Met1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains

Abstract

Linear (Met1-linked) ubiquitination is involved inflammatory and innate immune signaling. Previous studies have characterized enzymes regulating the addition and removal of this modification in mammalian systems. However, only a few plant-derived deubiquitinases targeting Met1-linked ubiquitin chains have been reported and their mechanism of action remains elusive. Here, using a dehydroalanine-bearing Met1-diubiquitin suicide probe, we discover OTUB1 from Oryza sativa (OsOTUB1) as a Met1-linked ubiquitin chain-targeting deubiquitinase. By solving crystal structures of apo OsOTUB1 and an OsOTUB1/Met1-diubiquitin complex, we find that Met1 activity is conferred by Met1-specific motifs in the S1’ pocket of OsOTUB1. Large-scale sequence alignments and hydrolysis experiments provide evidence that these motifs are a general determinant of Met1 activity in the OTUB subfamily across species. Analysis of the species distribution of OTUBs capable of hydrolysing Met1-linked ubiquitin chains shows that this activity is conserved in green plants (Viridiplantae) and does not exist in metazoans, providing insights into the evolutionary differentiation between primitive plants and animals.

Neutron-encoded diubiquitins to profile linkage selectivity of deubiquitinating enzymes

“…OTUB1 has previously been annotated as Lys48 specific 24 , but we also observed cleavage of Lys63- and Met1-linked chains (Supplementary Data 2a ). Although the processing of Lys63-linked linkages has previously been observed 63 , the processing of Met1-linked chains was only recently described for OsOTUB1, a homologue of human OTUB1 64 . We found OTUB2 to also process Lys6 diUb but only at elevated enzyme concentration and upon almost full consumption of its known target linkages Lys63, Lys48, and Lys11 (Fig.…”

Emerging Biopharmaceuticals from Pimpinella Genus

“…Pseudoisoeugenol, as a representative chemical marker of Pimpinella , possessed a peculiar skeleton of 1-hydroxy-2-propyl-4-methoxybenzene, which has been found exclusively in the genus Pimpinella so far [ 28 ]. Since the first pseudoisoeugenol was discovered from the P. anisum by G. T. Carter et al [ 29 ] in 1977, scientists have successively obtained 12 pseudoisoeugenol ( 1 – 12 ) from the Chinese herb P. thellungiana , and llungianin A ( 1 ) and llungianin B ( 2 ), which presented significant antihypertensive activity [ 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 ].…”

Secretory molecules from secretion systems fine-tune the host-beneficial bacteria (PGPRs) interaction

“…However, the role of SS in the establishment of beneficial microbe-plant interaction is limited to rhizobia and not thoroughly reviewed. Recently, Lomovatskaya et al reviewed the recent updates on the organization and operational aspects of SS of plant pathogens and a few beneficial bacteria and their importance in suppressing plant defense responses ( Parizad et al, 2016 ; Lomovatskaya and Romanenko, 2020 ; Lu et al, 2022 ). Therefore, the present review updates the mechanistic aspects of the secretion system in chemotaxis, initiation of infection, colonization, and establishment of beneficial bacteria in the host.…”