{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Peter Newell"],"organism":["Pseudomonas fluorescens Pf0-1"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-30681"],"description":["Whole genome gene expression study comparing Pseudomonas fluorescens Pf0-1 (Wt) relative to a delta-pst mutant (deletion of the pstSCAB operon) that consitutively expresses the Pho regulon Mutants used in this study are further described  in Monds, R.D. Newell, P.D., Gross, R.H., O'Toole, G.A. (2007) Phosphate-dependent modulation of c-di-GMP levels regulates Pseudomonas fluorescens Pf0-1 biofilm formation by controlling secretion of the adhesin LapA. Mol. Microbiol. 63(3): 656-679 A four chip study using total RNA recovered from two independent wild-type cultures of wild type strain Pseudomonas fluorescens Pf0-1 and two independent cultures of  Pseudomonas fluorescens Pf0-1 delta pst mutant (deletion of the pstSCAB operon). Each chip measures the expression level of 5733 open reading frames (ORFs) genes from Pseudomonas fluorescens Pf0-1 (Refseq: NC_007492) with twenty 60-mer postive match (PM) probes per gene, with three-fold technical redundancy."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Processing - RNA was stabilized before extraction by addition mixing of culture directly with RNAprotect reagent (Qiagen) in a 1:2 ratio. Samples were frozen at -80 degrees celcius until RNA extraction.","Hybridization - Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.","Growth Protocol - Strains were grown overnight in 5 mL LB medium before diluting 1:50 into 5 mL K10T-1 medium (Monds et al (2007) Mol. Microbiol. 63(3): 656-679) and grown with shaking to mid exponential phase (OD600 = 0.6).","Nucleic Acid Extraction - RNA was extracted using an RNeasy kit (QIAGEN, Valencia, CA) according to the manufacturer's instructions, except that a postcolumn DNase treatment was performed using 15 U of RQ1 DNase (Promega, Madison, WI). The RNA was subsequently purified using the RNeasy kit. RNA integrity was assessed by gel electrophoresis, and genomic DNA contamination was assessed by PCR.","Labeling - Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Assay Data Transformation - ID_REF = <br>VALUE = RMA-normalized, averaged gene-level signal intensity","Image Adquisition - Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.","Feature Extraction - The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["Cyclic di-GMP (c-di-GMP) is a broadly conserved, intracellular second-messenger molecule that regulates biofilm formation by many bacteria. The synthesis of c-di-GMP is catalyzed by diguanylate cyclases (DGCs) containing the GGDEF domain, while its degradation is achieved through the phosphodiesterase activities of EAL and HD-GYP domains. c-di-GMP controls biofilm formation by Pseudomonas fluorescens Pf0-1 by promoting the cell surface localization of a large adhesive protein, LapA. LapA localization is regulated posttranslationally by a c-di-GMP effector system consisting of LapD and LapG, which senses cytoplasmic c-di-GMP and modifies the LapA protein in the outer membrane. Despite the apparent requirement for c-di-GMP for biofilm formation by P. fluorescens Pf0-1, no DGCs from this strain have been characterized to date. In this study, we undertook a systematic mutagenesis of 30 predicted DGCs and found that mutations in just 4 cause reductions in biofilm formation by P. fluorescens Pf0-1 under the conditions tested. These DGCs were characterized genetically and biochemically to corroborate the hypothesis that they function to produce c-di-GMP in vivo. The effects of DGC gene mutations on phenotypes associated with biofilm formation were analyzed. One DGC preferentially affects LapA localization, another DGC mainly controls swimming motility, while a third DGC affects both LapA and motility. Our data support the conclusion that different c-di-GMP-regulated outputs can be specifically controlled by distinct DGCs."],"study_type":["transcription profiling by array"],"species":["Pseudomonas fluorescens Pf0-1"],"pubmed_title":["Systematic analysis of diguanylate cyclases that promote biofilm formation by Pseudomonas fluorescens Pf0-1."],"pubmed_authors":["Russell Monds","George O'Toole","Newell PD, Yoshioka S, Hvorecny KL, Monds RD, O'Toole GA","Peter Newell"],"additional_accession":[]},"is_claimable":false,"name":"Expression analysis of Pseudomonas fluorescens Pf0-1 (Wt) and delta-pst mutant grown in K10T-1 medium","description":"Whole genome gene expression study comparing Pseudomonas fluorescens Pf0-1 (Wt) relative to a delta-pst mutant (deletion of the pstSCAB operon) that consitutively expresses the Pho regulon Mutants used in this study are further described  in Monds, R.D. Newell, P.D., Gross, R.H., O'Toole, G.A. (2007) Phosphate-dependent modulation of c-di-GMP levels regulates Pseudomonas fluorescens Pf0-1 biofilm formation by controlling secretion of the adhesin LapA. Mol. Microbiol. 63(3): 656-679 A four chip study using total RNA recovered from two independent wild-type cultures of wild type strain Pseudomonas fluorescens Pf0-1 and two independent cultures of  Pseudomonas fluorescens Pf0-1 delta pst mutant (deletion of the pstSCAB operon). Each chip measures the expression level of 5733 open reading frames (ORFs) genes from Pseudomonas fluorescens Pf0-1 (Refseq: NC_007492) with twenty 60-mer postive match (PM) probes per gene, with three-fold technical redundancy.","dates":{"release":"2011-07-13T00:00:00Z","modification":"2023-08-17T04:25:21.6Z","creation":"2022-02-08T00:54:44.455Z"},"accession":"E-GEOD-30681","cross_references":{"GEO":["GSE30681"],"pubmed":["21764921"],"EFO":["EFO_0002768"],"doi":["10.1128/JB.05483-11"]}}