Phylogenetic analysis and classification of the fungal bHLH domain

The basic Helix-Loop-Helix (bHLH) domain is an essential highly conserved DNA-binding domain found in many transcription factors in all eukaryotic organisms. The bHLH domain has been well studied in the Animal and Plant Kingdoms but has yet to be characterized within Fungi. Herein, we obtained and e...

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Bibliographic Details
Published in:Molecular biology and evolution 2012-05, Vol.29 (5), p.1301-1318
Main Authors: Sailsbery, Joshua K, Atchley, William R, Dean, Ralph A
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Amino acids
Ascomycota
Ascomycota - genetics
Basidiomycota - genetics
Classification
Computer programs
Conservation
Conserved sequence
Decision Trees
Discriminant Analysis
Fungal Proteins - chemistry
Fungal Proteins - classification
Fungal Proteins - genetics
Fungi
Genome, Fungal
Genomes
Genomics
Helix-Loop-Helix Motifs - genetics
Helix-loop-helix proteins
Models, Biological
Molecular Sequence Annotation
Molecular Sequence Data
Phylogenetics
Phylogeny
Proteins
Sensitivity and Specificity
software
Transcription factors
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Summary:The basic Helix-Loop-Helix (bHLH) domain is an essential highly conserved DNA-binding domain found in many transcription factors in all eukaryotic organisms. The bHLH domain has been well studied in the Animal and Plant Kingdoms but has yet to be characterized within Fungi. Herein, we obtained and evaluated the phylogenetic relationship of 490 fungal-specific bHLH containing proteins from 55 whole genome projects composed of 49 Ascomycota and 6 Basidiomycota organisms. We identified 12 major groupings within Fungi (F1-F12); identifying conserved motifs and functions specific to each group. Several classification models were built to distinguish the 12 groups and elucidate the most discerning sites in the domain. Performance testing on these models, for correct group classification, resulted in a maximum sensitivity and specificity of 98.5% and 99.8%, respectively. We identified 12 highly discerning sites and incorporated those into a set of rules (simplified model) to classify sequences into the correct group. Conservation of amino acid sites and phylogenetic analyses established that like plant bHLH proteins, fungal bHLH-containing proteins are most closely related to animal Group B. The models used in these analyses were incorporated into a software package, the source code for which is available at www.fungalgenomics.ncsu.edu.
ISSN:0737-4038
1537-1719
DOI:10.1093/molbev/msr288