Understanding - Transcriptional regulation

Sigma(σ)-factors are responsible for recognising cis-acting sequence elements in the promoter regions. They orchestrate the global pattern of initiation, or repression, of promoter-specific transcription. They are the key regulatory elements that control the different classes of promoters in response to intra- or extracellular stimuli. Despite their key role, the information on the cis-acting DNA sequence elements in the promoter regions is far from resolved for each the σ-factors in bacteria.

We are using both in vivo and microfluidics-based in vitro transcription methods to decode σ-factor-specific cis-acting DNA sequences in bacteria.

Controlling - Artificial gene expression engineering

We develop platforms that enable the design and fabrication of context-dependent artificial 5' regulatory sequences in a wide range of microorganisms.

The microorganisms we work with are:

Gram-negative bacteria

• Escherichia coli, Pseudomonas putida, Synechococcus sp., Thermus thermophilus, Vibrio natriegens

Gram-positive bacteria

• Bacillus subtilis, Corynebacterium glutamicum, Streptomyces albus, Streptomyces lividans

Yeast

• Saccharomyces cerevisiae

Collaborations

• Anil Wipat, Newcastle University, School of Computing, England.
  Collaboration in promoter engineering in B. subtilis.

• Bjørn T. Stokke, Deparment of Physics, NTNU.
  Collaboration in microfluidics.

• Florian Hollfelder, Department of Biochemistry, University of Cambridge, England.
  Collaboration in cell lysis in microdroplets and alternative bacterial hosts.

• Jörn Kalinowski, Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Germany.
  Collaboration in DNA and RNA sequencing.

• Magnar Bjørås, Department of Clinical and Molecular Medicine, NTNU. Collaboration in enzyme production, gene expression and pathway engineering.

• Rita S. Dias, Deparment of Physics, NTNU.
  Collaboration in transcription factor target site search and gene regulation, and in vitro DNA condensation by bridging proteins.

• Victor de Lorenzo, Systems Biology Department, National Centre of Biotechnology, Spain.
  Collaboration in non-functional DNA.

• Victoria Shingler, Department of Molecular Biology, University of Umeå, Umeå, Sweden.
  Collaboration in in vitro transcription.

Ongoing projects

• Horizon Europe, EU. Innovative Tools for Sustainable Exploration of Marine Microbiomes: Towards A Circular Blue Bioeconomy and Healthier Marine Environments.

• RCN-FRIPRO, Norway. An interdisciplinary data-driven approach to resolve sigma-factor-specific promoter dependency in bacteria.

Finalised projects

• H2020, EU. Advanced toolbox for rapid and cost-effective functional metagenomic screening – microbiology meets microfluidics.

• EPSRC, UK. Design the Future 2: Thinking Soils: Engineered bacteria as computational agents in the design and manufacture of new materials and structures.

• RCN-FORNY2020, Norway. Fast-X-Press

• NTNU-Discovery, Norway. SUPERAP – fast track for efficient protein production in novel hosts.