Project description:Lariat RNAs, generated as by-products of RNA splicing from excised introns, must be removed. RNA debranching enzyme (DBR1) is the core factor responsible for lariat RNA removal. However, the mechanism by which DBR1 debranches lariat RNAs remains unclear. Here, we demonstrate that six ALBA (Acetylation Lowers Binding Affinity) proteins interact with DBR1 to enhance its debranching activity and facilitate DBR1's accessibility to lariat RNAs, thereby promoting lariat RNA turnover. Similar to dbr1, alba mutants exhibit pleiotropic developmental defects and accumulate lariat RNAs. ALBAs bind to lariat RNAs via their C-terminal RGG/RG-rich repeats and assist DBR1 in binding to these RNAs. The N-terminal ALBA domain mediates the interaction with DBR1 and enhances its enzymatic activity. Cold stress induces lariat RNA accumulation by attenuating the ALBA–DBR1 interaction, which in turn reduces the induction of cold-responsive genes by impairing their transcription. Together, these findings uncover that lariat RNA turnover requires ALBA proteins.
Project description:The Poplar transcriptome was analyzed in Populus tremulaxPopulus alba clone 717-1B4 control roots and in two poplar lines overexpressing MiSSP7. We performed 9 hybridizations (NimbleGen) with samples derived from Populus tremulaxPopulus alba clone 717-1B4 control roots, as well as from roots of LINE1 and LINE2 MiSSP7 overexpressor poplars (3 biological replicates each). All samples were labeled with Cy3.
Project description:This study characterizes the transcriptomic alterations of P. tremula x P. alba at three weeks after inoculation with the ectomycorrhizal fungus Laccaria bicolor. We performed 6 hybridizations (NimbleGen) with samples derived from Populus tremula x P. alba control roots and mycorrhizal root tips. Samples were taken after 3 weeks of interaction (three biological replicates). All samples were labeled with Cy3.
Project description:Klebsiella pneumoniae is designated as one of six priority ESKAPE pathogens by the World Health Organisation (WHO). It is the causative agent of a number of serious infections, including pneumonia, and worryingly strains are known to have resistance to the four major antibiotic classes. Pyrrolobenzodiazepines (PBDs) with a C8-linked aliphatic heterocycle have been developed as a new class of potent antibacterial compounds. They are active against multidrug resistant (MDR) Gram-negative pathogens, including K. pneumoniae. When K. pneumoniae isolates were exposed to PBDs, they acquired resistance, with an increase in minimum inhibitory concentration (MIC) from 1-4 µg/mL to >32 µg/mL. Resistant strains showed mutations in genes associated with resistance to albicidin, a natural antimicrobial produced by Xanthomonas albilineans, specifically tsx and merR-family regulator albA. Heterologous expression of AlbA in Escherichia coli, and introduction of a proposed resistance-mediating single-nucleotide modification (AlbA L120Q) into the genome of a sensitive K. pneumoniae strain confers both PBD and albicidin resistance. This is further supported by proteomic analysis of the recombineered K. pneumoniae strain (NCTC 7427 AlbA L120Q) together with two strains that have acquired PBD resistance (NCTC 13438 AlbA L120Q and NCTC 13368 AlbA H50N), which all show significantly elevated levels of the AlbA protein compared to isogenic wild-type strains. Crystallographic studies with the purified antibiotic binding domain of K. oxytoca AlbA (termed AlbAS) show binding of KMR-14-14 to the same groove which has been previously shown to bind albicidin, but with a stoichiometry of two PBD bound to each molecule of AlbAS protein. Given the parallels between these two structurally unrelated compound classes, these mechanisms may offer resistance to further antibiotics in K. pneumoniae and should be considered in future antibiotic discovery.
