Repertoire of plant RING E3 ubiquitin ligases revisited: New groups counting gene families and single genes

Abstract

E3 ubiquitin ligases of the ubiquitin proteasome system (UPS) mediate recognition of substrates and later transfer the ubiquitin (Ub). They are the most expanded components of the system. The Really Interesting New Gene (RING) domain contains 40–60 residues that are highly represented among E3 ubiquitin ligases. The Arabidopsis thaliana E3 ubiquitin ligases with a RING finger primarily contain RING-HC or RING-H2 type domains or less frequently RING-v, RING-C2, RING-D, RING-S/T and RING-G type domains. Our previous work on three E3 ubiquitin ligase families with a RING-H2 type domain, ATL, BTL, and CTL, suggested that a phylogenetic distribution based on the RING domain allowed for the creation a catalog of known domains or unknown conserved motifs. This work provided a useful and comprehensive view of particular families of RING E3 ubiquitin ligases. We updated the annotation of A. thaliana RING proteins and surveyed RING proteins from 30 species across eukaryotes. Based on domain architecture profile of the A. thaliana proteins, we catalogued 4711 RING finger proteins into 107 groups, including 66 previously described gene families or single genes and 36 novel families or undescribed genes. Forty-four groups were specific to a plant lineage while 41 groups consisted of proteins found in all eukaryotic species. Our present study updates the current classification of plant RING finger proteins and reiterates the importance of these proteins in plant growth and adaptation.

Research Progress on Plant RING-Finger Proteins

“…However, the latest study suggests that there are 508 RING domains predicted in Arabidopsis thaliana due to the improved annotation of the A. thaliana genome. These are also divided into seven subtypes: RING-H2(258), RING-HC(191), RING-v(26), RING-C2 (16), RING-D(7), RING-S/T(3), and RING-G(1) [12]. According to the type of the fifth conserved ML, the ML containing histidine is called RING-H2, and the one containing cysteine is called RING-HC.…”

High throughput in vitro seed germination screen identified new ABA responsive RING-type ubiquitin E3 ligases in Arabidopsis thaliana

“…RING-type Ubiquitin E3 ligases are a large protein family with diverse additional domains determining the upstream regulation and downstream targets (Stone et al 2005;Jiménez-López et al 2018). Through the complex structural characteristics RING-type ubiquitin E3 ligases are involved in many developmental or signalling processes, including ABA (Sadanandom et al 2012;Yu et al 2016).…”

“…The E3 ligases are the most abundant UPS components; there are more than a thousand E3 ligase genes in Arabidopsis genome (Stone et al 2005;Jiménez-López et al 2018). The E3 ligases found in plants belong to one of seven subtypes that can be divided in two: genes with either a Homology to E6-AP C-Terminus (HECT) or Really Interesting New Gene (RING)/U-box domain (Sadanandom et al 2012;Jiménez-López et al 2018).…”

“…The E3 ligases are the most abundant UPS components; there are more than a thousand E3 ligase genes in Arabidopsis genome (Stone et al 2005;Jiménez-López et al 2018). The E3 ligases found in plants belong to one of seven subtypes that can be divided in two: genes with either a Homology to E6-AP C-Terminus (HECT) or Really Interesting New Gene (RING)/U-box domain (Sadanandom et al 2012;Jiménez-López et al 2018). The RING-type E3 proteins are the most abundant among the single subunit E3 ligases and can be divided in seven RING finger domain classes distributed in 30 groups (Stone et al 2005;Jiménez-López et al 2018).…”

“…The E3 ligases found in plants belong to one of seven subtypes that can be divided in two: genes with either a Homology to E6-AP C-Terminus (HECT) or Really Interesting New Gene (RING)/U-box domain (Sadanandom et al 2012;Jiménez-López et al 2018). The RING-type E3 proteins are the most abundant among the single subunit E3 ligases and can be divided in seven RING finger domain classes distributed in 30 groups (Stone et al 2005;Jiménez-López et al 2018). However, only few E3 ligases have been functionally analysed and their substrates identified.…”