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Luna-Flores CH, Stowers CC, Cox BM, Nielsen LK, Marcellin E. Linking genotype and phenotype in an economically viable propionic acid biosynthesis process. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:224. [PMID: 30123322 PMCID: PMC6090647 DOI: 10.1186/s13068-018-1222-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/03/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Propionic acid (PA) is used as a food preservative and increasingly, as a precursor for the synthesis of monomers. PA is produced mainly through hydrocarboxylation of ethylene, also known as the 'oxo-process'; however, Propionibacterium species are promising biological PA producers natively producing PA as their main fermentation product. However, for fermentation to be competitive, a PA yield of at least 0.6 g/g is required. RESULTS A new strain able to reach the required yield was obtained using genome shuffling. To gain insight into the changes leading to the improved phenotype, the genome of the new strain was sequenced, and metabolomics and transcriptomics data were obtained. In combination, the data revealed three key mutations: (i) a mutation in the promoter region of a sugar transporter which enables an increase in the uptake rate of sucrose; (ii) a mutation in a polar amino acid transporter which improves consumption of amino acids and acid tolerance; and (iii) a mutation in a gene annotated as a cytochrome C biogenesis gene, which is likely responsible for the coupling of the Wood-Werkman cycle to ATP production were responsible for the phenotype. The bioprocess was further enhanced with a feeding strategy that achieved 70 g/L of product. The proposed bioprocess is expected to outperform the economics of the current 'oxo-process' by 2020. CONCLUSIONS In this study, using genome shuffling, we obtained a strain capable of producing PA exceeding the commercial needs. The multiomics comparison between the novel strain and the wild type revealed overexpression of amino acid pathways, changes in sucrose transporters and an increased activity in the methylglyoxal and the glucuronate interconversion pathways. The analysis also suggests that a mutation in the cytochrome C biogenesis gene, coupled with ATP production through the Wood-Werkman cycle, may be responsible for the increased PA production.
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Affiliation(s)
- Carlos H. Luna-Flores
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
| | - Chris C. Stowers
- BioEngineering and Bioprocessing R&D, Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268 USA
| | - Brad M. Cox
- BioEngineering and Bioprocessing R&D, Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268 USA
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072 Australia
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Rakicka M, Lazar Z, Dulermo T, Fickers P, Nicaud JM. Lipid production by the oleaginous yeast Yarrowia lipolytica using industrial by-products under different culture conditions. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:104. [PMID: 26213570 PMCID: PMC4513389 DOI: 10.1186/s13068-015-0286-z] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND Microbial lipid production using renewable feedstock shows great promise for the biodiesel industry. RESULTS In this study, the ability of a lipid-engineered Yarrowia lipolytica strain JMY4086 to produce lipids using molasses and crude glycerol under different oxygenation conditions and at different inoculum densities was evaluated in fed-batch cultures. The greatest lipid content, 31% of CDW, was obtained using a low-density inoculum, a constant agitation rate of 800 rpm, and an oxygenation rate of 1.5 L/min. When the strain was cultured for 450 h in a chemostat containing a nitrogen-limited medium (dilution rate of 0.01 h(-1); 250 g/L crude glycerol), volumetric lipid productivity was 0.43 g/L/h and biomass yield was 60 g CDW/L. The coefficient of lipid yield to glycerol consumption (Y L/gly) and the coefficient of lipid yield to biomass yield (Y L/X ) were equal to 0.1 and 0.4, respectively. CONCLUSIONS These results indicate that lipids may be produced using renewable feedstock, thus providing a means of decreasing the cost of biodiesel production. Furthermore, using molasses for biomass production and recycling glycerol from the biodiesel industry should allow biolipids to be sustainably produced.
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Affiliation(s)
- Magdalena Rakicka
- />INRA, UMR1319 Micalis, 78350, Jouy-en-Josas, France
- />AgroParisTech, UMR Micalis, Jouy-en-Josas, France
- />Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego Str. 37/41, 51-630 Wrocław, Poland
- />Institut Micalis, INRA-AgroParisTech, UMR1319, Team BIMLip: Biologie Intégrative du Métabolisme Lipidique, CBAI, 78850 Thiverval-Grignon, France
| | - Zbigniew Lazar
- />INRA, UMR1319 Micalis, 78350, Jouy-en-Josas, France
- />AgroParisTech, UMR Micalis, Jouy-en-Josas, France
- />Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego Str. 37/41, 51-630 Wrocław, Poland
| | - Thierry Dulermo
- />INRA, UMR1319 Micalis, 78350, Jouy-en-Josas, France
- />AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Patrick Fickers
- />Microbial Processes and Interactions, Gembloux Agro Bio-Tech, Université de Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium
| | - Jean Marc Nicaud
- />INRA, UMR1319 Micalis, 78350, Jouy-en-Josas, France
- />AgroParisTech, UMR Micalis, Jouy-en-Josas, France
- />Institut Micalis, INRA-AgroParisTech, UMR1319, Team BIMLip: Biologie Intégrative du Métabolisme Lipidique, CBAI, 78850 Thiverval-Grignon, France
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Glyoxalase Centennial conference: introduction, history of research on the glyoxalase system and future prospects. Biochem Soc Trans 2014; 42:413-8. [DOI: 10.1042/bst20140014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
On 27–29 November 2013, researchers gathered at the University of Warwick, Coventry, U.K., to celebrate the centennial of the discovery of the glyoxalase pathway. The glyoxalase system was discovered and reported in papers by Carl Neuberg and by Henry Drysdale Dakin and Harold Ward Dudley in 1913. All three were leading extraordinary investigators in the pioneering years of biochemistry. Neuberg proposed glyoxalase as the pathway of mainstream glycolysis and Gustav Embden correctly discounted this, later confirmed by Otto Meyerhof. Albert Szent-Györgyi proposed glyoxalase I as the regulator of cell growth and others discounted this. In the meantime, molecular, structural and mechanistic properties of the enzymatic components of the system, glyoxalase I and glyoxalase II, have been characterized. The physiological function of the glyoxalase pathway of enzymatic defence against dicarbonyl glycation, particularly by endogenous methylglyoxal, now seems secure. We are now in an era of investigation of the regulation of the glyoxalase system where a role in aging and disease, physiological stress and drug resistance and development of healthier foods and new pharmaceuticals is emerging. The history of glyoxalase research illustrates the scientific process of hypothesis proposal, testing and rejection or acceptance with further investigation, standing testament to the need for intuition guided by experience and expertise, as well as indefatigable experimentation.
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Kalapos MP. Methylglyoxal and glucose metabolism: a historical perspective and future avenues for research. ACTA ACUST UNITED AC 2008; 23:69-91. [PMID: 18533365 DOI: 10.1515/dmdi.2008.23.1-2.69] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Methylglyoxal, an alpha-oxoaldehyde discovered in the 1880s, has had a hectic scientific career, at times being considered of fundamental importance and at other times viewed as playing a very subordinate role. Much has been learned about methylglyoxal, but the function of its production in the metabolic machinery is still unknown. This paper gives an overview of the changing role of methylglyoxal from a historical aspect and arrives at the conclusion that methylglyoxal is tightly bound to glycolysis from an evolutionary perspective, its production therefore being inevitable. It is not situated in the main stream of the glycolytic sequence, but a role can be assigned to its production in the phosphate supply of operating glycolysis in some prokaryotes and yeast under conditions of phosphate deficiency. This function is presumed to be performed by the enzyme methylglyoxal synthase, which is specialized for the conversion of dihydroxyacetone-phosphate to methylglyoxal. However, it is still unknown whether this enzyme and this kind of regulation also exist in animals.
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Martins AM, Cordeiro CA, Ponces Freire AM. In situ analysis of methylglyoxal metabolism in Saccharomyces cerevisiae. FEBS Lett 2001; 499:41-4. [PMID: 11418108 DOI: 10.1016/s0014-5793(01)02519-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Methylglyoxal metabolism was studied during Saccharomyces cerevisiae grown with D-glucose as the sole carbon and energy source. Using for the first time a specific assay for methylglyoxal in yeast, metabolic fluxes of its formation and D-lactate production were determined. D-Glucose consumption and ethanol production were determined during growth. Metabolic fluxes were also determined in situ, at the glycolytic triose phosphate levels and glyoxalase pathway. Maximum fluxes of ethanol production and glucose consumption correspond to maxima of methylglyoxal and D-lactate formation fluxes during growth. Methylglyoxal formation is quantitatively related to glycolysis, representing 0.3% of the total glycolytic flux in S. cerevisiae.
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Affiliation(s)
- A M Martins
- Grupo de Enzimologia, Centro de Estudos de Bioquímica e Fisiologia, and Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, 1749-016, Lisbon, Portugal
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Huang K, Rudolph FB, Bennett GN. Characterization of methylglyoxal synthase from Clostridium acetobutylicum ATCC 824 and its use in the formation of 1, 2-propanediol. Appl Environ Microbiol 1999; 65:3244-7. [PMID: 10388730 PMCID: PMC91483 DOI: 10.1128/aem.65.7.3244-3247.1999] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A gene encoding a putative 150-amino-acid methylglyoxal synthase was identified in Clostridium acetobutylicum ATCC 824. The enzyme was overexpressed in Escherichia coli and purified. Methylglyoxal synthase has a native molecular mass of 60 kDa and an optimum pH of 7.5. The Km and Vmax values for the substrate dihydroxyacetone phosphate were 0.53 mM and 1.56 mmol min(-1) microgram(-1), respectively. When E. coli glycerol dehydrogenase was coexpressed with methylglyoxal synthase in E. coli BL21(DE3), 3.9 mM 1,2-propanediol was produced.
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Affiliation(s)
- K Huang
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005-1892, USA
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Kaliterna J, Weusthuis RA, Castrillo JI, Van Dijken JP, Pronk JT. Transient responses of Candida utilis to oxygen limitation: regulation of the Kluyver effect for maltose. Yeast 1995; 11:317-25. [PMID: 7785332 DOI: 10.1002/yea.320110404] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The facultatively fermentative yeast Candida utilis exhibits the Kluyver effect for maltose: this disaccharide is respired and assimilated but, in contrast to glucose, it cannot be fermented. To study the mechanism of the Kluyver effect, metabolic responses of C. utilis to a transition from aerobic, sugar-limited growth to oxygen-limited conditions were studied in chemostat cultures. Unexpectedly, the initial response of maltose-grown cultures to oxygen limitation was very similar to that of glucose-grown cultures. In both cases, alcoholic fermentation occurred after a lag phase of 1 h, during which glycerol, pyruvate and D-lactate were the main fermentation products. After ca. 10 h the behaviour of the maltose- and glucose-grown cultures diverged: ethanol disappeared from the maltose-grown cultures, whereas fermentation continued in steady-state, oxygen-limited cultures grown on glucose. The disappearance of alcoholic fermentation in oxygen-limited chemostat cultures growing on maltose was not due to a repression of the synthesis of pyruvate decarboxylase and alcohol dehydrogenase. The results demonstrate that the Kluyver effect for maltose in C. utilis does not reflect an intrinsic inability of this yeast to ferment maltose, but is caused by a regulatory phenomenon that affects a key enzyme in maltose metabolism, probably the maltose carrier. The observed kinetics indicate that this regulation occurs at the level of enzyme synthesis rather than via modification of existing enzyme activity.
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Affiliation(s)
- J Kaliterna
- Department of Microbiology and Enzymology, Kluyer Laboratory of Biotechnology, Delft University of Technology, The Netherlands
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Affiliation(s)
- M J Penninckx
- Unité de Physiologie et Ecologie Microbiennes, Faculté des Sciences, Université libre de Bruxelles, Instut Pasteur Brabant, Belgium
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Hofmann KH, Polnisch E. Catabolite inactivation, cyclic AMP and protein phosphorylation in the methylotrophic yeast Hansenula polymorpha. Antonie Van Leeuwenhoek 1991; 60:49-54. [PMID: 1724594 DOI: 10.1007/bf00580441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The inactivation of the peroxisomal enzyme alcohol oxidase and the cytoplasmic enzymes fructose-1,6-bisphosphatase, malate dehydrogenase and phosphoenolpyruvate carboxykinase was found to occur after addition of glucose to methanol-grown cells of the yeast Hansenula polymorpha. The concentration of cyclic AMP increased nearly twofold within 3 min under the same conditions. In crude extracts of H. polymorpha about 20 proteins are phosphorylated by cyclic AMP dependent protein kinases, among them also fructose-1,6-bisphosphatase. No phosphorylation of the alcohol oxidase protein could be detected. From this fact, it was concluded that the inactivation of the peroxisomal alcohol oxidase is independent of cyclic AMP-dependent protein phosphorylation.
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Affiliation(s)
- K H Hofmann
- Institut für Angewandte und Technische Mikrobiologie, Ernst-Moritz-Arndt-Universität Greifswald, Germany
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Penninckx MJ, Jaspers CJ, Legrain MJ. The glutathione-dependent glyoxalase pathway in the yeast Saccharomyces cerevisiae. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32368-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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