Article
Biochemistry & Molecular Biology
Han Xue, Qingfeng Zhang, Panqin Wang, Bijin Cao, Chongchong Jia, Ben Cheng, Yuhua Shi, Wei-Feng Guo, Zhenlong Wang, Ze-Xian Liu, Han Cheng
Summary: The paper introduces an integrative database of quantitative PTMs in plants named qPTMplants, which includes experimentally identified PTM events for 123,551 proteins at 429,821 nonredundant sites under 583 conditions for 43 plant species from 293 published studies. This database is expected to be a valuable resource for further research on PTMs in plants.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Cell Biology
Rohan Gupta, Mehar Sahu, Devesh Srivastava, Swati Tiwari, Rashmi K. Ambasta, Pravir Kumar
Summary: Post-translational modifications play a crucial role in the pathogenesis of neurodegenerative diseases by regulating protein homeostasis and signaling cascades, leading to enhanced neuroprotection and potentially reversing misfolded protein accumulation.
AGEING RESEARCH REVIEWS
(2021)
Review
Oncology
Hashnu Dutta, Nishant Jain
Summary: Post-translational modifications are crucial regulatory mechanisms that alter the properties and functions of proteins, expanding the diversity of the proteome. They play a key role in physiological processes and have clinical relevance in diseases. These modifications involve covalently attaching modified chemical groups to amino acid residues, causing changes in protein activity, structure, location, and function.
FRONTIERS IN ONCOLOGY
(2023)
Review
Biology
Koyo Harada, Simon M. Carr, Amit Shrestha, Nicholas B. La Thangue
Summary: Post-translational modifications play a crucial role in disease pathogenesis and progression. Protein arginine citrullination, a type of modification catalyzed by peptidylarginine deiminases (PADs), is emerging as a potential therapeutic target in cancer. This review discusses the functions of PADs in cancer biology and their interplay with other types of modifications, shedding light on downstream biological events.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Review
Biotechnology & Applied Microbiology
Ruiqin Zhang, Chenghao Cao, Jiahua Bi, Yanjun Li
Summary: This article systematically summarizes the issues of protein engineering and post-translational modifications of fungal cellulases, pointing out the current challenges and opportunities, providing reference for further improvement of cellulase properties.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Review
Microbiology
Natalie A. Counihan, Hope C. Chernih, Tania F. de Koning-Ward
Summary: Post-translational modifications play a crucial role in regulating cellular processes in eukaryotic proteins, and lipidation is particularly important in Plasmodium parasites. This review discusses lipid modification processes and their potential as drug targets for malaria.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Zhuojun Wu, Vera Jankowski, Joachim Jankowski
Summary: Despite the use of medication for the prevention of cardiovascular diseases, it remains the leading cause of death globally. Non-enzymatic post-translational modifications of proteins and lipoproteins play a significant role in the development of cardiovascular diseases. Factors such as renal insufficiency and metabolic imbalance contribute to the increased frequency of these modifications. Understanding these modifications can provide new insights for risk assessment, prevention, and treatment of cardiovascular diseases.
MOLECULAR ASPECTS OF MEDICINE
(2022)
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)
Article
Nanoscience & Nanotechnology
Pablo Martin-Baniandres, Wei-Hsuan Lan, Stephanie Board, Mercedes Romero-Ruiz, Sergi Garcia-Manyes, Yujia Qing, Hagan Bayley
Summary: Electro-osmosis in an anion-selective alpha-hemolysin nanopore is utilized for capturing, unfolding, and transporting polypeptides with more than 1,200 residues. By monitoring the ionic current at a single-molecule resolution, this method enables the mapping of post-translational modifications in polypeptide chains. The application of nanopore technology holds potential for identifying full-length proteoforms.
NATURE NANOTECHNOLOGY
(2023)
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)
Review
Cell Biology
Zhu Liang, Andreas Damianou, Elena Di Daniel, Benedikt M. Kessler
Summary: This review discusses the potential therapeutic targets for a number of inflammatory diseases by focusing on post-translational modification enzymes that regulate NLRP3 inflammasome function. It highlights the importance of kinases, ubiquitin processing enzymes, and other PTM enzymes in controlling inflammasome activation and signal termination.
CELL COMMUNICATION AND SIGNALING
(2021)
Review
Chemistry, Multidisciplinary
Lin-hui Zhai, Kai-feng Chen, Bing-bing Hao, Min-jia Tan
Summary: Protein post-translational modifications (PTMs) are crucial for protein activity regulation and are involved in diseases. PTM regulatory enzymes are important drug targets. Mass spectrometry-based proteomics enables systematic characterization of PTMs for drug target identification, mechanism elucidation and biomarker discovery in personalized therapy.
ACTA PHARMACOLOGICA SINICA
(2022)
Review
Clinical Neurology
Rosie Bell, Michele Vendruscolo
Summary: This article discusses the features and pathophysiology of Parkinson's disease and related synucleinopathies, emphasizing the potential importance of the dysregulation of lipid homeostasis and alpha-synuclein homeostasis in disease development. It also explores the role of post-translational modifications in modulating the interactions of alpha-synuclein with lipid membranes, and the impact of these advancements on the development of new diagnostic and therapeutic tools.
FRONTIERS IN NEUROLOGY
(2021)
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)
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.
Article
Biochemistry & Molecular Biology
Tomonori Saotome, Sawaros Onchaiya, Subbaian Brindha, Taichi Mezaki, Satoru Unzai, Keiichi Noguchi, Jose C. Martinez, Shun-ichi Kidokoro, Yutaka Kuroda
Summary: The third PDZ domain of PSD95 has a propensity to form amyloid fibrils at high temperatures. It exhibits reversible oligomerization at high temperatures, which is unusual for a small globular protein like PDZ3. By suppressing the high-temperature oligomerization, amyloid formation can be inhibited.
Article
Biochemistry & Molecular Biology
Subbaian Brindha, Yutaka Kuroda
Summary: The use of a solubility-enhancing peptide tag containing nine arginine residues can significantly improve the solubility of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein expressed in Escherichia coli. This discovery has the potential to accelerate the development of anti-COVID-19 therapeutics. The folded RBD-C9R demonstrated binding activity with the host cell receptor and elicited a strong immune response in mice.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Sawaros Onchaiya, Tomonori Saotome, Kenji Mizutani, Jose C. Martinez, Jeremy R. H. Tame, Shun-ichi Kidokoro, Yutaka Kuroda
Summary: Researchers reverse-engineered the PDZ3-F340A variant to induce high-temperature reversible oligomerization (RO) and amyloidogenesis. By mutating specific amino acids, they successfully triggered the formation of high-temperature RO and concurrent amyloid-like structures in the PDZ3-F340A variant.
Article
Chemistry, Physical
Shin Kohara, Yuki Matsuzawa, Yutaka Kuroda
Summary: We present a lattice model to study the influence of protein surface charge distributions on protein solubility, aggregation, and condensation. Our findings show that proteins with the same isoelectric point can exhibit different aggregation propensities depending on the arrangement of surface charges. Additionally, mixing two particle types in a heterogeneous intracellular environment can affect the aggregation properties of each individual type.
CHEMICAL PHYSICS LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Tomoyuki Takeda, Kazumasa Shirai, You-wang Kim, Mieko Higuchi-Takeuchi, Minami Shimizu, Takayuki Kondo, Tomokazu Ushijima, Tomonao Matsushita, Kazuo Shinozaki, Kousuke Hanada
Summary: A large-scale intergenomic gene transfer event in Arabidopsis thaliana created a small coding gene that regulates floral timing. This de novo gene derived from the mitochondrial genome has an important regulatory effect on floral transition. Transcriptomic and phenotypic analyses support these findings.
PLANT MOLECULAR BIOLOGY
(2023)
Review
Multidisciplinary Sciences
Kazuo Shinozaki, Kazuko Yamaguchi-Shinozaki
Summary: This review article describes the 30-year experience of the authors in using functional genomics to understand the sophisticated molecular mechanisms of plant response and adaptation to environmental stress conditions. They focused on drought-inducible genes and their regulation, as well as the perception and cellular signal transduction of stress signals. Key genes and factors involved in complex responses and tolerance to dehydration and temperature stresses were identified.
PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Md. Din Islam, Tahmina Sharmin, Imrul Hasan Tipo, Antara Saha, Sanjida Yesmin, Moushumi Ghosh Roy, Subbaian Brindha, Yutaka Kuroda, M. Monirul Islam
Summary: This study reveals disparities in the immunogenicity of DENV envelope protein domain 3 (ED3) among different DENV serotypes, which may contribute to the development of hemorrhagic fever and dengue shock syndrome. Understanding these disparities is crucial for the development of a tetravalent subunit vaccine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Retraction
Biochemistry & Molecular Biology
Lianwei Peng, Yoichiro Fukao, Fumiyoshi Myouga, Reiko Motohashi, Kazuo Shinozaki, Toshiharu Shikanai
Review
Plant Sciences
June-Sik Kim, Keiichi Mochida, Kazuo Shinozaki
Summary: This review provides an overview of the current knowledge on ER stress sensing, activation, and downstream regulation of the unfolded protein response (UPR). Recent studies have shown that the UPR is also involved in plant growth and development, and it modulates both plant growth and stress tolerance by maintaining ER homeostasis.
Article
Biochemistry & Molecular Biology
Md. Golam Kibria, Yukari Shiwaku, Subbaian Brindha, Yutaka Kuroda
Summary: In this study, the researchers investigated whether the biophysical properties of amorphous oligomers can affect immunogenicity using a domain of dengue virus serotype 3 envelope protein. They prepared different formulations of amorphous oligomers and found that controlled oligomerization can increase the immunogenicity of the protein, suggesting a potential method for enhancing protein-based vaccines without the need for adjuvants.
Article
Multidisciplinary Sciences
Satoshi Kidokoro, Izumi Konoura, Fumiyuki Soma, Kazuo Shinozaki, Takamasa Suzuki, Masaru Tanokura, Takuya Miyakawa, Takato Imaizumi, Kazuko Yamaguchi-Shinozaki
Summary: Plants respond to severe temperature changes by inducing the expression of numerous genes whose products enhance stress tolerance and responses. DREB1 genes are rapidly and strongly induced by cold stress and their molecular mechanisms are vital for recognizing the initial responses to cold stress in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Takahiro Yoshizue, Subbaian Brindha, Rawiwan Wongnak, Hitoshi Takemae, Mami Oba, Tetsuya Mizutani, Yutaka Kuroda
Summary: E. coli-expressed proteins as a subunit vaccine antigen can induce neutralizing antibodies if properly folded. In this study, we compared the effectiveness of an E. coli-expressed SARS-CoV-2 receptor-binding domain (RBD) with the mammalian cell-produced S1 subunit as antigens. Mice immunized with two injections of RBD or S1 alone showed some protection against SARS-CoV-2, but a mixed injection scheme provided significantly higher protection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Materials Science, Ceramics
Haruki Zayasu, Takahiko Kawaguchi, Hiroki Nakane, Nobuyoshi Koshida, Kazuo Shinozaki, Hisao Suzuki, Naonori Sakamoto, Naoki Wakiya
Summary: Epitaxial growth of yttria-stabilized zirconia (YSZ) thin film on through-hole-type porous silicon (tht-PSi(001)) was achieved, and the strain applied to the YSZ thin film was found to affect the ionic conduction.
JOURNAL OF THE CERAMIC SOCIETY OF JAPAN
(2022)
Meeting Abstract
Biophysics
Yuanpeng Janet Huang, Ning Zhang, Beate Bersch, Krzysztof Fidelis, Masayori Inouye, Yojiro Ishida, Andriy Kryshtafovych, Naohiro Kobayashi, Yutaka Kuroda, Gaohua Liu, Andy Li Wang, G. V. T. Swapna, Nan Wu, Toshio Yamazaki, Gaetano T. Montelione
BIOPHYSICAL JOURNAL
(2022)
Article
Plant Sciences
Fabiane Kletke de Oliveira, Cristiane Jovelina Da-Silva, Natalia Garcia, Darwin Alexis Pomagualli Agualongo, Ana Claudia Barneche de Oliveira, Norihito Kanamori, Hironori Takasaki, Kaoru Urano, Kazuo Shinozaki, Kazuo Nakashima, Kazuko Yamaguchi-Shinozaki, Alexandre Lima Nepomuceno, Liliane Marcia Mertz Henning, Luciano do Amarante
Summary: Soil waterlogging has a major impact on plant growth and agricultural productivity. This study found that overexpression of the NCED gene increases the sensitivity of soybean plants to waterlogging and reoxygenation, leading to increased lipid peroxidation levels, decreased antioxidant activity and alcohol dehydrogenase activity, as well as reduced seed weight and grain yield.