Article
Biochemistry & Molecular Biology
Ricardo L. Couto-Rodriguez, Jin Koh, Sixue Chen, Julie A. Maupin-Furlow
Summary: Oxidative stress adaptation strategies are important for cell function and are associated with cardiac, neurodegenerative disease, and cancer. The halophilic archaeon Haloferax volcanii is used as a model organism due to its extreme tolerance to oxidants and close evolutionary relationship with eukaryotes. A study on H. volcanii reveals the association of lysine acetylation with oxidative stress responses, and the dynamic changes in the lysine acetylome in response to hypochlorite. These findings provide insights into the role of lysine acetylation in key biological processes and PTM crosstalk in Archaea.
Article
Plant Sciences
Jianfei Guo, Zhigang Ma, Ce Deng, Junqiang Ding, Yuxiao Chang
Summary: Lysine-epsilon-acetylation (Kac) is a reversible post-translational modification that plays important roles in plant-pathogen interactions. This study analyzed the changes in protein abundance and lysine acetylation in maize infected with Puccinia polysora, highlighting the role of Kac in cellular processes and defense responses. The findings provide valuable insights into protein acetylation in plant-pathogen interactions and the plant immune response.
Article
Biochemical Research Methods
Mingya Zhang, TianXian Liu, Le Wang, Yuqi Huang, Rufeng Fan, Ke Ma, Yunbo Kan, Minjia Tan, Jun-Yu Xu
Summary: This study provides a comprehensive analysis of several lysine acylomes using high-affinity antibody enrichment and high-resolution LC-MS/MS. Multiple acylated sites were identified and their potential roles in metabolism and physiology of bacteria were revealed.
JOURNAL OF PROTEOMICS
(2023)
Article
Biochemistry & Molecular Biology
Kevin P. Gillespie, Ross Pirnie, Clementina Mesaros, Ian A. Blair
Summary: It has been found that cisplatin treatment can induce secretion of HMGB1 from human non-small cell lung cancer cells, while carboplatin cannot. This secretion is dose-dependent and regulated by nuclear exportin 1. Additionally, the secreted HMGB1 after cisplatin treatment is mainly in the fully reduced form.
Review
Biochemistry & Molecular Biology
Keith E. Keenan, Derek K. Zachman, Matthew D. Hirschey
Summary: Protein modifications play a significant role in cell biology across various organisms. Discoveries in the early 20th century challenged traditional definitions of amino acids, and the advent of mass-spectrometry-based proteomics in the latter part led to a rapid increase in known protein modifications, with over 500 identified today. New computational tools in data science, machine learning, and artificial intelligence are expected to further advance the discovery and understanding of protein modifications in the future.
Article
Microbiology
Yafang Tan, Wanbing Liu, Yuling Chen, Yazhou Zhou, Kai Song, Shiyang Cao, Yuan Zhang, Yajun Song, Haiteng Deng, Ruifu Yang, Zongmin Du
Summary: Yersinia pestis is the causative agent of plague, responsible for three global pandemics. The recent plague epidemic in Madagascar highlighted the ongoing threat of Y. pestis worldwide. This study provides valuable insights into lysine acetylation in Y. pestis and its functional role in bacterial physiology.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Kazuya Tsumagari, Yasushi Ishihama
Summary: A novel enrichment method for acylated peptides was developed in this study without the use of antibodies, where endogenously acylated peptides are deacylated by recombinant lysine deacylases and enriched by N-hydroxysuccinimidyl chemistry for identification of the acylated sites. The acylomics platform was proven valid through its application on chemically acylated model protein samples and endogenous acylated sites in HeLa cell nuclei.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Marta Tomczyk, Mariola Olkowicz, Ewa M. Slominska, Ryszard T. Smolenski
Summary: The heart has a flexible energy metabolism and can utilize various carbon substrates, with substrate preference potentially impacting cardiac pathologies. A simple method was developed to analyze cardiac metabolic substrate use, allowing for fast estimation of glucose and amino acid utilization in mice and high-throughput analysis of changes in pathology and after pharmacological treatments.
Article
Multidisciplinary Sciences
Simon Maria Kienle, Tobias Schneider, Katrin Stuber, Christoph Globisch, Jasmin Jansen, Florian Stengel, Christine Peter, Andreas Marx, Michael Kovermann, Martin Scheffner
Summary: Ubiquitin is a highly versatile posttranslational modifier that is also subject to modifications such as acetylation. Acetylation at different sites has specific impacts on ubiquitin structure and function, linking different acetylated variants to distinct cellular pathways.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Shuwen Hua, Bing Wang, Chuan-Fan Ding, Yinghua Yan
Summary: The analysis of low abundance phosphopeptides and specific capture exosomes is crucial in understanding the pathogenesis of diseases. A carbon-based material, G@C@Ti-Zr-HMCT, was developed using titanium-zirconium ions and dopamine and polyimide tubes. This material showed satisfactory capability of enriching phosphopeptides and capturing exosomes.
Article
Chemistry, Analytical
Wei Luo, Teris A. van Beek, Bo Chen, Han Zuilhof, Gert I. J. Salentijn
Summary: A fast and simple quantitative boronate affinity paper spray tandem mass spectrometric (PS-MS/MS) method is established for the analysis of catecholamines in urine, which improves selectivity and reduces ion suppression without the need for instrumental chromatography. This method utilizes the property of boronic acids to selectively bind catecholamines under alkaline conditions. Compared to HPLC-MS/MS, the PS-MS/MS method is faster, cheaper, and easier to operate while maintaining good performance in terms of precision, accuracy, and limit of detection.
ANALYTICA CHIMICA ACTA
(2022)
Article
Microbiology
Timothy R. Howard, Marni S. Crow, Todd M. Greco, Krystal K. Lum, Tuo Li, Ileana M. Cristea
Summary: The research indicates that IFIX plays a significant role in impacting both nuclear and cytoplasmic proteomes, leading to alterations in immune signaling, DNA damage response, and vesicle-mediated transport proteins. Additionally, IFIX is shown to have multifunctional roles in immune signaling, DNA damage response, and transcriptional regulation within the host cell.
Article
Biochemistry & Molecular Biology
Artem Artiukhov, Ekaterina F. Kolesanova, Aleksandra Boyko, Anastasiya A. Chashnikova, Sergei N. Gnedoy, Thilo Kaehne, Daria A. Ivanova, Alyona Kolesnichenko, Vasily A. Aleshin, Victoria Bunik
Summary: The study focuses on the glutarylation of lysine residues in proteins, revealing sample-specific patterns of protein glutarylation in rat tissues and mitochondria. Time-dependent fragmentation of glutarylated proteins in rat tissue homogenates was observed, complicating the investigation of acylation regulators' effects. The affinity-purified anti(epsilon-glutaryllysine)-antibodies proved to be an effective tool for characterizing protein glutarylation and showing its specific pattern compared to other acylation types in complex protein mixtures.
Article
Biochemical Research Methods
Wenbo Dong, Lin Chen, Li Jia, Zexuan Chen, Jiechen Shen, Pengfei Li, Shisheng Sun
Summary: The low abundance and heterogeneity of N-glycosylation at the peptide level poses a great challenge in the field of glycobiology. In this study, different combinations of desalting and enrichment columns were compared for the enrichment of intact N-glycopeptides from mouse brain tissues. Results showed that the C18 column was slightly superior to the HLB column, and the use of both MAX and HILIC columns complemented each other in the enrichment of intact N-glycopeptides. Based on these findings, sequential enrichment of glycopeptides using HILIC and then MAX columns is recommended for in-depth analysis of site-specific glycoproteome.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Review
Cell Biology
Zakery N. Baker, Patrick Forny, David J. Pagliarini
Summary: Mitochondria are multifunctional organelles with diverse roles in cellular processes, bioenergetics, and disease. The development of a comprehensive mitochondrial protein map has revolutionized our understanding of mitochondrial biology and its clinical implications. Advances in technology and computational methods continue to refine this map, providing insights into new proteins and their functions.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Review
Microbiology
Jordan Blum, Mihiri Silva, Samantha J. Byrne, Catherine A. Butler, Geoffrey G. Adams, Eric C. Reynolds, Stuart G. Dashper
Summary: The human oral microbiome plays important roles in health and disease beyond the oral cavity. It is influenced by various factors, especially the neonate diet. Early childhood and prenatal influences have long-term effects on the development of the oral microbiome. Further research is needed to understand the specific roles of early colonizing bacteria in relation to health and disease.
CRITICAL REVIEWS IN MICROBIOLOGY
(2022)
Review
Dentistry, Oral Surgery & Medicine
P. D. Veith, M. D. Glew, D. G. Gorasia, E. Cascales, E. C. Reynolds
Summary: Bacteria in severe periodontitis utilize the T9SS system to release virulence factors that dysregulate the host immune response, leading to chronic inflammatory destruction of tooth supporting tissues. The molecular structure and secretion mechanism of T9SS are crucial for understanding this process.
JOURNAL OF DENTAL RESEARCH
(2022)
Article
Microbiology
Dhana G. Gorasia, Ignacio Lunar Silva, Catherine A. Butler, Maialene Chabalier, Thierry Doan, Eric Cascales, Paul D. Veith, Eric C. Reynolds
Summary: The type IX secretion system (T9SS) is an important system that transports cargo proteins from the outer membrane of bacteria to the cell surface. It plays a crucial role in pathogenesis, gliding motility, and degradation of carbon sources. However, the spatial organization and interaction of its modules have been unknown. In this study, researchers characterized the protein interactome of the Sov translocon in Porphyromonas gingivalis and identified PorW as the missing link that completes the interaction network from the PorUM motor to the Sov translocon, providing a pathway for cargo delivery and energy transduction from the inner membrane to the secretion pore for the first time.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Paul D. Veith, Mikio Shoji, Nichollas E. Scott, Eric C. Reynolds
Summary: Porphyromonas gingivalis, an important human pathogen and model organism, has been shown to have O-glycosylation. This study identified 257 putative glycosylation sites in 145 glycoproteins and revealed the structure of the major O-glycan. The O-glycosylation system in P. gingivalis plays a role in establishing the physicochemical properties of the periplasm.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Dhana G. Gorasia, Christine A. Seers, Jacqueline E. Heath, Michelle D. Glew, Hamid Soleimaninejad, Catherine A. Butler, Mark J. McBride, Paul D. Veith, Eric C. Reynolds
Summary: This study identified a complex comprising PorP, PorE, and PG1035, and supported direct interactions between PorE-PorP and PorP-PG1035. Additionally, it was found that type B-CTD proteins may anchor to the cell surface by binding to PorP-like proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
S. J. Byrne, D. Chang, G. G. Adams, C. A. Butler, E. C. Reynolds, I. B. Darby, S. G. Dashper
Summary: This study aimed to compare the microbiome of sites that did not respond to non-surgical debridement treatment with those that responded well. The results showed no significant differences in clinical parameters and microbial communities between good responding and non-responding sites before and after treatment. In non-responding sites, the pathogenic bacterial community was not disrupted by the treatment.
JOURNAL OF ORAL MICROBIOLOGY
(2022)
Article
Microbiology
Catherine A. Butler, Geoffrey G. Adams, Jordan Blum, Samantha J. Byrne, Lauren Carpenter, Mark G. Gussy, Hanny Calache, Deanne Catmull, Eric C. Reynolds, Stuart G. Dashper
Summary: This study investigates the effect of exposure to breastmilk on the assembly of the infant oral microbiome during the first 20 months of life. The results show significant differences in the development of the oral microbiomes of never breastfed and breastfed infants. Breastmilk likely plays a prebiotic role in selecting health-associated oral bacteria. The microbiomes of both groups become more heterogeneous following the introduction of solid foods.
JOURNAL OF ORAL MICROBIOLOGY
(2022)
Review
Microbiology
Sixin Liu, Catherine A. Butler, Scott Ayton, Eric C. Reynolds, Stuart G. Dashper
Summary: The cause and pathophysiological mechanisms of Alzheimer's disease (AD) are still unknown in medical science. Oral bacteria, especially Porphyromonas gingivalis, are associated with AD pathophysiology in some individuals. P. gingivalis produces proteins that cause tissue damage and inflammation. This bacterium's outer membrane vesicles (OMVs) can cross the blood brain barrier and contribute to neuroinflammation, plaque/tangle formation, and neuronal death.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Article
Microbiology
Paul D. D. Veith, Dhana G. G. Gorasia, Eric C. C. Reynolds
Summary: In this study, the O-glycoproteome of F. johnsoniae was characterized and 325 O-glycosylation sites were identified among 226 glycoproteins. The glycosylated domains were mainly located in the periplasm, which is believed to be beneficial for protein folding and stability. Additionally, six proteins associated with gliding motility or the T9SS were shown to be O-glycosylated.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Multidisciplinary Sciences
Abu Sayeed M. Mahmud, Christine A. Seers, N. Laila Huq, Lianyi Zhang, Catherine A. Butler, Caroline Moore, Keith J. Cross, Eric C. Reynolds
Summary: The Arg-specific gingipains of Porphyromonas gingivalis RgpA and RgpB have similar catalytic domains but different propeptides. A modification of rgpA allowed the isolation of monomeric RgpA (rRgpAH) for kinetic comparisons with RgpB. The kinetic data showed that rRgpAH and RgpB have similar properties in the absence of glycylglycine, but differ in their responses to glycylglycine. Recombinant RgpA propeptide exhibited stronger inhibition on rRgpAH and RgpB compared to RgpB propeptide, possibly due to the divergent propeptide sequences.
SCIENTIFIC REPORTS
(2023)
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)