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Sun S, Wang Y, Shu L, Lu X, Wang Q, Zhu C, Shi J, Lye GJ, Baganz F, Hao J. Redirection of the central metabolism of Klebsiella pneumoniae towards dihydroxyacetone production. Microb Cell Fact 2021; 20:123. [PMID: 34187467 PMCID: PMC8243499 DOI: 10.1186/s12934-021-01608-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 06/08/2021] [Indexed: 11/28/2022] Open
Abstract
Background Klebsiella pneumoniae is a bacterium that can be used as producer for numerous chemicals. Glycerol can be catabolised by K. pneumoniae and dihydroxyacetone is an intermediate of this catabolism pathway. Here dihydroxyacetone and glycerol were produced from glucose by this bacterium based a redirected glycerol catabolism pathway. Results tpiA, encoding triosephosphate isomerase, was knocked out to block the further catabolism of dihydroxyacetone phosphate in the glycolysis. After overexpression of a Corynebacterium glutamicum dihydroxyacetone phosphate dephosphorylase (hdpA), the engineered strain produced remarkable levels of dihydroxyacetone (7.0 g/L) and glycerol (2.5 g/L) from glucose. Further increase in product formation were obtained by knocking out gapA encoding an iosenzyme of glyceraldehyde 3-phosphate dehydrogenase. There are two dihydroxyacetone kinases in K. pneumoniae. They were both disrupted to prevent an inefficient reaction cycle between dihydroxyacetone phosphate and dihydroxyacetone, and the resulting strains had a distinct improvement in dihydroxyacetone and glycerol production. pH 6.0 and low air supplement were identified as the optimal conditions for dihydroxyacetone and glycerol production by K, pneumoniae ΔtpiA-ΔDHAK-hdpA. In fed batch fermentation 23.9 g/L of dihydroxyacetone and 10.8 g/L of glycerol were produced after 91 h of cultivation, with the total conversion ratio of 0.97 mol/mol glucose. Conclusions This study provides a novel and highly efficient way of dihydroxyacetone and glycerol production from glucose. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01608-0.
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Affiliation(s)
- Shaoqi Sun
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China.,School of Life Science, Shanghai University, Shanghai, 200444, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yike Wang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China.,School of Life Science, Shanghai University, Shanghai, 200444, People's Republic of China
| | - Lin Shu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiyang Lu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Qinghui Wang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Chenguang Zhu
- School of Life Science, Shanghai University, Shanghai, 200444, People's Republic of China
| | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Gary J Lye
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK
| | - Frank Baganz
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK.
| | - Jian Hao
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China. .,Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK. .,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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2,3-Dihydroxyisovalerate production by Klebsiella pneumoniae. Appl Microbiol Biotechnol 2020; 104:6601-6613. [PMID: 32519119 DOI: 10.1007/s00253-020-10711-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 02/28/2020] [Accepted: 06/01/2020] [Indexed: 01/04/2023]
Abstract
2,3-Dihydroxyisovalerate is an intermediate of valine and leucine biosynthesis pathway; however, no natural microorganism has been found yet that can accumulate this compound. Klebsiella pneumoniae is a useful bacterium that can be used as a workhorse for the production of a range of industrially desirable chemicals. Dihydroxy acid dehydratase, encoded by the ilvD gene, catalyzes the reaction of 2-ketoisovalerate formation from 2,3-dihydroxyisovalerate. In this study, an ilvD disrupted strain was constructed which resulted in the inability to synthesize 2-ketoisovalerate, yet accumulate 2,3-dihydroxyisovalerate in its culture broth. 2,3-Butanediol is the main metabolite of K. pneumoniae and its synthesis pathway and the branched-chain amino acid synthesis pathway share the same step of the α-acetolactate synthesis. By knocking out the budA gene, carbon flow into the branched-chain amino acid synthesis pathway was upregulated, which resulted in a distinct increase in 2,3-dihydroxyisovalerate levels. Lactic acid was identified as a by-product of the process and by blocking the lactic acid synthesis pathway, a further increase in 2,3-dihydroxyisovalerate levels was obtained. The culture parameters of 2,3-dihydroxyisovalerate fermentation were optimized, which include acidic pH and medium level oxygen supplementation to favor 2,3-dihydroxyisovalerate synthesis. At optimal conditions (pH 6.5, 400 rpm), 36.5 g/L of 2,3-dihydroxyisovalerate was produced in fed-batch fermentation over 45 h, with a conversion ratio of 0.49 mol/mol glucose. Thus, a biological route of 2,3-dihydroxyisovalerate production with high conversion ratio and final titer was developed, providing a basis for an industrial process. Key Points • A biological route of 2,3-dihydroxyisovalerate production was setup. • Disruption of budA causes 2,3-dihydroxuisovalerate accumulation in K. pneumoniae. • Disruption of ilvD prevents 2,3-dihydroxyisovalerate reuse by the cell. • 36.5 g/L of 2,3-dihydroxyisovalerate was obtained in fed-batch fermentation.
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Hendrata M, Birnir B. Dynamic-energy-budget-driven fruiting-body formation in myxobacteria. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:061902. [PMID: 20866435 DOI: 10.1103/physreve.81.061902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2008] [Revised: 03/11/2010] [Indexed: 05/29/2023]
Abstract
We develop an interacting particle model to simulate the life cycle of myxobacteria, which consists of two main stages--the swarming stage and the development (fruiting body formation) stage. As experiments have shown that the phase transition from swarming to development stage is triggered by starvation, we incorporate into the simulation a system of ordinary differential equations (ODEs) called the dynamic energy budget, which controls the uptake and use of energy by individuals. This inclusion successfully automates the phase transition in our simulation. Only one parameter, namely, the food density, controls the entire simulation of the life cycle.
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Affiliation(s)
- M Hendrata
- Department of Mathematics, California State University, 5151 State University Drive, Los Angeles, California 90032, USA.
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Pan JG, Rhee JS. Biomass yields and energetic yields of oleaginous yeasts in batch culture. Biotechnol Bioeng 2009; 28:112-4. [PMID: 18553850 DOI: 10.1002/bit.260280117] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This article provides the analysis on biomass yields and energetic yields of the oleaginous yeasts. The biomass yields of the oleaginous yeasts are consistently lower than nonoleaginous microorganisms, whereas their energetic yields are higher. Data inconsistencies of literature are explained by the variation of energy contents of oleaginous yeasts.
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Affiliation(s)
- J G Pan
- Department of Biological Science and Engineering, Korea Advanced Institute of Science and Technology, POB 150, Chongyang, Seoul, Korea
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Sousa T, Mota R, Domingos T, Kooijman SALM. Thermodynamics of organisms in the context of dynamic energy budget theory. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 74:051901. [PMID: 17279933 DOI: 10.1103/physreve.74.051901] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Revised: 08/10/2006] [Indexed: 05/13/2023]
Abstract
We carry out a thermodynamic analysis to an organism. It is applicable to any type of organism because (1) it is based on a thermodynamic formalism applicable to all open thermodynamic systems and (2) uses a general model to describe the internal structure of the organism--the dynamic energy budget (DEB) model. Our results on the thermodynamics of DEB organisms are the following. (1) Thermodynamic constraints for the following types of organisms: (a) aerobic and exothermic, (b) anaerobic and exothermic, and (c) anaerobic and endothermic; showing that anaerobic organisms have a higher thermodynamic flexibility. (2) A way to compute the changes in the enthalpy and in the entropy of living biomass that accompany changes in growth rate solving the problem of evaluating the thermodynamic properties of biomass as a function of the amount of reserves. (3) Two expressions for Thornton's coefficient that explain its experimental variability and theoretically underpin its use in metabolic studies. (4) A mechanism that organisms in non-steady-state use to rid themselves of internal entropy production: "dilution of entropy production by growth." To demonstrate the practical applicability of DEB theory to quantify thermodynamic changes in organisms we use published data on Klebsiella aerogenes growing aerobically in a continuous culture. We obtain different values for molar entropies of the reserve and the structure of Klebsiella aerogenes proving that the reserve density concept of DEB theory is essential in discussions concerning (a) the relationship between organization and entropy and (b) the mechanism of storing entropy in new biomass. Additionally, our results suggest that the entropy of dead biomass is significantly different from the entropy of living biomass.
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Affiliation(s)
- Tânia Sousa
- Environment and Energy Section, DEM, Instituto Superior Técnico, Avenida Rovisco Pais, 1. 1049-001 Lisbon, Portugal.
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Scherer P, Lippert H, Wolff G. Composition of the major elements and trace elements of 10 methanogenic bacteria determined by inductively coupled plasma emission spectrometry. Biol Trace Elem Res 1983; 5:149-63. [PMID: 24263482 DOI: 10.1007/bf02916619] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/1982] [Accepted: 12/29/1982] [Indexed: 12/01/2022]
Abstract
The elemental composition of 10 methanogenic species was determined by inductively coupled plasma emission spectrometry and by a C-H-N-analyzer. The 10 species were representative of all three orders of the methanogens and were cultivated under defined conditions. Special emphasis was given toMethanosarcina barkeri, represented by 5 strains and cultivated on various substrates. The following elements with the lowest and highest values in parentheses were determined: C (37-44%, w/w), H (5.5-6.5%), N (9.5-12,8%); Na (0.3-4.0%), K (0.13-5.0%), S (0.56-1.2%), P (0.5-2.8%), Ca (order I: 85-550 ppm; order II: 1000-4500 ppm), Mg (0.09-0.53%), Fe (0.07-0.28%), Ni (65-180 ppm), Co (10-120 ppm). Mo (10-70 ppm), Zn (50-630 ppm), Cu (<10-160 ppm), Mn (<5-25 ppm). The biggest variations were found with respect to N and K, which both seem to have important physiological functions. Although it is unknown whether zinc and copper are essential trace elements for methanogens, all investigated species contained remarkably high zinc contents, whereas copper seemed to be present only in some species.
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Affiliation(s)
- P Scherer
- Institut für Allgemeine Botanik, Abteilung Mikrobiologie, Universität Hamburg, Ohnhornststr. 18, D-2000, Hamburg 52, West Germany
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