Proteogenomic insights into uranium tolerance of a Chernobyl's Microbacterium bacterial isolate

Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10μM uranyl nitrate sampled at three previously identified phases of uranyl tolerance. We experimentally detected and annotated 1532 proteins and highlighted a total of 591 proteins for which abundances were significantly differing between conditions. Notably, proteins involved in phosphate and iron metabolisms show high dynamics. A large ratio of proteins more abundant upon uranyl stress, are distant from functionally-annotated known proteins, highlighting the lack of fundamental knowledge regarding numerous key molecular players from soil bacteria. Microbacterium oleivorans A9 is an interesting environmental model to understand biological processes engaged in tolerance to radionuclides. Using an innovative proteogenomics approach, we explored its molecular mechanisms involved in uranium tolerance. We sequenced its genome, interpreted high-throughput proteomic data against a six-reading frame ORF database deduced from the draft genome, annotated the identified proteins and compared protein abundances from cells exposed or not to uranyl stress after a cascade search. These data show that a complex cellular response to uranium occurs in Microbacterium oleivorans A9, where one third of the experimental proteome is modified. In particular, the uranyl stress perturbed the phosphate and iron metabolic pathways. Furthermore, several transporters have been identified to be specifically associated to uranyl stress, paving the way to the development of biotechnological tools for uranium decontamination. [Display omitted] •In-depth comparative analysis of the proteome of Microbacterium oleivorans A9 which is a uranium-tolerant actinobacteria.•The data highlight that uranyl stress perturbed the phosphate and iron metabolic pathways of Microbacterium.•Several transporters have been identified to be specifically associated to uranyl stress.