Review
Biochemistry & Molecular Biology
Yuwei Duan, Weijing Niu, Linlin Pang, Xiaoying Bian, Youming Zhang, Guannan Zhong
Summary: This review summarizes the unique post-translational modifications (PTMs) of lasso peptides uncovered to date, providing important insights for future research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Plant Sciences
Feng Yu, Ming Li, Dongli He, Pingfang Yang
Summary: Seed germination and seedling establishment are crucial developmental processes that undergo complex physiological changes, precisely regulated at transcriptional and translational levels. Phytohormones like ABA and GA play key roles in modulating this process, while proteins such as ABI5 and DELLA are central in seed germination. Post-translational modifications, particularly phosphorylation and ubiquitination, are shown to be decisive in regulating seed germination.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Rong Yi, Xiaoyi Shan
Summary: This article provides an overview of post-translational modifications (PTMs) identified in the biosynthetic and signaling pathways of jasmonate (JA), and discusses the mechanisms by which PTMs modulate JA responses.
PLANT CELL REPORTS
(2023)
Review
Cell Biology
Li Chen, Anna Kashina
Summary: Post-translational modifications (PTM) involve enzyme-mediated covalent addition of functional groups to proteins during or after synthesis, greatly increasing biological complexity and playing a crucial role in biological regulation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Piengtawan Tappiban, Yining Ying, Feifei Xu, Jinsong Bao
Summary: The study focuses on the proteomics and posttranslational modifications (PTMs) of starch biosynthesis-related proteins in rice endosperm, highlighting the differential expression of these proteins in developing seeds. Most proteins involved in starch biosynthesis increase at 6-20 days after flowering and decrease under high-temperature conditions. Various PTMs, including phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, target starch biosynthesis proteins in rice seeds. Further research on the role of these PTMs in starch biosynthesis is ongoing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Mohd Shariq, Neha Quadir, Javaid Ahmad Sheikh, Alok Kumar Singh, William R. Bishai, Nasreen Z. Ehtesham, Seyed E. Hasnain
Summary: The host utilizes ubiquitin pathway to combat intracellular pathogens, while pathogens like Mycobacterium tuberculosis exploit this pathway to dampen host innate immune response.
Review
Biochemistry & Molecular Biology
Yanxiang Meng, Jarrod J. Sandow, Peter E. Czabotar, James M. Murphy
Summary: This article discusses the role of phosphorylation, ubiquitylation, GlcNAcylation, proteolytic cleavage, and disulfide bonding in regulating necroptotic signaling, with a focus on RIPK1, RIPK3, and MLKL. Understanding of these post-translational modifications can be valuable in efforts to therapeutically modulate necroptosis.
CELL DEATH AND DIFFERENTIATION
(2021)
Review
Cell Biology
Linbin Zhou, Danny Siu-Chun Ng, Jason C. Yam, Li Jia Chen, Clement C. Tham, Chi Pui Pang, Wai Kit Chu
Summary: This review summarizes recent findings on the impact of post-translational modifications (PTMs) on the functions of retinoblastoma protein (pRb). PTMs on pRb play crucial roles in cell cycle regulation, cell survival, and differentiation, and altered PTMs can lead to anomalies in cell proliferation and tumorigenesis. Understanding the post-translational modulation of pRb could facilitate the development of novel therapeutic strategies for various human diseases.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Review
Microbiology
Kunlong Yang, Jun Tian, Nancy P. Keller
Summary: Post-translational modifications (PTMs) are important for regulating secondary metabolite biosynthesis in Aspergillus species. Histone modifications can be manipulated to activate silent biosynthetic gene clusters (BGCs), while non-histone PTMs also play critical roles in regulating secondary metabolism.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Review
Cell Biology
Takashi Akera
Summary: Haploid gametes are generated from diploid parents via meiosis, a process essential for sexually reproducing eukaryotes. While the precise mechanism of faithful chromosome segregation in meiosis is not fully understood, it is increasingly evident that tubulin post-translational modifications (PTMs) play crucial roles in regulating microtubule functions during meiosis. This review highlights recent advances in understanding the roles of tubulin PTMs in meiotic spindles, particularly their involvement in spindle integrity, oocyte aging, and non-Mendelian inheritance.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Review
Physiology
Kelsey S. Kalous, Sarah L. Wynia-Smith, Brian C. Smith
Summary: Increased sirtuin deacylase activity is associated with longer lifespan and lower susceptibility to aging-related diseases in eukaryotes, while decreased activity is linked to higher disease risk. Oxidative post-translational modifications such as cysteine nitrosation and glutathionylation can inhibit sirtuin deacylase activity, potentially providing a mechanistic link between cellular oxidants and age-related disease development.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Biology
Huanping Guo, Lin Xia, Wei Wang, Wei Xu, Xipeng Shen, Xiao Wu, Tong He, Xuelin Jiang, Yinying Xu, Pan Zhao, Dongmei Tan, Xi Zhang, Yunfang Zhang
Summary: This study explores the tissue-specific distribution pattern of RNA modifications in mouse tissues under hypobaric hypoxia exposure. The abundance of RNA modifications is found to be tissue-specific and responsive to hypoxia exposure. Dysregulation of tRNA modifications under hypoxia attenuates cell proliferation rate and affects overall protein synthesis.
Review
Biochemistry & Molecular Biology
Eugene Varfolomeev, Domagoj Vucic
Summary: Receptor interacting protein 1 (RIP1) kinase is a critical regulator of inflammation and cell death signaling, and its post-translational modifications, such as ubiquitination, phosphorylation, and cleavage, greatly impact its function in signaling pathways.
BIOCHEMICAL JOURNAL
(2022)
Review
Multidisciplinary Sciences
Ji Min Lee, Henrik M. Hammaren, Mikhail M. Savitski, Sung Hee Baek
Summary: Post-translational modifications (PTMs) on specific amino acids control the stability of target proteins. These PTM-regulated degrons act as signals for protein degradation or stabilization. This review summarizes the current knowledge of PTM-mediated protein stability regulation to enhance the identification of novel drug targets.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Julia Kraxner, Charlotta Lorenz, Julia Menzel, Iwan Parfentev, Ivan Silbern, Manuela Denz, Henning Urlaub, Blanche Schwappach, Sarah Koester
Summary: The mechanical properties of biological cells are influenced by the cytoskeleton, with phosphorylation serving as a fast mechanism for mechanical modulation. Phosphorylation can soften filaments, and the binding of 14-3-3 protein to phosphorylated filaments further enhances this effect, potentially preserving the softening and altering cell mechanics in the cell.
Article
Environmental Sciences
Mingwei Cai, Xiuran Yin, Xiaoyu Tang, Cuijing Zhang, Qingfei Zheng, Meng Li
Summary: The study investigated methanogens in vegetated coastal ecosystems and found that mangroves have more diverse methane-producing archaea compared to saltmarshes and seagrasses, where methylotrophic methanogenesis is predominant. The research identified 13 groups of methanogenic archaea being transcribed in VCEs, with Methanosarcinales being the most predominant. This suggests potential distinct methane production contributions in different VCEs to global warming.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Devin M. Ray, Erin Q. Jennings, Igor Maksimovic, Xander Chai, James J. Galligan, Yael David, Qingfei Zheng
Summary: In this study, glyoxal modifications on histones were characterized using quantitative proteomics and a GO-reactive probe derived from aniline. It was found that glycation regulatory proteins can reduce the levels of histone GO adducts. A two-round pull-down method was employed to enrich histone H3 GO glycation and map these adducts to specific chromatin regions.
ACS CHEMICAL BIOLOGY
(2022)
Article
Ecology
Xiuran Yin, Guowei Zhou, Mingwei Cai, Qing-Zeng Zhu, Tim Richter-Heitmann, David A. Aromokeye, Yang Liu, Rolf Nimzyk, Qingfei Zheng, Xiaoyu Tang, Marcus Elvert, Meng Li, Michael W. Friedrich
Summary: The study found that multiple low-abundance archaeal groups are actually catabolic protein degraders, while the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism. In addition, the catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.
Article
Microbiology
Mingwei Cai, Shruthi Kandalai, Xiaoyu Tang, Qingfei Zheng
Summary: There is increasing evidence that archaea are associated with human diseases, including cancer. This study provides the first framework of the diversity and distribution of human-associated archaea across different body sites, such as the gut and oral cavity, and identifies potential archaeal metabolites that may influence the tumor microenvironment and carcinogenesis.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Ge Ye, Weihuan Huang, Zeping Chen, Hao Zhong, Junhao Zhong, Xiaoxin Guo, Yuheng Huang, Shruthi Kandalai, Xiaozhuang Zhou, Nan Zhang, Yang Zhou, Qingfei Zheng, Haiyan Tian
Summary: Bufadienolides are toxic components found in amphibious toads and have a wide range of biological activities. This study identified and characterized several 3-epi-bufadienolides with unique structures from the bile of the Asiatic toad. Toxicology assays showed that 3-hydroxyl epimerization significantly decreased the toxicity of bufadienolides. Furthermore, a hydroxyl epimerase enzyme, HSE-1, was discovered in the toad liver, which regulates the toxicity of natural animal-derived products.
Review
Biochemistry & Molecular Biology
Farzana Hossain, Shruthi Kandalai, Xiaozhuang Zhou, Nan Zhang, Qingfei Zheng
Summary: In this review, synthetic approaches for antigen-based cancer vaccines are highlighted, along with the discussion of various bioconjugation strategies. The progress of genetically modified cancer vaccines in clinical research is also summarized. Additionally, the synthesis of adjuvants and utilization of biomaterial scaffolds for enhancing immune responses are mentioned.
Article
Chemistry, Organic
Xiaozhuang Zhou, Nan Zhang, Farzana Hossain, Shruthi Kandalai, Haiyan Tian, Qingfei Zheng
Summary: Lactate is a common metabolite generated during anaerobic glycolysis and plays important roles in health and disease, especially cancer development. This study reveals that DJ-1, an epigenetic eraser enzyme, can convert methylglyoxal (MGO) into D- and L-lactate through glyoxalase and deglycase activities. The findings provide chemical evidence confirming DJ-1 as a bona fide deglycase and offer new insights into its pathological effects in carcinogenesis.
Article
Chemistry, Multidisciplinary
Hongbo Wang, Yike Zou, Miao Li, Zhijun Tang, Jiabao Wang, Zhenhua Tian, Nina Strassner, Qian Yang, Qingfei Zheng, Yujiao Guo, Wen Liu, Lifeng Pan, K. N. Houk
Summary: In this study, PloI4, a beta-barrel-fold protein homologous to exo-selective 4 + 2 cyclase, was found to catalyze competitive 2 + 2 and 4 + 2 cycloaddition reactions. The versatility of PloI4 was rationalized through biochemical characterizations, computational analyses, (co)crystal structures, and mutagenesis outcomes. Mechanistic studies involved directed engineering of PloI4 to preferentially produce exo-4 + 2, endo-4 + 2, or exo-2 + 2 products. These findings demonstrate enzymatic thermal 2 + 2 cycloaddition and provide evidence for the co-evolution of an enzyme and its substrate for specialization and activity improvement.
Article
Nanoscience & Nanotechnology
Xiaozhuang Zhou, Nan Zhang, Shruthi Kandalai, Huapeng Li, Farzana Hossain, Shiqi Zhang, Jiangjiang Zhu, Junran Zhang, Jiaxi Cui, Qingfei Zheng
Summary: Electro-responsive dynamic hydrogels with robust mechanical properties and precise spatiotemporal resolution are reported. These hydrogels are based on the rearrangement of sodium dodecyl sulfate (SDS) micelles induced by direct current voltage (DCV). The hydrogels show enlarged mesh size, high stretchability (>6000%), and toughness (507 J/m2). They also possess self-healing and malleable properties. These hydrogels have potential applications in wearable bioelectronics and smart drug delivery systems.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Polymer Science
Xiaozhuang Zhou, Shruthi Kandalai, Farzana Hossain, Nan Zhang, Huapeng Li, Qingfei Zheng
Summary: A new class of pH-responsive and recyclable hydrogels with versatile gas-releasing and scavenging properties is reported in this study. The hydrogels can be reversibly controlled through pH changes, allowing for disassembly and reassembly of the gel network. The disassembled copolymer chains can reform hydrogels, and the mineral salts used in the process can function as gas donors or scavengers. This research provides a facile and environmentally friendly method to recycle hydrogels with gas-releasing and gas-scavenging properties, with potential applications in wound healing, wastewater management, and gas therapy for diseases.
MACROMOLECULAR RAPID COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Anthony D. Rish, Zhangfei Shen, Zhenhang Chen, Nan Zhang, Qingfei Zheng, Tian-Min Fu
Summary: This study reports two cryo-EM structures of RuvB, revealing the mechanism of HJ branch migration. RuvB assembles into a spiral staircase, ring-like hexamer, enveloping double-stranded DNA. The asymmetric assembly of RuvB explains the 6:4 stoichiometry of the RuvB/RuvA complex in coordinating HJ migration in bacteria. These findings provide a mechanistic understanding of HJ branch migration facilitated by RuvB, which may be universally shared by prokaryotic and eukaryotic organisms.
NATURE COMMUNICATIONS
(2023)
Review
Chemistry, Multidisciplinary
Rasmus Pihl, Qingfei Zheng, Yael David
Summary: Manipulating the chemical composition of proteins and peptides is crucial for improving polypeptide-based therapeutics and addressing challenging biological questions. Protein ligation, a process of covalently linking polypeptides, offers a powerful strategy for generating semisynthetic products and controlling polypeptide topology. Nature-inspired protein ligation strategies, utilizing enzymatic mechanisms, have been repurposed as tools in chemical biology to enhance control over polypeptide composition.
NATURE REVIEWS CHEMISTRY
(2023)
Review
Oncology
Shruthi Kandalai, Huapeng Li, Nan Zhang, Haidong Peng, Qingfei Zheng
Summary: Recent evidence has shown that the human microbiome is associated with various diseases, including cancer. The microbiomes present within local tissue, other regions, and tumors themselves have been shown to promote and restrict the development and progression of cancer, most often by affecting cancer cells or the host immune system. These microbes have also been shown to impact the efficacy of various cancer therapies, including radiation, chemotherapy, and immunotherapy.
CANCER BIOLOGY & THERAPY
(2023)
Review
Biochemistry & Molecular Biology
Mo E. Sun, Qingfei Zheng
Summary: DJ-1 is a highly conserved multifunctional enzyme found in humans and diverse species. Its enzymatic and non-enzymatic activities, along with its role as a transcriptional coactivator, make it an essential regulator in cellular processes and a potential therapeutic target for various diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Igor Maksimovic, Efrat Finkin-Groner, Yoshiyuki Fukase, Qingfei Zheng, Shan Sun, Mayako Michino, David J. Huggins, Robert W. Myers, Yael David
Summary: This study utilized the recent understanding of DJ-1 deglycation mechanism to develop a method for evaluating potential drug leads, establishing a new platform for targeting DJ-1.
RSC MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Organic
Faiza Diaba, Gisela Trenchs
Summary: The first violet light-mediated synthesis of gamma- and delta-lactams from N-alkenyl trichloroacetamides is reported in this paper. The reactions are conducted in tetrahydrofuran or 2-methyltetrahydrofuran as the sole solvent without catalysts or additives, under non-anhydrous conditions in an air atmosphere where the solvent serves as the radical initiator.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Feroze Hussain, Sajjad Ahmed, Ashiq Hussain Padder, Qazi Naveed Ahmed
Summary: This study reports a novel and efficient one-pot synthesis method for mixed phosphorotrithioates, which does not require supplementary additives and shows broad applicability.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Hyunjin Oh, Ikyon Kim
Summary: A new 1,2,4-triazole-pyrrolo[1,2-a]pyrazine hybrid system, 6-acylpyrrolo[1,2-a][1,2,4]triazolo[5,1-c]pyrazine, was synthesized using a catalyst-free method. This method involved sequential exposure of pyrrole-2-carbonitrile-derived substrates to DMF-DMA and acyl hydrazide, resulting in the formation of acylated pyrazine and 1,2,4-triazole rings, enabling the installation of various substituents at specific positions on the core skeleton.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Ming Yan, Si-fan Wang, Yong-po Zhang, Jin-zhong Zhao, Zhuo Tang, Guang-xun Li
Summary: Here we developed an efficient photocatalytic approach for the convenient preparation of sulfinamides. The reaction allows for the gram-scale preparation of sulfinamides and the one-pot synthesis of various sulfonyl amides.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Farzaneh Bandehali-Naeini, Zahra Tanbakouchian, Noushin Farajinia-Lehi, Nicolas Mayer, Morteza Shiri, Martin Breugst
Summary: Two tandem catalytic systems were developed for the synthesis of novel 3,4-disubstituted maleimides using the same Ugi adducts. Different maleimide structures can be synthesized using either Pd or Cu catalysis.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Tanya Raghava, Anjan Chattopadhyay, Subhadeep Banerjee, Nivedita Sarkar
Summary: Amine substitution of two ortho fluorine atoms of tetrafluoroterephthalonitrile through SNAr chemistry is easily achievable. But further fluorine substitution is only possible under forcing conditions, yielding valuable fluorophores for bioimaging.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Review
Chemistry, Organic
Anju Chadha, Santosh Kumar Padhi, Selvaraj Stella, Sowmyalakshmi Venkataraman, Thangavelu Saravanan
Summary: Alcohol dehydrogenases are enzymes that use cofactors for oxidation or reduction reactions of alcohols or carbonyl compounds. They are utilized in green chemistry and have applications in the production of pharmaceuticals. Recombinant enzymes have solved the challenge of producing purified enzymes in large quantities. Engineered alcohol dehydrogenases have been used in asymmetric synthesis in industry. Various methods have been established for regenerating expensive cofactors to make the enzymatic process more efficient and economically viable.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)