Mariëlle van Kooten

All Publications

• The transcriptional landscape of a rewritten bacterial genome reveals control elements and genome design principles NATURE COMMUNICATIONS van Kooten, M. M., Scheidegger, C. A., Christen, M., Christen, B. 2021; 12 (1): 3053

  Abstract

  Sequence rewriting enables low-cost genome synthesis and the design of biological systems with orthogonal genetic codes. The error-free, robust rewriting of nucleotide sequences can be achieved with a complete annotation of gene regulatory elements. Here, we compare transcription in Caulobacter crescentus to transcription from plasmid-borne segments of the synthesized genome of C. ethensis 2.0. This rewritten derivative contains an extensive amount of supposedly neutral mutations, including 123'562 synonymous codon changes. The transcriptional landscape refines 60 promoter annotations, exposes 18 termination elements and links extensive transcription throughout the synthesized genome to the unintentional introduction of sigma factor binding motifs. We reveal translational regulation for 20 CDS and uncover an essential translational regulatory element for the expression of ribosomal protein RplS. The annotation of gene regulatory elements allowed us to formulate design principles that improve design schemes for synthesized DNA, en route to a bright future of iteration-free programming of biological systems.

  View details for DOI 10.1038/s41467-021-23362-y

  View details for Web of Science ID 000658769900005

  View details for PubMedID 34031412

  View details for PubMedCentralID PMC8144410