Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56.

The mitochondrial C-to-U RNA editing factor PPR56 of the moss Physcomitrium patens is an RNA-binding pentatricopeptide repeat protein equipped with a terminal DYW-type cytidine deaminase domain. Transferred into Escherichia coli, PPR56 works faithfully on its two native RNA editing targets, nad3eU230SL and nad4eU272SL, and also converts cytidines into uridines at over 100 off-targets in the bacterial transcriptome. Accordingly, PPR56 is attractive for detailed mechanistic studies in the heterologous bacterial setup, allowing for scoring differential RNA editing activities of many target and protein variants in reasonable time. Here, we report (i) on the effects of numerous individual and combined PPR56 protein and target modifications, (ii) on the spectrum of off-target C-to-U editing in the bacterial background transcriptome for PPR56 and two variants engineered for target re-direction and (iii) on combinations of targets in tandem or separately at the 5'- and 3'-ends of large mRNAs. The latter experimentation finds enhancement of RNA editing at weak targets in many cases, including cox3eU290SF as a new candidate mitogenome target. We conclude that C-to-U RNA editing can be much enhanced by transcript features also outside the region ultimately targeted by PPRs of a plant editing factor, possibly facilitated by its enrichment or scanning along transcripts

DNA barcoding reveals an extensive number of cryptic introductions of bladed Bangiales (Rhodophyta) in the Southern North Sea

Using a DNA barcoding approach, we document an extensive number of inter-species cryptic introductions of bladed Bangiales (Pyropia) at an historic oyster aquaculture site in the Southern North Sea. We sampled the intertidal of 20 locations along the Belgian and Dutch coastline, ranging from sheltered to exposed, between February 2022 and April 2023 for bladed Bangiales. 230 individuals of bladed Bangiales were collected, morphological and ecological characteristics described and identified based on chloroplast rbcL gene sequences, revealing the presence of 13 species belonging to the genera Porphyra and Pyropia. While seven species (P. dioica, P. linearis, P. purpurea, P. umbilicalis, Py. collinsii, Py. elongata, Py. leucosticta) are regarded as native to the Northeast Atlantic, four species (Py. katadae, Py. koreana, Py. kinositae and Py. yezoensis) are considered non-indigenous. The records of Py. katadae, Py. kinositae and Py. koreana are the first confirmed observations for the Northeast Atlantic region. In addition, we identified two distinct rbcL clades, for which a definite species identification could not be established due to a lack of matching reference sequences. Species diversity was generally higher during winter and at exposed sites facing the open North Sea. The surprisingly high species diversity of the bladed Bangiales could only be revealed by molecular identification – a crucial tool for reliable species identification in this group of organisms

2018 Research & Innovation Day Program

A one day showcase of applied research, social innovation, scholarship projects and activities.https://first.fanshawec.ca/cri_cripublications/1005/thumbnail.jp