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Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites
BACKGROUND: The highly conserved bHLH (basic Helix-Loop-Helix) domain, found in many transcription factors, has been well characterized separately in Plants, Animals, and Fungi. While conserved, even functionally constrained sites have varied since the Eukarya split. Our research identifies those sl...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502508/ https://www.ncbi.nlm.nih.gov/pubmed/22920570 http://dx.doi.org/10.1186/1471-2148-12-154 |
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author | Sailsbery, Joshua K Dean, Ralph A |
author_facet | Sailsbery, Joshua K Dean, Ralph A |
author_sort | Sailsbery, Joshua K |
collection | PubMed |
description | BACKGROUND: The highly conserved bHLH (basic Helix-Loop-Helix) domain, found in many transcription factors, has been well characterized separately in Plants, Animals, and Fungi. While conserved, even functionally constrained sites have varied since the Eukarya split. Our research identifies those slightly variable sites that were highly characteristic of Plants, Animals, or Fungi. RESULTS: Through discriminant analysis, we identified five highly discerning DNA-binding amino acid sites. Additionally, by incorporating Kingdom specific HMMs, we were able to construct a tool to quickly and accurately identify and classify bHLH sequences using these sites. CONCLUSIONS: We conclude that highly discerning sites identified through our analysis were likely under functional constraints specific to each Kingdom. We also demonstrated the utility of our tool by identifying and classifying previously unknown bHLH domains in both characterized genomes and from sequences in a large environmental sample. |
format | Online Article Text |
id | pubmed-3502508 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35025082012-11-21 Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites Sailsbery, Joshua K Dean, Ralph A BMC Evol Biol Research Article BACKGROUND: The highly conserved bHLH (basic Helix-Loop-Helix) domain, found in many transcription factors, has been well characterized separately in Plants, Animals, and Fungi. While conserved, even functionally constrained sites have varied since the Eukarya split. Our research identifies those slightly variable sites that were highly characteristic of Plants, Animals, or Fungi. RESULTS: Through discriminant analysis, we identified five highly discerning DNA-binding amino acid sites. Additionally, by incorporating Kingdom specific HMMs, we were able to construct a tool to quickly and accurately identify and classify bHLH sequences using these sites. CONCLUSIONS: We conclude that highly discerning sites identified through our analysis were likely under functional constraints specific to each Kingdom. We also demonstrated the utility of our tool by identifying and classifying previously unknown bHLH domains in both characterized genomes and from sequences in a large environmental sample. BioMed Central 2012-08-24 /pmc/articles/PMC3502508/ /pubmed/22920570 http://dx.doi.org/10.1186/1471-2148-12-154 Text en Copyright ©2012 Sailsbery and Dean; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Sailsbery, Joshua K Dean, Ralph A Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites |
title | Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites |
title_full | Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites |
title_fullStr | Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites |
title_full_unstemmed | Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites |
title_short | Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites |
title_sort | accurate discrimination of bhlh domains in plants, animals, and fungi using biologically meaningful sites |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502508/ https://www.ncbi.nlm.nih.gov/pubmed/22920570 http://dx.doi.org/10.1186/1471-2148-12-154 |
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