Article
Microbiology
Hailin Zheng, Nana Song, Xiaowei Zhou, Huan Mei, Dongmei Li, Xiaofang Li, Weida Liu
Summary: The study examined the biological impact of lysine 2-hydroxyisobutyrylation on Candida albicans, identifying 1,438 Khib-modified proteins with various cellular functions. Functional enrichment analysis revealed significant pathways like ribosome biogenesis and carbon metabolism being affected by Khib modification, suggesting a potential role in regulating protein translation in this fungal pathogen.
Article
Neurosciences
Maria Bichmann, Nuria Prat Oriol, Ebru Ercan-Herbst, David C. Schoendorf, Borja Gomez Ramos, Vera Schwaerzler, Marie Neu, Annabelle Schlueter, Xue Wang, Liang Jin, Chenqi Hu, Yu Tian, Janina S. Ried, Per Haberkant, Laura Gasparini, Dagmar E. Ehrnhoefer
Summary: This study identified novel lysine methylation events on Tau protein in human Alzheimer's disease (AD) brain tissue and a mouse model of Tauopathy, demonstrating that methylated Tau levels increase with Tau pathology stage. Methylated Tau is enriched in soluble brain extracts, preferentially localizes to the cell soma and nuclear fractions, and is not associated with hyperphosphorylated, high molecular weight Tau species. The identification of SETD7 as a novel lysine methyltransferase for Tau suggests that methylated Tau may play a role in translocation to different subcellular compartments, shedding light on disease-associated phenomena related to Tau mislocalization.
MOLECULAR NEURODEGENERATION
(2021)
Review
Biochemistry & Molecular Biology
Juan Liu, Cen Zhang, Xue Wang, Wenwei Hu, Zhaohui Feng
Summary: p53 is a key tumor suppressor and is involved in various physiological and pathological processes. TRIM proteins, characterized by specific domains, play important roles in regulating fundamental biological processes. There is a cross-talk between p53 and TRIM proteins, impacting cellular processes, cancer, and other diseases.
Review
Pharmacology & Pharmacy
Samarth Dwivedi, Atharva Chavan, Atish T. Paul
Summary: This review focuses on the role of SET7 in the onset and progression of diabetic nephropathy (DN), and its potential as a therapeutic target to combat renal disorders.
DRUG DISCOVERY TODAY
(2023)
Article
Biotechnology & Applied Microbiology
Yibo Dong, Ping Li, Chao Chen
Summary: Lysine succinylation is a common post-translational modification that plays important roles in regulating protein structure and function, as well as cellular metabolism. A recent study investigated the effects of lysine succinylation on the growth, development, and physiology of paper mulberry. The results suggested that lysine-succinylated proteins may play key regulatory roles in metabolism, particularly in photosynthesis and oxidative phosphorylation.
Article
Chemistry, Multidisciplinary
Edgars Lakis, Sarolt Magyari, Jorn Piel
Summary: The study focuses on ribosomally synthesized and post-translationally modified peptides (RiPPs) and their untapped potential for protein engineering. The researchers report the incorporation of alpha-keto-beta-amino acids into proteins in E. coli using a family of enzymes that splice XYG sites in RiPPs. The approach offers new possibilities for introducing beta-amino acids or ketone-bearing moieties in chemical biology.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Chemistry, Multidisciplinary
Xin Li, Xiang David Li
Summary: The hereditary blueprint of a eukaryotic cell is encoded in genomic DNA compacted into chromatin with histone proteins. Histone posttranslational modifications (PTMs) regulate DNA-templated processes and are associated with human disease pathogenesis. The dynamic fluctuations of histone PTMs emphasize the importance of fully deciphering the histone code.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Agriculture, Multidisciplinary
Qibin Wu, Zhenxiang Li, Jingtao Yang, Fu Xu, Xueqin Fu, Liping Xu, Chuihuai You, Dongjiao Wang, Yachun Su, Youxiong Que
Summary: This study reports the first comprehensive analysis of protein lysine acetylation, 2-hydroxyisobutyrylation, and lysine lactylation in sugarcane. These post-translational modifications were found to be involved in energy metabolism and stress response. The results provide new insights into the molecular mechanisms of protein PTMs in sugarcane.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Microbiology
Yongqian Zhang, Nuomin Li, Qiushi Wei, Rui Min, Feng Liu, Fuli Wang, Yulin Deng
Summary: D. radiodurans is the most radioresistant organism known to date. Lysine acetylation, a highly conserved posttranslational modification, plays a crucial role in cellular regulation and may contribute to its extraordinary radioresistance. In this study, we used antibody enrichment technology and high-resolution liquid chromatography mass spectrometry to analyze the lysine acetylation of D. radiodurans. We identified 4,364 lysine acetylation sites on 1,410 proteins, making it the largest acetylome dataset reported for D. radiodurans. The acetylated proteins are involved in various metabolic pathways and DNA damage repair, suggesting the importance of lysine acetylation in the organism's robust resistance to radiation.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Erna Davydova, Tadahiro Shimazu, Maren Kirstin Schuhmacher, Magnus E. Jakobsson, Hanneke L. D. M. Willemen, Tongri Liu, Anders Moen, Angela Y. Y. Ho, Jedrzej Malecki, Lisa Schroer, Rita Pinto, Takehiro Suzuki, Ida A. Gronsberg, Yoshihiro Sohtome, Mai Akakabe, Sara Weirich, Masaki Kikuchi, Jesper V. Olsen, Naoshi Dohmae, Takashi Umehara, Mikiko Sodeoka, Valentina Siino, Michael A. McDonough, Niels Eijkelkamp, Christopher J. Schofield, Albert Jeltsch, Yoichi Shinkai, Pal O. Falnes
Summary: Post-translational methylation, specifically protein histidine methylation, is crucial for optimizing protein function. METTL9 is identified as a broad-specificity methyltransferase responsible for the majority of 1-methylhistidine modifications in mouse and human proteomes. The methylation catalyzed by METTL9 enhances respiration via Complex I, and reduces the zinc binding affinity of HxH-containing peptides.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Gemma Serra-Bardenys, Sandra Peiro
Summary: Oxidoreductases catalyze oxidation-reduction reactions and constitute a large and diverse group of enzymes. Carbonylation, particularly in lysine residues, is a significant oxidative modification in proteins that can impact protein structure and function.
Review
Endocrinology & Metabolism
Mingyang Li, Yanan Hou, Ziwei Zhang, Bowen Zhang, Ting Huang, Aiqin Sun, Genbao Shao, Qiong Lin
Summary: SETD5, an uncharacterized member of the protein lysine methyltransferase family, regulates transcription machinery by methylating histone H3 on lysine 36 (H3K36). Its well-known functions include transcription regulation, euchromatin formation, and RNA elongation and splicing. Mutations and hyperactivity of SETD5 are frequently observed in neurodevelopmental disorders and cancer, and it can be down-regulated through the ubiquitin-proteasome pathway. However, the underlying biochemical mechanisms of this dysregulation are poorly understood. This article provides an update on the enzymatic activity and substrate specificity of SETD5, its biological importance, and its impact on normal physiology and disease, with potential therapeutic options.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Pharmacology & Pharmacy
Zhifei Xu, Wentong Wu, Hao Yan, Yuhuai Hu, Qiaojun He, Peihua Luo
Summary: The tumor suppressor protein p53 plays a crucial role in controlling key biological functions and its mutation is associated with various diseases. Regulation of p53 stability is important for maintaining normal functions and targeting p53 for degradation could be a potential therapeutic strategy against cancer.
BIOCHEMICAL PHARMACOLOGY
(2021)
Review
Cell Biology
Jia Wen, Donglai Wang
Summary: The genome guardian p53 undergoes multiple posttranslational modifications in response to diverse stresses, which coordinate to precisely modulate its diverse properties in different biological contexts. These modifications can recruit 'reader' proteins that specifically recognize them, facilitating the functional readout of p53. Targeting the interplay between posttranslational modifications and reader proteins has become a promising cancer therapeutic strategy.
JOURNAL OF MOLECULAR CELL BIOLOGY
(2021)
Review
Endocrinology & Metabolism
Ye-Chi Cao, Su-Kang Shan, Bei Guo, Chang-Chun Li, Fu-Xing-Zi Li, Ming-Hui Zheng, Qiu-Shuang Xu, Yi Wang, Li-Min Lei, Ke-Xin Tang, Wen-Lu Ou-Yang, Jia-Yue Duan, Yun-Yun Wu, Muhammad Hasnain Ehsan Ullah, Zhi-Ang Zhou, Feng Xu, Xiao Lin, Feng Wu, Xiao-Bo Liao, Ling-Qing Yuan
Summary: Histone methylation modification may play a key role in the development of vascular calcification, which involves various complex pathophysiological processes. Comprehensive research on the role and mechanism of lysine methylation modification in VC is crucial for identifying new therapeutic targets and developing new drugs.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ksenia S. Egorova, Alexandra Posvyatenko, Sergey S. Larin, Valentine P. Ananikov
Summary: Operations with nucleic acids play a crucial role in studying gene function mechanisms and developing molecular medicine and gene therapy. Recently, the use of ionic liquids in manipulating nucleic acids has gained significant attention due to their unique physicochemical properties, offering potential advantages in the field.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Physical
Ksenia S. Egorova, Alexandra Posvyatenko, Artem N. Fakhrutdinov, Alexey S. Galushko, Marina M. Seitkalieva, Valentine P. Ananikov
Summary: This study applied NMR spectroscopy and scanning electron microscopy to investigate the interactions between ionic liquids and anticancer drugs, revealing synergistic or antagonistic cytotoxic effects in some mixtures. The observed cytotoxic effects were found to be cell type-dependent, with all test substances inducing cell death via necrosis in the CaCo-2 cell line. The study suggests potential benefits of utilizing ionic liquids in drug formulations.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Multidisciplinary
Marina M. Seitkalieva, Anna V. Vavina, Alexandra Posvyatenko, Ksenia S. Egorova, Alexey S. Kashin, Evgeniy G. Gordeev, Elena N. Strukova, Leonid Romashov, Valentine P. Ananikov
Summary: A new family of protic ammonium ionic liquids (ILs) with various inorganic anions was synthesized from bio-derived 5-HMF, showing potential sustainable applications and unique multifunctional intrinsic organization. The interaction nature between the cations and anions of the ILs was mapped at the molecular level, impacting cytotoxicity and potential dissolution properties. The results suggest the potential for biological and medicinal applications with structural adjustments for regulation of ILs' biological activity.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2021)
Review
Biochemistry & Molecular Biology
Anatoly N. Vereshchagin, Nikita A. Frolov, Ksenia S. Egorova, Marina M. Seitkalieva, Valentine P. Ananikov
Summary: Quaternary ammonium compounds (QACs) are well-known cationic biocides with a broad spectrum of antimicrobial activity, used in various products from personal care to disinfectants. Research focuses on developing new types of QACs and ILs to meet the increasing demand for efficient antimicrobials in modern society.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Alexei A. Kotov, Sergei S. Bazylev, Vladimir E. Adashev, Aleksei S. Shatskikh, Ludmila V. Olenina
Summary: The Y chromosome is a sex chromosome found in male animals and undergoes dynamic evolutionary changes. It is characterized by unique chromatin landscapes and is enriched in tandem repeats and transposons. Despite structural divergence, Y-linked genes are mainly associated with spermatogenesis and male-specific selection shapes the evolution of Y chromosomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Marina M. Seitkalieva, Evgeniy G. Gordeev, Elena N. Strukova, Ksenia S. Egorova, Valentine P. Ananikov, Anna V. Vavina, Alexandra Posvyatenko
Summary: Solubility in water, interactions with the solvent medium, and tuning of molecular conformation in the liquid phase are crucial for the discovery of new biologically active molecules and the understanding of their mechanisms. This article presents the synthesis, structural and biological activity studies, and computational modeling of new ionic compounds. Combining the structural frameworks of well-known imidazolium, pyridinium, and cholinium ionic liquids with naturally occurring cinnamic acid allows for the modulation of solubility, physicochemical properties, and biological activity. The biological activity of the resulting molecules was significantly increased, and the structure-activity relationship was investigated through cytotoxicity mapping and molecular dynamics simulation.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Inorganic & Nuclear
Evgeniy O. Pentsak, Lilya U. Dzhemileva, Vladimir A. D'yakonov, Ruslan R. Shaydullin, Alexey S. Galushko, Ksenia S. Egorova, Valentine P. Ananikov
Summary: Transition metals are crucial in fine organic synthesis, but their toxicity and environmental pollution have raised concerns. The comparison between supported catalysts and soluble metal complex catalysts revealed that supported catalysts have lower cytotoxicity, but their overall impact on the environment can vary depending on the preparation procedure and may have neglected biological effects. Both types of catalysts did not significantly contribute to the overall toxicity of the systems, while commonly ignored byproducts showed higher overall biological influence.
JOURNAL OF ORGANOMETALLIC CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Philip Toukach, Ksenia S. Egorova
Summary: The Carbohydrate Structure Database (CSDB) is a curated repository that stores glycans data from bacterial, fungal, and plant sources. It provides free access to the database content and tools through a web interface. This paper presents CSDB source data files and a self-contained SQL dump, demonstrating their potential application in glycan-related studies.
Article
Environmental Sciences
Ksenia S. Egorova, Alexandra V. Posvyatenko, Alexey S. Galushko, Valentine P. Ananikov
Summary: We introduce new quantitative environmental metrics - cytotoxicity potentials - for preliminary evaluation of chemical reactions' safety. We propose the concept of bio-Profiles, including common cytotoxicity scale and a more compact representation, bio-Strips, for fast estimation of potential environmental dangers. These improvements allow direct comparisons of synthetic routes and faster assessment of reactions' overall cytotoxicity.
Article
Chemistry, Physical
Ksenia S. Egorova, Marina M. Seitkalieva, Alexey S. Kashin, Evgeniy G. Gordeev, Anna V. Vavina, Alexandra V. Posvyatenko, Valentine P. Ananikov
Summary: This study investigated the cytotoxicity of chemically relevant imidazolium PILs with different alkyl side chains and compared it with aprotic analogues. The results highlighted the role of anion type in determining the cytotoxicity of ILs with short alkyl side chains. Even low-toxic PILs showed harmful effects on eukaryotic cells when used as cryopreservation agents, and the studied IL/water mixtures tended to form simple solid hydrates due to the weak amphiphilic properties of imidazolium cations with short alkyl side chains.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Philip V. Toukach, Ksenia S. Egorova
Summary: This paper presents a systematic statistical analysis of the fungal glycome compared to prokaryotic and protistal glycomes. It assesses the composition, modifications, linkages, sizes, branching degree, and net charge of glycans. The obtained information can help identify carbohydrate molecular markers for different fungal classes, aid in the development of diagnostic tools and carbohydrate-based vaccines against pathogenic fungi, and reveal specific glycosyltransferases active in particular fungal species.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
K. S. Egorova, A. S. Galushko, L. U. Dzhemileva, V. A. D'yakonov, V. P. Ananikov
Summary: This work investigates the contribution of different solvents to the overall cytotoxicity of chemical reactions using bio-Profiles and bio-Factors, with the synthesis of 1,1'-biphenyl as an example. The analyzed solvents include ethanol, N-methylpyrrolidone, and four ionic liquids.
Article
Chemistry, Multidisciplinary
Lilya U. Dzhemileva, Vladimir A. D'yakonov, Marina M. Seitkalieva, Natalia S. Kulikovskaya, Ksenia S. Egorova, Valentine P. Ananikov
Summary: This study systematically investigated the cytotoxic mechanisms of various classes of ionic liquids, demonstrating that most of them induce apoptosis in cells. The new data revealed that ILs trigger apoptosis through the mitochondrial pathway, shedding light on the detailed mechanisms of IL cytotoxicity.
Meeting Abstract
Biophysics
Ksenia S. Egorova, Alexandra V. Posvyatenko, Valentine P. Ananikov
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Ksenia S. Egorova, Nadezhda S. Smirnova, Philip Toukach
Summary: CSDB_GT is a novel manually curated database that provides close-to-complete coverage on experimentally confirmed glycosyltransferases (GTs) from the three most studied model organisms in the plantae, bacteria, and fungi kingdoms.
