High-throughput, quantitative analyses of genetic interactions in E. coli

Typas, Athanasios; Nichols, Robert J.; Siegele, Deborah A.; Shales, Michael; Collins, Sean R.; Lim, Bentley; Braberg, Hannes; Yamamoto, Nobuto; Takeuchi, Rikiya; Wanner, Barry L.; Mori, Hirotada; Weissman, Jonathan S.; Krogan, Nevan J.; Gross, Carol A.

doi:10.1038/nmeth.1240

Cited by 220 publications

(230 citation statements)

References 36 publications

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“…A ⌬surA mutation did not aggravate the OMP assembly defect of the ⌬GNA2091 mutant. In contrast, studies in E. coli where SurA is considered to be the major OMP chaperone revealed synthetic lethality between yraP and surA mutations (16,35), suggesting that these proteins may have overlapping functions. However, in N. meningitidis, a surA single mutant is not noticeably affected in OMP assembly (18).…”

Section: Discussionmentioning

confidence: 90%

Involvement of Neisseria meningitidis Lipoprotein GNA2091 in the Assembly of a Subset of Outer Membrane Proteins

Bos

Grijpstra

Boxtel

et al. 2014

Journal of Biological Chemistry

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Background: Outer membrane protein assembly is an incompletely understood process in Gram-negative bacteria. Results: A Neisseria meningitidis mutant lacking the lipoprotein GNA2091 is affected in growth and accumulates unassembled outer membrane proteins. Conclusion:We identified a novel component involved in outer membrane biogenesis. Significance: Our findings contribute to the understanding of a fundamental process occurring in Gram-negative bacteria.

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Section: Discussionmentioning

confidence: 90%

Involvement of Neisseria meningitidis Lipoprotein GNA2091 in the Assembly of a Subset of Outer Membrane Proteins

Bos

Grijpstra

Boxtel

et al. 2014

Journal of Biological Chemistry

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“…In the REGRES procedure ( Fig. 1), one first constructs a collection of Hfr (high frequency of recombination) donor strains (19,20) from one or more recA + pir -parent strains by introducing suicide F plasmids for homology-targeted integration at different genomic locations (21). Each of these unique Hfr strains is capable of initiating genome transfer at a specific locus determined by the orientation of the oriT site in its chromosomally integrated F plasmid.…”

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confidence: 99%

“…To begin REGRES, suicide F plasmids targeting the galS and rhaM loci were introduced into CZB154 by conjugative transfer with subsequent antibiotic selection for chromosomal integration (21). The resulting library of CZB154 Hfr donor strains was then mated to REL607 cells containing a plasmid-encoded kanamycin resistance marker.…”

mentioning

confidence: 99%

Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli

Quandt

Deatherage²,

Ellington

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Evolutionary innovations often arise from complex genetic and ecological interactions, which can make it challenging to understand retrospectively how a novel trait arose. In a long-term experiment, Escherichia coli gained the ability to use abundant citrate (Cit + ) in the growth medium after ∼31,500 generations of evolution. Exploiting this previously untapped resource was highly beneficial: later Cit + variants achieve a much higher population density in this environment. All Cit + individuals share a mutation that activates aerobic expression of the citT citrate transporter, but this mutation confers only an extremely weak Cit + phenotype on its own. To determine which of the other >70 mutations in early Cit + clones were needed to take full advantage of citrate, we developed a recursive genomewide recombination and sequencing method (REGRES) and performed genetic backcrosses to purge mutations not required for Cit + from an evolved strain. We discovered a mutation that increased expression of the dctA C 4 -dicarboxylate transporter greatly enhanced the Cit + phenotype after it evolved.

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“…This is a classical genetic way to assign genes to specific functional groups and has been widely used in model organisms, such as yeast and Escherichia coli, to understand gene functions and the architecture of signaling networks (Collins et al 2006(Collins et al , 2007Roguev et al 2007; Breslow et al 2008;Typas et al 2008). Arabidopsis is also a premier system for this type of genetic analysis.…”

mentioning

confidence: 99%

Genetic Dissection of Salicylic Acid-Mediated Defense Signaling Networks in Arabidopsis

Ng¹,

Seabolt²,

Zhang

et al. 2011

Genetics

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Properly coordinated defense signaling networks are critical for the fitness of plants. One hub of the defense networks is centered on salicylic acid (SA), which plays a key role in activating disease resistance in plants. However, while a number of genes are known to affect SA-mediated defense, relatively little is known about how these gene interact genetically with each other. Here we exploited the unique defense-sensitized Arabidopsis mutant accelerated cell death (acd) 6-1 to dissect functional relationships among key components in the SA hub. We show that while enhanced disease susceptibility (eds) 1-2 and phytoalexin deficient (pad) 4-1 suppressed acd6-1-conferred small size, cell death, and defense phenotypes, a combination of these two mutations did not incur additive suppression. This suggests that EDS1 and PAD4 act in the same signaling pathway. To further evaluate genetic interactions among SA regulators, we constructed 10 pairwise crosses in the acd6-1 background among mutants defective in: SA INDUCTION-DEFICIENT 2 for SA biosynthesis; AGD2-LIKE DEFENSE 1, EDS5, and PAD4 for SA accumulation; and NONEXPRESSOR OF PR GENES 1 for SA signaling. Systematic analysis of the triple mutants based on their suppression of acd6-1-conferred phenotypes revealed complex and interactive genetic relationships among the tested SA genes. Our results suggest a more comprehensive view of the gene networks governing SA function and provide a framework for further interrogation of the important roles of SA and possibly other signaling molecules in regulating plant disease resistance. IN response to pathogen infection, plants can activate different layers of defense responses and undergo global gene expression reprogramming (Maleck et al. 2000;Tao et al. 2003;Katagiri 2004). A major challenge of the postgenomic era is to identify genes that control plant innate immunity and to elucidate how they are organized into networks to orchestrate host defense responses.One key hub in plant defense signaling networks is centered on the small phenolic molecule salicylic acid (SA). SA is important for basal defense, resistance proteinmediated defense, and systemic acquired resistance (HammondKosack and Jones 1996;Ryals et al. 1996;Tsuda et al. 2008). The SA hub of Arabidopsis includes many genes, which can be further grouped into three types on the basis of how they affect SA-mediated defense (Lu 2009). Type I SA genes encode enzymes that are directly involved in SA biosynthesis. One example is SA INDUCTION-DEFICIENT 2/ENHANCED DISEASE SUSCEPTIBILITY 16 (SID2/EDS16), which encodes isochorismate synthase contributing to bulk SA biosynthesis (Wildermuth et al. 2001). Type II SA genes encode proteins that do not act directly as SA biosynthetic enzymes. Mutations in these genes lead to partially compromised SA accumulation and enhanced disease susceptibility to pathogen infection, which can be rescued by exogenous SA treatment. The precise mechanism of action for each type II SA gene, however, still remains to be resolved. Example...

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High-throughput, quantitative analyses of genetic interactions in E. coli

Cited by 220 publications

References 36 publications

Involvement of Neisseria meningitidis Lipoprotein GNA2091 in the Assembly of a Subset of Outer Membrane Proteins

Involvement of Neisseria meningitidis Lipoprotein GNA2091 in the Assembly of a Subset of Outer Membrane Proteins

Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli

Genetic Dissection of Salicylic Acid-Mediated Defense Signaling Networks in Arabidopsis

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