Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa

Álam, Intikhab; Yang, Yanqing; Wang, Yong; Zhu, Minhao; Wang, Hengbo; Chalhoub, Boulos; Lu, Yong-Zai

doi:10.1038/srep40690

Cited by 26 publications

(40 citation statements)

References 60 publications

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“…It is tempting to speculate that the RING-G and RING-D types evolved from RING-H2 proteins and that changes were fixed during evolution. This idea is in agreement with the exclusive detection of the RING-D type in plant species belonging to the Brasicaceae family [10, 12]. Our phylogenetic analysis supports this speculation since both types are grouped with RING-H2 sequences (Fig 2).…”

Section: Discussionsupporting

confidence: 90%

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

et al. 2018

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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.

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Section: Discussionsupporting

confidence: 90%

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

et al. 2018

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“…Eighty percent of rice RING-finger proteins have been shown to possess E3 ligase activity [16,17]. At the same time, 731 RING-finger domains in 715 predicted proteins were divided into eight types: RING-H2 (371), RING-HCa (215), RING-HCb (47),RING-v (44), RING-C2 (38), RING-D (10), RING-S/T (5), and RING-G (1) [18]. A total of 756 RING domains in 734 predicted proteins were identified in the whole Brassica oleracea proteome.…”

Section: Introductionmentioning

confidence: 99%

Research Progress on Plant RING-Finger Proteins

Sun

Ahmed

et al. 2019

Genes

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E3 ubiquitin ligases are the most expanded components of the ubiquitin proteasome system (UPS). They mediate the recognition of substrates and later transfer the ubiquitin (Ub) of the system. Really Interesting New Gene (RING) finger proteins characterized by the RING domain, which contains 40–60 residues, are thought to be E3 ubiquitin ligase. RING-finger proteins play significant roles in plant growth, stress resistance, and signal transduction. In this study, we mainly describe the structural characteristics, classifications, and subcellular localizations of RING-finger proteins, as well the physiological processes of RING-finger proteins in plant growth and development. We also summarize the functions of plant RING-finger proteins in plant stress resistance. Finally, further research on plant RING-finger proteins is suggested, thereby establishing a strong foundation for the future study of plant RING-finger proteins.

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“…Except for a large number of components related to optical responses, plant hormone regulation, growth and development, and stress were also common upstream of different VyRCHCs. This situation is in fact rather common in RING genes of all species [25][26][27][28]. Ubiquitin ligase SDIR1 regulates stress-responsive abscisic acid signal by interacting with ABRE abscisic acid response element [39].…”

Section: Discussionmentioning

confidence: 99%

“…The RING C3H2C3 gene family has since been identi ed in many plant species [25][26][27][28]. Related studies have shown that RING genes are involved in a variety of biological processes, growth and development and hormonal responses, as well as plant responses to abiotic stresses [29].…”

Section: Discussionmentioning

confidence: 99%

Identification of Ubiquitin Ligase From Grapevine Ring C3H2C3E3 and Characterization of Drought Resistance Function of VyRCHC114

Yang

et al. 2020

Preprint

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Background: RING is one of the largest E3 ubiquitin ligase families and C3H2C3 type is the largest subfamily of RING, playing an important role in plants’ development and growth and their biotic and abiotic stress responses. Results: A total of 143 RING C3H2C3-type genes (RCHCs) were discovered from the grapevine genome and separated into groups (I-XI) according to their phylogenetic analysis, with these genes named according to their positions on chromosomes. Gene replication analysis showed that tandem duplications play a predominant role in the expansion of VyRCHCs family together. Structural analysis showed that most VyRCHCs(67.13%) had no more than 2 introns, while genes clustered together based on phylogenetic trees had similar motifs and evolutionarily conserved structures. Cis-acting element analysis showed the diversity of VyRCHCs regulation. The expression profiles of eight DEGs in RNA-Seq after drought stress were similar to those in qRT-PCR analysis. The in vitro ubiquitin experiment showed that VyRCHC114 had E3 ubiquitin ligase activity, overexpression of VyRCHC114 in Arabidopsis improved drought tolerance, moreover, the transgenic plant survival rate increased by 30%, accompanied by changing of electrolyte leakage, chlorophyll content and the activities of SOD, POD, APX and CAT were changed. AtCOR15a, AtRD29A, AtERD15 and AtP5CS1 were expressed quantitatively, the results showed that they participated in the drought stress response may be regulated by the expression of VyRCHC114.Conclusions: Valuable new information on the evolution of grapevine RCHCs and its relevance for studying the functional characteristics of grapevine VyRCHC114 genes under drought stress emerged from this research.

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Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa

Cited by 26 publications

References 60 publications

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

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

Research Progress on Plant RING-Finger Proteins

Identification of Ubiquitin Ligase From Grapevine Ring C3H2C3E3 and Characterization of Drought Resistance Function of VyRCHC114

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