BIOLOGY OF MOLECULES, CELLS AND TISSUES
‘Biomolecular networks within and between cells’
Professor at University TUD – Department of Biotechnology
Jack Pronk (1963) is professor in Industrial Microbiology and leads the Department of Biotechnology at TU Delft. His research aims to understand and improve microbial performance in industrial processes and integrates quantitative physiology, genomics, synthetic biology and evolutionary engineering. Jack (co-)authored 270 scientific publications and is an inventor on 25 patent applications. From 2003-2014, Jack led the Kluyver Centre for Genomics of Industrial Fermentation, a Netherlands-based Centre of Excellence. Results from research that he and his colleagues and students performed on engineering of yeast for biofuels production from agricultural waste streams and for increased product yields on sugar feedstocks are applied at industrial scale. Jack loves to teach and coach students and in 2015 he was awarded the TU Delft Best Professor Award (“Leermeesterprijs”). In 2018 Jack received the International Metabolic Engineering Award and in 2019 the Stevin Prize, the highest distinction for application-inspired research in the Netherlands. Read more
Modifying the metabolic network of yeast for efficient production of fuels and chemicals
Bakers’ yeast (Saccharomyces cerevisiae), a ‘jack of all trades’ in biotechnology, is used in industry to convert renewable, sugar-containing feedstocks to products ranging from car fuels to pharmaceuticals. Spectacular developments in Cas9-mediated genome editing, in vivo DNA assembly and genome resequencing now enable single-step, accurate introduction of entire biochemical pathways into S. cerevisiae. In our research, we explore strategies for modifying the native metabolic network of this yeast to enable optimal integration of new metabolic pathways and cost-effective product formation. For example, enabling synthesis of cofactors that do not naturally occur in S. cerevisiae, helped expand the range of non-native pathways that can be functionally expressed in this yeast. However, the mere presence of a functional product-formation or substrate-consumption pathway does not guarantee economically related product titers, rates of product formation and product yields on the (sugar) substrate. In practice, achieving these objectives requires extensive rewiring of the native yeast metabolic network into which the new pathways become embedded, for example by optimizing the supply of product precursors that are derived from central carbon metabolism. Even for the well-established yeast-based production of ethanol, at 100 Mton·year-1 the largest-volume product of industrial biotechnology, engineering of redox-cofactor coupling enabled higher product yields on sugar without compromising conversion rates.
Professor at the University of California, Riverside, USA – Center for Plant Cell Biology
Julia Bailey-Serres is professor of genetics, director of the Center for Plant Cell Biology, and a member of the Institute for Integrative Genome Biology at the University of California, Riverside. Since 2008 she is also attached to Utrecht University, as professor of Molecular Physiology of Rice.
Julia is being recognized for her role in the discovery and characterization of a gene that allows rice to survive under water. That Sub1A gene has subsequently been introduced through breeding by the International Rice Research Institute and others, creating flood-tolerant rice varieties that are grown by more than five million farmers in flood-prone areas of Asia.
The Bailey-Serres group performs translational plant biology from gene to field. They aim to harness genetic mechanisms that provide climate change resilience to crops, particularly flooding, drought and nutrient stress resilience. They work from the single cell to whole plant level. Their studies have defined
mechanisms of low oxygen sensing and post-transcriptional gene regulation, from the epigenome to the “mRNPome” and translatome. This knowledge is of importance to efforts that seek to stabilize crop yields as Earth’s population grows, arable land decreases, and climatic patterns change. Read more
Plastic networks of root cell populations control climate-resilience traits
Future food security requires improvement of crop resilience to climate variability, including floods and droughts. Pathways to climate resilient crops include harnessing natural genetic variants that aid survival and the targeted editing of genomes. Since growth environments can fluctuate during a single day and over the life cycle, resilience mechanisms that are temporal and have minimal negative impact on growth are highly desirable. In rice, the survival of water extremes involves changes in undifferentiated and differentiated cells of roots that influence metabolism and morphology. Even with single-cell sequencing technologies, it is challenging to monitor how environmental signals activate or perturb gene regulatory networks in specific sub-populations of cells, such as those undergoing rapid cell division or becoming the water-transporting xylem. We have used methods applicable to diverse multicellular organisms to monitor dynamics in chromatin and translated mRNAs in specific populations of cells to better understand transient and determinant responses to flooding and water deficit resilience. The data uncover reversible and determinant gene regulatory networks controlling cell division, root architecture and adaptive changes in cell anatomy of roots as well as ubiquitous acclimation responses. These data can guide genome editing and recognition of relevant non-coding sequence variants to aid rice improvement. Funded by the US National Science Foundation (IOS-1810468; IOS-1856749).