The ATL Gene Family from Arabidopsis thaliana and Oryza sativa Comprises a Large Number of Putative Ubiquitin Ligases of the RING-H2 Type

Abstract

Ubiquitin ligases play an important regulatory role in the control of protein degradation processes via the ubiquitin/26S proteasome pathway in eukaryotes. These enzymes participate in substrate specification and mediate the transfer of ubiquitin to target proteins. A large number of ubiquitin ligases are predicted in the eukaryotes whose genomes have been sequenced; in Arabidopsis thaliana more than 1300 genes are thought to encode ubiquitin ligases. At least three classes of ubiquitin ligases are present in Arabidopsis, one of which comprises about 470 RING zinc-finger domain proteins. Within this class we have characterized the ATL family that encodes a RING-H2 finger. We identified 80 members of this family in A. thaliana and 121 in Oryza sativa. About 60% of the rice ATLs are clustered with A. thaliana ATLs, and in many cases the gene products showed sequence similarities beyond the ATL's conserved features, suggesting that they could be orthologous genes. Ninety percent of the ATLs are intronless genes, suggesting that the structure of the basic ATL protein may have evolved as a functional module. We carried out a survey of T-DNA insertions in 30% of the Arabidopsis ATL genes and screened for possible phenotypes. Four of these genes are likely to be essential for viability, since homozygous plants for the T-DNA insertion were not recovered. One of them, ATL8, is mainly expressed in young siliques, suggesting a role during embryogenesis. We also recovered a line carrying a T-DNA insertion in ATL43 that showed an ABA-insensitive phenotype, suggesting a role of this gene in the ABA response. The organization of ATLs in Arabidopsis and rice in this study will be a valuable comprehensive guide for this multigene family.

Phosphorylation of Arabidopsis Ubiquitin Ligase ATL31 Is Critical for Plant Carbon/Nitrogen Nutrient Balance Response and Controls the Stability of 14-3-3 Proteins

“…The C-terminal region of ATL proteins is predicted to recognize specific target proteins for ubiquitination because the region is not conserved among the ATL family, unlike the N-terminal hydrophobic region and RING domain (11). According to this hypothesis, our study demonstrates that the interaction of ATL31 with 14-3-3 proteins is mediated by the phosphorylation of specific Ser/Thr residues in the C-terminal region.…”

“…ATL31 overexpression led to a carbon/nitrogen-insensitive phenotype of carbon/nitrogen insensitive 1-dominant (cni1-D) plants and resulted in expansion of green-colored cotyledon under high carbon/low nitrogen conditions, whereas the loss-of-function mutant of ATL31 showed a hypersensitive phenotype (9). ATL31 is a member of the plant-specific ATL ubiquitin ligase family, which comprises proteins that contain a transmembrane-like hydrophobic region at the N terminus, a GLD region, a RING-H2 type zinc finger domain, and a nonconserved C-terminal region (11). Biochemical and genetic studies demonstrated the membrane localization and ubiquitin ligase activity of ATL31, both of which are required for the regulation of C/N-nutrient response in plants (9).…”

Interactions between theS-Domain Receptor Kinases and AtPUB-ARM E3 Ubiquitin Ligases Suggest a Conserved Signaling Pathway in Arabidopsis

“…KEG has been implicated in the regulation of ABI5 protein levels in the absence of stress (Stone et al, 2006). ATL43 has been proposed to function as a positive regulator of ABA responses because atl43 mutant T-DNA lines were moderately insensitive at high concentration of ABA during germination (Serrano et al, 2006). Increased expression of XERICO was found to increase endogenous ABA levels and XERICO was thought to regulate the expression of an ABA biosynthesis gene (Ko et al, 2006).…”

Isolation of putative embryo-specific genes using stress induction of carrot somatic embryos

“…RING-finger proteins are a group of E3 ligases that mediate the transfer of ubiquitin to proteins and target substrates to the proteasome, an important part of the protein degradation system, via the ubiquitin/26S proteasome pathway (Glickman and Ciechanover 2002). Ubiquitinmediated proteasome pathways have been suggested to play an important role in the early stages of plant embryogenesis (Shen et al 2002, Hellmann et al 2003, Liu et al 2004, and Arabidopsis mutants of RING-finger type E3 ligase show seed deficiency (Serrano et al 2006). Based on these observations, E-14-2 was expected to be an embryospecific gene with an important role in early embryogenesis.…”