The metagenomic telescope

Balázs Szalkai, Ildikó Scheer, Kinga Nagy, B. Vértessy, Vince Grolmusz

Research output: Contribution to journalArticle

2 Citations (Scopus)

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.

Original languageEnglish
Article numbere101605
JournalPLoS One
Volume9
Issue number7
DOIs
Publication statusPublished - Jul 23 2014

Fingerprint

Telescopes
Metagenomics
DNA repair
DNA Repair
Repair
Genes
Proteins
proteins
DNA
Metagenome
organisms
genes
DNA Repair Enzymes
telescopes
DNA Mismatch Repair
DNA Breaks
artificial intelligence
Artificial Intelligence
Archaea
Cluster analysis

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Szalkai, B., Scheer, I., Nagy, K., Vértessy, B., & Grolmusz, V. (2014). The metagenomic telescope. PLoS One, 9(7), [e101605]. https://doi.org/10.1371/journal.pone.0101605

The metagenomic telescope. / Szalkai, Balázs; Scheer, Ildikó; Nagy, Kinga; Vértessy, B.; Grolmusz, Vince.

In: PLoS One, Vol. 9, No. 7, e101605, 23.07.2014.

Research output: Contribution to journalArticle

Szalkai, B, Scheer, I, Nagy, K, Vértessy, B & Grolmusz, V 2014, 'The metagenomic telescope', PLoS One, vol. 9, no. 7, e101605. https://doi.org/10.1371/journal.pone.0101605
Szalkai B, Scheer I, Nagy K, Vértessy B, Grolmusz V. The metagenomic telescope. PLoS One. 2014 Jul 23;9(7). e101605. https://doi.org/10.1371/journal.pone.0101605
Szalkai, Balázs ; Scheer, Ildikó ; Nagy, Kinga ; Vértessy, B. ; Grolmusz, Vince. / The metagenomic telescope. In: PLoS One. 2014 ; Vol. 9, No. 7.
@article{60f5f0dff8af4d83938a823749898ea6,
title = "The metagenomic telescope",
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.",
author = "Bal{\'a}zs Szalkai and Ildik{\'o} Scheer and Kinga Nagy and B. V{\'e}rtessy and Vince Grolmusz",
year = "2014",
month = "7",
day = "23",
doi = "10.1371/journal.pone.0101605",
language = "English",
volume = "9",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "7",

}

TY - JOUR

T1 - The metagenomic telescope

AU - Szalkai, Balázs

AU - Scheer, Ildikó

AU - Nagy, Kinga

AU - Vértessy, B.

AU - Grolmusz, Vince

PY - 2014/7/23

Y1 - 2014/7/23

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84904639125&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84904639125&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0101605

DO - 10.1371/journal.pone.0101605

M3 - Article

VL - 9

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 7

M1 - e101605

ER -