DNA Double-Strand Break Repair at −15°C

Abstract

The survival of microorganisms in ancient glacial ice and permafrost has been ascribed to their ability to persist in a dormant, metabolically inert state. An alternative possibility, supported by experimental data, is that microorganisms in frozen matrices are able to sustain a level of metabolic function that is sufficient for cellular repair and maintenance. To examine this experimentally, frozen populations of Psychrobacter arcticus 273-4 were exposed to ionizing radiation (IR) to simulate the damage incurred from natural background IR sources in the permafrost environment from over ϳ225 kiloyears (ky). High-molecularweight DNA was fragmented by exposure to 450 Gy of IR, which introduced an average of 16 double-strand breaks (DSBs) per chromosome. During incubation at ؊15°C for 505 days, P. arcticus repaired DNA DSBs in the absence of net growth. Based on the time frame for the assembly of genomic fragments by P. arcticus, the rate of DNA DSB repair was estimated at 7 to 10 DSBs year ؊1 under the conditions tested. Our results provide direct evidence for the repair of DNA lesions, extending the range of complex biochemical reactions known to occur in bacteria at frozen temperatures. Provided that sufficient energy and nutrient sources are available, a functional DNA repair mechanism would allow cells to maintain genome integrity and augment microbial survival in icy terrestrial or extraterrestrial environments. The results from decades of studying the stability of DNA in bacteria may be summarized in two uncomplicated axioms. First, genomic DNA is not inert; the genetic material will degrade with time, and damage will accumulate unless that degradation is repaired. And second, if this degradation is not reversed, the cell will die. The repair processes that cope with DNA damage are integral to life, and it is assumed that all species express means of maintaining genetic integrity.The importance of DNA repair to cell viability motivated extensive study of the biochemistry and molecular biology of these repair processes in model organisms such as Escherichia coli (1). Although the advantages of using this species for such studies are well documented, there is a question as to whether detailed knowledge of DNA repair in E. coli as observed under standard laboratory conditions adequately represents the full spectrum of bacterial responses to DNA damage. For instance, DNA repair is an energy-intensive activity (2, 3), but microbial species in nature rarely experience optimal conditions for growth or have access to nutrient excess. Without a generous supply of energy, cells may need to generate a more measured response, rationing available resources in a manner that prioritizes the most important tasks for survival. Moreover, viability in the absence of cellular reproduction is sustained only by cells that do not accumulate a level of damage (e.g., to DNA) that exceeds a threshold beyond which effective repair is no longer possible.Genomic DNA and viable bacteria are preserved in ancient ice and permafrost for hun...

Proteomics of Colwellia psychrerythraea at subzero temperatures – a life with limited movement, flexible membranes and vital DNA repair

“…The metabolic activity of psychrotolerant and psychrophilic bacteria at subzero temperatures has been previously reported (e.g., Dieser et al, 2013;Junge et al, 2006;Mykytczuk et al, 2013); however, this is the first study that uses proteomics to elucidate some of the molecular mechanisms behind the ability of these bacteria to metabolize during extended periods of time at cold temperatures in saline ice. By combining metabolic assays (DNA and protein metabolism) with discoverybased proteomics, we provide direct evidence of metabolic pathways that allow C. psychrerythraea to survive at subzero temperatures.…”

“…Our leucine incorporation results showed protein synthesis in Cp34H down to −10°C over the course of 8 weeks. At very low temperatures, low rates of metabolism may offset cellular and macromolecular damage in permafrost bacteria (Dieser et al, 2013), thereby allowing for survival over prolonged time frames ). Maximum [3H]-leu incorporation occurred at the 24 h time point for all temperatures and was greatest in the −1°C treatment and lowest at −10°C.…”

“…Despite experimental challenges, research into the elusive nature of microbial processes at subzero temperatures remains active (e.g., Bakermans and Skidmore, 2011;Piette et al, 2011;Collins and Deming, 2013;Dieser et al, 2013;Tuorto et al, 2014). The emerging picture of microbial metabolism of psychrotolerant (i.e., eurypsychrophiles: cold-active; growth at >20°C, Bakermans and Skidmore, 2011) terrestrial bacteria at temperatures below −5°C suggests that low rates of metabolism may offset cellular and macromolecular damage, thereby allowing for survival over prolonged time frames Dieser et al, 2014).…”

Survivability of Soil and Permafrost Microbial Communities after Irradiation with Accelerated Electrons under Simulated Martian and Open Space Conditions

“…There are a lot of studies testifies possibility of it. Microbial metabolism is revealed at temperatures at least down to −33 • C [88,89]. Moreover, it is shown that econiches with liquid water and positive temperatures can occur on the current Mars [88,[90][91][92][93].…”

Evolution with a seed bank: The population genetic consequences of microbial dormancy

“…However, many microorganisms within the permafrost may not be completely dormant. For example, psychrophilic taxa isolated from the permafrost are capable of genome replication at temperatures as low as −20°C (Tuorto et al, 2014) and evidence of DNA repair has been found in taxa that have persisted in the permafrost for hundreds of thousands to millions of years (Dieser et al, 2013;Johnson et al, 2007). This does not suggest that there are no dormant microorganisms within the permafrost, as the generation-time effect can still occur if growth rate is correlated with season and the energetic cost of DNA repair is thought to be negligible (see section 2.2).…”