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Qin M, Han S, Chen M, Li P, Wang Y, Niu W, Gao C, Wang H, Li Y. Biofilm formation of Hafnia paralvei induced by c-di-GMP through facilitating bcsB gene expression promotes spoilage of Yellow River carp (Cyprinus carpio). Food Microbiol 2024; 120:104482. [PMID: 38431313 DOI: 10.1016/j.fm.2024.104482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 03/05/2024]
Abstract
Hafnia paralvei, a Gram-negative foodborne pathogen, is found ubiquitously in various aquatic animals and seafoods, which can form biofilm as a dominant virulence factor that contributes to its pathogenesis. However, the biofilm formation mechanism of H. paralvei and its effect on food spoilage has not been fully characterized. Here we show that biofilm formation, is regulated by c-di-GMP which mediated by bcsB, can increase the spoilage ability of H. paralvei. We found that GTP was added exogenously to enhance the synthesis of c-di-GMP, which further promoted biofilm formation. The gene dgcC, one of 11 genes encoding GGDEF domain-containing proteins in H. paralvei, was significantly upregulated with GTP as substrate. The upregulation of dgcC contributes to a significant increase of c-di-GMP and the formation of biofilm. In addition, the overexpression of dgcC induced upregulation of bcsB, a reported effector protein encoding gene, which was further demonstrated that overexpression of bcsB can encourage the synthesis of bacterial cellulose and biofilm formation. The effect of biofilm formation induced by c-di-GMP on spoilage of Yellow River carp (Cyprinus carpio) was evaluated by sensory evaluation, the total viable count, and the total volatile basic nitrogen, which showed that biofilm formation can significantly increase the spoilage ability of H. paralvei on C. carpio. Our findings provide the regulation of c-di-GMP on expression of bcsB, that can contribute to biofilm formation and spoilage ability of H. paralvei, which is favor to understanding the pathogenesis of Hafnia paralvei and its role in food spoilage.
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Affiliation(s)
- Mengyuan Qin
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Shuo Han
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Miaomiao Chen
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Pengju Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Yuqi Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Wenfang Niu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Chao Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Hailei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China; Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore, 637141, Singapore
| | - Yi Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China.
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Panda SP, Roy P, Soren D, Ranjan Sahoo D, Dehury B, Rout AK, Behera BK, Das BK. Structural insights of Labeo catla (catla) myxovirus resistance protein,GTP binding recognition and constitutive expression induced with Poly I:C. J Biomol Struct Dyn 2024; 42:3520-3534. [PMID: 37227778 DOI: 10.1080/07391102.2023.2213345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
The Myxovirus resistance (Mx) proteins are critical effectors belonging to the super-family of guanidine triphosphatase, often stimulated by type I interferon (IFN) and mediates antiviral responses to restrict the replication of numerous viral genes in fishes. In teleosts, Mx proteins display diverse and complicated antiviral activity in different species. The present investigation seeks to characterize the Mx gene from Labeo catla upon induction by double-stranded (ds) RNA, polyinosinic-polycytidylic acid, (poly I: C). Molecular modeling and all-atoms molecular dynamics (MD) simulations were employed to understand the architecture of the GTPase domain and its plausible mode of GTP recognition in Mx protein. The full-length L. catla Mx (LcMx) gene sequence (1821 bp nucleotides) encodes an open reading frame of 606 amino acids. Domain search indicated conserved tripartite domain architecture of LcMx and forms a major cluster with the Mx from other teleosts. The positively charged Arginine and polar Glutamine residues from helix 3 and 4 of stalk region LcMx aid in homo-oligomerization. MD simulation portrayed the role of conserved critical residues aid in GTP recognition by the GTPase domain which perfectly corroborates with experimental findings and prior MD studies. After injection of poly I:C, the temporal mRNA profile showed that LcMx expression was significantly elevated in the spleen, brain, kidney, liver, muscle, heart, intestine, and gill tissues. Collectively, these results suggest that the elevated expression of the major innate immune defense gene Mx was able to inhibit the poly I: C mediated virulence in fish.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumya Prasad Panda
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
- Department of Zoology, Ravenshaw University, Cuttack, Odisha, India
| | - Pragyan Roy
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Dhananjay Soren
- Department of Zoology, Ravenshaw University, Cuttack, Odisha, India
| | | | - Budheswar Dehury
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Ajaya Kumar Rout
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Bijay Kumar Behera
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
| | - Basanta Kumar Das
- Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, West Bengal, India
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Chen Y, Liu QP, Xie H, Ding J. From bench to bedside: current development and emerging trend of KRAS-targeted therapy. Acta Pharmacol Sin 2024; 45:686-703. [PMID: 38049578 PMCID: PMC10943119 DOI: 10.1038/s41401-023-01194-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) is the most frequently mutated oncogene in human cancers with mutations predominantly occurring in codon 12. These mutations disrupt the normal function of KRAS by interfering with GTP hydrolysis and nucleotide exchange activity, making it prone to the GTP-bound active state, thus leading to sustained activation of downstream pathways. Despite decades of research, there has been no progress in the KRAS drug discovery until the groundbreaking discovery of covalently targeting the KRASG12C mutation in 2013, which led to revolutionary changes in KRAS-targeted therapy. So far, two small molecule inhibitors sotorasib and adagrasib targeting KRASG12C have received accelerated approval for the treatment of non-small cell lung cancer (NSCLC) harboring KRASG12C mutations. In recent years, rapid progress has been achieved in the KRAS-targeted therapy field, especially the exploration of KRASG12C covalent inhibitors in other KRASG12C-positive malignancies, novel KRAS inhibitors beyond KRASG12C mutation or pan-KRAS inhibitors, and approaches to indirectly targeting KRAS. In this review, we provide a comprehensive overview of the molecular and mutational characteristics of KRAS and summarize the development and current status of covalent inhibitors targeting the KRASG12C mutation. We also discuss emerging promising KRAS-targeted therapeutic strategies, with a focus on mutation-specific and direct pan-KRAS inhibitors and indirect KRAS inhibitors through targeting the RAS activation-associated proteins Src homology-2 domain-containing phosphatase 2 (SHP2) and son of sevenless homolog 1 (SOS1), and shed light on current challenges and opportunities for drug discovery in this field.
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Affiliation(s)
- Yi Chen
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiu-Pei Liu
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Department of Chemical and Environment Engineering, Science and Engineering Building, The University of Nottingham Ningbo China, Ningbo, 315100, China
| | - Hua Xie
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.
| | - Jian Ding
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Ma J, Gong F, Kim E, Du JX, Leung C, Song Q, Logsdon CD, Luo Y, Li X, Lu W. Early elevations of RAS protein level and activity are critical for the development of PDAC in the context of inflammation. Cancer Lett 2024; 586:216694. [PMID: 38307409 PMCID: PMC11032208 DOI: 10.1016/j.canlet.2024.216694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Abstract
The KRASG12D mutation was believed to be locked in a GTP-bound form, rendering it fully active. However, recent studies have indicated that the presence of mutant KRAS alone is insufficient; it requires additional activation through inflammatory stimuli to effectively drive the development of pancreatic ductal adenocarcinoma (PDAC). It remains unclear to what extent RAS activation occurs during the development of PDAC in the context of inflammation. Here, in a mouse model with the concurrent expression of KrasG12D/+ and inflammation mediator IKK2 in pancreatic acinar cells, we showed that, compared to KRASG12D alone, the cooperative interaction between KRASG12D and IKK2 rapidly elevated both the protein level and activity of KRASG12D and NRAS in a short term. This high level was sustained throughout the rest phase of PDAC development. These results suggest that inflammation not only rapidly augments the activity but also the protein abundance, leading to an enhanced total amount of GTP-bound RAS (KRASG12D and NRAS) in the early stage. Notably, while KRASG12D could be further activated by IKK2, not all KRASG12D proteins were in the GTP-bound state. Overall, our findings suggest that although KRASG12D is not fully active in the context of inflammation, concurrent increases in both the protein level and activity of KRASG12D as well as NRAS at the early stage by inflammation contribute to the rise in total GTP-bound RAS.
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Affiliation(s)
- Jianjia Ma
- School of Pharmaceutical Sciences & the First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Fanghua Gong
- School of Pharmaceutical Sciences & the First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Eunice Kim
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - James Xianxing Du
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA; Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, 500 W. University Ave, El Paso, TX, 79968, USA
| | - Cindy Leung
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Qingchun Song
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, 500 W. University Ave, El Paso, TX, 79968, USA
| | - Craig D Logsdon
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yongde Luo
- School of Pharmaceutical Sciences & the First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Xiaokun Li
- School of Pharmaceutical Sciences & the First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Weiqin Lu
- Department of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA; Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, 500 W. University Ave, El Paso, TX, 79968, USA.
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Zhu M, Wu N, Zhong J, Chen C, Liu W, Ren Y, Wang X, Jin H. N 6-methyladenosine modification of the mRNA for a key gene in purine nucleotide metabolism regulates virus proliferation in an insect vector. Cell Rep 2024; 43:113821. [PMID: 38368611 DOI: 10.1016/j.celrep.2024.113821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 02/20/2024] Open
Abstract
The titer of viruses that persist and propagate in their insect vector must be high enough for transmission yet not harm the insect, but the mechanism of this dynamic balance is unclear. Here, expression of inosine monophosphate dehydrogenase (LsIMPDH), a rate-limiting enzyme for guanosine triphosphate (GTP) synthesis, is shown to be downregulated by increased levels of N6-methyladenosine (m6A) on LsIMPDH mRNA in rice stripe virus (RSV)-infected small brown planthoppers (SBPHs; Laodelphax striatellus), the RSV vector, which decreases GTP content, thus limiting viral proliferation. Moreover, planthopper methyltransferase-like protein 3 (LsMETTL3) and m6A reader protein LsYTHDF3 are found to catalyze and recognize the m6A on LsIMPDH mRNA, respectively, and cooperate in destabilizing LsIMPDH transcripts. Co-silencing assays show that negative regulation of viral proliferation by both LsMETTL3 and LsYTHDF3 is partially dependent on LsIMPDH. This distinct mechanism limits virus replication in an insect vector, providing a potential gene target to block viral transmission.
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Affiliation(s)
- Mengjie Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiayi Zhong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chen Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingdang Ren
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Huaibing Jin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Okamoto H, Tanaka Y, Shibagaki Y, Kuronuma S, Miyatani Y, Umeda S, Mishiro-Sato E, Takeuchi O, Hattori S, Kobayashi T, Okuwaki M. Measurement of the intracellular active metabolites of thiopurine drugs to evaluate the enzymatic activity of nudix hydrolase 15 in human blood samples. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1234:123993. [PMID: 38246006 DOI: 10.1016/j.jchromb.2024.123993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 12/13/2023] [Accepted: 01/01/2024] [Indexed: 01/23/2024]
Abstract
Thiopurine is metabolized to 6-thio-(deoxy) guanosine triphosphate (6-thio-(d) GTP), which is then incorporated into DNA or RNA and causes cytotoxicity. Nudix hydrolase 15 (NUDT15) reduces the cytotoxic effects of thiopurine by converting 6-thio-(d) GTP to 6-thio-(d) guanosine monophosphate (6-thio-(d) GMP). NUDT15 polymorphisms like the Arg139Cys variant are strongly linked to thiopurine-induced severe leukocytopenia and alopecia. Therefore, measurement of NUDT15 enzymatic activity in individual patients can help predict thiopurine tolerability and adjust the dosage. We aimed to develop a quantitative assay for NUDT15 enzymatic activity in human blood samples. Blood samples were collected from donors whose NUDT15 genetic status was determined. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to assess the 6-thio-GTP metabolic activity in cell extracts. Because 6-thio-guanosine diphosphate (6-thio-GDP) and 6-thio-GMP were generated upon incubation of 6-thio-GTP with human blood cell extracts, the method detecting 6-thio-GTP, 6-thio-GDP, and 6-thio-GMP was validated. All three metabolites were linearly detected, and the lower limit of quantification (LLOQ) of 6-thio-GTP, 6-thio-GDP, and 6-thio-GMP were 5 μM, 1 μM, and 2 μM, respectively. Matrix effects of human blood cell extracts to detect 6-thio-GTP, 6-thio-GDP, and 6-thio-GMP were 99.0 %, 100.5 %, and 101.4 %, respectively, relative to the signals in the absence of blood cell extracts. The accuracy and precision of the method and the stability of the samples were also assessed. Using this established method, the genotype-dependent differences in NUDT15 activities were successfully determined using cell extracts derived from human blood cells with NUDT15 wild-type (WT) or Arg139Cys variant and 6-thio-GTP (100 μM) as a substrate (18.1, 14.9, and 6.43 μM/h/106 cells for WT, Arg139Cys heterozygous, and homozygous variant, respectively). We developed a method for quantifying intracellular NUDT15 activity in peripheral blood mononuclear cells (PBMCs), which we defined as the conversion of 6-thio-GTP to 6-thio-GMP. Although PBMCs preparation takes some time, its reproducibility in experiments makes it a promising candidate for clinical application. This method can tell the difference between WT and Arg139Cys homozygous blood samples. Even in patients with WT NUDT15, WT samples showed variations in NUDT15 activity, which may correlate with variations in thiopurine dosage.
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Affiliation(s)
- Hitomi Okamoto
- Laboratory of Biochemistry, Graduate School of Pharmaceutical Sciences, Japan; Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Yoichi Tanaka
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan; Division of Medicinal Safety Science, National Institute of Health Sciences, Kanagawa, Japan.
| | - Yoshio Shibagaki
- Laboratory of Biochemistry, Graduate School of Pharmaceutical Sciences, Japan
| | - Satoshi Kuronuma
- Biomedical Laboratory, Department of Research, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Yusuke Miyatani
- Center for Advanced IBD Research and Treatment, Kitasato University Kitasato Institute Hospital, Tokyo, Japan; Department of Gastroenterology and Hepatology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Satoko Umeda
- Center for Advanced IBD Research and Treatment, Kitasato University Kitasato Institute Hospital, Tokyo, Japan; Department of Gastroenterology and Hepatology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Emi Mishiro-Sato
- Laboratory of Biochemistry, Graduate School of Pharmaceutical Sciences, Japan
| | - Osamu Takeuchi
- Biomedical Laboratory, Department of Research, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Seisuke Hattori
- Laboratory of Biochemistry, Graduate School of Pharmaceutical Sciences, Japan
| | - Taku Kobayashi
- Center for Advanced IBD Research and Treatment, Kitasato University Kitasato Institute Hospital, Tokyo, Japan; Department of Gastroenterology and Hepatology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Mitsuru Okuwaki
- Laboratory of Biochemistry, Graduate School of Pharmaceutical Sciences, Japan.
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Fisch U, Kliem P, Grzonka P, Sutter R. Performance of large language models on advocating the management of meningitis: a comparative qualitative study. BMJ Health Care Inform 2024; 31:e100978. [PMID: 38307617 PMCID: PMC10840049 DOI: 10.1136/bmjhci-2023-100978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/15/2024] [Indexed: 02/04/2024] Open
Abstract
OBJECTIVES We aimed to examine the adherence of large language models (LLMs) to bacterial meningitis guidelines using a hypothetical medical case, highlighting their utility and limitations in healthcare. METHODS A simulated clinical scenario of a patient with bacterial meningitis secondary to mastoiditis was presented in three independent sessions to seven publicly accessible LLMs (Bard, Bing, Claude-2, GTP-3.5, GTP-4, Llama, PaLM). Responses were evaluated for adherence to good clinical practice and two international meningitis guidelines. RESULTS A central nervous system infection was identified in 90% of LLM sessions. All recommended imaging, while 81% suggested lumbar puncture. Blood cultures and specific mastoiditis work-up were proposed in only 62% and 38% sessions, respectively. Only 38% of sessions provided the correct empirical antibiotic treatment, while antiviral treatment and dexamethasone were advised in 33% and 24%, respectively. Misleading statements were generated in 52%. No significant correlation was found between LLMs' text length and performance (r=0.29, p=0.20). Among all LLMs, GTP-4 demonstrated the best performance. DISCUSSION Latest LLMs provide valuable advice on differential diagnosis and diagnostic procedures but significantly vary in treatment-specific information for bacterial meningitis when introduced to a realistic clinical scenario. Misleading statements were common, with performance differences attributed to each LLM's unique algorithm rather than output length. CONCLUSIONS Users must be aware of such limitations and performance variability when considering LLMs as a support tool for medical decision-making. Further research is needed to refine these models' comprehension of complex medical scenarios and their ability to provide reliable information.
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Affiliation(s)
- Urs Fisch
- Department of Neurology, University Hospital Basel, Basel, Switzerland
| | - Paulina Kliem
- Clinic for Intensive Care Medicine, University Hospital Basel, Basel, Switzerland
| | - Pascale Grzonka
- Clinic for Intensive Care Medicine, University Hospital Basel, Basel, Switzerland
| | - Raoul Sutter
- Department of Neurology, University Hospital Basel, Basel, Switzerland
- Clinic for Intensive Care Medicine, University Hospital Basel, Basel, Switzerland
- Medical Faculty, University Basel, Basel, Switzerland
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Toyoda S, Handa T, Yong H, Takahashi H, Shiwaku H. IMPDH2 forms spots at branching sites and distal ends of astrocyte stem processes. Genes Cells 2024; 29:150-158. [PMID: 38009721 DOI: 10.1111/gtc.13088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme in the de novo GTP biosynthesis pathway. Recent studies suggest that IMPDH2, an isoform of IMPDH, can localize to specific subcellular compartments under certain conditions and regulate site-specific GTP availability and small GTPase activity in invasive cancer cells. However, it is unclear whether IMPDH2 plays a site-specific regulatory role in subcellular functions in healthy cells. In this study, we focused on brain cells and examined the localization pattern of IMPDH2. We discovered that IMPDH2 forms localized spots in the astrocytes of the adult mouse hippocampus. Further analysis of spot distribution in primary astrocyte cultures revealed that IMPDH2 spots are predominantly localized on branching sites and distal ends of astrocyte stem processes. Our findings suggest a potential unidentified role for IMPDH2 and GTP synthesis specifically at specialized nodes of astrocyte branches.
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Affiliation(s)
- Saori Toyoda
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Takehisa Handa
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Huang Yong
- Department of Neuropathology, Medical Research Institute and Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hidehiko Takahashi
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Hiroki Shiwaku
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
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Gaikwad S, Ghobakhlou F, Zhang H, Hinnebusch AG. Yeast eIF2A has a minimal role in translation initiation and uORF-mediated translational control in vivo. eLife 2024; 12:RP92916. [PMID: 38266075 PMCID: PMC10945734 DOI: 10.7554/elife.92916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
Initiating translation of most eukaryotic mRNAs depends on recruitment of methionyl initiator tRNA (Met-tRNAi) in a ternary complex (TC) with GTP-bound eukaryotic initiation factor 2 (eIF2) to the small (40S) ribosomal subunit, forming a 43S preinitiation complex (PIC) that attaches to the mRNA and scans the 5'-untranslated region (5' UTR) for an AUG start codon. Previous studies have implicated mammalian eIF2A in GTP-independent binding of Met-tRNAi to the 40S subunit and its recruitment to specialized mRNAs that do not require scanning, and in initiation at non-AUG start codons, when eIF2 function is attenuated by phosphorylation of its α-subunit during stress. The role of eIF2A in translation in vivo is poorly understood however, and it was unknown whether the conserved ortholog in budding yeast can functionally substitute for eIF2. We performed ribosome profiling of a yeast deletion mutant lacking eIF2A and isogenic wild-type (WT) cells in the presence or absence of eIF2α phosphorylation induced by starvation for amino acids isoleucine and valine. Whereas starvation of WT confers changes in translational efficiencies (TEs) of hundreds of mRNAs, the eIF2AΔ mutation conferred no significant TE reductions for any mRNAs in non-starved cells, and it reduced the TEs of only a small number of transcripts in starved cells containing phosphorylated eIF2α. We found no evidence that eliminating eIF2A altered the translation of mRNAs containing putative internal ribosome entry site (IRES) elements, or harboring uORFs initiated by AUG or near-cognate start codons, in non-starved or starved cells. Thus, very few mRNAs (possibly only one) appear to employ eIF2A for Met-tRNAi recruitment in yeast cells, even when eIF2 function is attenuated by stress.
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Affiliation(s)
- Swati Gaikwad
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Fardin Ghobakhlou
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Hongen Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
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10
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Gypakis A, Adelt S, Lemoine H, Vogel G, Wasner HK. Activated Inositol Phosphate, Substrate for Synthesis of Prostaglandylinositol Cyclic Phosphate (Cyclic PIP)-The Key for the Effectiveness of Inositol-Feeding. Int J Mol Sci 2024; 25:1362. [PMID: 38338641 PMCID: PMC10855042 DOI: 10.3390/ijms25031362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/12/2024] Open
Abstract
The natural cyclic AMP antagonist, prostaglandylinositol cyclic phosphate (cyclic PIP), is biosynthesized from prostaglandin E (PGE) and activated inositol phosphate (n-Ins-P), which is synthesized by a particulate rat-liver-enzyme from GTP and a precursor named inositol phosphate (pr-Ins-P), whose 5-ring phosphodiester structure is essential for n-Ins-P synthesis. Aortic myocytes, preincubated with [3H] myo-inositol, synthesize after angiotensin II stimulation (30 s) [3H] pr-Ins-P (65% yield), which is converted to [3H] n-Ins-P and [3H] cyclic PIP. Acid-treated (1 min) [3H] pr-Ins-P co-elutes with inositol (1,4)-bisphosphate in high performance ion chromatography, indicating that pr-Ins-P is inositol (1:2-cyclic,4)-bisphosphate. Incubation of [3H]-GTP with unlabeled pr-Ins-P gave [3H]-guanosine-labeled n-Ins-P. Cyclic PIP synthase binds the inositol (1:2-cyclic)-phosphate part of n-Ins-P to PGE and releases the [3H]-labeled guanosine as [3H]-GDP. Thus, n-Ins-P is most likely guanosine diphospho-4-inositol (1:2-cyclic)-phosphate. Inositol feeding helps patients with metabolic conditions related to insulin resistance, but explanations for this finding are missing. Cyclic PIP appears to be the key for explaining the curative effect of inositol supplementation: (1) inositol is a molecular constituent of cyclic PIP; (2) cyclic PIP triggers many of insulin's actions intracellularly; and (3) the synthesis of cyclic PIP is decreased in diabetes as shown in rodents.
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Affiliation(s)
- Antonios Gypakis
- General Secretariat for Research and Innovation, GR-11527 Athens, Greece;
| | - Stephan Adelt
- Fachbereich C—Biochemie, Bergische University, 42119 Wuppertal, Germany;
| | - Horst Lemoine
- Institute for Laser-Medicine, Molecular Drug-Research Group, Heinrich-Heine-University, 40225 Düsseldorf, Germany;
| | - Günter Vogel
- Fachbereich C—Biochemie, Bergische University, 42119 Wuppertal, Germany;
| | - Heinrich K. Wasner
- BioReg Biopharm, Technology Innovation Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA
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11
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Romero ME, McElhenney SJ, Yu J. Trapping a non-cognate nucleotide upon initial binding for replication fidelity control in SARS-CoV-2 RNA dependent RNA polymerase. Phys Chem Chem Phys 2024; 26:1792-1808. [PMID: 38168789 DOI: 10.1039/d3cp04410f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The RNA dependent RNA polymerase (RdRp) in SARS-CoV-2 is a highly conserved enzyme responsible for viral genome replication/transcription. To understand how the viral RdRp achieves fidelity control during such processes, here we computationally investigate the natural non-cognate vs. cognate nucleotide addition and selectivity during viral RdRp elongation. We focus on the nucleotide substrate initial binding (RdRp active site open) to the prechemical insertion (active site closed) of the RdRp. The current studies were first carried out using microsecond ensemble equilibrium all-atom molecular dynamics (MD) simulations. Due to the slow conformational changes (from open to closed) during nucleotide insertion and selection, enhanced or umbrella sampling methods have been further employed to calculate the free energy profiles of the nucleotide insertion. Our studies find notable stability of noncognate dATP and GTP upon initial binding in the active-site open state. The results indicate that while natural cognate ATP and Remdesivir drug analogue (RDV-TP) are biased toward stabilization in the closed state to facilitate insertion, the natural non-cognate dATP and GTP can be well trapped in off-path initial binding configurations and prevented from insertion so that to be further rejected. The current work thus presents the intrinsic nucleotide selectivity of SARS-CoV-2 RdRp for natural substrate fidelity control, which should be considered in antiviral drug design.
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Affiliation(s)
- Moises E Romero
- Department of Chemistry, University of California, Irvine, CA 92697, USA
| | | | - Jin Yu
- Department of Physics and Astronomy, Department of Chemistry, NSF-Simmons Center for Multi-scale Cell Fate Research, University of California, Irvine, CA 92697, USA.
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12
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Zhou W, Zhao Z, Lin A, Yang JZ, Xu J, Wilder-Romans K, Yang A, Li J, Solanki S, Speth JM, Walker N, Scott AJ, Wang L, Wen B, Andren A, Zhang L, Kothari AU, Yao Y, Peterson ER, Korimerla N, Werner CK, Ullrich A, Liang J, Jacobson J, Palavalasa S, O’Brien AM, Elaimy AL, Ferris SP, Zhao SG, Sarkaria JN, Győrffy B, Zhang S, Al-Holou WN, Umemura Y, Morgan MA, Lawrence TS, Lyssiotis CA, Peters-Golden M, Shah YM, Wahl DR. GTP Signaling Links Metabolism, DNA Repair, and Responses to Genotoxic Stress. Cancer Discov 2024; 14:158-175. [PMID: 37902550 PMCID: PMC10872631 DOI: 10.1158/2159-8290.cd-23-0437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/07/2023] [Accepted: 10/19/2023] [Indexed: 10/31/2023]
Abstract
How cell metabolism regulates DNA repair is incompletely understood. Here, we define a GTP-mediated signaling cascade that links metabolism to DNA repair and has significant therapeutic implications. GTP, but not other nucleotides, regulates the activity of Rac1, a guanine nucleotide-binding protein, which promotes the dephosphorylation of serine 323 on Abl-interactor 1 (Abi-1) by protein phosphatase 5 (PP5). Dephosphorylated Abi-1, a protein previously not known to activate DNA repair, promotes nonhomologous end joining. In patients and mouse models of glioblastoma, Rac1 and dephosphorylated Abi-1 mediate DNA repair and resistance to standard-of-care genotoxic treatments. The GTP-Rac1-PP5-Abi-1 signaling axis is not limited to brain cancer, as GTP supplementation promotes DNA repair and Abi-1-S323 dephosphorylation in nonmalignant cells and protects mouse tissues from genotoxic insult. This unexpected ability of GTP to regulate DNA repair independently of deoxynucleotide pools has important implications for normal physiology and cancer treatment. SIGNIFICANCE A newly described GTP-dependent signaling axis is an unexpected link between nucleotide metabolism and DNA repair. Disrupting this pathway can overcome cancer resistance to genotoxic therapy while augmenting it can mitigate genotoxic injury of normal tissues. This article is featured in Selected Articles from This Issue, p. 5.
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Affiliation(s)
- Weihua Zhou
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Zitong Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Oncology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shan Xi, PR China
| | - Angelica Lin
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - John Z Yang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Jie Xu
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Kari Wilder-Romans
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Annabel Yang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Jing Li
- Cell Signaling Technology, Inc., Danvers, MA, USA
| | - Sumeet Solanki
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer M Speth
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Natalie Walker
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Andrew J Scott
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lu Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Bo Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Anthony Andren
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Li Zhang
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Ayesha U Kothari
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Yangyang Yao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Oncology, the First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, PR China
| | - Erik R Peterson
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Navyateja Korimerla
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Christian K Werner
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Alexander Ullrich
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Jessica Liang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Janna Jacobson
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Sravya Palavalasa
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra M O’Brien
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Ameer L Elaimy
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Sean P Ferris
- Department of Pathology, Division of Neuropathology, University of Michigan, Ann Arbor, MI, USA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin Madison, WI, USA
| | | | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary; and TTK Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Shuqun Zhang
- Department of Oncology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shan Xi, PR China
| | - Wajd N Al-Holou
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, United States
| | - Yoshie Umemura
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States
| | - Meredith A Morgan
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Theodore S Lawrence
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology and Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marc Peters-Golden
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel R Wahl
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Lead contact
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Lin P, Qian J, Huang CC, Xu WM, Wang YY, Gao ZR, Zheng SQ, Wang P, Jia DQ, Feng Q, Yang JL. RGD-p21Ras-scFv expressed prokaryotically on a pilot scale inhibits ras-driven colorectal cancer growth by blocking p21Ras-GTP. BMC Cancer 2024; 24:71. [PMID: 38216883 PMCID: PMC10787443 DOI: 10.1186/s12885-023-11686-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/28/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Ras gene mutation and/or overexpression are drivers in the progression of cancers, including colorectal cancer. Blocking the Ras signaling has become a significant strategy for cancer therapy. Previously, we constructed a recombinant scFv, RGD-p21Ras-scFv by linking RGD membrane-penetrating peptide gene with the anti-p21Ras scFv gene. Here, we expressed prokaryotically RGD-p21Ras-scFv on a pilot scale, then investigated the anti-tumor effect and the mechanism of blocking Ras signaling. METHODS The E. coli bacteria which could highly express RGD-p21Ras-scFv was screened and grown in 100 L fermentation tank to produce RGD-p21Ras-scFv on optimized induced expression conditions. The scFv was purified from E. coli bacteria using His Ni-NTA column. ELISA was adopted to test the immunoreactivity of RGD-p21Ras-scFv against p21Ras proteins, and the IC50 of RGD-p21Ras-scFv was analyzed by CCK-8. Immunofluorescence colocalization and pull-down assays were used to determine the localization and binding between RGD-p21Ras-scFv and p21Ras. The interaction forces between RGD-p21Ras-scFv and p21Ras after binding were analyzed by molecular docking, and the stability after binding was determined by molecular dynamics simulations. p21Ras-GTP interaction was detected by Ras pull-down. Changes in the MEK-ERK /PI3K-AKT signaling paths downstream of Ras were detected by WB assays. The anti-tumor activity of RGD-p21Ras-scFv was investigated by nude mouse xenograft models. RESULTS The technique of RGD-p21Ras-scFv expression on a pilot scale was established. The wet weight of the harvested bacteria was 31.064 g/L, and 31.6 mg RGD-p21Ras-scFv was obtained from 1 L of bacterial medium. The purity of the recombinant antibody was above 85%, we found that the prepared on a pilot scale RGD-p21Ras-scFv could penetrate the cell membrane of colon cancer cells and bind to p21Ras, then led to reduce of p21Ras-GTP (active p21Ras). The phosphorylation of downstream effectors MEK-ERK /PI3K-AKT was downregulated. In vivo antitumor activity assays showed that the RGD-p21Ras-scFv inhibited the proliferation of colorectal cancer cell lines. CONCLUSION RGD-p21Ras-scFv prokaryotic expressed on pilot-scale could inhibited Ras-driven colorectal cancer growth by partially blocking p21Ras-GTP and might be able to be a hidden therapeutic antibody for treating RAS-driven tumors.
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Affiliation(s)
- Peng Lin
- Medical school, Kunming University of Science and Technology, Kunming, 650500, P.R. China
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Jing Qian
- Medical school, Kunming University of Science and Technology, Kunming, 650500, P.R. China
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
- Faculty of Life science and Technology, Kunming University of Science and Technology, Kunming, 650500, P.R. China
| | - Cheng-Cheng Huang
- Medical school, Kunming University of Science and Technology, Kunming, 650500, P.R. China
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Wen-Mang Xu
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Yuan-Yuan Wang
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Zi-Ran Gao
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Shi-Qi Zheng
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
- The Graduate School, Kunming Medical University, Kunming, 650500, P.R. China
| | - Peng Wang
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
| | - Da-Qi Jia
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China
- The Graduate School, Kunming Medical University, Kunming, 650500, P.R. China
| | - Qiang Feng
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China.
| | - Ju-Lun Yang
- Department of Pathology, 920th Hospital of the Joint Logistics Support Force of PLA, 212 Daguan Rd, Kunming, 650032, P.R. China.
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14
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McCormick LA, Cleary JM, Hancock WO, Rice LM. Interface-acting nucleotide controls polymerization dynamics at microtubule plus- and minus-ends. eLife 2024; 12:RP89231. [PMID: 38180336 PMCID: PMC10945504 DOI: 10.7554/elife.89231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
GTP-tubulin is preferentially incorporated at growing microtubule ends, but the biochemical mechanism by which the bound nucleotide regulates the strength of tubulin:tubulin interactions is debated. The 'self-acting' (cis) model posits that the nucleotide (GTP or GDP) bound to a particular tubulin dictates how strongly that tubulin interacts, whereas the 'interface-acting' (trans) model posits that the nucleotide at the interface of two tubulin dimers is the determinant. We identified a testable difference between these mechanisms using mixed nucleotide simulations of microtubule elongation: with a self-acting nucleotide, plus- and minus-end growth rates decreased in the same proportion to the amount of GDP-tubulin, whereas with interface-acting nucleotide, plus-end growth rates decreased disproportionately. We then experimentally measured plus- and minus-end elongation rates in mixed nucleotides and observed a disproportionate effect of GDP-tubulin on plus-end growth rates. Simulations of microtubule growth were consistent with GDP-tubulin binding at and 'poisoning' plus-ends but not at minus-ends. Quantitative agreement between simulations and experiments required nucleotide exchange at terminal plus-end subunits to mitigate the poisoning effect of GDP-tubulin there. Our results indicate that the interfacial nucleotide determines tubulin:tubulin interaction strength, thereby settling a longstanding debate over the effect of nucleotide state on microtubule dynamics.
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Affiliation(s)
- Lauren A McCormick
- Department of Biophysics and Biochemistry, the University of Texas Southwestern Medical CenterDallasUnited States
| | - Joseph M Cleary
- Department of Biomedical Engineering, Pennsylvania State UniversityState CollegeUnited States
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State UniversityState CollegeUnited States
| | - Luke M Rice
- Department of Biophysics and Biochemistry, the University of Texas Southwestern Medical CenterDallasUnited States
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15
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Zhu Y, Vvedenskaya IO, Sze SH, Nickels BE, Kaplan CD. Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels. Nat Struct Mol Biol 2024; 31:190-202. [PMID: 38177677 PMCID: PMC10928753 DOI: 10.1038/s41594-023-01171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
Abstract
Transcription start site (TSS) selection is a key step in gene expression and occurs at many promoter positions over a wide range of efficiencies. Here we develop a massively parallel reporter assay to quantitatively dissect contributions of promoter sequence, nucleoside triphosphate substrate levels and RNA polymerase II (Pol II) activity to TSS selection by 'promoter scanning' in Saccharomyces cerevisiae (Pol II MAssively Systematic Transcript End Readout, 'Pol II MASTER'). Using Pol II MASTER, we measure the efficiency of Pol II initiation at 1,000,000 individual TSS sequences in a defined promoter context. Pol II MASTER confirms proposed critical qualities of S. cerevisiae TSS -8, -1 and +1 positions, quantitatively, in a controlled promoter context. Pol II MASTER extends quantitative analysis to surrounding sequences and determines that they tune initiation over a wide range of efficiencies. These results enabled the development of a predictive model for initiation efficiency based on sequence. We show that genetic perturbation of Pol II catalytic activity alters initiation efficiency mostly independently of TSS sequence, but selectively modulates preference for the initiating nucleotide. Intriguingly, we find that Pol II initiation efficiency is directly sensitive to guanosine-5'-triphosphate levels at the first five transcript positions and to cytosine-5'-triphosphate and uridine-5'-triphosphate levels at the second position genome wide. These results suggest individual nucleoside triphosphate levels can have transcript-specific effects on initiation, representing a cryptic layer of potential regulation at the level of Pol II biochemical properties. The results establish Pol II MASTER as a method for quantitative dissection of transcription initiation in eukaryotes.
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Affiliation(s)
- Yunye Zhu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Irina O Vvedenskaya
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Sing-Hoi Sze
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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16
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Rabara D, Stephen AG. Measurement of KRAS-GTPase Activity. Methods Mol Biol 2024; 2797:91-102. [PMID: 38570454 DOI: 10.1007/978-1-0716-3822-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Oncogenic mutations in KRAS typically impact the GAP-mediated and intrinsic GTP hydrolysis activity resulting in elevated levels of cellular KRAS-GTP. The development of biochemical assays for GTPase activity provides an opportunity to quantitatively measure the impact of these mutations on GTP hydrolysis. Here we describe a biochemical assay that measures the release of free phosphate upon hydrolysis of the GTP nucleotide and allows the measurement of intrinsic or GAP-stimulated GTP hydrolysis by KRAS. This assay can be used to measure GTPase activity under single turnover conditions.
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Affiliation(s)
- Dana Rabara
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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Akrout M, Cirone KD, Vender R. Evaluation of Vision LLMs GTP-4V and LLaVA for the Recognition of Features Characteristic of Melanoma. J Cutan Med Surg 2024; 28:98-99. [PMID: 38174854 DOI: 10.1177/12034754231220934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Affiliation(s)
- Mohamed Akrout
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- AIP Labs, Budapest, Hungary
| | - Katrina D Cirone
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Ronald Vender
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Dermatrials Research Inc., Hamilton, ON, Canada
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18
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Biagetti E, Gislon G, Martella A, Zucali M, Bava L, Franco S, Sandrucci A. Comparison of the use of life cycle assessment and ecological footprint methods for evaluating environmental performances in dairy production. Sci Total Environ 2023; 905:166845. [PMID: 37709092 DOI: 10.1016/j.scitotenv.2023.166845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/12/2023] [Accepted: 09/03/2023] [Indexed: 09/16/2023]
Abstract
One popular methodology for assessing the environmental impact of livestock sector is Life Cycle Assessment (LCA), that quantifies the environmental impact of a product. Ecological Footprint (EF) performs an environmental sustainability assessment, by comparing the demand for natural capital by an economic activity with the offer of such capital within a certain territory. The aim of the study was the comparison between LCA and EF in assessing the environmental performances of milk production, assuming as case study three cattle farms with increasing levels of production intensity. Different metrics and functional units (FU) (i.e., fat and protein corrected milk, FPCM and hectare) were adopted for LCA analysis, considering some of the major impact categories. For greenhouse gases emissions, the Global Warming Potential (GWP) and the Global Temperature Potential (GTP) were considered. Both metrics were calculated assuming or not the distinction between biogenic and fossil methane. Adopting GWP as a metric, the results per kg of FPCM provided by the LCA highlighted a different trade off compared to the EF method: the farm with the highest productive intensity produced the least impactful milk in terms of GWP but had the most negative Ecological Balance (EB). The same occurred for the other impact categories. When GTP was adopted, or the hectare was considered as FU, the least intensive farm, characterized by greater feed self-sufficiency, became the one that produced the least impactful milk and had the least negative EB. The study highlighted the scientific significance of the integration between the two approaches for creating a comprehensive representation of the effects of human activities on the environment. The LCA method evaluates impacts intensity referred to a specific functional unit and its results are strongly influenced by productive efficiency; the EF method evaluates environmental sustainability of productions in relation to the territory that supports them.
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Affiliation(s)
- E Biagetti
- Università della Tuscia, Dipartimento di Economia, Ingegneria, Società e Impresa, via del Paradiso 47, 01100 Viterbo, Italy
| | - G Gislon
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali, via Celoria 2, 20133 Milano, Italy.
| | - A Martella
- Università della Tuscia, Dipartimento di Economia, Ingegneria, Società e Impresa, via del Paradiso 47, 01100 Viterbo, Italy
| | - M Zucali
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali, via Celoria 2, 20133 Milano, Italy
| | - L Bava
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali, via Celoria 2, 20133 Milano, Italy
| | - S Franco
- Università della Tuscia, Dipartimento di Economia, Ingegneria, Società e Impresa, via del Paradiso 47, 01100 Viterbo, Italy
| | - A Sandrucci
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali, via Celoria 2, 20133 Milano, Italy
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Schaefer A, Hodge RG, Zhang H, Hobbs GA, Dilly J, Huynh M, Goodwin CM, Zhang F, Diehl JN, Pierobon M, Baldelli E, Javaid S, Guthrie K, Rashid NU, Petricoin EF, Cox AD, Hahn WC, Aguirre AJ, Bass AJ, Der CJ. RHOA L57V drives the development of diffuse gastric cancer through IGF1R-PAK1-YAP1 signaling. Sci Signal 2023; 16:eadg5289. [PMID: 38113333 PMCID: PMC10791543 DOI: 10.1126/scisignal.adg5289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 11/03/2023] [Indexed: 12/21/2023]
Abstract
Cancer-associated mutations in the guanosine triphosphatase (GTPase) RHOA are found at different locations from the mutational hotspots in the structurally and biochemically related RAS. Tyr42-to-Cys (Y42C) and Leu57-to-Val (L57V) substitutions are the two most prevalent RHOA mutations in diffuse gastric cancer (DGC). RHOAY42C exhibits a gain-of-function phenotype and is an oncogenic driver in DGC. Here, we determined how RHOAL57V promotes DGC growth. In mouse gastric organoids with deletion of Cdh1, which encodes the cell adhesion protein E-cadherin, the expression of RHOAL57V, but not of wild-type RHOA, induced an abnormal morphology similar to that of patient-derived DGC organoids. RHOAL57V also exhibited a gain-of-function phenotype and promoted F-actin stress fiber formation and cell migration. RHOAL57V retained interaction with effectors but exhibited impaired RHOA-intrinsic and GAP-catalyzed GTP hydrolysis, which favored formation of the active GTP-bound state. Introduction of missense mutations at KRAS residues analogous to Tyr42 and Leu57 in RHOA did not activate KRAS oncogenic potential, indicating distinct functional effects in otherwise highly related GTPases. Both RHOA mutants stimulated the transcriptional co-activator YAP1 through actin dynamics to promote DGC progression; however, RHOAL57V additionally did so by activating the kinases IGF1R and PAK1, distinct from the FAK-mediated mechanism induced by RHOAY42C. Our results reveal that RHOAL57V and RHOAY42C drive the development of DGC through distinct biochemical and signaling mechanisms.
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Affiliation(s)
- Antje Schaefer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Richard G. Hodge
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Haisheng Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - G. Aaron Hobbs
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julien Dilly
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Minh Huynh
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig M. Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Feifei Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - J. Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Sehrish Javaid
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karson Guthrie
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Naim U. Rashid
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Adrienne D. Cox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William C. Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew J. Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Adam J. Bass
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Herbert Irving Comprehensive Cancer Center at Columbia University, New York, NY 10032, USA
| | - Channing J. Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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20
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Zhang H, Xu T, Liang J, Wu B, Yang X, Wang J, Zhou Z, Wang H. Controlling Supramolecular Fiber Formation of Nucleopeptide by Guanosine Triphosphate. Biomacromolecules 2023; 24:5678-5686. [PMID: 37934694 DOI: 10.1021/acs.biomac.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Cells use dynamic self-assembly to construct functional structures for maintaining cellular homeostasis. However, using a natural biological small molecule to mimic this phenomenon remains challenging. This work reports the dynamic microfiber formation of nucleopeptide driven by guanosine triphosphate, the small molecule that controls microtubule polymerization in living cells. Deactivation of GTP by enzyme dissociates the fibers, which could be reactivated by adding GTP. Molecular dynamic simulation unveils the mystery of microfiber formation of GBM-1 and GTP. Moreover, the microfiber formation can also be controlled by diffusion-driven GTP gradients across a semipermeable membrane in bulk conditions and the microfluidic method in the defined droplets. This study provides a new platform to construct dynamic self-assembly materials of molecular building blocks driven by GTP.
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Affiliation(s)
- Hongyue Zhang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, P. R. China
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Tengyan Xu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Juan Liang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Bihan Wu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Xuejiao Yang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Jing Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Ziao Zhou
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Huaimin Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
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21
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Iwagami M, Seol J, Hiei T, Tani A, Chiba S, Kanbayashi T, Kondo H, Tanaka T, Yanagisawa M. Association between electroencephalogram-based sleep characteristics and physical health in the general adult population. Sci Rep 2023; 13:21545. [PMID: 38066043 PMCID: PMC10709300 DOI: 10.1038/s41598-023-47979-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
We examined the associations between electroencephalogram (EEG)-based sleep characteristics and physical health parameters in general adults via a cross-sectional study recruiting 100 volunteers aged 30-59 years. Sleep characteristics were measured at home using a portable multichannel electroencephalography recorder. Using the k-means + + clustering method, according to 10 EEG-based parameters, participants were grouped into better (n = 39), middle (n = 46), and worse (n = 15) sleep groups. Comparing 50 physical health parameters among the groups, we identified four signals of difference (P < 0.05), including systolic (sBP) and diastolic blood pressure (dBP), γ-glutamyl transpeptidase (γ-GTP), and serum creatinine, where sBP reached a Bonferroni-corrected threshold (P < 0.001). The sBP was higher by 7.9 (95% confidence interval 1.9-13.9) and 15.7 (7.3-24.0) mmHg before adjustment and 5.4 (- 0.1-10.9) and 8.7 (1.1-16.3) mmHg after adjustment for age, sex, body mass index, smoking, drinking habits, and 3% oxygen desaturation index in the middle and worse sleep groups, respectively, than in the better group. As another approach, among 500 combinations of EEG-based and physical health parameters, there were 45 signals of correlation, of which 4 (N1% and sBP, dBP, γ-GTP, and triglycerides) reached a Bonferroni-corrected threshold (P < 0.0001). Thus, EEG-based sleep characteristics are associated with several physical health parameters, particularly sBP.
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Affiliation(s)
- Masao Iwagami
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- Department of Health Services Research, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Jaehoon Seol
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Research Center for Overwork-Related Disorders, National Institute of Occupational Safety and Health, Japan (JNIOSH), Kawasaki, Kanagawa, 214-8585, Japan
- R&D Center for Tailor-Made QOL, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Tetsuro Hiei
- S'UIMIN Inc., 1-51-1 Hatsudai, Shibuya, Tokyo, 151-0061, Japan
| | - Akihiro Tani
- S'UIMIN Inc., 1-51-1 Hatsudai, Shibuya, Tokyo, 151-0061, Japan
| | - Shigeru Chiba
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Ibaraki Prefectural Medical Center of Psychiatry, 654 Asahimachi, Kasama, Ibaraki, 309-1717, Japan
- Minamisaitama Hospital, 252 Masumori, Koshigaya, Ibaraki, 343-0012, Japan
| | - Takashi Kanbayashi
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Ibaraki Prefectural Medical Center of Psychiatry, 654 Asahimachi, Kasama, Ibaraki, 309-1717, Japan
| | - Hideaki Kondo
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Department of General Medicine, Institute of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8521, Japan
| | - Takashi Tanaka
- KRD Nihombashi, 4-4-2 Nihonbashi Honcho, Chuo, Tokyo, 103-0023, Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
- S'UIMIN Inc., 1-51-1 Hatsudai, Shibuya, Tokyo, 151-0061, Japan.
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22
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Leisten ED, Woods AC, Wong YC. Super-resolution microscopy: Insights into mitochondria-lysosome crosstalk in health and disease. J Cell Biol 2023; 222:e202305032. [PMID: 37917024 PMCID: PMC10621667 DOI: 10.1083/jcb.202305032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Live super-resolution microscopy has allowed for new insights into recently identified mitochondria-lysosome contact sites, which mediate crosstalk between mitochondria and lysosomes, including co-regulation of Rab7 GTP hydrolysis and Drp1 GTP hydrolysis. Here, we highlight recent findings and future perspectives on this dynamic pathway and its roles in health and disease.
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Affiliation(s)
- Eric D. Leisten
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Abby C. Woods
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yvette C. Wong
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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23
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Baek HS, Kim B, Lee SH, Lim DJ, Kwon HS, Chang SA, Han K, Yun JS. Long-Term Cumulative Exposure to High γ-Glutamyl Transferase Levels and the Risk of Cardiovascular Disease: A Nationwide Population-Based Cohort Study. Endocrinol Metab (Seoul) 2023; 38:770-781. [PMID: 37926990 PMCID: PMC10764996 DOI: 10.3803/enm.2023.1726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/04/2023] [Accepted: 08/11/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGRUOUND Elevated γ-glutamyl transferase (γ-GTP) levels are associated with metabolic syndrome. We investigated the association of cumulative exposure to high γ-GTP with the risk of cardiovascular disease (CVD) in a large-scale population. METHODS Using nationally representative data from the Korean National Health Insurance system, 1,640,127 people with 4 years of consecutive γ-GTP measurements from 2009 to 2012 were included and followed up until the end of 2019. For each year of the study period, participants were grouped by the number of exposures to the highest γ-GTP quartile (0-4), and the sum of quartiles (0-12) was defined as cumulative γ-GTP exposure. The hazard ratio for CVD was evaluated using the Cox proportional hazards model. RESULTS During the 6.4 years of follow-up, there were 15,980 cases (0.97%) of myocardial infarction (MI), 14,563 (0.89%) of stroke, 29,717 (1.81%) of CVD, and 25,916 (1.58%) of death. Persistent exposure to high γ-GTP levels was associated with higher risks of MI, stroke, CVD, and death than those without such exposure. The risks of MI, stroke, CVD, and mortality increased in a dose-dependent manner according to total cumulative γ-GTP (all P for trend <0.0001). Subjects younger than 65 years, with a body mass index <25 kg/m2, and without hypertension or fatty liver showed a stronger relationship between cumulative γ-GTP and the incidence of MI, CVD, and death. CONCLUSION Cumulative γ-GTP elevation is associated with CVD. γ-GTP could be more widely used as an early marker of CVD risk, especially in individuals without traditional CVD risk factors.
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Affiliation(s)
- Han-Sang Baek
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Bongseong Kim
- Department of Statistics and Actuarial Science, Soongsil University, Seoul, Korea
| | - Seung-Hwan Lee
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Dong-Jun Lim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyuk-Sang Kwon
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang-Ah Chang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyungdo Han
- Department of Statistics and Actuarial Science, Soongsil University, Seoul, Korea
| | - Jae-Seung Yun
- Division of Endocrinology and Metabolism, Department of Internal Medicine, St. Vincent’s Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
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24
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Leung AC, Nahmias JT, Roman KM, Kirby KA, Qazi AS, Joe VC. Unnecessary Early Gastrostomy for Trauma Patients. Am Surg 2023; 89:6338-6341. [PMID: 37148330 DOI: 10.1177/00031348231173986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
While early gastrostomy tube placement (GTP) may decrease hospital length of stay and facilitate disposition, GTP may be unnecessary as some patients regain the ability to eat earlier than expected. No guidelines currently exist regarding optimal GTP timing or minimum duration of need indicating appropriateness of GTP. This retrospective (9/2017-12/2019) single center study evaluated the incidence of adequate (>75%) oral caloric intake (ACI) after GTP during index hospitalization and associated characteristics before discharge. Bivariate analyses were performed to compare patients achieving ACI and patients not achieving ACI at discharge. By discharge, 10 (12.5%) patients achieved ACI and 6 (7.5%) had their GT removed prior to discharge suggesting many patients undergo unnecessary GTP. Also, 6 (7.5%) patients suffered GTP-related complications. Future multicenter studies are needed to corroborate these findings and establish GTP guidelines for trauma patients to avoid unnecessary GT procedures and associated morbidities.
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Affiliation(s)
- Amanda C Leung
- Division of Trauma, Burns, and Surgical Critical Care, Department of Surgery, University of California Irvine, Orange, CA, USA
| | - Jeffry T Nahmias
- Division of Trauma, Burns, and Surgical Critical Care, Department of Surgery, University of California Irvine, Orange, CA, USA
| | - Kelsey M Roman
- Division of Trauma, Burns, and Surgical Critical Care, Department of Surgery, University of California Irvine, Orange, CA, USA
| | - Katharine A Kirby
- Center for Statistical Consulting, Department of Statistics, University of California Irvine, Irvine, CA, USA
| | - Alliya S Qazi
- Division of Trauma, Burns, and Surgical Critical Care, Department of Surgery, University of California Irvine, Orange, CA, USA
| | - Victor C Joe
- Division of Trauma, Burns, and Surgical Critical Care, Department of Surgery, University of California Irvine, Orange, CA, USA
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25
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Guan L, Wen X, Zhang Z, Wang L, Zhang X, Yang M, Wang S, Qin Q. Grouper Rab1 inhibits nodovirus infection by affecting virus entry and host immune response. Fish Shellfish Immunol 2023; 143:109136. [PMID: 37839541 DOI: 10.1016/j.fsi.2023.109136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023]
Abstract
Rab1, a GTPase, is present in all eukaryotes, and is mainly involved in vesicle trafficking between the endoplasmic reticulum and Golgi, thereby regulating many cellular activities and pathogenic infections. However, little is known of how Rab1 functions in fish during virus infection. Groupers (Epinephelus spp.) are high in economic value and widely cultivated in China and Southeast Asia, although they often suffer from diseases. Red-spotted grouper nervous necrosis virus (RGNNV), a highly pathogenic RNA virus, is a major pathogen in cultured groupers, and causes huge economic losses. A series of host cellular proteins involved in RGNNV infection was identified. However, the impact of Rab1 on RGNNV infection has not yet been reported. In this study, a novel Rab1 homolog (EcRab1) from Epinephelus coioides was cloned, and its roles during virus infection and host immune responses were investigated. EcRab1 encoded a 202 amino acid polypeptide, showing 98% and 78% identity to Epinephelus lanceolatus and Homo sapiens, respectively. After challenge with RGNNV or poly(I:C), the transcription of EcRab1 was altered both in vitro and in vivo, implying that EcRab1 was involved in virus infection. Subcellular localization showed that EcRab1 was displayed as punctate structures in the cytoplasm, which was affected by EcRab1 mutants. The dominant negative (DN) EcRab1, enabling EcRab1 to remain in the GDP-binding state, caused EcRab1 to be diffusely distributed in the cytoplasm. Constitutively active (CA) EcRab1, enabling EcRab1 to remain in the GTP-binding state, induced larger cluster structures of EcRab1. During the late stage of RGNNV infection, some EcRab1 co-localized with RGNNV, and the size of EcRab1 clusters was enlarged. Importantly, overexpression of EcRab1 significantly inhibited RGNNV infection, and knockdown of EcRab1 promoted RGNNV infection. Furthermore, EcRab1 inhibited the entry of RGNNV to host cells. Compared with EcRab1, overexpression of DN EcRab1 or CA EcRab1 also promoted RGNNV infection, suggesting that EcRab1 regulated RGNNV infection, depending on the cycles of GTP- and GDP-binding states. In addition, EcRab1 positively regulated interferon (IFN) immune and inflammatory responses. Taken together, these results suggest that EcRab1 affects RGNNV infection, possibly by regulating host immunity. Our study furthers the understanding of Rab1 function during virus infection, thus helping to design new antiviral strategies.
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Affiliation(s)
- Lingfeng Guan
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Xiaozhi Wen
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zihan Zhang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Liqun Wang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Xinyue Zhang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Min Yang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Shaowen Wang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511464, China.
| | - Qiwei Qin
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511464, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, 519000, China.
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26
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Abstract
Metastatic progression is regulated by metastasis promoter and suppressor genes. NME1, the prototypic and first described metastasis suppressor gene, encodes a nucleoside diphosphate kinase (NDPK) involved in nucleotide metabolism; two related family members, NME2 and NME4, are also reported as metastasis suppressors. These proteins physically interact with members of the GTPase dynamin family, which have key functions in membrane fission and fusion reactions necessary for endocytosis and mitochondrial dynamics. Evidence supports a model in which NDPKs provide GTP to dynamins to maintain a high local GTP concentration for optimal dynamin function. NME1 and NME2 are cytosolic enzymes that provide GTP to dynamins at the plasma membrane, which drive endocytosis, suggesting that these NMEs are necessary to attenuate signaling by receptors on the cell surface. Disruption of NDPK activity in NME-deficient tumors may thus drive metastasis by prolonging signaling. NME4 is a mitochondrial enzyme that interacts with the dynamin OPA1 at the mitochondria inner membrane to drive inner membrane fusion and maintain a fused mitochondrial network. This function is consistent with the current view that mitochondrial fusion inhibits the metastatic potential of tumor cells whereas mitochondrial fission promotes metastasis progression. The roles of NME family members in dynamin-mediated endocytosis and mitochondrial dynamics and the intimate link between these processes and metastasis provide a new framework to understand the metastasis suppressor functions of NME proteins.
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Affiliation(s)
- Céline Prunier
- Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Philippe Chavrier
- Actin and Membrane Dynamics Laboratory, Institut Curie - Research Center, CNRS UMR144, PSL Research University, Paris, France
| | - Mathieu Boissan
- Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France.
- Laboratoire de Biochimie Endocrinienne Et Oncologique, Oncobiologie Cellulaire Et Moléculaire, APHP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Paris, France.
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27
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Wang Y, Li D, Lv Z, Feng B, Li T, Weng X. Efficacy and safety of Gutong Patch compared with NSAIDs for knee osteoarthritis: A real-world multicenter, prospective cohort study in China. Pharmacol Res 2023; 197:106954. [PMID: 37832860 DOI: 10.1016/j.phrs.2023.106954] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/25/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
The Gutong Patch (GTP) is common in clinical practice for bone diseases. This study compared the efficacy and safety of GTP and nonsteroidal anti-inflammatory drugs (NSAIDs) for KOA patients from 35 medical centers assigned to GTP, selective COX-2 inhibitor (SCI), GTP + SCI, non-selective COX-2 inhibitor (NSCI), and GTP + NSCI groups. The visual analog scale (VAS) pain score, EuroQol-VAS, EuroQol 5D-3 L, time to articular pain relief / disappearance, and joint motion recovery were the efficacy assessments. Safety assessments included contact dermatitis, gastrointestinal disorders, etc. The p-value < 0.05 was considered statistically significant. After statistical analysis, the SCI and GTP + SCI groups showed better improvement of VAS than the GTP group; the time to articular pain relief in the NSCI group was shorter than that in GTP and SCI group; the time to joint motion recovery in the GTP + NSCI group was longer than that in the SCI group. Additionally, the improvement of the quality of life in all groups was significant after treatments. While the incidence of gastrointestinal adverse events in the NSAIDs group was higher than that in the GTP and GTP + NSAIDs groups. GTP and NSAIDs are effective for KOA patients, and GTP is more suitable for KOA patients with cardiovascular and gastrointestinal comorbidities. This study was approved by the Ethics Committee at Peking Union Medical College Hospital (HS-1766) and registered in the Chinese Clinical Trial Registry (ChiCTR2100046391).
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Affiliation(s)
- Yingjie Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Dandan Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Zehui Lv
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Bin Feng
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi'an 710032, China.
| | - Xisheng Weng
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China.
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Zhang M, Wang W, Liu K, Jia C, Hou Y, Bai G. Astragaloside IV protects against lung injury and pulmonary fibrosis in COPD by targeting GTP-GDP domain of RAS and downregulating the RAS/RAF/FoxO signaling pathway. Phytomedicine 2023; 120:155066. [PMID: 37690229 DOI: 10.1016/j.phymed.2023.155066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/21/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Pulmonary fibrosis is a chronic progressive interstitial lung disease characterized by the replacement of lung parenchyma with fibrous scar tissue, usually as the final stage of lung injury like COPD. Astragaloside IV (AST), a bioactive compound found in the Astragalus membranaceus (Fisch.) used in traditional Chinese medicine, has been shown to improve pulmonary function and exhibit anti-pulmonary fibrosis effects. However, the exact molecular mechanisms through which it combats pulmonary fibrosis, especially in COPD, remain unclear. PURPOSE This study aimed to identify the potential therapeutic target and molecular mechanisms for AST in improving lung injury especially treating COPD type pulmonary fibrosis both in vivo and in vitro. METHODS Multi lung injury models were established in mice using lipopolysaccharide (LPS), cigarette smoke (CS), or LPS plus CS to simulate the processes of pulmonary fibrosis in COPD. The effect of AST on lung function protection was evaluated, and proteomic and metabolomic analysis were applied to identify the signaling pathway affected by AST and to find potential targets of AST. The interaction between AST and wild-type and mutant RAS proteins was studied. The RAS/RAF/FoxO signaling pathway was stimulated in BEAS-2B cells and in mice lung tissues by LPS plus CS to investigate the anti-pulmonary fibrosis mechanism of AST analyzed by western blotting. The regulatory effects of AST on the RAS/RAF/FoxO pathway dependent on RAS were further confirmed using RAS siRNA. RESULTS RAS was predicted and identified as the target protein of AST in anti-pulmonary fibrosis in COPD and improving lung function. The administration of AST was observed to impede the conversion of fibroblasts into myofibroblasts, reduce the manifestation of inflammatory factors and extracellular matrix, and hinder the activation of epithelial mesenchymal transition (EMT). Furthermore, AST significantly suppressed the RAS/RAF/FoxO signaling pathway in both in vitro and in vivo settings. CONCLUSION AST exhibited lung function protection and anti-pulmonary fibrosis effect by inhibiting the GTP-GDP domain of RAS, which downregulated the RAS/RAF/FoxO signaling pathway. This study revealed AST as a natural candidate molecule for the protection of pulmonary fibrosis in COPD.
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Affiliation(s)
- Man Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Wenshuang Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Kaixin Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Chao Jia
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Yuanyuan Hou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China.
| | - Gang Bai
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China.
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Larasati YA, Solis GP, Koval A, Griffiths ST, Berentsen R, Aukrust I, Lesca G, Chatron N, Ville D, Korff CM, Katanaev VL. Clinical Cases and the Molecular Profiling of a Novel Childhood Encephalopathy-Causing GNAO1 Mutation P170R. Cells 2023; 12:2469. [PMID: 37887313 PMCID: PMC10605901 DOI: 10.3390/cells12202469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/29/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
De novo mutations in GNAO1, the gene encoding the major neuronal G protein Gαo, cause a spectrum of pediatric encephalopathies with seizures, motor dysfunction, and developmental delay. Of the >80 distinct missense pathogenic variants, many appear to uniformly destabilize the guanine nucleotide handling of the mutant protein, speeding up GTP uptake and deactivating GTP hydrolysis. Zinc supplementation emerges as a promising treatment option for this disease, as Zn2+ ions reactivate the GTP hydrolysis on the mutant Gαo and restore cellular interactions for some of the mutants studied earlier. The molecular etiology of GNAO1 encephalopathies needs further elucidation as a prerequisite for the development of efficient therapeutic approaches. In this work, we combine clinical and medical genetics analysis of a novel GNAO1 mutation with an in-depth molecular dissection of the resultant protein variant. We identify two unrelated patients from Norway and France with a previously unknown mutation in GNAO1, c.509C>G that results in the production of the Pro170Arg mutant Gαo, leading to severe developmental and epileptic encephalopathy. Molecular investigations of Pro170Arg identify this mutant as a unique representative of the pathogenic variants. Its 100-fold-accelerated GTP uptake is not accompanied by a loss in GTP hydrolysis; Zn2+ ions induce a previously unseen effect on the mutant, forcing it to lose the bound GTP. Our work combining clinical and molecular analyses discovers a novel, biochemically distinct pathogenic missense variant of GNAO1 laying the ground for personalized treatment development.
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Affiliation(s)
- Yonika A. Larasati
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland (G.P.S.); (A.K.)
| | - Gonzalo P. Solis
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland (G.P.S.); (A.K.)
| | - Alexey Koval
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland (G.P.S.); (A.K.)
| | - Silja T. Griffiths
- Department of Pediatrics, Haukeland University Hospital, 5009 Bergen, Norway
| | - Ragnhild Berentsen
- Department of Medical Genetics, Haukeland University Hospital, 5009 Bergen, Norway; (R.B.)
| | - Ingvild Aukrust
- Department of Medical Genetics, Haukeland University Hospital, 5009 Bergen, Norway; (R.B.)
- Department of Clinical Science, University of Bergen, 5008 Bergen, Norway
| | - Gaetan Lesca
- Department of Medical Genetics, University Hospital of Lyon, 69002 Lyon, France; (G.L.); (N.C.)
| | - Nicolas Chatron
- Department of Medical Genetics, University Hospital of Lyon, 69002 Lyon, France; (G.L.); (N.C.)
| | - Dorothée Ville
- Pediatric Neurology Department, University Hospital of Lyon, 69002 Lyon, France;
| | - Christian M. Korff
- Pediatric Neurology Unit, University Hospitals of Geneva, CH-1211 Geneva, Switzerland;
| | - Vladimir L. Katanaev
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland (G.P.S.); (A.K.)
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok 690090, Russia
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Li J, Chang X, Chen X, Ma R, Qi R, Liu W, Li Y, Wan Y, Qiu Q, Shao Q, Liu A, Zhan K. Effects of green tea powder on production performance, egg quality, and blood biochemical parameters in laying hens. Poult Sci 2023; 102:102924. [PMID: 37542941 PMCID: PMC10407902 DOI: 10.1016/j.psj.2023.102924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/28/2023] [Accepted: 07/02/2023] [Indexed: 08/07/2023] Open
Abstract
The paper aimed to evaluate the effects of dietary inclusion of green tea powder (GTP) on laying performance, egg quality, and blood biochemical parameters of laying hens. A total of 240 Jingfen No. 6 laying hens (age, 24 wk) were randomly allocated into 4 groups: control group (CON, basal diet), GTP0.5, GTP0.75, and GTP1.0 (basal diet included 0.5, 0.75, and 1.0% GTP, respectively). Each group has 5 replicates with 12 birds each. The feeding trial lasted 8 wk. The results showed that the hen-day egg production rate in GTP0.5 and GTP 0.75 group was higher than that of GTP1.0 group (P < 0.05), hen-day egg production rate in the GTP1.0 group was lower compared to the CON group (P > 0.05), the feed conversion ratio (FCR) in the GTP0.75 group was lower than that in CON and GTP 1.0 group (P < 0.05) during the entire experimental period. Albumen height and Haugh unit were higher in the GTP0.75 and GTP1.0 group compared to the CON group at d 56 (P < 0.05). At the end of experiment, plasma TG content in the GTP0.75 and GTP1.0 group was lower than that in the CON group (P < 0.05), the T-CH concentration in the GTP0.5 and GTP0.75 group was lower compared to the CON group (P < 0.05), plasma LDL-C and CORT concentrations were decreased by dietary GTP supplementation (P < 0.05), the HDL-C and BUN concentrations in the GTP0.75 and GTP1.0 group were higher than that in the CON group (P < 0.05). The antibody titers of H5N1 in the GTP0.75 and GTP1.0 group, and H7N9 in the GTP1.0 group were lower than that in the CON group (P < 0.05). In conclusion, dietary GTP inclusion could affect laying performance, regulate lipid metabolism, and have no favorable influence on antibody titers of H5N1 and H7N9, herein, dietary 0.5% GTP inclusion is suggested for Jingfen No. 6 laying hens during the peak laying period.
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Affiliation(s)
- Junying Li
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xueling Chang
- College of Animal Science, Anhui Science and Technology University, Bengbu 233100, China
| | - Xiangming Chen
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Ruiyu Ma
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Renrong Qi
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Wei Liu
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yan Li
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yi Wan
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Qinqin Qiu
- Anhui Ningqing Tea Co., Ltd., Xuancheng 245300, China
| | - Qiance Shao
- Anhui Ningqing Tea Co., Ltd., Xuancheng 245300, China
| | - Aiqiao Liu
- Beijing Huadu Yukou Poultry Industry Co., Ltd., Beijing 101206, China
| | - Kai Zhan
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
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Yuan H, Zhao Z, Xu J, Zhang R, Ma L, Han J, Zhao W, Guo M, Song Y. Hypoxia-induced TMTC3 expression in esophageal squamous cell carcinoma potentiates tumor angiogenesis through Rho GTPase/STAT3/VEGFA pathway. J Exp Clin Cancer Res 2023; 42:249. [PMID: 37752569 PMCID: PMC10521530 DOI: 10.1186/s13046-023-02821-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/02/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Hypoxia is one of most typical features in the tumor microenvironment of solid tumor and an inducer of endoplasmic reticulum (ER) stress, and HIF-1α functions as a key transcription factor regulator to promote tumor angiogenesis in the adaptive response to hypoxia. Increasing evidence has suggested that hypoxia plays an important regulatory role of ER homeostasis. We previously identified TMTC3 as an ER stress mediator under nutrient-deficiency condition in esophageal squamous cell carcinoma (ESCC), but the molecular mechanism in hypoxia is still unclear. METHODS RNA sequencing data of TMTC3 knockdown cells and TCGA database were analyzed to determine the association of TMTC3 and hypoxia. Moreover, ChIP assay and dual-luciferase reporter assay were performed to detect the interaction of HIF-1α and TMTC3 promoter. In vitro and in vivo assays were used to investigate the function of TMTC3 in tumor angiogenesis. The molecular mechanism was determined using co-immunoprecipitation assays, immunofluorescence assays and western blot. The TMTC3 inhibitor was identified by high-throughput screening of FDA-approved drugs. The combination of TMTC3 inhibitor and cisplatin was conducted to confirm the efficiency in vitro and in vivo. RESULTS The expression of TMTC3 was remarkably increased under hypoxia and regulated by HIF-1α. Knockdown of TMTC3 inhibited the capability of tumor angiogenesis and ROS production in ESCC. Mechanistically, TMTC3 promoted the production of GTP through interacting with IMPDH2 Bateman domain. The activity of Rho GTPase/STAT3, regulated by cellular GTP levels, decreased in TMTC3 knockdown cells, whereas reversed by IMPDH2 overexpression. Additionally, TMTC3 regulated the expression of VEGFA through Rho GTPase/STAT3 pathway. Allopurinol inhibited the expression of TMTC3 and further reduced the phosphorylation and activation of STAT3 signaling pathway in a dose-dependent manner in ESCC. Additionally, the combination of allopurinol and cisplatin significantly inhibited the cell viability in vitro and tumor growth in vivo, comparing with single drug treatment, respectively. CONCLUSIONS Collectively, our study clarified the molecular mechanism of TMTC3 in regulating tumor angiogenesis and highlighted the potential therapeutic combination of TMTC3 inhibitor and cisplatin, which proposed a promising strategy for the treatment of ESCC.
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Affiliation(s)
- Hongyu Yuan
- Department of Gastroenterology & Hepatology, The First Medical Center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Zitong Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jing Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ruiping Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Liying Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jing Han
- Department of Medical Oncology, Hebei Medical University Fourth Affiliated Hospital and Hebei Provincial Tumor Hospital, Shijiazhuang, 050000, Hebei, China
| | - Weihong Zhao
- Medical Department, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, The First Medical Center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Zhou J, Wang A, Song Y, Liu N, Wang J, Li Y, Liang X, Li G, Chu H, Wang HW. Structural insights into the mechanism of GTP initiation of microtubule assembly. Nat Commun 2023; 14:5980. [PMID: 37749104 PMCID: PMC10519996 DOI: 10.1038/s41467-023-41615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
In eukaryotes, the dynamic assembly of microtubules (MT) plays an important role in numerous cellular processes. The underlying mechanism of GTP triggering MT assembly is still unknown. Here, we present cryo-EM structures of tubulin heterodimer at their GTP- and GDP-bound states, intermediate assembly states of GTP-tubulin, and final assembly stages of MT. Both GTP- and GDP-tubulin heterodimers adopt similar curved conformations with subtle flexibility differences. In head-to-tail oligomers of tubulin heterodimers, the inter-dimer interface of GDP-tubulin exhibits greater flexibility, particularly in tangential bending. Cryo-EM of the intermediate assembly states reveals two types of tubulin lateral contacts, "Tube-bond" and "MT-bond". Further, molecular dynamics (MD) simulations show that GTP triggers lateral contact formation in MT assembly in multiple sequential steps, gradually straightening the curved tubulin heterodimers. Therefore, we propose a flexible model of GTP-initiated MT assembly, including the formation of longitudinal and lateral contacts, to explain the nucleation and assembly of MT.
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Affiliation(s)
- Ju Zhou
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
- University of California Berkeley, Berkeley, CA, USA
| | - Anhui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Yinlong Song
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nan Liu
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Xin Liang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China.
| | - Hong-Wei Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China.
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Boegholm N, Petriman NA, Loureiro‐López M, Wang J, Vela MIS, Liu B, Kanie T, Ng R, Jackson PK, Andersen JS, Lorentzen E. The IFT81-IFT74 complex acts as an unconventional RabL2 GTPase-activating protein during intraflagellar transport. EMBO J 2023; 42:e111807. [PMID: 37606072 PMCID: PMC10505919 DOI: 10.15252/embj.2022111807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/24/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
Cilia are important cellular organelles for signaling and motility and are constructed via intraflagellar transport (IFT). RabL2 is a small GTPase that localizes to the basal body of cilia via an interaction with the centriolar protein CEP19 before downstream association with the IFT machinery, which is followed by initiation of IFT. We reconstituted and purified RabL2 with CEP19 or IFT proteins to show that a reconstituted pentameric IFT complex containing IFT81/74 enhances the GTP hydrolysis rate of RabL2. The binding site on IFT81/74 that promotes GTP hydrolysis in RabL2 was mapped to a 70-amino-acid-long coiled-coil region of IFT81/74. We present structural models for RabL2-containing IFT complexes that we validate in vitro and in cellulo and demonstrate that Chlamydomonas IFT81/74 enhances GTP hydrolysis of human RabL2, suggesting an ancient evolutionarily conserved activity. Our results provide an architectural understanding of how RabL2 is incorporated into the IFT complex and a molecular rationale for why RabL2 dissociates from anterograde IFT trains soon after departure from the ciliary base.
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Affiliation(s)
- Niels Boegholm
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | - Narcis A Petriman
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | - Marta Loureiro‐López
- Department for Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Jiaolong Wang
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | | | - Beibei Liu
- Department of Cell BiologyUniversity of Oklahoma Health Science CenterOklahomaOKUSA
| | - Tomoharu Kanie
- Department of Cell BiologyUniversity of Oklahoma Health Science CenterOklahomaOKUSA
- Baxter Laboratory, Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
| | - Roy Ng
- Baxter Laboratory, Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Jens S Andersen
- Department for Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Esben Lorentzen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
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Li D, Cheng Y, Zeng X, Li Y, Xia Z, Yang X, Ren D. Polysaccharide from Ziyang Selenium-Enriched Green Tea Prevents Obesity and Promotes Adipose Thermogenesis via Modulating the Gut Microbiota. J Agric Food Chem 2023; 71:13363-13375. [PMID: 37647585 DOI: 10.1021/acs.jafc.3c04193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The objective of the current study was to explore the potential mechanism of Ziyang selenium-enriched green tea polysaccharide (Se-GTP) against obesity. The results showed that Se-GTP significantly alleviated obesity and related metabolic disorders caused by high-fat diet (HFD) in mice. 16S rRNA gene sequencing results revealed that Se-GTP improved gut microbiota disturbance of obese mice and facilitated proliferation of probiotics such as Bacteroides, Bifidobacterium, Lactobacillus, and Akkermansia. In addition, the colonic content of succinate, a product of microbial metabolite in connection with adipocyte thermogenesis, was significantly enhanced by Se-GTP treatment. Therefore, Se-GTP facilitated brown adipose tissue (BAT) thermogenesis and inguinal white adipose tissue (iWAT) browning in obese mice, which could be revealed by increased expressions of thermogenic marker proteins UCP1, PGC-1α, and CIDEA in BAT and iWAT. Interestingly, Se-GTP intervention also observably increased the content of M2-like macrophages in iWAT of obese mice. To summarize, the results of this study are the first to show that Se-GTP can stimulate the browning of iWAT and BAT thermogenesis to counteract obesity, which may be pertinent with the alteration of gut microbiota in obese mice.
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Affiliation(s)
- Donglu Li
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, and Shaanxi Key Laboratory for Hazard Factors Assessment in Processing and Storage of Agricultural Products, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Yukun Cheng
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, and Shaanxi Key Laboratory for Hazard Factors Assessment in Processing and Storage of Agricultural Products, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Xiaoqian Zeng
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, and Shaanxi Key Laboratory for Hazard Factors Assessment in Processing and Storage of Agricultural Products, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Yixiao Li
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, and Shaanxi Key Laboratory for Hazard Factors Assessment in Processing and Storage of Agricultural Products, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Zengrun Xia
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs/National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang 725000, China
| | - Xingbin Yang
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, and Shaanxi Key Laboratory for Hazard Factors Assessment in Processing and Storage of Agricultural Products, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Daoyuan Ren
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, and Shaanxi Key Laboratory for Hazard Factors Assessment in Processing and Storage of Agricultural Products, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
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35
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McQuown AJ, Nelliat AR, Reif D, Sabbarini IM, Membreno BS, Wu CCC, Denic V. A Zpr1 co-chaperone mediates folding of eukaryotic translation elongation factor 1A via a GTPase cycle. Mol Cell 2023; 83:3108-3122.e13. [PMID: 37597513 PMCID: PMC10528422 DOI: 10.1016/j.molcel.2023.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/23/2023] [Accepted: 07/27/2023] [Indexed: 08/21/2023]
Abstract
General protein folding is mediated by chaperones that utilize ATP hydrolysis to regulate client binding and release. Zinc-finger protein 1 (Zpr1) is an essential ATP-independent chaperone dedicated to the biogenesis of eukaryotic translation elongation factor 1A (eEF1A), a highly abundant GTP-binding protein. How Zpr1-mediated folding is regulated to ensure rapid Zpr1 recycling remains an unanswered question. Here, we use yeast genetics and microscopy analysis, biochemical reconstitution, and structural modeling to reveal that folding of eEF1A by Zpr1 requires GTP hydrolysis. Furthermore, we identify the highly conserved altered inheritance of mitochondria 29 (Aim29) protein as a Zpr1 co-chaperone that recognizes eEF1A in the GTP-bound, pre-hydrolysis conformation. This interaction dampens Zpr1⋅eEF1A GTPase activity and facilitates client exit from the folding cycle. Our work reveals that a bespoke ATP-independent chaperone system has mechanistic similarity to ATPase chaperones but unexpectedly relies on client GTP hydrolysis to regulate the chaperone-client interaction.
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Affiliation(s)
- Alexander J McQuown
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anjali R Nelliat
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dvir Reif
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ibrahim M Sabbarini
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Britnie Santiago Membreno
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Colin Chih-Chien Wu
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Vladimir Denic
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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36
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McLeod MJ, Holyoak T. Biochemical, structural, and kinetic characterization of PP i -dependent phosphoenolpyruvate carboxykinase from Propionibacterium freudenreichii. Proteins 2023; 91:1261-1275. [PMID: 37226637 DOI: 10.1002/prot.26513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/26/2023]
Abstract
Phosphoenolpyruvate carboxykinases (PEPCK) are a well-studied family of enzymes responsible for the regulation of TCA cycle flux, where they catalyze the interconversion of oxaloacetic acid (OAA) and phosphoenolpyruvate (PEP) using a phosphoryl donor/acceptor. These enzymes have typically been divided into two nucleotide-dependent classes, those that use ATP and those that use GTP. In the 1960's and early 1970's, a group of papers detailed biochemical properties of an enzyme named phosphoenolpyruvate carboxytransphosphorylase (later identified as a third PEPCK) from Propionibacterium freudenreichii (PPi -PfPEPCK), which instead of using a nucleotide, utilized PPi to catalyze the same interconversion of OAA and PEP. The presented work expands upon the initial biochemical experiments for PPi -PfPEPCK and interprets these data considering both the current understanding of nucleotide-dependent PEPCKs and is supplemented with a new crystal structure of PPi -PfPEPCK in complex with malate at a putative allosteric site. Most interesting, the data are consistent with PPi -PfPEPCK being a Fe2+ activated enzyme in contrast with the Mn2+ activated nucleotide-dependent enzymes which in part results in some unique kinetic properties for the enzyme when compared to the more widely distributed GTP- and ATP-dependent enzymes.
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Affiliation(s)
- Matthew J McLeod
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Department of Physics, Cornell University, Ithaca, New York, USA
| | - Todd Holyoak
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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37
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Choi J, DiMaio D. Noncanonical Rab9a action supports retromer-mediated endosomal exit of human papillomavirus during virus entry. PLoS Pathog 2023; 19:e1011648. [PMID: 37703297 PMCID: PMC10519607 DOI: 10.1371/journal.ppat.1011648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/25/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023] Open
Abstract
Rab GTPases play key roles in controlling intracellular vesicular transport. GTP-bound Rab proteins support vesicle trafficking. Here, we report that, unlike cellular protein cargos, retromer-mediated delivery of human papillomaviruses (HPV) into the retrograde transport pathway during virus entry is inhibited by Rab9a in its GTP-bound form. Knockdown of Rab9a inhibits HPV entry by modulating the HPV-retromer interaction and impairing retromer-mediated endosome-to-Golgi transport of the incoming virus, resulting in the accumulation of HPV in the endosome. Rab9a is in proximity to HPV as early as 3.5 h post-infection, prior to the Rab7-HPV interaction, and HPV displays increased association with retromer in Rab9a knockdown cells, even in the presence of dominant negative Rab7. Thus, Rab9a can regulate HPV-retromer association independently of Rab7. Surprisingly, excess GTP-Rab9a impairs HPV entry, whereas excess GDP-Rab9a reduces association between L2 and Rab9a and stimulates entry. These findings reveal that HPV and cellular proteins utilize the Rab9a host trafficking machinery in distinct ways during intracellular trafficking.
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Affiliation(s)
- Jeongjoon Choi
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Yale Cancer Center, New Haven, Connecticut, United States of America
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38
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Shin DY, Takagi H, Hiroshima M, Matsuoka S, Ueda M. Sphingomyelin metabolism underlies Ras excitability for efficient cell migration and chemotaxis. Cell Struct Funct 2023; 48:145-160. [PMID: 37438131 DOI: 10.1247/csf.23045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023] Open
Abstract
In eukaryotic motile cells, the active Ras (Ras-GTP)-enriched domain is generated in an asymmetric manner on the cell membrane through the excitable dynamics of an intracellular signaling network. This asymmetric Ras signaling regulates pseudopod formation for both spontaneous random migration and chemoattractant-induced directional migration. While membrane lipids, such as sphingomyelin and phosphatidylserine, contribute to Ras signaling in various cell types, whether they are involved in the Ras excitability for cell motility is unknown. Here we report that functional Ras excitability requires the normal metabolism of sphingomyelin for efficient cell motility and chemotaxis. The pharmacological blockade of sphingomyelin metabolism by an acid-sphingomyelinase inhibitor, fendiline, and other inhibitors suppressed the excitable generation of the stable Ras-GTP-enriched domain. The suppressed excitability failed to invoke enough basal motility to achieve directed migration under shallow chemoattractant gradients. The fendiline-induced defects in Ras excitability, motility and stimulation-elicited directionality were due to an accumulation of sphingomyelin on the membrane, which could be recovered by exogenous sphingomyelinase or phosphatidylserine without changing the expression of Ras. These results indicate a novel regulatory mechanism of the excitable system by membrane lipids, in which sphingomyelin metabolism provides a membrane environment to ensure Ras excitation for efficient cellular motility and chemotaxis.Key words: cell polarity, cell migration, Ras, excitability, sphingomyelin.
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Affiliation(s)
- Da Young Shin
- Laboratory of Single Molecule Biology, Department of Biological Sciences, Graduate School of Science, Osaka University
- Laboratory for Cell Signaling Dynamics, Center for Biosystems Dynamics Research, RIKEN
| | - Hiroaki Takagi
- Laboratory for Cell Signaling Dynamics, Center for Biosystems Dynamics Research, RIKEN
- Department of Physics, School of Medicine, Nara Medical University
| | - Michio Hiroshima
- Laboratory for Cell Signaling Dynamics, Center for Biosystems Dynamics Research, RIKEN
- Laboratory of Single Molecule Biology, Graduate School of Frontier Biosciences, Osaka University
| | - Satomi Matsuoka
- Laboratory of Single Molecule Biology, Department of Biological Sciences, Graduate School of Science, Osaka University
- Laboratory for Cell Signaling Dynamics, Center for Biosystems Dynamics Research, RIKEN
- Laboratory of Single Molecule Biology, Graduate School of Frontier Biosciences, Osaka University
- PRESTO, JST
| | - Masahiro Ueda
- Laboratory of Single Molecule Biology, Department of Biological Sciences, Graduate School of Science, Osaka University
- Laboratory for Cell Signaling Dynamics, Center for Biosystems Dynamics Research, RIKEN
- Laboratory of Single Molecule Biology, Graduate School of Frontier Biosciences, Osaka University
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Alotaibi BS. Targeting Filamenting temperature-sensitive mutant Z (FtsZ) with bioactive phytoconstituents: An emerging strategy for antibacterial therapy. PLoS One 2023; 18:e0290852. [PMID: 37647309 PMCID: PMC10468062 DOI: 10.1371/journal.pone.0290852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
The rise and widespread occurrence of bacterial resistance has created an evident need for novel antibacterial drugs. Filamenting temperature-sensitive mutant Z (FtsZ) is a crucial bacterial protein that forms a ring-like structure known as the Z-ring, playing a significant role in cell division. Targeting FtsZ is an effective approach for developing antibiotics that disrupt bacterial cell division and halt growth. This study aimed to use a virtual screening approach to search for bioactive phytoconstituents with the potential to inhibit FtsZ. The screening process proceeded with the filtering compounds from the IMPPAT library of phytochemicals based on their physicochemical properties using the Lipinski rule of five. This was followed by molecular docking, Pan-assay interference compounds (PAINS) filter, absorption, distribution, metabolism, excretion, and toxicity (ADMET), prediction of activity spectra for biologically active substances (PASS), and molecular dynamics (MD) simulations. These filters ensured that any adverse effects that could impede the identification of potential inhibitors of FtsZ were eliminated. Following this, two phytocompounds, Withaperuvin C and Trifolirhizin, were selected after the screening, demonstrating noteworthy binding potential with FtsZ's GTP binding pocket, acting as potent GTP-competitive inhibitors of FtsZ. The study suggested that these compounds could be further investigated for developing a novel class of antibiotics after required studies.
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Affiliation(s)
- Bader Saud Alotaibi
- Department of Laboratories Sciences, College of Applied Medical Sciences, Shaqra University, Alquwayiyah, Saudi Arabia
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40
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Ha HJ, Kim JH, Lee GH, Kim S, Park HH. Structural basis of IRGB10 oligomerization by GTP hydrolysis. Front Immunol 2023; 14:1254415. [PMID: 37705969 PMCID: PMC10495984 DOI: 10.3389/fimmu.2023.1254415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/11/2023] [Indexed: 09/15/2023] Open
Abstract
Immunity-related GTPase B10 (IRGB10) is a crucial member of the interferon (IFN)-inducible GTPases and plays a vital role in host defense mechanisms. Following infection, IRGB10 is induced by IFNs and functions by liberating pathogenic ligands to activate the inflammasome through direct disruption of the pathogen membrane. Despite extensive investigation into the significance of the cell-autonomous immune response, the precise molecular mechanism underlying IRGB10-mediated microbial membrane disruption remains elusive. Herein, we present two structures of different forms of IRGB10, the nucleotide-free and GppNHp-bound forms. Based on these structures, we identified that IRGB10 exists as a monomer in nucleotide-free and GTP binding states. Additionally, we identified that GTP hydrolysis is critical for dimer formation and further oligomerization of IRGB10. Building upon these observations, we propose a mechanistic model to elucidate the working mechanism of IRGB10 during pathogen membrane disruption.
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Affiliation(s)
- Hyun Ji Ha
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Ju Hyeong Kim
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Republic of Korea
| | - Gwan Hee Lee
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Republic of Korea
| | - Subin Kim
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Republic of Korea
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41
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Zhao Y, Rai J, Li H. Regulation of translation by ribosomal RNA pseudouridylation. Sci Adv 2023; 9:eadg8190. [PMID: 37595043 PMCID: PMC10438446 DOI: 10.1126/sciadv.adg8190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023]
Abstract
Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such as ribosome, however, remains elusive owing to the lack of structures without this natural modification. Here, we studied the translation of a hypopseudouridylated ribosome initiated by the internal ribosome entry site (IRES) elements. We analyzed eight cryo-electron microscopy structures of the ribosome bound with the Taura syndrome virus IRES in multiple functional states. We found widespread loss of pseudouridine-mediated interactions through water and long-range base pairings. In the presence of the translocase, eukaryotic elongation factor 2, and guanosine 5'-triphosphate hydrolysis, the hypopseudouridylated ribosome favors a rare unconducive conformation for decoding that is partially recouped in the ribosome population that remains modified at the P-site uridine. The structural principles learned establish the link between functional defects and modification loss and are likely applicable to other pseudouridine-associated processes.
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Affiliation(s)
- Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Jay Rai
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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42
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Senthilvelan A, Shanmugasundaram M, Kore AR. Protocols for Efficient Chemical Synthesis of N 2 -Modified Guanosine Phosphate Derivatives: Versatile Probes for mRNA Labeling. Curr Protoc 2023; 3:e863. [PMID: 37639626 DOI: 10.1002/cpz1.863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
A facile, reliable, and efficient method for the synthesis of N2 -modified guanosine nucleotides such as N2 -[benzyl-N-(propyl)carbamate]-guanosine-5'-O-monophosphate, N2 -[benzyl-N-(propyl)carbamate]-guanosine-5'-O-diphosphate, N2 -[benzyl-N-(propyl)carbamate]-guanosine-5'-O-triphosphate, and N2 -[benzyl-N-(propyl)carbamate]-N7 -methyl-guanosine-5'-O-diphosphate, starting from the corresponding nucleotide is described. The general process entails condensation between the exocyclic amine of guanosine nucleotide and 3-[(benzyloxycarbonyl)amino]propionaldehyde in aqueous methanol, followed by reduction using sodium cyanoborohydride to furnish the corresponding N2 -modified guanosine nucleotide in moderate yield with high purity (>99.5%). © 2023 Wiley Periodicals LLC. Basic Protocol: Synthesis of N2 -modified guanosine derivatives.
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences and Laboratory Products Group, Thermo Fisher Scientific, Austin, Texas
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43
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O'Neill AG, Burrell AL, Zech M, Elpeleg O, Harel T, Edvardson S, Mor-Shaked H, Rippert AL, Nomakuchi T, Izumi K, Kollman JM. Neurodevelopmental disorder mutations in the purine biosynthetic enzyme IMPDH2 disrupt its allosteric regulation. J Biol Chem 2023; 299:105012. [PMID: 37414152 PMCID: PMC10407431 DOI: 10.1016/j.jbc.2023.105012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/08/2023] Open
Abstract
Inosine 5' monophosphate dehydrogenase (IMPDH) is a critical regulatory enzyme in purine nucleotide biosynthesis that is inhibited by the downstream product GTP. Multiple point mutations in the human isoform IMPDH2 have recently been associated with dystonia and other neurodevelopmental disorders, but the effect of the mutations on enzyme function has not been described. Here, we report the identification of two additional missense variants in IMPDH2 from affected individuals and show that all of the disease-associated mutations disrupt GTP regulation. Cryo-EM structures of one IMPDH2 mutant suggest this regulatory defect arises from a shift in the conformational equilibrium toward a more active state. This structural and functional analysis provides insight into IMPDH2-associated disease mechanisms that point to potential therapeutic approaches and raises new questions about fundamental aspects of IMPDH regulation.
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Affiliation(s)
- Audrey G O'Neill
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Anika L Burrell
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Simon Edvardson
- Alyn Hospital, Hebrew University School of Medicine, Jerusalem, Israel
| | - Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alyssa L Rippert
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tomoki Nomakuchi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kosuke Izumi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington, USA.
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44
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Fu W, Wu G. Design of negative-regulating proteins of Rheb/mTORC1 with much-reduced sizes of the tuberous sclerosis protein complex. Protein Sci 2023; 32:e4731. [PMID: 37462942 PMCID: PMC10382911 DOI: 10.1002/pro.4731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
The mTORC1 signaling pathway regulates cell growth and metabolism in a variety of organisms from yeast to human, and inhibition of the mTORC1 pathway has the prospect to treat cancer or achieve longevity. The tuberous sclerosis protein complex (TSCC) is a master negative regulator of the mTORC1 signaling pathway through hydrolyzing the GTP loaded on the small GTPase Rheb, which is a key activator of mTOR. However, the large size (~700 kDa) and complex structural organization of TSCC render it vulnerable to degradation and inactivation, thus limiting its potential application. In this work, based on thorough analysis and understanding of the structural mechanism of how the stabilization domain of TSC2 secures the association of TSC2-GAP with Rheb and thus enhances its GAP activity, we designed two proteins, namely SSG-MTM (short stabilization domain and GAP domain-membrane targeting motif) and SSG-TSC1N, which were able to function like TSCC to negatively regulate Rheb and mTORC1, but with much-reduced sizes (~1/15 and ~ 1/9 of the size of TSCC, respectively). Biochemical and cell biological assays demonstrated that these designed proteins indeed could promote the GTPase activity of Rheb to hydrolyze GTP, inhibit the kinase activity of mTORC1, and prevent mTORC1 from down-regulating catabolism and autophagy.
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Affiliation(s)
- Wencheng Fu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, the Joint International Research Laboratory of Metabolic & Developmental Sciences MOEShanghai Jiao Tong UniversityShanghaiChina
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, the Joint International Research Laboratory of Metabolic & Developmental Sciences MOEShanghai Jiao Tong UniversityShanghaiChina
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45
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Park JC, Luebbers A, Dao M, Semeano A, Nguyen AM, Papakonstantinou MP, Broselid S, Yano H, Martemyanov KA, Garcia-Marcos M. Fine-tuning GPCR-mediated neuromodulation by biasing signaling through different G protein subunits. Mol Cell 2023; 83:2540-2558.e12. [PMID: 37390816 PMCID: PMC10527995 DOI: 10.1016/j.molcel.2023.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/28/2023] [Accepted: 06/02/2023] [Indexed: 07/02/2023]
Abstract
G-protein-coupled receptors (GPCRs) mediate neuromodulation through the activation of heterotrimeric G proteins (Gαβγ). Classical models depict that G protein activation leads to a one-to-one formation of Gα-GTP and Gβγ species. Each of these species propagates signaling by independently acting on effectors, but the mechanisms by which response fidelity is ensured by coordinating Gα and Gβγ responses remain unknown. Here, we reveal a paradigm of G protein regulation whereby the neuronal protein GINIP (Gα inhibitory interacting protein) biases inhibitory GPCR responses to favor Gβγ over Gα signaling. Tight binding of GINIP to Gαi-GTP precludes its association with effectors (adenylyl cyclase) and, simultaneously, with regulator-of-G-protein-signaling (RGS) proteins that accelerate deactivation. As a consequence, Gαi-GTP signaling is dampened, whereas Gβγ signaling is enhanced. We show that this mechanism is essential to prevent the imbalances of neurotransmission that underlie increased seizure susceptibility in mice. Our findings reveal an additional layer of regulation within a quintessential mechanism of signal transduction that sets the tone of neurotransmission.
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Affiliation(s)
- Jong-Chan Park
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Alex Luebbers
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Maria Dao
- U.F. Scripps Biomedical Research, University of Florida, Jupiter, FL 33458, USA
| | - Ana Semeano
- Department of Pharmaceutical Sciences, Center for Drug Discovery, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Anh Minh Nguyen
- Department of Pharmaceutical Sciences, Center for Drug Discovery, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Maria P Papakonstantinou
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Stefan Broselid
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Hideaki Yano
- Department of Pharmaceutical Sciences, Center for Drug Discovery, School of Pharmacy and Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | | | - Mikel Garcia-Marcos
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; Department of Biology, College of Arts & Sciences, Boston University, Boston, MA 02115, USA.
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46
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Zhang Y, Chen S, Choi T, Qi Y, Wang Q, Li G, Zhao Y. Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1. J Comput Aided Mol Des 2023; 37:301-312. [PMID: 37286854 DOI: 10.1007/s10822-023-00508-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023]
Abstract
Cell division control protein 42 homolog (Cdc42), which controls a variety of cellular functions including rearrangements of the cell cytoskeleton, cell differentiation and proliferation, is a potential cancer therapeutic target. As an endogenous negative regulator of Cdc42, the Rho GDP dissociation inhibitor 1 (RhoGDI1) can prevent the GDP/GTP exchange of Cdc42 to maintain Cdc42 into an inactive state. To investigate the inhibition mechanism of Cdc42 through RhoGDI1 at the atomic level, we performed molecular dynamics (MD) simulations. Without RhoGDI1, Cdc42 has more flexible conformations, especially in switch regions which are vital for binding GDP/GTP and regulators. In the presence of RhoGDI1, it not only can change the intramolecular interactions of Cdc42 but also can maintain the switch regions into a closed conformation through extensive interactions with Cdc42. These results which are consistent with findings of biochemical and mutational studies provide deep structural insights into the inhibition mechanisms of Cdc42 by RhoGDI1. These findings are beneficial for the development of novel therapies targeting Cdc42-related cancers.
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Affiliation(s)
- Yijing Zhang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Shiyao Chen
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Taeyoung Choi
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yuzheng Qi
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Qianhui Wang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Guanyi Li
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yaxue Zhao
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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47
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Gupta A, Kelty-Stephen DG, Mangalam M, McKindles RJ, Stirling L. Walking speed and dual task input modality impact performance on a self-paced treadmill. Appl Ergon 2023; 109:103986. [PMID: 36753790 DOI: 10.1016/j.apergo.2023.103986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/18/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Interference between a walking task (target speeds on a self-paced treadmill) and dual visual and tactile-visual response time task was investigated. Ambulatory dual-task scenarios reveal how attention is divided between walking and additional tasks, but the impact of walking speed and dual-task modality on gait characteristics and dual-task performance is unclear. The purpose of this study was to evaluate the effect of visual and tactile-visual dual-task on gait performance. Participants (n=15) targeted four speeds (0.5, 1.0, 1.3, and 1.5 m/s) on a self-paced treadmill with a visual speed indicator (a green region centered at the target speed). Participants completed the same speed profile on the treadmill without (Self-Paced) and with a response time dual task (Self-Paced with Dual Task) requiring finger-tap responses to go/no-go cues. Six gait characteristics were calculated: proportion of time in the desired speed green region (GTP), speed ratio (ratio of mean to target speed), time to green region after target speed change (NRT), normalized stride width (NSW), normalized stride length (NSL), and stride time (ST). Both stride length and width were normalized by participant leg length. Lower GTP and greater speed ratio at slower speeds during dual tasking indicate speed-dependent changes in gait characteristics. Changes in NSL and ST were more affected by speed than dual task. These findings support that when speed is a parameter that is tracked, participants do not universally decrease speed in the presence of a dual task. These findings can support the decisions made when designing new wearable technologies that support navigation, communication, and mobility.
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Affiliation(s)
- Aditi Gupta
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Damian G Kelty-Stephen
- Department of Psychology, State University of New York at New Paltz, New Paltz, NY 12561, USA.
| | - Madhur Mangalam
- Department of Biomechanics, University of Nebraska Omaha, Omaha, NE 68182, USA.
| | - Ryan J McKindles
- MIT Lincoln Laboratory, Human Health & Performance Systems, Lexington, MA 02421, USA.
| | - Leia Stirling
- Industrial and Operations Engineering Department, Robotics Department, University of Michigan, Ann Arbor, MI 48109, USA.
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48
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Martínez RAS, Pinky PD, Harlan BA, Brewer GJ. GTP energy dependence of endocytosis and autophagy in the aging brain and Alzheimer's disease. GeroScience 2023; 45:757-780. [PMID: 36622562 PMCID: PMC9886713 DOI: 10.1007/s11357-022-00717-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
Increased interest in the aging and Alzheimer's disease (AD)-related impairments in autophagy in the brain raise important questions about regulation and treatment. Since many steps in endocytosis and autophagy depend on GTPases, new measures of cellular GTP levels are needed to evaluate energy regulation in aging and AD. The recent development of ratiometric GTP sensors (GEVALS) and findings that GTP levels are not homogenous inside cells raise new issues of regulation of GTPases by the local availability of GTP. In this review, we highlight the metabolism of GTP in relation to the Rab GTPases involved in formation of early endosomes, late endosomes, and lysosomal transport to execute the autophagic degradation of damaged cargo. Specific GTPases control macroautophagy (mitophagy), microautophagy, and chaperone-mediated autophagy (CMA). By inference, local GTP levels would control autophagy, if not in excess. Additional levels of control are imposed by the redox state of the cell, including thioredoxin involvement. Throughout this review, we emphasize the age-related changes that could contribute to deficits in GTP and AD. We conclude with prospects for boosting GTP levels and reversing age-related oxidative redox shift to restore autophagy. Therefore, GTP levels could regulate the numerous GTPases involved in endocytosis, autophagy, and vesicular trafficking. In aging, metabolic adaptation to a sedentary lifestyle could impair mitochondrial function generating less GTP and redox energy for healthy management of amyloid and tau proteostasis, synaptic function, and inflammation.
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Affiliation(s)
| | - Priyanka D. Pinky
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 USA
| | - Benjamin A. Harlan
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 USA
| | - Gregory J. Brewer
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 USA
- Center for Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA 92697 USA
- MIND Institute, University of California Irvine, Irvine, CA 92697 USA
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49
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Koval A, Larasati YA, Savitsky M, Solis GP, Good JM, Quinodoz M, Rivolta C, Superti-Furga A, Katanaev VL. In-depth molecular profiling of an intronic GNAO1 mutant as the basis for personalized high-throughput drug screening. Med 2023; 4:311-325.e7. [PMID: 37001522 DOI: 10.1016/j.medj.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023]
Abstract
BACKGROUND The GNAO1 gene, encoding the major neuronal G protein Gαo, is mutated in a subset of pediatric encephalopathies. Most such mutations consist of missense variants. METHODS In this study, we present a precision medicine workflow combining next-generation sequencing (NGS) diagnostics, molecular etiology analysis, and personalized drug discovery. FINDINGS We describe a patient carrying a de novo intronic mutation (NM_020988.3:c.724-8G>A), leading to epilepsy-negative encephalopathy with motor dysfunction from the second decade. Our data show that this mutation creates a novel splice acceptor site that in turn causes an in-frame insertion of two amino acid residues, Pro-Gln, within the regulatory switch III region of Gαo. This insertion misconfigures the switch III loop and creates novel interactions with the catalytic switch II region, resulting in increased GTP uptake, defective GTP hydrolysis, and aberrant interactions with effector proteins. In contrast, intracellular localization, Gβγ interactions, and G protein-coupled receptor (GPCR) coupling of the Gαo[insPQ] mutant protein remain unchanged. CONCLUSIONS This in-depth analysis characterizes the heterozygous c.724-8G>A mutation as partially dominant negative, providing clues to the molecular etiology of this specific pathology. Further, this analysis allows us to establish and validate a high-throughput screening platform aiming at identifying molecules that could correct the aberrant biochemical functions of the mutant Gαo. FUNDING This work was supported by the Joint Seed Money Funding scheme between the University of Geneva and the Hebrew University of Jerusalem.
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Affiliation(s)
- Alexey Koval
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Yonika A Larasati
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Mikhail Savitsky
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Gonzalo P Solis
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Vladimir L Katanaev
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690090 Vladivostok, Russia.
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50
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Nikonov OS, Nikonova EY, Tarabarova AG, Mikhaylina AO, Kravchenko OV, Nevskaya NA, Nikonov SV. Recognition of γ-Subunit by β-Subunit in Translation Initiation Factor 2. Stabilization of the GTP-Bound State of I/F 2 in Archaea and Eukaryotes. Biochemistry Moscow 2023; 88:221-230. [PMID: 37072332 DOI: 10.1134/s0006297923020062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Eukaryotic and archaeal translation initiation factor 2 (e/aIF2) functions as a heterotrimeric complex. It consists of three subunits (α, β, γ). α- and β-subunits are bound to γ-subunit by hydrogen bonds and van der Waals interactions, but do not contact each other. Although main functions of the factor are performed by the γ-subunit, reliable formation of αγ and βγ complexes is necessary for its proper functioning. In this work, we introduced mutations in the recognition part of the βγ interface and showed that hydrophobic effect plays a crucial role in the recognition of subunits both in eukaryotes and archaea. Shape and properties of the groove on the surface of γ-subunit facilitates transition of the disordered recognition part of the β-subunit into an α-helix containing approximately the same number of residues in archaea and eukaryotes. In addition, based on the newly obtained data, it was concluded that in archaea and eukaryotes, transition of the γ-subunit to the active state leads to additional contact between the region of switch 1 and C-terminal part of the β-subunit, which stabilizes helical conformation of the switch.
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Affiliation(s)
- Oleg S Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Ekaterina Yu Nikonova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Anastasiia G Tarabarova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alisa O Mikhaylina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Olesya V Kravchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Natalia A Nevskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Stanislav V Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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