Agrobacterium tumefaciens ExoR controls acid response genes and impacts exopolysaccharide synthesis, horizontal gene transfer and virulence gene expression.
Ontology highlight
ABSTRACT:
ORGANISM(S): Agrobacterium tumefaciens
SUBMITTER: Aaron Buechlein
PROVIDER: E-GEOD-59790 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Agrobacterium tumefaciens exoR controls acid response genes and impacts exopolysaccharide synthesis, horizontal gene transfer, and virulence gene expression.
Heckel Brynn C BC Tomlinson Amelia D AD Morton Elise R ER Choi Jeong-Hyeon JH Fuqua Clay C
Journal of bacteriology 20140630 18
Agrobacterium tumefaciens is a facultative plant pathogen and the causative agent of crown gall disease. The initial stage of infection involves attachment to plant tissues, and subsequently, biofilms may form at these sites. This study focuses on the periplasmic ExoR regulator, which was identified based on the severe biofilm deficiency of A. tumefaciens exoR mutants. Genome-wide expression analysis was performed to elucidate the complete ExoR regulon. Overproduction of the exopolysaccharide su ...[more]
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Project description:Agrobacterium tumefaciens is a facultative plant pathogen and the causative agent of crown gall disease. The initial stage of infection involves attachment to plant tissues and, subsequently, biofilms may form at these sites. This study focuses on the periplasmic ExoR regulator, which was identified based on the severe biofilm deficiency of A. tumefaciens exoR mutants. Genome-wide expression analysis was performed to elucidate the complete ExoR regulon. Overproduction of the exopolysaccharide succinoglycan is a dramatic phenotype of exoR mutants. Comparative expression analyses revealed that the core ExoR regulon is unaffected by succinoglycan synthesis. Several findings are consistent with previous observations: genes involved in succinoglycan biosynthesis, motility, and type VI secretion are differentially expressed in the ΔexoR mutant. In addition, these studies revealed new functional categories regulated by ExoR including genes related to virulence, conjugation of the pAtC58 megaplasmid, ABC transporters, and cell envelope architecture. To address how ExoR exerts a broad impact on gene expression from its periplasmic location, a genetic screen was performed to isolate suppressor mutants that mitigate the exoR motility phenotype and identify downstream components of the ExoR regulatory pathway. This suppression analysis identified the acid-sensing two-component system ChvG-ChvI, and the suppressor mutant phenotypes suggest that all or most of the characteristic exoR properties are mediated through ChvG-ChvI. Subsequent analysis indicates that exoR mutants are simulating a response to acidic conditions, even in neutral media. This work expands the model for ExoR regulation in A. tumefaciens and underscores the global role this regulator plays on gene expression. Four biological replicates, Independent RNA preparations, Two dye-swaps
2014-07-26 | E-GEOD-59788 | biostudies-arrayexpress
Project description:Agrobacterium tumefaciens is a facultative plant pathogen and the causative agent of crown gall disease. The initial stage of infection involves attachment to plant tissues and, subsequently, biofilms may form at these sites. This study focuses on the periplasmic ExoR regulator, which was identified based on the severe biofilm deficiency of A. tumefaciens exoR mutants. Genome-wide expression analysis was performed to elucidate the complete ExoR regulon. Overproduction of the exopolysaccharide succinoglycan is a dramatic phenotype of exoR mutants. Comparative expression analyses revealed that the core ExoR regulon is unaffected by succinoglycan synthesis. Several findings are consistent with previous observations: genes involved in succinoglycan biosynthesis, motility, and type VI secretion are differentially expressed in the ?exoR mutant. In addition, these studies revealed new functional categories regulated by ExoR including genes related to virulence, conjugation of the pAtC58 megaplasmid, ABC transporters, and cell envelope architecture. To address how ExoR exerts a broad impact on gene expression from its periplasmic location, a genetic screen was performed to isolate suppressor mutants that mitigate the exoR motility phenotype and identify downstream components of the ExoR regulatory pathway. This suppression analysis identified the acid-sensing two-component system ChvG-ChvI, and the suppressor mutant phenotypes suggest that all or most of the characteristic exoR properties are mediated through ChvG-ChvI. Subsequent analysis indicates that exoR mutants are simulating a response to acidic conditions, even in neutral media. This work expands the model for ExoR regulation in A. tumefaciens and underscores the global role this regulator plays on gene expression. Three biological replicates, Independent RNA preparations, One dye-swap
2014-07-26 | E-GEOD-59789 | biostudies-arrayexpress
Project description:Many bacteria colonize surfaces and transition to a sessile mode of growth. The plant pathogen Agrobacterium tumefaciens produces a unipolar polysaccharide (UPP) adhesin at single cell poles that contact surfaces. Here we report that elevated levels of the intracellular signal cyclic diguanosine monophosphate (c-di-GMP) lead to surface-contact-independent UPP production and a red colony phenotype due to production of UPP and the exopolysaccharide cellulose, when A. tumefaciens is incubated with the polysaccharide stain Congo Red. Transposon mutations with elevated Congo Red staining identified presumptive UPP-negative regulators, mutants for which were hyperadherent, producing UPP irrespective of surface contact. Multiple independent mutations were obtained in visN and visR, activators of flagellar motility in A. tumefaciens, now found to inhibit UPP and cellulose production. Expression analysis in a visR mutant and isolation of suppressor mutations, identified three diguanylate cyclases inhibited by VisR. Null mutations for two of these genes decrease attachment and UPP production, but do not alter cellular c-di-GMP levels. However, analysis of catalytic site mutants revealed their GGDEF motifs are required to increase UPP production and surface attachment. Mutations in a specific presumptive c-di-GMP phosphodiesterase also elevate UPP production and attachment, consistent with c-di-GMP activation of surface-dependent adhesin deployment. Three biological replicates, independent RNA preparations, one dye swap.
2014-08-21 | E-GEOD-60565 | biostudies-arrayexpress
Project description:A conserved regulatory pathway directs developmental transitions and asymmetries in Agrobacterium tumefaciens. Core components of this coordination of division and development (CDD) pathway include two integrated phosphorelays. One of these phosphorelays includes at least four histidine sensor kinase homologues, DivJ, PleC, PdhS1, and PdhS2, and at least two response regulators, DivK and PleD. Previously we demonstrated that PdhS2 reciprocally regulates biofilm formation and swimming motility. In the current study we further dissect the architecture of the CDD pathway in A. tumefaciens with respect to PdhS2. We show that PdhS2-dependent effects on attachment and motility require the response regulator, DivK, but do not require PdhS2 autokinase or phosphotransfer activities. We also demonstrate that PdhS2 regulation of biofilm formation is dependent upon multiple diguanylate cyclases, including PleD, DgcA, and DgcB, implying that PdhS2 regulation of this process intersects with pathways regulating levels of the second messenger cyclic-di-GMP. Finally, we show that upon cell division a GFP fusion to PdhS2 dynamically localizes to the new pole of the bacterium suggesting that PdhS2 controls processes in the daughter cell compartment of predivisional cells. These observations suggest that PdhS2 negatively regulates DivK, and possibly PleD, activity to control developmental processes in the daughter cell compartment of predivisional cells, as well as in newly released motile daughter cells. Three biological replicates, independent RNA preparations, one dye swap.
2015-07-24 | E-GEOD-71267 | biostudies-arrayexpress
Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. We demonstrate that A. tumefaciens biofilm formation is reduced under limiting iron conditions. Treatment of A. tumefaciens cultures with EDDHA, an iron-specific extracellular chelator, inhibited both planktonic growth rate and adherent biomass. These effects were reversed upon addition of exogenous ferrous iron. This reduced biofilm formation effect is independent of the known iron-responsive regulators Irr and RirA. Transcriptome analysis comparing gene expression under iron-replete versus iron-deficient conditions identified hundreds of genes that are differentially regulated. Downregulated genes suggest an iron sparing response. Four biological replicates, independent RNA preparations, one dye swap.
2015-07-22 | E-GEOD-71138 | biostudies-arrayexpress
Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. In several systems intracellular levels of the redox-active manganous (Mn2+) and ferrous (Fe2+) ions are interrelated and have tight corresponding regulation with respect to one another. We show that limiting manganese concentrations elicit similar growth and biofilm phenotypes to those seen under iron-limiting conditions. Microarray analysis comparing gene expression in manganese-replete versus manganese-limiting conditions identified a small number of differentially regulated transcripts. These results indicate that the redox-active manganous and ferrous ions are required for wild-type levels of growth and biofilm formation, and that the manganese-dependent response is primarily post-transcriptional and complementary to, but not redundant with, the iron-dependent response. Four biological replicates, independent RNA preparations, two dye swaps.
2015-07-24 | E-GEOD-71266 | biostudies-arrayexpress
Project description:To learn more about the global effects of phosphatidylcholine (PC)-deficiency in A. tumefaciens, we performed transcriptomic studies comparing the wild type and a PC-deficient DpmtA Dpcs mutant. We expanded the number of affected virulence genes and showed that the loss of PC was correlated with altered expression of multiple genes encoding membrane or membrane-associated proteins and proteins which fulfil their function at the membrane. The PC-deficient mutant analyzed in this study is further described in Sonja Klüsener, Stephanie Hacker, Yun-Long Tsai, Julia E. Bandow, Ronald Gust, Erh-Min Lai and Franz Narberhaus. 2010. Proteomic and transcriptomic characterization of a virulence-deficient phosphatidylcholine-negative Agrobacterium tumefaciens mutant. Total RNA was extracted from A. tumefaciens C58 wild-type and PC-deficient mutant cells grown under virulence-induced and non-induced conditions. The 4-plex NimbleGen Gene Expression Array for A. tumefaciens (Design ID 080630) represents 5344 genes and is based on NCBI reference sequences NC_003062, NC_003063, NC_003064 and NC_003065. Each gene is represented by 6 probes (45mer-60mer oligonucleotides), each in two copies on different locations on the array. Three biological replicates for each cultivation condition were analyzed for A. tumefaciens wild-type and PC-deficient mutant strains.
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Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 leafs in response to A. tumefaciens C58 for the identification of differentially expressed genes. 3-week-old A.thaliana Col-0 seedlings were selected for growth in hydroponic systems. A. tumefaciens C58 was inoculated into the hydroponic system and co-cultivation persisted for 8 hours. Leaf tissue was seperated for RNA extraction and hybridization to the ATH1 Affymetrix microarray.
2014-10-28 | E-GEOD-62749 | biostudies-arrayexpress
Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 roots in response to A. tumefaciens C58 for the identification of differentially expressed genes. 3-week-old A.thaliana Col-0 seedlings were selected for growth in hydroponic systems. A. tumefaciens C58 was inoculated into the hydroponic system and co-cultivation persisted for 8 hours. Root tissue was seperated for RNA extraction and hybridization to the ATH1 Affymetrix microarray.
2014-10-28 | E-GEOD-62750 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-10-28 | E-GEOD-62751 | biostudies-arrayexpress