Ubiquitin Specific Protease 15 Has an Important Role in Regulating Grain Width and Size in Rice

Abstract

Ubiquitination and deubiquitination are reversible processes that play crucial roles in regulating organ size in plants. However, information linking deubiquitination and seed size in rice (Oryza sativa) is limited. Here, we characterized a dominant large-grain mutant, large grain1-D (lg1-D), with a 30.8% increase in seed width and a 34.5% increase in 1,000-grain weight relative to the wild type. The lg1-D mutant had more cells oriented in the lateral direction of the spikelet hull compared with the wild type. Mapbased cloning showed that LG1 encodes a constitutively expressed ubiquitin-specific protease15 (OsUBP15) that possesses deubiquitination activity in vitro. Loss-of-function and down-regulated expression of OsUBP15 produced narrower and smaller grains than the control. A set of in vivo experiments indicated that the mutant Osubp15 had enhanced protein stability relative to wild-type OsUBP15. Further experiments verified that OsDA1 directly interacted with OsUBP15. Genetic data indicated that OsUBP15 and GRAIN WIDTH 2 (GW2) were not independent in regulating grain width and size. In summary, we identified OsUBP15 as a positive regulator of grain width and size in rice and provide a promising strategy for improvement of grain yield by pyramiding OsUBP15 and gw2.

Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population

“…The rice deubiquitinase gene OsOTUB1/WTG1 encodes an otubain-like protease and affects grain size (Huang et al, 2017;Liu et al, 2018). Recently, LG1 encoding for ubiquitin specific protease 15 (OsUBP15) was reported to function as a positive regulator of GW in rice (Shi et al, 2019). The other potential candidate gene, OsCLP6 (LOC_Os03g29810), encoding a putative chitinaselike protein (Clp) protease homolog was identified in both populations across all the three testing environments.…”

Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

“…and TraesCS6D01G179700, is OsUBP15/LG1 (Figure 7 and Table S9). OsUBP15/LG1 encodes a constitutively expressed ubiquitin-specific protease 15 (OsUBP15) that possesses de-ubiquitination activity in vitro and is a positive regulator of grain width and size in rice [49]. These results suggest that the orthologue of WGRG9 in the corresponding P genomic region could serve as a candidate gene of controlling thousand-grain weight in Pubing 3035 for functional verification in the next study.…”

“…Therefore, a comparative genomics map between the 6P chromosome fragment in Pubing 3035 and the wheat 6A chromosome was constructed by developing polymorphic molecular markers of conserved homologous genes between the 6P and 6A chromosomes. The results show that A. cristatum transcript/7882 corresponds with TraesCS6A01G192600, TraesCS6B01G231700 and TraesCS6D01G179700 (Figure 7 and Table S9) and is homologous to rice gene OsUBP15/LG1, which encodes a constitutively expressed ubiquitin-specific protease 15 (OsUBP15) that possesses de-ubiquitination activity in vitro and is a positive regulator of grain width and size in rice [49], suggesting that their orthologue in the corresponding P genomic region could serve as a candidate gene for controlling thousand-grain weight in Pubing 3035. The effective research method used in this study can be applied in other studies to discover candidate genes in wheat and wild relative-derived translocation lines with prominent traits.…”

The ubiquitin system affects agronomic plant traits

“…The rice (Oryza sativa) UBP15 ortholog OsUBP15 promotes large grain size (73). Seeds from plants with a dominant mutation in Osubp15 that produces a truncated protein lacking 160 amino acids at the C-terminus are larger and weigh 34.5% more than seeds from wild-type plants.…”

“…Plants overexpressing OsUBP15 have the opposite: longer, thicker grains than wild-type plants. Like Arabidopsis UBP15 and DA1, OsUBP15 has deubiquitinase activity and interacts with OsDA1 (73).…”