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Zhang X, Liu X, Chen X, Feng J, Zhao Q, Wu Q, Zhu D. Identification and structure-based engineering of a dipeptidase CpPepD from Clostridium perfringens for the synthesis of l-carnosine. J Biotechnol 2024; 389:86-93. [PMID: 38718874 DOI: 10.1016/j.jbiotec.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/12/2024]
Abstract
l-Carnosine (l-Car), an endogenous dipeptide presents in muscle and brain tissues of various vertebrates, has a wide range of application values. The enzymatic preparation of l-Car is a promising synthetic method because it avoids the protection and deprotection steps. In the present study, a dipeptidase gene (CpPepD) from Clostridium perfringens with high l-Car synthetic activity was cloned and characterized. In an effort to improve the performance of this enzyme, we carried out site saturation mutagenesis using CpPepD as the template. By the o-phthalaldehyde (OPA)-derived high throughput screening method, mutant A171S was obtained with 2.2-fold enhanced synthetic activity. The enzymatic properties of CpPepD and mutant A171S were investigated. Under the optimized conditions, 63.94 mM (14.46 g L-1) or 67.02 mM (15.16 g L-1) l-Car was produced at the substrate concentrations of 6 M β-Ala and 0.2 M l-His using wild-type or mutant A171S enzyme, respectively. Although the mutation enhanced the enzyme activity, the reaction equilibrium was barely affected.
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Affiliation(s)
- Xiaohan Zhang
- School of Biotechnology, Tianjin University of Science and Technology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, PR China; National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Xiangtao Liu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Xi Chen
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jinhui Feng
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Qing Zhao
- School of Biotechnology, Tianjin University of Science and Technology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, PR China; Tibet NWS Biotechnology Co., Ltd, Tibet 854000, PR China.
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China.
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2
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Perera CJ, Hosen SZ, Khan T, Fang H, Mekapogu AR, Xu Z, Falasca M, Chari ST, Wilson JS, Pirola R, Greening DW, Apte MV. Proteomic profiling of small extracellular vesicles derived from mouse pancreatic cancer and stellate cells: Role in pancreatic cancer. Proteomics 2024; 24:e2300067. [PMID: 38570832 DOI: 10.1002/pmic.202300067] [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: 08/09/2023] [Revised: 02/17/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Small extracellular vesicles (sEVs) are cell-derived vesicles evolving as important elements involved in all stages of cancers. sEVs bear unique protein signatures that may serve as biomarkers. Pancreatic cancer (PC) records a very poor survival rate owing to its late diagnosis and several cancer cell-derived proteins have been reported as candidate biomarkers. However, given the pivotal role played by stellate cells (PSCs, which produce the collagenous stroma in PC), it is essential to also assess PSC-sEV cargo in biomarker discovery. Thus, this study aimed to isolate and characterise sEVs from mouse PC cells and PSCs cultured alone or as co-cultures and performed proteomic profiling and pathway analysis. Proteomics confirmed the enrichment of specific markers in the sEVs compared to their cells of origin as well as the proteins that are known to express in each of the culture types. Most importantly, for the first time it was revealed that PSC-sEVs are enriched in proteins (including G6PI, PGAM1, ENO1, ENO3, and LDHA) that mediate pathways related to development of diabetes, such as glucose metabolism and gluconeogenesis revealing a potential role of PSCs in pancreatic cancer-related diabetes (PCRD). PCRD is now considered a harbinger of PC and further research will enable to identify the role of these components in PCRD and may develop as novel candidate biomarkers of PC.
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Affiliation(s)
- Chamini J Perera
- Pancreatic Research Group, South Western Sydney Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Ingham Institute of Applied Medical Research, Liverpool, NSW, Australia
| | - Sm Zahid Hosen
- Pancreatic Research Group, South Western Sydney Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Ingham Institute of Applied Medical Research, Liverpool, NSW, Australia
| | - Tanzila Khan
- Pancreatic Research Group, South Western Sydney Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Ingham Institute of Applied Medical Research, Liverpool, NSW, Australia
| | - Haoyun Fang
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, Australia
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Department of Cardiovascular Research, Translation and Implementation, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
| | - Alpha Raj Mekapogu
- Pancreatic Research Group, South Western Sydney Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Ingham Institute of Applied Medical Research, Liverpool, NSW, Australia
| | - Zhihong Xu
- Pancreatic Research Group, South Western Sydney Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Ingham Institute of Applied Medical Research, Liverpool, NSW, Australia
| | - Marco Falasca
- Metabolic Signalling Group, Curtin Medical School Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Suresh T Chari
- Department of Gastroenterology, Hepatology and Nutrition, M. D Anderson Cancer Centre, University of Texas, Houston, Texas, USA
| | - Jeremy S Wilson
- Pancreatic Research Group, South Western Sydney Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Ingham Institute of Applied Medical Research, Liverpool, NSW, Australia
| | - Ron Pirola
- Pancreatic Research Group, South Western Sydney Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Ingham Institute of Applied Medical Research, Liverpool, NSW, Australia
| | - David W Greening
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, Australia
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Department of Cardiovascular Research, Translation and Implementation, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
| | - Minoti V Apte
- Pancreatic Research Group, South Western Sydney Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Ingham Institute of Applied Medical Research, Liverpool, NSW, Australia
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3
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Chmielewska K, Vittorio S, Gervasoni S, Dzierzbicka K, Inkielewicz-Stepniak I, Vistoli G. Human carnosinases: A brief history, medicinal relevance, and in silico analyses. Drug Discov Today 2024; 29:103860. [PMID: 38128717 DOI: 10.1016/j.drudis.2023.103860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/03/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Carnosine, an endogenous dipeptide, has been found to have a plethora of medicinal properties, such as antioxidant, antiageing, and chelating effects, but with one downside: a short half-life. Carnosinases and two hydrolytic enzymes, which remain enigmatic, are responsible for these features. Hence, here we emphasize why research is valuable for better understanding crucial concepts like ageing, neurodegradation, and cancerogenesis, given that inhibition of carnosinases might significantly prolong carnosine bioavailability and allow its further use in medicine. Herein, we explore the literature regarding carnosinases and present a short in silico analysis aimed at elucidating the possible recognition pattern between CN1 and its ligands.
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Affiliation(s)
- Klaudia Chmielewska
- Department of Organic Chemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Serena Vittorio
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy
| | - Silvia Gervasoni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy; Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Krystyna Dzierzbicka
- Department of Organic Chemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | | | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy.
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4
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Kobayashi S, Homma T, Okumura N, Han J, Nagaoka K, Sato H, Konno H, Yamada S, Takao T, Fujii J. Carnosine dipeptidase II (CNDP2) protects cells under cysteine insufficiency by hydrolyzing glutathione-related peptides. Free Radic Biol Med 2021; 174:12-27. [PMID: 34324979 DOI: 10.1016/j.freeradbiomed.2021.07.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/06/2021] [Accepted: 07/25/2021] [Indexed: 01/18/2023]
Abstract
The knockout (KO) of the cystine transporter xCT causes ferroptosis, a type of iron-dependent necrotic cell death, in mouse embryonic fibroblasts, but this does not occur in macrophages. In this study, we explored the gene that supports cell survival under a xCT deficiency using a proteomics approach. Analysis of macrophage-derived peptides that were tagged with iTRAQ by liquid chromatography-mass spectrometry revealed a robust elevation in the levels of carnosine dipeptidase II (CNDP2) in xCT KO macrophages. The elevation in the CNDP2 protein levels was confirmed by immunoblot analyses and this elevation was accompanied by an increase in hydrolytic activity towards cysteinylglycine, the intermediate degradation product of glutathione after the removal of the γ-glutamyl group, in xCT KO macrophages. Supplementation of the cystine-free media of Hepa1-6 cells with glutathione or cysteinylglycine extended their survival, whereas the inclusion of bestatin, an inhibitor of CNDP2, counteracted the effects of these compounds. We established CNDP2 KO mice by means of the CRISPR/Cas9 system and found a decrease in dipeptidase activity in the liver, kidney, and brain. An acetaminophen overdose (350 mg/kg) showed not only aggravated hepatic damage but also renal injury in the CNDP2 KO mice, which was not evident in the wild-type mice that were receiving the same dose. The aggravated renal damage in the CNDP2 KO mice was consistent with the presence of abundant levels of CNDP2 in the kidney, the organ prone to developing ferroptosis. These collective data imply that cytosolic CNDP2, in conjugation with the removal of the γ-glutamyl group, recruits Cys from extracellular GSH and supports redox homeostasis of cells, particularly in epithelial cells of proximal tubules that are continuously exposed to oxidative insult from metabolic wastes that are produced in the body.
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Affiliation(s)
- Sho Kobayashi
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, 2-2-2 Iidanishi, Yamagata, Yamagata, 990-9585, Japan
| | - Takujiro Homma
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, 2-2-2 Iidanishi, Yamagata, Yamagata, 990-9585, Japan
| | - Nobuaki Okumura
- Laboratory of Biomolecular Analysis, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Jia Han
- Department of Pathology and Laboratory Medicine, Kanazawa Medical University, 1-1 Uchinada, Ishikawa, 920-0293, Japan
| | - Keita Nagaoka
- Department of Biological Engineering, Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata, 992-8510, Japan
| | - Hideyo Sato
- Laboratory of Biochemistry and Molecular Biology, Department of Medical Technology, Faculty of Medicine, Niigata University, 746-2 Asahimachi-dori, Chuo-ku, Niigata, 951-8518, Japan
| | - Hiroyuki Konno
- Department of Biological Engineering, Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata, 992-8510, Japan
| | - Sohsuke Yamada
- Department of Pathology and Laboratory Medicine, Kanazawa Medical University, 1-1 Uchinada, Ishikawa, 920-0293, Japan
| | - Toshifumi Takao
- Laboratory of Protein Profiling and Functional Proteomics, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, 2-2-2 Iidanishi, Yamagata, Yamagata, 990-9585, Japan.
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5
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Holtrup S, Heimerl T, Linne U, Altegoer F, Noll F, Waidner B. Biochemical characterization of the Helicobacter pylori bactofilin-homolog HP1542. PLoS One 2019; 14:e0218474. [PMID: 31233532 PMCID: PMC6590870 DOI: 10.1371/journal.pone.0218474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/03/2019] [Indexed: 01/11/2023] Open
Abstract
The human pathogen Helicobacter pylori is known for its colonization of the upper digestive system, where it escapes the harsh acidic environment by hiding in the mucus layer. One factor promoting this colonization is the helical cell shape of H. pylori. Among shape determining proteins are cytoskeletal elements like the recently discovered bactofilins. Bactofilins constitute a widespread family of polymer-forming bacterial proteins whose biology is still poorly investigated. Here we describe the first biochemical analysis of the bactofilin HP1542 of H. pylori reference strain 26695. Purified HP1542 forms sheet-like 2D crystalline assemblies, which clearly depend on a natively structured C-terminus. Polymerization properties and protein stability were investigated. Additionally, we also could demarcate HP1542 from amyloid proteins that share similarities with the bactofilin DUF domain. By using zonal centrifugation of total H. pylori cell lysates and immunfluorescence analysis we revealed peripheral membrane association of HP1542 mostly pronounced near mid-cell. Interestingly our results indicate that H. pylori bactofilin does not contribute to cell wall stability. This study might act as a starting point for biophysical studies of the H. pylori bactofilin biology as well as for the investigation of bactofilin cell physiology in this organism. Importantly, this study is the first biochemical analysis of a bactofilin in a human pathogen.
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Affiliation(s)
- Sven Holtrup
- LOEWE Center for Synthetic Microbiology, Philipps-Universität, Marburg, Germany
- Faculty of Chemistry, Philipps-Universität, Marburg, Germany
| | - Thomas Heimerl
- LOEWE Center for Synthetic Microbiology, Philipps-Universität, Marburg, Germany
- Faculty of Biology, Philipps-Universität, Marburg, Germany
| | - Uwe Linne
- Faculty of Chemistry, Philipps-Universität, Marburg, Germany
| | - Florian Altegoer
- LOEWE Center for Synthetic Microbiology, Philipps-Universität, Marburg, Germany
- Faculty of Chemistry, Philipps-Universität, Marburg, Germany
| | - Frank Noll
- Faculty of Chemistry, Philipps-Universität, Marburg, Germany
| | - Barbara Waidner
- LOEWE Center for Synthetic Microbiology, Philipps-Universität, Marburg, Germany
- Faculty of Chemistry, Philipps-Universität, Marburg, Germany
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6
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Andreyeva EN, Ogienko AA, Dubatolova TD, Oshchepkova AL, Kozhevnikova EN, Ivankin AV, Pavlova GA, Kopyl SA, Pindyurin AV. A toolset to study functions of Cytosolic non-specific dipeptidase 2 (CNDP2) using Drosophila as a model organism. BMC Genet 2019; 20:31. [PMID: 30885138 PMCID: PMC6421639 DOI: 10.1186/s12863-019-0726-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Expression of the CNDP2 gene is frequently up- or down-regulated in different types of human cancers. However, how the product of this gene is involved in cell growth and proliferation is poorly understood. Moreover, our knowledge of the functions of the CNDP2 orthologs in well-established model organisms is scarce. In particular, the function of the D. melanogaster ortholog of CNDP2, encoded by the CG17337 gene (hereafter referred to as dCNDP2), is still unknown. Results This study was aimed at developing a set of genetic and molecular tools to study the roles of dCNDP2. We generated a dCNDP2 null mutation (hereafter ∆dCNDP2) using CRISPR/Cas9-mediated homologous recombination (HR) and found that the ∆dCNDP2 mutants are homozygous viable, morphologically normal and fertile. We also generated transgenic fly lines expressing eGFP-tagged and non-tagged dCNDP2 protein, all under the control of the UAS promoter, as well as polyclonal antibodies specific to dCNDP2. Using these tools, we demonstrate that only one of the two predicted dCNDP2 isoforms is expressed throughout the different tissues tested. dCNDP2 was detected in both the cytoplasm and the nucleus, and was found to be associated with multiple sites in the salivary gland polytene chromosomes. Conclusions The dCNDP2 gene is not essential for fly viability under standard laboratory conditions. The subcellular localization pattern of dCNDP2 suggests that this protein might have roles in both the cytoplasm and the nucleus. The genetic and molecular tools developed in this study will allow further functional characterization of the conserved CNDP2 protein using D. melanogaster as a model system. Electronic supplementary material The online version of this article (10.1186/s12863-019-0726-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evgeniya N Andreyeva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Anna A Ogienko
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Tatiana D Dubatolova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Anastasiya L Oshchepkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Elena N Kozhevnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Anton V Ivankin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Gera A Pavlova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Sergei A Kopyl
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
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7
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Yin DY, Pan J, Zhu J, Liu YY, Xu JH. A green-by-design bioprocess forl-carnosine production integrating enzymatic synthesis with membrane separation. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01622h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This simple and clean bioprocess enables the economically attractive and environmentally benign production of the bioactive dipeptidel-Car.
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Affiliation(s)
- Dong-Ya Yin
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
| | - Jiang Pan
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
| | - Jie Zhu
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
| | - You-Yan Liu
- College of Chemistry and Chemical Engineering
- Guangxi University
- Nanning 530004
- P.R. China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
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8
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Jeyaharan D, Brackstone C, Schouten J, Davis P, Dixon AM. Characterisation of the Carboxypeptidase G2 Catalytic Site and Design of New Inhibitors for Cancer Therapy. Chembiochem 2018; 19:1959-1968. [PMID: 29968955 DOI: 10.1002/cbic.201800186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Indexed: 11/08/2022]
Abstract
The enzyme carboxypeptidase G2 (CPG2) is used in antibody-directed enzyme prodrug therapy (ADEPT) to catalyse the formation of an active drug from an inert prodrug. Free CPG2 in the bloodstream must be inhibited before administration of the prodrug in order to avoid a systemic reaction in the patient. Although a few small-molecule CPG2 inhibitors have been reported, none has been taken forward thus far. This lack of progress is due in part to a lack of structural understanding of the CPG2 active site as well as the absence of small molecules that can block the active site whilst targeting the complex for clearance. The work described here aimed to address both areas. We report the structural/functional impact of extensive point mutation across the putative CPG2 catalytic site and adjacent regions for the first time, revealing that residues outside the catalytic region (K208A, S210A and T357A) are crucial to enzyme activity. We also describe novel molecules that inhibit CPG2 whilst maintaining the accessibility of galactosylated moieties aimed at targeting the enzyme for clearance. This work acts as a platform for the future development of high-affinity CPG2 inhibitors that occupy new chemical space and will advance the safe application of ADEPT in cancer treatment.
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Affiliation(s)
| | - Carla Brackstone
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - James Schouten
- Mologic Ltd, Bedford Technology Park, Thurleigh, Bedford, MK44 2YP, UK
| | - Paul Davis
- Mologic Ltd, Bedford Technology Park, Thurleigh, Bedford, MK44 2YP, UK
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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9
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Okumura N, Takao T. The zinc form of carnosine dipeptidase 2 (CN2) has dipeptidase activity but its substrate specificity is different from that of the manganese form. Biochem Biophys Res Commun 2017; 494:484-490. [PMID: 29056506 DOI: 10.1016/j.bbrc.2017.10.100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/19/2017] [Indexed: 12/11/2022]
Abstract
Carnosine dipeptidase II (CN2), a metallopeptidase present in the cytosol of various vertebrate tissues, catalyzes the hydrolysis of carnosine and several other dipeptides in the presence of Mn2+. Although the metal-binding center of mouse CN2 is also able to associate with Zn2+in vitro, it was not known whether the zinc form of CN2 has any enzymatic activity. In the present study, we show that Zn2+ has a higher affinity for binding to CN2 than Mn2+, as evidenced by native mass spectrometry. The issue of whether the zinc form of CN2 has enzymatic activity was also examined using various dipeptides as substrates. The findings indicate that the zinc form of CN2 catalyzes the hydrolysis of several different dipeptides including Leu-His, Met-His and Ala-His at a reaction rate comparable to that for its manganese form. On the other hand, the zinc form of CN2 did not catalyze the hydrolysis of carnosine and several other dipeptides that are hydrolyzed by the manganese form of CN2. Substrate specificity was also examined in HEK293T cells expressing CN2, and the findings indicate that Leu-His, Met-His, but not carnosine, were hydrolyzed in the cell culture. These results suggest that the zinc form of CN2 is an active enzyme, but with a different substrate specificity from that of the manganese form.
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Affiliation(s)
- Nobuaki Okumura
- Institute for Protein Research, Osaka University, Suita, Osaka 5650871, Japan.
| | - Toshifumi Takao
- Institute for Protein Research, Osaka University, Suita, Osaka 5650871, Japan
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10
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Ishii K, Zhou M, Uchiyama S. Native mass spectrometry for understanding dynamic protein complex. Biochim Biophys Acta Gen Subj 2017; 1862:275-286. [PMID: 28965879 DOI: 10.1016/j.bbagen.2017.09.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/17/2017] [Accepted: 09/19/2017] [Indexed: 12/13/2022]
Abstract
Biomolecules have evolved to perform specific and sophisticated activities in a highly coordinated manner organizing into multi-component complexes consisting of proteins, nucleic acids, cofactors or ligands. Understanding such complexes represents a task in earnest for modern bioscience. Traditional structural techniques when extrapolating to macromolecules of ever increasing sizes are confronted with limitations posed by the difficulty in enrichment, solubility, stability as well as lack of homogeneity of these complexes. Alternative approaches are therefore prompted to bridge the gap, one of which is native mass spectrometry. Here we demonstrate the strength of native mass spectrometry, used alone or in combination with other biophysical methods such as analytical ultracentrifugation, small-angle neutron scattering, and small-angle X-ray scattering etc., in addressing dynamic aspects of protein complexes including structural reorganization, subunit exchange, as well as the assembly/disassembly processes in solution that are dictated by transient non-covalent interactions. We review recent studies from our laboratories and others applying native mass spectrometry to both soluble and membrane-embedded assemblies. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Min Zhou
- Institute of Bio-analytical Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China.
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Yachnin BJ, Khare SD. Engineering carboxypeptidase G2 circular permutations for the design of an autoinhibited enzyme. Protein Eng Des Sel 2017; 30:321-331. [PMID: 28160000 PMCID: PMC6283397 DOI: 10.1093/protein/gzx005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/11/2017] [Accepted: 01/18/2017] [Indexed: 11/14/2022] Open
Abstract
Carboxypeptidase G2 (CPG2) is an Food and Drug Administration (FDA)-approved enzyme drug used to treat methotrexate (MTX) toxicity in cancer patients receiving MTX treatment. It has also been used in directed enzyme-prodrug chemotherapy, but this strategy has been hampered by off-site activation of the prodrug by the circulating enzyme. The development of a tumor protease activatable CPG2, which could be achieved using a circular permutation of CPG2 fused to an inactivating 'prodomain', would aid in these applications. We report the development of a protease accessibility-based screen to identify candidate sites for circular permutation in proximity of the CPG2 active site. The resulting six circular permutants showed similar expression, structure, thermal stability, and, in four cases, activity levels compared to the wild-type enzyme. We rationalize these results based on structural models of the permutants obtained using the Rosetta software. We developed a cell growth-based selection system, and demonstrated that when fused to periplasm-directing signal peptides, one of our circular permutants confers MTX resistance in Escherichia coli with equal efficiency as the wild-type enzyme. As the permutants have similar properties to wild-type CPG2, these enzymes are promising starting points for the development of autoinhibited, protease-activatable zymogen forms of CPG2 for use in therapeutic contexts.
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Affiliation(s)
- Brahm J. Yachnin
- Department of Chemistry & Chemical Biology and the Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
| | - Sagar D. Khare
- Department of Chemistry & Chemical Biology and the Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
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