The metagenomic telescope.

Szalkai, Balázs and Scheer, Ildikó and Nagy, Kinga and G. Vértessy, Beáta and Grolmusz, Vince (2014) The metagenomic telescope. PLOS ONE, 9 (7). e101605. ISSN 1932-6203

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Abstract

Next generation sequencing technologies led to the discovery of numerous new microbe species in diverse environmental samples. Some of the new species contain genes never encountered before. Some of these genes encode proteins with novel functions, and some of these genes encode proteins that perform some well-known function in a novel way. A tool, named the Metagenomic Telescope, is described here that applies artificial intelligence methods, and seems to be capable of identifying new protein functions even in the well-studied model organisms. As a proof-of-principle demonstration of the Metagenomic Telescope, we considered DNA repair enzymes in the present work. First we identified proteins in DNA repair in well-known organisms (i.e., proteins in base excision repair, nucleotide excision repair, mismatch repair and DNA break repair); next we applied multiple alignments and then built hidden Markov profiles for each protein separately, across well-researched organisms; next, using public depositories of metagenomes, originating from extreme environments, we identified DNA repair genes in the samples. While the phylogenetic classification of the metagenomic samples are not typically available, we hypothesized that some very special DNA repair strategies need to be applied in bacteria and Archaea living in those extreme circumstances. It is a difficult task to evaluate the results obtained from mostly unknown species; therefore we applied again the hidden Markov profiling: for the identified DNA repair genes in the extreme metagenomes, we prepared new hidden Markov profiles (for each genes separately, subsequent to a cluster analysis); and we searched for similarities to those profiles in model organisms. We have found well known DNA repair proteins, numerous proteins with unknown functions, and also proteins with known, but different functions in the model organisms.

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