A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

被引：505

作者：

Peters, Jason M. ^{[1
]}

Colavin, Alexandre ^{[2
]}

Shi, Handuo ^{[3
]}

Czarny, Tomasz L. ^{[4
,11
]}

Larson, Matthew H. ^{[5
,6
,7
,8
]}

Wong, Spencer ^{[5
]}

Hawkins, John S. ^{[1
,9
]}

Lu, Candy H. S. ^{[1
]}

Koo, Byoung-Mo ^{[1
]}

Marta, Elizabeth ^{[1
]}

Shiver, Anthony L. ^{[1
,9
]}

Whitehead, Evan H. ^{[5
,7
,10
]}

Weissman, Jonathan S. ^{[5
,6
,7
,8
,10
]}

Brown, Eric D. ^{[4
,11
]}

Qi, Lei S. ^{[3
,12
,13
]}

Huang, Kerwyn Casey ^{[2
,3
,14
]}

Gross, Carol A. ^{[1
]}

机构：

[1] Univ Calif San Francisco, Dept Microbiol & Immunol, San Francisco, CA 94158 USA

[2] Stanford Univ, Biophys Program, Stanford, CA 94305 USA

[3] Stanford Univ, Dept Bioengn, Stanford, CA 94305 USA

[4] McMaster Univ, Dept Biochem & Biomed Sci, Hamilton, ON L8S 3Z5, Canada

[5] Univ Calif San Francisco, Dept Cellular & Mol Pharmacol, San Francisco, CA 94158 USA

[6] Univ Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94158 USA

[7] Calif Inst Quantitat Biomed Res, San Francisco, CA 94158 USA

[8] Univ Calif Berkeley, Ctr RNA Syst Biol, Berkeley, CA 94720 USA

[9] Univ Calif San Francisco, Biophys Grad Program, San Francisco, CA 94158 USA

[10] Univ Calif San Francisco, UCSF Ctr Syst & Synthet Biol, San Francisco, CA 94158 USA

[11] McMaster Univ, Michael G DeGroote Inst Infect Dis Res, Hamilton, ON L8N 3Z5, Canada

[12] Stanford Univ, Dept Chem & Syst Biol, Stanford, CA 94305 USA

[13] Stanford Univ, ChEM H, Stanford, CA 94305 USA

[14] Stanford Univ, Dept Microbiol & Immunol, Med, Stanford, CA 94305 USA

来源：

CELL | 2016年 / 165卷 / 06期

基金：

加拿大健康研究院;

关键词：

PENICILLIN-BINDING PROTEINS; SEQUENCE-SPECIFIC CONTROL; BACILLUS-SUBTILIS; ESCHERICHIA-COLI; ROD SHAPE; GENOME; GROWTH; EXPRESSION; IDENTIFICATION; BIOSYNTHESIS;

D O I：

10.1016/j.cell.2016.05.003

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Essential gene functions underpin the core reactions required for cell viability, but their contributions and relationships are poorly studied in vivo. Using CRISPR interference, we created knockdowns of every essential gene in Bacillus subtilis and probed their phenotypes. Our high-confidence essential gene network, established using chemical genomics, showed extensive interconnections among distantly related processes and identified modes of action for uncharacterized antibiotics. Importantly, mild knockdown of essential gene functions significantly reduced stationary-phase survival without affecting maximal growth rate, suggesting that essential protein levels are set to maximize outgrowth from stationary phase. Finally, high-throughput microscopy indicated that cell morphology is relatively insensitive to mild knockdown but profoundly affected by depletion of gene function, revealing intimate connections between cell growth and shape. Our results provide a framework for systematic investigation of essential gene functions in vivo broadly applicable to diverse microorganisms and amenable to comparative analysis.

引用

页码：1493 / 1506

页数：14

共 45 条

[1] Failsafe Mechanisms Couple Division and DNA Replication in Bacteria [J].

Arjes, Heidi A. ;

Kriel, Allison ;

Sorto, Nohemy A. ;

Shaw, Jared T. ;

Wang, Jue D. ;

Levin, Petra Anne .

CURRENT BIOLOGY, 2014, 24 (18) :2149-2155

[2] Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants:: the Keio collection [J].

Baba, Tomoya ;

Ara, Takeshi ;

Hasegawa, Miki ;

Takai, Yuki ;

Okumura, Yoshiko ;

Baba, Miki ;

Datsenko, Kirill A. ;

Tomita, Masaru ;

Wanner, Barry L. ;

Mori, Hirotada .

MOLECULAR SYSTEMS BIOLOGY, 2006, 2 (1) :2006.0008

[3] Gene essentiality and synthetic lethality in haploid human cells [J].

Blomen, Vincent A. ;

Majek, Peter ;

Jae, Lucas T. ;

Bigenzahn, Johannes W. ;

Nieuwenhuis, Joppe ;

Staring, Jacqueline ;

Sacco, Roberto ;

van Diemen, Ferdy R. ;

Olk, Nadine ;

Stukalov, Alexey ;

Marceau, Caleb ;

Janssen, Hans ;

Carette, Jan E. ;

Bennett, Keiryn L. ;

Colinge, Jacques ;

Superti-Furga, Giulio ;

Brummelkamp, Thijn R. .

SCIENCE, 2015, 350 (6264) :1092-1096

[4] A comprehensive strategy enabling high-resolution functional analysis of the yeast genome [J].

Breslow, David K. ;

Cameron, Dale M. ;

Collins, Sean R. ;

Schuldiner, Maya ;

Stewart-Ornstein, Jacob ;

Newman, Heather W. ;

Braun, Sigurd ;

Madhani, Hiten D. ;

Krogan, Nevan J. ;

Weissman, Jonathan S. .

NATURE METHODS, 2008, 5 (08) :711-718

[5] Bacterial Actin and Tubulin Homologs in Cell Growth and Division [J].

Busiek, Kimberly K. ;

Margolin, William .

CURRENT BIOLOGY, 2015, 25 (06) :R243-R254

[6] Antibiotics that inhibit cell wall biosynthesis induce expression of the Bacillus subtilis σW and σM regulons [J].

Cao, M ;

Wang, T ;

Ye, R ;

Helmann, JD .

MOLECULAR MICROBIOLOGY, 2002, 45 (05) :1267-1276

[7] The essential genome of a bacterium [J].

Christen, Beat ;

Abeliuk, Eduardo ;

Collier, John M. ;

Kalogeraki, Virginia S. ;

Passarelli, Ben ;

Coller, John A. ;

Fero, Michael J. ;

McAdams, Harley H. ;

Shapiro, Lucy .

MOLECULAR SYSTEMS BIOLOGY, 2011, 7

[8] Discovery of Novel Cell Wall-Active Compounds Using PywaC, a Sensitive Reporter of Cell Wall Stress, in the Model Gram-Positive Bacterium Bacillus subtilis [J].

Czarny, T. L. ;

Perri, A. L. ;

French, S. ;

Brown, E. D. .

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 2014, 58 (06) :3261-3269

[9] The Metabolic Enzyme ManA Reveals a Link between Cell Wall Integrity and Chromosome Morphology [J].

Elbaz, Maya ;

Ben-Yehuda, Sigal .

PLOS GENETICS, 2010, 6 (09)

[10] A genome-wide strategy for the identification of essential genes in Staphylococcus aureus [J].

Forsyth, RA ;

Haselbeck, RJ ;

Ohlsen, KL ;

Yamamoto, RT ;

Xu, H ;

Trawick, JD ;

Wall, D ;

Wang, LS ;

Brown-Driver, V ;

Froelich, JM ;

Kedar, GC ;

King, P ;

McCarthy, M ;

Malone, C ;

Misiner, B ;

Robbins, D ;

Tan, ZH ;

Zhu, ZY ;

Carr, G ;

Mosca, DA ;

Zamudio, C ;

Foulkes, JG ;

Zyskind, JW .

MOLECULAR MICROBIOLOGY, 2002, 43 (06) :1387-1400

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