Projects

Our ongoing and previous projects are

EU collaborative project (2017 – 2021)

FALCON aims to convert the lignin waste stream from lignocellulose-based bioethanol plants to a crude oil, which can be used directly as a low-sulphur marine fuel (value chain 1) or, alternatively, as a renewable feedstock for aromatic fuel additives (value chain 2) and chemical building blocks (value chain 3) such as substituted monomeric phenols. These three new value chains can be readily linked to existing second generation (2G) biofuel plants and thus contribute to their viability. In addition, the valorization of the lignin-rich waste stream will support the creation of the ‘zero-waste biorefinery’ concept.

Project members:

Kristiina Hildén (PI), Miia Mäkelä (co-PI), Jussi Sipilä (co-PI), Paula Nousiainen (Postdoc), Mika Kähkönen (Postdoc), Riku Maltari (PhD student)

Academy of Finland project (2017-2022)

The lignocellulose network in plant cell walls consists of polymeric compounds – cellulose, hemicelluloses and lignin. Basidiomycete fungi are the only organisms that efficiently modify and degrade all these polymers, mainly by producing extracellular enzymes. In the ESCaPADE project, regulation of the plant biomass degradation process in basidiomycete fungi will be investigated at the molecular level. The results will promote the exploitation of fungal enzymes in biotechnological applications, which use plant biomass as a raw material.

Project members:

Miia Mäkelä (PI), Joanna Kowalczyk (Postdoc), Astrid Müller (MSc student)

Academy of Finland project (2016-2020)

AromaFung project aims to identify the metabolic response of the model basiodiomycete white rot fungus including the most important genes and enzymes involved in its aromatic metabolism. Aromatic compounds are present in high concentrations in plant biomass as the aromatic polymer lignin and as side-groups on the polysaccharides xylan and pectin. They are released and fully converted mainly by plant biomass degrading fungi. Although the release of aromatic compounds from plant biomass by fungi has been studied extensively, relatively little attention has been given to the metabolic pathways that convert the resulting compounds.

Project members:

Kristiina Hildén (PI), Miia Mäkelä (co-PI), Jussi Sipilä (co-PI), Jussi Kontro (PhD student), Jaana Kuuskeri (Postdoc), Joona Mikkilä (Postdoc), Christina Lyra (post-doc), Mila Marinovic (PhD student)

Novo Nordisk project (2016-2019)

The aim of the LIGNICAT project is to explore the potential of enzymatic valorisation of industrial derived technical lignins. We will create basic knowledge on enzymatic reactions to modify processed lignins for sustainable catalytic processes suitable for potential value-added use in industrial applications.

Project members:

Kristiina Hildén (PI), Miia Mäkelä (co-PI), Jussi Sipilä (co-PI), Joona Mikkilä (Postdoc), Zane Dekere (technician)

EU collaborative project (2013 – 2017)

OPTIBIOCAT is aimed at developing biocatalysts based on feruloyl esterases (FAEs) and glucuronoyl esterases (GEs) for production of phenolic fatty- and sugar- esters with antioxidant activity for cosmetic industry. OPTIBIOCAT involves a highly skilled and multidisciplinary partnership of 16 partners from 8 EU countries that cover the entire development process from genome and microbial mining to application.
Our task in this project is to identify and characterize putative candidate enzymes that have different properties and may therefore be able to produce different antioxidants. A second task is to improve the production of these enzymes to levels that are suitable for applications tests.

Project members:

Kristiina Hildén (PI), Miia Mäkelä (co-PI), Jaana Kuuskeri (Postdoc), Harri Hinkka (MSc student)

EU MC-ITN project (2013 – 2017)

The goal of a sustainable society requires the efficient use of renewable or sustainable materials and demands the development of selective new methodologies for the preparation of desirable products. In this context we require:
(i) a change from traditional stoichiometric, high energy methods that produce huge amounts of chemical waste to mild and clean catalytic processes and
(ii) a major step change in chemicals production with fossil fuels being replaced by renewable resources as chemical starter units.

The challenge to change our societies reliance for chemical production from fossil-fuel based to all-renewable resources is a challenge of enormous scale. This change must be broken down into smaller, manageable components capable of demonstrating the effectiveness of this strategy in order to showcase the transition necessary. In the SUBICAT project we will establish links with world leading experts to develop leading examples of this approach and have identified several areas where we believe collaboration can impact. Using the complementary multidisciplinary expertise from the network partners we will develop optimal catalysts for ether cleavage in 'real life samples' of lignin for maximising the potential of lignocellulose as a source of fuels and fine chemicals. The most successful catalyst systems developed will be immobilized using advanced fluids and these systems will be fully explored and optimised through collaboration within this ITN consortium.

Project members:

Kristiina Hildén (PI), Miia Mäkelä (co-PI), Mila Marinovic (PhD student)

Collaborators:
Prof. Dr. Paul Kamer, University of St Andrews, United Kingdom
Prof. Dr. Bert Weckhuysen, Utrecht University, The Netherlands
Prof. Dr. Walter Leitner, Rheinisch-Westfaelische Technische Hochschule Aachen, Germany
Prof. Ronald de Vries, Westerdijk Institute, Utrecht, The Netherlands
Prof. Dr. Johannes de Vries, University of Groningen, The Netherlands
Dr. Erik Abbenhuis, Hybrid Catalysis BV, The Netherlands

Collaborative project (2014 onwards) with The Westerdijk Institute, Utrecht, The Netherlands, the Finnish Museum of Natural History, University of Helsinki and JGI

Despite the rapidly increasing number of fungal genomes, many of these are associated with relatively well studied taxonomical clades, while other clades remain largely unaddressed. The 1000 Fungal Genome project of JGI provides an opportunity to obtain genome sequences of these poorly studies species.
In this project we will perform genomic, taxonomic and physiological studies on basidiomycete species of poorly studied clades. Depending on the results of genome annotation and growth profiling, follow up studies on selective species will be performed to delve deeper into their characteristics and compare them to other basidiomycetes.

Project members:

Otto Miettinen (PI), Kristiina Hildén (PI), Miia Mäkelä (PI), Ronald de Vries (PI)

JGI project (2014 onwards)

During wood degradation Obba rivulosa degrades lignin selectively, making it a particularly interesting fungus for studying the enzymatic machinery of white-rot. The mechanism behind lignin degradation is not understood fully, and study of selective delignifiers will be highly useful in advancing that understanding. Selective delignification is potentially a useful character in biotechnological applications.

Obba rivulosa and Gelatoporia subvermispora are both selective delignifiers. Results of this genome sequencing will be used to compare genomes and transcriptomes of these two species against each other as well as against other, non-selective white-rot fungi.

Project members:

Otto Miettinen (PI), Joseph Spatafora (PI), Kristiina Hildén (PI), Miia Mäkelä (PI), Mila Marinovic (PhD student), Igor Grigoriev (PI), David Hibbett (PI), Dan Cullen (PI), Ronald de Vries (PI), Bernard Henrissat (PI)

JGI-EMSL project (2014 onwards)

In this study we aim to dissect the diversity of isolates of the white rot basidiomycete Dichomitus squalens. This species is commonly found in North America (known as Western Red Rot that causes significant damage to Ponderosa Pine (Pinus ponderosa)) as well as around the globe. In addition D. squalens is able to grow and degrade hardwood. The collections at CBS and UH contain a range of mono- and dikaryotic strains that have already been shown to have different carbon source growth profiles. Rather than comparing specific aspects of the wood decay process, we aim to analyze the differences between a selection of the isolates in a systems biology fashion. Samples from different D. squalens isolates grown on wood will be taken at two time points and used for extraction of RNA and metabolites, for transcriptomics and metabolomics, respectively. Extracellular and intracellular proteins will be extracted from the cultures and used for proteomics and enzyme assays. These data will be supplemented by visualization of wood colonization by the isolates using a combination of Helium-ion microscopy, cryo transmission electron microscopy and (confocal) fluorescence microscopy. In addition, we aim to de novo sequence three isolates that have significantly different carbon source growth profiles and compare these to the reference sequence already generated by JGI to identify the genomic difference within the species. This approach is chosen instead of re-sequencing since the later approach would not identify regions in the genomes of the new isolates that were absent in the reference genome.

Project members:

Kristiina Hildén (PI), Miia Mäkelä (PI), Ronald de Vries (PI), Sara Casado Lopez (PhD student), Igor Grigoriev (PI), Robby Robinson (PI), Scott Baker (PI)

Collaborative project (2012 onwards)

Although the enzymatic machinery of ascomycetes and basidiomycetes for plant biomass degradation has significant differences, both phyla contain enzymes of the same families in varying combinations. In contrast, no homologs could be found in basidiomycetes for any of the ascomycete transcriptional activators involved in this process. However, similar regulatory systems appear to be present in both phyla as co-regulation of genes encoding cellulose and/or xylan degrading enzymes is observed in basidiomycetes as well as ascomycetes. This suggests that while there are no sequence-homologs of the ascomycete activators in basidiomycetes, there are functional homologs.

In this project we aim to identify the differences in the molecular mechanisms underlying plant biomass degradation in ascomycetes and basidiomycetes, focusing not only on regulatory systems, but also on specific enzyme classes and metabolic pathways.

Based on an initial discussion in 2012 and the realisation of common interest and complementary background Kristiina Hildén, Miia Mäkelä and Ronald de Vries decided to initiate a collaborative approach to perform collaborative studies between ascomycete and basidiomycete fungi as well as more detailed studies in model fungi and use this as a backbone from collaborative project proposals.

Project members:

Kristiina Hildén (PI), Miia Mäkelä (PI), Ronald de Vries (PI), Ad Wiebenga (Technician)