An inter-species landscape of DNA repair proteins based on extreme metagenomes and repeated HMM profiling

Grolmusz, V. and Szalkai, B. and Vértessy G., Beáta and Scher, I. (2013) An inter-species landscape of DNA repair proteins based on extreme metagenomes and repeated HMM profiling. FEBS Journal, 280 (Supl 1). p. 66. ISSN 1742-464X

Preview

Text febs280_p66.pdf Download (72kB) | Preview

Abstract

Next generation sequencing technologies made possible the discovery of numerous new microbe species in environmental samples. Perhaps it is more important to discover new genes of remarkable functions and properties. In this study, 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 (with CLUSTAL) and then built HMMER profiles for each protein separately, across the well-researched (model- and non-model organisms); next, using public depositories of metagenomes, originating from extremely hot, extremely cold, or extreme pH environments, we identified DNA repair genes in the samples. Note, that the phylogenetic classification of the 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 HMMER profiling: for the identified DNA repair genes in the extreme metagenomes, we prepared new HMMER profiles (for each genes separately, subsequent to a cluster analysis); and we searched for similarities to those profiles in well-known model organisms. We have found well known DNA repair proteins, lots of proteins with unknown functions, and also proteins with known, but different functions in the model organisms. We describe the results of this work in our presentation.

Actions (login required)

Edit Item