1
|
Korhonen PK, Wang T, Young ND, Byrne JJ, Campos TL, Chang BC, Taki AC, Gasser RB. Analysis of Haemonchus embryos at single cell resolution identifies two eukaryotic elongation factors as intervention target candidates. Comput Struct Biotechnol J 2024; 23:1026-1035. [PMID: 38435301 PMCID: PMC10907403 DOI: 10.1016/j.csbj.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 03/05/2024] Open
Abstract
Advances in single cell technologies are allowing investigations of a wide range of biological processes and pathways in animals, such as the multicellular model organism Caenorhabditis elegans - a free-living nematode. However, there has been limited application of such technology to related parasitic nematodes which cause major diseases of humans and animals worldwide. With no vaccines against the vast majority of parasitic nematodes and treatment failures due to drug resistance or inefficacy, new intervention targets are urgently needed, preferably informed by a deep understanding of these nematodes' cellular and molecular biology - which is presently lacking for most worms. Here, we created the first single cell atlas for an early developmental stage of Haemonchus contortus - a highly pathogenic, C. elegans-related parasitic nematode. We obtained and curated RNA sequence (snRNA-seq) data from single nuclei from embryonating eggs of H. contortus (150,000 droplets), and selected high-quality transcriptomic data for > 14,000 single nuclei for analysis, and identified 19 distinct clusters of cells. Guided by comparative analyses with C. elegans, we were able to reproducibly assign seven cell clusters to body wall muscle, hypodermis, neuronal, intestinal or seam cells, and identified eight genes that were transcribed in all cell clusters/types, three of which were inferred to be essential in H. contortus. Two of these genes (i.e. Hc-eef-1A and Hc-eef1G), coding for eukaryotic elongation factors (called Hc-eEF1A and Hc-eEF1G), were also demonstrated to be transcribed and expressed in all key developmental stages of H. contortus. Together with these findings, sequence- and structure-based comparative analyses indicated the potential of Hc-eEF1A and/or Hc-eEF1G as intervention targets within the protein biosynthesis machinery of H. contortus. Future work will focus on single cell studies of all key developmental stages and tissues of H. contortus, and on evaluating the suitability of the two elongation factor proteins as drug targets in H. contortus and related nematodes, with a view to finding new nematocidal drug candidates.
Collapse
Affiliation(s)
- Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joseph J. Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tulio L. Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bill C.H. Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aya C. Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
2
|
Wang G, Wu Z, Li M, Liang X, Wen Y, Zheng Q, Li D, An T. Microbial production of 5- epi-jinkoheremol, a plant-derived antifungal sesquiterpene. Appl Environ Microbiol 2024; 90:e0119124. [PMID: 39283105 PMCID: PMC11497823 DOI: 10.1128/aem.01191-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 08/21/2024] [Indexed: 10/25/2024] Open
Abstract
Synthetic biology using microbial chassis is emerging as a powerful tool for the production of natural chemicals. In the present study, we constructed a microbial platform for the high-level production of a sesquiterpene from Catharanthus roseus, 5-epi-jinkoheremol, which exhibits strong fungicidal activity. First, the mevalonate and sterol biosynthesis pathways were optimized in engineered yeast to increase the metabolic flux toward the biosynthesis of the precursor farnesyl pyrophosphate. Then, the transcription factor Hac1- and m6A writer Ime4-based metabolic engineering strategies were implemented in yeast to increase 5-epi-jinkoheremol production further. Next, protein engineering was performed to improve the catalytic activity and enhance the stability of the 5-epi-jinkoheremol synthase TPS18, resulting in the variant TPS18I21P/T414S, with the most improved properties. Finally, the titer of 5-epi-jinkoheremol was elevated to 875.25 mg/L in a carbon source-optimized medium in shake flask cultivation. To the best of our knowledge, this is the first study to construct an efficient microbial cell factory for the sustainable production of this antifungal sesquiterpene.IMPORTANCEBiofungicides represent a new and sustainable tool for the control of crop fungal diseases. However, hindered by the high cost of biofungicide production, their use is not as popular as expected. Synthetic biology using microbial chassis is emerging as a powerful tool for the production of natural chemicals. We previously identified a promising sesquiterpenoid biofungicide, 5-epi-jinkoheremol. Here, we constructed a microbial platform for the high-level production of this chemical. The metabolic engineering of the terpene biosynthetic pathway was firstly employed to increase the metabolic flux toward 5-epi-jinkoheremol production. However, the limited catalytic activity of the key enzyme, TPS18, restricted the further yield of 5-epi-jinkoheremol. By using protein engineering, we improved its catalytic efficiency, and combined with the optimization of regulation factors, the highest production of 5-epi-jinkoheremol was achieved. Our work was useful for the larger-scale efficient production of this antifungal sesquiterpene.
Collapse
Affiliation(s)
- Guoli Wang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Zhenke Wu
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Mingkai Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Xiqin Liang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Yiwei Wen
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Qiusheng Zheng
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Defang Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Tianyue An
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| |
Collapse
|
3
|
Sehgal E, Wohlenberg C, Soukup EM, Viscardi MJ, Serrão VHB, Arribere JA. High-resolution reconstruction of a C. elegans ribosome sheds light on evolutionary dynamics and tissue specificity. RNA (NEW YORK, N.Y.) 2024; 30:1513-1528. [PMID: 39209556 PMCID: PMC11482609 DOI: 10.1261/rna.080103.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Caenorhabditis elegans is an important model organism for human health and disease, with foundational contributions to the understanding of gene expression and tissue patterning in animals. An invaluable tool in modern gene expression research is the presence of a high-resolution ribosome structure, though no such structure exists for C. elegans Here, we present a high-resolution single-particle cryogenic electron microscopy (cryo-EM) reconstruction and molecular model of a C. elegans ribosome, revealing a significantly streamlined animal ribosome. Many facets of ribosome structure are conserved in C. elegans, including overall ribosomal architecture and the mechanism of cycloheximide, whereas other facets, such as expansion segments and eL28, are rapidly evolving. We identify uL5 and uL23 as two instances of tissue-specific ribosomal protein paralog expression conserved in Caenorhabditis, suggesting that C. elegans ribosomes vary across tissues. The C. elegans ribosome structure will provide a basis for future structural, biochemical, and genetic studies of translation in this important animal system.
Collapse
Affiliation(s)
- Enisha Sehgal
- Department of MCD Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Chloe Wohlenberg
- Department of MCD Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Evan M Soukup
- Department of MCD Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Marcus J Viscardi
- Department of MCD Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Vitor Hugo Balasco Serrão
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
- Biomolecular Cryoelectron Microscopy Facility, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Joshua A Arribere
- Department of MCD Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
- RNA Center, University of California at Santa Cruz, Santa Cruz, California 95064, USA
- Genomics Institute, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| |
Collapse
|
4
|
McLellan JL, Morales-Hernandez B, Saeger S, Hanson KK. A high content imaging assay for identification of specific inhibitors of native Plasmodium liver stage protein synthesis. Antimicrob Agents Chemother 2024; 68:e0079324. [PMID: 39254294 PMCID: PMC11459927 DOI: 10.1128/aac.00793-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 08/22/2024] [Indexed: 09/11/2024] Open
Abstract
Plasmodium parasite resistance to antimalarial drugs is a serious threat to public health in malaria-endemic areas. Compounds that target core cellular processes like translation are highly desirable, as they should be capable of killing parasites in their liver and blood stage forms, regardless of molecular target or mechanism. Assays that can identify these compounds are thus needed. Recently, specific quantification of native Plasmodium berghei liver stage protein synthesis, as well as that of the hepatoma cells supporting parasite growth, was achieved via automated confocal feedback microscopy of the o-propargyl puromycin (OPP)-labeled nascent proteome, but this imaging modality is limited in throughput. Here, we developed and validated a miniaturized high content imaging (HCI) version of the OPP assay that increases throughput, before deploying this approach to screen the Pathogen Box. We identified only two hits; both of which are parasite-specific quinoline-4-carboxamides, and analogs of the clinical candidate and known inhibitor of blood and liver stage protein synthesis, DDD107498/cabamiquine. We further show that these compounds have strikingly distinct relationships between their antiplasmodial and translation inhibition efficacies. These results demonstrate the utility and reliability of the P. berghei liver stage OPP HCI assay for the specific, single-well quantification of Plasmodium and human protein synthesis in the native cellular context, allowing the identification of selective Plasmodium translation inhibitors with the highest potential for multistage activity.
Collapse
Affiliation(s)
- James L. McLellan
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Beatriz Morales-Hernandez
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Sarah Saeger
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Kirsten K. Hanson
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas, USA
| |
Collapse
|
5
|
Liu L, Li Z, Wu W. Harnessing natural inhibitors of protein synthesis for cancer therapy: A comprehensive review. Pharmacol Res 2024; 209:107449. [PMID: 39368568 DOI: 10.1016/j.phrs.2024.107449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 09/27/2024] [Accepted: 10/01/2024] [Indexed: 10/07/2024]
Abstract
Cancer treatment remains a formidable challenge in modern medicine, necessitating a nuanced understanding of its molecular underpinnings and the identification of novel therapeutic modalities. Among the intricate web of cellular pathways implicated in oncogenesis, protein synthesis has emerged as a fundamental process warranting meticulous investigation. This review elucidates the multifaceted role of protein synthesis pathways in tumor initiation and progression, highlighting the potential of targeting key nodes within these pathways as viable therapeutic strategies. Natural products have long served as a source of bioactive compounds with therapeutic potential owing to their structural diversity and evolutionary honing. Within this framework, we provide a thorough examination of natural inhibitors of protein synthesis as promising candidates for cancer therapy, drawing upon recent advancements and mechanistic insights. By synthesizing current evidence and elucidating key challenges and opportunities, this review aims to galvanize further research into the development of natural product-based anticancer therapeutics, thereby advancing the clinical armamentarium against malignancies.
Collapse
Affiliation(s)
- Liqin Liu
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhihui Li
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Wenshuang Wu
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| |
Collapse
|
6
|
Pierron A, Balbo LC, Soler L, Pinton P, Puel S, Laffitte J, Albin M, Bracarense APFRL, Rodriguez MA, Oswald IP. Deoxynivalenol Induces Local Inflammation and Lesions in Tissues at Doses Recommended by the EU. Int J Mol Sci 2024; 25:9790. [PMID: 39337277 PMCID: PMC11432646 DOI: 10.3390/ijms25189790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/24/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
The mycotoxin deoxynivalenol (DON) is frequently present in cereals at low levels, resulting in its occurrence in food and feed. DON has been proven to alter the immune response and induce inflammation in all species, with pigs exhibiting heightened sensitivity and exposure. However, no study has yet evaluated the effects of exposure to DON at the recommended levels in pig feed. In two separate trials, piglets were subjected to control feed or feed contaminated with a low level of purified DON (0.83 mg/kg feed in trial 1 and 0.85 mg/kg feed in trial 2) for either three weeks (trial 1) or two weeks (trial 2). Additionally, a group of animals exposed to 2.85 mg/kg feed of DON was included as a positive control in Trial 1. The impact of DON on porcine tissues (intestine, liver, and spleen) was evaluated through histological and qPCR analyses of immune-related genes. Additionally, biochemical analyses and acute-phase proteins were examined in plasma samples. Lesions were identified in the intestine (jejunum and ileum), the liver, and the spleen of pigs receiving diets contaminated with low and high concentrations of DON. The low level of DON also resulted in impaired expression of genes associated with intestinal barrier integrity, intestinal immune responses, and liver function. In conclusion, the results of the two trials demonstrate the impact of DON exposure even at doses below the recommended level of 0.9 mg/kg feed set by the European Union. This suggests that the current recommended level should be reconsidered to ensure the optimal health and well-being of pigs.
Collapse
Affiliation(s)
- Alix Pierron
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (A.P.); (L.S.); (P.P.); (S.P.); (J.L.); (M.A.)
| | - Luciana C. Balbo
- Laboratory of Animal Pathology, Universidade Estadual de Londrina, Londrina 86057-970, Brazil; (L.C.B.); (A.-P.F.R.L.B.)
| | - Laura Soler
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (A.P.); (L.S.); (P.P.); (S.P.); (J.L.); (M.A.)
| | - Philippe Pinton
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (A.P.); (L.S.); (P.P.); (S.P.); (J.L.); (M.A.)
| | - Sylvie Puel
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (A.P.); (L.S.); (P.P.); (S.P.); (J.L.); (M.A.)
| | - Joëlle Laffitte
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (A.P.); (L.S.); (P.P.); (S.P.); (J.L.); (M.A.)
| | - Mickaël Albin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (A.P.); (L.S.); (P.P.); (S.P.); (J.L.); (M.A.)
| | | | | | - Isabelle P. Oswald
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (A.P.); (L.S.); (P.P.); (S.P.); (J.L.); (M.A.)
| |
Collapse
|
7
|
Tsirogianni A, Ntinou N, Karampatsou K, Dinos G, Kournoutou GG, Athanassopoulos CM. Chemical Modification of Pactamycin Leads to New Compounds with Retained Antimicrobial Activity and Reduced Toxicity. Molecules 2024; 29:4169. [PMID: 39275017 PMCID: PMC11397182 DOI: 10.3390/molecules29174169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 08/27/2024] [Accepted: 08/28/2024] [Indexed: 09/16/2024] Open
Abstract
Pactamycin (PCT), an antibiotic produced by Streptomyces pactum, is a five-membered ring aminocyclitol that is active against a variety of Gram-positive and Gram-negative microorganisms, as well as several animal tumor lines in culture and in vivo. Pactamycin targets the small ribosomal subunit and inhibits protein synthesis in bacteria, archaea, and eukaryotes, but due to its toxicity is used only as a tool for biochemical research. Prompted by the successful and well-established procedure for the derivatization of antibiotics, we modified pactamycin by tethering basic amino acids to the free primary amino group of the aminocyclitol ring. Specifically, lysine, ornithine, and histidine were conjugated via an amide bond, and the antimicrobial activity of the derivatives was evaluated both in vivo and in vitro. According to our results, their antimicrobial activity was maintained at almost equal levels, while their toxicity was reduced compared to the parent molecule. These findings suggest that the new pactamycin derivatives can be considered as promising pharmacophores for the development of new antimicrobials that are able to combat the dangerously increasing resistance of pathogens to antibiotics.
Collapse
Affiliation(s)
- Artemis Tsirogianni
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, University of Patras, 26504 Patras, Greece
| | - Nikolina Ntinou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Konstantina Karampatsou
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, University of Patras, 26504 Patras, Greece
| | - George Dinos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Georgia G Kournoutou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | | |
Collapse
|
8
|
He W, Yang P, Huang T, Liu Y, Zhang Y, Zhang W, Zhang T, Zheng M, Ma L, Zhao C, Li H, Liao Y, Wu A, Zhang J. Detoxifying bacterial genes for deoxynivalenol epimerization confer durable resistance to Fusarium head blight in wheat. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2395-2409. [PMID: 38593377 PMCID: PMC11331793 DOI: 10.1111/pbi.14353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/26/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Fusarium head blight (FHB) and the presence of mycotoxin deoxynivalenol (DON) pose serious threats to wheat production and food safety worldwide. DON, as a virulence factor, is crucial for the spread of FHB pathogens on plants. However, germplasm resources that are naturally resistant to DON and DON-producing FHB pathogens are inadequate in plants. Here, detoxifying bacteria genes responsible for DON epimerization were used to enhance the resistance of wheat to mycotoxin DON and FHB pathogens. We characterized the complete pathway and molecular basis leading to the thorough detoxification of DON via epimerization through two sequential reactions in the detoxifying bacterium Devosia sp. D6-9. Epimerization efficiently eliminates the phytotoxicity of DON and neutralizes the effects of DON as a virulence factor. Notably, co-expressing of the genes encoding quinoprotein dehydrogenase (QDDH) for DON oxidation in the first reaction step, and aldo-keto reductase AKR13B2 for 3-keto-DON reduction in the second reaction step significantly reduced the accumulation of DON as virulence factor in wheat after the infection of pathogenic Fusarium, and accordingly conferred increased disease resistance to FHB by restricting the spread of pathogenic Fusarium in the transgenic plants. Stable and improved resistance was observed in greenhouse and field conditions over multiple generations. This successful approach presents a promising avenue for enhancing FHB resistance in crops and reducing mycotoxin contents in grains through detoxification of the virulence factor DON by exogenous resistance genes from microbes.
Collapse
Affiliation(s)
- Wei‐Jie He
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Peng Yang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Jiangsu Ruihua Agricultural Science and Technology Co., Ltd.SuqianChina
| | - Tao Huang
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yu‐Fan Liu
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yu‐Wei Zhang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Wen‐Min Zhang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Tian‐Tian Zhang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Meng‐Ru Zheng
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ling Ma
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Chang‐Xing Zhao
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - He‐Ping Li
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yu‐Cai Liao
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ai‐Bo Wu
- SIBS‐UGENT‐SJTU Joint Laboratory of Mycotoxin Research, CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and HealthUniversity of Chinese Academy of Sciences, Chinese Academy of SciencesShanghaiChina
| | - Jing‐Bo Zhang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
9
|
Qiao Y, Wang J, Zhang D, Zheng X, Lin B, Huang Y, Liao Y, Deng Z, Kong L, You D. Biosynthesis of the benzylpyrrolidine precursor in anisomycin by a unique ThDP-dependent enzyme. Synth Syst Biotechnol 2024; 10:76-85. [PMID: 39263350 PMCID: PMC11387542 DOI: 10.1016/j.synbio.2024.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/03/2024] [Accepted: 08/19/2024] [Indexed: 09/13/2024] Open
Abstract
Anisomycin (compound 1), a multifunctional pyrrolidine antibiotic, primarily inhibits protein biosynthesis by binding to the ribosome. Upon binding to the ribosome, the para-phenol moiety of anisomycin inserts completely into the hydrophobic crevice of the A-site and blocks the access of the incoming aminoacyl-tRNAs, disrupting peptide bond formation. Hence, the para-methoxyphenyl group serves as a starting point for developing novel anisomycin analogs with potent antifungal and insecticidal properties. However, the activation and condensation mechanism of phenylpyruvic acid has not yet been elucidated. In this study, genetic manipulations of aniP and its homologue siAniP confirmed their indispensable role in 1 biosynthesis. Bioinformatics analysis suggested that AniP and siAniP function as transketolase. siAniP was found to catalyzed condensation between 4-hydroxyphenylpyruvic acid (3) and glyceraldehyde (GA), initiating pyrrolidine synthesis. siAniP was specific for aromatic keto acids and tolerant of aliphatic and aromatic aldehydes, and was able to catalyze the asymmetric intermolecular condensation of two keto acids, leading to the formation of 24 α-hydroxy ketone. To the best of our knowledge, siAniP is the first TK that catalyzes the transfer of a C2 ketol and symmetrical intermolecular coupling using aromatic keto acids as donor substrates. Structural analysis, docking model construction, and site-directed mutagenesis identified that I220, H275, R322 and W391 were crucial for substrate binding. Moreover, sequence similarity network (SSN)-based genome neighborhood network (GNN) analyses of AniP suggested the widespread occurrence of the AniP-like-mediated reaction in the biosynthesis of 1 and its analogs, particularly in the assembly of benzylpyrrolidine. These findings not only expand the repertoire of TKs but also provide a potent biocatalyst that could be used for the structural innovation of 1 and its derivatives.
Collapse
Affiliation(s)
- Yongjian Qiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Junbo Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Dashan Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiaoqing Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Baixin Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yongkang Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yulin Liao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| |
Collapse
|
10
|
Trivellin C, Torello Pianale L, Olsson L. Robustness quantification of a mutant library screen revealed key genetic markers in yeast. Microb Cell Fact 2024; 23:218. [PMID: 39098937 PMCID: PMC11298085 DOI: 10.1186/s12934-024-02490-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/24/2024] [Indexed: 08/06/2024] Open
Abstract
BACKGROUND Microbial robustness is crucial for developing cell factories that maintain consistent performance in a challenging environment such as large-scale bioreactors. Although tools exist to assess and understand robustness at a phenotypic level, the underlying metabolic and genetic mechanisms are not well defined, which limits our ability to engineer more strains with robust functions. RESULTS This study encompassed four steps. (I) Fitness and robustness were analyzed from a published dataset of yeast mutants grown in multiple environments. (II) Genes and metabolic processes affecting robustness or fitness were identified, and 14 of these genes were deleted in Saccharomyces cerevisiae CEN.PK113-7D. (III) The mutants bearing gene deletions were cultivated in three perturbation spaces mimicking typical industrial processes. (IV) Fitness and robustness were determined for each mutant in each perturbation space. We report that robustness varied according to the perturbation space. We identified genes associated with increased robustness such as MET28, linked to sulfur metabolism; as well as genes associated with decreased robustness, including TIR3 and WWM1, both involved in stress response and apoptosis. CONCLUSION The present study demonstrates how phenomics datasets can be analyzed to reveal the relationship between phenotypic response and associated genes. Specifically, robustness analysis makes it possible to study the influence of single genes and metabolic processes on stable microbial performance in different perturbation spaces. Ultimately, this information can be used to enhance robustness in targeted strains.
Collapse
Affiliation(s)
- Cecilia Trivellin
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Luca Torello Pianale
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
| |
Collapse
|
11
|
Saita K, Iida T, Takai Y, Aihara M, Uchida K, Iwagawa T, Kawamura T, Watanabe S. The mechanism of multistep progression of the transcriptional cascade in activated microglia as approached by a proteome approach. Cytokine 2024; 180:156655. [PMID: 38824862 DOI: 10.1016/j.cyto.2024.156655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 06/04/2024]
Abstract
The ocular cytokine network plays pivotal roles in terms of the initiation and progression of retinal degeneration. Several types of immunocompetent cells such as microglia participate in inflammation, and a temporal transition in the molecular events of inflammation has been hypothesized. We previously found that the Csf2 gene was induced in the early phase of retinal degeneration. CSF2 participates in the transcriptional activation of several cytokines expressed by microglia; however, whether CSF2 is essential in this context is not known. In this work, we approach this question by using anti-CSF2 neutralizing bntibody and the protein synthesis inhibitor cycloheximide (CHX). We first revealed that CSF2 positively regulated the cytokine induction cascade using a CSF2-neutralizing antibody (anti-CSF2) to treat the microglial cell line that were activated by lipopolysaccharide (LPS). LPS or Lipid A stimulation in the presence of the protein synthesis inhibitor cycloheximide (CHX) led to cytokine superinduction, but suppression of the expression of a few cytokines was also noted in MG5 cells. To examine transitions of the molecular events within LPS-activated microglia, we next performed proteome analysis of MG5 cells stimulated with LPS for 0, 4, and 9 h. The Database for Annotation, Visualization, and Integrated Discovery analysis of differentially expressed proteins showed that various mRNA-modifying molecules were induced after LPS stimulation, in addition to molecules involved in inflammation. However, the numbers of common proteins founded in the comparison between the induced proteins of 4 and 9 h were only one-third and one-half of induced proteins at 4 and 9 h, respectively, suggesting dynamic transition of the induced proteins. LPS-induced mRNA-modifying proteins were almost completely suppressed by CHX, as expected, suggesting that transient induction of transcription-editing proteins plays an important role in terms of the phenotype of inflammation that develops in microglia after LPS stimulation.
Collapse
Affiliation(s)
- Kosuke Saita
- Department of Retinal Development and Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeru Iida
- Department of Retinal Development and Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Ophthalmology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yoshihiro Takai
- Pharmacological Research Group, Basic Research Development Division, Rohto Pharmaceutical Co., Ltd., Kyoto, Japan
| | - Makoto Aihara
- Department of Ophthalmology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kanji Uchida
- Department of Anesthesiology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Toshiro Iwagawa
- Department of Retinal Development and Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Sumiko Watanabe
- Department of Retinal Development and Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Ophthalmology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan; Department of Lipid Signaling, National Center for Global Health and Medicine, Tokyo, Japan.
| |
Collapse
|
12
|
Kim B, Nguyen MV, Park J, Kim YS, Han JW, Lee JY, Jeon J, Son H, Choi GJ, Kim H. Edeine B 1 produced by Brevibacillus brevis reduces the virulence of a plant pathogenic fungus by inhibiting mitochondrial respiration. mBio 2024; 15:e0135124. [PMID: 38860787 PMCID: PMC11253638 DOI: 10.1128/mbio.01351-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 06/12/2024] Open
Abstract
Plant pathogenic fungi cause serious diseases, which result in the loss of crop yields and reduce the quality of crops worldwide. To counteract the escalating risks of chemical fungicides, interest in biological control agents to manage plant diseases has significantly increased. In this study, we comprehensively screened microbial culture filtrates using a yeast screening system to find microbes exhibiting respiratory inhibition activity. Consequently, we found a soil-borne microbe Brevibacillus brevis HK544 strain exhibiting a respiration inhibitory activity and identified edeine B1 (EB1) from the culture filtrate of HK544 as the active compound of the respiration inhibition activity. Furthermore, against a plant pathogenic fungus Fusarium graminearum, our results showed that EB1 has effects on multiple aspects of respiration with the downregulation of most of the mitochondrial-related genes based on transcriptome analysis, differential EB1-sensitivity from targeted mutagenesis, and the synergistic effects of EB1 with electron transport chain complex inhibitors. With the promising plant disease control efficacy of B. brevis HK544 producing EB1, our results suggest that B. brevis HK544 has potential as a biocontrol agent for Fusarium head blight.IMPORTANCEAs a necrotrophic fungus, Fusarium graminearum is a highly destructive pathogen causing severe diseases in cereal crops and mycotoxin contamination in grains. Although chemical control is considered the primary approach to control plant disease caused by F. graminearum, fungicide-resistant strains have been detected in the field after long-term continuous application of fungicides. Moreover, applying chemical fungicides that trigger mycotoxin biosynthesis is a great concern for many researchers. Biocontrol of Fusarium head blight (FHB) by biological control agents (BCAs) represents an alternative approach and could be used as part of the integrated management of FHB and mycotoxin production. The most extensive studies on bacterial BCAs-fungal communications in agroecosystems have focused on antibiosis. Although many BCAs in agricultural ecology have already been used for fungal disease control, the molecular mechanisms of antibiotics produced by BCAs remain to be elucidated. Here, we found a potential BCA (Brevibacillus brevis HK544) with a strong antifungal activity based on the respiration inhibition activity with its active compound edeine B1 (EB1). Furthermore, our results showed that EB1 secreted by HK544 suppresses the expression of the mitochondria-related genes of F. graminearum, subsequently suppressing fungal development and the virulence of F. graminearum. In addition, EB1 exhibited a synergism with complex I inhibitors such as rotenone and fenazaquin. Our work extends our understanding of how B. brevis HK544 exhibits antifungal activity and suggests that the B. brevis HK544 strain could be a valuable source for developing new crop protectants to control F. graminearum.
Collapse
Affiliation(s)
- Bomin Kim
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea
| | - Minh Van Nguyen
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea
| | - Jiyeun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yeong Seok Kim
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea
| | - Jae Woo Han
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Joo-Youn Lee
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Hokyoung Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Gyung Ja Choi
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea
| | - Hun Kim
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea
| |
Collapse
|
13
|
Zheng W, Zhang Y, Wang J, Wang S, Chai P, Bailey EJ, Guo W, Devarkar SC, Wu S, Lin J, Zhang K, Liu J, Lomakin IB, Xiong Y. Visualizing the translation landscape in human cells at high resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601723. [PMID: 39005351 PMCID: PMC11244987 DOI: 10.1101/2024.07.02.601723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Obtaining comprehensive structural descriptions of macromolecules within their natural cellular context holds immense potential for understanding fundamental biology and improving health. Here, we present the landscape of protein synthesis inside human cells in unprecedented detail obtained using an approach which combines automated cryo-focused ion beam (FIB) milling and in situ single-particle cryo-electron microscopy (cryo-EM). With this in situ cryo-EM approach we resolved a 2.19 Å consensus structure of the human 80S ribosome and unveiled its 21 distinct functional states, nearly all higher than 3 Å resolution. In contrast to in vitro studies, we identified protein factors, including SERBP1, EDF1 and NAC/3, not enriched on purified ribosomes. Most strikingly, we observed that SERBP1 binds to the ribosome in almost all translating and non-translating states to bridge the 60S and 40S ribosomal subunits. These newly observed binding sites suggest that SERBP1 may serve an important regulatory role in translation. We also uncovered a detailed interface between adjacent translating ribosomes which can form the helical polysome structure. Finally, we resolved high-resolution structures from cells treated with homoharringtonine and cycloheximide, and identified numerous polyamines bound to the ribosome, including a spermidine that interacts with cycloheximide bound at the E site of the ribosome, underscoring the importance of high-resolution in situ studies in the complex native environment. Collectively, our work represents a significant advancement in detailed structural studies within cellular contexts.
Collapse
|
14
|
Burgers LD, Ciurus S, Engel P, Kuntschar S, Raue R, Kiprina A, Primke T, Schmid T, Weigert A, Schmidtko A, Fürst R. (Homo-)harringtonine prevents endothelial inflammation through IRF-1 dependent downregulation of VCAM1 mRNA expression and inhibition of cell adhesion molecule protein biosynthesis. Biomed Pharmacother 2024; 176:116907. [PMID: 38865849 DOI: 10.1016/j.biopha.2024.116907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
The plant alkaloid homoharringtonine (HHT) is a Food and Drug Administration (FDA)-approved drug for the treatment of hematologic malignancies. In addition to its well-established antitumor activity, accumulating evidence attributes anti-inflammatory effects to HHT, which have mainly been studied in leukocytes to date. However, a potential influence of HHT on inflammatory activation processes in endothelial cells, which are a key feature of inflammation and a prerequisite for the leukocyte-endothelial cell interaction and leukocyte extravasation, remains poorly understood. In this study, the anti-inflammatory potential of HHT and its derivative harringtonine (HT) on the TNF-induced leukocyte-endothelial cell interaction was assessed, and the underlying mechanistic basis of these effects was elucidated. HHT affected inflammation in vivo in a murine peritonitis model by reducing leukocyte infiltration and proinflammatory cytokine expression as well as ameliorating abdominal pain behavior. In vitro, HT and HHT impaired the leukocyte-endothelial cell interaction by decreasing the expression of the endothelial cell adhesion molecules intracellular adhesion molecule -1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1). This effect was mediated by a bipartite mechanism. While HHT did not affect the prominent TNF-induced pro-inflammatory NF-ĸB signaling cascade, the compound downregulated the VCAM1 mRNA expression in an IRF-1-dependent manner and diminished active ICAM1 mRNA translation as determined by polysome profiling. This study highlights HHT as an anti-inflammatory compound that efficiently hampers the leukocyte-endothelial cell interaction by targeting endothelial activation processes.
Collapse
Affiliation(s)
- Luisa D Burgers
- Institute of Pharmaceutical Biology, Faculty of Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt am Main, Germany
| | - Sarah Ciurus
- Institute of Pharmaceutical Biology, Faculty of Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt am Main, Germany
| | - Patrick Engel
- Institute of Pharmacology and Clinical Pharmacy, Faculty of Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt am Main, Germany
| | - Silvia Kuntschar
- Institute of Biochemistry I, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Rebecca Raue
- Institute of Biochemistry I, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Anastasiia Kiprina
- Institute of Biochemistry I, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Tobias Primke
- Institute of Pharmaceutical Biology, Faculty of Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt am Main, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Andreas Weigert
- Institute of Biochemistry I, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Achim Schmidtko
- Institute of Pharmacology and Clinical Pharmacy, Faculty of Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt am Main, Germany
| | - Robert Fürst
- Institute of Pharmaceutical Biology, Faculty of Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt am Main, Germany; LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany; Pharmaceutical Biology, Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
| |
Collapse
|
15
|
Qiu X, Zhang H, Tang Z, Fan Y, Yuan W, Feng C, Chen C, Cui P, Cui Y, Qi Z, Li T, Zhu Y, Xie L, Peng F, Deng T, Jiang X, Peng L, Dai H. Homoharringtonine promotes heart allograft acceptance by enhancing regulatory T cells induction in a mouse model. Chin Med J (Engl) 2024; 137:1453-1464. [PMID: 37962205 PMCID: PMC11188914 DOI: 10.1097/cm9.0000000000002813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Homoharringtonine (HHT) is an effective anti-inflammatory, anti-viral, and anti-tumor protein synthesis inhibitor that has been applied clinically. Here, we explored the therapeutic effects of HHT in a mouse heart transplant model. METHODS Healthy C57BL/6 mice were used to observe the toxicity of HHT in the liver, kidney, and hematology. A mouse heart transplantation model was constructed, and the potential mechanism of HHT prolonging allograft survival was evaluated using Kaplan-Meier analysis, immunostaining, and bulk RNA sequencing analysis. The HHT-T cell crosstalk was modeled ex vivo to further verify the molecular mechanism of HHT-induced regulatory T cells (Tregs) differentiation. RESULTS HHT inhibited the activation and proliferation of T cells and promoted their apoptosis ex vivo . Treatment of 0.5 mg/kg HHT for 10 days significantly prolonged the mean graft survival time of the allografts from 7 days to 48 days ( P <0.001) without non-immune toxicity. The allografts had long-term survival after continuous HHT treatment for 28 days. HHT significantly reduced lymphocyte infiltration in the graft, and interferon-γ-secreting CD4 + and CD8 + T cells in the spleen ( P <0.01). HHT significantly increased the number of peripheral Tregs (about 20%, P <0.001) and serum interleukin (IL)-10 levels. HHT downregulated the expression of T cell receptor (TCR) signaling pathway-related genes ( CD4 , H2-Eb1 , TRAT1 , and CD74 ) and upregulated the expression of IL-10 and transforming growth factor (TGF)-β pathway-related genes and Treg signature genes ( CTLA4 , Foxp3 , CD74 , and ICOS ). HHT increased CD4 + Foxp3 + cells and Foxp3 expression ex vivo , and it enhanced the inhibitory function of inducible Tregs. CONCLUSIONS HHT promotes Treg cell differentiation and enhances Treg suppressive function by attenuating the TCR signaling pathway and upregulating the expression of Treg signature genes and IL-10 levels, thereby promoting mouse heart allograft acceptance. These findings may have therapeutic implications for organ transplant recipients, particularly those with viral infections and malignancies, which require a more suitable anti-rejection medication.
Collapse
Affiliation(s)
- Xia Qiu
- Medical College, Guangxi University, Nanning, Guangxi 530004, China
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Hedong Zhang
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Zhouqi Tang
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Yuxi Fan
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Wenjia Yuan
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Chen Feng
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Chao Chen
- Medical College, Guangxi University, Nanning, Guangxi 530004, China
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Pengcheng Cui
- Medical College, Guangxi University, Nanning, Guangxi 530004, China
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Yan Cui
- Medical College, Guangxi University, Nanning, Guangxi 530004, China
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Zhongquan Qi
- Medical College, Guangxi University, Nanning, Guangxi 530004, China
| | - Tengfang Li
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Yuexing Zhu
- Medical College, Guangxi University, Nanning, Guangxi 530004, China
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Liming Xie
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Fenghua Peng
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Tuo Deng
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Xin Jiang
- Department of Organ Transplantation, The Fifth Clinical Medical College of Henan University of Chinese Medicine (Zhengzhou People's Hospital), Zhengzhou, Henan 450000, China
| | - Longkai Peng
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Helong Dai
- Medical College, Guangxi University, Nanning, Guangxi 530004, China
- Department of Kidney Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
- Department of Organ Transplantation, The Fifth Clinical Medical College of Henan University of Chinese Medicine (Zhengzhou People's Hospital), Zhengzhou, Henan 450000, China
| |
Collapse
|
16
|
McLellan JL, Hanson KK. Differential effects of translation inhibitors on Plasmodium berghei liver stage parasites. Life Sci Alliance 2024; 7:e202302540. [PMID: 38575357 PMCID: PMC10994859 DOI: 10.26508/lsa.202302540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/06/2024] Open
Abstract
Increasing numbers of antimalarial compounds are being identified that converge mechanistically at inhibition of cytoplasmic translation, regardless of the molecular target or mechanism. A deeper understanding of how their effectiveness as liver stage translation inhibitors relates to their chemoprotective potential could prove useful. Here, we probed that relationship using the Plasmodium berghei-HepG2 liver stage infection model. After determining translation inhibition EC50s for five compounds, we tested them at equivalent effective concentrations to compare the parasite response to, and recovery from, a brief period of translation inhibition in early schizogony, followed by parasites to 120 h post-infection to assess antiplasmodial effects of the treatment. We show compound-specific heterogeneity in single parasite and population responses to translation inhibitor treatment, with no single metric strongly correlated to the release of hepatic merozoites for all compounds. We also demonstrate that DDD107498 is capable of exerting antiplasmodial effects on translationally arrested liver stage parasites and uncover unexpected growth dynamics during the liver stage. Our results demonstrate that translation inhibition efficacy does not determine antiplasmodial efficacy for these compounds.
Collapse
Affiliation(s)
- James L McLellan
- https://ror.org/01kd65564 Department of Molecular Microbiology and Immunology and STCEID, University of Texas at San Antonio, San Antonio, TX, USA
| | - Kirsten K Hanson
- https://ror.org/01kd65564 Department of Molecular Microbiology and Immunology and STCEID, University of Texas at San Antonio, San Antonio, TX, USA
| |
Collapse
|
17
|
McLellan JL, Morales-Hernandez B, Saeger S, Hanson KK. A high content imaging assay for identification of specific inhibitors of native Plasmodium liver stage protein synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596519. [PMID: 38854116 PMCID: PMC11160711 DOI: 10.1101/2024.05.29.596519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Plasmodium parasite resistance to antimalarial drugs is a serious threat to public health in malaria-endemic areas. Compounds that target core cellular processes like translation are highly desirable, as they should be multistage actives, capable of killing parasites in the liver and blood, regardless of molecular target or mechanism. Assays that can identify these compounds are thus needed. Recently, specific quantification of native Plasmodium berghei liver stage protein synthesis as well as that of the hepatoma cells supporting parasite growth, was achieved via automated confocal feedback microscopy of the o-propargyl puromycin (OPP)-labeled nascent proteome, but this imaging modality is limited in throughput. Here, we developed and validated a miniaturized high content imaging (HCI) version of the OPP assay that increases throughput, before deploying this approach to screen the Pathogen Box. We identified only two hits, both of which are parasite-specific quinoline-4-carboxamides, and analogues of the clinical candidate and known inhibitor of blood and liver stage protein synthesis, DDD107498/cabamiquine. We further show that these compounds have strikingly distinct relationships between their antiplasmodial and translation inhibition efficacies. These results demonstrate the utility and reliability of the P. berghei liver stage OPP HCI assay for specific, single-well quantification of Plasmodium and human protein synthesis in the native cellular context, allowing identification of selective Plasmodium translation inhibitors with the highest potential for multistage activity.
Collapse
Affiliation(s)
- James L. McLellan
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
| | - Beatriz Morales-Hernandez
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
| | - Sarah Saeger
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
| | - Kirsten K. Hanson
- Department of Molecular Microbiology and Immunology, and the South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
| |
Collapse
|
18
|
Jiang J, Li H, Tang M, Lei L, Li HY, Dong B, Li JR, Wang XK, Sun H, Li JY, Xu JC, Gong Y, Jiang JD, Peng ZG. Upregulation of Hepatic Glutathione S-Transferase Alpha 1 Ameliorates Metabolic Dysfunction-Associated Steatosis by Degrading Fatty Acid Binding Protein 1. Int J Mol Sci 2024; 25:5086. [PMID: 38791126 PMCID: PMC11120891 DOI: 10.3390/ijms25105086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/02/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common metabolic disease of the liver, characterized by hepatic steatosis in more than 5% of hepatocytes. However, despite the recent approval of the first drug, resmetirom, for the management of metabolic dysfunction-associated steatohepatitis, decades of target exploration and hundreds of clinical trials have failed, highlighting the urgent need to find new druggable targets for the discovery of innovative drug candidates against MASLD. Here, we found that glutathione S-transferase alpha 1 (GSTA1) expression was negatively associated with lipid droplet accumulation in vitro and in vivo. Overexpression of GSTA1 significantly attenuated oleic acid-induced steatosis in hepatocytes or high-fat diet-induced steatosis in the mouse liver. The hepatoprotective and anti-inflammatory drug bicyclol also attenuated steatosis by upregulating GSTA1 expression. A detailed mechanism showed that GSTA1 directly interacts with fatty acid binding protein 1 (FABP1) and facilitates the degradation of FABP1, thereby inhibiting intracellular triglyceride synthesis by impeding the uptake and transportation of free fatty acids. Conclusion: GSTA1 may be a good target for the discovery of innovative drug candidates as GSTA1 stabilizers or enhancers against MASLD.
Collapse
Affiliation(s)
- Jing Jiang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
| | - Hu Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mei Tang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
| | - Lei Lei
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
| | - Hong-Ying Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
| | - Biao Dong
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jian-Rui Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xue-Kai Wang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
| | - Han Sun
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
| | - Jia-Yu Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
| | - Jing-Chen Xu
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
| | - Yue Gong
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
| | - Jian-Dong Jiang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zong-Gen Peng
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China (H.-Y.L.)
- Key Laboratory of Biotechnology of Antibiotics, The National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| |
Collapse
|
19
|
Félix-Pérez T, Mora-García M, Rebolloso-Gómez Y, DelaGarza-Varela A, Castro-Velázquez G, Peña-Gómez SG, Riego-Ruiz L, Sánchez-Olea R, Calera MR. Translation initiation factor eIF1A rescues hygromycin B sensitivity caused by deleting the carboxy-terminal tail in the GPN-loop GTPase Npa3. FEBS J 2024; 291:2191-2208. [PMID: 38431777 DOI: 10.1111/febs.17106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 12/20/2023] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
The essential yeast protein GPN-loop GTPase 1 (Npa3) plays a critical role in RNA polymerase II (RNAPII) assembly and subsequent nuclear import. We previously identified a synthetic lethal interaction between a mutant lacking the carboxy-terminal 106-amino acid tail of Npa3 (npa3ΔC) and a bud27Δ mutant. As the prefoldin-like Bud27 protein participates in ribosome biogenesis and translation, we hypothesized that Npa3 may also regulate these biological processes. We investigated this proposal by using Saccharomyces cerevisiae strains episomally expressing either wild-type Npa3 or hypomorphic mutants (Npa3ΔC, Npa3K16R, and Npa3G70A). The Npa3ΔC mutant fully supports RNAPII nuclear localization and activity. However, the Npa3K16R and Npa3G70A mutants only partially mediate RNAPII nuclear targeting and exhibit a higher reduction in Npa3 function. Cell proliferation in these strains displayed an increased sensitivity to protein synthesis inhibitors hygromycin B and geneticin/G418 (npa3G70A > npa3K16R > npa3ΔC > NPA3 cells) but not to transcriptional elongation inhibitors 6-azauracil, mycophenolic acid or 1,10-phenanthroline. In all three mutant strains, the increase in sensitivity to both aminoglycoside antibiotics was totally rescued by expressing NPA3. Protein synthesis, visualized by quantifying puromycin incorporation into nascent-polypeptide chains, was markedly more sensitive to hygromycin B inhibition in npa3ΔC, npa3K16R, and npa3G70A than NPA3 cells. Notably, high-copy expression of the TIF11 gene, that encodes the eukaryotic translation initiation factor 1A (eIF1A) protein, completely suppressed both phenotypes (of reduced basal cell growth and increased sensitivity to hygromycin B) in npa3ΔC cells but not npa3K16R or npa3G70A cells. We conclude that Npa3 plays a critical RNAPII-independent and previously unrecognized role in translation initiation.
Collapse
Affiliation(s)
- Tania Félix-Pérez
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Mexico
| | | | | | | | | | | | - Lina Riego-Ruiz
- División de Biología Molecular, IPICYT, San Luis Potosí, Mexico
| | | | - Mónica R Calera
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Mexico
| |
Collapse
|
20
|
Tanaka M, Yokoyama T, Saito H, Nishimoto M, Tsuda K, Sotta N, Shigematsu H, Shirouzu M, Iwasaki S, Ito T, Fujiwara T. Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat Chem Biol 2024; 20:605-614. [PMID: 38267667 DOI: 10.1038/s41589-023-01513-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 11/24/2023] [Indexed: 01/26/2024]
Abstract
In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is downregulated in response to an excess amount of boric acid in the environment through upstream open reading frames (uORFs) that consist of only AUG and stop codons. However, the molecular details of how this minimum uORF controls translation of the downstream main ORF in a boric acid-dependent manner have remained unclear. Here, by combining ribosome profiling, translation complex profile sequencing, structural analysis with cryo-electron microscopy and biochemical assays, we show that the 80S ribosome assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 on the 80S ribosome on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.
Collapse
Affiliation(s)
- Mayuki Tanaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeshi Yokoyama
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hironori Saito
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Madoka Nishimoto
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Kengo Tsuda
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Naoyuki Sotta
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hideki Shigematsu
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Sayo, Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Shintaro Iwasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- RIKEN Cluster for Pioneering Research, Wako, Japan.
| | - Takuhiro Ito
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan.
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
21
|
Rauscher R, Eggers C, Dimitrova-Paternoga L, Shankar V, Rosina A, Cristodero M, Paternoga H, Wilson DN, Leidel SA, Polacek N. Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes. Nucleic Acids Res 2024; 52:4021-4036. [PMID: 38324474 DOI: 10.1093/nar/gkae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms for enhanced translation fidelity. Indeed, eukaryal ribosomes are more accurate than bacterial counterparts, despite their virtually identical, conserved active centers. During the evolution of eukaryotic organisms ribosome expansions at the rRNA and protein level occurred, which potentially increases the options for translation regulation and cotranslational events. Here we tested the hypothesis that ribosomal RNA expansions can modulate the core function of the ribosome, faithful protein synthesis. We demonstrate that a short expansion segment present in all eukaryotes' small subunit, ES7S, is crucial for accurate protein synthesis as its presence adjusts codon-specific velocities and guarantees high levels of cognate tRNA selection. Deletion of ES7S in yeast enhances mistranslation and causes protein destabilization and aggregation, dramatically reducing cellular fitness. Removal of ES7S did not alter ribosome architecture but altered the structural dynamics of inter-subunit bridges thus affecting A-tRNA selection. Exchanging the yeast ES7S sequence with the human ES7S increases accuracy whereas shortening causes the opposite effect. Our study demonstrates that ES7S provided eukaryal ribosomes with higher accuracy without perturbing the structurally conserved decoding center.
Collapse
Affiliation(s)
- Robert Rauscher
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Cristian Eggers
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Lyudmila Dimitrova-Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vaishnavi Shankar
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Alessia Rosina
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marina Cristodero
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Sebastian A Leidel
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Norbert Polacek
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| |
Collapse
|
22
|
Ütkür K, Mayer K, Liu S, Brinkmann U, Schaffrath R. Functional Integrity of Radical SAM Enzyme Dph1•Dph2 Requires Non-Canonical Cofactor Motifs with Tandem Cysteines. Biomolecules 2024; 14:470. [PMID: 38672486 PMCID: PMC11048331 DOI: 10.3390/biom14040470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The Dph1•Dph2 heterodimer from yeast is a radical SAM (RS) enzyme that generates the 3-amino-3-carboxy-propyl (ACP) precursor for diphthamide, a clinically relevant modification on eukaryotic elongation factor 2 (eEF2). ACP formation requires SAM cleavage and atypical Cys-bound Fe-S clusters in each Dph1 and Dph2 subunit. Intriguingly, the first Cys residue in each motif is found next to another ill-defined cysteine that we show is conserved across eukaryotes. As judged from structural modeling, the orientation of these tandem cysteine motifs (TCMs) suggests a candidate Fe-S cluster ligand role. Hence, we generated, by site-directed DPH1 and DPH2 mutagenesis, Dph1•Dph2 variants with cysteines from each TCM replaced individually or in combination by serines. Assays diagnostic for diphthamide formation in vivo reveal that while single substitutions in the TCM of Dph2 cause mild defects, double mutations almost entirely inactivate the RS enzyme. Based on enhanced Dph1 and Dph2 subunit instability in response to cycloheximide chases, the variants with Cys substitutions in their cofactor motifs are particularly prone to protein degradation. In sum, we identify a fourth functionally cooperative Cys residue within the Fe-S motif of Dph2 and show that the Cys-based cofactor binding motifs in Dph1 and Dph2 are critical for the structural integrity of the dimeric RS enzyme in vivo.
Collapse
Affiliation(s)
- Koray Ütkür
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany;
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Shihui Liu
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany;
| |
Collapse
|
23
|
Bulygin KN, Malygin AA, Graifer DM. Functional involvement of a conserved motif in the middle region of the human ribosomal protein eL42 in translation. Biochimie 2024; 218:96-104. [PMID: 37716853 DOI: 10.1016/j.biochi.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023]
Abstract
Ribosomal protein eL42 (formerly known as L36A), a small protein of the large (60S) subunit of the eukaryotic ribosome, is a component of its exit (E) site. The residue K53 of this protein resides within the motif QSGYGGQTK mainly conserved in eukaryotes, and it is located in the immediate vicinity of the CCA-terminus of the ribosome-bound tRNA in the hybrid P/E state. To examine the role of this eL42 motif in translation, we obtained HEK293T cells producing the wild-type FLAG-tagged protein or its mutant forms with either single substitutions of conserved amino acid residues in the above motif, or simultaneous replacements in positions 45 and 51 or 45 and 53. Examination of the level of exogenous eL42 in fractions of polysome profiles from the target protein-producing cells by the Western blotting revealed that neither single substitution affects the assembly of 60S ribosomal subunits and 80S ribosomes or critically decreases the level of polysomes, but the latter was observed with the double replacements. Analysis of tRNAs bound to 80S ribosomes containing eL42 with double substitutions and examination their peptidyl transferase activity enabled estimation the stage of the elongation cycle, in which amino acid residues of the conserved eL42 motif are involved. We clearly show that cooperative interactions implicating the eL42 residues Q45, Q51, and K53 play a critical role in the ability of the human ribosome to perform properly elongation cycle at the step of deacylated tRNA dissociation from the E site in the human cell.
Collapse
Affiliation(s)
- Konstantin N Bulygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Dmitri M Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia.
| |
Collapse
|
24
|
Yang J, Liang K, Ke H, Zhang Y, Meng Q, Gao L, Fan J, Li G, Zhou H, Xiao J, Lei X. Enzymatic Degradation of Deoxynivalenol with the Engineered Detoxification Enzyme Fhb7. JACS AU 2024; 4:619-634. [PMID: 38425922 PMCID: PMC10900206 DOI: 10.1021/jacsau.3c00696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 03/02/2024]
Abstract
In the era of global climate change, the increasingly severe Fusarium head blight (FHB) and deoxynivalenol (DON) contamination have caused economic losses and brought food and feed safety concerns. Recently, an FHB resistance gene Fhb7 coding a glutathione-S transferase (GST) to degrade DON by opening the critical toxic epoxide moiety was identified and opened a new window for wheat breeding and DON detoxification. However, the poor stability of Fhb7 and the elusiveness of the catalytic mechanism hinder its practical application. Herein, we report the first structure of Fhb7 at 2.41 Å and reveal a unique catalytic mechanism of epoxide opening transformation in GST family proteins. Furthermore, variants V29P and M10 showed that 5.5-fold and 266.7-fold longer half-life time than wild-type, respectively, were identified. These variants offer broad substrate scope, and the engineered biosafe Bacillus subtilis overexpressing the variants shows excellent DON degradation performance, exhibiting potential at bacterium engineering to achieve DON detoxification in the feed and biomedicine industry. This work provides a profound mechanistic insight into the enzymatic activities of Fhb7 and paves the way for further utilizing Fhb7-related enzymes in crop breeding and DON detoxification by synthetic biology.
Collapse
Affiliation(s)
- Jun Yang
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Academy
for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Kai Liang
- School
of Life Sciences, Peking University, Beijing 100871, China
| | - Han Ke
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuebin Zhang
- Laboratory
of Molecular Modeling and Design, State Key Laboratory of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Qian Meng
- Analytical
Research Center for Organic and Biological Molecules, State Key Laboratory
of Drug Research, Shanghai Institute of
Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lei Gao
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junping Fan
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Guohui Li
- Laboratory
of Molecular Modeling and Design, State Key Laboratory of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hu Zhou
- Analytical
Research Center for Organic and Biological Molecules, State Key Laboratory
of Drug Research, Shanghai Institute of
Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University
of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Junyu Xiao
- School
of Life Sciences, Peking University, Beijing 100871, China
- Academy
for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Academy
for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Institute
for Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518107, China
| |
Collapse
|
25
|
Pierron A, Kleber A, Mayer E, Gerner W. Effect of DON and ZEN and their metabolites DOM-1 and HZEN on B cell proliferation and antibody production. Front Immunol 2024; 15:1338937. [PMID: 38449861 PMCID: PMC10915041 DOI: 10.3389/fimmu.2024.1338937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/24/2024] [Indexed: 03/08/2024] Open
Abstract
Introduction The mycotoxins deoxynivalenol (DON) and zearalenone (ZEN), produced by Fusarium fungi, are frequently found in the cereal-rich diet of pigs and can modulate the immune system. Some enzymes or bacteria present in the digestive tract can de-epoxydize DON to deepoxy-deoxynivalenol (DOM-1) and biotransform ZEN into hydrolyzed ZEN (HZEN). The effects of these metabolites on immune cells, particularly with respect to the vaccine responses, are poorly documented. The aim of this study was to address the impact of DON and ZEN and their respective derivatives, on proliferation, and antibody production of porcine B cells in vitro. Methods Peripheral blood mononuclear cells (PBMCs), isolated from healthy pigs, were stimulated with the Toll-like receptor (TLR) 7/8-agonist Resiquimod (R848) or the TLR/1/2-agonist Pam3Cys-SKKKK in combination with DON [0.1-1.6 µM] or DOM-1 [1.6 µM and 16 µM] and ZEN [2.5-40 µM] or HZEN [40 µM]. Results A strong decrease in B-cell proliferation was observed at DON concentrations equal to or exceeding 0.8 µM and at ZEN concentrations equal to or exceeding 20 µM. Treatment with 1.6 µM DON or 40 µM ZEN led to almost a complete loss of live CD79α+ B cells. Moreover, CD21 expression of proliferating IgG+ and IgM+ B-cell subsets was decreased at DON concentrations equal to and exceeding 0.4 µM and at ZEN concentrations equal to or exceeding 10 µM. ELISpot assays revealed a decrease of IgG-secreting B cells at concentrations of and exceeding 0.4 µM and at ZEN concentrations equal to and exceeding 10 µM. ELISA assays showed a decrease of IgM, IgG, and IgA secretion at concentrations equal to or exceeding 0.4 µM DON. ZEN reduced IgM secretion at 20-40 µM (both R848 and Pam3Cys-SKKKK), IgG secretion at 40 µM (both R848 and Pam3Cys-SKKKK) and IgA secretion at 20-40 µM. Discussion Our in vitro experiments show that while DON and ZEN impair immunoglobulin production and B-cell proliferation, this effect is abrogated by HZEN and DOM-1.
Collapse
Affiliation(s)
- Alix Pierron
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine, Vienna, Austria
| | - Alexandra Kleber
- dsm-firmenich, Animal Nutrition and Health R&D Center, Tulln, Austria
| | - Elisabeth Mayer
- dsm-firmenich, Animal Nutrition and Health R&D Center, Tulln, Austria
| | - Wilhelm Gerner
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine, Vienna, Austria
| |
Collapse
|
26
|
Nogami R, Nagata M, Imada R, Kai K, Kawaguchi T, Tani S. Cycloheximide in the nanomolar range inhibits seed germination of Orobanche minor. JOURNAL OF PESTICIDE SCIENCE 2024; 49:22-30. [PMID: 38450089 PMCID: PMC10912901 DOI: 10.1584/jpestics.d23-038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/29/2023] [Indexed: 03/08/2024]
Abstract
From the 992 samples of culture extracts of microorganisms isolated from soil in Japan, we found that the extract of Streptomyces sp. no. 226 inhibited Orobanche minor seed germination without significantly affecting the seed germination of Trifolium pratense and the growth of Aspergillus oryzae and Escherichia coli. Using ESI-MS, 1H-NMR, and 13C-NMR, we identified the active compound as cycloheximide. Cycloheximide had half-maximum inhibitory concentrations of 2.6 ng/mL for the inhibition of seed germination of O. minor and 2.5 µg/mL for that of the conidial germination of A. oryzae. Since cycloheximide is known to inhibit translation by interacting with ribosomal protein L28 (RPL28) in yeast, we investigated whether RPL protein of O. minor plays a critical role in the inhibition of O. minor seed germination. Our data suggested that O. minor RPL27A was not sensitive to cycloheximide by comparing it to the strain expressing S. cerevisiae RPL28. These findings suggest the presence of an unidentified mechanism by which cycloheximide hinders O. minor seed germination.
Collapse
Affiliation(s)
- Ryosuke Nogami
- Graduate School of Agriculture, Osaka Metropolitan University
| | - Mari Nagata
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Risa Imada
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Kenji Kai
- Graduate School of Agriculture, Osaka Metropolitan University
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Takashi Kawaguchi
- Graduate School of Agriculture, Osaka Metropolitan University
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Shuji Tani
- Graduate School of Agriculture, Osaka Metropolitan University
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| |
Collapse
|
27
|
Chen X, Varghese S, Zhang Z, Du J, Ruan B, Baell JB, Liu X. Drug discovery and optimization based on the co-crystal structure of natural product with target. Eur J Med Chem 2024; 266:116126. [PMID: 38232464 DOI: 10.1016/j.ejmech.2024.116126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Due to their structural diversities and prevalent biological activities, natural products (NPs) are momentous resources for drug discovery. Although NPs have a wide range of biological activities, many exhibit structural complexity that leads to synthetic difficulties, which combines with inefficient biological activity, toxicity, and unfavorable pharmacokinetic characteristics and ultimately imparts poor safety and efficacy outcomes. Progress in crystallization and computational techniques allow crystallography to have a seasonable influences on drug discovery. By co-crystallizing with proteins, therapeutic targets of NPs in specific diseases can be identified. By analyzing the co-crystal information, the structure-activity relationships (SARs) of NPs targeting specific proteins can be grasped. Under the guidance of co-crystal information, directional structural modification and simplification are powerful strategies for overcoming limitations of NPs, improving the success rate of NP-based drug discovery, and obtaining NP-based drugs with high selectivity, low toxicity and favorable pharmacokinetic characteristics. Here, we review the co-crystal information of a selection of NPs, focusing on the SARs of NPs reflected by co-crystal information and the modification and simplification strategies of NPs, and discuss how to apply co-crystal information in the optimization of NP-based lead compound.
Collapse
Affiliation(s)
- Xing Chen
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China; School of Public Health, Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Hefei, 230032, PR China.
| | - Swapna Varghese
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, Victoria, 3052, Australia.
| | - Zhaoyan Zhang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China.
| | - Juncheng Du
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China.
| | - Banfeng Ruan
- Key Lab of Biofabrication of Anhui Higher Education, Hefei University, Hefei, 230601, PR China.
| | - Jonathan B Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, Victoria, 3052, Australia.
| | - Xinhua Liu
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, 230032, PR China.
| |
Collapse
|
28
|
Anadolu MN, Sun J, Li JTY, Graber TE, Ortega J, Sossin WS. Puromycin reveals a distinct conformation of neuronal ribosomes. Proc Natl Acad Sci U S A 2024; 121:e2306993121. [PMID: 38315848 PMCID: PMC10873636 DOI: 10.1073/pnas.2306993121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
Puromycin is covalently added to the nascent chain of proteins by the peptidyl transferase activity of the ribosome and the dissociation of the puromycylated peptide typically follows this event. It was postulated that blocking the translocation of the ribosome with emetine could retain the puromycylated peptide on the ribosome, but evidence against this has recently been published [Hobson et al., Elife 9, e60048 (2020); and Enam et al., Elife 9, e60303 (2020)]. In neurons, puromycylated nascent chains remain in the ribosome even in the absence of emetine, yet direct evidence for this has been lacking. Using biochemistry and cryoelectron microscopy, we show that the puromycylated peptides remain in the ribosome exit channel in the large subunit in a subset of neuronal ribosomes stalled in the hybrid state. These results validate previous experiments to localize stalled polysomes in neurons and provide insight into how neuronal ribosomes are stalled. Moreover, in these hybrid-state neuronal ribosomes, anisomycin, which usually blocks puromycylation, competes poorly with puromycin in the puromycylation reaction, allowing a simple assay to determine the proportion of nascent chains that are stalled in this state. In early hippocampal neuronal cultures, over 50% of all nascent peptides are found in these stalled polysomes. These results provide insights into the stalling mechanisms of neuronal ribosomes and suggest that puromycylated peptides can be used to reveal subcellular sites of hybrid-state stalled ribosomes in neurons.
Collapse
Affiliation(s)
- Mina N. Anadolu
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QCH3A 2B4, Canada
| | - Jingyu Sun
- Department of Anatomy and Cell Biology, McGill University, Montreal, QCH3A 0C7, Canada
- Centre for Structural Biology, McGill University, Montreal, QCH3G 0B1, Canada
| | - Jewel T.-Y. Li
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QCH3A 2B4, Canada
| | - Tyson E. Graber
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QCH3A 2B4, Canada
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, QCH3A 0C7, Canada
- Centre for Structural Biology, McGill University, Montreal, QCH3G 0B1, Canada
| | - Wayne S. Sossin
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QCH3A 2B4, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, QCH3A 0C7, Canada
| |
Collapse
|
29
|
Perochon A, Doohan FM. Trichothecenes and Fumonisins: Key Players in Fusarium-Cereal Ecosystem Interactions. Toxins (Basel) 2024; 16:90. [PMID: 38393168 PMCID: PMC10893083 DOI: 10.3390/toxins16020090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Fusarium fungi produce a diverse array of mycotoxic metabolites during the pathogenesis of cereals. Some, such as the trichothecenes and fumonisins, are phytotoxic, acting as non-proteinaceous effectors that facilitate disease development in cereals. Over the last few decades, we have gained some depth of understanding as to how trichothecenes and fumonisins interact with plant cells and how plants deploy mycotoxin detoxification and resistance strategies to defend themselves against the producer fungi. The cereal-mycotoxin interaction is part of a co-evolutionary dance between Fusarium and cereals, as evidenced by a trichothecene-responsive, taxonomically restricted, cereal gene competing with a fungal effector protein and enhancing tolerance to the trichothecene and resistance to DON-producing F. graminearum. But the binary fungal-plant interaction is part of a bigger ecosystem wherein other microbes and insects have been shown to interact with fungal mycotoxins, directly or indirectly through host plants. We are only beginning to unravel the extent to which trichothecenes, fumonisins and other mycotoxins play a role in fungal-ecosystem interactions. We now have tools to determine how, when and where mycotoxins impact and are impacted by the microbiome and microfauna. As more mycotoxins are described, research into their individual and synergistic toxicity and their interactions with the crop ecosystem will give insights into how we can holistically breed for and cultivate healthy crops.
Collapse
Affiliation(s)
| | - Fiona M. Doohan
- UCD School of Biology and Environmental Science, UCD Earth Institute and UCD Institute of Food and Health, University College Dublin, D04 V1W8 Dublin, Ireland
| |
Collapse
|
30
|
Zhang D, Gao Y, Zhu L, Wang Y, Li P. Advances and opportunities in methods to study protein translation - A review. Int J Biol Macromol 2024; 259:129150. [PMID: 38171441 DOI: 10.1016/j.ijbiomac.2023.129150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024]
Abstract
It is generally believed that the regulation of gene expression involves protein translation occurring before RNA transcription. Therefore, it is crucial to investigate protein translation and its regulation. Recent advancements in biological sciences, particularly in the field of omics, have revolutionized protein translation research. These studies not only help characterize changes in protein translation during specific biological or pathological processes but also have significant implications in disease prevention and treatment. In this review, we summarize the latest methods in ribosome-based translation omics. We specifically focus on the application of fluorescence imaging technology and omics technology in studying overall protein translation. Additionally, we analyze the advantages, disadvantages, and application of these experimental methods, aiming to provide valuable insights and references to researchers studying translation.
Collapse
Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| |
Collapse
|
31
|
Wimmer B, Friedrich A, Poeltner K, Edobor G, Mosshammer C, Temaj G, Rathner A, Karl T, Krauss J, von Hagen J, Gerner C, Breitenbach M, Hintner H, Bauer JW, Breitenbach-Koller H. En Route to Targeted Ribosome Editing to Replenish Skin Anchor Protein LAMB3 in Junctional Epidermolysis Bullosa. JID INNOVATIONS 2024; 4:100240. [PMID: 38282649 PMCID: PMC10810840 DOI: 10.1016/j.xjidi.2023.100240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 01/30/2024] Open
Abstract
Severe junctional epidermolysis bullosa is a rare genetic, postpartum lethal skin disease, predominantly caused by nonsense/premature termination codon (PTC) sequence variants in LAMB3 gene. LAMB3 encodes LAMB3, the β subunit of epidermal-dermal skin anchor laminin 332. Most translational reads of a PTC mRNA deliver truncated, nonfunctional proteins, whereas an endogenous PTC readthrough mechanism produces full-length protein at minimal and insufficient levels. Conventional translational readthrough-inducing drugs amplify endogenous PTC readthrough; however, translational readthrough-inducing drugs are either proteotoxic or nonselective. Ribosome editing is a more selective and less toxic strategy. This technique identified ribosomal protein L35/uL29 (ie, RpL35) and RpL35-ligands repurposable drugs artesunate and atazanavir as molecular tools to increase production levels of full-length LAMB3. To evaluate ligand activity in living cells, we monitored artesunate and atazanavir treatment by dual luciferase reporter assays. Production levels of full-length LAMB3 increased up to 200% upon artesunate treatment, up to 150% upon atazanavir treatment, and up to 170% upon combinatorial treatment of RpL35 ligands at reduced drug dosage, with an unrelated PTC reporter being nonresponsive. Proof of bioactivity of RpL35 ligands in selective increase of full-length LAMB3 provides the basis for an alternative, targeted therapeutic route to replenish LAMB3 in severe junctional epidermolysis bullosa.
Collapse
Affiliation(s)
- Bjoern Wimmer
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Andreas Friedrich
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Katharina Poeltner
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Genevieve Edobor
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Claudia Mosshammer
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | | | - Adriana Rathner
- Institute of Biochemistry, Johannes Kepler University of Linz, Linz, Austria
| | - Thomas Karl
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Jan Krauss
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
- SKM-IP PartGmbB, Munich, Germany
| | - Joerg von Hagen
- Merck KGaA, Gernsheim, Germany
- ryon-Greentech Accelerator, Gernsheim, Germany
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna, Vienna, Austria
| | - Michael Breitenbach
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Helmut Hintner
- Department of Dermatology and Allergology, University Hospital Salzburg, Salzburg, Austria
| | - Johann W. Bauer
- Department of Dermatology and Allergology, University Hospital Salzburg, Salzburg, Austria
| | | |
Collapse
|
32
|
McLellan JL, Sausman W, Reers AB, Bunnik EM, Hanson KK. Single-cell quantitative bioimaging of P. berghei liver stage translation. mSphere 2023; 8:e0054423. [PMID: 37909773 PMCID: PMC10732057 DOI: 10.1128/msphere.00544-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Plasmodium parasites cause malaria in humans. New multistage active antimalarial drugs are needed, and a promising class of drugs targets the core cellular process of translation, which has many potential molecular targets. During the obligate liver stage, Plasmodium parasites grow in metabolically active hepatocytes, making it challenging to study core cellular processes common to both host cells and parasites, as the signal from the host typically overwhelms that of the parasite. Here, we present and validate a flexible assay to quantify Plasmodium liver stage translation using a technique to fluorescently label the newly synthesized proteins of both host and parasite followed by computational separation of their respective nascent proteomes in confocal image sets. We use the assay to determine whether a test set of known compounds are direct or indirect liver stage translation inhibitors and show that the assay can also predict the mode of action for novel antimalarial compounds.
Collapse
Affiliation(s)
- James L. McLellan
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas, USA
| | - William Sausman
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Ashley B. Reers
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Evelien M. Bunnik
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Kirsten K. Hanson
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas, USA
| |
Collapse
|
33
|
McLellan JL, Hanson KK. Translation inhibition efficacy does not determine the Plasmodium berghei liver stage antiplasmodial efficacy of protein synthesis inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570699. [PMID: 38106175 PMCID: PMC10723475 DOI: 10.1101/2023.12.07.570699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Protein synthesis is a core cellular process, necessary throughout the complex lifecycle of Plasmodium parasites, thus specific translation inhibitors would be a valuable class of antimalarial drugs, capable of both treating symptomatic infections in the blood and providing chemoprotection by targeting the initial parasite population in the liver, preventing both human disease and parasite transmission back to the mosquito host. As increasing numbers of antiplasmodial compounds are identified that converge mechanistically at inhibition of cytoplasmic translation, regardless of molecular target or mechanism, it would be useful to gain deeper understanding of how their effectiveness as liver stage translation inhibitors relates to their chemoprotective potential. Here, we probed that relationship using the P. berghei-HepG2 liver stage infection model. Using o-propargyl puromycin-based labeling of the nascent proteome in P. berghei-infected HepG2 monolayers coupled with automated confocal feedback microscopy to generate unbiased, single parasite image sets of P. berghei liver stage translation, we determined translation inhibition EC50s for five compounds, encompassing parasite-specific aminoacyl tRNA synthetase inhibitors, compounds targeting the ribosome in both host and parasite, as well as DDD107498, which targets Plasmodium eEF2, and is a leading antimalarial candidate compound being clinically developed as cabamiquine. Compounds were then tested at equivalent effective concentrations to compare the parasite response to, and recovery from, a brief period of translation inhibition in early schizogony, with parasites followed up to 120 hours post-infection to assess liver stage antiplasmodial effects of the treatment. Our data conclusively show that translation inhibition efficacy per se does not determine a translation inhibitor's antiplasmodial efficacy. DDD107498 was the least effective translation inhibitor, yet exerted the strongest antimalarial effects at both 5x- and 10x EC50 concentrations. We show compound-specific heterogeneity in single parasite and population responses to translation inhibitor treatment, with no single metric strongly correlated to release of hepatic merozoites for all compound, demonstrate that DDD107498 is capable of exerting antiplasmodial effects on translationally arrested liver stage parasites, and uncover unexpected growth dynamics during the liver stage. Our results demonstrate that translation inhibition efficacy cannot function as a proxy for antiplasmodial effectiveness, and highlight the importance of exploring the ultimate, as well as proximate, mechanisms of action of these compounds on liver stage parasites.
Collapse
Affiliation(s)
- James L. McLellan
- University of Texas at San Antonio, Department of Molecular Microbiology and Immunology and STCEID, San Antonio TX, USA
| | - Kirsten K. Hanson
- University of Texas at San Antonio, Department of Molecular Microbiology and Immunology and STCEID, San Antonio TX, USA
| |
Collapse
|
34
|
Sung HM, Schott J, Boss P, Lehmann JA, Hardt MR, Lindner D, Messens J, Bogeski I, Ohler U, Stoecklin G. Stress-induced nuclear speckle reorganization is linked to activation of immediate early gene splicing. J Cell Biol 2023; 222:e202111151. [PMID: 37956386 PMCID: PMC10641589 DOI: 10.1083/jcb.202111151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 07/13/2023] [Accepted: 09/29/2023] [Indexed: 11/15/2023] Open
Abstract
Current models posit that nuclear speckles (NSs) serve as reservoirs of splicing factors and facilitate posttranscriptional mRNA processing. Here, we discovered that ribotoxic stress induces a profound reorganization of NSs with enhanced recruitment of factors required for splice-site recognition, including the RNA-binding protein TIAR, U1 snRNP proteins and U2-associated factor 65, as well as serine 2 phosphorylated RNA polymerase II. NS reorganization relies on the stress-activated p38 mitogen-activated protein kinase (MAPK) pathway and coincides with splicing activation of both pre-existing and newly synthesized pre-mRNAs. In particular, ribotoxic stress causes targeted excision of retained introns from pre-mRNAs of immediate early genes (IEGs), whose transcription is induced during the stress response. Importantly, enhanced splicing of the IEGs ZFP36 and FOS is accompanied by relocalization of the corresponding nuclear mRNA foci to NSs. Our study reveals NSs as a dynamic compartment that is remodeled under stress conditions, whereby NSs appear to become sites of IEG transcription and efficient cotranscriptional splicing.
Collapse
Affiliation(s)
- Hsu-Min Sung
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
- Brussels Center for Redox Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Johanna Schott
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Philipp Boss
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Department of Biology, Humboldt University, Berlin, Germany
| | - Janina A. Lehmann
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Marius Roland Hardt
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Doris Lindner
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Joris Messens
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
- Brussels Center for Redox Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Department of Biology, Humboldt University, Berlin, Germany
| | - Georg Stoecklin
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| |
Collapse
|
35
|
Gutiérrez-Sánchez A, Plasencia J, Monribot-Villanueva JL, Rodríguez-Haas B, Ruíz-May E, Guerrero-Analco JA, Sánchez-Rangel D. Virulence factors of the genus Fusarium with targets in plants. Microbiol Res 2023; 277:127506. [PMID: 37783182 DOI: 10.1016/j.micres.2023.127506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Fusarium spp. comprise various species of filamentous fungi that cause severe diseases in plant crops of both agricultural and forestry interest. These plant pathogens produce a wide range of molecules with diverse chemical structures and biological activities. Genetic functional analyses of some of these compounds have shown their role as virulence factors (VF). However, their mode of action and contributions to the infection process for many of these molecules are still unknown. This review aims to analyze the state of the art in Fusarium VF, emphasizing their biological targets on the plant hosts. It also addresses the current experimental approaches to improve our understanding of their role in virulence and suggests relevant research questions that remain to be answered with a greater focus on species of agroeconomic importance. In this review, a total of 37 confirmed VF are described, including 22 proteinaceous and 15 non-proteinaceous molecules, mainly from Fusarium oxysporum and Fusarium graminearum and, to a lesser extent, in Fusarium verticillioides and Fusarium solani.
Collapse
Affiliation(s)
- Angélica Gutiérrez-Sánchez
- Laboratorios de Fitopatología y Biología Molecular, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico; Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico
| | - Javier Plasencia
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Juan L Monribot-Villanueva
- Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico
| | - Benjamín Rodríguez-Haas
- Laboratorios de Fitopatología y Biología Molecular, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico
| | - Eliel Ruíz-May
- Laboratorio de Proteómica, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico
| | - José A Guerrero-Analco
- Laboratorio de Química de Productos Naturales, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico.
| | - Diana Sánchez-Rangel
- Laboratorios de Fitopatología y Biología Molecular, Red de Estudios Moleculares Avanzados, Clúster BioMimic®, Instituto de Ecología, A. C. Xalapa, Veracruz 91073, Mexico; Investigador por México - CONAHCyT en la Red de Estudios Moleculares Avanzados del Instituto de Ecología, A. C. (INECOL), Carretera antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico.
| |
Collapse
|
36
|
Lucas BA, Himes BA, Grigorieff N. Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias. eLife 2023; 12:RP90486. [PMID: 38010355 PMCID: PMC10681363 DOI: 10.7554/elife.90486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and cellular background (Lucas et al., 2021; Lucas et al., 2022). Here, we show that once localized, these particles may be averaged together to generate high-resolution 3D reconstructions. However, regions included in the template may suffer from template bias, leading to inflated resolution estimates and making the interpretation of high-resolution features unreliable. We evaluate conditions that minimize template bias while retaining the benefits of high-precision localization, and we show that molecular features not present in the template can be reconstructed at high resolution from targets found by 2DTM, extending prior work at low-resolution. Moreover, we present a quantitative metric for template bias to aid the interpretation of 3D reconstructions calculated with particles localized using high-resolution templates and fine angular sampling.
Collapse
Affiliation(s)
- Bronwyn A Lucas
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Department of Molecular and Cell Biology, University of California BerkeleyBerkeleyUnited States
- Center for Computational Biology, University of California BerkeleyBerkeleyUnited States
| | - Benjamin A Himes
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Nikolaus Grigorieff
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| |
Collapse
|
37
|
Fedorovskiy AG, Burakov AV, Terenin IM, Bykov DA, Lashkevich KA, Popenko VI, Makarova NE, Sorokin II, Sukhinina AP, Prassolov VS, Ivanov PV, Dmitriev SE. A Solitary Stalled 80S Ribosome Prevents mRNA Recruitment to Stress Granules. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1786-1799. [PMID: 38105199 DOI: 10.1134/s000629792311010x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/31/2023] [Accepted: 09/11/2023] [Indexed: 12/19/2023]
Abstract
In response to stress stimuli, eukaryotic cells typically suppress protein synthesis. This leads to the release of mRNAs from polysomes, their condensation with RNA-binding proteins, and the formation of non-membrane-bound cytoplasmic compartments called stress granules (SGs). SGs contain 40S but generally lack 60S ribosomal subunits. It is known that cycloheximide, emetine, and anisomycin, the ribosome inhibitors that block the progression of 80S ribosomes along mRNA and stabilize polysomes, prevent SG assembly. Conversely, puromycin, which induces premature termination, releases mRNA from polysomes and stimulates the formation of SGs. The same effect is caused by some translation initiation inhibitors, which lead to polysome disassembly and the accumulation of mRNAs in the form of stalled 48S preinitiation complexes. Based on these and other data, it is believed that the trigger for SG formation is the presence of mRNA with extended ribosome-free segments, which tend to form condensates in the cell. In this study, we evaluated the ability of various small-molecule translation inhibitors to block or stimulate the assembly of SGs under conditions of severe oxidative stress induced by sodium arsenite. Contrary to expectations, we found that ribosome-targeting elongation inhibitors of a specific type, which arrest solitary 80S ribosomes at the beginning of the mRNA coding regions but do not interfere with all subsequent ribosomes in completing translation and leaving the transcripts (such as harringtonine, lactimidomycin, or T-2 toxin), completely prevent the formation of arsenite-induced SGs. These observations suggest that the presence of even a single 80S ribosome on mRNA is sufficient to prevent its recruitment into SGs, and the presence of extended ribosome-free regions of mRNA is not sufficient for SG formation. We propose that mRNA entry into SGs may be mediated by specific contacts between RNA-binding proteins and those regions on 40S subunits that remain inaccessible when ribosomes are associated.
Collapse
Affiliation(s)
- Artem G Fedorovskiy
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Materials Science, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anton V Burakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Sirius University of Science and Technology, Sirius, Krasnodar Region, 354340, Russia
| | - Dmitry A Bykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Kseniya A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Vladimir I Popenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Nadezhda E Makarova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ivan I Sorokin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anastasia P Sukhinina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Vladimir S Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Pavel V Ivanov
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Boston, MA 02115, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| |
Collapse
|
38
|
Wittenstein A, Caspi M, Rippin I, Elroy-Stein O, Eldar-Finkelman H, Thoms S, Rosin-Arbesfeld R. Nonsense mutation suppression is enhanced by targeting different stages of the protein synthesis process. PLoS Biol 2023; 21:e3002355. [PMID: 37943958 PMCID: PMC10684085 DOI: 10.1371/journal.pbio.3002355] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/28/2023] [Accepted: 09/29/2023] [Indexed: 11/12/2023] Open
Abstract
The introduction of premature termination codons (PTCs), as a result of splicing defects, insertions, deletions, or point mutations (also termed nonsense mutations), lead to numerous genetic diseases, ranging from rare neuro-metabolic disorders to relatively common inheritable cancer syndromes and muscular dystrophies. Over the years, a large number of studies have demonstrated that certain antibiotics and other synthetic molecules can act as PTC suppressors by inducing readthrough of nonsense mutations, thereby restoring the expression of full-length proteins. Unfortunately, most PTC readthrough-inducing agents are toxic, have limited effects, and cannot be used for therapeutic purposes. Thus, further efforts are required to improve the clinical outcome of nonsense mutation suppressors. Here, by focusing on enhancing readthrough of pathogenic nonsense mutations in the adenomatous polyposis coli (APC) tumor suppressor gene, we show that disturbing the protein translation initiation complex, as well as targeting other stages of the protein translation machinery, enhances both antibiotic and non-antibiotic-mediated readthrough of nonsense mutations. These findings strongly increase our understanding of the mechanisms involved in nonsense mutation readthrough and facilitate the development of novel therapeutic targets for nonsense suppression to restore protein expression from a large variety of disease-causing mutated transcripts.
Collapse
Affiliation(s)
- Amnon Wittenstein
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Caspi
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Rippin
- The Department of Human Molecular Genetics & Biochemistry School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Elroy-Stein
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hagit Eldar-Finkelman
- The Department of Human Molecular Genetics & Biochemistry School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sven Thoms
- Biochemistry and Molecular Medicine, Medical School EWL, Bielefeld University, Bielefeld, Germany
| | - Rina Rosin-Arbesfeld
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
39
|
Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S. A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response. Nat Cell Biol 2023; 25:1600-1615. [PMID: 37857833 PMCID: PMC11005034 DOI: 10.1038/s41556-023-01248-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 09/01/2023] [Indexed: 10/21/2023]
Abstract
A widespread strategy employed by pathogens to establish infection is to inhibit host-cell protein synthesis. Legionella pneumophila, an intracellular bacterial pathogen and the causative organism of Legionnaires' disease, secretes a subset of protein effectors into host cells that inhibit translation elongation. Mechanistic insights into how the bacterium targets translation elongation remain poorly defined. We report here that the Legionella effector SidI functions in an unprecedented way as a transfer-RNA mimic that directly binds to and glycosylates the ribosome. The 3.1 Å cryo-electron microscopy structure of SidI reveals an N-terminal domain with an 'inverted L' shape and surface-charge distribution characteristic of tRNA mimicry, and a C-terminal domain that adopts a glycosyl transferase fold that licenses SidI to utilize GDP-mannose as a sugar precursor. This coupling of tRNA mimicry and enzymatic action endows SidI with the ability to block protein synthesis with a potency comparable to ricin, one of the most powerful toxins known. In Legionella-infected cells, the translational pausing activated by SidI elicits a stress response signature mimicking the ribotoxic stress response, which is activated by elongation inhibitors that induce ribosome collisions. SidI-mediated effects on the ribosome activate the stress kinases ZAKα and p38, which in turn drive an accumulation of the protein activating transcription factor 3 (ATF3). Intriguingly, ATF3 escapes the translation block imposed by SidI, translocates to the nucleus and orchestrates the transcription of stress-inducible genes that promote cell death, revealing a major role for ATF3 in the response to collided ribosome stress. Together, our findings elucidate a novel mechanism by which a pathogenic bacterium employs tRNA mimicry to hijack a ribosome-to-nuclear signalling pathway that regulates cell fate.
Collapse
Affiliation(s)
- Advait Subramanian
- G.W. Hooper Foundation, University of California at San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Lan Wang
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Tom Moss
- G.W. Hooper Foundation, University of California at San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA
| | - Smriti Sangwan
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Erica Stevenson
- Gladstone Institute of Data Science and Biotechnology, J. Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California at San Francisco, San Francisco, CA, USA
| | - Ernst H Pulido
- Gladstone Institute of Data Science and Biotechnology, J. Gladstone Institutes, San Francisco, CA, USA
| | - Samentha Kwok
- Department of Cell and Tissue Biology, University of California at San Francisco, San Francisco, CA, USA
| | - Robert J Chalkley
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Kathy H Li
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Nevan J Krogan
- Gladstone Institute of Data Science and Biotechnology, J. Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California at San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- Gladstone Institute of Data Science and Biotechnology, J. Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California at San Francisco, San Francisco, CA, USA
| | - Alma L Burlingame
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter Walter
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.
- Bay Area Institute of Science, Altos Labs, Redwood City, CA, USA.
| | - Shaeri Mukherjee
- G.W. Hooper Foundation, University of California at San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
40
|
Yang Z, Zhou N, Jiang X, Wang L. Loop Evolutionary Patterns Shape Catalytic Efficiency of TRI101/201 for Trichothecenes: Insights into Protein-Substrate Interactions. J Chem Inf Model 2023; 63:6316-6331. [PMID: 37821422 DOI: 10.1021/acs.jcim.3c00787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Trichothecenes are highly toxic mycotoxins produced by Fusarium fungi, while TRI101/201 family enzymes play a crucial role in detoxification through acetylation. Studies on the substrate specificity and catalytic kinetics of TRI101/201 have revealed distinct kinetic characteristics, with significant differences observed in catalytic efficiency toward deoxynivalenol, while the catalytic efficiency for T-2 toxin remains relatively consistent. In this study, we used structural bioinformatics analysis and a molecular dynamics simulation workflow to investigate the mechanism underlying the differential catalytic activity of TRI101/201. The findings revealed that the binding stability between trichothecenes and TRI101/201 hinges primarily on a hydrophobic cage structure within the binding site. An intrinsic disordered loop, termed loop cover, defined the evolutionary patterns of the TRI101/201 protein family that are categorized into four subfamilies (V1/V2/V3/M). Furthermore, the unique loop displayed different conformations among these subfamilies' structures, which served to disrupt (V1/V2/V3) or reinforce (M) the hydrophobic cages. The disrupted cages enhanced the water exposure of the hydrophilic moieties of substrates like deoxynivalenol and thereby hindered their binding to the catalytic sites of V-type enzymes. In contrast, this water exposure does not affect substrates like T-2 toxin, which have more hydrophobic substituents, resulting in a comparable catalytic efficiency of both V- and M-type enzymes. Overall, our studies provide theoretical support for understanding the catalytic mechanism of TRI101/201, which shows how an intrinsic disordered loop could impact the protein-ligand binding and suggests a direction for rational protein design in the future.
Collapse
Affiliation(s)
- Zezheng Yang
- Taishan College, Shandong University, 266237 Qingdao, China
| | - Nana Zhou
- COFCO Nutrition and Health Research Institute, 102209 Beijing, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, 266237 Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| |
Collapse
|
41
|
Garofalo M, Payros D, Taieb F, Oswald E, Nougayrède JP, Oswald IP. From ribosome to ribotoxins: understanding the toxicity of deoxynivalenol and Shiga toxin, two food borne toxins. Crit Rev Food Sci Nutr 2023:1-13. [PMID: 37862145 DOI: 10.1080/10408398.2023.2271101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Ribosomes that synthesize proteins are among the most central and evolutionarily conserved organelles. Given the key role of proteins in cellular functions, prokaryotic and eukaryotic pathogens have evolved potent toxins to inhibit ribosomal functions and weaken their host. Many of these ribotoxin-producing pathogens are associated with food. For example, food can be contaminated with bacterial pathogens that produce the ribotoxin Shiga toxin, but also with the fungal ribotoxin deoxynivalenol. Shiga toxin cleaves ribosomal RNA, while deoxynivalenol binds to and inhibits the peptidyl transferase center. Despite their distinct modes of action, both groups of ribotoxins hinder protein translation, but also trigger other comparable toxic effects, which depend or not on the activation of the ribotoxic stress response. Ribotoxic stress response-dependent effects include inflammation and apoptosis, whereas ribotoxic stress response-independent effects include endoplasmic reticulum stress, oxidative stress, and autophagy. For other effects, such as cell cycle arrest and cytoskeleton modulation, the involvement of the ribotoxic stress response is still controversial. Ribotoxins affect one organelle yet induce multiple toxic effects with multiple consequences for the cell. The ribosome can therefore be considered as the cellular "Achilles heel" targeted by food borne ribotoxins. Considering the high toxicity of ribotoxins, they pose a substantial health risk, as humans are highly susceptible to widespread exposure to these toxins through contaminated food sources.
Collapse
Affiliation(s)
- Marion Garofalo
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Delphine Payros
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Frederic Taieb
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Toulouse, France
| | | | - Isabelle P Oswald
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| |
Collapse
|
42
|
Subbaiah S P V, Uttamrao PP, Das U, Sundaresan S, Rathinavelan T. Concentration and time-dependent amyloidogenic characteristics of intrinsically disordered N-terminal region of Saccharomyces cerevisiae Stm1. Front Microbiol 2023; 14:1206945. [PMID: 37928673 PMCID: PMC10620681 DOI: 10.3389/fmicb.2023.1206945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
Saccharomyces cerevisiae Stm1 protein is a ribosomal association factor, which plays an important role in preserving ribosomes in a nutrition-deprived environment. It is also shown to take part in apoptosis-like cell death. Stm1 N-terminal region (Stm1_N1-113) is shown to recognize purine motif DNA triplex and G-quadruplex. Circular dichroism (CD) spectra of Stm1_N1-113 (enriched in positively-charged Lysine and Arginine; negatively-charged Aspartate; polar-uncharged Threonine, Asparagine, Proline and Serine; hydrophobic Alanine, Valine, and Glycine) collected after 0 and 24 h indicate that the protein assumes beta-sheet conformation at the higher concentrations in contrast to intrinsically disordered conformation seen for its monomeric form found in the crystal structure. Thioflavin-T kinetics experiments indicate that the lag phase is influenced by the salt concentration. Atomic force microscopy (AFM) images collected for a variety of Stm1_N1-113 concentrations (in the range of 1-400 μM) in the presence of 150 mM NaCl at 0, 24, and 48 h indicate a threshold concentration requirement to observe the time-dependent amyloid formation. This is prominent seen at the physiological salt concentration of 150 mM NaCl with the fibrillation observed for 400 μM concentration at 48 h, whereas oligomerization or proto-fibrillation is seen for the other concentrations. Such concentration-dependent fibrillation of Stm1_N1-113 explains that amyloid fibrils formed during the overexpression of Stm1_N1-113 may act as a molecular device to trigger apoptosis-like cell death.
Collapse
Affiliation(s)
- Venkata Subbaiah S P
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Patil Pranita Uttamrao
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Uttam Das
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Sruthi Sundaresan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | | |
Collapse
|
43
|
Pietra F. Do Naturally Modified Nucleotides Contribute to Stabilizing Complexes between Ribosomes and Small Molecules? A Case Study with the Antitumor Drug Homoharringtonine. ChemMedChem 2023; 18:e202300095. [PMID: 37548261 DOI: 10.1002/cmdc.202300095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/08/2023]
Abstract
Modified nucleotides are ubiquitous with RNAs, also in contact with drugs that target the ribosome. Whether this represents a stabilization of the drug-ribosome complex, thus affecting the drug's affinity and possibly also intrinsic efficacy, remains an open question, however. The challenge of answering this question has been taken here with the only human-ribosome-targeting small-molecule currently in clinical use, the antitumor plant alkaloid homoharringtonine (HHT). The approach consisted in dissecting HHT-nucleotide interaction energies from QM-MM simulations in explicit water. What emerged is a network of mostly weak interactions of the large, branched HHT with standard nucleotides and a single modified nucleotide, out of the four ones present at PCT's A site. This is unlike the case of the small, compact marine antitumor alkaloid agelastatin A, which displays only a few, albeit strong, interactions with site-A ribosome nucleotides. This should aid tailoring drugs targeting the ribosome.
Collapse
Affiliation(s)
- Francesco Pietra
- Accademia Lucchese di Scienze Lettere e Arti, Classe di Scienze, Palazzo Pretorio, Via Vittorio Veneto 1, 55100, Lucca, Italy
| |
Collapse
|
44
|
Qin K, Yu S, Liu Y, Guo R, Guo S, Fei J, Wang Y, Jia K, Xu Z, Chen H, Li F, Niu M, Dai MS, Dai L, Cao Y, Zhang Y, Xiao ZXJ, Yi Y. USP36 stabilizes nucleolar Snail1 to promote ribosome biogenesis and cancer cell survival upon ribotoxic stress. Nat Commun 2023; 14:6473. [PMID: 37833415 PMCID: PMC10575996 DOI: 10.1038/s41467-023-42257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Tumor growth requires elevated ribosome biogenesis. Targeting ribosomes is an important strategy for cancer therapy. The ribosome inhibitor, homoharringtonine (HHT), is used for the clinical treatment of leukemia, yet it is ineffective for the treatment of solid tumors, the reasons for which remain unclear. Here we show that Snail1, a key factor in the regulation of epithelial-to-mesenchymal transition, plays a pivotal role in cellular surveillance response upon ribotoxic stress. Mechanistically, ribotoxic stress activates the JNK-USP36 signaling to stabilize Snail1 in the nucleolus, which facilitates ribosome biogenesis and tumor cell survival. Furthermore, we show that HHT activates the JNK-USP36-Snail1 axis in solid tumor cells, but not in leukemia cells, resulting in solid tumor cell resistance to HHT. Importantly, a combination of HHT with the inhibition of the JNK-USP36-Snail1 axis synergistically inhibits solid tumor growth. Together, this study provides a rationale for targeting the JNK-USP36-Snail1 axis in ribosome inhibition-based solid tumor therapy.
Collapse
Affiliation(s)
- Kewei Qin
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Shuhan Yu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Yang Liu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Rongtian Guo
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Shiya Guo
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Junjie Fei
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Yuemeng Wang
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Kaiyuan Jia
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Zhiqiang Xu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Hu Chen
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chengdu Medical College, 610500, Chengdu, China
| | - Fengtian Li
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Mengmeng Niu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Mu-Shui Dai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Lunzhi Dai
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Yujun Zhang
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Zhi-Xiong Jim Xiao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China.
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China.
| | - Yong Yi
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China.
| |
Collapse
|
45
|
Cheatham AM, Sharma NR, Satpute-Krishnan P. Competition for calnexin binding regulates secretion and turnover of misfolded GPI-anchored proteins. J Cell Biol 2023; 222:e202108160. [PMID: 37702712 PMCID: PMC10499038 DOI: 10.1083/jcb.202108160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/19/2023] [Accepted: 08/10/2023] [Indexed: 09/14/2023] Open
Abstract
In mammalian cells, misfolded glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs) are cleared out of the ER to the Golgi via a constitutive and a stress-inducible pathway called RESET. From the Golgi, misfolded GPI-APs transiently access the cell surface prior to rapid internalization for lysosomal degradation. What regulates the release of misfolded GPI-APs for RESET during steady-state conditions and how this release is accelerated during ER stress is unknown. Using mutants of prion protein or CD59 as model misfolded GPI-APs, we demonstrate that inducing calnexin degradation or upregulating calnexin-binding glycoprotein expression triggers the release of misfolded GPI-APs for RESET. Conversely, blocking protein synthesis dramatically inhibits the dissociation of misfolded GPI-APs from calnexin and subsequent turnover. We demonstrate an inverse correlation between newly synthesized calnexin substrates and RESET substrates that coimmunoprecipitate with calnexin. These findings implicate competition by newly synthesized substrates for association with calnexin as a key factor in regulating the release of misfolded GPI-APs from calnexin for turnover via the RESET pathway.
Collapse
Affiliation(s)
- Amber M. Cheatham
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Nishi Raj Sharma
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Prasanna Satpute-Krishnan
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| |
Collapse
|
46
|
O'Mara SP, Broz K, Schwister EM, Singh L, Dong Y, Elmore JM, Kistler HC. The Fusarium graminearum Transporters Abc1 and Abc6 Are Important for Xenobiotic Resistance, Trichothecene Accumulation, and Virulence to Wheat. PHYTOPATHOLOGY 2023; 113:1916-1923. [PMID: 37260101 DOI: 10.1094/phyto-09-22-0345-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The plant pathogenic fungus Fusarium graminearum is the causal agent of Fusarium head blight (FHB) disease on small-grain cereals. F. graminearum produces trichothecene mycotoxins such as deoxynivalenol (DON) that are required for full virulence. DON must be exported outside the cell to cause FHB disease, a process that may require the involvement of membrane-bound transporters. In this study, we show that the deletion of membrane-bound transporters results in reduced DON accumulation as well as reduced FHB symptoms on wheat. Deletion of the ATP-binding cassette (ABC) transporter gene Abc1 results in the greatest reduction in DON accumulation and virulence. Deletion of another ABC transporter gene, Abc6, also reduces FHB symptoms to a lesser degree. Combining deletions fails to reduce DON accumulation or virulence in an additive fashion, even when a ∆abc1 deletion is included. Heterologous expression of F. graminearum transporters in a DON-sensitive strain of yeast confirms Abc1 as a major DON resistance mechanism; furthermore, it suggests that Abc1 is directly participating in DON transport rather than facilitating DON transport though other means. Yeast expression further indicates that multiple transporters, including Abc1, play an important role in resistance to the wheat phytoalexin 2-benzoxazolinone (BOA) and other xenobiotics. Thus, Abc1 may contribute to virulence on wheat both by facilitating export of DON and by providing resistance to the wheat phytoalexin BOA. This research provides useful information that may aid in designing novel management techniques of FHB or other destructive plant diseases.
Collapse
Affiliation(s)
- Sean P O'Mara
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - Karen Broz
- U.S. Department of Agriculture-Agricultural Research Service Cereal Disease Laboratory, St. Paul, MN 55108
| | - Erin M Schwister
- U.S. Department of Agriculture-Agricultural Research Service Cereal Disease Laboratory, St. Paul, MN 55108
| | - Lovepreet Singh
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - Yanhong Dong
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - J Mitch Elmore
- U.S. Department of Agriculture-Agricultural Research Service Cereal Disease Laboratory, St. Paul, MN 55108
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - H Corby Kistler
- U.S. Department of Agriculture-Agricultural Research Service Cereal Disease Laboratory, St. Paul, MN 55108
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| |
Collapse
|
47
|
Wang Z, Guo X, Lian J, Ji Y, Li K. Prognostic value of amino acid metabolism-related gene expression in invasive breast carcinoma. J Cancer Res Clin Oncol 2023; 149:11117-11133. [PMID: 37340191 DOI: 10.1007/s00432-023-04985-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND An increasing number of studies indicated that metabolic reprogramming of amino acid metabolism may either promote or inhibit tumor progression. The purpose of this study was to investigate the ability of a gene risk signature associated with amino acid metabolism to predict the prognosis and immune characteristics of invasive breast carcinoma. METHODS LASSO Cox regression analysis was performed to construct and validate the prognostic risk signature based on the expression of 9 amino acid metabolism-related genes. The predictive value of the signature, immune characteristics, and chemotherapeutic drugs was also predicted. Finally, 9 significant genes were examined in MDA-MB-231 and MCF-7 cells, and the predicted chemotherapeutic drugs were also verified. RESULTS The prognosis of the low-risk group was better than that of the high-risk group. The areas under the curve (AUCs) at 1, 2, and 3 years were 0.852, 0.790, and 0.736, respectively. In addition, the GSEA results for KEGG and GO revealed that samples with a high-risk score exhibited a variety of highly malignant manifestations. The high-risk group was characterized by an increased number of M2 macrophages, a high level of tumor purity, low levels of APC co-stimulation, cytolytic activity, HLA, para-inflammation, and type I IFN response. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) confirmed that MDA-MB-231 and MCF-7 cells express 9 amino acid metabolism-related genes differently. In addition, cell experiments were conducted to examine the effect of cephaeline-induced on cell viability, migration ability, and protein expression of the PI3K/AKT signaling pathway and HIF-1α. CONCLUSION We established a risk signature based on 9 amino acid metabolism-related genes for invasive breast carcinoma. Further analyses revealed that this risk signature is superior to other clinical indexes in survival prediction and that the subgroups identified by the risk signature exhibit distinct immune characteristics. Cephaeline was determined to be a superior option for patients in high-risk groups.
Collapse
Affiliation(s)
- Zilin Wang
- Department of Radiology, School of Medicine, Shanghai General Hospital, Shanghai Jiaotong University, No. 650 New Songjiang Road, Shanghai, 200080, People's Republic of China
| | - Xinyu Guo
- Department of Radiology, School of Medicine, Shanghai General Hospital, Shanghai Jiaotong University, No. 650 New Songjiang Road, Shanghai, 200080, People's Republic of China
| | - Jingge Lian
- Department of Radiology, School of Medicine, Shanghai General Hospital, Shanghai Jiaotong University, No. 650 New Songjiang Road, Shanghai, 200080, People's Republic of China
| | - Ying Ji
- Department of Radiology, School of Medicine, Shanghai General Hospital, Shanghai Jiaotong University, No. 650 New Songjiang Road, Shanghai, 200080, People's Republic of China
| | - Kangan Li
- Department of Radiology, School of Medicine, Shanghai General Hospital, Shanghai Jiaotong University, No. 650 New Songjiang Road, Shanghai, 200080, People's Republic of China.
| |
Collapse
|
48
|
Yayli G, Bernardini A, Mendoza Sanchez PK, Scheer E, Damilot M, Essabri K, Morlet B, Negroni L, Vincent SD, Timmers HTM, Tora L. ATAC and SAGA co-activator complexes utilize co-translational assembly, but their cellular localization properties and functions are distinct. Cell Rep 2023; 42:113099. [PMID: 37682711 PMCID: PMC10591836 DOI: 10.1016/j.celrep.2023.113099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
To understand the function of multisubunit complexes, it is of key importance to uncover the precise mechanisms that guide their assembly. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here, we demonstrate that the core modules of ATAC (ADA-two-A-containing) and SAGA (Spt-Ada-Gcn5-acetyltransferase), two lysine acetyl transferase-containing transcription co-activator complexes, assemble co-translationally in the cytoplasm of mammalian cells. In addition, a SAGA complex containing all of its modules forms in the cytoplasm and acetylates non-histone proteins. In contrast, ATAC complex subunits cannot be detected in the cytoplasm of mammalian cells. However, an endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related co-activators, ATAC and SAGA, assemble using co-translational pathways, but their subcellular localization, cytoplasmic abundance, and functions are distinct.
Collapse
Affiliation(s)
- Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Mylène Damilot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Karim Essabri
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - H T Marc Timmers
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Freiburg, Germany; Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France.
| |
Collapse
|
49
|
Nguyen AMT, Shalev-Benami M, Rosa-Teijeiro C, Ibarra-Meneses AV, Yonath A, Bashan A, Jaffe CL, Olivier M, Fernandez-Prada C, Lubell WD. Systematic Exploration of Functional Group Relevance for Anti-Leishmanial Activity of Anisomycin. Biomedicines 2023; 11:2541. [PMID: 37760981 PMCID: PMC10526209 DOI: 10.3390/biomedicines11092541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Assessment of structure-activity relationships for anti-protozoan activity revealed a strategy for preparing potent anisomycin derivatives with reduced host toxicity. Thirteen anisomycin analogs were synthesized by modifying the alcohol, amine, and aromatic functional groups. Examination of anti-protozoal activity against various strains of Leishmania and cytotoxicity against leucocytes with comparison against the parent natural product demonstrated typical losses of activity with modifications of the alcohol, amine, and aromatic meta-positions. On the other hand, the para-phenol moiety of anisomycin proved an effective location for introducing substituents without significant loss of anti-protozoan potency. An entry point for differentiating activity against Leishmania versus host has been uncovered by this systematic study.
Collapse
Affiliation(s)
| | - Moran Shalev-Benami
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (M.S.-B.); (A.Y.); (A.B.)
| | - Chloé Rosa-Teijeiro
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (C.R.-T.); (A.V.I.-M.); (C.F.-P.)
- The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, Université de Montréal, Montreal, QC J2S 2M2, Canada
| | - Ana Victoria Ibarra-Meneses
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (C.R.-T.); (A.V.I.-M.); (C.F.-P.)
- The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, Université de Montréal, Montreal, QC J2S 2M2, Canada
| | - Ada Yonath
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (M.S.-B.); (A.Y.); (A.B.)
| | - Anat Bashan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (M.S.-B.); (A.Y.); (A.B.)
| | - Charles L. Jaffe
- Department of Microbiology & Molecular Genetics, Kuvin Center for the Study of Tropical & Infectious Diseases, Institute for Medical Research (IMRIC), Hadassah Hebrew University Medical Center, Jerusalem 9112102, Israel;
| | - Martin Olivier
- Departments of Medicine, and of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, QC H3A 2B4, Canada;
- The Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, QC H4A 3J1, Canada
| | - Christopher Fernandez-Prada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (C.R.-T.); (A.V.I.-M.); (C.F.-P.)
- The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, Université de Montréal, Montreal, QC J2S 2M2, Canada
| | - William D. Lubell
- Department of Chemistry, Université de Montréal, Montreal, QC H3T 1J4, Canada
| |
Collapse
|
50
|
Ishimura R, Ito S, Mao G, Komatsu-Hirota S, Inada T, Noda NN, Komatsu M. Mechanistic insights into the roles of the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control. SCIENCE ADVANCES 2023; 9:eadh3635. [PMID: 37595036 PMCID: PMC10438457 DOI: 10.1126/sciadv.adh3635] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like protein covalently conjugated with intracellular proteins through ufmylation, similar to ubiquitylation. Ufmylation is involved in processes such as endoplasmic reticulum (ER)-associated protein degradation, ribosome-associated protein quality control (RQC) at the ER (ER-RQC), and ER-phagy. However, it remains unclear how ufmylation regulates such distinct ER-related functions. Here, we provide insights into the mechanism of the UFM1 E3 complex in not only ufmylation but also ER-RQC. The E3 complex consisting of UFL1 and UFBP1 interacted with UFC1, UFM1 E2, and, subsequently, CDK5RAP3, an adaptor for ufmylation of ribosomal subunit RPL26. Upon disome formation, the E3 complex associated with ufmylated RPL26 on the 60S subunit through the UFM1-interacting region of UFBP1. Loss of E3 components or disruption of the interaction between UFBP1 and ufmylated RPL26 attenuated ER-RQC. These results provide insights into not only the molecular basis of the ufmylation but also its role in proteostasis.
Collapse
Affiliation(s)
- Ryosuke Ishimura
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Sota Ito
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Gaoxin Mao
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Satoko Komatsu-Hirota
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Kita-Ku, Sapporo 060-0815, Japan
- Institute of Microbial Chemistry (Bikaken), Shinagawa-ku, Tokyo 141-0021, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| |
Collapse
|