Article
Biochemistry & Molecular Biology
Fumiyo Ikeda
Summary: The ubiquitin-proteasomal system and the autophagy-lysosome system are two major degradation systems in mammalian cells. Ubiquitin not only regulates proteasomal degradation of substrates but also regulates the autophagy pathway. Ubiquitin plays a key role in autophagy regulation by recruiting cargos to phagophore in a ubiquitin-dependent manner.
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
Cell Biology
Gun West, Minttu Turunen, Anna Aalto, Laura Virtanen, Song-Ping Li, Tiina Helio, Annika Meinander, Pekka Taimen
Summary: This study reveals the intricate interplay between mutant lamins A and C and the protein degradation machinery. Mutant lamins A and C reduce the activity of the ubiquitin-proteasome system (UPS), leading to accumulation of K48-ubiquitin chains. However, compensatory enhanced autophagy can degrade the mutant lamins A and C. Furthermore, pharmacological interventions that enhance protein degradation can be beneficial for maintaining cellular homeostasis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Cell Biology
James L. Shen, Tina M. Fortier, Ruoxi Wang, Eric H. Baehrecke
Summary: Defects in autophagy can lead to issues in metabolism, development, and disease. The loss of Vps13D affects mitophagy, regulated by the core autophagy machinery. Pink1 and Vps13D play roles in Pink1-dependent mitophagy, with Park contributing to mitochondrial clearance through a pathway parallel to Vps13D.
JOURNAL OF CELL BIOLOGY
(2021)
Review
Cell Biology
Yamen Abu Ahmad, Avital Oknin-Vaisman, Eliya Bitman-Lotan, Amir Orian
Summary: The dysregulation of protein turnover in cancer involves multiple mechanisms, including increased stabilization of oncoproteins, inactivation of degradation pathways, and the ability of specific sequences to evade degradation. These mechanisms lead to the accumulation of multiple active oncoproteins in tumor cells, ultimately contributing to the development of degradation-resistant cancer cells.
Article
Biochemistry & Molecular Biology
Fang Liu, Wei Yang, Minghui Hu, Yong Zhang, Beicheng Sun, Hao Yang, Juergen Brosius, Cheng Deng
Summary: This study identifies a group of GPCRs that exhibit constitutive activity and play potentially important roles in physiological functions through rapid ubiquitin-dependent degradation, with GPR26 showing anti-tumor activity in liver cancer cells.
Article
Biology
Chao Hou, Yuxuan Li, Mengyao Wang, Hong Wu, Tingting Li
Summary: Degpred is a deep learning-based model that predicts general degrons directly from protein sequences. It successfully captures typical degron-related sequence properties and predicts degrons beyond those identified by motif-based methods. Furthermore, it constructs a regulatory network of protein degradation by assigning predicted degrons to specific E3 ubiquitin ligases with calculated motifs.
Article
Biochemistry & Molecular Biology
Yang Wang, Randy Y. C. Poon
Summary: The anti-apoptotic protein MCL1 is gradually degraded during mitotic arrest, and the initial level of MCL1 is determined by the mitochondrial ubiquitin ligase MARCH5. Knockout of MARCH5 increases mitotic MCL1 but paradoxically enhances mitotic apoptosis in a BAK-dependent manner. MARCH5 regulates mitotic apoptosis through mechanisms independent of MCL1, including mitochondrial maintenance.
CELL DEATH AND DIFFERENTIATION
(2023)
Article
Rheumatology
Tadashi Hosoya, Tetsuya Saito, Hiroyuki Baba, Nao Tanaka, Seiji Noda, Youji Komiya, Yasuhiro Tagawa, Akio Yamamoto, Fumitaka Mizoguchi, Kimito Kawahata, Nobuyuki Miyasaka, Hitoshi Kohsaka, Shinsuke Yasuda
Summary: This study reveals that inhibiting CDK4/6 activity can attenuate cartilage destruction and MMP-3 production, providing chondroprotective effects. These effects were achieved by impairing AP-1 transcriptional activity and destabilizing JUN.
Article
Oncology
Kumar Nikhil, Hanan S. Haymour, Mohini Kamra, Kavita Shah
Summary: This study identified that LIMK2 degrades SPOP by direct phosphorylation and creates a feedback loop to promote oncogenicity in prostate cancer. Understanding the relationship between LIMK2 and SPOP provides a powerful opportunity to inhibit LIMK2 and retain WT-SPOP, effectively halting disease progression.
BRITISH JOURNAL OF CANCER
(2021)
Article
Multidisciplinary Sciences
Matteo Gentili, Bingxu Liu, Malvina Papanastasiou, Deborah Dele-Oni, Marc A. Schwartz, Rebecca J. Carlson, Aziz M. Al'Khafaji, Karsten Krug, Adam Brown, John G. Doench, Steven A. Carr, Nir Hacohen
Summary: In this study, genes regulating STING trafficking were systematically characterized, and their impact on STING-mediated responses was examined. The study revealed that the ESCRT complex promotes STING degradation and terminates STING signaling. Furthermore, a UBAP1 mutation was found to increase steady-state STING-dependent responses. Overall, this study uncovers the role of the ESCRT complex in regulating STING signaling.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Reo Kurusu, Yuki Fujimoto, Hideaki Morishita, Daisuke Noshiro, Shuhei Takada, Koji Yamano, Hideaki Tanaka, Ritsuko Arai, Shun Kageyama, Tomoko Funakoshi, Satoko Komatsu-Hirota, Hikari Taka, Saiko Kazuno, Yoshiki Miura, Masato Koike, Toshifumi Wakai, Satoshi Waguri, Nobuo N. Noda, Masaaki Komatsu
Summary: In addition to membranous organelles, autophagy selectively degrades p62 bodies, including the cargo vault, to prevent diseases such as cancer. The study established a purification method for p62 bodies using human cell lines and identified vault as a constituent using mass spectrometry. The major vault protein directly interacts with NBR1 to recruit vault into p62 bodies, facilitating their efficient degradation.
DEVELOPMENTAL CELL
(2023)
Article
Biochemistry & Molecular Biology
Ping Liu, Xiaoji Cong, Shengjie Liao, Xinglong Jia, Xiaomin Wang, Wei Dai, Linhui Zhai, Lei Zhao, Jing Ji, Duan Ni, Zhiwei Liu, Yulu Chen, Lulu Pan, Wei Liu, Jian Zhang, Min Huang, Bin Liu, Minjia Tan
Summary: This study identified phosphorylation-dependent SCF substrates using a quantitative phosphoproteome approach, demonstrating the mechanism by which SCFFBXO22 recognizes a phosphodegron. FBXO22 was shown to mediate BAG3 ubiquitination and degradation, impacting tumor growth, apoptosis, and cell cycle progression.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Cell Biology
Nur Mehpare Kocaturk, Nesibe Peker, Karin Eberhart, Yunus Akkoc, Gamze Deveci, Joern Dengjel, Devrim Gozuacik
Summary: Autophagy is a cellular mechanism that degrades and recycles cytosolic fragments, proteins, and organelles. This study identifies novel protein complexes involving autophagy protein ATG5 and ubiquitin-proteasome system (UPS) components. The results suggest that these proteins interact and participate in various protein complexes during mitochondrial stress. Interestingly, specific protein components play important roles in PARK2-PARK6-mediated mitophagy and proteasome activity following mitochondrial stress.
CELL DEATH & DISEASE
(2022)
Article
Cell Biology
Sreedhar Nellaepalli, Anne Sophie Lau, R. Paul Jarvis
Summary: Chloroplasts play a crucial role in photosynthesis and other metabolic and signaling processes for plant growth and development. This article presents the mechanistic details of protein import and the regulation of chloroplast proteins by the ubiquitin-proteasome system (UPS).
JOURNAL OF CELL SCIENCE
(2023)
Article
Genetics & Heredity
Young-Dan Cho, Bong-Su Kim, Woo-Jin Kim, Hyun-Jung Kim, Jeong-Hwa Baek, Kyung-Mi Woo, Yang-Jo Seol, Young Ku, Hyun-Mo Ryoo
Review
Biochemistry & Molecular Biology
Woo-Jin Kim, Hye-Lim Shin, Bong-Soo Kim, Hyun-Jung Kim, Hyun-Mo Ryoo
EXPERIMENTAL AND MOLECULAR MEDICINE
(2020)
Article
Biochemistry & Molecular Biology
Young-Dan Cho, Woo-Jin Kim, Sungtae Kim, Young Ku, Hyun-Mo Ryoo
Summary: The study found that the surface roughness of titanium implants affects their osteogenic potential, with sandblasted/large-grit/acid-etched (SLA) surfaces showing superior osteogenic response compared to machined surfaces, likely due to a different epigenetic landscape, particularly DNA methylation of the Alp gene.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Bong-Soo Kim, Hye-Rim Shin, Hyun-Jung Kim, Heein Yoon, Young-Dan Cho, Kang-Young Choi, Je-Yong Choi, Woo-Jin Kim, Hyun-Mo Ryoo
Summary: Midface hypoplasia in Apert syndrome is associated with abnormal nasal septum cartilage. Surgical correction of the nasal septum cartilage may improve the prognosis of patients with midface hypoplasia and respiratory problems in Apert syndrome.
SCIENTIFIC REPORTS
(2021)
Review
Oncology
Young-Dan Cho, Woo-Jin Kim, Hyun-Mo Ryoo, Hong-Gee Kim, Kyoung-Hwa Kim, Young Ku, Yang-Jo Seol
Summary: The ENCODE project has increased our understanding of functional elements in the genome and epigenome. Current research trends focus on the link between epigenetics and periodontal diseases, with a growing interest in oral health and systemic health. Advances in sequencing technology have expanded the scope of epigenetic studies from specific genes to genome-wide analyses, providing crucial information for comprehensive dental medicine.
CLINICAL EPIGENETICS
(2021)
Article
Dentistry, Oral Surgery & Medicine
Young-Dan Cho, Woo-Jin Kim, Hyun-Mo Ryoo, Young Ku
Summary: This study evaluated the current status of patents on dental implants and found that the technology is in the decline stage. The United States holds the largest number of patents, and profit-oriented companies are the main contributors to development.
CLINICAL IMPLANT DENTISTRY AND RELATED RESEARCH
(2021)
Article
Dentistry, Oral Surgery & Medicine
Maria Akhtar, Kyung Mi Woo, Muhammad Tahir, Wenhui Wu, Jeevithan Elango, Munazza R. Mirza, Maryam Khan, Saba Shamim, Praveen R. Arany, Saeed Ur Rahman
Summary: The study demonstrated that LiCl-incorporated nanofiber scaffolds can enhance osteoblast differentiation by promoting cell proliferation and increasing expression of proteins associated with osteogenesis.
CLINICAL ORAL INVESTIGATIONS
(2022)
Article
Cell Biology
Hye-Rim Shin, Bong-Soo Kim, Hyun-Jung Kim, Heein Yoon, Woo-Jin Kim, Je-Yong Choi, Hyun-Mo Ryoo
Summary: This study finds that the main cause of limb shortening in Apert syndrome resulting from FGFR2 gene mutations is the excessive expression of RANKL, which leads to an imbalance in osteoblast and osteoclast coupling.
JOURNAL OF CELLULAR PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hyun-Jung Kim, Woo-Jin Kim, Hye-Rim Shin, Hee-In Yoon, Jae- Moon, Eunji Lee, Jin-Muk Lim, Young-Dan Cho, Mi-Hye Lee, Hong-Gee Kim, Hyun-Mo Ryoo
Summary: Cellular senescence is closely related to tissue aging, including bone. Oxidative stress caused by the accumulation of reactive oxygen species (ROS) accelerates cellular senescence and dysfunction of osteoblasts. This study identified PADI2 as a regulator of ROS-accelerated senescence of osteoblasts and provided new insights into excessive ROS-promoted cellular senescence and aging-related bone diseases.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Engineering, Biomedical
Saeed Ur Rahman, Woo-Jin Kim, Shin Hye Chung, Kyung Mi Woo
Summary: This study demonstrates that the fibrous topography of scaffolds can direct the differentiation of odontoblast-lineage cells to have the three-dimensional structure of odontoblasts. The altered responsiveness to Wnt5a on the nanofibrous substrate mediated the phosphorylation of JNK and polarity growth signaling, leading to the regeneration of tubular dentin with odontoblast processes. These findings suggest the potential application of nanofibrous scaffolds for dentin regeneration and provide evidence for the distinctive cell responsiveness to their micro-environments.
MATERIALS TODAY BIO
(2022)
Review
Engineering, Biomedical
Woo Jin Kim, Young-Dan Cho, Young Ku, Hyun-Mo Ryoo
Summary: As the society ages, improving quality of life has become an important issue. With implants being accepted as a core component of oral rehabilitation treatment, competition to develop related technologies is intensifying. The analysis of 32,237 dental implant patents reveals advancements in technology, diverse geography, and a convergence towards combining various technological areas in the field. Dental implant technology has transitioned from conventional materials and surface treatments to new material technologies like zirconium and tantalum, as well as software technologies for diagnosis and prognosis. The growth of dental implant technology is expanding rapidly in East Asian countries, along with the growth of the Asian market. Overall, dental implant technology is developing by merging with different technological areas based on the local market environment.
BIOMATERIALS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jae- Moon, Woo-Jin Kim, Ki-Tae Kim, Hyun-Jung Kim, Hye-Rim Shin, Heein Yoon, Seung Gwa Park, Min-Sang Park, Young-Dan Cho, Pil-Jong Kim, Hyun-Mo Ryoo
Summary: An innovative automated image analysis method is presented in this study for precise quantification of subcellular foci within the cell nucleus. The method, called Foci-Xpress, is significantly faster and equally accurate compared to other conventional methods. Its automation eliminates biases caused by researchers and enhances experimental efficiency.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Heein Yoon, Seung Gwa Park, Hyun-Jung Kim, Hye-Rim Shin, Ki-Tae Kim, Young-Dan Cho, Jae- Moon, Min-Sang Park, Woo-Jin Kim, Hyun-Mo Ryoo
Summary: A study found that a form of vitamin B3 called nicotinamide (NAM) can prevent or treat bone diseases related to oxidative stress by increasing the production of antioxidant enzymes. NAM enhances mitochondrial function, increases the production of antioxidant enzymes, and promotes the formation of bone-building cells called osteoblasts. NAM increases mitochondrial biogenesis and antioxidant enzyme expression through activation of the SIRT3-FOXO3A axis, enhancing osteoblast differentiation.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2023)
Article
Dentistry, Oral Surgery & Medicine
H. Yoon, H. J. Kim, H. R. Shin, B. S. Kim, W. J. Kim, Y. D. Cho, H. M. Ryoo
Summary: The study demonstrates that nicotinamide improves delayed tooth eruption in Runx2(+/-) mice through the restoration of decreased osteoclastogenesis, suggesting it as a potential therapeutic drug for dental abnormalities in patients with CCD.
JOURNAL OF DENTAL RESEARCH
(2021)
Article
Dentistry, Oral Surgery & Medicine
Mi Hyun Seo, Min Young Lee, Mi Young Eo, Suk Keun Lee, Kyung Mi Woo, Soung Min Kim
JOURNAL OF THE KOREAN ASSOCIATION OF ORAL AND MAXILLOFACIAL SURGEONS
(2020)