Efficient enzymatic conversion of biomass to bio-based compounds

Application period: 11 June – 10 August, 2026

Research project description

Biomass serves as a renewable, carbon-neutral alternative to fossil fuels. This PhD project focuses on enzyme-driven processes for converting renewable lignocellulosic biomasses into bio-oils and high-value biobased chemicals. The project aims to exploit non‑phosphorylative metabolic pathway enzymes for converting pentose sugars—particularly xylose and arabinose derived from lignocellulosic biomass—into high‑value bio‑based chemicals.

Xylonolactonase and pentonate dehydratases of the Weimberg/Dahms pathway are Fe-dependent enzymes. One of the objectives of the project is to study the Fe-dependency of the enzymes by native mass spectrometry. The work also integrates structural biology and enzyme engineering to improve the catalytic efficiency of key enzymes of the pathway. Through tailored enzymes, the project aims to convert pentose sugars into polymer precursors and/or fine chemicals.

Ultimately, the project supports the transition toward a circular bioeconomy by enabling low‑emission production of renewable fuels and chemicals from non‑fossil raw materials while reducing waste and enhancing the valorisation of biomass resources.

Academic background and skills of the applicant

An ideal candidate holds a master’s degree in chemistry, chemical engineering, biotechnology, or a closely related field. The candidate is expected to have an understanding of biophysical and bioanalytical methods for protein characterization. Excellent scientific writing and oral communication skills in English are essential for the position. Strong analytical thinking and problem-solving abilities are required, together with the ability to work effectively as part of a team and a genuine interest in laboratory-based research. Prior experience in protein expression and purification is considered an advantage, and familiarity with X-ray crystallography and/or native mass spectrometry is regarded as a further asset. The selected candidate must fulfil the language skills requirements of the Doctoral Programme in Science, Forestry and Technology at UEF (see https://www.uef.fi/en/degree-programme/doctoral-programme-in-science-forestry-and-technology (Eligibility and admission criteria)).

Doctoral programme and research group

Doctoral education in the University of Eastern Finland is arranged in seven discipline specific or thematic doctoral programmes. This research project will be located in the Doctoral Programme in Science, Forestry and Technology, and the submitting department is the Department of Chemistry and Sustainable Technology. The PhD researcher will join the research group of Bio-organic Chemistry.

Partners / Secondments

Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), hosted by Prof. Tu Tao

BIOCEV Institute of Microbiology of the CAS, Prague, Czech Republic, hosted by Dr. Petr Novak

Other interdisciplinary, international and/or intersectoral collaboration

This project involves potential collaboration with VTT Technical Research Center of Finland.

Intersectoral and interdisciplinary collaboration is strengthened through DP-FOBI’s three summer schools involving academic supervisors, non-academic partners, and other stakeholders, enabling hands-on interaction and knowledge exchange.

Supervisors and related research

Nina Hakulinen

Docent Nina Hakulinen is a University Lecturer at the University of Eastern Finland. She was awarded the title of Docent in 2011 and served as an Academy Researcher from 2012 to 2017. She has extensive experience in X-ray crystallography and native mass spectrometric characterization of a wide range of proteins, including numerous metalloenzymes, and has contributed more than 70 published protein structures to the Protein Data Bank (PDB). She received project funding from the Research Council of Finland for the period 2019–2023 to support structural studies of enzymes involved in pentose metabolism.

Hakulinen has substantial experience in the supervision and training of graduate students, having supervised more than 10 PhD students (with one currently ongoing) and 23 MSc students (with three currently ongoing).

Janne Jänis

Professor Janne Jänis has extensive experience in biomolecular mass spectrometry and bioanalytical chemistry, with a strong track record spanning proteomics, metabolomics, petroleomics, and environmental analysis. In recent years, his research has focused on thermochemical biorefining and the characterization of highly complex mixtures using advanced high-resolution mass spectrometry, contributing to molecular-level understanding and application-oriented solutions. He has secured funding (2010–2025) from sources including the Research Council of Finland, Business Finland, EU Horizon 2020/MSCA, foundations, and industry.

In supervision and training, he has guided more than 120 BSc, MSc, and PhD theses and supervised nine postdoctoral researchers, and currently supervises or co-supervises two MSCA Doctoral Network researchers.

Ren, Y., Eronen, V. Blomster Andberg, M., Koivula, A and Hakulinen, N. (2022) Structure and function of aldopentose catabolism enzymes involved into oxidative non-phosphorylative pathways, Biotechnology for Biofuels and Bioproducts 15, 147.

Ren, Y., Vettenranta, E., Penttinen, L., Andberg, M., Koivula, A., Rouvinen, J. and Hakulinen N. (2024) Unveiling the importance of the C-terminus in the sugar acid dehydratase of the IlvD/EDD superfamily, Applied Microbiology and Biotechnology 108, 436.

Pääkkönen, J.; Penttinen, L.; Andberg, M.; Koivula, A.; Hakulinen, N.; Rouvinen, J.; Jänis, J. Xylonolactonase from Caulobacter crescentus is a mononuclear nonheme iron hydrolase. Biochemistry 2021, 60 (41), 3046–3049.