and remodeling occur in diabetic patients even without comorbidities, which is referred to as diabetic cardiomyopathy. Investigations in recent decades have demonstrated that the production of reactive oxygen species (ROS), impaired handling of intracellular Ca2+, and alterations in energy metabolism are involved in the development of diabetic cardiomyopathy. AMP deaminase (AMPD) directly regulates adenine nucleotide metabolism and energy transfer by adenylate kinase and indirectly modulates xanthine oxidoreductase-mediated pathways and AMP-activated protein kinase-mediated signaling. Upregulation of AMPD in diabetic hearts was first reported more than 30 years ago, and subsequent studies showed similar upregulation in the liver and skeletal muscle. Evidence for the roles of AMPD in diabetes-induced fatty liver, sarcopenia, and heart failure has been accumulating. A series of our recent studies showed that AMPD localizes in the mitochondria-associated endoplasmic reticulum membrane as well as the sarcoplasmic reticulum and cytosol and participates in the regulation of mitochondrial Ca2+ and suggested that upregulated AMPD contributes to contractile dysfunction in diabetic cardiomyopathy via increased generation of ROS, adenine nucleotide depletion, and impaired mitochondrial respiration. The detrimental effects of AMPD were manifested at times of increased cardiac workload by pressure loading. In this review, we briefly summarize the expression and functions of AMPD in the heart and discuss the roles of AMPD in diabetic cardiomyopathy, mainly focusing on contractile dysfunction caused by this disorder.
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Affiliation(s)
- Tetsuji Miura
- Department of Cardiovascular, Renal and Metabolic Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan.
- Department of Clinical Pharmacology, Faculty of Pharmaceutical Sciences, Hokkaido University of Science, 15-4-1, Maeda-7, Teine-Ku, Sapporo, 006-8585, Japan.
| | - Hidemichi Kouzu
- Department of Cardiovascular, Renal and Metabolic Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masaya Tanno
- Department of Cardiovascular, Renal and Metabolic Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Nursing, Sapporo Medical University School of Health Sciences, Sapporo, Japan
| | - Yuki Tatekoshi
- Department of Pharmacology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Atsushi Kuno
- Department of Pharmacology, Sapporo Medical University School of Medicine, Sapporo, Japan
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20
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Wang J, Saiki N, Tanimura A, Noma T, Niwa A, Nakahata T, Saito MK. UK-5099, a mitochondrial pyruvate carrier inhibitor, recovers impaired neutrophil maturation caused by AK2 deficiency in human pluripotent stem cell models. Biochem Biophys Res Commun 2023; 687:149211. [PMID: 37949028 DOI: 10.1016/j.bbrc.2023.149211] [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: 10/27/2023] [Revised: 10/29/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
Reticular dysgenesis (RD) is a rare genetic disease caused by gene mutations in the ATP:AMP phosphotransferase, adenylate kinase 2 (AK2). Patients with RD suffer from severe combined immunodeficiency with neutrophil maturation arrest. Although hematopoietic stem cell transplantation can be a curative option, it is invasive, and complications of agranulocytosis-induced infection worsen the prognosis. Here, we report that the use of UK-5099, an inhibitor of the mitochondrial pyruvate carrier (MPC), on hemo-angiogenic progenitor cells (HAPCs) derived from AK2-deficient induced pluripotent stem cells improved neutrophil maturation. Reactive oxygen species (ROS) levels in AK2-deficient HAPCs remained unchanged throughout all experiments, implying that UK-5099 improved the phenotype without affecting ROS levels. Overall, our results suggest that the MPC is a potential therapeutic target for the treatment of neutrophil maturation defects in RD.
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Affiliation(s)
- Jingxin Wang
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Norikazu Saiki
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan; Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ayako Tanimura
- Division of Food and Health Environmental Sciences, Department of Environmental and Symbiotic Sciences, Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto, 862-8502, Japan; Department of Health and Nutrition, Faculty of Nursing and Nutrition, The University of Shimane, Izumo, 693-8550, Japan
| | - Takafumi Noma
- Department of Nutrition and Health, Faculty of Human Life Studies, Hiroshima Jogakuin University, Hiroshima, 732-0063, Japan
| | - Akira Niwa
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Tastutoshi Nakahata
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan; Central Institute for Experimental Animals, Kawasaki, 210-0821, Japan
| | - Megumu K Saito
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan.
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21
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Nakamura I, Amesaka H, Hara M, Yonezawa K, Okamoto K, Kamikubo H, Tanaka S, Matsuo T. Conformation state-specific monobodies regulate the functions of flexible proteins through conformation trapping. Protein Sci 2023; 32:e4813. [PMID: 37861467 PMCID: PMC10659937 DOI: 10.1002/pro.4813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023]
Abstract
Synthetic binding proteins have emerged as modulators of protein functions through protein-protein interactions (PPIs). Because PPIs are influenced by the structural dynamics of targeted proteins, investigating whether the synthetic-binders-based strategy is applicable for proteins with large conformational changes is important. This study demonstrates the applicability of monobodies (fibronectin type-III domain-based synthetic binding proteins) in regulating the functions of proteins that undergo tens-of-angstroms-scale conformational changes, using an example of the A55C/C77S/V169C triple mutant (Adktm ; a phosphoryl transfer-catalyzing enzyme with a conformational change between OPEN/CLOSED forms). Phage display successfully developed monobodies that recognize the OPEN form (substrate-unbound form), but not the CLOSED form of Adktm . Two OPEN form-specific clones (OP-2 and OP-4) inhibited Adktm kinase activity. Epitope mapping with a yeast-surface display/flow cytometry indicated that OP-2 binds to the substrate-entry side of Adktm , whereas OP-4 binding occurs at another site. Small angle X-ray scattering coupled with size-exclusion chromatography (SEC-SAXS) indicated that OP-4 binds to the hinge side opposite to the substrate-binding site of Adktm , retaining the whole OPEN-form structure of Adktm . Titration of the OP-4-Adktm complex with Ap5 A, a transition-state analog of Adktm , showed that the conformational shift to the CLOSED form was suppressed although Adktm retained the OPEN-form (i.e., substrate-binding ready form). These results show that OP-4 captures and stabilizes the OPEN-form state, thereby affecting the hinge motion. These experimental results indicate that monobody-based modulators can regulate the functions of proteins that show tens-of-angstroms-scale conformational changes, by trapping specific conformational states generated during large conformational change process that is essential for function exertion.
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Affiliation(s)
- Ibuki Nakamura
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
| | - Hiroshi Amesaka
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Mizuho Hara
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Kento Yonezawa
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
- Center for Digital Green‐innovationNara Institute of Science and Technology (NAIST)NaraJapan
| | - Keisuke Okamoto
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
- Center for Digital Green‐innovationNara Institute of Science and Technology (NAIST)NaraJapan
| | - Shun‐ichi Tanaka
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
- Department of Biotechnology, College of Life SciencesRitsumeikan UniversityKusatsuJapan
| | - Takashi Matsuo
- Division of Materials Science, Graduate School of Science and TechnologyNara Institute of Science and Technology (NAIST)NaraJapan
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22
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Branovets J, Soodla K, Vendelin M, Birkedal R. Rat and mouse cardiomyocytes show subtle differences in creatine kinase expression and compartmentalization. PLoS One 2023; 18:e0294718. [PMID: 38011179 PMCID: PMC10681188 DOI: 10.1371/journal.pone.0294718] [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: 06/06/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
Creatine kinase (CK) and adenylate kinase (AK) are energy transfer systems. Different studies on permeabilized cardiomyocytes suggest that ADP-channelling from mitochondrial CK alone stimulates respiration to its maximum, VO2_max, in rat but not mouse cardiomyocytes. Results are ambiguous on ADP-channelling from AK to mitochondria. This study was undertaken to directly compare the CK and AK systems in rat and mouse hearts. In homogenates, we assessed CK- and AK-activities, and the CK isoform distribution. In permeabilized cardiomyocytes, we assessed mitochondrial respiration stimulated by ADP from CK and AK, VO2_CK and VO2_AK, respectively. The ADP-channelling from CK or AK to mitochondria was assessed by adding PEP and PK to competitively inhibit the respiration rate. We found that rat compared to mouse hearts had a lower aerobic capacity, higher VO2_CK/VO2_max, and different CK-isoform distribution. Although rat hearts had a larger fraction of mitochondrial CK, less ADP was channeled from CK to the mitochondria. This suggests different intracellular compartmentalization in rat and mouse cardiomyocytes. VO2_AK/VO2_max was similar in mouse and rat cardiomyocytes, and AK did not channel ADP to the mitochondria. In the absence of intracellular compartmentalization, the AK- and CK-activities in homogenate should have been similar to the ADP-phosphorylation rates estimated from VO2_AK and VO2_CK in permeabilized cardiomyocytes. Instead, we found that the ADP-phosphorylation rates estimated from permeabilized cardiomyocytes were 2 and 9 times lower than the activities recorded in homogenate for CK and AK, respectively. Our results highlight the importance of energetic compartmentalization in cardiac metabolic regulation and signalling.
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Affiliation(s)
- Jelena Branovets
- Laboratory of Systems Biology, Department of Cybernetics, Tallinn University of Technology, Tallinn, Estonia
| | - Kärol Soodla
- Laboratory of Systems Biology, Department of Cybernetics, Tallinn University of Technology, Tallinn, Estonia
| | - Marko Vendelin
- Laboratory of Systems Biology, Department of Cybernetics, Tallinn University of Technology, Tallinn, Estonia
| | - Rikke Birkedal
- Laboratory of Systems Biology, Department of Cybernetics, Tallinn University of Technology, Tallinn, Estonia
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23
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Kuang S, Zhu B, Zhang J, Yang F, Wu B, Ding W, Yang L, Shen S, Liang SH, Mondal P, Kumar M, Tanzi RE, Zhang C, Chao H, Ran C. A Photolabile Curcumin-Diazirine Analogue Enables Phototherapy with Physically and Molecularly Produced Light for Alzheimer's Disease Treatment. Angew Chem Int Ed Engl 2023; 62:e202312519. [PMID: 37721455 PMCID: PMC10615883 DOI: 10.1002/anie.202312519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/19/2023]
Abstract
The development of Alzheimer's disease (AD) drugs has recently witnessed substantial achievement. To further enhance the pool of drug candidates, it is crucial to explore non-traditional therapeutic avenues. In this study, we present the use of a photolabile curcumin-diazirine analogue, CRANAD-147, to induce changes in properties, structures (sequences), and neurotoxicity of amyloid beta (Aβ) species both in cells and in vivo. This manipulation was achieved through irradiation with LED light or molecularly generated light, dubbed as "molecular light", emitted by the chemiluminescence probe ADLumin-4. Next, aided by molecular chemiluminescence imaging, we demonstrated that the combination of CRANAD-147/LED or CRANAD-147/ADLumin-4 (molecular light) could effectively slow down the accumulation of Aβs in transgenic 5xFAD mice in vivo. Leveraging the remarkable tissue penetration capacity of molecular light, phototherapy employing the synergistic effect of a photolabile Aβ ligand and molecular light emerges as a promising alternative to conventional AD treatment interventions.
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Affiliation(s)
- Shi Kuang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Building 149, Charlestown, Boston, MA-02129, USA
| | - Biyue Zhu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Building 149, Charlestown, Boston, MA-02129, USA
| | - Jing Zhang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Building 149, Charlestown, Boston, MA-02129, USA
| | - Fan Yang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Building 149, Charlestown, Boston, MA-02129, USA
| | - Bo Wu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Building 149, Charlestown, Boston, MA-02129, USA
| | - Weihua Ding
- MGH Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA-02129, USA
| | - Liuyue Yang
- MGH Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA-02129, USA
| | - Shiqian Shen
- MGH Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA-02129, USA
| | - Seven H Liang
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA-02114, USA
| | - Prasenjit Mondal
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA-02129, USA
| | - Mohanraja Kumar
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA-02139, USA
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA-02129, USA
| | - Can Zhang
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA-02129, USA
| | - Hui Chao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Building 149, Charlestown, Boston, MA-02129, USA
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24
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O’Callaghan E, Navarrete-Lopez P, Štiavnická M, Sánchez JM, Maroto M, Pericuesta E, Fernández-González R, O’Meara C, Eivers B, Kelleher MM, Evans RD, Mapel XM, Lloret-Villas A, Pausch H, Balastegui-Alarcón M, Avilés M, Sanchez-Rodriguez A, Roldan ERS, McDonald M, Kenny DA, Fair S, Gutiérrez-Adán A, Lonergan P. Adenylate kinase 9 is essential for sperm function and male fertility in mammals. Proc Natl Acad Sci U S A 2023; 120:e2305712120. [PMID: 37812723 PMCID: PMC10589668 DOI: 10.1073/pnas.2305712120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/23/2023] [Indexed: 10/11/2023] Open
Abstract
Despite passing routine laboratory tests for semen quality, bulls used in artificial insemination exhibit significant variation in fertility. Routine analysis of fertility data identified a dairy bull with extreme subfertility (10% pregnancy rate). To characterize the subfertility phenotype, a range of in vitro, in vivo, and molecular assays were carried out. Sperm from the subfertile bull exhibited reduced motility and severely reduced caffeine-induced hyperactivation compared to controls. Ability to penetrate the zona pellucida, cleavage rate, cleavage kinetics, and blastocyst yield after IVF or AI were significantly lower than in control bulls. Whole-genome sequencing from semen and RNA sequencing of testis tissue revealed a critical mutation in adenylate kinase 9 (AK9) that impaired splicing, leading to a premature termination codon and a severely truncated protein. Mice deficient in AK9 were generated to further investigate the function of the gene; knockout males were phenotypically indistinguishable from their wild-type littermates but produced immotile sperm that were incapable of normal fertilization. These sperm exhibited numerous abnormalities, including a low ATP concentration and reduced motility. RNA-seq analysis of their testis revealed differential gene expression of components of the axoneme and sperm flagellum as well as steroid metabolic processes. Sperm ultrastructural analysis showed a high percentage of sperm with abnormal flagella. Combined bovine and murine data indicate the essential metabolic role of AK9 in sperm motility and/or hyperactivation, which in turn affects sperm binding and penetration of the zona pellucida. Thus, AK9 has been found to be directly implicated in impaired male fertility in mammals.
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Affiliation(s)
- Elena O’Callaghan
- Animal and Crop Sciences, School of Agriculture and Food Science, University College Dublin, Belfield, DublinD04 V1W8, Ireland
| | - Paula Navarrete-Lopez
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Miriama Štiavnická
- Department of Biological Sciences, Bernal Institute, Faculty of Science and Engineering, University of Limerick, LimerickV94 T9PX, Ireland
| | - José M. Sánchez
- Animal and Crop Sciences, School of Agriculture and Food Science, University College Dublin, Belfield, DublinD04 V1W8, Ireland
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Maria Maroto
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Eva Pericuesta
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Raul Fernández-González
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Ciara O’Meara
- National Cattle Breeding Centre, County KildareW91 WF59, Ireland
| | - Bernard Eivers
- National Cattle Breeding Centre, County KildareW91 WF59, Ireland
| | - Margaret M. Kelleher
- Irish Cattle Breeding Federation, Link Road, Ballincollig, County CorkP31 D452, Ireland
| | - Ross D. Evans
- Irish Cattle Breeding Federation, Link Road, Ballincollig, County CorkP31 D452, Ireland
| | - Xena M. Mapel
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Zürich8092, Switzerland
| | - Audald Lloret-Villas
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Zürich8092, Switzerland
| | - Hubert Pausch
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Zürich8092, Switzerland
| | - Miriam Balastegui-Alarcón
- Departamento de Biología Celular e Histología, Universidad de Murcia-Instituto Murciano de Investigación Biosanitaria Pascual Parrilla, Murcia30120, Spain
| | - Manuel Avilés
- Departamento de Biología Celular e Histología, Universidad de Murcia-Instituto Murciano de Investigación Biosanitaria Pascual Parrilla, Murcia30120, Spain
| | - Ana Sanchez-Rodriguez
- Departmento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, Madrid28006, Spain
| | - Eduardo R. S. Roldan
- Departmento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, Madrid28006, Spain
| | - Michael McDonald
- Animal and Crop Sciences, School of Agriculture and Food Science, University College Dublin, Belfield, DublinD04 V1W8, Ireland
| | - David A. Kenny
- Animal and Bioscience Department, Teagasc, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, County MeathC15 PW93, Ireland
| | - Sean Fair
- Department of Biological Sciences, Bernal Institute, Faculty of Science and Engineering, University of Limerick, LimerickV94 T9PX, Ireland
| | - Alfonso Gutiérrez-Adán
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro Nacional integrado en la Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid28040, Spain
| | - Patrick Lonergan
- Animal and Crop Sciences, School of Agriculture and Food Science, University College Dublin, Belfield, DublinD04 V1W8, Ireland
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25
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Calderari S, Archilla C, Jouneau L, Daniel N, Peynot N, Dahirel M, Richard C, Mourier E, Schmaltz-Panneau B, Vitorino Carvalho A, Rousseau-Ralliard D, Lager F, Marchiol C, Renault G, Gatien J, Nadal-Desbarats L, Couturier-Tarrade A, Duranthon V, Chavatte-Palmer P. Alteration of the embryonic microenvironment and sex-specific responses of the preimplantation embryo related to a maternal high-fat diet in the rabbit model. J Dev Orig Health Dis 2023; 14:602-613. [PMID: 37822211 DOI: 10.1017/s2040174423000260] [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: 10/13/2023]
Abstract
The maternal metabolic environment can be detrimental to the health of the offspring. In a previous work, we showed that maternal high-fat (HH) feeding in rabbit induced sex-dependent metabolic adaptation in the fetus and led to metabolic syndrome in adult offspring. As early development representing a critical window of susceptibility, in the present work we aimed to explore the effects of the HH diet on the oocyte, preimplantation embryo and its microenvironment. In oocytes from females on HH diet, transcriptomic analysis revealed a weak modification in the content of transcripts mainly involved in meiosis and translational control. The effect of maternal HH diet on the embryonic microenvironment was investigated by identifying the metabolite composition of uterine and embryonic fluids collected in vivo by biomicroscopy. Metabolomic analysis revealed differences in the HH uterine fluid surrounding the embryo, with increased pyruvate concentration. Within the blastocoelic fluid, metabolomic profiles showed decreased glucose and alanine concentrations. In addition, the blastocyst transcriptome showed under-expression of genes and pathways involved in lipid, glucose and amino acid transport and metabolism, most pronounced in female embryos. This work demonstrates that the maternal HH diet disrupts the in vivo composition of the embryonic microenvironment, where the presence of nutrients is increased. In contrast to this nutrient-rich environment, the embryo presents a decrease in nutrient sensing and metabolism suggesting a potential protective process. In addition, this work identifies a very early sex-specific response to the maternal HH diet, from the blastocyst stage.
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Affiliation(s)
- Sophie Calderari
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Catherine Archilla
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Luc Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Nathalie Daniel
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Nathalie Peynot
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Michele Dahirel
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Christophe Richard
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
- Plateforme MIMA2-CIMA, Jouy en Josas, France
| | - Eve Mourier
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
- Plateforme MIMA2-CIMA, Jouy en Josas, France
| | - Barbara Schmaltz-Panneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Anaïs Vitorino Carvalho
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Delphine Rousseau-Ralliard
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Franck Lager
- Université Paris Cité, Institut Cochin, Inserm, CNRS, ParisF-75014, France
| | - Carmen Marchiol
- Université Paris Cité, Institut Cochin, Inserm, CNRS, ParisF-75014, France
| | - Gilles Renault
- Université Paris Cité, Institut Cochin, Inserm, CNRS, ParisF-75014, France
| | - Julie Gatien
- Research and Development Department, Eliance, Nouzilly, France
| | - Lydie Nadal-Desbarats
- UMR 1253, iBrain, University of Tours, Inserm, Tours, France
- PST-ASB, University of Tours, Tours, France
| | - Anne Couturier-Tarrade
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Véronique Duranthon
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
| | - Pascale Chavatte-Palmer
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort94700, France
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26
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Sha Y, Liu W, Li S, Osadchuk LV, Chen Y, Nie H, Gao S, Xie L, Qin W, Zhou H, Li L. Deficiency in AK9 causes asthenozoospermia and male infertility by destabilising sperm nucleotide homeostasis. EBioMedicine 2023; 96:104798. [PMID: 37713809 PMCID: PMC10507140 DOI: 10.1016/j.ebiom.2023.104798] [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: 04/24/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Asthenozoospermia is the primary cause of male infertility; however, its genetic aetiology remains poorly understood. Adenylate kinase 9 (AK9) is highly expressed in the testes of humans and mice and encodes a type of adenosine kinase that is functionally involved in cellular nucleotide homeostasis and energy metabolism. We aimed to assess whether AK9 is involved in asthenozoospermia. METHODS One-hundred-and-sixty-five Chinese men with idiopathic asthenozoospermia were recruited. Whole-exome sequencing (WES) and Sanger sequencing were performed for genetic analyses. Papanicolaou staining, Haematoxylin and eosin staining, scanning electron microscopy, and transmission electron microscopy were used to observe the sperm morphology and structure. Ak9-knockout mice were generated using CRISPR-Cas9. Sperm adenosine was detected by liquid chromatography-mass spectrometry. Targeted sperm metabolomics was performed. Intracytoplasmic sperm injection (ICSI) was used to treat patients. FINDINGS We identified five patients harbouring bi-allelic AK9 mutations. Spermatozoa from men harbouring bi-allelic AK9 mutations have a decreased ability to sustain nucleotide homeostasis. Moreover, bi-allelic AK9 mutations inhibit glycolysis in sperm. Ak9-knockout male mice also presented similar phenotypes of asthenozoospermia. Interestingly, ICSI was effective in bi-allelic AK9 mutant patients in achieving good pregnancy outcomes. INTERPRETATION Defects in AK9 induce asthenozoospermia with defects in nucleotide homeostasis and energy metabolism. This sterile phenotype could be rescued by ICSI. FUNDING The National Natural Science Foundation of China (82071697), Medical Innovation Project of Fujian Province (2020-CXB-051), open project of the NHC Key Laboratory of Male Reproduction and Genetics in Guangzhou (KF202004), Medical Research Foundation of Guangdong Province (A2021269), Guangdong Provincial Reproductive Science Institute Innovation Team grants (C-03), and Outstanding Young Talents Program of Capital Medical University (B2205).
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Affiliation(s)
- Yanwei Sha
- Department of Andrology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Wensheng Liu
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, Guangdong, China
| | - Shu Li
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Ludmila V Osadchuk
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yongjie Chen
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Dongcheng, Beijing, China
| | - Hua Nie
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, Guangdong, China
| | - Shuai Gao
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Linna Xie
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Weibing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, Guangdong, China.
| | - Huiliang Zhou
- Department of Andrology, First Affiliated Hospital of Fujian Medical University, No.20, Chazhong Road, Fuzhou, Fujian, China.
| | - Lin Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Dongcheng, Beijing, China.
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27
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Sheridan J, Grata A, Suva EE, Bresteau E, Mitchell LR, Hassan O, Mitchell B. Novel centriolar defects underlie a primary ciliary dyskinesia phenotype in an adenylate kinase 7 deficient ciliated epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550535. [PMID: 37546962 PMCID: PMC10402086 DOI: 10.1101/2023.07.25.550535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The skin of Xenopus embryos contains numerous multiciliated cells (MCCs), which collectively generate a directed fluid flow across the epithelial surface essential for distributing the overlaying mucous. MCCs develop into highly specialized cells to generate this flow, containing approximately 150 evenly spaced centrioles that give rise to motile cilia. MCC-driven fluid flow can be impaired when ciliary dysfunction occurs, resulting in primary ciliary dyskinesia (PCD) in humans. Mutations in a large number of genes (~50) have been found to be causative to PCD. Recently, studies have linked low levels of Adenylate Kinase 7 (AK7) gene expression to patients with PCD; however, the mechanism for this link remains unclear. Additionally, AK7 mutations have been linked to multiple PCD patients. Adenylate kinases modulate ATP production and consumption, with AK7 explicitly associated with motile cilia. Here we reproduce an AK7 PCD-like phenotype in Xenopus and describe the cellular consequences that occur with manipulation of AK7 levels. We show that AK7 localizes throughout the cilia in a DPY30 domain-dependent manner, suggesting a ciliary function. Additionally, we find that AK7 overexpression increases centriole number, suggesting a role in regulating centriole biogenesis. We find that in AK7-depleted embryos, cilia number, length, and beat frequency are all reduced, which in turn, significantly decreases the tissue-wide mucociliary flow. Additionally, we find a decrease in centriole number and an increase in sub-apical centrioles, implying that AK7 influences both centriole biogenesis and docking, which we propose underlie its defect in ciliogenesis. We propose that AK7 plays a role in PCD by impacting centriole biogenesis and apical docking, ultimately leading to ciliogenesis defects that impair mucociliary clearance.
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Affiliation(s)
- Jennifer Sheridan
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Aline Grata
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Eve E. Suva
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Enzo Bresteau
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Linus R. Mitchell
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Osama Hassan
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
| | - Brian Mitchell
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology
- Northwestern University, Lurie Cancer Center
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28
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Tsutsumi R, Ueberheide B, Liang FX, Neel BG, Sakai R, Saito Y. Endocytic vesicles act as vehicles for glucose uptake in response to growth factor stimulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.23.550235. [PMID: 37546742 PMCID: PMC10402005 DOI: 10.1101/2023.07.23.550235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Glycolysis is a fundamental cellular process, yet its regulatory mechanisms remain incompletely understood. Here, we show that a subset of glucose transporter 1 (GLUT1/SLC2A1) co-endocytoses with platelet-derived growth factor (PDGF) receptor (PDGFR) upon PDGF-stimulation. Furthermore, multiple glycolytic enzymes localize to these endocytosed PDGFR/GLUT1-containing vesicles adjacent to mitochondria. Contrary to current models, which emphasize the importance of glucose transporters on the cell surface, we find that PDGF-stimulated glucose uptake depends on receptor/transporter endocytosis. Our results suggest that growth factors generate glucose-loaded endocytic vesicles that deliver glucose to the glycolytic machinery in proximity to mitochondria, and argue for a new layer of regulation for glycolytic control governed by cellular membrane dynamics.
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Affiliation(s)
- Ryouhei Tsutsumi
- Kitasato University School of Medicine; Sagamihara 252-0374, Kanagawa, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University; Sendai 980-8578, Miyagi, Japan
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
| | - Beatrix Ueberheide
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
- Proteomics Laboratory, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
- Department of Biochemistry and Molecular Pharmacology and Department of Neurology, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
| | - Feng-Xia Liang
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
- Microscopy Laboratory, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA.Paste the full affiliation list here
| | - Benjamin G. Neel
- Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health; New York, NY 10016, USA
| | - Ryuichi Sakai
- Kitasato University School of Medicine; Sagamihara 252-0374, Kanagawa, Japan
| | - Yoshiro Saito
- Graduate School of Pharmaceutical Sciences, Tohoku University; Sendai 980-8578, Miyagi, Japan
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Rebane-Klemm E, Reinsalu L, Puurand M, Shevchuk I, Bogovskaja J, Suurmaa K, Valvere V, Moreno-Sanchez R, Kaambre T. Colorectal polyps increase the glycolytic activity. Front Oncol 2023; 13:1171887. [PMID: 37342183 PMCID: PMC10277630 DOI: 10.3389/fonc.2023.1171887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
In colorectal cancer (CRC) energy metabolism research, the precancerous stage of polyp has remained rather unexplored. By now, it has been shown that CRC has not fully obtained the glycolytic phenotype proposed by O. Warburg and rather depends on mitochondrial respiration. However, the pattern of metabolic adaptations during tumorigenesis is still unknown. Understanding the interplay between genetic and metabolic changes that initiate tumor development could provide biomarkers for diagnosing cancer early and targets for new cancer therapeutics. We used human CRC and polyp tissue material and performed high-resolution respirometry and qRT-PCR to detect changes on molecular and functional level with the goal of generally describing metabolic reprogramming during CRC development. Colon polyps were found to have a more glycolytic bioenergetic phenotype than tumors and normal tissues. This was supported by a greater GLUT1, HK, LDHA, and MCT expression. Despite the increased glycolytic activity, cells in polyps were still able to maintain a highly functional OXPHOS system. The mechanisms of OXPHOS regulation and the preferred substrates are currently unclear and would require further investigation. During polyp formation, intracellular energy transfer pathways become rearranged mainly by increasing the expression of mitochondrial adenylate kinase (AK) and creatine kinase (CK) isoforms. Decreased glycolysis and maintenance of OXPHOS activity, together with the downregulation of the CK system and the most common AK isoforms (AK1 and AK2), seem to play a relevant role in CRC development.
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Affiliation(s)
- Egle Rebane-Klemm
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
| | - Leenu Reinsalu
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
| | - Marju Puurand
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Igor Shevchuk
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Jelena Bogovskaja
- Clinic of Diagnostics, North Estonia Medical Centre, Tallinn, Estonia
| | - Kulliki Suurmaa
- Department of Gastroenterology, West Tallinn Central Hospital, Tallinn, Estonia
| | - Vahur Valvere
- Oncology and Hematology Clinic, North Estonia Medical Centre, Tallinn, Estonia
| | - Rafael Moreno-Sanchez
- Laboratorio de Control Metabólico, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Iztacala, Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, Mexico
| | - Tuuli Kaambre
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
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30
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Bizerra PFV, Itou da Silva FS, Gilglioni EH, Nanami LF, Klosowski EM, de Souza BTL, Raimundo AFG, Paulino Dos Santos KB, Mewes JM, Constantin RP, Mito MS, Ishii-Iwamoto EL, Constantin J, Mingatto FE, Esquissato GNM, Marchiosi R, Dos Santos WD, Ferrarese-Filho O, Constantin RP. The harmful acute effects of clomipramine in the rat liver: impairments in mitochondrial bioenergetics. Toxicol Lett 2023:S0378-4274(23)00184-4. [PMID: 37217012 DOI: 10.1016/j.toxlet.2023.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/14/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
Clomipramine, a tricyclic antidepressant used to treat depression and obsessive-compulsive disorder, has been linked to a few cases of acute hepatotoxicity. It is also recognized as a compound that hinders the functioning of mitochondria. Hence, the effects of clomipramine on mitochondria should endanger processes that are somewhat connected to energy metabolism in the liver. For this reason, the primary aim of this study was to examine how the effects of clomipramine on mitochondrial functions manifest in the intact liver. For this purpose, we used the isolated perfused rat liver, but also isolated hepatocytes and isolated mitochondria as experimental systems. According to the findings, clomipramine harmed metabolic processes and the cellular structure of the liver, especially the membrane structure. The considerable decrease in oxygen consumption in perfused livers strongly suggested that the mechanism of clomipramine toxicity involves the disruption of mitochondrial functions. Coherently, it could be observed that clomipramine inhibited both gluconeogenesis and ureagenesis, two processes that rely on ATP production within the mitochondria. Half-maximal inhibitory concentrations for gluconeogenesis and ureagenesis ranged from 36.87μM to 59.64μM. The levels of ATP as well as the ATP/ADP and ATP/AMP ratios were reduced, but distinctly, between the livers of fasted and fed rats. The results obtained from experiments conducted on isolated hepatocytes and isolated mitochondria unambiguously confirmed previous propositions about the effects of clomipramine on mitochondrial functions. These findings revealed at least three distinct mechanisms of action, including uncoupling of oxidative phosphorylation, inhibition of the FoF1-ATP synthase complex, and inhibition of mitochondrial electron flow. The elevation in activity of cytosolic and mitochondrial enzymes detected in the effluent perfusate from perfused livers, coupled with the increase in aminotransferase release and trypan blue uptake observed in isolated hepatocytes, provided further evidence of the hepatotoxicity of clomipramine. It can be concluded that impaired mitochondrial bioenergetics and cellular damage are important factors underlying the hepatotoxicity of clomipramine and that taking excessive amounts of clomipramine can lead to several risks including decreased ATP production, severe hypoglycemia, and potentially fatal outcomes.
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Affiliation(s)
- Paulo Francisco Veiga Bizerra
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Fernanda Sayuri Itou da Silva
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Eduardo Hideo Gilglioni
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Letícia Fernanda Nanami
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Eduardo Makiyama Klosowski
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Byanca Thais Lima de Souza
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Ana Flávia Gatto Raimundo
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Karina Borba Paulino Dos Santos
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Juliana Moraes Mewes
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Renato Polimeni Constantin
- Department of Biochemistry, Laboratory of Plant Biochemistry, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Márcio Shigueaki Mito
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Emy Luiza Ishii-Iwamoto
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Jorgete Constantin
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Fábio Ermínio Mingatto
- Laboratory of Metabolic and Toxicological Biochemistry, São Paulo State University, Dracena 17900-000, São Paulo, Brazil.
| | | | - Rogério Marchiosi
- Department of Biochemistry, Laboratory of Plant Biochemistry, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Wanderley Dantas Dos Santos
- Department of Biochemistry, Laboratory of Plant Biochemistry, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Osvaldo Ferrarese-Filho
- Department of Biochemistry, Laboratory of Plant Biochemistry, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
| | - Rodrigo Polimeni Constantin
- Department of Biochemistry, Laboratory of Biological Oxidations, State University of Maringá, Maringá 87020-900, Paraná, Brazil; Department of Biochemistry, Laboratory of Plant Biochemistry, State University of Maringá, Maringá 87020-900, Paraná, Brazil.
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Liu Z, Tang C, Teng X, Mohamed ZA, Fan J. Adenylate kinase 2 is a biomarker related to the prognosis of glioma and the immune microenvironment. J Clin Lab Anal 2023:e24892. [PMID: 37161605 DOI: 10.1002/jcla.24892] [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: 01/03/2023] [Revised: 04/12/2023] [Accepted: 04/22/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Among the brain and the other central nervous system, gliomas are the most prevalent malignant primary tumors. Adenylate kinase 2 (AK2) is generally thought to be crucial for energy metabolism and signal transduction. Several disorders are correlated with its aberrant expression. However, it is unclear what functions AK2 might have in gliomas. METHODS We investigated the relationship between AK2 expression and clinicopathological features of glioma patients using information obtained from public databases and patient tissue microarrays. AK2 knockdown glioma cell lines were constructed to explore how AK2 affects glioma progress. The association between AK2 and the immune microenvironment in gliomas was evaluated by multiple methods. RESULTS AK2 expression was higher in glioma samples than in normal brain tissues. Older patients and those with higher-grade, IDH-wildtype, 1p/19q codeletion-free, and MGMT-unmethylated tumors had higher levels of AK2 expression, linking to poor outcomes. Thus, gliomas with high AK2 expression have a worse prognosis. GO and KEGG analyses demonstrated that AK2 was relevant to cell division and DNA replication. Downregulation of AK2 suppresses cell proliferation, migration, and colony formation of glioma cell lines in vitro. AK2 expression was positively connected to the inhibitory immune checkpoints, also correlating with immune infiltration degree. CONCLUSIONS In this study, AK2 may be a potential biological target for more precise molecular therapy of gliomas, since its high expression is associated with worse outcomes and a more malignant immune microenvironment.
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Affiliation(s)
- Zhichen Liu
- Department of Pediatrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chunjiao Tang
- Department of Pediatrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xu Teng
- Department of Pediatrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | | | - Jingyi Fan
- Department of Pediatrics, Zhongnan Hospital of Wuhan University, Wuhan, China
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Song HY, Zhan JF, Hua RQ, He X, Du XD, Xu J, He R, Xie Y, Gu XB, Peng XR, Yang GY. Molecular characterization and immunological properties of Echinococcus granulosus sensu stricto (G1) ADK1 and ADK8. Parasitol Res 2023:10.1007/s00436-023-07857-9. [PMID: 37148368 DOI: 10.1007/s00436-023-07857-9] [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: 09/22/2022] [Accepted: 04/24/2023] [Indexed: 05/08/2023]
Abstract
Adenylate kinases (ADKs) are one of the important enzymes regulating adenosine triphosphate (ATP) metabolism in Echinococcus granulosus sensu lato. The objective of the present study was to explore the molecular characteristics and immunological properties of E. granulosus sensu stricto (G1) adenylate kinase 1 (EgADK1) and adenylate kinase 8 (EgADK8). EgADK1 and EgADK8 were cloned and expressed, and the molecular characteristics of EgADK1 and EgADK8 were analyzed through different bioinformatics tools. Western blotting was used to examine the reactogenicity of recombinant adenylate kinase 1 (rEgADK1) and recombinant adenylate kinase 8 (rEgADK8) and to evaluate their diagnostic value. The expression profiles of EgADK1 and EgADK8 in 18-day-old strobilated worms and protoscoleces were analyzed by quantitative real-time PCR, and their distribution in 18-day-old strobilated worms, the germinal layer, and protoscoleces was determined by immunofluorescence localization. EgADK1 and EgADK8 were successfully cloned and expressed. Bioinformatics analysis predicted that EgADK1 and EgADK8 have multiple phosphorylation sites and B-cell epitopes. Compared with EgADK8, EgADK1 and other parasite ADKs have higher sequence similarity. In addition, both cystic echinococcosis (CE)-positive sheep sera and Cysticercus tenuicollis-infected goat sera could recognize rEgADK1 and rEgADK8. EgADK1 and EgADK8 were localized in protoscoleces, the germinal layer, and 18-day-old strobilated worms. EgADK1 and EgADK8 showed no significant difference in their transcription level in 18-day-old strobilated worms and protoscoleces, suggesting that EgADK1 and EgADK8 may play an important role in the growth and development of E. granulosus sensu lato. Since EgADK1 and EgADK8 can be recognized by other parasite-positive sera, they are not suitable as candidate antigens for the diagnosis of CE.
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Affiliation(s)
- Hong-Yu Song
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Jia-Fei Zhan
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Rui-Qi Hua
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xue He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xiao-Di Du
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xiao-Bin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xue-Rong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Guang-You Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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Scheerer D, Adkar BV, Bhattacharyya S, Levy D, Iljina M, Riven I, Dym O, Haran G, Shakhnovich EI. Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase. Proc Natl Acad Sci U S A 2023; 120:e2219855120. [PMID: 37094144 PMCID: PMC10160949 DOI: 10.1073/pnas.2219855120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/22/2023] [Indexed: 04/26/2023] Open
Abstract
Enzymes play a vital role in life processes; they control chemical reactions and allow functional cycles to be synchronized. Many enzymes harness large-scale motions of their domains to achieve tremendous catalytic prowess and high selectivity for specific substrates. One outstanding example is provided by the three-domain enzyme adenylate kinase (AK), which catalyzes phosphotransfer between ATP to AMP. Here we study the phenomenon of substrate inhibition by AMP and its correlation with domain motions. Using single-molecule FRET spectroscopy, we show that AMP does not block access to the ATP binding site, neither by competitive binding to the ATP cognate site nor by directly closing the LID domain. Instead, inhibitory concentrations of AMP lead to a faster and more cooperative domain closure by ATP, leading in turn to an increased population of the closed state. The effect of AMP binding can be modulated through mutations throughout the structure of the enzyme, as shown by the screening of an extensive AK mutant library. The mutation of multiple conserved residues reduces substrate inhibition, suggesting that substrate inhibition is an evolutionary well conserved feature in AK. Combining these insights, we developed a model that explains the complex activity of AK, particularly substrate inhibition, based on the experimentally observed opening and closing rates. Notably, the model indicates that the catalytic power is affected by the microsecond balance between the open and closed states of the enzyme. Our findings highlight the crucial role of protein motions in enzymatic activity.
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Affiliation(s)
- David Scheerer
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Bharat V Adkar
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | | | - Dorit Levy
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Marija Iljina
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Orly Dym
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
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Neri-Silva R, Monteiro-Batista RDC, Fonseca-Pereira PD, Nunes MD, Viana-Silva AL, Palhares Ribeiro T, Pérez-Díaz JL, Medeiros DB, Araújo WL, Fernie AR, Nunes-Nesi A. On the Significance of the ADNT1 Carrier in Arabidopsis thaliana under Waterlogging Conditions. Biomolecules 2023; 13:biom13050731. [PMID: 37238601 DOI: 10.3390/biom13050731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Among the adenylate carriers identified in Arabidopsis thaliana, only the AMP/ATP transporter ADNT1 shows increased expression in roots under waterlogging stress conditions. Here, we investigated the impact of a reduced expression of ADNT1 in A. thaliana plants submitted to waterlogging conditions. For this purpose, an adnt1 T-DNA mutant and two ADNT1 antisense lines were evaluated. Following waterlogging, ADNT1 deficiency resulted in a reduced maximum quantum yield of PSII electron transport (significantly for adnt1 and antisense Line 10), indicating a higher impact caused by the stress in the mutants. In addition, ADNT1 deficient lines showed higher levels of AMP in roots under nonstress condition. This result indicates that the downregulation of ADNT1 impacts the levels of adenylates. ADNT1-deficient plants exhibited a differential expression pattern of hypoxia-related genes with an increase in non-fermenting-related-kinase 1 (SnRK1) expression and upregulation of adenylate kinase (ADK) under stress and non-stress conditions. Together, these results indicated that the lower expression of ADNT1 is associated with an early "hypoxic status" due to the perturbation of the adenylate pool caused by reduced AMP import by mitochondria. This perturbation, which is sensed by SnRK1, results in a metabolic reprogramming associated with early induction of the fermentative pathway in ADNT1 deficient plants.
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Affiliation(s)
- Roberto Neri-Silva
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Rita de Cássia Monteiro-Batista
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Paula da Fonseca-Pereira
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Mateus Dias Nunes
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Ana Luiza Viana-Silva
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Tamara Palhares Ribeiro
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Jorge L Pérez-Díaz
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - David B Medeiros
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Wagner L Araújo
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Adriano Nunes-Nesi
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil
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Rafii S, Ghouzlani A, Naji O, Ait Ssi S, Kandoussi S, Lakhdar A, Badou A. A2AR as a Prognostic Marker and a Potential Immunotherapy Target in Human Glioma. Int J Mol Sci 2023; 24:ijms24076688. [PMID: 37047660 PMCID: PMC10095519 DOI: 10.3390/ijms24076688] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/05/2023] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
Gliomas are considered one of the most malignant tumors in the body. The immune system has the ability to control the initiation and development of tumors, including gliomas. Thus, immune cells find themselves controlled by various molecular pathways, inhibiting their activation, such as the immunosuppressive adenosine 2A receptor (A2AR). Our objective was to establish the expression profile and role of A2AR at the transcriptomic level, using real-time RT-PCR in Moroccan glioma patients, in addition to TCGA and CGGA cohorts. The real-time RT-PCR results in Moroccan patients showed that high expression of this gene was associated with poor survival in males. Our study on the CGGA cohort corroborated these results. In addition, there was a positive association of A2AR with T-cell exhaustion genes. A2AR also correlated strongly with genes that are primarily enriched in focal adhesion and extracellular matrix interactions, inducing epithelial mesenchymal transition, angiogenesis, and glioma growth. However, in the TCGA cohort, the A2AR showed results that were different from the two previously examined cohorts. In fact, this gene was instead linked to a good prognosis in patients with the astrocytoma histological type. The correlation and enrichment results reinforced the prognostic role of A2AR in this TCGA cohort, in which its high expression was shown to be related to lymphocyte differentiation and a successful cytolytic response, suggesting a more efficient anti-tumor immune response. Correlations and differential analyses based on A2AR gene expression, to understand the cause of the association of this gene with two different prognoses (CGGA males and TCGA Astrocytoma), showed that the overexpression of A2AR in Chinese male patients could be associated with the overexpression of extracellular adenosine, which binds to A2AR to induce immunosuppression and consequently a poor prognosis. However, in the second group (TCGA astrocytomas), the overexpression of the gene could be associated with an adenosine deficiency, and therefore this receptor does not undergo activation. The absence of A2AR activation in these patients may have protected them from immunosuppression, which could reflect the good prognosis. A2AR can be considered a promising therapeutic target in male CGGA and Moroccan patients with gliomas.
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Affiliation(s)
- Soumaya Rafii
- Immuno-Genetics and Human Pathologies Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca 20000, Morocco
| | - Amina Ghouzlani
- Immuno-Genetics and Human Pathologies Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca 20000, Morocco
| | - Oumayma Naji
- Immuno-Genetics and Human Pathologies Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca 20000, Morocco
| | - Saadia Ait Ssi
- Immuno-Genetics and Human Pathologies Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca 20000, Morocco
| | - Sarah Kandoussi
- Immuno-Genetics and Human Pathologies Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca 20000, Morocco
| | | | - Abdallah Badou
- Immuno-Genetics and Human Pathologies Laboratory, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca 20000, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco and Mohammed VI University of Sciences and Health, Casablanca 82403, Morocco
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Shrestha GS, Vijay AK, Stapleton F, White A, Pickford R, Carnt N. Human tear metabolites associated with nucleoside-signalling pathways in bacterial keratitis. Exp Eye Res 2023; 228:109409. [PMID: 36775205 DOI: 10.1016/j.exer.2023.109409] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/17/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
OBJECTIVE The study aimed to profile and quantify tear metabolites associated with bacterial keratitis using both untargeted and targeted metabolomic platforms. METHODS Untargeted metabolomic analysis using liquid-chromatography-Q Exactive-HF mass-spectrometry explored tear metabolites significantly associated with bacterial keratitis (n = 6) compared to healthy participants (n = 6). Differential statistics and principal component analysis determined meaningful metabolite differences between cases and controls. Purines and nucleosides were further quantified and compared between 15 cases and 15 controls in the targeted metabolomic platform using TSQ quantum access triple quadrupole mass spectrometry. Compound quantification was done by plotting the calibration curves and the difference in the compound levels was evaluated using the Wilcoxon rank-sum test. RESULTS In the untargeted analysis, 49 tear metabolites (27 upregulated and 22 downregulated) were differentially expressed between cases and controls. The untargeted analysis indicated that the purine metabolism pathway was the most affected by bacterial keratitis. Metabolite quantification in the targeted analysis further confirmed the upregulation of xanthine (P = 0.02) and downregulation of adenine (P < 0.0001), adenosine (P < 0.0001) and cytidine (P < 0.0001) in the tears of participants with bacterial keratitis compared to that of healthy participants. CONCLUSIONS Bacterial keratitis significantly changes the tear metabolite profile, including five major compound classes such as indoles, amino acids, nucleosides, carbohydrates, and steroids. This study also indicates that tear fluids can be used to map the metabolic pathways and uncover metabolic markers associated with bacterial keratitis. Conceivably, the inhibition of nucleoside synthesis may contribute to the pathophysiology of bacterial keratitis because nucleosides are required for maintaining cellular energy homeostasis and immune adaptability.
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Affiliation(s)
| | | | - Fiona Stapleton
- School of Optometry and Vision Science, UNSW Sydney, Australia
| | - Andrew White
- Department of Ophthalmology, Westmead Hospital, University of Sydney, Australia; Westmead Institute for Medical Research, University of Sydney, Australia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, UNSW Sydney, Australia
| | - Nicole Carnt
- School of Optometry and Vision Science, UNSW Sydney, Australia; Westmead Institute for Medical Research, University of Sydney, Australia; Institute of Ophthalmology, University College London, United Kingdom
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Fiorentini R, Tarenzi T, Potestio R. Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins. J Chem Inf Model 2023; 63:1260-1275. [PMID: 36735551 PMCID: PMC9976289 DOI: 10.1021/acs.jcim.2c01311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 02/04/2023]
Abstract
In recent years, a few multiple-resolution modeling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, with the remainder of the system being concurrently treated using a coarse-grained model. In most cases, the parametrization of the latter requires lengthy reference all-atom simulations and/or the usage of off-shelf coarse-grained force fields, whose interactions have to be refined to fit the specific system under examination. Here, we overcome these limitations through a novel multiresolution modeling scheme for proteins, dubbed coarse-grained anisotropic network model for variable resolution simulations, or CANVAS. This scheme enables a user-defined modulation of the resolution level throughout the system structure; a fast parametrization of the potential without the necessity of reference simulations; and the straightforward usage of the model on the most commonly used molecular dynamics platforms. The method is presented and validated with two case studies, the enzyme adenylate kinase and the therapeutic antibody pembrolizumab, by comparing the results obtained with the CANVAS model against fully atomistic simulations. The modeling software, implemented in Python, is made freely available for the community on a collaborative github repository.
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Affiliation(s)
- Raffaele Fiorentini
- Department
of Physics, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento
Institute for Fundamental Physics and Applications, via Sommarive 14, I-38123 Trento, Italy
| | - Thomas Tarenzi
- Department
of Physics, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento
Institute for Fundamental Physics and Applications, via Sommarive 14, I-38123 Trento, Italy
| | - Raffaello Potestio
- Department
of Physics, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento
Institute for Fundamental Physics and Applications, via Sommarive 14, I-38123 Trento, Italy
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Ito C, Makino T, Mutoh T, Kikkawa M, Toshimori K. The association of ODF4 with AK1 and AK2 in mice is essential for fertility through its contribution to flagellar shape. Sci Rep 2023; 13:2969. [PMID: 36804949 PMCID: PMC9941515 DOI: 10.1038/s41598-023-28177-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 01/12/2023] [Indexed: 02/22/2023] Open
Abstract
Normal sperm flagellar shape and movement are essential for fertilization. The integral protein outer dense fiber 4 (ODF4) localizes to ODFs, but its function remains unclear. Adenylate kinase (AK) is a phosphotransferase that catalyzes the interconversion and controls the concentration equilibrium of adenine nucleotides. AK shuttles ATP to energy-consuming sites. Here, we report on the relationship of flagellar shape and movement with ODF4, AK1 and AK2 by using Odf4-deletion (Odf4-/-) mice. Soluble ODF4 is coimmunoprecipitated with AK1 and AK2 in Odf4+/+ spermatozoa. ODF4, AK1 and AK2 localize to whole flagella (plasmalemma, mitochondria, ODFs, and residual cytoplasmic droplets (CDs)), principal pieces, and midpieces, respectively. Odf4-/- sperm flagella lose ODF4 and reduce AK1 and AK2 but produce ATP. The flagellum is bent (hairpin flagellum) with a large CD in the midpiece. There is no motility in the midpiece, but the principal piece is motile. Odf4-/- spermatozoa progress backward and fail to ascend in the uterus. Thus, Odf4-/- males are infertile owing to abnormal flagellar shape and movement caused mainly by the loss of ODF4 with AK1 and AK2. This study is supported by the rescue experiment; the abnormalities and male infertility caused by Odf4 deletion were reversed by Odf4 restoration.
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Affiliation(s)
- Chizuru Ito
- Department of Functional Anatomy, Reproductive Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.
| | - Tsukasa Makino
- grid.26999.3d0000 0001 2151 536XDepartment of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tohru Mutoh
- grid.136304.30000 0004 0370 1101Department of Functional Anatomy, Reproductive Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, 260-8670 Japan
| | - Masahide Kikkawa
- grid.26999.3d0000 0001 2151 536XDepartment of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyotaka Toshimori
- Department of Functional Anatomy, Reproductive Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan. .,Future Medicine Research Center, Chiba University, Chiba, 260-8670, Japan.
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Biros E, Birosova E, Moran CS. Mechanistic considerations for adenosine-lidocaine-magnesium (ALM) in controlling coagulopathy. Trends Pharmacol Sci 2023; 44:324-334. [PMID: 36805364 DOI: 10.1016/j.tips.2023.01.006] [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: 12/05/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/21/2023]
Abstract
Adenosine-lidocaine-magnesium (ALM) mixture is a cardioplegic agent that improves survivability in rodent, but not swine, models of noncompressible torso hemorrhage (NCTH). However, despite protection from comorbid coagulopathy being the one common effect reported in both NCTH models, the underlying prothrombotic mechanism for ALM has not been elucidated in either. Here, we undertook a component-based approach focusing on individual drugs in the mixture to elaborate on the protective mechanism against coagulopathy within the frames of adenosine signaling and metabolic pathways. Additionally, the translational potential of small and large animal models of NCTH for human survival is critically appraised, owing to substantial quantitative/qualitative differences between humans and rodents, particularly regarding the genetics of G protein-coupled receptors (GPCRs) interacting with ALM's constituents.
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Affiliation(s)
- Erik Biros
- College of Medicine and Dentistry, James Cook University, Townsville, Australia.
| | - Eva Birosova
- College of Medicine and Dentistry, James Cook University, Townsville, Australia
| | - Corey S Moran
- College of Medicine and Dentistry, James Cook University, Townsville, Australia; School of Dentistry, The University of Queensland, Herston, Brisbane, Australia
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40
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Gessner P, Lum J, Frenguelli BG. The mammalian purine salvage pathway as an exploitable route for cerebral bioenergetic support after brain injury. Neuropharmacology 2023; 224:109370. [PMID: 36493858 DOI: 10.1016/j.neuropharm.2022.109370] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/21/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]
Abstract
Purine-based molecules play ancient, fundamental, and evolutionarily-conserved roles across life on Earth, ranging from DNA and RNA, to the universal energy currency, ATP. In mammals, the two primary routes for the synthesis of the adenine nucleotides ATP, ADP and AMP, and, as a consequence, the major bioactive metabolite adenosine, are the de novo purine biosynthesis (DNPB) pathway, and the purine salvage pathway (PSP). Of the two, the PSP dominates in both the mammalian brain and heart. This is because the PSP utilizes the breakdown products of ATP, occasioned by the high energy demands of these organs, to rapidly regenerate adenine nucleotides. This resynthesis route, while efficient and energetically favourable, leaves these organs vulnerable to loss of salvageable metabolites, with the potential for protracted depletion of the means to synthesize ATP, and the ability to deploy neuro- and cardioprotective adenosine. Having previously shown that hippocampal cellular ATP and adenosine release can be increased by supplying substrates for the PSP (d-ribose and adenine), we now explore the expression of DNPB and PSP enzymes in hippocampal neurons and astrocytes based on available transcriptomic data. We find that key enzymes of the PSP are expressed at higher levels than those in the DNPB pathway, and that PSP enzymes are expressed at higher levels in neurons than in astrocytes. These data reflect the importance of the PSP in the mammalian brain and imply that pharmacological targeting of the PSP may be particularly beneficial to neurons at times of metabolic stress. This article is part of the Special Issue on 'Purinergic Signaling: 50 years'.
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Affiliation(s)
- Philipp Gessner
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jenni Lum
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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Ünal İ, Cansız D, Sürmen MG, Sürmen S, Sezer Z, Beler M, Üstündağ ÜV, Güzel E, Alturfan AA, Emekli-Alturfan E. Identification of molecular network of gut-brain axis associated with neuroprotective effects of PPARδ-ligand erucic acid in rotenone-induced Parkinson's disease model in zebrafish. Eur J Neurosci 2023; 57:585-606. [PMID: 36564343 DOI: 10.1111/ejn.15904] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 12/10/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
Disruption of the gut-brain axis in Parkinson's disease (PD) may lead to motor symptoms and PD pathogenesis. Recently, the neuroprotective potential of different PPARδ-agonists has been shown. We aimed to reveal the effects of erucic acid, peroxisome proliferator-activated receptors (PPARs)-ligand in rotenone-induced PD model in zebrafish, focusing on the gut-brain axis. Adult zebrafish were exposed to rotenone and erucic acid for 30 days. Liquid chromatography-mass spectrometry and tandem mass spectrometry (LC-MS/MS) analysis was performed. Raw files were analysed by Proteome Discoverer 2.4 software; peptide lists were searched against Danio rerio proteins. STRING database was used for protein annotations or interactions. Lipid peroxidation (LPO), nitric oxide (No), alkaline phosphatase, superoxide dismutase, glutathione S-transferase (GST), acetylcholinesterase and the expressions of PD-related genes were determined. Immunohistochemical tyrosine hydroxylase (TH) staining was performed. LC-MS/MS analyses allowed identification of over 2000 proteins in each sample. The 2502 and 2707 proteins overlapped for intestine and brain. The 196 and 243 significantly dysregulated proteins in the brain and intestines were found in rotenone groups. Erucic acid treatment corrected the changes in the expression of proteins associated with cytoskeletal organisation, transport and localisation and improved locomotor activity, expressions of TH, PD-related genes (lrrk2, park2, park7, pink1) and oxidant-damage in brain and intestines in the rotenone group as evidenced by decreased LPO, No and increased GST. Our results showed beneficial effects of erucic acid as a PPARδ-ligand in neurotoxin-induced PD model in zebrafish. We believe that our study will shed light on the mechanism of the effects of PPARδ agonists and ω9-fatty acids in the gut-brain axis of PD.
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Affiliation(s)
- İsmail Ünal
- Institute of Health Sciences, Department of Biochemistry, Marmara University, Istanbul, Turkey
| | - Derya Cansız
- Faculty of Medicine, Department of Medical Biochemistry, Istanbul Medipol University, Istanbul, Turkey
| | - Mustafa Gani Sürmen
- Hamidiye Institute of Health Sciences, Department of Molecular Medicine, University of Health Sciences, Istanbul, Turkey
| | - Saime Sürmen
- Hamidiye Institute of Health Sciences, Department of Molecular Medicine, University of Health Sciences, Istanbul, Turkey
| | - Zehra Sezer
- Cerrahpasa Faculty of Medicine, Department of Histology and Embryology, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Merih Beler
- Institute of Health Sciences, Department of Biochemistry, Marmara University, Istanbul, Turkey
| | - Ünsal Veli Üstündağ
- Faculty of Medicine, Department of Medical Biochemistry, Istanbul Medipol University, Istanbul, Turkey
| | - Elif Güzel
- Cerrahpasa Faculty of Medicine, Department of Histology and Embryology, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - A Ata Alturfan
- Faculty of Medicine, Department of Biochemistry, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Ebru Emekli-Alturfan
- Faculty of Dentistry, Department of Basic Medical Sciences, Marmara University, Istanbul, Turkey
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42
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Jaroensuk J, Chuaboon L, Chaiyen P. Biochemical reactions for in vitro ATP production and their applications. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2023.112937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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43
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Suwara J, Radzikowska-Cieciura E, Chworos A, Pawlowska R. The ATP-dependent Pathways and Human Diseases. Curr Med Chem 2023; 30:1232-1255. [PMID: 35319356 DOI: 10.2174/0929867329666220322104552] [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: 08/22/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 11/22/2022]
Abstract
Adenosine triphosphate (ATP) is one of the most important molecules of life, present both inside the cells and extracellularly. It is an essential building block for nucleic acids biosynthesis and crucial intracellular energy storage. However, one of the most interesting functions of ATP is the role of a signaling molecule. Numerous studies indicate the involvement of ATP-dependent pathways in maintaining the proper functioning of individual tissues and organs. Herein, the latest data indicating the ATP function in the network of intra- and extracellular signaling pathways including purinergic signaling, MAP kinase pathway, mTOR and calcium signaling are collected. The main ATP-dependent processes maintaining the proper functioning of the nervous, cardiovascular and immune systems, as well as skin and bones, are summarized. The disturbances in the ATP amount, its cellular localization, or interaction with target elements may induce pathological changes in signaling pathways leading to the development of serious diseases. The impact of an ATP imbalance on the development of dangerous health dysfunctions such as neurodegeneration diseases, cardiovascular diseases (CVDs), diabetes mellitus, obesity, cancers and immune pathogenesis are discussed here.
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Affiliation(s)
- Justyna Suwara
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
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44
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Rezaei T, Kamounah FS, Khodadadi E, Mehramouz B, Gholizadeh P, Yousefi L, Ganbarov K, Ghotaslou R, Yousefi M, Asgharzadeh M, Eslami H, Taghizadeh S, Pirzadeh T, Kafil HS. Comparing proteome changes involved in biofilm formation by Streptococcus mutans after exposure to sucrose and starch. Biotechnol Appl Biochem 2023. [PMID: 36588392 DOI: 10.1002/bab.2442] [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: 06/05/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023]
Abstract
Streptococcus mutans is a main organism of tooth infections including tooth decay and periodontitis. The aim of this study was to assess the influence of sucrose and starch on biofilm formation and proteome profile of S. mutans ATCC 35668 strain. The biofilm formation was assessed by microtiter plating method. Changes in bacterial proteins after exposure to sucrose and starch carbohydrates were analyzed using matrix-assisted laser desorption/ionization mass spectrometry. The biofilm formation of S. mutans was increased to 391.76% in 1% sucrose concentration, 165.76% in 1% starch, and 264.27% in the 0.5% sucrose plus 0.5% starch in comparison to biofilm formation in the media without sugars. The abundance of glutamines, adenylate kinase, and 50S ribosomal protein L29 was increased under exposure to sucrose. Upregulation of lactate utilization protein C, 5-hydroxybenzimidazole synthase BzaA, and 50S ribosomal protein L16 was formed under starch exposure. Ribosome-recycling factor, peptide chain release factor 1, and peptide methionine sulfoxide reductase MsrB were upregulated under exposure to sucrose in combination with starch. The results demonstrated that the carbohydrates increase microbial pathogenicity. In addition, sucrose and starch carbohydrates can induce biofilm formation of S. mutans via various mechanisms such as changes in the expression of special proteins.
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Affiliation(s)
- Tohid Rezaei
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Ehsaneh Khodadadi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Bahareh Mehramouz
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Yousefi
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khudaverdi Ganbarov
- Research Laboratory of Microbiology and Virology, Baku State University, Baku, Azerbaijan
| | - Reza Ghotaslou
- Research Laboratory of Microbiology and Virology, Baku State University, Baku, Azerbaijan
| | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hosein Eslami
- Dental and Periodontal Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepehr Taghizadeh
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tahereh Pirzadeh
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Discovery of Hepatotoxic Equivalent Markers and Mechanism of Polygonum multiflorum Thunb. by Metabolomics Coupled with Molecular Docking. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010025. [PMID: 36615221 PMCID: PMC9822512 DOI: 10.3390/molecules28010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Polygonum multiflorum Thunb. (PMT), a commonly used Chinese herbal medicine for treating diseases such as poisoning and white hair, has attracted constant attention due to the frequent occurrence of liver injury incidents. To date, its hepatotoxic equivalent markers (HEMs) and potential hepatotoxic mechanisms are still unclear. In order to clarify the HEMs of PMT and further explore the potential mechanisms of hepatotoxicity, firstly, the chemical constituents in PMT extract were globally characterized, and the fingerprints of PMT extracts were established along with the detection of their hepatotoxicity in vivo. Then, the correlations between hepatotoxic features and component contents were modeled by chemometrics to screen HEMs of PMT, which were then further evaluated. Finally, the hepatotoxic mechanisms of PMT were investigated using liver metabolomics and molecular docking. The results show that the chemical combination of 2,3,5,4-tetrahydroxystilbene-2-O-β-D-glucoside (TSG) and emodin-8-O-glucoside (EG) was discovered as the HEMs of PMT through pre-screening and verifying process. Liver metabolomics revealed that PMT caused liver injury by interfering with purine metabolism, which might be related to mitochondrial function disorder and oxidative injury via the up-regulations of xanthosine and xanthine, and the down-regulation of 5' nucleotidase (NT5E) and adenylate kinase 2 (AK2). This study not only found that the HEMs of PMT were TSG and EG, but also clarified that PMT might affect purine metabolism to induce liver injury, which contributed to our understanding of the underlying mechanisms of PMT hepatotoxicity.
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da Graça Cabreira M, Wang X, Critsinelis A, Setegne M, Lotfi P, Wan YW, Barrios G, Mei Z, Gee AP, Buja LM, Perin E. Environmental oxygen affects ex vivo growth and proliferation of mesenchymal progenitors by modulating mitogen-activated protein kinase and mammalian target of rapamycin signaling. Cytotherapy 2022; 24:1201-1210. [PMID: 36109320 DOI: 10.1016/j.jcyt.2022.06.005] [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: 12/16/2021] [Revised: 04/16/2022] [Accepted: 06/13/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND AIMS Stem and progenitor cells of hematopoietic and mesenchymal lineages reside in the bone marrow under low oxygen (O2) saturation. O2 levels used in ex vivo expansion of multipotent mesenchymal stromal cells (MSCs) affect proliferation, metabolism and differentiation. METHODS Using cell-based assays and transcriptome and proteome data, the authors compared MSC cultures simultaneously grown under a conventional 19.95% O2 atmosphere or at 5% O2. RESULTS In 5% O2, MSCs showed better proliferation and higher self-renewal ability, most probably sustained by enhanced signaling activity of mitogen-activated protein kinase and mammalian target of rapamycin pathways. Non-oxidative glycolysis-based energy metabolism supported growth and proliferation in 5% O2 cultures, whereas MSCs grown under 19.95% O2 also utilized oxidative phosphorylation. Cytoprotection mechanisms used by cells under 5% O2 differed from 19.95% O2 suggesting differences in the triggers of cell stress between these two O2 conditions. CONCLUSIONS Based on the potential benefits for the growth and metabolism of MSCs, the authors propose the use of 5% O2 for MSC culture.
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Affiliation(s)
| | - Xiaohong Wang
- Department of Dermatology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Mekedlawit Setegne
- Chemistry-Biology Interface Predoctoral Training Program, Stanford University, Stanford, California, USA
| | - Parisa Lotfi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Ying-Wooi Wan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Gabriela Barrios
- Department of Regenerative Medicine Research, Texas Heart Institute, Houston, Texas, USA
| | - Zhuyong Mei
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA
| | - Adrian P Gee
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, Texas, USA
| | - Louis Maximilian Buja
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Emerson Perin
- Center for Clinical Research, Texas Heart Institute, Houston, Texas, USA
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Zeng Z, Li M, Jiang Z, Lan Y, Chen L, Chen Y, Li H, Hui J, Zhang L, Hu X, Xia H. Integrated transcriptomic and metabolomic profiling reveals dysregulation of purine metabolism during the acute phase of spinal cord injury in rats. Front Neurosci 2022; 16:1066528. [PMID: 36507345 PMCID: PMC9727392 DOI: 10.3389/fnins.2022.1066528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction Spinal cord injury (SCI) results in drastic dysregulation of microenvironmental metabolism during the acute phase, which greatly affects neural recovery. A better insight into the potential molecular pathways of metabolic dysregulation by multi-omics analysis could help to reveal targets that promote nerve repair and regeneration in the future. Materials and methods We established the SCI model and rats were randomly divided into two groups: the acute-phase SCI (ASCI) group (n = 14, 3 days post-SCI) and the sham group with day-matched periods (n = 14, without SCI). In each group, rats were sacrificed at 3 days post-surgery for histology study (n = 3), metabolome sequencing (n = 5), transcriptome sequencing (n = 3), and quantitative real-time polymerase chain reaction (n = 3). The motor function of rats was evaluated by double-blind Basso, Beattie, and Bresnahan (BBB) Locomotor Scores at 0, 1, 2, 3 days post-SCI in an open field area. Then the transcriptomic and metabolomic data were integrated in SCI model of rat to reveal the underlying molecular pathways of microenvironmental metabolic dysregulation. Results The histology of the microenvironment was significantly altered in ASCI and the locomotor function was significantly reduced in rats. Metabolomics analysis showed that 360 metabolites were highly altered during the acute phase of SCI, of which 310 were up-regulated and 50 were down-regulated, and bioinformatics analysis revealed that these differential metabolites were mainly enriched in arginine and proline metabolism, D-glutamine and D-glutamate metabolism, purine metabolism, biosynthesis of unsaturated fatty acids. Transcriptomics results showed that 5,963 genes were clearly altered, of which 2,848 genes were up-regulated and 3,115 genes were down-regulated, and these differentially expressed genes were mainly involved in response to stimulus, metabolic process, immune system process. Surprisingly, the Integrative analysis revealed significant dysregulation of purine metabolism at both transcriptome and metabolome levels in the acute phase of SCI, with 48 differential genes and 16 differential metabolites involved. Further analysis indicated that dysregulation of purine metabolism could seriously affect the energy metabolism of the injured microenvironment and increase oxidative stress as well as other responses detrimental to nerve repair and regeneration. Discussion On the whole, we have for the first time combined transcriptomics and metabolomics to systematically analyze the potential molecular pathways of metabolic dysregulation in the acute phase of SCI, which will contribute to broaden our understanding of the sophisticated molecular mechanisms of SCI, in parallel with serving as a foundation for future studies of neural repair and regeneration after SCI.
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Affiliation(s)
- Zhong Zeng
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Craniocerebral Diseases, Ningxia Medical University, Yinchuan, China
| | - Mei Li
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Craniocerebral Diseases, Ningxia Medical University, Yinchuan, China
| | - Zhanfeng Jiang
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Yuanxiang Lan
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Lei Chen
- Department of Neurosurgery, The First People’s Hospital of Shizuishan, Shizuishan, China
| | - Yanjun Chen
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Hailiang Li
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Craniocerebral Diseases, Ningxia Medical University, Yinchuan, China
| | - Jianwen Hui
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Lijian Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Hebei University, Baoding, China
| | - Xvlei Hu
- Department of Neurosurgery, Shanxi Provincial People’s Hospital, Taiyuan, China
| | - Hechun Xia
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China,Ningxia Key Laboratory of Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,*Correspondence: Hechun Xia,
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Wang G, Zou R, Liu L, Wang Z, Zou Z, Tan S, Xu W, Fan X. A circular network of purine metabolism as coregulators of dilated cardiomyopathy. J Transl Med 2022; 20:532. [PMID: 36401332 PMCID: PMC9673417 DOI: 10.1186/s12967-022-03739-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The crosstalk of purine biosynthesis and metabolism exists to balance the cell energy production, proliferation, survival and cytoplasmic environment stability, but disorganized mechanics of with respect to developing heart failure (HF) is currently unknown. METHODS We conducted a multi-omics wide analysis, including microarray-based transcriptomes, and full spectrum metabolomics with respect to chronic HF. Based on expression profiling by array, we applied a bioinformatics platform of quantifiable metabolic pathway changes based on gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), Shapley Additive Explanations (SHAP), and Xtreme Gradient Boosting (XGBoost) algorithms to comprehensively analyze the dynamic changes of metabolic pathways and circular network in the HF development. Additionally, left ventricular tissue from patients undergoing myocardial biopsy and transplantation were collected to perform the protein and full spectrum metabolic mass spectrometry. RESULTS Systematic bioinformatics analysis showed the purine metabolism reprogramming was significantly detected in dilated cardiomyopathy. In addition, this result was also demonstrated in metabolomic mass spectrometry. And the differentially expressed metabolites analysis showing the guanine, urea, and xanthine were significantly detected. Hub markers, includes IMPDH1, ENTPD2, AK7, AK2, and CANT1, also significantly identified based on XGBoost, SHAP model and PPI network. CONCLUSION The crosstalk in the reactions involved in purine metabolism may involving in DCM metabolism reprogramming, and as coregulators of development of HF, which may identify as potential therapeutic targets. And the markers of IMPDH1, ENTPD2, AK7, AK2, and CANT1, and metabolites involved in purine metabolism shown an important role.
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Affiliation(s)
- Ge Wang
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Rongjun Zou
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Libao Liu
- Department of Cardiothoracic Surgery, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Zongtao Wang
- The First Affiliated Hospital of Guangdong Pharmaceutical University, School of Clinical Medicine of Guangdong Pharmaceutical University, Guangzhou, 510008, Guangdong, China
| | - Zengxiao Zou
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Songtao Tan
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Wenliu Xu
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Xiaoping Fan
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China.
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China.
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.
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Germanova E, Khmil N, Pavlik L, Mikheeva I, Mironova G, Lukyanova L. The Role of Mitochondrial Enzymes, Succinate-Coupled Signaling Pathways and Mitochondrial Ultrastructure in the Formation of Urgent Adaptation to Acute Hypoxia in the Myocardium. Int J Mol Sci 2022; 23:ijms232214248. [PMID: 36430733 PMCID: PMC9696391 DOI: 10.3390/ijms232214248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/21/2022] [Accepted: 11/13/2022] [Indexed: 11/19/2022] Open
Abstract
The effect of a single one-hour exposure to three modes of hypobaric hypoxia (HBH) differed in the content of O2 in inhaled air (FiO2-14%, 10%, 8%) in the development of mitochondrial-dependent adaptive processes in the myocardium was studied in vivo. The following parameters have been examined: (a) an urgent reaction of catalytic subunits of mitochondrial enzymes (NDUFV2, SDHA, Cyt b, COX2, ATP5A) in the myocardium as an indicator of the state of the respiratory chain electron transport function; (b) an urgent activation of signaling pathways dependent on GPR91, HIF-1α and VEGF, allowing us to assess their role in the formation of urgent mechanisms of adaptation to hypoxia in the myocardium; (c) changes in the ultrastructure of three subpopulations of myocardial mitochondria under these conditions. The studies were conducted on two rat phenotypes: rats with low resistance (LR) and high resistance (HR) to hypoxia. The adaptive and compensatory role of the mitochondrial complex II (MC II) in maintaining the electron transport and energy function of the myocardium in a wide range of reduced O2 concentrations in the initial period of hypoxic exposure has been established. The features of urgent reciprocal regulatory interaction of NAD- and FAD-dependent oxidation pathways in myocardial mitochondria under these conditions have been revealed. The data indicating the participation of GPR91, HIF-1a and VEGF in this process have been obtained. The ultrastructure of the mitochondrial subpopulations in the myocardium of LR and HR rats differed in normoxic conditions and reacted differently to hypoxia of varying severity. The parameters studied together are highly informative indicators of the quality of cardiac activity and metabolic biomarkers of urgent adaptation in various hypoxic conditions.
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Affiliation(s)
- Elita Germanova
- Institute of General Pathology and Pathophysiology, 8 Baltijskaya Str., Moscow 125315, Russia
| | - Natalya Khmil
- Institute of Theoretical and Experimental Biophysics RAS, 3 Institutskaya Str., Pushchino 142290, Moscow Region, Russia
| | - Lyubov Pavlik
- Institute of Theoretical and Experimental Biophysics RAS, 3 Institutskaya Str., Pushchino 142290, Moscow Region, Russia
| | - Irina Mikheeva
- Institute of Theoretical and Experimental Biophysics RAS, 3 Institutskaya Str., Pushchino 142290, Moscow Region, Russia
| | - Galina Mironova
- Institute of Theoretical and Experimental Biophysics RAS, 3 Institutskaya Str., Pushchino 142290, Moscow Region, Russia
- Correspondence: (G.M.); (L.L.)
| | - Ludmila Lukyanova
- Institute of General Pathology and Pathophysiology, 8 Baltijskaya Str., Moscow 125315, Russia
- Correspondence: (G.M.); (L.L.)
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50
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Konieczka P, Żelechowska E, Przybylski W, Jaworska D, Sałek P, Kinsner M, Jankowski J. The Sarcoplasmic Protein Profile of Breast Muscle in Turkeys in Response to Different Dietary Ratios of Limiting Amino Acids and Clostridium perfringens-Induced Inflammation. Poult Sci 2022; 101:102195. [PMID: 36257075 PMCID: PMC9574763 DOI: 10.1016/j.psj.2022.102195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 12/23/2022] Open
Abstract
In this study, the effects of the Arginine/Lysine (Arg/Lys) ratio in low- and high-methionine (Met) diets on the sarcoplasmic protein profile of breast muscles from turkeys reared under optimal or challenge (Clostridium perfringens infection) conditions were determined. One-day-old Hybrid Converter female turkey poults (216 in total) obtained from a commercial hatchery on hatching day, and on the basis of their average initial body weight were randomly allocated to 12 pens (4 m2 each; 2.0 m × 2.0 m) containing litter bedding and were reared over a 42-day experimental period. Diets with high levels of Lys contained approximately 1.80% and 1.65% Lys and were offered in two successive feeding periods (days 1–28 and days 29–42). The supplemental levels of Lys were consistent with the nutritional specifications for birds at their respective ages as established in the Management Guidelines for Raising Commercial Turkeys. The experiment was based on a completely randomized 3 × 2 × 2 factorial design with three levels of Arg (90%, 100% and 110%) relative to the content of dietary Met (30 or 45%) and without (−) or with (+) C. perfringens challenge at 34, 36, or 37 d of age. Meat samples were investigated in terms of pH, color, and sarcoplasmic protein profile. The experimental factors did not influence meat quality but the dietary Arg content affected meat color. The sarcoplasmic protein profile was influenced by all studied factors, and glycolytic enzymes were the most abundant. This study evidenced strong association between the challenge conditions and the involvement of glycolytic enzymes in cell metabolism, particularly in inflammatory processes, and DNA replication and maintenance in turkeys. The results showed an effect of C. perfringens infection and feeding with different doses of Arg and Met may lead to significant consequences in cell metabolism.
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Affiliation(s)
- Paweł Konieczka
- Department of Poultry Science and Apiculture, University of Warmia and Mazury, Olsztyn, Poland.
| | - Elżbieta Żelechowska
- Institute of Human Nutrition Sciences, Warsaw University of Life Sciences, Warsaw, Poland
| | - Wiesław Przybylski
- Institute of Human Nutrition Sciences, Warsaw University of Life Sciences, Warsaw, Poland
| | - Danuta Jaworska
- Institute of Human Nutrition Sciences, Warsaw University of Life Sciences, Warsaw, Poland
| | - Piotr Sałek
- Institute of Human Nutrition Sciences, Warsaw University of Life Sciences, Warsaw, Poland
| | - Misza Kinsner
- Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Jabłonna, Poland
| | - Jan Jankowski
- Department of Poultry Science and Apiculture, University of Warmia and Mazury, Olsztyn, Poland
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