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Sun Y, Jia X, Yang Z, Fu Q, Yang H, Xu X. Genome-Wide Identification of PEBP Gene Family in Solanum lycopersicum. Int J Mol Sci 2023; 24:ijms24119185. [PMID: 37298136 DOI: 10.3390/ijms24119185] [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: 04/05/2023] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
The PEBP gene family is crucial for the growth and development of plants, the transition between vegetative and reproductive growth, the response to light, the production of florigen, and the reaction to several abiotic stressors. The PEBP gene family has been found in numerous species, but the SLPEBP gene family has not yet received a thorough bioinformatics investigation, and the members of this gene family are currently unknown. In this study, bioinformatics was used to identify 12 members of the SLPEBP gene family in tomato and localize them on the chromosomes. The physicochemical characteristics of the proteins encoded by members of the SLPEBP gene family were also examined, along with their intraspecific collinearity, gene structure, conserved motifs, and cis-acting elements. In parallel, a phylogenetic tree was built and the collinear relationships of the PEBP gene family among tomato, potato, pepper, and Arabidopsis were examined. The expression of 12 genes in different tissues and organs of tomato was analyzed using transcriptomic data. It was also hypothesized that SLPEBP3, SLPEBP5, SLPEBP6, SLPEBP8, SLPEBP9, and SLPEBP10 might be related to tomato flowering and that SLPEBP2, SLPEBP3, SLPEBP7, and SLPEBP11 might be related to ovary development based on the tissue-specific expression analysis of SLPEBP gene family members at five different stages during flower bud formation to fruit set. This article's goal is to offer suggestions and research directions for further study of tomato PEBP gene family members.
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Affiliation(s)
- Yimeng Sun
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Xinyi Jia
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Zhenru Yang
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Qingjun Fu
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Huanhuan Yang
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
| | - Xiangyang Xu
- Laboratory of Genetic Breeding in Tomato, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Mucai Street 59, Harbin 150030, China
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102
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Yang A, Zeng K, Huang H, Liu D, Song X, Qian Y, Yu X, Liu D, Zha X, Zhang H, Chai X, Tu P, Hu Z. Usenamine A induces apoptosis and autophagic cell death of human hepatoma cells via interference with the Myosin-9/actin-dependent cytoskeleton remodeling. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154895. [PMID: 37229890 DOI: 10.1016/j.phymed.2023.154895] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/09/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a major cause of cancer-associated mortality worldwide. Myosin-9's role in HCC and the anti-HCC effect of the drugs targeting Myosin-9 remain poorly understood so far. Candidate antitumor agents obtained from natural products have attracted worldwide attention. Usenamine A is a novel product, which was first extracted in our laboratory from the lichen Usnea longissima. According to published reports, usenamine A exhibits good antitumor activity, while the mechanisms underlying its antitumor effects remain to be elucidated. PURPOSE The present study investigated the anti-hepatoma effect of usenamine A and the underlying molecular mechanisms, along with evaluating the therapeutic potential of targeting Myosin-9 in HCC. METHODS The CCK-8, Hoechst staining, and FACS assays were conducted in the present study to investigate how usenamine A affected the growth and apoptosis of human hepatoma cells. Moreover, TEM, acridine orange staining, and immunofluorescence assay were performed to explore the induction of autophagy by usenamine A in human hepatoma cells. The usenamine A-mediated regulation of protein expression in human hepatoma cells was analyzed using immunoblotting. MS analysis, SPR assay, CETSA, and molecular modeling were performed to identify the direct target of usenamine A. Immunofluorescence assay and co-immunoprecipitation assay were conducted to determine whether usenamine A affected the interaction between Myosin-9 and the actin present in human hepatoma cells. In addition, the anti-hepatoma effect of usenamine A was investigated in vivo using a xenograft tumor model and the IHC analysis. RESULTS The present study initially revealed that usenamine A could suppress the proliferation of HepG2 and SK-HEP-1 cells (hepatoma cell lines). Furthermore, usenamine A induced cell apoptosis via the activation of caspase-3. In addition, usenamine A enhanced autophagy. Moreover, usenamine A administration could dramatically suppress the carcinogenic ability of HepG2 cells, as evidenced by the nude mouse xenograft tumor model. Importantly, it was initially revealed that Myosin-9 was a direct target of usenamine A. Usenamine A could block cytoskeleton remodeling through the disruption of the interaction between Myosin-9 and actin. Myosin-9 participated in suppressing proliferation while inducing apoptosis and autophagy in response to treatment with usenamine A. In addition, Myosin-9 was revealed as a potential oncogene in HCC. CONCLUSIONS Usenamine A was initially revealed to suppress human hepatoma cells growth by interfering with the Myosin-9/actin-dependent cytoskeleton remodeling through the direct targeting of Myosin-9. Myosin-9 is, therefore, a promising candidate target for HCC treatment, while usenamine A may be utilized as a possible anti-HCC therapeutic, particularly in the treatment of HCC with aberrant Myosin-9.
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Affiliation(s)
- Ailin Yang
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Kewu Zeng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Huiming Huang
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Dongxiao Liu
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiaomin Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yi Qian
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xuelong Yu
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Dan Liu
- Proteomics Laboratory, Medical and Healthy Analytical Center, Peking University Health Science Center, Beijing 100191, China
| | - Xiaojun Zha
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Hongbing Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Physiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Xingyun Chai
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China.
| | - Pengfei Tu
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China.
| | - Zhongdong Hu
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China.
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Pfister P, Diehl C, Hammarlund E, Carrillo M, Erb TJ. Enhancing the Substrate Specificity of Clostridium Succinyl-CoA Reductase for Synthetic Biology and Biocatalysis. Biochemistry 2023. [PMID: 37207322 DOI: 10.1021/acs.biochem.3c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Succinyl-CoA reductase (SucD) is an acylating aldehyde reductase that catalyzes the NADPH-dependent reduction of succinyl-CoA to succinic semialdehyde. The reaction sequence from succinate to crotonyl-CoA is of particular interest for several new-to-nature CO2-fixation pathways, such as the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, in which SucD plays a key role. However, pathways like the CETCH cycle feature several CoA-ester intermediates, which could be potentially side substrates for this enzyme. Here, we show that the side reaction for most CETCH cycle metabolites is relatively small (<2%) with the exception of mesaconyl-C1-CoA (16%), which represents a competing substrate in this pathway. We addressed this promiscuity by solving the crystal structure of a SucD of Clostridium kluyveri in complex with NADP+ and mesaconyl-C1-CoA. We further identified two residues (Lys70 and Ser243) that coordinate mesaconyl-C1-CoA at the active site. We targeted those residues with site-directed mutagenesis to improve succinyl-CoA over mesaconyl-C1-CoA reduction. The best resulting SucD variant, K70R, showed a strongly reduced side activity for mesaconyl-C1-CoA, but the substitution also reduced the specific activity for succinyl-CoA by a factor of 10. Transferring the same mutations into a SucD homologue from Clostridium difficile similarly decreases the side reaction of this enzyme for mesaconyl-C1-CoA from 12 to 2%, notably without changing the catalytic efficiency for succinyl-CoA. Overall, our structure-based engineering efforts provided a highly specific enzyme of interest for several applications in biocatalysis and synthetic biology.
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Affiliation(s)
- Pascal Pfister
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Christoph Diehl
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Eric Hammarlund
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Martina Carrillo
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
- SYNMIKRO Center for Synthetic Microbiology, Karl-von-Frisch Str., 14, 35032 Marburg, Germany
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104
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Zhou L, Meng Q, Zhang R, Jiang B, Wu Q, Chen J, Zhang T. Improving thermostability of a PL 5 family alginate lyase with combination of rational design strategies. Int J Biol Macromol 2023; 242:124871. [PMID: 37201879 DOI: 10.1016/j.ijbiomac.2023.124871] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
Alginate lyases with strict substrate specificity possess potential in directed production of alginate oligosaccharides with specific composition. However, their poor thermostability hampered their applications in industry. In this study, an efficient comprehensive strategy including sequence-based analysis, structure-based analysis, and computer-aid ΔΔGfold value calculation was proposed. It was successfully performed on alginate lyase (PMD) with strict poly-β-D-mannuronic acid substrate specificity. Four single-point variants A74V, G75V, A240V, and D250G with increased Tm of 3.94 °C, 5.21 °C, 2.56 °C, and 4.80 °C, respectively, were selected out. After ordered combined mutations, a four-point mutant (M4) was finally generated which displayed remarkable increase on thermostability. The Tm of M4 increased from 42.25 °C to 51.59 °C and its half-life at 50 °C was about 58.9-fold of PMD. Meanwhile, there was no obvious loss of enzyme activity (more than 90% retained). Molecular dynamics simulation analysis insisted that the improvement of thermostability might be attribute to the rigidified region A which might be caused by the newly formed hydrogen bonds and salt bridges introduced by mutations, the lower distance of original hydrogen bonds, and the more compact overall structures.
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Affiliation(s)
- Licheng Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qing Meng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ran Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Qun Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jingjing Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
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105
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Zhao Y, Zheng Z, Zhang Z, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of High-Molecular-Mass Hyaluronic Acid is Associated with Subterranean Lifestyle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539764. [PMID: 37215017 PMCID: PMC10197608 DOI: 10.1101/2023.05.08.539764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hyaluronic acid (HA) is a major component of extracellular matrix (ECM) which plays an important role in development, cellular response to injury and inflammation, cell migration, and cancer. The naked mole-rat (NMR, Heterocephalus glaber ) contains abundant high-molecular-mass HA (HMM-HA) in its tissues, which contributes to this species' cancer resistance and possibly longevity. Here we report that abundant HMM-HA is found in a wide range of subterranean mammalian species, but not in phylogenetically related aboveground species. These species accumulate abundant HMM-HA by regulating the expression of genes involved in HA degradation and synthesis and contain unique mutations in these genes. The abundant high molecular weight HA may benefit the adaptation to subterranean environment by increasing skin elasticity and protecting from oxidative stress due to hypoxic subterranean environment. HMM-HA may also be coopted to confer cancer resistance and longevity to subterranean mammals. Our work suggests that HMM-HA has evolved with subterranean lifestyle.
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106
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Fan X, Xu L, Zhang J, Wang Y, Wu Z, Sun W, Yao X, Wang X, Guan S, Shan Y. Mechanism Exploration of Amyloid-β-42 Disaggregation by Single-Chain Variable Fragments of Alzheimer's Disease Therapeutic Antibodies. Int J Mol Sci 2023; 24:ijms24098371. [PMID: 37176076 PMCID: PMC10179127 DOI: 10.3390/ijms24098371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Alzheimer's disease (AD) is a specific neurodegenerative disease. This study adopts single-chain variable fragments (scFvs) as a potential immunotherapeutic precursor for AD. According to the remarkable effects of monoclonal antibodies, such as the depolymerization or promotion of Aβ42 efflux by Crenezumab, Solanezumab, and 12B4, it is attractive to prepare corresponding scFvs targeting amyloid-β-42 protein (Aβ42) and investigate their biological activities. Crenezumab-like scFv (scFv-C), Solanezumab-like scFv (scFv-S), and 12B4-like scFv (scFv-12B4) were designed and constructed. The thermal stabilities and binding ability to Aβ42 of scFv-C, scFv-S, and scFv-12B4 were evaluated using unfolding profile and enzyme-linked immunosorbent assay. As the results indicated that scFv-C could recognize Aβ42 monomer/oligomer and promote the disaggregation of Aβ42 fiber as determined by the Thioflavin-T assay, the potential mechanism of its interaction with Aβ42 was investigated using molecular dynamics analysis. Interactions involving hydrogen bonds and salt bonds were predicted between scFv-C and Aβ42 pentamer, suggesting the possibility of inhibiting further aggregation of Aβ42. The successfully prepared scFvs, especially scFv-C, with favorable biological activity targeting Aβ42, might be developed for a potentially efficacious clinical application for AD.
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Affiliation(s)
- Xing Fan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Lipeng Xu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jianhao Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yidan Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zirui Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Wenjing Sun
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xin Yao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Shanshan Guan
- College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun 130052, China
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
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107
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Nguyen LT, Rananaware SR, Yang LG, Macaluso NC, Ocana-Ortiz JE, Meister KS, Pizzano BLM, Sandoval LSW, Hautamaki RC, Fang ZR, Joseph SM, Shoemaker GM, Carman DR, Chang L, Rakestraw NR, Zachary JF, Guerra S, Perez A, Jain PK. Engineering highly thermostable Cas12b via de novo structural analyses for one-pot detection of nucleic acids. Cell Rep Med 2023; 4:101037. [PMID: 37160120 DOI: 10.1016/j.xcrm.2023.101037] [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: 12/08/2022] [Revised: 01/31/2023] [Accepted: 04/14/2023] [Indexed: 05/11/2023]
Abstract
CRISPR-Cas-based diagnostics have the potential to elevate nucleic acid detection. CRISPR-Cas systems can be combined with a pre-amplification step in a one-pot reaction to simplify the workflow and reduce carryover contamination. Here, we report an engineered Cas12b with improved thermostability that falls within the optimal temperature range (60°C-65°C) of reverse transcription-loop-mediated isothermal amplification (RT-LAMP). Using de novo structural analyses, we introduce mutations to wild-type BrCas12b to tighten its hydrophobic cores, thereby enhancing thermostability. The one-pot detection assay utilizing the engineered BrCas12b, called SPLENDID (single-pot LAMP-mediated engineered BrCas12b for nucleic acid detection of infectious diseases), exhibits robust trans-cleavage activity up to 67°C in a one-pot setting. We validate SPLENDID clinically in 80 serum samples for hepatitis C virus (HCV) and 66 saliva samples for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high specificity and accuracy. We obtain results in as little as 20 min, and with the extraction process, the entire assay can be performed within an hour.
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Affiliation(s)
- Long T Nguyen
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Santosh R Rananaware
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Lilia G Yang
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Nicolas C Macaluso
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Julio E Ocana-Ortiz
- Department of Chemical Engineering, University of Puerto Rico, Mayagüez, PR, USA
| | - Katelyn S Meister
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Brianna L M Pizzano
- Department of Agricultural and Biological Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Luke Samuel W Sandoval
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Raymond C Hautamaki
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, USA
| | - Zoe R Fang
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, USA
| | - Sara M Joseph
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Grace M Shoemaker
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Dylan R Carman
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Liwei Chang
- Department of Chemistry and Quantum Theory Project, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Noah R Rakestraw
- Department of Graduate Education, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jon F Zachary
- Department of Graduate Education, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Sebastian Guerra
- Genetics Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Piyush K Jain
- Department of Chemical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA; Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA; UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
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108
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Lesko MA, Chandrashekarappa DG, Jordahl EM, Oppenheimer KG, Bowman RW, Shang C, Durrant JD, Schmidt MC, O’Donnell AF. Changing course: Glucose starvation drives nuclear accumulation of Hexokinase 2 in S. cerevisiae. PLoS Genet 2023; 19:e1010745. [PMID: 37196001 PMCID: PMC10228819 DOI: 10.1371/journal.pgen.1010745] [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: 02/27/2023] [Revised: 05/30/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Glucose is the preferred carbon source for most eukaryotes, and the first step in its metabolism is phosphorylation to glucose-6-phosphate. This reaction is catalyzed by hexokinases or glucokinases. The yeast Saccharomyces cerevisiae encodes three such enzymes, Hxk1, Hxk2, and Glk1. In yeast and mammals, some isoforms of this enzyme are found in the nucleus, suggesting a possible moonlighting function beyond glucose phosphorylation. In contrast to mammalian hexokinases, yeast Hxk2 has been proposed to shuttle into the nucleus in glucose-replete conditions, where it reportedly moonlights as part of a glucose-repressive transcriptional complex. To achieve its role in glucose repression, Hxk2 reportedly binds the Mig1 transcriptional repressor, is dephosphorylated at serine 15 and requires an N-terminal nuclear localization sequence (NLS). We used high-resolution, quantitative, fluorescent microscopy of live cells to determine the conditions, residues, and regulatory proteins required for Hxk2 nuclear localization. Countering previous yeast studies, we find that Hxk2 is largely excluded from the nucleus under glucose-replete conditions but is retained in the nucleus under glucose-limiting conditions. We find that the Hxk2 N-terminus does not contain an NLS but instead is necessary for nuclear exclusion and regulating multimerization. Amino acid substitutions of the phosphorylated residue, serine 15, disrupt Hxk2 dimerization but have no effect on its glucose-regulated nuclear localization. Alanine substation at nearby lysine 13 affects dimerization and maintenance of nuclear exclusion in glucose-replete conditions. Modeling and simulation provide insight into the molecular mechanisms of this regulation. In contrast to earlier studies, we find that the transcriptional repressor Mig1 and the protein kinase Snf1 have little effect on Hxk2 localization. Instead, the protein kinase Tda1 regulates Hxk2 localization. RNAseq analyses of the yeast transcriptome dispels the idea that Hxk2 moonlights as a transcriptional regulator of glucose repression, demonstrating that Hxk2 has a negligible role in transcriptional regulation in both glucose-replete and limiting conditions. Our studies define a new model of cis- and trans-acting regulators of Hxk2 dimerization and nuclear localization. Based on our data, the nuclear translocation of Hxk2 in yeast occurs in glucose starvation conditions, which aligns well with the nuclear regulation of mammalian orthologs. Our results lay the foundation for future studies of Hxk2 nuclear activity.
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Affiliation(s)
- Mitchell A. Lesko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Dakshayini G. Chandrashekarappa
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Eric M. Jordahl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Katherine G. Oppenheimer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ray W. Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chaowei Shang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Martin C. Schmidt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Allyson F. O’Donnell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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109
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Zhu R, Sang X, Zhou J, Meng Q, Huang LSM, Xu Y, An J, Huang Z. CXCR4 Recognition by L- and D-Peptides Containing the Full-Length V3 Loop of HIV-1 gp120. Viruses 2023; 15:1084. [PMID: 37243169 PMCID: PMC10221217 DOI: 10.3390/v15051084] [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: 04/06/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) recognizes one of its principal coreceptors, CXC chemokine receptor 4 (CXCR4), on the host cell via the third variable loop (V3 loop) of HIV-1 envelope glycoprotein gp120 during the viral entry process. Here, the mechanism of the molecular recognition of HIV-1 gp120 V3 loop by coreceptor CXCR4 was probed by synthetic peptides containing the full-length V3 loop. The two ends of the V3 loop were covalently linked by a disulfide bond to form a cyclic peptide with better conformational integrity. In addition, to probe the effect of the changed side-chain conformations of the peptide on CXCR4 recognition, an all-D-amino acid analog of the L-V3 loop peptide was generated. Both of these cyclic L- and D-V3 loop peptides displayed comparable binding recognition to the CXCR4 receptor, but not to another chemokine receptor, CCR5, suggesting their selective interactions with CXCR4. Molecular modeling studies revealed the important roles played by many negative-charged Asp and Glu residues on CXCR4 that probably engaged in favorable electrostatic interactions with the positive-charged Arg residues present in these peptides. These results support the notion that the HIV-1 gp120 V3 loop-CXCR4 interface is flexible for ligands of different chiralities, which might be relevant in terms of the ability of the virus to retain coreceptor recognition despite the mutations at the V3 loop.
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Affiliation(s)
- Ruohan Zhu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohong Sang
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jiao Zhou
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Qian Meng
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lina S. M. Huang
- Division of Infectious Diseases and Global Public Heath, Department of Medicine, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yan Xu
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jing An
- Division of Infectious Diseases and Global Public Heath, Department of Medicine, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ziwei Huang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
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110
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Qu P, Faraone JN, Evans JP, Zheng YM, Carlin C, Anghelina M, Stevens P, Fernandez S, Jones D, Panchal AR, Saif LJ, Oltz EM, Zhang B, Zhou T, Xu K, Gumina RJ, Liu SL. Enhanced evasion of neutralizing antibody response by Omicron XBB.1.5, CH.1.1, and CA.3.1 variants. Cell Rep 2023; 42:112443. [PMID: 37104089 DOI: 10.1016/j.celrep.2023.112443] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Omicron subvariants continuingly challenge current vaccination strategies. Here, we demonstrate nearly complete escape of the XBB.1.5, CH.1.1, and CA.3.1 variants from neutralizing antibodies stimulated by three doses of mRNA vaccine or by BA.4/5 wave infection, but neutralization is rescued by a BA.5-containing bivalent booster. CH.1.1 and CA.3.1 show strong immune escape from monoclonal antibody S309. Additionally, XBB.1.5, CH.1.1, and CA.3.1 spike proteins exhibit increased fusogenicity and enhanced processing compared with BA.2. Homology modeling reveals the key roles of G252V and F486P in the neutralization resistance of XBB.1.5, with F486P also enhancing receptor binding. Further, K444T/M and L452R in CH.1.1 and CA.3.1 likely drive escape from class II neutralizing antibodies, whereas R346T and G339H mutations could confer the strong neutralization resistance of these two subvariants to S309-like antibodies. Overall, our results support the need for administration of the bivalent mRNA vaccine and continued surveillance of Omicron subvariants.
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Affiliation(s)
- Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Julia N Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - John P Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Mirela Anghelina
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick Stevens
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Soledad Fernandez
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Ashish R Panchal
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Linda J Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Xu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Richard J Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA.
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111
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Huang J, Wang X, Chen X, Li H, Chen Y, Hu Z, Yang S. Adaptive Laboratory Evolution and Metabolic Engineering of Zymomonas mobilis for Bioethanol Production Using Molasses. ACS Synth Biol 2023; 12:1297-1307. [PMID: 37036829 DOI: 10.1021/acssynbio.3c00056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Molasses with abundant sugars is widely used for bioethanol production. Although the ethanologenic bacterium Zymomonas mobilis can use glucose, fructose, and sucrose for ethanol production, levan production from sucrose reduces the ethanol yield of molasses fermentation. To increase ethanol production from sucrose-rich molasses, Z. mobilis was adapted in molasses, sucrose, and fructose in parallel. Adaptation in fructose is the most effective route to generate an evolved strain F74 with improved molasses utilization, which is majorly due to a G99S mutation in Glf for enhanced fructose import. Subsequent sacB deletion and sacC overexpression in F74 to divert sucrose metabolism from levan production to ethanol production further enhanced ethanol productivity 28.6% to 1.35 g/L/h. The efficient utilization of molasses by diverting sucrose metabolic flux through adaptation and genome engineering not only generated an excellent ethanol producer using molasses but also provided the strategy for developing microbial cell factories.
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Affiliation(s)
- Ju Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xia Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiangyu Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Han Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yunhao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhousheng Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
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112
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Kreida S, Narita A, Johnson MD, Tocheva EI, Das A, Ghosal D, Jensen GJ. Cryo-EM structure of the Agrobacterium tumefaciens T4SS-associated T-pilus reveals stoichiometric protein-phospholipid assembly. Structure 2023; 31:385-394.e4. [PMID: 36870333 PMCID: PMC10168017 DOI: 10.1016/j.str.2023.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 01/08/2023] [Accepted: 02/07/2023] [Indexed: 03/06/2023]
Abstract
Agrobacterium tumefaciens causes crown gall disease in plants by the horizontal transfer of oncogenic DNA. The conjugation is mediated by the VirB/D4 type 4 secretion system (T4SS) that assembles an extracellular filament, the T-pilus, and is involved in mating pair formation between A. tumefaciens and the recipient plant cell. Here, we present a 3 Å cryoelectron microscopy (cryo-EM) structure of the T-pilus solved by helical reconstruction. Our structure reveals that the T-pilus is a stoichiometric assembly of the VirB2 major pilin and phosphatidylglycerol (PG) phospholipid with 5-start helical symmetry. We show that PG head groups and the positively charged Arg 91 residues of VirB2 protomers form extensive electrostatic interactions in the lumen of the T-pilus. Mutagenesis of Arg 91 abolished pilus formation. While our T-pilus structure is architecturally similar to previously published conjugative pili structures, the T-pilus lumen is narrower and positively charged, raising questions of whether the T-pilus is a conduit for ssDNA transfer.
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Affiliation(s)
- Stefan Kreida
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Akihiro Narita
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Matthew D Johnson
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada
| | - Anath Das
- Department of Biochemistry, Molecular Biology and Biophysics, and Microbial and Plant Genomics Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84604, USA.
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113
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Chang YL, Huang LM, Kuo XZ, Chen YY, Lin ST, Jeng MF, Yeh HH, Tsai WC, Chen HH. PbABCG1 and PbABCG2 transporters are required for the emission of floral monoterpenes in Phalaenopsis bellina. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:279-292. [PMID: 36738107 DOI: 10.1111/tpj.16133] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 12/17/2022] [Accepted: 01/30/2023] [Indexed: 05/10/2023]
Abstract
Terrestrial plants emit volatiles into the atmosphere to attract both pollinators and the enemies of herbivores, for defense. Phalaenopsis bellina is a scented orchid species in which the main scent components are monoterpenes, including linalool and geraniol, and their derivatives. Here, we investigated whether ABC transporters are involved in floral scent emission. We carried out whole-genome identification of ABC transporter-related genes using four floral transcriptomics libraries of P. bellina. We identified 86 ABC subfamily G genes related to terpenoid transport. After comparing the gene expression patterns of P. bellina with that of Phalaenopsis aphrodite subsp. formosana, a scentless species, followed by gene-to-gene correlation analysis, PbABCG1 and PbABCG2 were selected. The temporal expression of both PbABCG1 and PbABCG2 was highly correlated with that of the key enzyme PbGDPS and the major transcription factor PbbHLH4 in monoterpene biosynthesis, with optimal expression on day 5 post-anthesis. Spatial gene expression analysis showed that PbABCG1 was highly expressed in sepals, whereas PbABCG2 was expressed in the lip. Subcellular localization with a GFP fusion protein revealed that both PbABCG1 and PbABCG2 are cytoplasmic membrane proteins. Co-downregulation of PbABCG1 and PbABCG2 using both double-strand RNA interference and tobacco rattle virus-based gene silencing led to a significant decrease in monoterpene emission, accompanied by an increase in the internal monoterpene pools. Furthermore, ectopic expression of PbABCG1 and PbABCG2 in an ABC16- mutant yeast strain rescued its tolerance to geraniol. Altogether, our results indicate that PbABCG1 and PbABCG2 play substantial roles in monoterpene transport/emission in P. bellina floral scent.
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Affiliation(s)
- Ya-Lan Chang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Li-Min Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Xuan-Zhou Kuo
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - You-Yi Chen
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shao-Ting Lin
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Mei-Fen Jeng
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan
| | - Hsin-Hung Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan
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114
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Hou S, Li Y, Fu Y. me53 encoded by Autographa californica multiple nucleopolyhedrovirus: from mechanism to function. Virus Genes 2023; 59:188-194. [PMID: 36229721 DOI: 10.1007/s11262-022-01943-3] [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: 06/27/2022] [Accepted: 10/05/2022] [Indexed: 10/17/2022]
Abstract
me53, a highly conserved immediate early gene in all Lepidoptera baculoviruses, has been of great interest in recent years. Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is in the family Baculoviridae, genus Alphabaculovirus. The me53 gene of AcMNPV has been sequenced, and it was transcribed late after infection. The structure of ME53 protein and its roles in the infection of host cells were summarized and discussed, including that (1) the production of Budding Virus (BV); (2) nucleocapsid formation in the host nuclei; (3) ME53 forms a lesion on the cell membrane of AcMNPV-infected cells and co-locates with GP64 and the primary capsid protein VP39; (4) the nuclear translocation signal sequence of ME53 is essential for optimal baculovirus production. In this review, we focus on the emerging roles of ME53 by discussing novel mechanisms identified to mediate or interact by ME53, which provides an important reference for the effective transformation, utilization and improvement of the anti-insect activity of AcMNPV.
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Affiliation(s)
- Shuoyu Hou
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Yingqi Li
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Yuejun Fu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, People's Republic of China.
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115
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Investigation of the effects of N-Acetylglucosamine on the stability of the spike protein in SARS-CoV-2 by molecular dynamics simulations. COMPUT THEOR CHEM 2023; 1222:114049. [PMID: 36743995 PMCID: PMC9890939 DOI: 10.1016/j.comptc.2023.114049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023]
Abstract
A lot of effort has been made in developing vaccine and therapeutic agents against the SARS-CoV-2, concentrating on the Spike protein that binds angiotensin-converting enzyme 2 on human cells. Nowadays, some researches study the role of the N-linked glycans as potential targets for vaccines and new agents. Due to the flexibility and diversity of the N-linked glycans, in this work, we focus on the N-Acetylglucosamine moiety, which is the precursor of nearly all eukaryotic glycans. We performed molecular dynamics simulations to study the effects of the N-Acetylglucosamine on the stability of the spike glycoprotein in SARS-CoV-2. After a 100 ns of simulation on the spike proteins without and with the N-Acetylglucosamine molecules, we found that the presence of N-Acetylglucosamine increases the local stability in their vicinity; even though their effect on the full structure is negligible. Thus; it can be inferred that the N-Acetylglucosamine moieties can potentially affect the interaction of the S protein with the ACE2 receptor. We also found that the S1 domain is more flexible than the S2 domain. We propose which of the experimentally observed glycans found on the spike may be more functional than the others. Detailed understanding of glycans is key for the development of new therapeutic strategies.
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116
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Otarigho B, Falade MO. Computational Screening of Approved Drugs for Inhibition of the Antibiotic Resistance Gene mecA in Methicillin-Resistant Staphylococcus aureus (MRSA) Strains. BIOTECH 2023; 12:biotech12020025. [PMID: 37092469 PMCID: PMC10123713 DOI: 10.3390/biotech12020025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Antibiotic resistance is a critical problem that results in a high morbidity and mortality rate. The process of discovering new chemotherapy and antibiotics is challenging, expensive, and time-consuming, with only a few getting approved for clinical use. Therefore, screening already-approved drugs to combat pathogens such as bacteria that cause serious infections in humans and animals is highly encouraged. In this work, we aim to identify approved antibiotics that can inhibit the mecA antibiotic resistance gene found in methicillin-resistant Staphylococcus aureus (MRSA) strains. The MecA protein sequence was utilized to perform a BLAST search against a drug database containing 4302 approved drugs. The results revealed that 50 medications, including known antibiotics for other bacterial strains, targeted the mecA antibiotic resistance gene. In addition, a structural similarity approach was employed to identify existing antibiotics for S. aureus, followed by molecular docking. The results of the docking experiment indicated that six drugs had a high binding affinity to the mecA antibiotic resistance gene. Furthermore, using the structural similarity strategy, it was discovered that afamelanotide, an approved drug with unclear antibiotic activity, had a strong binding affinity to the MRSA-MecA protein. These findings suggest that certain already-approved drugs have potential in chemotherapy against drug-resistant pathogenic bacteria, such as MRSA.
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117
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Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Recent advances in simultaneous thermostability-activity improvement of industrial enzymes through structure modification. Int J Biol Macromol 2023; 232:123440. [PMID: 36708895 DOI: 10.1016/j.ijbiomac.2023.123440] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Engineered thermostable microbial enzymes are widely employed to catalyze chemical reactions in numerous industrial sectors. Although high thermostability is a prerequisite of industrial applications, enzyme activity is usually sacrificed during thermostability improvement. Therefore, it is vital to select the common and compatible strategies between thermostability and activity improvement to reduce mutants̕ libraries and screening time. Three functional protein engineering approaches, including directed evolution, rational design, and semi-rational design, are employed to manipulate protein structure on a genetic basis. From a structural standpoint, integrative strategies such as increasing substrate affinity; introducing electrostatic interaction; removing steric hindrance; increasing flexibility of the active site; N- and C-terminal engineering; and increasing intramolecular and intermolecular hydrophobic interactions are well-known to improve simultaneous activity and thermostability. The current review aims to analyze relevant strategies to improve thermostability and activity simultaneously to circumvent the thermostability and activity trade-off of industrial enzymes.
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Affiliation(s)
- Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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Dominelli N, Regaiolo A, Willy L, Heermann R. Interkingdom Signaling of the Insect Pathogen Photorhabdus luminescens with Plants Via the LuxR solo SdiA. Microorganisms 2023; 11:microorganisms11040890. [PMID: 37110313 PMCID: PMC10143992 DOI: 10.3390/microorganisms11040890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
In bacteria, group-coordinated behavior such as biofilm formation or virulence are often mediated via cell–cell communication, a process referred to as quorum sensing (QS). The canonical QS system of Gram-negative bacteria uses N-acyl homoserine lactones (AHLs) as communication molecules, which are produced by LuxI-type synthases and sensed by cognate LuxR-type receptors. These receptors act as transcriptional regulators controlling the expression of specific genes. Some bacteria harbor LuxR-type receptors lacking a cognate LuxI-type synthases, designated as LuxR solos. Among many other LuxR solos, the entomopathogenic enteric bacterium Photorhabdus luminescens harbors a SdiA-like LuxR solo containing an AHL signal-binding domain, for which a respective signal molecule and target genes have not been identified yet. Here we performed SPR analysis to demonstrate that SdiA acts as a bidirectional regulator of transcription, tightly controlling its own expression and the adjacent PluDJC_01670 (aidA) gene in P. luminescens, a gene supposed to be involved in the colonization of eukaryotes. Via qPCR we could further determine that in sdiA deletion mutant strains, aidA is upregulated, indicating that SdiA negatively affects expression of aidA. Furthermore, the ΔsdiA deletion mutant exhibited differences in biofilm formation and motility compared with the wild-type. Finally, using nanoDSF analysis we could identify putative binding ability of SdiA towards diverse AHLs, but also to plant-derived signals, modulating the DNA-binding capacity of SdiA, suggesting that this LuxR solo acts as an important player in interkingdom signaling between P. luminescens and plants.
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119
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Lobo V, Rocha A, Castro TG, Carvalho MA. Synthesis of Novel 2,9-Disubstituted-6-morpholino Purine Derivatives Assisted by Virtual Screening and Modelling of Class I PI3K Isoforms. Polymers (Basel) 2023; 15:polym15071703. [PMID: 37050317 PMCID: PMC10096987 DOI: 10.3390/polym15071703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The phosphatidylinositol-3 kinase (PI3K) pathway is one of the most frequently activated pathogenic signalling cascades in a wide variety of cancers. In the last 15 years, there has been an increase in the search for selective inhibitors of the four class I isoforms of PI3K, as they demonstrate better specificity and reduced toxicity in comparison to existing inhibitors. A ligand-based and target-based rational drug design strategy was employed to build a virtual library of 105 new compounds. Through this strategy, the four isoforms were compared regarding their activity pocket availability, amino acid sequences, and prone interactions. Additionally, a known active scaffold was used as a molecular base to design new derivatives. The virtual screening of the resultant library toward the four isoforms points to the obtention of 19 selective inhibitors for the PI3Kα and PI3Kγ targets. Three selective ligands, one for α-isoform and two for γ-isoform, present a ∆ (∆Gbinding) equal or greater than 1.5 Kcal/mol and were identified as the most promising candidates. A principal component analysis was used to establish correlations between the affinity data and some of the physicochemical and structural properties of the ligands. The binding modes and interactions established by the selective ligands in the active centre of the α and γ isoforms of PI3K were also investigated. After modelling studies, a synthetic approach to generate selective ligands was developed and applied in synthesising a set of derivatives that were obtained in good to excellent yield.
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Meena J, Hasija Y. Rare deleterious mutations in Bruton's tyrosine kinase as biomarkers for ibrutinib-based therapy: an in silico insight. J Mol Model 2023; 29:120. [PMID: 36991253 DOI: 10.1007/s00894-023-05515-6] [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: 11/21/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023]
Abstract
CONTEXT Squamous cell carcinoma (SCC) is the second most common type of skin cancer caused by malignant keratinocytes. Multiple studies have shown that protein mutations have a significant impact on the development and progression of cancer, including SCC. We attempted to decode the effect of single amino acid mutations in the Bruton's tyrosine kinase (BTK) protein in this study. Molecular dynamic (MD) simulations were performed on selected deleterious mutations of the BTK protein, revealing that the variants adversely affect the protein, indicating that they may contribute to the prognosis of SCC by making the protein unstable. Then, we investigated the interaction between the protein and its mutants with ibrutinib, a drug designed to treat SCC. Even though the mutations have deleterious effects on protein structure, they bind to ibrutinib similarly to their wild type counterpart. This study demonstrates that the effect of detected missense mutations is unfavorable and can result in function loss, which is severe for SCC, but that ibrutinib-based therapy can still be effective on them, and the mutations can be used as biomarkers for Ibrutinib-based treatment. METHODS Seven different computational techniques were used to compute the effect of SAVs in accordance with the experimental requirements of this study. To understand the differences in protein and mutant dynamics, MD simulation and trajectory analysis, including RMSD, RMSF, PCA, and contact analysis, were performed. The free binding energy and its decomposition for each protein-drug complex were determined using docking, MM-GBSA, MM-PBSA, and interaction analysis (wild and mutants).
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Affiliation(s)
- Jaishree Meena
- Department of Biotechnology, Delhi Technological University, Delhi, 110042, India
| | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University, Delhi, 110042, India.
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Gisriel CJ, Elias E, Shen G, Soulier NT, Flesher DA, Gunner MR, Brudvig GW, Croce R, Bryant DA. Helical allophycocyanin nanotubes absorb far-red light in a thermophilic cyanobacterium. SCIENCE ADVANCES 2023; 9:eadg0251. [PMID: 36961897 PMCID: PMC10038336 DOI: 10.1126/sciadv.adg0251] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
To compete in certain low-light environments, some cyanobacteria express a paralog of the light-harvesting phycobiliprotein, allophycocyanin (AP), that strongly absorbs far-red light (FRL). Using cryo-electron microscopy and time-resolved absorption spectroscopy, we reveal the structure-function relationship of this FRL-absorbing AP complex (FRL-AP) that is expressed during acclimation to low light and that likely associates with chlorophyll a-containing photosystem I. FRL-AP assembles as helical nanotubes rather than typical toroids due to alterations of the domain geometry within each subunit. Spectroscopic characterization suggests that FRL-AP nanotubes are somewhat inefficient antenna; however, the enhanced ability to harvest FRL when visible light is severely attenuated represents a beneficial trade-off. The results expand the known diversity of light-harvesting proteins in nature and exemplify how biological plasticity is achieved by balancing resource accessibility with efficiency.
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Affiliation(s)
| | - Eduard Elias
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nathan T. Soulier
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - David A. Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - M. R. Gunner
- Department of Physics, City College of New York, New York, NY 10031, USA
| | - Gary W. Brudvig
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Roberta Croce
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Li Z, Fu Z, Zhang S, Zhang X, Xue X, Chen Y, Zhang Z, Lai Z, Lin Y. Genome-wide analysis of the GLP gene family and overexpression of GLP1-5-1 to promote lignin accumulation during early somatic embryo development in Dimocarpus longan. BMC Genomics 2023; 24:138. [PMID: 36944911 PMCID: PMC10029309 DOI: 10.1186/s12864-023-09201-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/21/2023] [Indexed: 03/23/2023] Open
Abstract
Longan (Dimocarpus longan Lour.) is an economically important subtropical fruit tree. Its fruit quality and yield are affected by embryo development. As a plant seed germination marker gene, the germin-like protein (GLP) gene plays an important role in embryo development. However, the mechanism underlying the role of the GLP gene in somatic embryos is still unclear. Therefore, we conducted genome-wide identification of the longan GLP (DlGLP) gene and preliminarily verified the function of DlGLP1-5-1. Thirty-five genes were identified as longan GLP genes and divided into 8 subfamilies. Based on transcriptome data and qRT‒PCR results, DlGLP genes exhibited the highest expression levels in the root, and the expression of most DlGLPs was upregulated during the early somatic embryogenesis (SE) in longan and responded to high temperature stress and 2,4-D treatment; eight DlGLP genes were upregulated under MeJA treatment, and four of them were downregulated under ABA treatment. Subcellular localization showed that DlGLP5-8-2 and DlGLP1-5-1 were located in the cytoplasm and extracellular stroma/chloroplast, respectively. Overexpression of DIGLP1-5-1 in the globular embryos (GEs) of longan promoted the accumulation of lignin and decreased the H2O2 content by regulating the activities of ROS-related enzymes. The results provide a reference for the functional analysis of DlGLPs and related research on improving lignin accumulation in the agricultural industry through genetic engineering.
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Affiliation(s)
- Zhuoyun Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhuoran Fu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaodong Xue
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Jaciuk M, Scherf D, Kaszuba K, Gaik M, Rau A, Kościelniak A, Krutyhołowa R, Rawski M, Indyka P, Graziadei A, Chramiec-Głąbik A, Biela A, Dobosz D, Lin TY, Abbassi NEH, Hammermeister A, Rappsilber J, Kosinski J, Schaffrath R, Glatt S. Cryo-EM structure of the fully assembled Elongator complex. Nucleic Acids Res 2023; 51:2011-2032. [PMID: 36617428 PMCID: PMC10018365 DOI: 10.1093/nar/gkac1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eukaryotes, wobble uridines are modified by Elongator, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero-hexamer. The structure of the fully assembled complex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 Å. We validate the obtained structure by complementary mutational analyses in vitro and in vivo. In addition, we determined various structures of the murine Elongator complex, including the fully assembled mouse Elongator complex at 5.9 Å resolution. Our results confirm the structural conservation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analyses with the biochemical characterization of the assembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes.
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Affiliation(s)
- Marcin Jaciuk
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - David Scherf
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Karol Kaszuba
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
| | - Monika Gaik
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Alexander Rau
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Michał Rawski
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Paulina Indyka
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Andrea Graziadei
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | | | - Anna Biela
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Dominika Dobosz
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Nour-el-Hana Abbassi
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw 02-091, Poland
| | - Alexander Hammermeister
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jan Kosinski
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Raffael Schaffrath
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Sebastian Glatt
- To whom correspondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902;
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Al-Mamun A, Ahammad I, Ahmed SS, Akter F, Hossain SI, Chowdhury ZM, Bhattacharjee A, Das KC, Keya CA, Salimullah M. Pharmacoinformatics and molecular dynamics simulation approach to identify anti-diarrheal potentials of Centella asiatica (L.) Urb. against Vibrio cholerae. J Biomol Struct Dyn 2023; 41:14730-14743. [PMID: 36927394 DOI: 10.1080/07391102.2023.2191736] [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: 12/13/2022] [Accepted: 03/07/2023] [Indexed: 03/18/2023]
Abstract
Vibrio cholerae, the etiological agent of cholera, causes dehydration and severe diarrhea with the production of cholera toxin. Due to the acquired antibiotic resistance, V. cholerae has drawn attention to the establishment of novel medications to counteract the virulence and viability of the pathogen. Centella asiatica is a medicinal herb native to Bangladesh that has a wide range of medicinal and ethnobotanical applications including anti-bacterial properties. In the present investigation, a total of 25 bioactive phytochemicals of C. asiatica have been screened virtually through molecular docking, ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses, and molecular dynamics simulation. Our results revealed four lead compounds as Viridiflorol (-8.7 Kcal/mol), Luteolin (-8.1 Kcal/mol), Quercetin (-8.0 Kcal/mol) and, Geranyl acetate (-7.1 Kcal/mol) against V. cholerae Toxin co-regulated pilus virulence regulatory protein (ToxT). All the lead compounds have been found to possess favorable pharmacokinetic, pharmacodynamics, and molecular dynamics properties. Toxicity analysis revealed satisfactory results with no major side effects. Molecular dynamics simulation was performed for 100 ns that revealed noteworthy conformational stability and structural compactness for all the lead compounds, especially for Quercetin. Target class prediction unveiled enzymes in most of the cases and some experimental and investigational drugs were found as structurally similar analogs of the lead compounds. These findings could aid in the development of novel therapeutics targeting Cholera disease and we strongly recommend in vitro trials of our experimental findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullah Al-Mamun
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Sheikh Sunzid Ahmed
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Farzana Akter
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Shah Imran Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | | | | | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
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Bertschi A, Wang P, Galvan S, Teixeira AP, Fussenegger M. Combinatorial protein dimerization enables precise multi-input synthetic computations. Nat Chem Biol 2023; 19:767-777. [PMID: 36894721 DOI: 10.1038/s41589-023-01281-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 02/01/2023] [Indexed: 03/11/2023]
Abstract
Bacterial transcription factors (TFs) with helix-turn-helix (HTH) DNA-binding domains have been widely explored to build orthogonal transcriptional regulation systems in mammalian cells. Here we capitalize on the modular structure of these proteins to build a framework for multi-input logic gates relying on serial combinations of inducible protein-protein interactions. We found that for some TFs, their HTH domain alone is sufficient for DNA binding. By fusing the HTH domain to TFs, we established dimerization dependent rather than DNA-binding-dependent activation. This enabled us to convert gene switches from OFF-type into more widely applicable ON-type systems and to create mammalian gene switches responsive to new inducers. By combining both OFF and ON modes of action, we built a compact, high-performance bandpass filter. Furthermore, we were able to show cytosolic and extracellular dimerization. Cascading up to five pairwise fusion proteins yielded robust multi-input AND logic gates. Combinations of different pairwise fusion proteins afforded a variety of 4-input 1-output AND and OR logic gate configurations.
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Affiliation(s)
- Adrian Bertschi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Pengli Wang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Silvia Galvan
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ana Palma Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,University of Basel, Faculty of Science, Basel, Switzerland.
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Le J, Min JH. Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein. J Biomol Struct Dyn 2023; 41:13535-13562. [PMID: 36890638 PMCID: PMC10485178 DOI: 10.1080/07391102.2023.2177349] [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: 07/29/2022] [Accepted: 01/27/2023] [Indexed: 03/10/2023]
Abstract
Xeroderma pigmentosum C (XPC) is a key initiator in the global genome nucleotide excision repair pathway in mammalian cells. Inherited mutations in the XPC gene can cause xeroderma pigmentosum (XP) cancer predisposition syndrome that dramatically increases the susceptibility to sunlight-induced cancers. Various genetic variants and mutations of the protein have been reported in cancer databases and literature. The current lack of a high-resolution 3-D structure of human XPC makes it difficult to assess the structural impact of the mutations/genetic variations. Using the available high-resolution crystal structure of its yeast ortholog, Rad4, we built a homology model of human XPC protein and compared it with a model generated by AlphaFold. The two models are largely consistent with each other in the structured domains. We have also assessed the degree of conservation for each residue using 966 sequences of XPC orthologs. Our structure- and sequence conservation-based assessments largely agree with the variant's impact on the protein's structural stability, computed by FoldX and SDM. Known XP missense mutations such as Y585C, W690S, and C771Y are consistently predicted to destabilize the protein's structure. Our analyses also reveal several highly conserved hydrophobic regions that are surface-exposed, which may indicate novel intermolecular interfaces that are yet to be characterized.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jennifer Le
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
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Tuning charge density of chimeric antigen receptor optimizes tonic signaling and CAR-T cell fitness. Cell Res 2023; 33:341-354. [PMID: 36882513 PMCID: PMC10156745 DOI: 10.1038/s41422-023-00789-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
Tonic signaling of chimeric antigen receptor (CAR), i.e., the spontaneous CAR activation in the absence of tumor antigen stimulation, is considered to be a pivotal event controlling CAR-T efficacy. However, the molecular mechanism underlying the spontaneous CAR signals remains elusive. Here, we unveil that positively charged patches (PCPs) on the surface of the CAR antigen-binding domain mediate CAR clustering and result in CAR tonic signaling. For CARs with high tonic signaling (e.g., GD2.CAR and CSPG4.CAR), reducing PCPs on CARs or boosting ionic strength in the culture medium during ex vivo CAR-T cell expansion minimizes spontaneous CAR activation and alleviates CAR-T cell exhaustion. In contrast, introducing PCPs into the CAR with weak tonic signaling, such as CD19.CAR, results in improved in vivo persistence and superior antitumor function. These results demonstrate that CAR tonic signaling is induced and maintained by PCP-mediated CAR clustering. Notably, the mutations we generated to alter the PCPs maintain the antigen-binding affinity and specificity of the CAR. Therefore, our findings suggest that the rational tuning of PCPs to optimize tonic signaling and in vivo fitness of CAR-T cells is a promising design strategy for the next-generation CAR.
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Cruz-Castillo AU, Rodríguez-Valdez LM, Correa-Basurto J, Nogueda-Torres B, Andrade-Ochoa S, Nevárez-Moorillón GV. Terpenic Constituents of Essential Oils with Larvicidal Activity against Aedes Aegypti: A QSAR and Docking Molecular Study. Molecules 2023; 28:molecules28062454. [PMID: 36985426 PMCID: PMC10054420 DOI: 10.3390/molecules28062454] [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: 01/31/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/30/2023] Open
Abstract
Aedes aegypti is a vector for the arbovirus responsible for yellow fever, Zika and Chikungunya virus. Essential oils and their constituents are known for their larvicidal properties and are strong candidates for mosquito control. This work aimed to develop a quantitative structure-activity study and molecular screening for the search and design of new larvicidal agents. Twenty-five monoterpenes with previously evaluated larvicidal activity were built and optimized using computational tools. QSAR models were constructed through genetic algorithms from the larvicidal activity and the calculation of theoretical descriptors for each molecule. Docking studies on acetylcholinesterase (AChE) and sterol carrier protein (SCP-2) were also carried out. Results demonstrate that the epoxide groups in the structure of terpenes hinder larvicidal activity, while lipophilicity plays an important role in enhancing biological activity. Larvicidal activity correlates with the interaction of the sterol-carrier protein. Of the 25 compounds evaluated, carvacrol showed the highest larvicidal activity with an LC50 of 8.8 µg/mL. The information included in this work contributes to describing the molecular, topological, and quantum mechanical properties related to the larvicidal activity of monoterpenes and their derivatives.
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Affiliation(s)
- Adrián Ulises Cruz-Castillo
- Campus Coyoacán, Universidad del Valle de México, Calzada De Tlalpan No. 3016 y 3058, Ex Hacienda Coapa, Delegación Coyoacán, Ciudad de México 04910, Mexico
| | - Luz María Rodríguez-Valdez
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario S/N Campus Universitario II, Chihuahua 31125, Mexico
| | - José Correa-Basurto
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón S/N Col. Santo Tomas, Ciudad de México 11340, Mexico
| | - Benjamín Nogueda-Torres
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N Col. Santo Tomas, Ciudad de México 11340, Mexico
| | - Sergio Andrade-Ochoa
- Campus Coyoacán, Universidad del Valle de México, Calzada De Tlalpan No. 3016 y 3058, Ex Hacienda Coapa, Delegación Coyoacán, Ciudad de México 04910, Mexico
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Bu XL, Zhao WS, Li WX, Zou H, Wu SG, Li M, Wang GT. Mitochondrial metabolism of the facultative parasite Chilodonella uncinata (Alveolata, Ciliophora). Parasit Vectors 2023; 16:92. [PMID: 36882771 PMCID: PMC9993649 DOI: 10.1186/s13071-023-05695-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/03/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Chilodonella uncinata is an aerobic ciliate capable of switching between being free-living and parasitic on fish fins and gills, causing tissue damage and host mortality. It is widely used as a model organism for genetic studies, but its mitochondrial metabolism has never been studied. Therefore, we aimed to describe the morphological features and metabolic characteristics of its mitochondria. METHODS Fluorescence staining and transmission electron microscopy (TEM) were used to observe the morphology of mitochondria. Single-cell transcriptome data of C. uncinata were annotated by the Clusters of Orthologous Genes (COG) database. Meanwhile, the metabolic pathways were constructed based on the transcriptomes. The phylogenetic analysis was also made based on the sequenced cytochrome c oxidase subunit 1 (COX1) gene. RESULTS Mitochondria were stained red using Mito-tracker Red staining and were stained slightly blue by DAPI dye. The cristae and double membrane structures of the mitochondria were observed by TEM. Besides, many lipid droplets were evenly distributed around the macronucleus. A total of 2594 unigenes were assigned to 23 functional classifications of COG. Mitochondrial metabolic pathways were depicted. The mitochondria contained enzymes for the complete tricarboxylic acid (TCA) cycle, fatty acid metabolism, amino acid metabolism, and cytochrome-based electron transport chain (ETC), but only partial enzymes involved in the iron-sulfur clusters (ISCs). CONCLUSIONS Our results showed that C. uncinata possess typical mitochondria. Stored lipid droplets inside mitochondria may be the energy storage of C. uncinata that helps its transmission from a free-living to a parasitic lifestyle. These findings also have improved our knowledge of the mitochondrial metabolism of C. uncinata and increased the volume of molecular data for future studies of this facultative parasite.
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Affiliation(s)
- Xia-Lian Bu
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, The People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, The People's Republic of China.,Protist 10,000 Genomics Project (P10K) Consortium, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, The People's Republic of China
| | - Wei-Shan Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, The People's Republic of China.,Protist 10,000 Genomics Project (P10K) Consortium, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, The People's Republic of China
| | - Wen-Xiang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, The People's Republic of China
| | - Hong Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, The People's Republic of China
| | - Shan-Gong Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, The People's Republic of China
| | - Ming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, The People's Republic of China. .,Protist 10,000 Genomics Project (P10K) Consortium, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, The People's Republic of China.
| | - Gui-Tang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, The People's Republic of China
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Sangeeta, Sonaxi, Tomar R, Agrawal S, Sarkar A. 1,3‐Benzodioxole Tagged Lidocaine Based Ionic Liquids as Anticancer Drug: Synthesis, Characterization and
In Silico
Study. ChemistrySelect 2023. [DOI: 10.1002/slct.202204535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Affiliation(s)
- Sangeeta
- Department of Chemistry Netaji Subhas University of Technology, Dwarka Delhi 110078 India
| | - Sonaxi
- Department of Chemistry Baba Mastnath University, Rohtak Haryana 124021 India
| | - Ravi Tomar
- Department of Chemistry University Center for Research & Development Chandigarh University, Mohali Punjab 140413 India
- Department of Chemical Engineering IIT Delhi New Delhi-110016 India
| | - Swati Agrawal
- Department of Chemistry Motilal Nehru College University of Delhi New Delhi 110021 India
| | - Anjana Sarkar
- Department of Chemistry Netaji Subhas University of Technology, Dwarka Delhi 110078 India
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131
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Bouqellah NA. In silico and in vitro investigation of the antifungal activity of trimetallic Cu-Zn-magnetic nanoparticles against Fusarium oxysporum with stimulation of the tomato plant's drought stress tolerance response. Microb Pathog 2023; 178:106060. [PMID: 36889369 DOI: 10.1016/j.micpath.2023.106060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
Abstract
Fusarium oxysporum is the fungus responsible for Fusarium wilt. Tomatoes and other plants acquire Fusarium wilt through their root systems. Occasionally, fungicides applied to the soil are used to combat the disease; however, some strains have developed resistance. Carboxymethyl cellulose (CMC) trimetallic magnetic zinc and copper nanoparticles CMC-Cu-Zn-FeMNPs are one of the most promising antifungal agents against a wide range of fungi. One of the most important aspects of using magnetic nanoparticles is their ability to target cells, which confirms the drug's potent fungicidal activity. Using a UV-spectrophotometer, the characterization of synthesized CMC-Cu-Zn-FeMNPs revealed four peaks at226,271, 321 and 335 nm, as well as spherical nanoparticles with a mean size of 5.905 nm and a surface potential of -61.7 mv. In this study, CMC-Cu-Zn-FeMNPs were used to inhibit the growth of F. oxysporum by interfering with the ergosterol production metabolic pathway. Molecular docking experiments demonstrated that the nanoparticles were able to bind to sterol 14-alpha demethylase responsible for inhibiting ergosterol biosynthesis. Real-time PCR analysis showed that the nanoparticles upregulated tomato plants and other assessed parameters under drought stress and downregulated the velvet complex and virulence factors of F. oxysporum on plants. The study results indicate that CMC-Cu-Zn-FeMNPs may be a promising and eco-friendly solution with low potential of accumulation and easy to collected alternative to conventional chemical pesticides that can have negative impacts on the environment and human health. Furthermore, it could provide a sustainable solution for managing Fusarium wilt disease, which can significantly reduce tomato yield and quality.
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Affiliation(s)
- Nahla Alsayd Bouqellah
- Taibah University, Science College, Biology Department, 42317- 8599, Al Madinah Al Munawwarah, Saudi Arabia.
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132
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Sarkar S, Gupta VK, Sharma S, Shen T, Gupta V, Mirzaei M, Graham SL, Chitranshi N. Computational refinement identifies functional destructive single nucleotide polymorphisms associated with human retinoid X receptor gene. J Biomol Struct Dyn 2023; 41:1458-1478. [PMID: 34971346 DOI: 10.1080/07391102.2021.2021991] [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: 01/18/2023]
Abstract
Alterations in the nuclear retinoid X receptor (RXRs) signalling have been implicated in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, stroke, multiple sclerosis and glaucoma. Single nucleotide polymorphisms (SNPs) are the main cause underlying single nucleic acid variations which in turn determine heterogeneity within various populations. These genetic polymorphisms have been suggested to associate with various degenerative disorders in population-wide analysis. This bioinformatics study was designed to investigate, search, retrieve and identify deleterious SNPs which may affect the structure and function of various RXR isoforms through a computational and molecular modelling approach. Amongst the 1,813 retrieved SNPs several were found to be deleterious with rs140464195_G139R, rs368400425_R358W and rs368586400_L383F RXRα mutant variants being the most detrimental ones causing changes in the interatomic interactions and decreasing the flexibility of the mutant proteins. Molecular genetics analysis identified seven missense mutations in RXRα/β/γ isoforms. Two novel mutations SNP IDs (rs1588299621 and rs1057519958) were identified in RXRα isoform. We used several in silico prediction tools such as SIFT, PolyPhen, I-Mutant, Protein Variation Effect Analyzer (PROVEAN), PANTHER, SNP&Go, PhD-SNP and SNPeffect to predict pathogenicity and protein stability associated with RXR mutations. The structural assessment by DynaMut tool revealed that hydrogen bonds were affected along with hydrophobic and carbonyl interactions resulting in reduced flexibility at the mutated residue positions but ultimately stabilizing the molecule as a whole. Summarizing, analysis of the missense mutations in RXR isoforms showed a mix of conclusive and inconclusive genotype-phenotype correlations suggesting the use of sophisticated computational analysis tools for studying RXR variants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumalya Sarkar
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Vivek K Gupta
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Samridhi Sharma
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Ting Shen
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Veer Gupta
- School of Medicine, Deakin University, Melbourne, Australia
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Stuart L Graham
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Nitin Chitranshi
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
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133
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Pavlik P, Jost P, Rehulka P, Vozandychova V, Link M, Spidlova P. Epigallocatechin gallate inhibits Francisella tularensis growth and suppresses the function of DNA-binding protein HU. Microb Pathog 2023; 176:105999. [PMID: 36702369 DOI: 10.1016/j.micpath.2023.105999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/11/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023]
Abstract
Francisella tularensis is a highly infectious intracellular bacterium causing tularemia disease and is regarded as a potential biological weapon. The development of a vaccine, effective treatment, or prophylactic substances targeted against tularemia is in the forefront of interest and could help to prevent or mitigate possible malevolent acts by bioterrorism utilizing F. tularensis. The viability of F. tularensis, and thus of a tularemia disease outbreak, might potentially be suppressed by simple commonly available natural substances. Epigallocatechin gallate (EGCG) is contained in green tea and its antimicrobial effect has been described. Here, we show that EGCG can suppress F. tularensis growth and is able to reduce the bacterium's ability to replicate inside mouse bone marrow-derived macrophages (BMMs) without side effects on BMMs' own viability. We suggest one (but not the only) mechanism of EGCG action. We demonstrate that EGCG can block the main functions of HU protein, the important regulator of F. tularensis virulence, leading to overall attenuation of F. tularensis viability. EGCG can delay death of mice infected by F. tularensis and can be used as a prophylactic agent against tularemia disease. Postponing death by up to 2 days can provide sufficient opportunity to administer another treatment agent.
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Affiliation(s)
- Pavla Pavlik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
| | - Petr Jost
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
| | - Pavel Rehulka
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
| | - Vera Vozandychova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
| | - Marek Link
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
| | - Petra Spidlova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic.
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134
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Hollmann NM, Jagtap PKA, Linse JB, Ullmann P, Payr M, Murciano B, Simon B, Hub JS, Hennig J. Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein. Nucleic Acids Res 2023; 51:1895-1913. [PMID: 36688322 PMCID: PMC9976900 DOI: 10.1093/nar/gkac1277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/24/2023] Open
Abstract
RNA binding proteins (RBPs) often engage multiple RNA binding domains (RBDs) to increase target specificity and affinity. However, the complexity of target recognition of multiple RBDs remains largely unexplored. Here we use Upstream of N-Ras (Unr), a multidomain RBP, to demonstrate how multiple RBDs orchestrate target specificity. A crystal structure of the three C-terminal RNA binding cold-shock domains (CSD) of Unr bound to a poly(A) sequence exemplifies how recognition goes beyond the classical ππ-stacking in CSDs. Further structural studies reveal several interaction surfaces between the N-terminal and C-terminal part of Unr with the poly(A)-binding protein (pAbp). All interactions are validated by mutational analyses and the high-resolution structures presented here will guide further studies to understand how both proteins act together in cellular processes.
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Philip Ullmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Marco Payr
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jochen S Hub
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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135
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Wang C, Yang W, Li X, Zhou C, Liu J, Jin L, Jiang Q, Wang Y. A Novel PAX6 Frameshift Mutation Identified in a Large Chinese Family with Congenital Aniridia. J Pers Med 2023; 13:jpm13030442. [PMID: 36983625 PMCID: PMC10052173 DOI: 10.3390/jpm13030442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/25/2023] [Accepted: 02/26/2023] [Indexed: 03/05/2023] Open
Abstract
Congenital aniridia is a rare autosomal dominant congenital ocular disorder. Genetic studies suggest that heterozygous mutations in the developmental regulator PAX6 gene or the related regulatory regions leading to haploinsufficiency are the main cause of congenital aniridia. In this study, the clinical characteristics and pathogenic mutation of a four-generation Chinese family with congenital aniridia were investigated. All members recruited in this study underwent comprehensive ophthalmic examinations. Targeted gene capture sequencing and Sanger sequencing were performed to screen and confirm the candidate pathogenicity gene and its mutation. A multiple alignment of homologous sequences covering the identified mutation from different species was investigated, and the mutant protein structure was predicted using Swiss-Model. Additionally, the prediction of pathogenicity was analyzed using the ACMG Guidelines. Thirteen patients in this pedigree were diagnosed with congenital aniridia. A novel heterozygous frameshift mutation (c.391_398dupATACCAAG, p.Ser133Argfs*8) in exon 7 of the PAX6 gene was identified in all affected individuals in the family. This study demonstrates that this frameshift mutation of the PAX6 gene might be the causative genetic defect of congenital aniridia in this family. This mutation is predicted to cause the premature truncation of the PAX6 protein, leading to the functional haploinsufficiency of PAX6, which may be the major molecular mechanism underlying the aniridia phenotype. To the best of our knowledge, this is the first report of a novel pathogenic PAX6 gene variant c.391_398dupATACCAAG(p.Ser133Argfs*8) identified in a Chinese family with congenital aniridia.
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Affiliation(s)
- Chenghu Wang
- Eye Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Weihua Yang
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen 518040, China
| | - Xiumiao Li
- Eye Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Chenchen Zhou
- Eye Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Jinghua Liu
- Eye Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Ling Jin
- Eye Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Qin Jiang
- Eye Hospital, Nanjing Medical University, Nanjing 210029, China
- Correspondence: (Q.J.); (Y.W.)
| | - Yun Wang
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen 518040, China
- Correspondence: (Q.J.); (Y.W.)
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136
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Fischer S, Bürgi J, Gabay-Maskit S, Maier R, Mastalski T, Yifrach E, Obarska-Kosinska A, Rudowitz M, Erdmann R, Platta HW, Wilmanns M, Schuldiner M, Zalckvar E, Oeljeklaus S, Drepper F, Warscheid B. Phosphorylation of the receptor protein Pex5p modulates import of proteins into peroxisomes. Biol Chem 2023; 404:135-155. [PMID: 36122347 PMCID: PMC9929924 DOI: 10.1515/hsz-2022-0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/23/2022] [Indexed: 11/15/2022]
Abstract
Peroxisomes are organelles with vital functions in metabolism and their dysfunction is associated with human diseases. To fulfill their multiple roles, peroxisomes import nuclear-encoded matrix proteins, most carrying a peroxisomal targeting signal (PTS) 1. The receptor Pex5p recruits PTS1-proteins for import into peroxisomes; whether and how this process is posttranslationally regulated is unknown. Here, we identify 22 phosphorylation sites of Pex5p. Yeast cells expressing phospho-mimicking Pex5p-S507/523D (Pex5p2D) show decreased import of GFP with a PTS1. We show that the binding affinity between a PTS1-protein and Pex5p2D is reduced. An in vivo analysis of the effect of the phospho-mimicking mutant on PTS1-proteins revealed that import of most, but not all, cargos is affected. The physiological effect of the phosphomimetic mutations correlates with the binding affinity of the corresponding extended PTS1-sequences. Thus, we report a novel Pex5p phosphorylation-dependent mechanism for regulating PTS1-protein import into peroxisomes. In a broader view, this suggests that posttranslational modifications can function in fine-tuning the peroxisomal protein composition and, thus, cellular metabolism.
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Affiliation(s)
- Sven Fischer
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
| | - Jérôme Bürgi
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, D-22607Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246Hamburg, Germany
| | - Shiran Gabay-Maskit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Renate Maier
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
| | - Thomas Mastalski
- Biochemistry of Intracellular Transport, Medical Faculty, Ruhr University Bochum, D-44780Bochum, Germany
| | - Eden Yifrach
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Agnieszka Obarska-Kosinska
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, D-22607Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246Hamburg, Germany
| | - Markus Rudowitz
- Systems Biochemistry, Medical Faculty, Ruhr-University Bochum, D-44780Bochum, Germany
| | - Ralf Erdmann
- Systems Biochemistry, Medical Faculty, Ruhr-University Bochum, D-44780Bochum, Germany
| | - Harald W. Platta
- Biochemistry of Intracellular Transport, Medical Faculty, Ruhr University Bochum, D-44780Bochum, Germany
| | - Matthias Wilmanns
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, D-22607Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246Hamburg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Silke Oeljeklaus
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany
| | - Friedel Drepper
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, D-79104Freiburg, Germany
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137
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Hernandez CC, Shen Y, Hu N, Shen W, Narayanan V, Ramsey K, He W, Zou L, Macdonald RL. GABRG2 Variants Associated with Febrile Seizures. Biomolecules 2023; 13:414. [PMID: 36979350 PMCID: PMC10046037 DOI: 10.3390/biom13030414] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Febrile seizures (FS) are the most common form of epilepsy in children between six months and five years of age. FS is a self-limited type of fever-related seizure. However, complicated prolonged FS can lead to complex partial epilepsy. We found that among the GABAA receptor subunit (GABR) genes, most variants associated with FS are harbored in the γ2 subunit (GABRG2). Here, we characterized the effects of eight variants in the GABAA receptor γ2 subunit on receptor biogenesis and channel function. Two-thirds of the GABRG2 variants followed the expected autosomal dominant inheritance in FS and occurred as missense and nonsense variants. The remaining one-third appeared as de novo in the affected probands and occurred only as missense variants. The loss of GABAA receptor function and dominant negative effect on GABAA receptor biogenesis likely caused the FS phenotype. In general, variants in the GABRG2 result in a broad spectrum of phenotypic severity, ranging from asymptomatic, FS, genetic epilepsy with febrile seizures plus (GEFS+), and Dravet syndrome individuals. The data presented here support the link between FS, epilepsy, and GABRG2 variants, shedding light on the relationship between the variant topological occurrence and disease severity.
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Affiliation(s)
- Ciria C. Hernandez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yanwen Shen
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Ningning Hu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wangzhen Shen
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Wen He
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Liping Zou
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Robert L. Macdonald
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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138
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Hot spot-based engineering of ketopantoate hydroxymethyltransferase for the improvement of D-pantothenic acid production in Escherichia coli. J Biotechnol 2023; 364:40-49. [PMID: 36708995 DOI: 10.1016/j.jbiotec.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/10/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023]
Abstract
D-Pantothenic acid (D-PA) is an essential vitamin with wide applications. However, the biotechnological production of D-PA is still not competitive with the chemical synthesis in terms of production cost. Ketopantoate hydroxymethyltransferase is a crucial enzyme in the D-PA synthetic pathway in Escherichia coli encoded by the panB gene. Here a hot spots study was applied to a ketopantoate hydroxymethyltransferase from Corynebacterium glutamicum (CgKPHMT) to relieve the product inhibitory effect and thus improve the D-PA production. Compared with the wild type, the double-site variant CgKPHMT-K25A/E189S showed 1.8 times higher enzyme activity and 2.1 times higher catalytic efficiency, 1.88 and 3.32 times higher inhibitory constant of α-ketoisovalerate and D-PA, respectively. The D-PA yield using E. coli W3110 adopted the double-site variant was 41.17 g·L-1 within 48 h, a 9.80 g·L-1 increase. Structural analysis of K25A/E189S revealed the expansion of the entry channel and the change of the electric charge from negative to uncharged due to the substitution from glutamic acid to serine at site 189. Our study emphasized the positive roles of ketopantoate hydroxymethyltransferase in D-PA production and paved the way by analyzing critical enzymes in the synthetic pathway of E. coli to increase the D-PA yield.
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139
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Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI. Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus. SCIENCE ADVANCES 2023; 9:eade7093. [PMID: 36753546 PMCID: PMC9908020 DOI: 10.1126/sciadv.ade7093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the adenosine triphosphate-dependent RNA translocase/helicase Rho, which causes RNA/DNA dissociation from the RNAP elongation complex (EC). However, the structural basis of the interplay between Rho and RNAP remains obscure. Here, we report the cryo-electron microscopy structure of the Thermus thermophilus RNAP EC engaged with Rho. The Rho hexamer binds RNAP through the carboxyl-terminal domains, which surround the RNA exit site of RNAP, directing the nascent RNA seamlessly from the RNA exit to its central channel. The β-flap tip at the RNA exit is critical for the Rho-dependent RNA release, and its deletion causes an alternative Rho-RNAP binding mode, which is irrelevant to termination. The Rho binding site overlaps with the binding sites of other macromolecules, such as ribosomes, providing a general basis of gene regulation.
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Affiliation(s)
- Yuko Murayama
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Haruhiko Ehara
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mari Aoki
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mie Goto
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shun-ichi Sekine
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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140
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Hirsch M, Hofmann L, Shenberger Y, Gevorkyan-Airapetov L, Ruthstein S. Conformations and Local Dynamics of the CopY Metal Sensor Revealed by EPR Spectroscopy. Biochemistry 2023; 62:797-807. [PMID: 36691693 DOI: 10.1021/acs.biochem.2c00480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Metal transcription factors regulate metal concentrations in eukaryotic and prokaryotic cells. Copper is a metal ion that is being tightly regulated, owing to its dual nature. Whereas copper is an essential nutrient for bacteria, it is also toxic at high concentrations. CopY is a metal-sensitive transcription factor belonging to the copper-responsive repressor family found in Gram-positive bacteria. CopY represses transcription in the presence of Zn(II) ions and initiates transcription in the presence of Cu(I) ions. The complete crystal structure of CopY has not been reported yet, therefore most of the structural information on this protein is based on its similarity to the well-studied MecI protein. In this study, electron paramagnetic resonance (EPR) spectroscopy was used to characterize structural and local dynamical changes in Streptococcus pneumoniae CopY as a function of Zn(II), Cu(I), and DNA binding. We detected different conformations and changes in local dynamics when CopY bound Zn(II), as opposed to Cu(I) ions. Furthermore, we explored the effects of metal ions and DNA on CopY conformation. Our results revealed the sensitivity and selectivity of CopY towards metal ions and provide new insight into the structural mechanism of the CopY transcription factor.
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Affiliation(s)
- Melanie Hirsch
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Lukas Hofmann
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yulia Shenberger
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sharon Ruthstein
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
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141
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Azmi MB, Khan F, Asif U, Khurshid B, Wadood A, Qureshi SA, Ahmed SDH, Mudassir HA, Sheikh SI, Feroz N. In Silico Characterization of Withania coagulans Bioactive Compounds as Potential Inhibitors of Hydroxymethylglutaryl (HMG-CoA) Reductase of Mus musculus. ACS OMEGA 2023; 8:5057-5071. [PMID: 36777558 PMCID: PMC9909811 DOI: 10.1021/acsomega.2c07893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Hypercholesterolemia is a mediator for the etiology of cardiovascular diseases, which are characterized as the global leading cause of mortality. We aimed to investigate the inhibitory activity of Withania coagulans compounds against 3-hydroxy-3-methylglutaryl-coenzyme A reductase (Hmgcr) of Mus musculus using an extensive in silico approach. The 3D structure of the Hmgcr protein is not yet known, so we performed the homology modeling using MODELLER and SWISS-MODEL tools, followed with structural validation and assessment. The PROCHECK web server showed that the top-ranked homology model from SWISS-MODEL has 93.4% of residues in the most-favorable region, the quality factor was 98%, and the Verify3D score was 91.43%, compared to the other generated models. The druggable protein-binding cavities in a 3D model of Hmgcr were investigated with the aid of commonly prescribed statin compounds using the CB-dock approach. We compiled a 3D compound library of W. coagulans, followed by drug-likeness evaluation, and found 20 eligible compounds. The pattern of consensus residues obtained from the CB-dock procedure was then used for grid-box docking of W. coagulans compounds and statin drugs using AutoDock 4.2, respectively. The results showed that withanolide R (-10.77 kcal/mol), withanolide Q (-10.56 kcal/mol), withanolide J (-10.52 kcal/mol), atorvastatin (-8.99 kcal/mol), simvastatin (-8.66 kcal/mol), and rosuvastatin (-8.58 kcal/mol) were promising candidates that bind Hmgcr protein. The key residues involved in protein-ligand (withanolide R) interactions were Y516, C526, V529, I530, M533, I535, and V537, and the formation of a H-bond was at C526, M533, and I535 residues. M533 was the consensus residue having a tendency to form a H-bond with withanolide Q, too. Molecular dynamics simulations were used to validate the top-ranked docked complexes for the stability of the modeled protein. We also predicted the pharmacokinetic properties of binding affinity-based top-ranked compounds and concluded that they could be used as potential inhibitors of Hmgcr. However, further in vitro and in vivo studies are essential to completing the drug development process.
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Affiliation(s)
- Muhammad Bilal Azmi
- Department
of Biochemistry, Dow Medical College, Dow
University of Health Sciences, Karachi 74200, Pakistan
| | - Fearoz Khan
- Department
of Biochemistry, University of Karachi, Karachi 75270, Pakistan
- Rahman
Medical College, Peshawar 25000, Pakistan
| | - Uzma Asif
- Department
of Biochemistry, Medicine Program, Batterjee
Medical College, Jeddah 21442, Saudi Arabia
| | - Beenish Khurshid
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Abdul Wadood
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | | | - Syed Danish Haseen Ahmed
- Department
of Biochemistry, Dow Medical College, Dow
University of Health Sciences, Karachi 74200, Pakistan
| | - Hina Akram Mudassir
- Department
of Biochemistry, Federal Urdu University
of Arts, Science and Technology, Karachi 75300, Pakistan
| | - Sadia Ikhlaque Sheikh
- Department
of Biochemistry, Dow Medical College, Dow
University of Health Sciences, Karachi 74200, Pakistan
| | - Nazia Feroz
- Department
of Biochemistry, Dow Medical College, Dow
University of Health Sciences, Karachi 74200, Pakistan
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142
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N-Amidation of Nitrogen-Containing Heterocyclic Compounds: Can We Apply Enzymatic Tools? Bioengineering (Basel) 2023; 10:bioengineering10020222. [PMID: 36829716 PMCID: PMC9951958 DOI: 10.3390/bioengineering10020222] [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: 12/07/2022] [Revised: 01/20/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
Amide bond is often seen in value-added nitrogen-containing heterocyclic compounds, which can present promising chemical, biological, and pharmaceutical significance. However, current synthesis methods in the preparation of amide-containing N-heterocyclic compounds have low specificity (large amount of by-products) and efficiency. In this study, we focused on reviewing the feasible enzymes (nitrogen acetyltransferase, carboxylic acid reductase, lipase, and cutinase) for the amidation of N-heterocyclic compounds; summarizing their advantages and weakness in the specific applications; and further predicting candidate enzymes through in silico structure-functional analysis. For future prospects, current enzymes demand further engineering and improving for practical industrial applications and more enzymatic tools need to be explored and developed for a broader range of N-heterocyclic substrates.
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143
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Zhu F, Tan C, Li C, Ma S, Wen H, Yang H, Rao M, Zhang P, Peng W, Cui Y, Chen J, Pan P. Design of a multi-epitope vaccine against six Nocardia species based on reverse vaccinology combined with immunoinformatics. Front Immunol 2023; 14:1100188. [PMID: 36845087 PMCID: PMC9952739 DOI: 10.3389/fimmu.2023.1100188] [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: 11/16/2022] [Accepted: 01/13/2023] [Indexed: 02/12/2023] Open
Abstract
Background Nocardia genus, a complex group of species classified to be aerobic actinomycete, can lead to severe concurrent infection as well as disseminated infection, typically in immunocompromised patients. With the expansion of the susceptible population, the incidence of Nocardia has been gradually growing, accompanied by increased resistance of the pathogen to existing therapeutics. However, there is no effective vaccine against this pathogen yet. In this study, a multi-epitope vaccine was designed against the Nocardia infection using reverse vaccinology combined with immunoinformatics approaches. Methods First, the proteomes of 6 Nocardia subspecies Nocardia subspecies (Nocardia farcinica, Nocardia cyriacigeorgica, Nocardia abscessus, Nocardia otitidiscaviarum, Nocardia brasiliensis and Nocardia nova) were download NCBI (National Center for Biotechnology Information) database on May 1st, 2022 for the target proteins selection. The essential, virulent-associated or resistant-associated, surface-exposed, antigenic, non-toxic, and non-homologous with the human proteome proteins were selected for epitope identification. The shortlisted T-cell and B-cell epitopes were fused with appropriate adjuvants and linkers to construct vaccines. The physicochemical properties of the designed vaccine were predicted using multiple online servers. The Molecular docking and molecular dynamics (MD) simulation were performed to understand the binding pattern and binding stability between the vaccine candidate and Toll-like receptors (TLRs). The immunogenicity of the designed vaccines was evaluated via immune simulation. Results 3 proteins that are essential, virulent-associated or resistant-associated, surface-exposed, antigenic, non-toxic, and non-homologous with the human proteome were selected from 218 complete proteome sequences of the 6 Nocardia subspecies epitope identification. After screening, only 4 cytotoxic T lymphocyte (CTL) epitopes, 6 helper T lymphocyte (HTL) epitopes, and 8 B cell epitopes that were antigenic, non-allergenic, and non-toxic were included in the final vaccine construct. The results of molecular docking and MD simulation showed that the vaccine candidate has a strong affinity for TLR2 and TLR4 of the host and the vaccine-TLR complexes were dynamically stable in the natural environment. The results of the immune simulation indicated that the designed vaccine had the potential to induce strong protective immune responses in the host. The codon optimization and cloned analysis showed that the vaccine was available for mass production. Conclusion The designed vaccine has the potential to stimulate long-lasting immunity in the host, but further studies are required to validate its safety and efficacy.
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Affiliation(s)
- Fei Zhu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Caixia Tan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China,Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunhui Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China,Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shiyang Ma
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Haicheng Wen
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Hang Yang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Mingjun Rao
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Peipei Zhang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Wenzhong Peng
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Yanhui Cui
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Jie Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China,*Correspondence: Jie Chen, ; Pinhua Pan,
| | - Pinhua Pan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China,Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China,Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China,*Correspondence: Jie Chen, ; Pinhua Pan,
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144
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Torres-Arteaga I, Blanco-Labra A, Mendiola-Olaya E, García-Gasca T, Aguirre-Mancilla C, Ortega-de-Santiago AL, Barboza M, Lebrilla CB, Castro-Guillén JL. Comparative study, homology modelling and molecular docking with cancer associated glycans of two non-fetuin-binding Tepary bean lectins. Glycoconj J 2023; 40:69-84. [PMID: 36385669 DOI: 10.1007/s10719-022-10091-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/19/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022]
Abstract
We present the purification and characterization of the two most abundant isoforms of lectins isolated from Tepary bean (Phaseolus acutifolius) seeds, which have been shown to differentially affect the survival of different cancer cells. They were separated by concanavalin A-affinity chromatography. After purification, to release the N-glycans, they were digested with the endoglycosidases PNGase and Glycanase A. Fractions resulted from the hydrolysis products were analyzed to determine their carbohydrate composition. Mass spectrometry data indicated that both isoforms contained high mannose glycans being mannose 6 the most abundant form. Furthermore, based on sequence Ans-X-Ser/Thr, where X is any amino acid except proline, a glycosylation site was determined on asparagine 36. When their metal requirement to preserve their biological activity was determined, the lectins showed differences. While lectin A (LA) agglutination activity was best in the presence of magnesium, lectin B (LB) was best with calcium. Additionally, only LA exhibited affinity to human type-A erythrocytes. Although both lectins showed small differences in their properties, an identical structure-model for both lectins was generated by the homology modelling process. Also, the analysis of ligand binding sites and in silico glycosylation were achieved. Molecular docking with colon adenocarcinoma associated-N-glycans revealed some highly possible interactions and, on the other hand, that N-glycan interaction zones of Tepary bean lectins is not restricted to the carbohydrate binding domain but to an extended part of their surface, which could lead new strategies to explain their biological activity.
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Affiliation(s)
- Iovanna Torres-Arteaga
- Centro de Investigación y de Estudios Avanzados. Unidad Irapuato. Departamento de Biotecnología y Bioquímica., Libramiento Norte. Carretera Irapuato-León. Km. 9.6, 36824, Irapuato, Guanajuato, México
| | - Alejandro Blanco-Labra
- Centro de Investigación y de Estudios Avanzados. Unidad Irapuato. Departamento de Biotecnología y Bioquímica., Libramiento Norte. Carretera Irapuato-León. Km. 9.6, 36824, Irapuato, Guanajuato, México
| | - Elizabeth Mendiola-Olaya
- Centro de Investigación y de Estudios Avanzados. Unidad Irapuato. Departamento de Biotecnología y Bioquímica., Libramiento Norte. Carretera Irapuato-León. Km. 9.6, 36824, Irapuato, Guanajuato, México
| | - Teresa García-Gasca
- Universidad Autónoma de Querétaro. Campus Juriquilla. Facultad de Ciencias Naturales., Av. de las Ciencias s/n, Juriquilla, 76230, Santiago de Querétaro, Querétaro, México
| | - Cesar Aguirre-Mancilla
- Tecnológico Nacional de México / Instituto Tecnológico de Roque., Carretera Celaya-Juventino Rosas Km. 8., 38110, Celaya, Guanajuato, México
| | - Alondra L Ortega-de-Santiago
- Centro de Investigación y de Estudios Avanzados. Unidad Irapuato. Departamento de Biotecnología y Bioquímica., Libramiento Norte. Carretera Irapuato-León. Km. 9.6, 36824, Irapuato, Guanajuato, México
| | - Mariana Barboza
- University of California. Davis campus. Department of Chemistry, One Shields Ave. Chemistry Department 2465. Chemistry Annex., 95616, CA, Davis, USA
| | - Carlito B Lebrilla
- University of California. Davis campus. Department of Chemistry, One Shields Ave. Chemistry Department 2465. Chemistry Annex., 95616, CA, Davis, USA
| | - José Luis Castro-Guillén
- Tecnológico Nacional de México / Instituto Tecnológico Superior de Irapuato, Carretera Irapuato-Silao Km. 12.5. Colonia El Copal, 36821, Irapuato, Guanajuato, México.
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145
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Colombo S, Alonso A, Real R, Goswami R, Suarez MC, Ogueta S, Almeida M, Adhikary L, Malmierca MG, de Melo IS. Improvement of monoclonal antibody stability by modulating trace metal iron concentration in cell culture media: A case study. Process Biochem 2023. [DOI: 10.1016/j.procbio.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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146
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Mukherjee RP, Yow GY, Sarakbi S, Menegatti S, Gurgel PV, Carbonell RG, Bobay BG. Integrated in silico and experimental discovery of trimeric peptide ligands targeting Butyrylcholinesterase. Comput Biol Chem 2023; 102:107797. [PMID: 36463785 DOI: 10.1016/j.compbiolchem.2022.107797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/09/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022]
Abstract
Butyrylcholinesterase (BChE) is recognized as a high value biotherapeutic in the treatment of Alzheimer's disease and drug addiction. This study presents the rational design and screening of an in-silico library of trimeric peptides against BChE and the experimental characterization of peptide ligands for purification. The selected peptides consistently afforded high BChE recovery (> 90 %) and purity, yielding up to a 1000-fold purification factor. This study revealed a marked anti-correlated conformational movement governed by the ionic strength and pH of the aqueous environment, which ultimately controls BChE binding and release during chromatographic purification; and highlighted the role of residues within and allosteric to the catalytic triad of BChE in determining biorecognition, thus providing useful guidance for ligand design and affinity maturation.
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Affiliation(s)
- Rudra Palash Mukherjee
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27606, USA; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA
| | | | | | - Stefano Menegatti
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27606, USA; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA
| | - Patrick V Gurgel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA; Prometic Bioseparations Ltd, Cambridge CB23 7AJ, UK
| | - Ruben G Carbonell
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27606, USA; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA; William R. Kenan, Jr. Institute for Engineering, Technology and Science North Carolina State University, Raleigh, NC 27606, USA.
| | - Benjamin G Bobay
- Duke University NMR Center, Duke University Medical Center, Durham, NC 27710, USA; Department of Biochemistry, Duke University, Durham, NC 27710, USA; Department of Radiology, Duke University, Durham, NC 27710, USA.
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147
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Chen C, Zhou L, Zhu L, Luo G, Wang L, Zeng C, Zhou H, Li Y. TNFAIP3 mutation is an independent poor overall survival factor for patients with T-cell acute lymphoblastic leukemia. Cancer Med 2023; 12:3952-3961. [PMID: 36056685 PMCID: PMC9972139 DOI: 10.1002/cam4.5196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/06/2022] [Accepted: 08/19/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND It is imperative to explore potential biomarkers for predicting clinical outcome and developing targeted therapies for T-cell acute lymphoblastic leukemia (T-ALL). This study aimed to investigate the mutation patterns of tumor necrosis factor-alpha-inducing protein 3 (TNFAIP3, also known as A20) and its role in the prognosis of T-ALL patients. METHODS Polymerase chain reaction (PCR) and Sanger sequencing data from T-ALL (n = 49, JNU) and targeted sequencing data from T-ALL (n = 54, NFH) in our clinical center and a publicly available dataset (n = 121, PRJCA002270), were used to detect TNFAIP3 mutation. RESULTS Three TNFAIP3 single nucleotide polymorphisms (SNPs; g.3033 C > T, g.3910 G > A, and g.3904 A > G) were detected in T-ALL in the JNU dataset, and g.3033 C > T accounted for the highest proportion, reaching 60% (6/10). Interestingly, TNFAIP3 mutation mainly occurred in adults but not pediatric patients in all three datasets (JNU, NFH, and PRJCA002270). T-ALL patients carrying a TNFAIP3 mutation were associated with a trend of poor overall survival (OS) (p = 0.092). Moreover, TNFAIP3 mutation was also an independent factor for OS for T-ALL patients (p = 0.008). Further subgroup analysis suggested that TNFAIP3 mutation predicted poor OS for T-ALL patients who underwent chemotherapy only (p < 0.001), and it was positively correlated with high risk and early T-cell precursor ALL (ETP-ALL) in two independent validation datasets (NFH and PRJCA002270). CONCLUSION TNFAIP3 mutation mainly occurs in adult T-ALL patients, and it was associated with adverse clinical outcomes for T-ALL patients; thus, it might be a biomarker for prognostic stratification.
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Affiliation(s)
- Cunte Chen
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, China
| | - Lingling Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lihua Zhu
- Department of Rheumatism and Immunology, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Gengxin Luo
- Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Liang Wang
- Department of Oncology, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Chengwu Zeng
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, China
| | - Hongsheng Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yangqiu Li
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, China
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148
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Ximinies AD, Dou Y, Mishra A, Zhang K, Deivanayagam C, Wang C, Fletcher HM. The Oxidative Stress-Induced Hypothetical Protein PG_0686 in Porphyromonas gingivalis W83 Is a Novel Diguanylate Cyclase. Microbiol Spectr 2023; 11:e0441122. [PMID: 36719196 PMCID: PMC10101095 DOI: 10.1128/spectrum.04411-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/06/2023] [Indexed: 02/01/2023] Open
Abstract
The survival/adaptation of Porphyromonas gingivalis to the inflammatory environment of the periodontal pocket requires an ability to overcome oxidative stress. Several functional classes of genes, depending on the severity and duration of the exposure, were induced in P. gingivalis under H2O2-induced oxidative stress. The PG_0686 gene was highly upregulated under prolonged oxidative stress. PG_0686, annotated as a hypothetical protein of unknown function, is a 60 kDa protein that carries several domains including hemerythrin, PAS10, and domain of unknown function (DUF)-1858. Although PG_0686 showed some relatedness to several diguanylate cyclases (DGCs), it is missing the classical conserved, active site sequence motif (GGD[/E]EF), commonly observed in other bacteria. PG_0686-related proteins are observed in other anaerobic bacterial species. The isogenic mutant P. gingivalis FLL361 (ΔPG_0686::ermF) showed increased sensitivity to H2O2, and decreased gingipain activity compared to the parental strain. Transcriptome analysis of P. gingivalis FLL361 showed the dysregulation of several gene clusters/operons, known oxidative stress resistance genes, and transcriptional regulators, including PG_2212, CdhR and PG_1181 that were upregulated under normal anaerobic conditions. The intracellular level of c-di-GMP in P. gingivalis FLL361 was significantly decreased compared to the parental strain. The purified recombinant PG_0686 (rPG_0686) protein catalyzed the formation of c-di-GMP from GTP. Collectively, our data suggest a global regulatory property for PG_0686 that may be part of an unconventional second messenger signaling system in P. gingivalis. Moreover, it may coordinately regulate a pathway(s) vital for protection against environmental stress, and is significant in the pathogenicity of P. gingivalis and other anaerobes. IMPORTANCE Porphyromonas gingivalis is an important etiological agent in periodontitis and other systemic diseases. There is still a gap in our understanding of the mechanisms that P. gingivalis uses to survive the inflammatory microenvironment of the periodontal pocket. The hypothetical PG_0686 gene was highly upregulated under prolonged oxidative stress. Although the tertiary structure of PG_0686 showed little relatedness to previously characterized diguanylate cyclases (DGCs), and does not contain the conserved GGD(/E)EF catalytic domain motif sequence, an ability to catalyze the formation of c-di-GMP from GTP is demonstrated. The second messenger pathway for c-di-GMP was previously predicted to be absent in P. gingivalis. PG_0686 paralogs are identified in other anaerobic bacteria. Thus, PG_0686 may represent a novel class of DGCs, which is yet to be characterized. In conclusion, we have shown, for the first time, evidence for the presence of c-di-GMP signaling with environmental stress protective function in P. gingivalis.
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Affiliation(s)
- Alexia D. Ximinies
- Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
| | - Yuetan Dou
- Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
| | - Arunima Mishra
- Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
| | - Kangling Zhang
- Department of Pharmacology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Champion Deivanayagam
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama, USA
| | - Charles Wang
- Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
| | - Hansel M. Fletcher
- Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
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149
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Kulkarni V, Chellasamy SK, Dhangar S, Ghatanatti J, Vundinti BR. Comprehensive molecular analysis identifies eight novel variants in XY females with disorders of sex development. Mol Hum Reprod 2023; 29:6972780. [PMID: 36617173 PMCID: PMC10167928 DOI: 10.1093/molehr/gaad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/16/2022] [Indexed: 01/09/2023] Open
Abstract
Disorders of sex development (DSD) are a group of clinical conditions with variable presentation and genetic background. Females with or without development of secondary sexual characters and presenting with primary amenorrhea (PA) and a 46,XY karyotype are one of the classified groups in DSD. In this study, we aimed to determine the genetic mutations in 25 females with PA and a 46,XY karyotype to show correlations with their phenotypes. Routine Sanger sequencing with candidate genes like SRY, AR, SRD5A2, and SF1, which are mainly responsible for 46,XY DSD in adolescent females, was performed. In a cohort of 25 patients of PA with 46,XY DSD, where routine Sanger sequencing failed to detect the mutations, next-generation sequencing of a targeted gene panel with 81 genes was used for the molecular diagnosis. The targeted sequencing identified a total of 21 mutations including 8 novel variants in 20 out of 25 patients with DSD. The most frequently identified mutations in our series were in AR (36%), followed by SRD5A2 (20%), SF1 (12%), DHX37 (4%), HSD17B3 (4%), and DMRT2 (4%). We could not find any mutation in the DSD-related genes in five (20%) patients due to complex molecular mechanisms in 46,XY DSD, highlighting the possibility of new DSD genes which are yet to be discovered in these disorders. In conclusion, genetic testing, including cytogenetics and molecular genetics, is important for the diagnosis and management of 46,XY DSD cases.
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Affiliation(s)
- Vinayak Kulkarni
- Department of Anatomy, Lokmanya Tilak Municipal Medical College and General Hospital, Mumbai, India.,Department of Cytogenetics, ICMR-National Institute of Immunohematology, Mumbai, India
| | - Selvaa Kumar Chellasamy
- Bioinformatics Division, School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, Navi Mumbai, India
| | - Somprakash Dhangar
- Department of Cytogenetics, ICMR-National Institute of Immunohematology, Mumbai, India
| | | | - Babu Rao Vundinti
- Department of Cytogenetics, ICMR-National Institute of Immunohematology, Mumbai, India
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150
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Guo S, Zhao Q, Li Y, Chu S, He F, Li X, Sun N, Zong W, Liu R. Potential toxicity of bisphenol A to α-chymotrypsin and the corresponding mechanisms of their binding. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121910. [PMID: 36167003 DOI: 10.1016/j.saa.2022.121910] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
Bisphenol A (BPA) is an endocrine disruptor widely existing in plastics and resins, which can accumulate in animals and human bodies, posing a potential threat to the physiological and biochemical reactions of human beings or other organisms. α-Chymotrypsin is a kind of proteolytic enzyme existing in humans and animals, which can cause diseases when its activity is excessive. However, there is a lack of research on the mechanism of endocrine disruptors affecting α-chymotrypsin activity. In this study, the interaction between BPA and α-chymotrypsin was proved via multiple spectroscopic approaches, enzyme activity change, isothermal titration calorimetry and molecular docking. Results showed that α-chymotrypsin's polypeptide chains were unfolded, and protein skeletons were loosened with the exposure to BPA. α-Helix content increased and β-sheet content was decreased. The particle size of the BPA-α-chymotrypsin complex became smaller. Fluorescence sensitization may also be explained by a perturbation of the chromophore Trp 141. The thermodynamic parameters of the binding reaction were measured by isothermal titration calorimetry (ITC), which showed that there was hydrophobic interaction between BPA and α-chymotrypsin, which was consistent with the results of molecular docking. Moreover, BPA may stop near the active center of α-chymotrypsin and interact with the key residues His 57 and Ser 195. The above phenomenon explained the result that the activity of α-chymotrypsin increased to 139% when exposed to high dose BPA (40 μM). Taken together, the effects of BPA on the structure and function of α-chymotrypsin were clarified at the molecular level, which made up the gap in the mechanism of BPA on the proteolytic enzyme, and provided a reliable basis for disease avoidance and prevention.
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Affiliation(s)
- Shuqi Guo
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Qiang Zhao
- Shandong Provincial Eco-environment Monitoring Center, 3377 Jingshi Dong Lu, Jinan, Shandong 250100, PR China
| | - Yuze Li
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Shanshan Chu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Falin He
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Xiangxiang Li
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Ning Sun
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Wansong Zong
- College of Geography and Environment, Shandong Normal University, 88# East Wenhua Road, Jinan, Shandong 250014, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China.
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