Review
Biochemical Research Methods
Lan Huang, Dan Shao, Yan Wang, Xueteng Cui, Yufei Li, Qian Chen, Juan Cui
Summary: Recent research on body-fluid proteomes has resulted in the discovery of novel disease biomarkers and therapeutic drugs, with over 15,000 different proteins detected in major human body fluids. Challenges remain in effectively handling the variety of protein modifications in these fluids. Computational efforts using statistical and machine-learning approaches have shown promise in identifying biomarker proteins in specific human diseases.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Mengyun Hou, Jingnan Huang, Tianyuan Jia, Yudong Guan, Fan Yang, Hongchao Zhou, Piying Huang, Jigang Wang, Liang Yang, Lingyun Dai
Summary: In this study, the abundance dynamics of proteins in Pseudomonas aeruginosa reference strain PAO1 were analyzed using data-independent acquisition-based quantitative proteomics. The differentially expressed proteins during planktonic growth exhibited diverse expression patterns relevant to various biological processes, highlighting the continuous adaptation of the PAO1 proteome. By comparing protein expressions in biofilm and planktonic cells, the roles of known factors in biofilm formation were confirmed and new functional proteins were discovered. This study provides a valuable resource for understanding the proteomic dynamics of P. aeruginosa and advancing our knowledge of its physiology.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Plant Sciences
Penny Makhumbila, Molemi Rauwane, Hangwani Muedi, Sandiswa Figlan
Summary: Legume crops play a significant role in both human and animal diets, as well as in improving cropping systems. However, biotic stresses significantly limit their yield potential. Metabolomic studies can help understand the response pathways of leguminous crops to biotic stresses.
Article
Biochemical Research Methods
Mingzhe Fu, Yuchao Yan, Hong Su, Jingjing Wang, Xiaojie Shi, Hongchao Zhou, Qi Zhang, Xingang Xu
Summary: The study used proteomic analysis to investigate the immune response and molecular pathways in goats infected with C. pseudotuberculosis, identifying altered proteins and enriched pathways. Understanding the complexity of C. pseudotuberculosis infection and identifying potential therapeutic targets is crucial for disease management. The research sheds new light on the interaction between C. pseudotuberculosis and the host, particularly highlighting the disruption of the immune response mechanism and immune cell death caused by the infection in dairy goats.
JOURNAL OF PROTEOMICS
(2021)
Article
Chemistry, Multidisciplinary
Dustin T. King, Jesus E. Serrano-Negron, Yanping Zhu, Christopher L. Moore, Matthew D. Shoulders, Leonard J. Foster, David J. Vocadlo
Summary: Posttranslational modifications can alter protein stability and cellular physiology. This study presents an unbiased proteome-wide approach to explore the influence of protein modifications on thermodynamic stability. Using this approach, the authors identify a set of proteins that are destabilized by O-GlcNAc modification and form distinct macromolecular complexes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Environmental Sciences
Qiyu Qin, Yidi Yang, Changfu Yang, Leilihe Zhang, Haoyuan Yin, Fei Yu, Jie Ma
Summary: This study investigated the characteristics of biodegradable plastic PLA and its adsorption behavior with tetracycline under weathering conditions. The results showed that weathered PLA had cracks and holes on the surface, increased oxygen-containing functional groups, and enhanced adsorption capacity. However, the surface of microplastics weathered by seawater did not change significantly.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Chemistry, Multidisciplinary
Jiaying Li, Jiahua Zhou, Kailu Tian, He Zhu, Yao Chen, Yangyu Huang, Guosheng Wang, Zhou Gong, Hongqiang Qin, Mingliang Ye, Hao Xu
Summary: The quantitative profiling of residue reactivity in proteins can help identify covalent druggable targets for precise therapy. In this study, a chemical proteomics platform was developed to analyze the reactivity of histidine (His) residues. Through this platform, the reactivity of His residues in the human proteome was characterized, and a large number of His residues with high reactivity were identified. The findings suggest that these highly reactive residues are less likely to be phosphorylation sites, which requires further research to understand the underlying mechanism. This comprehensive map of His residue reactivity provides potential bindable sites for disrupting protein activities and offers new opportunities for developing covalent inhibitors using acrolein derivatives as reactive warheads.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Dari Shalon, Rebecca Neal Culver, Jessica A. Grembi, Jacob Folz, Peter V. Treit, Handuo Shi, Florian A. Rosenberger, Les Dethlefsen, Xiandong Meng, Eitan Yaffe, Andres Aranda-Diaz, Philipp E. Geyer, Johannes B. Mueller-Reif, Sean Spencer, Andrew D. Patterson, George Triadafilopoulos, Susan P. Holmes, Matthias Mann, Oliver Fiehn, David A. Relman, Kerwyn Casey Huang
Summary: This study developed an ingestible device that can collect samples from multiple regions of the human intestinal tract during normal digestion. Multi-omics analysis of the collected samples revealed significant differences in bacteria, phages, host proteins, and metabolites between the intestines and stool. The study provides insights into the roles of the gut microbiome and metabolome in human physiology and disease through non-invasive longitudinal profiling of microorganisms, proteins, and bile acids along the intestinal tract.
Article
Horticulture
Wanjie Xue, Lishan Wang, Xueqi Li, Mingwei Tang, Jingyao Li, Bing Ding, Saneyuki Kawabata, Yuhua Li, Yang Zhang
Summary: This study identified the most suitable reference genes for different treatments in Eustoma grandiflorum by analyzing 18 potential reference genes in different organs, at different developmental stages and under drought- and salt-stress treatments. The results provide important contributions to future studies on gene expression normalization in Eustoma grandiflorum.
Article
Biochemical Research Methods
Federica D'Onofrio, Pierina Visciano, Ivanka Krasteva, Marina Torresi, Manuela Tittarelli, Francesco Pomilio, Luigi Iannetti, Tiziana Di Febo, Antonello Paparella, Maria Schirone, Mirella Luciani
Summary: This study characterized the immunogenic protein profile of a sequence type 7 (ST7) strain of Listeria monocytogenes that caused severe listeriosis outbreaks in central Italy using a combined proteomics and bioinformatics approach. The results showed that the proteome of L. monocytogenes adapted and reshaped under mild stress conditions, involving cell motility, carbohydrate metabolism, oxidative stress, and DNA repair.
Article
Biochemical Research Methods
Amy L. George, Frances R. Sidgwick, Jessica E. Watt, Mathew P. Martin, Matthias Trost, Jose Luis Marin-Rubio, Maria Emilia Duenas
Summary: Thermal proteome profiling (TPP) is a powerful approach to studying the interactions of therapeutic molecules with proteins. Isobaric tandem mass tags (TMTs) are commonly used in TPP analysis, but data-independent acquisition (DIA) approaches offer higher sensitivity and protein coverage with reduced costs. In this study, different DIA-based label-free quantification approaches were compared to TMT-DDA for thermal shift quantitation, and it was found that DIA approaches are a cost-effective alternative.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Shanshan Li, Huoqing Luo, Ronghui Lou, Cuiping Tian, Chen Miao, Lisha Xia, Chen Pan, Xiaoxiao Duan, Ting Dang, Hui Li, Chengyu Fan, Pan Tang, Zhuangzhuang Zhang, Yan Liu, Yunxia Li, Fei Xu, Yaoyang Zhang, Guisheng Zhong, Ji Hu, Wenqing Shui
Summary: This study presents a new proteomic approach aided by deep learning models to comprehensively profile transmembrane protein families in multiple mouse brain regions. It highlights discrepancies between messenger RNA and protein distribution, predicts an endogenous GPCR interaction network in the brain, and reveals the transmembrane proteome remodeling landscape in a mouse depression model, leading to the identification of previously unknown GPCR regulators of depressive-like behaviors.
Article
Multidisciplinary Sciences
Haizhu Zhang, Zhaoyu Qin, Xuetong Yue, Yang Liu, Xiaogang Sun, Jinwen Feng, Ziyan Xu, Jiangyan Zhao, Kai Li, Jiange Qiu, Wenjun Yang, Fuchu He, Chen Ding
Summary: ATAC-MS is a method to identify transcriptional protein complexes assembled on accessible chromatin, providing insight into the protein machinery in open chromatin. Combined with ATAC-seq, it allows for high-resolution profiling of chromatin-transcriptional machinery. Additionally, the fusion protein ctATAC-MS enables systematic pinpointing of the transcriptional machinery at specific open chromatin regions.
Article
Multidisciplinary Sciences
Natalia Andelova, Iveta Waczulikova, Lukas Kunstek, Ivan Talian, Tanya Ravingerova, Magdalena Jasova, Simon Suty, Miroslav Ferko
Summary: The study identifies the effects of the drug DCA on protein interactions, calcium uptake, and ROS production in diabetic heart muscle, providing insights into the cardioprotective pathway.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Jiayun Xing, Jinjuan Tan, Hanqian Feng, Zhongjing Zhou, Min Deng, Hongbing Luo, Zhiping Deng
Summary: This study investigates the molecular mechanism of cold adaptation in maize by analyzing the proteome and phosphoproteome levels of maize seedlings under cold shock. The results reveal the early molecular events associated with cold response in maize, including changes in photosynthesis proteins, spliceosome proteins, kinases, and transcriptional factors. The study provides valuable insights into how C-4 plants respond to sudden temperature drops.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Annelies Bogaert, Esperanza Fernandez, Kris Gevaert
TRENDS IN BIOCHEMICAL SCIENCES
(2020)
Article
Biochemical Research Methods
Patrick Willems, Ursula Fels, An Staes, Kris Gevaert, Petra Van Damme
Summary: To study physiological responses in bacterial infections, an optimized hybrid library generation workflow for DIA mass spectrometry was found to significantly improve sensitivity and depth of protein detection, without the need for prior enrichment of bacterial pathogens.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Spectroscopy
Jarne Pauwels, Daria Fijalkowska, Sven Eyckerman, Kris Gevaert
Summary: The surfaceome, consisting of plasma membrane proteins, plays crucial roles in cell communication, transport regulation, and immune responses. However, challenges such as inefficient extraction and lower abundance compared to intracellular proteins hinder comprehensive analysis. To address these issues, innovative analytical methodologies have been developed.
MASS SPECTROMETRY REVIEWS
(2022)
Editorial Material
Biochemical Research Methods
Jarne Pauwels, Kris Gevaert
EXPERT REVIEW OF PROTEOMICS
(2021)
Review
Entomology
Pengyu Chen, Kristof De Schutter, Jarne Pauwels, Kris Gevaert, Els J. M. Van Damme, Guy Smagghe
Summary: Plant lectins in mammals have been shown to modulate immune responses, but their effects in insects are not well understood. Treatment of Drosophila melanogaster S2 cells with Orysata, a mannose-binding lectin, led to the upregulation of immunity-related proteins and antimicrobial peptides. Additionally, Orysata was found to interact with iron-binding proteins and reduces intracellular iron concentration in S2 cells. These findings provide new insights into the immunomodulatory properties of plant lectins in insects.
Article
Chemistry, Analytical
Kaatje Van Vlierberghe, Maxime Gavage, Marc Dieu, Patsy Renard, Thierry Arnould, Nathalie Gillard, Katleen Coudijzer, Marc de Loose, Kris Gevaert, Christof Van Poucke
Summary: This study aims to identify stable peptide markers for milk for the ultrahigh performance liquid chromatography-tandem mass spectrometry based detection of food allergens in different food products. By establishing tryptic peptide profiles from milk-incurred food materials undergoing various processing techniques, eight peptide biomarkers were selected for application in ultrahigh performance liquid chromatography-tandem mass spectrometry based milk detection methods. These robust markers can be used for the development of a robust detection method for milk in different food matrixes.
JOURNAL OF AOAC INTERNATIONAL
(2022)
Article
Plant Sciences
Pan Gong, Michiel Bontinck, Kirin Demuynck, Jolien De Block, Kris Gevaert, Dominique Eeckhout, Geert Persiau, Stijn Aesaert, Griet Coussens, Mieke Van Lijsebettens, Laurens Pauwels, Geert De Jaeger, Dirk Inze, Hilde Nelissen
Summary: SAMBA has been identified as a plant-specific regulator of the anaphase-promoting complex/cyclosome (APC/C) in Arabidopsis and maize. Two samba genome edited mutants in maize showed growth defects, with samba-1 representing a knockout allele and samba-3 producing a truncated protein that still interacted with APC/C but with altered activity. This suggests a dosage-dependent role for SAMBA in controlling developmental processes.
Article
Chemistry, Analytical
Maxime Gavage, Kaatje Van Vlierberghe, Marc Dieu, Patsy Renard, Thierry Arnould, Marc De Loose, Kris Gevaert, Nathalie Gillard, Christof Van Poucke
Summary: This study has successfully developed a robust method for detecting and quantifying multiple allergens in food, ensuring the safety of allergic consumers. The combination of specific incurred test materials, standard addition strategy, and stable isotope-labeled concatemer has provided the method with sufficient sensitivity and reliability.
JOURNAL OF AOAC INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
Petra Van Damme, Camilla Osberg, Veronique Jonckheere, Nina Glomnes, Kris Gevaert, Thomas Arnesen, Henriette Aksnes
Summary: N-terminal acetylation of proteins is a conserved modification in eukaryotes, and the yeast Saccharomyces cerevisiae is a valuable model for studying this process. The bulk of N-terminal acetylation in S. cerevisiae is catalyzed by NatA, NatB, and NatC. In this study, the authors identified 57 yeast NatC substrates using a combination of techniques. They also uncovered some non-NatC NAT activity, suggesting redundancy between NatC and NatE/Naa50. Furthermore, the authors demonstrated the evolutionary conservation of NatC from yeast to humans and its potential implications for studying pathogenic variants. Overall, this work provides valuable insights into NatC-mediated N-terminal acetylation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Oncology
Ana Teresa Pinto, Ana Beatriz Machado, Hugo Osorio, Marta Laranjeiro Pinto, Rui Vitorino, Goncalo Justino, Catia Santa, Flavia Castro, Tania Cruz, Carla Rodrigues, Jorge Lima, Jose Luis R. Sousa, Ana Patricia Cardoso, Rita Figueira, Armanda Monteiro, Margarida Marques, Bruno Manadas, Jarne Pauwels, Kris Gevaert, Marc Mareel, Sonia Rocha, Tiago Duarte, Maria Jose Oliveira
Summary: Resistance to radiotherapy is a major problem in cancer treatment. Investigating the response of macrophages to ionizing radiation could help overcome tumor radio resistance.
Article
Biochemistry & Molecular Biology
Patrick Willems, Valerie Van Ruyskensvelde, Takanori Maruta, Robin Pottie, Alvaro D. Fernandez-Fernandez, Jarne Pauwels, Matthew A. Hannah, Kris Gevaert, Frank Van Breusegem, Katrien Van der Kelen
Summary: Alternative splicing is an important gene regulatory process in plants, and its inhibition can alleviate cell death and enhance tolerance to oxidative stress.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Chemistry, Analytical
Maxime Gavage, Kaatje Van Vlierberghe, Marc Dieu, Patsy Renard, Thierry Arnould, Kris Gevaert, Marc De Loose, Christof Van Poucke, Anne-Catherine Huet, Nathalie Gillard
Summary: This interlaboratory study evaluated the potential of MS for food allergen detection and quantification using a standard addition quantification strategy and a stable isotope-labeled concatemer as an internal standard. Nine laboratories participated in the study and were able to detect allergens with sufficient sensitivity, although egg detection was more challenging. The encouraging results of this study contribute to harmonization among laboratories testing for allergens.
JOURNAL OF AOAC INTERNATIONAL
(2023)
Article
Biochemical Research Methods
Tine Claeys, Maxime Menu, Robbin Bouwmeester, Kris Gevaert, Lennart Martens
Summary: Using data from 183 public human data sets, a machine learning model was trained to identify tissue and cell-type specific protein patterns. The model achieved high accuracy in predicting tissues (98%) and cell types (99%) based on protein abundance. The results provide valuable insights into tissue-specific proteins and can be applied to various downstream applications.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Andreia Ferreira, Evy Timmerman, An Staes, Marnik Vuylsteke, Louis De Muynck, Kris Gevaert
Summary: By using affinity-enrichment mass spectrometry, we identified novel potential protein ligands that may interact with (3S-)HS. Our dataset expands the repertoire of proteins that depend on 3S-HS in (patho)physiological conditions, providing new insights into the molecular mechanisms involved.
Article
Chemistry, Multidisciplinary
Klaas W. Decoene, Kamil Unal, An Staes, Olivier Zwaenepoel, Jan Gettemans, Kris Gevaert, Johan M. Winne, Annemieke Madder
Summary: This study presents a new method for site-selective labeling of tyrosine and tryptophan residues in peptides and proteins. By lowering the pH of the solution, selective labeling of tryptophan can be achieved. This method does not rely on enzymes or unnatural amino acids, making it a promising approach for bioconjugation.
