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.
Highlights
The accurate maintenance of protein levels is an essential regulatory mechanism in all biological processes
The study showed that only 60% of the O. sativa ATLs were clustered with A. thaliana ATLs, suggesting that either an important expansion of ATLs in O. sativa or a dramatic contraction in A. thaliana occurred since their divergence about 140–145 million years ago [33,34]
We have continued our previous analysis on the ATL genes encoding a class of ubiquitin-ligases in plants incorporating the information from 24 complete genomes
Summary
The accurate maintenance of protein levels is an essential regulatory mechanism in all biological processes. The UPS performs several amazing and complex tasks It is involved in the regulation of key steps of almost all hormone responses, it participates in plant morphogenesis, has a role in chromatin structure and epigenetics, and modulates the defense response against diverse pathogens. Such diversity of roles may be a reason for the large number and variety of UPS pathway components in plants [1,2]. Ubiquitin-ligase genes encoding the RING-finger domain are highly abundant. The estimated number of single-subunit RING finger E3s is 477 in A. thaliana and 300 in humans [2,3]
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