Article
Multidisciplinary Sciences
Wenyu Han, Mingliang Jin, Caixuan Liu, Qiaoyu Zhao, Shutian Wang, Yifan Wang, Yue Yin, Chao Peng, Yanxing Wang, Yao Cong
Summary: Using cryo-electron microscopy, we investigated the folding mechanism of tubulin/actin under the assistance of the chaperonin TRiC and its co-chaperone plp2. Our findings revealed the interaction between plp2 and tubulin/actin in different chambers of TRiC, and provided insights into the folding mechanism of these cytoskeletal proteins. These findings enhance our understanding of cytoskeletal proteostasis and its relevance to human diseases.
Article
Biochemistry & Molecular Biology
John J. Kelly, Dale Tranter, Els Pardon, Gamma Chi, Holger Kramer, Lotta Happonen, Kelly M. Knee, Jay M. Janz, Jan Steyaert, Christine Bulawa, Ville O. Paavilainen, Juha T. Huiskonen, Wyatt W. Yue
Summary: The integrity of a cell's proteome relies on the correct folding of polypeptides, which is facilitated by the chaperonin TCP-1 ring complex (TRiC). Structural studies have provided insights into the architecture and substrate recognition of TRiC, but the fate of substrates inside the TRiC chamber has remained unclear. In this study, cryo-EM was used to determine the structure of endogenous human TRiC with substrates and cochaperone at different folding stages. The findings revealed the positioning of already-folded regions of client proteins at the chamber wall, allowing unstructured regions to achieve their native fold. The substrates engaged with different sections of the chamber during the folding process, while the cochaperone PhLP2A acted as a molecular strut between the substrate and TRiC chamber. These structural snapshots contribute to our understanding of client protein folding within TRiC.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Oscar Gutierrez-Gutierrez, Daniel A. Felix, Alessandra Salvetti, Elias M. Amro, Anne Thems, Stefan Pietsch, Andreas Koeberle, K. Lenhard Rudolph, Cristina Gonzalez-Estevez
Summary: Planarians can endure starvation by maintaining adult stem cell pools and regenerative capacity. TRiC/CCT subunits play a crucial role in maintaining regeneration under starvation conditions by modulating the unfolded protein response and maintaining ATP levels.
Article
Multidisciplinary Sciences
Miranda P. Collier, Karen Betancourt Moreira, Kathy H. Li, Yu-Chan Chen, Daniel Itzhak, Rahul Samant, Alexander Leitner, Alma Burlingame, Judith Frydman
Summary: The study characterized recombinant human TRiC (hTRiC) using mass spectrometry techniques, revealing post-translational processing of its subunits. Interestingly, some subunits can promiscuously re-assemble into dimers with non-canonical contacts. CCT5 was found to be the most stable subunit and engaged in the greatest number of non-canonical dimer pairings.
SCIENTIFIC REPORTS
(2021)
Article
Biology
Caixuan Liu, Mingliang Jin, Shutian Wang, Wenyu Han, Qiaoyu Zhao, Yifan Wang, Cong Xu, Lei Diao, Yue Yin, Chao Peng, Lan Bao, Yanxing Wang, Yao Cong
Summary: This study reveals the conformational landscape of TRiC-mediated tubulin folding along TRiC's ATPase cycle and the interaction sites between tubulin and the closed TRiC chamber using cryo-EM and XL-MS analyses.
COMMUNICATIONS BIOLOGY
(2023)
Article
Microbiology
Wei-Ru Huang, Jyun-Yi Li, Tsai-Ling Liao, Chuan-Ming Yeh, Chi-Young Wang, Hsiao-Wei Wen, Nien-Jen Hu, Yi-Ying Wu, Chao-Yu Hsu, Yu-Kang Chang, Ching-Dong Chang, Brent L. Nielsen, Hung-Jen Liu
Summary: This study demonstrates that the eukaryotic chaperonin T-complex protein-1 (TCP-1) ring complex (TRiC) is essential for avian reovirus (ARV) replication by stabilizing outer-capsid protein aC, inner core protein aA, and the non-structural protein aNS of ARV.
VETERINARY MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Karen Betancourt Moreira, Miranda P. Collier, Alexander Leitner, Kathy H. Li, Ivana L. Serrano Lachapel, Frank Mccarthy, Kwadwo A. Opoku-Nsiah, Fabian Morales-Polanco, Natalia Barbosa, Daniel Gestaut, Rahul S. Samant, Soung-hun Roh, Judith Frydman
Summary: The assembly pathway of the eukaryotic chaperonin TRiC/CCT involves the sequential addition of subunits, resulting in the formation of a stable holocomplex. Unincorporated subunits are highly unstable in cells, preventing the formation of alternative chaperonin complexes.
Article
Biochemistry & Molecular Biology
Daniel Gestaut, Yanyan Zhao, Junsun Park, Boxue Ma, Alexander Leitner, Miranda Collier, Grigore Pintilie, Soung-Hun Roh, Wah Chiu, Judith Frydman
Summary: The ATP-dependent ring-shaped chaperonin TRiC/CCT plays a crucial role in cellular proteostasis. It has been found that TRiC guides the folding pathway of its substrates through site-specific interactions with conserved regions in its chamber. The chamber of TRiC provides chemical and topological directives that shape the folding landscape of its obligate substrates.
Article
Biochemistry & Molecular Biology
Mark D. Wilkinson, Josie L. Ferreira, Morgan Beeby, Jake Baum, Keith R. Willison
Summary: This paper reviews the interaction of the eukaryotic chaperonin CCT with cytoskeletal proteins actin and tubulin and its role in the assembly of protein complexes. The authors present a new proteomic dataset for CCT purified from the human malarial parasite and incorporate it into the existing model of the CCT system. The study provides insights into the essential role of the CCT chaperonin system in eukaryotic cell growth control and cell cycle regulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Cell Biology
Heba Ghozlan, Amanda Cox, Daniel Nierenberg, Stephen King, Annette R. Khaled
Summary: Maintenance of the cellular proteome is crucial for cell function, and its deregulation can lead to diseases. Chaperonins, such as CCT, play a central role in folding proteins and preventing aggregation. CCT has unique features that allow it to fold large or complex proteins and complexes. Understanding the structure, function, and interactome of CCT is essential for studying its role in disease and potential diagnostic and therapeutic applications.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Alla Revittser, Ivan Selin, Yuri Negulyaev, Vladislav Chubinskiy-Nadezhdin
Summary: The actin cytoskeleton is crucial for cell motility and migration, thus playing a key role in tissue repair. To enhance the migration rate of stem cells, researchers are exploring methods such as co-cultivation and preconditioning with biologically active compounds. Quantitative estimation of F-actin structure changes can be challenging, with fluorescence intensity measurements not always providing accurate results.
Article
Multidisciplinary Sciences
Sofia S. Kudryavtseva, Evgeny B. Pichkur, Igor A. Yaroshevich, Aleksandra A. Mamchur, Irina S. Panina, Andrei V. Moiseenko, Olga S. Sokolova, Vladimir I. Muronetz, Tatiana B. Stanishneva-Konovalova
Summary: In this study, cryo-EM was used to resolve two nucleotide-bound structures of the bullet-shaped GroEL-GroES complex, revealing different orientations of their apical domains. The results suggest that the bound nucleotides correspond to ADP and appear at low ATP:ADP ratios.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Wen-Xiu Xu, Wei Song, Meng-Ping Jiang, Su-Jin Yang, Jian Zhang, Dan-Dan Wang, Jin-Hai Tang
Summary: This study systematically illustrated the expression profiles and distinct prognostic values of chaperonin TRiC in BCa, providing insights for further investigation of subunits of the chaperonin TRiC as novel therapeutic targets and potential prognostic biomarkers in BCa.
FRONTIERS IN GENETICS
(2021)
Review
Oncology
Liming Zheng, Xingyue Chen, Li Zhang, Nannan Qin, Jiaxing An, Jiaxing Zhu, Hai Jin, Biguang Tuo
Summary: Due to its involvement in the growth and development of various malignant tumors, the chaperonin containing TCP-1 (CCT) is considered to be a crucial factor in cancer. It assists in the folding of cancer-related proteins and its high expression in tumor cells has been associated with poor prognosis. Additionally, CCT affects the proliferation, invasion, and migration of cancer cells through various mechanisms. Therefore, CCT has the potential to serve as a new tumor marker or therapeutic target, providing guidance for early detection and prognosis of cancer.
INTERNATIONAL JOURNAL OF ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Nishkantha Arulkumaran, Mervyn Singer, Stefan Howorka, Jonathan R. R. Burns
Summary: In this study, the authors assemble DNA subunits into structural frameworks to support the formation of membrane-based protocells and prototissues, harnessing simplicity to create complexity.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Yue Zhu, Wenmin Qiu, Yuhong Li, Jinjuan Tan, Xiaojiao Han, Longhua Wu, Yugen Jiang, Zhiping Deng, Chao Wu, Renying Zhuo
Summary: Sedum plumbizincicola is a herbaceous species capable of accumulating excessive cadmium, especially with up-regulation of transport proteins, in response to Cd exposure. The study identified and quantified Cd-responsive membrane proteins in root, stem, and leaf tissues, showing significant changes in transport proteins such as ABC transporters and aquaporins after Cd treatment. The results provide insights into the molecular mechanisms of Cd hyper-tolerance and hyper-accumulation in S. plumbizincicola for potential applications in genetic engineering for phytoremediation purposes.
Article
Biochemistry & Molecular Biology
Hongtao Ji, Renhao Xiao, Xiangguang Lyu, Jiahuan Chen, Xuehai Zhang, Zhijuan Wang, Zhiping Deng, Yongliang Wang, Hui Wang, Ran Li, Qingqing Chai, Yongfang Hao, Qi Xu, Junwen Liao, Qian Wang, Yu Liu, Ruizhen Tang, Bin Liu, Xia Li
Summary: Darkness promotes root symbiotic nodulation, while blue light inhibits nodulation. Soybean TGACG motif-binding factors STF1 and STF2 regulate nodulation by repressing the transcription of the nodulation regulator GmNINa. Photoreceptor GmCRY1 promotes nodulation in darkness and mediates blue light-induced transcription of STF1 and STF2. The blue light receptor GmCRY1s-STF1/2 module plays a pivotal role in integrating darkness, blue light, and nodulation signals.
Article
Plant Sciences
Ruben Shrestha, Andres V. Reyes, Peter R. Baker, Zhi-Yong Wang, Robert J. Chalkley, Shou-Ling Xu
Summary: This article presents a workflow for N-15 stable-isotope labeled protein quantification and discusses important features such as ratio adjustment, statistical analysis of protein ratios, isotope cluster pattern matching, and fast retrieval of quantification results.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Zhi-Liang Yue, Ning Liu, Zhi-Ping Deng, Yu Zhang, Zhi-Ming Wu, Ji-Long Zhao, Ying Sun, Zhi-Yong Wang, Sheng-Wei Zhang
Summary: This study reveals the important role of the OsWAK11 gene in rice, which regulates agronomical traits and BR signaling by controlling cell elongation rates. OsWAK11 directly interacts with the BR receptor OsBRI1 and inhibits BR signaling. Additionally, OsWAK11 shows a stronger affinity for methyl-esterified pectin and is regulated by changes in pectin methylesterification in response to light.
Article
Biochemistry & Molecular Biology
Yang Bi, Ruben Shrestha, Zhenzhen Zhang, Chuan-Chih Hsu, Andres Reyes, Sumudu Karunadasa, Peter R. Baker, Jason C. Maynard, Yang Liu, Amirmansoor Hakimi, Daniel Lopez-Ferrer, Tahmid Hassan, Robert J. Chalkley, Shou-Ling Xu, Zhi-Yong Wang
Summary: The recent discovery of SPY-catalyzed protein O-fucosylation provides new insights into the regulation of nucleocytoplasmic protein functions in plants. This study identified hundreds of O-fucosylated proteins and demonstrated the involvement of SPY in sugar-dependent growth in Arabidopsis. The findings shed light on the signaling network underlying sugar regulation of plant growth and development.
Article
Biochemistry & Molecular Biology
Tae-Wuk Kim, Chan Ho Park, Chuan-Chih Hsu, Yeong-Woo Kim, Yeong-Woo Ko, Zhenzhen Zhang, Jia-Ying Zhu, Yu-Chun Hsiao, Tess Branon, Krista Kaasik, Evan Saldivar, Kevin Li, Asher Pasha, Nicholas J. Provart, Alma L. Burlingame, Shou-Ling Xu, Alice Y. Ting, Zhi-Yong Wang
Summary: Combining TurboID-mediated proximity labeling with quantitative phosphoproteomics, this study identified BIN2 signaling components including kinase substrates in vivo, revealing the cellular functions of BIN2. The TurboID-based proximity labeling effectively and specifically captures the substrates of kinases and phosphatases. The proteomic analysis establishes the BIN2 signaling network and uncovers important insights into the signaling network controlling key cellular functions in plant growth and acclimation.
Article
Biochemistry & Molecular Biology
Jihong Zhang, Yuqiong Li, Shenglong Du, Zhiping Deng, Quanwu Liang, Ge Song, Haihua Wang, Mingli Yan, Xuewen Wang
Summary: In this study, the global mechanism underlying (E)-2-hexenal-mediated regulation of biotic stress tolerance in tomato was investigated using transcriptomic and proteomic analyses. The results showed that (E)-2-hexenal treatment reduced susceptibility to B. cinerea and increased antioxidant enzyme activities. The analysis also revealed the modulation of genes involved in various metabolic pathways and the activities of defense response proteins.
PLANT MOLECULAR BIOLOGY
(2023)
Review
Plant Sciences
Hanqian Feng, Jinjuan Tan, Zhiping Deng
Summary: Ubiquitination and deubiquitination are crucial post-translational modifications in plants. UBP12 and UBP13, two deubiquitinating enzymes, play significant roles in regulating hormone signaling, developmental signaling, and transcription factor activity in plants.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Zhongjing Zhou, Zhiping Deng, Shuang Liang, Xiaowei Zou, Yi Teng, Weike Wang, Lizhong Fu
Summary: A rapid, precise, and dependable method for quantifying flavonoids in the fruiting bodies of Sanghuangporus was established using ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-QQQ-MS/MS). The method enabled simultaneous detection of 10 flavonoids and can be applied to analyze flavonoid content in different Sanghuangporus species. This protocol serves as a valuable tool for identifying species with high levels of specific flavonoid compounds.
Article
Plant Sciences
Xiaoran Xin, Donghui Wei, Lei Lei, Haiyan Zheng, Ian S. Wallace, Shundai Li, Ying Gu
Summary: Cellulose is crucial for plant cell walls and plays an important role in various industries such as food, paper, textiles, and biofuel. This study identified the protein kinase CPK32 as a key regulator of cellulose biosynthesis and uncovered a novel mechanism by which phosphorylation controls the stability of cellulose synthase complexes (CSCs).
Article
Plant Sciences
Mohammad Murshed, Donghui Wei, Ying Gu, Jin Wang
Summary: This study developed a computational modeling framework for microtubules in plant cells and found that the interaction between microtubules and cytoplasmic flow is crucial for their assembly and orientation.
Article
Biotechnology & Applied Microbiology
Thomas Hartwig, Michael Banf, Gisele Passaia Prietsch, Jia-Ying Zhu, Isabel Mora-Ramirez, Jos H. M. Schippers, Samantha J. Snodgrass, Arun S. Seetharam, Bruno Huettel, Judith M. Kolkman, Jinliang Yang, Julia Engelhorn, Zhi-Yong Wang
Summary: This study uses a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach to identify variations in target binding of the brassinosteroid-responsive TF ZmBZR1 in maize. These variations are enriched in promoter and enhancer regions and correlate with sequence variation in BZR1-binding motifs and haplotype-specific DNA methylation. Comparison with GWAS data shows linkage of many variations to important yield and disease-related traits. Therefore, this study provides a robust method for analyzing genome-wide variations of TF occupancy and identifies genetic and epigenetic variations of the brassinosteroid response transcription network in maize.
Article
Biochemistry & Molecular Biology
Yalikunjiang Aizezi, Hongming Zhao, Zhenzhen Zhang, Yang Bi, Qiuhua Yang, Guangshuo Guo, Hongliang Zhang, Hongwei Guo, Kai Jiang, Zhi-Yong Wang
Summary: Protein O-glycosylation is an important mechanism for cellular homeostasis, and SPY and SEC are key factors involved in this process in plants. A study identified a SPY O-fucosyltransferase inhibitor (SOFTI) that reduces protein O-fucosylation and affects plant growth and development.
Article
Plant Sciences
Chuanling Li, Xuetong Li, Zhiping Deng, Yuning Song, Xinye Liu, Xiaohan Alex Tang, Ziye Li, Ya Zhang, Baowen Zhang, Wenqiang Tang, Jian-Xiu Shang, Yu Sun
Article
Plant Sciences
Chan Ho Park, Yang Bi, Ji-Hyun Youn, So-Hee Kim, Jung-Gun Kim, Nicole Y. Xu, Ruben Shrestha, Alma L. Burlingame, Shou-Ling Xu, Mary Beth Mudgett, Seong-Ki Kim, Tae-Wuk Kim, Zhi-Yong Wang
Summary: This study reveals that two plant receptor kinases regulate different cellular responses through phosphorylation of a shared phosphatase. The results demonstrate the important role of BSU1 in immunity and show how different phosphorylation sites are used to transduce signals from brassinosteroid and flagellin receptors.
