The CDC48 complex mediates ubiquitin-dependent degradation of intra-chloroplast proteins in plants

Li, Jialong; Yuan, Jiarui; Li, Yuhong; Sun, Huilun; Ma, Tingting; Huai, Junling; Yang, Wenqiang; Zhang, Wenhao; Lin, Rongcheng

doi:10.1016/j.celrep.2022.110664

Cited by 46 publications

(59 citation statements)

References 79 publications

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“…Of the five reported Arabidopsis CDC48 homologous genes, CDC48A was found to be associated with the chloroplast exoplastid protein TOC33 for ubiquitination and transferring them to cytoplasmic 26S proteasome degradation [ 26 ]. Current report showed CDC48 complex can interact with plastid protein RbcL (RuBisCO large subunit) and AtpB (ATP synthase β subunit) and ubiquitinated them under ROS stress condition [ 27 ]. At the same time, our proteome dataset showed that the plastid protein and the mitochondrion protein increasingly enriched in upl5 mutants ( Figure 5 ), thus, UPL5 might alter protein allocation between organelles and cytoplasm.…”

Section: Discussionmentioning

confidence: 99%

Establishment of a Landscape of UPL5-Ubiquitinated on Multiple Subcellular Components of Leaf Senescence Cell in Arabidopsis

Lan

Zheng

Yang

et al. 2022

IJMS

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Catabolism of macromolecules is a major event in senescent cells, especially involving proteolysis of organelles and abnormally aggregated proteins, circulation of nutrients, and precise control of intracellular environmental balance. Proteasomes are distributed in the nucleus and cytoplasm; however, proteasomes in organelles are limited. In this study, multi-omics proteomic analyses of ubiquitinated proteins enriched by using antibody against “di-Gly-Lys” via a free labeling were used to investigate the global changes of protein levels and ubiquitination modification levels of upl5 mutant relative to wild-type plant; subcellular localization analysis of UPL5 was found to be located in the nucleus, cytoplasm, and plastid within the cell; and the direct lysine site patterns of UPL5 were screened by the H89R substitution in the tagged ubiquitinated assay. It suggests that UPL5 acting as a candidate of organelle E3 ligase either in the nucleus or cytoplasm or plastid modifies numerous targets related to nuclear transcription and plastid photosynthesis involving in Ca2+ and hormone signaling pathway in plant senescence and in response to (a)biotic stress protection.

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Section: Discussionmentioning

confidence: 99%

Establishment of a Landscape of UPL5-Ubiquitinated on Multiple Subcellular Components of Leaf Senescence Cell in Arabidopsis

Lan

Zheng

Yang

et al. 2022

IJMS

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“…Protease activities were detected in the chloroplast, such as a metalloprotease Fish Protease 6 (AtFtsH6), which is responsible for the degradation of LHCb1 and LHCb3 under high light and senescence [ 55 ]. Recently, a ubiquitin-dependent degradation process was observed during chloroplast degradation, and a degradation of intra-chloroplast proteins RbcL and AtpB was mediated by a chaperone-like CDC48 complex [ 56 ]. Interestingly, when the global proteome data were searched against the maize database using ubiquitination of lysine as a variable modification, 11 cold down-regulated photosynthesis proteins were found to contain ubiquitin sites, including six chlorophyll a-b binding proteins, three ATP synthase subunits (alpha, beta, and gamma) and one cytochrome f proteins ( Table S6 ).…”

Section: Discussionmentioning

confidence: 99%

Integrative Proteome and Phosphoproteome Profiling of Early Cold Response in Maize Seedlings

Xing

Tan

Feng

et al. 2022

IJMS

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Cold limits the growth and yield of maize in temperate regions, but the molecular mechanism of cold adaptation remains largely unexplored in maize. To identify early molecular events during cold shock, maize seedlings were treated under 4 °C for 30 min and 2 h, and analyzed at both the proteome and phosphoproteome levels. Over 8500 proteins and 19,300 phosphopeptides were quantified. About 660 and 620 proteins were cold responsive at protein abundance or site-specific phosphorylation levels, but only 65 proteins were shared between them. Functional enrichment analysis of cold-responsive proteins and phosphoproteins revealed that early cold response in maize is associated with photosynthesis light reaction, spliceosome, endocytosis, and defense response, consistent with similar studies in Arabidopsis. Thirty-two photosynthesis proteins were down-regulated at protein levels, and 48 spliceosome proteins were altered at site-specific phosphorylation levels. Thirty-one kinases and 33 transcriptional factors were cold responsive at protein, phosphopeptide, or site-specific phosphorylation levels. Our results showed that maize seedlings respond to cold shock rapidly, at both the proteome and phosphoproteome levels. This study provides a comprehensive landscape at the cold-responsive proteome and phosphoproteome in maize seedlings that can be a significant resource to understand how C4 plants respond to a sudden temperature drop.

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“…Furthermore, a chloroplast-associated protein degradation pathway (CHLORAD) was shown to target damaged TOC machinery [7]. In this pathway, SP1 interacts with Omp85-type β-barrel channel protein suppressor of ppi1 locus2 (SP2) and cell division control protein 48 (CDC48), a conserved AAA+ (ATPases associated with diverse cellular activities) chaperone, to form a complex that mediates TOC protein degradation via protein retrotranslocation and the UPS (Figure 1A) [7,38]. While SP1 is involved in mediating the process of ubiquitination in the presence of stress or developmental cues, the exact mode of target substrate recognition by SP1 remains largely elusive [7,36].…”

Section: Sp1 a Chloroplast-localized Ring-type E3 Ligasementioning

confidence: 99%

“…CDC48 is a highly conserved eukaryotic protein and ubiquitin-dependent segregase belonging to the AAA+ family [7,38]. Located in the cytosol and nucleus, CDC48 plays an important role in the CHLORAD pathway.…”

Section: Role Of Cdc48 In Intra-chloroplast Protein Degradationmentioning

confidence: 99%

“…More specifically, CDC48 provides the proper ATP-powered machinery needed to surpass the physical barriers presented by the chloroplast envelope membranes upon protein extraction [7]. To function, CDC48 requires a complex formation with Ubiquitin Fusion Degradation1 (UFD1)-Nuclear Protein Localization4 (NPL4), a heterodimeric cofactor that binds ubiquitin and small ubiquitin-like modifier proteins [38].…”

Section: Role Of Cdc48 In Intra-chloroplast Protein Degradationmentioning

confidence: 99%

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The Role of E3 Ubiquitin Ligases in Chloroplast Function

Hand¹,

Shabek²

2022

Preprint

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Chloroplasts are ancient organelles responsible for photosynthesis and various biosynthetic functions essential to most life on Earth. Many of these functions require tightly controlled regulatory processes to maintain homeostasis at the protein level. One such regulatory mechanism is the ubiquitin-proteasome system whose fundamental role is increasingly emerging in chloroplasts. In particular, the role of E3 ubiquitin ligases as determinants in the ubiquitination and degradation of specific intra-chloroplast proteins. Here, we highlight recent advances in understanding the roles of plant E3 ubiquitin ligases in chloroplast function.

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The CDC48 complex mediates ubiquitin-dependent degradation of intra-chloroplast proteins in plants

Cited by 46 publications

References 79 publications

Establishment of a Landscape of UPL5-Ubiquitinated on Multiple Subcellular Components of Leaf Senescence Cell in Arabidopsis

Establishment of a Landscape of UPL5-Ubiquitinated on Multiple Subcellular Components of Leaf Senescence Cell in Arabidopsis

Integrative Proteome and Phosphoproteome Profiling of Early Cold Response in Maize Seedlings

The Role of E3 Ubiquitin Ligases in Chloroplast Function

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