At the beginning of the project, (WP1) the Fellow identified DNA methyltransferases in ~ 5000 available complete genomes of A. baumannii. About 32000 predicted R-M-related proteins were grouped in 1055 groups by sequence similarity (% identity > 95%). Only one DNA methyltransferase was encoded in all analysed strains. This methyltransferase was chosen for further experimental study.
Then the Fellow created the methyltransferase deletion mutant for the A. baumannii AB5075 strain (WP2). Transcriptomic data analysis showed 496 differentially expressed genes between the methyltransferase deletion mutant and wild type. To charachterise the role of methylation, the Fellow performed several phenotypic assays, including motility test, antibiotic sensitivity test, biofilm formation, growth, infection of Galleria mellonella larvae, and eukaryotic cells for methyl-deficient mutant and wild-type strains. The mutant had several important phenotypic traits, including differences in growth, plastic surface attachment, biofilm formation, and motility.
We found 273 out of 496 differentially expressed genes have the RAATTY site in the upstream region (WP3). It can explain the difference in the expression of these genes in the mutant strain. We identified several potentially methylation-sensitive transcription factors.
During this project, the Fellow got training (WP4) in bioinformatics, molecular microbiology, RNA-seq data analysis, and infection models at Trinity College Dublin and University of Lyon. Additionally, the Fellow took courses on available at TCD. To facilitate knowledge transfer the Fellow co-supervised 3 BSc and 1 MSc diploma projects, focused on the study of A. baumannii at Trinity College Dublin. The MSc diploma results on characteristics of a rare species of Acinetobacter soli AS15, isolated from an Irish Hospital, were published recently. The new skills will help the Fellow to to facilitate her career prospects.
Results of the project were presented (WP5) at two conferences, ISMB/ECCB 2021 (online, ~2000 participants), AcinetoVibes 2022 (online, ~ 100 participants). Results of the ERA project will be reported in forthcoming papers on the epigenetic regulation of A. baumannii. Results of the project were presented to the general public during the European Researchers’ Night 2021.
The conclusion of the action
Scientific objectives of the project are achieved. We found that the AbaM deletion mutant has impaired growth, plastic attachment, and biofilm formation and is less virulent. We identified differentially expressed genes that cause the abaM deletion mutant phenotype.
Training objectives are achieved. The Fellow improved her skills in Data Analysis and Genomic/Transcriptomyc data handlyng, obtained new wet-lab skills. Additionally, the Fellow got transferrable skills, such as Project Management and Scientific Communication. The obtained skills and results will help the Fellow to establish herself as an independent investigator in the field of epigenomics and gene expression regulation.
