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Li W, Zhu L, Wu B, Liu Y, Li J, Xu L, Huangfu X, Shi D, Gu L, Chen C. Improving mesophilic anaerobic digestion of food waste by side-stream thermophilic reactor: Activation of methanogenic, key enzymes and metabolism. WATER RESEARCH 2023; 241:120167. [PMID: 37290195 DOI: 10.1016/j.watres.2023.120167] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/21/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Anaerobic digestion (AD) is a favorable way to convert organic pollutants, such as food waste (FW), into clean energy through microbial action. This work adopted a side-stream thermophilic anaerobic digestion (STA) strategy to improve a digestive system's efficiency and stability. Results showed that the STA strategy brought higher methane production as well as higher system stability. It quickly adapted to thermal stimulation and increased the specific methane production from 359 mL CH4/g·VS to 439 mL CH4/g·VS, which was also higher than 317 mL CH4/g·VS from single-stage thermophilic anaerobic digestion. Further exploration of the mechanism of STA using metagenomic and metaproteomic analysis revealed enhanced activity of key enzymes. The main metabolic pathway was up-regulated, while the dominant bacteria were concentrated, and the multifunctional Methanosarcina was enriched. These results indicate that STA optimized organic metabolism patterns, comprehensively promoted methane production pathways, and formed various energy conservation mechanisms. Further, the system's limited heating avoided adverse effects from thermal stimulation, and activated enzyme activity and heat shock proteins through circulating slurries, which improved the metabolic process, showing great application potential.
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Affiliation(s)
- Wen Li
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Lirong Zhu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Baocun Wu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Yongli Liu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Jinze Li
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Linji Xu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Xiaoliu Huangfu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Dezhi Shi
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Li Gu
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China.
| | - Cong Chen
- Key laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, Institute of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
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Tian X, Wei W, Cao Y, Ao T, Huang F, Javed R, Wang X, Fan J, Zhang Y, Liu Y, Lai L, Ao Q. Gingival mesenchymal stem cell-derived exosomes are immunosuppressive in preventing collagen-induced arthritis. J Cell Mol Med 2021; 26:693-708. [PMID: 34953015 PMCID: PMC8817124 DOI: 10.1111/jcmm.17086] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 10/26/2021] [Accepted: 11/16/2021] [Indexed: 01/08/2023] Open
Abstract
Due to the unsatisfied effects of clinical drugs used in rheumatoid arthritis (RA), investigators shifted their focus on the biotherapy. Although human gingival mesenchymal stem cells (GMSC) have the potential to be used in treating RA, GMSC‐based therapy has some inevitable side effects such as immunogenicity and tumorigenicity. As one of the most important paracrine mediators, GMSC‐derived exosomes (GMSC‐Exo) exhibit therapeutic effects via immunomodulation in a variety of disease models, bypassing potential shortcomings of the direct use of MSCs. Furthermore, exosomes are not sensitive to freezing and thawing, and can be readily available for use. GMSC‐Exo has been reported to promote tissue regeneration and wound healing, but have not been reported to be effective against autoimmune diseases. We herein compare the immunomodulatory functions of GMSC‐Exo and GMSC in collagen‐induced arthritis (CIA) model and in vitro CD4+ T‐cell co‐culture model. The results show that GMSC‐Exo has the same or stronger effects compared with GMSC in inhibiting IL‐17A and promoting IL‐10, reducing incidences and bone erosion of arthritis, via inhibiting IL‐17RA‐Act1‐TRAF6‐NF‐κB signal pathway. Our results suggest that GMSC‐Exo has many advantages in treating CIA, and may offer a promising new cell‐free therapy strategy for RA and other autoimmune diseases.
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Affiliation(s)
- Xiaohong Tian
- Department of Tissue Engineering, School of Intelligent Medicine, China Medical University, Shenyang, China
| | - Wumei Wei
- Department of Tissue Engineering, School of Intelligent Medicine, China Medical University, Shenyang, China
| | - Yue Cao
- Department of Tissue Engineering, School of Intelligent Medicine, China Medical University, Shenyang, China
| | - Tianrang Ao
- Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Feng Huang
- Department of Clinical Immunology, Sun Yat-sen University, Third Affiliated Hospital, Guangzhou, PR China
| | - Rabia Javed
- Department of Tissue Engineering, School of Intelligent Medicine, China Medical University, Shenyang, China
| | - Xiaohong Wang
- Department of Tissue Engineering, School of Intelligent Medicine, China Medical University, Shenyang, China
| | - Jun Fan
- Department of Tissue Engineering, School of Intelligent Medicine, China Medical University, Shenyang, China
| | - Yanhui Zhang
- Department of Tissue Engineering, School of Intelligent Medicine, China Medical University, Shenyang, China
| | - Yanying Liu
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing, China
| | - Laijun Lai
- Department of Allied Health Sciences, University of Connecticut, Storrs, Connecticut, USA
| | - Qiang Ao
- Department of Tissue Engineering, School of Intelligent Medicine, China Medical University, Shenyang, China.,National Engineering Research Center for Biomaterials, Institute of Regulatory Science for Medical Device, Sichuan University, Chengdu, China
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Proteomic perspectives on thermotolerant microbes: an updated review. Mol Biol Rep 2021; 49:629-646. [PMID: 34671903 DOI: 10.1007/s11033-021-06805-z] [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] [Received: 05/11/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Thermotolerant microbes are a group of microorganisms that survive in elevated temperatures. The thermotolerant microbes, which are found in geothermal heat zones, grow at temperatures of or above 45°C. The proteins present in such microbes are optimally active at these elevated temperatures. Hence, therefore, serves as an advantage in various biotechnological applications. In the last few years, scientists have tried to understand the molecular mechanisms behind the maintenance of the structural integrity of the cell and to study the stability of various thermotolerant proteins at extreme temperatures. Proteomic analysis is the solution for this search. Applying novel proteomic tools determines the proteins involved in the thermostability of microbes at elevated temperatures. METHODS Advanced proteomic techniques like Mass spectrometry, nano-LC-MS, protein microarray, ICAT, iTRAQ, and SILAC could enable the screening and identification of novel thermostable proteins. RESULTS This review provides up-to-date details on the protein signature of various thermotolerant microbes analyzed through advanced proteomic tools concerning relevant research articles. The protein complex composition from various thermotolerant microbes cultured at different temperatures, their structural arrangement, and functional efficiency of the protein was reviewed and reported. CONCLUSION This review provides an overview of thermotolerant microbes, their enzymes, and the proteomic tools implemented to characterize them. This article also reviewed a comprehensive view of the current proteomic approaches for protein profiling in thermotolerant microbes.
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Wang L, Wang X, He ZQ, Zhou SJ, Xu L, Tan XY, Xu T, Li BZ, Yuan YJ. Engineering prokaryotic regulator IrrE to enhance stress tolerance in budding yeast. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:193. [PMID: 33292418 PMCID: PMC7706047 DOI: 10.1186/s13068-020-01833-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Stress tolerance is one of the important desired microbial traits for industrial bioprocesses, and global regulatory protein engineering is an efficient approach to improve strain tolerance. In our study, IrrE, a global regulatory protein from the prokaryotic organism Deinococcus radiodurans, was engineered to confer yeast improved tolerance to the inhibitors in lignocellulose hydrolysates or high temperatures. RESULTS Three IrrE mutations were developed through directed evolution, and the expression of these mutants could improve the yeast fermentation rate by threefold or more in the presence of multiple inhibitors. Subsequently, the tolerance to multiple inhibitors of single-site mutants based on the mutations from the variants were then evaluated, and 11 mutants, including L65P, I103T, E119V, L160F, P162S, M169V, V204A, R244G, Base 824 Deletion, V299A, and A300V were identified to be critical for the improved representative inhibitors, i.e., furfural, acetic acid and phenol (FAP) tolerance. Further studies indicated that IrrE caused genome-wide transcriptional perturbation in yeast, and the mutant I24 led to the rapid growth of Saccharomyces cerevisiae by primarily regulating the transcription level of transcription activators/factors, protecting the intracellular environment and enhancing the antioxidant capacity under inhibitor environments, which reflected IrrE plasticity. Meanwhile, we observed that the expression of the wild-type or mutant IrrE could also protect Saccharomyces cerevisiae from the damage caused by thermal stress. The recombinant yeast strains were able to grow with glucose at 42 ℃. CONCLUSIONS IrrE from Deinococcus radiodurans can be engineered as a tolerance-enhancer for Saccharomyces cerevisiae. Systematic research on the regulatory model and mechanism of a prokaryotic global regulatory factor IrrE to increase yeast tolerance provided valuable insights for the improvements in microbial tolerance to complex industrial stress conditions.
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Affiliation(s)
- Li Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 P.R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 P.R. China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu P.R. China
| | - Zhi-Qiang He
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 P.R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 P.R. China
| | - Si-Jie Zhou
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 P.R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 P.R. China
| | - Li Xu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 P.R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 P.R. China
| | - Xiao-Yu Tan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 P.R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 P.R. China
| | - Tao Xu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 P.R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 P.R. China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 P.R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 P.R. China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 P.R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 P.R. China
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Sunny JS, Mukund N, Natarajan A, Saleena LM. Identifying heat shock response systems from the genomic assembly of Ureibacillus thermophilus LM102 using protein-protein interaction networks. Gene X 2020; 737:144449. [DOI: 10.1016/j.gene.2020.144449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/28/2020] [Accepted: 02/04/2020] [Indexed: 11/30/2022] Open
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Improvement of stress tolerance and riboflavin production of Bacillus subtilis by introduction of heat shock proteins from thermophilic bacillus strains. Appl Microbiol Biotechnol 2019; 103:4455-4465. [PMID: 30968162 DOI: 10.1007/s00253-019-09788-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/12/2019] [Accepted: 03/19/2019] [Indexed: 10/27/2022]
Abstract
In this study, stress tolerance devices consisting of heat shock protein (HSP) genes from thermophiles Geobacillus and Parageobacillus were introduced into riboflavin-producing strain Bacillus subtilis 446 to improve its stress tolerance and riboflavin production. The 12 HSP homologs were selected from 28 Geobacillus and Parageobacillus genomes according to their sequence clustering and phylogenetically analysis which represents the diversity of HSPs from thermophilic bacillus. The 12 HSP genes and 2 combinations of them (PtdnaK-PtdnaJ-PtgrpE and PtgroeL-PtgroeS) were heterologously expressed in B. subtilis 446 under the control of a strong constitutive promoter P43. Most of the 14 engineered strains showed increased cell density at 44 to 48 °C and less cell death at 50 °C compared with the control strains. Among them, strains B.s446-HSP20-3, B.s446-HSP20-2, and B.s446-PtDnaK-PtDnaJ-PtGrpE increased their cell densities over 25% at 44 to 48 °C. They also showed 5-, 4-, and 4-fold improved cell survivals after the 10-h heat shock treatment at 50 °C, respectively. These three strains also showed reduced cell death rates under osmotic stress of 10% NaCl, indicating that the introduction of HSPs improved not only the heat tolerance of B. subtilis 446 but also its osmotic tolerance. Fermentation of these three strains at higher temperatures of 39 and 43 °C showed 23-66% improved riboflavin titers, as well as 24-h shortened fermentation period. These results indicated that implanting HSPs from thermophiles to B. subtilis 446 would be an efficient approach to improve its stress tolerance and riboflavin production.
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Chamnipa N, Thanonkeo S, Klanrit P, Thanonkeo P. The potential of the newly isolated thermotolerant yeast Pichia kudriavzevii RZ8-1 for high-temperature ethanol production. Braz J Microbiol 2018; 49:378-391. [PMID: 29154013 PMCID: PMC5914142 DOI: 10.1016/j.bjm.2017.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 07/29/2017] [Accepted: 09/06/2017] [Indexed: 11/30/2022] Open
Abstract
High potential, thermotolerant, ethanol-producing yeasts were successfully isolated in this study. Based on molecular identification and phylogenetic analysis, the isolated thermotolerant yeasts were clustered in the genera of Pichia kudriavzevii, Candida tropicalis, Candida orthopsilosis, Candida glabrata and Kodamea ohmeri. A comparative study of ethanol production using 160g/L glucose as a substrate revealed several yeast strains that could produce high ethanol concentrations at high temperatures. When sugarcane bagasse (SCB) hydrolysate containing 85g/L glucose was used as a substrate, the yeast strain designated P. kudriavzevii RZ8-1 exhibited the highest ethanol concentrations of 35.51g/L and 33.84g/L at 37°C and 40°C, respectively. It also exhibited multi-stress tolerance, such as heat, ethanol and acetic acid tolerance. During ethanol fermentation at high temperature (42°C), genes encoding heat shock proteins (ssq1 and hsp90), alcohol dehydrogenases (adh1, adh2, adh3 and adh4) and glyceraldehyde-3-phosphate dehydrogenase (tdh2) were up-regulated, suggesting that these genes might play a crucial role in the thermotolerance ability of P. kudriavzevii RZ8-1 under heat stress. These findings suggest that the growth and ethanol fermentation activities of this organism under heat stress were restricted to the expression of genes involved not only in heat shock response but also in the ethanol production pathway.
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Affiliation(s)
- Nuttaporn Chamnipa
- Khon Kaen University, Graduate School, Khon Kaen, Thailand; Khon Kaen University, Faculty of Technology, Department of Biotechnology, Khon Kaen, Thailand
| | - Sudarat Thanonkeo
- Mahasarakam University, Walai Rukhavej Botanical Research Institute, Maha Sarakam, Thailand
| | - Preekamol Klanrit
- Khon Kaen University, Faculty of Technology, Department of Biotechnology, Khon Kaen, Thailand; Khon Kaen University, Fermentation Research Center for Value Added Agricultural Products, Khon Kaen, Thailand
| | - Pornthap Thanonkeo
- Khon Kaen University, Faculty of Technology, Department of Biotechnology, Khon Kaen, Thailand; Khon Kaen University, Fermentation Research Center for Value Added Agricultural Products, Khon Kaen, Thailand.
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Yan R, Zhang J, Zellmer L, Chen L, Wu D, Liu S, Xu N, Liao JD. Probably less than one-tenth of the genes produce only the wild type protein without at least one additional protein isoform in some human cancer cell lines. Oncotarget 2017; 8:82714-82727. [PMID: 29137297 PMCID: PMC5669923 DOI: 10.18632/oncotarget.20015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/30/2017] [Indexed: 11/25/2022] Open
Abstract
To estimate how many genes produce multiple protein isoforms, we electrophoresed proteins from MCF7 and MDA-MB231 (MB231) human breast cancer cells in SDS-PAGE and excised narrow stripes of the gel at the 48kD, 55kD and 72kD. Proteins in these stripes were identified using liquid chromatography and tandem mass spectrometry. A total of 765, 750 and 679 proteins from MB231 cells, as well as 470, 390 and 490 proteins from MCF7 cells, were identified from the 48kD, 55kD and 72kD stripes, respectively. We arbitrarily allowed a 10% technical variation from the proteins' theoretical molecular mass (TMM) and considered those proteins with their TMMs within the 43-53 kD, 49-61 kD and 65-79 kD ranges as the wild type (WT) expected from the corresponding stripe, whereas those with a TMM above or below this range as a smaller- or larger-group, respectively. Only 263 (34.4%), 269 (35.9%) and 151 (22.2%) proteins from MB231 cells and 117 (24.9%), 135 (34.6%) and 130 (26.5%) proteins from MCF7 cells from the 48kD, 55kD and 72kD stripes, respectively, belonged to the WT, while the remaining majority belonged to the smaller- or larger-groups. Only about 3-16%, on average about 10% regardless of the stripe and cell line, of the proteins appeared in only one stripe and within the WT range, while the remaining preponderance appeared also in additional stripe(s) or had a larger or smaller TMM. We conclude that few (fewer than 10%) of the human genes produce only the WT protein without additional isoform(s).
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Affiliation(s)
- Rui Yan
- Nephrology Department, Guizhou Medical University Hospital, Guiyang, P.R. China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Lucas Zellmer
- Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Lichan Chen
- Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Di Wu
- Beijing Protein Innovation Co., Ltd, Beijing, P.R. China
| | - Siqi Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Joshua D Liao
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, P.R. China
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Wang L, Fan C, Xu W, Zhang Y, Dong Z, Xiang J, Chen S. Characterization and functional analysis of a novel C1q-domain-containing protein in Japanese flounder (Paralichthys olivaceus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 67:322-332. [PMID: 27601208 DOI: 10.1016/j.dci.2016.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 09/02/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
The complement system is important in the innate immune response. C1q-domain-containing proteins have multiple functions and occur extensively in invertebrates and vertebrates. In this study, PoC1ql3 encoding a C1q-domain-containing protein in the Japanese flounder was identified. The 266-amino-acid polypeptide encoded, PoC1ql3, shares high sequence and structural similarity with orthologues in other fish and mammals. PoC1ql3 is abundantly expressed in the brain, but less in the blood, gills, and liver. Transcripts of PoC1ql3 were down-regulated in the spleen and liver 6-24 h after bacterial infection, but were significantly up-regulated after 48 h. Full-length PoC1ql3 (C1ql3-full) and its gC1q domain (C1ql3-part) were both exerted anti-Edwardsiella tarda activity. C1ql3-part bound to lipopolysaccharide and peptidoglycan, and exerted antibacterial effects against E. tarda in vivo, suggesting that C1ql3 functions as a pathogen-recognition receptor. Therefore, PoC1ql3 functions in the innate immune system, which would facilitate the investigation of the immune system in Japanese flounder.
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Affiliation(s)
- Lei Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Caixia Fan
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Wenteng Xu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yongzhen Zhang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Zhongdian Dong
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jinsong Xiang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Songlin Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Loder AJ, Zeldes BM, Conway JM, Counts JA, Straub CT, Khatibi PA, Lee LL, Vitko NP, Keller MW, Rhaesa AM, Rubinstein GM, Scott IM, Lipscomb GL, Adams MW, Kelly RM. Extreme Thermophiles as Metabolic Engineering Platforms: Strategies and Current Perspective. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Andrew J. Loder
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Benjamin M. Zeldes
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Jonathan M. Conway
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - James A. Counts
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Christopher T. Straub
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Piyum A. Khatibi
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Laura L. Lee
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Nicholas P. Vitko
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Matthew W. Keller
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Amanda M. Rhaesa
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gabe M. Rubinstein
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Israel M. Scott
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gina L. Lipscomb
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Michael W.W. Adams
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Robert M. Kelly
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
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Wang Q, Cen Z, Zhao J. The survival mechanisms of thermophiles at high temperatures: an angle of omics. Physiology (Bethesda) 2015; 30:97-106. [PMID: 25729055 DOI: 10.1152/physiol.00066.2013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Thermophiles are referred to as microorganisms with optimal growth temperatures of >60 °C. Over the past few years, a number of studies have been conducted regarding thermophiles, especially using the omics strategies. This review provides a systematic view of the survival physiology of thermophiles from an "omics" perspective, which suggests that the adaptive ability of thermophiles is based on a cooperative mode with multi-dimensional regulations integrating genomics, transcriptomics, and proteomics.
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Affiliation(s)
- Quanhui Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; and BGI-Shenzhen, Shenzhen, China
| | - Zhen Cen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; and
| | - Jingjing Zhao
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; and
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12
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Liu S, Lan J, Zhou B, Qin Y, Zhou Y, Xiao X, Yang J, Gou J, Qi J, Huang Y, Tang C. HbNIN2, a cytosolic alkaline/neutral-invertase, is responsible for sucrose catabolism in rubber-producing laticifers of Hevea brasiliensis (para rubber tree). THE NEW PHYTOLOGIST 2015; 206:709-25. [PMID: 25581169 DOI: 10.1111/nph.13257] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/29/2014] [Indexed: 05/21/2023]
Abstract
In Hevea brasiliensis, an alkaline/neutral invertase (A/N-Inv) is responsible for sucrose catabolism in latex (essentially the cytoplasm of rubber-producing laticifers, the source of natural rubber) and implicated in rubber yield. However, neither the gene encoding this enzyme nor its molecular and biochemical properties have been well documented. Three Hevea A/N-Inv genes, namely HbNIN1, 2 and 3, were first cloned and characterized in planta and in Escherichia coli. Cellular localizations of HbNIN2 mRNA and protein were probed. From latex, active A/N-Inv proteins were purified, identified, and explored for enzymatic properties. HbNIN2 was identified as the major A/N-Inv gene functioning in latex based on its functionality in E. coli, its latex-predominant expression, the conspicuous localization of its mRNA and protein in the laticifers, and its expressional correlation with rubber yield. An active A/N-Inv protein was partially purified from latex, and determined as HbNIN2. The enhancement of HbNIN2 enzymatic activity by pyridoxal is peculiar to A/N-Invs in other plants. We conclude that HbNIN2, a cytosolic A/N-Inv, is responsible for sucrose catabolism in rubber laticifers. The results contribute to the studies of sucrose catabolism in plants as a whole and natural rubber synthesis in particular.
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Affiliation(s)
- Shujin Liu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, China; College of Agronomy, Hainan University, Haikou, 570228, Hainan, China
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13
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Liu Y, Zhang G, Sun H, Sun X, Jiang N, Rasool A, Lin Z, Li C. Enhanced pathway efficiency of Saccharomyces cerevisiae by introducing thermo-tolerant devices. BIORESOURCE TECHNOLOGY 2014; 170:38-44. [PMID: 25118151 DOI: 10.1016/j.biortech.2014.07.063] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 06/03/2023]
Abstract
In this study, thermo-tolerant devices consisting of heat shock genes from thermophiles were designed and introduced into Saccharomyces cerevisiae for improving its thermo-tolerance. Among ten engineered thermo-tolerant yeasts, T.te-TTE2469, T.te-GroS2 and T.te-IbpA displayed over 25% increased cell density and 1.5-4-fold cell viability compared with the control. Physiological characteristics of thermo-tolerant strains revealed that better cell wall integrity, higher trehalose content and enhanced metabolic energy were preserved by thermo-tolerant devices. Engineered thermo-tolerant strain was used to investigate the impact of thermo-tolerant device on pathway efficiency by introducing β-amyrin synthesis pathway, showed 28.1% increased β-amyrin titer, 28-35°C broadened growth temperature range and 72h shortened fermentation period. The results indicated that implanting heat shock proteins from thermophiles to S. cerevisiae would be an efficient approach to improve its thermo-tolerance.
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Affiliation(s)
- Yueqin Liu
- School of Chemical Engineering, Tianjin University, Tianjin 300072, China
| | - Genli Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Huan Sun
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xiangying Sun
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Nisi Jiang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Aamir Rasool
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | | | - Chun Li
- School of Chemical Engineering, Tianjin University, Tianjin 300072, China; School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
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14
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Zhang J, Lou X, Shen H, Zellmer L, Sun Y, Liu S, Xu N, Liao DJ. Isoforms of wild type proteins often appear as low molecular weight bands on SDS-PAGE. Biotechnol J 2014; 9:1044-54. [PMID: 24906056 DOI: 10.1002/biot.201400072] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/03/2014] [Accepted: 06/04/2014] [Indexed: 11/08/2022]
Abstract
Immunoblotting, after polyacrylamide gel electrophoresis with sodium dodecyl sulfate (SDS-PAGE), is a technique commonly used to detect specific proteins. SDS-PAGE often results in the visualization of protein band(s) in addition to the one expected based on the theoretical molecular mass (TMM) of the protein of interest. To determine the likelihood of additional band(s) being nonspecific, we used liquid chromatography - mass spectrometry to identify proteins that were extracted from bands with the apparent molecular mass (MM) of 40 and 26 kD, originating from protein extracts derived from non-malignant HEK293 and cancerous MDA-MB231 (MB231) cells separated using SDS-PAGE. In total, approximately 57% and 21% of the MS/MS spectra were annotated as peptides in the two cell samples, respectively. Moreover, approximately 24% and 36.2% of the identified proteins from HEK293 and MB231 cells matched their TMMs. Of the identified proteins, 8% from HEK293 and 26% from MB231 had apparent MMs that were larger than predicted, and 67% from HEK293 and 37% from MB231 exhibited smaller MM values than predicted. These revelations suggest that interpretation of the positive bands of immunoblots should be conducted with caution. This study also shows that protein identification performed by mass spectrometry on bands excised from SDS-PAGE gels could make valuable contributions to the identification of cancer biomarkers, and to cancer-therapy studies.
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Affiliation(s)
- Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China
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15
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Liang X, Martyniuk CJ, Cheng G, Zha J, Wang Z. Pyruvate carboxylase as a sensitive protein biomarker for exogenous steroid chemicals. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2014; 189:184-193. [PMID: 24681510 DOI: 10.1016/j.envpol.2014.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 06/03/2023]
Abstract
Assessing protein responses to endocrine disrupting chemicals is critical for understanding the mechanisms of chemical action and for the assessment of hazards. In this study, the response of the liver proteome of male rare minnows (Gobiocypris rarus) treated with 17β-estradiol (E2) and females treated with 17α-methyltestosterone (MT) were analyzed. A total of 23 and 24 proteins were identified with differential expression in response to E2 and MT, respectively. Pyruvate carboxylase (PC) was the only common differentially expressed protein in both males and females after E2- and MT-treatments. The mRNA as well as the protein levels of PC were significantly down-regulated compared with that of the controls (p < 0.05). Our results suggest that endocrine disruptors interfere with genes and proteins of the TCA cycle and PC may be a sensitive biomarker of exposure to exogenous steroid chemicals in the liver of fish.
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Affiliation(s)
- Xuefang Liang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
| | - Christopher J Martyniuk
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada E2L 4L5
| | - Gang Cheng
- Key Lab for Biotechnology of National Commission for Nationalities, College of Life Science, South Central University for Nationalities, Wuhan 430074, China
| | - Jinmiao Zha
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China.
| | - Zijian Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China.
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16
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Liang X, Li W, Martyniuk CJ, Zha J, Wang Z, Cheng G, Giesy JP. Effects of dechlorane plus on the hepatic proteome of juvenile Chinese sturgeon (Acipenser sinensis). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 148:83-91. [PMID: 24463492 DOI: 10.1016/j.aquatox.2014.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 12/31/2013] [Accepted: 01/05/2014] [Indexed: 06/03/2023]
Abstract
Dechlorane Plus (DP), an alternative to decabromodiphenyl ether (BDE-209), is a widely used polychlorinated flame retardant that is frequently detected in aquatic ecosystems. While the mechanisms of toxicity of BDE-209 have been well documented, less is known about the toxicity of DP. In this study, juvenile Chinese sturgeon (Acipenser sinensis) were treated with DP at doses of 1, 10, and 100mg/kg wet weight for 14 days via a single intraperitoneal injection (i.p.). After 14 days, liver proteomes of juvenile Chinese sturgeon were analyzed using two-dimensional electrophoresis (2-DE) coupled matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). A total of 39 protein spots were significantly altered in abundance (>2-fold) and of these proteins, 27 were successfully identified. Proteins related to the stress response that included heat shock cognate protein 70 and T-complex protein 1 were significantly increased and decreased in abundance, respectively. Moreover, Ras-related protein Rab-6B and GDP dissociation inhibitor 2, proteins that are involved in small G-protein signal cascades, were decreased in abundance 2- to 5-fold. Annexin A4, which is associated with Ca(2+) signaling pathways, was also markedly decreased by 2-fold in the liver. Pathway analysis of differentially regulated proteins revealed that DP interfered with metabolism and was associated with proteins related to apoptosis and cell differentiation. Based upon protein responses, we suggest that DP has effects on the generalized stress response, small G-protein signal cascades, Ca(2+) signaling pathway, and metabolic process, and may induce apoptosis in the liver. This study offers novel mechanistic insight into the protein responses induced in the liver with DP, an increasingly used and understudied flame retardant.
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Affiliation(s)
- Xuefang Liang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wei Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Christopher J Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, NB, Canada E2L 4L5
| | - Jinmiao Zha
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Zijian Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Gang Cheng
- Key Lab for Biotechnology of National Commission for Nationalities, College of Life Science, South Central University for Nationalities, Wuhan 430074, China
| | - John P Giesy
- Department of Biomedical Veterinary Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada S7N 5B3; Department of Biology & Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, China
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17
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Deinhardt K, Darie CC. Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. Cell Mol Life Sci 2014; 71:205-28. [PMID: 23579629 PMCID: PMC11113707 DOI: 10.1007/s00018-013-1333-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 11/28/2022]
Abstract
Following the sequencing of the human genome and many other organisms, research on protein-coding genes and their functions (functional genomics) has intensified. Subsequently, with the observation that proteins are indeed the molecular effectors of most cellular processes, the discipline of proteomics was born. Clearly, proteins do not function as single entities but rather as a dynamic network of team players that have to communicate. Though genetic (yeast two-hybrid Y2H) and biochemical methods (co-immunoprecipitation Co-IP, affinity purification AP) were the methods of choice at the beginning of the study of protein-protein interactions (PPI), in more recent years there has been a shift towards proteomics-based methods and bioinformatics-based approaches. In this review, we first describe in depth PPIs and we make a strong case as to why unraveling the interactome is the next challenge in the field of proteomics. Furthermore, classical methods of investigation of PPIs and structure-based bioinformatics approaches are presented. The greatest emphasis is placed on proteomic methods, especially native techniques that were recently developed and that have been shown to be reliable. Finally, we point out the limitations of these methods and the need to set up a standard for the validation of PPI experiments.
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Affiliation(s)
- Armand G. Ngounou Wetie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Alisa G. Woods
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Urmi Roy
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Katrin Deinhardt
- Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
- Institute for Life Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
| | - Costel C. Darie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
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18
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Sun Y, Lou X, Yang M, Yuan C, Ma L, Xie BK, Wu JM, Yang W, Shen SX, Xu N, Liao DJ. Cyclin-dependent kinase 4 may be expressed as multiple proteins and have functions that are independent of binding to CCND and RB and occur at the S and G 2/M phases of the cell cycle. Cell Cycle 2013; 12:3512-25. [PMID: 24091631 DOI: 10.4161/cc.26510] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cyclin-dependent kinase 4 (CDK4) is known to be a 33 kD protein that drives G 1 phase progression of the cell cycle by binding to a CCND protein to phosphorylate RB proteins. Using different CDK4 antibodies in western blot, we detected 2 groups of proteins around 40 and 33 kD, respectively, in human and mouse cells; each group often appeared as a duplet or triplet of bands. Some CDK4 shRNAs could decrease the 33 kD wild-type (wt) CDK4 but increase some 40 kD proteins, whereas some other shRNAs had the opposite effects. Liquid chromatography-mass spectrometry/mass spectrometry analysis confirmed the existence of CDK4 isoforms smaller than 33 kD but failed to identify CDK4 at 40 kD. We cloned one CDK4 mRNA variant that lacks exon 2 and encodes a 26 kD protein without the first 74 amino acids of the wt CDK4, thus lacking the ATP binding sequence and the PISTVRE domain required for binding to CCND. Co-IP assay confirmed that this ΔE2 protein lost CCND1- and RB1-binding ability. Moreover, we found, surprisingly, that the wt CDK4 and the ΔE2 could inhibit G 1-S progression, accelerate S-G 2/M progression, and enhance or delay apoptosis in a cell line-specific manner in a situation where the cells were treated with a CDK4 inhibitor or the cells were serum-starved and then replenished. Hence, CDK4 seems to be expressed as multiple proteins that react differently to different CDK4 antibodies, respond differently to different shRNAs, and, in some situations, have previously unrecognized functions at the S-G 2/M phases of the cell cycle via mechanisms independent of binding to CCND and RB.
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Affiliation(s)
- Yuan Sun
- Hormel Institute; The University of Minnesota; Austin, MN USA
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19
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Thermal stability of glucokinases in Thermoanaerobacter tengcongensis. BIOMED RESEARCH INTERNATIONAL 2013; 2013:646539. [PMID: 24058911 PMCID: PMC3766608 DOI: 10.1155/2013/646539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/18/2013] [Indexed: 11/18/2022]
Abstract
In the genome of Thermoanaerobacter tengcongensis, three genes belonging to ROK (Repressor, ORF, and Kinase) family are annotated as glucokinases (GLKs). Using enzyme assays, the three GLKs were identified as ATP-dependent GLK (ATP-GLK), ADP-dependent GLK (ADP-GLK), and N-acetyl-glucosamine/mannosamine kinase (glu/man-NacK). The kinetic properties of the three GLKs such as Km, Vmax, optimal pH, and temperature were characterized, demonstrating that these enzymes performed the specific functions against varied substrates and under different temperatures. The abundance of ATP-GLK was attenuated when culture temperature was elevated and was almost undetectable at 80°C, whereas the ADP-GLK abundance was insensitive to temperature changes. Using degradation assays, ATP-GLK was found to have significantly faster degradation than ADP-GLK at 80°C. Co-immunoprecipitation results revealed that heat shock protein 60 (HSP60) could interact with ATP-GLK and ADP-GLK at 60 and 75°C, whereas at 80°C, the interaction was only effectively with ADP-GLK but not ATP-GLK. The functions of GLKs in T. tengcongensis are temperature dependent, likely regulated through interactions with HSP60.
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20
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Tong W, Chen Z, Cao Z, Wang Q, Zhang J, Bai X, Wang R, Liu S. Robustness analysis of a constraint-based metabolic model links cell growth and proteomics of Thermoanaerobacter tengcongensis under temperature perturbation. MOLECULAR BIOSYSTEMS 2013; 9:713-22. [PMID: 23396507 DOI: 10.1039/c3mb25278g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The integration of omic data with metabolic networks has been demonstrated to be an effective approach to elucidate the underlying metabolic mechanisms in life. Because the metabolic pathways of Thermoanaerobacter tengcongensis (T. tengcongensis) are incomplete, we used a 1-(13)C-glucose culture to monitor intracellular isotope-labeled metabolites by GC/MS and identified the gap gene in glucose catabolism, Re-citrate synthase. Based on genome annotation and biochemical information, we reconstructed the metabolic network of glucose metabolism and amino acid synthesis in T. tengcongensis, including 253 reactions, 227 metabolites, and 236 genes. Furthermore, we performed constraint based modeling (CBM)-derived robustness analysis on the model to study the dynamic changes of the metabolic network. By perturbing the culture temperature from 75 to 55 °C, we collected the bacterial growth rates and differential proteomes. Assuming that protein abundance changes represent metabolic flux variations, we proposed that the robustness analysis of the CBM model could decipher the effect of proteome change on the bacterial growth under perturbation. For approximately 73% of the reactions, the predicted cell growth changes due to such reaction flux variations matched the observed cell growth data. Our study, therefore, indicates that differential proteome data can be integrated with metabolic network modeling and that robustness analysis is a strong method for representing the dynamic change in cell phenotypes under perturbation.
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Affiliation(s)
- Wei Tong
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 101300, China
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21
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Zi J, Zhang J, Wang Q, Lin L, Tong W, Bai X, Zhao J, Chen Z, Fu X, Liu S. Proteomics study of rice embryogenesis: discovery of the embryogenesis-dependent globulins. Electrophoresis 2012; 33:1129-38. [PMID: 22539316 DOI: 10.1002/elps.201100398] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The plant embryo is the germination center of the seed. How an embryo forms during seed maturation remains unclear, especially in the case of monocotyledonous plants. Generally, the complex processes of embryogenesis result from the action of a coordinated network of genes. Thus, a large-scale survey of changes in protein abundance during embryogenesis is an effective approach to study the molecular events of embryogenesis. In this study, two-dimensional gel electrophoresis (2DE) was applied to separate rice embryo proteins collected during the three phases of embryogenesis: 6 days after pollination (DAP), 12 DAP, and 18 DAP. We then employed matrix-assisted laser desorption-ionization time of flight/time of flight mass spectrometry(MALDI TOF/TOF MS) to identify the phase-dependent differential 2DE spots. A total of 66 spots were discovered to be regulated during embryogenesis, and of these spots, 53 spots were identified. These proteins were further categorized into several functional classes, including storage, embryo development, stress response, glycolysis, and protein metabolism. Intriguingly, the major differential spots originated from three globulins. We further examined the possible mechanism underlying the globulins' multiple forms using Western blotting, proteolysis, and blue native gel electrophoresis techniques and found that the multiple forms of globulins were produced as a result of enhanced proteolysis during embryogenesis, indicating that these globulin forms may serve as chaperone proteins participating in the formation of multiple protein complexes during embryogenesis.
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Affiliation(s)
- Jin Zi
- China Agricultural University, Beijing, China
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22
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Liu B, Wang C, Yang H, Tan H. Establishment of a genetic transformation system and its application in Thermoanaerobacter tengcongensis. J Genet Genomics 2012; 39:561-70. [PMID: 23089366 DOI: 10.1016/j.jgg.2012.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 07/13/2012] [Accepted: 07/16/2012] [Indexed: 11/30/2022]
Abstract
The whole-genome sequence of Thermoanaerobacter tengcongensis, an anaerobic thermophilic bacterium isolated from the Tengchong hot spring in China, was completed in 2002. However, in vivo studies on the genes of this strain have been hindered in the absence of genetic manipulation system. In order to establish such a system, the plasmid pBOL01 containing the replication origin of the T. tengcongensis chromosome and a kanamycin resistance cassette, in which kanamycin resistance gene expression was controlled by the tte1482 promoter from T. tengcongensis, was constructed and introduced into T. tengcongensis via electroporation. Subsequently, the high transformation efficiency occurred when using freshly cultured T. tengcongensis cells without electroporation treatment, suggesting that T. tengcongensis is naturally competent under appropriate growth stage. A genetic transformation system for this strain was then established based on these important components, and this system was proved to be available for studying physiological characters of T. tengcongensis in vivo by means of hisG gene disruption and complementation.
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Affiliation(s)
- Bo Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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23
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Wang Q, Wang Q, Tong W, Bai X, Chen Z, Zhao J, Zhang J, Liu S. Regulation of enzyme activity of alcohol dehydrogenase through its interactions with pyruvate-ferredoxin oxidoreductase in Thermoanaerobacter tengcongensis. Biochem Biophys Res Commun 2011; 417:1018-23. [PMID: 22222371 DOI: 10.1016/j.bbrc.2011.12.083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 12/16/2011] [Indexed: 10/14/2022]
Abstract
Alcohol dehydrogenases (ADHs) from thermophilic microorganisms are interesting enzymes that have their potential applications in biotechnology and potentially provide insight into the mechanisms of action of thermo-tolerant proteins. The molecular mechanisms of ADHs under thermal stress in vivo have yet to be explored. Herein, we employed a proteomic strategy to survey the possible interactions of secondary-ADH (2-ADH) with other proteins in Thermoanaerobacter tengcongensis (T. tengcongensis) cultured at 75°C and found that 2-ADH, pyruvate-ferredoxin oxidoreductase (PFOR) and several glycolytic enzymes coexisted in a protein complex. Using anion exchange chromatography, the elution profile indicated that the native 2-ADH was present in two forms, PFOR-bound and PFOR-free. Immuno-precipitation and pull down analysis further validated the interactions between 2-ADH and PFOR. The kinetic behaviours of 2-ADH either in the recombinant or native form were evaluated with different substrates. The enzyme activity of 2-ADH was inhibited in a non-competitive mode by PFOR, implying the interaction of 2-ADH and PFOR negatively regulated alcohol formation. In T. tengcongensis, PFOR is an enzyme complex located at the upstream of 2-ADH in the alcohol generation pathway. These findings, therefore, offered a plausible mechanism for how alcohol metabolism is regulated by hetero-interactions between 2-ADH and PFOR, especially in anaerobic thermophiles.
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Affiliation(s)
- Qian Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China
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24
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Woods AG, Sokolowska I, Yakubu R, Butkiewicz M, LaFleur M, Talbot C, Darie CC. Blue Native PAGE and Mass Spectrometry as an Approach for the Investigation of Stable and Transient Protein-Protein Interactions. ACS SYMPOSIUM SERIES 2011. [DOI: 10.1021/bk-2011-1083.ch012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Alisa G. Woods
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Izabela Sokolowska
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Rama Yakubu
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Melissa Butkiewicz
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Martin LaFleur
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Christopher Talbot
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Costel C. Darie
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
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