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Diversity in the Architecture of ATLs, a Family of Plant Ubiquitin-Ligases, Leads to Recognition and Targeting of Substrates in Different Cellular Environments

Authors
Journal
PLoS ONE
1932-6203
Publisher
Public Library of Science
Publication Date
Volume
6
Issue
8
Identifiers
DOI: 10.1371/journal.pone.0023934
Keywords
  • Research Article
  • Biology
  • Computational Biology
  • Genomics
  • Genome Databases
  • Genome Evolution
  • Structure Prediction
  • Molecular Genetics
  • Gene Classes
  • Gene Duplication
  • Gene Identification And Analysis
  • Gene Regulation
  • Evolutionary Biology
  • Organismal Evolution
  • Plant Evolution
  • Genome Analysis Tools
  • Gene Prediction
  • Sequence Databases
  • Functional Genomics
  • Model Organisms
  • Plant And Algal Models
  • Arabidopsis Thaliana
  • Plant Science
  • Plants
  • Flowering Plants
  • Major Plant Groups
  • Plant Genomics
  • Plant Phylogenetics
Disciplines
  • Biology
  • Ecology
  • Geography

Abstract

Ubiquitin-ligases or E3s are components of the ubiquitin proteasome system (UPS) that coordinate the transfer of ubiquitin to the target protein. A major class of ubiquitin-ligases consists of RING-finger domain proteins that include the substrate recognition sequences in the same polypeptide; these are known as single-subunit RING finger E3s. We are studying a particular family of RING finger E3s, named ATL, that contain a transmembrane domain and the RING-H2 finger domain; none of the member of the family contains any other previously described domain. Although the study of a few members in A. thaliana and O. sativa has been reported, the role of this family in the life cycle of a plant is still vague. To provide tools to advance on the functional analysis of this family we have undertaken a phylogenetic analysis of ATLs in twenty-four plant genomes. ATLs were found in all the 24 plant species analyzed, in numbers ranging from 20–28 in two basal species to 162 in soybean. Analysis of ATLs arrayed in tandem indicates that sets of genes are expanding in a species-specific manner. To get insights into the domain architecture of ATLs we generated 75 pHMM LOGOs from 1815 ATLs, and unraveled potential protein-protein interaction regions by means of yeast two-hybrid assays. Several ATLs were found to interact with DSK2a/ubiquilin through a region at the amino-terminal end, suggesting that this is a widespread interaction that may assist in the mode of action of ATLs; the region was traced to a distinct sequence LOGO. Our analysis provides significant observations on the evolution and expansion of the ATL family in addition to information on the domain structure of this class of ubiquitin-ligases that may be involved in plant adaptation to environmental stress.

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