A novel phylogenetic tree based on the presence of protein domains in selected actinobacteria

Antonie van Leeuwenhoek
Indrani SarkarArnab Sen

Abstract

Protein functional domains are semi-autonomous parts of proteins capable of functioning independently. One protein may contain several domains and one domain may be present in different protein sequences. Thus, protein domains represent the niche specific adaptive nature of an organism. We hypothesized that the presence and absence of protein domains in an organism could be used to make a phylogenetic tree, which may better depict the biotope (niche). Here, we selected 100 actinobacteria and built a phylogenetic tree depending upon the presence and absence of protein domains. Strains of different genera from the same niche were found to cluster together suggesting niche specific domain acquisition among selected strains. Thus, the domain based phylogeny clustered the selected actinobacteria mainly according to their niche rather than their taxonomic classification.

References

Oct 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·P Bork, R F Doolittle
Jul 29, 1991·FEBS Letters·P Bork
Mar 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·M A Savageau
Mar 1, 1973·Proceedings of the National Academy of Sciences of the United States of America·D B Wetlaufer
Mar 1, 1993·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·J N DavidsonC B Kern
Jun 1, 1995·Protein Engineering·S A IslamM J Sternberg
Oct 20, 2000·Bioinformatics·S J WheelanS H Bryant
Jun 29, 2001·Journal of Molecular Biology·G ApicS A Teichmann
Jul 4, 2003·Genome Research·Gustavo Caetano-Anollés, Derek Caetano-Anollés
Dec 19, 2003·Nucleic Acids Research·Alex BatemanSean R Eddy
Jan 5, 2005·Proceedings of the National Academy of Sciences of the United States of America·Song YangPhilip E Bourne
Apr 6, 2005·Journal of Molecular Biology·Diana EkmanArne Elofsson
Dec 4, 2012·Nucleic Acids Research·Andrea FranceschiniLars J Jensen

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Methods Mentioned

BETA
proteins folding
protein folding

Software Mentioned

MLSA
STRING
NTsys

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