Modeling a whole organ using proteomics: The avian bursa of Fabricius

While advances in proteomics have improved proteome coverage and enhanced biological modeling, modeling function in multicellular organisms requires understanding how cells interact. Here we used the chicken bursa of Fabricius, a common experimental system for B cell function, to model organ functio...

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Bibliographic Details
Published in:Proteomics (Weinheim) 2006-05, Vol.6 (9), p.2759-2771
Main Authors: McCarthy, Fiona M., Cooksey, Amanda M., Wang, Nan, Bridges, Susan M., Pharr, G. Todd, Burgess, Shane C.
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Analytical, structural and metabolic biochemistry
Animals
B-Cell development
Biological and medical sciences
Bursa of Fabricius
Cells, Cultured
Chickens
Databases, Genetic
Functional proteomics
Fundamental and applied biological sciences. Psychology
Humans
Miscellaneous
Models, Biological
Molecular Sequence Data
Phylogenetics
Phylogeny
Proteins
Proteomics
Sequence Alignment
Transcription factors
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Summary:While advances in proteomics have improved proteome coverage and enhanced biological modeling, modeling function in multicellular organisms requires understanding how cells interact. Here we used the chicken bursa of Fabricius, a common experimental system for B cell function, to model organ function from proteomics data. The bursa has two major functional cell types: B cells and the supporting stromal cells. We used differential detergent fractionation‐multidimensional protein identification technology (DDF‐MudPIT) to identify 5198 proteins from all cellular compartments. Of these, 1753 were B cell specific, 1972 were stroma specific and 1473 were shared between the two. By modeling programmed cell death (PCD), cell differentiation and proliferation, and transcriptional activation, we have improved functional annotation of chicken proteins and placed chicken‐specific death receptors into the PCD process using phylogenetics. We have identified 114 transcription factors (TFs); 42 of the bursal B cell TFs have not been reported before in any B cells. We have also improved the structural annotation of a newly sequenced genome by confirming the in vivo expression of 4006 “predicted”, and 6623 ab initio, ORFs. Finally, we have developed a novel method for facilitating structural annotation, “expressed peptide sequence tags” (ePSTs) and demonstrate its utility by identifying 521 potential novel proteins from the chicken “unassigned chromosome”.
ISSN:1615-9853
1615-9861
DOI:10.1002/pmic.200500648