Mimivirus+Genomics+and+Phylogeny

=Mimivirus: Genomics and Phylogeny = Jennifer Koch May 20, 2010 The Mimivirus is a double-stranded DNA virus isolated from amoeba growing in England. It is categorized as a nucleocytoplasmic large DNA virus and is the largest virus identified thus far. It exhibits numerous genes never before seen in viruses and bridges the gap between viruses and cellular parasites. Genemoic data from the Mimivirus supports hypotheses that ancestral DNA viruses could have been involved in the emergence of cellular life.  ** ** Introduction ** The Mimivirus distinguishes itself from others because of its evolutionary history and massive genome. It challenges the conception of what it is to be “living” and fosters ideology of the origin of viruses and what lineage of organisms they might have arrived from. This topic stimulates such personal interest because of what little we know about these particles. The only clue they offer us is their genome of nucleotides that we must decipher to piece together how they have influenced our mysterious history of life on Earth.
 * Abstract

The Mimivirus genome was recently sequenced to determine its gene content and evolutionary position. It was assembled into a sequence of 1,181,404 base pairs. The genome of Mimivirus is larger than the published genomes of 20 cellular organisms from two domains of life, Bacteria and Archaea (Miller 2003). It contains two inverted sequences 900 nucleotides long near its extremities, which may suggest that it adopts a circular topology. The nucleotide composition was 72.0% A+T (Wagner 2008). Also found was significant strand asymmetry. 1262 open reading frames were identified. The length of the ORFs were >100 amino acid residues which corresponds to a theoretical coding density of 90.5% (Raoult 2004). The proteome exhibits a strong codon bias for A+T.
 * Discussion **



When looking at the function of the Mimivirus genes, researchers found a significant overrepresentation in the categories of translation, posttranslational modifications, and amino acid transport and metabolism (Raoult 2004). Analysis found genes that were never before seen in a virus. Some of these genes were thought to be the trademark of cellular organisms. The inability to perform protein synthesis independent from the host is one of the main characteristics that distinguishes viruses from cellular organisms. However, genes were found to code for tRNA-like proteins. Mimivirus genome encodes the first identified viral homolog of a tRNA modifying enzymes (Raoult 2004). The virus also has genes to repair DNA mismatch and damages caused by oxidation, alkylating agent, or UV light. Mimivirus also exhibits the first type 1A topoisomerase reported in a virus. It is also the first to encode a homolog to the lon //E. Coli // heat shock protein, an ATP dependent protease thought to dispose of unfolded polypeptides. Mimivirus exhibits four instances of self-excising intron, all in the RNA polymerase genes (Raoult 2004).



Mimivirus is categorized as a nucleocytoplasmic large DNA virus (NCLDVs). But based on the genomic analysis researchers suggest an independent branching of Mimivirus in the phylogenetic tree of NCLDVs (Yutin 2009). There are 63 sequences common to all known unicellular genomes from the three domains of life: Eukarya, Eubacteria, and Archaea (Tatusov 2003). Seven of them are now identified in the genome of Mimivirus. Based on this data, we can stipulate that Mimivirus branches out near the origin of Eukaryota domains. BLAST scores against the three domins of life indicate that most Mimivirus ORFs exhibit higher sequences similarities to Eukaryotic sequences than Prokaryotic sequences, and are equally distant from the four main Eukaryotic kingdoms: Protists, Animalia, Plantae, and Fungi (Tatusov 2003).

It seems as though the Mimivirus contains all the genes it needs to be a functional "living" organism, with the exception of ribosomes. Researchers have thus formulated two evolutionary scenarios as to how these viruses have come to acquire translational related genes. These genes could be the relics of a more complete ancestral protein-translation apparatus, which was gradually lost through a genome reduction process similar to the one governing the evolution of intracellular bacteria (Raoult 2004). Another speculation is that these genes could have been individually acquired from cellular organisms and used to control the host translation apparatus in favor of Mimivirus mRNAs. Phylogenetic analysis supports the loss rather than gain scenario. The theory currently is that the Mimivirus lineage originated from a more complex ancestor possibly exhibiting an even more complex protein-translation machinery (Raoult 2004). Results from experiments support hypotheses that a lineage of large DNA viruses could have emerged before the individualization of cellular organisms from the three domains of life or from an ancestor distinct of these three domains. This is consistent with hypothesis that ancestral DNA viruses were involved in the emergence of Eukaryotes. We could now possibly build a new tree of life, where Mimivirus appears to define a new branch distinct from the other three domains (Raoult 2004).


 * Literature Cited **

Miller et al,. //Microbial Molecular Biology// //.// Rev. 67, 86 (2003)

Raoult et al., 2004. <span style="font-family: 'Lucida Sans Unicode','Lucida Grande',sans-serif; font-size: 80%;">//The 1.2-Megabase Genome Sequence of Mimivirus// <span style="font-family: 'Lucida Sans Unicode','Lucida Grande',sans-serif;">. Published online in <span style="font-family: 'Lucida Sans Unicode','Lucida Grande',sans-serif; font-size: 80%;">Science 1344-1350. [|www.sciencemag.org/cgi/content/full/1101485/DC1] <span style="font-family: 'Lucida Sans Unicode','Lucida Grande',sans-serif;">

Tatusov et al., <span style="font-family: 'Lucida Sans Unicode','Lucida Grande',sans-serif; font-size: 80%;"> //BMC Bioinformatics// <span style="font-family: 'Lucida Sans Unicode','Lucida Grande',sans-serif;">. 4,41 (2003)

Wagner, E. 2008. <span style="font-family: 'Lucida Sans Unicode','Lucida Grande',sans-serif; font-size: 80%;">//Basic Virology//. Blackwell Publishing, MA. pp 149-150.

Yutin N, Koonin E. Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity. <span style="font-family: 'Lucida Sans Unicode','Lucida Grande',sans-serif;"> Biology Direct[serial online]. December 18, 2009;4 Available from: Biological Abstracts 1969 - Present, Ipswich, MA.