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Li G, Wang X, Zeng W, Qin Z, Li J, Chen J, Zhou J. Engineering Gluconbacter oxydans with efficient co-utilization of glucose and sorbitol for one-step biosynthesis of 2-keto-L-gulonic. BIORESOURCE TECHNOLOGY 2024; 406:131098. [PMID: 38986886 DOI: 10.1016/j.biortech.2024.131098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/03/2024] [Accepted: 07/07/2024] [Indexed: 07/12/2024]
Abstract
As the highest-demand vitamin, the development of a one-step vitamin C synthesis process has been slow for a long time. In previous research, a Gluconobacter oxydans strain (GKLG9) was constructed that can directly synthesize 2-keto-L-gulonic acid (2-KLG) from glucose, but carbon source utilization remained low. Therefore, this study first identified the gene 4kas (4-keto-D-arabate synthase) to reduce the loss of extracellular carbon and inhibit the browning of fermentation broth. Then, promoter engineering was conducted to enhance the intracellular glucose transport pathway and concentrate intracellular glucose metabolism on the pentose phosphate pathway to provide more reducing power. Finally, by introducing the D-sorbitol pathway, the titer of 2-KLG was increased to 38.6 g/L within 60 h in a 5-L bioreactor, with a glucose-to-2-KLG conversion rate of about 46 %. This study is an important step in the development of single-bacterial one-step fermentation to produce 2-KLG.
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Affiliation(s)
- Guang Li
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xuyang Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Zhijie Qin
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Wang X, Li D, Qin Z, Chen J, Zhou J. CRISPR/Cpf1-FOKI-induced gene editing in Gluconobacter oxydans. Synth Syst Biotechnol 2024; 9:369-379. [PMID: 38559425 PMCID: PMC10980938 DOI: 10.1016/j.synbio.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Gluconobacter oxydans is an important Gram-negative industrial microorganism that produces vitamin C and other products due to its efficient membrane-bound dehydrogenase system. Its incomplete oxidation system has many crucial industrial applications. However, it also leads to slow growth and low biomass, requiring further metabolic modification for balancing the cell growth and incomplete oxidation process. As a non-model strain, G. oxydans lacks efficient genome editing tools and cannot perform rapid multi-gene editing and complex metabolic network regulation. In the last 15 years, our laboratory attempted to deploy multiple CRISPR/Cas systems in different G. oxydans strains and found none of them as functional. In this study, Cpf1-based or dCpf1-based CRISPRi was constructed to explore the targeted binding ability of Cpf1, while Cpf1-FokI was deployed to study its nuclease activity. A study on Cpf1 found that the CRISPR/Cpf1 system could locate the target genes in G. oxydans but lacked the nuclease cleavage activity. Therefore, the CRISPR/Cpf1-FokI system based on FokI nuclease was constructed. Single-gene knockout with efficiency up to 100% and double-gene iterative editing were achieved in G. oxydans. Using this system, AcrVA6, the anti-CRISPR protein of G. oxydans was discovered for the first time, and efficient genome editing was realized.
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Affiliation(s)
- Xuyang Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Dong Li
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Zhijie Qin
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jian Chen
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China
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Román-Camacho JJ, García-García I, Santos-Dueñas IM, García-Martínez T, Mauricio JC. Latest Trends in Industrial Vinegar Production and the Role of Acetic Acid Bacteria: Classification, Metabolism, and Applications-A Comprehensive Review. Foods 2023; 12:3705. [PMID: 37835358 PMCID: PMC10572879 DOI: 10.3390/foods12193705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Vinegar is one of the most appreciated fermented foods in European and Asian countries. In industry, its elaboration depends on numerous factors, including the nature of starter culture and raw material, as well as the production system and operational conditions. Furthermore, vinegar is obtained by the action of acetic acid bacteria (AAB) on an alcoholic medium in which ethanol is transformed into acetic acid. Besides the highlighted oxidative metabolism of AAB, their versatility and metabolic adaptability make them a taxonomic group with several biotechnological uses. Due to new and rapid advances in this field, this review attempts to approach the current state of knowledge by firstly discussing fundamental aspects related to industrial vinegar production and then exploring aspects related to AAB: classification, metabolism, and applications. Emphasis has been placed on an exhaustive taxonomic review considering the progressive increase in the number of new AAB species and genera, especially those with recognized biotechnological potential.
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Affiliation(s)
- Juan J. Román-Camacho
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Inés M. Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Juan C. Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
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Engineering Gluconobacter cerinus CGMCC 1.110 for direct 2-keto-L-gulonic acid production. Appl Microbiol Biotechnol 2022; 107:153-162. [DOI: 10.1007/s00253-022-12310-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/25/2022] [Accepted: 05/17/2022] [Indexed: 12/02/2022]
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Fricke PM, Gries ML, Mürköster M, Höninger M, Gätgens J, Bott M, Polen T. The l-rhamnose-dependent regulator RhaS and its target promoters from Escherichia coli expand the genetic toolkit for regulatable gene expression in the acetic acid bacterium Gluconobacter oxydans. Front Microbiol 2022; 13:981767. [PMID: 36060754 PMCID: PMC9429829 DOI: 10.3389/fmicb.2022.981767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022] Open
Abstract
For regulatable target gene expression in the acetic acid bacterium (AAB) Gluconobacter oxydans only recently the first plasmids became available. These systems solely enable AraC- and TetR-dependent induction. In this study we showed that the l-rhamnose-dependent regulator RhaS from Escherichia coli and its target promoters PrhaBAD, PrhaT, and PrhaSR could also be used in G. oxydans for regulatable target gene expression. Interestingly, in contrast to the responsiveness in E. coli, in G. oxydans RhaS increased the expression from PrhaBAD in the absence of l-rhamnose and repressed PrhaBAD in the presence of l-rhamnose. Inserting an additional RhaS binding site directly downstream from the −10 region generating promoter variant PrhaBAD(+RhaS-BS) almost doubled the apparent RhaS-dependent promoter strength. Plasmid-based PrhaBAD and PrhaBAD(+RhaS-BS) activity could be reduced up to 90% by RhaS and l-rhamnose, while a genomic copy of PrhaBAD(+RhaS-BS) appeared fully repressed. The RhaS-dependent repression was largely tunable by l-rhamnose concentrations between 0% and only 0.3% (w/v). The RhaS-PrhaBAD and the RhaS-PrhaBAD(+RhaS-BS) systems represent the first heterologous repressible expression systems for G. oxydans. In contrast to PrhaBAD, the E. coli promoter PrhaT was almost inactive in the absence of RhaS. In the presence of RhaS, the PrhaT activity in the absence of l-rhamnose was weak, but could be induced up to 10-fold by addition of l-rhamnose, resulting in a moderate expression level. Therefore, the RhaS-PrhaT system could be suitable for tunable low-level expression of difficult enzymes or membrane proteins in G. oxydans. The insertion of an additional RhaS binding site directly downstream from the E. coli PrhaT −10 region increased the non-induced expression strength and reversed the regulation by RhaS and l-rhamnose from inducible to repressible. The PrhaSR promoter appeared to be positively auto-regulated by RhaS and this activation was increased by l-rhamnose. In summary, the interplay of the l-rhamnose-binding RhaS transcriptional regulator from E. coli with its target promoters PrhaBAD, PrhaT, PrhaSR and variants thereof provide new opportunities for regulatable gene expression in G. oxydans and possibly also for simultaneous l-rhamnose-triggered repression and activation of target genes, which is a highly interesting possibility in metabolic engineering approaches requiring redirection of carbon fluxes.
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Liu X, Zhang L, Cao C, Wang J, Sun X, Yuan J. Biorefining process of agricultural onions to functional vinegar. Prep Biochem Biotechnol 2022; 53:424-432. [PMID: 35857437 DOI: 10.1080/10826068.2022.2098321] [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: 10/17/2022]
Abstract
Biorefinery of onion vinegar (OV) is attractive as a method for producing functional foods from onions or onion by-products. In this study, a two-stage fermentation of OV using Saccharomyces cerevisiae ATCC9763 and Acetobacter pasteurianus CICC20001 was carried out at 28 °C, the titratable acidity reached 4.01%, and the YA/E was 69.64% at 72 h. Based on this, semi-continuous fermentation was performed, proceeded to charge-discharge consisting of three cycles, and the yield, productivity, and specific production rate were 76.71%, 17.73 g/(L·d), and 20.51 h-1, respectively, which was higher than fed-batch fermentation. The in vivo antioxidant experiments showed that OV significantly increased GSH-Px, SOD, and CAT enzyme activities of Caenorhabditis elegans at 271.57, 129.26, and 314.68%, respectively. Nutritional analysis revealed that the total flavonoids and polyphenols were 3.01 mg/mL and 976.76 µg/mL, respectively. It was also shown that the acetic acid to total organic acid (A/T) ratio of OV was 79.02%, and the total free amino acid content was 262.30 mg/100 mL, 1.78-7.44 times higher than other fruit vinegar. The OV prepared in this study showed higher quality than the commercial vinegar.
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Affiliation(s)
- Xinhua Liu
- Xinzhi College, Zhejiang Normal University, Lanxi, China.,Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Liangliang Zhang
- Xinzhi College, Zhejiang Normal University, Lanxi, China.,Key Laboratory of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, China
| | - Chunxin Cao
- Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Jianfeng Wang
- Xinzhi College, Zhejiang Normal University, Lanxi, China
| | - Xiaoming Sun
- Xinzhi College, Zhejiang Normal University, Lanxi, China.,Key Laboratory of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, China
| | - Jianfeng Yuan
- Xinzhi College, Zhejiang Normal University, Lanxi, China.,Key Laboratory of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, China
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Bertucci M, Ariano K, Zumsteg M, Schweiger P. Engineering a tunable bicistronic TetR autoregulation expression system in Gluconobacter oxydans. PeerJ 2022; 10:e13639. [PMID: 35873911 PMCID: PMC9306550 DOI: 10.7717/peerj.13639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 06/06/2022] [Indexed: 01/17/2023] Open
Abstract
Acetic acid bacteria are well-known for their ability to incompletely oxidize their carbon sources. Many of the products of these oxidations find industrial uses. Metabolic engineering of acetic acid bacteria would improve production efficiency and yield by allowing controllable gene expression. However, the molecular tools necessary for regulating gene expression have only recently started being explored. To this end the ability of the activation-dependent Plux system and two constitutive repression Ptet systems were examined for their ability to modulate gene expression in Gluconobacter oxydans. The activation-dependent Plux system increased gene expression approximately 5-fold regardless of the strength of the constitutive promoter used to express the luxR transcriptional activator. The Ptet system was tunable and had a nearly 20-fold induction when the tetR gene was expressed from the strong constitutive promoters P0169 and P264, but only had a 4-fold induction when a weak constitutive promoter (P452) was used for tetR expression. However, the Ptet system was somewhat leaky when uninduced. To mitigate this background activity, a bicistronic TetR expression system was constructed. Based on molecular modeling, this system is predicted to have low background activity when not induced with anhydrotetracycline. The bicistronic system was inducible up to >3,000-fold and was highly tunable with almost no background expression when uninduced, making this bicistronic system potentially useful for engineering G. oxydans and possibly other acetic acid bacteria. These expression systems add to the newly growing repertoire of suitable regulatable promoter systems in acetic acid bacteria.
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Wohlers K, Wirtz A, Reiter A, Oldiges M, Baumgart M, Bott M. Metabolic engineering of Pseudomonas putida for production of the natural sweetener 5-ketofructose from fructose or sucrose by periplasmic oxidation with a heterologous fructose dehydrogenase. Microb Biotechnol 2021; 14:2592-2604. [PMID: 34437751 PMCID: PMC8601194 DOI: 10.1111/1751-7915.13913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/13/2021] [Indexed: 11/30/2022] Open
Abstract
5-Ketofructose (5-KF) is a promising low-calorie natural sweetener with the potential to reduce health problems caused by excessive sugar consumption. It is formed by periplasmic oxidation of fructose by fructose dehydrogenase (Fdh) of Gluconobacter japonicus, a membrane-bound three-subunit enzyme containing FAD and three haemes c as prosthetic groups. This study aimed at establishing Pseudomonas putida KT2440 as a new cell factory for 5-KF production, as this host offers a number of advantages compared with the established host Gluconobacter oxydans. Genomic expression of the fdhSCL genes from G. japonicus enabled synthesis of functional Fdh in P. putida and successful oxidation of fructose to 5-KF. In a batch fermentation, 129 g l-1 5-KF were formed from 150 g l-1 fructose within 23 h, corresponding to a space-time yield of 5.6 g l-1 h-1 . Besides fructose, also sucrose could be used as substrate for 5-KF production by plasmid-based expression of the invertase gene inv1417 from G. japonicus. In a bioreactor cultivation with pulsed sucrose feeding, 144 g 5-KF were produced from 358 g sucrose within 48 h. These results demonstrate that P. putida is an attractive host for 5-KF production.
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Affiliation(s)
- Karen Wohlers
- IBG‐1: BiotechnologyInstitute of Bio‐ and GeosciencesForschungszentrum JülichJülich52425Germany
| | - Astrid Wirtz
- IBG‐1: BiotechnologyInstitute of Bio‐ and GeosciencesForschungszentrum JülichJülich52425Germany
| | - Alexander Reiter
- IBG‐1: BiotechnologyInstitute of Bio‐ and GeosciencesForschungszentrum JülichJülich52425Germany
- Institute of BiotechnologyRWTH Aachen UniversityAachen52062Germany
| | - Marco Oldiges
- IBG‐1: BiotechnologyInstitute of Bio‐ and GeosciencesForschungszentrum JülichJülich52425Germany
- Institute of BiotechnologyRWTH Aachen UniversityAachen52062Germany
| | - Meike Baumgart
- IBG‐1: BiotechnologyInstitute of Bio‐ and GeosciencesForschungszentrum JülichJülich52425Germany
| | - Michael Bott
- IBG‐1: BiotechnologyInstitute of Bio‐ and GeosciencesForschungszentrum JülichJülich52425Germany
- The Bioeconomy Science Center (BioSC)Forschungszentrum JülichJülichD‐52425Germany
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Fricke PM, Lürkens M, Hünnefeld M, Sonntag CK, Bott M, Davari MD, Polen T. Highly tunable TetR-dependent target gene expression in the acetic acid bacterium Gluconobacter oxydans. Appl Microbiol Biotechnol 2021; 105:6835-6852. [PMID: 34448898 PMCID: PMC8426231 DOI: 10.1007/s00253-021-11473-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/27/2022]
Abstract
Abstract For the acetic acid bacterium (AAB) Gluconobacter oxydans only recently the first tight system for regulatable target gene expression became available based on the heterologous repressor-activator protein AraC from Escherichia coli and the target promoter ParaBAD. In this study, we tested pure repressor-based TetR- and LacI-dependent target gene expression in G. oxydans by applying the same plasmid backbone and construction principles that we have used successfully for the araC-ParaBAD system. When using a pBBR1MCS-5-based plasmid, the non-induced basal expression of the Tn10-based TetR-dependent expression system was extremely low. This allowed calculated induction ratios of up to more than 3500-fold with the fluorescence reporter protein mNeonGreen (mNG). The induction was highly homogeneous and tunable by varying the anhydrotetracycline concentration from 10 to 200 ng/mL. The already strong reporter gene expression could be doubled by inserting the ribosome binding site AGGAGA into the 3’ region of the Ptet sequence upstream from mNG. Alternative plasmid constructs used as controls revealed a strong influence of transcription terminators and antibiotics resistance gene of the plasmid backbone on the resulting expression performance. In contrast to the TetR-Ptet-system, pBBR1MCS-5-based LacI-dependent expression from PlacUV5 always exhibited some non-induced basal reporter expression and was therefore tunable only up to 40-fold induction by IPTG. The leakiness of PlacUV5 when not induced was independent of potential read-through from the lacI promoter. Protein-DNA binding simulations for pH 7, 6, 5, and 4 by computational modeling of LacI, TetR, and AraC with DNA suggested a decreased DNA binding of LacI when pH is below 6, the latter possibly causing the leakiness of LacI-dependent systems hitherto tested in AAB. In summary, the expression performance of the pBBR1MCS-5-based TetR-Ptet system makes this system highly suitable for applications in G. oxydans and possibly in other AAB. Key Points • A pBBR1MCS-5-based TetR-Ptet system was tunable up to more than 3500-fold induction. • A pBBR1MCS-5-based LacI-PlacUV5 system was leaky and tunable only up to 40-fold. • Modeling of protein-DNA binding suggested decreased DNA binding of LacI at pH < 6. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11473-x.
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Affiliation(s)
- Philipp Moritz Fricke
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Martha Lürkens
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074 Aachen, Germany
| | - Max Hünnefeld
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Christiane K. Sonntag
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Michael Bott
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Tino Polen
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Institute of Bio- and Geosciences, 52425 Jülich, Germany
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FNR-Type Regulator GoxR of the Obligatorily Aerobic Acetic Acid Bacterium Gluconobacter oxydans Affects Expression of Genes Involved in Respiration and Redox Metabolism. Appl Environ Microbiol 2021; 87:AEM.00195-21. [PMID: 33741613 DOI: 10.1128/aem.00195-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Gene expression in the obligately aerobic acetic acid bacterium Gluconobacter oxydans responds to oxygen limitation, but the regulators involved are unknown. In this study, we analyzed a transcriptional regulator named GoxR (GOX0974), which is the only member of the fumarate-nitrate reduction regulator (FNR) family in this species. Evidence that GoxR contains an iron-sulfur cluster was obtained, suggesting that GoxR functions as an oxygen sensor similar to FNR. The direct target genes of GoxR were determined by combining several approaches, including a transcriptome comparison of a ΔgoxR mutant with the wild-type strain and detection of in vivo GoxR binding sites by chromatin affinity purification and sequencing (ChAP-Seq). Prominent targets were the cioAB genes encoding a cytochrome bd oxidase with low O2 affinity, which were repressed by GoxR, and the pnt operon, which was activated by GoxR. The pnt operon encodes a transhydrogenase (pntA1A2B), an NADH-dependent oxidoreductase (GOX0313), and another oxidoreductase (GOX0314). Evidence was obtained for GoxR being active despite a high dissolved oxygen concentration in the medium. We suggest a model in which the very high respiration rates of G. oxydans due to periplasmic oxidations cause an oxygen-limited cytoplasm and insufficient reoxidation of NAD(P)H in the respiratory chain, leading to inhibited cytoplasmic carbohydrate degradation. GoxR-triggered induction of the pnt operon enhances fast interconversion of NADPH and NADH by the transhydrogenase and NADH reoxidation by the GOX0313 oxidoreductase via reduction of acetaldehyde formed by pyruvate decarboxylase to ethanol. In fact, small amounts of ethanol were formed by G. oxydans under oxygen-restricted conditions in a GoxR-dependent manner.IMPORTANCE Gluconobacter oxydans serves as a cell factory for oxidative biotransformations based on membrane-bound dehydrogenases and as a model organism for elucidating the metabolism of acetic acid bacteria. Surprisingly, to our knowledge none of the more than 100 transcriptional regulators encoded in the genome of G. oxydans has been studied experimentally until now. In this work, we analyzed the function of a regulator named GoxR, which belongs to the FNR family. Members of this family serve as oxygen sensors by means of an oxygen-sensitive [4Fe-4S] cluster and typically regulate genes important for growth under anoxic conditions by anaerobic respiration or fermentation. Because G. oxydans has an obligatory aerobic respiratory mode of energy metabolism, it was tempting to elucidate the target genes regulated by GoxR. Our results show that GoxR affects the expression of genes that support the interconversion of NADPH and NADH and the NADH reoxidation by reduction of acetaldehyde to ethanol.
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Fricke PM, Klemm A, Bott M, Polen T. On the way toward regulatable expression systems in acetic acid bacteria: target gene expression and use cases. Appl Microbiol Biotechnol 2021; 105:3423-3456. [PMID: 33856535 PMCID: PMC8102297 DOI: 10.1007/s00253-021-11269-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/24/2021] [Accepted: 04/04/2021] [Indexed: 01/06/2023]
Abstract
Acetic acid bacteria (AAB) are valuable biocatalysts for which there is growing interest in understanding their basics including physiology and biochemistry. This is accompanied by growing demands for metabolic engineering of AAB to take advantage of their properties and to improve their biomanufacturing efficiencies. Controlled expression of target genes is key to fundamental and applied microbiological research. In order to get an overview of expression systems and their applications in AAB, we carried out a comprehensive literature search using the Web of Science Core Collection database. The Acetobacteraceae family currently comprises 49 genera. We found overall 6097 publications related to one or more AAB genera since 1973, when the first successful recombinant DNA experiments in Escherichia coli have been published. The use of plasmids in AAB began in 1985 and till today was reported for only nine out of the 49 AAB genera currently described. We found at least five major expression plasmid lineages and a multitude of further expression plasmids, almost all enabling only constitutive target gene expression. Only recently, two regulatable expression systems became available for AAB, an N-acyl homoserine lactone (AHL)-inducible system for Komagataeibacter rhaeticus and an L-arabinose-inducible system for Gluconobacter oxydans. Thus, after 35 years of constitutive target gene expression in AAB, we now have the first regulatable expression systems for AAB in hand and further regulatable expression systems for AAB can be expected. KEY POINTS: • Literature search revealed developments and usage of expression systems in AAB. • Only recently 2 regulatable plasmid systems became available for only 2 AAB genera. • Further regulatable expression systems for AAB are in sight.
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Affiliation(s)
- Philipp Moritz Fricke
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Angelika Klemm
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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Fricke PM, Link T, Gätgens J, Sonntag C, Otto M, Bott M, Polen T. A tunable L-arabinose-inducible expression plasmid for the acetic acid bacterium Gluconobacter oxydans. Appl Microbiol Biotechnol 2020; 104:9267-9282. [PMID: 32974745 PMCID: PMC7567684 DOI: 10.1007/s00253-020-10905-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 01/21/2023]
Abstract
Abstract The acetic acid bacterium (AAB) Gluconobacter oxydans incompletely oxidizes a wide variety of carbohydrates and is therefore used industrially for oxidative biotransformations. For G. oxydans, no system was available that allows regulatable plasmid-based expression. We found that the l-arabinose-inducible PBAD promoter and the transcriptional regulator AraC from Escherichia coli MC4100 performed very well in G. oxydans. The respective pBBR1-based plasmids showed very low basal expression of the reporters β-glucuronidase and mNeonGreen, up to 480-fold induction with 1% l-arabinose, and tunability from 0.1 to 1% l-arabinose. In G. oxydans 621H, l-arabinose was oxidized by the membrane-bound glucose dehydrogenase, which is absent in the multi-deletion strain BP.6. Nevertheless, AraC-PBAD performed similar in both strains in the exponential phase, indicating that a gene knockout is not required for application of AraC-PBAD in wild-type G. oxydans strains. However, the oxidation product arabinonic acid strongly contributed to the acidification of the growth medium in 621H cultures during the stationary phase, which resulted in drastically decreased reporter activities in 621H (pH 3.3) but not in BP.6 cultures (pH 4.4). These activities could be strongly increased quickly solely by incubating stationary cells in d-mannitol-free medium adjusted to pH 6, indicating that the reporters were hardly degraded yet rather became inactive. In a pH-controlled bioreactor, these reporter activities remained high in the stationary phase (pH 6). Finally, we created a multiple cloning vector with araC-PBAD based on pBBR1MCS-5. Together, we demonstrated superior functionality and good tunability of an AraC-PBAD system in G. oxydans that could possibly also be used in other AAB. Key points • We found the AraC-PBADsystem from E. coli MC4100 was well tunable in G. oxydans. • In the absence of AraC orl-arabinose, expression from PBADwas extremely low. • This araC-PBADsystem could also be fully functional in other acetic acid bacteria. Electronic supplementary material The online version of this article (10.1007/s00253-020-10905-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Philipp Moritz Fricke
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tobias Link
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jochem Gätgens
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Christiane Sonntag
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Maike Otto
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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Breeding of Gluconobacter oxydans with high PQQ-dependent D-sorbitol dehydrogenase for improvement of 6-(N-hydroxyethyl)-amino-6-deoxy-α-L-sorbofuranose production. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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14
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Hahn T, Torkler S, van der Bolt R, Gammel N, Hesse M, Möller A, Preylowski B, Hubracht V, Patzsch K, Zibek S. Determining different impact factors on the xylonic acid production using Gluconobacter oxydans DSM 2343. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Repeated production of 6-(N-hydroxyethyl)-amino-6-deoxy-α-L-sorbofuranose by immobilized Gluconobacter oxydans cells with a strategy of in situ exhaustive cell regeneration. Bioprocess Biosyst Eng 2020; 43:1781-1789. [PMID: 32399751 DOI: 10.1007/s00449-020-02368-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 04/26/2020] [Indexed: 01/04/2023]
Abstract
The major troubles in 6-(N-hydroxyethyl)-amino-6-deoxy-α-L-sorbofuranose (6NSL) production from N-2-hydroxyethyl glucamine (NHEG) by Gluconobacter oxydans were low cell yield during cell preparation and loss of cells' biocatalytic ability during biotransformation, resulting in high production cost and low 6NSL production. The target of this work was to enhance 6NSL production by reusing cells and improving the cells biocatalytic ability. First, inhibitory effects of substrate and product on 6NSL production, and optimization of cell regeneration condition were investigated, respectively. Then repeated production of 6NSL by immobilized cell using a strategy of in situ exhaustive cell regeneration in a bubble column bioreactor was developed. As a result, the bioprocess underwent nine cycles, the average 6NSL production and conversion rate of NHEG to 6NSL reached 42.6 g L-1 and 83.1% in each batch was achieved, respectively.
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Hu B, Wang M, Geng S, Wen L, Wu M, Nie Y, Tang YQ, Wu XL. Metabolic Exchange with Non-Alkane-Consuming Pseudomonas stutzeri SLG510A3-8 Improves n-Alkane Biodegradation by the Alkane Degrader Dietzia sp. Strain DQ12-45-1b. Appl Environ Microbiol 2020; 86:AEM.02931-19. [PMID: 32033953 PMCID: PMC7117941 DOI: 10.1128/aem.02931-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/05/2020] [Indexed: 02/07/2023] Open
Abstract
Biodegradation of alkanes by microbial communities is ubiquitous in nature. Interestingly, the microbial communities with high hydrocarbon-degrading performances are sometimes composed of not only hydrocarbon degraders but also nonconsumers, but the synergistic mechanisms remain unknown. Here, we found that two bacterial strains isolated from Chinese oil fields, Dietzia sp. strain DQ12-45-1b and Pseudomonas stutzeri SLG510A3-8, had a synergistic effect on hexadecane (C16 compound) biodegradation, even though P. stutzeri could not utilize C16 individually. To gain a better understanding of the roles of the alkane nonconsumer P. stutzeri in the C16-degrading consortium, we reconstructed a two-species stoichiometric metabolic model, iBH1908, and integrated in silico prediction with the following in vitro validation, a comparative proteomics analysis, and extracellular metabolomic detection. Metabolic interactions between P. stutzeri and Dietzia sp. were successfully revealed to have importance in efficient C16 degradation. In the process, P. stutzeri survived on C16 metabolic intermediates from Dietzia sp., including hexadecanoate, 3-hydroxybutanoate, and α-ketoglutarate. In return, P. stutzeri reorganized its metabolic flux distribution to fed back acetate and glutamate to Dietzia sp. to enhance its C16 degradation efficiency by improving Dietzia cell accumulation and by regulating the expression of Dietzia succinate dehydrogenase. By using the synergistic microbial consortium of Dietzia sp. and P. stutzeri with the addition of the in silico-predicted key exchanged metabolites, diesel oil was effectively disposed of in 15 days with a removal fraction of 85.54% ± 6.42%, leaving small amounts of C15 to C20 isomers. Our finding provides a novel microbial assembling mode for efficient bioremediation or chemical production in the future.IMPORTANCE Many natural and synthetic microbial communities are composed of not only species whose biological properties are consistent with their corresponding communities but also ones whose chemophysical characteristics do not directly contribute to the performance of their communities. Even though the latter species are often essential to the microbial communities, their roles are unclear. Here, by investigation of an artificial two-member microbial consortium in n-alkane biodegradation, we showed that the microbial member without the n-alkane-degrading capability had a cross-feeding interaction with and metabolic regulation to the leading member for the synergistic n-alkane biodegradation. Our study improves the current understanding of microbial interactions. Because "assistant" microbes showed importance in communities in addition to the functional microbes, our findings also suggest a useful "assistant-microbe" principle in the design of microbial communities for either bioremediation or chemical production.
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Affiliation(s)
- Bing Hu
- Institute for Synthetic Biosystems, Department of Biochemical Engineering, College of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, People's Republic of China
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Miaoxiao Wang
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Shuang Geng
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Liqun Wen
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Mengdi Wu
- School of Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yong Nie
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Yue-Qin Tang
- Department of Architecture and Environment, Sichuan University, Chengdu, People's Republic of China
| | - Xiao-Lei Wu
- Department of Energy and Resource Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
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17
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Battling S, Wohlers K, Igwe C, Kranz A, Pesch M, Wirtz A, Baumgart M, Büchs J, Bott M. Novel plasmid-free Gluconobacter oxydans strains for production of the natural sweetener 5-ketofructose. Microb Cell Fact 2020; 19:54. [PMID: 32131833 PMCID: PMC7055074 DOI: 10.1186/s12934-020-01310-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Background 5-Ketofructose (5-KF) has recently been identified as a promising non-nutritive natural sweetener. Gluconobacter oxydans strains have been developed that allow efficient production of 5-KF from fructose by plasmid-based expression of the fructose dehydrogenase genes fdhSCL of Gluconobacter japonicus. As plasmid-free strains are preferred for industrial production of food additives, we aimed at the construction of efficient 5-KF production strains with the fdhSCL genes chromosomally integrated. Results For plasmid-free 5-KF production, we selected four sites in the genome of G. oxydans IK003.1 and inserted the fdhSCL genes under control of the strong P264 promoter into each of these sites. All four recombinant strains expressed fdhSCL and oxidized fructose to 5-KF, but site-specific differences were observed suggesting that the genomic vicinity influenced gene expression. For further improvement, a second copy of the fdhSCL genes under control of P264 was inserted into the second-best insertion site to obtain strain IK003.1::fdhSCL2. The 5-KF production rate and the 5-KF yield obtained with this double-integration strain were considerably higher than for the single integration strains and approached the values of IK003.1 with plasmid-based fdhSCL expression. Conclusion We identified four sites in the genome of G. oxydans suitable for expression of heterologous genes and constructed a strain with two genomic copies of the fdhSCL genes enabling efficient plasmid-free 5-KF production. This strain will serve as basis for further metabolic engineering strategies aiming at the use of alternative carbon sources for 5-KF production and for bioprocess optimization.
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Affiliation(s)
- Svenja Battling
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Karen Wohlers
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Chika Igwe
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Angela Kranz
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Matthias Pesch
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Astrid Wirtz
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany.
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18
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Liu L, Zeng W, Du G, Chen J, Zhou J. Identification of NAD-Dependent Xylitol Dehydrogenase from Gluconobacter oxydans WSH-003. ACS OMEGA 2019; 4:15074-15080. [PMID: 31552350 PMCID: PMC6751703 DOI: 10.1021/acsomega.9b01867] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 08/20/2019] [Indexed: 05/08/2023]
Abstract
Gluconobacter oxydans plays an important role in the conversion of d-sorbitol to l-sorbose, which is an essential intermediate for the industrial-scale production of vitamin C. In the fermentation process, some d-sorbitol could be converted to d-fructose and other byproducts by uncertain dehydrogenases. Genome sequencing has revealed the presence of diverse genes encoding dehydrogenases in G. oxydans. However, the characteristics of most of these dehydrogenases remain unclear. Therefore, the analyses of these unknown dehydrogenases could be useful for identifying those related to the production of d-fructose and other byproducts. Accordingly, dehydrogenases in G. oxydans WSH-003, an industrial strain used for vitamin C production, were examined. A nicotinamide adenine dinucleotide (NAD)-dependent dehydrogenase, which was annotated as xylitol dehydrogenase 2, was identified, codon-optimized, and expressed in Escherichia coli BL21 (DE3) cells. The enzyme exhibited a high preference for NAD+ as the cofactor, while no activity with nicotinamide adenine dinucleotide phosphate, flavin adenine dinucleotide, or pyrroloquinoline quinone was noted. Although this enzyme presented high similarity with NAD-dependent xylitol dehydrogenase, it showed high activity to catalyze d-sorbitol to d-fructose. Unlike the optimum temperature and pH for most of the known NAD-dependent xylitol dehydrogenases (30-40 °C and about 6-8, respectively), those for the identified enzyme were 57 °C and 12, respectively. The values of K m and V max of the identified dehydrogenase toward l-sorbitol were 4.92 μM and 196.08 μM/min, respectively. Thus, xylitol dehydrogenase 2 can be useful for the cofactor-reduced nicotinamide adenine dinucleotide regeneration under alkaline conditions, or its knockout can improve the conversion ratio of d-sorbitol to l-sorbose.
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Affiliation(s)
- Li Liu
- School
of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry
of Education, National Engineering Laboratory for Cereal Fermentation Technology, The Key Laboratory of Carbohydrate
Chemistry and Biotechnology, Ministry of Education, and Jiangsu Provisional Research Center for
Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Weizhu Zeng
- School
of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry
of Education, National Engineering Laboratory for Cereal Fermentation Technology, The Key Laboratory of Carbohydrate
Chemistry and Biotechnology, Ministry of Education, and Jiangsu Provisional Research Center for
Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Guocheng Du
- School
of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry
of Education, National Engineering Laboratory for Cereal Fermentation Technology, The Key Laboratory of Carbohydrate
Chemistry and Biotechnology, Ministry of Education, and Jiangsu Provisional Research Center for
Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Jian Chen
- School
of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry
of Education, National Engineering Laboratory for Cereal Fermentation Technology, The Key Laboratory of Carbohydrate
Chemistry and Biotechnology, Ministry of Education, and Jiangsu Provisional Research Center for
Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Jingwen Zhou
- School
of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry
of Education, National Engineering Laboratory for Cereal Fermentation Technology, The Key Laboratory of Carbohydrate
Chemistry and Biotechnology, Ministry of Education, and Jiangsu Provisional Research Center for
Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- E-mail: . Tel/Fax: +86-510-85914317
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19
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L-Erythrulose production with a multideletion strain of Gluconobacter oxydans. Appl Microbiol Biotechnol 2019; 103:4393-4404. [DOI: 10.1007/s00253-019-09824-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/30/2019] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
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20
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Kranz A, Steinmann A, Degner U, Mengus-Kaya A, Matamouros S, Bott M, Polen T. Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H. BMC Genomics 2018; 19:753. [PMID: 30326828 PMCID: PMC6191907 DOI: 10.1186/s12864-018-5111-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/25/2018] [Indexed: 12/14/2022] Open
Abstract
Background Gluconobacter oxydans is a strictly aerobic Gram-negative acetic acid bacterium used industrially for oxidative biotransformations due to its exceptional type of catabolism. It incompletely oxidizes a wide variety of carbohydrates regio- and stereoselectively in the periplasm using membrane-bound dehydrogenases with accumulation of the products in the medium. As a consequence, only a small fraction of the carbon and energy source enters the cell, resulting in a low biomass yield. Additionally, central carbon metabolism is characterized by the absence of a functional glycolysis and absence of a functional tricarboxylic acid (TCA) cycle. Due to these features, G. oxydans is a highly interesting model organism. Here we analyzed global mRNA decay in G. oxydans to describe its characteristic features and to identify short-lived mRNAs representing potential bottlenecks in the metabolism for further growth improvement by metabolic engineering. Results Using DNA microarrays we estimated the mRNA half-lives in G. oxydans. Overall, the mRNA half-lives ranged mainly from 3 min to 25 min with a global mean of 5.7 min. The transcripts encoding GroES and GroEL required for proper protein folding ranked at the top among transcripts exhibiting both long half-lives and high abundance. The F-type H+-ATP synthase transcripts involved in energy metabolism ranked among the transcripts with the shortest mRNA half-lives. RNAseq analysis revealed low expression levels for genes of the incomplete TCA cycle and also the mRNA half-lives of several of those were short and below the global mean. The mRNA decay analysis also revealed an apparent instability of full-length 23S rRNA. Further analysis of the ribosome-associated rRNA revealed a 23S rRNA fragmentation pattern exhibiting new cleavage regions in 23S rRNAs which were previously not known. Conclusions The very short mRNA half-lives of the H+-ATP synthase, which is likely responsible for the ATP-proton motive force interconversion in G. oxydans under many or most conditions, is notably in contrast to mRNA decay data from other bacteria. Together with the short mRNA half-lives and low expression of some other central metabolic genes it could limit intended improvements of G. oxydans’ biomass yield by metabolic engineering. Also, further studies are needed to unravel the multistep process of the 23S rRNA fragmentation in G. oxydans. Electronic supplementary material The online version of this article (10.1186/s12864-018-5111-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Angela Kranz
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Andrea Steinmann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Ursula Degner
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Aliye Mengus-Kaya
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Susana Matamouros
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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21
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Sun W, Alexander T, Man Z, Xiao F, Cui F, Qi X. Enhancing 2-Ketogluconate Production of Pseudomonas plecoglossicida JUIM01 by Maintaining the Carbon Catabolite Repression of 2-Ketogluconate Metabolism. Molecules 2018; 23:molecules23102629. [PMID: 30322137 PMCID: PMC6222622 DOI: 10.3390/molecules23102629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 12/22/2022] Open
Abstract
2-Ketogluconate (2KGA) is an organic acid that is important for pharmaceutical, cosmetic, and environmental applications. Pseudomonas plecoglossicida JUIM01 strain is an important industrial 2KGA producer in China. In this paper, we found that P. plecoglossicida JUIM01 could convert glucose to 2KGA extracellularly, and the formed 2KGA was subsequently consumed after glucose was exhausted during the fermentation process. Experiments of glucose and 2KGA supplementation during fermentation process revealed that, only when glucose was exhausted, the strain started to consume the product 2KGA. Then, the mechanism of this phenomenon was investigated at transcription and protein levels, and the results indicated that P. plecoglossicida JUIM01 possesses carbon catabolite repression of 2KGA metabolism by glucose. Next, increasing the supply of glucose could attenuate 2KGA consumption and enhance the 2KGA yield from glucose. Finally, fed-batch fermentation of P. plecoglossicida JUIM01 resulted in 205.67 g/L of 2KGA with a productivity of 6.86 g/L/h and yield of 0.953 g/g glucose. These results can provide references for the industrial fermentation production of 2KGA and other fermentation products.
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Affiliation(s)
- Wenjing Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
- Parchn Sodium Isovitamin C Co. Ltd., Dexing, 334221, China.
| | - Tjahjasari Alexander
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Zaiwei Man
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Fangfang Xiao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Fengjie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
- Parchn Sodium Isovitamin C Co. Ltd., Dexing, 334221, China.
| | - Xianghui Qi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
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22
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Yan J, Xu J, Cao M, Li Z, Xu C, Wang X, Yang C, Xu P, Gao C, Ma C. Engineering of glycerol utilization in Gluconobacter oxydans 621H for biocatalyst preparation in a low-cost way. Microb Cell Fact 2018; 17:158. [PMID: 30296949 PMCID: PMC6174558 DOI: 10.1186/s12934-018-1001-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022] Open
Abstract
Background Whole cells of Gluconobacter oxydans are widely used in various biocatalytic processes. Sorbitol at high concentrations is commonly used in complex media to prepare biocatalysts. Exploiting an alternative process for preparation of biocatalysts with low cost substrates is of importance for industrial applications. Results G. oxydans 621H was confirmed to have the ability to grow in mineral salts medium with glycerol, an inevitable waste generated from industry of biofuels, as the sole carbon source. Based on the glycerol utilization mechanism elucidated in this study, the major polyol dehydrogenase (GOX0854) and the membrane-bound alcohol dehydrogenase (GOX1068) can competitively utilize glycerol but play no obvious roles in the biocatalyst preparation. Thus, the genes related to these two enzymes were deleted. Whole cells of G. oxydans ∆GOX1068∆GOX0854 can be prepared from glycerol with a 2.4-fold higher biomass yield than that of G. oxydans 621H. Using whole cells of G. oxydans ∆GOX1068∆GOX0854 as the biocatalyst, 61.6 g L−1 xylonate was produced from 58.4 g L−1 xylose at a yield of 1.05 g g−1. Conclusion This process is an example of efficient preparation of whole cells of G. oxydans with reduced cost. Besides xylonate production from xylose, other biocatalytic processes might also be developed using whole cells of metabolic engineered G. oxydans prepared from glycerol. Electronic supplementary material The online version of this article (10.1186/s12934-018-1001-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinxin Yan
- State Key Laboratory of Microbial Technology & Shenzhen Research Institute, Shandong University, 27 Shanda South Road, Jinan, 250100, People's Republic of China
| | - Jing Xu
- State Key Laboratory of Microbial Technology & Shenzhen Research Institute, Shandong University, 27 Shanda South Road, Jinan, 250100, People's Republic of China.,Dong Ying Oceanic and Fishery Bureau, 206 Yellow River Road, Dongying, 257091, People's Republic of China
| | - Menghao Cao
- State Key Laboratory of Microbial Technology & Shenzhen Research Institute, Shandong University, 27 Shanda South Road, Jinan, 250100, People's Republic of China
| | - Zhong Li
- State Key Laboratory of Microbial Technology & Shenzhen Research Institute, Shandong University, 27 Shanda South Road, Jinan, 250100, People's Republic of China
| | - Chengpeng Xu
- State Key Laboratory of Microbial Technology & Shenzhen Research Institute, Shandong University, 27 Shanda South Road, Jinan, 250100, People's Republic of China
| | - Xinyu Wang
- State Key Laboratory of Microbial Technology & Shenzhen Research Institute, Shandong University, 27 Shanda South Road, Jinan, 250100, People's Republic of China
| | - Chunyu Yang
- State Key Laboratory of Microbial Technology & Shenzhen Research Institute, Shandong University, 27 Shanda South Road, Jinan, 250100, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Chao Gao
- State Key Laboratory of Microbial Technology & Shenzhen Research Institute, Shandong University, 27 Shanda South Road, Jinan, 250100, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology & Shenzhen Research Institute, Shandong University, 27 Shanda South Road, Jinan, 250100, People's Republic of China.
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RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H. BMC Genomics 2018; 19:24. [PMID: 29304737 PMCID: PMC5756330 DOI: 10.1186/s12864-017-4415-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 12/22/2017] [Indexed: 01/05/2023] Open
Abstract
Background The acetic acid bacterium Gluconobacter oxydans 621H is characterized by its exceptional ability to incompletely oxidize a great variety of carbohydrates in the periplasm. The metabolism of this α-proteobacterium has been characterized to some extent, yet little is known about its transcriptomes and related data. In this study, we applied two different RNAseq approaches. Primary transcriptomes enriched for 5′-ends of transcripts were sequenced to detect transcription start sites, which allow subsequent analysis of promoter motifs, ribosome binding sites, and 5´-UTRs. Whole transcriptomes were sequenced to identify expressed genes and operon structures. Results Sequencing of primary transcriptomes of G. oxydans revealed 2449 TSSs, which were classified according to their genomic context followed by identification of promoter and ribosome binding site motifs, analysis of 5´-UTRs including validation of predicted cis-regulatory elements and correction of start codons. 1144 (41%) of all genes were found to be expressed monocistronically, whereas 1634 genes were organized in 571 operons. Together, TSSs and whole transcriptome data were also used to identify novel intergenic (18), intragenic (328), and antisense transcripts (313). Conclusions This study provides deep insights into the transcriptional landscapes of G. oxydans. The comprehensive transcriptome data, which we made publicly available, facilitate further analysis of promoters and other regulatory elements. This will support future approaches for rational strain development and targeted gene expression in G. oxydans. The corrections of start codons further improve the high quality genome reference and support future proteome analysis. Electronic supplementary material The online version of this article (10.1186/s12864-017-4415-x) contains supplementary material, which is available to authorized users.
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Kranz A, Vogel A, Degner U, Kiefler I, Bott M, Usadel B, Polen T. High precision genome sequencing of engineered Gluconobacter oxydans 621H by combining long nanopore and short accurate Illumina reads. J Biotechnol 2017; 258:197-205. [PMID: 28433722 DOI: 10.1016/j.jbiotec.2017.04.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 04/14/2017] [Accepted: 04/15/2017] [Indexed: 02/08/2023]
Abstract
State of the art and novel high-throughput DNA sequencing technologies enable fascinating opportunities and applications in the life sciences including microbial genomics. Short high-quality read data already enable not only microbial genome sequencing, yet can be inadequately to solve problems in genome assemblies and for the analysis of structural variants, especially in engineered microbial cell factories. Single-molecule real-time sequencing technologies generating long reads promise to solve such assembly problems. In our study, we wanted to increase the average read length of long nanopore reads with R9 chemistry and conducted a hybrid approach for the analysis of structural variants to check the genome stability of a recombinant Gluconobacter oxydans 621H strain (IK003.1) engineered for improved growth. Therefore we combined accurate Illumina sequencing technology and low-cost single-molecule nanopore sequencing using the MinION® device from Oxford Nanopore. In our hybrid approach with a modified library protocol we could increase the average size of nanopore 2D reads to about 18.9kb. Combining the long MinION nanopore reads with the high quality short Illumina reads enabled the assembly of the engineered chromosome into a single contig and comprehensive detection and clarification of 7 structural variants including all three known genetically engineered modifications. We found the genome of IK003.1 was stable over 70 generations of strain handling including 28h of process time in a bioreactor. The long read data revealed a novel 1420 bp transposon-flanked and ORF-containing sequence which was hitherto unknown in the G. oxydans 621H reference. Further analysis and genome sequencing showed that this region is already present in G. oxydans 621H wild-type strains. Our data of G. oxydans 621H wild-type DNA from different resources also revealed in 73 annotated coding sequences about 91 uniform nucleotide differences including InDels. Together, our results contribute to an improved high quality genome reference for G. oxydans 621H which is available via ENA accession PRJEB18739.
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Affiliation(s)
- Angela Kranz
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Alexander Vogel
- IBMG: Institute for Biology I, RWTH Aachen University, Worringer Weg 2, 52074 Aachen, Germany; IBG-2 Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ursula Degner
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ines Kiefler
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Björn Usadel
- IBMG: Institute for Biology I, RWTH Aachen University, Worringer Weg 2, 52074 Aachen, Germany; IBG-2 Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
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