Review
Plant Sciences
Changtian Pan, Simon Sretenovic, Yiping Qi
Summary: The precise genome editing mediated by the CRISPR/Cas system has revolutionized genome engineering, with the use of dCas variants expanding its applications to genetic and translational research without inducing DNA double-strand breaks. Fusion of effector domains to dCas proteins empowers the CRISPR/dCas system as a multifunctional platform, enabling gene expression regulation, epigenetic regulation, and sequence-specific imaging. This review highlights recent advances in transcriptional activation and repression, as well as epigenetic modifications, and discusses the future directions and broader applications of the CRISPR/dCas systems in plants.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Emilie Bourdonnay, Thomas Henry
Summary: Gasdermins (GSDM) are a family of proteins that play important roles in cell death, immune response, disease susceptibility, and treatment response. The expression of GSDM genes is influenced by various factors and has been associated with diseases such as asthma, inflammatory bowel disease, and cancer.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biology
Vivek Kumar Raxwal, Somya Singh, Manu Agarwal, Karel Riha
Summary: The study revealed that new genes in rice have relatively low expression levels, possibly controlled by distal enhancers and chromatin conformation at their TSS; the chromatin in TSS regions may be remodeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis are prone to nonsense-mediated RNA decay, restricting their expression.
Review
Oncology
Chuan Chen, Na Man, Fan Liu, Gloria Mas Martin, Hidehiro Itonaga, Jun Sun, Stephen D. Nimer
Summary: This review discusses the role of innate immune cells in cancer and the mechanisms underlying their regulation. It also explores new strategies for cancer control using innate immune cells and signaling molecules.
Review
Cell Biology
Qiuqin Ma, Shihui Long, Zhending Gan, Gianluca Tettamanti, Kang Li, Ling Tian
Summary: Autophagy, a widely conserved process in eukaryotes, is regulated by nutrient deprivation, energy stress, and other unfavorable conditions through multiple pathways. It is primarily governed at the RNA and protein levels in a synergistic manner.
Review
Biochemistry & Molecular Biology
Shuhan Bu, Krishna K. Singh
Summary: Autophagy plays a crucial role in cardiovascular diseases, with complex regulation involving epigenetic pathways. Understanding these pathways not only enhances the comprehension of CVDs, but may also offer new therapeutic targets and biomarkers for CVDs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Zengde Chi, Yan Lu, Yinlong Yang, Bingqing Li, Peiyuan Lu
Summary: PD-1 serves as a crucial co-inhibitory receptor in regulating T cell immunity and peripheral tolerance. It plays a dual role in preventing T cell overactivation and maintaining T cell exhaustion. Additionally, the PD-1 signaling pathway is exploited by tumor cells to evade immune responses and is essential for maintaining peripheral tolerance and preventing autoimmune diseases.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Saeid Ghavami, Mozhdeh Zamani, Mazaher Ahmadi, Mehran Erfani, Sanaz Dastghaib, Mahsa Darbandi, Sara Darbandi, Omid Vakili, Morvarid Siri, Beniamin Oskar Grabarek, Dariusz Boron, Maryam Zarghooni, Emilia Wiechec, Pooneh Mokarram
Summary: This article discusses the association between autophagy and epigenetics in gastrointestinal cancers (GICs), including their interplay, how epigenetic modifications affect cancer cell behavior, and how epigenetic drugs modulate autophagy to overcome chemoresistance in GICs.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2022)
Review
Cell Biology
Elly I. Lewerissa, Nael Nadif Kasri, Katrin Linda
Summary: Autophagy is a crucial metabolic process for maintaining cellular homeostasis and survival. Recent studies have shown the importance of autophagy in brain function, particularly in neuronal development and functioning. Mutations in autophagy-related genes as well as genes involved in epigenetic regulation have been linked to neurodevelopmental disorders (NDDs). This suggests that aberrant autophagic regulation may contribute to nervous system impairments in NDDs with disturbed epigenetic regulation.
Review
Plant Sciences
Hao Zhang, Xiaoyu Zhang, Jun Xiao
Summary: Nitrogen is a crucial nutrient for enhancing crop yield, but excessive use in agriculture leads to environmental and economic issues. This review focuses on recent advances in understanding the role of epigenetic modifications in nitrogen response and low-nitrogen adaptation. Decoding the epigenome at various levels is highlighted as important for accelerating the study of plant response to nitrogen availability. Understanding the epigenetic control of nitrogen signaling and adaptation can lead to new strategies for improving nitrogen use efficiency and enhancing sustainable crop productivity.
Review
Biochemistry & Molecular Biology
Consuelo Arias, Luis A. Salazar
Summary: Autophagy is a cellular mechanism that maintains cellular homeostasis. It declines in aging and is associated with osteoarthritis. MicroRNAs regulate autophagy, but only a few are involved in osteoarthritis. Epigenetic modifications could be a therapeutic opportunity for osteoarthritis. Polyphenols have the potential to reverse epigenetic alterations and modify autophagy in cartilage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Tanya J. Lupancu, Kevin M. C. Lee, Mahtab Eivazitork, Cecil Hor, Andrew J. Fleetwood, Andrew D. Cook, Moshe Olshansky, Stephen J. Turner, Richard de Steiger, Keith Lim, John A. Hamilton, Adrian A. Achuthan
Summary: Glucocorticoids can suppress GM-CSF-mediated upregulation of IRF4 and CCL17 expression by regulating the expression and activity of JMJD3. Treatment with GCs inhibits CCL17 expression and improves arthritic pain-like behavior and disease in mouse models of inflammatory arthritis. This pathway provides new therapeutic options for the treatment of inflammatory conditions where GCs are used as an anti-inflammatory drug.
Review
Immunology
Gustavo Ulises Martinez-Ruiz, Abigail Morales-Sanchez, Avinash Bhandoola
Summary: The thymus is crucial for the development of T cell subsets, with interest in manipulating thymic function for therapeutic purposes in various conditions. Thymic epithelial cells play essential roles in directing T cell development and are regulated by several transcription factors. While some transcription factors have been studied in detail, the roles of many others remain unclear, suggesting potential for new discoveries in this field.
IMMUNOLOGICAL REVIEWS
(2022)
Review
Plant Sciences
Aifu Li, Bin Hu, Chengcai Chu
Summary: Studies have shown the importance of nitrogen and phosphorus uptake and utilization for plant growth and crop yields, with epigenetic regulation playing a vital role in modulating plant responses to nutrient availability.
JOURNAL OF PLANT PHYSIOLOGY
(2021)
Article
Plant Sciences
Shuangrong Liu, Milan He, Xiaoya Lin, Fanjiang Kong
Summary: In response to seasonal changes, plants precisely control flowering initiation to ensure reproductive success. Day length is the key external cue for determining flowering time. Epigenetics plays a crucial role in regulating major developmental stages in plants, including floral transition. This article summarizes recent advances in the epigenetic regulation of photoperiod-mediated flowering in Arabidopsis and rice, discusses the potential of epigenetic regulation in crop improvement, and provides a brief outlook on future research trends.
Article
Chemistry, Multidisciplinary
Lok Wai Cola Ho, Cecilia Ka Wing Chan, Ruifang Han, Yolanda Fong Yung Lau, Huize Li, Yi-Ping Ho, Xiaohong Zhuang, Chung Hang Jonathan Choi
Summary: Understanding the mechanism of nanoparticle exocytosis from cells is important for designing nanoparticles with desirable cellular retention for nanomedicine applications. This study investigates the exocytosis mechanism of dodecyl-terminated, polyethylene glycol-coated gold nanoparticles and finds that the presence of alkyl chains promotes cellular uptake and improves exocytosis efficiency.
Article
Cell Biology
Shuangli Sun, Lanlan Feng, Kin Pan Chung, Ka-Ming Lee, Hayley Hei-Yin Cheung, Mengqian Luo, Kaike Ren, Kai Ching Law, Liwen Jiang, Kam-Bo Wong, Xiaohong Zhuang
Summary: The study uncovered an atypical interaction mode of Arabidopsis ATG8f with the plant unique adaptor protein SH3P2, showing unique conformational changes in ATG8f upon binding to the AIM sequence of the autophagic receptor NBR1. Additionally, the gel filtration assay revealed that the ubiquitin-associated domain of NBR1 outcompetes the SH3 domain of SH3P2 for ATG8f interaction. Biochemical and cellular analysis demonstrated distinct interfaces used by ATG8f to interact with NBR1 and SH3P2.
Meeting Abstract
Oncology
Haifeng Lin, Jie Ma, Manyun Zhuo, Chengsheng Zhang, Jingru Luo, Xiaohong Zhuang, Zhiming Zeng, Lihua Yang
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hongbo Li, Yanglan Liao, Xuanang Zheng, Xiaohong Zhuang, Caiji Gao, Jun Zhou
Summary: This review discusses the role of phosphorylation in the regulation of autophagosome biogenesis and autophagic degradation in plants, and summarizes the experimentally verified phosphorylation sites in the core autophagy machinery in plants. Several approaches to test the roles of phosphorylation in the regulation of plant autophagy are also proposed.
Article
Plant Sciences
Hongbo Li, Juan Wei, Yanglan Liao, Xiaoling Cheng, Shuhong Yang, Xiaohong Zhuang, Zhonghui Zhang, Wenjin Shen, Caiji Gao
Summary: This study reveals a previously unidentified function of plant-specific casein kinase I members in attenuating ABA signaling by regulating the phosphorylation and nuclear accumulation of FREE1.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Shuai Hu, Baiying Li, Fan Wu, Dongmei Zhu, Jan Zouhar, Caiji Gao, Tomoo Shimada, Enrique Rojo, Ikuko Hara-Nishimura, Liwen Jiang, Jinbo Shen
Summary: This study elucidates the role and mechanism of ALIX in regulating vacuolar transport of soluble proteins in plants. It is found that ALIX physically interacts with the retromer core subunits Vps26 and Vps29 and cooperatively regulates the trafficking of soluble vacuolar proteins. Depletion of ALIX disrupts the membrane recruitment of Vps26 and Vps29 and alters the endosomal localization of vacuolar sorting receptors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Xibao Li, Jun Liao, Haiyan Bai, Jieying Bei, Kailin Li, Ming Luo, Wenjin Shen, Chao Yang, Caiji Gao
Summary: SOC1 functions as a transcriptional repressor of autophagy by targeting the autophagy-related genes ATG4b, ATG7, and ATG18c. It negatively affects plant tolerance to long-term carbon starvation. This study highlights the important role of SOC1 in regulating plant autophagy and its cellular functions.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Editorial Material
Plant Sciences
Yan Bao, Caiji Gao, Tamar Avin-Wittenberg, Jie Zhou, Faqiang Li
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cell Biology
Yilin He, Jiayang Gao, Mengqian Luo, Caiji Gao, Youshun Lin, Hiu Yan Wong, Yong Cui, Xiaohong Zhuang, Liwen Jiang
Summary: This study identified and characterized two Arabidopsis SNAREs, AT4G15780/VAMP724 and AT1G04760/VAMP726, involved in plant autophagy. Phenotypic analysis showed that mutants of VAMP724 and VAMP726 are sensitive to nutrient-starved conditions. Further experiments demonstrated that VAMP724 and VAMP726 regulate autophagosome formation likely working together with ATG9 in Arabidopsis.
Article
Plant Sciences
Na Luo, Dandan Shang, Zhiwei Tang, Jinyan Mai, Xiao Huang, Li-Zhen Tao, Linchuan Liu, Caiji Gao, Yangwen Qian, Qingjun Xie, Faqiang Li
Summary: Protein-targeting technologies play crucial roles in biological research, but there is currently no direct method to degrade endogenous proteins in plants. In this study, a novel approach was developed to engineer autophagy receptors for targeted protein clearance, using a binder for target specificity and an ATG8-binding motif (AIM) to link targets to autophagosomes. The method was demonstrated to be specific and versatile in degrading different tagged proteins and peroxisomes in tobacco, and its feasibility was further confirmed in Arabidopsis. This concept of engineered AIM-based selective autophagy could serve as a convenient and robust research tool for manipulating endogenous proteins in plants.
Article
Biochemistry & Molecular Biology
Hongbo Li, Tingting Li, Yingzhu Li, Haiyan Bai, Yanghuan Dai, Yanglan Liao, Juan Wei, Wenjin Shen, Binglian Zheng, Zhonghui Zhang, Caiji Gao
Summary: The FYVE domain protein FREE1 is shown to have a negative regulatory role in plant miRNA biogenesis by interacting with the core microprocessor component in the nucleus.
Article
Multidisciplinary Sciences
Hongbo Li, Ruihua Huang, Yanglan Liao, Shuhong Yang, Bojin Feng, Hongting Qin, Jun Zhou, Yonglun Zeng, Jinbo Shen, Xiaohong Zhuang, Liwen Jiang, Marisa S. Otegui, Shengchun Zhang, Caiji Gao
Summary: The study identifies a plant-specific endosomal regulator, BLISTER (BLI), that interacts with the retromer complex and plays a crucial role in regulating endosomal trafficking in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Mengqian Luo, Kai Ching Law, Yilin He, Ka Kit Chung, Muk Kuen Po, Lanlan Feng, Kin Pan Chung, Caiji Gao, Xiaohong Zhuang, Liwen Jiang
Summary: This study reveals the role of AUTOPHAGY-RELATED2 in coordinating the trafficking of ATG18a and ATG9 to mediate autophagosome closure in Arabidopsis. Under normal conditions, ATG2 is essential for the transport of ATG18a and ATG9, and its depletion leads to unclosed autophagosome structures.
Article
Plant Sciences
Jun Zhou, Juncai Ma, Chao Yang, Xiu Zhu, Jing Li, Xuanang Zheng, Xibao Li, Siyu Chen, Lei Feng, Pengfei Wang, Man Ip Ho, Wenlong Ma, Jun Liao, Faqiang Li, Chao Wang, Xiaohong Zhuang, Liwen Jiang, Byung-Ho Kang, Caiji Gao
Summary: Short-term acute heat stress causes vacuolation of the Golgi apparatus, whereafter autophagy-related protein 8 (ATG8) translocates to the dilated Golgi membrane. The inactivation of the ATG conjugation system abolishes the targeting of ATG8 to the swollen Golgi, causing a delay in Golgi recovery after heat stress. CLATHRIN LIGHT CHAIN 2 (CLC2) is recruited to the cisternal membrane by ATG8, facilitating Golgi reassembly. This study reveals a hitherto unanticipated process of Golgi stack recovery from heat stress in plant cells and uncovers a previously unknown mechanism of organelle resilience involving ATG8.