Project description:KaiC is the central cog of the circadian clock in Cyanobacteria. Close homologs of this protein are widespread among bacteria not known to have a circadian physiology. The function, interaction network, and mechanism of action of these KaiC homologs are still largely unknown. Here, we focus on KaiC homologs found in environmental Pseudomonas species. We characterize experimentally the only KaiC homolog present in Pseudomonas putida KT2440 and Pseudomonas protegens CHA0. Through phenotypic assays and transcriptomics, we show that KaiC is involved in osmotic and oxidative stress resistance in P. putida and in biofilm production in both P. putida and P. protegens.
Project description:Transcriptomic profiling of Pseudomonas protegens Pf-5 comparing zinc-limited culture against zinc-amended culture in M9 minimal media
Project description:Transcriptomic profiling of a gacA mutant of Pseudomonas protegens Pf-5 in comparison to the wild-type Pf-5 strain grown on pea seed surfaces for 24h.
Project description:Transcriptomic profiling of an rpoS mutant of Pseudomonas protegens Pf-5 in comparison to the wild-type Pf-5 strain grown on pea seed surfaces for 24h.
Project description:Transcriptomic profiling of an rpoS mutant of Pseudomonas protegens Pf-5 in comparison to the wild-type Pf-5 strain grown in nutrient broth supplemented with 1% glycerol to OD600=2.0-2.4 (early stationary phase).
Project description:Transcriptomic profiles of Pseudomonas protegens H78 and its hfq mutant, which were grown to the late exponential phase (OD600 = 5.0 to 6.0) in the KMB media at 28 °C, were assessed by deep sequencing (RNA-seq) on Illumina HiSeq 2500.
Project description:Pf1, also known as Phf12 (plant homeodomain (PHD) zinc finger protein 12) is a member of the PHD zinc finger family. Pf1 was first identified in a yeast-two hybrid screen for proteins interacting with the paired amphipathic helix (PAH) 2 domain of mSin3A, and shown to function as a transcriptional repressor . We generated Pf1 knockout mice to define the physiological role of Pf1. To identify the molecular mechanisms underlying the cellular defects elicited by genetic inactivation of Pf1, we next examined the impact of a Pf1 deletion on genome-wide transcriptome. RNA extracted from wild-type and Pf1-depleted MEFs was profiled by hybridization to a whole genome microarray.
Project description:Transcriptomic profiles of Pseudomonas protegens H78 and its rpoN-deleted mutant (H78ΔrpoN), which were grown to the late exponential phase (OD600 = 4.0 to 5.0) in the KMB media at 28 °C, were assessed by deep sequencing (RNA-seq) on BGISEQ-500 (illumina).