1
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Lv P, Liu J, Liu X. The role of ubiquitin-conjugating enzyme in the process of spermatogenesis. Reprod Biol Endocrinol 2024; 22:110. [PMID: 39198846 PMCID: PMC11351103 DOI: 10.1186/s12958-024-01282-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 08/15/2024] [Indexed: 09/01/2024] Open
Abstract
The ubiquitination is crucial for controlling cellular homeostasis and protein modification, in which ubiquitin-conjugating enzyme (E2) acts as the central player in the ubiquitination system. Ubiquitin-conjugating enzymes, which have special domains that catalyse substrates, have sequence discrepancies and modulate various pathophysiological processes in different cells of multiple organisms. E2s take part in the mitosis of primordial germ cells, meiosis of spermatocytes and the formation of mature haploid spermatids to maintain normal male fertility. In this review, we summarize the various types of E2s and their functions during distinct stages of spermatogenesis.
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Affiliation(s)
- Peng Lv
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Andrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Institute of Andrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Xiaming Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Institute of Andrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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2
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Samant SB, Yadav N, Swain J, Joseph J, Kumari A, Praveen A, Sahoo RK, Manjunatha G, Seth CS, Singla-Pareek SL, Foyer CH, Pareek A, Gupta KJ. Nitric oxide, energy, and redox-dependent responses to hypoxia. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4573-4588. [PMID: 38557811 DOI: 10.1093/jxb/erae139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/30/2024] [Indexed: 04/04/2024]
Abstract
Hypoxia occurs when oxygen levels fall below the levels required for mitochondria to support respiration. Regulated hypoxia is associated with quiescence, particularly in storage organs (seeds) and stem cell niches. In contrast, environmentally induced hypoxia poses significant challenges for metabolically active cells that are adapted to aerobic respiration. The perception of oxygen availability through cysteine oxidases, which function as oxygen-sensing enzymes in plants that control the N-degron pathway, and the regulation of hypoxia-responsive genes and processes is essential to survival. Functioning together with reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2) and reactive nitrogen species (RNS), such as nitric oxide (·NO), nitrogen dioxide (·NO2), S-nitrosothiols (SNOs), and peroxynitrite (ONOO-), hypoxia signaling pathways trigger anatomical adaptations such as formation of aerenchyma, mobilization of sugar reserves for anaerobic germination, formation of aerial adventitious roots, and the hyponastic response. NO and H2O2 participate in local and systemic signaling pathways that facilitate acclimation to changing energetic requirements, controlling glycolytic fermentation, the γ-aminobutyric acid (GABA) shunt, and amino acid synthesis. NO enhances antioxidant capacity and contributes to the recycling of redox equivalents in energy metabolism through the phytoglobin (Pgb)-NO cycle. Here, we summarize current knowledge of the central role of NO and redox regulation in adaptive responses that prevent hypoxia-induced death in challenging conditions such as flooding.
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Affiliation(s)
- Sanjib Bal Samant
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nidhi Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jagannath Swain
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Josepheena Joseph
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Aprajita Kumari
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Afsana Praveen
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ranjan Kumar Sahoo
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | | | | | - Sneh Lata Singla-Pareek
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Ashwani Pareek
- National Agri-Food Biotechnology Institute, Mohali, Punjab, 140306, India
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3
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Shokeen K, Baroi MK, Chahar M, Das D, Saini H, Kumar S. Arginyltransferase 1 (ATE1)-mediated proteasomal degradation of viral haemagglutinin protein: a unique host defence mechanism. J Gen Virol 2024; 105. [PMID: 39207120 DOI: 10.1099/jgv.0.002020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
The extensive protein production in virus-infected cells can disrupt protein homeostasis and activate various proteolytic pathways. These pathways utilize post-translational modifications (PTMs) to drive the ubiquitin-mediated proteasomal degradation of surplus proteins. Protein arginylation is the least explored PTM facilitated by arginyltransferase 1 (ATE1) enzyme. Several studies have provided evidence supporting its importance in multiple physiological processes, including ageing, stress, nerve regeneration, actin formation and embryo development. However, its function in viral pathogenesis is still unexplored. The present work utilizes Newcastle disease virus (NDV) as a model to establish the role of the ATE1 enzyme and its activity in pathogenesis. Our data indicate a rise in levels of N-arginylated cellular proteins in the infected cells. Here, we also explore the haemagglutinin-neuraminidase (HN) protein of NDV as a presumable target for arginylation. The data indicate that the administration of Arg amplifies the arginylation process, resulting in reduced stability of the HN protein. ATE1 enzyme activity inhibition and gene expression knockdown studies were also conducted to analyse modulation in HN protein levels, which further substantiated the findings. Moreover, we also observed Arg addition and probable ubiquitin modification to the HN protein, indicating engagement of the proteasomal degradation machinery. Lastly, we concluded that the enhanced levels of the ATE1 enzyme could transfer the Arg residue to the N-terminus of the HN protein, ultimately driving its proteasomal degradation.
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Affiliation(s)
- Kamal Shokeen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Malay Kumar Baroi
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
| | - Manjeet Chahar
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Debapratim Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
| | - Harimohan Saini
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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4
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Lan X, Huang W, Kim SB, Fu D, Abeywansha T, Lou J, Balamurugan U, Kwon YT, Ji CH, Taylor DJ, Zhang Y. Oligomerization and a distinct tRNA-binding loop are important regulators of human arginyl-transferase function. Nat Commun 2024; 15:6350. [PMID: 39068213 PMCID: PMC11283454 DOI: 10.1038/s41467-024-50719-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 07/18/2024] [Indexed: 07/30/2024] Open
Abstract
The arginyl-transferase ATE1 is a tRNA-dependent enzyme that covalently attaches an arginine molecule to a protein substrate. Conserved from yeast to humans, ATE1 deficiency in mice correlates with defects in cardiovascular development and angiogenesis and results in embryonic lethality, while conditional knockouts exhibit reproductive, developmental, and neurological deficiencies. Despite the recent revelation of the tRNA binding mechanism and the catalytic cycle of yeast ATE1, the structure-function relationship of ATE1 in higher organisms is not well understood. In this study, we present the three-dimensional structure of human ATE1 in an apo-state and in complex with its tRNA cofactor and a peptide substrate. In contrast to its yeast counterpart, human ATE1 forms a symmetric homodimer, which dissociates upon binding of a substrate. Furthermore, human ATE1 includes a unique and extended loop that wraps around tRNAArg, creating extensive contacts with the T-arm of the tRNA cofactor. Substituting key residues identified in the substrate binding site of ATE1 abolishes enzymatic activity and results in the accumulation of ATE1 substrates in cells.
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Affiliation(s)
- Xin Lan
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Su Bin Kim
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Korea
| | - Dechen Fu
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Thilini Abeywansha
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Jiemin Lou
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA
| | | | - Yong Tae Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Korea
- AUTOTAC Bio Inc., Changkkyunggung-ro 254, Jongno-gu, Seoul, Korea
- Seoul National University Hospital, 71 Daehak ro, Seoul, Republic of Korea
| | - Chang Hoon Ji
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Korea.
- AUTOTAC Bio Inc., Changkkyunggung-ro 254, Jongno-gu, Seoul, Korea.
| | - Derek J Taylor
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA.
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| | - Yi Zhang
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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5
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Xu Z, Kombe Kombe AJ, Deng S, Zhang H, Wu S, Ruan J, Zhou Y, Jin T. NLRP inflammasomes in health and disease. MOLECULAR BIOMEDICINE 2024; 5:14. [PMID: 38644450 PMCID: PMC11033252 DOI: 10.1186/s43556-024-00179-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024] Open
Abstract
NLRP inflammasomes are a group of cytosolic multiprotein oligomer pattern recognition receptors (PRRs) involved in the recognition of pathogen-associated molecular patterns (PAMPs) and danger-associated molecular patterns (DAMPs) produced by infected cells. They regulate innate immunity by triggering a protective inflammatory response. However, despite their protective role, aberrant NLPR inflammasome activation and gain-of-function mutations in NLRP sensor proteins are involved in occurrence and enhancement of non-communicating autoimmune, auto-inflammatory, and neurodegenerative diseases. In the last few years, significant advances have been achieved in the understanding of the NLRP inflammasome physiological functions and their molecular mechanisms of activation, as well as therapeutics that target NLRP inflammasome activity in inflammatory diseases. Here, we provide the latest research progress on NLRP inflammasomes, including NLRP1, CARD8, NLRP3, NLRP6, NLRP7, NLRP2, NLRP9, NLRP10, and NLRP12 regarding their structural and assembling features, signaling transduction and molecular activation mechanisms. Importantly, we highlight the mechanisms associated with NLRP inflammasome dysregulation involved in numerous human auto-inflammatory, autoimmune, and neurodegenerative diseases. Overall, we summarize the latest discoveries in NLRP biology, their forming inflammasomes, and their role in health and diseases, and provide therapeutic strategies and perspectives for future studies about NLRP inflammasomes.
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Affiliation(s)
- Zhihao Xu
- Center of Disease Immunity and Intervention, College of Medicine, Lishui University, Lishui, 323000, China
| | - Arnaud John Kombe Kombe
- Laboratory of Structural Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Shasha Deng
- Laboratory of Structural Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Hongliang Zhang
- Center of Disease Immunity and Intervention, College of Medicine, Lishui University, Lishui, 323000, China
| | - Songquan Wu
- Center of Disease Immunity and Intervention, College of Medicine, Lishui University, Lishui, 323000, China
| | - Jianbin Ruan
- Department of Immunology, University of Connecticut Health Center, Farmington, 06030, USA.
| | - Ying Zhou
- Department of Obstetrics and Gynecology, Core Facility Center, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China.
| | - Tengchuan Jin
- Center of Disease Immunity and Intervention, College of Medicine, Lishui University, Lishui, 323000, China.
- Laboratory of Structural Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
- Department of Obstetrics and Gynecology, Core Facility Center, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China.
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science & Technology of China, Hefei, 230027, China.
- Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230001, China.
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6
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Verbič A, Lebar T, Praznik A, Jerala R. Subunits of an E3 Ligase Complex as Degrons for Efficient Degradation of Cytosolic, Nuclear, and Membrane Proteins. ACS Synth Biol 2024; 13:792-803. [PMID: 38404221 PMCID: PMC10949250 DOI: 10.1021/acssynbio.3c00588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Protein degradation is a highly regulated cellular process crucial to enable the high dynamic range of the response to external and internal stimuli and to balance protein biosynthesis to maintain cell homeostasis. Within mammalian cells, hundreds of E3 ubiquitin ligases target specific protein substrates and could be repurposed for synthetic biology. Here, we present a systematic analysis of the four protein subunits of the multiprotein E3 ligase complex as scaffolds for the designed degrons. While all of them were functional, the fusion of a fragment of Skp1 with the target protein enabled the most effective degradation. Combination with heterodimerizing peptides, protease substrate sites, and chemically inducible dimerizers enabled the regulation of protein degradation. While the investigated subunits of E3 ligases showed variable degradation efficiency of the membrane and cytosolic and nuclear proteins, the bipartite SSD (SOCSbox-Skp1(ΔC111)) degron enabled fast degradation of protein targets in all tested cellular compartments, including the nucleus and plasma membrane, in different cell lines and could be chemically regulated. These subunits could be employed for research as well as for diverse applications, as demonstrated in the regulation of Cas9 and chimeric antigen receptor proteins.
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Affiliation(s)
- Anže Verbič
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | | | - Arne Praznik
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
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7
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Charousova M, Kudlickova Peskova M, Takacsova P, Kapolkova K, Haddad Y, Bilek J, Sivak L, Bartejs T, Heger Z, Pekarik V. Engineered human H-chain ferritin with reversed charge of the internal cavity exhibits RNA-mediated spongelike effect for loading RNA/DNA-binding molecules. Biomater Sci 2024; 12:1249-1262. [PMID: 38247338 DOI: 10.1039/d3bm01257c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Ferritins are globular proteins with an internal cavity that enables the encapsulation of a plethora of low-mass compounds. Unfortunately, the overall negative surface charge of ferritin's internal cavity hampers efficient loading of negatively charged molecules. Therefore, we produced a genetically engineered human H-chain ferritin containing a cationic RKRK domain, reversing the natural net charge of the cavity to positive, thus allowing for efficient encapsulation of negatively charged siRNA. Due to the reversed, positive charge mediated by RKRK domains, the recombinant ferritin produced in E. coli inherently carries a load of bacterial RNA inside its cavity, turning the protein into an effective sponge possessing high affinity for DNA/RNA-binding substances that can be loaded with markedly higher efficiency compared to the wildtype protein. Using doxorubicin as payload, we show that due to its loading through the RNA sponge, doxorubicin is released in a sustained manner, with a cytotoxicity profile similar to the free drug. In summary, this is the first report demonstrating a ferritin/nucleic acid hybrid delivery vehicle with a broad spectrum of properties exploitable in various fields of biomedical applications.
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Affiliation(s)
- Marketa Charousova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia.
| | - Marie Kudlickova Peskova
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno CZ-625 00, Czechia.
| | - Paulina Takacsova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia.
| | - Katerina Kapolkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia.
| | - Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia.
| | - Jan Bilek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia.
| | - Ladislav Sivak
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia.
| | - Tomas Bartejs
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno CZ-625 00, Czechia.
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia.
| | - Vladimir Pekarik
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czechia.
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno CZ-625 00, Czechia.
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8
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Xu S, Xu X, Wang Z, Wu R. A Systematic Investigation of Proteoforms with N-Terminal Glycine and Their Dynamics Reveals Its Impacts on Protein Stability. Angew Chem Int Ed Engl 2024; 63:e202315286. [PMID: 38117010 PMCID: PMC10981938 DOI: 10.1002/anie.202315286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
The N-termini of proteins can regulate their degradation, and the same protein with different N-termini may have distinct dynamics. Recently, it was found that N-terminal glycine can serve as a degron recognized by two E3 ligases, but N-terminal glycine was also reported to stabilize proteins. Here we developed a chemoenzymatic method for selective enrichment of proteoforms with N-terminal glycine and integrated dual protease cleavage to further improve the enrichment specificity. Over 2000 unique peptides with protein N-terminal glycine were analyzed from >1000 proteins, and most of them are previously unknown, indicating the effectiveness of the current method to capture low-abundance proteoforms with N-terminal glycine. The degradation rates of proteoforms with N-terminal glycine were quantified along with those of proteins from the whole proteome. Bioinformatic analyses reveal that proteoforms with N-terminal glycine with the fastest and slowest degradation rates have different functions and localizations. Membrane proteins with N-terminal glycine and proteins with N-terminal glycine from the N-terminal methionine excision degrade more rapidly. Furthermore, the secondary structures, adjacent amino acid residues, and protease specificities for N-terminal glycine are also vital for protein degradation. The results advance our understanding of the effects of N-terminal glycine on protein properties and functions.
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Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zeyu Wang
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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9
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Madera D, Alonso-Gómez A, Delgado MJ, Valenciano AI, Alonso-Gómez ÁL. Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression. Int J Mol Sci 2023; 25:54. [PMID: 38203224 PMCID: PMC10779419 DOI: 10.3390/ijms25010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/05/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
The aim of this work is the full characterization of all the nocturnin (noc) paralogues expressed in a teleost, the goldfish. An in silico analysis of the evolutive origin of noc in Osteichthyes is performed, including the splicing variants and new paralogues appearing after teleostean 3R genomic duplication and the cyprinine 4Rc. After sequencing the full-length mRNA of goldfish, we obtained two isoforms for noc-a (noc-aa and noc-ab) with two splice variants (I and II), and only one for noc-b (noc-bb) with two transcripts (II and III). Using the splicing variant II, the prediction of the secondary and tertiary structures renders a well-conserved 3D distribution of four α-helices and nine β-sheets in the three noc isoforms. A synteny analysis based on the localization of noc genes in the patrilineal or matrilineal subgenomes and a phylogenetic tree of protein sequences were accomplished to stablish a classification and a long-lasting nomenclature of noc in goldfish, and valid to be extrapolated to allotetraploid Cyprininae. Finally, both goldfish and zebrafish showed a broad tissue expression of all the noc paralogues. Moreover, the enriched expression of specific paralogues in some tissues argues in favour of neo- or subfunctionalization.
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Affiliation(s)
| | | | | | | | - Ángel Luis Alonso-Gómez
- Departamento de Genética, Fisiología y Microbiología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.M.); (A.A.-G.); (M.J.D.); (A.I.V.)
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10
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Jeong DE, Lee HS, Ku B, Kim CH, Kim SJ, Shin HC. Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates. Commun Biol 2023; 6:1214. [PMID: 38030679 PMCID: PMC10687169 DOI: 10.1038/s42003-023-05602-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
The N-end rule pathway is a proteolytic system involving the destabilization of N-terminal amino acids, known as N-degrons, which are recognized by N-recognins. Dysregulation of the N-end rule pathway results in the accumulation of undesired proteins, causing various diseases. The E3 ligases of the UBR subfamily recognize and degrade N-degrons through the ubiquitin-proteasome system. Herein, we investigated UBR4, which has a distinct mechanism for recognizing type-2 N-degrons. Structural analysis revealed that the UBR box of UBR4 differs from other UBR boxes in the N-degron binding sites. It recognizes type-2 N-terminal amino acids containing an aromatic ring and type-1 N-terminal arginine through two phenylalanines on its hydrophobic surface. We also characterized the binding mechanism for the second ligand residue. This is the report on the structural basis underlying the recognition of type-2 N-degrons by the UBR box with implications for understanding the N-end rule pathway.
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Affiliation(s)
- Da Eun Jeong
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioscience & Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hye Seon Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, 34141, Republic of Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, 34141, Republic of Korea
| | - Cheol-Hee Kim
- Department of Bioscience & Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seung Jun Kim
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Ho-Chul Shin
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134, Republic of Korea.
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11
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Saini S, Sharma P, Singh P, Kumar V, Yadav P, Sharma A. Nitric oxide: An emerging warrior of plant physiology under abiotic stress. Nitric Oxide 2023; 140-141:58-76. [PMID: 37848156 DOI: 10.1016/j.niox.2023.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/05/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
The natural environment of plants comprises a complex set of various abiotic stresses and their capability to react and survive under this anticipated changing climate is highly flexible and involves a series of balanced interactions between signaling molecules where nitric oxide becomes a crucial component. In this article, we focussed on the role of nitric oxide (NO) in various signal transduction pathways of plants and its positive impact on maintaining cellular homeostasis under various abiotic stresses. Besides this, the recent data on interactions of NO with various phytohormones to control physiological and biochemical processes to attain abiotic stress tolerance have also been considered. These crosstalks modulate the plant's defense mechanism and help in alleviating the negative impact of stress. While focusing on the diverse functions of NO, an effort has been made to explore the functions of NO-mediated post-translational modifications, such as the N-end rule pathway, tyrosine nitration, and S-nitrosylation which revealed the exact mechanism and characterization of proteins that modify various metabolic processes in stressed conditions. Considering all of these factors, the present review emphasizes the role of NO and its interlinking with various phytohormones in maintaining developmental processes in plants, specifically under unfavorable environments.
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Affiliation(s)
- Sakshi Saini
- Department of Botany, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Priyanka Sharma
- Department of Botany, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Pooja Singh
- Department of Botany, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Vikram Kumar
- Department of Botany, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Priya Yadav
- Department of Botany, Zakir Husain Delhi College, University of Delhi, New Delhi, India.
| | - Asha Sharma
- Department of Botany, Maharshi Dayanand University, Rohtak, 124001, Haryana, India.
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12
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Zhao S, Olmayev-Yaakobov D, Ru W, Li S, Chen X, Zhang J, Yao X, Koren I, Zhang K, Xu C. Molecular basis for C-degron recognition by CRL2 APPBP2 ubiquitin ligase. Proc Natl Acad Sci U S A 2023; 120:e2308870120. [PMID: 37844242 PMCID: PMC10614623 DOI: 10.1073/pnas.2308870120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/11/2023] [Indexed: 10/18/2023] Open
Abstract
E3 ubiquitin ligases determine the specificity of eukaryotic protein degradation by selective binding to destabilizing protein motifs, termed degrons, in substrates for ubiquitin-mediated proteolysis. The exposed C-terminal residues of proteins can act as C-degrons that are recognized by distinct substrate receptors (SRs) as part of dedicated cullin-RING E3 ubiquitin ligase (CRL) complexes. APPBP2, an SR of Cullin 2-RING ligase (CRL2), has been shown to recognize R-x-x-G/C-degron; however, the molecular mechanism of recognition remains elusive. By solving several cryogenic electron microscopy structures of active CRL2APPBP2 bound with different R-x-x-G/C-degrons, we unveiled the molecular mechanisms underlying the assembly of the CRL2APPBP2 dimer and tetramer, as well as C-degron recognition. The structural study, complemented by binding experiments and cell-based assays, demonstrates that APPBP2 specifically recognizes the R-x-x-G/C-degron via a bipartite mechanism; arginine and glycine, which play critical roles in C-degron recognition, accommodate distinct pockets that are spaced by two residues. In addition, the binding pocket is deep enough to enable the interaction of APPBP2 with the motif placed at or up to three residues upstream of the C-end. Overall, our study not only provides structural insight into CRL2APPBP2-mediated protein turnover but also serves as the basis for future structure-based chemical probe design.
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Affiliation(s)
- Shidong Zhao
- Ministry of Education Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei230027, Peoples Republic of China
| | - Diana Olmayev-Yaakobov
- The Mina and Everard GoodmanFaculty of Life Sciences, Bar-Ilan University, Ramat-Gan5290002, Israel
| | - Wenwen Ru
- Ministry of Education Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei230027, Peoples Republic of China
| | - Shanshan Li
- Ministry of Education Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei230027, Peoples Republic of China
| | - Xinyan Chen
- Ministry of Education Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei230027, Peoples Republic of China
| | - Jiahai Zhang
- Ministry of Education Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei230027, Peoples Republic of China
| | - Xuebiao Yao
- Ministry of Education Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei230027, Peoples Republic of China
| | - Itay Koren
- The Mina and Everard GoodmanFaculty of Life Sciences, Bar-Ilan University, Ramat-Gan5290002, Israel
| | - Kaiming Zhang
- Ministry of Education Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei230027, Peoples Republic of China
| | - Chao Xu
- Ministry of Education Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei230027, Peoples Republic of China
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13
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Tokumon R, Sebastián I, Humbel BM, Okura N, Yamanaka H, Yamashiro T, Toma C. Degradation of p0071 and p120-catenin during adherens junction disassembly by Leptospira interrogans. Front Cell Infect Microbiol 2023; 13:1228051. [PMID: 37795382 PMCID: PMC10545952 DOI: 10.3389/fcimb.2023.1228051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/23/2023] [Indexed: 10/06/2023] Open
Abstract
Leptospira interrogans disseminates hematogenously to reach the target organs by disrupting epithelial adherens junctions (AJs), thus causing leptospirosis, which is a globally neglected zoonotic disease. L. interrogans induces E-cadherin (E-cad) endocytosis and cytoskeletal rearrangement during AJ disassembly, but the detailed mechanism remains unknown. Elucidation of AJ disassembly mechanisms will guide new approaches to developing vaccines and diagnostic methods. In this study, we combine proteomic and imaging analysis with chemical inhibition studies to demonstrate that disrupting the AJs of renal proximal tubule epithelial cells involves the degradation of two armadillo repeat-containing proteins, p0071 and p120-catenin, that stabilize E-cad at the plasma membrane. Combining proteasomal and lysosomal inhibitors substantially prevented p120-catenin degradation, and monolayer integrity destruction without preventing p0071 proteolysis. In contrast, the pan-caspase inhibitor Z-VAD-FMK inhibited p0071 proteolysis and displacement of both armadillo repeat-containing proteins from the cell-cell junctions. Our results show that L. interrogans induces p120-catenin and p0071 degradation, which mutually regulates E-cad stability by co-opting multiple cellular degradation pathways. This strategy may allow L. interrogans to disassemble AJs and disseminate through the body efficiently.
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Affiliation(s)
- Romina Tokumon
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Isabel Sebastián
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Bruno M. Humbel
- Provost Office, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Microscopy Center, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobuhiko Okura
- Department of Molecular Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hidenori Yamanaka
- Environmental Technology Department, Chemicals Evaluation and Research Institute, Saitama, Japan
| | - Tetsu Yamashiro
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Claudia Toma
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
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14
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Chang YH. Impact of Protein N α-Modifications on Cellular Functions and Human Health. Life (Basel) 2023; 13:1613. [PMID: 37511988 PMCID: PMC10381334 DOI: 10.3390/life13071613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Most human proteins are modified by enzymes that act on the α-amino group of a newly synthesized polypeptide. Methionine aminopeptidases can remove the initiator methionine and expose the second amino acid for further modification by enzymes responsible for myristoylation, acetylation, methylation, or other chemical reactions. Specific acetyltransferases can also modify the initiator methionine and sometimes the acetylated methionine can be removed, followed by further modifications. These modifications at the protein N-termini play critical roles in cellular protein localization, protein-protein interaction, protein-DNA interaction, and protein stability. Consequently, the dysregulation of these modifications could significantly change the development and progression status of certain human diseases. The focus of this review is to highlight recent progress in our understanding of the roles of these modifications in regulating protein functions and how these enzymes have been used as potential novel therapeutic targets for various human diseases.
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Affiliation(s)
- Yie-Hwa Chang
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University Medical School, Saint Louis, MO 63104, USA
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15
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Lee J, Sung KW, Bae EJ, Yoon D, Kim D, Lee JS, Park DH, Park DY, Mun SR, Kwon SC, Kim HY, Min JO, Lee SJ, Suh YH, Kwon YT. Targeted degradation of ⍺-synuclein aggregates in Parkinson's disease using the AUTOTAC technology. Mol Neurodegener 2023; 18:41. [PMID: 37355598 PMCID: PMC10290391 DOI: 10.1186/s13024-023-00630-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/31/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND There are currently no disease-modifying therapeutics for Parkinson's disease (PD). Although extensive efforts were undertaken to develop therapeutic approaches to delay the symptoms of PD, untreated α-synuclein (α-syn) aggregates cause cellular toxicity and stimulate further disease progression. PROTAC (Proteolysis-Targeting Chimera) has drawn attention as a therapeutic modality to target α-syn. However, no PROTACs have yet shown to selectively degrade α-syn aggregates mainly owing to the limited capacity of the proteasome to degrade aggregates, necessitating the development of novel approaches to fundamentally eliminate α-syn aggregates. METHODS We employed AUTOTAC (Autophagy-Targeting Chimera), a macroautophagy-based targeted protein degradation (TPD) platform developed in our earlier studies. A series of AUTOTAC chemicals was synthesized as chimeras that bind both α-syn aggregates and p62/SQSTM1/Sequestosome-1, an autophagic receptor. The efficacy of Autotacs was evaluated to target α-syn aggregates to phagophores and subsequently lysosomes for hydrolysis via p62-dependent macroautophagy. The target engagement was monitored by oligomerization and localization of p62 and autophagic markers. The therapeutic efficacy to rescue PD symptoms was characterized in cultured cells and mice. The PK/PD (pharmacokinetics/pharmacodynamics) profiles were investigated to develop an oral drug for PD. RESULTS ATC161 induced selective degradation of α-syn aggregates at DC50 of ~ 100 nM. No apparent degradation was observed with monomeric α-syn. ATC161 mediated the targeting of α-syn aggregates to p62 by binding the ZZ domain and accelerating p62 self-polymerization. These p62-cargo complexes were delivered to autophagic membranes for lysosomal degradation. In PD cellular models, ATC161 exhibited therapeutic efficacy to reduce cell-to-cell transmission of α-syn and to rescue cells from the damages in DNA and mitochondria. In PD mice established by injecting α-syn preformed fibrils (PFFs) into brain striata via stereotaxic surgery, oral administration of ATC161 at 10 mg/kg induced the degradation of α-syn aggregates and reduced their propagation. ATC161 also mitigated the associated glial inflammatory response and improved muscle strength and locomotive activity. CONCLUSION AUTOTAC provides a platform to develop drugs for PD. ATC161, an oral drug with excellent PK/PD profiles, induces selective degradation of α-syn aggregates in vitro and in vivo. We suggest that ATC161 is a disease-modifying drug that degrades the pathogenic cause of PD.
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Affiliation(s)
- Jihoon Lee
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- AUTOTAC Bio Inc., Changkyunggung-Ro 254, Jongno-Gu, Seoul, 03077, Republic of Korea
| | - Ki Woon Sung
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- AUTOTAC Bio Inc., Changkyunggung-Ro 254, Jongno-Gu, Seoul, 03077, Republic of Korea
| | - Eun-Jin Bae
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Neuroscience Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Dabin Yoon
- AUTOTAC Bio Inc., Changkyunggung-Ro 254, Jongno-Gu, Seoul, 03077, Republic of Korea
- Department of Physical Education, Sejong University, Seoul, 05006, Republic of Korea
| | - Dasarang Kim
- AUTOTAC Bio Inc., Changkyunggung-Ro 254, Jongno-Gu, Seoul, 03077, Republic of Korea
| | - Jin Saem Lee
- AUTOTAC Bio Inc., Changkyunggung-Ro 254, Jongno-Gu, Seoul, 03077, Republic of Korea
| | - Da-Ha Park
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Neuroscience Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Daniel Youngjae Park
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Su Ran Mun
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Soon Chul Kwon
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Hye Yeon Kim
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Joo-Ok Min
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Neuroscience Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Seung-Jae Lee
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Neuroscience Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
- Neuramedy Co. Ltd, Seoul, 04796, Republic of Korea
- Convergence Research Center for Dementia, Seoul National University Medical Research Center, Seoul, 03080, Republic of Korea
| | - Young Ho Suh
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.
- Neuroscience Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.
| | - Yong Tae Kwon
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.
- AUTOTAC Bio Inc., Changkyunggung-Ro 254, Jongno-Gu, Seoul, 03077, Republic of Korea.
- Convergence Research Center for Dementia, Seoul National University Medical Research Center, Seoul, 03080, Republic of Korea.
- Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.
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16
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Kwon SC, Lee J, Kwon YT, Heo AJ. Monitoring the interactions between N-degrons and N-recognins of the Arg/N-degron pathway. Methods Enzymol 2023; 686:165-203. [PMID: 37532399 DOI: 10.1016/bs.mie.2023.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
As defined by the N-degron pathway, single N-terminal (Nt) amino acids can function as N-degrons that induce the degradation of proteins and other biological materials. Central to this pathway is the selective recognition of N-degrons by cognate N-recognins that direct the substrates to either the ubiquitin (Ub)-proteasome system (UPS) or autophagy-lysosome pathway (ALP). Eukaryotic cells have developed diverse pathways to utilize all 20 amino acids in the genetic code as pro-N-degrons or N-degrons which can be generated through endoproteolytic cleavage or post-translational modifications. Amongst these, the arginine (Arg) N-degron plays a key role in both cis- and trans-degradation of a large spectrum of cellular materials by the proteasome or lysosome. In mammals, Arg/N-degrons can be generated through endoproteolytic cleavage or post-translational conjugation of the amino acid L-Arg by ATE1-encoded R-transferases (EC 2.3.2.8), which requires Arg-tRNAArg as a cofactor. Arg/N-degrons of short-lived substrates are recognized by a family of N-recognins characterized by the UBR box for polyubiquitination and proteasomal degradation. Under stresses, however, the same degrons can be recognized for autophagic degradation by the ZZ domain of the N-recognin p62/SQSTSM-1/Sequestosome-1 or KCMF1. Biochemical tools were developed to monitor the interaction of Arg/N-degrons with its cognate N-recognins. These assays were employed to identify new N-recognins and to characterize their biochemical properties and physiological functions. The principles of these assays may be applied for other types of N-degron pathways. Below, we describe the methods that analyze the interaction of Arg/N-degrons and their chemical mimics to N-recognins.
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Affiliation(s)
- Soon Chul Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, South Korea
| | - Jihoon Lee
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, South Korea; AUTOTAC Bio Inc., Seoul, South Korea
| | - Yong Tae Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, South Korea; AUTOTAC Bio Inc., Seoul, South Korea; Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul, South Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul, South Korea.
| | - Ah Jung Heo
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, South Korea.
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17
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Shim SM, Choi HR, Kwon SC, Kim HY, Sung KW, Jung EJ, Mun SR, Bae TH, Kim DH, Son YS, Jung CH, Lee J, Lee MJ, Park JW, Kwon YT. The Cys-N-degron pathway modulates pexophagy through the N-terminal oxidation and arginylation of ACAD10. Autophagy 2023; 19:1642-1661. [PMID: 36184612 PMCID: PMC10262816 DOI: 10.1080/15548627.2022.2126617] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/02/2022] Open
Abstract
In the N-degron pathway, N-recognins recognize cognate substrates for degradation via the ubiquitin (Ub)-proteasome system (UPS) or the autophagy-lysosome system (hereafter autophagy). We have recently shown that the autophagy receptor SQSTM1/p62 (sequestosome 1) is an N-recognin that binds the N-terminal arginine (Nt-Arg) as an N-degron to modulate autophagic proteolysis. Here, we show that the N-degron pathway mediates pexophagy, in which damaged peroxisomal fragments are degraded by autophagy under normal and oxidative stress conditions. This degradative process initiates when the Nt-Cys of ACAD10 (acyl-CoA dehydrogenase family, member 10), a receptor in pexophagy, is oxidized into Cys sulfinic (CysO2) or sulfonic acid (CysO3) by ADO (2-aminoethanethiol (cysteamine) dioxygenase). Under oxidative stress, the Nt-Cys of ACAD10 is chemically oxidized by reactive oxygen species (ROS). The oxidized Nt-Cys2 is arginylated by ATE1-encoded R-transferases, generating the RCOX N-degron. RCOX-ACAD10 marks the site of pexophagy via the interaction with PEX5 and binds the ZZ domain of SQSTM1/p62, recruiting LC3+-autophagic membranes. In mice, knockout of either Ate1 responsible for Nt-arginylation or Sqstm1/p62 leads to increased levels of peroxisomes. In the cells from patients with peroxisome biogenesis disorders (PBDs), characterized by peroxisomal loss due to uncontrolled pexophagy, inhibition of either ATE1 or SQSTM1/p62 was sufficient to recover the level of peroxisomes. Our results demonstrate that the Cys-N-degron pathway generates an N-degron that regulates the removal of damaged peroxisomal membranes along with their contents. We suggest that tannic acid, a commercially available drug on the market, has a potential to treat PBDs through its activity to inhibit ATE1 R-transferases.Abbreviations: ACAA1, acetyl-Coenzyme A acyltransferase 1; ACAD, acyl-Coenzyme A dehydrogenase; ADO, 2-aminoethanethiol (cysteamine) dioxygenase; ATE1, arginyltransferase 1; CDO1, cysteine dioxygenase type 1; ER, endoplasmic reticulum; LIR, LC3-interacting region; MOXD1, monooxygenase, DBH-like 1; NAC, N-acetyl-cysteine; Nt-Arg, N-terminal arginine; Nt-Cys, N-terminal cysteine; PB1, Phox and Bem1p; PBD, peroxisome biogenesis disorder; PCO, plant cysteine oxidase; PDI, protein disulfide isomerase; PTS, peroxisomal targeting signal; R-COX, Nt-Arg-CysOX; RNS, reactive nitrogen species; ROS, reactive oxygen species; SNP, sodium nitroprusside; UBA, ubiquitin-associated; UPS, ubiquitinproteasome system.
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Affiliation(s)
- Sang Mi Shim
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Ha Rim Choi
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Soon Chul Kwon
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hye Yeon Kim
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Ki Woon Sung
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
- AUTOTAC Bio Inc., Seoul, Republic of Korea
| | - Eui Jung Jung
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Su Ran Mun
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Tae Hyun Bae
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Dong Hyun Kim
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Korea
| | - Yeon Sung Son
- Neuroscience Research Institute, Medical Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Chan Hoon Jung
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jihoon Lee
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
- AUTOTAC Bio Inc., Seoul, Republic of Korea
| | - Min Jae Lee
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Joo-Won Park
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Yong Tae Kwon
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
- AUTOTAC Bio Inc., Seoul, Republic of Korea
- Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
- SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
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18
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Heo AJ, Kim SB, Kwon YT, Ji CH. The N-degron pathway: From basic science to therapeutic applications. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194934. [PMID: 36990317 DOI: 10.1016/j.bbagrm.2023.194934] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
The N-degron pathway is a degradative system in which single N-terminal (Nt) amino acids regulate the half-lives of proteins and other biological materials. These determinants, called N-degrons, are recognized by N-recognins that link them to the ubiquitin (Ub)-proteasome system (UPS) or autophagy-lysosome system (ALS). In the UPS, the Arg/N-degron pathway targets the Nt-arginine (Nt-Arg) and other N-degrons to assemble Lys48 (K48)-linked Ub chains by UBR box N-recognins for proteasomal proteolysis. In the ALS, Arg/N-degrons are recognized by the N-recognin p62/SQSTSM-1/Sequestosome-1 to induce cis-degradation of substrates and trans-degradation of various cargoes such as protein aggregates and subcellular organelles. This crosstalk between the UPS and ALP involves reprogramming of the Ub code. Eukaryotic cells developed diverse ways to target all 20 principal amino acids for degradation. Here we discuss the components, regulation, and functions of the N-degron pathways, with an emphasis on the basic mechanisms and therapeutic applications of Arg/N-degrons and N-recognins.
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Affiliation(s)
- Ah Jung Heo
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Su Bin Kim
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Yong Tae Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Republic of Korea; Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul 110-799, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 110-799, Republic of Korea.
| | - Chang Hoon Ji
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Republic of Korea.
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19
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Abeywansha T, Huang W, Ye X, Nawrocki A, Lan X, Jankowsky E, Taylor DJ, Zhang Y. The structural basis of tRNA recognition by arginyl-tRNA-protein transferase. Nat Commun 2023; 14:2232. [PMID: 37076488 PMCID: PMC10115844 DOI: 10.1038/s41467-023-38004-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Arginyl-tRNA-protein transferase 1 (ATE1) is a master regulator of protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The diverse functions of ATE1 arise from its unique enzymatic activity to covalently attach an arginine onto its protein substrates in a tRNA-dependent manner. However, how ATE1 (and other aminoacyl-tRNA transferases) hijacks tRNA from the highly efficient ribosomal protein synthesis pathways and catalyzes the arginylation reaction remains a mystery. Here, we describe the three-dimensional structures of Saccharomyces cerevisiae ATE1 with and without its tRNA cofactor. Importantly, the putative substrate binding domain of ATE1 adopts a previously uncharacterized fold that contains an atypical zinc-binding site critical for ATE1 stability and function. The unique recognition of tRNAArg by ATE1 is coordinated through interactions with the major groove of the acceptor arm of tRNA. Binding of tRNA induces conformational changes in ATE1 that helps explain the mechanism of substrate arginylation.
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Affiliation(s)
- Thilini Abeywansha
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xuan Ye
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Allison Nawrocki
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xin Lan
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Derek J Taylor
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Yi Zhang
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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20
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Heo AJ, Ji CH, Kwon YT. The Cys/N-degron pathway in the ubiquitin-proteasome system and autophagy. Trends Cell Biol 2023; 33:247-259. [PMID: 35945077 DOI: 10.1016/j.tcb.2022.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 10/15/2022]
Abstract
The N-degron pathway is a degradative system in which the N-terminal residues of proteins modulate the half-lives of proteins and other cellular materials. The majority of amino acids in the genetic code have the potential to induce cis or trans degradation in diverse processes, which requires selective recognition between N-degrons and cognate N-recognins. Of particular interest is the Cys/N-degron branch, in which the N-terminal cysteine (Nt-Cys) induces proteolysis via either the ubiquitin (Ub)-proteasome system (UPS) or the autophagy-lysosome pathway (ALP), depending on physiological conditions. Recent studies provided new insights into the central role of Nt-Cys in sensing the fluctuating levels of oxygen and reactive oxygen species (ROS). Here, we discuss the components, regulations, and functions of the Cys/N-degron pathway.
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Affiliation(s)
- Ah Jung Heo
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
| | - Chang Hoon Ji
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Korea
| | - Yong Tae Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Korea; Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul 110-799, Korea.
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21
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Shade O, Ryan A, Deiters A. Targeted protein degradation through light-activated E3 ligase recruitment. Methods Enzymol 2023; 681:265-286. [PMID: 36764761 DOI: 10.1016/bs.mie.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Optical control of protein function through proteasomal degradation benefits from the noninvasive nature and spatiotemporal precision of light as a trigger. In this chapter, light activation of protein degradation with an optically controlled degron, termed optoDeg, is discussed. This method utilizes genetic code expansion to insert a photocaged analog of lysine at the N-terminal position of a protein of interest for spatial and temporal control of the N-end pathway, inducing proteasomal degradation. Methods for the use of optoDeg for degradation of the fluorescent reporter EGFP and the kinase MEK1 are described. The system is fast, with complete degradation of proteins within minutes following irradiation, and highly specific, with genetically directed introduction of the light-activated degron.
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Affiliation(s)
- Olivia Shade
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Amy Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States.
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22
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Wang R, Wang Z, Lu H. Separation methods for system-wide profiling of protein terminome. Proteomics 2023; 23:e2100374. [PMID: 35997653 DOI: 10.1002/pmic.202100374] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022]
Abstract
Protein N- and C-termini have specific biochemical properties and functions. They play vital roles in various biological processes, such as protein stability and localization. In addition, post-translational modifications and proteolytic processing generate different proteoforms at protein termini. In recent years, terminomics has attracted significant attention, and numerous strategies have been developed to achieve high-throughput and global terminomics analysis. This review summarizes the recent protein N-termini and C-termini enrichment methods and their application in different samples. We also look ahead further application of terminomics in profiling protease substrates and discovery of disease biomarkers and therapeutic targets.
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Affiliation(s)
- Rui Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Zhongjie Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China.,Department of Chemistry and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai, People's Republic of China
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23
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Lee SJ, Kim HY, Lee MJ, Kim SB, Kwon YT, Ji CH. Characterization and chemical modulation of p62/SQSTM1/Sequestosome-1 as an autophagic N-recognin. Methods Enzymol 2023. [PMID: 37532402 DOI: 10.1016/bs.mie.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
In the Arg/N-degron pathway, single N-terminal (Nt) residues function as N-degrons recognized by UBR box-containing N-recognins that induce substrate ubiquitination and proteasomal degradation. Recent studies led to the discovery of the autophagic Arg/N-degron pathway, in which the autophagic receptor p62/SQSTM1/Sequestosome-1 acts as an N-recognin that binds the Nt-Arg and other destabilizing residues as N-degrons. Upon binding to Nt-Arg, p62 undergoes self-polymerization associated with its cargoes, accelerating the macroautophagic delivery of p62-cargo complexes to autophagosomes leading to degradation by lysosomal hydrolases. This autophagic mechanism is emerging as an important pathway that modulates the lysosomal degradation of various biomaterial ranging from protein aggregates and subcellular organelles to invading pathogens. Chemical mimics of the physiological N-degrons were developed to exert therapeutic efficacy in pathophysiological processes associated with neurodegeneration and other related diseases. Here, we describe the methods to monitor the activities of p62 in a dual role as an N-recognin and an autophagic receptor. The topic includes self-polymerization (for cargo condensation), its interaction with LC3 on autophagic membranes (for cargo targeting), and the degradation of p62-cargo complexes by lysosomal hydrolases. We also discuss the development and use of small molecule mimics of N-degrons that modulate p62-dependent macroautophagy in biological and pathophysiological processes.
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24
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Ji CH, Kim SB, Lee MJ, Kwon YT. Monitoring the Activation of Selective Autophagy via N-Terminal Arginylation. Methods Mol Biol 2023; 2620:243-252. [PMID: 37010767 DOI: 10.1007/978-1-0716-2942-0_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
In addition to generating N-degron-carrying substrates destined for proteolysis, N-terminal arginylation can globally upregulate selective macroautophagy via activation of the autophagic N-recognin and archetypal autophagy cargo receptor p62/SQSTM1/sequestosome-1. To evaluate the macroautophagic turnover of cellular substrates, including protein aggregates (aggrephagy) and subcellular organelles (organellophagy) mediated by N-terminal arginylation in vivo, we report here a protocol for assaying the activation of the autophagic Arg/N-degron pathway and degradation of cellular cargoes via N-terminal arginylation. These methods, reagents, and conditions are applicable across a wide spectrum of different cell lines, primary cultures, and/or animal tissues, thereby providing a general means for identification and validation of putative cellular cargoes degraded by Nt-arginylation-activated selective autophagy.
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Affiliation(s)
- Chang Hoon Ji
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Jongno-gu, Seoul, Republic of Korea
- AUTOTAC Bio Inc., Jongno-gu, Seoul, Republic of Korea
| | - Su Bin Kim
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Jongno-gu, Seoul, Republic of Korea
| | - Min Ju Lee
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Jongno-gu, Seoul, Republic of Korea
| | - Yong Tae Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Jongno-gu, Seoul, Republic of Korea.
- AUTOTAC Bio Inc., Jongno-gu, Seoul, Republic of Korea.
- Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea.
- SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea.
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25
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Lee YJ, Kim JK, Jung CH, Kim YJ, Jung EJ, Lee SH, Choi HR, Son YS, Shim SM, Jeon SM, Choe JH, Lee SH, Whang J, Sohn KC, Hur GM, Kim HT, Yeom J, Jo EK, Kwon YT. Chemical modulation of SQSTM1/p62-mediated xenophagy that targets a broad range of pathogenic bacteria. Autophagy 2022; 18:2926-2945. [PMID: 35316156 PMCID: PMC9673928 DOI: 10.1080/15548627.2022.2054240] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The N-degron pathway is a proteolytic system in which the N-terminal degrons (N-degrons) of proteins, such as arginine (Nt-Arg), induce the degradation of proteins and subcellular organelles via the ubiquitin-proteasome system (UPS) or macroautophagy/autophagy-lysosome system (hereafter autophagy). Here, we developed the chemical mimics of the N-degron Nt-Arg as a pharmaceutical means to induce targeted degradation of intracellular bacteria via autophagy, such as Salmonella enterica serovar Typhimurium (S. Typhimurium), Escherichia coli, and Streptococcus pyogenes as well as Mycobacterium tuberculosis (Mtb). Upon binding the ZZ domain of the autophagic cargo receptor SQSTM1/p62 (sequestosome 1), these chemicals induced the biogenesis and recruitment of autophagic membranes to intracellular bacteria via SQSTM1, leading to lysosomal degradation. The antimicrobial efficacy was independent of rapamycin-modulated core autophagic pathways and synergistic with the reduced production of inflammatory cytokines. In mice, these drugs exhibited antimicrobial efficacy for S. Typhimurium, Bacillus Calmette-Guérin (BCG), and Mtb as well as multidrug-resistant Mtb and inhibited the production of inflammatory cytokines. This dual mode of action in xenophagy and inflammation significantly protected mice from inflammatory lesions in the lungs and other tissues caused by all the tested bacterial strains. Our results suggest that the N-degron pathway provides a therapeutic target in host-directed therapeutics for a broad range of drug-resistant intracellular pathogens.Abbreviations: ATG: autophagy-related gene; BCG: Bacillus Calmette-Guérin; BMDMs: bone marrow-derived macrophages; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CFUs: colony-forming units; CXCL: C-X-C motif chemokine ligand; EGFP: enhanced green fluorescent protein; IL1B/IL-1β: interleukin 1 beta; IL6: interleukin 6; LIR: MAP1LC3/LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; Mtb: Mycobacterium tuberculosis; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; OPTN: optineurin; PB1: Phox and Bem1; SQSTM1/p62: sequestosome 1; S. Typhimurium: Salmonella enterica serovar Typhimurium; TAX1BP1: Tax1 binding protein 1; TNF: tumor necrosis factor; UBA: ubiquitin-associated.
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Affiliation(s)
- Yoon Jee Lee
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jin Kyung Kim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Korea,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Korea,Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Korea
| | - Chan Hoon Jung
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Young Jae Kim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Korea,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Korea,Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Korea
| | - Eui Jung Jung
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Su Hyun Lee
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Ha Rim Choi
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Yeon Sung Son
- Neuroscience Research Institute, Medical Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Sang Mi Shim
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Sang Min Jeon
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Korea,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Korea,Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Korea
| | - Jin Ho Choe
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Korea,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Korea,Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Korea
| | - Sang-Hee Lee
- Center for Research Equipment, Korea Basic Science Institute, Cheongju, Korea
| | - Jake Whang
- Korea Mycobacterium Resource Center (KMRC) & Basic Research Section, The Korean Institute of Tuberculosis (KIT), Cheongju, Korea
| | - Kyung-Cheol Sohn
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Korea,Department of Pharmacology, Chungnam National University School of Medicine, Daejeon, Korea
| | - Gang Min Hur
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Korea,Department of Pharmacology, Chungnam National University School of Medicine, Daejeon, Korea
| | - Hyun Tae Kim
- Chemistry R&D Center, AUTOTAC Bio Inc, Seoul, Republic of Korea
| | - Jinki Yeom
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea,Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Eun-Kyeong Jo
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Korea,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Korea,Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Korea,CONTACT Eun-Kyeong Jo Department of Microbiology, and Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon35015, Korea
| | - Yong Tae Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea,Chemistry R&D Center, AUTOTAC Bio Inc, Seoul, Republic of Korea,SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea,Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea,Yong Tae Kwon Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul110-799, Korea
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26
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Zheng Y, Zhang S, Luo Y, Li F, Tan J, Wang B, Zhao Z, Lin H, Zhang T, Liu J, Liu X, Guo J, Xie X, Chen L, Liu YG, Chu Z. Rice OsUBR7 modulates plant height by regulating histone H2B monoubiquitination and cell proliferation. PLANT COMMUNICATIONS 2022; 3:100412. [PMID: 35836378 PMCID: PMC9700165 DOI: 10.1016/j.xplc.2022.100412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/20/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Plant height is an important agronomic trait for lodging resistance and yield. Here, we report a new plant-height-related gene, OsUBR7 in rice (Oryza sativa L.); knockout of OsUBR7 caused fewer cells in internodes, resulting in a semi-dwarf phenotype. OsUBR7 encodes a putative E3 ligase containing a plant homeodomain finger and a ubiquitin protein ligase E3 component N-recognin 7 (UBR7) domain. OsUBR7 interacts with histones and monoubiquitinates H2B (H2Bub1) at lysine148 in coordination with the E2 conjugase OsUBC18. OsUBR7 mediates H2Bub1 at a number of chromatin loci for the normal expression of target genes, including cell-cycle-related and pleiotropic genes, consistent with the observation that cell-cycle progression was suppressed in the osubr7 mutant owing to reductions in H2Bub1 and expression levels at these loci. The genetic divergence of OsUBR7 alleles among japonica and indica cultivars affects their transcriptional activity, and these alleles may have undergone selection during rice domestication. Overall, our results reveal a novel mechanism that mediates H2Bub1 in plants, and UBR7 orthologs could be utilized as an untapped epigenetic resource for crop improvement.
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Affiliation(s)
- Yangyi Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Sensen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yanqiu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Fuquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Bin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zhe Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Huifang Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Tingting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jianhong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xupeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Zhizhan Chu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China.
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27
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Winichayakul S, Curran A, Moraga R, Cookson R, Xue H, Crowther T, Roldan M, Bryan G, Roberts N. An alternative angiosperm DGAT1 topology and potential motifs in the N-terminus. FRONTIERS IN PLANT SCIENCE 2022; 13:951389. [PMID: 36186081 PMCID: PMC9523541 DOI: 10.3389/fpls.2022.951389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
The highly variable cytoplasmic N-terminus of the plant diacylglycerol acyltransferase 1 (DGAT1) has been shown to have roles in oligomerization as well as allostery; however, the biological significance of the variation within this region is not understood. Comparing the coding sequences over the variable N-termini revealed the Poaceae DGAT1s contain relatively high GC compositional gradients as well as numerous direct and inverted repeats in this region. Using a variety of reciprocal chimeric DGAT1s from angiosperms we show that related N-termini had similar effects (positive or negative) on the accumulation of the recombinant protein in Saccharomyces cerevisiae. When expressed in Camelina sativa seeds the recombinant proteins of specific chimeras elevated total lipid content of the seeds as well as increased seed size. In addition, we combine N- and C-terminal as well as internal tags with high pH membrane reformation, protease protection and differential permeabilization. This led us to conclude the C-terminus is in the ER lumen; this contradicts earlier reports of the cytoplasmic location of plant DGAT1 C-termini.
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Affiliation(s)
- Somrutai Winichayakul
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Amy Curran
- ZeaKal Inc., San Diego, CA, United States
| | - Roger Moraga
- Bioinformatics and Statistics, AgResearch Ltd., Palmerston North, New Zealand
| | - Ruth Cookson
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Hong Xue
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Tracey Crowther
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Marissa Roldan
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
| | - Greg Bryan
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
- ZeaKal Inc., San Diego, CA, United States
| | - Nick Roberts
- Resilient Agriculture Innovation Centre of Excellence, AgResearch Ltd., Palmerston North, New Zealand
- ZeaKal Inc., San Diego, CA, United States
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28
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Castañeda-Sampedro A, Calvin-Cejudo L, Martin F, Gomez-Diaz C, Alcorta E. The Ntan1 gene is expressed in perineural glia and neurons of adult Drosophila. Sci Rep 2022; 12:14749. [PMID: 36042338 PMCID: PMC9427837 DOI: 10.1038/s41598-022-18999-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
The Drosophila Ntan1 gene encodes an N-terminal asparagine amidohydrolase that we show is highly conserved throughout evolution. Protein isoforms share more than 72% of similarity with their human counterparts. At the cellular level, this gene regulates the type of glial cell growth in Drosophila larvae by its different expression levels. The Drosophila Ntan1 gene has 4 transcripts that encode 2 protein isoforms. Here we describe that although this gene is expressed at all developmental stages and adult organs tested (eye, antennae and brain) there are some transcript-dependent specificities. Therefore, both quantitative and qualitative cues could account for gene function. However, widespread developmental stage and organ-dependent expression could be masking cell-specific constraints that can be explored in Drosophila by using Gal4 drivers. We report a new genetic driver within this gene, Mz317-Gal4, that recapitulates the Ntan1 gene expression pattern in adults. It shows specific expression for perineural glia in the olfactory organs but mixed expression with some neurons in the adult brain. Memory and social behavior disturbances in mice and cancer and schizophrenia in humans have been linked to the Ntan1 gene. Therefore, these new tools in Drosophila may contribute to our understanding of the cellular basis of these alterations.
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Affiliation(s)
- Ana Castañeda-Sampedro
- Facultad de Medicina y Ciencias de la Salud, Departamento de Biología Funcional (Área de Genética), Universidad de Oviedo, c/Julián Clavería S/N, 33006, Oviedo, Asturias, Spain.,Instituto de Neurociencias del Principado de Asturias (INEUROPA), Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Oviedo, Asturias, Spain
| | - Laura Calvin-Cejudo
- Facultad de Medicina y Ciencias de la Salud, Departamento de Biología Funcional (Área de Genética), Universidad de Oviedo, c/Julián Clavería S/N, 33006, Oviedo, Asturias, Spain.,Instituto de Neurociencias del Principado de Asturias (INEUROPA), Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Oviedo, Asturias, Spain
| | - Fernando Martin
- Facultad de Medicina y Ciencias de la Salud, Departamento de Biología Funcional (Área de Genética), Universidad de Oviedo, c/Julián Clavería S/N, 33006, Oviedo, Asturias, Spain.,Instituto de Neurociencias del Principado de Asturias (INEUROPA), Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Oviedo, Asturias, Spain
| | - Carolina Gomez-Diaz
- Facultad de Medicina y Ciencias de la Salud, Departamento de Biología Funcional (Área de Genética), Universidad de Oviedo, c/Julián Clavería S/N, 33006, Oviedo, Asturias, Spain. .,Instituto de Neurociencias del Principado de Asturias (INEUROPA), Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Oviedo, Asturias, Spain.
| | - Esther Alcorta
- Facultad de Medicina y Ciencias de la Salud, Departamento de Biología Funcional (Área de Genética), Universidad de Oviedo, c/Julián Clavería S/N, 33006, Oviedo, Asturias, Spain.,Instituto de Neurociencias del Principado de Asturias (INEUROPA), Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Oviedo, Asturias, Spain
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Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene. Int J Mol Sci 2022; 23:ijms23169352. [PMID: 36012613 PMCID: PMC9409418 DOI: 10.3390/ijms23169352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
In Arabidopsis thaliana, the breaking of seed dormancy in wild type (Col-0) by ethylene at 100 μL L-1 required at least 30 h application. A mutant of the proteolytic N-degron pathway, lacking the E3 ligase PROTEOLYSIS 6 (PRT6), was investigated for its role in ethylene-triggered changes in proteomes during seed germination. Label-free quantitative proteomics was carried out on dormant wild type Col-0 and prt6 seeds treated with (+) or without (-) ethylene. After 16 h, 1737 proteins were identified, but none was significantly different in protein levels in response to ethylene. After longer ethylene treatment (30 h), 2552 proteins were identified, and 619 Differentially Expressed Proteins (DEPs) had significant differences in protein abundances between ethylene treatments and genotypes. In Col, 587 DEPs were enriched for those involved in signal perception and transduction, reserve mobilization and new material generation, which potentially contributed to seed germination. DEPs up-regulated by ethylene in Col included S-adenosylmethionine synthase 1, methionine adenosyltransferase 3 and ACC oxidase involved in ethylene synthesis and of Pyrabactin Resistance1 acting as an ABA receptor, while DEPs down-regulated by ethylene in Col included aldehyde oxidase 4 involved in ABA synthesis. In contrast, in prt6 seeds, ethylene did not result in strong proteomic changes with only 30 DEPs. Taken together, the present work demonstrates that the proteolytic N-degron pathway is essential for ethylene-mediated reprogramming of seed proteomes during germination.
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30
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Ru Y, Yan X, Zhang B, Song L, Feng Q, Ye C, Zhou Z, Yang Z, Li Y, Zhang Z, Li Q, Mi W, Dong C. C-terminal glutamine acts as a C-degron targeted by E3 ubiquitin ligase TRIM7. Proc Natl Acad Sci U S A 2022; 119:e2203218119. [PMID: 35867826 PMCID: PMC9335266 DOI: 10.1073/pnas.2203218119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/06/2022] [Indexed: 01/24/2023] Open
Abstract
The exposed N-terminal or C-terminal residues of proteins can act, in cognate sequence contexts, as degradation signals (degrons) that are targeted by specific E3 ubiquitin ligases for proteasome-dependent degradation by N-degron or C-degron pathways. Here, we discovered a distinct C-degron pathway, termed the Gln/C-degron pathway, in which the B30.2 domain of E3 ubiquitin ligase TRIM7 (TRIM7B30.2) mediates the recognition of proteins bearing a C-terminal glutamine. By determining crystal structures of TRIM7B30.2 in complexes with various peptides, we show that TRIM7B30.2 forms a positively charged binding pocket to engage the "U"-shaped Gln/C-degron. The four C-terminal residues of a substrate play an important role in C-degron recognition, with C-terminal glutamine as the principal determinant. In vitro biochemical and cellular experiments were used to further analyze the substrate specificity and selective degradation of the Gln/C-degron by TRIM7.
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Affiliation(s)
- Yawei Ru
- Haihe Laboratory of Cell Ecosystem, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, 300070, China
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xiaojie Yan
- Haihe Laboratory of Cell Ecosystem, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, 300070, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Bing Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Lili Song
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, Tianjin Medical University, Tianjin, 300070, China
| | - Qiqi Feng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Chen Ye
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, Tianjin Medical University, Tianjin, 300070, China
| | - Zhili Zhou
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, Tianjin Medical University, Tianjin, 300070, China
| | - Zhenzhen Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yao Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Zhenjian Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, Tianjin Medical University, Tianjin, 300070, China
| | - Qianqian Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, Tianjin Medical University, Tianjin, 300070, China
| | - Wenyi Mi
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, Tianjin Medical University, Tianjin, 300070, China
| | - Cheng Dong
- Haihe Laboratory of Cell Ecosystem, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, 300070, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
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31
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Mi L, Min X, Chai Y, Zhang J, Chen X. NLRP1 Inflammasomes: A Potential Target for the Treatment of Several Types of Brain Injury. Front Immunol 2022; 13:863774. [PMID: 35707533 PMCID: PMC9189285 DOI: 10.3389/fimmu.2022.863774] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/28/2022] [Indexed: 12/28/2022] Open
Abstract
NOD-like receptor (NLR) family pyrin domain-containing 1 (NLRP1) is a member of the NLR family. The NLRP1 inflammasome consists of the NLRP1 protein, the adaptor protein apoptosis-associated speck-like protein containing a CARD domain, and the effector molecule pro-caspase-1. When stimulated, the inflammasome initiates the cleavage of pro-caspase-1 and converts it into its active form, caspase-1; then, caspase-1 facilitates the cleavage of the proinflammatory cytokines interleukin-1β and interleukin-18 into their active and secreted forms. In addition, caspase-1 also mediates the cleavage of gasdermin D, which leads to pyroptosis, an inflammatory form of cell death. Pathological events that damage the brain and result in neuropathological conditions can generally be described as brain injury. Neuroinflammation, especially that driven by NLRP1, plays a considerable role in the pathophysiology of brain injury, such as early brain injury (EBI) of subarachnoid hemorrhage, ischemic brain injury during stroke, and traumatic brain injury (TBI). In this article, a thorough overview of NLRP1 is presented, including its structure, mechanism of activation, and role in neuroinflammation. We also present recent studies on NLRP1 as a target for the treatment of EBI, ischemic brain injury, TBI, and other types of brain injury, thus highlighting the perspective of NLRP1 as an effective mediator of catastrophic brain injury.
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Affiliation(s)
- Liang Mi
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Neurological Institute, Key Laboratory of Posttrauma Neurorepair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, China
| | - Xiaobin Min
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
- Baodi Clinical College, Tianjin Medical University, Tianjin, China
| | - Yan Chai
- Tianjin Neurological Institute, Key Laboratory of Posttrauma Neurorepair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, China
| | - Jianning Zhang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Neurological Institute, Key Laboratory of Posttrauma Neurorepair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, China
| | - Xin Chen
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
- Tianjin Neurological Institute, Key Laboratory of Posttrauma Neurorepair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, China
- *Correspondence: Xin Chen,
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The ZZ domain of HERC2 is a receptor of arginylated substrates. Sci Rep 2022; 12:6063. [PMID: 35411094 PMCID: PMC9001736 DOI: 10.1038/s41598-022-10119-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 04/01/2022] [Indexed: 01/18/2023] Open
Abstract
AbstractThe E3 ubiquitin ligase HERC2 has been linked to neurological diseases and cancer, however it remains a poorly characterized human protein. Here, we show that the ZZ domain of HERC2 (HERC2ZZ) recognizes a mimetic of the Nt-R cargo degradation signal. NMR titration experiments and mutagenesis results reveal that the Nt-R mimetic peptide occupies a well-defined binding site of HERC2ZZ comprising of the negatively charged aspartic acids. We report the crystal structure of the DOC domain of HERC2 (HERC2DOC) that is adjacent to HERC2ZZ and show that a conformational rearrangement in the protein may occur when the two domains are linked. Immunofluorescence microscopy data suggest that the stimulation of autophagy promotes targeting of HERC2 to the proteasome. Our findings suggest a role of cytosolic HERC2 in the ubiquitin-dependent degradation pathways.
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33
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Nguyen KT, Ju S, Kim SY, Lee CS, Lee C, Hwang CS. N-Terminal Modifications of Ubiquitin via Methionine Excision, Deamination, and Arginylation Expand the Ubiquitin Code. Mol Cells 2022; 45:158-167. [PMID: 35253655 PMCID: PMC8926867 DOI: 10.14348/molcells.2022.2027] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/16/2021] [Accepted: 01/12/2022] [Indexed: 11/27/2022] Open
Abstract
Ubiquitin (Ub) is post-translationally modified by Ub itself or Ub-like proteins, phosphorylation, and acetylation, among others, which elicits a variety of Ub topologies and cellular functions. However, N-terminal (Nt) modifications of Ub remain unknown, except the linear head-to-tail ubiquitylation via Nt-Met. Here, using the yeast Saccharomyces cerevisiae and an Nt-arginylated Ub-specific antibody, we found that the detectable level of Ub undergoes Nt-Met excision, Nt-deamination, and Nt-arginylation. The resulting Nt-arginylated Ub and its conjugated proteins are upregulated in the stationary-growth phase or by oxidative stress. We further proved the existence of Nt-arginylated Ub in vivo and identified Nt-arginylated Ub-protein conjugates using stable isotope labeling by amino acids in cell culture (SILAC)-based tandem mass spectrometry. In silico structural modeling of Nt-arginylated Ub predicted that Nt-Arg flexibly protrudes from the surface of the Ub, thereby most likely providing a docking site for the factors that recognize it. Collectively, these results reveal unprecedented Nt-arginylated Ub and the pathway by which it is produced, which greatly expands the known complexity of the Ub code.
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Affiliation(s)
- Kha The Nguyen
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Shinyeong Ju
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Sang-Yoon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Chang-Seok Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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Bracci N, de la Fuente C, Saleem S, Pinkham C, Narayanan A, García-Sastre A, Balaraman V, Richt JA, Wilson W, Kehn-Hall K. Rift Valley fever virus Gn V5-epitope tagged virus enables identification of UBR4 as a Gn interacting protein that facilitates Rift Valley fever virus production. Virology 2022; 567:65-76. [PMID: 35032865 PMCID: PMC8877469 DOI: 10.1016/j.virol.2021.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/15/2021] [Accepted: 12/31/2021] [Indexed: 02/03/2023]
Abstract
Rift Valley fever virus (RVFV) is an arbovirus that was first reported in the Rift Valley of Kenya which causes significant disease in humans and livestock. RVFV is a tri-segmented, negative-sense RNA virus consisting of a L, M, and S segments with the M segment encoding the glycoproteins Gn and Gc. Host factors that interact with Gn are largely unknown. To this end, two viruses containing an epitope tag (V5) on the Gn protein in position 105 or 229 (V5Gn105 and V5Gn229) were generated using the RVFV MP-12 vaccine strain as a backbone. The V5-tag insertion minimally impacted Gn functionality as measured by replication kinetics, Gn localization, and antibody neutralization assays. A proteomics-based approach was used to identify novel Gn-binding host proteins, including the E3 ubiquitin-protein ligase, UBR4. Depletion of UBR4 resulted in a significant decrease in RVFV titers and a reduction in viral RNA production.
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Affiliation(s)
- Nicole Bracci
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University,National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Cynthia de la Fuente
- The National Institutes of Health, National Institute of Allergy and Infectious Diseases, DEA,National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Sahar Saleem
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Chelsea Pinkham
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University
| | | | - Velmurugan Balaraman
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University
| | - William Wilson
- National Bio and Agro-Defense Facility, Agricultural Research Service, USDA
| | - Kylene Kehn-Hall
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University,National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University,Center for Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University,Corresponding Author: Kylene Kehn-Hall, Ph.D., Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Integrated Life Sciences Building, 1981 Kraft Drive, Blacksburg, VA 24060 USA,
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35
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Dissecting the molecular mechanisms of mitochondrial import and maturation of peroxiredoxins from yeast and mammalian cells. Biophys Rev 2022; 13:983-994. [PMID: 35059022 DOI: 10.1007/s12551-021-00899-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/01/2021] [Indexed: 12/26/2022] Open
Abstract
Peroxiredoxins (Prxs) are cysteine-based peroxidases that play a central role in keeping the H2O2 at physiological levels. Eukaryotic cells express different Prxs isoforms, which differ in their subcellular locations and substrate specificities. Mitochondrial Prxs are synthesized in the cytosol as precursor proteins containing N-terminal cleavable presequences that act as mitochondrial targeting signals. Due to the fact that presequence controls the import of the vast majority of mitochondrial matrix proteins, the mitochondrial Prxs were initially predicted to be localized exclusively in the matrix. However, recent studies showed that mitochondrial Prxs are also targeted to the intermembrane space by mechanisms that remain poorly understood. While in yeast the IMP complex can translocate Prx1 to the intermembrane space, the maturation of yeast Prx1 and mammalian Prdx3 and Prdx5 in the matrix has been associated with sequential cleavages of the presequence by MPP and Oct1/MIP proteases. In this review, we describe the state of the art of the molecular mechanisms that control the mitochondrial import and maturation of Prxs of yeast and human cells. Once mitochondria are considered the major intracellular source of H2O2, understanding the mitochondrial Prx biogenesis pathways is essential to increase our knowledge about the H2O2-dependent cellular signaling, which is relevant to the pathophysiology of some human diseases.
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36
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Nishida H, Ishihama Y. One-Step Isolation of Protein C-Terminal Peptides from V8 Protease-Digested Proteins by Metal Oxide-Based Ligand-Exchange Chromatography. Anal Chem 2021; 94:944-951. [PMID: 34962382 DOI: 10.1021/acs.analchem.1c03722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed a one-step method to isolate protein C-terminal peptides from V8 protease-digested proteins by metal oxide-based ligand-exchange (MOLEX) chromatography. V8 protease cleaves the C-terminal side of Asp and Glu, affording a digested peptide with two carboxy groups at the C-terminus, whereas the protein C-terminal peptide has only one α-carboxy group. In MOLEX chromatography, a stable chelate is formed between dicarboxylates and metal atoms, so that the nonterminal (i.e., internal) peptide is retained, whereas the protein C-terminal peptide flows through the MOLEX column. After the optimization of the MOLEX chromatographic conditions, 1619 protein C-termini were identified from 30 μg of peptides (10 μg each, in triplicate) derived from human HeLa cells by means of nanoLC/MS/MS. When the MOLEX-isolated sample from 200 μg of HeLa peptides was further divided into six fractions by high-pH reversed-phase liquid chromatography (LC) prior to nanoLC/MS/MS, 2203 protein C-termini were identified with less than 3% contamination with internal peptides. We believe that this is the largest coverage with the highest purity reported to date in human protein C-terminomics. This fast, simple, sensitive, and selective method to isolate protein C-terminal peptides should be useful for profiling protein C-termini on a proteome-wide scale.
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Affiliation(s)
- Hiroshi Nishida
- Department of Molecular & Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,National Institute of Biomedical Innovation, Health and Nutrition, Laboratory of Clinical and Analytical Chemistry, Ibaraki, Osaka 567-0085, Japan
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37
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Wang X, Gomes MM, Bailly C, Nambara E, Corbineau F. Role of ethylene and proteolytic N-degron pathway in the regulation of Arabidopsis seed dormancy. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:2110-2122. [PMID: 34542217 DOI: 10.1111/jipb.13173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/16/2021] [Indexed: 05/22/2023]
Abstract
Primary dormant seeds of Arabidopsis thaliana did not germinate in darkness at temperature higher than 10-15°C. Ethylene improved the germination of dormant wild-type (Col-0) seeds at 25°C in darkness but seeds of the mutant affected in the proteolytic N-degron pathway, proteolysis6 (prt6), were insensitive to ethylene suggesting that PRT6 was involved in dormancy release by ethylene. The substrates of the N-degron pathway, the Ethylene Response Factors from group VII (HRE1, HRE2, RAP2.2, RAP2.3, and RAP2.12), were identified to be involved in this insensitivity with an increased germination in prt6 rap2.2 rap2.3 rap2.12 rather than in prt6 hre1 hre2, which also indicated that the three RAPs acted downstream of PRT6, while the two HREs acted upstream of PRT6. Ethylene reduced the expression of the three RAPs in Col-0 seeds but they were maintained or induced by ethylene in prt6 seeds. The promoting effect of ethylene was associated with a down-regulation of dormancy-related genes in gibberellins (GAs) and abscisic acid (ABA) signaling, such as RGA, RGL2, and ABI5, and with a strong decrease in ABA/GA4 ratio in the presence of ethylene. In contrast, we show that the insensitivity of prt6 seeds to ethylene was mainly related to GA signaling disturbance.
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Affiliation(s)
- Xu Wang
- UMR7622 Biologie du Développement, Sorbonne Université, IBPS, CNRS, Paris, F-75005, France
| | - Malaika Maraya Gomes
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Christophe Bailly
- UMR7622 Biologie du Développement, Sorbonne Université, IBPS, CNRS, Paris, F-75005, France
| | - Eiji Nambara
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Françoise Corbineau
- UMR7622 Biologie du Développement, Sorbonne Université, IBPS, CNRS, Paris, F-75005, France
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Signaling Pathways Regulated by UBR Box-Containing E3 Ligases. Int J Mol Sci 2021; 22:ijms22158323. [PMID: 34361089 PMCID: PMC8346999 DOI: 10.3390/ijms22158323] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/31/2022] Open
Abstract
UBR box E3 ligases, also called N-recognins, are integral components of the N-degron pathway. Representative N-recognins include UBR1, UBR2, UBR4, and UBR5, and they bind destabilizing N-terminal residues, termed N-degrons. Understanding the molecular bases of their substrate recognition and the biological impact of the clearance of their substrates on cellular signaling pathways can provide valuable insights into the regulation of these pathways. This review provides an overview of the current knowledge of the binding mechanism of UBR box N-recognin/N-degron interactions and their roles in signaling pathways linked to G-protein-coupled receptors, apoptosis, mitochondrial quality control, inflammation, and DNA damage. The targeting of these UBR box N-recognins can provide potential therapies to treat diseases such as cancer and neurodegenerative diseases.
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Chen L, Kashina A. Post-translational Modifications of the Protein Termini. Front Cell Dev Biol 2021; 9:719590. [PMID: 34395449 PMCID: PMC8358657 DOI: 10.3389/fcell.2021.719590] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Post-translational modifications (PTM) involve enzyme-mediated covalent addition of functional groups to proteins during or after synthesis. These modifications greatly increase biological complexity and are responsible for orders of magnitude change between the variety of proteins encoded in the genome and the variety of their biological functions. Many of these modifications occur at the protein termini, which contain reactive amino- and carboxy-groups of the polypeptide chain and often are pre-primed through the actions of cellular machinery to expose highly reactive residues. Such modifications have been known for decades, but only a few of them have been functionally characterized. The vast majority of eukaryotic proteins are N- and C-terminally modified by acetylation, arginylation, tyrosination, lipidation, and many others. Post-translational modifications of the protein termini have been linked to different normal and disease-related processes and constitute a rapidly emerging area of biological regulation. Here we highlight recent progress in our understanding of post-translational modifications of the protein termini and outline the role that these modifications play in vivo.
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Affiliation(s)
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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40
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Choi SR, Wang HM, Shin MH, Lim HS. Hydrophobic Tagging-Mediated Degradation of Transcription Coactivator SRC-1. Int J Mol Sci 2021; 22:6407. [PMID: 34203850 PMCID: PMC8232704 DOI: 10.3390/ijms22126407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 01/19/2023] Open
Abstract
Steroid receptor coactivator-1 (SRC-1) is a transcription coactivator playing a pivotal role in mediating a wide range of signaling pathways by interacting with related transcription factors and nuclear receptors. Aberrantly elevated SRC-1 activity is associated with cancer metastasis and progression, and therefore, suppression of SRC-1 is emerging as a promising therapeutic strategy. In this study, we developed a novel SRC-1 degrader for targeted degradation of cellular SRC-1. This molecule consists of a selective ligand for SRC-1 and a bulky hydrophobic group. Since the hydrophobic moiety on the protein surface could mimic a partially denatured hydrophobic region of a protein, SRC-1 could be recognized as an unfolded protein and experience the chaperone-mediated degradation in the cells through the ubiquitin-proteasome system (UPS). Our results demonstrate that a hydrophobic-tagged chimeric molecule is shown to significantly reduce cellular levels of SRC-1 and suppress cancer cell migration and invasion. Together, these results highlight that our SRC-1 degrader represents a novel class of therapeutic candidates for targeting cancer metastasis. Moreover, we believe that the hydrophobic tagging strategy would be widely applicable to develop peptide-based protein degraders with enhanced cellular activity.
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Affiliation(s)
- So Ra Choi
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea; (S.R.C.); (H.M.W.)
| | - Hee Myeong Wang
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea; (S.R.C.); (H.M.W.)
| | - Min Hyeon Shin
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea; (S.R.C.); (H.M.W.)
- POSTECH Biotech Center, Pohang 37673, Korea
| | - Hyun-Suk Lim
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea; (S.R.C.); (H.M.W.)
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41
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Ryan A, Liu J, Deiters A. Targeted Protein Degradation through Fast Optogenetic Activation and Its Application to the Control of Cell Signaling. J Am Chem Soc 2021; 143:9222-9229. [PMID: 34121391 DOI: 10.1021/jacs.1c04324] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Development of methodologies for optically triggered protein degradation enables the study of dynamic protein functions, such as those involved in cell signaling, that are difficult to be probed with traditional genetic techniques. Here, we describe the design and implementation of a novel light-controlled peptide degron conferring N-end pathway degradation to its protein target. The degron comprises a photocaged N-terminal amino acid and a lysine-rich, 13-residue linker. By caging the N-terminal residue, we were able to optically control N-degron recognition by an E3 ligase, consequently controlling ubiquitination and proteasomal degradation of the target protein. We demonstrate broad applicability by applying this approach to a diverse set of target proteins, including EGFP, firefly luciferase, the kinase MEK1, and the phosphatase DUSP6 (also known as MKP3). The caged degron can be used with minimal protein engineering and provides virtually complete, light-triggered protein degradation on a second to minute time scale.
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Affiliation(s)
- Amy Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jihe Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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42
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Kabir MT, Uddin MS, Abdeen A, Ashraf GM, Perveen A, Hafeez A, Bin-Jumah MN, Abdel-Daim MM. Evidence Linking Protein Misfolding to Quality Control in Progressive Neurodegenerative Diseases. Curr Top Med Chem 2021; 20:2025-2043. [PMID: 32552649 DOI: 10.2174/1568026620666200618114924] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/25/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022]
Abstract
Several proteolytic systems including ubiquitin (Ub)-proteasome system (UPS), chaperonemediated autophagy (CMA), and macroautophagy are used by the mammalian cells to remove misfolded proteins (MPs). UPS mediates degradation of most of the MPs, where Ub-conjugated substrates are deubiquitinated, unfolded, and passed through the proteasome's narrow chamber, and eventually break into smaller peptides. It has been observed that the substrates that show a specific degradation signal, the KFERQ sequence motif, can be delivered to and go through CMA-mediated degradation in lysosomes. Macroautophagy can help in the degradation of substrates that are prone to aggregation and resistant to both the CMA and UPS. In the aforesaid case, cargoes are separated into autophagosomes before lysosomal hydrolase-mediated degradation. Even though the majority of the aggregated and MPs in the human proteome can be removed via cellular protein quality control (PQC), some mutant and native proteins tend to aggregate into β-sheet-rich oligomers that exhibit resistance to all identified proteolytic processes and can, therefore, grow into extracellular plaques or inclusion bodies. Indeed, the buildup of protease-resistant aggregated and MPs is a usual process underlying various protein misfolding disorders, including neurodegenerative diseases (NDs) for example Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and prion diseases. In this article, we have focused on the contribution of PQC in the degradation of pathogenic proteins in NDs.
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Affiliation(s)
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh.,Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
| | - Ahmed Abdeen
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Saharanpur, India
| | - Abdul Hafeez
- Glocal School of Pharmacy, Glocal University, Saharanpur, India
| | - May N Bin-Jumah
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11474, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt.,Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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43
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Stevens LM, Kim G, Koromila T, Steele JW, McGehee J, Stathopoulos A, Stein DS. Light-dependent N-end rule-mediated disruption of protein function in Saccharomyces cerevisiae and Drosophila melanogaster. PLoS Genet 2021; 17:e1009544. [PMID: 33999957 PMCID: PMC8158876 DOI: 10.1371/journal.pgen.1009544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 05/27/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
Here we describe the development and characterization of the photo-N-degron, a peptide tag that can be used in optogenetic studies of protein function in vivo. The photo-N-degron can be expressed as a genetic fusion to the amino termini of other proteins, where it undergoes a blue light-dependent conformational change that exposes a signal for the class of ubiquitin ligases, the N-recognins, which mediate the N-end rule mechanism of proteasomal degradation. We demonstrate that the photo-N-degron can be used to direct light-mediated degradation of proteins in Saccharomyces cerevisiae and Drosophila melanogaster with fine temporal control. In addition, we compare the effectiveness of the photo-N-degron with that of two other light-dependent degrons that have been developed in their abilities to mediate the loss of function of Cactus, a component of the dorsal-ventral patterning system in the Drosophila embryo. We find that like the photo-N-degron, the blue light-inducible degradation (B-LID) domain, a light-activated degron that must be placed at the carboxy terminus of targeted proteins, is also effective in eliciting light-dependent loss of Cactus function, as determined by embryonic dorsal-ventral patterning phenotypes. In contrast, another previously described photosensitive degron (psd), which also must be located at the carboxy terminus of associated proteins, has little effect on Cactus-dependent phenotypes in response to illumination of developing embryos. These and other observations indicate that care must be taken in the selection and application of light-dependent and other inducible degrons for use in studies of protein function in vivo, but importantly demonstrate that N- and C-terminal fusions to the photo-N-degron and the B-LID domain, respectively, support light-dependent degradation in vivo. Much of what we know about biological processes has come from the analysis of mutants whose loss-of-function phenotypes provide insight into their normal functions. However, for genes that are required for viability and which have multiple functions in the life of a cell or organism one can only observe mutant phenotypes produced up to the time of death. Normal functions performed in wild-type individuals later than the time of death of mutants cannot be observed. In one approach to overcoming this limitation, a class of peptide degradation signals (degrons) have been developed, which when fused to proteins-of-interest, can target those proteins for degradation in response to various stimuli (temperature, chemical agents, co-expressed proteins, or light). Here we describe a new inducible degron (the photo-N-degron or PND), which when fused to the N-terminus of a protein, can induce N-end rule-mediated degradation in response to blue-light illumination and have validated its use in both yeast and Drosophila embryos. Moreover, using the Drosophila embryonic patterning protein Cactus, we show that like the PND, the previously-described B-LID domain, but not the previously-described photosensitive degron (psd), can produce detectable light-inducible phenotypes in Drosophila embryos that are consistent with the role of Cactus in dorsal-ventral patterning.
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Affiliation(s)
- Leslie M. Stevens
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Goheun Kim
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Theodora Koromila
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - John W. Steele
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - James McGehee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (AS); (DSS)
| | - David S. Stein
- Department of Molecular Biosciences and Institute for Molecular and Cellular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (AS); (DSS)
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44
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Maturation of Mitochondrially Targeted Prx V Involves a Second Cleavage by Mitochondrial Intermediate Peptidase That Is Sensitive to Inhibition by H 2O 2. Antioxidants (Basel) 2021; 10:antiox10030346. [PMID: 33669127 PMCID: PMC7996597 DOI: 10.3390/antiox10030346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/09/2021] [Accepted: 02/22/2021] [Indexed: 12/14/2022] Open
Abstract
Prx V mRNA contains two in-frame AUG codons, producing a long (L-Prx V) and short form of Prx V (S-Prx V), and mouse L-Prx V is expressed as a precursor protein containing a 49-amino acid N-terminal mitochondria targeting sequence. Here, we show that the N-terminal 41-residue sequence of L-Prx V is cleaved by mitochondrial processing peptidase (MPP) in the mitochondrial matrix to produce an intermediate Prx V (I-Prx V) with a destabilizing phenylalanine at its N-terminus, and further, that the next 8-residue sequence is cleaved by mitochondrial intermediate peptidase (MIP) to convert I-Prx V to a stabilized mature form that is identical to S-Prx V. Further, we show that when mitochondrial H2O2 levels are increased in HeLa cells using rotenone, in several mouse tissues by deleting Prx III, and in the adrenal gland by deleting Srx or by exposing mice to immobilized stress, I-Prx V accumulates transiently and mature S-Prx V levels decrease in mitochondria over time. These findings support the view that MIP is inhibited by H2O2, resulting in the accumulation and subsequent degradation of I-Prx V, identifying a role for redox mediated regulation of Prx V proteolytic maturation and expression in mitochondria.
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45
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Yeh CW, Huang WC, Hsu PH, Yeh KH, Wang LC, Hsu PWC, Lin HC, Chen YN, Chen SC, Yeang CH, Yen HCS. The C-degron pathway eliminates mislocalized proteins and products of deubiquitinating enzymes. EMBO J 2021; 40:e105846. [PMID: 33469951 PMCID: PMC8013793 DOI: 10.15252/embj.2020105846] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 01/22/2023] Open
Abstract
Protein termini are determinants of protein stability. Proteins bearing degradation signals, or degrons, at their amino‐ or carboxyl‐termini are eliminated by the N‐ or C‐degron pathways, respectively. We aimed to elucidate the function of C‐degron pathways and to unveil how normal proteomes are exempt from C‐degron pathway‐mediated destruction. Our data reveal that C‐degron pathways remove mislocalized cellular proteins and cleavage products of deubiquitinating enzymes. Furthermore, the C‐degron and N‐degron pathways cooperate in protein removal. Proteome analysis revealed a shortfall in normal proteins targeted by C‐degron pathways, but not of defective proteins, suggesting proteolysis‐based immunity as a constraint for protein evolution/selection. Our work highlights the importance of protein termini for protein quality surveillance, and the relationship between the functional proteome and protein degradation pathways.
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Affiliation(s)
- Chi-Wei Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Wei-Chieh Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Pang-Hung Hsu
- Department of Life Science, Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Kun-Hai Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Li-Chin Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | | | - Hsiu-Chuan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Yi-Ning Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Chuan Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chen-Hsiang Yeang
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.,Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Hsueh-Chi S Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
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46
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Kaushal P, Lee C. N-terminomics - its past and recent advancements. J Proteomics 2020; 233:104089. [PMID: 33359939 DOI: 10.1016/j.jprot.2020.104089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/22/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023]
Abstract
N-terminomics is a rapidly evolving branch of proteomics that encompasses the study of protein N-terminal sequence. A proteome-wide collection of such sequences has been widely used to understand the proteolytic cascades and in annotating the genome. Over the last two decades, various N-terminomic strategies have been developed for achieving high sensitivity, greater depth of coverage, and high-throughputness. We, in this review, cover how the field of N-terminomics has evolved to date, including discussion on various sample preparation and N-terminal peptide enrichment strategies. We also compare different N-terminomic methods and highlight their relative benefits and shortcomings in their implementation. In addition, an overview of the currently available bioinformatics tools and data analysis pipelines for the annotation of N-terminomic datasets is also included. SIGNIFICANCE: It has been recognized that proteins undergo several post-translational modifications (PTM), and a number of perturbed biological pathways are directly associated with modifications at the terminal sites of a protein. In this regard, N-terminomics can be applied to generate a proteome-wide landscape of mature N-terminal sequences, annotate their source of generation, and recognize their significance in the biological pathways. Besides, a system-wide study can be used to study complicated proteolytic machinery and protease cleavage patterns for potential therapeutic targets. Moreover, due to unprecedented improvements in the analytical methods and mass spectrometry instrumentation in recent times, the N-terminomic methodologies now offers an unparalleled ability to study proteoforms and their implications in clinical conditions. Such approaches can further be applied for the detection of low abundant proteoforms, annotation of non-canonical protein coding sites, identification of candidate disease biomarkers, and, last but not least, the discovery of novel drug targets.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea.
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47
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Saurabh K, Shah PP, Doll MA, Siskind LJ, Beverly LJ. UBR-box containing protein, UBR5, is over-expressed in human lung adenocarcinoma and is a potential therapeutic target. BMC Cancer 2020; 20:824. [PMID: 32867711 PMCID: PMC7457484 DOI: 10.1186/s12885-020-07322-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/19/2020] [Indexed: 11/13/2022] Open
Abstract
Background N-end rule ubiquitination pathway is known to be disrupted in many diseases, including cancer. UBR5, an E3 ubiquitin ligase, is mutated and/or overexpressed in human lung cancer cells suggesting its pathological role in cancer. Methods We determined expression of UBR5 protein in multiple lung cancer cell lines and human patient samples. Using immunoprecipitation followed by mass spectrometry we determined the UBR5 interacting proteins. The impact of loss of UBR5 for lung adenocarcinoma cell lines was analyzed using cell viability, clonogenic assays and in vivo xenograft models in nude mice. Additional Western blot analysis was performed to assess the loss of UBR5 on downstream signaling. Statistical analysis was done by one-way ANOVA for in vitro studies and Wilcoxon paired t-test for in vivo tumor volumes. Results We show variability of UBR5 expression levels in lung adenocarcinoma cell lines and in primary human patient samples. To gain better insight into the role that UBR5 may play in lung cancer progression we performed unbiased interactome analyses for UBR5. Data indicate that UBR5 has a wide range of interacting protein partners that are known to be involved in critical cellular processes such as DNA damage, proliferation and cell cycle regulation. We have demonstrated that shRNA-mediated loss of UBR5 decreases cell viability and clonogenic potential of lung adenocarcinoma cell lines. In addition, we found decreased levels of activated AKT signaling after the loss of UBR5 in lung adenocarcinoma cell lines using multiple means of UBR5 knockdown/knockout. Furthermore, we demonstrated that loss of UBR5 in lung adenocarcinoma cells results in significant reduction of tumor volume in nude mice. Conclusions These findings demonstrate that deregulation of the N-end rule ubiquitination pathway plays a crucial role in the etiology of some human cancers, and blocking this pathway via UBR5-specific inhibitors, may represent a unique therapeutic target for human cancers.
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Affiliation(s)
- Kumar Saurabh
- James Graham Brown Cancer Center, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Parag P Shah
- James Graham Brown Cancer Center, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Mark A Doll
- James Graham Brown Cancer Center, School of Medicine, University of Louisville, Louisville, KY, USA.,Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
| | - Leah J Siskind
- James Graham Brown Cancer Center, School of Medicine, University of Louisville, Louisville, KY, USA.,Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
| | - Levi J Beverly
- James Graham Brown Cancer Center, School of Medicine, University of Louisville, Louisville, KY, USA. .,Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA. .,Division of Hematology and Oncology, School of Medicine, University of Louisville, Louisville, KY, USA.
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48
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Lee Y, Heo J, Jeong H, Hong KT, Kwon DH, Shin MH, Oh M, Sable GA, Ahn GO, Lee JS, Song HK, Lim HS. Targeted Degradation of Transcription Coactivator SRC-1 through the N-Degron Pathway. Angew Chem Int Ed Engl 2020; 59:17548-17555. [PMID: 33026161 DOI: 10.1002/anie.202005004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/01/2020] [Indexed: 01/12/2023]
Abstract
Aberrantly elevated steroid receptor coactivator-1 (SRC-1) expression and activity are strongly correlated with cancer progression and metastasis. Here we report, for the first time, the development of a proteolysis targeting chimera (PROTAC) that is composed of a selective SRC-1 binder linked to a specific ligand for UBR box, a unique class of E3 ligases recognizing N-degrons. We showed that the bifunctional molecule efficiently and selectively induced the degradation of SRC-1 in cells through the N-degron pathway. Importantly, given the ubiquitous expression of the UBR protein in most cells, PROTACs targeting the UBR box could degrade a protein of interest regardless of cell types. We also showed that the SRC-1 degrader significantly suppressed cancer cell invasion and migration in vitro and in vivo. Together, these results demonstrate that the SRC-1 degrader can be an invaluable chemical tool in the studies of SRC-1 functions. Moreover, our findings suggest PROTACs based on the N-degron pathway as a widely useful strategy to degrade disease-relevant proteins.
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Affiliation(s)
- Yeongju Lee
- Department of Chemistry and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, South Korea
| | - Jiwon Heo
- School of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea
| | - Hoibin Jeong
- Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Kyung Tae Hong
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), 5. Hwarang-ro, 14-gil, Seongbuk-gu, Seoul, 02792, South Korea
| | - Do Hoon Kwon
- School of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea
| | - Min Hyeon Shin
- Department of Chemistry and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, South Korea
| | - Misook Oh
- Department of Chemistry and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, South Korea
| | - Ganesh A Sable
- Department of Chemistry and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, South Korea
| | - G-One Ahn
- Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), 5. Hwarang-ro, 14-gil, Seongbuk-gu, Seoul, 02792, South Korea
| | - Hyun Kyu Song
- School of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea
| | - Hyun-Suk Lim
- Department of Chemistry and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, South Korea
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49
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Lee Y, Heo J, Jeong H, Hong KT, Kwon DH, Shin MH, Oh M, Sable GA, Ahn G, Lee J, Song HK, Lim H. Targeted Degradation of Transcription Coactivator SRC‐1 through the N‐Degron Pathway. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yeongju Lee
- Department of Chemistry and Division of Advanced Materials Science Pohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang 37673 South Korea
| | - Jiwon Heo
- School of Life Sciences and Biotechnology Korea University 145 Anam-ro, Seongbuk-gu Seoul 02841 South Korea
| | - Hoibin Jeong
- Research Institute for Veterinary Science and College of Veterinary Medicine Seoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 South Korea
| | - Kyung Tae Hong
- Molecular Recognition Research Center Korea Institute of Science and Technology (KIST) 5. Hwarang-ro, 14-gil, Seongbuk-gu Seoul 02792 South Korea
| | - Do Hoon Kwon
- School of Life Sciences and Biotechnology Korea University 145 Anam-ro, Seongbuk-gu Seoul 02841 South Korea
| | - Min Hyeon Shin
- Department of Chemistry and Division of Advanced Materials Science Pohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang 37673 South Korea
| | - Misook Oh
- Department of Chemistry and Division of Advanced Materials Science Pohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang 37673 South Korea
| | - Ganesh A. Sable
- Department of Chemistry and Division of Advanced Materials Science Pohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang 37673 South Korea
| | - G‐One Ahn
- Research Institute for Veterinary Science and College of Veterinary Medicine Seoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 South Korea
| | - Jun‐Seok Lee
- Molecular Recognition Research Center Korea Institute of Science and Technology (KIST) 5. Hwarang-ro, 14-gil, Seongbuk-gu Seoul 02792 South Korea
| | - Hyun Kyu Song
- School of Life Sciences and Biotechnology Korea University 145 Anam-ro, Seongbuk-gu Seoul 02841 South Korea
| | - Hyun‐Suk Lim
- Department of Chemistry and Division of Advanced Materials Science Pohang University of Science and Technology (POSTECH) 77 Cheongam-Ro, Nam-Gu Pohang 37673 South Korea
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50
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Yin L, Hu Q. Chimera induced protein degradation: PROTACs and beyond. Eur J Med Chem 2020; 206:112494. [PMID: 32890974 DOI: 10.1016/j.ejmech.2020.112494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/28/2020] [Accepted: 05/28/2020] [Indexed: 12/13/2022]
Abstract
Ubiquitin-proteasome system, autophagy-lysosome pathway and N-end rule pathway are crucial protein quality control mechanisms in human body. Hijacking these endogenous protein degrading measures by chimera degraders could be a revolutionary strategy for the discovery of small-molecule drugs. As the most advanced chimera degraders, PROTACs have demonstrated the potential by delivering two drug candidates into clinical trials. The development of chimera degraders exploiting these three pathways are reviewed, a focus is given on the chemical structures and their influences on biological effects from a viewpoint of medicinal chemistry.
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Affiliation(s)
- Lina Yin
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232 East Waihuan Road, 51006, Guangzhou, PR China.
| | - Qingzhong Hu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232 East Waihuan Road, 51006, Guangzhou, PR China.
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