Exploration of gene functions and library construction for engineering strains from a synthetic biology perspective

ZHANG Yiqing; LIU Gaowen

doi:10.12211/2096-8280.2024-079

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Exploration of gene functions and library construction for engineering strains from a synthetic biology perspective

Invited Review | 更新时间：2025-07-07

- Exploration of gene functions and library construction for engineering strains from a synthetic biology perspective
- Synthetic Biology Journal Vol. 6, Issue 3, Pages: 685-700(2025)
- 作者机构：
  
  1.中国科学院深圳先进技术研究院，深圳合成生物学创新研究院，深圳合成基因组学重点实验室，广东省合成基因组学重点实验室，定量合成生物学重点实验室，广东深圳 518055
  2.中国科学院大学，北京 100049
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2024-079
  CLC： Q812
- Received：11 November 2024，
  
  Revised：2025-02-20，
  
  Published：30 June 2025
- 稿件说明：
移动端阅览
章益蜻，刘高雯. 合成生物学视角下的基因功能探索与酵母工程菌株文库构建［J］. 合成生物学， 2025， 6（3）： 685-700

ZHANG Yiqing， LIU Gaowen. Exploration of gene functions and library construction for engineering strains from a synthetic biology perspective［J］. Synthetic Biology Journal， 2025， 6（3）： 685-700
章益蜻，刘高雯. 合成生物学视角下的基因功能探索与酵母工程菌株文库构建［J］. 合成生物学， 2025， 6（3）： 685-700 DOI： 10.12211/2096-8280.2024-079.

ZHANG Yiqing， LIU Gaowen. Exploration of gene functions and library construction for engineering strains from a synthetic biology perspective［J］. Synthetic Biology Journal， 2025， 6（3）： 685-700 DOI： 10.12211/2096-8280.2024-079.

摘要

合成生物学作为一门通过设计、构建和改造生物系统来实现其特定功能的学科，被广泛应用于生物制造、环境保护和药物合成等领域。基因功能的系统性探索和工程菌株文库的构建是推动合成生物学发展的重要手段。本文重点介绍了不同酵母文库在合成生物学中的构建方法及其应用前景。随着基因组测序和高通量技术的快速进展，酿酒酵母和裂殖酵母等微生物文库在系统性研究中发挥了关键作用。基因缺失文库、过表达文库、转座子插入文库等多种类型的酵母文库为基因组合优化和代谢路径设计提供了重要工具，促进了代谢工程和合成生物学的创新应用。这些文库在工业生产中支持高产菌株的构建，如用于生物燃料和化学品的高效生产；在环境领域，通过基因改造筛选，生成具备污染物降解能力的菌株，为生态修复提供解决方案；在药物合成方面，文库帮助构建高效合成药用化合物的菌株，推动生物制药的发展。然而，当前文库构建和应用仍面临诸如构建成本、基因组编辑的精确度及筛选效率等技术瓶颈。未来，自动化、数字化和新型筛选技术的进步有望突破这些瓶颈，推动酵母文库的快速构建和高效筛选，从而加速合成生物学在可持续发展和生态工程中的应用。

Abstract

Synthetic biology

as a discipline that designs

constructs

and modifies biological systems to achieve specific functions

is widely applied in biomanufacturing

the biodegradation of environmental pollutants

and drug synthesis. Systematic exploration of gene functions and construction of libraries for engineered strains are driving forces of the development of synthetic biology. These libraries serve as foundational tools for understanding complex biological processes and engineering microorganisms for potential applications. This review focuses on the construction methods and application prospects of various yeast libraries in synthetic biology. With the rapid advancement of genome sequencing and high-throughput screening technologies

microbial libraries

such as those of

Saccharomyces

cerevisiae

and

Schizosaccharomyces

pombe

play a pivotal role in systematic research. Yeast libraries

including gene knockout libraries

overexpression libraries

and transposon insertion libraries

provide valuable tools for optimizing gene combinations and designing metabolic pathways

thus promoting applications in metabolic engineering and synthetic biology. These libraries facilitate the development of robust industrial strains

driving improvements in biofuel production

emical synthesis

and other biotechnological processes. In the environmental field

the screening of modified genes generates strains with pollutant degradation capabilities

contributing to ecological restoration. In drug synthesis

these libraries aid in constructing strains for the efficient production of pharmaceutical compounds

advancing the development of biopharmaceuticals. Despite these successes

there remain challenges in library construction and application

such as the high cost of library generation

difficulty in precise genome editing

and limitation in screening efficiency. In the future

advances in automation

digitization

and novel screening technologies are expected to overcome these barriers

facilitating the rapid construction and efficient screening of yeast libraries. No doubt

synthetic biology holds immense promise

with improvements in library construction and screening processes expected to accelerate the development of sustainable solutions in industrial production

environmental protection

and healthcare

thereby driving innovations in biotechnology.

关键词

Keywords

references

PRZYBYLA L , GILBERT L A . A new era in functional genomics screens [J ] . Nature Reviews Genetics , 2022 , 23 ( 2 ): 89 - 103 .

GALANIE S , THODEY K , TRENCHARD I J , et al . Complete biosynthesis of opioids in yeast [J ] . Science , 2015 , 349 ( 6252 ): 1095 - 1100 .

RUNGUPHAN W , KEASLING J D . Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid-derived biofuels and chemicals [J ] . Metabolic Engineering , 2014 , 21 : 103 - 113 .

SHENG J Y , FENG X Y . Metabolic engineering of yeast to produce fatty acid-derived biofuels: bottlenecks and solutions [J ] . Frontiers in Microbiology , 2015 , 6 : 554 .

SAMAL S K , PREETAM S . Synthetic biology: refining human health [M/OL ] //SUAR M, MISRA N, DASH C. Microbial engineering for therapeutics . Singapore: Springer Nature Singapore, 2022 : 57 - 70 [2024-11-01] . https://doi.org/10.1007/978-981-19-3979-2_3 https://doi.org/10.1007/978-981-19-3979-2_3 .

TSAI C S , KWAK S , TURNER T L , et al . Yeast synthetic biology toolbox and applications for biofuel production [J ] . FEMS Yeast Research , 2015 , 15 ( 1 ): 1 - 15 .

GOFFEAU A , BARRELL B G , BUSSEY H , et al . Life with 6000 genes [J ] . Science , 1996 , 274 ( 5287 ): 546 - 567 .

ARITA Y , KIM G , LI Z J , et al . A genome-scale yeast library with inducible expression of individual genes [J ] . Molecular Systems Biology , 2021 , 17 ( 6 ): e10207 .

WOOD V , GWILLIAM R , RAJANDREAM M A , et al . The genome sequence of Schizosaccharomyces pombe [J ] . Nature , 2002 , 415 ( 6874 ): 871 - 880 .

GREWAL S I S , JIA S T . Heterochromatin revisited [J ] . Nature Reviews Genetics , 2007 , 8 ( 1 ): 35 - 46 .

ROGUEV A , RYAN C J , HARTSUIKER E , et al . High-throughput quantitative genetic interaction mapping in the fission yeast Schizosaccharomyces pombe [J ] . Cold Spring Harbor Protocols , 2018 , 2018 ( 2 ): pdb.top079905.

ZHANG W , GENG A L . Improved ethanol production by a xylose-fermenting recombinant yeast strain constructed through a modified genome shuffling method [J ] . Biotechnology for Biofuels , 2012 , 5 ( 1 ): 46 .

BOTSTEIN D , FINK G R . Yeast: an experimental organism for 21st century biology [J ] . Genetics , 2011 , 189 ( 3 ): 695 - 704 .

RODRIGUEZ A , STRUCKO T , STAHLHUT S G , et al . Metabolic engineering of yeast for fermentative production of flavonoids [J ] . Bioresource Technology , 2017 , 245 : 1645 - 1654 .

MYBURGH M W , FAVARO L , VAN ZYL W H , et al . Engineered yeast for the efficient hydrolysis of polylactic acid [J ] . Bioresource Technology , 2023 , 378 : 129008 .

CHEN J S , BECKLEY J R , MCDONALD N A , et al . Identification of new players in cell division, DNA damage response, and morphogenesis through construction of Schizosaccharomyces pombe deletion strains [J ] . G 3 Genes|Genomes|Genetics, 2015, 5 ( 3 ): 361 - 370 .

TURCO G , CHANG C , WANG R Y , et al . Global analysis of the yeast knockout phenome [J ] . Science Advances , 2023 , 9 ( 21 ): eadg5702 .

KIM D U , HAYLES J , KIM D , et al . Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe [J ] . Nature Biotechnology , 2010 , 28 ( 6 ): 617 - 623 .

SCHERENS B , GOFFEAU A . The uses of genome-wide yeast mutant collections [J ] . Genome Biology , 2004 , 5 ( 7 ): 229 .

GIAEVER G , NISLOW C . The yeast deletion collection: a decade of functional genomics [J ] . Genetics , 2014 , 197 ( 2 ): 451 - 465 .

SOPKO R , HUANG D Q , PRESTON N , et al . Mapping pathways and phenotypes by systematic gene overexpression [J ] . Molecular Cell , 2006 , 21 ( 3 ): 319 - 330 .

MATSUYAMA A , ARAI R , YASHIRODA Y , et al . ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe [J ] . Nature Biotechnology , 2006 , 24 ( 7 ): 841 - 847 .

TONG A H , EVANGELISTA M , PARSONS A B , et al . Systematic genetic analysis with ordered arrays of yeast deletion mutants [J ] . Science , 2001 , 294 ( 5550 ): 2364 - 2368 .

ROGUEV A , WIREN M , WEISSMAN J S , et al . High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe [J ] . Nature Methods , 2007 , 4 ( 10 ): 861 - 866 .

GIAEVER G , CHU A M , NI L , et al . Functional profiling of the Saccharomyces cerevisiae genome [J ] . Nature , 2002 , 418 ( 6896 ): 387 - 391 .

HWANG Y C , LIN C C , CHANG J Y , et al . Predicting essential genes based on network and sequence analysis [J ] . Molecular BioSystems , 2009 , 5 ( 12 ): 1672 - 1678 .

JEONG H , MASON S P , BARABÁSI A L , et al . Lethality and centrality in protein networks [J ] . Nature , 2001 , 411 ( 6833 ): 41 - 42 .

LI Z J , VIZEACOUMAR F J , BAHR S , et al . Systematic exploration of essential yeast gene function with temperature-sensitive mutants [J ] . Nature Biotechnology , 2011 , 29 ( 4 ): 361 - 367 .

SHORTLE D , NOVICK P , BOTSTEIN D . Construction and genetic characterization of temperature-sensitive mutant alleles of the yeast actin gene [J ] . Proceedings of the National Academy of Sciences of the United States of America , 1984 , 81 ( 15 ): 4889 - 4893 .

BEN-AROYA S , COOMBES C , KWOK T , et al . Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae [J ] . Molecular Cell , 2008 , 30 ( 2 ): 248 - 258 .

POULTNEY C S , BUTTERFOSS G L , GUTWEIN M R , et al . Rational design of temperature-sensitive alleles using computationalstructure prediction [J ] . PLoS One , 2011 , 6 ( 9 ): e23947 .

CHAKSHUSMATHI G , MONDAL K , LAKSHMI G S , et al . Design of temperature-sensitive mutants solely from amino acid sequence [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2004 , 101 ( 21 ): 7925 - 7930 .

TAN G H , CHEN M , FOOTE C , et al . Temperature-sensitive mutations made easy: generating conditional mutations by using temperature-sensitive inteins that function within different temperature ranges [J ] . Genetics , 2009 , 183 ( 1 ): 13 - 22 .

WIDLUND P O , DAVIS T N . A high-efficiency method to replace essential genes with mutant alleles in yeast [J ] . Yeast , 2005 , 22 ( 10 ): 769 - 774 .

KOFOED M , MILBURY K L , CHIANG J H , et al . An updated collection of sequence barcoded temperature-sensitive alleles of yeast essential genes [J ] . G3 Genes|Genomes|Genetics , 2015 , 5 ( 9 ): 1879 - 1887 .

MNAIMNEH S , DAVIERWALA A P , HAYNES J , et al . Exploration of essential gene functions via titratable promoter alleles [J ] . Cell , 2004 , 118 ( 1 ): 31 - 44 .

BRESLOW D K , CAMERON D M , COLLINS S R , et al . A comprehensive strategy enabling high-resolution functional analysis of the yeast genome [J ] . Nature Methods , 2008 , 5 ( 8 ): 711 - 718 .

SCHULDINER M , COLLINS S R , THOMPSON N J , et al . Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile [J ] . Cell , 2005 , 123 ( 3 ): 507 - 519 .

LIU G W , YONG M Y J , YURIEVA M , et al . Gene essentiality is a quantitative property linked to cellular evolvability [J ] . Cell , 2015 , 163 ( 6 ): 1388 - 1399 .

GUO Y B , PARK J M , CUI B W , et al . Integration profiling of gene function with dense maps of transposon integration [J ] . Genetics , 2013 , 195 ( 2 ): 599 - 609 .

EVERTTS A G , PLYMIRE C , CRAIG N L , et al . The Hermes transposon of Musca domestica is an efficient tool for the mutagenesis of Schizosaccharomyces pombe [J ] . Genetics , 2007 , 177 ( 4 ): 2519 - 2523 .

PARK J M , EVERTTS A G , LEVIN H L . The Hermes transposon of Musca domestica and its use as a mutagen of Schizosaccharomyces pombe [J ] . Methods , 2009 , 49 ( 3 ): 243 - 247 .

GANGADHARAN S , MULARONI L , FAIN-THORNTON J , et al . DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2010 , 107 ( 51 ): 21966 - 21972 .

CAIN A K , BARQUIST L , GOODMAN A L , et al . A decade of advances in transposon-insertion sequencing [J ] . Nature Reviews Genetics , 2020 , 21 ( 9 ): 526 - 540 .

MICHEL A H , HATAKEYAMA R , KIMMIG P , et al . Functional mapping of yeast genomes by saturated transposition [J ] . eLife , 2017 , 6 : e23570 .

BLAKE BILLMYRE R , EICKBUSH M T , CRAIG C J , et al . Genome-wide quantification of contributions to sexual fitness identifies genes required for spore viability and health in fission yeast [J ] . PLoS Genetics , 2022 , 18 ( 10 ): e1010462 .

ADAMES N R , GALLEGOS J E , PECCOUD J . Yeast genetic interaction screens in the age of CRISPR/Cas [J ] . Current Genetics , 2019 , 65 ( 2 ): 307 - 327 .

LI L , LIU X C , WEI K K , et al . Synthetic biology approaches for chromosomal integration of genes and pathways in industrial microbial systems [J ] . Biotechnology Advances , 2019 , 37 ( 5 ): 730 - 745 .

GASIUNAS G , BARRANGOU R , HORVATH P , et al . Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2012 , 109 ( 39 ): E2579 - E2586 .

QI L S , LARSON M H , GILBERT L A , et al . Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression [J ] . Cell , 2021 , 184 : 844 .

LIAN J Z , HAMEDIRAD M , HU S M , et al . Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system [J ] . Nature Communications , 2017 , 8 ( 1 ): 1688 .

GUO X G , CHAVEZ A , TUNG A , et al . High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast [J ] . Nature Biotechnology , 2018 , 36 ( 6 ): 540 - 546 .

SI T , CHAO R , MIN Y H , et al . Automated multiplex genome-scale engineering in yeast [J ] . Nature Communications , 2017 , 8 : 15187 .

SAKAI A , SHIMIZU Y , HISHINUMA F . Integration of heterologous genes into the chromosome of Saccharomyces cerevisiae using a delta sequence of yeast retrotransposon Ty [J ] . Applied Microbiology and Biotechnology , 1990 , 33 ( 3 ): 302 - 306 .

DICARLO J E , CONLEY A J , PENTTILÄ M , et al . Yeast oligo-mediated genome engineering (YOGE) [J ] . ACS Synthetic Biology , 2013 , 2 ( 12 ): 741 - 749 .

BARBIERI E M , MUIR P , AKHUETIE-ONI B O , et al . Precise editing at DNA replication forks enables multiplex genome engineering in eukaryotes [J ] . Cell , 2017 , 171 ( 6 ): 1453 - 1467.e13 .

JAKOČIŪNAS T , RAJKUMAR A S , ZHANG J , et al . CasEMBLR: Cas9-facilitated multiloci genomic integration of in vivo assembled DNA parts in Saccharomyces cerevisiae [J ] . ACS Synthetic Biology , 2015 , 4 ( 11 ): 1226 - 1234 .

LIU R M , LIANG L Y , CHOUDHURY A , et al . Multiplex navigation of global regulatory networks (MINR) in yeast for improved ethanol tolerance and production [J ] . Metabolic Engineering , 2019 , 51 : 50 - 58 .

KUZMIN E , VANDERSLUIS B , NGUYEN BA A N , et al . Exploring whole-genome duplicate gene retention with complex genetic interaction analysis [J ] . Science , 2020 , 368 ( 6498 ): eaaz5667 .

PENG J R . Gene redundancy and gene compensation: an updated view [J ] . Journal of Genetics and Genomics , 2019 , 46 ( 7 ): 329 - 333 .

MERZ S , WESTERMANN B . Genome-wide deletion mutant analysis reveals genes required for re spiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae [J ] . Genome Biology , 2009 , 10 ( 9 ): R95 .

LOUCA S , POLZ M F , MAZEL F , et al . Function and functional redundancy in microbial systems [J ] . Nature Ecology & Evolution , 2018 , 2 ( 6 ): 936 - 943 .

BIDLINGMAIER S , LIU B . Construction of yeast surface-displayed cDNA libraries [J ] . Methods in Molecular Biology , 2011 , 729 : 199 - 210 .

LIU Z H , TYO K E J , MARTÍNEZ J L , et al . Different expression systems fo r production of recombinant proteins in Saccharomyces cerevisiae [J ] . Biotechnology and Bioengineering , 2012 , 109 ( 5 ): 1259 - 1268 .

SMITH V , BOTSTEIN D , BROWN P O . Genetic footprinting: a genomic strategy for determining a gene’s function given its sequence [J ] . Proceedings of the National Academy of Sciences of the United States of America , 1995 , 92 ( 14 ): 6479 - 6483 .

SMITH V , CHOU K N , LASHKARI D , et al . Functional analysis of the genes of yeast chromosome Ⅴ by genetic footprinting [J ] . Science , 1996 , 274 ( 5295 ): 2069 - 2074 .

HAN T X , XU X Y , ZHANG M J , et al . Global fitness profiling of fission yeast deletion strains by barcode sequencing [J ] . Genome Biology , 2010 , 11 ( 6 ): R60 .

STEINMETZ L M , SCHARFE C , DEUTSCHBAUER A M , et al . Systematic screen for human disease genes in yeast [J ] . Nature Genetics , 2002 , 31 ( 4 ): 400 - 404 .

WARRINGER J , ERICSON E , FERNANDEZ L , et al . High-resolution yeast phenomics resolves different physiological features in the saline response [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2003 , 100 ( 26 ): 15724 - 15729 .

BIRRELL G W , BROWN J A , IRENE WU H , et al . Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2002 , 99 ( 13 ): 8778 - 8783 .

CHANG M , BELLAOUI M , BOONE C , et al . A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2002 , 99 ( 26 ): 16934 - 16939 .

PARSONS A B , BROST R L , DING H M , et al . Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways [J ] . Nature Biotechnology , 2004 , 22 ( 1 ): 62 - 69 .

PARSONS A B , LOPEZ A , GIVONI I E , et al . Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast [J ] . Cell , 2006 , 126 ( 3 ): 611 - 625 .

ENYENIHI A H , SAUNDERS W S . Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae [J ] . Genetics , 2003 , 163 ( 1 ): 47 - 54 .

MATECIC M , SMITH D L , PAN X W , et al . A microarray-based genetic screen for yeast chronological aging factors [J ] . PLoS Genetics , 2010 , 6 ( 4 ): e1000921 .

ROMILA C A , TOWNSEND S , MALECKI M , et al . Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast [J ] . Microbial Cell , 2021 , 8 ( 7 ): 146 - 160 .

FERRARI S , BERETTA S , JACOB A , et al . BAR-Seq clonal tracking of gene-edited cells [J ] . Nature Protocols , 2021 , 16 ( 6 ): 2991 - 3025 .

RALLIS C , LÓPEZ-MAURY L , GEORGESCU T , et al . Systematic screen for mutants resistant to TORC1 inhibition in fission yeast reveals genes involved in cellular ageing and growth [J ] . Biology Open , 2014 , 3 ( 2 ): 161 - 171 .

KENNEDY P J , VASHISHT A A , HOE K L , et al . A genome-wide screen of genes involved in cadmium tolerance in Schizosaccharomyces pombe [J ] . Toxicological Sciences , 2008 , 106 ( 1 ): 124 - 139 .

RODRÍGUEZ-LÓPEZ M , BORDIN N , LEES J , et al . Broad functional profiling of fission yeast proteins using phenomics and machine learning [J ] . eLife , 2023 , 12 : RP88229 .

NI L , SNYDER M . A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae [J ] . Molecular Biology of the Cell , 2001 , 12 ( 7 ): 2147 - 2170 .

KELLY F D , NURSE P . Spatial control of Cdc42 activation determines cell width in fission yeast [J ] . Molecular Biology of the Cell , 2011 , 22 ( 20 ): 3801 - 3811 .

NAVARRO F J , NURSE P . A systematic screen reveals new elements acting at the G2/M cell cycle control [J ] . Genome Biology , 2012 , 13 ( 5 ): R36 .

BLYTH J , MAKRANTONI V , BARTON R E , et al . Genes important for Schizosaccharomyces pombe meiosis identified through a functional genomics screen [J ] . Genetics , 2018 , 208 ( 2 ): 589 - 603 .

DESHPANDE G P , HAYLES J , HOE K L , et al . Screening a genome-wide S. pombe deletion library identifies novel genes and pathways involved in genome stability maintenance [J ] . DNA Repair , 2009 , 8 ( 5 ): 672 - 679 .

PAN X , LEI B K , ZHOU N , et al . Identification of novel genes involved in DNA damage response by screening a genome-wide Schizosaccharomyces pombe deletion library [J ] . BMC Genomics , 2012 , 13 : 662 .

COSTANZO M , VANDERSLUIS B , KOCH E N , et al . A global genetic interaction network maps a wiring diagram of cellular function [J ] . Science , 2016 , 353 ( 6306 ): aaf1420 .

ROSS-MACDONALD P , COELHO P S , ROEMER T , et al . Large-scale analysis of the yeast genome by transposon tagging and gene disruption [J ] . Nature , 1999 , 402 ( 6760 ): 413 - 418 .

WHITE W H , JOHNSON D I . Characterization of synthetic-lethal mutants reveals a role for the Saccharomyces cerevisiae guanine-nucleotide exchange factor Cdc24p in vacuole function and Na + tolerance [J ] . Genetics , 1997 , 147 ( 1 ): 43 - 55 .

HUH W K , FALVO J V , GERKE L C , et al . Global analysis of protein localization in budding yeast [J ] . Nature , 2003 , 425 ( 6959 ): 686 - 691 .

RAZDAIBIEDINA A , BRECHALOV A , FRIESEN H , et al . PIFiA: self-supervised approach for protein functional annotation from single-cell imaging data [J ] . Molecular Systems Biology , 2024 , 20 ( 5 ): 521 - 548 .

CHONG Y T , KOH J L Y , FRIESEN H , et al . Yeast proteome dynamics from single cell imaging and automated analysis [J ] . Cell , 2015 , 161 : 1413 - 1424

HAYASHI A , DING D Q , TSUTSUMI C , et al . Localization of gene products using a chromosomally tagged GFP-fusion library in the fission yeast Schizosaccharomyces pombe [J ] . Genes to Cells , 2009 , 14 ( 2 ): 217 - 225 .

JIA B , WU Y , LI B Z , et al . Precise control of SCRaMbLE in synthetic haploid and diploid yeast [J ] . Nature Communications , 2018 , 9 ( 1 ): 1933 .

SI T , LUO Y Z , BAO Z H , et al . RNAi-assisted genome evolution in Saccharomyces cerevisiae for complex phenotype engineering [J ] . ACS Synthetic Biology , 2015 , 4 ( 3 ): 283 - 291 .

ZENG W Z , GUO L K , XU S , et al . High-throughput screening technology in industrial biotechnology [J ] . Trends in Biotechnology , 2020 , 38 ( 8 ): 888 - 906 .

RUGBJERG P , SOMMER M O A . Overcoming genetic heterogeneity in industrial fermentations [J ] . Nature Biotechnology , 2019 , 37 ( 8 ): 869 - 876 .

WEHRS M , TANJORE D , ENG T , et al . Engineering robust production microbes for large-scale cultivation [J ] . Trends in Microbiology , 2019 , 27 ( 6 ): 524 - 537 .

JAKOČIŪNAS T , BONDE I , HERRGÅRD M , et al . Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae [J ] . Metabolic Engineering , 2015 , 28 : 213 - 222 .

LI Y H , MOLYNEAUX N , ZHANG H T , et al . A multiplexed, three-dimensional pooling and next-generation sequencing strategy for creating barcoded mutant arrays: construction of a Schizosaccharomyces pombe transposon insertion library [J ] . Nucleic Acids Research , 2022 , 50 ( 17 ): e102 .

COOPE R J N , MATIC N , PANDOH P K , et al . Automated library construction and analysis for high-throughput nanopore sequencing of SARS-CoV-2 [J ] . The Journal of Applied Laboratory Medicine , 2022 , 7 ( 5 ): 1025 - 1036 .

SANTACRUZ D , ENANE F O , FUNDEL-CLEMENS K , et al . Automation of high-throughput mRNA-seq library preparation: a robust, hands-free and time efficient methodology [J ] . SLAS Discovery , 2022 , 27 ( 2 ): 140 - 147 .

VAN DEVENTER J A , WITTRUP K D . Yeast surface display for antibody isolation: library construction, library screening, and affinity maturation [J ] . Methods in Molecular Biology , 2014 , 1131 : 151 - 181 .

YOFE I , WEILL U , MEURER M , et al . One library to make them all: streamlining the creation of yeast libraries via a SWAp-tag strategy [J ] . Nature Methods , 2016 , 13 ( 4 ): 371 - 378 .

COSTANZO M , HOU J , MESSIER V , et al . Environmental robustness of the global yeast genetic interaction network [J ] . Science , 2021 , 372 ( 6542 ): eabf8424 .

KUZMIN E , VANDERSLUIS B , WANG W , et al . Systematic analysis of complex genetic interactions [J ] . Science , 2018 , 360 ( 6386 ): eaao1729 .

PENNISI E . Building the ultimate yeast genome [J ] . Science , 2014 , 343 ( 6178 ): 1426 - 1429 .

ZHAO Y , COELHO C , HUGHES A L , et al . Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions [J ] . Cell , 2023 , 186 ( 24 ): 5220 - 5236.e16 .

SCHINDLER D , WALKER R S K , JIANG S Y , et al . Design, construction, and functional characterization of a tRNA neochromosome in yeast [J ] . Cell , 2023 , 186 ( 24 ): 5237 - 5253.e22 .

ZHANG W M , LAZAR-STEFANITA L , YAMASHITA H , et al . Manipulating the 3D organization of the largest synthetic yeast chromosome [J ] . Molecular Cell , 2023 , 83 ( 23 ): 4424 - 4437.e5 .

DAI J B , BOEKE J D , LUO Z Q , et al . Sc3.0: revamping and minimizing the yeast genome [J ] . Genome Biology , 2020 , 21 ( 1 ): 205 .

SHAO Y Y , LU N , WU Z F , et al . Creating a functional single-chromosome yeast [J ] . Nature , 2018 , 560 ( 7718 ): 331 - 335 .

WANG P , LIN Y , ZOU C J , et al . Construction and screening of a glycosylphosphatidylinositol protein deletion library in Pichia pastoris [J ] . BMC Microbiology , 2020 , 20 ( 1 ): 262 .

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Related Author

ZHANG Yiqing

LIU Gaowen

SONG Chengzhi

LIN Yihan

HUANG Yang

LI Yiye

NIE Guangjun

HUANG Ruping

Related Institution

Shenzhen Key Laboratory of Synthetic Genomics， Guangdong Provincial Key Laboratory of Synthetic Genomics， Key Laboratory of Quantitative Synthetic Biology， Shenzhen Institute of Synthetic Biology， Shenzhen Institute of Advanced Technology， Chinese Academy of Sciences

Center for Quantitative Biology， Peking-Tsinghua Center for Life Sciences， Academy for Advanced Interdisciplinary Studies， Peking University

The MOE Key Laboratory of Cell Proliferation and Differentiation， School of Life Sciences， Peking University

Chengdu Academy for Advanced Interdisciplinary Biotechnologies， Peking University

CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety， CAS Center for Excellence in Nanoscience， National Center for Nanoscience and Technology of China

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