Article
Agriculture, Multidisciplinary
Qibin Wu, Zhenxiang Li, Jingtao Yang, Fu Xu, Xueqin Fu, Liping Xu, Chuihuai You, Dongjiao Wang, Yachun Su, Youxiong Que
Summary: This study reports the first comprehensive analysis of protein lysine acetylation, 2-hydroxyisobutyrylation, and lysine lactylation in sugarcane. These post-translational modifications were found to be involved in energy metabolism and stress response. The results provide new insights into the molecular mechanisms of protein PTMs in sugarcane.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Rachel E. Lacoursiere, Dania Hadi, Gary S. Shaw
Summary: Ubiquitination is a complex process controlled by a series of enzymes. Recent studies have shown that these enzymes can be further modified through acetylation or phosphorylation, and alterations in these modifications have been observed in different diseases.
Review
Plant Sciences
William Agbemafle, Min May Wong, Diane C. Bassham
Summary: This review summarizes key regulatory mechanisms for modulating autophagy through post-translational modification or transcriptional regulation. Plants activate cellular responses to adapt to changing environmental conditions, one of which is autophagy, where cellular components are delivered to the vacuole for degradation. Autophagy is activated by various conditions, and the pathways controlling its activation are being elucidated. However, there is still much to discover regarding how these factors work together to properly modulate autophagy in response to specific signals.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Plant Sciences
Huijia Kang, Tianyi Fan, Jiabing Wu, Yan Zhu, Wen-Hui Shen
Summary: Plants, as sessile organisms, are constantly exposed to diverse stresses, including pathogen invasion. Recent studies have found that pathogen infections can induce epigenetic changes in plants, leading to the reprogramming of plant defense genes. These mechanisms could be used in the design of stress-resistant plant varieties.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Suresh Poudel, David Vanderwall, Zuo-Fei Yuan, Zhiping Wu, Junmin Peng, Yuxin Li
Summary: A computational pipeline JUMPptm was presented to extract PTMs from unenriched whole proteome. The deep brain proteome of Alzheimer's disease (AD) was analyzed using JUMPptm, revealing dysregulated PTM peptides during AD progression and establishing a valuable pan-PTM profile for AD research.
Article
Biochemistry & Molecular Biology
Karlie R. Platz, Emma J. Rudisel, Katelynn V. Paluch, Taylor R. Laurin, Kristin E. Dittenhafer-Reed
Summary: The mitochondrial proteome undergoes various post-translational modifications, and this study focused on the effects of acetylation and phosphorylation on the function of mitochondrial RNA polymerase (POLRMT). While some modifications showed slight decrease in the binding ability of POLRMT, there were minimal biological impacts observed in terms of viability, mtDNA content, and mitochondrial transcript levels.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Chemistry, Multidisciplinary
Lin-hui Zhai, Kai-feng Chen, Bing-bing Hao, Min-jia Tan
Summary: Protein post-translational modifications (PTMs) are crucial for protein activity regulation and are involved in diseases. PTM regulatory enzymes are important drug targets. Mass spectrometry-based proteomics enables systematic characterization of PTMs for drug target identification, mechanism elucidation and biomarker discovery in personalized therapy.
ACTA PHARMACOLOGICA SINICA
(2022)
Article
Plant Sciences
Irma Y. Mora-Ocampo, Carlos P. Pirovani, Edna D. M. N. Luz, Angra P. B. Rego, Edson M. A. Silva, Mateo Rhodes-Valbuena, Ronan X. Correa
Summary: The study revealed the mechanisms used by resistant and susceptible cacao genotypes against Ceratocystis cacaofunesta through proteomics, systems biology, and enzymatic analyses. Different accumulation of proteins and key defense factors were identified in resistant and susceptible genotypes during infection with Ceratocystis cacaofunesta.
Review
Plant Sciences
Marco Zarattini, Mahsa Farjad, Alban Launay, David Cannella, Marie-Christine Soulie, Giovanni Bernacchia, Mathilde Fagard
Summary: Current environmental and climate changes significantly impact plant-pathogen interactions, with abiotic stresses affecting the expression of plant defense genes and pathogen virulence. This can lead to modifications in existing pathosystems and the emergence of new pathogens.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Review
Chemistry, Multidisciplinary
Wei-hua Wang, Tao Yuan, Mei-jia Qian, Fang-jie Yan, Liu Yang, Qiao-jun He, Bo Yang, Jin-jian Lu, Hong Zhu
Summary: This review discusses the regulatory mode of post-translational modifications on KRAS, including prenylation, phosphorylation, and more, while highlighting recent studies targeting these modifications that have shown potent anti-tumor activities.
ACTA PHARMACOLOGICA SINICA
(2021)
Review
Biochemistry & Molecular Biology
Ramesh Kumar, Divya Mehta, Nimisha Mishra, Debasis Nayak, Sujatha Sunil
Summary: Viruses depend on host cells for replication and survival, utilizing post-translational modifications (PTMs) to control viral replication. Host proteins use PTMs to inhibit viral protein synthesis, eliminate viruses, while PTMs of viral proteins can increase their solubility and virulence.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Ashish Prasad, Shambhavi Sharma, Manoj Prasad
Summary: This article discusses the importance of post-translational modifications (PTMs) in plant-virus interaction. The interactions between viral proteins and components of PTM pathways play a crucial role in regulating the function of viral proteins and gene expression.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2023)
Review
Cell Biology
Linbin Zhou, Danny Siu-Chun Ng, Jason C. Yam, Li Jia Chen, Clement C. Tham, Chi Pui Pang, Wai Kit Chu
Summary: This review summarizes recent findings on the impact of post-translational modifications (PTMs) on the functions of retinoblastoma protein (pRb). PTMs on pRb play crucial roles in cell cycle regulation, cell survival, and differentiation, and altered PTMs can lead to anomalies in cell proliferation and tumorigenesis. Understanding the post-translational modulation of pRb could facilitate the development of novel therapeutic strategies for various human diseases.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Review
Oncology
Katie Dunphy, Paul Dowling, Despina Bazou, Peter O'Gorman
Summary: This review discusses techniques used for PTM analysis and their applications in blood cancer research. Mass spectrometry-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with high sensitivity and specificity. Immuno-based techniques remain popular, with improvements in the quality of commercially available modification-specific antibodies facilitating the detection of modified proteins with high affinity. PTM-focused studies on blood cancers have provided information on altered cellular processes that contribute to the malignant phenotype, while many blood cancer therapies target protein modifications to exert their anti-cancer effects. Continued optimization of protocols and techniques for PTM analysis in blood cancer research will lead to novel insights into mechanisms of malignant transformation and the identification of new biomarkers and therapeutic targets.
Review
Immunology
Chong Feng, Lening Zhang, Xin Chang, Dongliang Qin, Tao Zhang
Summary: The immune checkpoint molecules PD-1 and PD-L1 are promising targets for tumor immunotherapy. PD-L1 overexpression on tumor cells inhibits T cell activation by binding to PD-1, leading to tumor immune escape. Targeting PD-1/PD-L1 involves blocking this binding and restoring immune cell killing effect.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Margaret R. Woodhouse, Shatabdi Sen, David Schott, John L. Portwood, Michael Freeling, Justin W. Walley, Carson M. Andorf, James C. Schnable
Summary: RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. The comparative gene expression tool qTeller has been revamped to take advantage of the growing number of public RNA-Seq datasets, enabling users to evaluate gene expression data in a defined genomic interval and perform two-gene comparisons across multiple user-chosen tissues. The updated qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets, along with support for additional data formats and a modernized interface.
Article
Plant Sciences
Lirong Xiang, Trevor M. Nolan, Yin Bao, Mitch Elmore, Taylor Tuel, Jingyao Gai, Dylan Shah, Ping Wang, Nicole M. Huser, Ashley M. Hurd, Sean A. McLaughlin, Stephen H. Howell, Justin W. Walley, Yanhai Yin, Lie Tang
Summary: The development of the RoAD system aims to conduct BR and drought response experiments in soil-grown Arabidopsis plants using a robotic system, accurately measuring morphological and growth-related traits of both Arabidopsis and maize plants through machine learning algorithms, offering insights into the BR-mediated control of plant growth and stress responses.
Article
Biology
Suryatapa Ghosh Jha, Alexander T. Borowsky, Benjamin J. Cole, Noah Fahlgren, Andrew Farmer, Shao-Shan Carol Huang, Purva Karia, Marc Libault, Nicholas J. Provart, Selena L. Rice, Maite Saura-Sanchez, Pinky Agarwal, Amir H. Ahkami, Christopher R. Anderton, Steven P. Briggs, Jennifer An Brophy, Peter Denolf, Luigi F. Di Costanzo, Moises Exposito-Alonso, Stefania Giacomello, Fabio Gomez-Cano, Kerstin Kaufmann, Dae Kwani Ko, Sagar Kumar, Andrey Malkovskiy, Naomi Nakayama, Toshihiro Obata, Marisa S. Otegui, Gergo Palfalvi, Elsa H. Quezada-Rodriguez, Rajveer Singh, R. Glen Uhrig, Jamie Waese, Klaas Van Wijk, R. Clay Wright, David W. Ehrhardt, Kenneth D. Birnbaum, Seung Y. Rhee
Summary: With growing populations and urgent environmental issues, the future economy will be increasingly plant-based. Reimagining plant science as a critical component across various fields is crucial. The concept of a Plant Cell Atlas (PCA) is proposed to better understand and engineer plant development, physiology, and environmental responses. A workshop was held to discuss the purpose and utility of this initiative, highlighting current knowledge gaps and technical challenges.
Article
Plant Sciences
Linkan Dash, Robert E. McEwan, Christian Montes, Ludvin Mejia, Justin W. Walley, Brian P. Dilkes, Dior R. Kelley
Summary: This study identified a novel regulator of plant growth and advanced our understanding of the molecular mechanisms in seedling development, particularly in linking light signaling to auxin-dependent cell elongation. Furthermore, it highlighted the importance of confirming the genetic identity of research material before attributing phenotypes to known mutations sourced from T-YDNA stocks.
Review
Plant Sciences
James M. Elmore, Brianna D. Griffin, Justin W. Walley
Summary: This article discusses the signaling networks triggered by pathogen infection in plant cells, as well as the different methods for studying the functional proteomes of plants and pathogens, and how integrating other profiling data can provide a more comprehensive understanding of plant diseases.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Antony V. E. Chapman, J. Mitch Elmore, Maxwell McReynolds, Justin W. Walley, Roger P. Wise
Summary: The Mla gene of barley plays a role in cereal immunity against fungal pathogens. Functional analysis of Sgt1, which is important for the resistance conferred by Mla, has been challenging. This study identified a Sgt1 mutation that weakens its interaction with Mla and affects the resistance. It is proposed that the strength of the interaction between plant CC-NLRs and Sgt1 determines the impact of Sgt1 silencing on resistance.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2022)
Article
Multidisciplinary Sciences
Natalie M. Clark, Trevor M. Nolan, Ping Wang, Gaoyuan Song, Christian Montes, Conner T. Valentine, Hongqing Guo, Rosangela Sozzani, Yanhai Yin, Justin W. Walley
Summary: This study analyzed the BR signaling in Arabidopsis by integrating multiple omics datasets and inferring networks, identifying a BR-regulated transcription factor BRONTOSAURUS that affects cell division in roots. The research provides insights into the molecular signaling events during BR response through integrative network analysis applied to multi-omic data.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Ping Wang, Natalie M. Clark, Trevor M. Nolan, Gaoyuan Song, Parker M. Bartz, Ching-Yi Liao, Christian Montes-Serey, Ella Katz, Joanna K. Polko, Joseph J. Kieber, Daniel J. Kliebenstein, Diane C. Bassham, Justin W. Walley, Yanhai Yin, Hongqing Guo
Summary: This study identified novel functions of FERONIA in ER body formation and glucosinolate biosynthesis, as well as its regulation of ABI5 in ABA signaling through multi-omics data analysis. These findings provide new insights into the molecular interplay of FER.
Article
Plant Sciences
Christian Montes, Ping Wang, Ching-Yi Liao, Trevor M. Nolan, Gaoyuan Song, Natalie M. Clark, J. Mitch Elmore, Hongqing Guo, Diane C. Bassham, Yanhai Yin, Justin W. Walley
Summary: This study reveals the crosstalk between Brassinosteroids and Target of Rapamycin Complex in coordinating plant growth and stress responses. By quantifying the levels of transcripts, proteins, and phosphorylation sites, the researchers found that mutants with altered levels of key players in BR and TORC signaling affect a common set of gene-products involved in growth and stress responses. Additionally, a predictive network was reconstructed to define the molecular interactions between BR- or TORC-regulated growth and autophagy.
Article
Cell Biology
Ching-Yi Liao, Yunting Pu, Trevor M. Nolan, Christian Montes, Hongqing Guo, Justin W. Walley, Yanhai Yin, Diane C. Bassham
Summary: This study reveals that TOR modulates brassinosteroid (BR) regulation of plant growth and stress response pathways. By phosphorylating and reducing the inhibition of RAPTOR1B, TOR helps to maintain the balance between BR and TOR signaling pathways through regulating autophagy activity.
Article
Plant Sciences
Ping Wang, Natalie M. Clark, Trevor M. Nolan, Gaoyuan Song, Olivia G. Whitham, Ching-Yi Liao, Christian Montes-Serey, Diane C. Bassham, Justin W. Walley, Yanhai Yin, Hongqing Guo
Summary: This study reveals a previously unknown mechanism by which FER negatively regulates autophagy through TOR.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Hsin-Yen Larry Wu, Qiaoyun Ai, Rita Teresa Teixeira, Phong H. T. Nguyen, Gaoyuan Song, Christian Montes, J. Mitch Elmore, Justin W. Walley, Polly Yingshan Hsu
Summary: By improving the coverage of super-resolution Ribo-seq, previously uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes in Arabidopsis have been revealed. These events include untranslated ORFs in noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events.
Letter
Plant Sciences
Devang Mehta, Amir H. H. Ahkami, Justin Walley, Shou-Ling Xu, R. Glen Uhrig
Article
Plant Sciences
Natalie M. Clark, James Mitch Elmore, Justin W. Walley
Summary: Recent advances in single-cell proteomics can be applied to plants, increasing our understanding of plant development, response to stimuli, and cell-to-cell signaling.
Article
Biochemistry & Molecular Biology
Ping Wang, Trevor M. Nolan, Natalie M. Clark, Hao Jiang, Christian Montes-Serey, Hongqing Guo, Diane C. Bassham, Justin W. Walley, Yanhai Yin
Summary: The research identified BES1-ASSOCIATED F-BOX1 (BAF1) as an E3 ubiquitin ligase that interacts with BES1 and regulates its degradation through selective autophagy pathway. BAF1 inhibits BR signaling and its overexpression increases BR-regulated growth. Under sucrose starvation, plants with BAF1 overexpression show higher tolerance, while baf1 mutants and plants with BAF1-Delta F overexpression are more sensitive to sucrose starvation.