Article
Plant Sciences
Jingyan Zheng, Xiaodi Yang, Yan Huang, Shiping Yang, Stefan Wuchty, Ziding Zhang
Summary: The authors introduce a deep learning framework called DeepAraPPI, using sequence, domain, and Gene Ontology information to predict protein-protein interactions in Arabidopsis. DeepAraPPI combines the prediction results of three individual predictors and shows superior performance compared to existing methods. It also exhibits better cross-species predictive ability in rice. DeepAraPPI is freely accessible online.
Article
Biochemistry & Molecular Biology
Timothy O. Jobe, Qi Yu, Felix Hauser, Qingqing Xie, Yuan Meng, Tim Maassen, Stanislav Kopriva, Julian I. Schroeder
Summary: The SLIM1 transcription factor plays a crucial role in arsenic-induced gene expression and tolerance mechanisms. Mutant alleles in SLIM1 exhibit higher sensitivity to arsenic than cadmium, leading to increased oxidative stress and impaired sulfur assimilation. Enhanced arsenic accumulation in roots of slim1 mutants suggests altered redox status as a possible cause for their severe arsenic sensitivity.
Article
Plant Sciences
Merve Yilmaz, Merle Paulic, Thorsten Seidel
Summary: This study reports a protein-protein interaction network of Arabidopsis thaliana, combining various types of information such as subcellular localization, gene ontologies, biochemical properties, and co-expression. The resulting network shows enrichment in nuclear, cytosolic, and plasma membrane proteins, while being depleted in extracellular and mitochondrial proteins. Additionally, proteins involved in transcription are highly abundant in the network.
Review
Biochemistry & Molecular Biology
Ze-Hua Guo, Shiu-Cheung Lung, Mohd Fadhli Hamdan, Mee-Len Chye
Summary: Lipids play diverse biological functions, including signal transduction, cellular membrane biogenesis, and carbon storage. Fatty acids are synthesized in the plastids and then transported to the endoplasmic reticulum for further acylation to form triacylglycerols or incorporation into phosphatidylcholine. Acyl-CoA-binding proteins (ACBPs) play a crucial role in lipid transfer and maintaining intracellular acyl-CoA pools, while other proteins such as lipid transfer proteins and annexins are also important in lipid binding.
PROGRESS IN LIPID RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Michael Busche, M. Regina Scarpin, Robert Hnasko, Jacob O. Brunkard
Summary: The TOR protein kinase in plants regulates nucleotide synthesis and metabolic balance by promoting the activity of cytosolic phosphoribosyl pyrophosphate synthetase (PRS4). Knockout of the prs4 gene leads to embryo lethality in Arabidopsis, while silencing of PRS4 expression causes various developmental abnormalities in Nicotiana benthamiana.
Article
Biochemistry & Molecular Biology
Romulo Pedro Macedo Lima, Alessandra Vasconcellos Nunes-Laitz, Mariana de Lara Campos Arcuri, Felipe Girotto Campos, Thais Arruda Costa Joca, Gean Charles Monteiro, Helio Kushima, Giuseppina Pace Pereira Lima, Luiz Fernando Rolim de Almeida, Pedro Barreto, Ivan de Godoy Maia
Summary: In Arabidopsis, UCP2 and UCP3 have complementary functions with UCP1 in plant reproductive and vegetative organs/tissues, as well as in stress adaptation. There is partial redundancy between the UCP isoforms.
Article
Plant Sciences
Lujun Yin, Xiaodong Chen, Qi Chen, Dongqing Wei, Xiang-Yang Hu, Ai-Qun Jia
Summary: This study evaluated the effects of 12 synthesized diketopiperazines (DKPs) on Arabidopsis thaliana roots and found that they promote lateral root development and root hair formation. The DKPs enhance the polar transport of auxin and interfere with auxin receptor transporter inhibitor response protein, leading to accelerated root growth and the development of lateral roots and root hair.
PLANT AND CELL PHYSIOLOGY
(2022)
Editorial Material
Cell Biology
Hui Zhang, Qihua Ling
Summary: This article introduces a significant cellular process, autophagy, which degrades unwanted or damaged macromolecules and organelles through the lysosome or vacuole for recycling. Selective autophagy was found to play a crucial role in regulating chloroplast protein import and enhancing stress tolerance in plants.
Article
Plant Sciences
Nathan Diplock, Mael Baudin, Leslie Harden, Christopher J. Silva, Melissa L. Erickson-Beltran, Jana A. Hassan, Jennifer D. Lewis
Summary: The highly conserved angiosperm immune receptor ZAR1 recognizes diverse pathogen effector proteins by monitoring the ZRK family. The study found that ZAR1 can interact with most ZRKs, except ZRK7, in Arabidopsis thaliana. Alternative splicing of ZRK7 generates a protein that can still interact with ZAR1. The findings suggest a greater diversity of ZAR1 interactions with kinases and the potential for expanding ZAR1 immunodiversity.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Biochemical Research Methods
Fee Faysal Ahmed, Mst Shamima Khatun, Md Parvez Mosharaf, Md Nurul Haque Mollah
Summary: The study developed an effective PPI prediction model for Arabidopsis thaliana using partial training samples in a machine learning framework, combining random forest classifier and autocorrelation sequence encoding features. The proposed model showed higher performance scores in both training and test datasets compared to other candidate predictors, suggesting its potential utility in elucidating the biological function of unseen PPIs in Arabidopsis thaliana.
CURRENT BIOINFORMATICS
(2021)
Article
Plant Sciences
Kaihang Li, Kexin Cheng, Haochen Wang, Qi Zhang, Yan Yang, Yi Jin, Xiaoqing He, Rongling Wu
Summary: The leaf microbiota plays a crucial role in plant development, yet the detailed mechanisms behind microbe-plant relationships remain unclear. In this study, network mapping and genetic analysis were used to identify plant genes that mediate the topological architecture of microbial networks and uncover their molecular pathways related to leaf growth, stress responses, disease resistance, and nutrition uptake. Path analysis also revealed how genetic variants in Arabidopsis affect its fecundity through the leaf microbiome. This study provides new insights into the role of microbial networks in connecting plant genotype to end-point phenotypes, and highlights the importance of further research in plant breeding and synthetic microbial consortia.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Juyoung Kim, Ryeo Jin Kim, Saet Buyl Lee, Mi Chung Suh
Summary: Interactions between KCS9 and other proteins in the fatty acid elongase complex are essential for the synthesis of very-long-chain fatty acids (VLCFAs). This study provides insights into the quaternary structure and protein-protein interactions of the fatty acid elongase complex, highlighting their importance for efficient VLCFA synthesis.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Nadav Eisner, Tzofia Maymon, Ester Cancho Sanchez, Dana Bar-Zvi, Sagie Brodsky, Ruth Finkelstein, Dudy Bar-Zvi
Summary: ABI4 transcription factor plays multiple roles in regulating plant growth, with phosphorylation of S114 being necessary for responses to ABA, glucose, salt stress, and lateral root development. Phosphorylation of S114 is required for the regulation of 35% of repressed genes by ABI4, while only 17% of induced genes are affected.
Article
Biochemistry & Molecular Biology
Emmanuel Baudouin, Juliette Puyaubert, Patrice Meimoun, Melisande Blein-Nicolas, Marlene Davanture, Michel Zivy, Christophe Bailly
Summary: This study investigated the remodeling of Arabidopsis seed phosphoproteome during imbibition using stable isotope dimethyl labeling and nanoLC-MS/MS analysis. The study identified a large repertoire of phosphopeptides and phosphoproteins involved in seed germination control, including protein kinases and key regulators like DOG1. Gene ontology analysis revealed their involvement in various biological processes. The study provides evidence of the major role of phosphosignaling in the regulation of Arabidopsis seed germination.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Yanbing Wang, Joshua Coomey, Kari Miller, Gregory S. Jensen, Elizabeth S. Haswell
Summary: Cells have multiple systems, including ion channels and the cell wall integrity pathway, to maintain cellular integrity. Through studying pollen, it has been discovered that mechanosensitive ion channels modulate callose deposition and interact with the cell wall integrity pathway to maintain cell integrity.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Michael W. Shane, Regina Feil, John E. Lunn, William C. Plaxton
Article
Biochemistry & Molecular Biology
Eric T. Fedosejevs, Suzanne A. Gerdis, Sheng Ying, Michal Pyc, Erin M. Anderson, Wayne A. Snedden, Robert T. Mullen, Yi-Min She, William C. Plaxton
BIOCHEMICAL JOURNAL
(2016)
Review
Biotechnology & Applied Microbiology
Shijian Ge, Pascale Champagne, William C. Plaxton, Gustavo B. Leite, Francesca Marazzi
BIOFUELS BIOPRODUCTS & BIOREFINING-BIOFPR
(2017)
Article
Plant Sciences
Isabel Ruiz-Ballesta, Guillermo Baena, Jacinto Gandullo, Liqun Wang, Yi-Min She, William Charles Plaxton, Cristina Echevarria
JOURNAL OF EXPERIMENTAL BOTANY
(2016)
Article
Biochemistry & Molecular Biology
Eric T. Fedosejevs, Leo N. C. Liu, Megan Abergel, Yi-Min She, William C. Plaxton
Article
Plant Sciences
Michael K. Y. Ting, Yi-Min She, William C. Plaxton
JOURNAL OF EXPERIMENTAL BOTANY
(2017)
Article
Plant Sciences
Sheng Ying, Allyson T. Hill, Michal Pyc, Erin M. Anderson, Wayne A. Snedden, Robert T. Mullen, Yi-Min She, William C. Plaxton
Article
Biotechnology & Applied Microbiology
Nicole Unterlander, Pascale Champagne, William C. Plaxton
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2017)
Article
Biochemistry & Molecular Biology
Eric T. Fedosejevs, Regina Feil, John E. Lunn, William C. Plaxton
Review
Plant Sciences
D. M. S. B. Dissanayaka, William C. Plaxton, Hans Lambers, Meike Siebers, Buddhi Marambe, Jun Wasaki
PLANT CELL AND ENVIRONMENT
(2018)
Article
Plant Sciences
Mina Ghahremani, Hue Tran, Sanaz G. Biglou, Bryden O'Gallagher, Yi-Min She, William C. Plaxton
PLANT CELL AND ENVIRONMENT
(2019)
Article
Biochemistry & Molecular Biology
Matthew B. Connell, Michael J. Y. Lee, Jerry Li, William C. Plaxton, Zongchao Jia
JOURNAL OF STRUCTURAL BIOLOGY
(2018)
Review
Plant Sciences
William C. Plaxton
PLANT AND CELL PHYSIOLOGY
(2019)
Article
Plant Sciences
Ian R. Willick, William C. Plaxton, Susan J. Lolle, Sheila M. Macfie
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2019)