Developing a 3rd-generation genome pipeline to uncover novel metabolic activities in Galdieria: a focus on secreted enzyme activities

Galdieria is a red alga that exhibits wide metabolic versatility and displays enormous capacity to thrive at highly acidic conditions (down to pH 0) and temperatures above 55 degrees C, which is the limit of eukaryotic life. Its extremophile lifestyle makes it a fascinating organism to study from both a mechanistic viewpoint and to find novel species with properties that have industrial biotechnological (IB) applications. To exploit Galdieria, one must understand the constellation of diversity in metabolic capacity. We have assembled a sub-collection of lines that are strikingly different in metabolic capacity. In investigating the potential of third-generation genomics to provide rapid, affordable long-read capacity, this project develops nanopore genome sequencing to define Galdieria strains that have the greatest IB utility. In phase 1 the student will use short-read genome-sequencing as a starting point to further develop nanopore, third-generation genomics. Here it is expected that dozens of complete Galdieria genomes would be produced, and the extent of wide-scale phylogenomic diversity would be appraised. From there, full genome annotations lead to descriptions of metabolic capacities in these diverse Galdieria. In phase 2, informatic descriptions will be made for excreted enzymes that can function under very low pH and elevated temperature. From the large range of such classified enzymes, searches will be used to identify encoded enzymes, such as xylanases and other cellulases, proteases and oxidative enzymes. In phase 3, the student will perform enzyme production and characterisation. By definition, these enzymes must function at high temperature and very low pH and could be the most resistant enzymes ever isolated from a eukaryote. Taken together this project provides direct links between mechanistic biology of an interesting extremophile, with biochemical coupling to genomic-based informatics, to define exciting translational potentials for enzyme discovery.