1
|
Mothersole RG, Mothersole MK, Goddard HG, Liu J, Van Hamme JD. Enzyme Catalyzed Formation of CoA Adducts of Fluorinated Hexanoic Acid Analogues using a Long-Chain acyl-CoA Synthetase from Gordonia sp. Strain NB4-1Y. Biochemistry 2024; 63:2153-2165. [PMID: 39152907 PMCID: PMC11376266 DOI: 10.1021/acs.biochem.4c00336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2024]
Abstract
Per and polyfluoroalkyl substances (PFAS) are a large family of anthropogenic fluorinated chemicals of increasing environmental concern. Over recent years, numerous microbial communities have been found to be capable of metabolizing some polyfluoroalkyl substances, generating a range of low-molecular-weight PFAS metabolites. One proposed pathway for the microbial breakdown of fluorinated carboxylates includes β-oxidation, this pathway is initiated by the formation of a CoA adduct. However, until recently no PFAS-CoA adducts had been reported. In a previous study, we were able to use a bacterial medium-chain acyl-CoA synthetase (mACS) to form CoA adducts of fluorinated adducts of propanoic acid and pentanoic acid but were not able to detect any products of fluorinated hexanoic acid analogues. Herein, we expressed and purified a long-chain acyl-CoA synthetase (lACS) and a A461K variant of mACS from the soil bacterium Gordonia sp. strain NB4-1Y and performed an analysis of substrate scope and enzyme kinetics using fluorinated and nonfluorinated carboxylates. We determined that lACS can catalyze the formation of CoA adducts of 1:5 fluorotelomer carboxylic acid (FTCA), 2:4 FTCA and 3:3 FTCA, albeit with generally low turnover rates (<0.02 s-1) compared with the nonfluorinated hexanoic acid (5.39 s-1). In addition, the A461K variant was found to have an 8-fold increase in selectivity toward hexanoic acid compared with wild-type mACS, suggesting that Ala-461 has a mechanistic role in selectivity toward substrate chain length. This provides further evidence to validate the proposed activation step involving the formation of CoA adducts in the enzymatic breakdown of PFAS.
Collapse
Affiliation(s)
- Robert G Mothersole
- Department of Chemistry, Thompson Rivers University, 805 TRU Way, Kamloops, British Columbia V2C 0C8, Canada
| | - Mina K Mothersole
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, British Columbia V2C 0C8, Canada
| | - Hannah G Goddard
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, British Columbia V2C 0C8, Canada
| | - Jinxia Liu
- Department of Civil Engineering, McGill University, 817 Sherbrooke Street West, Montreal, Québec H3A 0C3, Canada
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, British Columbia V2C 0C8, Canada
| |
Collapse
|
2
|
Yu J, Guo M, Liu Y, Li S, Ni J, Feng YQ, Ding J. An 8-(Diazomethyl) Quinoline Derivatized Acyl-CoA in Silico Mass Spectral Library Reveals the Landscape of Acyl-CoA in Aging Mouse Organs. Anal Chem 2024. [PMID: 39150895 DOI: 10.1021/acs.analchem.4c02113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2024]
Abstract
Acyl-Coenzyme As (acyl-CoAs) are essential intermediates to incorporate carboxylic acids into the bioactive metabolic network across all species, which play important roles in lipid remodeling, fatty acids, and xenobiotic carboxylic metabolism. However, due to the poor liquid chromatographic behavior, the relatively low mass spectrometry (MS) sensitivity, and lack of authentic standards for annotation, the in-depth untargeted profiling of acyl-CoAs is challenging. We developed a chemical derivatization strategy of acyl-CoAs by employing 8-(diazomethyl) quinoline (8-DMQ) as the labeling reagent, which increased the detection sensitivity by 625-fold with good peak shapes. By applying the MS/MS fragmentation rules learned from the MS/MS spectra of 8-DMQ-acyl-CoA authentic standards, an 8-DMQ-acyl-CoA in silico mass spectral library containing 33,344 high-resolution tandem mass spectra of 8,336 acyl-CoA species was created. The in silico library facilitated the high-throughput and automatic annotation of acyl-CoA using multiple metabolomic data processing tools, such as NIST MS Search and MSDIAL. The feasibility of the in silico library in a complex sample was demonstrated by profiling endogenous acyl-CoAs in multiple organs of an aging mouse. 53 acyl-CoA species were annotated, including 12 oxidized fatty acyl-CoAs and 3 novel nonfatty acyl-CoAs. False positive annotations were further screened by developing an eXtreme Gradient Boosting (XGBoost) based retention time prediction model. The organ distribution and the aging dynamics of acyl-CoAs in a mouse model were discussed for the first time, which helped to elucidate the organ-specific function of acyl-CoAs and the role of different acyl-CoA species during aging.
Collapse
Affiliation(s)
- Jinhui Yu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Menghao Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ye Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Sha Li
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430071, China
| | - Jian Ni
- Renmin Hospital of Wuhan University, Wuhan University, 430072 Wuhan, P. R. China
| | - Yu-Qi Feng
- School of Bioengineering and Health, Wuhan Textile University, Wuhan 430200, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430071, China
| | - Jun Ding
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
- Renmin Hospital of Wuhan University, Wuhan University, 430072 Wuhan, P. R. China
| |
Collapse
|
3
|
Mothersole R, Wynne FT, Rota G, Mothersole MK, Liu J, Van Hamme JD. Formation of CoA Adducts of Short-Chain Fluorinated Carboxylates Catalyzed by Acyl-CoA Synthetase from Gordonia sp. Strain NB4-1Y. ACS OMEGA 2023; 8:39437-39446. [PMID: 37901528 PMCID: PMC10601079 DOI: 10.1021/acsomega.3c05147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/20/2023] [Indexed: 10/31/2023]
Abstract
Perfluoroalkyl and polyfluoroalkyl substances (PFAS) make up a group of anthropogenic chemicals with a myriad of applications. However, some PFAS have been shown to negatively impact human health and the environment, leading to increased regulation, with some countries making efforts to phase out their use. PFAS fate in the environment is driven by physical, chemical, and biological processes, with microbial communities in matrices such as soil and sewage sludge being known to generate a range of low-molecular-weight PFAS metabolites. Proposed metabolic intermediates for both mixed and pure microbial cultures include fluorinated carboxylates that may be activated by CoA prior to β-oxidation and defluorination, although thus far, no PFAS-CoA adducts have been reported. Herein, we expressed and purified acyl-CoA synthetase (ACS) from the soil bacterium Gordonia sp. strain NB4-1Y and performed an analysis of substrate scope and enzyme kinetics using fluorinated and nonfluorinated carboxylates. We determined that ACS was able to catalyze the formation of CoA adducts of 3,3,3-trifluoropropionic acid, 5,5,5-trifluoropentanoic acid, 4,5,5-trifluoropent-4-enoic acid, and 4,4,5,5,5-pentafluoropentanoic acid. Kinetic analysis revealed a 90-98% decrease in kcat between nonfluorinated carboxylates and their fluorinated analogues. This provides evidence to validate proposed enzymatic pathways for microbial PFAS metabolism that proceed via an activation step involving the formation of CoA adducts.
Collapse
Affiliation(s)
- Robert
G. Mothersole
- Department
of Biological Sciences, Thompson Rivers
University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Foster T. Wynne
- Department
of Biological Sciences, Thompson Rivers
University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Gaia Rota
- Department
of Biological Sciences, Thompson Rivers
University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Mina K. Mothersole
- Department
of Biological Sciences, Thompson Rivers
University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Jinxia Liu
- Department
of Civil Engineering, McGill University, 817 Sherbrooke Street West, Montreal, QC H3A
0C3, Canada
| | - Jonathan D. Van Hamme
- Department
of Biological Sciences, Thompson Rivers
University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| |
Collapse
|
4
|
Ma Y, Cao Y, Song X, Xu W, Luo Z, Shan J, Zhou J. Integration of semi-empirical MS/MS library with characteristic features for the annotation of novel amino acid-conjugated bile acids. Analyst 2023; 148:5380-5389. [PMID: 37743718 DOI: 10.1039/d3an01237a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Recently, amino acids other than glycine and taurine were found to be conjugated with bile acids by the gut microbiome in mouse and human. As potential diagnostic markers for inflammatory bowel disease and farnesoid X receptor agonists, their physiological effects and mechanisms, however, remain to be elucidated. A tool for the rapid and comprehensive annotation of such new metabolites is required. Thus, we developed a semi-empirical MS/MS library for bile acids conjugated with 18 common amino acids, including alanine, arginine, asparagine, aspartate, glutamine, glutamate, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine. To investigate their fragmentation rules, these amino acids were chemically conjugated with lithocholic acid, deoxycholic acid, and cholic acid, and their accurate-mass MS/MS spectra were acquired. The common fragmentation patterns from the amino acid moieties were combined with 10 general bile acid skeletons to generate a semi-empirical MS/MS library of 180 structures. Software named BAFinder 2.0 was developed to combine the semi-empirical library in negative mode and the characteristic fragments in positive mode for automatic unknown identification. As a proof of concept, this workflow was applied to the LC-MS/MS analysis of the feces of human, beagle dogs, and rats. In total, 171 common amino acid-conjugated bile acids were annotated and 105 of them were confirmed with the retention times of synthesized compounds. To explore other potential bile acid conjugates, user-defined small molecules were in-silico conjugated with bile acids and searched in the fecal dataset. Four novel bile acid conjugates were discovered, including D-Ala-D-Ala, Lys(iso)-Gly, L-2-aminobutyric acid, and ornithine.
Collapse
Affiliation(s)
- Yan Ma
- National Institute of Biological Sciences, Beijing, Beijing 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Yang Cao
- National Institute of Biological Sciences, Beijing, Beijing 102206, China.
| | - Xiaocui Song
- National Institute of Biological Sciences, Beijing, Beijing 102206, China.
| | - Weichen Xu
- Institute of Pediatrics, Jiangsu Key Laboratory of Pediatric Respiratory Disease, Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zichen Luo
- Institute of Pediatrics, Jiangsu Key Laboratory of Pediatric Respiratory Disease, Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jinjun Shan
- Institute of Pediatrics, Jiangsu Key Laboratory of Pediatric Respiratory Disease, Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jingjie Zhou
- The Affiliated Jiangyin Hospital of Nanjing University of Chinese Medicine, Jiangyin 214400, China
| |
Collapse
|
5
|
Li S, Zhang Z, Liu FL, Yuan BF, Liu TG, Feng YQ. Comprehensive Profiling of Phosphomonoester Metabolites in Saccharomyces cerevisiae by the Chemical Isotope Labeling-LC-MS Method. J Proteome Res 2023; 22:114-122. [PMID: 36484485 DOI: 10.1021/acs.jproteome.2c00507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphomonoesters are important biosynthetic and energy metabolism intermediates in microorganisms. A comprehensive analysis of phosphomonoester metabolites is of great significance for the understanding of their metabolic phosphorylation process and inner mechanism. In this study, we established a pair of isotope reagent d0/d5-2-diazomethyl-N-methyl-phenyl benzamide-labeling-based LC-MS method for the comprehensive analysis of phosphomonoester metabolites. By this method, the labeled phosphomonoester metabolites specifically produced characteristic isotope paired peaks with an m/z difference of 5.0314 in the MS1 spectra and a pair of diagnostic ions (m/z 320.0693/325.1077) in the MS2 spectra. Based on this, a diagnostic ion-based strategy was established for the rapid screening, identification, and relative quantification of phosphomonoester metabolites. Using this strategy, 42 phosphomonoester metabolites were highly accurately identified fromSaccharomyces cerevisiae (S. cerevisiae). Notably, two phosphomonoesters were first detected fromS. cerevisiae. The relative quantification results indicated that the contents of nine phosphomonoester metabolites including two intermediates (Ru5P and S7P) in the pentose phosphate pathway (PPP) were significantly different between lycopene-producible and wild-type S. cerevisiae. A further enzyme assay indicated that the activity of the PPP was closely related to the production of lycopene. Our findings provide new perspectives for the related mechanism study and valuable references for making informed microbial engineering decisions.
Collapse
Affiliation(s)
- Sha Li
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Zheng Zhang
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Fei-Long Liu
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Tian-Gang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Public Health, Wuhan University, Wuhan 430071, China
| |
Collapse
|
6
|
Tian Z, Liu F, Li D, Fernie AR, Chen W. Strategies for structure elucidation of small molecules based on LC–MS/MS data from complex biological samples. Comput Struct Biotechnol J 2022; 20:5085-5097. [PMID: 36187931 PMCID: PMC9489805 DOI: 10.1016/j.csbj.2022.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/03/2022] [Accepted: 09/03/2022] [Indexed: 11/06/2022] Open
Abstract
LC–MS/MS is a major analytical platform for metabolomics, which has become a recent hotspot in the research fields of life and environmental sciences. By contrast, structure elucidation of small molecules based on LC–MS/MS data remains a major challenge in the chemical and biological interpretation of untargeted metabolomics datasets. In recent years, several strategies for structure elucidation using LC–MS/MS data from complex biological samples have been proposed, these strategies can be simply categorized into two types, one based on structure annotation of mass spectra and for the other on retention time prediction. These strategies have helped many scientists conduct research in metabolite-related fields and are indispensable for the development of future tools. Here, we summarized the characteristics of the current tools and strategies for structure elucidation of small molecules based on LC–MS/MS data, and further discussed the directions and perspectives to improve the power of the tools or strategies for structure elucidation.
Collapse
|