Synthetic yeast genomes for studying chromosomal features

Jiang, Shuangying; Zhao, Shijun; Cai, Zelin; Tang, Yuanwei; Dai, Junbiao

doi:10.1016/j.coisb.2020.09.001

Cited by 7 publications

(7 citation statements)

References 76 publications

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“…Given that the native genes could be relocated to neochromosome with little effects on function, we next asked if both the coding and regulatory sequences are able to be reconstructed with completely synthetic ones. Previously, it has been shown that E. coli with only 61 codons survives (Fredens et al, 2019) and yeast strains lacking TAG codon in one chromosome grows indistinguishable from that of wild type (Annaluru et al, 2014; Jiang et al, 2020a). In addition, synthetic promoters and terminators have been designed and showed varied activities (Curran et al, 2015; de Boer et al, 2020; Redden and Alper, 2015).…”

Section: Resultsmentioning

confidence: 99%

“…However, we observed several single nucleotide substitutions and insertions in the neochromosome (Figure S1H-1I) which do not affect the function of each essential gene (see below), and therefore, no further correction was performed. Interestingly, we found that the telomeric TG repeats, in both neochromosomes, significantly expanded (Figure S1J-1K), indicating the TeSS end grew a new telomere successfully, as designed (Jiang et al, 2020a;Richardson et al, 2017).…”

Section: Construction Of Neochromosomes Carrying Essential Genes From...mentioning

confidence: 91%

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Reconstruct a eukaryotic chromosome arm by de novo design and synthesis

Jiang¹,

Luo

Kang³

et al. 2022

Preprint

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The genome of an organism is inherited from its ancestor and keeps evolving over time, however, how much the current version could be altered remains unknown. Here, we use the left arm of chromosome XII (chrXIIL) as an example to probe the genome plasticity in Saccharomyces cerevisiae. A neochromosome was designed to harbor originally dispersed genes. The essentiality of sequences in chrXIIL was dissected by targeted DNA removal, chromosome truncation and random deletion. Notably, 12 genes were sufficient for survival, while 25 genes are required to retain robust fitness. Next, we demonstrated these genes could be reconstructed using synthetic regulatory sequences and recoded open-reading frames with "one-amino-acid-one-codon" strategy. Finally, we built a neochromsome, which could substitute for chrXIIL for cell viability, with these reconstructed genes. Our work not only highlights the high plasticity of yeast genome, but also illustrates the possibility of making functional chromosomes with completely artificial sequences.

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Section: Resultsmentioning

confidence: 99%

Section: Construction Of Neochromosomes Carrying Essential Genes From...mentioning

confidence: 91%

Reconstruct a eukaryotic chromosome arm by de novo design and synthesis

Jiang¹,

Luo

Kang³

et al. 2022

Preprint

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“…Assembling large fragments of genomic DNA in vitro remains a technical challenge for synthetic biology. The three most common methods currently used for this process are artificial synthesis, fosmid library construction, and TAR cloning, which have successfully been used to assemble 770 kb, 35.6 kb, and 300 kb fragments, respectively (Jiang et al 2020, Kouprina and Larionov 2006, Liu et al 2017). Direct artificial synthesis in vitro can be used for codon optimization.…”

Section: Discussionmentioning

confidence: 99%

“…Direct artificial synthesis in vitro can be used for codon optimization. For example, the yeast chromosome (Sc2.0 Project) (12 Mb) had been over half synthesized in vitro using artificial synthesis technology (Jiang et al 2020). However, the high cost of this technique limits its application.…”

Section: Discussionmentioning

confidence: 99%

Reconstitution and Expression of mcy Gene Cluster in The Model Cyanobacterium Synechococcus 7942 Reveals a Roll of MC-LR in Cell Division

Zheng

Xue

Chen

et al. 2022

Preprint

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Cyanobacterial blooms pose a serious threat to public health due to the presence of cyanotoxins. The most common cyanotoxins, microcystins (MCs), can cause acute poisoning at high concentrations and hepatocellular carcinoma following chronic exposure. Among all MC variants, MC-LR produced by Microcystis aeruginosa PCC 7806 is the most common toxic MC. Although the biosynthetic pathway for MC-LR has been proposed, experimental support of this pathway is lacking. In an effort to experimentally validate this pathway, we expressed the 55 kb microcystin biosynthetic gene cluster (mcy cluster) (mcyA-J) and produced MC-LR in the model cyanobacterium Synechococcus 7942. We designed and constructed the strong bidirectional promoter biPpsbA2 between mcyA and mcyD, reassembled the mcy cluster in yeast by transformation-associated recombination (TAR cloning), transformed the gene cluster into the NSII site of Synechococcus 7942, and successfully expressed MC-LR at a level of 0.006-0.018 fg cell-1 day-1. The expression of MC-LR led to abnormal cell division and the filamentation of Synechococcus 7942 cells, further analysis proved a role of MC-LR in functional assembly of the cell division protein FtsZ, by competing its GTP binding site. These results represent the first synthetic biological expression of the mcy cluster and the autotrophic production of MC-LR in a photosynthetic model organism, which lays the foundation for resolving the MC biosynthesis pathway. The suggested role of MC-LR in cell division reveals a mechanism of how blooming cyanobacteria gain a competitive edge over their non-blooming counterparts.

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“…When synthesizing viral and bacterial genomes, an attempt to synthesize eukaryotic genomes, called the Synthetic Yeast Genome Project (Sc2.0), was initiated, an effort that is only now nearing completion (Jiang et al, 2020a;Luo et al, 2020;Luo et al, 2018;Zhang et al, 2020b). Sc2.0 aims to synthesize the entire genome of Saccharomyces cerevisiae (~12 Mb, divided into 16 chromosomes), with numerous changes to explore fundamental biological questions about genome function.…”

Section: Brief History Of Genome Synthesismentioning

confidence: 99%

Enabling technology and core theory of synthetic biology

Zhang

Liu

Dai

et al. 2023

Sci. China Life Sci.

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Synthetic biology provides a new paradigm for life science research (“build to learn”) and opens the future journey of biotechnology (“build to use”). Here, we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology, including synthesis and assembly of a genome, DNA storage, gene editing, molecular evolution and de novo design of function proteins, cell and gene circuit engineering, cell-free synthetic biology, artificial intelligence (AI)-aided synthetic biology, as well as biofoundries. We also introduce the concept of quantitative synthetic biology, which is guiding synthetic biology towards increased accuracy and predictability or the real rational design. We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.

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Synthetic yeast genomes for studying chromosomal features

Cited by 7 publications

References 76 publications

Reconstruct a eukaryotic chromosome arm by de novo design and synthesis

Reconstruct a eukaryotic chromosome arm by de novo design and synthesis

Reconstitution and Expression of mcy Gene Cluster in The Model Cyanobacterium Synechococcus 7942 Reveals a Roll of MC-LR in Cell Division

Enabling technology and core theory of synthetic biology

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