Expansion and Diversification of BTL Ring-H2 Ubiquitin Ligases in Angiosperms: Putative Rabring7/BCA2 Orthologs

Abstract

RING finger E3 ligases are components of the ubiquitin proteasome system (UPS) that mediate the transfer of ubiquitin to substrates. Single-subunit RING finger E3s binds the E2 ubiquitin-conjugating enzyme and contains recognition sequences for the substrate within the same polypeptide. Here we describe the characterization of a class of RING finger E3 ligases that is conserved among eukaryotes. This class encodes a RING-H2 domain related in sequence to the ATL RING-H2 domain, another class of E3 ligases, and a C2/C2 zing finger at the amino-terminus, formerly described as BZF. In viridiplantae (green algae and land plants), we designed this family as BTL for BZF ATLs. BTLs are putative orthologs of the mammalian Rabring7/BCA2 RING-H2 E3s that have expanded in angiosperms. They are found in numbers ranging from three to thirty-one, which is in contrast to the one to three members normally found in animals, fungi, and protists. Furthermore, the number of sequence LOGOs generated in angiosperms is four times greater than that in other eukaryotes. In contrast to ATLs, which show expansion by tandem duplication, tandemly duplicated BTLs are scarce. The mode of action of Rabring7/BCA2 and BTLs may be similar since both the Rabring7/BCA2 BZF and the ath|BTL4 BZF are likely to mediate the binding of ubiquitin. This study introduces valuable information on the evolution and domain structure of the Rabring7/BCA2/BTL class of E3 ligases which may be important for core eukaryotic genes.

Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members

“…The survey of the grapevine genome retrieved 96 ATL genes, consistent with the ATL families described in Arabidopsis and rice12, but higher than the 30 ATL genes and the seven BTL genes identified in the first draft (V0, 8X prediction) grapevine genome sequence13. Among the 96 ATL proteins we identified, 10 contain a proline residue before the third cysteine residue of the canonical RING-H2 domain and therefore belong to the BTL subfamily.…”

“…We surveyed the grapevine genome ( V. vinifera cv Pinot Noir, genotype PN40024) to identify all genes containing a canonical ATL-type RING-H2 domain1342. Each potential RING-H2 domain was analysed for the presence of, and the distance between, each of the Zn-coordinating cysteine and histidine residues, as well as the presence of a proline residue before the third cysteine according to the original ATL definition reported for the ATL family in Arabidopsis12.…”

“…Only 19 further domains in 14 sequences were detected in addition to the common RING-H2 sequence (Table 1). Ten of the ATL proteins contained an N-terminal BZF domain (C2/C2 zf-RING_3: PF14369)15 as described for the BTL subfamily in Arabidopsis13. We also identified three domain-of-unknown-function (DUF) 1117 motifs, also present, among others, in two Arabidopsis RING domain-containing E3 ubiquitin ligases ( AtRDUF1 and AtRDUF2 )46, and two protease-associated domains (PF02225), which could act as a lid covering the remnants of the active site of catalytically inactive proteins47.…”

“…Other features conserved in most known ATL proteins are a tryptophan residue located three residues downstream from the forth cysteine residue, an N-terminal hydrophobic region, a GLD motif, and a basic region, but these modules are not always present and therefore are not considered a requirement for ATL classification12. A variant of the ATL protein structure was recently described in Arabidopsis in which an additional BCA2 Zinc Finger (BZF) domain replaces the typical hydrophobic domain at the N-terminus13. The BZF domain, first identified in the N-terminal region of the human BCA2 RING E3 ligase14, interacts with ubiquitin and is required for E3 ligase activity15.…”

“…In these proteins, the proline residue associated with the RING-H2 domain is immediately adjacent to the third cysteine residue (P-Cys instead of P-X-Cys). Seventeen such BTL proteins have been described in Arabidopsis thus far13.…”