title: Quantitative Selection Analysis of Bacteriophage φCbK Susceptibility in Caulobacter crescentus.
abstract: Classical molecular genetics uses stringent selective conditions to identify mutants with distinct phenotypic responses. Mutations giving rise to less pronounced phenotypes are often missed. However, to gain systems-level insights into complex genetic interaction networks requires genome-wide assignment of quantitative phenotypic traits. In this paper, we present a quantitative selection approach coupled with transposon sequencing (QS-TnSeq) to globally identify the cellular components that orchestrate susceptibility of the cell cycle model bacterium Caulobacter crescentus toward bacteriophage φCbK infection. We found that 135 genes representing 3.30% of the Caulobacter genome exhibit significant accumulation of transposon insertions upon φCbK selection. More than 85% thereof consist of new factors not previously associated with phage φCbK susceptibility. Using hierarchical clustering of dose-dependent TnSeq datasets, we grouped these genes into functional modules that correlate with different stages of the φCbK infection process. We assign φCbK susceptibility to eight new genes that represent novel components of the pilus secretion machinery. Further, we demonstrate that, from 86 motility genes, only seven genes encoding structural and regulatory components of the flagellar hook increase phage resistance when disrupted by transposons, suggesting a link between flagellar hook assembly and pili biogenesis. In addition, we observe high recovery of Tn5 insertions within regulatory sequences of the genes encoding the essential NADH:ubiquinone oxidoreductase complex indicating that intact proton motive force is crucial for effective phage propagation. In sum, QS-TnSeq is broadly applicable to perform quantitative and genome-wide systems-genetics analysis of complex phenotypic traits.
authors.affiliation: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland.
authors.forename: Matthias
authors.initials: M
authors.lastname: Christen
authors.affiliation: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: Beusch
authors.affiliation: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Bösch
authors.affiliation: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland.
authors.forename: Dario
authors.initials: D
authors.lastname: Cerletti
authors.affiliation: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland; Life Science Zürich PhD Program on Systems Biology, Zürich, Switzerland.
authors.forename: Carlos Eduardo
authors.initials: CE
authors.lastname: Flores-Tinoco
authors.affiliation: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland.
authors.forename: Luca
authors.initials: L
authors.lastname: Del Medico
authors.affiliation: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland.
authors.forename: Flavia
authors.initials: F
authors.lastname: Tschan
authors.affiliation: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland. Electronic address: beat.christen@imsb.biol.ethz.ch.
authors.forename: Beat
authors.initials: B
authors.lastname: Christen
mesh_terms: D001435:Bacteriophages / Q000254:growth & development*; D016935:Caulobacter crescentus / Q000235:genetics / Q000821:virology*; D003600:Cytosol / Q000737:chemistry; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D042967:Electron Transport Complex I / Q000235:genetics; D005798:Genes, Bacterial; D026901:Membrane Transport Proteins / Q000235:genetics; D016254:Mutagenesis, Insertional; D019655:Quantitative Trait, Heritable; D011809:Quinones / Q000032:analysis; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D026901:Membrane Transport Proteins; D011809:Quinones; D042967:Electron Transport Complex I
keywords: Caulobacter crescentus; bacteriophage; systems biology; transposon sequencing; type IV pili biogenesis; φCbK