Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles

Cao

et al. 2021

Nucleic Acids Research

Self Cite

As a crucial molecular mechanism, post-translational modifications (PTMs) play critical roles in a wide range of biological processes in plants. Recent advances in mass spectrometry-based proteomic technologies have greatly accelerated the profiling and quantification of plant PTM events. Although several databases have been constructed to store plant PTM data, a resource including more plant species and more PTM types with quantitative dynamics still remains to be developed. In this paper, we present an integrative database of quantitative PTMs in plants named qPTMplants (http://qptmplants.omicsbio.info), which hosts 1 242 365 experimentally identified PTM events for 429 821 nonredundant sites on 123 551 proteins under 583 conditions for 23 PTM types in 43 plant species from 293 published studies, with 620 509 quantification events for 136 700 PTM sites on 55 361 proteins under 354 conditions. Moreover, the experimental details, such as conditions, samples, instruments and methods, were manually curated, while a variety of annotations, including the sequence and structural characteristics, were integrated into qPTMplants. Then, various search and browse functions were implemented to access the qPTMplants data in a user-friendly manner. Overall, we anticipate that the qPTMplants database will be a valuable resource for further research on PTMs in plants.

Section: Discussionmentioning

confidence: 99%

“…Recently, the rapid progress of high-throughput proteomic techniques has made great strides in the profiling and quantification of plant PTMs in different tissues under various conditions ( 17 - 20 ). For example, based on phosphoproteome and acetylome quantification, Uhrig et al.…”

Section: Introductionmentioning

confidence: 99%

qPTMplants: an integrative database of quantitative post-translational modifications in plants

Han

Cao

et al. 2021

Nucleic Acids Research

Self Cite

“…2G ). Indeed, the ubiquitinated lysine K following A residue has been previously described to be a sequence feature for ubiquitination in wheat, maize, and rice ( Zhang et al , 2017 ; Wang et al , 2019 ; Zhu et al , 2020 ), but not in petunia, Paeonia , and tobacco ( Guo et al , 2017 ; Gu et al , 2019 ; Zhan et al , 2020 ), in which glutamic acid (E) was found upstream of the ubiquitinated K. These results suggest that the preference of ubiquitination sites exhibit species specificity.…”

Section: Resultsmentioning

confidence: 88%

“…Recently, a state-of-the-art technique, which couples high-resolution mass spectrometry (MS) with a commercialized antibody that specifically recognizes the lysine residues modified by diglycine remnant (K-ɛ-GG), an adduct left at sites of ubiquitination after trypsin digestion, has achieved significant improvement in the detection of ubiquitinated proteins and the corresponding ubiquitination sites ( Xu et al , 2010 ). This enables researchers to identify a large number of ubiquitinated proteins in different eukaryotic species including crop plants ( Zhang et al , 2017 ; Wang et al , 2019 ; Zhu et al , 2020 ). Strawberry is not only a commonly consumed fresh fruit, but also a model system for ripening analysis of non-climacteric fruits ( Giovannoni, 2004 ; T. Chen et al , 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Global ubiquitinome analysis reveals the role of E3 ubiquitin ligase FaBRIZ in strawberry fruit ripening

Kong

Journal of Experimental Botany

et al. 2022

Ubiquitination is an important post-translational modification that mediates protein degradation in eukaryotic cell, participating in multiple biological processes. However, the profiling of protein ubiquitination and the function of this crucial modification in fruit ripening remain largely unknown. In this study, we found that suppression of proteasome by the inhibitor MG132 retarded strawberry fruit ripening. By using K-ɛ-GG antibody enrichment combined with high-resolution mass spectrometry, we performed a comprehensive ubiquitinome analysis in strawberry fruit. We identified 2947 ubiquitination sites for 2878 peptides within 1487 proteins, which are involved in a variety of cellular functions. The lysine at position 48 (K48)-linked poly-ubiquitin chains appeared to be the most prevalent types of modification among the identified ubiquitinated proteins. A large number of ubiquitination sites exhibited altered ubiquitination levels after proteasome inhibition, including those within ripening-related proteins associated with sugar and acid metabolism, cell wall metabolism, anthocyanin synthesis, and ABA biosynthesis and signaling. We further demonstrated that FaBRIZ, a RING-type E3 ligase, functions as a negative regulator of ripening in strawberry fruit. Our findings highlight the critical regulatory roles of protein ubiquitination in fruit ripening. The ubiquitinome data provide a basis for further exploration of the function of ubiquitination on specific proteins.

“…We previously identified 1543 proteins containing ubiquitinated sites in two studies [ 12 , 13 ]. In addition, 1163 and 895 ubiquitinated proteins were recently isolated from germinating rice seeds and young panicles, respectively [ 19 , 20 ]. These studies led to the identification of 2362 ubiquitinated proteins (Additional file 1 : Fig.…”

Section: Resultsmentioning

confidence: 99%

An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome

et al. 2022

Background Ubiquitination is essential for many cellular processes in eukaryotes, including 26S proteasome-dependent protein degradation, cell cycle progression, transcriptional regulation, and signal transduction. Although numerous ubiquitinated proteins have been empirically identified, their cognate ubiquitin E3 ligases remain largely unknown. Results Here, we generate a complete ubiquitin E3 ligase-encoding open reading frames (UbE3-ORFeome) library containing 98.94% of the 1515 E3 ligase genes in the rice (Oryza sativa L.) genome. In the test screens with four known ubiquitinated proteins, we identify both known and new E3s. The interaction and degradation between several E3s and their substrates are confirmed in vitro and in vivo. In addition, we identify the F-box E3 ligase OsFBK16 as a hub-interacting protein of the phenylalanine ammonia lyase family OsPAL1–OsPAL7. We demonstrate that OsFBK16 promotes the degradation of OsPAL1, OsPAL5, and OsPAL6. Remarkably, we find that overexpression of OsPAL1 or OsPAL6 as well as loss-of-function of OsFBK16 in rice displayed enhanced blast resistance, indicating that OsFBK16 degrades OsPALs to negatively regulate rice immunity. Conclusions The rice UbE3-ORFeome is the first complete E3 ligase library in plants and represents a powerful proteomic resource for rapid identification of the cognate E3 ligases of ubiquitinated proteins and establishment of functional E3–substrate interactome in plants.