Project description:Paenibacillus polymyxa is an agriculturally important plant growth promoting rhizobacterium (PGPR). Many Paenibacillus species are known to be engaged in complex bacteria-bacteria and bacteria-host interactions, which in other bacteria were shown to necessitate quorum sensing communication, but to date no quorum sensing systems have been described in Paenibacillus. Here we show that the type strain P. polymyxa ATCC 842 encodes at least 16 peptide-based communication systems. Each of these systems comprises a pro-peptide that is secreted to the growth medium and further processed to generate a mature short peptide. Each peptide has a cognate intracellular receptor of the RRNPP family, and we show that external addition of P. polymyxa communication peptides to the medium leads to reprogramming of the transcriptional response. We found that these quorum sensing systems are conserved across hundreds of species belonging to the Paenibacillaceae family, with some species encoding more than 25 different peptide-receptor pairs, representing a record number of quorum sensing systems encoded in a single genome.
Project description:Transcriptional profiling of the bacteria Paenibacillus vortex comparing control untreated cells with kanamycin treated cells after 18 hours of exposure. Goal was to determine the effect of the antibiotic kanamycin in concentration which affect the colony morphology on global bacteria gene expression.
Project description:X1 is the most abundant transcript variant of BRAF mRNA and has a long 3’UTR, but its involvement in post-transcriptional regulatory circuits has not been investigated yet. Here, we describe 20 microRNAs that bind directly to the X1 3’UTR. They were identified in BRAFV600E mutant A375 melanoma cells using miR-CATCHv2.0, an implemented experimental method that combines RNA affinity purification with small RNA sequencing and an ad hoc analytical workflow. X1-targeting microRNAs fall into 4 classes, according to the effect that they exert (decrease/increase in BRAFV600E mRNA and protein levels) and on the mechanism they use to achieve it (destabilization/stabilization of X1 mRNA or decrease/increase in its translation). In many cases, the microRNA-induced variations in BRAFV600E protein levels are coupled to consistent variations in pMEK levels and, in turn, to melanoma cell proliferation and sensitivity to the BRAF inhibitor vemurafenib. However, examples exist of microRNAs that uncouple the degree of activation of the ERK pathway from the levels of BRAFV600E protein. Our study describes miR-CATCHv2.0 as an effective tool for the identification of direct microRNA-target interactions and unveils the complexity of the post-transcriptional regulation to which BRAFV600E and the ERK pathway are subjected in melanoma cells.
Project description:Transcriptional profiling of the bacteria Paenibacillus vortex comparing control untreated cells with kanamycin treated cells after 18 hours of exposure. Goal was to determine the effect of the antibiotic kanamycin in concentration which affect the colony morphology on global bacteria gene expression. Two-condition experiment, control cells vs. kanamycin treated cells. Biological replicates: 2 control replicates, 2 treated replicates. Pooling of 5 technical replicates for each biological replicate.
