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Metabolic engineering

Let us harness the microbial metabolism for your benefit!

​Metabolic engineering uses genetic and regulatory engineering of cellular metabolism for the production of desired chemicals with microbial cells (i.e. cell factories): in this way, customised, cost-efficient, and sustainable production processes can be created. There is a clear need for competitive biotechnical production processes, which are independent of fossil resources and can reduce the energy demand. These processes need our trimmed microbes.

Science - for engineering cell factories

We are experts in metabolic engineering of different yeasts, filamentous fungi, and cyanobacteria. We identify novel production hosts with desired process and physiological properties and develop genetic tools for their engineering. We work closely with other expert teams at VTT, applying the latest methods of synthetic biology, systems biology, modelling, bioinformatics, enzymology, analytics, and bioprocess technology for efficient pathway engineering. Our projects are customised to fit your needs, and we deliver strains from proof-of-concept level to those ready for industrial scale production. We are especially interested in the production of organic acids, lipids and their derivatives, alkanes, terpenes – you name it!

The People who make biology work

Our key resource is people, their knowledge, enthusiasm, interest and love of natural sciences. With the attitude of making biology really work for your project, and with the business mind set, we can serve you better than anyone else. In addition, we do have excellent research facilities in a multidiciplinary environment. We are part of national and international networks.

We serve a wide variety of industrial sectors, including energy, pulp and paper, chemical, food and feed, malting and brewing, flavour and fragrance industries. At the moment we are focusing especially on the transition of the traditional oil and chemical industry towards bioeconomy.

Our Metabolic Engineering know-how is applicable in production of platform and high value chemicals, liquid biofuels, in food, feed and beverages applications as well as in carbon capture.

As well as servicing customers, we also protect our IPR and license or develop further the ideas with customers.


​Scientific publications



Overexpression of PAD1 and FDC1 results in significant cinnamic acid decarboxylase activity in Saccharomyces cerevisiae. Richard P, Viljanen K, Penttilä M. AMB Express. 2015 Feb 18;5:12.

Metabolic engineering of the fungal D-galacturonate pathway for L-ascorbic acid production. Kuivanen J, Penttilä M, Richard P. Microb Cell Fact. 2015 Jan 8;14(1):2.



L-lactic acid production from D-xylose with Candida sonorensis expressing a heterologous lactate dehydrogenase encoding gene. Koivuranta KT, Ilmén M, Wiebe MG, Ruohonen L, Suominen P, Penttilä M. Microb Cell Fact. 2014 Aug 8;13:107

Transcriptome of Saccharomyces cerevisiae during production of D-xylonate. Mojzita D, Oja M, Rintala E, Wiebe M, Penttilä M, Ruohonen L. BMC Genomics. 2014 Sep 5;15:763.

Single cell and in vivo analyses elucidate the effect of xylC lactonase during production of D-xylonate in Saccharomyces cerevisiae. Nygård Y, Maaheimo H, Mojzita D, Toivari M, Wiebe M, Resnekov O, Gustavo Pesce C, Ruohonen L, Penttilä M. Metab Eng. 2014 Sep;25:238-47.

The diverse role of Pdr12 in resistance to weak organic acids. Nygård Y, Mojzita D, Toivari M, Penttilä M, Wiebe MG, Ruohonen L. Yeast. 2014 Jun;31(6):219-32.

L-arabinose/D-galactose 1-dehydrogenase of Rhizobium leguminosarum bv. trifolii characterised and applied for bioconversion of L-arabinose to L-arabonate with Saccharomyces cerevisiae. Aro-Kärkkäinen N, Toivari M, Maaheimo H, Ylilauri M, Pentikäinen OT, Andberg M, Oja M, Penttilä M, Wiebe MG, Ruohonen L, Koivula A. Appl Microbiol Biotechnol. 2014 Dec;98(23):9653-65.

Categorisation of sugar acid dehydratases in Aspergillus niger. Motter FA, Kuivanen J, Keränen H, Hilditch S, Penttilä M, Richard P. Fungal Genet Biol. 2014 Mar;64:67-72.

Effect of oxygenation and temperature on glucose-xylose fermentation in Kluyveromyces marxianus CBS712 strain. Signori L, Passolunghi S, Ruohonen L, Porro D, Branduardi P. Microb Cell Fact. 2014 Apr 8;13(1):51



Yeast oligo-mediated genome engineering (YOGE). DiCarlo JE, Conley AJ, Penttilä M, Jäntti J, Wang HH, Church GM. ACS Synth Biol. 2013 Dec 20;2(12):741-9.

Glycolic acid production in the engineered yeasts Saccharomyces cerevisiae and Kluyveromyces lactis. Koivistoinen OM, Kuivanen J, Barth D, Turkia H, Pitkänen JP, Penttilä M, Richard P. Microb Cell Fact. 2013 Sep 23;12:82.

Production of L-lactic acid by the yeast Candida sonorensis expressing heterologous bacterial and fungal lactate dehydrogenases. Ilmén M, Koivuranta K, Ruohonen L, Rajgarhia V, Suominen P, Penttilä M. Microb Cell Fact. 2013 May 25;12:53

Low pH D-xylonate production with Pichia kudriavzevii. Toivari M, Vehkomäki ML, Nygård Y, Penttilä M, Ruohonen L, Wiebe MG. Bioresour Technol. 2013 Apr;133:555-62.

Single-cell measurements of enzyme levels as a predictive tool for cellular fates during organic acid production. Zdraljevic S, Wagner D, Cheng K, Ruohonen L, Jäntti J, Penttilä M, Resnekov O, Pesce CG. Appl Environ Microbiol. 2013 Dec;79(24):7569-82.

Overexpression of NADH-dependent fumarate reductase improves D-xylose fermentation in recombinant Saccharomyces cerevisiae. Salusjärvi L, Kaunisto S, Holmström S, Vehkomäki ML, Koivuranta K, Pitkänen JP, Ruohonen L. J Ind Microbiol Biotechnol. 2013 Dec;40(12):1383-92



Lipid production in batch and fed-batch cultures of Rhodosporidium toruloides from 5 and 6 carbon carbohydrates. Wiebe MG, Koivuranta K, Penttilä M, Ruohonen L. BMC Biotechnol. 2012 May 30;12:26.

Engineering filamentous fungi for conversion of D-galacturonic acid to L-galactonic acid. Kuivanen J, Mojzita D, Wang Y, Hilditch S, Penttilä M, Richard P, Wiebe MG. Appl Environ Microbiol. 2012 Dec;78(24):8676-83.

Microbial D-xylonate production. Toivari MH, Nygård Y, Penttilä M, Ruohonen L, Wiebe MG. Appl Microbiol Biotechnol. 2012 Oct;96(1):1-8.

Metabolic engineering of Saccharomyces cerevisiae for bioconversion of D-xylose to D-xylonate. Toivari M, Nygård Y, Kumpula EP, Vehkomäki ML, Benčina M, Valkonen M, Maaheimo H, Andberg M, Koivula A, Ruohonen L, Penttilä M, Wiebe MG. Metab Eng. 2012 Jul;14(4):427-36.

Characterization of a novel Agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-deoxy-2-keto-L-threo-hexarate. Andberg M, Maaheimo H, Boer H, Penttilä M, Koivula A, Richard P. J Biol Chem. 2012 May 18;287(21):17662-71

Sorbitol dehydrogenase of Aspergillus niger, SdhA, is part of the oxido-reductive D-galactose pathway and essential for D-sorbitol catabolism. Koivistoinen OM, Richard P, Penttilä M, Ruohonen L, Mojzita D. FEBS Lett. 2012 Feb 17;586(4):378-83.

Identification of the galactitol dehydrogenase, LadB, that is part of the oxido-reductive D-galactose catabolic pathway in Aspergillus niger. Mojzita D, Koivistoinen OM, Maaheimo H, Penttilä M, Ruohonen L, Richard P. Fungal Genet Biol. 2012 Feb;49(2):152-9.

Characterisation of the gene cluster for l-rhamnose catabolism in the yeast Scheffersomyces (Pichia) stipitis. Koivistoinen OM, Arvas M, Headman JR, Andberg M, Penttilä M, Jeffries TW, Richard P. Gene. 2012 Jan 15;492(1):177-85.

Identification and characterization of a novel diterpene gene cluster in Aspergillus nidulans. Bromann K, Toivari M, Viljanen K, Vuoristo A, Ruohonen L, Nakari-Setälä T. PLoS One. 2012;7(4):e35450.



High level secretion of cellobiohydrolases by Saccharomyces cerevisiae. Ilmén M, den Haan R, Brevnova E, McBride J, Wiswall E, Froehlich A, Koivula A, Voutilainen SP, Siika-Aho M, la Grange DC, Thorngren N, Ahlgren S, Mellon M, Deleault K, Rajgarhia V, van Zyl WH, Penttilä M. Biotechnol Biofuels. 2011 Sep 12;4:30.

Bioconversion of d-xylose to d-xylonate with Kluyveromyces lactis. Nygård Y, Toivari MH, Penttilä M, Ruohonen L, Wiebe MG. Metab Eng. 2011 Jul;13(4):383-91.

Transcriptional responses of Saccharomyces cerevisiae to shift from respiratory and respirofermentative to fully fermentative metabolism. Rintala E, Jouhten P, Toivari M, Wiebe MG, Maaheimo H, Penttilä M, Ruohonen L. OMICS. 2011 Jul-Aug;15(7-8):461-76.

Cloning of two genes (LAT1,2) encoding specific L: -arabinose transporters of the L: -arabinose fermenting yeast Ambrosiozyma monospora. Verho R, Penttilä M, Richard P. Appl Biochem Biotechnol. 2011 Jul;164(5):604-11.

Identification of regulatory elements in the AGT1 promoter of ale and lager strains of brewer's yeast. Vidgren V, Kankainen M, Londesborough J, Ruohonen L. Yeast. 2011 Aug;28(8):579-94.



Metabolic engineering of fungal strains for conversion of D-galacturonate to meso-galactarate. Mojzita D, Wiebe M, Hilditch S, Boer H, Penttilä M, Richard P. Appl Environ Microbiol. 2010 Jan;76(1):169-75.

Bioconversion of D-galacturonate to keto-deoxy-L-galactonate (3-deoxy-L-threo-hex-2-ulosonate) using filamentous fungi. Wiebe MG, Mojzita D, Hilditch S, Ruohonen L, Penttilä M. BMC Biotechnol. 2010 Aug 26;10:63.

Saccharomyces cerevisiae engineered to produce D-xylonate. Toivari MH, Ruohonen L, Richard P, Penttilä M, Wiebe MG. Appl Microbiol Biotechnol. 2010 Oct;88(3):751-60.

Enhancing the flux of D-glucose to the pentose phosphate pathway in Saccharomyces cerevisiae for the production of D-ribose and ribitol. Toivari MH, Maaheimo H, Penttilä M, Ruohonen L. Appl Microbiol Biotechnol. 2010 Jan;85(3):731-9.

The 'true' L-xylulose reductase of filamentous fungi identified in Aspergillus niger. Mojzita D, Vuoristo K, Koivistoinen OM, Penttilä M, Richard P. FEBS Lett. 2010 Aug 20;584(16):3540-4.

Identification of an L-arabinose reductase gene in Aspergillus niger and its role in L-arabinose catabolism. Mojzita D, Penttilä M, Richard P.J Biol Chem. 2010 Jul 30;285(31):23622-8.