Article
Biochemistry & Molecular Biology
Lin Gao, Qing Liu, Ming Zhong, Nannan Zeng, Weixian Deng, Yaxing Li, Dong Wang, Siyuan Liu, Qin Wang
Summary: Plants have two cryptochrome photoreceptors, CRY1 and CRY2, which mediate overlapping and distinct physiological responses. This study identified 19 phosphorylation sites in CRY1 and analyzed the physiological and photobiochemical activities of CRY1 variants with phosphosite substitutions. The results showed that phosphorylation of CRY1 is necessary for its degradation, physiological functions, and interaction with the E3 ubiquitin ligase COP1. Additionally, the phosphorylation of CRY1 by photoregulatory protein kinases (PPKs) is critical for CRY1 signaling and regulation.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Plant Sciences
Hiroyuki Imai, Yukio Kawamura, Akira Nagatani, Matsuo Uemura
Summary: The study reveals that blue light and its photoreceptor cryptochrome play a crucial role in regulating cold acclimation pathways in plants. Blue light enhances freezing tolerance in wild type plants through CRY signaling, while unexpectedly cry1cry2 mutants show higher freezing tolerance after cold acclimation. Blue light affects gene expression related to anthocyanin biosynthesis and CBF/COR genes during cold acclimation, indicating a complex regulatory network involving the blue light-CRY system.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Jiaxin Yang, Lan Li, Xin Li, Ming Zhong, Xinmei Li, Lina Qu, Hui Zhang, Dongying Tang, Xuanming Liu, Chongsheng He, Xiaoying Zhao
Summary: The study reveals that blue light induces m(6)A RNA modification partially via CRY1, and CRY1 mediates the expression of FIP37, which is associated with m(6)A modification. CRY1 and FIP37 regulate m(6)A modification on photomorphogenesis-related genes and determine their transcript stability.
Article
Plant Sciences
Langxi Miao, Jiachen Zhao, Guangqiong Yang, Peng Xu, Xiaoli Cao, Shasha Du, Feng Xu, Lu Jiang, Shilong Zhang, Xuxu Wei, Yao Liu, Huiru Chen, Zhilei Mao, Tongtong Guo, Shuang Kou, Wenxiu Wang, Hong-Quan Yang
Summary: Arabidopsis cryptochrome 1 (CRY1) undergoes degradation through ubiquitination and the 26S proteasome pathway in response to high-intensity blue light (HBL), involving E3 ubiquitin ligases COP1 and LRBs. Additionally, a blue-light inhibitor of cryptochromes 1 interacts with CRY1 in a blue-light-dependent manner to inhibit its dimerization/oligomerization and suppress HBL-induced degradation of CRY1.
Article
Biochemistry & Molecular Biology
Sonal Kedia, Eve Marder
Summary: In this study, the researchers serendipitously discovered that the crab STG exhibits increased neuronal activity upon exposure to blue light. They found that this response may be mediated by cryptochromes, which are blue-light photoreceptors involved in circadian behaviors.
Article
Plant Sciences
Han Dong, Chaoyi Hu, Chaochao Liu, Jiachun Wang, Yanhong Zhou, Jingquan Yu
Summary: The study reveals that the blue light signal plays a critical role in regulating starch accumulation in tomato chloroplasts through the CRY1a-mediated HY5 transcription factor, affecting starch degradation. HY5 directly binds to the promoters of starch degradation-related genes, activating their transcription and impacting the accumulation of starch and soluble sugars.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Xiangguang Lyu, Qican Cheng, Chao Qin, Yinghui Li, Xinying Xu, Ronghuan Ji, Ruolan Mu, Hongyu Li, Tao Zhao, Jun Liu, Yonggang Zhou, Haiyan Li, Guodong Yang, Qingshan Chen, Bin Liu
Summary: It was found that low blue light mainly induces excessive stem elongation in soybean, while the integration of GmCRY1-mediated signals with the GA metabolic pathway can regulate soybean leaf phototropic growth and improve agronomic traits.
Article
Microbiology
Zhongyi Zhang, Tianli Han, Jikang Sui, Hui Wang
Summary: Blue light can trigger carotenoid accumulation in microalgae, which is mediated by cryptochromes as photoreceptors.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Jin Hu, Yinmeng Hu, Mengran Yang, Xiaotong Hu, Xuelu Wang
Summary: Ubiquitin-dependent protein degradation is important in plant development, with the SINA RING-type E3 ligases (SINATs) exhibiting light-dependent regulation. The study found that the degradation of SINATs is self-regulated, and they interact with photoreceptors phyB and CRY1 in the cytoplasm.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Vladimir D. Kreslavski, Aleksandra Yu Khudyakova, Valeria V. Strokina, Galina N. Shirshikova, Pavel P. Pashkovskiy, Tamara Balakhnina, Anatoly A. Kosobryukhov, Vladimir V. Kuznetsov, Suleyman Allakhverdiev
Summary: This study investigated the effects of high-intensity light and UV-B radiation on photosynthetic activity, pigment content, antioxidant enzyme activity, and gene expression in Arabidopsis plants. Results showed that the absence of cryptochrome 1 in the mutant hy4 led to greater impacts on photosynthetic activity under high-intensity blue light, potentially linked to lower levels of UAP and carotenoids. These findings suggest a connection between light intensity, cryptochrome function, and stress resistance in plants.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Louise N. Lindback, Yuzhao Hu, Amanda Ackermann, Oliver Artz, Ullas Pedmale
Summary: Light is a crucial signal sensed by CRY receptors to regulate growth and circadian clock. This study uncovers the role of UBP12/13 deubiquitinases in negatively regulating CRY2 and modulating hypocotyl growth. UBP12/13 interacts with COP1 to stabilize it, leading to degradation of CRY2 under blue light. The findings provide insight into the regulation of deubiquitinase activity and its role in controlling plant growth.
Article
Agronomy
Yun Kong, Youbin Zheng
Summary: By comparing wild-type Arabidopsis with its cryptochrome-deficient mutants and cryptochrome-overexpressing transgenic plants, it was found that the promotion effects of stem elongation and flowering are mainly related to low activity of CRY1, with partial involvement of high-activity CRY2.
CANADIAN JOURNAL OF PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Ming Zhong, Bingjie Zeng, Dongying Tang, Jiaxin Yang, Lina Qu, Jindong Yan, Xiaochuan Wang, Xin Li, Xuanming Liu, Xiaoying Zhao
Summary: This study reveals that blue light inhibits the degradation of DELLA proteins induced by GA through the major photoreceptor CRY1, thereby repressing the GA response during hypocotyl elongation and affecting plant photomorphogenesis. The findings provide new insights into the antagonistic interaction between blue light and GA in regulating plant development processes.
Article
Plant Sciences
Shengguan Cai, Yuqing Huang, Fei Chen, Xin Zhang, Emily Sessa, Chenchen Zhao, D. Blaine Marchant, Dawei Xue, Guang Chen, Fei Dai, James H. Leebens-Mack, Guoping Zhang, Sergey Shabala, John M. Christie, Michael R. Blatt, Eviatar Nevo, Pamela S. Soltis, Douglas E. Soltis, Peter J. Franks, Feibo Wu, Zhong-Hua Chen
Summary: The study found that modern ferns have faster stomatal response to blue light, which is linked to specific genes in the blue light signaling pathway. Cryptochromes in the Polypodiales underwent gene duplication events when angiosperms emerged, aiding modern ferns in thriving beneath angiosperm forest canopies.
Article
Biochemistry & Molecular Biology
Xiaolin Jia, Meifang Song, Shaoci Wang, Tong Liu, Lijian Wang, Lin Guo, Liang Su, Yong Shi, Xu Zheng, Jianping Yang
Summary: In Arabidopsis, the involvement of phytochrome A (phyA) and phytochrome B (phyB) in blue light signaling has been demonstrated. However, the mechanism of how blue light-activated phytochromes modulate the activity of the COP1-SPA1 E3 complex remains unclear. This study reveals that phyA responds to early and weak blue light, while phyB responds to sustainable and strong blue light. Activation of both phyA and phyB inhibits SPA1 activity by promoting their nuclear import and binding to SPA1, disrupting SPA1's interaction with HY5 and promoting seedling photomorphogenesis.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Biochemical Research Methods
Weixian Deng, Jihui Sha, Kathrin Plath, James A. Wohlschlegel
Summary: In bottom-up proteomics, achieving deep proteome coverage requires peptide-level fractionation to simplify the complex peptide mixture. CIF is an effective offline separation strategy capable of increasing the depth of peptide analyte coverage.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Plant Sciences
Yuning Wu, Qin Wang, Jing Qu, Wen Liu, Xuejuan Gao, Xiang Li, Xinhao Ouyang, Chentao Lin, Jianwei Shuai
Summary: Cryptochromes photoreceptors CRY1 and CRY2 play important roles in mediating blue light responses in plants and metazoa. The study reveals that BIC negatively modulates CRY2 phosphorylation, while COP1-SPA can strongly inhibit the phosphorylation response of CRY2 and positively regulate CRY2 phosphorylation by CRY1. The model predicts that the CRY1-HY5 axis, rather than the CRY2-HY5 pathway, dominates in blue-light-dependent photomorphogenesis.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Multidisciplinary Sciences
Yadi Chen, Xiaohua Hu, Siyuan Liu, Tiantian Su, Hsiaochi Huang, Huibo Ren, Zhensheng Gao, Xu Wang, Deshu Lin, James A. Wohlschlegel, Qin Wang, Chentao Lin
Summary: The degradation of the plant blue light receptor CRY2 is determined by two distinct E3 ubiquitin ligases, Cul4(COP1/SPAs) and Cul3(LRBs), regulating the function of CRY2 under different light conditions.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Weixian Deng, Elsie C. Jacobson, Amanda J. Collier, Kathrin Plath
Summary: The understanding of iPSC reprogramming has provided insights into the mechanisms that safeguard somatic cell identity, drive epigenetic reprogramming, and underlie cell fate specification in vivo. The combinatorial action of TFs has emerged as the key mechanism for the direct and indirect effects of reprogramming factors that induce the remodelling of the enhancer landscape. The interplay of TFs in iPSC reprogramming also yields trophectoderm-and extraembryonic endoderm-like cell populations, uncovering an intriguing plasticity of cell states and opening new avenues for exploring cell fate decisions during early embryogenesis.
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2021)
Article
Cell Biology
Wendy A. Herbst, Weixian Deng, James A. Wohlschlegel, Jennifer M. Achiro, Kelsey C. Martin
Summary: By using nucleus-specific proteomic mapping in silenced and stimulated neurons, researchers revealed an understudied mechanism of nuclear proteome regulation: activity-dependent proteasome-mediated degradation. They found that the tumor suppressor protein PDCD4 undergoes rapid stimulus-induced degradation in the nucleus of neurons. This degradation of PDCD4 is crucial for normal activity-dependent transcription, impacting genes involved in synapse formation, remodeling, and transmission.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lin Gao, Qing Liu, Ming Zhong, Nannan Zeng, Weixian Deng, Yaxing Li, Dong Wang, Siyuan Liu, Qin Wang
Summary: Plants have two cryptochrome photoreceptors, CRY1 and CRY2, which mediate overlapping and distinct physiological responses. This study identified 19 phosphorylation sites in CRY1 and analyzed the physiological and photobiochemical activities of CRY1 variants with phosphosite substitutions. The results showed that phosphorylation of CRY1 is necessary for its degradation, physiological functions, and interaction with the E3 ubiquitin ligase COP1. Additionally, the phosphorylation of CRY1 by photoregulatory protein kinases (PPKs) is critical for CRY1 signaling and regulation.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Plant Sciences
Yubang Gao, Xuqing Liu, Yandong Jin, Ji Wu, Shuang Li, Yaxing Li, Binqing Chen, Yaxin Zhang, Linxiao Wei, Wei Li, Ruili Li, Chentao Lin, Anireddy S. N. Reddy, Pankaj Jaiswal, Lianfeng Gu
Summary: In this study, the epitranscriptomic and proteomic regulation induced by drought treatment in poplar SDX was examined using Nanopore direct RNA sequencing and tandem mass tag-based proteomic analysis. The results showed that drought stress increased RNA degradation, reduced transcription and translation, and had an impact on the interplay among m(6)A, polyadenylation, PAL, and translation in the SDX of P. trichocarpa.
Article
Multidisciplinary Sciences
Zhiyuan Mao, Pavlo A. Nesterenko, Jami McLaughlin, Weixian Deng, Giselle Burton Sojo, Donghui Cheng, Miyako Noguchi, William Chour, Diana C. DeLucia, Kathryn A. Finton, Yu Qin, Matthew B. Obusan, Wendy Tran, Liang Wang, Nathanael J. Bangayan, Lisa Ta, Chia-Chun Chen, Christopher S. Seet, Gay M. Crooks, John W. Phillips, James R. Heath, Roland K. Strong, John K. Lee, James A. Wohlschlegel, Owen N. Witte
Summary: This study used a multimodal immunopeptidomic approach to analyze the peptides of prostatic acid phosphatase (PAP) on HLA-A*02:01. They identified 11 potentially A*02:01-restricted PAP peptides and screened 7 cognate TCR sequences that can recognize different epitopes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Oncology
Zhentao Yang, Yan Wang, Sixue Liu, Weixian Deng, Shirley H. Lomeli, Gatien Moriceau, James Wohlschlegel, Marco Piva, Roger S. Lo
Summary: MAPKi therapy induces accumulation of PD-L1 on melanoma cells, leading to immune evasion and therapy resistance. ITCH degrades PD-L1, enhancing anti-tumor T-cell immunity. Degrading tumor cell-surface PD-L1 and/or activating intrinsic ITCH may overcome MAPKi resistance.
Article
Genetics & Heredity
Duo Chen, Xue Yuan, Xuehai Zheng, Jingping Fang, Gang Lin, Rongmao Li, Jiannan Chen, Wenjin He, Zhen Huang, Wenfang Fan, Limin Liang, Chentao Lin, Jinmao Zhu, Youqiang Chen, Ting Xue
Summary: This study presents a comprehensive analysis of the regulatory networks for fucoxanthin (Fx) biosynthesis in Isochrysis galbana, a potential bait for functional foods and nutraceuticals. A high-quality genome assembly of I. galbana LG007 was obtained, which revealed its phylogenetic relationship with other Haptophytes. Evolutionary analysis provided insights into the divergence time between I. galbana and Emiliania huxleyi. Gene family and metabolome analyses identified key genes and environmental factors influencing Fx content in I. galbana. These findings contribute to the understanding of Fx biosynthesis and regulation, providing valuable references for food and pharmaceutical applications.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Chemistry, Analytical
Weixian Deng, Jihui Sha, Fanglei Xue, Yasaman Jami-Alahmadi, Kathrin Plath, James Wohlschlegel
Summary: In this study, we characterized the molecular factors underlying peptide separation in high-field asymmetric waveform ion mobility spectrometry (FAIMS) and used machine learning to predict optimized compensation voltage values for peptides. These findings improve parallel reaction monitoring workflows and highlight the utility of FAIMS in targeted proteomic applications.
ANALYTICAL CHEMISTRY
(2022)
Article
Cell Biology
Michael S. Hoetker, Masaki Yagi, Bruno Di Stefano, Justin Langerman, Simona Cristea, Lai Ping Wong, Aaron J. Huebner, Jocelyn Charlton, Weixian Deng, Chuck Haggerty, Ruslan I. Sadreyev, Alexander Meissner, Franziska Michor, Kathrin Plath, Konrad Hochedlinger
Summary: Hoetker et al. demonstrate the dual role of H3K36 methylation in cell identity maintenance: integrating TGF-β signals to keep mesenchymal targets active and preventing the activation of alternative lineage programs through enhancer methylation. This study uncovers the crucial role of H3K36 methylation in maintaining cell identities across different developmental contexts.
NATURE CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Chenjin Wen, Zhen Yuan, Xiaotian Zhang, Hao Chen, Lin Luo, Wanying Li, Tian Li, Nana Ma, Fei Mao, Dongmei Lin, Zhanxi Lin, Chentao Lin, Tongda Xu, Peitao Lu, Juncheng Lin, Fangjie Zhu
Summary: The cistrome is composed of cis-acting regulatory elements recognized by transcription factors (TFs), but only a fraction of them are active in specific tissues. This study introduces a low-input method called sea-ATI to profile the active cistrome in plants and identify previously unidentified cis-regulatory vocabularies. The functionality of the new cis-elements was confirmed through ATAC-seq and RNA-seq analyses, and sea-ATI was shown to be able to identify both positive and negative regulatory cis-elements.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Bochen Jiang, Zhenhui Zhong, Jun Su, Tengfei Zhu, Timothy Yueh, Jielena Bragasin, Victoria Bu, Charles Zhou, Chentao Lin, Xu Wang
Summary: Research shows that Cryptochromes (CRYs) in plants regulate gene expressions to mediate plant photoresponses. It has been discovered that MAC3A and 3B proteins interact with CRY2 and form nuclear protein condensates. The study reveals that MAC3A/3B proteins positively regulate hypocotyl growth.
Correction
Plant Sciences
Xu Wang, Bochen Jiang, Lianfeng Gu, Yadi Chen, Manuel Mora, Mulangma Zhu, Eliace Noory, Qin Wang, Chentao Lin