AsianScientist (Mar. 17, 2017) – A team of researchers led by Professor Yuan Ying-Jin from Tianjin University (TJU) has created two synthetic yeast chromosomes, synV and synX. Their results, part of an international collaboration which released a total of five synthetic chromosomes, have been published in two papers in Science.
The publications are part of the effort to chemically synthesize the designer yeast genome (Sc 2.0), in collaboration with NYU and John Hopkins in the US, Tsinghua University, BGI-Shenzhen in China, the University of Edinburgh in the UK, and the Institut Pasteur and Sorbonne Universités in France, as well as industry partners.
During the synthesis of the designer chromosome SynV, the “Build-A-Genome (BAG) China” course played a crucial role. In this innovative educational course, sixty-one students participated in the construction of building blocks and minichunks for synthetic chromosome V, although the majority of the students had little or no experience in DNA synthesis before.
Through the BAG training, they developed advanced experimental skills and obtained first-hand experiences essential to promote their trouble-shooting ability. Several students even became specialists in DNA synthesis and constructed DNA segments with complicated sequences.
“The goal of the BAG course at TJU is to train the next generation of synthetic biologists with a global perspective, innovative spirit, and practical abilities,” said Yuan.
This goal was reached during the process of the Sc2.0 project, linking the course to practical scientific work. The first authors of the synV and synX articles, PhD candidates from Yuan’s team, Xie Zexiong and Wu Yi, were both participants of the BAG course.
To construct a synthetic eukaryotic chromosome perfectly matching the designer sequence, the research team had to overcome significant obstacles. Randomly distributed mutations and other unpredictable events corrected in the designed sequence and performed with a similar fitness compared with native strains.
Certain genetic alternations in the chromosome would affect cell fitness and cause “bugs”; debugging is therefore imperative for successfully building a synthetic genome. The malfunction of synthetic genomes remains one of the most common obstacles, as it is difficult to uncover the underlying reasons.
In a bid to tackle this problem, TJU developed a highly efficient debugging method called pooled PCRTag mapping (PoPM) by using a pooling strategy and the Sc2.0 PCRTag system, which is generalized to watermarked synthetic chromosomes. PoPM is a powerful tool for synthetic yeast genome debugging which accelerated the progress of the whole Sc2.0 project.
“During synX assembly, the PoPM method was applied to identify and eliminate genetic alternations that affect cell fitness, sequences we refer to as ‘bugs,’ and several details of yeast biology were uncovered by debugging. PoPM represents an efficient strategy for phenotype-genotype mapping which will be applicable for expanding understanding of yeast genomic and cellular functions,” according to Wu.
“Together with my colleagues, I spent almost 18 months mapping the bugs and correcting errors that led to the yeast being non-viable or having growth defects,” Xie added.
Aiming to provide a model with which to study human ring chromosome disorders, the linear synV was converted to a ring synthetic chromosome, and it can extend genome design principles, as well as providing an insight into genomic rearrangement and ring chromosome evolution.
The articles can be found at:
Xie et al. (2017) “Perfect” Designer Chromosome V and Behavior of a Ring Derivative.
Wu et al. (2017) Bug Mapping and Fitness Testing of Chemically Synthesized Chromosome X.
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Source: Tianjin University; Photo: Shutterstock.
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