Review
Biochemistry & Molecular Biology
Samuel Smalley, Hanjo Hellmann
Summary: This review provides an overview of how ubiquitin and similar proteins modify target proteins in plants to rapidly change their stability and activity, with a focus on their contribution to stress tolerance. The study also explores the potential use of these pathways for generating more robust crop plants to cope with stress situations.
Article
Biochemistry & Molecular Biology
Catherine Kim, Meredith Juncker, Ryan Reed, Arthur Haas, Jessie Guidry, Michael Matunis, Wei-Chih Yang, Joshua Schwartzenburg, Shyamal Desai
Summary: In cells treated with mitochondrial stressors, SUMOylation of Mfn1/2 facilitates the aggregation of damaged mitochondria at the perinuclear region, potentially through acting as a molecular glue to interact with other proteins.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2021)
Article
Biochemistry & Molecular Biology
Shanshan Xu, Maria E. Gierisch, Anna Katharina Schellhaus, Ina Poser, Simon Alberti, Florian A. Salomons, Nico P. Dantuma
Summary: The absence of stress granules in cells has a negative impact on the functionality of the nuclear ubiquitin-proteasome system (UPS). Defective ribosome products (DRiPs) in stress granule-deficient cells accumulated at nucleoli instead of stress granules, accompanied by redistribution and enhanced degradation of SUMOylated proteins. Depletion of the SUMO-targeted ubiquitin ligase RNF4 restored the functionality of the nuclear UPS in stress granule-deficient cells. Stress granule-deficient cells showed increased formation of mutant ataxin-1 nuclear inclusions under thermal stress. These findings highlight the importance of stress granules in sequestering cytosolic misfolded proteins and preventing their accumulation in the nucleus.
Review
Cell Biology
Satyendra Chandra Tripathi, Disha Vedpathak, Edwin Justin Ostrin
Summary: Cell-mediated immunity is driven by antigenic peptide presentation on major histocompatibility complex (MHC) molecules. Immunoproteasomes, with inducible activity by inflammatory stimuli, play central roles in cancer, autoimmunity, and inflammation by altering the catalytic activity of the proteasome.Understanding the roles of immunoproteasome in different cancers offers insights into developing targeted therapies.
Review
Microbiology
Kenneth H. Wolfe, Geraldine Butler
Summary: This review focuses on recent progress in understanding the origins and evolution of mating-type switching systems in budding yeasts, highlighting the multiple independent occurrences and convergent evolution of these mechanisms, as well as the diversity of self-fertilization mechanisms.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2022)
Review
Biochemistry & Molecular Biology
Yilun Sun, John L. Nitiss, Yves Pommier
Summary: Topoisomerases play crucial roles in DNA metabolism by manipulating DNA structures and are regulated by post-translational modifications. Damage repair of topoisomerase malfunction is also regulated by various conditions and modifications.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Plant Sciences
Catherine M. Doorly, Emmanuelle Graciet
Summary: Hypoxia is a significant stress factor for both plants and mammals, leading to crop losses in plants and pathological conditions in mammals. Understanding the shared mechanisms of how plants and mammals sense and respond to hypoxia can provide insights for crop improvement and therapeutic development. The ubiquitin/proteasome system and SUMO protein play essential roles in regulating hypoxia responses in both plants and mammals, highlighting the potential for future interdisciplinary research in this area.
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
Biochemistry & Molecular Biology
Abramo J. Manfredonia, Daniel A. Kraut
Summary: The ubiquitin-proteasome system is responsible for protein degradation in eukaryotic cells. The study showed that degradation of ubiquitin-independent degrons (UbIDs) is slower and relies on loosely folded substrates. Furthermore, UbID degradation is ATP-independent.
Article
Multidisciplinary Sciences
Hyein G. Lee, Abigail A. Lemmon, Christopher D. Lima
Summary: The Ufd1/Npl4/Cdc48 complex enhances unfolding of substrates modified by SUMO-polyubiquitin hybrid chains through interactions with SUMO. It exhibits a stronger effect on substrates modified by these chains compared to polyubiquitin chains when given a choice. Cryo-EM structures reveal the interactions between Ufd1/Npl4/Cdc48 and ubiquitin during the unfolding process. These findings confirm the significance of SUMO and ubiquitin modifications in cellular functions and support a model where Ufd1/Npl4/Cdc48, SUMO, and ubiquitin conjugation pathways converge to promote clearance of proteins modified with SUMO and polyubiquitin.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Wenyan Yang, Shiqun Wang, Shengqiang Tong, Wei-Dong Zhang, Jiang-Jiang Qin
Summary: This article provides an overview of the ubiquitin-proteasome system (UPS) and its role in pancreatic cancer. Studies indicate that mutations or aberrant expression of UPS members can lead to rewriting of the ubiquitination code, affecting tumor growth, metastasis, immune evasion, and drug resistance. The article also reviews current UPS modulators and analyzes their potential as cancer therapies.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2024)
Article
Biochemistry & Molecular Biology
Hae-Seul Choi, Eun-Su Lim, Kwang-Hyun Baek
Summary: The study identified the deubiquitinating enzyme USP12 as being associated with Bax and showed that USP12 regulates Bax by detaching ubiquitin on K63-linked chains. The site-directed mutagenesis of putative ubiquitination sites on Bax confirmed the half-life of the protein.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Lucas W. Henderson, Edie M. Sharon, Amit K. S. Gautam, Adam J. Anthony, Martin F. Jarrold, David H. Russell, Andreas Matouschek, David E. Clemmer
Summary: Mass spectrometry studies show that the stability of S. cerevisiae 20S proteasome undergoes related configurations and transitions during temperature changes, possibly linked to the opening of the proteolytic core. The study indicates that the proteasome remains intact and all transitions are reversible. Three types of structures are identified based on thermodynamic analysis: energetically stabilized closed configurations, high-entropy precursor states, and open pore structures. Opening of the 20S pore in the absence of the regulatory unit involves a charge-priming process. However, only a small fraction of precursor configurations actually open to expose the catalytic cavity.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Mrinal Sharma, Prranshu Yadav, Ankita Doshi, Hemang D. Brahmbhatt, C. Ratna Prabha
Summary: The study examined the effects of six double mutants derived from the ubiquitin mutant UbEP42 on cell functions, finding that the double mutation L50P-I61T had the most detrimental impact. Overall, these double mutations made cells more sensitive, and the negative effects under certain conditions could be compensated for by each other.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Editorial Material
Biochemistry & Molecular Biology
Xiaodong Cheng
Summary: Protein SUMOylation is an essential post-translational modification for maintaining cellular homeostasis. Recent evidence suggests that liquid-liquid phase separation (LLPS)/ biomolecular condensates play a role in regulating cellular SUMOylation, providing insights into its cellular mechanism.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Review
Genetics & Heredity
Jianhui Li, Mark Hochstrasser
Article
Multidisciplinary Sciences
Jason M. Berk, Christopher Lim, Judith A. Ronau, Apala Chaudhuri, Hongli Chen, John F. Beckmann, J. Patrick Loria, Yong Xiong, Mark Hochstrasser
NATURE COMMUNICATIONS
(2020)
Review
Biochemistry & Molecular Biology
Hong-Yeoul Ryu, Seong Hoon Ahn, Mark Hochstrasser
EXPERIMENTAL AND MOLECULAR MEDICINE
(2020)
Review
Genetics & Heredity
Hongli Chen, Mengwen Zhang, Mark Hochstrasser
Article
Chemistry, Multidisciplinary
Adam E. Richardson, Zachary A. Zentz, Antonio E. Chambers, Siara N. Sandwith, Michael A. Reisinger, Destinee W. Saunders, Joshua D. Tompkins, Arthur D. Riggs, Eric D. Routh, Eric M. Rubenstein, Melissa A. Smaldino, James P. Vaughn, Robert A. Haney, Philip J. Smaldino
Article
Biochemistry & Molecular Biology
Hong-Yeoul Ryu, Dejian Zhao, Jianhui Li, Dan Su, Mark Hochstrasser
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Hong-Yeoul Ryu, Mark Hochstrasser
Summary: Histone sumoylation plays diverse roles in regulating chromatin structure, transcription processes, DNA repair, and chromosome segregation, and is involved in complex signaling codes with other histone modifications and RNAPII-CTD.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Jianhui Li, Mark Hochstrasser
Summary: The proteasome is involved in proteolysis and can be degraded through macroautophagy and microautophagy pathways. AMPK-dependent ESCRT-mediated microautophagy regulates proteasome trafficking and degradation in low-glucose conditions. Aberrant proteasomes are more likely to undergo microautophagy, suggesting that the ESCRT system fine-tunes proteasome quality control in response to low-glucose stress.
JOURNAL OF CELL SCIENCE
(2022)
Article
Microbiology
Guangxin Sun, Mengwen Zhang, Hongli Chen, Mark Hochstrasser
Summary: Wolbachia is a bacterium that can affect the reproduction of arthropod hosts through cytoplasmic incompatibility (CI). Researchers have found that the expression of the CinB gene alone in fruit fly males can cause a decrease in embryo viability, but this sterility can be rescued when the females express the corresponding CinA gene. These findings have important implications for understanding the impact of bacteria and insect control.
Review
Biochemistry & Molecular Biology
Carolyn Allain Breckel, Mark Hochstrasser
Summary: The proper folding of proteins is vital for their diverse functions, and misfolded proteins can potentially harm cells by forming aggregates. Protein quality control pathways are responsible for repairing or degrading abnormal proteins, with the ubiquitin-proteasome system being commonly employed.
Article
Biochemistry & Molecular Biology
Mengwen Zhang, Jason M. Berk, Adrian B. Mehrtash, Jean Kanyo, Mark Hochstrasser
Summary: Protein ubiquitylation is a crucial posttranslational modification, and the OtUBD tool offers an efficient way to detect and purify ubiquitylated proteins. It enables selective purification of covalently ubiquitylated proteins or co-isolation of both ubiquitylated proteins and their interacting proteins.
Article
Immunology
Haley E. Adcox, Jason M. Berk, Mark Hochstrasser, Jason A. Carlyon
Summary: This study reveals the expression, localization, and interactome of OtDUB during O. tsutsugamushi infection and establishes a strong link between OtDUB and the host endocytic pathway. OtDUB peripherally associates with the O. tsutsugamushi cell wall and interacts with adapter protein complex 2 and other endosomal membrane traffic regulators.
INFECTION AND IMMUNITY
(2022)
Article
Biochemistry & Molecular Biology
Chin Leng Cheng, Michael K. Wong, Yanjie Li, Mark Hochstrasser
Summary: The study reveals the importance of proline residues in the proteasome-activating nucleotidase for efficient assembly of the 26S proteasome base in eukaryotes and archaea. Investigation of equivalent prolines in Rpt2, Rpt3, and Rpt5 suggests their crucial role in specific ATPase heterodimerization during proteasome base assembly.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Microbiology
Guangxin Sun, Mengwen Zhang, Hongli Chen, Mark Hochstrasser
Summary: The study investigates the mechanism of cytoplasmic incompatibility (CI) induced by Wolbachia bacteria in arthropod hosts. It identifies that the CinB protein alone from a specific clade of cif genes can cause male sterility, which is rescued by the cognate CinA protein in female germ line. These findings highlight the role of Cif proteins in inducing CI and provide insights for using CI in insect control.
Article
Genetics & Heredity
Christopher M. Hickey, Carolyn Breckel, Mengwen Zhang, William C. Theune, Mark Hochstrasser
Summary: Intracellular proteolysis through the ubiquitin-proteasome system regulates various processes in eukaryotes, with specific E3 ligases targeting proteins for degradation based on different signals. This study identified E3 ligases in yeast responsible for degrading proteins with different degradation signals, showing differential recognition of PQC substrates by the ubiquitin system in the cytoplasm and nucleus. Results in human cells confirmed these findings, indicating the ability of the ubiquitin system to target natural hydrophobic C-termini as degrons.