Eastwood Zhao, Allan Bisnar, Garrett Hinchey
University of British Columbia
March 2009

In this report, the organism Deinococcus radiodurans is examined in detail, with a specific focus on its incredible resistance to radiation, as well as its ability to survive in a multitude of different environments.  Also covered are D. radiodurans gene and cell structure and a description of its metabolic systems.  Finally, specific qualities within the DNA of D. radiodurans are described in depth, particularly its damage resistance and ability to repair itself rapidly, and how these abilities can be used in both ecological and medical applications.

The Deinococcus genus consists of approximately 30 different species of bacteria and is derived from the Greek adjective, deinos, meaning strange or unusual (Cox et al. 2005). Spherically shaped, this berry-like bacterium is considered ‘strange’ due to its unique radiation-resistant ability (Daly 2009). As the first extremophile bacteria with a fully sequenced genome, Deinococcus radiodurans has been extensively studied and published in a number of scientific journals (Kim et al. 2002). With numerous potential health and ecological applications, our research into D. radiodurans looks into the the physical and chemical significance of this organism and its importance for further research.

Deinococcus radiodurans is a tetrad-forming extremophile bacterium, 1-2um in size, found in a wide variety of conditions. From soils in highly radioactive nuclear-waste sites and the Alps to desert substratum and Antarctic ice, this bacterium has been found in a wide range of extreme environments (Daly 2009). D. radiodurans is also characterized as a polyextromophile, with remarkable resistance to a range of severe damage-causing agents, including ionizing radiation, desiccation, ultra-violet radiation, oxidizing agents, and electrophilic mutagens (Kim et al. 2002). Though this organism is able to survive in highly uninhabitable conditions, oxygen and organic sources of nutrients such as amino acids, sugars are still required for growth, survival, and reproduction (Makarova et al. 2001). As an obligate aerobe and heterotroph, D. radiodurans cannot produce food for itself and must rely on the environment for sources of energy, using similar, yet less diverse metabolic pathways to that of Escherichia coli (Makarova et al. 2001). D. radiodurans do not possess as many enzymes or genes as do E. coli, however D. radiodurans possess genes that code for enzymes that are more complex and efficient (Markarova et al. 2001).

The genome of D. radiodurans contains many genes that are also present in other organisms, where they are expressed to partake in metabolic processes (Makarova et al. 2001). However, D. radiodurans does not express these genes for metabolic needs, and their function is still unclear (Makarova et al. 2001). For example, D. radiodurans has two functional genes that are responsible for ammonia utilization — glutamate ammonia ligase and carbamoyl-phosphate synthase (Makarova et al. 2001). Despite the presence of these genes, it has been determined through experiments that D. radiodurans does not utilize ammonia present in the soil as a nitrogen source (Makarova et al. 2001). Rather, D. radiodurans consumes sulfur-containing amino acids as an effective source of nitrogen (Makarova et al. 2001). Because it would seem energetically unfavorable for D. radiodurans to express both ammonia-catalyzing genes, there must be alternative explanations as to what the significance of these enzymes are, and whether these genes will be secondarily lost over time due to evolution.

D. radiodurans possesses genes for various metabolic pathways responsible for the catalysis and consumption of glucose, including glycolysis, gluconeogenesis, pentose phosphate shunt, and the tricarboxylic acid cycle, among many others (Makarova et al. 2001). A distinct feature of the organism is its vacuolar-type (V-type) membrane-bound ATP synthase (Makarova et al. 2001).  This type of protein is more prevalent in eukaryotes and archaea, while eubacteria possess F1/Fo ATP synthase (Makarova et at. 2001).

D. radiodurans is a Gram-positive bacterium (Cuypers et al. 2007). Its cell envelope is unusual both in terms of structure and composition, giving the organism Gram-negative characteristics (Makarova et al. 2001). Unlike other Gram-positive bacteria, D. radiodurans possesses at least 6 distinct layers of membranes, including the plasma membrane, the peptidoglycan-containing cell wall, a compartmentalized membrane layer, the outer membrane, an electrolucent zone, and a layer of hexagonally-packed protein subunits known as the S-layer (Makarova et al. 2001). There are H+/Na+ antiporter proteins in the membranes of D. radiodurans, which suggest that this bacterium cannot make acidic phospholipids due to its lacking of a gene common to most other bacteria, one that codes for phosphatidylglycerophosphate synthase (Makarova et al. 2001).

One feature that distinguishes Deinococcus radiodurans apart from all other bacteria is its unique resistance to ionizing radiation, that is, radiation that has sufficient energy to ionize molecules (Cox et al. 2005). When D. radiodurans is subjected to high levels of ionizing radiation, hundreds of double-strands are broken within the genome (Cox et al. 2005). However, before the next cycle of cell division begins, the genome is accurately reassembled, aided by both passive and enzymatic processes (Cox et al. 2005). It has been suggested that the desiccation tolerance of D. radiodurans contributes to a resistance to lethal ionizing radiation (Cox et al. 2005).

There are a number of passive mechanisms that contribute to Deinococcus radiodurans’ resistance to ionizing radiation. D. radiodurans has no less than four copies of its genome present within the cell, which decreases the probability of a gene being inactivated by radiation, therefore increasing the cell’s chance of survival (Cox et al. 2005). One hypothesis is that genome redundancy contributes to the radiation resistance of the Deinococcus species (Cox et al. 2005). Another, more controversial hypothesis is that the tightly structured, ring-like nucleoids of D. radiodurans passively contribute to the organism’s radioresistance by continuing to maintain the linear continuity of the genome even when fragmentation has occurred (Cox et al. 2005). Furthermore, experiments have shown that the presence of Manganese(II) contributes to the condensation of the D. radiodurans genome, neutralizing the repulsing effects of the phosphate backbone and enabling the organism to better tolerate radiation (Cox et al. 2005).

Within a few hours following a high dose treatment of ionizing radiation, Deinococcus radiodurans is able to repair all of the genomic double-strand breaks that have occurred with a 100% rate of survival and 0% rate of mutagenesis (Nitzan et al. 1999). The enzymatic processes fixing the genomic breaks are extensive and highly complex. Immediately following radiation exposure, a noticeable period is observed where the organism’s growth and division is inhibited due to limited fragmentation of the chromosomal DNA (Makarova et al. 2001). After 1.5 hours, the RecA-dependent repair process begins, initiating a phase where one-third of the double-strands will be repaired (Cox et al. 2005). This process becomes more important several hours later, where it predominates in the process of genome reformation (Cox et al. 2005).  Other large numbers of phenotypes are also directly responsible for genome repair through the processes of DNA end-protection, RecA-independent double-strand-break repair, and recombinational DNA repair, where DdrA and other proteins bind to the ends of exposed DNA to prevent nuclease digestion (Cox et al. 2005). Breaks in the condensed chromosome are repaired by using redundant genome information (Cox et al. 2005).

Unlike other deinobacterial species, Deinococcus radiodurans possesses DNA that is easily manipulated via genetic engineering processes due to its natural ability to transform by both high-molecular-weight chromosomal DNA and plasmid DNA (Makarova et al. 2001). This creates many possibilities for genetic research for both medical and ecological applications. Deinococcus radiodurans has a very powerful ability to accurately fix DNA breaks after being exposed to a mutagen. If we could better understand the function behind this efficient mechanism, we may be able to find and devise cures for many genetic diseases, including those associated with chromosome breaks and misalignment.  Another possible application of this organism’s unique abilities involve potentially genetically engineering D. Radiodurans to metabolize radioactive chemicals, therefore assisting with the removal of nuclear waste.  By ensuring research continues on the many functions of D. Radiodurans, not only will we gain a further appreciation of its incredibly unique characteristics, but also realize its immense potential in a wide variety of scientific applications.

Works Cited

Cox, M.M., and Bassista, J.R.  2005. Deinococcus radiodurans — the consummate survivor.  Nature reviews. Microbiology, (11): 882–92.

Cuypers, M.G., Mitchell, E.P., Romão, C.V., McSweeney, S.M.  2007. The Crystal Structure of the Dps2 from Deinococcus radiodurans Reveals an Unusual Pore Profile with a Non-specific Metal Binding Site.  Journal of Molecular Biology. 371, 787-799.

Daly, M.J.  2009.  A new perspective on radiation resistance based on Deinococcus radiodurans.  Nature Reviews Microbiology.  7: 237-45.

Kim, J., Sharma, A.K., Abbott, S.N., Wood, E.A., Dwyer, D.W., Jambura, A., Minton, K.W., Inman, R.B., Daly, M.J., Cox, M.M.  2002.  RecA Protein from the Extremely Radioresistant Bacterium Deinococcus radiodurans: Expression, Purification, and Characterization.  Journal of Bacteriology.  184(6): 1649-60.

Makarova, K.S., Aravind, L., Wolf, Y.I., Tatusov, R.L., Minton, K.W., Koonin, E.V., Daly, M.J.  2001.  Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics.  Microbiology and Molecular Biology Reviews.  65(1): 44-79.

Nitzan Y., and Ashkenazi H.  1999.  Photoinactivation of Deinococcus radiodurans: An Unusual Gram-Positive Microorganism.  Photochemistry and Photobiology.  69(4): 505-51.