Compacting a synthetic yeast chromosome arm.
Essential gene array
Minimal genome
SCRaMbLE-based genome compaction
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
04 01 2021
04 01 2021
Historique:
received:
18
06
2020
accepted:
10
12
2020
entrez:
5
1
2021
pubmed:
6
1
2021
medline:
4
1
2022
Statut:
epublish
Résumé
Redundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction, removing sequences nonessential for given conditions, provides a novel way to understand the core principles of life. The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system is a unique feature implanted in the synthetic yeast genome (Sc2.0), which is proposed as an effective tool for genome minimization. As the Sc2.0 project is nearing its completion, we have begun to explore the application of the SCRaMbLE system in genome compaction. We develop a method termed SCRaMbLE-based genome compaction (SGC) and demonstrate that a synthetic chromosome arm (synXIIL) can be efficiently reduced. The pre-introduced episomal essential gene array significantly enhances the compacting ability of SGC, not only by enabling the deletion of nonessential genes located in essential gene containing loxPsym units but also by allowing more chromosomal sequences to be removed in a single SGC process. Further compaction is achieved through iterative SGC, revealing that at least 39 out of 65 nonessential genes in synXIIL can be removed collectively without affecting cell viability at 30 °C in rich medium. Approximately 40% of the synthetic sequence, encoding 28 genes, is found to be dispensable for cell growth at 30 °C in rich medium and several genes whose functions are needed under specified conditions are identified. We develop iterative SGC with the aid of eArray as a generic yet effective tool to compact the synthetic yeast genome.
Sections du résumé
BACKGROUND
Redundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction, removing sequences nonessential for given conditions, provides a novel way to understand the core principles of life. The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system is a unique feature implanted in the synthetic yeast genome (Sc2.0), which is proposed as an effective tool for genome minimization. As the Sc2.0 project is nearing its completion, we have begun to explore the application of the SCRaMbLE system in genome compaction.
RESULTS
We develop a method termed SCRaMbLE-based genome compaction (SGC) and demonstrate that a synthetic chromosome arm (synXIIL) can be efficiently reduced. The pre-introduced episomal essential gene array significantly enhances the compacting ability of SGC, not only by enabling the deletion of nonessential genes located in essential gene containing loxPsym units but also by allowing more chromosomal sequences to be removed in a single SGC process. Further compaction is achieved through iterative SGC, revealing that at least 39 out of 65 nonessential genes in synXIIL can be removed collectively without affecting cell viability at 30 °C in rich medium. Approximately 40% of the synthetic sequence, encoding 28 genes, is found to be dispensable for cell growth at 30 °C in rich medium and several genes whose functions are needed under specified conditions are identified.
CONCLUSIONS
We develop iterative SGC with the aid of eArray as a generic yet effective tool to compact the synthetic yeast genome.
Identifiants
pubmed: 33397424
doi: 10.1186/s13059-020-02232-8
pii: 10.1186/s13059-020-02232-8
pmc: PMC7780613
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5Subventions
Organisme : BBSRC Grant
ID : R121730
Références
Science. 2010 Jan 22;327(5964):425-31
pubmed: 20093466
Nat Biotechnol. 2016 Jun 9;34(6):623-4
pubmed: 27281422
Genome Res. 2016 Jan;26(1):36-49
pubmed: 26566658
Nat Commun. 2020 Feb 13;11(1):868
pubmed: 32054834
Nature. 2002 Jul 25;418(6896):387-91
pubmed: 12140549
Sci China Life Sci. 2018 Dec;61(12):1515-1527
pubmed: 30465231
Cell. 2015 Jul 2;162(1):108-19
pubmed: 26119342
Science. 2011 Aug 19;333(6045):1026-30
pubmed: 21852501
Science. 2017 Mar 10;355(6329):1040-1044
pubmed: 28280199
Nat Rev Genet. 2018 Jan;19(1):34-49
pubmed: 29033457
Nature. 1997 Sep 4;389(6646):40-6
pubmed: 9288963
Science. 2010 Jul 2;329(5987):52-6
pubmed: 20488990
Science. 2017 Mar 10;355(6329):
pubmed: 28280150
Science. 2016 Mar 25;351(6280):aad6253
pubmed: 27013737
Nat Methods. 2018 Jun;15(6):461-468
pubmed: 29713083
Methods Enzymol. 1987;154:164-75
pubmed: 3323810
BMC Genet. 2009 Jul 13;10:36
pubmed: 19594932
Genome Biol. 2004;5(2):R12
pubmed: 14759262
Science. 2008 Feb 29;319(5867):1215-20
pubmed: 18218864
Nat Commun. 2018 Sep 17;9(1):3783
pubmed: 30224715
Science. 2017 Mar 10;355(6329):
pubmed: 28280149
Sci China Life Sci. 2019 Mar;62(3):381-393
pubmed: 30900161
Science. 2017 Mar 10;355(6329):
pubmed: 28280152
Microb Cell Fact. 2019 Mar 11;18(1):52
pubmed: 30857530
Science. 2007 Feb 2;315(5812):653-5
pubmed: 17272723
Science. 2017 Mar 10;355(6329):
pubmed: 28280151
Genome Res. 2017 Feb;27(2):289-299
pubmed: 27965289
Nucleic Acids Res. 2018 Jul 2;46(W1):W11-W16
pubmed: 29901812
Nat Commun. 2018 May 22;9(1):1935
pubmed: 29789594
Nature. 2019 Jun;570(7759):117-121
pubmed: 31068692
DNA Res. 2008 Apr 30;15(2):73-81
pubmed: 18334513
EMBO J. 2004 Dec 8;23(24):4847-56
pubmed: 15565172
Elife. 2019 Jan 18;8:
pubmed: 30657448
Mol Cell Biol. 2000 Jan;20(2):648-55
pubmed: 10611243
Nat Commun. 2018 May 22;9(1):1937
pubmed: 29789533
Nat Commun. 2018 May 22;9(1):1936
pubmed: 29789543
Nature. 2011 Sep 14;477(7365):471-6
pubmed: 21918511
Methods Enzymol. 2002;350:3-41
pubmed: 12073320
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Nat Commun. 2018 May 22;9(1):1932
pubmed: 29789540
Science. 2017 Mar 10;355(6329):
pubmed: 28280153
Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10268-73
pubmed: 8816789
Science. 2016 Sep 23;353(6306):
pubmed: 27708008
Science. 2018 Apr 20;360(6386):
pubmed: 29674565
Nucleic Acids Res. 2013 May 1;41(10):5382-99
pubmed: 23563150
Science. 2014 Apr 4;344(6179):55-8
pubmed: 24674868
Appl Microbiol Biotechnol. 2007 Jun;75(3):589-97
pubmed: 17345083
Science. 2007 Aug 3;317(5838):632-8
pubmed: 17600181
Nat Commun. 2018 May 22;9(1):1931
pubmed: 29789561
Nat Commun. 2018 May 22;9(1):1933
pubmed: 29789567
Science. 1996 Oct 25;274(5287):546, 563-7
pubmed: 8849441
Science. 2007 Feb 2;315(5812):649-52
pubmed: 17272722
Science. 1999 Aug 6;285(5429):901-6
pubmed: 10436161
Science. 2017 Mar 10;355(6329):
pubmed: 28280154
Science. 1999 Dec 10;286(5447):2165-9
pubmed: 10591650
Science. 2006 May 19;312(5776):1044-6
pubmed: 16645050
Nat Commun. 2018 May 22;9(1):1930
pubmed: 29789541
Nat Commun. 2018 May 22;9(1):1934
pubmed: 29789590
Bioeng Bugs. 2012 May-Jun;3(3):168-71
pubmed: 22572789
Genome Biol. 2015 Dec 01;16:259
pubmed: 26619908
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242