Linked Life Data

15822920

Source:http://linkedlifedata.com/resource/pubmed/id/15822920

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2005-4-12
pubmed:abstractText
The domain graph of domains and domain combinations of Arabidopsis thaliana is established based on pfam 14.0 database and analyzed via comparison with 10 eukaryotic, 30 bacterial, and 16 archaeal proteomes. The comparative analysis of the domain graphs provides a useful platform for revealing global insights on the evolution of plant kingdom. More importantly, it is a powerful tool for searching not only the possible new function of both plant-specific and nonspecific domains via specific domain combinations in Arabidopsis thaliana but also the functional role of unknown domains. As an example, we present the functional link between ubiquitin and Myb_DNA-binding domains via Bromodomain as the plant specific evidence for the association between transcription and ubiquitin. We further show that PentatricoPeptide Repeats (PPR) proteins have plant-specific links with a wide variety of domains responsible for RNA binding/metabolism, modulation of protein-protein interactions, ubiquitin-conjugation, cell growth/maintenance, catalysis, and others. This further supports the recently proposed association of PPR proteins with specific RNA transcripts and defined effector proteins. Moreover, the domain graph built from tissue-specific genes is frequently associated with DNA binding domains, suggesting that the differentiation of tissue cell types is contributed mostly by tissue-specific transcriptional process. DOGMA (DOmain Graph via coMparitive analysis for Arabidopsis thaliana) is available on-line with a variety of search tools at http://theory.med.buffalo.edu/DOGMA. The database, which allows user-specified search for plant specific domains and their combinations, will be useful as an additional tool for annotation of the proteins that play specific roles in plants and other organisms.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:issn
1535-3893
pubmed:author
pubmed:issnType
Print
pubmed:volume
4
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
435-44
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed:articleTitle
Domain graph of Arabidopsis proteome by comparative analysis.
pubmed:affiliation
Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology & Biophysics, State University of New York at Buffalo, 124 Sherman Hall, Buffalo, New York 14214, USA.
pubmed:publicationType
Journal Article, Comparative Study, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural