The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16.

Arenas-Lopez C, Locker J, Orol D, Walter F, Busche T, Kalinowski J, Minton NP, Kovacs K, Winzer K (2019)
Biotechnology for biofuels 12(1): 150.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Autor*in
Arenas-Lopez, Christian; Locker, Jessica; Orol, Diego; Walter, Frederik; Busche, TobiasUniBi; Kalinowski, JörnUniBi; Minton, Nigel P; Kovacs, Katalin; Winzer, Klaus
Abstract / Bemerkung
Background: 3-Hydroxypropionic acid (3-HP) is a promising platform chemical with various industrial applications. Several metabolic routes to produce 3-HP from organic substrates such as sugars or glycerol have been implemented in yeast, enterobacterial species and other microorganisms. In this study, the native 3-HP metabolism of Cupriavidus necator was investigated and manipulated as it represents a promising chassis for the production of 3-HP and other fatty acid derivatives from CO2 and H2.; Results: When testing C. necator for its tolerance towards 3-HP, it was noted that it could utilise the compound as the sole source of carbon and energy, a highly undesirable trait in the context of biological 3-HP production which required elimination. Inactivation of the methylcitrate pathway needed for propionate utilisation did not affect the organism's ability to grow on 3-HP. Putative genes involved in 3-HP degradation were identified by bioinformatics means and confirmed by transcriptomic analyses, the latter revealing considerably increased expression in the presence of 3-HP. Genes identified in this manner encoded three putative (methyl)malonate semialdehyde dehydrogenases (mmsA1, mmsA2 and mmsA3) and two putative dehydrogenases (hpdH and hbdH). These genes, which are part of three separate mmsA operons, were inactivated through deletion of the entire coding region, either singly or in various combinations, to engineer strains unable to grow on 3-HP. Whilst inactivation of single genes or double deletions could only delay but not abolish growth, a triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain was unable utilise 3-HP as the sole source of carbon and energy. Under the used conditions this strain was also unable to co-metabolise 3-HP alongside other carbon and energy sources such as fructose and CO2/H2. Further analysis suggested primary roles for the different mmsA operons in the utilisation of beta-alanine generating substrates (mmsA1), degradation of 3-HP (mmsA2), and breakdown of valine (mmsA3).; Conclusions: Three different (methyl)malonate semialdehyde dehydrogenases contribute to 3-HP breakdown in C. necator H16. The created triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain represents an ideal chassis for autotrophic 3-HP production.
Erscheinungsjahr
2019
Zeitschriftentitel
Biotechnology for biofuels
Band
12
Ausgabe
1
Art.-Nr.
150
ISSN
1754-6834
Page URI
https://pub.uni-bielefeld.de/record/2936260

Zitieren

Arenas-Lopez C, Locker J, Orol D, et al. The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16. Biotechnology for biofuels. 2019;12(1): 150.
Arenas-Lopez, C., Locker, J., Orol, D., Walter, F., Busche, T., Kalinowski, J., Minton, N. P., et al. (2019). The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16. Biotechnology for biofuels, 12(1), 150. doi:10.1186/s13068-019-1489-5
Arenas-Lopez, C., Locker, J., Orol, D., Walter, F., Busche, T., Kalinowski, J., Minton, N. P., Kovacs, K., and Winzer, K. (2019). The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16. Biotechnology for biofuels 12:150.
Arenas-Lopez, C., et al., 2019. The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16. Biotechnology for biofuels, 12(1): 150.
C. Arenas-Lopez, et al., “The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16.”, Biotechnology for biofuels, vol. 12, 2019, : 150.
Arenas-Lopez, C., Locker, J., Orol, D., Walter, F., Busche, T., Kalinowski, J., Minton, N.P., Kovacs, K., Winzer, K.: The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16. Biotechnology for biofuels. 12, : 150 (2019).
Arenas-Lopez, Christian, Locker, Jessica, Orol, Diego, Walter, Frederik, Busche, Tobias, Kalinowski, Jörn, Minton, Nigel P, Kovacs, Katalin, and Winzer, Klaus. “The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16.”. Biotechnology for biofuels 12.1 (2019): 150.

59 References

Daten bereitgestellt von Europe PubMed Central.

A proteomic view of the facultatively chemolithoautotrophic lifestyle of Ralstonia eutropha H16.
Schwartz E, Voigt B, Zuhlke D, Pohlmann A, Lenz O, Albrecht D, Schwarze A, Kohlmann Y, Krause C, Hecker M, Friedrich B., Proteomics 9(22), 2009
PMID: 19798673
Dissimilation of aromatic compounds by Alcaligenes eutrophus.
Johnson BF, Stanier RY., J. Bacteriol. 107(2), 1971
PMID: 5113598
Biosynthesis and biodegradation of 3-hydroxypropionate-containing polyesters.
Andreessen B, Steinbuchel A., Appl. Environ. Microbiol. 76(15), 2010
PMID: 20543057
Rhodobacter sphaeroides uses a reductive route via propionyl coenzyme A to assimilate 3-hydroxypropionate.
Schneider K, Asao M, Carter MS, Alber BE., J. Bacteriol. 194(2), 2011
PMID: 22056933
Candida albicans utilizes a modified β-oxidation pathway for the degradation of toxic propionyl-CoA.
Otzen C, Bardl B, Jacobsen ID, Nett M, Brock M., J. Biol. Chem. 289(12), 2014
PMID: 24497638
Development of a deletion mutant of Pseudomonas denitrificans that does not degrade 3-hydroxypropionic acid.
Zhou S, Ashok S, Ko Y, Kim DM, Park S., Appl. Microbiol. Biotechnol. 98(10), 2014
PMID: 24519457
Characterization of propionate CoA-transferase from Ralstonia eutropha H16.
Volodina E, Schurmann M, Lindenkamp N, Steinbuchel A., Appl. Microbiol. Biotechnol. 98(8), 2013
PMID: 24057402
Direct fermentation route for the production of acrylic acid.
Chu HS, Ahn JH, Yun J, Choi IS, Nam TW, Cho KM., Metab. Eng. 32(), 2015
PMID: 26319589
Investigations on the microbial catabolism of the organic sulfur compounds TDP and DTDP in Ralstonia eutropha H16 employing DNA microarrays.
Peplinski K, Ehrenreich A, Doring C, Bomeke M, Steinbuchel A., Appl. Microbiol. Biotechnol. 88(5), 2010
PMID: 20924576
The methylcitric acid pathway in Ralstonia eutropha: new genes identified involved in propionate metabolism.
Bramer CO, Steinbuchel A., Microbiology (Reading, Engl.) 147(Pt 8), 2001
PMID: 11495997
Production of 3-hydroxypropionic acid from glycerol by recombinant Pseudomonas denitrificans.
Zhou S, Catherine C, Rathnasingh C, Somasundar A, Park S., Biotechnol. Bioeng. 110(12), 2013
PMID: 23775313
Cloning, expression and characterization of 3-hydroxyisobutyrate dehydrogenase from Pseudomonas denitrificans ATCC 13867.
Zhou S, Mohan Raj S, Ashok S, Edwardraja S, Lee SG, Park S., PLoS ONE 8(5), 2013
PMID: 23658760
Inducible gene expression system by 3-hydroxypropionic acid.
Zhou S, Ainala SK, Seol E, Nguyen TT, Park S., Biotechnol Biofuels 8(), 2015
PMID: 26500695
The catalytic property of 3-hydroxyisobutyrate dehydrogenase from Bacillus cereus on 3-hydroxypropionate.
Yao T, Xu L, Ying H, Huang H, Yan M., Appl. Biochem. Biotechnol. 160(3), 2009
PMID: 19517068
KEGG: new perspectives on genomes, pathways, diseases and drugs.
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K., Nucleic Acids Res. 45(D1), 2016
PMID: 27899662
ReadXplorer--visualization and analysis of mapped sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
PMID: 24790157
ReadXplorer 2-detailed read mapping analysis and visualization from one single source.
Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A., Bioinformatics 32(24), 2016
PMID: 27540267
Differential expression analysis for sequence count data.
Anders S, Huber W., Genome Biol. 11(10), 2010
PMID: 20979621
Production of 3-hydroxypropionic acid in engineered Methylobacterium extorquens AM1 and its reassimilation through a reductive route.
Yang YM, Chen WJ, Yang J, Zhou YM, Hu B, Zhang M, Zhu LP, Wang GY, Yang S., Microb. Cell Fact. 16(1), 2017
PMID: 29084554
Genomic view of energy metabolism in Ralstonia eutropha H16.
Cramm R., J. Mol. Microbiol. Biotechnol. 16(1-2), 2008
PMID: 18957861
Manipulation of Ralstonia eutropha carbon storage pathways to produce useful bio-based products.
Brigham CJ, Zhila N, Shishatskaya E, Volova TG, Sinskey AJ., Subcell. Biochem. 64(), 2012
PMID: 23080259
The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems.
Kim KS, Pelton JG, Inwood WB, Andersen U, Kustu S, Wemmer DE., J. Bacteriol. 192(16), 2010
PMID: 20400551
Recent advances in biological production of 3-hydroxypropionic acid.
Kumar V, Ashok S, Park S., Biotechnol. Adv. 31(6), 2013
PMID: 23473969
Biosynthetic pathways for 3-hydroxypropionic acid production.
Jiang X, Meng X, Xian M., Appl. Microbiol. Biotechnol. 82(6), 2009
PMID: 19221732
Recent advances in the metabolic engineering of microorganisms for the production of 3-hydroxypropionic acid as C3 platform chemical.
Valdehuesa KN, Liu H, Nisola GM, Chung WJ, Lee SH, Park SJ., Appl. Microbiol. Biotechnol. 97(8), 2013
PMID: 23494623
Identification of a gene cluster enabling Lactobacillus casei BL23 to utilize myo-inositol.
Yebra MJ, Zuniga M, Beaufils S, Perez-Martinez G, Deutscher J, Monedero V., Appl. Environ. Microbiol. 73(12), 2007
PMID: 17449687
Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16.
Pohlmann A, Fricke WF, Reinecke F, Kusian B, Liesegang H, Cramm R, Eitinger T, Ewering C, Potter M, Schwartz E, Strittmatter A, Voss I, Gottschalk G, Steinbuchel A, Friedrich B, Bowien B., Nat. Biotechnol. 24(10), 2006
PMID: 16964242
Properties of purified methylmalonate semialdehyde dehydrogenase of Pseudomonas aeruginosa.
Bannerjee D, Sanders LE, Sokatch JR., J. Biol. Chem. 245(7), 1970
PMID: 4314598
Methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis: substrate specificity and coenzyme A binding.
Talfournier F, Stines-Chaumeil C, Branlant G., J. Biol. Chem. 286(25), 2011
PMID: 21515690
Regulation and evolution of malonate and propionate catabolism in proteobacteria.
Suvorova IA, Ravcheev DA, Gelfand MS., J. Bacteriol. 194(12), 2012
PMID: 22505679
The glyoxylate bypass of Ralstonia eutropha.
Wang ZX, Bramer CO, Steinbuchel A., FEMS Microbiol. Lett. 228(1), 2003
PMID: 14612238
The Alcaligenes eutrophus H16 hoxX gene participates in hydrogenase regulation.
Lenz O, Schwartz E, Dernedde J, Eitinger M, Friedrich B., J. Bacteriol. 176(14), 1994
PMID: 8021224
Formation and utilization of poly-beta-hydroxybutyric acid by Knallgas bacteria (Hydrogenomonas).
SCHLEGEL HG, GOTTSCHALK G, VON BARTHA R., Nature 191(), 1961
PMID: 13747776
A novel multicomponent regulatory system mediates H2 sensing in Alcaligenes eutrophus.
Lenz O, Friedrich B., Proc. Natl. Acad. Sci. U.S.A. 95(21), 1998
PMID: 9770510
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B., Bioinformatics 30(15), 2014
PMID: 24695404
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup., Bioinformatics 25(16), 2009
PMID: 19505943
Database resources of the National Center for Biotechnology Information.
NCBI Resource Coordinators, Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, Bolton E, Bourexis D, Brister JR, Bryant SH, Canese K, Charowhas C, Clark K, DiCuccio M, Dondoshansky I, Federhen S, Feolo M, Funk K, Geer LY, Gorelenkov V, Hoeppner M, Holmes B, Johnson M, Khotomlianski V, Kimchi A, Kimelman M, Kitts P, Klimke W, Krasnov S, Kuznetsov A, Landrum MJ, Landsman D, Lee JM, Lipman DJ, Lu Z, Madden TL, Madej T, Marchler-Bauer A, Karsch-Mizrachi I, Murphy T, Orris R, Ostell J, O'Sullivan C, Panchenko A, Phan L, Preuss D, Pruitt KD, Rodarmer K, Rubinstein W, Sayers EW, Schneider V, Schuler GD, Sherry ST, Sirotkin K, Siyan K, Slotta D, Soboleva A, Soussov V, Starchenko G, Tatusova TA, Todorov K, Trawick BW, Vakatov D, Wang Y, Ward M, Wilbur WJ, Yaschenko E, Zbicz K., Nucleic Acids Res. 44(D1), 2015
PMID: 26615191
Elucidation of beta-oxidation pathways in Ralstonia eutropha H16 by examination of global gene expression.
Brigham CJ, Budde CF, Holder JW, Zeng Q, Mahan AE, Rha C, Sinskey AJ., J. Bacteriol. 192(20), 2010
PMID: 20709892
Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis.
Schwartz E, Henne A, Cramm R, Eitinger T, Friedrich B, Gottschalk G., J. Mol. Biol. 332(2), 2003
PMID: 12948488

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 31236137
PubMed | Europe PMC

Suchen in

Google Scholar