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Miura D, Tsurigami R, Kato H, Wariishi H, Shimizu M. Pathway crosstalk between the central metabolic and heme biosynthetic pathways in Phanerochaete chrysosporium. Appl Microbiol Biotechnol 2024; 108:37. [PMID: 38183476 PMCID: PMC10771590 DOI: 10.1007/s00253-023-12846-0] [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: 04/26/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 01/08/2024]
Abstract
A comprehensive analysis to survey heme-binding proteins produced by the white-rot fungus Phanerochaete chrysosporium was achieved using a biotinylated heme-streptavidin beads system. Mitochondrial citrate synthase (PcCS), glyceraldehyde 3-phosphate dehydrogenase (PcGAPDH), and 2-Cys thioredoxin peroxidase (mammalian HBP23 homolog) were identified as putative heme-binding proteins. Among these, PcCS and PcGAPDH were further characterized using heterologously expressed recombinant proteins. Difference spectra of PcCS titrated with hemin exhibited an increase in the Soret absorbance at 414 nm, suggesting that the axial ligand of the heme is a His residue. The activity of PcCS was strongly inhibited by hemin with Ki oxaloacetate of 8.7 μM and Ki acetyl-CoA of 5.8 μM. Since the final step of heme biosynthesis occurred at the mitochondrial inner membrane, the inhibition of PcCS by heme is thought to be a physiological event. The inhibitory mode of the heme was similar to that of CoA analogues, suggesting that heme binds to PcCS at His347 at the AcCoA-CoA binding site, which was supported by the homology model of PcCS. PcGAPDH was also inhibited by heme, with a lower concentration than that for PcCS. This might be caused by the different location of these enzymes. From the integration of these phenomena, it was concluded that metabolic regulations by heme in the central metabolic and heme synthetic pathways occurred in the mitochondria and cytosol. This novel pathway crosstalk between the central metabolic and heme biosynthetic pathways, via a heme molecule, is important in regulating the metabolic balance (heme synthesis, ATP synthesis, flux balance of the tricarboxylic acid (TCA) cycle and cellular redox balance (NADPH production) during fungal aromatic degradation. KEY POINTS: • A comprehensive survey of heme-binding proteins in P. chrysosporium was achieved. • Several heme-binding proteins including CS and GAPDH were identified. • A novel metabolic regulation by heme in the central metabolic pathways was found.
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Affiliation(s)
- Daisuke Miura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan.
| | - Ryoga Tsurigami
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Hiroyuki Kato
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Hiroyuki Wariishi
- Faculty of Arts and Science, Kyushu University, Fukuoka, Fukuoka, 819-0395, Japan
| | - Motoyuki Shimizu
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan.
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Bhattacharya S, Dutta A, Khanra PK, Gupta N, Dutta R, Tzvetkov NT, Milella L, Ponticelli M. In silico exploration of 4(α-l-rhamnosyloxy)-benzyl isothiocyanate: A promising phytochemical-based drug discovery approach for combating multi-drug resistant Staphylococcus aureus. Comput Biol Med 2024; 179:108907. [PMID: 39033680 DOI: 10.1016/j.compbiomed.2024.108907] [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: 06/04/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Multidrug-resistant (MDR) Staphylococcus aureus infections significantly threaten global health. With rising resistance to current antibiotics and limited solutions, the urgent discovery of new, effective, and affordable antibacterials with low toxicity is imperative to combat diverse MDR S. aureus strains. Hence, in this study, we introduce an in silico phytochemical-based approach for discovering novel antibacterial agents, underscoring the potential of computational approaches in therapeutic discovery. Glucomoringin Isothiocyanate (GMG-ITC) from Moringa oleifera Lam. is one of the phytochemical compounds with several biological activities, including antimicrobial, anti-inflammatory, and antioxidant activities, and is also effective against S. aureus. This study focuses on screening GMG-ITC as a potential drug candidate to combat MDR S. aureus infections through a molecular docking approach. Moreover, interaction amino acid analysis, in silico pharmacokinetics, compound target prediction, pathway enrichment analysis and molecular dynamics (MD) simulations were conducted for further investigation. Molecular docking and interaction analysis showed strong binding affinity towards S. aureus lipase, dihydrofolate reductase, and other MDR S. aureus proteins, including penicillin-binding protein 2a, MepR, D-Ala:D-Ala ligase, and RPP TetM, through hydrophilic and hydrophobic interactions. GMG-ITC also showed a strong binding affinity to cyclooxygenase-2 and FAD-dependent NAD(P)H oxidase, suggesting that it is a potential anti-inflammatory and antioxidant candidate that may eliminate inflammation and oxidative stress associated with S. aureus infections. MD simulations validated the stability of the GMG-ITC molecular interactions determined by molecular docking. In silico pharmacokinetic analysis highlights its potency as a drug candidate, showing strong absorption, distribution, and excretion properties in combination with low toxicity. It acts as an active protease and enzyme inhibitor with moderate activity against GPCR ligands, ion channels, nuclear receptor ligands, and kinases. Enrichment analysis further elucidated its involvement in important biological, molecular, and cellular functions with potential therapeutic applications in diseases like cancer, hepatitis B, and influenza. Results suggest that GMG-ITC is an effective antibacterial agent that could treat MDR S. aureus-associated infections.
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Affiliation(s)
- Soham Bhattacharya
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol, 165 00, Czech Republic
| | - Adrish Dutta
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Pijush Kanti Khanra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 39, Assam, India
| | - Neha Gupta
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Ritesh Dutta
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, India
| | - Nikolay T Tzvetkov
- Department of Biochemical Pharmacology & Drug Design, Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences (BAS), Acad. G. Bonchev Str., Bl. 21, 1113, Sofia, Bulgaria
| | - Luigi Milella
- Department of Science, University of Basilicata, Via Dell'Ateneo Lucano 10, 85100, Potenza, Italy.
| | - Maria Ponticelli
- Department of Biochemical Pharmacology & Drug Design, Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences (BAS), Acad. G. Bonchev Str., Bl. 21, 1113, Sofia, Bulgaria; Department of Science, University of Basilicata, Via Dell'Ateneo Lucano 10, 85100, Potenza, Italy
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Nagaoka A, Hino M, Izumi R, Shishido R, Ishibashi M, Hatano M, Sainouchi M, Kakita A, Tomita H, Kunii Y. Availability of individual proteins for quantitative analysis in postmortem brains preserved in two different brain banks. Neuropsychopharmacol Rep 2024; 44:399-409. [PMID: 38558385 PMCID: PMC11144605 DOI: 10.1002/npr2.12430] [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: 08/31/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
AIM Postmortem brain research is necessary for elucidating the pathology of schizophrenia; an increasing number of studies require a combination of suitable tissue samples preserved at multiple brain banks. In this study, we examined whether a comparative study of protein expression levels can be conducted using postmortem brain samples preserved in different facilities. METHODS We compared the demographic factors of postmortem brain samples preserved in two institutions and measured and compared the expression levels of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and glial fibrillary acidic protein (GFAP) in the prefrontal cortex and superior temporal gyrus. GAPDH is generally used as a loading control for western blotting, and GFAP is considered as an astrocyte marker in the brain. RESULTS We found significant differences between the two institutions in postmortem interval, age at death, and preservation time. To reduce the effects of these differences on our measurements, the parameters were set as covariates in our analyses of covariance. Subsequently, no differences in GAPDH and GFAP expression were found between institutions. CONCLUSIONS When studies are conducted using brain samples preserved in different brain banks, differences in demographic factors should be carefully considered and taken into account by statistical methods to minimize their impact as much as possible. Since there was no significant difference in the protein expression levels of GAPDH and GFAP in either region between the two institutions that preserved the postmortem brains, we concluded that it is possible to perform protein quantitative analysis assuming that there is no effect of difference between two institutions.
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Affiliation(s)
- Atsuko Nagaoka
- Department of PsychiatryTohoku University HospitalSendaiJapan
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | - Mizuki Hino
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
- Department of Disaster Psychiatry, International Research Institute of Disaster ScienceTohoku UniversitySendaiJapan
| | - Ryuta Izumi
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | - Risa Shishido
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | - Miki Ishibashi
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | - Masataka Hatano
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | - Makoto Sainouchi
- Department of Pathology, Brain Research InstituteNiigata UniversityNiigataJapan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research InstituteNiigata UniversityNiigataJapan
| | - Hiroaki Tomita
- Department of PsychiatryTohoku University HospitalSendaiJapan
- Department of Disaster Psychiatry, International Research Institute of Disaster ScienceTohoku UniversitySendaiJapan
- Department of Psychiatry, Graduate School of MedicineTohoku UniversitySendaiJapan
| | - Yasuto Kunii
- Department of PsychiatryTohoku University HospitalSendaiJapan
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
- Department of Disaster Psychiatry, International Research Institute of Disaster ScienceTohoku UniversitySendaiJapan
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von Montfort C, Aplak E, Ebbert L, Wenzel CK, Klahm NP, Stahl W, Brenneisen P. The role of GAPDH in the selective toxicity of CNP in melanoma cells. PLoS One 2024; 19:e0300718. [PMID: 38512909 PMCID: PMC10956844 DOI: 10.1371/journal.pone.0300718] [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: 06/30/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Malignant melanoma is the most aggressive form of skin cancer with a rather poor prognosis. Standard chemotherapy often results in severe side effects on normal (healthy) cells finally being difficult to tolerate for the patients. Shown by us earlier, cerium oxide nanoparticles (CNP, nanoceria) selectively killed A375 melanoma cells while not being cytotoxic at identical concentrations on non-cancerous cells. In conclusion, the redox-active CNP exhibited both prooxidative as well as antioxidative properties. In that context, CNP induced mitochondrial dysfunction in the studied melanoma cells via generation of reactive oxygene species (primarily hydrogen peroxide (H2O2)), but that does not account for 100% of the toxicity. AIM Cancer cells often show an increased glycolytic rate (Warburg effect), therefore we focused on CNP mediated changes of the glucose metabolism. RESULTS It has been shown before that glyceraldehyde 3-phosphate dehydrogenase (GAPDH) activity is regulated via oxidation of a cysteine in the active center of the enzyme with a subsequent loss of activity. Upon CNP treatment, formation of cellular lactate and GAPDH activity were significantly lowered. The treatment of melanoma cells and melanocytes with the GAPDH inhibitor heptelidic acid (HA) decreased viability to a much higher extent in the cancer cells than in the studied normal (healthy) cells, highlighting and supporting the important role of GAPDH in cancer cells. CONCLUSION We identified glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as a target protein for CNP mediated thiol oxidation.
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Affiliation(s)
- Claudia von Montfort
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Elif Aplak
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Lara Ebbert
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Chantal-Kristin Wenzel
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Niklas P. Klahm
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Wilhelm Stahl
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Peter Brenneisen
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
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5
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Aoki R, Tanaka T. Pathogenesis of Warthin's Tumor: Neoplastic or Non-Neoplastic? Cancers (Basel) 2024; 16:912. [PMID: 38473274 DOI: 10.3390/cancers16050912] [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: 01/04/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Warthin's tumor is the second most frequent neoplasm next to pleomorphic adenoma in the salivary gland, mostly in the parotid gland. The epithelial cells constituting a tumor are characterized by the presence of mitochondria that undergo structural and functional changes, resulting in the development of oncocytes. In addition to containing epithelial cells, Warthin's tumors contain abundant lymphocytes with lymph follicles (germinal centers) that are surrounded by epithelial cells. The pathogenesis of Warthin's tumor is not fully understood, and several hypotheses have been proposed. The risk factors for the development of Warthin's tumor, which predominantly occurs in males, include aging, smoking, and radiation exposure. Recently, it has been reported that chronic inflammation and aging cells promote the growth of Warthin's tumor. Several reports regarding the origin of the tumor have suggested that (1) Warthin's tumor is an IgG4-related disease, (2) epithelial cells that compose Warthin's tumor accumulate mitochondria, and (3) Warthin's tumor is a metaplastic lesion in the lymph nodes. It is possible that the pathogenesis of Warthin's tumor includes mitochondrial metabolic abnormalities, accumulation of aged cells, chronic inflammation, and senescence-associated secretory phenotype (SASP). In this short review, we propose that DNA damage, metabolic dysfunction of mitochondria, senescent cells, SASP, human papillomavirus, and IgG4 may be involved in the development of Warthin's tumor.
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Affiliation(s)
- Ryogo Aoki
- Department of Diagnostic Pathology (DDP) & Research Center of Diagnostic Pathology (RC-DiP), Gifu Municipal Hospital, 7-l Kashima-Cho, Gifu City 500-8513, Gifu, Japan
| | - Takuji Tanaka
- Department of Diagnostic Pathology (DDP) & Research Center of Diagnostic Pathology (RC-DiP), Gifu Municipal Hospital, 7-l Kashima-Cho, Gifu City 500-8513, Gifu, Japan
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Lee CH, Wu CJ, Yang YY, Wang WC, Leu SJ, Wu CT, Kao PS, Liu KJ, Tsai BY, Chiang YW, Mao YC, Benedict Dlamini N, Chang J. Characterization of chicken-derived antibody against Alpha-Enolase of Streptococcus pneumoniae. Int Immunopharmacol 2024; 128:111476. [PMID: 38185035 DOI: 10.1016/j.intimp.2023.111476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/24/2023] [Accepted: 12/29/2023] [Indexed: 01/09/2024]
Abstract
Streptococcus pneumoniae is a clinically relevant pathogen notorious for causing pneumonia, meningitis, and otitis media in immunocompromised patients. Currently, antibiotic therapy is the most efficient treatment for fighting pneumococcal infections. However, an arise in antimicrobial resistance in S. pneumoniae has become a serious health issue globally. To resolve the problem, alternative and cost-effective strategies, such as monoclonal antibody-based targeted therapy, are needed for combating bacterial infection. S. pneumoniae alpha-enolase (spEno1), which is thought to be a great target, is a surface protein that binds and converts human plasminogen to plasmin, leading to accelerated bacterial infections. We first purified recombinant spEno1 protein for chicken immunization to generate specific IgY antibodies. We next constructed two single-chain variable fragments (scFv) antibody libraries by phage display technology, containing 7.2 × 107 and 4.8 × 107 transformants. After bio-panning, ten scFv antibodies were obtained, and their binding activities to spEno1 were evaluated on ELISA, Western blot and IFA. The epitopes of spEno1 were identified by these scFv antibodies, which binding affinities were determined by competitive ELISA. Moreover, inhibition assay displayed that the scFv antibodies effectively inhibit the binding between spEno1 and human plasminogen. Overall, the results suggested that these scFv antibodies have the potential to serve as an immunotherapeutic drug against S. pneumoniae infections.
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Affiliation(s)
- Chi-Hsin Lee
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan; Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Chao-Jung Wu
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan; Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Yi-Yuan Yang
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan; Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan; Core Laboratory of Antibody Generation and Research, Taipei Medical University, Taipei 110301, Taiwan
| | - Wei-Chu Wang
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Sy-Jye Leu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan; Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Cheng-Tsang Wu
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Pei-Shih Kao
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Ko-Jiunn Liu
- National Institute of Cancer Research, National Health Research Institutes, Tainan 70456, Taiwan
| | - Bor-Yu Tsai
- Navi Bio-Therapeutics Inc., Taipei 10351, Taiwan
| | - Yu-Wei Chiang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Yan-Chiao Mao
- Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Nhlanhla Benedict Dlamini
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110301, Taiwan
| | - Jungshan Chang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan; International Master/Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan.
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Pezzotti G, Adachi T, Imamura H, Bristol DR, Adachi K, Yamamoto T, Kanamura N, Marin E, Zhu W, Kawai T, Mazda O, Kariu T, Waku T, Nichols FC, Riello P, Rizzolio F, Limongi T, Okuma K. In Situ Raman Study of Neurodegenerated Human Neuroblastoma Cells Exposed to Outer-Membrane Vesicles Isolated from Porphyromonas gingivalis. Int J Mol Sci 2023; 24:13351. [PMID: 37686157 PMCID: PMC10488263 DOI: 10.3390/ijms241713351] [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: 08/08/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
The aim of this study was to elucidate the chemistry of cellular degeneration in human neuroblastoma cells upon exposure to outer-membrane vesicles (OMVs) produced by Porphyromonas gingivalis (Pg) oral bacteria by monitoring their metabolomic evolution using in situ Raman spectroscopy. Pg-OMVs are a key factor in Alzheimer's disease (AD) pathogenesis, as they act as efficient vectors for the delivery of toxins promoting neuronal damage. However, the chemical mechanisms underlying the direct impact of Pg-OMVs on cell metabolites at the molecular scale still remain conspicuously unclear. A widely used in vitro model employing neuroblastoma SH-SY5Y cells (a sub-line of the SK-N-SH cell line) was spectroscopically analyzed in situ before and 6 h after Pg-OMV contamination. Concurrently, Raman characterizations were also performed on isolated Pg-OMVs, which included phosphorylated dihydroceramide (PDHC) lipids and lipopolysaccharide (LPS), the latter in turn being contaminated with a highly pathogenic class of cysteine proteases, a key factor in neuronal cell degradation. Raman characterizations located lipopolysaccharide fingerprints in the vesicle structure and unveiled so far unproved aspects of the chemistry behind protein degradation induced by Pg-OMV contamination of SH-SY5Y cells. The observed alterations of cells' Raman profiles were then discussed in view of key factors including the formation of amyloid β (Aβ) plaques and hyperphosphorylated Tau neurofibrillary tangles, and the formation of cholesterol agglomerates that exacerbate AD pathologies.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy;
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Tetsuya Adachi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan
| | - Hayata Imamura
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Davide Redolfi Bristol
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Keiji Adachi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
| | - Toshihisa Kawai
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, 3301 College Avenue, Fort Lauderdale, FL 33314, USA;
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
| | - Toru Kariu
- Department of Life Science, Shokei University, Chuo-ku, Kuhonji, Kumamoto 862-8678, Japan;
| | - Tomonori Waku
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan;
| | - Frank C. Nichols
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut, 263 Farmington Avenue, Storrs, CT 06030, USA;
| | - Pietro Riello
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Flavio Rizzolio
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Tania Limongi
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy;
| | - Kazu Okuma
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan
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Soultanas P, Janniere L. The metabolic control of DNA replication: mechanism and function. Open Biol 2023; 13:230220. [PMID: 37582405 PMCID: PMC10427196 DOI: 10.1098/rsob.230220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023] Open
Abstract
Metabolism and DNA replication are the two most fundamental biological functions in life. The catabolic branch of metabolism breaks down nutrients to produce energy and precursors used by the anabolic branch of metabolism to synthesize macromolecules. DNA replication consumes energy and precursors for faithfully copying genomes, propagating the genetic material from generation to generation. We have exquisite understanding of the mechanisms that underpin and regulate these two biological functions. However, the molecular mechanism coordinating replication to metabolism and its biological function remains mostly unknown. Understanding how and why living organisms respond to fluctuating nutritional stimuli through cell-cycle dynamic changes and reproducibly and distinctly temporalize DNA synthesis in a wide-range of growth conditions is important, with wider implications across all domains of life. After summarizing the seminal studies that founded the concept of the metabolic control of replication, we review data linking metabolism to replication from bacteria to humans. Molecular insights underpinning these links are then presented to propose that the metabolic control of replication uses signalling systems gearing metabolome homeostasis to orchestrate replication temporalization. The remarkable replication phenotypes found in mutants of this control highlight its importance in replication regulation and potentially genetic stability and tumorigenesis.
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Affiliation(s)
- Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
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Shegay PV, Shatova OP, Zabolotneva AA, Shestopalov AV, Kaprin AD. Moonlight functions of glycolytic enzymes in cancer. Front Mol Biosci 2023; 10:1076138. [PMID: 37449059 PMCID: PMC10337784 DOI: 10.3389/fmolb.2023.1076138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Since an extensive genome research has started, basic principle "one gene-one protein-one function" was significantly revised. Many proteins with more than one function were identified and characterized as "moonlighting" proteins, which activity depend not only on structural peculiarities but also on compartmentation and metabolic environment. It turned out that "housekeeping" glycolytic enzymes show important moonlight functions such as control of development, proliferation, apoptosis, migration, regulation of transcription and cell signaling. Glycolytic enzymes emerged very early in evolution and because of the limited content of genomes, they could be used as ancient regulators for intercellular and intracellular communication. The multifunctionality of the constitutively expressed enzymes began to serve cancer cell survival and growth. In the present review we discuss some moonlight functions of glycolytic enzymes that important for malignant transformation and tumor growth.
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Affiliation(s)
- Petr V. Shegay
- Federal State Budget Institution, National Medical Research Radiology Center of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Olga P. Shatova
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Biochemistry Department, Peoples’ Friendship University of Russia, Moscow, Russia
| | - Anastasia A. Zabolotneva
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- National Medical Research Centre for Endocrinology, Laboratory of Biochemistry of Signaling Pathways, Moscow, Russia
| | - Aleksandr V. Shestopalov
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- National Medical Research Centre for Endocrinology, Laboratory of Biochemistry of Signaling Pathways, Moscow, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrei D. Kaprin
- Federal State Budget Institution, National Medical Research Radiology Center of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
- Biochemistry Department, Peoples’ Friendship University of Russia, Moscow, Russia
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10
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Yao H, Wang W, Cao Y, Liang Z, Zhang P. Interaction Network Construction and Functional Analysis of the Plasma Membrane H +-ATPase in Bangia fuscopurpurea (Rhodophyta). Int J Mol Sci 2023; 24:ijms24087644. [PMID: 37108805 PMCID: PMC10142769 DOI: 10.3390/ijms24087644] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Salinity is a serious threat to most land plants. Although seaweeds adapt to salty environments, intertidal species experience wide fluctuations in external salinities, including hyper- and hypo-saline stress. Bangia fuscopurpurea is an economic intertidal seaweed with a strong tolerance to hypo-salinity. Until now, the salt stress tolerance mechanism has remained elusive. Our previous study showed that the expression of B. fuscopurpurea plasma membrane H+-ATPase (BfPMHA) genes were the most upregulated under hypo-salinity. In this study, we obtained the complete sequence of BfPMHA, traced the relative expression of this BfPMHA gene in B. fuscopurpurea under hypo-salinity, and analyzed the protein structure and properties based on the gene's sequence. The result showed that the expression of BfPMHA in B. fuscopurpurea increased significantly with varying hypo-salinity treatments, and the higher the degree of low salinity stress, the higher the expression level. This BfPMHA had typical PMHA structures with a Cation-N domain, an E1-E2 ATPase domain, a Hydrolase domain, and seven transmembrane domains. In addition, through the membrane system yeast two-hybrid library, three candidate proteins interacting with BfPMHA during hypo-saline stress were screened, fructose-bisphosphate aldolase (BfFBA), glyceraldehyde 3-phosphate dehydrogenase (NADP+) (phosphorylating) (BfGAPDH), and manganese superoxide dismutase (BfMnSOD). The three candidates and BfPMHA genes were successfully transferred and overexpressed in a BY4741 yeast strain. All of them significantly enhanced the yeast tolerance to NaCl stress, verifying the function of BfPMHA in salt stress response. This is the first study to report the structure and topological features of PMHA in B. fuscopurpurea and its candidate interaction proteins in response to salt stress.
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Affiliation(s)
- Haiqin Yao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 106 Nanjing Road, Qingdao 266071, China
| | - Wenjun Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 106 Nanjing Road, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Yuan Cao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 106 Nanjing Road, Qingdao 266071, China
| | - Zhourui Liang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 106 Nanjing Road, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Pengyan Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No. 106 Nanjing Road, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
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11
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Zhang G, Zhang Z, Wan Q, Zhou H, Jiao M, Zheng H, Lu Y, Rao S, Wu G, Chen J, Yan F, Peng J, Wu J. Selection and Validation of Reference Genes for RT-qPCR Analysis of Gene Expression in Nicotiana benthamiana upon Single Infections by 11 Positive-Sense Single-Stranded RNA Viruses from Four Genera. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040857. [PMID: 36840204 PMCID: PMC9964245 DOI: 10.3390/plants12040857] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 05/17/2023]
Abstract
Quantitative real-time PCR (RT-qPCR) is a widely used method for studying alterations in gene expression upon infections caused by diverse pathogens such as viruses. Positive-sense single-stranded (ss(+)) RNA viruses form a major part of all known plant viruses, and some of them are damaging pathogens of agriculturally important crops. Analysis of gene expression following infection by ss(+) RNA viruses is crucial for the identification of potential anti-viral factors. However, viral infections are known to globally affect gene expression and therefore selection and validation of reference genes for RT-qPCR is particularly important. In this study, the expression of commonly used reference genes for RT-qPCR was studied in Nicotiana benthamiana following single infection by 11 ss(+) RNA viruses, including five tobamoviruses, four potyviruses, one potexvirus and one polerovirus. Stability of gene expression was analyzed in parallel by four commonly used algorithms: geNorm, NormFinder, BestKeeper, and Delta CT, and RefFinder was finally used to summarize all the data. The most stably expressed reference genes differed significantly among the viruses, even when those viruses were from the same genus. Our study highlights the importance of the selection and validation of reference genes upon different viral infections.
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Affiliation(s)
- Ge Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhuo Zhang
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Qionglian Wan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Huijie Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Mengting Jiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Shaofei Rao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Guanwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Correspondence: (J.P.); (J.W.)
| | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Correspondence: (J.P.); (J.W.)
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12
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Tringides ML, Zhang Z, Morgan CE, Su CC, Yu EW. A cryo-electron microscopic approach to elucidate protein structures from human brain microsomes. Life Sci Alliance 2023; 6:6/2/e202201724. [PMID: 36450447 PMCID: PMC9713474 DOI: 10.26508/lsa.202201724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
We recently developed a "Build and Retrieve" cryo-electron microscopy (cryo-EM) methodology, which is capable of simultaneously producing near-atomic resolution cryo-EM maps for several individual proteins from a heterogeneous, multiprotein sample. Here we report the use of "Build and Retrieve" to define the composition of a raw human brain microsomal lysate. From this sample, we simultaneously identify and solve cryo-EM structures of five different brain enzymes whose functions affect neurotransmitter recycling, iron metabolism, glycolysis, axonal development, energy homeostasis, and retinoic acid biosynthesis. Interestingly, malfunction of these important proteins has been directly linked to several neurodegenerative disorders, such as Alzheimer's, Huntington's, and Parkinson's diseases. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
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Affiliation(s)
- Marios L Tringides
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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13
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Shatova OP, Shegay PV, Zabolotneva AA, Shestopalov AV, Kaprin AD. Evolutionary Acquisition of Multifunctionality by Glycolytic Enzymes. J EVOL BIOCHEM PHYS+ 2023. [DOI: 10.1134/s002209302301009x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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14
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Morgan CE, Zhang Z, Miyagi M, Golczak M, Yu EW. Toward structural-omics of the bovine retinal pigment epithelium. Cell Rep 2022; 41:111876. [PMID: 36577381 PMCID: PMC9875382 DOI: 10.1016/j.celrep.2022.111876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 10/12/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on determining the structure of a particular biomacromolecule of interest. Here, we report the use of cryoelectron microscopy (cryo-EM) to define the composition of a raw bovine retinal pigment epithelium (RPE) lysate. From this sample, we simultaneously identify and solve cryo-EM structures of seven different RPE enzymes whose functions affect neurotransmitter recycling, iron metabolism, gluconeogenesis, glycolysis, axonal development, and energy homeostasis. Interestingly, dysfunction of these important proteins has been directly linked to several neurodegenerative disorders, including Huntington's disease, amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, and schizophrenia. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
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Affiliation(s)
- Christopher E. Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Department of Chemistry, Thiel College, Greenville, PA 16125, USA,These authors contributed equally
| | - Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,These authors contributed equally
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Marcin Golczak
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Lead contact,Correspondence:
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15
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Grossenbacher P, Essers MC, Moser J, Singer SA, Häusler S, Stieger B, Rougier JS, Lochner M. Bioorthogonal site-selective conjugation of fluorescent dyes to antibodies: method and potential applications. RSC Adv 2022; 12:28306-28317. [PMID: 36320493 PMCID: PMC9533196 DOI: 10.1039/d2ra05580e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022] Open
Abstract
Antibodies are immensely useful tools for biochemical research and have found application in numerous protein detection and purification methods. Moreover, monoclonal antibodies are increasingly utilised as therapeutics or, conjugated to active pharmaceutical ingredients, in targeted chemotherapy. Several reagents and protocols are reported to synthesise fluorescent antibodies for protein target detection and immunofluorescence applications. However, most of these protocols lead to non-selective conjugation, over-labelling or in the worst case antigen binding site modification. Here, we have used the antibody disulphide cleavage and re-bridging strategy to introduce bright fluorescent dyes without loss of the antibody function. The resulting fluorescent IgG1 type antibodies were shown to be effective imaging tools in western blot and direct immunofluorescence experiments.
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Affiliation(s)
- Philipp Grossenbacher
- Institute of Biochemistry and Molecular Medicine, University of BernBühlstrasse 283012 BernSwitzerland
| | - Maria C. Essers
- Institute of Biochemistry and Molecular Medicine, University of BernBühlstrasse 283012 BernSwitzerland
| | - Joël Moser
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of BernFreiestrasse 33012 BernSwitzerland
| | - Simon A. Singer
- Institute of Biochemistry and Molecular Medicine, University of BernBühlstrasse 283012 BernSwitzerland
| | - Stephanie Häusler
- Department of Clinical Pharmacology and Toxicology, University Hospital Zürich, University of ZürichRämistrasse 1008091 ZürichSwitzerland
| | - Bruno Stieger
- Department of Clinical Pharmacology and Toxicology, University Hospital Zürich, University of ZürichRämistrasse 1008091 ZürichSwitzerland
| | - Jean-Sébastien Rougier
- Institute of Biochemistry and Molecular Medicine, University of BernBühlstrasse 283012 BernSwitzerland
| | - Martin Lochner
- Institute of Biochemistry and Molecular Medicine, University of BernBühlstrasse 283012 BernSwitzerland
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16
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Tawa M, Okamura T. Factors influencing the soluble guanylate cyclase heme redox state in blood vessels. Vascul Pharmacol 2022; 145:107023. [PMID: 35718342 DOI: 10.1016/j.vph.2022.107023] [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: 03/11/2022] [Revised: 06/09/2022] [Accepted: 06/12/2022] [Indexed: 11/15/2022]
Abstract
Soluble guanylate cyclase (sGC) plays an important role in maintaining vascular homeostasis, as an acceptor for the biological messenger nitric oxide (NO). However, only reduced sGC (with a ferrous heme) can be activated by NO; oxidized (ferric heme) and apo (absent heme) sGC cannot. In addition, the proportions of reduced, oxidized, and apo sGC change under pathological conditions. Although diseased blood vessels often show decreased NO bioavailability in the vascular wall, a shift of sGC heme redox balance in favor of the oxidized/apo forms can also occur. Therefore, sGC is of growing interest as a drug target for various cardiovascular diseases. Notably, the balance between NO-sensitive reduced sGC and NO-insensitive oxidized/apo sGC in the body is regulated in a reversible manner by various biological molecules and proteins. Many studies have attempted to identify endogenous factors and determinants that influence this redox state. For example, various reactive nitrogen and oxygen species are capable of inducing the oxidation of sGC heme. Conversely, a heme reductase and some antioxidants reduce the ferric heme in sGC to the ferrous state. This review summarizes the factors and mechanisms identified by these studies that operate to regulate the sGC heme redox state.
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Affiliation(s)
- Masashi Tawa
- Department of Pathological and Molecular Pharmacology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka 569-1094, Japan.
| | - Tomio Okamura
- Emeritus Professor, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan
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17
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Dual-hairpin ligation amplification enabled ultra-sensitive and selective ATP detection for cancer monitor. Biosens Bioelectron 2022; 212:114402. [PMID: 35653851 DOI: 10.1016/j.bios.2022.114402] [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: 04/29/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022]
Abstract
Abnormal concentration of ATP is related to many diseases such as Parkinson's disease, hypoglycaemia, inflammation and cancer. However, most of the reported strategies exhibit moderate sensitivity with ∼nM level detection limit and few of them can distinguish ATP from its analogues, such as GTP, CTP, UTP and adenosine. Herein, we report an ultra-sensitive and selective ATP detection strategy that combines dual hairpin ligation-induced isothermal amplification (DHLA) with ATP-dependent enzymatic reaction. A good linear relationship between Cq value and ATP concentration in the range from 16 fM to 160 nM is acquired. Meanwhile, the strategy can distinguish ATP from its analogues with high selectivity. Furthermore, our proposed strategy has been successfully utilized to detect ATP from colon cell line and cell culture media with great potential applications in cell metabolism and cancer diagnosis.
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18
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Guo H, Zhang Y, Hu Z, Wang L, Du H. Screening and identification of biomarkers associated with the immune infiltration of intracerebral hemorrhage. J Clin Lab Anal 2022; 36:e24361. [PMID: 35318719 PMCID: PMC9102626 DOI: 10.1002/jcla.24361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Recent studies showed that inflammation and immunity might play essential roles in the progression of intracerebral hemorrhage (ICH). However, the underlying mechanisms for changes at the cellular and molecular levels after ICH remain unclear. METHODS We downloaded the microarray dataset of ICH from the Gene Expression Omnibus (GEO) database. The differential expression gene analysis was obtained by weighted gene co-expression network analysis (WGCNA). We got the hub genes and performed the biological functions and signaling pathways of these genes by Metascape. GSVA algorithm was used to evaluate the potential physical function of time-varying ICH samples. We used single-sample gene set enrichment analysis (ssGSEA) to assess the immune signatures infiltration and analyzed the correlation between hub genes and immune signatures. RESULTS The data sets of all 22 ICH samples in GSE125512 were examined by the WGCNA R package. We finally screened five hub genes (GAPDH, PF4, SELP, APP, and PPBP) in the royal blue module. Metascape analysis displayed the biological processes related to inflammation and immunology. Cell adhesion molecule binding, myeloid leukocyte activation, CXCR chemokine receptor binding, and regulation of cytokine production were the most enriched pathophysiological process. The immune signatures infiltration analyses showed that ICH patients' early and late samples had different activity and abundance of immune-related cells and types. CONCLUSIONS GAPDH, PF4, SELP, APP, and PPBP are identified as potential biomarkers for predicting the progression of ICH. This study may help us better understand the immunologic mechanism and shed new light on the promising approaches of immunotherapy for ICH patients.
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Affiliation(s)
- Hao Guo
- The First Central Clinical School, Tianjin Medical University, Tianjin, China.,Department of Anesthesiology, Shanxi provincial people's Hospital, Taiyuan, China
| | - Yanjun Zhang
- The First Central Clinical School, Tianjin Medical University, Tianjin, China.,Department of Anesthesiology, Tianjin Children's Hospital, Tianjin, China
| | - Zhanfei Hu
- The First Central Clinical School, Tianjin Medical University, Tianjin, China.,Department of Anesthesiology, Chifeng Municipal Hospital, Chifeng, China
| | - Li Wang
- The First Central Clinical School, Tianjin Medical University, Tianjin, China
| | - Hongyin Du
- The First Central Clinical School, Tianjin Medical University, Tianjin, China
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19
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Horemans S, Pitoulias M, Holland A, Pateau E, Lechaplais C, Ekaterina D, Perret A, Soultanas P, Janniere L. Pyruvate kinase, a metabolic sensor powering glycolysis, drives the metabolic control of DNA replication. BMC Biol 2022; 20:87. [PMID: 35418203 PMCID: PMC9009071 DOI: 10.1186/s12915-022-01278-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/11/2022] [Indexed: 12/04/2022] Open
Abstract
Background In all living organisms, DNA replication is exquisitely regulated in a wide range of growth conditions to achieve timely and accurate genome duplication prior to cell division. Failures in this regulation cause DNA damage with potentially disastrous consequences for cell viability and human health, including cancer. To cope with these threats, cells tightly control replication initiation using well-known mechanisms. They also couple DNA synthesis to nutrient richness and growth rate through a poorly understood process thought to involve central carbon metabolism. One such process may involve the cross-species conserved pyruvate kinase (PykA) which catalyzes the last reaction of glycolysis. Here we have investigated the role of PykA in regulating DNA replication in the model system Bacillus subtilis. Results On analysing mutants of the catalytic (Cat) and C-terminal (PEPut) domains of B. subtilis PykA we found replication phenotypes in conditions where PykA is dispensable for growth. These phenotypes are independent from the effect of mutations on PykA catalytic activity and are not associated with significant changes in the metabolome. PEPut operates as a nutrient-dependent inhibitor of initiation while Cat acts as a stimulator of replication fork speed. Disruption of either PEPut or Cat replication function dramatically impacted the cell cycle and replication timing even in cells fully proficient in known replication control functions. In vitro, PykA modulates activities of enzymes essential for replication initiation and elongation via functional interactions. Additional experiments showed that PEPut regulates PykA activity and that Cat and PEPut determinants important for PykA catalytic activity regulation are also important for PykA-driven replication functions. Conclusions We infer from our findings that PykA typifies a new family of cross-species replication control regulators that drive the metabolic control of replication through a mechanism involving regulatory determinants of PykA catalytic activity. As disruption of PykA replication functions causes dramatic replication defects, we suggest that dysfunctions in this new family of universal replication regulators may pave the path to genetic instability and carcinogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01278-3.
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Affiliation(s)
- Steff Horemans
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Matthaios Pitoulias
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Alexandria Holland
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Emilie Pateau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Christophe Lechaplais
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Dariy Ekaterina
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France.
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20
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Gao H, Niu J, Zhao W, Zhang D, Li S, Xu Y, Liu Y. The Effect and Regulation Mechanism of Powdery Mildew on Wheat Grain Carbon Metabolism. STARCH-STARKE 2022. [DOI: 10.1002/star.202100239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hongyun Gao
- School of Life Sciences Zhengzhou Normal University Zhengzhou 450044 China
| | - Jishan Niu
- National Centre of Engineering and Technological Research for Wheat Henan Agricultural University Zhengzhou 450046 China
| | - Wanyong Zhao
- College of Food and Bioengineering Zhengzhou University of Light Industry Zhengzhou 450000 China
| | - Dale Zhang
- School of Life Sciences Henan University Kaifeng 475004 China
| | - Suoping Li
- School of Life Sciences Henan University Kaifeng 475004 China
| | - Yanhua Xu
- School of Life Sciences Zhengzhou Normal University Zhengzhou 450044 China
| | - Yumiao Liu
- School of Life Sciences Zhengzhou Normal University Zhengzhou 450044 China
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21
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Canarelli SE, Swalm BM, Larson ET, Morrison MJ, Weerapana E. Monitoring GAPDH activity and inhibition with cysteine-reactive chemical probes. RSC Chem Biol 2022; 3:972-982. [PMID: 35866162 PMCID: PMC9257626 DOI: 10.1039/d2cb00091a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a central enzyme in glycolysis that regulates the Warburg effect in cancer cells. In addition to its role in metabolism, GAPDH is also implicated in diverse cellular processes, including transcription and apoptosis. Dysregulated GAPDH activity is associated with a variety of pathologies, and GAPDH inhibitors have demonstrated therapeutic potential as anticancer and immunomodulatory agents. Given the critical role of GAPDH in pathophysiology, it is important to have access to tools that enable rapid monitoring of GAPDH activity and inhibition within a complex biological system. Here, we report an electrophilic peptide-based probe, SEC1, which covalently modifies the active-site cysteine, C152, of GAPDH to directly report on GAPDH activity within a proteome. We demonstrate the utility of SEC1 to assess changes in GAPDH activity in response to oncogenic transformation, reactive oxygen species (ROS) and small-molecule GAPDH inhibitors, including Koningic acid (KA). We then further evaluated KA, to determine the detailed mechanism of inhibition. Our mechanistic studies confirm that KA is a highly effective irreversible inhibitor of GAPDH, which acts through a NAD+-uncompetitive and G3P-competitive mechanism. Proteome-wide evaluation of the cysteine targets of KA demonstrated high selectivity for the active-site cysteine of GAPDH over other reactive cysteines within the proteome. Lastly, the therapeutic potential of KA was investigated in an autoimmune model, where treatment with KA resulted in decreased cytokine production by Th1 effector cells. Together, these studies describe methods to evaluate GAPDH activity and inhibition within a proteome, and report on the high potency and selectivity of KA as an irreversible inhibitor of GAPDH. Cysteine-reactive chemical probes can covalently modify the active-site cysteine of GAPDH.![]()
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Affiliation(s)
- Sarah E. Canarelli
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | | | - Eric T. Larson
- Rheos Medicines, Inc, Cambridge, Massachusetts 02142, USA
| | | | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
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22
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Levi H, Bar E, Cohen-Adiv S, Sweitat S, Kanner S, Galron R, Mitiagin Y, Barzilai A. Dysfunction of cerebellar microglia in Ataxia-telangiectasia. Glia 2021; 70:536-557. [PMID: 34854502 DOI: 10.1002/glia.24122] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022]
Abstract
Ataxia-telangiectasia (A-T) is a multisystem autosomal recessive disease caused by mutations in the ATM gene and characterized by cerebellar atrophy, progressive ataxia, immunodeficiency, male and female sterility, radiosensitivity, cancer predisposition, growth retardation, insulin-resistant diabetes, and premature aging. ATM phosphorylates more than 1500 target proteins, which are involved in cell cycle control, DNA repair, apoptosis, modulation of chromatin structure, and other cytoplasmic as well as mitochondrial processes. In our quest to better understand the mechanisms by which ATM deficiency causes cerebellar degeneration, we hypothesized that specific vulnerabilities of cerebellar microglia underlie the etiology of A-T. Our hypothesis is based on the recent finding that dysfunction of glial cells affect a variety of process leading to impaired neuronal functionality (Song et al., 2019). Whereas astrocytes and neurons descend from the neural tube, microglia originate from the hematopoietic system, invade the brain at early embryonic stage, and become the innate immune cells of the central nervous system and important participants in development of synaptic plasticity. Here we demonstrate that microglia derived from Atm-/- mouse cerebellum display accelerated cell migration and are severely impaired in phagocytosis, secretion of neurotrophic factors, and mitochondrial activity, suggestive of apoptotic processes. Interestingly, no microglial impairment was detected in Atm-deficient cerebral cortex, and Atm deficiency had less impact on astroglia than microglia. Collectively, our findings validate the roles of glial cells in cerebellar attrition in A-T.
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Affiliation(s)
- Hadar Levi
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ela Bar
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Stav Cohen-Adiv
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Suzan Sweitat
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sivan Kanner
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ronit Galron
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yulia Mitiagin
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ari Barzilai
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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23
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Cui C, Zhu L, Tang X, Xing J, Sheng X, Chi H, Zhan W. Differential white spot syndrome virus-binding proteins in two hemocyte subpopulations of Chinese shrimp (Fenneropenaeus chinensis). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 125:104215. [PMID: 34324898 DOI: 10.1016/j.dci.2021.104215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
A number of white spot syndrome virus (WSSV)-binding proteins have been identified previously in the hemocytes of Fenneropenaeus chinensis. In order to further investigate the differential WSSV-binding proteins in hemocyte subpopulations, granular hemocytes and hyalinocytes were sorted from WSSV-infected shrimp by immunomagnetic bead (IMB) method. The results of ELISA and immuno-dot blot assay showed that the WSSV-binding activity of granular hemocytes proteins was much stronger than that of hyalinocytes proteins. And the percentage of WSSV-positive granular hemocytes was significantly higher than that of hyalinocytes post WSSV infection, indicating that granular hemocytes were more susceptible to WSSV infection. Moreover, a total of 9 WSSV-binding proteins were successfully identified in granular hemocytes and hyalinocytes by two-dimensional virus overlay protein binding assay (2D-VOPBA) and MALDI-TOF MS analysis, of which 3 binding proteins (arginine kinase, protease 1 and transglutaminase) existing in both hyalinocytes and granular hemocytes and 6 proteins (F1ATP synthase β-chain, hnRNPs, GAPDH, RACK1, β-actin and cellular retinoic acid) detected only in granular hemocytes. Among these identified WSSV-binding proteins, the transglutaminase (TG) was further recombinantly expressed, and the recombinant TG could be bound with WSSV. Subsequently, quantitative real-time PCR analysis showed that differential expression levels of WSSV-binding proteins were observed in granular hemocytes and hyalinocytes. The results of this study revealed that the WSSV-binding proteins were differentially expressed in granular hemocytes and hyalinocytes, which provided a deeper insight into the interaction between WSSV and hemocyte subpopulations.
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Affiliation(s)
- Chuang Cui
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China
| | - Lei Zhu
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China
| | - Xiaoqian Tang
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| | - Jing Xing
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xiuzhen Sheng
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China
| | - Heng Chi
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China
| | - Wenbin Zhan
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
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24
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Dar GH, Mendes CC, Kuan WL, Speciale AA, Conceição M, Görgens A, Uliyakina I, Lobo MJ, Lim WF, El Andaloussi S, Mäger I, Roberts TC, Barker RA, Goberdhan DCI, Wilson C, Wood MJA. GAPDH controls extracellular vesicle biogenesis and enhances the therapeutic potential of EV mediated siRNA delivery to the brain. Nat Commun 2021; 12:6666. [PMID: 34795295 PMCID: PMC8602309 DOI: 10.1038/s41467-021-27056-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 10/17/2021] [Indexed: 01/04/2023] Open
Abstract
Extracellular vesicles (EVs) are biological nanoparticles with important roles in intercellular communication, and potential as drug delivery vehicles. Here we demonstrate a role for the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in EV assembly and secretion. We observe high levels of GAPDH binding to the outer surface of EVs via a phosphatidylserine binding motif (G58), which promotes extensive EV clustering. Further studies in a Drosophila EV biogenesis model reveal that GAPDH is required for the normal generation of intraluminal vesicles in endosomal compartments, and promotes vesicle clustering. Fusion of the GAPDH-derived G58 peptide to dsRNA-binding motifs enables highly efficient loading of small interfering RNA (siRNA) onto the EV surface. Such vesicles efficiently deliver siRNA to multiple anatomical regions of the brain in a Huntington's disease mouse model after systemic injection, resulting in silencing of the huntingtin gene in different regions of the brain.
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Affiliation(s)
- Ghulam Hassan Dar
- Department of Paediatrics, University of Oxford, Oxford, OX1 3QX, UK
| | - Cláudia C Mendes
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK
| | - Wei-Li Kuan
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0PY, UK
| | - Alfina A Speciale
- Department of Paediatrics, University of Oxford, Oxford, OX1 3QX, UK
| | - Mariana Conceição
- Department of Paediatrics, University of Oxford, Oxford, OX1 3QX, UK
| | - André Görgens
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, 14186, Stockholme, Sweden
| | - Inna Uliyakina
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK
| | - Miguel J Lobo
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK
| | - Wooi F Lim
- Department of Paediatrics, University of Oxford, Oxford, OX1 3QX, UK
| | - Samir El Andaloussi
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, 14186, Stockholme, Sweden
| | - Imre Mäger
- Department of Paediatrics, University of Oxford, Oxford, OX1 3QX, UK
| | - Thomas C Roberts
- Department of Paediatrics, University of Oxford, Oxford, OX1 3QX, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, OX2 9DU, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0PY, UK
| | - Deborah C I Goberdhan
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK
| | - Clive Wilson
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK.
| | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, Oxford, OX1 3QX, UK.
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, OX2 9DU, UK.
- Oxford-Harrington Rare Disease Centre, University of Oxford, Oxford, OX2 9DU, UK.
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25
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Dube DK, Wang J, Fan Y, Dube S, Abbott L, Sanger JM, Channaveerappa D, Darie CC, Poiesz BJ, Sanger JW. Effect of MG-132 on myofibrillogenesis and the ubiquitination of GAPDH in quail myotubes. Cytoskeleton (Hoboken) 2021; 78:375-390. [PMID: 34698442 DOI: 10.1002/cm.21690] [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: 08/17/2021] [Revised: 10/07/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022]
Abstract
In the three-step myofibrillogenesis model, mature myofibrils are formed through two intermediate structures: premyofibrils and nascent myofibrils. We have recently reported that several inhibitors of the Ubiquitin Proteosome System, for example, MG-132, and DBeQ, reversibly block progression of nascent myofibrils to mature myofibrils. In this investigation, we studied the effects of MG132 and DBeQ on the expression of various myofibrillar proteins including actin, myosin light and heavy chains, tropomyosin, myomesin, and myosin binding protein-C in cultured embryonic quail myotubes by western blotting using two loading controls-α-tubulin and glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Surprisingly, we found that MG-132 affected the level of expression of GAPDH but DBeQ did not. Reverse transcription polymerase chain reaction (RT-PCR) and quantitative reverse transcription-PCR (qRT-PCR) showed no significant effect of MG-132 on GAPDH transcription. Two-dimensional (2D) western blot analyses with extracts of control and MG-132-treated cells using anti-ubiquitin antibody indicated that MG132-treated myotubes show a stronger emitter-coupled logic signal. However, Spot% and Spot volume calculations for all spots from both western blot film signals and matched Coomassie-stained 2D polyacrylamide gel electrophoresis showed that the intensity of staining in a spot of ~39 kDa protein is 3.5-fold lower in the gel of MG-132-treated extracts. Mass spectrometry analyses identified the ~39 kDa protein as quail GAPDH. Immunohistochemical analysis of fixed MG-132-treated myotubes with anti-GAPDH antibody showed extensive clump formation, which may be analogous to granule formation by stress response factors in MG132-treated cells. This is the first report on in vivo ubiquitination of GAPDH. This may be essential for the moonlighting (Jeffery, 1999) activity of GAPDH for tailoring stress in myotubes.
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Affiliation(s)
- Dipak K Dube
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Jushuo Wang
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Yingli Fan
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Syamalima Dube
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Lynn Abbott
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Jean M Sanger
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Devika Channaveerappa
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, USA
| | - Bernard J Poiesz
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Joseph W Sanger
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, New York, USA
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26
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Glyceraldehyde-3-Phosphate Dehydrogenase Restricted in Cytoplasmic Location by Viral GP5 Facilitates Porcine Reproductive and Respiratory Syndrome Virus Replication via Its Glycolytic Activity. J Virol 2021; 95:e0021021. [PMID: 34160254 DOI: 10.1128/jvi.00210-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important endemic swine pathogens, causing enormous losses in the global swine industry. Commercially available vaccines only partially prevent or counteract the virus infection and correlated losses. PRRSV's replication mechanism has not been well understood. In this study, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was screened to bind with the viral major envelope glycoprotein 5 (GP5) after PRRSV infection. The interacting sites are located within a 13-amino-acid (aa) region (aa 93 to 105) of GP5 and at Lys227 of GAPDH. Interestingly, viral GP5 restricts the translocation of GAPDH from the cytoplasm to the nucleus. Moreover, cytoplasmic GAPDH facilitates PRRSV replication by virtue of its glycolytic activity. The results suggest that PRRSV GP5 restricts GAPDH to the nucleus and exploits its glycolytic activity to stimulate virus replication. The data provide insight into the role of GAPDH in PRRSV replication and reveal a potential target for controlling viral infection. IMPORTANCE PRRSV poses a severe economic threat to the pig industry. PRRSV GP5, the major viral envelope protein, plays an important role in viral infection, pathogenicity, and immunity. However, interactions between GP5 and host proteins have not yet been well studied. Here, we show that GAPDH interacts with GP5 through binding a 13-aa sequence (aa 93 to 105) in GP5, while GP5 interacts with GAPDH at the K277 amino acid residue of GAPDH. We demonstrate that GP5 interacts with GAPDH in the cytoplasm during PPRSV infection, inhibiting GAPDH entry into the nucleus. PRRSV exploits the glycolytic activity of GAPDH to promote viral replication. These results enrich our understanding of PRRSV infection and pathogenesis and open a new avenue for antiviral prevention and PRRSV treatment strategies.
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27
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Chaudhary S, Dhiman A, Dilawari R, Chaubey GK, Talukdar S, Modanwal R, Patidar A, Malhotra H, Raje CI, Raje M. Glyceraldehyde-3-Phosphate Dehydrogenase Facilitates Macroautophagic Degradation of Mutant Huntingtin Protein Aggregates. Mol Neurobiol 2021; 58:5790-5798. [PMID: 34406601 DOI: 10.1007/s12035-021-02532-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/11/2021] [Indexed: 11/29/2022]
Abstract
Protein aggregate accumulation is a pathological hallmark of several neurodegenerative disorders. Autophagy is critical for clearance of aggregate-prone proteins. In this study, we identify a novel role of the multifunctional glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in clearance of intracellular protein aggregates. Previously, it has been reported that though clearance of wild-type huntingtin protein is mediated by chaperone-mediated autophagy (CMA), however, degradation of mutant huntingtin (mHtt with numerous poly Q repeats) remains impaired by this route as mutant Htt binds with high affinity to Hsc70 and LAMP-2A. This delays delivery of misfolded protein to lysosomes and results in accumulation of intracellular aggregates which are degraded only by macroautophagy. Earlier investigations also suggest that mHtt causes inactivation of mTOR signaling, causing upregulation of autophagy. GAPDH had earlier been reported to interact with mHtt resulting in cellular toxicity. Utilizing a cell culture model of mHtt aggregates coupled with modulation of GAPDH expression, we analyzed the formation of intracellular aggregates and correlated this with autophagy induction. We observed that GAPDH knockdown cells transfected with N-terminal mutant huntingtin (103 poly Q residues) aggregate-prone protein exhibit diminished autophagy. GAPDH was found to regulate autophagy via the mTOR pathway. Significantly more and larger-sized huntingtin protein aggregates were observed in GAPDH knockdown cells compared to empty vector-transfected control cells. This correlated with the observed decrease in autophagy. Overexpression of GAPDH had a protective effect on cells resulting in a decreased load of aggregates. Our results demonstrate that GAPDH assists in the clearance of protein aggregates by autophagy induction. These findings provide a new insight in understanding the mechanism of mutant huntingtin aggregate clearance. By studying the molecular mechanism of protein aggregate clearance via GAPDH, we hope to provide a new approach in targeting and understanding several neurodegenerative disorders.
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Affiliation(s)
- Surbhi Chaudhary
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh, India, 160036
| | - Asmita Dhiman
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh, India, 160036
| | - Rahul Dilawari
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh, India, 160036
| | | | - Sharmila Talukdar
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh, India, 160036
| | - Radheshyam Modanwal
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh, India, 160036
| | - Anil Patidar
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh, India, 160036
| | - Himanshu Malhotra
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh, India, 160036
| | - Chaaya Iyengar Raje
- National Institute of Pharmaceutical Education & Research, Phase X, Sector 67, SAS Nagar, Punjab, India, 160062
| | - Manoj Raje
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh, India, 160036.
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28
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Chaudhary S, Dhiman A, Patidar A, Malhotra H, Talukdar S, Dilawari R, Chaubey GK, Modanwal R, Raje CI, Raje M. Moonlighting glyceraldehyde-3-phosphate dehydrogenase (GAPDH) modulates protein aggregation. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166202. [PMID: 34144092 DOI: 10.1016/j.bbadis.2021.166202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 11/18/2022]
Abstract
Onset of protein aggregation reflects failure of the cellular folding machinery to keep aggregation-prone protein from misfolding and accumulating into a non-degradable state. FRET based analysis and biochemical data reveal that cytosolic prion (cyPrP) and httQ-103 interact with the multifunctional protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) leading to few detectable aggregates in GAPDH-over expressing cells.The preventive effect of GAPDH suggests that this abundant and long-lived cytoplasmic protein has an active role in the shielding and maintenance, in soluble form of proteins as heterogeneous as huntingtin and cyPrP.
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Affiliation(s)
- Surbhi Chaudhary
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Asmita Dhiman
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Anil Patidar
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Himanshu Malhotra
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Sharmila Talukdar
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Rahul Dilawari
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | | | - Radheshyam Modanwal
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India
| | - Chaaya Iyengar Raje
- National Institute of Pharmaceutical Education & Research, Phase X, Sector 67, SAS Nagar, Punjab 160062, India
| | - Manoj Raje
- Institute of Microbial Technology, CSIR, Sector 39A, Chandigarh 160036, India.
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29
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Iwamoto A, Inoue Y, Tachibana H, Kawahara H. Immunomodulatory effect of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in allergic conditions in vitro and in vivo. Cytotechnology 2021; 73:333-342. [PMID: 34149169 PMCID: PMC8166990 DOI: 10.1007/s10616-020-00438-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022] Open
Abstract
We found that strawberry extract suppressed immunoglobulin (Ig) E production in vitro and in vivo, and identified glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as one of the IgE suppressor in the extract. We report here the effect of GAPDH on various Ig productions in vitro and in vivo. GAPDH suppressed IgE and enhanced IgA, IgG and IgM productions in ovalbumin (OVA)-stimulated human peripheral blood mononuclear cells. Oral administration of GAPDH at 10 mg/kg/day to OVA-induced allergy model mice tended to decrease total IgE level and increase total IgA and IgG levels in sera, and also decreased OVA-specific IgE and IgG levels. It is known that the increase of total IgA as well as the decrease of total and specific IgE is important for alleviating allergic symptoms. In addition, GAPDH accelerated IgA production and increased some cytokine secretions such as IL-4, TGF-β1 and IFN-γ in the OVA-immunized mice spleen lymphocytes. These cytokines involved in the class-switching, IgA enhancement, and IgE suppression, respectively, supporting above results. Our study suggests a possibility that oral administration of GAPDH may induce the immunomodulation in allergic responses.
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Affiliation(s)
- Akira Iwamoto
- Division of Applied Biological Chemistry, Department of Bioscience and Biochemistry, Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395 Japan
| | - Yuichi Inoue
- Department of Creative Engineering, National Institute of Technology, Kitakyushu College, 5-20-1 Shii, Kokuraminami-ku, Kitakyushu, Fukuoka, 802-0985 Japan
| | - Hirofumi Tachibana
- Division of Applied Biological Chemistry, Department of Bioscience and Biochemistry, Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395 Japan
| | - Hiroharu Kawahara
- Department of Creative Engineering, National Institute of Technology, Kitakyushu College, 5-20-1 Shii, Kokuraminami-ku, Kitakyushu, Fukuoka, 802-0985 Japan
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30
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Curcio C, Brugiapaglia S, Bulfamante S, Follia L, Cappello P, Novelli F. The Glycolytic Pathway as a Target for Novel Onco-Immunology Therapies in Pancreatic Cancer. Molecules 2021; 26:1642. [PMID: 33804240 PMCID: PMC7998946 DOI: 10.3390/molecules26061642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/11/2021] [Indexed: 02/08/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal forms of human cancer, characterized by unrestrained progression, invasiveness and treatment resistance. To date, there are limited curative options, with surgical resection as the only effective strategy, hence the urgent need to discover novel therapies. A platform of onco-immunology targets is represented by molecules that play a role in the reprogrammed cellular metabolism as one hallmark of cancer. Due to the hypoxic tumor microenvironment (TME), PDA cells display an altered glucose metabolism-resulting in its increased uptake-and a higher glycolytic rate, which leads to lactate accumulation and them acting as fuel for cancer cells. The consequent acidification of the TME results in immunosuppression, which impairs the antitumor immunity. This review analyzes the genetic background and the emerging glycolytic enzymes that are involved in tumor progression, development and metastasis, and how this represents feasible therapeutic targets to counteract PDA. In particular, as the overexpressed or mutated glycolytic enzymes stimulate both humoral and cellular immune responses, we will discuss their possible exploitation as immunological targets in anti-PDA therapeutic strategies.
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Affiliation(s)
- Claudia Curcio
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (S.B.); (S.B.); (L.F.); (P.C.)
- Centro Ricerche Medicina Sperimentale, Azienda Ospedaliera Universitaria, Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Silvia Brugiapaglia
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (S.B.); (S.B.); (L.F.); (P.C.)
- Centro Ricerche Medicina Sperimentale, Azienda Ospedaliera Universitaria, Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Sara Bulfamante
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (S.B.); (S.B.); (L.F.); (P.C.)
- Centro Ricerche Medicina Sperimentale, Azienda Ospedaliera Universitaria, Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Laura Follia
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (S.B.); (S.B.); (L.F.); (P.C.)
- Computer Science Department, University of Turin, 10126 Turin, Italy
| | - Paola Cappello
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (S.B.); (S.B.); (L.F.); (P.C.)
- Centro Ricerche Medicina Sperimentale, Azienda Ospedaliera Universitaria, Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Francesco Novelli
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy; (C.C.); (S.B.); (S.B.); (L.F.); (P.C.)
- Centro Ricerche Medicina Sperimentale, Azienda Ospedaliera Universitaria, Città della Salute e della Scienza di Torino, 10126 Turin, Italy
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Guimaraes de Souza Melo C, Nelisis Zanoni J, Raquel Garcia de Souza S, Zignani I, de Lima Leite A, Domingues Heubel A, Vanessa Colombo Martins Perles J, Afonso Rabelo Buzalaf M. Global Proteomic Profile Integrated to Quantitative and Morphometric Assessment of Enteric Neurons: Investigation of the Mechanisms Involved in the Toxicity Induced by Acute Fluoride Exposure in the Duodenum. Neurotox Res 2021; 39:800-814. [PMID: 33689147 DOI: 10.1007/s12640-020-00296-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/20/2020] [Accepted: 10/11/2020] [Indexed: 10/21/2022]
Abstract
The enteric nervous system is responsible for controlling the gastrointestinal tract (GIT) functions. Enteric neuropathies are highly correlated to the development of several intestinal disturbances. Fluoride (F) is extensively applied for dental health improvement and its ingestion can promote systemic toxicity with mild to severe GIT symptomatology and neurotoxicity. Although F harmful effects have been published, there is no information regarding noxiousness of a high acute F exposure (25 mg F/kg) on enteric neurons and levels of expression of intestinal proteins in the duodenum. Quantitative proteomics of the duodenum wall associated to morphometric and quantitative analysis of enteric neurons displayed F effects of a high acute exposure. F-induced myenteric neuroplasticity was characterized by a decrease in the density of nitrergic neurons and morphometric alterations in the general populations of neurons, nitrergic neurons, and substance P varicosities. Proteomics demonstrated F-induced alterations in levels of expression of 356 proteins correlated to striated muscle cell differentiation; generation of precursor metabolites and energy; NADH and glutathione metabolic process and purine ribonucleoside triphosphate biosynthesis. The neurochemical role of several intestinal proteins was discussed specially related to the modulation of enteric neuroplasticity. The results provide a new perspective on cell signaling pathways of gastrointestinal symptomatology promoted by acute F toxicity.
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Affiliation(s)
| | | | | | - Isabela Zignani
- Department of Morphophysiological Sciences, State University of Maringá, Paraná, Brazil
| | - Aline de Lima Leite
- Department of Biological Sciences, School of Dentistry, University of São Paulo, Bauru, Brazil
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Sirover MA. The role of posttranslational modification in moonlighting glyceraldehyde-3-phosphate dehydrogenase structure and function. Amino Acids 2021; 53:507-515. [PMID: 33651246 DOI: 10.1007/s00726-021-02959-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/06/2021] [Indexed: 11/26/2022]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a moonlighting protein exhibiting distinct activities apart from its classical role in glycolysis. Regulation of its moonlighting functions and its subcellular localization may be dependent on its posttranslational modification (PTM). The latter include its phosphorylation, which is required for its role in intermembrane trafficking, synaptic transmission and cancer survival; nitrosylation, which is required for its function in apoptosis, heme metabolism and the immune response; acetylation which is necessary for its modulation of apoptotic gene regulation; and N-acetylglucosamine modification which may induce changes in GAPDH oligomeric structure. These findings suggest a structure function relationship between GAPDH posttranslational modification and its diverse moonlighting activities.
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Affiliation(s)
- Michael A Sirover
- Department of Pharmacology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.
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Kalyanasundaram A, Henry BJ, Henry C, Kendall RJ. Molecular phylogenetic and in silico analysis of glyceraldeyde-3-phosphate dehydrogenase (GAPDH) gene from northern bobwhite quail (Colinus virginianus). Mol Biol Rep 2021; 48:1093-1101. [PMID: 33580461 DOI: 10.1007/s11033-021-06186-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/28/2021] [Indexed: 10/22/2022]
Abstract
Many recent studies have been focused on prevalence and impact of two helminth parasites, eyeworm Oxyspirura petrowi and caecal worm Aulonocephalus pennula, in the northern bobwhite quail (Colinus virginianus). However, few studies have attempted to examine the effect of these parasites on the bobwhite immune system. This is likely due to the lack of proper reference genes for relative gene expression studies. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme that is often utilized as a reference gene, and in this preliminary study, we evaluated the similarity of bobwhite GAPDH to GAPDH in other avian species to evaluate its potential as a reference gene in bobwhite. GAPDH was identified in the bobwhite full genome sequence and multiple sets of PCR primers were designed to generate overlapping PCR products. These products were then sequenced and then aligned to generate the sequence for the full-length open reading frame (ORF) of bobwhite GAPDH. Utilizing this sequence, phylogenetic analyses and comparative analysis of the exon-intron pattern were conducted that revealed high similarity of GAPDH encoding sequences among bobwhite and other Galliformes. Additionally, This ORF sequence was also used to predict the encoded protein and its three-dimensional structure which like the phylogenetic analyses reveal that bobwhite GAPDH is similar to GAPDH in other Galliformes. Finally, GAPDH qPCR primers were designed, standardized, and tested with bobwhite both uninfected and infected with O. petrowi, and this preliminary test showed no statistical difference in expression of GAPDH between the two groups. These analyses are the first to investigate GAPDH in bobwhite. These efforts in phylogeny, sequence analysis, and protein structure suggest that there is > 97% conservation of GADPH among Galliformes. Furthermore, the results of these in silico tests and the preliminary qPCR indicate that GAPDH is a prospective candidate for use in gene expression analyses in bobwhite.
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Affiliation(s)
| | - Brett J Henry
- The Wildlife Toxicology Laboratory, Texas Tech University, Lubbock, TX, 79409-3290, USA
| | - Cassandra Henry
- The Wildlife Toxicology Laboratory, Texas Tech University, Lubbock, TX, 79409-3290, USA
| | - Ronald J Kendall
- The Wildlife Toxicology Laboratory, Texas Tech University, Lubbock, TX, 79409-3290, USA.
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Boreiko S, Silva M, Iulek J. Structure determination and analyses of the GAPDH from the parasite Schistosoma mansoni, the first one from a platyhelminth. Biochimie 2021; 184:18-25. [PMID: 33524435 DOI: 10.1016/j.biochi.2021.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/18/2021] [Accepted: 01/24/2021] [Indexed: 10/22/2022]
Abstract
The enzyme Glyceraldehyde-3-Phosphate Dehydrogenase from Schistosoma mansoni (SmGAPDH) is characterized as a therapeutical target for schistosomiasis. In this context, we report here the experimental structure, structural analyses and comparisons of SmGAPDH, the first one from a Platyhelminth. The enzyme was expressed, purified and assayed for crystallization, what allowed the obtainment of crystals of sufficient quality to collect X-ray diffraction data up to 2.51 Å resolution. SmGAPDH is the only GAPDH to present the sequence NNR (its residues 114-116) which leads to (especially R116) a hydrogen bond network that possibly reflects on the flexibility of residues to interact with the adenine part of NAD+, speculated to be important for differential drug design.
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Affiliation(s)
- Sheila Boreiko
- Department of Chemistry, State University of Ponta Grossa, Ponta Grossa - PR, 84030-900, Brazil
| | - Marcio Silva
- Department of Education, Federal Technological University of Paraná, Ponta Grossa - PR, 84016-210, Brazil
| | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, Ponta Grossa - PR, 84030-900, Brazil.
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Bioinformatic analysis of key pathways and genes involved in pediatric atopic dermatitis. Biosci Rep 2021; 41:227178. [PMID: 33289509 PMCID: PMC7789805 DOI: 10.1042/bsr20193517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/26/2020] [Accepted: 12/02/2020] [Indexed: 01/16/2023] Open
Abstract
The initiation of atopic dermatitis (AD) typically happens very early in life, but most of our understanding of AD is derived from studies on AD patients in adult. The aim of the present study was to identify gene signature speficic to pediatric AD comapred with adult AD. The gene expression profiles of four datasets (GSE32924, GSE36842, GSE58558, and GSE107361) were downloaded from the GEO database. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed, and protein–protein interaction (PPI) network was constructed by Cytoscape software. Total 654 differentially expressed genes (DEGs) (394 up-regulated and 260 down-regulated) were identified in pediatric AD samples with adult AD samples as control. The up-regulated DEGs were significantly enriched in the migration and chemotaxis of granulocyte and neutrophil, while down-regulated DEGs were significantly enriched in biological adhesion. KEGG pathway analysis showed that up-regulated DEGs participated in chemokine signaling pathway while down-regulated DEGs participated in adherens junction, focal adhesion, and regulation of actin cytoskeleton. The top 10 hub genes GAPDH, EGFR, ACTB, ESR1, CDK1, CXCL8, CD44, KRAS, PTGS2, and SMC3 were involved in chemokine signaling pathway, cytokine–cytokine receptor interaction, interleukin-17 signaling pathway, and regulation of actin cytoskeleton. In conclusion, we identified DEGs and hub genes involved in pediatric AD, which might be used as therapeutic targets and diagnostic biomarkers for pediatric AD.
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Nocua PA, Requena JM, Puerta CJ. Identification of the interactomes associated with SCD6 and RBP42 proteins in Leishmania braziliensis. J Proteomics 2020; 233:104066. [PMID: 33296709 DOI: 10.1016/j.jprot.2020.104066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/16/2020] [Accepted: 11/29/2020] [Indexed: 02/04/2023]
Abstract
Leishmania are protozoan parasites responsible for leishmaniasis. These parasites present a precise gene regulation that allows them to survive different environmental conditions during their digenetic life cycle. This adaptation depends on the regulation of the expression of a wide variety of genes, which occurs, mainly at the post-transcriptional level. This differential gene expression is achieved by mechanisms based mainly in RNA binding proteins that regulate the translation and/or stability of mRNA targets by interaction with cis elements principally located in the untranslated regions (UTR). In recent studies, our group identified and characterized two proteins, SCD6 and RBP42, as RNA binding proteins in Leishmania braziliensis. To find clues about the cellular processes in which these proteins are involved, this work was aimed to determine the SCD6- and RBP42-interacting proteins (interactome) in L. braziliensis promastigotes. For this purpose, after an in vivo UV cross-linking, cellular extracts were used to immunoprecipitated, by specific antibodies, protein complexes in which SCD6 or RBP42 were present. Protein mass spectrometry analysis of the immunoprecipitated proteins identified 96 proteins presumably associated with SCD6 and 173 proteins associated with RBP42. Notably, a significant proportion of the identified proteins were shared in both interactomes, indicating a possible functional relationship between SCD6 and RBP42. Remarkably, many of the proteins identified in the SCD6 and RBP42 interactomes are related to RNA metabolism and translation processes, and many of them have been described as components of ribonucleoprotein (RNP) granules in Leishmania and related trypanosomatids. Thus, these results support a role of SCD6 and RBP42 in the assembly and/or function of mRNA-protein complexes, participating in the fate (decay/accumulation/translation) of L. braziliensis transcripts. SIGNIFICANCE: Parasites of the Leishmania genus present a particular regulation of gene expression, operating mainly at the post-transcriptional level, surely aimed to modulate quickly both mRNA and protein levels to survive the sudden environmental changes that occur during a parasite's life cycle as it moves from one host to another. This regulation of gene expression processes would be governed by the interaction of mRNA with RNA binding proteins. Nevertheless, the entirety of protein networks involved in these regulatory processes is far from being understood. In this regard, our work is contributing to stablish protein networks in which the L. braziliensis SCD6 and RBP42 proteins are involved; these proteins, in previous works, have been described as RNA binding proteins and found to participate in gene regulation in different cells and organisms. Additionally, our data point out a possible functional relationship between SCD6 and RBP42 proteins as constituents of mRNA granules, like processing bodies or stress granules, which are essential structures in the regulation of gene expression. This knowledge could provide a new approach for the development of therapeutic targets to control Leishmania infections.
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Affiliation(s)
- Paola A Nocua
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia; Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - José M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - Concepción J Puerta
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
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Naghiyan Fesharaki S, Naghiyan Fesharaki S, Esmaeili A, Azadeh M, Ghaedi K. SNP rs1803622 in hsa-miR-548g binding site at GAPDH alters susceptibility to breast cancer. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Melnikova AK, Kuravsky ML, Kulikova KV, Sevostyanova IA, Muronetz VI. [Expression of sperm-specific glyceraldehyde-3-phosphate dehydrogenase in melanoma cells changes their energy metabolism]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2020; 66:372-377. [PMID: 33140730 DOI: 10.18097/pbmc20206605372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The somatic isoform of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC1.2.1.12) is involved in such crucial for cancer cells development pathways as induction of apoptosis and glycolytic regulation. At the same time, sperm-specific isoform (GAPDHS) does not exhibit all the same functions as somatic enzyme. The expression of sperm-specific GAPDH without N-terminal domain in some melanoma cells along with somatic isoenzyme, shown in our previous work, has led to the proposal of this unusual enzyme's possible role in regulation of cancer cells glycolysis. In the presented work we have tested production of GAPDHS in 13 additional melanoma cell lines by immunoblotting. We have also gathered data on energy metabolism in 5 selected cell lines by evaluation of glucose uptake and lactate production in differing conditions. We have demonstrated that in standard cultivation media glucose uptake by MelP cells, producing substantial amounts of GAPDHS protein was higher than in MelKor cells, producing lesser amounts of GAPDHS. All other analyzed cell lines that do not produce GAPDHS (MelMS, MelSi and Malme3M) had even a lower glucose uptake rate.
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Affiliation(s)
- A K Melnikova
- Faculty of Bioengineering and Bioinformatics Moscow State University, Moscow, Russia
| | - M L Kuravsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - K V Kulikova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - I A Sevostyanova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - V I Muronetz
- Faculty of Bioengineering and Bioinformatics Moscow State University, Moscow, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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Ribosome-Engineered Lacticaseibacillus rhamnosus Strain GG Exhibits Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Accumulation and Enhanced Adhesion to Human Colonic Mucin. Appl Environ Microbiol 2020; 86:AEM.01448-20. [PMID: 32801170 PMCID: PMC7531950 DOI: 10.1128/aem.01448-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/03/2020] [Indexed: 01/02/2023] Open
Abstract
We sought to apply ribosome engineering (RE) to probiotic lactic acid bacteria and to verify RE’s impact. Here, we showed that one mutant of RE Lacticaseibacillus rhamnosus GG (LGG-MTK56N) bore a GAPDH on the cell surface; the GAPDH was exported via an ABC transporter. Compared to the wild-type parent, LGG-MTK56N adhered more strongly to human colonic mucin and exhibited a distinct cell size and shape. These findings demonstrate that RE in LGG-MTK56N yielded dramatic changes in protein synthesis, protein transport, and cell morphology and affected adherence to human colonic mucin. Differences in individual host responses have emerged as an issue regarding the health benefits of probiotics. Here, we applied ribosome engineering (RE) technology, developed in an actinomycete study, to Lacticaseibacillus rhamnosus GG (LGG). RE can effectively enhance microbial potential by using antibiotics to induce spontaneous mutations in the ribosome and/or RNA polymerase. In this study, we identified eight types of streptomycin resistance mutations in the LGG rpsL gene, which encodes ribosomal protein S12. Notably, LGG harboring the K56N mutant (LGG-MTK56N) expressed high levels of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) on the cell surface compared with the LGG wild type (LGG-WT). GAPDH plays a key role in colonic mucin adhesion. Indeed, LGG-MTK56N significantly increased type A human colonic mucin adhesion compared to LGG-WT in experiments using the Biacore system. The ability to adhere to the colon is an important property of probiotics; thus, these results suggest that RE is an effective breeding strategy for probiotic lactic acid bacteria. IMPORTANCE We sought to apply ribosome engineering (RE) to probiotic lactic acid bacteria and to verify RE’s impact. Here, we showed that one mutant of RE Lacticaseibacillus rhamnosus GG (LGG-MTK56N) bore a GAPDH on the cell surface; the GAPDH was exported via an ABC transporter. Compared to the wild-type parent, LGG-MTK56N adhered more strongly to human colonic mucin and exhibited a distinct cell size and shape. These findings demonstrate that RE in LGG-MTK56N yielded dramatic changes in protein synthesis, protein transport, and cell morphology and affected adherence to human colonic mucin.
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Narula S, Tandon S, Kumar D, Varshney S, Adlakha K, Sengupta S, Singh SK, Tandon C. Human kidney stone matrix proteins alleviate hyperoxaluria induced renal stress by targeting cell-crystal interactions. Life Sci 2020; 262:118498. [PMID: 32991878 DOI: 10.1016/j.lfs.2020.118498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/10/2020] [Accepted: 09/20/2020] [Indexed: 12/19/2022]
Abstract
Increased levels of urinary oxalate also known as hyperoxaluria, increase the likelihood of kidney stone formation through enhanced calcium oxalate (CaOx) crystallization. The management of lithiatic renal pathology requires investigations at the initial macromolecular stages. Hence, the current study was designed to unravel the protein make-up of human kidney stones and its impact on renal cells' altered proteome, induced as the consequence of CaOx injury. CaOx kidney stones were collected from patients; stones were pooled for entire cohort, followed by protein extraction. Immunocytochemistry, RT-PCR and flow-cytometric analysis revealed the promising antilithiatic activity of kidney stone matrix proteins. The iTRAQ analysis of renal cells showed up-regulation of 12 proteins and down-regulation of 41 proteins due to CaOx insult, however, this differential expression was normalized in the presence of kidney stone matrix proteins. Protein network analysis revealed involvement of up-regulated proteins in apoptosis, calcium-binding, inflammatory and stress response pathways. Moreover, seven novel antilithiatic proteins were identified from human kidney stones' matrix: Tenascin-X-isoform2, CCDC-144A, LIM domain kinase-1, Serine/Arginine receptor matrix protein-2, mitochondrial peptide methionine sulfoxide reductase, volume-regulated anion channel subunit-LRRC8A and BMPR2. In silico analysis concluded that these proteins exert antilithiatic potential through crystal binding, thereby inhibiting the crystal-cell interaction, a pre-requisite to initiate inflammatory response. Thus, the outcomes of this study provide insights into the molecular events of CaOx induced renal toxicity and subsequent progression into nephrolithiasis.
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Affiliation(s)
- Shifa Narula
- Amity Institute of Biotechnology (AIB), Amity University, Noida, Uttar Pradesh 201301, India
| | - Simran Tandon
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh 201301, India
| | - Dhruv Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh 201301, India
| | - Swati Varshney
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Khushboo Adlakha
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Shantanu Sengupta
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Shrawan Kumar Singh
- Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Chanderdeep Tandon
- Amity Institute of Biotechnology (AIB), Amity University, Noida, Uttar Pradesh 201301, India.
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Pachauri S, Gupta GD, Mukherjee PK, Kumar V. Expression of a heptelidic acid-insensitive recombinant GAPDH from Trichoderma virens, and its biochemical and biophysical characterization. Protein Expr Purif 2020; 175:105697. [PMID: 32681951 DOI: 10.1016/j.pep.2020.105697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/08/2020] [Accepted: 06/26/2020] [Indexed: 12/30/2022]
Abstract
Trichoderma virens genome harbors two isoforms of GAPDH, one (gGPD) involved in glycolysis and the other one (vGPD) in secondary metabolism. vGPD is expressed as part of the "vir" cluster responsible for the biosynthesis of volatile sesquiterpenes. The secondary metabolism-associated GAPDH is tolerant to the anti-cancer metabolite heptelidic acid (HA), produced by T. virens. Characterizing the HA-tolerant form of GAPDH, thus has implications in cancer therapy. In order to get insight into the mechanism of HA-tolerance of vGPD, we have purified recombinant form of this protein. The protein displays biochemical and biophysical characteristics analogous to the gGPD isoform. It exists as a tetramer with Tm of about 56.5 °C, and displays phosphorylation enzyme activity with Km and Kcat of 0.38 mM and 2.55 sec-1, respectively. The protein weakly binds to the sequence upstream of the vir4 gene that codes for the core enzyme (a terpene cyclase) of the "vir" cluster. The EMSA analysis indicates that vGPD may not act as a transcription factor driving the "vir" cluster, at least not by directly binding to the promoter region. We also succeeded in obtaining small crystals of this protein. We have constructed structural models of vGPD and gGPD of T. virens. In silico constrained docking analysis reveals weaker binding of heptelidic acid in vGPD, compared to gGPD protein.
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Affiliation(s)
- Shikha Pachauri
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Gagan D Gupta
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India; Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
| | - Vinay Kumar
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
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Muronetz VI, Melnikova AK, Saso L, Schmalhausen EV. Influence of Oxidative Stress on Catalytic and Non-glycolytic Functions of Glyceraldehyde-3-phosphate Dehydrogenase. Curr Med Chem 2020; 27:2040-2058. [PMID: 29848267 DOI: 10.2174/0929867325666180530101057] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) is a unique enzyme that, besides its main function in glycolysis (catalysis of glyceraldehyde-3-phosphate oxidation), possesses a number of non-glycolytic activities. The present review summarizes information on the role of oxidative stress in the regulation of the enzymatic activity as well as non-glycolytic functions of GAPDH. METHODS Based on the analysis of literature data and the results obtained in our research group, mechanisms of the regulation of GAPDH functions through the oxidation of the sulfhydryl groups in the active site of the enzyme have been suggested. RESULTS Mechanism of GAPDH oxidation includes consecutive oxidation of the catalytic Cysteine (Cys150) into sulfenic, sulfinic, and sulfonic acid derivatives, resulting in the complete inactivation of the enzyme. The cysteine sulfenic acid reacts with reduced glutathione (GSH) to form a mixed disulfide (S-glutathionylated GAPDH) that further reacts with Cys154 yielding the disulfide bond in the active site of the enzyme. In contrast to the sulfinic and sulfonic acids, the mixed disulfide and the intramolecular disulfide bond are reversible oxidation products that can be reduced in the presence of GSH or thioredoxin. CONCLUSION Oxidation of sulfhydryl groups in the active site of GAPDH is unavoidable due to the enhanced reactivity of Cys150. The irreversible oxidation of Cys150 is prevented by Sglutathionylation and disulfide bonding with Cys154. The oxidation/reduction of the sulfhydryl groups in the active site of GAPDH can be used for regulation of glycolysis and numerous side activities of this enzyme including the induction of apoptosis.
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Affiliation(s)
- Vladimir I Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Aleksandra K Melnikova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer"Sapienza, University of Rome, Rome, Italy
| | - Elena V Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
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Arabiyat AS, Becerra-Bayona S, Kamaldinov T, Munoz-Pinto DJ, Hahn MS. Hydrogel Properties May Influence Mesenchymal Stem Cell Lineage Progression Through Modulating GAPDH Activity. REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE 2020. [DOI: 10.1007/s40883-020-00164-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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44
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Lin L, Zhang Y, Li Y, Fu H, Hu J, Zhou Y, Xu Y, Xia G, Sun X, Yang H, Shen Y. Identification of signature proteins of processed Bombyx batryticatus by comparative proteomic analysis. Int J Biol Macromol 2020; 153:289-296. [DOI: 10.1016/j.ijbiomac.2020.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/02/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022]
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Tsai CW, Tsai CF, Lin KH, Chen WJ, Lin MS, Hsieh CC, Lin CC. An investigation of the correlation between the S-glutathionylated GAPDH levels in blood and Alzheimer's disease progression. PLoS One 2020; 15:e0233289. [PMID: 32469899 PMCID: PMC7259681 DOI: 10.1371/journal.pone.0233289] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/03/2020] [Indexed: 11/24/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disease characterized by two aggregates, namely, amyloid-β (Aβ) plaques and neurofibrillary tangles (NFTs) of hyperphosphorylated tau protein (tau-p), which are released into the blood in a very small amount and cannot be easily detected. An increasing number of recent studies have suggested that S-glutathionylated glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is highly correlated with Aβ in patients with AD and that S-glutathionylated GAPDH plays a role as a proapoptotic factor in AD. We found that S-glutathionylated GAPDH is abundant in the blood of AD patients, which is unusual because S-glutathionylated GAPDH cannot exist in the blood under normal conditions. The aim of this study was to further explore the correlation between the S-glutathionylated GAPDH levels in blood plasma and AD progression. As controls, we recruited 191 people without AD, which included 111 healthy individuals and 37 patients with depression and insomnia, in the psychosomatic clinic. Moreover, 47 patients with AD (aged 40–89 years) were recruited at the neurology clinic. The blood S-glutathionylated GAPDH levels in the AD patients were significantly (p < 0.001) higher (752.7 ± 301.7 ng/dL) than those in the controls (59.92 ± 122.4 ng/dL), irrespective of gender and age. For AD diagnosis, the criterion blood S-glutathionylated GAPDH level > 251.62 ng/dL exhibited 95.74% sensitivity and 92.67% specificity. In fact, the individuals aged 70–89 years, namely, 37 patients from the psychosomatic clinic and 42 healthy individuals, showed significant blood S-glutathionylated GAPDH levels (230.5 ± 79.3 and 8.05 ± 20.51 ng/dL, respectively). This finding might indicate neurodegenerative AD progression in psychosomatic patients and suggests that the degree of neuronal apoptosis during AD progression might be sensitively evaluated based on the level of S-glutathionylated GAPDH in blood.
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Affiliation(s)
- Chen Wei Tsai
- Department of Biotechnology and Animal Science, College of Bioresources, National Ilan University, Yilan City, Taiwan
| | - Chia Fan Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Kuan Hung Lin
- Department of Neurology, Taiwan Adventist Hospital, Taipei, Taiwan
| | - Wei Jung Chen
- Department of Biotechnology and Animal Science, College of Bioresources, National Ilan University, Yilan City, Taiwan
| | - Muh Shi Lin
- Department of Biotechnology and Animal Science, College of Bioresources, National Ilan University, Yilan City, Taiwan.,Department of Surgery, Kuang Tien General Hospital, Taichung, Taiwan.,Department of Biotechnology, College of Medical and Health Care, Hung Kuang University, Taichung, Taiwan.,Department of Health Business Administration, College of Medical and Health Care, Hung Kuang University, Taichung, Taiwan
| | | | - Chai Ching Lin
- Department of Biotechnology and Animal Science, College of Bioresources, National Ilan University, Yilan City, Taiwan
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Leu SJ, Lee YC, Lee CH, Liao PY, Chiang CW, Yang CM, Su CH, Ou TY, Liu KJ, Lo HJ, Tsai BY, Yang YY. Generation and Characterization of Single Chain Variable Fragment against Alpha-Enolase of Candida albicans. Int J Mol Sci 2020; 21:ijms21082903. [PMID: 32326294 PMCID: PMC7215377 DOI: 10.3390/ijms21082903] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 11/16/2022] Open
Abstract
Candida albicans (C. albicans) is an opportunistic human pathogen responsible for approximately a half of clinical candidemia. The emerging Candida spp. with resistance to azoles is a major challenge in clinic, suggesting an urgent demand for new drugs and therapeutic strategies. Alpha–enolase (Eno1) is a multifunctional protein and represents an important marker for invasive candidiasis. Thus, C. albicans Eno1 (CaEno1) is believed to be an important target for the development of therapeutic agents and antibody drugs. Recombinant CaEno1 (rCaEno1) was first used to immunize chickens. Subsequently, we used phage display technology to construct two single chain variable fragment (scFv) antibody libraries. A novel biopanning procedure was carried out to screen anti-rCaEno1 scFv antibodies, whose specificities were further characterized. The polyclonal IgY antibodies showed binding to rCaEno1 and native CaEno1. A dominant scFv (CaS1) and its properties were further characterized. CaS1 attenuated the growth of C. albicans and inhibited the binding of CaEno1 to plasminogen. Animal studies showed that CaS1 prolonged the survival rate of mice and zebrafish with candidiasis. The fungal burden in kidney and spleen, as well as level of inflammatory cytokines were significantly reduced in CaS1-treated mice. These results suggest CaS1 has potential of being immunotherapeutic drug against C. albicans infections.
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Affiliation(s)
- Sy-Jye Leu
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (S.-J.-L.); (C.-H.S.)
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (P.-Y.L.); (C.-W.C.); (C.-M.Y.)
- Center for Reproductive Medicine and Sciences, Taipei Medical University, Taipei 11031, Taiwan
| | - Yu-Ching Lee
- The Center of Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan;
| | - Chi-Hsin Lee
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (C.-H.L.); (K.-J.L.)
| | - Po-Yen Liao
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (P.-Y.L.); (C.-W.C.); (C.-M.Y.)
| | - Chen-Wei Chiang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (P.-Y.L.); (C.-W.C.); (C.-M.Y.)
| | - Chieh-Ming Yang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (P.-Y.L.); (C.-W.C.); (C.-M.Y.)
| | - Ching-Hua Su
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (S.-J.-L.); (C.-H.S.)
| | - Tsong-Yih Ou
- Division of Infectious Diseases, Department of Internal Medicine, School of Medicine, College of Medicine, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan;
| | - Ko-Jiunn Liu
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (C.-H.L.); (K.-J.L.)
- National Institute of Cancer Research, National Health Research Institutes, Tainan 70456, Taiwan
| | - Hsiu-Jung Lo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70456, Taiwan;
- School of Dentistry, China Medical University, Taichung 40402, Taiwan
| | - Bor-Yu Tsai
- Navi Bio-Therapeutics Inc., Taipei 10351, Taiwan;
| | - Yi-Yuan Yang
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (C.-H.L.); (K.-J.L.)
- Core Laboratory of Antibody Generation and Research, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Correspondence: ; Tel.: +886-2-27361661 (ext. 3325); Fax: +886-2-27324510
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47
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Genome association of carcass and palatability traits from Bos indicus-Bos taurus crossbred steers within electrical stimulation status and correspondence with steer temperament 2. Palatability. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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48
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Zamani A, Powell KL, May A, Semple BD. Validation of reference genes for gene expression analysis following experimental traumatic brain injury in a pediatric mouse model. Brain Res Bull 2020; 156:43-49. [PMID: 31904409 DOI: 10.1016/j.brainresbull.2019.12.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/02/2019] [Accepted: 12/30/2019] [Indexed: 01/01/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) is the gold standard method in targeted analysis of messenger RNA (mRNA) levels in a tissue. To minimize methodological errors, a reference gene (or a combination of reference genes) is routinely used for normalization to account for technical variables such as RNA quality and sample size. While presumed to have stable expression, reference genes in the brain can change during normal development, as well as in response to injury, such as traumatic brain injury (TBI). This study is the first to evaluate the stability of reference genes in a controlled cortical impact (CCI) model in the pediatric mouse brain, using two methods of qPCR normalization for optimal reference gene selection. Three week old mice were subjected to unilateral CCI at two severity of injuries (mild or severe), compared to sham controls. At 1 and 8 weeks post-injury, the ipsilateral hemisphere was analyzed to determine reference gene stability. Five commonly-used reference genes were compared: tyrosine 3 monooxygenase/tryptophan 5 monooxygenase activation protein zeta (Ywhaz), cyclophilin A (Ppia), hypoxanthine phosphoribosyl transferase (Hprt), glyceraldehyde-3-phosphate dehydrogenase (Gapdh) and β-actin (Actb). Ppia and Hprt were chosen as the most stable combination of genes using GeNORM software analysis. These results highlight the instability of several commonly used reference genes after TBI, and provide a selection of validated genes for future gene expression analyses in the injured pediatric mouse brain.
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Affiliation(s)
- Akram Zamani
- Department of Neuroscience, Monash University, Melbourne, VIC, 3004, Australia.
| | - Kim L Powell
- Department of Neuroscience, Monash University, Melbourne, VIC, 3004, Australia; Department of Medicine (Royal Melbourne Hospital), The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Ashleigh May
- Department of Neuroscience, Monash University, Melbourne, VIC, 3004, Australia
| | - Bridgette D Semple
- Department of Neuroscience, Monash University, Melbourne, VIC, 3004, Australia; Department of Medicine (Royal Melbourne Hospital), The University of Melbourne, Parkville, VIC, 3052, Australia
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Fatsini E, Rey S, Ibarra-Zatarain Z, Boltaña S, Mackenzie S, Duncan NJ. Linking stress coping styles with brain mRNA abundance of selected transcripts for Senegalese sole (Solea senegalensis) juveniles. Physiol Behav 2020; 213:112724. [PMID: 31682888 DOI: 10.1016/j.physbeh.2019.112724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/17/2019] [Accepted: 10/25/2019] [Indexed: 11/24/2022]
Abstract
In fish, proactive and reactive individual stress copying styles (SCS) have been used to resolve variation in molecular expression data. Stress coping styles have been previously described in several stages of Solea senegalensis by validating for the species the use of standard behavioural screening tests. The present study aimed to link behavioural SCS tests with brain transcript abundance in early Senegalese sole juveniles in order to observe the natural variation in a molecular pathway in this species. A total of 50 juveniles were subjected to three individual behavioural (Restraining, New environment and Confinement) and one group (Risk-taking) screening tests. The fish were classified in SCS categories by applying a hierarchical cluster to the variable "Total activity" (the total activity time that the fish was moving in each individual test). Three categories were defined, proactive, intermediate and reactive sole. Six transcripts were chosen and tested, one related to basic metabolism (gapdh-2), three to feeding behaviour (per1, igf-Ia, pparß) and two to the stress response (crh-BP and hsp90aa) in 30 juveniles (10 individuals per SCS category) using rt-qPCR to observe differences in the abundance of those transcripts among SCS. Four transcripts were differentially expressed (DETs) among them. The transcript gapdh-2 showed up-regulation for proactive and intermediate SCS sole while reactive individuals showed down-regulation. Target mRNAs per1, igf-Ia and pparß, showed different levels of up-regulation for proactive and reactive fish while intermediates were highly down-regulated. Surprisingly no differences in stress related transcripts were observed. Correlations were found between variation in coping styles and variation in the abundance of mRNAs involved in important biological functions in Senegalese sole. These results are the first evidence of the relationship between the behavioural individual variation and the fluctuation in brain transcripts abundance in Senegalese sole.
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Affiliation(s)
- Elvira Fatsini
- IRTA, Ctra. Poble Nou, km. 5.5, 43540 Sant Carles de la Ràpita, Tarragona Spain; Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro Portugal.
| | - Sonia Rey
- Institute of Aquaculture, University of Stirling, FK9 4LU Stirling Scotland UK
| | - Zohar Ibarra-Zatarain
- Centro Nayarita de Innovación y Transferencia Tecnológica (CENIT(2)), 63173 Tepic Mexico
| | | | - Simon Mackenzie
- Institute of Aquaculture, University of Stirling, FK9 4LU Stirling Scotland UK
| | - Neil J Duncan
- IRTA, Ctra. Poble Nou, km. 5.5, 43540 Sant Carles de la Ràpita, Tarragona Spain
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50
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Randez-Gil F, Sánchez-Adriá IE, Estruch F, Prieto JA. The formation of hybrid complexes between isoenzymes of glyceraldehyde-3-phosphate dehydrogenase regulates its aggregation state, the glycolytic activity and sphingolipid status in Saccharomyces cerevisiae. Microb Biotechnol 2019; 13:562-571. [PMID: 31743950 PMCID: PMC7017825 DOI: 10.1111/1751-7915.13513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/14/2019] [Accepted: 11/02/2019] [Indexed: 11/29/2022] Open
Abstract
The glycolytic enzyme glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) has been traditionally considered a housekeeping protein involved in energy generation. However, evidence indicates that GAPDHs from different origins are tightly regulated and that this regulation may be on the basis of glycolysis‐related and glycolysis‐unrelated functions. In Saccharomyces cerevisiae, Tdh3 is the main GAPDH, although two other isoenzymes encoded by TDH1 and TDH2 have been identified. Like other GAPDHs, Tdh3 exists predominantly as a tetramer, although dimeric and monomeric forms have also been isolated. Mechanisms of Tdh3 regulation may thus imply changes in its oligomeric state or be based in its ability to interact with Tdh1 and/or Tdh2 to form hybrid complexes. However, no direct evidence of the existence of these interactions has been provided and the exact function of Tdh1,2 is unknown. Here, we show that Tdh1,2 immunopurified with a GFP‐tagged version of Tdh3 and that lack of this interaction stimulates the Tdh3’s aggregation. Furthermore, we found that the combined knockout of TDH1 and TDH2 promotes the loss of cell’s viability and increases the growing rate, glucose consumption and CO2 production, suggesting a higher glycolytic flux in the mutant cells. Consistent with this, the tdh3 strain, which displays impaired in vitro GAPDH activity, exhibited the opposite phenotypes. Quite remarkably, tdh1 tdh2 mutant cells show increased sensitivity to aureobasidin A, an inhibitor of the inositolphosphoryl ceramide synthase, while cells lacking Tdh3 showed improved tolerance. The results are in agreement with a link between glycolysis and sphingolipid (SLs) metabolism. Engineering Tdh activity could be thus exploited to alter the SLs status with consequences in different aspects of yeast biotechnology.
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Affiliation(s)
- Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7., Paterna, 46980, Valencia, Spain
| | - Isabel E Sánchez-Adriá
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7., Paterna, 46980, Valencia, Spain
| | - Francisco Estruch
- Departament of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, Burjassot, 46100, Spain
| | - Jose A Prieto
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7., Paterna, 46980, Valencia, Spain
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