Bug mapping and fitness testing of chemically synthesized chromosome X
Authors: Wu Yi , Li Bing-Zhi , Zhao Meng , Mitchell Leslie A. , Xie Ze-Xiong , Lin Qiu-Hui , Wang Xia , Xiao Wen-Hai , Wang Ying , Zhou Xiao , Liu Hong , Li Xia , Ding Ming-Zhu , Liu Duo , Zhang Lu , Liu Bao-Li , Wu Xiao-Le , Li Fei-Fei , Dong Xiu-Tao , Jia Bin , Zhang Wen-Zheng , Jiang Guo-Zhen , Liu Yue , Bai Xue , Song Tian-Qing , Chen Yan , Zhou Si-Jie , Zhu Rui-Ying , Gao Feng , Kuang Zheng , Wang Xuya , Shen Michael , Yang Kun , Stracquadanio Giovanni , Richardson Sarah M. , Lin Yicong , Wang Lihui , Walker Roy , Luo Yisha , Ma Ping-Sheng , Yang Huanming , Cai Yizhi , Dai Junbiao , Bader Joel S. , Boeke Jef D. , Yuan Ying-Jin 
Published: July 2017

INTRODUCTION

Design and construction of an extensively modified yeast genome is a direct means to interrogate the integrity, comprehensiveness, and accuracy of the knowledge amassed by the yeast community to date. The international synthetic yeast genome project (Sc2.0) aims to build an entirely designer, synthetic
Saccharomyces cerevisiae
genome. The synthetic genome is designed to increase genome stability and genetic flexibility while maintaining cell fitness near that of the wild type. A major challenge for a genome synthesis lies in identifying and eliminating fitness-reducing sequence variants referred to as “bugs.”

RATIONALE
Debugging is imperative for successfully building a fit strain encoding a synthetic genome. However, it is time-consuming and laborious to replace wild-type genes and measure strain fitness systematically. The Sc2.0 PCRTag system, which specifies recoded sequences within open reading frames (ORFs), is designed to distinguish synthetic from wild-type DNA in a simple polymerase chain reaction (PCR) assay. This system provides an opportunity to efficiently map bugs to the related genes by using a pooling strategy and subsequently correct them. Further, as we identify bugs in designer sequences, we will identify gaps in our knowledge and gain a deeper understanding of genome biology, allowing refinement of future design strategies.

RESULTS

We chemically synthesized yeast chromosome X, synX, designed to be 707,459 base pairs. A high-throughput mapping strategy called pooled PCRTag mapping (PoPM) was developed to identify unexpected bugs during chromosome assembly. With this method, the genotypes of pools of colonies with normal or defective fitness are assessed by PCRTag analysis. The PoPM method exploits the patchwork structure of synthetic and wild-type sequences observed in the majority of putative synthetic DNA integrants or meiotic progeny derived from synthetic/wild-type strain backcross. PCRTag analysis with both synthetic and wild-type specific primers, carried out with genomic DNA extracted from the two pools of clones (normal fitness versus a specific growth defect), can be used to identify regions of synthetic DNA missing from the normal fitness pool and, analogously, sections of wild-type DNA absent from the specific growth-defect pool. In this way, the defect can be efficiently mapped to a very small overlapping region, and subsequent systematic analysis of designed changes in that region can be used to identify the bug. Several bugs were identified and corrected, including a growth defect mapping to a specific synonymously recoded PCRTag sequence in the essential
FIP1
ORF and the effect of introducing a loxPsym site that unexpectedly altered the the promoter function of a nearby gene,
ATP2.
In addition, meiotic crossover was employed to repair the massive duplications and rearrangements in the synthetic chromosome. The debugged synX strain exhibited high fitness under a variety of conditions tested and in competitive growth with the wild-type strain.

CONCLUSION
Synthetic yeast chromosome X was chemically synthesized from scratch, a rigorous, incremental step toward complete synthesis of the whole yeast genome. Thousands of designer modifications in synX revealed extensive flexibility of the yeast genome. We developed an efficient mapping method, PoPM, to identify bugs during genome synthesis, generalizable to any watermarked synthetic chromosome, and several details of yeast biology were uncovered by debugging. Considering the numerous gene-associated PCRTags available in the synthetic chromosomes, PoPM may represent a powerful tool to map interesting phenotypes of mutated synthetic strains or even mutated wild-type strains to the relevant genes. It may also be useful to study yeast genetic interactions when an unexpected phenotype is generated by alterations in two or more genes, substantially expanding understanding of yeast genomic and cellular functions. The PoPM method is also likely to be useful for mapping phenotype(s) resulting from the genome SCRaMbLE system.

Characterization of synX and debugging by pooled PCRTag mapping.

(
Top
) Design overview of synthetic chromosome X. (
Bottom
) Flow diagram of pooled PCRTag mapping (PoPM).