Article
Biochemistry & Molecular Biology
Van-An Duong, Onyou Nam, EonSeon Jin, Jong-Moon Park, Hookeun Lee
Summary: Emiliania huxleyi, a cosmopolitan coccolithophore, was studied for the global discovery of post-translational modifications (PTMs) using a three-dimensional separation method combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Methylation was found to be the most frequent PTM, with lysine being the most frequently modified amino acid. The number of identified proteins increased by 22.5% after the PTM search, with some proteins showing a significant increase in intensity.
Review
Biochemistry & Molecular Biology
Gengjun Zhu, Lifang Jin, Wanchun Sun, Shuang Wang, Ning Liu
Summary: This review highlights the importance of post-translational modifications (PTMs) in colorectal cancer (CRC) and discusses their role in diagnosis, prognosis, and treatment. The review summarizes the proteomic profiling strategies for key PTMs and describes the methods used to delineate the global landscapes of each PTM. The review also discusses the current status of PTM research in CRC and provides future perspectives on the role of PTM regulation in translational medicine for CRC.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2022)
Review
Biochemistry & Molecular Biology
Juliane Hermann, Leon Schurgers, Vera Jankowski
Summary: Post-translational modifications play a key role in protein function and disease progression, but their reliable detection and quantification remain a challenge in clinical diagnosis. Mass spectrometry offers a solution, but its clinical translation still faces challenges.
MOLECULAR ASPECTS OF MEDICINE
(2022)
Article
Parasitology
Sebastian Miles, Javier Magnone, Joaquin Garcia-Luna, Sylvia Dematteis, Gustavo Mourglia-Ettlin
Summary: This study provides insights into the post-translational modifications (PTMs) of proteins in E. granulosus s.l., including the identification of new PTMs and the enzymes involved. These findings expand our knowledge on PTMs in platyhelminthes.
Article
Biochemical Research Methods
Elizabeth A. Mojica, Dietmar Kultz
Summary: This study developed a workflow for analyzing histone post-translational modifications (PTMs) in nonmodel organisms, and validated it in Mozambique tilapia. By using mass spectrometry methods, 214 biologically relevant histone PTMs were reliably quantified. The study found that 91.59% of histone PTMs were tissue-dependent. The developed workflow and tools are now publicly available for investigating the influence of environmental stress on histone PTMs in nonmodel organisms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Ji Woo Park, Matthew D. Tyl, Ileana M. Cristea
Summary: The regulation of mitochondria structure and function is crucial for viral infections. Post-translational modification of mitochondrial proteins plays a critical role in controlling energy metabolism, apoptosis, and immune signaling. Understanding these modifications and their effects is important for the development of therapeutic strategies.
Article
Plant Sciences
Jonas Giese, Juergen Eirich, Dirk Walther, Youjun Zhang, Ines Lassowskat, Alisdair R. Fernie, Marlene Elsaesser, Veronica G. Maurino, Markus Schwarzlaender, Iris Finkemeier
Summary: The transition from dark to light in the diurnal cycle causes significant physiological changes in plant metabolism, which require specific modes of regulation. While the activities of key metabolic enzymes regulated by light-dependent post-translational modifications (PTMs) have been extensively studied at the protein level, a comprehensive understanding of the global dynamics of light-dependent PTMs is lacking. In this study, we investigated the changes in the metabolome and proteome in Arabidopsis rosettes in response to light in a time-dependent manner, focusing on phosphorylation, lysine acetylation, and cysteine-based redox switches. Our findings revealed that over 1700 out of more than 24,000 detected PTM sites were altered during the transition from dark to light, with different compartments showing distinct PTM changes at different timepoints.
Review
Microbiology
Yiman Li, Zhihui Song, Ente Wang, Liming Dong, Jie Bai, Dong Wang, Jinyan Zhu, Chao Zhang
Summary: Invasive aspergillosis is a significant cause of death in patients with hematological malignancies and transplant recipients. Antifungal drug resistance has become a concern in managing infections, and understanding histone posttranslational modifications may provide insights for developing new antifungal drugs.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Daniel Salas-Lloret, Roman Gonzalez-Prieto
Summary: Ubiquitination and SUMOylation are dynamic post-translational modifications that regulate cellular processes. The understanding of these modifications has been increased by the development of mass spectrometry-based approaches. This translated article provides a concise overview of the basic mechanisms of ubiquitination and SUMOylation, as well as recent MS-based approaches for specific target identification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Roberta Noberini, Evelyn Oliva Savoia, Stefania Brandini, Francesco Greco, Francesca Marra, Giovanni Bertalot, Giancarlo Pruneri, Liam A. McDonnell, Tiziana Bonaldi
Summary: This study simplified the protein extraction process from low-amount clinical samples and developed a protocol that allows MS-based analysis of histone PTMs from laser microdissected tissue areas with as low as 1000 cells, which is approximately 500 times lower than what is required by available methods. This method opens the possibility for spatial epi-proteomics, facilitating the investigation of epigenetic features in tissue and tumor heterogeneity and aiding in the discovery of novel epigenetic biomarkers and mechanisms.
CLINICAL EPIGENETICS
(2021)
Article
Multidisciplinary Sciences
Rafael Fogaca de Almeida, Matheus Fernandes, Lyris Martins Franco de Godoy
Summary: Histone post-translational modifications (hPTMs) are abundant and varied in Trypanosoma cruzi, indicating potential conserved epigenetic functions. The comprehensive map of hPTMs provided by this study can serve as a basis for further research on epigenetic mechanisms and the development of epigenetic drugs against trypanosomatids.
Article
Food Science & Technology
Teodora Dukic, Katarina Smiljanic, Jelena Mihailovic, Ivana Prodic, Danijela Apostolovic, Shu-Hua Liu, Michelle M. Epstein, Marianne van Hage, Dragana Stanic-Vucinic, Tanja Cirkovic Velickovic
Summary: This study investigates the impact of peanut roasting on the post-translational modification (PTM) profiles of major peanut allergens. It finds that roasting can induce changes in certain PTMs, and Ara h 1 is the most modified major allergen in both raw and roasted samples.
Review
Chemistry, Multidisciplinary
Bingjie Zhang, Shanshan Li, Wenqing Shui
Summary: G protein-coupled receptors (GPCRs) are a large family of proteins that play significant roles in cellular and physiological responses. Post-translational modifications (PTMs) of GPCRs, such as glycosylation, phosphorylation, ubiquitination and palmitoylation, have important regulatory functions in receptor folding, biosynthesis, trafficking, dimerization and signaling. This review provides an overview of PTMs in GPCRs, focusing on their types, locations, cross talk and dynamic regulation, which can shed light on the molecular basis of GPCRs and contribute to structure-based drug discovery.
FRONTIERS IN CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Poornima Ramesh, Santosh Kumar Behera, Chinmaya Narayana Kotimoole, Varshasnata Mohanty, Rajesh Raju, T. S. Keshava Prasad, Jalaluddin Akbar Kandel Codi
Summary: Gastric cancers are characterized by late diagnosis and poor prognosis, and protein post-translational modifications (PTMs) have been associated with cancer development and metastasis. However, limited data is available on PTMs in gastric cancers. This study used an iterative searching strategy to analyze mass spectrometry data and identified 21,710 unique modification sites on 16,364 modified peptides. The majority of the altered PTMs/proteins were found in cytoskeletal and extracellular matrix proteins, which are known to be perturbed in gastric cancer.
Article
Multidisciplinary Sciences
Nathalie Kyalu Ngoie Zola, Clemence Balty, Sebastien Pyr dit Ruys, Axelle A. T. Vanparys, Nicolas D. G. Huyghe, Gaetan Herinckx, Manuel Johanns, Emilien Boyer, Pascal Kienlen-Campard, Mark H. Rider, Didier Vertommen, Bernard J. Hanseeuw
Summary: Tau isoforms in insoluble aggregates differ between tauopathies, but not in soluble brain extracts. This study characterizes the post-translational modifications of aggregated and soluble tau protein in various tauopathies, revealing specific soluble signatures for each tauopathy.
NATURE COMMUNICATIONS
(2023)
Article
Infectious Diseases
Jackson Alves da Silva Queiroz, Rita de Cassia Pontello Rampazzo, Ediva Basilio da Silva Filho, Gabriella Sgorlon Oliveira, Suyane da Costa Oliveira, Luan Felipo Botelho Souza, Soraya dos Santos Pereira, Moreno Magalhaes de Souza Rodrigues, Adriana Cristina Salvador Maia, Cicileia Correia da Silva, Aline Linhares Ferreira de Melo Mendonca, Celina Aparecida Bertoni Lugtenburg, Francisco de Assis Araujo Aguiar, Rosiane de Souza Soares Rodrigues, Caio Henrique Nemeth Santos, Alice Paula Di Sabatino Guimaraes, Fernando Rodrigues Maximo, Alcione de Oliveira dos Santos, Marco Aurelio Krieger, Juan Miguel Villalobos Salcedo, Deusilene Souza Vieira Dall'Acqua
Summary: This study aimed to develop a high-precision quantitative one-step RT-qPCR reaction that can quantify as few as 2.5 copies per reaction, showing 100% agreement with a qualitative RT-qPCR assay. The assay successfully quantified viral load in patients and accurately diagnosed negative cases in a population of 244 selected patients.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Bernardo Bonilauri, Marlon D. M. Santos, Amanda Caroline Camillo-Andrade, Saloe Bispo, Fabio C. S. Nogueira, Paulo C. Carvalho, Nilson I. T. Zanchin, Juliana de S. da G. Fischer
Summary: The delay in blood-processing time directly impacts the proteomic profile of human PBMC, possibly through granulocyte contamination and activation.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2021)
Article
Microbiology
Ueriton Dias de Oliveira, Fred Luciano Neves Santos, Bernardo Galvao-Castro, Marco Aurelio Krieger, Nilson Ivo Tonin Zanchin
Summary: This study successfully produced recombinant antigenic proteins derived from HTLV-1 and HTLV-2, highlighting the strong potential of HTLV-1 antigens for serological diagnosis of HTLV-1 infections. However, there was a high level of cross-reaction between HTLV-1-positive samples and HTLV-2 antigens, which can be attributed to the sequence conservation between the structural proteins of these two closely related viruses.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Gisele Fernanda Assine Picchi-Constante, Eloise Pavao Guerra-Slompo, Ana Carolina Tahira, Monica Visnieski Alcantara, Murilo Sena Amaral, Arthur Schveitzer Ferreira, Michel Batista, Cassiano Martin Batista, Samuel Goldenberg, Sergio Verjovski-Almeida, Nilson Ivo Tonin Zanchin
Summary: This study investigated the function of T. cruzi histone deacetylase 4 (TcHDAC4) and found that TcHDAC4 deficiency leads to chromatin alterations and abnormal gene expression regulation.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Martin Marek, Elizabeth Ramos-Morales, Gisele F. A. Picchi-Constante, Theresa Bayer, Carina Norstrom, Daniel Herp, Policarpo A. Sales-Junior, Eloise P. Guerra-Slompo, Kristin Hausmann, Alokta Chakrabarti, Tajith B. Shaik, Annika Merz, Edouard Troesch, Karin Schmidtkunz, Samuel Goldenberg, Raymond J. Pierce, Marina M. Mourao, Manfred Jung, Johan Schultz, Wolfgang Sippl, Nilson I. T. Zanchin, Christophe Romier
Summary: The zinc-dependent histone deacetylases in the protozoan parasite Trypanosoma cruzi have significantly diverged from their human counterparts, with tcDAC2 displaying essential deacetylase activity and major structural differences. Targeting these atypical HDACs can lead to selective chemical impairment of parasites.
Article
Multidisciplinary Sciences
Arthur Schveitzer Ferreira, Amanda Lopacinski, Michel Batista, Priscila Mazzocchi Hiraiwa, Beatriz Gomes Guimaraes, Nilson Ivo Tonin Zanchin
Summary: Epidermal growth factors (EGF) play important roles in various aspects, including embryogenesis, skin development, and immune response homeostasis. However, recombinant production of these factors in prokaryotic systems is challenging due to their structural organization. This study presents a reliable method for producing seven human growth factors of the EGF family in Escherichia coli, demonstrating their folded and stable conformation and high activity at low concentrations.
SCIENTIFIC REPORTS
(2022)
Article
Infectious Diseases
Natalia Erdens Maron Freitas, Emily Ferreira Santos, Leonardo Maia Leony, Angelo Antonio Oliveira Silva, Ramona Tavares Daltro, Larissa de Carvalho Medrado Vasconcelos, Gabriela Agra Duarte, Cristiane Oliveira da Mota, Edimilson Domingos Silva, Paola Alejandra Fiorani Celedon, Nilson Ivo Tonin Zanchin, Fred Luciano Neves Santos
Summary: The chimeric antigens IBMP-8.1, IBMP-8.2, IBMP-8.3, and IBMP-8.4 were evaluated in the double-antigen sandwich ELISA platform. The diagnostic performance of the DAgS-ELISA was promising, but improvements are being considered to increase its sensitivity.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Medicine, General & Internal
Emily Ferreira dos Santos, angelo Antonio Oliveira Silva, Natalia Erdens Maron Freitas, Leonardo Maia Leony, Ramona Tavares Daltro, Carlos Antonio de Souza Teles Santos, Maria da Conceicao Chagas de Almeida, Fernando Luiz Vieira de Araujo, Paola Alejandra Fiorani Celedon, Marco Aurelio Krieger, Nilson Ivo Tonin Zanchin, Mitermayer Galvao dos Reis, Fred Luciano Neves Santos
Summary: Chagas disease (CD) is a major cause of inability to donate blood. The current blood screening methods for anti-Trypanosoma cruzi antibodies have high false positive rates. A research group has developed four chimeric proteins that have shown high performance and low cross-reactivity rates. These proteins can be used to screen for CD in blood donations, reducing the risk of unnecessary blood disposal or T. cruzi transmission.
FRONTIERS IN MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Arthur Schveitzer Ferreira, Amanda Lopacinski, Michel Batista, Priscila Mazzocchi Hiraiwa, Natalia Fernanda Bueno, Beatriz Gomes Guimaraes, Nilson I. T. Zanchin
Summary: NRG1 is a growth factor family involved in signaling pathways of various normal cell types and human diseases. In this study, the hNRG1 alpha EGF domain was successfully expressed and purified in E. coli, demonstrating its high activity in cell proliferation and migration.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Giovanna Cesaro, Heloisa Tramontin da Soler, Eloise Pavao Guerra-Slompo, Ahmed Haouz, Pierre Legrand, Nilson Ivo Tonin Zanchin, Beatriz Gomes Guimaraes
Summary: Rrp44/Dis3 is a conserved eukaryotic ribonuclease that plays a role in processing and degradation of almost all types of RNA. Depletion of Rrp44 in Trypanosoma brucei blocks maturation of ribosomal RNA, leading to disruption of ribosome synthesis and inhibition of cell proliferation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Eloise Pavao Guerra-Slompo, Giovanna Cesaro, Beatriz Gomes Guimaraes, Nilson Ivo Tonin Zanchin
Summary: Trypanosoma brucei, a protozoan with fragmented large subunit rRNA, requires additional processing for the maturation of its LSU rRNA. TbRRP44, a nuclease, is essential for this maturation process, where its RNB domain and physical presence of the PIN domain play crucial roles. A new endonucleolytic cleavage site was identified in ITS1, and TbRRP44 is also involved in the degradation of 5'-ETS and part of ITS1 during the maturation of 18S rRNA 3'-end.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Infectious Diseases
Ramona Tavares Daltro, Emily Ferreira Santos, Angelo Antonio Oliveira Silva, Natalia Erdens Maron Freitas, Leonardo Maia Leony, Larissa Carvalho Medrado Vasconcelos, Alejandro Ostermayer Luquetti, Paola Alejandra Fiorani Celedon, Nilson Ivo Tonin Zanchin, Carlos Gustavo Regis-Silva, Fred Luciano Neves Santos
Summary: This study evaluated the diagnostic potential of four chimeric recombinant antigens for diagnosing chronic Chagas disease. The results showed that these antigens can effectively discriminate between T. cruzi-positive and -negative samples.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Biochemical Research Methods
Eloise Pavao Guerra-Slompo, Gisele Fernanda Assine Picchi-Constante, Martin Marek, Christophe Romier, Wolfgang Sippl, Nilson Ivo Tonin Zanchin
Summary: We present a combined in cellulo and in vivo approach to identify compounds with high potential for inhibiting Trypanosoma cruzi. The in cellulo assays consist of two phases - one for excluding inactive or toxic compounds and the other for determining IC50, CC50, and selective index (SI). Compounds with high SI are further tested in in vivo infection models to evaluate their efficacy compared to benznidazole, a reference drug for Chagas disease treatment. For more details, refer to Marek et al. (2021).
Article
Biochemical Research Methods
Gisele Fernanda Assine Picchi-Constante, Priscila Mazzocchi Hiraiwa, Martin Marek, Vanessa Zulkievicz Rogerio, Eloise Pavao Guerra-Slompo, Christophe Romier, Nilson Ivo Tonin Zanchin
Summary: This study presents a novel genetic complementation strategy for investigating gene function in Trypanosoma cruzi, the parasite responsible for Chagas disease. By combining CRISPR-Cas9 technology with recombination of resistant variants of the target gene containing desired mutations, detailed exploration of protein function is made possible. This experimental approach overcomes some of the limitations associated with traditional gene knockouts in T. cruzi.