Exposure of Shewanella oneidensis MR-1 to Sublethal Doses of Ionizing Radiation Triggers Short-Term SOS Activation and Longer-Term Prophage Activation

Abstract

The bacterial minimum threshold of sensitivity to ionizing radiation (IR) is poorly understood, which hinders our understanding of how living systems recover from the doses of IR experienced in medical, industrial, and off-world environments. Using a transcriptome-wide approach, we studied how in the highly radiosensitive bacterium S. oneidensis , genes (including the SOS regulon and the So Lambda prophage) are activated after exposure to low doses of IR.

Geometric changes in the nucleoids of Deinococcus radiodurans reveal involvement of new proteins in recovery from ionizing radiation

“…Specifically, the average cell area is greater following IR, and the average nucleoid eccentricity is lower, for all radiation doses tested (Figure 3A, Supplementary Figure S7, Table 1). The increase in cell area is consistent with the idea that bacterial cells under stress divide less frequently and therefore may grow to larger sizes before division [34,49]. The changes in nucleoid eccentricity and circularity both point to the nucleoid becoming a more-compact and more-spherical shape after radiative stress than before.…”

“…The area enclosed by the membrane mask was used to measure the cross-sectional area of each cell (Cell Area), and the area covered by the nucleoid mask was used to measure the cross-sectional area of each nucleoid (Nucleoid Area). Measuring cell area allows assessment of spatial changes in cells that are not directly related to any change in nucleoid properties but are likely to arise from radiative damage [34]. Given that changes in relative cell and nucleoid area sizes are easily conflated with changes in absolute size following qualitative inspection by the human eye, we provide a quantitative measure of relative cell-nucleoid sizes by introducing the parameter nucleoid fractional area (NFA); this is the ratio of nucleoid cross-sectional area to cell cross-sectional area, using the matched pairs of each cell's membrane and nucleoid masks.…”

TolRad: A model for predicting radiation tolerance using Pfam annotations identifies novel radiosensitive bacterial species from reference genomes and MAGs

“…While genetic explanations have been offered for the sensitivity of specific bacteria, such as a large number of proteins with heme (i.e. iron-binding) domains in the radiosensitive bacteria S. oneidensis (26) (49) a broadly applicable understanding of the genetic origins of radiation sensitivity has not been proposed. The construction of TolRad required the identification of Pfam domains informative of radiation tolerance; we present these findings, as well as the Mean Decrease in Accuracy and examples of Escherichia coli genes with these domains, in Table 2 .…”

“…There are several applications for TolRad, including providing context for metagenomic studies of bacterial communities after IR exposure (19), searching for bacterial sources of low-dose biomarkers (49), and as a guide for selecting against radiosensitive species for bioremediation development (17). Currently, the only way to determine the sensitivity of a bacteria species to IR is to conduct extensive experimentation, requiring both the ability to culture the bacteria of interest and a high-powered source of IR.…”