Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond

Leslie A Mitchell; Ann Wang; Giovanni Stracquadanio; Zheng Kuang; Xuya Wang; Kun Yang; Sarah Richardson; J Andrew Martin; Yu Zhao; Roy Walker; Yisha Luo; Hongjiu Dai; Kang Dong; Zuojian Tang; Yanling Yang; Yizhi Cai; Adriana Heguy; Beatrix Ueberheide; David Fenyö; Junbiao Dai; Joel S Bader; Jef D Boeke

doi:10.1126/science.aaf4831

Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond

Leslie A Mitchell, Ann Wang, Giovanni Stracquadanio, Zheng Kuang, Xuya Wang, Kun Yang, Sarah Richardson, J Andrew Martin, Yu Zhao, Roy Walker, Yisha Luo, Hongjiu Dai, Kang Dong, Zuojian Tang, Yanling Yang, Yizhi Cai, Adriana Heguy, Beatrix Ueberheide, David Fenyö, Junbiao DaiJoel S Bader, Jef D Boeke

Research output: Contribution to journal › Article › peer-review

Abstract

We describe design, rapid assembly, and characterization of synthetic yeast Sc2.0 chromosome VI (synVI). A mitochondrial defect in the synVI strain mapped to synonymous coding changes within PRE4 (YFR050C), encoding an essential proteasome subunit; Sc2.0 coding changes reduced Pre4 protein accumulation by half. Completing Sc2.0 specifies consolidation of 16 synthetic chromosomes into a single strain. We investigated phenotypic, transcriptional, and proteomewide consequences of Sc2.0 chromosome consolidation in poly-synthetic strains. Another "bug" was discovered through proteomic analysis, associated with alteration of the HIS2 transcription start due to transfer RNA deletion and loxPsym site insertion. Despite extensive genetic alterations across 6% of the genome, no major global changes were detected in the poly-synthetic strain "omics" analyses. This work sets the stage for completion of a designer, synthetic eukaryotic genome.

Original language	English
Article number	eaaf4831
Journal	Science
Volume	355
Issue number	6329
DOIs	https://doi.org/10.1126/science.aaf4831
Publication status	Published - 10 Mar 2017

Keywords

Journal Article
Research Support, Non-U.S. Gov't

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10.1126/science.aaf4831

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Mitchell, L. A., Wang, A., Stracquadanio, G., Kuang, Z., Wang, X., Yang, K., Richardson, S., Martin, J. A., Zhao, Y., Walker, R., Luo, Y., Dai, H., Dong, K., Tang, Z., Yang, Y., Cai, Y., Heguy, A., Ueberheide, B., Fenyö, D., ... Boeke, J. D. (2017). Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science, 355(6329), Article eaaf4831. https://doi.org/10.1126/science.aaf4831

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title = "Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond",

abstract = "We describe design, rapid assembly, and characterization of synthetic yeast Sc2.0 chromosome VI (synVI). A mitochondrial defect in the synVI strain mapped to synonymous coding changes within PRE4 (YFR050C), encoding an essential proteasome subunit; Sc2.0 coding changes reduced Pre4 protein accumulation by half. Completing Sc2.0 specifies consolidation of 16 synthetic chromosomes into a single strain. We investigated phenotypic, transcriptional, and proteomewide consequences of Sc2.0 chromosome consolidation in poly-synthetic strains. Another {"}bug{"} was discovered through proteomic analysis, associated with alteration of the HIS2 transcription start due to transfer RNA deletion and loxPsym site insertion. Despite extensive genetic alterations across 6% of the genome, no major global changes were detected in the poly-synthetic strain {"}omics{"} analyses. This work sets the stage for completion of a designer, synthetic eukaryotic genome.",

keywords = "Journal Article, Research Support, Non-U.S. Gov't",

author = "Mitchell, {Leslie A} and Ann Wang and Giovanni Stracquadanio and Zheng Kuang and Xuya Wang and Kun Yang and Sarah Richardson and Martin, {J Andrew} and Yu Zhao and Roy Walker and Yisha Luo and Hongjiu Dai and Kang Dong and Zuojian Tang and Yanling Yang and Yizhi Cai and Adriana Heguy and Beatrix Ueberheide and David Feny{\"o} and Junbiao Dai and Bader, {Joel S} and Boeke, {Jef D}",

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month = mar,

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doi = "10.1126/science.aaf4831",

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Mitchell, LA, Wang, A, Stracquadanio, G, Kuang, Z, Wang, X, Yang, K, Richardson, S, Martin, JA, Zhao, Y, Walker, R, Luo, Y, Dai, H, Dong, K, Tang, Z, Yang, Y, Cai, Y, Heguy, A, Ueberheide, B, Fenyö, D, Dai, J, Bader, JS & Boeke, JD 2017, 'Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond', Science, vol. 355, no. 6329, eaaf4831. https://doi.org/10.1126/science.aaf4831

TY - JOUR

T1 - Synthesis, debugging, and effects of synthetic chromosome consolidation

T2 - synVI and beyond

AU - Mitchell, Leslie A

AU - Wang, Ann

AU - Stracquadanio, Giovanni

AU - Kuang, Zheng

AU - Wang, Xuya

AU - Yang, Kun

AU - Richardson, Sarah

AU - Martin, J Andrew

AU - Zhao, Yu

AU - Walker, Roy

AU - Luo, Yisha

AU - Dai, Hongjiu

AU - Dong, Kang

AU - Tang, Zuojian

AU - Yang, Yanling

AU - Cai, Yizhi

AU - Heguy, Adriana

AU - Ueberheide, Beatrix

AU - Fenyö, David

AU - Dai, Junbiao

AU - Bader, Joel S

AU - Boeke, Jef D

PY - 2017/3/10

Y1 - 2017/3/10

N2 - We describe design, rapid assembly, and characterization of synthetic yeast Sc2.0 chromosome VI (synVI). A mitochondrial defect in the synVI strain mapped to synonymous coding changes within PRE4 (YFR050C), encoding an essential proteasome subunit; Sc2.0 coding changes reduced Pre4 protein accumulation by half. Completing Sc2.0 specifies consolidation of 16 synthetic chromosomes into a single strain. We investigated phenotypic, transcriptional, and proteomewide consequences of Sc2.0 chromosome consolidation in poly-synthetic strains. Another "bug" was discovered through proteomic analysis, associated with alteration of the HIS2 transcription start due to transfer RNA deletion and loxPsym site insertion. Despite extensive genetic alterations across 6% of the genome, no major global changes were detected in the poly-synthetic strain "omics" analyses. This work sets the stage for completion of a designer, synthetic eukaryotic genome.

AB - We describe design, rapid assembly, and characterization of synthetic yeast Sc2.0 chromosome VI (synVI). A mitochondrial defect in the synVI strain mapped to synonymous coding changes within PRE4 (YFR050C), encoding an essential proteasome subunit; Sc2.0 coding changes reduced Pre4 protein accumulation by half. Completing Sc2.0 specifies consolidation of 16 synthetic chromosomes into a single strain. We investigated phenotypic, transcriptional, and proteomewide consequences of Sc2.0 chromosome consolidation in poly-synthetic strains. Another "bug" was discovered through proteomic analysis, associated with alteration of the HIS2 transcription start due to transfer RNA deletion and loxPsym site insertion. Despite extensive genetic alterations across 6% of the genome, no major global changes were detected in the poly-synthetic strain "omics" analyses. This work sets the stage for completion of a designer, synthetic eukaryotic genome.

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

UR - http://repository.essex.ac.uk/19587/

U2 - 10.1126/science.aaf4831

DO - 10.1126/science.aaf4831

M3 - Article

C2 - 28280154

SN - 0036-8075

VL - 355

JO - Science

JF - Science

IS - 6329

M1 - eaaf4831

ER -

Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond

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