Review
Biochemical Research Methods
Jan-Simon Behnke, Leonhard H. Urner
Summary: This article reviews the role of detergents in mass spectrometry for studying membrane proteins and highlights the importance of optimizing detergent chemistry and handling. It also introduces a new research direction: the optimization of mass spectrometry detergents for different applications in mass spectrometry-based membrane proteomics. The review focuses on qualitative design aspects, including their relevance in bottom-up proteomics, top-down proteomics, native mass spectrometry, and Nativeomics. In addition to established design aspects, such as charge, concentration, degradability, detergent removal, and exchange, detergent heterogeneity is identified as a promising driver for innovation. Rationalizing the role of detergent structures in membrane proteomics is expected to enable the analysis of challenging biological systems.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Urology & Nephrology
Claire E. Martin, Noah J. Phippen, Ava Keyvani Chahi, Manali Tilak, Sara L. Banerjee, Peihua Lu, Laura A. New, Casey R. Williamson, Mathew J. Platt, Jeremy A. Simpson, Mira Krendel, Nicolas Bisson, Anne-Claude Gingras, Nina Jones
Summary: This study reveals the distinct and complementary roles of Nck proteins in regulating podocyte adhesion, controlling GBM composition, and sustaining filtration barrier integrity.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2022)
Article
Multidisciplinary Sciences
Dongxue Zhang, Fan Yin, Qin Qin, Liang Qiao
Summary: Bacterial antimicrobial resistance (AMR) is a major challenge to current society, and understanding the molecular changes during bacterial self-saving responses can lead to new inhibition methods. This study used microfluidics mass spectrometry to identify metabolic changes in extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) during filamentation. The up-regulation of cyclic dinucleotide c-di-GMP, which is related to bacterial resistance and tolerance, was observed. By inhibiting the synthesis of c-di-GMP through a chemical inhibitor, the minimum inhibitory concentration of ceftriaxone against ESBL-E. coli was significantly decreased. This study uncovers molecular changes during bacterial filamentation and proposes a method to inhibit antibiotic-resistant bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Joseph Puccini, Jia Wei, Liang Tong, Dafna Bar-Sagi
Summary: Macropinocytosis is a nonselective endocytosis process that facilitates the uptake of extracellular fluid-phase cargoes. Tumor cells exploit this process to acquire macromolecules for cell growth and proliferation under nutrient-limiting conditions. This study reveals that the enzyme ATP citrate lyase (ACLY) is a key regulator of macropinocytosis, and it is involved in the actin cytoskeleton. The findings demonstrate a mechanism that links regional acetyl-CoA availability with dynamic protein acetylation, supporting the spatial and temporal modulation of membrane-cytoskeletal interactions required for macropinocytosis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Simon Czolkoss, Xenia Safronov, Sascha Rexroth, Lisa R. Knoke, Meriyem Aktas, Franz Narberhaus
Summary: Research has shown that the cell membranes of Agrobacterium tumefaciens contain specialized microdomains enriched with specific proteins related to cell envelope biogenesis, transport, secretion, bacterial motility and chemotaxis. Additionally, proteins associated with the pathogenicity of A. tumefaciens were found to be compartmentalized into these functional microdomains.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
J. Michael Henderson, Nina Ljubojevic, Sevan Belian, Thibault Chaze, Daryl Castaneda, Aude Battistella, Quentin Giai Gianetto, Mariette Matondo, Stephanie Descroix, Patricia Bassereau, Chiara Zurzolo
Summary: Tunnelling nanotubes (TNTs) are specialized actin-based protrusions that bridge distant cells to facilitate direct intercellular communication and cargo transfer in both physiological and pathological contexts. Linear actin filament elongation induced by Eps8 and IRSp53 is shown to promote functional and stable TNT formation. A micropatterning approach shows that TNTs originate via actin polymerization rather than cell dislodgement and exceed the length of conventional filopodia. Inhibition of Arp2/3 activity promotes functional TNT formation due to enhanced actin filament polymerization and elongation, suggesting a shift from branched to linear actin. An interaction between Eps8 and the I-BAR domain protein IRSp53 promotes formation of functional TNTs with an increased lifetime. Arp2/3 inhibition leads to reduction of Eps8 interactions with proteins facilitating actin filament depolymerization and turnover. Inhibition of branched actin networks reveals the role of linear actin filament polymerization in the formation of functional tunnelling nanotubes.
Review
Biochemistry & Molecular Biology
Meletia Kallianta, Eftychia Pappa, Heleni Vastardis, Christos Rahiotis
Summary: Mass Spectrometry (MS) is a highly sensitive and universal analytical technique that has rapidly developed in recent decades. It has various applications in dentistry, including research on dental materials and agents, laboratory analysis of biospecimens, and real-time diagnostics in oral surgery and pathology. MS can provide valuable insights into the clinical behavior, toxicity, antimicrobial properties, and biomarkers of dental materials and agents. It is also effective in detecting biomarkers in saliva and providing a comprehensive understanding of cellular functions through metabolite analysis. Additionally, MS shows promising potential for surgical approaches to oral malignant disorders. Overall, MS has revolutionized dental research and has the potential to advance personalized dentistry.
Article
Oncology
Monika Kmetova Sivonova, Zuzana Tatarkova, Jana Jurecekova, Jan Kliment, Mark Hives, Lucia Lichardusova, Peter Kaplan
Summary: Comparing the proteomic profiles of prostate tumors and benign prostatic hyperplasia tissues revealed ten different proteins potentially serving as biomarkers for prostate cancer. These proteins are involved in regulating actin dynamics, the cytoskeleton, and cell motility, suggesting they could be useful molecular targets for prostate cancer diagnostics and therapies. Verification through western blot and RT-PCR assays confirmed the observations obtained by proteomic analysis.
Article
Microbiology
Samuel I. de Jong, Dimitry Y. Sorokin, Mark C. M. van Loosdrecht, Martin Pabst, Duncan G. G. McMillan
Summary: Proteomics has advanced the understanding of microorganism biochemistry. The study focuses on the thermoalkaliphile Caldalkalibacillus thermarum TA2.A1 to investigate alkaliphiles' adaptation to extreme conditions. The research combines different proteomics methods to detect membrane proteins and reveals important metabolic pathways and transporters in C. thermarum TA2.A1.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Endocrinology & Metabolism
Siva S. V. P. Sakamuri, Venkata N. Sure, Lokanatha Oruganti, William Wisen, Partha K. Chandra, Ning Liu, Vivian A. Fonseca, Xiaoying Wang, Jennifer Klein, Prasad V. G. Katakam
Summary: Hypoglycemia affects the proteome of brain microvessels, potentially impairing cellular cytoskeleton and RNA processing.
JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM
(2023)
Article
Cell Biology
Ilijana Begcevic Brkovic, Madlen Reinicke, Soroth Chey, Ingo Bechmann, Uta Ceglarek
Summary: An analytical protocol for the quantitative assessment of sterol composition in microglia cell membrane microdomains was developed and validated. It was found that non-cholesterol sterols accounted for about 38% of the total sterol content in microglia membrane microdomains. Further studies are needed to clarify the impact of non-sterol composition changes on membrane fluidity and cell signaling.
Article
Biochemistry & Molecular Biology
Jessica H. van Wonderen, Jason C. Crack, Marcus J. Edwards, Thomas A. Clarke, Gerhard Saalbach, Carlo Martins, Julea N. Butt
Summary: Electrogenic bacteria transfer excess respiratory electrons to metal oxide particles and electrodes through the MtrCAB complex. The crystal structure of MtrCAB from S. baltica OS185 was resolved, and liquid chromatography mass spectrometry was used to determine the mass values of the three proteins in purified MtrCAB complexes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemical Research Methods
Masato Taoka, Kota Kamei, Akiko Kashima, Yuko Nobe, Takahiro Takekiyo, Takamasa Uekita, Tohru Ichimura
Summary: Many ion channels and receptor proteins are potential targets for new drugs. This study presents a novel proteomic sample preparation platform that allows for the processing of sub-microgram level starting materials using an ionic liquid-based sample preparation strategy and an in-StageTip technique. This approach enables the rapid solubilization and analysis of integral membrane proteins from human samples, surpassing the performance of conventional methods.
ANALYTICAL BIOCHEMISTRY
(2023)
Review
Cell Biology
Beatrice Benoit, Christian Pous, Anita Baillet
Summary: The cytoskeleton is composed of different structures, including actin microfilaments, microtubules, intermediate filaments, and recently studied dynamic assemblies such as septins and the ESCRT complex. These filament-forming proteins control various cell functions through interactions with each other and with membranes. Recent research has focused on understanding how septins bind to membranes and influence their properties and functions, either directly or indirectly through other cytoskeleton elements.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sumaiya Nazli, Kip D. Zimmerman, Angelica M. Riojas, Laura A. Cox, Michael Olivier
Summary: The proteomic analysis of plasma has great potential for precision medicine and biomarker identification. However, detecting and quantifying low abundance proteins in plasma is challenging. This study developed a mass spectrometry approach using tandem mass tags (TMT) and a tissue reference sample, which successfully identified and quantified numerous proteins in nonhuman primate plasma samples. The methodology promises to increase the number of putative disease biomarkers by efficiently quantifying plasma proteins released from specific tissues.
Article
Multidisciplinary Sciences
Elena Uyy, Viorel Suica, Raluca M. Boteanu, Aurel Cerveanu-Hogas, Luminita Ivan, Rune Hansen, Felicia Antohe
Summary: Non-apoptotic regulated cell death and DAMPs play important roles in the progression of atherosclerotic plaques, with inadequate response to lipid-lowering treatment. Dysregulation of certain proteins involved in non-apoptotic regulated cell death and associated DAMPs may contribute to the silent evolution of atherosclerosis and possess therapeutic potential.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Raluca Maria Boteanu, Viorel-Iulian Suica, Elena Uyy, Luminita Ivan, Aurel Cerveanu-Hogas, Razvan Gheorghita Mares, Maya Simionescu, Alexandru Schiopu, Felicia Antohe
Summary: This study investigates the effects of S100A9 blockade on the biological processes during recovery after myocardial infarction (MI). The results suggest that blockade of S100A9 regulates the expression of proteins involved in leukocyte cell-cell adhesion, muscle cell apoptosis, cardiac muscle hypertrophy, and other biological processes. It prevents compensatory hypertrophy and reduces post-ischemic stress in the heart.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Gastroenterology & Hepatology
Luminita Ivan, Elena Uyy, Viorel Suica, Raluca M. Boteanu, Aurel Cerveanu-Hogas, Rune Hansen, Felicia Antohe
Summary: This study used high performance mass spectrometry-based proteomics to investigate the effects of lipid accumulation on signaling pathways and liver proteome in a rabbit atherosclerotic model with hypercholesterolemia. The results showed that hyperlipidemia caused mitochondrial dysfunction, altered fatty acid metabolism, and induced local inflammation and liver steatosis and fibrosis through the release of alarmins. Lipid-lowering treatment was found to up-regulate the expression of certain proteins.
JOURNAL OF CLINICAL AND TRANSLATIONAL HEPATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Viorel Suica, Elena Uyy, Luminita Ivan, Raluca M. Boteanu, Aurel Cerveanu-Hogas, Rune Hansen, Felicia Antohe
Summary: Increased levels of low-density lipoproteins are the main risk factor in the initiation and progression of atherosclerosis. This study suggests that a specific panel of stress-sensing molecules (alarmins) may indicate the persistence of residual risk in silent atherosclerosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, Research & Experimental
Elena Georgiana Bernea, Elena Uyy, Doina-Andrada Mihai, Iuliana Ceausu, Constantin Ionescu-Tirgoviste, Viorel-Iulian Suica, Luminita Ivan, Felicia Antohe
Summary: This study analyzed the factors associated with insulin resistance and beta-cell dysfunction in the pathophysiology of GDM complicated with macrosomia. It also assessed the relationship between GDM with macrosomia and various anthropometric, clinical, and paraclinical parameters.
EXPERIMENTAL AND THERAPEUTIC MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Elena G. Bernea, Viorel Suica, Elena Uyy, Aurel Cerveanu-Hogas, Raluca M. Boteanu, Luminita Ivan, Iuliana Ceausu, Doina A. Mihai, Constantin Ionescu-Tirgoviste, Felicia Antohe
Summary: This study found that the protein composition of serum exosomes in gestational diabetes mellitus (GDM) patients is associated with inflammation and vascular dysfunction. Pathways related to complement and coagulation cascades, platelet activation, prothrombotic factors, and cholesterol metabolism may play important roles in the pathophysiology of GDM.