Improving Hox protein classification across the major model organisms.

The family of Hox-proteins has been a major focus of research for over 30 years. Hox-proteins are crucial to the correct development of bilateral organisms, however, some uncertainty remains as to which Hox-proteins are functionally equivalent across different species. Initial classification of Hox-...

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Autores principales:	Stefanie D Hueber, Georg F Weiller, Michael A Djordjevic, Tancred Frickey
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4eb3f5379d21417b9cba6fb0d7542c40
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spelling	oai:doaj.org-article:4eb3f5379d21417b9cba6fb0d7542c402021-12-02T20:21:23ZImproving Hox protein classification across the major model organisms.1932-620310.1371/journal.pone.0010820https://doaj.org/article/4eb3f5379d21417b9cba6fb0d7542c402010-05-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20520839/?tool=EBIhttps://doaj.org/toc/1932-6203The family of Hox-proteins has been a major focus of research for over 30 years. Hox-proteins are crucial to the correct development of bilateral organisms, however, some uncertainty remains as to which Hox-proteins are functionally equivalent across different species. Initial classification of Hox-proteins was based on phylogenetic analysis of the 60 amino acid homeodomain. This approach was successful in classifying Hox-proteins with differing homeodomains, but the relationships of Hox-proteins with nearly identical homeodomains, yet distinct biological functions, could not be resolved. Correspondingly, these 'problematic' proteins were classified into one large unresolved group. Other classifications used the relative location of the Hox-protein coding genes on the chromosome (synteny) to further resolve this group. Although widely used, this synteny-based classification is inconsistent with experimental evidence from functional equivalence studies. These inconsistencies led us to re-examine and derive a new classification for the Hox-protein family using all Hox-protein sequences available in the GenBank non-redundant protein database (NCBI-nr). We compare the use of the homeodomain, the homeodomain with conserved flanking regions (the YPWM and linker region), and full length Hox-protein sequences as a basis for classification of Hox-proteins. In contrast to previous attempts, our approach is able to resolve the relationships for the 'problematic' as well as ABD-B-like Hox-proteins. We highlight differences to previous classifications and clarify the relationships of Hox-proteins across the five major model organisms, Caenorhabditis elegans, Drosophila melanogaster, Branchiostoma floridae, Mus musculus and Danio rerio. Comparative and functional analysis of Hox-proteins, two fields crucial to understanding the development of bilateral organisms, have been hampered by difficulties in predicting functionally equivalent Hox-proteins across species. Our classification scheme offers a higher-resolution classification that is in accordance with phylogenetic as well as experimental data and, thereby, provides a novel basis for experiments, such as comparative and functional analyses of Hox-proteins.Stefanie D HueberGeorg F WeillerMichael A DjordjevicTancred FrickeyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 5, p e10820 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Stefanie D Hueber Georg F Weiller Michael A Djordjevic Tancred Frickey Improving Hox protein classification across the major model organisms.
description	The family of Hox-proteins has been a major focus of research for over 30 years. Hox-proteins are crucial to the correct development of bilateral organisms, however, some uncertainty remains as to which Hox-proteins are functionally equivalent across different species. Initial classification of Hox-proteins was based on phylogenetic analysis of the 60 amino acid homeodomain. This approach was successful in classifying Hox-proteins with differing homeodomains, but the relationships of Hox-proteins with nearly identical homeodomains, yet distinct biological functions, could not be resolved. Correspondingly, these 'problematic' proteins were classified into one large unresolved group. Other classifications used the relative location of the Hox-protein coding genes on the chromosome (synteny) to further resolve this group. Although widely used, this synteny-based classification is inconsistent with experimental evidence from functional equivalence studies. These inconsistencies led us to re-examine and derive a new classification for the Hox-protein family using all Hox-protein sequences available in the GenBank non-redundant protein database (NCBI-nr). We compare the use of the homeodomain, the homeodomain with conserved flanking regions (the YPWM and linker region), and full length Hox-protein sequences as a basis for classification of Hox-proteins. In contrast to previous attempts, our approach is able to resolve the relationships for the 'problematic' as well as ABD-B-like Hox-proteins. We highlight differences to previous classifications and clarify the relationships of Hox-proteins across the five major model organisms, Caenorhabditis elegans, Drosophila melanogaster, Branchiostoma floridae, Mus musculus and Danio rerio. Comparative and functional analysis of Hox-proteins, two fields crucial to understanding the development of bilateral organisms, have been hampered by difficulties in predicting functionally equivalent Hox-proteins across species. Our classification scheme offers a higher-resolution classification that is in accordance with phylogenetic as well as experimental data and, thereby, provides a novel basis for experiments, such as comparative and functional analyses of Hox-proteins.
format	article
author	Stefanie D Hueber Georg F Weiller Michael A Djordjevic Tancred Frickey
author_facet	Stefanie D Hueber Georg F Weiller Michael A Djordjevic Tancred Frickey
author_sort	Stefanie D Hueber
title	Improving Hox protein classification across the major model organisms.
title_short	Improving Hox protein classification across the major model organisms.
title_full	Improving Hox protein classification across the major model organisms.
title_fullStr	Improving Hox protein classification across the major model organisms.
title_full_unstemmed	Improving Hox protein classification across the major model organisms.
title_sort	improving hox protein classification across the major model organisms.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/4eb3f5379d21417b9cba6fb0d7542c40
work_keys_str_mv	AT stefaniedhueber improvinghoxproteinclassificationacrossthemajormodelorganisms AT georgfweiller improvinghoxproteinclassificationacrossthemajormodelorganisms AT michaeladjordjevic improvinghoxproteinclassificationacrossthemajormodelorganisms AT tancredfrickey improvinghoxproteinclassificationacrossthemajormodelorganisms
_version_	1718374106802421760

Improving Hox protein classification across the major model organisms.

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