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Cai R, Wang Y. Chemoproteomic Profiling of Geranyl Pyrophosphate-Binding Proteins. Methods Mol Biol 2023; 2603:127-138. [PMID: 36370275 DOI: 10.1007/978-1-0716-2863-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Chemical proteomics has been widely applied in the identification and quantification of targeted proteins. Here we describe a chemoproteomic method, in combination with stable isotope labeling by amino acids in cell culture (SILAC), for the proteome-wide profiling of geranyl pyrophosphate (GPP)-binding proteins. After labeling using a desthiobiotin-GPP acyl phosphate probe, desthiobiotin-conjugated peptides of GPP-binding proteins could be enriched from the tryptic digestion products of complex protein mixtures and subsequently identified with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. To exclude nonspecific binding proteins, we applied SILAC, together with competitive labeling experiments, including high vs. low concentrations of GPP probe, GPP vs. ATP probes, and GPP probe labeling with or without the presence of GPP. Several known or candidate GPP-binding proteins were identified with this method, suggesting the potential application of this method in the study of isoprenoid-interacting proteins and biological functions of isoprenoids.
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Affiliation(s)
- Rong Cai
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, CA, USA
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Hung CY, Zhu C, Kittur FS, He M, Arning E, Zhang J, Johnson AJ, Jawa GS, Thomas MD, Ding TT, Xie J. A plant-based mutant huntingtin model-driven discovery of impaired expression of GTPCH and DHFR. Cell Mol Life Sci 2022; 79:553. [PMID: 36251090 PMCID: PMC9576654 DOI: 10.1007/s00018-022-04587-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/13/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022]
Abstract
Pathophysiology associated with Huntington's disease (HD) has been studied extensively in various cell and animal models since the 1993 discovery of the mutant huntingtin (mHtt) with abnormally expanded polyglutamine (polyQ) tracts as the causative factor. However, the sequence of early pathophysiological events leading to HD still remains elusive. To gain new insights into the early polyQ-induced pathogenic events, we expressed Htt exon1 (Httex1) with a normal (21), or an extended (42 or 63) number of polyQ in tobacco plants. Here, we show that transgenic plants accumulated Httex1 proteins with corresponding polyQ tracts, and mHttex1 induced protein aggregation and affected plant growth, especially root and root hair development, in a polyQ length-dependent manner. Quantitative proteomic analysis of young roots from severely affected Httex1Q63 and unaffected Httex1Q21 plants showed that the most reduced protein by polyQ63 is a GTP cyclohydrolase I (GTPCH) along with many of its related one-carbon (C1) metabolic pathway enzymes. GTPCH is a key enzyme involved in folate biosynthesis in plants and tetrahydrobiopterin (BH4) biosynthesis in mammals. Validating studies in 4-week-old R6/2 HD mice expressing a mHttex1 showed reduced levels of GTPCH and dihydrofolate reductase (DHFR, a key folate utilization/alternate BH4 biosynthesis enzyme), and impaired C1 and BH4 metabolism. Our findings from mHttex1 plants and mice reveal impaired expressions of GTPCH and DHFR and may contribute to a better understanding of mHtt-altered C1 and BH4 metabolism, and their roles in the pathogenesis of HD.
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Affiliation(s)
- Chiu-Yueh Hung
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, 27707, USA
| | - Chuanshu Zhu
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, 27707, USA.,College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Farooqahmed S Kittur
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, 27707, USA
| | - Maotao He
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, 27707, USA.,Department of Pathology, Weifang Medical University, Weifang, Shandong, 261000, China
| | - Erland Arning
- Baylor Scott and White Research Institute, Institute of Metabolic Disease, Dallas, TX, 75204, USA
| | - Jianhui Zhang
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, 27707, USA
| | - Asia J Johnson
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, 27707, USA
| | - Gurpreet S Jawa
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, 27707, USA.,DePuy Synthes Companies of Johnson & Johnson, West Chester, PA, 19380, USA
| | - Michelle D Thomas
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, 27707, USA.,University of North Carolina, Eshelman School of Pharmacy, Chapel Hill, NC, 27599, USA
| | - Tomas T Ding
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, 27707, USA.
| | - Jiahua Xie
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, 27707, USA.
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Min Lim K, Kim S, Yeom J, Choi Y, Lee Y, An J, Gil M, Abdal Dayem A, Kim K, Kang GH, Kim A, Hong K, Kim K, Cho SG. Advanced 3D dynamic culture system with transforming growth factor-β3 enhances production of potent extracellular vesicles with modified protein cargoes via upregulation of TGF-β signaling. J Adv Res 2022; 47:57-74. [PMID: 36130685 PMCID: PMC10173176 DOI: 10.1016/j.jare.2022.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/29/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Mesenchymal stromal cells (MSCs) release extracellular vesicles (MSC-EVs) containing various cargoes. Although MSC-EVs show significant therapeutic effects, the low production of EVs in MSCs hinders MSC-EV-mediated therapeutic development. OBJECTIVES Here, we developed an advanced three-dimensional (a3D) dynamic culture technique with exogenous transforming growth factor beta-3 (TGF-β3) treatment (T-a3D) to produce potent MSC-EVs. METHODS Our system enabled preparation of a highly concentrated EV-containing medium for efficient EV isolation and purification with higher yield and efficacy. RESULTS MSC spheroids in T-a3D system (T-a3D spheroids) showed high expression of CD9 and TGF-β3, which was dependent on TGF-β signaling. Treatment with EVs produced under T-a3D conditions (T-a3D-EVs) led to significantly improved migration of dermal fibroblasts and wound closure in an excisional wound model. The relative total efficacy (relative yield of single-batch EVs (10-11-fold) × relative regeneration effect of EVs (2-3-fold)) of T-a3D-EVs was approximately up to 33-fold higher than that of 2D-EVs. Importantly the quantitative proteomic analyses of the T-a3D spheroids and T-a3D-EVs supported the improved EV production as well as the therapeutic potency of T-a3D-EVs. CONCLUSION TGF-β signalling differentially regulated by fluid shear stress produced in our system and exogenous TGF-β3 addition was confirmed to play an important role in the enhanced production of EVs with modified protein cargoes. We suggest that the T-a3D system leads to the efficient production of MSC-EVs with high potential in therapies and clinical development.
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Affiliation(s)
- Kyung Min Lim
- Department of Stem Cell & Regenerative Biotechnology and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; R&D Team, StemExOne Co., Ltd., 303, Life Science Bldg, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Sehee Kim
- Department of Stem Cell & Regenerative Biotechnology and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Jeonghun Yeom
- Convergence Medicine Research Center, Asan Institute for Life Sciences, Asan Medical Center, 88-gil, 43 Olympic-ro, Songpa-gu, Seoul 05505, Republic of Korea.
| | - Yujin Choi
- Department of Stem Cell & Regenerative Biotechnology and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Yoonjoo Lee
- Department of Stem Cell & Regenerative Biotechnology and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Jongyub An
- Department of Stem Cell & Regenerative Biotechnology and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Minchan Gil
- Department of Stem Cell & Regenerative Biotechnology and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Ahmed Abdal Dayem
- Department of Stem Cell & Regenerative Biotechnology and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Kyeongseok Kim
- Department of Stem Cell & Regenerative Biotechnology and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Geun-Ho Kang
- Department of Stem Cell & Regenerative Biotechnology and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; R&D Team, StemExOne Co., Ltd., 303, Life Science Bldg, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Aram Kim
- Department of Urology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul 05029, Republic of Korea.
| | - Kwonho Hong
- Department of Stem Cell & Regenerative Biotechnology and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Kyunggon Kim
- Convergence Medicine Research Center, Asan Institute for Life Sciences, Asan Medical Center, 88-gil, 43 Olympic-ro, Songpa-gu, Seoul 05505, Republic of Korea; Biomedical Research Center, Asan Institute for Life Sciences, Asan Medical Center, 88-gil, 43 Olympic-ro, Songpa-gu, Seoul 05505, Republic of Korea; Department of Convergence Medicine, University of Ulsan College of Medicine, 88-gil, 43 Olympic-ro, Songpa-gu, Seoul 05505, Republic of Korea.
| | - Ssang-Goo Cho
- Department of Stem Cell & Regenerative Biotechnology and Institute of Advanced Regenerative Science, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; R&D Team, StemExOne Co., Ltd., 303, Life Science Bldg, 120, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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Deng M, Sun J, Peng L, Huang Y, Jiang W, Wu S, Zhou L, Chung SK, Cheng X. Scutellarin acts on the AR-NOX axis to remediate oxidative stress injury in a mouse model of cerebral ischemia/reperfusion injury. Phytomedicine 2022; 103:154214. [PMID: 35689902 DOI: 10.1016/j.phymed.2022.154214] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/11/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Oxidative stress plays an important role in the pathology of ischemic stroke. Studies have confirmedthat scutellarin has antioxidant effects against ischemic injury, and we also reported that the involvement of Aldose reductase (AR) in oxidative stress and cerebral ischemic injury, in this study we furtherly explicit whether the antioxidant effect of scutellarin on cerebral ischemia injury is related to AR gene regulation and its specific mechanism. METHODS C57BL/6N mice (Wild-type, WT) and AR knockout (AR-/-) mice suffered from transient middle cerebral artery occlusion (tMCAO) injury (1 h occlusion followed by 3 days reperfusion), and scutellarin was administered from 2 h before surgery to 3 days after surgery. Subsequently, neurological function was assessed by the modified Longa score method, the histopathological morphology observed with 2,3,5-triphenyltetrazolium chloride (TTC) and hematoxylin-eosin (HE) staining. Enzyme-linked immunosorbent assay (Elisa) was used to detect the levels of ROS, 4-hydroxynonenal (4-HNE), 8-hydroxydeoxyguanosine (8-OHDG), Neurotrophin-3 (NT-3), poly ADP-ribose polymerase-1 (PARP1) and 3-nitrotyrosine (3-NT) in the ischemic penumbra regions. Quantitative proteomics profiling using quantitative nano-HPLC-MS/MS were performed to compare the protein expression difference between AR-/- and WT mice with or without tMCAO injury. The expression of AR, nicotinamide adenine dinucleotide phosphate oxidases (NOX1, NOX2 and NOX4) in the ipsilateral side of ischemic brain were detected by qRT-PCR, Western blot and immunofluorescence co-staining with NeuN. RESULTS Scutellarin treatment alleviated brain damage in tMCAO stroke model such as improved neurological function deficit, brain infarct area and neuronal injury and reduced the expression of oxidation-related products, moreover, also down-regulated tMCAO induced AR mRNA and protein expression. In addition, the therapeutic effect of scutellarin on the reduction of cerebral infarction area and neurological function deficits abolished in AR-/- mice under ischemia cerebral injury, which indicated that the effect of scutellarin treatment on tMCAO injury is through regulating AR gene. Proteomic analysis of AR-/- and WT mice indicated AR knockout would affect oxidation reaction even as NADPH related process and activity in mice under cerebral ischemia conditions. Moreover, NOX isoforms (NOX1, NOX2 and NOX4) mRNA and protein expression were significant decreased in neurons of penumbra region in AR-/- mice compared with that in WT mice at 3d after tMCAO injury, which indicated that AR should be the upstream protein regulating NOX after cerebral ischemia. CONCLUSIONS We first reported that AR directly regulates NOX subtypes (not only NOX2 but also NOX1 and NOX4) after cerebral ischaemic injury. Scutellarin specifically targets the AR-NOX axis and has antioxidant effects in mice with cerebral ischaemic injury, providing a theoretical basis and accurate molecular targets for the clinical application of scutellarin.
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Affiliation(s)
- Minzhen Deng
- Department of Neurology, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China; Department of Second Institute of Clinical Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Jingbo Sun
- Department of Neurology, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Second Institute of Clinical Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, China; Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China
| | - Lilin Peng
- Department of Second Institute of Clinical Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Yan Huang
- Department of Neurology, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Second Institute of Clinical Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, China; Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China
| | - Wen Jiang
- Department of Second Institute of Clinical Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Shuang Wu
- Department of Second Institute of Clinical Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Lihua Zhou
- Department of Anatomy, Sun Yat-Sen School of Medicine, Sun Yat-Sen University, Shenzhen, China
| | - Sookja Kim Chung
- Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Xiao Cheng
- Department of Neurology, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Second Institute of Clinical Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, China; Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China.
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Feng C, Wu Y, Chen Y, Xiong X, Li P, Peng X, Li C, Weng W, Zhu Y, Zhou D, Li Y. Arsenic trioxide increases apoptosis of SK-N-BE (2) cells partially by inducing GPX4-mediated ferroptosis. Mol Biol Rep 2022; 49:6573-6580. [PMID: 35598199 DOI: 10.1007/s11033-022-07497-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/21/2022] [Indexed: 01/18/2023]
Abstract
BACKGROUND Neuroblastoma (NB) is the most common extracranial tumor in central nervous system threatening children's health with limited therapeutic options. Arsenic trioxide (ATO) has been identified the cytotoxicity in NB cells but the potential mechanism remains unclear. In this study, we attempted to obtain some insight into the mechanisms of cell death induced by ATO in NB cells. METHODS AND RESULTS Proteomic analyses found that ATO can affect the signaling pathway associated with ferroptosis, including the upregulation of iron absorption (FTL, FTH1, HO-1), ferritinophagy (LC3, P62, ATG7, NCOA4) and modifier of glutathione synthesis (GCLM); downregulation of glutamine synthetase (GS) and GPX4, which was the critical inhibitor of ferroptosis. Western blot analysis revealing GPX4 expression in SK-N-BE (2) cells decreased after treatment with ATO (7.3 µM), resulting in a loss of GPX4 activity. Furthermore, Ferroptosis inhibitor ferrostatin-1 partially blocked ATO-induced cell death. CONCLUSIONS Our study revealed that ATO may induce ferroptosis in neuroblastoma cell SK-N-BE (2) by facilitating the downregulation of GPX4, ultimately resulting in iron-dependent oxidative death.
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Affiliation(s)
- Chuchu Feng
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Yu Wu
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Yantao Chen
- Department of Orthopaedics, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Xilin Xiong
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Peng Li
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Kaiyuan Avenue, No. 190, Guangzhou, 510530, China
| | - Xiaomin Peng
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Chunmou Li
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Wenjun Weng
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Yafeng Zhu
- Medical Researcher Center, Sun Yat-Sen University Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Dunhua Zhou
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China.
| | - Yang Li
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China.
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Zhang Y, Zhao Y, Zhang J, Gao Y, Li S, Chang C, Yu D, Yang G. Ginkgolide B inhibits NLRP3 inflammasome activation and promotes microglial M2 polarization in Aβ 1-42-induced microglia cells. Neurosci Lett 2021; 764:136206. [PMID: 34478813 DOI: 10.1016/j.neulet.2021.136206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/14/2021] [Accepted: 08/24/2021] [Indexed: 12/20/2022]
Abstract
Nucleotide-binding oligomerization domain (NOD)-like receptor protein 3 (NLRP3) inflammasome-mediated chronic neuroinflammation plays a crucial role in the progression of Alzheimer's disease (AD), which is related to microglial activation. Using quantitative proteomic analysis, we identified 25 up-regulated and 83 down-regulated proteins in amyloid beta (Aβ)1-42-induced BV2 cells. Among the differentiallyexpressedproteins involved in inflammation, the NLRP3 protein level increased dramatically. Ginkgolide B (GB) prevents Aβ-induced neuroinflammation and neurotoxic effects in multiple neurodegenerative disorders. However, its role in NLRP3 inflammasome-mediated neuroinflammation in AD remain unknown. We found that GB treatment ameliorated Aβ1-42-induced pathological damages and inhibited NLRP3 inflammasome activation. Furthermore, GB enhanced the expression of M2 microglial markers and suppressed the expression of M1 microglial markers. Our findings suggest that GB treatment prevents the pathological processes of AD and suppresses neuroinflammation by inhibiting NLRP3 inflammasome activation and promoting microglial M2 polarization.
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Ma J, Yue H, Li H, Zhang J, Zhang Y, Wang X, Gong S, Liu GQ. Selective delignification of poplar wood with a newly isolated white-rot basidiomycete Peniophora incarnata T-7 by submerged fermentation to enhance saccharification. Biotechnol Biofuels 2021; 14:135. [PMID: 34118970 PMCID: PMC8199694 DOI: 10.1186/s13068-021-01986-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/05/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Pretreatment is a critical step required for efficient conversion of woody biomass into biofuels and platform chemicals. Fungal pretreatment is regarded as one of the most promising technology for woody biomass conversion but remains challenging for industrial application. The exploration of potential fungus strain with high efficient delignification and less processing time for woody biomass pretreatment will be valuable for development of biorefinery industry. Here, a newly isolated white-rot basidiomycete Peniophora incarnate T-7 was employed for poplar wood pretreatment. RESULTS The chemical component analysis showed that cellulose, hemicellulose and lignin from poplar wood declined by 16%, 48% and 70%, respectively, after 7 days submerged fermentation by P. incarnate T-7. Enzymatic saccharification analysis revealed that the maximum yields of glucose and xylose from 7 days of P. incarnate T-7 treated poplar wood reached 33.4% and 27.6%, respectively, both of which were enhanced by sevenfold relative to the untreated group. Fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM), X-ray diffraction (XRD) and pyrolysis gas chromatography-mass spectrometry (Py-GC/MS) characterization confirmed that lignocellulosic structure of poplar wood was largely broken by P. incarnate T-7, including delignification and de-crystalline of cellulose. Meanwhile, lignin component of poplar wood was selectively degraded by P. incarnate T-7, and G-type unit of lignin was preferentially attacked by the strain. Furthermore, quantitative proteomic analysis revealed that a considerable amount of lignocellulolytic enzymes were detected in the secretory proteins of P. incarnate T-7, especially with high abundance of lignin-degrading enzymes and hemicellulases. Combination of quantitative proteomic with transcriptomic analysis results showed that most of those lignocellulolytic enzymes were highly upregulated on poplar wood substrate compared to glucose substrate. CONCLUSIONS This study showed that P. incarnate T-7 could selectively delignify poplar wood by submerged fermentation with short time of 7 days, which greatly improved its enzymatic saccharification efficiency. Our results suggested that P. incarnate T-7 might be a promising candidate for industrial woody biomass pretreatment.
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Affiliation(s)
- Jiangshan Ma
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
| | - Huimin Yue
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
| | - Hongqian Li
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
| | - Jing Zhang
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
| | - Yanghong Zhang
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
| | - Xiaoling Wang
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
| | - Si Gong
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
| | - Gao-Qiang Liu
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
- International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan P.R. China
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Tang R, Lan P, Ding C, Wang J, Zhang T, Wang X. A new perspective on the toxicity of arsenic-contaminated soil: Tandem mass tag proteomics and metabolomics in earthworms. J Hazard Mater 2020; 398:122825. [PMID: 32768809 DOI: 10.1016/j.jhazmat.2020.122825] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/23/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
The toxicity of low-level arsenic (As)-contaminated soil is not well understood. An integrated proteomic and metabolomic approach combined with morphological examination was used to investigate the potential biological toxicity of As-contaminated soil based on an exposure experiment with the earthworm Eisenia fetida. The results showed that the earthworm hindgut accumulated high As concentrations resulting in injury to the intestinal epithelia, chloragogenous tissues and coelom tissues. Furthermore, As-contaminated soil induced a significant increase in betaine levels and a decrease in dimethylglycine and myo-inositol levels in the earthworms, suggesting that the osmoregulatory metabolism of the earthworms may have been disturbed. The significantly altered levels of asparagine and dimethylglycine were proposed as potential biomarkers of As-contaminated soil. The upregulation of soluble calcium-binding proteins and profilin, the downregulation of sodium/potassium-transporting ATPase, and the proteins changes identified by gene ontology enrichment analysis confirmed that the earthworms suffered from osmotic stress. In addition, the significant changes in glycine-tRNA ligase activity and coelomic tissue injury revealed that As accumulation may disturb the earthworm immune system. This work provided new insight into the proteomic and metabolic toxicity of low-level As-contaminated soil ecosystems in earthworms, extended our knowledge of dual omics and highlighted the mechanisms underlying toxicity.
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Affiliation(s)
- Ronggui Tang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Changfeng Ding
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Junsong Wang
- Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210014, China
| | - Taolin Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xingxiang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China.
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9
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Yan W, Mukherjee M, Zhou Y. Direct interspecies electron transfer (DIET) can be suppressed under ammonia-stressed condition - Reevaluate the role of conductive materials. Water Res 2020; 183:116094. [PMID: 32668350 DOI: 10.1016/j.watres.2020.116094] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/17/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
Thermal hydrolysis pretreatment (THP) and anaerobic digestion (AD) integrated (THP-AD) process is a promising process for sludge management. However, the high ammonia production during the THP-AD process severely affects system's stability and performance. Conductive materials are widely reported to stimulate AD, thus they are potentially helpful in alleviating ammonia inhibition. This study investigated the effects of three widely studied conductive materials, i.e. zero-valent iron (ZVI), magnetite nanoparticles (Mag.) and powder activated carbon (PAC), on THP-AD process. Results showed that all the tested materials could effectively stimulate methanogenesis process under non-ammonia inhibition conditions. However, upon ammonia stress, these materials behaved distinctively with the best methanogenic performance in ZVI group followed by Mag. Group, and even worsened inhibition occurred in PAC group. The mechanisms behind were investigated from two levels-the reaction kinetics of each anaerobic digestion step and the responses of intracellular metabolism. It is revealed that ZVI effectively promoted all AD reactions, especially the energy unfavorable propanoate and butanoate metabolism and overall methanogenesis. In addition, ZVI likely acted as intracellular electron shuttles, and the conjunction point of ZVI to electron transfer system was identified as EtfAB: quinone oxidoreductase. On the contrary, the declined methanogenic performance in PAC group was attributed to selectively stimulated the growth of acetoclastic methanogen - Methanosaeta, which is sensitive to ammonia toxicity. The proteomic information further revealed that ammonia stress was unfavorable to the formation of direct interspecies electron transfer between syntrophic anaerobes. Overall, the present study provides fundamental knowledge about the role of different conductive materials in AD systems from intracellular proteomic level.
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Affiliation(s)
- Wangwang Yan
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore
| | - Manisha Mukherjee
- Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 639798, Singapore
| | - Yan Zhou
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore.
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10
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Mitaki S, Nagai A, Wada Y, Onoda K, Md Sheikh A, Adachi E, Matsumoto KI, Yamaguchi S. iTRAQ-based proteomic analysis after mesenchymal stem cell line transplantation for ischemic stroke. Brain Res 2020; 1742:146900. [PMID: 32445714 DOI: 10.1016/j.brainres.2020.146900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 05/01/2020] [Accepted: 05/18/2020] [Indexed: 02/01/2023]
Abstract
Transplantation with mesenchymal stem cells (MSCs) has been reported to promote functional recovery in animal models of ischemic stroke. However, the molecular mechanisms underlying the therapeutic effects of MSC transplantation have been only partially elucidated. The purpose of this study was to comprehensively identify changes in brain proteins in rats treated with MSCs for ischemic stroke, and to explore the multi-target mechanisms of MSCs using a proteomics-based strategy. Twenty-eight proteins were found to be differentially expressed following B10 MSC transplantation in adult male Wistar rats, as assessed using isobaric tagging for relative and absolute protein quantification (iTRAQ). Subsequent bioinformatic analysis revealed that these proteins were mainly associated with energy metabolism, glutamate excitotoxicity, oxidative stress, and brain structural and functional plasticity. Immunohistochemical staining revealed decreased expression of EAAT1 in the phosphate-buffered saline group as opposed to normal levels in the B10 transplantation group. Furthermore, ATP levels were also significantly higher in the B10 transplantation group, thus supporting the iTRAQ results. Our results suggest that the therapeutic effects of B10 transplantation might arise from the modulation of the acute ischemic cascade via multiple molecular pathways. Thus, our findings provide valuable clues to elucidate the mechanisms underlying the therapeutic effects of MSC transplantation in ischemic stroke.
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11
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Ohira T, Ino Y, Nakai Y, Morita H, Kimura A, Kurata Y, Kagawa H, Kimura M, Egashira K, Moriya S, Hiramatsu K, Kawakita M, Kimura Y, Hirano H. Proteomic analysis revealed different responses to hypergravity of soleus and extensor digitorum longus muscles in mice. J Proteomics 2020; 217:103686. [PMID: 32061808 DOI: 10.1016/j.jprot.2020.103686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/30/2020] [Accepted: 02/12/2020] [Indexed: 01/01/2023]
Abstract
Investigating protein abundance profiles is important to understand the differences in the slow and fast skeletal muscle characteristics. The profiles in soleus (Sol) and extensor digitorum longus (EDL) muscles in mice exposed to 1 g or 3 g for 28 d were compared. The biological implications of the profiles revealed that hypergravity exposure activated a larger number of pathways involved in protein synthesis in Sol. In contrast, the inactivation of signalling pathways involved in oxidative phosphorylation were conspicuous in EDL. These results suggested that the reactivity of molecular pathways in Sol and EDL differed. Additionally, the levels of spermidine synthase and spermidine, an important polyamine for cell growth, increased in both muscles following hypergravity exposure, whereas the level of spermine oxidase (SMOX) increased in EDL alone. The SMOX level was negatively correlated with spermine content, which is involved in muscle atrophy, and was higher in EDL than Sol, even in the 1 g group. These results indicated that the contribution of SMOX to the regulation of spermidine and spermine contents in Sol and EDL differed. However, contrary to expectations, the difference in the SMOX level did not have a significant impact on the growth of these muscles following hypergravity exposure. SIGNIFICANCE: The skeletal muscle-specific protein abundance profiles result in differences in the characteristics of slow and fast skeletal muscles. We investigated differences in the profiles in mouse slow-twitch Sol and fast-twitch EDL muscles following 28-d of 1 g and 3 g exposure by LC-MS/MS analysis and label-free quantitation. A two-step solubilisation of the skeletal muscle proteins increased the coverage of proteins identified by LC-MS/MS analysis. Additionally, this method reduced the complexity of samples more easily than protein or peptide fractionation by SDS-PAGE and offline HPLC while maintaining the high operability of samples and was reproducible. A larger number of hypergravity-responsive proteins as well as a prominent increase in the wet weights was observed in Sol than EDL muscles. The biological implications of the difference in the protein abundance profiles in 1 g and 3 g groups revealed that the reactivity of each molecular pathway in Sol and EDL muscles to hypergravity exposure differed significantly. In addition, we found that the biosynthetic and interconversion pathway of polyamines, essential factors for cell growth and survival in mammals, was responsive to hypergravity exposure; spermidine and spermine contents in Sol and EDL muscles were regulated by different mechanisms even in the 1 g group. However, our results indicated that the difference in the mechanism regulating polyamine contents is unlikely to have a significant effect on the differences in Sol and EDL muscle growth following hypergravity exposure.
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Affiliation(s)
- Takashi Ohira
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Yoko Ino
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Yusuke Nakai
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Hironobu Morita
- Department of Physiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Ayuko Kimura
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Yoichi Kurata
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Hiroyuki Kagawa
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Mitsuo Kimura
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Kenji Egashira
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Shunsuke Moriya
- Department of Advanced Research for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kyoko Hiramatsu
- Department of Advanced Research for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masao Kawakita
- Department of Advanced Research for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan.
| | - Hisashi Hirano
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan.
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12
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Liu W, Zeng L, Li N, Wang F, Jiang C, Guo F, Chen X, Su T, Xu C, Zhang S, Fang C. Quantitative proteomic analysis for novel biomarkers of buccal squamous cell carcinoma arising in background of oral submucous fibrosis. BMC Cancer 2016; 16:584. [PMID: 27485544 PMCID: PMC4971621 DOI: 10.1186/s12885-016-2650-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 07/28/2016] [Indexed: 12/28/2022] Open
Abstract
Background In South and Southeast Asian, the majority of buccal squamous cell carcinoma (BSCC) can arise from oral submucous fibrosis (OSF). BSCCs develop in OSF that are often not completely resected, causing local relapse. The aim of our study was to find candidate protein biomarkers to detect OSF and predict prognosis in BSCCs by quantitative proteomics approaches. Methods We compared normal oral mucosa (NBM) and paired biopsies of BSCC and OSF by quantitative proteomics using isobaric tags for relative and absolute quantification (iTRAQ) to discover proteins with differential expression. Gene Ontology and KEGG networks were analyzed. The prognostic value of biomarkers was evaluated in 94 BSCCs accompanied with OSF. Significant associations were assessed by Kaplan-Meier survival and Cox-proportional hazards analysis. Results In total 30 proteins were identified with significantly different expression (false discovery rate < 0.05) among three tissues. Two consistently upregulated proteins, ANXA4 and FLNA, were validated. The disease-free survival was negatively associated with the expression of ANXA4 (hazard ratio, 3.4; P = 0.000), FLNA (hazard ratio, 2.1; P = 0.000) and their combination (hazard ratio, 8.8; P = 0.002) in BSCCs. Conclusion The present study indicates that iTRAQ quantitative proteomics analysis for tissues of BSCC and OSF is a reliable strategy. A significantly up-regulated ANXA4 and FLNA could be not only candidate biomarkers for BSCC prognosis but also potential targets for its therapy. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2650-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wen Liu
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Lijuan Zeng
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Ning Li
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China.
| | - Fei Wang
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Canhua Jiang
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Feng Guo
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Xinqun Chen
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Tong Su
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Chunjiao Xu
- Department of Oral Medicine, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Shanshan Zhang
- Department of Oral Medicine, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Changyun Fang
- Department of Oral Medicine, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
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Takagi T, Morisaka H, Aburaya S, Tatsukami Y, Kuroda K, Ueda M. Putative Alginate Assimilation Process of the Marine Bacterium Saccharophagus degradans 2-40 Based on Quantitative Proteomic Analysis. Mar Biotechnol (NY) 2016; 18:15-23. [PMID: 26458373 DOI: 10.1007/s10126-015-9667-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 08/15/2015] [Indexed: 06/05/2023]
Abstract
Quantitative proteomic analysis was conducted to assess the assimilation processes of Saccharophagus degradans cultured with glucose, pectin, and alginate as carbon sources. A liquid chromatography-tandem mass spectrometry approach was used, employing our unique, long monolithic silica capillary column. In an attempt to select candidate proteins that correlated to alginate assimilation, the production of 23 alginate-specific proteins was identified by statistical analyses of the quantitative proteomic data. Based on the analysis, we propose that S. degradans has an alginate-specific gene cluster for efficient alginate utilization. The alginate-specific proteins of S. degradans were comprised of alginate lyases, enzymes related to carbohydrate metabolism, membrane transporters, and transcription factors. Among them, the short-chain dehydrogenase/reductase Sde_3281 annotated in the alginate-specific cluster showed 4-deoxy-L-erythro-5-hexoseulose uronic acid reductase (DehR) activity. Furthermore, we found two different genes (Sde_3280 and Sde_0939) encoding 2-keto-3-deoxy-D-gluconic acid (KDG) kinases (KdgK) that metabolize the KDG derived from alginate and pectin in S. degradans. S. degradans used Sde_3280 to phosphorylate the KDG derived from alginate and Sde_0939 to phosphorylate the KDG derived from pectin. The distinct selection of KdgKs provides an important clue toward the elucidation of how S. degradans recognizes and processes polysaccharides.
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Affiliation(s)
- Toshiyuki Takagi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
- JST, CREST, Kawaguchi, Saitama, 332-0012, Japan.
- Japan Society for the Promotion of Science, Sakyo, Kyoto, 606-8502, Japan.
| | - Hironobu Morisaka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
- JST, CREST, Kawaguchi, Saitama, 332-0012, Japan.
| | - Shunsuke Aburaya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
- JST, CREST, Kawaguchi, Saitama, 332-0012, Japan.
| | - Yohei Tatsukami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
- JST, CREST, Kawaguchi, Saitama, 332-0012, Japan.
- Japan Society for the Promotion of Science, Sakyo, Kyoto, 606-8502, Japan.
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
- JST, CREST, Kawaguchi, Saitama, 332-0012, Japan.
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
- JST, CREST, Kawaguchi, Saitama, 332-0012, Japan.
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