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Paul Hudson

Paul Hudson
KTH Royal Institute of Technology

Research Interests

We are pursuing applied and fundamental research into the metabolism of autotrophic (CO2-fixing) bacteria. Most of our expertise is on photosynthetic cyanobacteria though we are also exploring lithoautotrophic, H2-consuming bacteria. We aim to engineer new strains that can efficiently convert CO2 to chemicals, in particular biofuels. This often involves significant modifications to the native metabolism. One area of research is to quantify the energy investments of the autotrophic cell under different conditions, such as its metabolome, proteome, and translatome. A second arm is to use this information to guide metabolic engineering. For example, we can design and insert new metabolic pathways to biofuel that are better matched with the host metabolism. Our lab uses genome-scale modeling, systems biology, CRISPR/Cas-based gene regulation, and adaptive evolution.

More information about my group:

Group members

Paul Hudson (Associate Professor, PI)
Lun Yao (Postdoc)
Michael Jahn (Postdoc)
Ivana Cengic (Graduate student)
Kiyan Shabestary (Graduate student)
Markus Janasch (Graduate student)
Johannes Asplund-Samuelsson (Graduate student)
Jan Karlsen (Graduate student)
Johann Bauerfeind (Visiting researcher)

Key publications

Jahn M, Vialas V, Karlsen J, Maddalo G, Edfors F, Forsström B, Uhlen M, Käll L, Hudson EP*.  Growth of Cyanobacteria Is Constrained by the Abundance of Light and Carbon Assimilation Proteins (2018). Cell Reports 25. P478-486.
The proteome of cyanobacteria grown under different conditions was investigated by shotgun proteomics. A resource-allocation model showed that proteins involved in carbon fixation are not optimally regulated. This paper will be an important resource for basic cyanobacteria research

Karlsen J+, Asplund-Samuelsson J+, Thomas Q, Jahn M, Hudson EP*. Ribosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon Starvation (2018). mSystems 3. P1-12
First genome-wide ribosome profiling report of cyanobacteria. Ribosome profiling allows estimation of translation rate of each gene. We found that during low CO2 conditions, several genes had increased translation efficiency (#ribosomes per mRNA). Also, we saw evidence that ribosomes “hibernate” in the 5’UTR of select genes during carbon starvation. Suggests a type of ribosome sequestration.

Asplund-Samuelsson J, Janasch, M, Hudson EP*Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential (2018). Metabolic Engineering 45 223-236
We developed the POPPY software that creates and analyzes thousands of potential metabolic pathways to different biofuels and chemicals. POPPY evaluates the potential of each pathway in terms of thermodynamic driving force that the host cyanobacteria can impart. Compared to E. coli. Will be useful in metabolic engineering.

Yao L, Cengic I, Anfelt J, Hudson EP*. Multiple gene repression in cyanobacteria using CRISPRi.(2015) ACS Synthetic Biology 5, 207−212
First demonstration of CRISPR interference in cyanobacteria. We optimized this gene-repression tool so that it was inducible and could be multiplexed. In the following years, we have used this tool to alter the native cyanobacteria metabolism and divert carbon to biofuels.

Anfelt J, Kaczmarzyk D, Shabestary K, Renberg B, Rockberg R, Nielsen J, Uhlen M, Hudson EP*. Genetic and nutrient modulation of acetyl-CoA levels in Synechocystis for n-butanol production.(2015) Microbial Cell Factories 14 (1) 1-12
We show that a heterologous phosphoketolase enzyme can improve butanol production in cyanobacteria. This enzyme enables a shortcut from the Calvin cycle to acetyl-CoA, an important building block for chemicals and fuels such as butanol.

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