Article
Multidisciplinary Sciences
Uwe Schulte, Fabian den Brave, Alexander Haupt, Arushi Gupta, Jiyao Song, Catrin S. S. Mueller, Jeannine Engelke, Swadha Mishra, Christoph Martensson, Lars Ellenrieder, Chantal Priesnitz, Sebastian P. P. Straub, Kim Nguyen Doan, Bogusz Kulawiak, Wolfgang Bildl, Heike Rampelt, Nils Wiedemann, Nikolaus Pfanner, Bernd Fakler, Thomas Becker
Summary: This study presents a quantitative mapping of mitochondrial protein assemblies using high-resolution complexome profiling. The results reveal the complex organization of mitochondrial protein assemblies involved in various cellular processes. It also identifies quality-control factors and elucidates a constitutive pathway for preprotein removal.
Review
Cell Biology
Alfredo Cabrera-Orefice, Alisa Potter, Felix Evers, Johannes F. Hevler, Sergio Guerrero-Castillo
Summary: Complexome profiling is an advanced method for studying the composition and abundance of protein complexes in biological samples, as well as their dynamics and the impact of mutations. It has been used to discover novel protein interactors and investigate pathophysiological mechanisms.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Petra Palenikova, Michael E. Harbour, Federica Prodi, Michal Minczuk, Massimo Zeviani, Anna Ghelli, Erika Fernandez-Vizarra
Summary: Complexome Profiling (CP) combines size separation of native multimeric complexes with protein identification by mass spectrometry (MS), resulting in protein abundance profiles for visual output of protein assembly status. Stable isotope labeling by amino acids in cell culture (SILAC) allows quantitative proteomics with duplexing in MS analysis and comparison of relative protein abundances between samples. The combination of SILAC and CP enables direct comparison of protein migration and abundance in mitochondrial respiratory chain complexes in different samples.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Biochemical Research Methods
Petra Palenikova, Michal Minczuk, Pedro Rebelo-Guiomar
Summary: This study presents a flexible setup for the analysis of dynamic macromolecular complexes in near-native conditions. The human mitochondrial ribosome was analyzed using density gradient ultracentrifugation coupled to quantitative mass spectrometry, providing standardized analysis of the complex.
Article
Biochemistry & Molecular Biology
Helene Roehricht, Joram Schwartzmann, Etienne H. Meyer
Summary: The mitochondrial ATP synthase, responsible for producing the energy needed for eucaryotic life, is structurally similar across species but exhibits some variations in plant-specific subunits. While assembly of this enzyme has been extensively studied in bacteria, yeast, and mammals, little is known about its assembly in plants. Through complexome profiling, researchers have identified assembly intermediates and proposed a model for the assembly pathway of plant mitochondria's ATP synthase, revealing that plant-specific subunits are also present in other organisms. This study demonstrates that the subunit composition and assembly pathway of plant mitochondria's ATP synthase are largely conserved with other mitochondrial enzymes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Multidisciplinary Sciences
Maik Pietzner, Eleanor Wheeler, Julia Carrasco-Zanini, Nicola D. Kerrison, Erin Oerton, Mine Koprulu, Jian'an Luan, Aroon D. Hingorani, Steve A. Williams, Nicholas J. Wareham, Claudia Langenberg
Summary: This study integrates two proteomic technologies to analyze the effects of protein quantitative trait loci, showing that each technique captures different aspects of protein biology. The results provide a benchmark for future cross-platform discoveries and highlight the inconsistency in genetically predicted effect directions between different assays.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Erika Fernandez-Vizarra, Sandra Lopez-Calcerrada, Luke E. Formosa, Rafael Perez-Perez, Shujing Ding, Ian M. Fearnley, Joaquin Arenas, Miguel A. Martin, Massimo Zeviani, Michael T. Ryan, Cristina Ugalde
Summary: The study of mitochondrial respiratory chain function in relation to its structural organization is essential for understanding eukaryotic cell metabolism. The complexome profiling technique has provided valuable information on the composition and assembly of MRC complexes, including larger supercomplexes and respirasomes. SCAFI plays a role in connecting individual MRC complexes III and IV, but is not the main player in respirasome formation as previously thought.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Food Science & Technology
Jivanka Mohan, Naeem Sheik Abdul, Savania Nagiah, Terisha Ghazi, Anil A. Chuturgoon
Summary: This study found that the mycotoxin FB2 produced by soil fungi can increase mitochondrial stress and promote mitophagy in human kidney cells.
Article
Biochemistry & Molecular Biology
Ochuko L. Erukainure, Nicholisha Narainpersad, Veronica F. Salau, Moganavelli Singh, Neil A. Koorbanally, Md. Shahidul Islam
Summary: The study explores the cytotoxic effect of the chemical fractions of Allium cepa on Human Embryonic Kidney cells. The ethyl acetate fraction showed cytotoxic effects, altering oxidative, inflammatory, and apoptotic activities in the cells. Further research is needed to assess the safety and potential risks associated with the use of Allium cepa.
JOURNAL OF FOOD BIOCHEMISTRY
(2021)
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
Biochemistry & Molecular Biology
Petra Palenikova, Michael E. Harbour, Shujing Ding, Ian M. Fearnley, Lindsey Van Haute, Joanna Rorbach, Rick Scavetta, Michal Minczuk, Pedro Rebelo-Guiomar
Summary: The method described utilizes density separation and mass spectrometric quantitation for quantitative analysis of native protein or ribonucleoprotein complexes, with the ComPrAn software package providing tools for data organization, analysis, and visualization. This technology can be applied to study the assembly and dynamic properties of macromolecular complexes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Biology
Barbara Uszczynska-Ratajczak, Sreedevi Sugunan, Monika Kwiatkowska, Maciej Migdal, Silvia Carbonell-Sala, Anna Sokol, Cecilia L. Winata, Agnieszka Chacinska
Summary: Most mitochondrial proteins are encoded by nuclear genes, synthesized in the cytosol, and targeted into the organelle. The presence of nuclear-encoded mRNA5 in the mitochondrial fraction confirms that large proteins with specific properties, like transmembrane domains, are predominantly encoded. Under proteostatic stress conditions, the population of transcripts on the mitochondrial surface is further restricted, allowing only the largest and most evolutionarily conserved proteins to be synthesized there.
LIFE SCIENCE ALLIANCE
(2022)
Article
Reproductive Biology
Chunxia Lu, Changbin Liu, Xieping Sun, Pengcheng Wan, Jianhong Ni, Limin Wang, Yong Ji, Yanhua Guo, Shouliang Lu
Summary: This study analyzed the codon bias of the ovPAG-7 gene and optimized it for improved expression efficiency in HEK293 cells. Predictions of the protein structure and function were made using bioinformatics tools, providing insights into the characteristics of ovPAG-7. The study successfully expressed the recombinant ovPAG-7 protein in HEK293 cells and identified important features such as glycosylation sites, epitopes, and secondary structure, which can facilitate functional research and antibody screening for ovPAG-7.
Article
Neurosciences
Juliet Goldsmith, Alban Ordureau, J. Wade Harper, Erika L. F. Holzbaur
Summary: This study reveals the importance of autophagy in maintaining neuronal health. By isolating autophagic vesicles and using proteomics, the researchers identified mitochondrial proteins as a major cargo engulfed in autophagosomes. They also found that nucleoid-associated proteins are enriched in autophagic engulfment of nucleoid-enriched mitochondrial fragments, and this process requires the mitochondrial fission machinery protein Drp1.
Article
Chemistry, Multidisciplinary
He Wang, Zhiting Wang, Hang Gao, Jianhui Liu, Zichun Qiao, Baofeng Zhao, Zhen Liang, Bo Jiang, Lihua Zhang, Yukui Zhang
Summary: This paper presents a photo-oxidation driven proximity labeling strategy for profiling the mitochondrial proteome with high spatiotemporal resolution in living cells. By selectively labeling mitochondrial proteins and quantifying their dynamics, this strategy provides solid technical support for the study of subcellular biology.
Article
Hematology
Oyindamola Christiana Adebayo, DieuMerci Kabasele Betukumesu, Agathe Bikupe Nkoy, Oluyomi Modupe Adesoji, Pepe Mfutu Ekulu, Lambertus P. Van den Heuvel, Elena N. Levtchenko, Veerle Labarque
Summary: The study found a high burden of kidney damage among Congolese children and provided evidence of the possible role of APOL1 and HMOX1 in making children more susceptible to kidney complications.
BRITISH JOURNAL OF HAEMATOLOGY
(2022)
Article
Pediatrics
Marloes A. H. M. Michels, Kioa L. Wijnsma, Roel A. J. Kurvers, Dineke Westra, Michiel F. Schreuder, Joanna A. E. van Wijk, Antonia H. M. Bouts, Valentina Gracchi, Flore A. P. T. Engels, Mandy G. Keijzer-Veen, Eiske M. Dorresteijn, Elena B. Volokhina, Lambertus P. W. J. van den Heuvel, Nicole C. A. J. van de Kar
Summary: The study provides an extensive description of the clinical and laboratory findings of an exclusively pediatric C3G cohort. The outcomes were relatively benign with persistent low C3 levels correlated with the presence of C3NeF, and C3GN was associated with higher sC5b-9 and lower properdin levels. Prospective studies are needed to further understand the pathogenic mechanisms of C3G and guide personalized medicine with complement therapeutics.
PEDIATRIC NEPHROLOGY
(2022)
Article
Endocrinology & Metabolism
Selma L. van Esveld, Richard J. Rodenburg, Fathiya Al-Murshedi, Eiman Al-Ajmi, Sana Al-Zuhaibi, Martijn A. Huynen, Johannes N. Spelbrink
Summary: In this study, two patients with a mutation in the SUPV3L1 gene were reported. They showed a neurodegenerative phenotype characterized by progressive spastic paraparesis, growth restriction, hypopigmentation, and predisposition to autoimmune disease. The mutation resulted in reduced expression of the truncated protein, decreased levels of mature mRNA, and accumulation of double-stranded RNA. Lentiviral complementation with the full-length SUPV3L1 gene partially restored the RNA abnormalities, indicating that the mutation is pathogenic and causes the disease.
JOURNAL OF INHERITED METABOLIC DISEASE
(2022)
Article
Transplantation
Mendy ter Avest, Romy N. Bouwmeester, Caroline Duineveld, Kioa L. Wijnsma, Elena B. Volokhina, Lambertus P. W. J. van den Heuvel, David M. Burger, Jack F. M. Wetzels, Nicole C. A. J. van de Kar, Rob ter Heine
Summary: This study evaluated the pharmacokinetics and pharmacodynamics of eculizumab in patients with atypical haemolytic uraemic syndrome (aHUS) and proposed improved dosing strategies. The study found that individualized dosing strategy could improve treatment response and reduce treatment costs by prolonging the dosing interval.
NEPHROLOGY DIALYSIS TRANSPLANTATION
(2023)
Review
Pediatrics
Tjessa Bondue, Lambertus van den Heuvel, Elena Levtchenko, Roland Brock
Summary: Inherited kidney diseases affect different nephron segments and can lead to kidney failure. Advances in genetic testing have increased our understanding of the molecular basis and pathophysiology of these diseases, revealing new potential therapeutic targets. RNA-based therapies, which have revolutionized molecular therapy, are now emerging in the field of kidney diseases.
PEDIATRIC NEPHROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Dirk J. W. den Braanker, Rutger J. H. Maas, Guido van Mierlo, Naomi M. J. Parr, Marinka Bakker-van Bebber, Jeroen K. J. Deegens, Pascal W. T. C. Jansen, Jolein Gloerich, Brigith Willemsen, Henry B. B. Dijkman, Alain J. J. van Gool, Jack F. M. Wetzels, Markus M. M. Rinschen, Michiel Vermeulen, Tom Nijenhuis, Johan van der Vlag
Summary: This study aimed to investigate the possible factors and mechanisms leading to recurrence of focal segmental glomerulosclerosis (FSGS) after kidney transplantation. It was found that a protein called perilipin-2 was significantly increased in infiltrating cells of patients' glomeruli and was associated with lipid droplet accumulation, suggesting it as a potential biomarker. Further research should focus on understanding how these factors alter lipid metabolism in podocytes and provide new treatment strategies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Pediatrics
Oyindamola C. C. Adebayo, Agathe B. B. Nkoy, Lambertus P. P. van den Heuvel, Veerle Labarque, Elena Levtchenko, Pierre Delanaye, Hans Pottel
Summary: This review explores the pathophysiological mechanisms of GHF in relation to various clinical conditions in the pediatric population. It discusses the role and mechanism of action of important factors such as gender, low birth weight, and race in the pathogenesis of GHF. Furthermore, it highlights the consequences of GHF in the progression of kidney disease.
PEDIATRIC NEPHROLOGY
(2023)
Review
Pediatrics
Agathe B. Nkoy, Pepe M. Ekulu, Veerle Labarque, Lambertus P. van den Heuvel, Elena N. Levtchenko
Summary: HIV infection remains a significant health threat globally, especially in children living in resource-limited settings. Limited access to ART in sub-Saharan Africa puts HIV-infected children at risk of developing HIVAN without appropriate treatment.
PEDIATRIC NEPHROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Federica Conte, Angel Ashikov, Rachel Mijdam, Eline G. P. van de Ven, Monique van Scherpenzeel, Raisa Veizaj, Seyed P. Mahalleh-Yousefi, Merel A. Post, Karin Huijben, Daan M. Panneman, Richard J. T. Rodenburg, Nicol C. Voermans, Alejandro Garanto, Werner J. H. Koopman, Hans J. C. T. Wessels, Marek J. Noga, Dirk J. Lefeber
Summary: Phosphoglucomutase 1 (PGM1) is a key enzyme involved in energy metabolism and its deficiency causes a wide range of symptoms. D-galactose supplementation has been shown to improve some symptoms, but its effects on skeletal muscle and heart remain unclear. In this study, a muscle cell model for PGM1 deficiency was established, which revealed that D-galactose failed to restore the reduced energy production capacity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Esther Willems, Jolein Gloerich, Anouk Suppers, Michiel van der Flier, Lambert P. van den Heuvel, Nicole van de Kar, Ria H. L. A. Philipsen, Maurice van Dael, Myrsini Kaforou, Victoria J. Wright, Jethro A. Herberg, Federico Martinon Torres, Michael Levin, Ronald de Groot, Alain J. van Gool, Dirk J. Lefeber, Hans J. C. T. Wessels, Marien I. de Jonge
Summary: Mechanisms of infection and pathogenesis have mainly focused on differential gene or protein expression, with less emphasis on posttranslational modifications. In this study, a novel glycoproteomics approach was applied to investigate systemic proteome-wide glycosylation in response to infection. Through characterization of site-specific protein glycosylation in plasma samples from controls and patients, a glycopeptide signature was identified that could significantly differentiate between bacterial and viral infections. Additionally, machine learning algorithm-based analysis demonstrated the ability to identify the causative pathogens based on distinct host blood plasma glycopeptide signatures. These findings highlight the potential of glycoproteomics as an innovative approach to enhance the interpretation of relevant biological changes during infection.
Meeting Abstract
Pediatrics
Oyindamola C. Adebayo, Cheng Cheng, Agathe B. Nkoy, Pepe M. Ekulu, Lambertus P. Van Den Heuvel, Elena Levtchenko, Veerle Labarque
PEDIATRIC NEPHROLOGY
(2022)
Meeting Abstract
Pediatrics
Sante Princiero Berlingerio, Sarah Tassinari, Tjessa Bondue, Marc Fransen, Benedetta Bussolati, Lambertus Van Den Heuvel, Elena Levtchenko
PEDIATRIC NEPHROLOGY
(2022)
Meeting Abstract
Pediatrics
Tjessa Bondue, Lambertus Van Den Heuvel, Rik Gijsbers, Roland Brock, Elena Levtchenko
PEDIATRIC NEPHROLOGY
(2022)
Meeting Abstract
Pediatrics
Agathe Nkoy, Ndiyo Yoly, Matoka Therance, Odio Matondo, Betukumesu Dieumerci, Kazadi Orly, Veerle Labarque, Lambertus P. Van Den Heuvel, Levtchenko Elena, Ekulu Pepe
PEDIATRIC NEPHROLOGY
(2022)