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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Hempen M, Herman L. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 12: suitability of taxonomic units notified to EFSA until March 2020. EFSA J 2020; 18:e06174. [PMID: 32760463 PMCID: PMC7331632 DOI: 10.2903/j.efsa.2020.6174] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. It is based on an assessment of the taxonomic identity, the body of knowledge, safety concerns and antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs of the 39 microorganisms notified to EFSA between October 2019 and March 2020, 33 were excluded, including five filamentous fungi, five Escherichia coli, two Enterococcus faecium, two Streptomyces spp. and 19 TUs already evaluated. Six TUs were evaluated. Akkermansia muciniphila was not recommended for QPS status due to safety concerns. Clostridium butyricum was not recommended because some strains contain pathogenicity factors. This TU was excluded for further QPS evaluation. Galdieria sulphuraria and Pseudomonas chlororaphis were also rejected due to a lack of body of knowledge. The QPS status of Corynebacterium ammoniagenes (with the qualification 'for production purposes only') and of Komagataella pastoris (with the qualification 'for enzyme production') was confirmed. In relation to the taxonomic revision of the Lactobacillus genus, previously designated Lactobacillus species will be reassigned to the new species and both the old and new names will be retained in the QPS list.
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Hou Y, Chen S, Wang J, Liu G, Wu S, Tao Y. Isolating promoters from Corynebacterium ammoniagenes ATCC 6871 and application in CoA synthesis. BMC Biotechnol 2019; 19:76. [PMID: 31718625 PMCID: PMC6849255 DOI: 10.1186/s12896-019-0568-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/10/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Corynebacterium ammoniagenes is an important industrial organism that is widely used to produce nucleotides and the potential for industrial production of coenzyme A by C. ammoniagenes ATCC 6871 has been shown. However, the yield of coenzyme A needs to be improved, and the available constitutive promoters are rather limited in this strain. RESULTS In this study, 20 putative DNA promoters derived from genes with high transcription levels and 6 promoters from molecular chaperone genes were identified. To evaluate the activity of each promoter, red fluorescence protein (RFP) was used as a reporter. We successfully isolated a range of promoters with different activity levels, and among these a fragment derived from the upstream sequence of the 50S ribosomal protein L21 (Prpl21) exhibited the strongest activity among the 26 identified promoters. Furthermore, type III pantothenate kinase from Pseudomonas putida (PpcoaA) was overexpressed in C. ammoniagenes under the control of Prpl21, CoA yield increased approximately 4.4 times. CONCLUSIONS This study provides a paradigm for rational isolation of promoters with different activities and their application in metabolic engineering. These promoters will enrich the available promoter toolkit for C. ammoniagenes and should be valuable in current platforms for metabolic engineering and synthetic biology for the optimization of pathways to extend the product spectrum or improve the productivity in C. ammoniagenes ATCC 6871 for industrial applications.
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Affiliation(s)
- Yingshuo Hou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Siyu Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Jianjun Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Guizhen Liu
- Kaiping Genuine Biochemical Pharmaceutical Co. Ltd, Kaiping, People's Republic of China
| | - Sheng Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
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Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 10: Suitability of taxonomic units notified to EFSA until March 2019. EFSA J 2019; 17:e05753. [PMID: 32626372 PMCID: PMC7009089 DOI: 10.2903/j.efsa.2019.5753] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The qualified presumption of safety (QPS) procedure was developed to provide a harmonised generic pre-evaluation to support safety risk assessments of biological agents performed by EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance were assessed. Safety concerns identified for a taxonomic unit (TU) are, where possible and reasonable in number, reflected by 'qualifications' which should be assessed at the strain level by the EFSA's Scientific Panels. During the current assessment, no new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA from applications for market authorisation was updated with 47 biological agents, received between October 2018 and March 2019. Of these, 19 already had QPS status, 20 were excluded from the QPS exercise by the previous QPS mandate (11 filamentous fungi) or from further evaluations within the current mandate (9 notifications of Escherichia coli). Sphingomonas elodea, Gluconobacter frateurii, Corynebacterium ammoniagenes, Corynebacterium casei, Burkholderia ubonensis, Phaeodactylum tricornutum, Microbacterium foliorum and Euglena gracilis were evaluated for the first time. Sphingomonas elodea cannot be assessed for a possible QPS recommendation because it is not a valid species. Corynebacterium ammoniagenes and Euglena gracilis can be recommended for the QPS list with the qualification 'for production purposes only'. The following TUs cannot be recommended for the QPS list: Burkholderia ubonensis, due to its potential and confirmed ability to generate biologically active compounds and limited of body of knowledge; Corynebacterium casei, Gluconobacter frateurii and Microbacterium foliorum, due to lack of body of knowledge; Phaeodactylum tricornutum, based on the lack of a safe history of use in the food chain and limited knowledge on its potential production of bioactive compounds with possible toxic effects.
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Liu Y, Wang J, Xu C, Chen Y, Yang J, Liu D, Niu H, Jiang Y, Yang S, Ying H. Efficient multi-enzyme-catalyzed CDP-choline production driven by an ATP donor module. Appl Microbiol Biotechnol 2016; 101:1409-1417. [PMID: 27738720 DOI: 10.1007/s00253-016-7874-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 09/05/2016] [Accepted: 09/20/2016] [Indexed: 10/20/2022]
Abstract
Cytidine diphosphate choline (CDP-choline) has been applied for treating acute craniocerebral injury and allowing recovery of consciousness after brain surgery. In this study, an acetate kinase (ACK)/acetyl phosphate system was used to supply ATP and combined with Escherichia coli-overexpressed CMP kinase (CMK), NDP kinase (NDK), choline phosphate cytidylyltransferase (CCT), and choline kinase (CKI) to produce CDP-choline from CMP and choline chloride. Within 1 h, 49 mM CDP-choline was produced, for a molar yield of 89.9 and 68.4 % based on CMP and choline chloride, respectively; the utilization efficiency of energy (UEE) was 79.5 %. Acetyl phosphate, sodium acetate, and CTP inhibited the reaction when the concentration exceeded 18.5, 600, and 30 mM, respectively. This inhibition could be overcome by controlling the rate of acetyl phosphate, CMP addition or using KOH instead of NaOH to regulate the pH in fed-batch transformation. After 24 h, the maximum titer was 124.1 ± 2.7 mM, the productivity was 5.1 ± 0.1 mM l-1 h-1, the molar yield to CMP and choline chloride were 83.8 and 63.7 %, respectively, and the UEE was 58.2 %. This high yield and productivity of CDP-choline through biocatalysis suggest future application at the industrial scale.
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Affiliation(s)
- Yingmiao Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 211816, People's Republic of China.,National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, People's Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, 211816, People's Republic of China
| | - Junzhi Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 211816, People's Republic of China.,National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, People's Republic of China
| | - Chongmao Xu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yong Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 211816, People's Republic of China.,National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, People's Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, 211816, People's Republic of China
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dong Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 211816, People's Republic of China.,National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, People's Republic of China
| | - Huanqing Niu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 211816, People's Republic of China.,National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, People's Republic of China
| | - Yu Jiang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sheng Yang
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, 211816, People's Republic of China. .,Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 211816, People's Republic of China.,National Engineering Technique Research Center for Biotechnology, Nanjing, 211816, People's Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, 211816, People's Republic of China
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