Domain graph of Arabidopsis proteome by comparative analysis

Song Liu, Chi Zhang, Yaoqi Zhou

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)435-444
Number of pages10
JournalJournal of proteome research
Volume4
Issue number2
DOIs
StatePublished - Mar 1 2005

Fingerprint

Proteome
Arabidopsis
Ubiquitin
Proteins
Tissue
Databases
Molecular Sequence Annotation
Plant Proteins
Association reactions
RNA
Buffaloes
DNA
Catalysis
Cell growth
Transcription
Cell Differentiation
Catalyst supports
Metabolism
Maintenance
Genes

Keywords

  • Arabidopsis thaliana
  • Domain combination
  • Domain graph
  • Pentatricopeptide repeats

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Domain graph of Arabidopsis proteome by comparative analysis. / Liu, Song; Zhang, Chi; Zhou, Yaoqi.

In: Journal of proteome research, Vol. 4, No. 2, 01.03.2005, p. 435-444.

Research output: Contribution to journalArticle

Liu, Song ; Zhang, Chi ; Zhou, Yaoqi. / Domain graph of Arabidopsis proteome by comparative analysis. In: Journal of proteome research. 2005 ; Vol. 4, No. 2. pp. 435-444.
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