Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection

Abstract

Ionizing radiation (IR) is lethal to most organisms at high doses, damaging every cellular macromolecule via induction of reactive oxygen species (ROS). Utilizing experimental evolution and continuing previous work, we have generated the most IR-resistant Escherichia coli populations developed to date. After 100 cycles of selection, the dose required to kill 99% the four replicate populations (IR9-100, IR10-100, IR11-100, and IR12-100) has increased from 750 Gy to approximately 3,000 Gy. Fitness trade-offs, specialization, and clonal interference are evident. Long-lived competing subpopulations are present in three of the four lineages. In IR9, one lineage accumulates the heme precursor, porphyrin, leading to generation of yellow-brown colonies. Major genomic alterations are present. IR9 and IR10 exhibit major deletions and/or duplications proximal to the chromosome replication terminus. Contributions to IR resistance have expanded beyond the alterations in DNA repair systems documented previously. Variants of proteins involved in ATP synthesis (AtpA), iron-sulfur cluster biogenesis (SufD) and cadaverine synthesis (CadA) each contribute to IR resistance in IR9-100. Major genomic and physiological changes are emerging. An isolate from IR10 exhibits protein protection from ROS similar to the extremely radiation resistant bacterium Deinococcus radiodurans, without evident changes in cellular metal homeostasis. Selection is continuing with no limit to IR resistance in evidence as our E. coli populations approach levels of IR resistance typical of D. radiodurans.

Proteome Damage Inflicted by Ionizing Radiation: Advancing a Theme in the Research of Miroslav Radman

“…In order to provide several comparative proteomes from IR-resistant species, we carried out identical experiments as laid out above with (a) two isolates from a population that had been subjected to 150 rounds of selection for IR resistance as part of a long-term evolution trial to generate high levels of IR resistance [ 17 , 18 ] and (b) the highly radioresistant bacterium Deinococcus radiodurans . The isolates from the experimental evolution trial are both from one population (IR9) and are denoted IR9-150-1 and IR9-150-2.…”

“…All E. coli strains used are derivatives of E. coli K-12 derivative MG1655 [ 22 ], two of which (IR9-150-1 and IR9-150-2) were generated through 150 cycles of selection with ionizing radiation [ 17 , 18 ]. D. radiodurans is an R1 derivative (ATCC13939) [ 23 ].…”

“…Using experimental evolution, we have been pursuing a long-term project to generate populations of Escherichia coli that are as radiation resistant as the bacterium Deinococcus radiodurans [ 17 , 18 , 19 , 20 ]. Progress reports have been published [ 17 , 18 ]. IR resistance has continued to increase.…”

“…In the present report, we examine proteome damage inflicted by much higher doses of IR. We compare Escherichia coli and Deinococcus radiodurans , as well as two isolates from highly evolved populations generated in the evolution trials [ 17 , 18 ]. Our goal was to continue cataloguing the types of protein oxidation events that occur as well as to begin to determine the extent to which IR-resistance is contingent on a capacity for amelioration of protein oxidation comparable to Deinococcus .…”

PprI: The Key Protein in Response to DNA Damage in Deinococcus

“…The efficiency of the PprI–DdrO response system also relies on the antioxidant intracellular environment protecting the proteome, which is provided and kept by the extraordinary antioxidant system ( Daly et al, 2004 , 2010 ; Slade and Radman, 2011 ). The domestication of the high-resistant E. coli by 100-cycle selection exhibits reduced level of hydroxylation, which further indicates the relationship between DNA damage repair and antioxidant system ( Bruckbauer et al, 2020 ). In other words, both DDR system and antioxidant system are important, without which the radiation resistance will be greatly impaired.…”