Article
Multidisciplinary Sciences
Joan Blanco-Fernandez, Alexis A. Jourdain
Summary: This article presents a protocol for isolating high-quality mitochondria from primary cells and tissues. The method involves mechanical homogenization and differential centrifugation to isolate crude mitochondria, followed by tag-free immune capture to obtain pure organelles and remove contaminants. The mitochondrial proteins from each purification stage are analyzed by quantitative mass spectrometry, enabling the discovery of novel mitochondrial proteins through subtractive proteomics. This protocol offers a sensitive and comprehensive approach to studying mitochondrial content in cell lines, primary cells, and tissues.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2023)
Article
Chemistry, Analytical
Sam B. Choi, Abigail M. Polter, Peter Nemes
Summary: The integration of patch-clamp electrophysiology with high-resolution mass spectrometry enables the identification and quantification of proteins within neurons. By improving sample processing and detection methods, the study was able to detect approximately 275 different proteins in somal aspirates from cultured neurons.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Dirk F. Moore, David E. Sleat, Peter Lobel
Summary: Knowledge of cellular location is crucial for understanding protein function. Subcellular fractionation followed by mass spectrometry is a commonly used method for assigning cellular locations to proteins. However, proteins can reside in multiple compartments, which requires a more accurate method for localization. In this article, the constrained proportional assignment (CPA) method is introduced, along with data transformations and R-based programs for analyzing subcellular proteomics data.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Chemistry, Multidisciplinary
Qiuxin Zhang, Weiyi Tan, Bing Xu
Summary: Enzymatic noncovalent synthesis (ENS) is a mechanism that utilizes enzymatic reactions to produce spatially organized higher-order supramolecular assemblies, which can modulate cellular processes. This Review highlights the recent progress in the application of ENS for targeted subcellular organelles, showcasing its potential in understanding diseases, controlling cell behaviors, and developing new therapeutics.
Article
Pharmacology & Pharmacy
Haifeng Hu, Peng Li, Jie Qiu, Meiji Zhao, Mingjie Kuang, Zhaoyan Zhang, Dachuan Wang
Summary: This study used two-photon laser confocal microscopy to analyze the uptake and subcellular distribution of red fluorescent graphene quantum dots (Red-GQDs) in HeLa cells and discussed their effects on cell metabolism. The results showed that Red-GQDs were well-absorbed by HeLa cells and distributed in lysosomes and mitochondria in a time-dependent manner. Additionally, Red-GQDs significantly affected cell functions, inducing autophagy at low concentrations and promoting cell death and exosome secretion at high concentrations.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Maria J. Sarmento, Alicia Llorente, Toni Petan, Denis Khnykin, Iuliana Popa, Matea Nikolac Perkovic, Marcela Konjevod, Morana Jaganjac
Summary: Lipids in cell membranes and subcellular compartments are important for cellular processes, and specific organelle lipidomes are characterized by lipid synthesis, metabolism, trafficking, and homeostasis. Identifying the lipid fingerprints of cellular organelles has been challenging due to the variety and complexity of lipids, and the variability in their abundance. This review summarizes the available information on the lipid composition of mammalian cell organelles and discusses the dynamics of subcellular lipidomes under physiological and pathological conditions, as well as the challenges in mapping organelle lipidomes.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Review
Plant Sciences
Jiahui Bian, Xiao Su, Xiaoyan Yuan, Yuan Zhang, Jinxing Lin, Xiaojuan Li
Summary: This review focuses on the structural organization, dynamics, and physiological functions of membrane contact sites between the endoplasmic reticulum and various organelles, particularly in plants. Membrane contact sites play a vital role in development and response to stress by facilitating highly dynamic and organized interactions among organelles. The endoplasmic reticulum acts as an architectural scaffold to maintain the spatial distribution of other membrane-bound organelles. Future research directions related to membrane contact sites are also discussed.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemical Research Methods
Martin Rusilowicz, David W. Newman, Declan R. Creamer, James Johnson, Kareena Adair, Victoria M. Harman, Chris M. Grant, Robert J. Beynon, Simon J. Hubbard
Summary: Protein quantitation via mass spectrometry requires the use of peptide proxies, and accurate quantitation often relies on the addition of an external standard. AlacatDesigner is a tool that assists in selecting suitable peptide candidates for recombinant protein standards. It considers factors such as target protein, existing databases, literature occurrence, potential post-translational modifications, and ionization potential within the mass spectrometer.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Qi Guo, Lei Liu, Won C. Yim, John C. Cushman, Bronwyn J. Barkla
Summary: The study utilized Free Flow Electrophoresis for high-resolution membrane fractionation of plant leaf tissue, combined with mass spectrometry-based proteomics, allowing simultaneous profiling of multiple cellular membranes. Comparison of protein profiles of fractionated membranes with known cellular compartment markers revealed protein functions and provided new evidence for multiple subcellular localizations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Chuankai Zhou
Summary: A major recent advance in cell biology is the understanding of the mechanisms and dynamics of biogenesis of membrane-less condensates. These condensates interact with membrane-bound organelles and are regulated by cellular signaling, metabolic states, and proteostasis network.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Analytical
Siyuan Qin, Yuxin Zhang, Yuan Tian, Fengguo Xu, Pei Zhang
Summary: Metabolomics, a technique profiling global small molecules in biological samples, has become crucial for disease diagnosis and mechanism research. Organelles in cells, where diverse metabolic activities happen orderly, play a significant role in various pathological conditions. Characterizing the metabolic pool in compartmentalized system is important for understanding the role of organelles in physiological functions and diseases.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2022)
Article
Cell Biology
Katharina Stillger, Ines Neundorf
Summary: Personal medicine aims to tailor diagnostics and treatments, especially in targeting intracellular sites of action. Peptides are being explored as delivery vehicles that can overcome the cell membrane and achieve the final intracellular destination. These tools allow modulation of a drug's pharmacological properties without compromising its biological activity, making them valuable for targeting protein-protein interactions (PPIs), a growing therapeutic focus. This review provides an update on recent advances in cell-permeable peptides targeting subcellular destinations, including chimeric peptide probes and peptides with inherent cell-permeability that are utilized in PPI targeting.
CELLULAR SIGNALLING
(2023)
Article
Cell Biology
Xiaowen Ma, Sharon Manley, Hui Qian, Yuan Li, Chen Zhang, Kevin Li, Benjamin Ding, Fengli Guo, Allen Chen, Xing Zhang, Meilian Liu, Meihua Hao, Benjamin Kugler, E. Matthew Morris, John Thyfault, Ling Yang, Hiromi Sesaki, Hong-Min Ni, Heidi McBride, Wen-Xing Ding
Summary: During hepatocyte dedifferentiation, a newly discovered intracellular organelle called the mitochondria-lysosome-related organelle (MLRO) plays a crucial role in regulating mitochondrial homeostasis. The MLRO is formed through the fusion of mitochondria-derived vesicles (MDVs) with lysosomes and is involved in mitochondrial protein degradation and hepatocyte dedifferentiation. This organelle, resembling damaged lysosomes, can be cleared by overexpression of the transcription factor EB (TFEB). The MLRO acts as an alternative mechanism for mitochondrial quality control during cell dedifferentiation, independent of canonical autophagy/mitophagy.
Article
Environmental Sciences
Yiteng Xia, Wen-Xiong Wang
Summary: Acute toxicity determination is crucial for ecological risk assessment. Traditional methods require large numbers of animals and take days to obtain results. A cell-based fluorescent assay was developed as an alternative, which allows visualization and quantification of subcellular responses, providing a faster and cheaper method for predicting the acute toxicity of sewage effluents.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Review
Plant Sciences
Xin Wang, Setsuko Komatsu
Summary: Climate change poses a threat to soybean production through reduced seed yield and quality. This review summarizes the morphophysiological changes in soybeans under abiotic stress and discusses cellular metabolisms and regulatory mechanisms in response to organellar stress using subcellular proteomics. The communication pathways involving reactive oxygen species scavenging, molecular chaperones, and phytohormone signals among subcellular compartments are highlighted. Given the complexity of climate change and plant limitations in coping with multiple abiotic stresses, a generic response involving calcium and abscisic acid signals in subcellular organelles is proposed. This review provides an overview of subcellular proteomics research on stressed soybeans and discusses the future potential of subcellular proteomics in enhancing climate-tolerant crops.
Article
Biochemical Research Methods
Vadim Demichev, Christoph B. Messner, Spyros I. Vernardis, Kathryn S. Lilley, Markus Ralser
Review
Biochemistry & Molecular Biology
Tom Smith, Eneko Villanueva, Rayner M. L. Queiroz, Charlotte S. Dawson, Mohamed Elzek, Erika C. Urdaneta, Anne E. Willis, Benedikt M. Beckmann, Jeroen Krijgsveld, Kathryn S. Lilley
CURRENT OPINION IN CHEMICAL BIOLOGY
(2020)
Article
Oncology
Johanna S. Rees, Lawrence C. C. Cheung, Samir W. Hamaia, Gareth Davies, Alan Sandercock, Kathryn S. Lilley, Natalie Tigue, Antony P. Jackson
INTERNATIONAL JOURNAL OF ONCOLOGY
(2020)
Correction
Multidisciplinary Sciences
Michael A. S. Thorne, Nina Kocevar Britovsek, Liam Hawkins, Kathryn S. Lilley, Kenneth B. Storey
Article
Biology
Siqi Fang, Paul D. W. Kirk, Marcus Bantscheff, Kathryn S. Lilley, Oliver M. Crook
Summary: Thermal proteome profiling is a method for monitoring protein thermal stability that can provide insights into protein function, drug targets, and off-targets. The use of Bayesian functional data analysis tools can improve sensitivity and identify new drug-protein associations.
COMMUNICATIONS BIOLOGY
(2021)
Review
Biochemical Research Methods
Josie A. Christopher, Aikaterini Geladaki, Charlotte S. Dawson, Owen L. Vennard, Kathryn S. Lilley
Summary: The internal environment of cells is crowded with molecules, requiring spatial organization through subcellular compartmentalization. These compartments provide specific conditions for molecules to carry out their biological functions, and molecules traffic between these compartments. Aberrant localization of proteins or RNA species is associated with various pathological conditions. Differential expression studies often overlook the importance of subcellular information, and subcellular transcriptomics and proteomics data do not always overlap, highlighting their complementary nature.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Letter
Biotechnology & Applied Microbiology
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser, Juri Rappsilber
NATURE BIOTECHNOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser, Juri Rappsilber
Article
Multidisciplinary Sciences
Vadim Demichev, Lukasz Szyrwiel, Fengchao Yu, Guo Ci Teo, George Rosenberger, Agathe Niewienda, Daniela Ludwig, Jens Decker, Stephanie Kaspar-Schoenefeld, Kathryn S. Lilley, Michael Muelleder, Alexey Nesvizhskii, Markus Ralser
Summary: The dia-PASEF technology utilizes ion mobility separation to reduce signal interference and enhance sensitivity in proteomic experiments. This study introduces a novel algorithm and software solution that significantly improves proteomic depth in dia-PASEF experiments, particularly for fast experiments and those with limited sample sizes.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Clarissa Braccia, Josie A. Christopher, Oliver M. Crook, Lisa M. Breckels, Rayner M. L. Queiroz, Nara Liessi, Valeria Tomati, Valeria Capurro, Tiziano Bandiera, Simona Baldassari, Nicoletta Pedemonte, Kathryn S. Lilley, Andrea Armirotti
Summary: This study investigates the impact of pharmacological rescue treatment on the proteome of a CF model. The results suggest that VX-809 treatment induces extensive structural and functional remodeling of mitochondria and peroxisomes. These findings are important for further understanding the therapeutic mechanisms and drug research of CF.
Article
Multidisciplinary Sciences
Oliver M. Crook, Colin T. R. Davies, Lisa M. Breckels, Josie A. Christopher, Laurent Gatto, Paul D. W. Kirk, Kathryn S. Lilley
Summary: The steady-state localisation and re-localisation of proteins are crucial for understanding their function and cellular dynamics, with high-throughput methods like BANDLE using Bayesian principles to accurately compute differential protein localisation probabilities upon cellular perturbation, reducing errors compared to existing approaches.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Alistair R. Hines, Matthew Edgeworth, Paul W. A. Devine, Samuel Shepherd, Nicholas Chatterton, Claire Turner, Kathryn S. Lilley, Xiaoyu Chen, Nicholas J. Bond
Summary: Antibody-drug conjugates (ADCs) have been widely developed, leading to new approvals and improved standard of care for cancer patients. This study describes the development of a mass-spectrometry-based method that can simultaneously monitor four quality attributes of ADCs, providing new insights into their properties and manufacturing processes. The study identified variations in thiol state, N-linked glycosylation, reduction of disulfide bonds, and polypeptide fragmentation in ADCs. The method offers a high-throughput approach to support the development of engineered antibody scaffolds.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Multidisciplinary Sciences
Nicola M. Moloney, Konstantin Barylyuk, Eelco Tromer, Oliver M. Crook, Lisa M. Breckels, Kathryn S. Lilley, Ross F. Waller, Paula MacGregor
Summary: This study maps the spatial proteomes of two African trypanosome species, Trypanosoma brucei and Trypanosoma congolense, providing insights into the molecular basis for diversity within and between these pathogen species. Comparative analysis reveals key routes of parasitic adaptation to different biological niches.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Claudius Marondedze, Ludivine Thomas, Kathryn S. Lilley, Chris Gehring
FRONTIERS IN MOLECULAR BIOSCIENCES
(2020)
Article
Biology
David-Paul Minde, Manasa Ramakrishna, Kathryn S. Lilley
COMMUNICATIONS BIOLOGY
(2020)
