Metagenomic Study of Deinococcus Radiodurans

===Bacteria Overview===
The bacteria Deinococcus radiodurans is especially known for its resistance to high doses of radiation and its ability to survive in nutrient deficient environments.  Its genome consists of two chromosomes and two plasmids; 4 copies of the genome are present in its resting state and up to 10 copies of the genome are present during its growth phase and/or during exposure to DNA damaging environments. 
There are three attributes of this bacterium that are thought to contribute to its radioresistance.  The most prominent attribute is its many (38+) DNA repair genes, the other is its highly complex 6 layer cell membrane that is highly effective at transport of nutrients into the cytoplasm from its environment and last is the bacterias ability to reduce oxidative stress by having less sulfur-iron complexes in its oxidative phosphorylation mechanism and by having mechanisms that skip over parts of energy production that produce free radicals.  For more general information on this bacteria please see the Deinococcus radiodurans R1 Wikia page.
===Meta-Genomics Overview of Deinococcus & Thermus spp. (1,2)===
Deinococcus spp. and Thermus spp. are believed to belong to a specific branch of bacteria known as the Deinococcus-Thermus group and are thought to be a bridge between gram (+) and gram (-) bacteria.  The support for this theory is found in the strong linkage in the phylogenetic tree of ribosomal RNA's along with several conserved ribosomal proteins, RNA polymerase subunits and in the RecA gene (a gene used for DNA recombination).
Despite the lack of radioresistance displayed by the Thermus spp. and the inability for Deinococcus spp. to survive at temperatures above 39 degrees Celsius, it is believed that these two species share a common ancestor but have deviated in preferred living environments due to four evolutionary processes:
#Gene loss and gain
#Horizontal gene transfer (HGT) followed by loss of ancestral ortholog genes
#Lineage specific expansion of paralogs
#Modification of amino acid composition that could affect protein stability
By evaluating COGs of 62 sequenced genomes of prokaryotes and unicellular eukaryotes a gene construct tree was made which shows that Deinococcus & Thermus are sister species.  The construct map also showed that the two bacteria share a branch with actinobacteria and cyanobacteria, several of which are known for their resistance to radiation and dry environments.  With further evaluation of COGs it was found that the two bacteria share 14 COGs that are not shared with any other bacteria, but are shared with archaea and prokaryotes.  
In order to determine where the gains and losses of genetic material are between the two species an evolutionary scenario for divergence of genomes was constructed by evaluating presence of COGs (genes) after branching from their last bacterial common ancestor (LBCA).  The diagram shows that DR/TT have 1,310 genes in common after undergoing the gain of 202 genes and loss of 161 genes from their LBCA.  This diagram also shows that Deinococcus has undergone substantial genome growth by gaining 272 genes while only loosing 59.  
===Gain and Loss of Genes in D.radiodurans (1)===
As the Diagram above shows, D.radiodurans has undergone more gene gain than loss.  A majority of the genes lost were responsible for energy metabolism and biosynthesis of cofactors. Examples of genes lost are as follows:
#Loss of the three subunits of pyruvate: ferridoxin oxioreductase which is responsible for oxidation of pyruvate.
#Loss of the three subunits of NAD/NADP transhydrogenase which is responsible for reduction of NADH+.
#Loss of 4 enzymes responsible for NAD biosynthesis, rendering the bacteria dependant on exogenous sources of NAD for growth.
Genes gained by D.radiodurans are abundant. Being the bacteria is highly transformable and has a knack for 'absorbing' molecules and substances from its environment, it is easily believable that the gain of many genes occurred as a result of horizontal gene transfer. The following are examples of the types of genes and generic functions gained:
#Genes responsible for protein degradation and amino acid catabolism; ex. urease and a predicted urea transporter.
#Gain of two complexes of aerobic type carbon monoxide dehydrogenase. This allows the bacteria to utilize oxidation of carbon monoxide as an energy source.
#Gain of many inorganic ion transport systems. It is thought that this may be indirectly linked the bacterias oxidative stress resistance by providing regulation of ion gradients and Mn/Fe homeostasis. Mn/Fe homeostasis is thought to be responsible for clearing reactive oxygen species (ROSs) and hence, reducing oxidative stress.
#Gain of many genes involved in an elaborate signal transduction system. The functions of many of these genes are unclear and some are thought to serve no function; such as the gene for the protein DR0724 which contains the SARP domain. The SARP domain is involved in apoptosis related signaling pathways in eukaryotes, but the function in bacteria remains unknown.
#Gain of several genes (total after gain = 25 genes) related to microbial defense including 7 genes for restriction-modification systems and several genes for antibiotic resistance. It is thought that the gain of these genes is due to its need for a nutrient rich environment for growth. While in this nutrient rich environment, the bacteria is likely to encounter many microbial species.
#15 genes were gained via HGT from eukaryotes and viruses. Several of which are thought to be related to the bacterias ability to survive in very dry environments, but none that are related to radioresistance.
The loss and gain of these genes is consistent with the bacterias ability to maintain low levels of oxidative stress by having many mechanisms in place for cleaning up ROSs, reducing the occurrence of ROSs and by obtaining molecules related to energy production from its exogenous environment.
References:
#Omelchenko, MV, Et al.  Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evolutionary Biology. 2005, Vol 5, pg 57.
#Makarova, K.S., Et Al. Genome of the Extremely Radiation-Resistant Bacterium Deinococcus Radiodurans Views from the Perspective of Comparative Genomics. Microbiology and Molecular Biology Reviews. Vol 65, No.1, p.44-79. Mar 2001.