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Biology of Extreme Radiation Resistance:The Way of Deinococcus radiodurans

Anita Krisko1 and Miroslav Radman1,2

1Mediterranean Institute for Life Sciences, 21000 Split, Croatia2Faculte de Medecine, Universite Rene Descartes—Paris V, INSERM U1001, 75015 Paris, France

Correspondence: [email protected]

The bacterium Deinococcus radiodurans is a champion of extreme radiation resistance that isaccounted for by a highly efficient protection against proteome, but not genome, damage. Awell-protected functional proteome ensures cell recovery from extensive radiation damageto other cellular constituents by molecular repair and turnover processes, including anefficient repair of disintegrated DNA. Therefore, cell death correlates with radiation-induced protein damage, rather than DNA damage, in both robust and standard species.From the reviewed biology of resistance to radiation and other sources of oxidative damage,we conclude that the impact of protein damage on the maintenance of life has been largelyunderestimated in biology and medicine.

Several recent reviews comprehensively pres-ent the extraordinary bacterium Deinococ-

cus radiodurans, best known for its biologicalrobustness involving an extremely efficientDNA repair system (Cox and Battista 2005; Bla-sius et al. 2008; Daly 2009; Slade and Radman2011). The aim of this short review of the biol-ogy of D. radiodurans is to single out a generalconcept of the primacy of biological function(proteome) over information (genome) in themaintenance of life. A cell dies when its vitalfunctions performed by the proteome cease,for example, because of the direct loss of prote-ome functionality or via the loss of membraneintegrity, whereas genome integrity is required(in addition to an active proteome) for the per-petuation of cells that have survived. But sur-vival itself depends primarily on the proteome

rather than the genome. A cell that instantlyloses its genome can function for some time,unlike one that loses its proteome. In otherwords, the proteome sustains and maintainslife, whereas the genome ensures the perpetua-tion of life by renewing the proteome, a processcontingent on a preexisting proteome that re-pairs, replicates, and expresses the genome. Inaddition to the functional integrity of the pro-teome, small metabolites and other cofactorsfor catalysis and protein interactions are equallyimportant for proteome functionality. Howev-er, chemical damage to cofactors is not a likelyprimary bottleneck in survival because of theirhigh molar concentrations, compared with pro-teins. And, finally, it is the proteome that syn-thesizes metabolites and imports vital metal co-factors and ions. Although obvious, the concept

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that the prime target in cell degeneracy anddeath is proteome activity—ensuring all vitalfunctions including genome integrity—is con-spicuously absent in biological and medical sci-ences. This overview of the biology of a prokary-otic cell that survives conditions lethal to otherspecies is to define and elaborate a general con-cept of sustainability of life that applies to allliving cells.

ROBUSTNESS AND LIFESTYLE OFDeinococcus radiodurans (DRA)

Since its anecdotal discovery as a contaminantin radiation-sterilized corned beef cans (Ander-son et al. 1956; Duggan et al. 1963), Deinococcusradiodurans (Dra) has fascinated biologists byits extraordinary resistance to ionizing radia-tion. Radiation biology—the study of how ra-diation alters and destroys life—brought aboutthe birth of a DNA-centered molecular biology.Thus, when it was shown that (1) Dra DNA is assensitive to radiation-induced breakage as thegenomes of other bacteria (Burrell et al. 1971;Bonura and Smith 1976; Gerard et al. 2001), and(2) the analyses of its genome and proteomeshowed nothing extraordinary (White et al.1999), some fundamental queries surfaced (be-low). Because the extreme radiation resistancedid correlate with an extraordinary capacity torepair massive DNA damage inflicted by ioniz-ing radiation or ultraviolet light, several ques-tions arose: What is the mechanism of suchspectacular DNA repair capacity? Can extremeresistance to radiation be acquired by other or-ganisms, for instance, human? Why and howdid robust life evolve, in particular, because noradiation sources on Earth are known that couldproduce doses comparable to those of Dra re-sistance? The hypothesis of an extraterrestrialorigin of Dra (Pavlov et al. 2006) should placeits genome outside the terrestrial phylogenetictree (which is not true; see below), unless allDNA-sequenced terrestrial life was seeded byDra, that is, descended from a deinococcal pan-spermia. In that case, Dra should be at the rootof the current DNA-based terrestrial phyloge-netic tree.

Mattimore and Battista (1996) proposed amore plausible hypothesis that the resistance toradiation is a by-product of a primary selectionfor resistance to desiccation. Moreover, such ahypothesis is sensible because some other rareunrelated bacteria, as well as some archaea,plants, and small animals, for example, bdelloidrotifers and tardigrada, also acquired coincidentresistance to desiccation and radiation. In otherwords, mechanisms of recovery from desiccationdamage ensure recovery from radiation damage.But why did the selection for resistance to desic-cation operate on Dra rather than on all otherbacteria? The answer might lie in the lifestyle andecological distribution of Dra.

Unlike the well-known enterobacteria, Drais ubiquitous in nature but its populations areminor compared with other bacteria occupyingthe same ecological niches. The likely reason isthat other bacteria overgrow Dra in Nature,because in the standard laboratory media theygrow faster than Dra. It looks as if Dra made an“investment” in the efficiency of survival (ro-bustness), whereas other bacteria made an in-vestment in the efficiency of growth (reproduc-tion). The nature of such an “investment” isdiscussed below. Robustness is the characteris-tic of individual cells and does not imply win-ning the race, at the level of populations, withless robust but faster growing competitors, par-ticularly in mild natural habitats. However,under harsh life conditions—arid environmentssuch as deserts—desiccated Dra populationsdominate the less-resilient species by their ca-pacity to regrow after rehydration.

The lifestyle and metabolism of Dra suggestthat this bacterium is a scavenger of food pro-duced by (or composed of ) other (dead) organ-isms: It feeds on amino acids from degradedproteins and sugars from degraded polymersby excreting diverse hydrolytic enzymes. Itsmosaic genome composition and remarkablegenomic variability (below) are consistent withan evolved preadaptation to diverse environ-ments scattered among the deinococcal popula-tions and species, hence, the ubiquitous pres-ence of similar deinococcal variants in differenthabitats (White et al. 1999; for review, see Sladeand Radman 2011).

A. Krisko and M. Radman

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THE ECOLOGY AND THE GENOME OFD. radiodurans

The genome of Dra R1 consists of two largeDNAs (3.06 Mb) called chromosomes and twosmaller DNAs (223 kb) called plasmids (Whiteet al. 1999). Sequence-wise, the Dra genome is amosaic of Bacillus subtilis- and Thermus ther-mophilus-like genomes with some individualgenes that could have been acquired even fromother kingdoms of life. Such interkingdom hor-izontal gene transfer could originate from DNA-scavenging events facilitated by the high naturaltransformability of Dra. Genome sequencingof 37 natural isolates (Deinove, pers. comm.)showed a very high diversity that, astonishingly,appears similar worldwide (see Slade and Rad-man 2011). There is even a factor of two in thegenome size and gene content between thesmallest and largest sequenced deinococcal ge-nomes (Jung et al. 2010; Deinove, pers. comm.).

The ubiquitous ecological distribution ofdeinococcal diversity may account for the re-sults of genome analyses in the following way.The desiccated bacteria are constituents of thedust occasionally blown up by the winds intothe atmosphere and stratosphere. where bacte-ria from different geographic origins mix whilebeing exposed to UVC light 100 to 1000 timesmore intense than on Earth’s surface. They even-tually rehydrate when falling back on Earth withthe rain and snow (this is how Francois-XavierPellay in our laboratory collects robust bacteria)and—depending on their genomic constitu-tion—develop, or not, in the ecological nichesinto which they happen to fall. Indeed, the mostefficient cellulose degraders are deinococcifound growing in the waist of the wood-sawingindustry (Deinove, pers. comm.).

The resistance of D. radiodurans is not ex-clusive to radiation and desiccation but extendsalso to many toxic chemicals and conditions(Lown et al. 1978). Therefore, Dra is called apolyextremophile, a robust “generalist,” to bedistinguished from specialized extremophileswith an evolutionary redesign of their proteome(e.g., proteins purified from thermophiles arethermostable in vitro) (see Smole et al. 2011).Unlike specialized extremophiles, Dra does not

thrive on extreme conditions—indeed, it doesnot grow while desiccated or when heavily irra-diated—but it can reproduce under standardgrowth conditions after recovering from dam-age inflicted by chronic moderate, or acute in-tense, exposures to cytotoxic conditions. This“resurrection” following diverse kinds of dam-age lethal to most organisms raises the question:How did the multiresistance evolve? Was it bymany parallel strategies, each selected for a spe-cific resistance, or by a single polyvalent strategygenerating resistance to many different condi-tions lethal to most species? The latter seems tobe the case of Dra (see below).

ROBUST DNA REPAIR IN D. radiodurans

The science of molecular biology was dominat-ed by the notion of information, its storage,transmission, and evolution as encrypted inthe nucleotide sequence of nucleic acids. Butthe biological information is relevant to lifeonly to the extent of its translation into usefulbiological functions performed, directly or in-directly, by proteins; that is, selection operateson phenotypes. Because proteins repair DNA,the destiny of genetic information depends di-rectly on the function of dedicated proteins.Thus, when the extent of DNA breakage by ion-izing radiation was studied in Dra, it came as asurprise that it is the same as in the most sensi-tive bacterial and animal cells; that is, there isno special protection of DNA to account forits resistance to radiation (Burrell et al. 1971;Bonura and Smith 1976; Gerard et al. 2001).What seemed to correlate with radiation re-sistance is the extraordinary capacity to repairhundreds, sometimes thousands, of radiation-induced DNA double-strand breaks (DSBs) percell, whereas standard species’ cells can repaironly a dozen (Cox and Battista 2005; Slade andRadman 2011). Therefore, at the time, it hadseemed reasonable to anticipate the discoveryof a novel repair mechanism or of improved“smart” repair proteins that are more efficientin Dra than in most other species.

Eventually, the basic mechanism of DSB re-pair in Dra was discovered and called extendedsynthesis-dependent strand annealing (ESDSA)

Extreme Radiation Resistance of D. radiodurans

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(Fig. 1) whose elementary act is similar to thesynthesis-dependent strand annealing (SDSA)(Zahradka et al. 2006), well known to operatein other species including eukaryotic meiosis, inwhich DNA is broken by a topoisomerase. Theterm “extended” refers to the capability of per-forming the elementary act of DSB repair manyhundred times in the same cell.

A NEW PARADIGM FOR ALL SPECIES: THEPROTEOME RATHER THAN THE GENOMEIS THE PRIME TARGET IN RADIATION-INDUCED CELL DEATH

When the extensive analysis of the mechanismand genes/proteins involved in the repair ofDSBs in Dra showed no novelty (Makarovaet al. 2000; Omelchenko et al. 2005; Slade et al.2009), the puzzle of a “smart” mechanism ofrepair turned into a puzzle of unexplained effi-ciency of a standard DNA repair system. Neitherthe specific activity of purified key repair pro-teins nor their cellular amounts could accountfor the extreme efficiencyof repair (see Slade andRadman 2011). The puzzle of Dra robustnessremained until several old studies revived andextended by the recent research from MichaelDaly’s group (Daly et al. 2007) changed the par-adigm: Radiation-induced oxidative damage toproteins inactivates their function, for example,DNA repair and other vital functions, becomingthe principal cause of the sensitivity of the stan-dard organisms. Dra has a way of protecting itsproteins from oxidative damage, thereby pre-serving their activity. This paradigm got supportfrom research in Daly’s and our laboratories andwithstands rigorous experimental tests.

Reactive oxygen species (ROS) and, conse-quently, protein carbonylation (PC)—a widelyused marker of irreversible oxidative proteomedamage—are found at much lower levels in un-irradiated Dra than in other bacteria and so-matic cells of animal species (Table 1) (Kriskoand Radman 2010; Krisko et al. 2012). Further-more, the dose ranges of g rays and UVC lightthat saturate PC in Escherichia coli show no effecton carbonylation of the Dra proteome (Table 1)(Krisko and Radman 2010). Only, and preciselyat doses of radiation that become lethal, doesthere commence an increase in PC such thatthe killing and PC curves coincide for bothE. coli and Dra, albeit at widely different doseranges (Table 1) (Krisko and Radman 2010).

Radiation-induced PC levels saturate at thesame level in E. coli and Dra, meaning that theintrinsic susceptibility of proteins to carbonyl-ation is similar in the two species (Fig. 2) andthat a proteome protection system consumed by

ESDSA

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Figure 1. Extended synthesis-dependent strand an-nealing (ESDSA) pathway for reassembly of brokenDNA in D. radiodurans. Several genomic copies pres-ent in D. radiodurans undergo radiation-induced ran-dom DNA double-strand breakage, producing nu-merous fragments. The end-recessed fragments (step1) prime synthesis use the homologous regions ofpartially overlapping fragments as a template (step2), presumably through a moving D-loop (bracketedintermediate). The strand extension can run to theend of the template, producing fragments with long,newly synthesized (red) single-stranded overhangs(step 3) that can a priori engage in several roundsof extension until they find a complementary partnerstrand (steps 4 and 5). Hydrogen bonds are indicatedonly for interfragment associations. Long linear frag-ments mature into unit-size circular chromosomesby homologous recombination (crossover).





radiation is present at much higher levels ofactivity in Dra than in E. coli cells. When ex-tracts of broken E. coli and Dra cells are exposedto radiation, the same difference in PC is foundas with intact cells (Krisko and Radman 2010).Mixing of the two extracts before radiationshowed that the Dra resistance to radiation-in-

duced PC is dominant: Apparently, a diffusibleentity from the Dra cell extract protects E. coliproteins equally effectively as its own proteins.That protective entity is composed of moie-ties smaller than 3 kDa (Daly et al. 2010; Kriskoand Radman 2010) and acts by preventing ROSproduction, or neutralizing ROS, induced by

Table 1. Dose ranges of g rays and UVC light that saturate PC in E. coli show no effect on carbonylationof the Dra proteome

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Figure 2. Single correlation between cell killing and protein carbonylation. A similar correlation is observed forthe two bacterial (E. coli and D. radiodurans) and the two animal (bdelloid rotifer Adineta vaga and the wormCaenorhabditis elegans) species of widely different radiation resistance. (Data from Krisko and Radman 2010;Krisko et al. 2012.)





ionizing radiation and UVC light as measuredby intracellular dihydrorhodamine fluorescence(Krisko and Radman 2010).

MULTIPLE ANTIOXIDANT SYSTEMSIN D. radiodurans

Based on whole-genome comparisons, there isin Dra a remarkable abundance of genes encod-ing catabolic enzymes including phosphatases,nucleases, and proteases, which would be ex-pected to give rise to the pool of small antioxi-dant molecules found in the Dra ultrafiltrate(Daly et al. 2010). There are several mechanismsfor maintenance of low ROS levels in Dra thatcontribute to its resilience. They can be belong toat least three independent, but complementarygroups: (1) increased ROS-scavenging and ROS-detoxifying activities (high levels of constitu-tive catalase and superoxide dismutase activity,increased amount of manganese complexes, andsmall antioxidant molecules) (Makarova et al.2000; Daly et al. 2010); (2) altered metabolicactivities that result in a decreased ROS produc-tion, for example, glyoxylate bypass of the TCAcycle (Liu et al. 2003; Ghosal et al. 2005); and (3)reduction of the proteins containing Fe-S clus-ters, as well as reduction of the number of respi-ratory chain enzymes (Ghosal et al. 2005).

Divalent iron is a source of production ofthe most reactive ROS, the hydroxyl radical. As aconsequence of the redundancy of the antioxi-dant mechanisms in Dra, single pathways can beinactivated without significantly compromisingthe resilience of the bacterium. For example,inactivation of the deinococcal pigment deino-xanthin, one of the most potent antioxidantsknown to date, has very little effect on the resil-ience of Dra (Lemee et al. 1997; Ji 2010). On theother hand, the production of deinoxanthinand the cytosolic antioxidant pyrroloquinolinequinone in E. coli increases its resistance to ox-idative damage (Misra et al. 2012). Moreover,Dra extract of molecules smaller than 3 kDaprovides antioxidant protection to E. coli pro-teins in vitro (Daly et al. 2010; Krisko and Rad-man 2010) and human Jurkat T cells in culture(Daly et al. 2010). The group of Michael Dalyhas characterized the composition of the Dra

ultrafiltrate. In addition to the abundance ofmanganese complexes, they have found elevatedconcentrations of orthophosphate, nucleotides,and their derivatives, as well as amino acidsand peptides. The radioprotective propertiesof the D. radiodurans ultrafiltrate have alsobeen assigned to the abundance of metaboliteslike TCA cycle products (Daly et al. 2010).

Apart from low ROS production in Dra,there are several additional metabolic propertiesthat contribute to its robustness: for instance,highly efficient proteolysis, import of exogenousamino acids and peptides, and the conversionof glucose into precursors for dNTPs, as well ascarbohydrate and polyphosphate storage (seeSlade and Radman 2011). D. radiodurans is aproteolytic bacterium and, as such, contains re-dundant mechanisms for protein degradationand amino acids catabolism. Interestingly, pro-teolytic activities are induced following ionizingradiation (Daly et al. 2010). The degradation ofproteins produces amino acids and peptidesthat can be reused during the energetically de-manding recovery period, thus enabling an ef-ficient damage repairand finallysurvival (Omel-chenko et al. 2005). Furthermore, the pool ofamino acids and peptides has been suggestedto have a role as ROS scavengers during irradia-tion (Daly et al. 2010). The source of the largeamino acid and peptide pool can be accountedforalso by their import: Namely,Drahas as manyas 90 ABC transporters dedicated to amino acidand peptide uptake (de Groot et al. 2009).

Glucose metabolism also contributes to theremarkable resistance of D. radiodurans. Forexample, mutants with G6PDH deficiency (up-regulated in the wild type during the postirra-diation recovery) are more sensitive to UV-in-duced oxidative stress, as well as H2O2 andmitomycin C (Zhang et al. 2005). Glucose canbe metabolized into NADPH, which can be aprecursor of dNTPs as well as a cofactor in theproduction of glutathione and thioredoxin. Asmentioned above, ROS production in Dra ispresumably also reduced owing to fewer pro-teins with iron–sulfur clusters. A negative corre-lation between the proportion of iron–sulfurcluster proteins and radiation resistance hasbeen observed over several species. For example,





the radiation-sensitive bacterium Shewanellaoneidensis encodes 65% more iron–sulfur clus-ter proteins compared with Dra (Ghosal et al.2005).

One of the mechanisms maintaining lowROS levels in Dra is the activity of the manga-nese complexes. A strong correlation has beenshown between intracellular Mn/Fe concentra-tion ratios and bacterial resistance to radiation,in which the most resistant bacteria containedabout 300 times more Mn2þ and about threetimes less Fe2þ than the most radiation-sensi-tive bacteria (Daly et al. 2007). However, thenature of Mn-facilitated resistance to ionizingradiation was at first unclear, and the questionpersisted why many bacteria that encode a nor-mal complement of repair functions are killedby doses of ionizing radiation that cause little orno DNA damage?

A potential answer can be found in the re-sults showing that the amount of protein dam-age caused by a given dose of g radiation is verydifferent for resistant and sensitive bacteria(Daly et al. 2007). High levels of protein pro-tection during irradiation correlate with highintracellular Mn/Fe concentration ratios andhigh levels of resistance, whereas proteins in ra-diation-sensitive cells were highly susceptibleto radiation-induced oxidation. When cell ex-tracts are devoid of the small-molecular-weight(,3 kDa) moieties by ultrafiltration, then D.radiodurans and E. coli proteomes are equallysusceptible to radiation-induced PC, and the(re)addition of Dra ultrafiltrate bestows the re-silience to radiation-induced PC to either of thetwo species’ proteomes (Krisko and Radman2010). It is obvious that the biosynthetic “invest-ment” providing prevention against oxidativeproteome damage, required for radiation anddesiccation resistance, is quite significant andevolved under selective pressure for robustness.

PROTEIN, NOT DNA, DAMAGE PREDICTSDEATH BY RADIATION

The above experiments and the observation thatpurified individual proteins from resistant andstandard species appear to be similarly suscep-tible to oxidation in vitro argue that the over-

whelming proteome protection against oxida-tive damage resides in a small-molecular-weightfraction of the cytosol. It is this constitutiveprotection, present in cells before irradiation,whose exhaustion determines the sensitivityof the species to radiation and other oxidativedamage.

Indeed, in all bacterial and animal speciestested (E. coli, D. radiodurans, C. elegans, andA. vaga), we have found a characteristic quanti-tative relationship between g- and UVC-light-induced cell mortality and total protein carbon-ylation, regardless of their intrinsic potentialto resist oxidative damage as seen at the levelof PC saturation upon high radiation exposures(Fig. 2) (Krisko and Radman 2010; Krisko et al.2012). This observation suggests that the func-tionality of the proteome of all tested speciesis similarly sensitive to incurred PC; however,all species do not accumulate oxidative proteindamage at the same radiation exposures. Thebasis of the remarkable robustness of resilientspecies is predominantly the antioxidant pro-tection of the cellular proteome.

Having established that PC indeed corre-lates with cell mortality over a wide range ofdoses of two different cytotoxic agents, the keyquestion remained: Is high PC the cause or theconsequence of the process of cell death? Eventhe activity of refrigerated purified proteinsmust be routinely protected by antioxidants(e.g., DTT); therefore, it is likely that the decayof cellular functions culminating in cell deathis a direct result of the accumulated oxidativedamage to the proteome. To measure the prote-ome’s biosynthetic efficacy independently ofcell death, we have used a “parasite” of E. coli,the bacteriophage l, as a quantitative probe.Upon entering the host cell, phage l DNA hi-jacks biosynthetic machineries of E. coli anddirects them to its own reproduction. That in-volves host cell replication and transcriptionand translation machineries, all of which requiremultiple protein interactions and catalytic reac-tions expected to be sensitive to PC. Exposure ofE. coli to ionizing radiation or UVC light beforeinfection with undamaged bacteriophage l re-sults in a progressive loss of phage productioncorrelating with PC levels better than cell death





(Fig. 3). In other words, this experiment showedthat an intact phage genome fails to replicateand express when host cell proteome incurs acritical amount of oxidative damage.

The chemistry of DNA damage in cells ex-posed to ionizing radiation and UV light is dis-tinctly different. Exposure to ionizing radiationprimarily generates DNA strand breaks and basedamage, whereas exposure to UV light primar-ily generates photoproducts (Friedberg et al.2004). The cellular responses to these types ofDNA damage are also distinctive. Therefore, theobservation that saturation levels of PC are thesame in D. radiodurans and E. coli heavily ex-posed to either source of damage shows thatoxidative damage is a common correlate of tox-icity and that the intrinsic susceptibility to PCof the proteomes of these two bacterial species isindistinguishable. However, the doses at whichincreases in PC and cell killing commence arealways coincident, suggesting that protein dam-age—rather than DNA damage—might be thefundamental chemistry of cell killing (Kriskoand Radman 2010). The same conclusion wasreached by Daly and coworkers (Daly et al. 2007;Daly 2009). Thus, biological responses to geno-mic insults depend primarily on the integrityof the proteome, which includes proteins in-

volved in DNA repair, proteostasis, and struc-tural maintenance. This conclusion is the con-sequence of the fact that dedicated proteinsrepair DNA, and not vice versa. This paradigmis fundamental in its obviousness (no living cellcan function correctly with an oxidized prote-ome) and, if it is true, must be universal, that is,hold also for human cells.

EVOLVED RADIATION RESISTANCE IN E. coli

Is proteome protection the molecular basis ofthe radiation resistance also in other species? Toprovide an answer to this question, the groupsof John Battista and Michael Cox have producedradiation-resistant strains of E. coli by directedevolution in the laboratory (Harris et al. 2009).Genome sequencing of several independentlyobtained radiation-resistant E. coli strains hasrevealed more than 60 acquired mutations innonoverlapping genes that do not reveal genesalready associated with recognizable radio pro-tection or repair mechanisms. However, we havefound that both tested strains of radioresistantE. coli show the same correlation between radi-ation-induced loss of biosynthesis, mortality,and PC levels as seen in irradiated D. radiodur-ans and wild-type E. coli. Because neither gene

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Figure 3. Correlations between radiation-induced protein carbonylation (filled square), cellular capacity toproduce phage l (open circle), and cell death (filled circle) in E. coli. (A) g-radiation. (B) UVC radiation.(Data from Krisko and Radman 2010.)





acquisition nor any Deinococcus-like featuresevolved during selection of resistant E. coli inthe test tube, it is likely that many distinct mo-lecular mechanisms exist for increasing the re-sistance of bacteria to ionizing radiation, UVlight, and other toxic agents, but necessarily in-volve acquisition of proteome protection againstoxidative damage. This conclusion is supportedby the finding that the reproductive death byionizing radiation correlates with induced PCboth in radiation-sensitive (C. elegans) and ra-diation-resistant (A. vaga) invertebrates (Kriskoet al. 2012).

CONCLUSIONS

We draw the following general conclusions fromthe reviewed studies of naturally and experi-mentally evolved radiation resistance. Proteinactivities sustain life, whereas the genome per-petuates life by maintaining the levels of activeproteins. Hence, the acute cell killing occurs bydestroying the proteome’s functional integrity,not necessarily genome integrity, because evenan excessively damaged genome can be fully re-paired by an active proteome, even if it takesdays (Slade et al. 2009), ensuring the perpetua-tion of cellular life. Obviously, well-protectedproteome activities perform all vital cell func-tions including protein turnover, genome main-tenance, and its expression. D. radiodurans pre-sents a spectacular example. If this paradigmholds also for mammalian cells, then an effectivecancer therapy by tumor cell killing should tar-get the proteome, or both the proteome and thegenome, rather than the genome alone.

PERSPECTIVES: PROTEIN DAMAGE ANDAGING

Progressive cell dysfunction and massive celldeath are at the basis of aging of multicellularorganisms. A cell dies when it loses its activitiesand/or structures necessary for vital cellularfunctions. Studying Dra has shown that life de-pends acutely on proteome quality (function),whereas membrane integrity (structure—cellu-larity) has long been the standard diagnostic ofcell death.

Is it reasonable to make ad hoc connectionsbetween the biological effect of oxidative proteindamage caused by radiation and the same dam-age caused by (or just accompanying) aging (seeRichardson 2009)? Is protein damage the causeor the consequence of cellulardegeneracycausedby radiation or aging? The deleterious cellulareffects of the inactivation of the proteasomethat degrades oxidized proteins (Servant et al.2007; Bayot et al. 2010) argues that accumulatingprotein damage is likely the original cause ofgeneral degradation of cellular functions.

We posit that studying the most robust or-ganisms can bring about the definition of mo-lecular “wear and tear” mechanisms in standardorganisms. Such mechanisms are likely to berelevant to aging and age-related diseases. Thereis a possibility that such knowledge and theavailability of highly efficient natural antioxi-dants from robust species could have a majorimpact on public health.

The pioneering work of Earl Stadtman andassociates in the late 1980s showed that the ex-ponentially accumulating oxidative damage tothe proteome is the best biomarker and the likelyfundamental cause of aging and age-related dis-eases because it correlates in the same exponen-tial way with the fraction of life span of differentspecies (extending from 3 weeks to 100 years)(Oliver et al. 1987) and with the Gompertz curveof incidence of disease and death in human andanimal populations (Sas et al. 2012). We pro-pose here the concept that aging and age-relateddiseases are the emerging phenotypes of accu-mulating proteome damage whose severity andcomplexity increase with time. Current researchin the cell biology of aging deals usually with thecomplicated consequences of aging, but noth-ing seems to contradict the hypothesis that aginghas a simple cause with increasingly complexconsequences. Aging and age-related diseasescould be progressively complex phenotypes ofaccumulating proteome damage.

ACKNOWLEDGMENTS

This review is supported by a generous giftfrom Jean-Noel Thorel, who also supported allquoted unpublished work at the Mediterranean





Institute for Life Sciences. M.R. receives supportfrom the two affiliated institutions (Universityof Paris Vand Institut National pour la Sante etla Recherche Medicale). A.K. receives supportfrom the Mediterranean Institute for Life Sci-ences. We thank Dr. Jean-Paul Leonetti and Dr.Jacques Biton of the Paris-based Deinove com-pany for allowing us to quote the company’sunpublished work.

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2013; doi: 10.1101/cshperspect.a012765Cold Spring Harb Perspect Biol Anita Krisko and Miroslav Radman radiodurans

DeinococcusBiology of Extreme Radiation Resistance: The Way of

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Akira Yasui IntactDNA Repair at Telomeres: Keeping the Ends

ZakianChristopher J. Webb, Yun Wu and Virginia A.

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