title: RNA sequencing analysis of the broad-host-range strain Sinorhizobium fredii NGR234 identifies a large set of genes linked to quorum sensing-dependent regulation in the background of a traI and ngrI deletion mutant.
abstract: The alphaproteobacterium Sinorhizobium fredii NGR234 has an exceptionally wide host range, as it forms nitrogen-fixing nodules with more legumes than any other known microsymbiont. Within its 6.9-Mbp genome, it encodes two N-acyl-homoserine-lactone synthase genes (i.e., traI and ngrI) involved in the biosynthesis of two distinct autoinducer I-type molecules. Here, we report on the construction of an NGR234-ΔtraI and an NGR234-ΔngrI mutant and their genome-wide transcriptome analysis. A high-resolution RNA sequencing (RNA-seq) analysis of early-stationary-phase cultures in the NGR234-ΔtraI background suggested that up to 316 genes were differentially expressed in the NGR234-ΔtraI mutant versus the parent strain. Similarly, in the background of NGR234-ΔngrI 466 differentially regulated genes were identified. Accordingly, a common set of 186 genes was regulated by the TraI/R and NgrI/R regulon. Coregulated genes included 42 flagellar biosynthesis genes and 22 genes linked to exopolysaccharide (EPS) biosynthesis. Among the genes and open reading frames (ORFs) that were differentially regulated in NGR234-ΔtraI were those linked to replication of the pNGR234a symbiotic plasmid and cytochrome c oxidases. Biotin and pyrroloquinoline quinone biosynthesis genes were differentially expressed in the NGR234-ΔngrI mutant as well as the entire cluster of 21 genes linked to assembly of the NGR234 type III secretion system (T3SS-II). Further, we also discovered that genes responsible for rhizopine catabolism in NGR234 were strongly repressed in the presence of high levels of N-acyl-homoserine-lactones. Together with nodulation assays, the RNA-seq-based findings suggested that quorum sensing (QS)-dependent gene regulation appears to be of higher relevance during nonsymbiotic growth rather than for life within root nodules.
authors.affiliation: Biozentrum Klein Flottbek, Abteilung für Mikrobiologie und Biotechnologie, Universität Hamburg, Hamburg, Germany.
authors.forename: Dagmar
authors.initials: D
authors.lastname: Krysciak
authors.affiliation: Biozentrum Klein Flottbek, Abteilung für Mikrobiologie und Biotechnologie, Universität Hamburg, Hamburg, Germany.
authors.forename: Jessica
authors.initials: J
authors.lastname: Grote
authors.affiliation: Biozentrum Klein Flottbek, Abteilung für Mikrobiologie und Biotechnologie, Universität Hamburg, Hamburg, Germany.
authors.forename: Mariita
authors.initials: M
authors.lastname: Rodriguez Orbegoso
authors.affiliation: Biozentrum Klein Flottbek, Abteilung für Mikrobiologie und Biotechnologie, Universität Hamburg, Hamburg, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Utpatel
authors.affiliation: Core Unit Systems Medicine, Universität Würzburg, Würzburg, Germany.
authors.forename: Konrad U
authors.initials: KU
authors.lastname: Förstner
authors.affiliation: Core Unit Systems Medicine, Universität Würzburg, Würzburg, Germany Institut für Molekulare Infektionsbiologie, Universität Würzburg, Würzburg, Germany.
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.affiliation: Biozentrum Klein Flottbek, Abteilung für Mikrobiologie und Biotechnologie, Universität Hamburg, Hamburg, Germany.
authors.forename: Christel
authors.initials: C
authors.lastname: Schmeisser
authors.affiliation: Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, Missouri, USA.
authors.forename: Hari B
authors.initials: HB
authors.lastname: Krishnan
authors.affiliation: Biozentrum Klein Flottbek, Abteilung für Mikrobiologie und Biotechnologie, Universität Hamburg, Hamburg, Germany wolfgang.streit@uni-hamburg.de.
authors.forename: Wolfgang R
authors.initials: WR
authors.lastname: Streit
mesh_terms: D058947:Bacterial Secretion Systems / Q000235:genetics; D005407:Flagella / Q000235:genetics; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D058507:Host Specificity; D008025:Ligases / Q000235:genetics; D053858:Metabolic Networks and Pathways / Q000235:genetics; D053038:Quorum Sensing; D017423:Sequence Analysis, RNA; D017384:Sequence Deletion; D042181:Sinorhizobium fredii / Q000235:genetics / Q000502:physiology*
chemical_list: D058947:Bacterial Secretion Systems; D008025:Ligases; C449816:N-acylhomoserine lactone synthase