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

Galdieria是一种红色的植物，具有广泛的代谢多样性，并在高酸性条件（低至pH 0）和高于55摄氏度的温度下（这是真核生物的极限）表现出巨大的生长能力。它的极端生活方式使其成为一种迷人的生物体，从机械学的角度进行研究，并发现具有工业生物技术（IB）应用特性的新物种。要开发Galdieria，必须了解代谢能力的多样性。我们已经组装了一个子集合的线是惊人的不同的代谢能力。在研究第三代基因组学提供快速，负担得起的长读能力的潜力时，该项目开发了纳米孔基因组测序，以确定具有最大IB效用的Galdieria菌株。在第一阶段，学生将使用短读基因组测序作为起点，进一步开发纳米孔，第三代基因组学。在这里，预计将产生数十个完整的Galdieria基因组，并评估大规模Galdieria基因组多样性的程度。从那里，全基因组注释导致这些不同Galdieria的代谢能力的描述。在第2阶段，将对可在极低pH值和高温下发挥作用的排泄酶进行信息描述。从大范围的这种分类的酶中，搜索将用于鉴定编码的酶，例如木聚糖酶和其他纤维素酶、蛋白酶和氧化酶。在第3阶段，学生将进行酶的生产和表征。根据定义，这些酶必须在高温和非常低的pH值下起作用，并且可能是从真核生物中分离出的最具抗性的酶。总之，该项目提供了一个有趣的极端微生物的机械生物学之间的直接联系，与生物化学耦合到基于基因组的信息学，定义酶的发现令人兴奋的翻译潜力。

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.