Article
Plant Sciences
Therese C. Rytz, Juanjuan Feng, Jessica A. S. Barros, Richard D. D. Vierstra
Summary: The reversible conjugation of SUMO to other proteins plays an important role in plant development and stress defense. SUMO can be further modified by SUMOylation and ubiquitylation, but the functions of these modifications are not well understood. By replacing the essential SUMO isoforms with a lysine-null variant, the researchers found that these secondary modifications are involved in stress defense, DNA repair, and hormone signaling. The study also generated a new tool for investigating SUMO in plants.
Review
Biochemistry & Molecular Biology
Lingkuan Meng, Wai-Sum Chan, Lei Huang, Linjing Liu, Xingjian Chen, Weitong Zhang, Fuzhou Wang, Ke Cheng, Hongyan Sun, Ka -Chun Wong
Summary: This paper reviews the recent works in deep learning for identifying various types of PTMs and discusses PTM databases and future research directions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biology
Zhenkai Dai, Kayvan Etebari, Sassan Asgari
Summary: The analysis of m(6)A RNA modifications in the mosquito transcriptome and their changes during dengue virus infection provides insights into the role of epigenetics in regulating viral replication in mosquitoes.
COMMUNICATIONS BIOLOGY
(2022)
Review
Cell Biology
Fredrik Trulsson, Alfred C. O. Vertegaal
Summary: This review discusses the biological importance of site-specific modifications by ubiquitin and SUMO in regulating the DNA damage response, protein quality control, and cell cycle progression. The review also explores the machinery responsible for these modifications and methods to identify ubiquitin and SUMO modified sites. The authors emphasize the need for further innovation in the field to address challenges and long-standing questions.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Krishna M. Chauhan, Yingxiao Chen, Yiyi Chen, Andrew T. Liu, Xiao-Xin Sun, Mu-Shui Dai
Summary: The study reveals that SENP1 is a critical p53 deSUMOylating enzyme, and its depletion induces p53 transactivation activity and synergizes with DNA damage-inducing agent etoposide to activate p53 and inhibit cancer cell growth.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Xiaoxia Shi, Yixin Du, Shujing Li, Huijian Wu
Summary: SUMOylation, a reversible post-translational modification process, plays crucial roles in cell physiology, including cell cycle regulation, DNA damage repair, and protein trafficking and turnover. Dysregulated SUMO E3 ligases may be associated with the occurrence and development of cancers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Oncology
Ana Gonzalez-Garcia, Antonio Garrido, Ana C. Carrera
Summary: Genetic alterations in the PI3-kinase/PTEN pathway are common in cancer cells. Current efforts to treat PTEN-dependent tumors mainly focus on PI3-kinase inhibition, but modulating PTEN post-translational modifications could provide alternative therapeutic strategies.
Article
Biochemical Research Methods
Hauh-Jyun Candy Chen, Yan-Ling Liao
Summary: Although malondialdehyde and methylglyoxal have the same molecular formula, they have different chemistry in forming protein adducts. The major lysine adduct of malondialdehyde in hemoglobin is the N-propenal type, while that of methylglyoxal is N6-(1-carboxyethyl)lysine. This Letter provides evidence that the methylglyoxal-like hemoglobin adducts are not derived from malondialdehyde. This Letter also discusses the quantification of malondialdehyde-induced post-translational modifications in human hemoglobin by different mass spectrometry-based methods.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Microbiology
Junping Li, Libin Liang, Li Jiang, Qian Wang, Xia Wen, Yuhui Zhao, Pengfei Cui, Yaping Zhang, Guangwen Wang, Qibing Li, Guohua Deng, Jianzhong Shi, Guobin Tian, Xianying Zeng, Yongping Jiang, Liling Liu, Hualan Chen, Chengjun Li
Summary: Our study demonstrates the vital role of PB1 K612 SUMOylation in the pathogenesis and transmission of IAVs, providing a potential target for anti-influenza therapies. The SUMOylation at K612 is crucial for PB1 to efficiently bind viral RNA, facilitating the transcription and replication of the viral genome.
Article
Plant Sciences
Reetu Singh, Monika Mahajan, Sheetal Das, Vinay Kumar
Summary: Post-translational modification, such as the small ubiquitin-like modification (SUMOylation), plays a crucial role in various cellular signaling events and environmental stress responses in plants. SUMOylation has been shown to regulate plant growth and development, as well as defense against pathogens. This review provides insight into the SUMO conjugation machinery and its isoforms, and their potential roles in cellular processes and stress conditions in plants. Understanding SUMOylation mechanisms can contribute to the development of stress tolerance and resistance mechanisms.
SOUTH AFRICAN JOURNAL OF BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Fang Yu, Jiangbo Wei, Xiaolong Cui, Chunjie Yu, Wei Ni, Jorg Bungert, Lizi Wu, Chuan He, Zhijian Qian
Summary: The RNA demethylase ALKBH5 serves as a key regulator in protecting cells from DNA damage and apoptosis during ROS-induced stress. ROS induces global mRNA N-6-methyladenosine levels by modulating ALKBH5 post-translational modifications, leading to the rapid induction of genes involved in DNA damage repair. Additionally, ROS activates the ERK/JNK/ALKBH5-PTMs/m(6)A axis in hematopoietic stem/progenitor cells in mice, indicating a physiological role of this pathway in maintaining genome stability.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Plant Sciences
Shumei Fang, Xue Hou, Xilong Liang
Summary: SUMOylation is a crucial posttranslational modification in eukaryotes, involved in metabolic regulation under various stresses. SIZ1, a SUMO E3 ligase, plays a vital role in substrate-specific recognition and facilitates the binding of SUMO proteins to target proteins. This review provides insights into the characteristics of SUMOylation and the role of SIZ1 in plant adaptation to abiotic stresses, offering valuable references for crop improvement and future research on plant responses to environmental stress.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Article
Multidisciplinary Sciences
Robert V. Williams, Chin Huang, Connor McDermott, Tanvir Ahmed, Linda Columbus, Kelley W. Moremen, James H. Prestegard, I. Jonathan Amster
Summary: This study demonstrates the kinetics of glycan addition by the OST-B enzyme and suggests that the order and efficiency of posttranslational glycosylation are influenced by steric cross-talk between adjoining acceptor sites. The findings provide insight into the function of these important enzymes and the site-specific recognition of glycosylation sequons by OST-B.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Kinga Gostomska-Pampuch, Jacek R. Wisniewski, Karol Sowinski, Wieslaw Gruszecki, Andrzej Gamian, Magdalena Staniszewska
Summary: The study found that the glycation product MAGE, generated from the reaction of melibiose with a protein, is more efficiently formed under dry conditions compared to aqueous conditions. Different structures of myoglobin with melibiose were identified, including crosslinking and non-crosslinking modifications. The results suggest that MAGE adduct is initiated by coupling melibiose to a model myoglobin protein and can further rearrange into more advanced structures.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Andrada-Maria Birladeanu, Malgorzata Rogalska, Myrto Potiri, Vasiliki Papadaki, Margarita Andreadou, Dimitris L. Kontoyiannis, Joe D. Lewis, Zoi Erpapazoglou, Panagiota Kafasla
Summary: The cytosolic scaffold protein IQGAP1 regulates the subnuclear localization of spliceosome components and assists in stress-related splicing mechanisms in gastric cancer cells. It co-regulates cell cycle-related RNA splicing with hnRNPM, promoting gastric cancer cell proliferation. The study reveals a previously unknown link between stress signals and alternative splicing regulation.
Article
Gastroenterology & Hepatology
Sumit Kumar, Mark J. A. Schoonderwoerd, Jessie S. Kroonen, Ilona J. de Graaf, Marjolein Sluijter, Dina Ruano, Roman Gonzalez-Prieto, Matty Verlaan-de Vries, Jasper Rip, Ramon Arens, Noel F. C. C. de Miranda, Lukas J. A. C. Hawinkels, Thorbald van Hall, Alfred C. O. Vertegaal
Summary: The pharmacological inhibition of the SUMO pathway represents a potential strategy for targeting PDAC by inhibiting cancer cell cycle progression and activating anti-tumor immunity through interferon signaling. TAK-981, a novel small molecule inhibitor, has shown potential in reducing SUMOylation and inhibiting the proliferation of PDAC cells.
Review
Cell Biology
Fredrik Trulsson, Alfred C. O. Vertegaal
Summary: This review discusses the biological importance of site-specific modifications by ubiquitin and SUMO in regulating the DNA damage response, protein quality control, and cell cycle progression. The review also explores the machinery responsible for these modifications and methods to identify ubiquitin and SUMO modified sites. The authors emphasize the need for further innovation in the field to address challenges and long-standing questions.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Fredrik Trulsson, Vyacheslav Akimov, Mihaela Robu, Nila van Overbeek, David Aureliano Perez Berrocal, Rashmi G. Shah, Juergen Cox, Girish M. Shah, Blagoy Blagoev, Alfred C. O. Vertegaal
Summary: This study compares the regulatory effects of the proteasome and deubiquitinating enzymes (DUBs) on the ubiquitinated proteome. The authors find preferential sets of substrates regulated by DUBs or by the proteasome. Moreover, they find that PARP1 is hyper-ubiquitinated in response to DUB inhibition, which increases its enzymatic activity.
NATURE COMMUNICATIONS
(2022)
Review
Cell Biology
Alfred C. O. Vertegaal
Summary: Sumoylation is an essential post-translational modification that regulates many nuclear processes. Recent studies have revealed its roles in liquid-liquid phase separation, immunity, pluripotency, and disease, offering new therapeutic opportunities.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yara Huppelschoten, Rishov Mukhopadhyay, Jens Buchardt, Thomas E. E. Nielsen, Alfred C. O. Vertegaal, Huib Ovaa, Gerbrand J. van Der Heden J. van Noort
Summary: Researchers synthesized a large number of SUMO-based fluorescence polarization reagents to study enzyme preferences. Screening of five SENPs revealed differences in deconjugation activity and substrate preferences. The findings provide important evidence for understanding the mechanism of SENP-specific binding to SUMO.
Article
Cardiac & Cardiovascular Systems
Jurrien H. Kuneman, Sophie E. van Rosendael, Pieter van der Bijl, Alexander R. van Rosendael, Pieter H. Kitslaar, Johan H. C. Reiber, J. Wouter Jukema, Martin B. Leon, Nina Ajmone Marsan, Juhani Knuuti, Jeroen J. Bax
Summary: This study compared the pericoronary adipose tissue (PCAT) attenuation between acute coronary syndrome and stable coronary artery disease patients. The results showed that the PCAT attenuation in culprit lesion precursors of acute coronary syndrome patients was significantly higher than nonculprit lesions and lesions of stable coronary artery disease patients. Therefore, PCAT attenuation may be a novel marker for identifying high-risk plaques.
CIRCULATION-CARDIOVASCULAR IMAGING
(2023)
Article
Biochemistry & Molecular Biology
Tariq O. Faquih, N. Ahmad Aziz, Sarah L. Gardiner, Ruifang Li-Gao, Renee de Mutsert, Yuri Milaneschi, Stella Trompet, J. Wouter Jukema, Frits R. Rosendaal, Astrid van Hylckama Vlieg, Ko Willems van Dijk, Dennis O. Mook-Kanamori
Summary: Based on the data from three European cohorts, this study found that non-pathogenic CAG repeat sizes below 36 in the HTT gene are associated with abnormal metabolite levels, which may be mediated through lower BMI.
HUMAN MOLECULAR GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Muhanad Ali, Miriam E. van Gent, Amy M. de Waal, Bjorn R. van Doodewaerd, Erik Bos, Roman I. Koning, Robert A. Cordfunke, Jan Wouter Drijfhout, Peter H. Nibbering
Summary: The formulation of SAAP-148 in PLGA nanoparticles improves its selectivity index and enables sustained release of the peptide. The nanoparticles exhibit favorable physiochemical properties and demonstrate increased activity against antimicrobial resistant bacteria and biofilms over time. This suggests that SAAP-148 nanoparticles have promising potential as a treatment for bacterial infections.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Correction
Multidisciplinary Sciences
Sarah Tessier, Omar Ferhi, Marie-Claude Geoffroy, Roman Gonzalez-Prieto, Antoine Canat, Samuel Quentin, Marika Pla, Michiko Niwa-Kawakita, Pierre Bercier, Domitille Rerolle, Marilyn Tirard, Pierre Therizols, Emmanuelle Fabre, Alfred C. O. Vertegaal, Hugues de The, Valerie Lallemand-Breitenbach
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Bharath Sampadi, Sylvia Vermeulen, Branislav Misovic, Jan J. J. Boei, Tanveer S. S. Batth, Jer-Gung Chang, Michelle T. T. Paulsen, Brian Magnuson, Joost Schimmel, Hanneke Kool, Cyriel S. S. Olie, Bart Everts, Alfred C. O. Vertegaal, Jesper V. V. Olsen, Mats Ljungman, Penny A. A. Jeggo, Leon H. F. Mullenders, Harry Vrieling
Summary: In this study, using temporal multi-omic systems analyses, it was found that the DNA damage response (DDR) displayed dose proportionality, but many other molecular and cellular responses did not. Additionally, a novel mode of phospho-signaling and large-scale dephosphorylation events that regulate mitotic exit control and the G2/M checkpoint were uncovered. Furthermore, after low dose radiation exposure, reactive oxygen species and antioxidant defense were prominently activated, while DDR genes were prominently activated after high dose radiation.
Article
Pharmacology & Pharmacy
Miriam E. E. van Gent, Tom van Baaren, Sylvia N. N. Klodzinska, Muhanad Ali, Natasja Dolezal, Bjorn R. R. van Doodewaerd, Erik Bos, Amy M. M. de Waal, Roman I. I. Koning, Jan Wouter Drijfhout, Hanne Morck Nielsen, Peter H. H. Nibbering
Summary: Synthetic antibacterial and antibiofilm peptide (SAAP)-148 is an alternative treatment for chronic wound infections, but its therapeutic potential is limited due to its peptidic nature and cytotoxicity. Encapsulation of SAAP-148 in nanogels composed of OSA-modified HA overcomes these limitations. The formulated SAAP-148-loaded nanogels sustainably release the peptide and exhibit antimicrobial activity without cytotoxicity.
Article
Cardiac & Cardiovascular Systems
Alberico L. Catapano, Raffaele De Caterina, J. Wouter Jukema, Robert Klempfner, Ulf Landmesser, Francois Schiele, Alessandro Sionis
Summary: The ACS EuroPath III project was conducted to improve LDL-C management for post-ACS patients. Five areas of improvement were identified, including developing a standardized GP discharge letter and treatment algorithm.
CLINICAL CARDIOLOGY
(2023)
Article
Oncology
Jessie S. Kroonen, Ilona J. de Graaf, Sumit Kumar, Dennis F. G. Remst, Anne K. Wouters, Mirjam H. M. Heemskerk, Alfred C. O. Vertegaal
Summary: Combination therapies using SUMO inhibition and DNA hypomethylation can effectively reduce cell proliferation in MYC-driven hematopoietic malignancies. In vivo experiments also showed promising results in reducing tumor growth with the combined treatment. Tailored combination therapies based on molecular mechanisms have the potential to improve cancer treatment efficacy.
Article
Infectious Diseases
Colin Bournez, Martijn Riool, Leonie de Boer, Robert A. Cordfunke, Leonie de Best, Remko van Leeuwen, Jan Wouter Drijfhout, Sebastian A. J. Zaat, Gerard J. P. van Westen
Summary: To combat infection, host organisms possess defense peptides, including antimicrobial peptides (AMPs), which can target a wide range of pathogenic microorganisms. Researchers have developed a machine learning model called CalcAMP that can predict the activity of AMPs. This model can help in identifying potential short AMPs quickly, which can be an effective solution to the growing issue of multi-drug resistance. CalcAMP is based on a new data set constructed from available public data on AMPs and experimental antimicrobial activities, and it can predict activity against both Gram-positive and Gram-negative bacteria.
Article
Multidisciplinary Sciences
Laura A. Claessens, Matty Verlaan-de Vries, Ilona J. de Graaf, Alfred C. O. Vertegaal
Summary: The SUMO protease SENP6 plays a crucial role in maintaining genomic stability by disassembling SUMO2/3 polymers from DNA damage response proteins, preventing their trapping at sites of DNA damage and nuclear condensates.
NATURE COMMUNICATIONS
(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)
