Deinococcus radiodurans: “Conan the Bacterium”

If you had to name the most epic, mindboggling bacteria in the world, Deinococcus radiodurans would be a top contestant. D. radiodurans has managed to make it into the Guinness Book of World Records, quite the feat for microbiology, and is pretty darned close to invulnerable. It is the most DNA damage-tolerant organism we have ever discovered. One of its natural habitats is the frigid dry valleys of Antarctica and it can also survive in a vacuum (think outer space!). There is no phage or virus capable of infecting it, and it can survive over six years with no water [2,3]. D. radiodurans shrugs off having its genome shattered into thousands of pieces, while other organisms die with only a handful of breaks. Last but not least, it can survive 2,000 to 6,666 times the gamma radiation that would kill a human and 250 to 5,000 times the UV radiation used to kill microbes in our water supply [2,4]. Luckily for us, it is so focused on being the coolest microbe around that it has no pathogenic qualities. In fact, there’s no sign of it ecologically interacting with any other organism out there.

      Deinococcus radiodurans

Meet the Microbe

D. radiodurans bacterium was first isolated from a tin of meat in 1956 after someone noticed a bacterial colony had survived the sterilizing dose of gamma radiation used on tinned food. Hopefully they gave him a raise. Either way, the event brought this fascinating microbe into the spotlight and the bacterium soon became the focus of microbiology nerds everywhere. D. radiodurans is a polyextremophile: it is highly resistant to many extreme conditions that are often considered fatal. It is a simple looking little microbe, a reddish, pink, or orange sphere that tends to group up in pairs or tetrads with its fellows. It doesn’t actually do very much, being completely stationary, and it does not form spores (normally, a spore phase provides a microbe with protection against extreme conditions. Obviously D. radiodurans is in no need of such aid). The bacterium takes 80 minutes to replicate and is Gram positive. Gram classification is based on the ability to use Gram staining on a microbe, which is dependent on the structure of the microbe. Gram positive microbes have a thick outer cell barrier made of peptidoglycan, which allows the uptake of dye. Gram negative microbes tend to have a thinner version of this peptidoglycan barrier, and have an outer membrane beyond it that prevents the dye from taking. While D. radiodurans is Gram positive, it actually has a complex outer cell-membrane somewhat similar to that of Gram negative microbes [2,4,11].

Unsurprisingly, D. radiodurans is found worldwide. No one has managed to pinpoint this bacteria’s natural habitat because it can grow anywhere from Antarctica to your backyard soil, sewage, tinned meat, dried food, and on medical instruments. Furthermore, no relationships or ecological interactions between D. radiodurans and any other organisms have been observed. It is a multigenomic organism, which means that it carries multiple copies of the entirety of its genetic information (generally 2-6 copies! We humans have two copies of our DNA in each cell). Each genome is made up of two chromosomes, a megaplasmid, and a smaller plasmid (in contrast, all our DNA is stored in chromosomes. Plasmids are circular DNA molecules).

Basically, D. radiodurans is one of the toughest, nigh invulnerable microbes around and all it does is sit around in pink little colonies, minding its own business.

DNA Damage

DNADamage

DNA damage is a constant problem for all living organisms. It underlies aging and numerous human diseases such as cancer. When oxidative stress damages an organisms’ DNA through normal biological processes, radiation, or chemical agents, the damage and mutations can be inherited in each subsequent cell, causing cell death and the degradation of the organisms (oxidative stress was previously described in this post). Apart from base mutations, damage presents in DNA in two main ways: single-strand and double-strand breaks. Double-strand breaks are the most severe form damage. As mutations and DNA breakage occur occasionally in all cells, there are various repair mechanisms in place. Unfortunately, a major genomic injury causing several breaks at once is often fatal for the cell. In contrast, not only does D. radiodurans show a resistance to all oxidative-stress causing agents, but it can survive over a thousand double-strand breaks. This bacterium repairs completely shattered chromosomes without batting an eyelash and continues chugging along in its thrilling, stationary life [13,16].

Gamma Radiation

Gamma

Gamma radiation is an electromagnetic radiation as well as an ionizing radiation, the latter of which is of greater interest here. Ionizing radiation means that the radiation is made of up particles that have the energy to release electrons from atoms or molecules it interacts with, turning them into a charged atom or molecule that is highly reactive and, consequently, biologically harmful. When organisms are exposed to high enough levels, it damages cellular molecules including proteins and DNA. For humans, being exposed to 5 Gray of gamma radiation will result in a 50% mortality rate. If humans are exposed to 7.5 Gy or higher, it is an irreversible death sentence. Meanwhile, Deinococcus radiodurans is completely resistant to up to 5,000 Gy of gamma radiation, cultures routinely survive exposure to 15,000 Gy, and some strains have been reported to have survived 50,000 Gy of radiation [2,4].

When exposed to gamma radiation, D. radiodurans does sustain damage: 3,000 Gy causes ~100 double-strand DNA breaks and 5,000 Gy causes ~200 double strand breaks. However, within three hours the bacteria completely repairs itself, with no loss of viability or mutations [2,4]!

Ultraviolet Radiation

UV

Ultraviolet, or UV, radiation is another electromagnetic radiation, probably one that you’re far more familiar with as it is the source of tans and sunburns. Most UV radiation is non-ionizing, but the entire spectrum can still cause biological damage (aside from the heating effects which result in burns) because the photons in UV rays contain enough power to change chemical bonds in cells. Unfortunately, I can’t find a fatal dose for humans for comparative purposes; however D. radiodurans can survive doses as high as 1000 J/m2, with a complete survival resistance up to 500 J/m2 thanks to its efficient DNA repair mechanisms. To give you a sense of how much that is, according to my calculations (in other words, worth taking with a grain of salt) 0.2 to 4 J/m2 is generally used to irradiate and purify water and kill all the microorganisms in it [2,4].

Desiccation

Dessication

Water is vital to life. It is necessary to maintain both the structure of cells and for nearly all biochemical functions and metabolism. The loss of water from cells is deadly, not only because it halts most of the necessary chemical reactions, but also by causing breaks and mutations in DNA, RNA, lipids, and proteins [3]. Water accounts for about 65% of the mass of the human body and, generally, we will die if we are deprived of water for a mere three days. D. radiodurans once again puts us to shame, with cultures of the bacteria surviving in desiccators (container that removes all water from the air and items inside of it) for six years with 10% viability [2]. Not only can they survive without water, but when they are dehydrated they actually have increased resistance to radiation and heat [3]!

What are D. radiodurans’ secrets for survival?

Gamma2

While we do not completely understand all the tricks D. radiodurans has up its sleeve, we currently attribute its amazing resistances to a combination of unique traits and DNA repair efficiency.

Genome sequencing and scientific research has shown that the repair mechanisms of D. radiodurans do not appear to be novel, but, rather, that it uses common repair systems much more efficiently along with expanded systems involved in salvage. While it utilizes a classical set of repair enzymes, novel genes associated with them have been discovered [4, 6]. When exposed to irradiation, approximately 60 genes are induced which prompt repair pathways to reassemble DNA accurately and repair it efficiently, preventing any further cellular division until all damage is fixed (this is key, as otherwise the damage is passed onto daughter cells) [9, 10]. D. radiodurans uses four types of repair mechanisms to fix double stranded breaks, which further increases the efficiency of repair and allows complete chromosomal reconstruction within a few hours. The first, homologous recombination, uses an intact copy of the DNA (from another chromosome or genome, as this microbe has several spare) as a template to fill in or fix the break or mutated section of DNA. Extended synthesis-dependent strand annealing is the second type, which also uses an existing copy of DNA to connect and build DNA from fragments. Similarly, single-strand annealing synthesizes missing sections on a strand using another copy of DNA. Finally, non homologous end joining is a type of repair that does not require another copy of DNA. Instead, broken ends are recognized and proteins join the ends back together [4,16]!

Apart from their incredibly efficient DNA repair, D. radiodurans has several unique traits that help resist radiation damage or aid in repair. Their thick cellular envelope (unusual for Gram positive bacteria), along with the pigments contained in it, help protect against some of the radiation damage. Additionally, their DNA is unusually densely packed, possibly preventing the movement or loss of damaged fragments of DNA which facilitates repair [3]. The fact that they have numerous copies of their genome no doubt also aids in DNA repair, as it provides several copies of the DNA that can be used as templates to fix damaged sections. Finally, D. radiodurans has an unusually high accumulation of manganese (in the form of Mn(II)) in its cytoplasm along with phosphate, nucleosides, DNA bases, and peptides. When this intracellular fluid is removed from the bacteria and filtered to extract the proteins, it was found to help prevent protein oxidation under extremely high ionizing radiation levels. Recent research has suggested that high concentrations of these Mn(II) ions increase radiation tolerance and form complexes that protect proteins [7,8,10].

In summary, the key to D. radiodurans incredible ability to survive damage seems to be using multiple, but not unique, repair pathways far more efficiently than other organisms along with various unique protective and repair-enhancing traits.

Is there anything that can kill it?!

Death copy

Actually, yes! Despite its fabulous radioactive resistance, D. radiodurans is a mesophile: it prefers to grow at temperatures under 39C (102F), and can be killed by incubating it at higher temperatures for an extended duration [13]. High enough radiation levels (gamma or UV) would also kill it, although that’s likely an expensive and dangerous way to go about an execution. Finally, a recent study discovered that it can also be killed by cold atmospheric plasma (a state of matter containing charged particles) at the same concentration and duration needed to kill the antibiotic-resistant MRSA strain [10]. Of course, as D. radiodurans is not a pathogen and would make the coolest microbial pet ever, I’m not sure why anyone would want to kill it.

Application: Toxic Waste Remediation

Since D. radiodurans is unwilling to do anything cool with its near immortality, humans have stepped up to the plate and are busy finding uses for it. This bacterium is currently being developed to treat radioactive waste. Radioactive waste sites from nuclear weapon production are quite a problem; in the US, there are 3,000 such sites and the estimated cost to clean them with current methods is $265 billion [5]. Unsurprisingly, there is a lot of research investigating cheaper alternatives. Strains of D. radiodurans have been created with a gene cloned into them providing ionic mercury resistance. This allows them to not only flourish in these radioactive sites, but to grow on ionic mercury and detoxify it, helping remediate these waste sites [5]. Other researchers have engineered strains of these bacteria to express acid phosphatase, which allows the remediation of aqueous nuclear waste that results from reprocessing spent fuel rods (heavy in beta and gamma radiation), and another gene to precipitate uranium [12]!

Application: Post-Apocalyptic Data Storage

info

Personally, I’ve always been a little worried about what would happen if, despite the implausibility, all digital and electronic memory was lost. Could you imagine no more Wikipedia or Google? What would people do (libraries would get a business boost, for one)?

Apparently I was not the only one concerned about this prospect. One scientist has already created a patent for storing information in a manner that would survive a nuclear apocalypse. Commenting on how “bones and stone erode, paper disintegrates, and electronic memory degrades,” Pak Chung Wong et al. describe the process for storing information in DNA inside of bacteria such as D. radiodurans. Together, they stored the lyrics of “It’s a Small World” in synthesized DNA, inserted it into 7 different bacteria, and later recovered the information without a hitch. Considering the amount of DNA that a single bacteria can contain (beyond comprehension, really), and the fact that 1 ml of liquid can contain 10,000,000,000 bacteria, the capacity of DNA memory storage is incredible. Stick data into a microbe like D. radiodurans and it will be passed through generations of the bacteria, could exist for possibly millions of years, and survive pretty much any disaster you could imagine [14]. Of course, the chances of humans surviving such a disaster, retaining the knowledge that such information is stored in the bacteria, and having the technology to recover it don’t seem too high.

Application: Cure to aging and cancer?

I’ve already mentioned that oxidative stress is behind a plethora of human diseases, including cancer, as well as the phenomenon of aging. While it is unlikely too many of D. radiodurans tricks could be applied to humans due to genomic differences, thoroughly understanding the pathways of protection and repair in this bacteria could have possible medical applications down the road [13]. You know, in case we never find the elusive fountain of youth.

Extraterrestrial Life

Space

In a study published in the journal of Astrobiology (I was quite excited to discover this journal existed), researchers exposed bacteria, including D. radiodurans to vacuum conditions simultaneously with UV radiation. The resulting survival fractions, while only 1% at high (1350 J/m2) fluency, still suggest the possibility of interplanetary transfer of living microorganisms and the possible existence of microbial life in environments like those found on Jupiter’s moons and Mars. Chances are, if we discover alien neighbors they’ll probably be little organisms like D. radiodurans and other such microbes. Maybe they’ll even contain a library-worth of information from a previous advanced civilization…

 

References

[1] Auda H. and Emborg, C. “Studies onpost-irradiation DNA degradation inMi-crococcus radiodurans, Strain RII5.” Ra-diat. 1973. 53:273–80.

[2] Battista, J. “Against all odds: the survival strategies of Deinococcus radiodurans.” Annual Review of Microbiology. 1997. 51:203-224.

[3] Bauermeister, A. et al. “”Effect of relative humidity on Deinococcus radiodurans’ resistance to prolonged dessication, heat, ionizing, germicidal, and environmentally relevant UV radiation.” Microb Ecol. 2011. 61:715-722.

[4] Blasius, M. et al. “Deinococcus radiodurans: what belongs to the survival kit?” Critical Reviews in Biochemistry and Molecular Biology. 2008. 43:221-238.

[5] Brim, H. et al. “Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments.” Nature Biotechnology. 2000. 18:85-90.

[6] Cox, M. et al. “Rising from the ashes: DNA repair in Deinococcus radiodurans.” PloS Genetics. 2010. 6(1).

[7] Daly, M. et al. “Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance.” Science. 2004. 306:1025-1028.

[8] Daly, M. et al. “Small-molecule antioxidant proteome-shields in Deinococcus radiodurans.” PloS One. 2010. 5(9).

[9] Krisko, A. and Radman, M. “Protein damage and death by radiation in Escherichia coli and Deinococcus radiodurans.” PNAS. 2010. 107(32): 14373-14377.

[10] Maisch, T. et al. “Contact-free cold atmospheric plasma treatment of Deinococcus radiodurans.” J Ind Microbiol Biotechnol. 2012. 39(9):1367-1375.

[11] Makarova, K. et al. “Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics.” Microbiology and Molecular Biology Reviews. 2001. 65(1):44-79.

[12] Misra, C. et al. “Recombinant D. radiodurans cells for bioremediation of heavy metals from acidic/neutral aqueous wastes.” Bioengineered Bugs. 2012. 3(1):44-48.

[13] Slade, D. and Radman, M. “Oxidative stress resistance in Deinococcus radiodurans.” Microbiology and Molecular Biology Reviews. 2011. 5(1):133-191.

[14] Wong, P. et al. “Organic data memory using the DNA approach.” Communications of the ACM. 2003. 46(1): 95-98.

[15] Ximena, C. et al. “Comparative survival analysis of Deinococcus radiodurans and the haloarchaea Natrialba magadii and Haloferax volcanii, exposed to vacuum ultraviolet irradiation.” Astrobiology. 2011. 11(10):1034-1040.

[16] Zahradka, K. et al. “Reassembly of shattered chromosomes in Deinococcus radiodurans.” Nature (Letters). 2006. 44(5).

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2 thoughts on “Deinococcus radiodurans: “Conan the Bacterium”

  1. Pingback: Tardigrades: Animal Survivors | Biogeekery

  2. VERY NICE. FEEL FREE TO CONTACT IF YOU WANT TO HEAR WHAT’S NEW – PARTICULARLY HOW THE Mn2+ PEPTIDE COMPLEXES ARE BEING USED IN PREPARING IRRADIATED VACCINES. M. DALY

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