1
|
Abril AG, Calo-Mata P, Villa TG, Böhme K, Barros-Velázquez J, Sánchez-Pérez Á, Pazos M, Carrera M. Comprehensive shotgun proteomic characterization and virulence factors of seafood spoilage bacteria. Food Chem 2024; 448:139045. [PMID: 38537549 DOI: 10.1016/j.foodchem.2024.139045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/01/2024] [Accepted: 03/13/2024] [Indexed: 04/24/2024]
Abstract
This article summarizes the characterization, by shotgun proteomics, of 11 bacterial strains identified as responsible for seafood spoilage. A total of 4455 peptide spectrum matches, corresponding to 4299 peptides and 3817 proteins were identified. Analyses of data determined the functional pathways they are involved in. The proteins identified were integrated into a protein-protein network that involves 371 nodes and 3016 edges. Those proteins are implicated in energy pathways, peptidoglycan biosynthesis, spermidine/putrescine metabolism. An additional 773 peptides were characterized as virulence factors, that participates in bacterial pathogenesis; while 14 peptides were defined as biomarkers, as they can be used to differentiate the bacterial species present. This report represents the most extensive proteomic repository available in the field of seafood spoilage bacteria; the data substantially advances the understanding of seafood decay, as well as provides fundamental bases for the recognition of the bacteria existent in seafood that cause spoilage during food processing/storage.
Collapse
Affiliation(s)
- Ana G Abril
- Institute of Marine Research (IIM-CSIC), Department of Food Technology, Spanish National Research Council (CSIC), 36208 Vigo, Spain; Faculty of Pharmacy, University of Santiago de Compostela, Department of Microbiology and Parasitology, 15898 Santiago de Compostela, Spain.
| | - Pilar Calo-Mata
- School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, 27002 Lugo, Spain.
| | - Tomás G Villa
- Faculty of Pharmacy, University of Santiago de Compostela, Department of Microbiology and Parasitology, 15898 Santiago de Compostela, Spain.
| | - Karola Böhme
- School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, 27002 Lugo, Spain.
| | - Jorge Barros-Velázquez
- School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, 27002 Lugo, Spain.
| | - Ángeles Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia.
| | - Manuel Pazos
- Institute of Marine Research (IIM-CSIC), Department of Food Technology, Spanish National Research Council (CSIC), 36208 Vigo, Spain.
| | - Mónica Carrera
- Institute of Marine Research (IIM-CSIC), Department of Food Technology, Spanish National Research Council (CSIC), 36208 Vigo, Spain.
| |
Collapse
|
2
|
Production of the Food Enzyme Acetolactate Decarboxylase (ALDC) from Bacillus subtilis ICA 56 Using Agro-Industrial Residues as Feedstock. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During the beer brewing process, some compounds are formed in the primary fermentation step and may affect the final quality of beer. These compounds, called off flavors, such as diacetyl, are produced during fermentation and are related to a buttery taste. The use of acetolactate decarboxylase (ALDC) in the traditional beer brewing process may significantly increase productivity since it allows for a faster decrease in the adverse flavor caused by diacetyl. However, production costs directly impact its application. For this reason, we analyzed the effect of different cultivation media on ALDC production by Bacillus subtilis ICA 56 and process economics. Different carbon and nitrogen sources, including agro-industrial residues, were evaluated. The best result was obtained using sugarcane molasses and corn steep solids (CSS), allowing a 74% reduction in ALDC production cost and an enzyme activity of 4.43 ± 0.12 U·mL−1. The enzymatic extract was then characterized, showing an optimum temperature at 40 °C and stability at different pH levels, being able to maintain more than 80% of its catalytic capacity between pH values of 3.6 and 7.0, with higher enzymatic activity at pH 6.0 (50 mM MES Buffer), reaching an ALDC activity of 5.30 ± 0.06 U·mL−1.
Collapse
|
3
|
Characterization of acetolactate decarboxylase of Streptococcus thermophilus and its stereoselectivity in decarboxylation of α-hydroxy-β-ketoacids. Bioorg Chem 2022; 122:105719. [DOI: 10.1016/j.bioorg.2022.105719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/29/2022] [Accepted: 03/02/2022] [Indexed: 11/22/2022]
|
4
|
Cui Z, Wang Z, Zheng M, Chen T. Advances in biological production of acetoin: a comprehensive overview. Crit Rev Biotechnol 2021; 42:1135-1156. [PMID: 34806505 DOI: 10.1080/07388551.2021.1995319] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Acetoin, a high-value-added bio-based platform chemical, is widely used in foods, cosmetics, agriculture, and the chemical industry. It is an important precursor for the synthesis of: 2,3-butanediol, liquid hydrocarbon fuels and heterocyclic compounds. Since the fossil resources are becoming increasingly scarce, biological production of acetoin has received increasing attention as an alternative to chemical synthesis. Although there are excellent reviews on the: application, catabolism and fermentative production of acetoin, little attention has been paid to acetoin production via: electrode-assisted fermentation, whole-cell biocatalysis, and in vitro/cell-free biocatalysis. In this review, acetoin biosynthesis pathways and relevant key enzymes are firstly reviewed. In addition, various strategies for biological acetoin production are summarized including: cell-free biocatalysis, whole-cell biocatalysis, microbial fermentation, and electrode-assisted fermentation. The advantages and disadvantages of the different approaches are discussed and weighed, illustrating the increasing progress toward economical, green and efficient production of acetoin. Additionally, recent advances in acetoin extraction and recovery in downstream processing are also briefly reviewed. Moreover, the current issues and future prospects of diverse strategies for biological acetoin production are discussed, with the hope of realizing the promises of industrial acetoin biomanufacturing in the near future.
Collapse
Affiliation(s)
- Zhenzhen Cui
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Zhiwen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Meiyu Zheng
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| |
Collapse
|
5
|
Ji F, Feng Y, Li M, Long F, Yang Y, Wang T, Wang J, Bao Y, Xue S. Structure and catalytic mechanistic insight into Enterobacter aerogenes acetolactate decarboxylase. Enzyme Microb Technol 2019; 126:9-17. [PMID: 31000168 DOI: 10.1016/j.enzmictec.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 02/20/2019] [Accepted: 03/04/2019] [Indexed: 11/25/2022]
Abstract
α-Acetolactate decarboxylase (ALDC) catalyses α-acetolactate into acetoin (3-hydroxy-2-butanone, AC) and is considered to be the rate-limiting enzyme in the synthesis of 2,3-butanediol. In this work, the enzymatic activity of ALDC from Enterobacter aerogenes ALDC (E.a.-ALDC) was fully characterized with enzyme kinetics, indicating a Km of 14.83 ± 0.87 mM and a kcat of 0.81 ± 0.09 s-1. However, compared with the activities of ALDCs reported from other bacteria, the activity of E.a.-ALDC was determined to present a relatively lower value of 849.08 ± 35.21 U/mg. The enzyme showed maximum activity at pH 5.5. In addition, the activity of E.a.-ALDC was promoted by Mg2+. The crystal structure of E.a.-ALDC firstly solved by X-ray crystallography at resolution of 2.4 Å revealed a chelated zinc ion with conserved His199, His201, His212, Glu70 and Glu259. In the active center, the conservative Arg150 was particularly proven to deviate from the zinc ion of the active centre, by adopting a flexible conformational change, resulting in a weak interaction network of the enzyme and the substrate. Further in silico docking of E.a.-ALDC with two enantiomers, (R)-acetolactate and (S)-acetolactate, unaltered the interaction network of E.a.-ALDC from the apo structure, which confirmed the weakened role of Arg150 in the catalytic properties of E.a.-ALDC. Our results reveal a unique structure-function relationship of acetolactate decarboxylase and provide a fundamental basis for the enzymatic synthesis of acetoin.
Collapse
Affiliation(s)
- Fangling Ji
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China.
| | - Yanbin Feng
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, PR China
| | - Mingyang Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China
| | - Feida Long
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China
| | - Yongliang Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China
| | - Tianqi Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China
| | - Jingyun Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China
| | - Yongming Bao
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China; School of Food and Environment Science and Engineering, Dalian University of Technology, Panjin, Liaoning, 12422, PR China
| | - Song Xue
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, PR China.
| |
Collapse
|
6
|
Ji F, Feng Y, Li M, Yang Y, Wang T, Wang J, Bao Y, Xue S. Studies on structure-function relationships of acetolactate decarboxylase from Enterobacter cloacae. RSC Adv 2018; 8:39066-39073. [PMID: 35558320 PMCID: PMC9090609 DOI: 10.1039/c8ra07379a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/15/2018] [Indexed: 12/29/2022] Open
Abstract
Acetoin is an important bio-based platform chemical with wide applications. Among all bacterial strains, Enterobacter cloacae is a well-known acetoin producer via α-acetolactate decarboxylase (ALDC), which converts α-acetolactate into acetoin and is identified as the key enzyme in the biosynthetic pathway of acetoin. In this work, the enzyme properties of Enterobacter cloacae ALDC (E.c.-ALDC) were characterized, revealing a K m value of 12.19 mM and a k cat value of 0.96 s-1. Meanwhile, the optimum pH of E.c.-ALDC was 6.5, and the activity of E.c.-ALDC was activated by Mn2+, Ba2+, Mg2+, Zn2+ and Ca2+, while Cu2+ and Fe2+ significantly inhibited ALDC activity. More importantly, we solved and reported the first crystal structure of E.c.-ALDC at 2.4 Å resolution. The active centre consists of a zinc ion coordinated by highly conserved histidines (199, 201 and 212) and glutamates (70 and 259). However, the conserved Arg150 in E.c.-ALDC orients away from the zinc ion in the active centre of the molecule, losing contact with the zinc ion. Molecular docking of the two enantiomers of α-acetolactate, (R)-acetolactate and (S)-acetolactate allows us to further investigate the interaction networks of E.c.-ALDC with the unique conformation of Arg150. In the models, no direct contacts are observed between Arg150 and the substrates, which is unlikely to maintain the stabilization function of Arg150 in the catalytic reaction. The structure of E.c.-ALDC provides valuable information about its function, allowing a deeper understanding of the catalytic mechanism of ALDCs.
Collapse
Affiliation(s)
- Fangling Ji
- School of Life Science and Biotechnology, Dalian University of Technology Dalian Liaoning 116024 P. R. China
| | - Yanbin Feng
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian Liaoning 116023 P. R. China
| | - Mingyang Li
- School of Life Science and Biotechnology, Dalian University of Technology Dalian Liaoning 116024 P. R. China
| | - Yongliang Yang
- School of Life Science and Biotechnology, Dalian University of Technology Dalian Liaoning 116024 P. R. China
| | - Tianqi Wang
- School of Life Science and Biotechnology, Dalian University of Technology Dalian Liaoning 116024 P. R. China
| | - Jingyun Wang
- School of Life Science and Biotechnology, Dalian University of Technology Dalian Liaoning 116024 P. R. China
| | - Yongming Bao
- School of Life Science and Biotechnology, Dalian University of Technology Dalian Liaoning 116024 P. R. China
- School of Food and Environment Science and Engineering, Dalian University of Technology Panjin Liaoning 12422 P. R. China
| | - Song Xue
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian Liaoning 116023 P. R. China
| |
Collapse
|
7
|
Ji F, Li M, Feng Y, Wu S, Wang T, Pu Z, Wang J, Yang Y, Xue S, Bao Y. Structural and enzymatic characterization of acetolactate decarboxylase from Bacillus subtilis. Appl Microbiol Biotechnol 2018; 102:6479-6491. [DOI: 10.1007/s00253-018-9049-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/25/2022]
|
8
|
Tian G, Liu Y. Mechanistic insights into the catalytic reaction of ferulic acid decarboxylase from Aspergillus niger: a QM/MM study. Phys Chem Chem Phys 2018; 19:7733-7742. [PMID: 28262890 DOI: 10.1039/c6cp08811b] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ubiquinone plays a pivotal role in the aerobic cellular respiratory electron transport chain, whereas ferulic acid decarboxylase (FDC) is involved in the biosynthesis of ubiquinone precursor. Recently, the complete crystal structure of FDC (based on the co-expression of the A. niger fdc1 gene in E. coli with the associated ubix gene from E. coli) at high resolution was reported. Herein, the detailed catalytic non-oxidative decarboxylation mechanism of FDC has been investigated by a combined quantum mechanics/molecular mechanics (QM/MM) approach. Calculation results indicate that, after the 1,3-dipolar cycloaddition of the substrate and cofactor, the carboxylic group can readily split off from the adduct, and the overall energy barrier of the whole catalytic reaction is 23.5 kcal mol-1. According to the energy barrier analysis, the protonation step is rate-limiting. The conserved protonated Glu282 is suggested to be the proton donor through a "water bridge". Besides, two cases, that is, the generated CO2 escapes from the active site or remains in the active site, were considered. It was found that the prolonged leaving of CO2 can facilitate the protonation of the intermediate. In particular, our calculations shed light on the detailed function of both cofactors prFMNiminium and prFMNketamine in the decarboxylation step. The cofactor prFMNiminium is the catalytically relevant species compared with prFMNketamine.
Collapse
Affiliation(s)
- Ge Tian
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
| |
Collapse
|
9
|
Ling B, Wang X, Su H, Liu R, Liu Y. Protonation state and fine structure of the active site determine the reactivity of dehydratase: hydration and isomerization of β-myrcene catalyzed by linalool dehydratase/isomerase from Castellaniella defragrans. Phys Chem Chem Phys 2018; 20:17342-17352. [DOI: 10.1039/c8cp02362j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Linalool dehydratase/isomerase (LinD) from Castellaniella defragrans is a bifunctional enzyme that catalyzes the hydration of β-myrcene to (S)-linalool and isomerization of (S)-linalool to geraniol.
Collapse
Affiliation(s)
- Baoping Ling
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu
- China
- School of Chemistry and Chemical Engineering & Environmental Science and Engineering
| | - Xiya Wang
- School of Chemistry and Chemical Engineering & Environmental Science and Engineering
- Shandong University
- Jinan
- China
| | - Hao Su
- School of Chemistry and Chemical Engineering & Environmental Science and Engineering
- Shandong University
- Jinan
- China
| | - Rutao Liu
- School of Chemistry and Chemical Engineering & Environmental Science and Engineering
- Shandong University
- Jinan
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering & Environmental Science and Engineering
- Shandong University
- Jinan
- China
| |
Collapse
|
10
|
Jia X, Liu Y, Han Y. A thermophilic cell-free cascade enzymatic reaction for acetoin synthesis from pyruvate. Sci Rep 2017; 7:4333. [PMID: 28659601 PMCID: PMC5489476 DOI: 10.1038/s41598-017-04684-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/18/2017] [Indexed: 11/09/2022] Open
Abstract
Acetoin (3-hydroxy-2-butanone) is an important bio-based platform chemical with wide applications. In vitro enzyme catalysed synthesis exhibits great feasibility in the production of chemicals with high purity. In the present work, a synthetic pathway involving a two-step continuous reaction was constructed in vitro for acetoin production from pyruvate at improved temperature. Thermostable candidates, acetolactate synthase (coAHASL1 and coAHASL2 from Caldicellulosiruptor owensensis OL) and α-acetolactate decarboxylase (bsALDC from Bacillus subtilis IPE5-4) were cloned, heterologously expressed, and characterized. All the enzymes showed maximum activities at 65–70 °C and pH of 6.5. Enzyme kinetics analysis showed that coAHASL1 had a higher activity but lower affinity against pyruvate than that of coAHASL2. In addition, the activities of coAHASL1 and bsALDC were promoted by Mn2+ and NADPH. The cascade enzymatic reaction was optimized by using coAHASL1 and bsALDC based on their kinetic properties. Under optimal conditions, a maximum concentration of 3.36 ± 0.26 mM acetoin was produced from 10 mM pyruvate after reaction for 24 h at 65 °C. The productivity of acetoin was 0.14 mM h−1, and the yield was 67.80% compared with the theoretical value. The results confirmed the feasibility of synthesis of acetoin from pyruvate with a cell-free enzyme catalysed system at improved temperature.
Collapse
Affiliation(s)
- Xiaojing Jia
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ying Liu
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China.
| |
Collapse
|