Functional modelling of an equine bronchoalveolar lavage fluid proteome provides experimental confirmation and functional annotation of equine genome sequences

L. A. Bright, N. Mujahid, B. Nanduri, Fiona M McCarthy, L. R R Costa, Shane C Burgess, C. E. Swiderski

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

The equine genome sequence enables the use of high-throughput genomic technologies in equine research, but accurate identification of expressed gene products and interpreting their biological relevance require additional structural and functional genome annotation. Here, we employ the equine genome sequence to identify predicted and known proteins using proteomics and model these proteins into biological pathways, identifying 582 proteins in normal cell-free equine bronchoalveolar lavage fluid (BALF). We improved structural and functional annotation by directly confirming the in vivo expression of 558 (96%) proteins, which were computationally predicted previously, and adding Gene Ontology (GO) annotations for 174 proteins, 108 of which lacked functional annotation. Bronchoalveolar lavage is commonly used to investigate equine respiratory disease, leading us to model the associated proteome and its biological functions. Modelling of protein functions using Ingenuity Pathway Analysis identified carbohydrate metabolism, cell-to-cell signalling, cellular function, inflammatory response, organ morphology, lipid metabolism and cellular movement as key biological processes in normal equine BALF. Comparative modelling of protein functions in normal cell-free bronchoalveolar lavage proteomes from horse, human, and mouse, performed by grouping GO terms sharing common ancestor terms, confirms conservation of functions across species. Ninety-one of 92 human GO categories and 105 of 109 mouse GO categories were conserved in the horse. Our approach confirms the utility of the equine genome sequence to characterize protein networks without antibodies or mRNA quantification, highlights the need for continued structural and functional annotation of the equine genome and provides a framework for equine researchers to aid in the annotation effort.

Original languageEnglish (US)
Pages (from-to)395-405
Number of pages11
JournalAnimal Genetics
Volume42
Issue number4
DOIs
StatePublished - Aug 2011
Externally publishedYes

Fingerprint

Bronchoalveolar Lavage Fluid
Proteome
proteome
Horses
Genome
horses
genome
Gene Ontology
Proteins
proteins
Bronchoalveolar Lavage
genes
fluids
Horse Diseases
Molecular Sequence Annotation
Biological Phenomena
cells
cell communication
Carbohydrate Metabolism
mice

Keywords

  • bronchoalveolar lavage
  • equine
  • genome annotation
  • proteomics

ASJC Scopus subject areas

  • Genetics
  • Animal Science and Zoology

Cite this

Functional modelling of an equine bronchoalveolar lavage fluid proteome provides experimental confirmation and functional annotation of equine genome sequences. / Bright, L. A.; Mujahid, N.; Nanduri, B.; McCarthy, Fiona M; Costa, L. R R; Burgess, Shane C; Swiderski, C. E.

In: Animal Genetics, Vol. 42, No. 4, 08.2011, p. 395-405.

Research output: Contribution to journalArticle

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