Article
Plant Sciences
Kati Mielke, Raik Wagner, Laxmi S. Mishra, Fatih Demir, Andreas Perrar, Pitter F. Huesgen, Christiane Funk
Summary: FtsH12 plays a crucial role in seedling development of Arabidopsis thaliana, affecting plastid import machinery and chloroplast development. Changes in FtsH12 abundance lead to alterations in protein composition and structure of the chloroplast, impacting overall plant growth and leaf coloration.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Sara Zandalinas, Luhua Song, Rachel Nechushtai, David G. Mendoza-Cozatl, Ron Mittler
Summary: NEET proteins are conserved 2Fe-2S proteins that regulate iron and reactive oxygen species levels in plant and mammalian cells. Disrupting AtNEET function causes oxidative stress, chloroplast iron overload, activation of iron-deficiency responses, and cell death. This study reveals new roles for AtNEET in supporting the ferredoxin-thioredoxin network, iron mobilization, and cytosolic 2Fe-2S cluster assembly in plants.
Article
Biology
Kazusato Oikawa, Takuto Imai, Chonprakun Thagun, Kiminori Toyooka, Takeshi Yoshizumi, Kazuya Ishikawa, Yutaka Kodama, Keiji Numata
Summary: The researchers investigated the rate and trajectory of mitochondria in Arabidopsis thaliana mesophyll cells using confocal laser-scanning microscopy. They discovered that mitochondria migrate through wiggling during their association with chloroplasts, shedding light on the impact of mitochondria-chloroplast interaction on mitochondrial movement.
COMMUNICATIONS BIOLOGY
(2021)
Article
Plant Sciences
Estefania Mancini, Antoni Garcia-Molina
Summary: This study investigated the effect of alternative splicing (AS) on the transcriptome of rosette leaves under single and simultaneous copper (Cu) and iron (Fe) deficiency. It was found that differentially spliced genes (DSGs) and differentially expressed genes (DEGs) showed minimal overlap in number, indicating distinct responses to the double deficiency. Furthermore, it was observed that AS might act as a regulatory mechanism to modify the stability and/or functionality of enzymes involved in amino acid production during the combinatorial response to simultaneous Cu and Fe deficiency.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Manasa B. Satyanarayan, Jun Zhao, Jessica Zhang, Fei Yu, Yan Lu
Summary: Iron-sulfur clusters are essential in various biological processes, and NFU proteins in Arabidopsis thaliana play important roles in their biogenesis. Through mutant analysis, it was found that NFU2 and NFU3 have additive effects on the production of 4Fe-4S clusters. Loss-of-function mutations in NFU1 also result in significant declines in iron-sulfur cluster-containing proteins.
Article
Plant Sciences
R. Glen Uhrig, Sira Echevarria-Zomeno, Pascal Schlapfer, Jonas Grossmann, Bernd Roschitzki, Niklas Koerber, Fabio Fiorani, Wilhelm Gruissem
Summary: The study reports the changes in the Arabidopsis leaf rosette proteome and phosphoproteome during the diurnal cycle, indicating proteins involved in nitrogen and hormone metabolism undergo simultaneous changes in protein abundance and phosphorylation status. The phosphoproteome at light-dark transitions reveals dynamic changes at phosphorylation sites.
PLANT CELL AND ENVIRONMENT
(2021)
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
Thomas Waksman, Noriyuki Suetsugu, Pawel Hermanowicz, James Ronald, Stuart Sullivan, Justyna Labuz, John M. Christie
Summary: Directional movements in plants are regulated by the protein RPT2, which is phosphorylated by phot1 and phot2. This phosphorylation is important for leaf positioning, phototropism, and chloroplast accumulation movement, and highlights the significance of the C-terminal region of NRL proteins in phot receptor signaling.
Article
Plant Sciences
Leah J. Kim, Kaitlyn M. Tsuyuki, Fengling Hu, Emily Y. Park, Jingwen Zhang, Jennifer G. Iraheta, Ju-Chen Chia, Rong Huang, Avery E. Tucker, Madeline Clyne, Claire Castellano, Angie Kim, Daniel D. Chung, Christopher T. DaVeiga, Elizabeth M. Parsons, Olena K. Vatamaniuk, Jeeyon Jeong
Summary: This study reveals the essential role of Arabidopsis ferroportin 3 (FPN3) in maintaining optimal iron homeostasis in mitochondria and chloroplasts. Lack of FPN3 leads to disrupted iron levels and abnormal ultrastructure in mitochondria, affecting plant growth under iron-deficient conditions.
Article
Plant Sciences
Ahmet Bakirbas, Elsbeth L. Walker
Summary: This study identified an iron-regulated lncRNA, COS, in Arabidopsis that is involved in leaf and seed iron levels, chlorophyll levels, root length, and singlet oxygen accumulation during iron deficiency.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Maria N. Danilova, Natalia Kudryakova, Anastasia S. Doroshenko, Amina G. Daminova, Ralf Oelmuller, Victor V. Kusnetsov
Summary: The study investigates the role of cytokinin in the senescence process of detached Arabidopsis leaves. It finds that cytokinin inhibits photosynthesis activity and chlorophyll content while promoting anthocyanin accumulation and ROS production. Additionally, cytokinin stimulates starch accumulation and alters the expression of extracellular cell wall enzyme genes.
PLANT GROWTH REGULATION
(2023)
Article
Plant Sciences
Wei-Liang Kong, Ya-Hui Wang, Xiao-Qin Wu
Summary: The study found that volatile organic compounds (VOCs) released by the rhizobacterium R. aquatilis JZ-GX1 can enhance plant tolerance to iron deficiency stress by promoting root development and regulating gene expression. These VOCs have the potential to promote iron absorption in plants, thereby enhancing plant growth.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Ana Perea-Garcia, Sergi Puig, Lola Penarrubia
Summary: This review proposes that post-transcriptional modulators of metalloprotein mRNA (ModMeR) are good candidates for metal prioritization under metal-limited conditions. ModMeR targets high quota or redundant metalloproteins and acts as internal metal distribution valves by adjusting their synthesis. Inappropriate metalation of ModMeR targets could compete with metal delivery to essential metalloproteins and interfere with metal-sensitive processes.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Developmental Biology
Yingzhang Huang, Limeng Zhou, Chunhui Hou, Dianjing Guo
Summary: This study reveals the proteome landscape of Arabidopsis early embryogenesis through nanoproteomic analysis, and identifies gene enrichment related to ribosome biogenesis and auxin signaling. The positive correlation between mRNA and protein is confirmed by integrating RNA-sequencing data. This work provides valuable insights for further investigation into plant embryo development.
Article
Biochemistry & Molecular Biology
Ranju Chutia, Sarah Scharfenberg, Steffen Neumann, Steffen Abel, Joerg Ziegler
Summary: The research reveals the important roles of iron and phosphate in plant growth and metabolic regulation, showing their interdependency and interaction which affect plant growth and development under different nutrient conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Arvind S. Pillai, Shane A. Chandler, Yang Liu, Anthony Signor, Carlos R. Cortez-Romero, Justin L. P. Benesch, Arthur Laganowsky, Jay F. Storz, Georg K. A. Hochberg, Joseph W. Thornton
Article
Chemistry, Analytical
Shiyu Dong, Mehdi Shirzadeh, Liqi Fan, Arthur Laganowsky, David H. Russell
ANALYTICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Samantha Schrecke, Yun Zhu, Jacob W. McCabe, Mariah Bartz, Charles Packianathan, Minglei Zhao, Ming Zhou, David Russell, Arthur Laganowsky
Summary: The study shows that the two isoforms of K(2P)4.1 have distinct preferences for binding to lipids, including acyl chain length, position, and fatty acid linkage. Phosphatidic acid has the best activation effect on the channel.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Truc Viet Pham, Drake M. Mellott, Zahra Moghadamchargari, Kevin Chen, Inna Krieger, Arthur Laganowsky, James C. Sacchettini, Thomas D. Meek
Summary: This study identified cis-2,3-epoxysuccinate as the most potent inactivator of Mycobacterium tuberculosis ICL1, providing a new lead for the development of antituberculosis agents.
ACS CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Analytical
Jacob W. McCabe, Mehdi Shirzadeh, Thomas E. Walker, Cheng-Wei Lin, Benjamin J. Jones, Vicki H. Wysocki, David P. Barondeau, David E. Clemmer, Arthur Laganowsky, David H. Russell
Summary: The stability and structure of proteins are influenced by various factors in their local environment, and a new variable-temperature electrospray ionization (vT-ESI) source has been developed to study the effects of temperature on protein folding and ligand binding. This apparatus allows for rapid and precise control of solution temperature changes, enabling research on temperature-dependent protein reactions with high efficiency.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Zahra Moghadamchargari, Mehdi Shirzadeh, Chang Liu, Samantha Schrecke, Charles Packianathan, David H. Russell, Minglei Zhao, Arthur Laganowsky
Summary: This study investigated the interaction of oncogenic Ras mutants with SOS using native ion mobility-mass spectrometry and structural analysis, revealing different molecular assemblies and the potent modulatory effects of certain mutants on SOS. The findings provide insights into potential therapeutic interventions for Ras-driven cancers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Analytical
Tarick J. El-Baba, Shannon A. Raab, Rachel P. Buckley, Christopher J. Brown, Corinne A. Lutomski, Lucas W. Henderson, Daniel W. Woodall, Jiangchuan Shen, Jonathan C. Trinidad, Hengyao Niu, Martin F. Jarrold, David H. Russell, Arthur Laganowsky, David E. Clemmer
Summary: The method characterizes the thermal stabilities of endogenous proteins and protein assemblies in complex mixtures by directly measuring melting transitions. Structural transitions related to protein complexes can be monitored based on changes in charge states and masses.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Linfeng Li, Bala C. Chenna, Kai S. Yang, Taylor R. Cole, Zachary T. Goodall, Miriam Giardini, Zahra Moghadamchargari, Elizabeth A. Hernandez, Jana Gomez, Claudia M. Calvet, Jean A. Bernatchez, Drake M. Mellott, Jiyun Zhu, Andrew Rademacher, Diane Thomas, Lauren R. Blankenship, Aleksandra Drelich, Arthur Laganowsky, Chien-Te K. Tseng, Wenshe R. Liu, A. Joshua Wand, Jorge Cruz-Reyes, Jair L. Siqueira-Neto, Thomas D. Meek
Summary: A novel class of self-masked aldehyde inhibitors has been developed for the major cysteine protease of Chagas disease, showing potent and reversible inhibition while potentially improving pharmacokinetic properties. The study also elucidated the kinetic and chemical mechanism of these inhibitors and applied the strategy to design anti-SARS-CoV-2 drugs.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Shannon A. Raab, Tarick J. El-Baba, Arthur Laganowsky, David H. Russell, Stephen J. Valentine, David E. Clemmer
Summary: The article discusses the impact of differences in time scales between protons and proteins on the conformation trapping during the electrospray process. It highlights the mechanisms of conformational changes and proton exchange at different time scales, as well as the immobilization of protons specific to protein conformations in the vacuum of the mass spectrometer.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Review
Biophysics
Arthur Laganowsky, David E. Clemmer, David H. Russell
Summary: This review highlights the application of vT-ESI-MS in studying the structures and thermodynamic properties of proteins and their interactions with ligands. The technology provides direct measurements of stability and heat-induced processes in different conformers of proteins.
ANNUAL REVIEW OF BIOPHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Pei Qiao, Samantha Schrecke, Jixing Lyu, Yun Zhu, Tianqi Zhang, Amanda Benavides, Arthur Laganowsky
Summary: The study found that Kir3.4 displays binding preferences for PIPs, and the interactions between Kir3.4 and PIPs are weaker compared to Kir3.2. Additionally, the type of acyl chains can influence the binding preferences of Kir3.4 for PIPs.
Article
Chemistry, Physical
Pei Qiao, Samantha Schrecke, Thomas Walker, Jacob W. McCabe, Jixing Lyu, Yun Zhu, Tianqi Zhang, Smriti Kumar, David Clemmer, David H. Russell, Arthur Laganowsky
Summary: This study used variable-temperature native mass spectrometry to investigate the thermodynamics of lipid binding events to the human G-protein-gated inward rectifier potassium channel, Kir3.2, revealing distinct thermodynamic strategies for different types of phosphatidylinositol and phosphorylated forms. The acyl chain of the lipid and the number of phosphate groups have significant impacts on the binding thermodynamics, with entropy and enthalpy playing key roles in the interactions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Drake M. Mellott, Dan Torres, Inna Krieger, Scott A. Cameron, Zahra Moghadamchargari, Arthur Laganowsky, James C. Sacchettini, Thomas D. Meek, Lawrence D. Harris
Summary: The research shows that 5-NIC can serve as an effective inactivator of ICL1. Its design aims to lower the overall charge for improved cell permeability, facilitating the synthesis of pro-drug forms for M. tuberculosis cell-infection models.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemical Research Methods
Jacob W. McCabe, Benjamin J. Jones, Thomas E. Walker, Robert L. Schrader, Adam P. Huntley, Jixing Lyu, Nathan M. Hoffman, Gordon A. Anderson, Peter T. A. Reilly, Arthur Laganowsky, Vicki H. Wysocki, David H. Russell
Summary: This study presents a digital-waveform dual-quadrupole mass spectrometer to improve the performance of a drift tube FT-IMS high-resolution Orbitrap mass spectrometer in studying large proteins and protein complexes. The dual-quadrupole analyzer allows for low-energy collisional activation of ions and precise mass selection using digital-waveform technology, enhancing the capabilities of the instrument at a lower cost compared to traditional RF drivers.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Multidisciplinary
Mia L. Abramsson, Cagla Sahin, Jonathan T. S. Hopper, Rui M. M. Branca, Jens Danielsson, Mingming Xu, Shane A. Chandler, Nicklas Osterlund, Leopold L. Ilag, Axel Leppert, Joana Costeira-Paulo, Lisa Lang, Kaare Teilum, Arthur Laganowsky, Justin L. P. Benesch, Mikael Oliveberg, Carol Robinson, Erik G. Marklund, Timothy M. Allison, Jakob R. Winther, Michael Landreh
Summary: The presence of ionizable side chains in proteins affect their charging under native conditions, with preferential protonation sites. Absence of ionizable side chains results in similar charge state distributions under native-like and denaturing conditions, while an excess of ionizable side chains effectively modulates protein ion stability.
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)