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Zhan Y, Xu H, Tan HT, Ho YS, Yang D, Chen S, Ow DSW, Lv X, Wei F, Bi X, Chen S. Systematic Adaptation of Bacillus licheniformis to 2-Phenylethanol Stress. Appl Environ Microbiol 2023; 89:e0156822. [PMID: 36752618 PMCID: PMC9972911 DOI: 10.1128/aem.01568-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 01/12/2023] [Indexed: 02/09/2023] Open
Abstract
The compound 2-phenylethanol (2-PE) is a bulk flavor and fragrance with a rose-like aroma that can be produced by microbial cell factories, but its cellular toxicity inhibits cellular growth and limits strain performance. Specifically, the microbe Bacillus licheniformis has shown a strong tolerance to 2-PE. Understanding these tolerance mechanisms is crucial for achieving the hyperproduction of 2-PE. In this report, the mechanisms of B. licheniformis DW2 resistance to 2-PE were studied by multi-omics technology coupled with physiological and molecular biological approaches. 2-PE induced reactive oxygen species formation and affected nucleic acid, ribosome, and cell wall synthesis. To manage 2-PE stress, the antioxidant and global stress response systems were activated; the repair system of proteins and homeostasis of the ion and osmotic were initiated. Furthermore, the tricarboxylic acid cycle and NADPH synthesis pathways were upregulated; correspondingly, scanning electron microscopy revealed that cell morphology was changed. These results provide deeper insights into the adaptive mechanisms of B. licheniformis to 2-PE and highlight the potential targets for genetic manipulation to enhance 2-PE resistance. IMPORTANCE The ability to tolerate organic solvents is essential for bacteria producing these chemicals with high titer, yield, and productivity. As exemplified by 2-PE, bioproduction of 2-PE represents a promising alternative to chemical synthesis and plant extraction approaches, but its toxicity hinders successful large-scale microbial production. Here, a multi-omics approach is employed to systematically study the mechanisms of B. licheniformis DW2 resistance to 2-PE. As a 2-PE-tolerant strain, B. licheniformis displays multifactorial mechanisms of 2-PE tolerance, including activating global stress response and repair systems, increasing NADPH supply, changing cell morphology and membrane composition, and remodeling metabolic pathways. The current work yields novel insights into the mechanisms of B. licheniformis resistance to 2-PE. This knowledge can also be used as a clue for improving bacterial performances to achieve industrial-scale production of 2-PE and potentially applied to the production of other relevant organic solvents, such as tyrosol and hydroxytyrosol.
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Affiliation(s)
- Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei, People’s Republic of China
| | - Haixia Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei, People’s Republic of China
| | - Hween Tong Tan
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dongxiao Yang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dave Siak-Wei Ow
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xin Lv
- Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, People’s Republic of China
| | - Fang Wei
- Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei, People’s Republic of China
| | - Xuezhi Bi
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei, People’s Republic of China
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2
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Re A, Mazzoli R. Current progress on engineering microbial strains and consortia for production of cellulosic butanol through consolidated bioprocessing. Microb Biotechnol 2022; 16:238-261. [PMID: 36168663 PMCID: PMC9871528 DOI: 10.1111/1751-7915.14148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/01/2022] [Accepted: 09/07/2022] [Indexed: 01/27/2023] Open
Abstract
In the last decades, fermentative production of n-butanol has regained substantial interest mainly owing to its use as drop-in-fuel. The use of lignocellulose as an alternative to traditional acetone-butanol-ethanol fermentation feedstocks (starchy biomass and molasses) can significantly increase the economic competitiveness of biobutanol over production from non-renewable sources (petroleum). However, the low cost of lignocellulose is offset by its high recalcitrance to biodegradation which generally requires chemical-physical pre-treatment and multiple bioreactor-based processes. The development of consolidated processing (i.e., single-pot fermentation) can dramatically reduce lignocellulose fermentation costs and promote its industrial application. Here, strategies for developing microbial strains and consortia that feature both efficient (hemi)cellulose depolymerization and butanol production will be depicted, that is, rational metabolic engineering of native (hemi)cellulolytic or native butanol-producing or other suitable microorganisms; protoplast fusion of (hemi)cellulolytic and butanol-producing strains; and co-culture of (hemi)cellulolytic and butanol-producing microbes. Irrespective of the fermentation feedstock, biobutanol production is inherently limited by the severe toxicity of this solvent that challenges process economic viability. Hence, an overview of strategies for developing butanol hypertolerant strains will be provided.
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Affiliation(s)
- Angela Re
- Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTorinoItaly,Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems BiologyUniversity of TorinoTorinoItaly
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Multi-Omics Integration and Network Analysis Reveal Potential Hub Genes and Genetic Mechanisms Regulating Bovine Mastitis. Curr Issues Mol Biol 2022; 44:309-328. [PMID: 35723402 PMCID: PMC8928958 DOI: 10.3390/cimb44010023] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/29/2021] [Accepted: 01/08/2022] [Indexed: 02/07/2023] Open
Abstract
Mastitis, inflammation of the mammary gland, is the most prevalent disease in dairy cattle that has a potential impact on profitability and animal welfare. Specifically designed multi-omics studies can be used to prioritize candidate genes and identify biomarkers and the molecular mechanisms underlying mastitis in dairy cattle. Hence, the present study aimed to explore the genetic basis of bovine mastitis by integrating microarray and RNA-Seq data containing healthy and mastitic samples in comparative transcriptome analysis with the results of published genome-wide association studies (GWAS) using a literature mining approach. The integration of different information sources resulted in the identification of 33 common and relevant genes associated with bovine mastitis. Among these, seven genes—CXCR1, HCK, IL1RN, MMP9, S100A9, GRO1, and SOCS3—were identified as the hub genes (highly connected genes) for mastitis susceptibility and resistance, and were subjected to protein-protein interaction (PPI) network and gene regulatory network construction. Gene ontology annotation and enrichment analysis revealed 23, 7, and 4 GO terms related to mastitis in the biological process, molecular function, and cellular component categories, respectively. Moreover, the main metabolic-signalling pathways responsible for the regulation of immune or inflammatory responses were significantly enriched in cytokine–cytokine-receptor interaction, the IL-17 signaling pathway, viral protein interaction with cytokines and cytokine receptors, and the chemokine signaling pathway. Consequently, the identification of these genes, pathways, and their respective functions could contribute to a better understanding of the genetics and mechanisms regulating mastitis and can be considered a starting point for future studies on bovine mastitis.
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Costa P, Usai G, Re A, Manfredi M, Mannino G, Bertea CM, Pessione E, Mazzoli R. Clostridium cellulovorans Proteomic Responses to Butanol Stress. Front Microbiol 2021; 12:674639. [PMID: 34367082 PMCID: PMC8336468 DOI: 10.3389/fmicb.2021.674639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Combination of butanol-hyperproducing and hypertolerant phenotypes is essential for developing microbial strains suitable for industrial production of bio-butanol, one of the most promising liquid biofuels. Clostridium cellulovorans is among the microbial strains with the highest potential for direct production of n-butanol from lignocellulosic wastes, a process that would significantly reduce the cost of bio-butanol. However, butanol exhibits higher toxicity compared to ethanol and C. cellulovorans tolerance to this solvent is low. In the present investigation, comparative gel-free proteomics was used to study the response of C. cellulovorans to butanol challenge and understand the tolerance mechanisms activated in this condition. Sequential Window Acquisition of all Theoretical fragment ion spectra Mass Spectrometry (SWATH-MS) analysis allowed identification and quantification of differentially expressed soluble proteins. The study data are available via ProteomeXchange with the identifier PXD024183. The most important response concerned modulation of protein biosynthesis, folding and degradation. Coherent with previous studies on other bacteria, several heat shock proteins (HSPs), involved in protein quality control, were up-regulated such as the chaperones GroES (Cpn10), Hsp90, and DnaJ. Globally, our data indicate that protein biosynthesis is reduced, likely not to overload HSPs. Several additional metabolic adaptations were triggered by butanol exposure such as the up-regulation of V- and F-type ATPases (involved in ATP synthesis/generation of proton motive force), enzymes involved in amino acid (e.g., arginine, lysine, methionine, and branched chain amino acids) biosynthesis and proteins involved in cell envelope re-arrangement (e.g., the products of Clocel_4136, Clocel_4137, Clocel_4144, Clocel_4162 and Clocel_4352, involved in the biosynthesis of saturated fatty acids) and a redistribution of carbon flux through fermentative pathways (acetate and formate yields were increased and decreased, respectively). Based on these experimental findings, several potential gene targets for metabolic engineering strategies aimed at improving butanol tolerance in C. cellulovorans are suggested. This includes overexpression of HSPs (e.g., GroES, Hsp90, DnaJ, ClpC), RNA chaperone Hfq, V- and F-type ATPases and a number of genes whose function in C. cellulovorans is currently unknown.
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Affiliation(s)
- Paolo Costa
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giulia Usai
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.,Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy.,Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Angela Re
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Marcello Manfredi
- Center for Translational Research on Autoimmune and Allergic Diseases, Università del Piemonte Orientale, Novara, Italy.,Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Giuseppe Mannino
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Cinzia Margherita Bertea
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Enrica Pessione
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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Ibrahim M, Raajaraam L, Raman K. Modelling microbial communities: Harnessing consortia for biotechnological applications. Comput Struct Biotechnol J 2021; 19:3892-3907. [PMID: 34584635 PMCID: PMC8441623 DOI: 10.1016/j.csbj.2021.06.048] [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: 04/02/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Microbes propagate and thrive in complex communities, and there are many benefits to studying and engineering microbial communities instead of single strains. Microbial communities are being increasingly leveraged in biotechnological applications, as they present significant advantages such as the division of labour and improved substrate utilisation. Nevertheless, they also present some interesting challenges to surmount for the design of efficient biotechnological processes. In this review, we discuss key principles of microbial interactions, followed by a deep dive into genome-scale metabolic models, focussing on a vast repertoire of constraint-based modelling methods that enable us to characterise and understand the metabolic capabilities of microbial communities. Complementary approaches to model microbial communities, such as those based on graph theory, are also briefly discussed. Taken together, these methods provide rich insights into the interactions between microbes and how they influence microbial community productivity. We finally overview approaches that allow us to generate and test numerous synthetic community compositions, followed by tools and methodologies that can predict effective genetic interventions to further improve the productivity of communities. With impending advancements in high-throughput omics of microbial communities, the stage is set for the rapid expansion of microbial community engineering, with a significant impact on biotechnological processes.
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Affiliation(s)
- Maziya Ibrahim
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Lavanya Raajaraam
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Karthik Raman
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
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Li P, Li ZH. Tributyltin Induces the Tissue-Specific Stresses in Zebrafish, a Study in Various Tissues of Muscle, Gill and Intestine. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 105:847-852. [PMID: 33211132 DOI: 10.1007/s00128-020-03048-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
Because the mechanism of tissue-specific toxicity of tributyltin (TBT) in aquatic organisms has not been explained clearly, the aim of this study is to investigate the effect of chronic exposure to TBT on muscle-related energy metabolism, gill-related ATPase enzymatic system and intestine-related digestive enzymes activities in zebrafish. Male zebrafish were exposed to sub-lethal concentrations of TBT (10, 100 and 300 ng/L) for 6 weeks. Multiple biomarkers were measured (such as glucose, lactate, hexokinase, pyruvate kinase, lactate dehydrogenase, ATP content, ATPases, trypsin, lipase and amylase), which reflected more serious physiological stress with increasing TBT concentrations during the experimental period. Through principal component analysis (PCA) and integrated biomarker response (IBR) analysis, the toxic effect of TBT in zebrafish was in a concentration-dependent manner. Shortly, the results of this study can provide new evidence for a comprehensive understanding of the toxic effects of TBT.
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Affiliation(s)
- Ping Li
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
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Zhai Q, Xiao Y, Narbad A, Chen W. Comparative metabolomic analysis reveals global cadmium stress response of Lactobacillus plantarum strains. Metallomics 2019; 10:1065-1077. [PMID: 29998247 DOI: 10.1039/c8mt00095f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Our previous work demonstrated the protective effects of Lactobacillus plantarum (L. plantarum) strains against cadmium (Cd) toxicity in vivo, and also indicated that the Cd tolerance of the strains played an important role in this protection. The goal of this study was to investigate the Cd resistance mechanism of L. plantarum by liquid chromatography-mass spectrometry (LC-MS) based metabolomic analysis, with a focus on the global Cd stress response. L. plantarum CCFM8610 (strongly resistant to Cd) and L. plantarum CCFM191 (sensitive to Cd) were selected as target strains, and their metabolomic profiles with and without Cd exposure were compared. The underlying mechanisms of the intra-species distinction between CCFM8610 and CCFM191 in terms of Cd tolerance can be attributed to the following aspects: (a) CCFM8610 possesses a higher intracellular content of osmolytes; (b) CCFM8610 can induce more effective biosynthesis of extracellular polymeric substance (EPS) to sequestrate Cd;
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Affiliation(s)
- Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
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Luo J, Song Z, Ning J, Cheng Y, Wang Y, Cui F, Shen Y, Wang M. The ethanol-induced global alteration in Arthrobacter simplex and its mutants with enhanced ethanol tolerance. Appl Microbiol Biotechnol 2018; 102:9331-9350. [DOI: 10.1007/s00253-018-9301-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/22/2018] [Accepted: 08/03/2018] [Indexed: 11/27/2022]
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9
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Jiménez-Munguía I, Calderón-Santiago M, Rodríguez-Franco A, Priego-Capote F, Rodríguez-Ortega MJ. Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4. PeerJ 2018; 6:e4966. [PMID: 29915696 PMCID: PMC6004102 DOI: 10.7717/peerj.4966] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/23/2018] [Indexed: 11/20/2022] Open
Abstract
We applied multi-omics approaches (transcriptomics, proteomics and metabolomics) to study the effect of iron starvation on the Gram-positive human pathogen Streptococcus pneumoniae to elucidate global changes in the bacterium in a condition similar to what can be found in the host during an infectious episode. We treated the reference strain TIGR4 with the iron chelator deferoxamine mesylate. DNA microarrays revealed changes in the expression of operons involved in multiple biological processes, with a prevalence of genes coding for ion binding proteins. We also studied the changes in protein abundance by 2-DE followed by MALDI-TOF/TOF analysis of total cell extracts and secretome fractions. The main proteomic changes were found in proteins related to the primary and amino sugar metabolism, especially in enzymes with divalent cations as cofactors. Finally, the metabolomic analysis of intracellular metabolites showed altered levels of amino sugars involved in the cell wall peptidoglycan metabolism. This work shows the utility of multi-perspective studies that can provide complementary results for the comprehension of how a given condition can influence global physiological changes in microorganisms.
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Affiliation(s)
- Irene Jiménez-Munguía
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3, Córdoba, Spain
| | - Mónica Calderón-Santiago
- Departamento de Química Analítica, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3, Córdoba, Spain
| | - Antonio Rodríguez-Franco
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3, Córdoba, Spain
| | - Feliciano Priego-Capote
- Departamento de Química Analítica, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3, Córdoba, Spain
| | - Manuel J Rodríguez-Ortega
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3, Córdoba, Spain
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Zdarta A, Tracz J, Luczak M, Guzik U, Kaczorek E. Hydrocarbon-induced changes in proteins and fatty acids profiles of Raoultella ornithinolytica M03. J Proteomics 2017; 164:43-51. [DOI: 10.1016/j.jprot.2017.05.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/25/2017] [Accepted: 05/31/2017] [Indexed: 01/04/2023]
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11
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Zhang S, Shi J, Shan C, Huang C, Wu Y, Ding R, Xue Y, Liu W, Zhou Q, Zhao Y, Xu P, Gao X. Stable isotope N -phosphoryl amino acids labeling for quantitative profiling of amine-containing metabolites using liquid chromatography mass spectrometry. Anal Chim Acta 2017; 978:24-34. [DOI: 10.1016/j.aca.2017.04.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/10/2017] [Accepted: 04/20/2017] [Indexed: 12/16/2022]
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Mahipant G, Paemanee A, Roytrakul S, Kato J, Vangnai AS. The significance of proline and glutamate on butanol chaotropic stress in Bacillus subtilis 168. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:122. [PMID: 28503197 PMCID: PMC5425972 DOI: 10.1186/s13068-017-0811-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Butanol is an intensively used industrial solvent and an attractive alternative biofuel, but the bioproduction suffers from its high toxicity. Among the native butanol producers and heterologous butanol-producing hosts, Bacillus subtilis 168 exhibited relatively higher butanol tolerance. Nevertheless, organic solvent tolerance mechanisms in Bacilli and Gram-positive bacteria have relatively less information. Thus, this study aimed to elucidate butanol stress responses that may involve in unique tolerance of B. subtilis 168 to butanol and other alcohol biocommodities. RESULTS Using comparative proteomics approach and molecular analysis of butanol-challenged B. subtilis 168, 108 butanol-responsive proteins were revealed, and classified into seven groups according to their biological functions. While parts of them may be similar to the proteins reportedly involved in solvent stress response in other Gram-positive bacteria, significant role of proline in the proline-glutamate-arginine metabolism was substantiated. Detection of intracellular proline and glutamate accumulation, as well as glutamate transient conversion during butanol exposure confirmed their necessity, especially proline, for cellular butanol tolerance. Disruption of the particular genes in proline biosynthesis pathways clarified the essential role of the anabolic ProB-ProA-ProI system over the osmoadaptive ProH-ProA-ProJ system for cellular protection in response to butanol exposure. Molecular modifications to increase gene dosage for proline biosynthesis as well as for glutamate acquisition enhanced butanol tolerance of B. subtilis 168 up to 1.8% (vol/vol) under the conditions tested. CONCLUSION This work revealed the important role of proline as an effective compatible solute that is required to protect cells against butanol chaotropic effect and to maintain cellular functions in B. subtilis 168 during butanol exposure. Nevertheless, the accumulation of intracellular proline against butanol stress required a metabolic conversion of glutamate through the specific biosynthetic ProB-ProA-ProI route. Thus, exogenous addition of glutamate, but not proline, enhanced butanol tolerance. These findings serve as a practical knowledge to enhance B. subtilis 168 butanol tolerance, and demonstrate means to engineer the bacterial host to promote higher butanol/alcohol tolerance of B. subtilis 168 for the production of butanol and other alcohol biocommodities.
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Affiliation(s)
- Gumpanat Mahipant
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Atchara Paemanee
- Proteomics Research Laboratory, Genome Institute Biotechnology, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, 12120 Thailand
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, Genome Institute Biotechnology, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, 12120 Thailand
| | - Junichi Kato
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, 739-8530 Japan
| | - Alisa S. Vangnai
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand
- Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, 10330 Thailand
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13
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Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology. Anal Chim Acta 2016; 938:18-32. [DOI: 10.1016/j.aca.2016.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023]
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14
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Ye J, Zhang Y, Huang L, Li Q, Huang J, Lu J, Li Y, Zhang X. An optimized guanidination method for large-scale proteomic studies. Proteomics 2016; 16:1837-46. [DOI: 10.1002/pmic.201500226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 04/11/2016] [Accepted: 05/09/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Juanying Ye
- State Key Laboratory of Genetic Engineering; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai P. R. China
| | - Yang Zhang
- State Key Laboratory of Genetic Engineering; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai P. R. China
| | - Lin Huang
- State Key Laboratory of Genetic Engineering; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai P. R. China
| | - Qingqing Li
- State Key Laboratory of Genetic Engineering; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai P. R. China
| | - Jingnan Huang
- State Key Laboratory of Genetic Engineering; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai P. R. China
| | - Jianan Lu
- State Key Laboratory of Genetic Engineering; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai P. R. China
| | - Yanhong Li
- State Key Laboratory of Genetic Engineering; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai P. R. China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai P. R. China
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Alves E, Esteves AC, Correia A, Cunha Â, Faustino MAF, Neves MGPMS, Almeida A. Protein profiles of Escherichia coli and Staphylococcus warneri are altered by photosensitization with cationic porphyrins. Photochem Photobiol Sci 2016; 14:1169-78. [PMID: 25959378 DOI: 10.1039/c4pp00194j] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Oxidative stress induced by photodynamic treatment of microbial cells causes irreversible damages to vital cellular components such as proteins. Photodynamic inactivation (PDI) of bacteria, a promising therapeutic approach for the treatment of superficial and localized skin and oral infections, can be achieved by exciting a photosensitizing agent with visible light in an oxygenated environment. Although some studies have addressed the oxidative alterations of PDI in bacterial proteins, the present study is the first to compare the electrophoretic profiles of proteins of Gram-positive and Gram-negative bacteria, having two structurally different porphyrins, with different kinetics of photoinactivation. The cationic porphyrins 5,10,15-tris(1-methylpyridinium-4-yl)-20-(pentafluorophenyl)porphyrin tri-iodide (Tri-Py(+)-Me-PF) and 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin tetra-iodide (Tetra-Py(+)-Me) were used to photosensitize Escherichia coli and Staphylococcus warneri upon white light irradiation at an irradiance of 4.0 mW cm(-2). After different photosensitization periods, proteins were extracted from bacteria and analyzed using one-dimensional SDS-PAGE. Apparent molecular weights and band intensities were determined after an irradiation period corresponding to a reduction of 4 log10 in cell viability. After photodynamic treatment, there was a general loss of bacterial proteins, assigned to large-scale protein degradation. Protein loss was more pronounced after PDI with Tri-Py(+)-Me-PF in both bacteria. There was also an increase in the concentration of some proteins as well as an increase in the molecular weight of other proteins. We show that proteins of E. coli and S. warneri are important targets of PDI. Although there is an attempt of cellular response to the PDI-induced damage by overexpression of a limited number of proteins, the damage is lethal. Our results show that changes occurring in the protein pattern during photodynamic treatment are different with the two photosensitizers, which helps to explain the different inactivation kinetics of the two bacteria. SDS-PAGE is a rational approach to assign the type of cellular response to stress that is being induced in the cells.
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Affiliation(s)
- Eliana Alves
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
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16
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Si HM, Zhang F, Wu AN, Han RZ, Xu GC, Ni Y. DNA microarray of global transcription factor mutant reveals membrane-related proteins involved in n-butanol tolerance in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:114. [PMID: 27252779 PMCID: PMC4888631 DOI: 10.1186/s13068-016-0527-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/11/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Escherichia coli has been explored as a platform host strain for biofuels production such as butanol. However, the severe toxicity of butanol is considered to be one major limitation for butanol production from E. coli. The goal of this study is therefore to construct butanol-tolerant E. coli strains and clarify the tolerance mechanisms. RESULTS A recombinant E. coli strain harboring σ(70) mutation capable of tolerating 2 % (v/v) butanol was isolated by the global transcription machinery engineering (gTME) approach. DNA microarrays were employed to assess the transcriptome profile of butanol-tolerant strain B8. Compared with the wild-type strain, 329 differentially expressed genes (197 up-regulated and 132 down-regulated) (p < 0.05; FC ≥ 2) were identified. These genes are involved in carbohydrate metabolism, energy metabolism, two-component signal transduction system, oxidative stress response, lipid and cell envelope biogenesis and efflux pump. CONCLUSIONS Several membrane-related proteins were proved to be involved in butanol tolerance of E. coli. Two down-regulated genes, yibT and yghW, were identified to be capable of affecting butanol tolerance by regulating membrane fatty acid composition. Another down-regulated gene ybjC encodes a predicted inner membrane protein. In addition, a number of up-regulated genes, such as gcl and glcF, contribute to supplement metabolic intermediates for glyoxylate and TCA cycles to enhance energy supply. Our results could serve as a practical strategy for the construction of platform E. coli strains as biofuel producer.
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Affiliation(s)
- Hai-Ming Si
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Fa Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - An-Ning Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Rui-Zhi Han
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Guo-Chao Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Ye Ni
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
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17
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Wu Y, Li L. Sample normalization methods in quantitative metabolomics. J Chromatogr A 2015; 1430:80-95. [PMID: 26763302 DOI: 10.1016/j.chroma.2015.12.007] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/30/2015] [Accepted: 12/02/2015] [Indexed: 12/31/2022]
Abstract
To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts.
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Affiliation(s)
- Yiman Wu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G2G2, Canada.
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18
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Huan T, Li L. Quantitative Metabolome Analysis Based on Chromatographic Peak Reconstruction in Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry. Anal Chem 2015; 87:7011-6. [DOI: 10.1021/acs.analchem.5b01434] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tao Huan
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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19
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Zhou R, Huan T, Li L. Development of versatile isotopic labeling reagents for profiling the amine submetabolome by liquid chromatography–mass spectrometry. Anal Chim Acta 2015; 881:107-16. [DOI: 10.1016/j.aca.2015.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/06/2015] [Accepted: 04/11/2015] [Indexed: 01/09/2023]
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20
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Fondi M, Liò P. Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology. Microbiol Res 2015; 171:52-64. [PMID: 25644953 DOI: 10.1016/j.micres.2015.01.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/02/2015] [Accepted: 01/03/2015] [Indexed: 12/27/2022]
Abstract
Integrated -omics approaches are quickly spreading across microbiology research labs, leading to (i) the possibility of detecting previously hidden features of microbial cells like multi-scale spatial organization and (ii) tracing molecular components across multiple cellular functional states. This promises to reduce the knowledge gap between genotype and phenotype and poses new challenges for computational microbiologists. We underline how the capability to unravel the complexity of microbial life will strongly depend on the integration of the huge and diverse amount of information that can be derived today from -omics experiments. In this work, we present opportunities and challenges of multi -omics data integration in current systems biology pipelines. We here discuss which layers of biological information are important for biotechnological and clinical purposes, with a special focus on bacterial metabolism and modelling procedures. A general review of the most recent computational tools for performing large-scale datasets integration is also presented, together with a possible framework to guide the design of systems biology experiments by microbiologists.
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Affiliation(s)
- Marco Fondi
- Florence Computational Biology Group (ComBo), University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, Florence 50019, Italy; Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, Florence 50019, Italy.
| | - Pietro Liò
- University of Cambridge, Computer Laboratory, 15 JJ Thomson Avenue, CB3 0FD Cambridge, UK
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21
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Yu CL, Summers RM, Li Y, Mohanty SK, Subramanian M, Pope RM. Rapid identification and quantitative validation of a caffeine-degrading pathway in Pseudomonas sp. CES. J Proteome Res 2014; 14:95-106. [PMID: 25350919 DOI: 10.1021/pr500751w] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding the genes and enzymes involved in caffeine metabolism can lead to applications such as production of methylxanthines and environmental waste remediation. Pseudomonas sp. CES may provide insights into these applications, since this bacterium degrades caffeine and thrives in concentrations of caffeine that are three times higher (9.0 g L(-1)) than the maximum tolerable levels of other reported bacteria. We took a novel approach toward identifying the enzymatic pathways in Pseudomonas sp. CES that metabolize caffeine, which largely circumvented the need for exhaustive isolation of enzymes and the stepwise reconstitution of their activities. Here we describe an optimized, rapid alternative strategy based on multiplexed LC-MS/MS assays and show its application by discovering caffeine-degrading enzymes in the CES strain based on quantitative comparison of proteomes from bacteria grown in the absence and presence of caffeine, the latter condition of which was found to have a highly induced capacity for caffeine degradation. Comparisons were made using stable isotope dimethyl labeling, differences in the abundance of particular proteins were substantiated by reciprocal labeling experiments, and the role of the identified proteins in caffeine degradation was independently verified by genetic sequencing. Overall, multiple new components of a N-demethylase system were identified that resulted in rapid pathway validation and gene isolation using this new approach.
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Affiliation(s)
- Chi Li Yu
- Proteomics Facility, University of Iowa , 355 EMRB, Iowa City, Iowa 52242, United States
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22
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Vandera E, Samiotaki M, Parapouli M, Panayotou G, Koukkou AI. Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose. J Proteomics 2014; 113:73-89. [PMID: 25257624 DOI: 10.1016/j.jprot.2014.08.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 07/18/2014] [Accepted: 08/22/2014] [Indexed: 10/24/2022]
Abstract
UNLABELLED In the present study, by applying comparative quantitative proteomics, we investigated the metabolic adaptation of Arthrobacter phenanthrenivorans Sphe3 when using phenanthrene, phthalate, glucose or glucose plus phenanthrene as sole carbon and energy sources. More than a third of the total Sphe3 proteins, with function prediction within the genome, were identified with confidence. Proteomic analysis data and annotated genomic information coincide, allowing us to clarify the phenanthrene catabolic pathway. We confirmed the implication of several proteins in aromatic substrate degradation by identifying those mediating the initial ring-hydroxylation and ring cleavage of phenanthrene to phthalate, phthalate degradation, as well as ortho- and meta-protocatechuate catabolism. Repression of catabolic genes by glucose was observed by both proteomic and transcriptional analyses. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in substrate and amino acid metabolism, stress response, detoxification and membrane and cell wall metabolism. Uptake and transport associated proteins differ in the substrates used, indicating the use of different uptake mechanisms for transport of each compound in the Sphe3 cells. Our results also suggest the activation of a glyoxylate shunt in the presence of aromatic compounds, based on the up-regulation of the key enzymes of this pathway. BIOLOGICAL SIGNIFICANCE A. phenanthrenivorans Sphe3, isolated from a creosote contaminated soil in Greece, can grow on phenanthrene as the sole source of carbon and energy. To explore the phenanthrene catabolic pathway by determining the key proteins involved in this pathway, as well as the global changes in proteins due to the adaptive response of Sphe3 cells grown on different substrates, we applied a gel-free quantitative proteomic analysis using nanoLC-MS/MS. To our knowledge this is the first study of comparative global proteomic changes occurring in the Sphe3 cells under exposure in different nutritional environments. The extended proteomic changes observed in Sphe3 grown on different substrates provide an insight in the complex interactions occurring in the presence of aromatic compounds and could serve as a basis for further investigations intended to elucidate the general regulatory mechanism by which Sphe3 adapts to such xenobiotic environments. This may light the way for more efficient engineering of bacteria towards more effective bioremediation applications.
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Affiliation(s)
- Elpiniki Vandera
- Sector of Organic Chemistry and Biochemistry, University of Ioannina, Greece
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Athens, Greece.
| | - Maria Parapouli
- Sector of Organic Chemistry and Biochemistry, University of Ioannina, Greece
| | - George Panayotou
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Athens, Greece
| | - Anna Irini Koukkou
- Sector of Organic Chemistry and Biochemistry, University of Ioannina, Greece.
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23
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Wu Y, Li L. Dansylation Metabolite Assay: A Simple and Rapid Method for Sample Amount Normalization in Metabolomics. Anal Chem 2014; 86:9428-33. [DOI: 10.1021/ac503359v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yiman Wu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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24
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Peng J, Guo K, Xia J, Zhou J, Yang J, Westaway D, Wishart DS, Li L. Development of isotope labeling liquid chromatography mass spectrometry for mouse urine metabolomics: quantitative metabolomic study of transgenic mice related to Alzheimer's disease. J Proteome Res 2014; 13:4457-69. [PMID: 25164377 DOI: 10.1021/pr500828v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Because of a limited volume of urine that can be collected from a mouse, it is very difficult to apply the common strategy of using multiple analytical techniques to analyze the metabolites to increase the metabolome coverage for mouse urine metabolomics. We report an enabling method based on differential isotope labeling liquid chromatography mass spectrometry (LC-MS) for relative quantification of over 950 putative metabolites using 20 μL of urine as the starting material. The workflow involves aliquoting 10 μL of an individual urine sample for ¹²C-dansylation labeling that target amines and phenols. Another 10 μL of aliquot was taken from each sample to generate a pooled sample that was subjected to ¹³C-dansylation labeling. The ¹²C-labeled individual sample was mixed with an equal volume of the ¹³C-labeled pooled sample. The mixture was then analyzed by LC-MS to generate information on metabolite concentration differences among different individual samples. The interday repeatability for the LC-MS runs was assessed, and the median relative standard deviation over 4 days was 5.0%. This workflow was then applied to a metabolomic biomarker discovery study using urine samples obtained from the TgCRND8 mouse model of early onset familial Alzheimer's disease (FAD) throughout the course of their pathological deposition of beta amyloid (Aβ). It was showed that there was a distinct metabolomic separation between the AD prone mice and the wild type (control) group. As early as 15-17 weeks of age (presymptomatic), metabolomic differences were observed between the two groups, and after the age of 25 weeks the metabolomic alterations became more pronounced. The metabolomic changes at different ages corroborated well with the phenotype changes in this transgenic mice model. Several useful candidate biomarkers including methionine, desaminotyrosine, taurine, N1-acetylspermidine, and 5-hydroxyindoleacetic acid were identified. Some of them were found in previous metabolomics studies in human cerebrospinal fluid or blood samples. This work illustrates the utility of this isotope labeling LC-MS method for biomarker discovery using mouse urine metabolomics.
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Affiliation(s)
- Jun Peng
- Department of Chemistry, ‡Department of Computing Science, §Department of Biological Sciences, and ∥Centre for Prions and Protein Folding Diseases, University of Alberta , Edmonton, Alberta T6G 2R3, Canada
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25
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Peng J, Chen YT, Chen CL, Li L. Development of a Universal Metabolome-Standard Method for Long-Term LC–MS Metabolome Profiling and Its Application for Bladder Cancer Urine-Metabolite-Biomarker Discovery. Anal Chem 2014; 86:6540-7. [DOI: 10.1021/ac5011684] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jun Peng
- Department
of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yi-Ting Chen
- Department
of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chien-Lun Chen
- Department
of Urology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Liang Li
- Department
of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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