1
|
Zhao X, Liu Y, Yan F, Lin Z, Zhao Y, Chen X, Zhang Y. OmpU and OmpC are the key OMPs for Litopenaeus vannamei hemocyanin recognizes Vibrio parahaemolyticus. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109409. [PMID: 38325593 DOI: 10.1016/j.fsi.2024.109409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/25/2023] [Accepted: 01/25/2024] [Indexed: 02/09/2024]
Abstract
Hemocyanin is a multifunctional protein present in arthropods and mollusks, responsible for oxygen transport and participating in multiple roles of immune defense including antibacterial activity. However, the molecular basis of how hemocyanin recognizes pathogens and exerts antibacterial activity remains poorly understood. In the present study, the pull-down assay was used to isolate Vibrio parahaemolyticus outer membrane proteins (OMPs) that bind to Litopenaeus vannamei hemocyanin. Two interacting OMPs bands were determined as OmpC and OmpU, and the heterogeneous interaction between hemocyanin and the two OMPs was further confirmed by far-Western blot. After construction of ompC and ompU deletion mutants, we found that the agglutinating activity and antibacterial activity of hemocyanin significantly decreased compared to the wild-type strain. After hemocyanin treatment, we identified four intracellular proteins of V. parahaemolyticus, including fructose-bisphosphate aldolase and ribosomal proteins could interact with rOmpC and rOmpU, respectively. Furthermore, we found that the mRNA levels of ompC, ompU, fbaA, rpsB and rpsC significantly decreased after hemocyanin treatment. These findings indicated that OmpC and OmpU are the key targets for L. vannamei hemocyanin recognize pathogens and exert its antibacterial activity.
Collapse
Affiliation(s)
- Xianliang Zhao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, 530021, China
| | - Yao Liu
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Fang Yan
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Zhongyang Lin
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Yongzhen Zhao
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, 530021, China
| | - Xiuli Chen
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, 530021, China
| | - Yueling Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China.
| |
Collapse
|
2
|
Sulaima JE, Lam H. Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens. Proteomics 2022; 22:e2100409. [PMID: 35143120 DOI: 10.1002/pmic.202100409] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 11/12/2022]
Abstract
Antibiotic resistance, the ability of a microbial pathogen to evade the effects of antibiotics thereby allowing them to grow under elevated drug concentrations, is an alarming health problem worldwide and has attracted the attention of scientists for decades. On the other hand, the clinical importance of persistence and tolerance as alternative mechanisms for pathogens to survive prolonged lethal antibiotic doses has recently become increasingly appreciated. Persisters and high-tolerance populations are thought to cause the relapse of infectious diseases, and provide opportunities for the pathogens to evolve resistance during the course of antibiotic therapy. Although proteomics and other omics methodology have long been employed to study resistance, its applications in studying persistence and tolerance are still limited. However, due to the growing interest in the topic and recent progress in method developments to study them, there have been some proteomic studies that yield fresh insights into the phenomenon of persistence and tolerance. Combined with the studies on resistance, these collectively guide us to novel molecular targets for the potential drugs for the control of these dangerous pathogens. In this review, we surveyed previous proteomic studies to investigate resistance, persistence, and tolerance mechanisms, and discussed emerging experimental strategies for studying these phenotypes with a combination of adaptive laboratory evolution and high-throughput proteomics. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Jordy Evan Sulaima
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| |
Collapse
|
3
|
Elevation of Fatty Acid Biosynthesis Metabolism Contributes to Zhongshengmycin Resistance in Xanthomonas oryzae. Antibiotics (Basel) 2021; 10:antibiotics10101166. [PMID: 34680747 PMCID: PMC8532796 DOI: 10.3390/antibiotics10101166] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/15/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Xanthomonas oryzae severely impacts the yield and quality of rice. Antibiotics are the most common control measure for this pathogen; however, the overuse of antibiotics in past decades has caused bacterial resistance to these antibiotics. The agricultural context is of particular importance as antibiotic-resistant bacteria are prevalent, but the resistance mechanism largely remains unexplored. Herein, using gas chromatography-mass spectrometry (GC-MS), we demonstrated that zhongshengmycin-resistant X. oryzae (Xoo-Rzs) and zhongshengmycin-sensitive X. oryzae (Xoo-S) have distinct metabolic profiles. We found that the resistance to zhongshengmycin (ZS) in X. oryzae is related to increased fatty acid biosynthesis. This was demonstrated by measuring the Acetyl-CoA carboxylase (ACC) activity, the expression levels of enzyme genes involved in the fatty acid biosynthesis and degradation pathways, and adding exogenous materials, i.e., triclosan and fatty acids. Our work provides a basis for the subsequent control of the production of antibiotic-resistant strains of X. oryzae and the development of coping strategies.
Collapse
|
4
|
Abstract
The Na+-NQR complex functions as a unique redox-driven sodium pump, generating membrane potential directly. However, whether it mediates generation of membrane potential indirectly is unknown. The present study shows that the Na+-NQR complex impacts membrane potential through other antiporter families Atp and Mnh. It proceeds by ATP and then cAMP/CRP regulon, which inhibits l-alanine catabolism and promotes l-alanine anabolism. When the Na+-NQR complex is reduced as in antibiotic-resistant bacteria, l-alanine is depressed, which is related to the antibiotic resistance phenotypes. However, exogenous l-alanine reverts the phenotype and promotes antibiotic-mediated killing. These findings suggest a novel mechanism by which the Na+-NQR system regulates antibiotic resistance via l-alanine metabolism in a cAMP/CRP complex-dependent manner. Sodium-translocating NADH:quinone oxidoreductase (Na+-NQR) functions as a unique redox-driven sodium pump, generating membrane potential, which is related to aminoglycoside antibiotic resistance. However, whether it modulates other metabolisms to confer antibiotic resistance is unknown. The present study showed that loss of nqrA or nqrF led to differential metabolomes with elevated resistance to aminoglycoside antibiotics. Decreased alanine, aspartate, and glutamate metabolism and depressed abundance of alanine were characterized as the most impacted pathway and crucial biomarker, respectively. Further data showed that higher viability was detected in ΔnqrA and ΔnqrF mutant strains than their parent strain ATCC 33787 in the presence of gentamicin but recovered by exogenous l-alanine. It proceeds by the following events. The loss of nqrA or nqrF led to the decrease of membrane potential, ATPase activity, and then ATP and cyclic AMP (cAMP), which reduced the cAMP/CRP (cAMP receptor protein) complex. The reduced cAMP/CRP complex promoted l-alanine catabolism and inhibited l-alanine anabolism, causing reduced levels of alanine. Reduced alanine affected the expression of antiporter families Atp and Mnh genes. Our results suggest a novel mechanism by which the Na+-NQR system regulates antibiotic resistance via l-alanine metabolism in a cAMP/CRP complex-dependent manner.
Collapse
|
5
|
Zhang S, Wang J, Jiang M, Xu D, Peng B, Peng X, Li H. Reduced redox‐dependent mechanism and glucose‐mediated reversal in gentamicin‐resistant
Vibrio alginolyticus. Environ Microbiol 2019; 21:4724-4739. [DOI: 10.1111/1462-2920.14811] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/21/2019] [Accepted: 09/24/2019] [Indexed: 01/22/2023]
Affiliation(s)
- Song Zhang
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio‐Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life SciencesSun Yat‐sen University, University City Guangzhou 510006 People's Republic of China
| | - Jie Wang
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio‐Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life SciencesSun Yat‐sen University, University City Guangzhou 510006 People's Republic of China
| | - Ming Jiang
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio‐Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life SciencesSun Yat‐sen University, University City Guangzhou 510006 People's Republic of China
| | - Di Xu
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio‐Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life SciencesSun Yat‐sen University, University City Guangzhou 510006 People's Republic of China
| | - Bo Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio‐Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life SciencesSun Yat‐sen University, University City Guangzhou 510006 People's Republic of China
- Laboratory for Marine Fisheries Science and Food Production ProcessesQingdao National Laboratory for Marine Science and Technology Qingdao 266071 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Zhuhai 519000 China
| | - Xuan‐xian Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio‐Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life SciencesSun Yat‐sen University, University City Guangzhou 510006 People's Republic of China
- Laboratory for Marine Fisheries Science and Food Production ProcessesQingdao National Laboratory for Marine Science and Technology Qingdao 266071 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Zhuhai 519000 China
| | - Hui Li
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio‐Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life SciencesSun Yat‐sen University, University City Guangzhou 510006 People's Republic of China
- Laboratory for Marine Fisheries Science and Food Production ProcessesQingdao National Laboratory for Marine Science and Technology Qingdao 266071 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Zhuhai 519000 China
| |
Collapse
|
6
|
Wen Q, Liu XJ, Zhu WC, Li L, Li MY, Peng XX, Li H. Characterization of balofloxacin-stressed proteomics and identification of balofloxacin-binding proteins pre-peptidase and integration host factor in Edwardsiella tarda. J Proteomics 2019; 205:103413. [DOI: 10.1016/j.jprot.2019.103413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/23/2019] [Accepted: 06/06/2019] [Indexed: 12/13/2022]
|
7
|
Yang J, Zeng ZH, Yang MJ, Cheng ZX, Peng XX, Li H. NaCl promotes antibiotic resistance by reducing redox states in Vibrio alginolyticus. Environ Microbiol 2018; 20:4022-4036. [PMID: 30307102 DOI: 10.1111/1462-2920.14443] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/27/2018] [Accepted: 10/05/2018] [Indexed: 01/22/2023]
Abstract
The development of antibiotic resistance in Vibrio alginolyticus represents a threat to human health and fish farming. Environmental NaCl regulation of bacterial physiology is well documented, but whether the regulation contributes to antibiotic resistance remains unknown. To explore this, we compared minimum inhibitory concentration (MIC) of V. alginolyticus cultured in different media with 0.5%-10% NaCl, and found that the MIC increased as the NaCl concentration increased, especially for aminoglycoside antibiotics. Consistent with this finding, internal NaCl also increased, while intracellular gentamicin level decreased. GC-MS-based metabolomics showed different distributions of pyruvate cycle intermediates among 0.5%, 4% and 10% NaCl. Differential activity of enzymes in the pyruvate cycle and altered expression of Na(+)-NQR led to a reducing redox state, characterized by decreased levels of NADH, proton motive force (PMF) and ATP. Meanwhile, NaCl negatively regulated PMF as a consequence of the reducing redox state. These together are responsible for the decreased intracellular gentamicin level with the increased external level of NaCl. Our study reveals a previously unknown redox state-dependent mechanism regulated by NaCl in V. alginolyticus that impacts antibiotic resistance.
Collapse
Affiliation(s)
- Jun Yang
- Center for Proteomics, State Key Laboratory of Bio-Control, School of Life Sciences, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou, 510006, People's Republic of China
| | - Zao-Hai Zeng
- Center for Proteomics, State Key Laboratory of Bio-Control, School of Life Sciences, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou, 510006, People's Republic of China
| | - Man-Jun Yang
- Center for Proteomics, State Key Laboratory of Bio-Control, School of Life Sciences, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou, 510006, People's Republic of China
| | - Zhi-Xue Cheng
- Center for Proteomics, State Key Laboratory of Bio-Control, School of Life Sciences, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou, 510006, People's Republic of China
| | - Xuan-Xian Peng
- Center for Proteomics, State Key Laboratory of Bio-Control, School of Life Sciences, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou, 510006, People's Republic of China
| | - Hui Li
- Center for Proteomics, State Key Laboratory of Bio-Control, School of Life Sciences, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou, 510006, People's Republic of China
| |
Collapse
|
8
|
The depressed central carbon and energy metabolisms is associated to the acquisition of levofloxacin resistance in Vibrio alginolyticus. J Proteomics 2018; 181:83-91. [DOI: 10.1016/j.jprot.2018.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 02/28/2018] [Accepted: 04/02/2018] [Indexed: 01/22/2023]
|
9
|
Li W, Zhang S, Wang X, Yu J, Li Z, Lin W, Lin X. Systematically integrated metabonomic-proteomic studies of Escherichia coli under ciprofloxacin stress. J Proteomics 2018. [PMID: 29522880 DOI: 10.1016/j.jprot.2018.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Many antibiotics are used to kill pathogenic Escherichia coli each year, resulting in an increase in the number of antibiotic-resistant strains. In this study, an integrated metabonomic-proteomic method was performed to systematically compare the profiles of metabolites and proteins with or without ciprofloxacin (CFLX) treatment. Proteomics identified 290 altered proteins including 143 with decreased and 147 increased expression, respectively. Metabonomics identified 65 altered metabolites including 58 and 7 with decreased and increased expression, respectively. The integrated analysis showed that the CFLX inhibited the DNA replication and increased the expression of DNA gyrase and DNA topoisomerase 1, while causing a sharp decrease in metabolic activity such as the alanine, aspartate and glutamate metabolism. Moreover, CFLX affected the biosynthesis of aminoacyl- transfer RNAs (tRNAs), leading to an increase in aminoacyl-tRNAs ligases, but limited the aminoacyl-tRNAs-mediated-biosynthesis of related amino acids. In this study, we identified the metabolite and protein profiles under CFLX stress, indicating the mode of action of antibiotics in E. coli. Furthermore, the decreasing metabolic activity in E. coli may be an effective strategy to escape killing by antimicrobials or toxic compounds. The results of this study will advance our understanding of the mechanisms underlying the resistance of bacteria to antibiotics. BIOLOGICAL SIGNIFICANCE To investigate the biological impact of antibiotics stress on Escherichia coli, we applied an integrated metabonomic-proteomic method to systematically compare the profiles of metabolites and proteins between with and without antibiotics ciprofloxacin (CFLX) treatment. Following bioinformatics analysis showed that CFLX inhibited the DNA replication and increased the expression of DNA gyrase and DNA topoisomerase, while causing a sharp increase in the alanine, aspartate and glutamate metabolism. Moreover, CFLX affected the biosynthesis of tRNAs and limited the generation of related amino acids metabolites. In a summary, our results will provide the metabolite and protein profiles under CFLX stress, indicating the mode of action of antibiotics in E. coli. The results of this study will advance our understanding of the mechanisms underlying the resistance of bacteria to antibiotics.
Collapse
Affiliation(s)
- Wanxin Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 35002, PR China
| | - Song Zhang
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, PR China
| | - Xiaoyun Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 35002, PR China
| | - Jing Yu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 35002, PR China
| | - Zeqi Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 35002, PR China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 35002, PR China
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 35002, PR China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 35002, PR China.
| |
Collapse
|
10
|
Zhang C, Zhu S, Jatt AN, Pan Y, Zeng M. Proteomic assessment of the role of N
-acyl homoserine lactone in Shewanella putrefaciens
spoilage. Lett Appl Microbiol 2017; 65:388-394. [DOI: 10.1111/lam.12795] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/29/2017] [Accepted: 06/19/2017] [Indexed: 11/29/2022]
Affiliation(s)
- C. Zhang
- College of Food Science and Engineering; Ocean University of China; Qingdao China
| | - S. Zhu
- College of Food Science and Engineering; Ocean University of China; Qingdao China
| | - A.-N. Jatt
- Institute of Microbiology; University of Sindh; Sindh Pakistan
| | - Y. Pan
- College of Food Science and Engineering; Ocean University of China; Qingdao China
| | - M. Zeng
- College of Food Science and Engineering; Ocean University of China; Qingdao China
| |
Collapse
|
11
|
Correia S, Hébraud M, Chafsey I, Chambon C, Viala D, Torres C, Caniça M, Capelo JL, Poeta P, Igrejas G. Subproteomic signature comparison of in vitro selected fluoroquinolone resistance and ciprofloxacin stress in Salmonella Typhimurium DT104B. Expert Rev Proteomics 2017; 14:941-961. [PMID: 28871888 DOI: 10.1080/14789450.2017.1375856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Fluoroquinolone resistance in nontyphoidal Salmonella is a situation of serious and international concern, particularly in S. Typhimurium DT104B multiresistant strains. Although known to be multifactorial, fluoroquinolone resistance is still far from a complete understanding. METHODS Subproteome changes between an experimentally selected fluoroquinolone-resistant strain (Se6-M) and its parent strain (Se6), and also in Se6-M under ciprofloxacin (CIP) stress, were evaluated in order to give new insights into the mechanisms involved. Proteomes were compared at the intracellular and membrane levels by a 2-DE~LC-MS/MS and a shotgun LC-MS/MS approach, respectively. RESULTS In total, 35 differentially abundant proteins were identified when comparing Se6 with Se6-M (25 more abundant in Se6 and 10 more abundant in Se6-M) and 82 were identified between Se6-M and Se6-M+CIP (51 more abundant in Se6-M and 31 more abundant under ciprofloxacin stress). CONCLUSION Several proteins with known and possible roles in quinolone resistance were identified which provide important information about mechanism-related differential protein expression, supporting the current knowledge and also leading to new testable hypotheses on the mechanism of action of fluoroquinolone drugs.
Collapse
Affiliation(s)
- Susana Correia
- a Functional Genomics and Proteomics Unit , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,b Department of Genetics and Biotechnology , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Veterinary Science Department , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal
| | - Michel Hébraud
- e UR454 Microbiology , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France.,f Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Ingrid Chafsey
- e UR454 Microbiology , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Christophe Chambon
- f Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Didier Viala
- f Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA , Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes , site de Theix , Saint-Genès Champanelle , France
| | - Carmen Torres
- g Área de Bioquímica y Biología Molecular , Universidad de La Rioja , Logroño , Spain
| | - Manuela Caniça
- h National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR-HAI), Department of Infectious Diseases , National Health Institute Doutor Ricardo Jorge (INSA) , Lisbon , Portugal
| | - José Luis Capelo
- d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal.,i Faculty of Sciences and Technology , ProteoMass Scientific Society , Caparica , Portugal
| | - Patrícia Poeta
- c Veterinary Science Department , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal
| | - Gilberto Igrejas
- a Functional Genomics and Proteomics Unit , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,b Department of Genetics and Biotechnology , University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,d UCIBIO-REQUIMTE, Faculty of Science and Technology , Nova University of Lisbon , Caparica , Portugal
| |
Collapse
|
12
|
Functional metabolomics: from biomarker discovery to metabolome reprogramming. Protein Cell 2015; 6:628-37. [PMID: 26135925 PMCID: PMC4537470 DOI: 10.1007/s13238-015-0185-x] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/28/2015] [Indexed: 12/14/2022] Open
Abstract
Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics. The crucial biomarkers can be used to reprogram a metabolome, leading to an aimed metabolic strategy to cope with alteration of internal and external environments, naming reprogramming metabolomics here. The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins. The reprogramming metabolomics approach can be used to clarify metabolic mechanisms of responding to changed internal and external environmental factors and to establish a framework to develop targeted tools for dealing with the changes such as controlling and/or preventing infection with pathogens and enhancing host immunity against pathogens. This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.
Collapse
|
13
|
Su YB, Peng B, Han Y, Li H, Peng XX. Fructose Restores Susceptibility of Multidrug-Resistant Edwardsiella tarda to Kanamycin. J Proteome Res 2015; 14:1612-20. [DOI: 10.1021/pr501285f] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yu-bin Su
- Center
for Proteomics and Metabolomics, State Key Laboratory of Biocontrol,
School of Life Sciences, MOE Key Lab Aquat Food Safety, School of
Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Bo Peng
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8197, United States
| | | | - Hui Li
- Center
for Proteomics and Metabolomics, State Key Laboratory of Biocontrol,
School of Life Sciences, MOE Key Lab Aquat Food Safety, School of
Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Xuan-xian Peng
- Center
for Proteomics and Metabolomics, State Key Laboratory of Biocontrol,
School of Life Sciences, MOE Key Lab Aquat Food Safety, School of
Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| |
Collapse
|
14
|
Liu XJ, Zhu WC, Su YB, Guo C, Zeng ZH, Zhu H, Li H, Peng XX. Characterization of ampicillin-stressed proteomics and development of a direct method for detecting drug-binding proteins in Edwardsiella tarda. J Proteomics 2015; 116:97-105. [PMID: 25596334 DOI: 10.1016/j.jprot.2014.12.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/25/2014] [Accepted: 12/10/2014] [Indexed: 02/01/2023]
Abstract
UNLABELLED Antibiotic-resistant Edwardsiella tarda poses a severe challenge to aquaculture. An understanding for antibiotic-resistant mechanisms is crucial to control the disease. The present study characterizes E. tarda ampicillin-stressed proteome and shows the importance of energy metabolism including the TCA cycle and glycolysis/gluconeogenesis in the antibiotic resistance. Further combination with antibiotic measurement develops a new method for identification of antibiotic-binding proteins out of differential abundances of proteins and results in determination of ETAE_0175 and ETAE_3367 as ampicillin-binding proteins in E. tarda. Genes of the two proteins are cloned and recombinant proteins are purified for validation of antibiotic-binding capability. Results show that higher binding capability is detected in ETAE_3367 than ETAE_0175. Out of the two proteins, ETAE_3367 is first reported here to be an antibiotic-binding protein, while ETAE_0175 homology in other bacteria has been shown to bind with other antibiotics. Bioinformatics analysis shows that ETAE_3367 may closely interact with aceF and sucA belonging to the TCA cycle and glycolysis/gluconeogenesis, respectively. These results indicate that energy metabolism contributes to ampicillin resistance in E. tarda and a new method to identify antibiotic-binding proteins is developed. These findings highlight the way to an understanding of antibiotic-resistant mechanisms in content of antibiotic-binding proteins. BIOLOGICAL SIGNIFICANCE Our data characterizes Edwardsiella tarda ampicillin-stressed proteome and shows the importance of energy metabolism including the TCA cycle and glycolysis/gluconeogenesis in the antibiotic resistance. Furthermore, a new method based 2-DE proteomics is developed for identification of antibiotic-binding proteins, which results in determination of ETAE_0175 and ETAE_3367 as ampicillin-binding proteins in E. tarda. ETAE_3367 is closely interacted with proteins of the TCA cycle and glycolysis/gluconeogenesis, suggesting the drug-resistant mechanism.
Collapse
Affiliation(s)
- Xian-jie Liu
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China
| | - Wei-cong Zhu
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China
| | - Yu-bin Su
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China
| | - Chang Guo
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China
| | - Zhao-hai Zeng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China
| | - Hai Zhu
- Shenzhen Bioeasy Biotechnologies Co., Ltd. No. 11 R&D Centre, Bao'an District, Shenzhen 518100, China
| | - Hui Li
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China
| | - Xuan-xian Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, MOE Key Lab Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China.
| |
Collapse
|
15
|
Lin XM, Yang MJ, Li H, Wang C, Peng XX. Decreased expression of LamB and Odp1 complex is crucial for antibiotic resistance in Escherichia coli. J Proteomics 2014; 98:244-53. [DOI: 10.1016/j.jprot.2013.12.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/18/2013] [Accepted: 12/29/2013] [Indexed: 01/06/2023]
|
16
|
Proteome studies of bacterial antibiotic resistance mechanisms. J Proteomics 2014; 97:88-99. [DOI: 10.1016/j.jprot.2013.10.027] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 10/12/2013] [Accepted: 10/19/2013] [Indexed: 01/10/2023]
|
17
|
Low abundance of respiratory nitrate reductase is essential for Escherichia coli in resistance to aminoglycoside and cephalosporin. J Proteomics 2013; 87:78-88. [DOI: 10.1016/j.jprot.2013.05.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 05/06/2013] [Accepted: 05/16/2013] [Indexed: 11/19/2022]
|
18
|
Liu X, She XT, Zhu QF, Li H, Peng XX. Heterogeneous interactome between Litopenaeus vannamei plasma proteins and Vibrio parahaemolyticus outer membrane proteins. FISH & SHELLFISH IMMUNOLOGY 2013; 34:192-198. [PMID: 23099052 DOI: 10.1016/j.fsi.2012.10.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 09/14/2012] [Accepted: 10/14/2012] [Indexed: 06/01/2023]
Abstract
A great loss has been suffered by microbial infectious diseases under intensive shrimp farming in recent years. In this background, the understanding of shrimp innate immunity becomes an importantly scientific issue, but little is known about the heterogeneous protein-protein interaction between pathogenic cells and hosts, which is a key step for the invading microbes to infect internet organs through bloodstream. In the present study, bacterial outer membrane (OM) protein array and pull-down approaches are used to isolate both Vibrio parahaemolyticus OM proteins that bind to shrimp serum proteins and the shrimp serum proteins that interact with bacterial cells, respectively. Three interacting shrimp serum proteins, hemocyanin, β-1,3-glucan binding protein and LV_HP_RA36F08r and thirty interacting OM proteins were determined. They form 63 heterogeneous protein-protein interactions. Nine out of the 30 OM proteins were randomly demonstrated to be up-regulated or down-regulated when bacterial cells were cultured with shrimp sera, indicating the biological significance of the network. The interesting findings uncover the complexity of struggle between host immunity and bacterial infection. Compared with our previous report on heterogeneous interactome between fish grill and bacterial OM proteins, the present study further extends the investigation from lower vertebrates to invertebrates and develops a bacterial OM protein array to identify the OM proteins bound with shrimp serum proteins, which elevates the frequencies of the bound OM proteins. Our results highlight the way to determine and understand the heterogeneous interaction between hosts and microbes.
Collapse
Affiliation(s)
- Xiang Liu
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | | | | | | | | |
Collapse
|
19
|
Zhang HL, Liu XJ, Zhang BW, Peng XX, Li H. Amphioxus CaVPT and creatine kinase are crucial immune-related molecules in response to bacterial infection and immunization. FISH & SHELLFISH IMMUNOLOGY 2012; 33:1139-1148. [PMID: 22960218 DOI: 10.1016/j.fsi.2012.08.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/16/2012] [Accepted: 08/27/2012] [Indexed: 06/01/2023]
Abstract
Although a great progress has been made, our understanding of innate immunity is incomplete. Here, we hypothesize that the innate immune response to pathogens is attributed into a group of functional proteins. The group contains information on host status post bacterial entry (infection or immunity) and bacterial species (Gram-positive or Gram-negative bacteria). Investigation of the group of proteins may result in disclosing of biomarkers identifying the status and species. For this regard, differential proteomics approach coupled with the pattern recognition methods are used to identify biomarkers from the proteins that being specifically regulated during the innate immune response of amphioxus to Gram-positive and Gram-negative bacteria with live or dead status. Four proteins, Calcium vector protein (CaVP), sarcoplasmic calcium-binding protein (SCP), CaVP-target protein (CaVPT) and creatine kinase (CK), are selected as the key biomarkers. Since immunoprotection of CaVP and SCP has been reported, the role of CaVPT and CK are further investigated. Gut CaVPT appears in dying amphioxus, whereas humoral fluid CK downregulates and gut CK keep no change in animals with immunity. The responses are stronger in Gram-negative than Gram-positive bacteria. These results indicate that CaVPT, CK, CaVP and SCP are the most important biomarkers to uncover amphioxus innate immunity to bacteria, and the approach is an efficient way to identify key biomarkers.
Collapse
Affiliation(s)
- Hai-Li Zhang
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510275, PR China
| | | | | | | | | |
Collapse
|
20
|
Lin X, Wang C, Guo C, Tian Y, Li H, Peng X. Differential regulation of OmpC and OmpF by AtpB in Escherichia coli exposed to nalidixic acid and chlortetracycline. J Proteomics 2012; 75:5898-910. [DOI: 10.1016/j.jprot.2012.08.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 08/13/2012] [Accepted: 08/22/2012] [Indexed: 12/27/2022]
|
21
|
Li H, Pan JY, Liu XJ, Gao JX, Wu HK, Wang C, Peng XX. Alterations of protein complexes and pathways in genetic information flow and response to stimulus contribute to Escherichia coli resistance to balofloxacin. MOLECULAR BIOSYSTEMS 2012; 8:2303-11. [PMID: 22729160 DOI: 10.1039/c2mb25090j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Protein-protein interactions are important biological processes and essential for a global understanding of cell functions. To date, little is known about the protein interactions and roles of the protein interacting networks and protein complexes in bacterial resistance to antibiotics. In the present study, we investigated protein complexes in Escherichia coli exposed to an antibiotic balofloxacin (BLFX). One homomeric and eight heteromeric protein complexes involved in BLFX resistance were detected. Potential roles of these complexes that are played in BLFX resistance were characterized and categorized into four functional areas: information streams, monosaccharide metabolism, response to stimulus and amino acid metabolic processes. Protein complexes involved in information streams and response to stimulus played more significant roles in the resistance. These results are consistent with previously published mechanisms on the acquired quinolone-resistance through the GyrA-GyrB complex, and two novel antibiotic-resistant pathways were identified: upregulation of genetic information flow and alteration of the response to a stimulus. The balance of the two pathways will be a viable means of reducing BLFX-resistance.
Collapse
Affiliation(s)
- Hui Li
- Center for Proteomics, State Key Laboratory of Bio-Control, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|