A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria
Jason M. Peters,Alexandre Colavin,Handuo Shi,Tomasz L. Czarny,Matthew H. Larson,Spencer Wong,John S. Hawkins,Candy H. S. Lu,Byoung-Mo Koo,Elizabeth Marta,Anthony L. Shiver,Evan H. Whitehead,Jonathan S. Weissman,Eric D. Brown,Lei S. Qi,Kerwyn Casey Huang,Carol A. Gross +16 more
Reads0
Chats0
TLDR
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.About:
This article is published in Cell.The article was published on 2016-06-02 and is currently open access. It has received 542 citations till now. The article focuses on the topics: Essential gene & CRISPR interference.read more
Citations
More filters
Journal ArticleDOI
Communication between viruses guides lysis–lysogeny decisions
Zohar Erez,Ida Steinberger-Levy,Ida Steinberger-Levy,Maya Shamir,Shany Doron,Avigail Stokar-Avihail,Yoav Peleg,Sarah Melamed,Azita Leavitt,Alon Savidor,Shira Albeck,Gil Amitai,Rotem Sorek +12 more
TL;DR: It is shown that viruses (phages) of the SPbeta group use a small-molecule communication system to coordinate lysis–lysogeny decisions, and that different phages encode different versions of the communication peptide, demonstrating a phage-specific peptide communication code for lysogenY decisions.
Journal ArticleDOI
Panning for gold: ‘model‐X’ knockoffs for high dimensional controlled variable selection
TL;DR: In this paper, the authors propose a new framework of "model-X" knockoffs, which reads from a different perspective the knockoff procedure that was originally designed for controlling the false discovery rate in linear models.
Journal ArticleDOI
Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform
Jeremy M. Rock,Forrest F. Hopkins,Alejandro Chavez,Alejandro Chavez,Marieme Diallo,Michael R. Chase,Elias R. Gerrick,Justin R. Pritchard,George M. Church,George M. Church,Eric J. Rubin,Christopher M. Sassetti,Dirk Schnappinger,Sarah M. Fortune,Sarah M. Fortune +14 more
TL;DR: The utility of the dCas9Sth1 CRISPRi system is demonstrated by addressing persistent controversies regarding drug synergies in the mycobacterial folate biosynthesis pathway by allowing high-resolution dissection of gene function in the context of bacterial operons.
Journal ArticleDOI
Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
Andrew D. Garst,Marcelo C. Bassalo,Gur Pines,Sean A. Lynch,Andrea L. Halweg-Edwards,Rongming Liu,Liya Liang,Zhiwen Wang,Ramsey I. Zeitoun,William G. Alexander,Ryan T. Gill +10 more
TL;DR: It is reported that CRISPR–Cas9 gene editing in combination with massively parallel oligomer synthesis can enable trackable editing on a genome-wide scale and preliminary evidence that CREATE will work in yeast is provided.
Journal ArticleDOI
A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection.
Amanda Jacobson,Lilian H. Lam,Manohary Rajendram,Fiona B. Tamburini,Jared Honeycutt,Trung H.M. Pham,Will Van Treuren,Kali M. Pruss,Stephen Russell Stabler,Kyler A. Lugo,Donna M. Bouley,Jose G. Vilches-Moure,Mark Smith,Justin L. Sonnenburg,Ami S. Bhatt,Kerwyn Casey Huang,Denise M. Monack +16 more
TL;DR: This work identifies a microbiota-mediated mechanism of colonization resistance against Salmonella enterica serovar Typhimurium by comparing high-complexity commensal communities with different levels of colonists resistance, and provides mechanistic understanding into the role of individualized microbial communities in host-to-host variability of pathogen transmission.
References
More filters
Journal ArticleDOI
STRING v10: protein–protein interaction networks, integrated over the tree of life
Damian Szklarczyk,Andrea Franceschini,Stefan Wyder,Kristoffer Forslund,Davide Heller,Jaime Huerta-Cepas,Milan Simonovic,Alexander Roth,Alberto Santos,Kalliopi Tsafou,Michael Kuhn,Peer Bork,Lars Juhl Jensen,Christian von Mering +13 more
TL;DR: H hierarchical and self-consistent orthology annotations are introduced for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution in the STRING database.
Journal ArticleDOI
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
Tomoya Baba,Takeshi Ara,Miki Hasegawa,Yuki Takai,Yoshiko Okumura,Miki Baba,Kirill A. Datsenko,Masaru Tomita,Barry L. Wanner,Hirotada Mori,Hirotada Mori +10 more
TL;DR: These mutants—the ‘Keio collection’—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome‐wide testing of mutational effects in a common strain background, E. coli K‐12 BW25113.
Journal ArticleDOI
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.
Lei S. Qi,Matthew H. Larson,Luke A. Gilbert,Jennifer A. Doudna,Jonathan S. Weissman,Adam P. Arkin,Adam P. Arkin,Wendell A. Lim +7 more
TL;DR: This RNA-guided DNA recognition platform provides a simple approach for selectively perturbing gene expression on a genome-wide scale and can efficiently repress expression of targeted genes in Escherichia coli, with no detectable off-target effects.
Journal ArticleDOI
Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis
Elizabeth A. Winzeler,Daniel D. Shoemaker,Anna Astromoff,Hong Liang,Keith Anderson,Bruno André,Rhonda Bangham,Rocío Benito,Jef D. Boeke,Howard Bussey,Angela M. Chu,Carla Connelly,Karen Davis,Fred S. Dietrich,Sally Dow,Mohamed El Bakkoury,Françoise Foury,Stephen H. Friend,Erik Gentalen,Guri Giaever,Johannes H. Hegemann,Ted Jones,Michael T. Laub,Hong Liao,Nicole Liebundguth,David J. Lockhart,Anca Lucau-Danila,Marc Lussier,Nasiha M'Rabet,Patrice Menard,Michael Mittmann,Chai Pai,Corinne Rebischung,José L. Revuelta,Linda Riles,Christopher J. Roberts,Petra Ross-Macdonald,Bart Scherens,Michael Snyder,Sharon Sookhai-Mahadeo,Reginald Storms,Steeve Veronneau,Marleen Voet,Guido Volckaert,Teresa R. Ward,Robert W. Wysocki,Grace Yen,Kexin Yu,Katja Zimmermann,Peter Philippsen,Mark Johnston,Ronald W. Davis +51 more
TL;DR: A total of 6925 Saccharomyces cerevisiae strains were constructed, by a high-throughput strategy, each with a precise deletion of one of 2026 ORFs (more than one-third of the ORFs in the genome), finding that 17 percent were essential for viability in rich medium.
Journal ArticleDOI
Modeling of the Bacterial Growth Curve
TL;DR: Several sigmoidal functions (logistic, Gompertz, Richards, Schnute, and Stannard) were compared to describe a bacterial growth curve by using the model of Schnutes, which is a comprehensive model, encompassing all other models.