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Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium

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Plant Communications 2022年第1期3卷 53-70页

作者： Dmitry A.Semchonok Jyotirmoy Mondal Connor J.Cooper Katrina Schlum Meng Li Muhamed Amin Carlos O.S.Sorzano Erney Ramirez-Aportela Panagiotis L.Kastritis Egbert J.Boekema Albert Guskov Barry D.Bruce Groningen Biomolecular Sciences&Biotechnology Institute University of GroningenGroningenthe Netherlands Biochemistry&Cellular and Molecular Biology Department University of TennesseeKnoxvilleTNUSA Program in Genome Science and Technology University of TennesseeKnoxvilleTNUSA Bredesen Center for Interdisciplinary Research&Education University of TennesseeKnoxvilleTNUSA Department of Sciences University College GroningenGroningenthe Netherlands Biocomputing Unit National Center for Biotechnology(CSIC)Darwin 3Campus Universidad Auto´noma de MadridCantoblanco28049 MadridSpain Universidad CEU San Pablo Campus Urb.Monteprı´ncipeBoadilla del Monte28668 MadridSpain Institute of Biochemistry and Biotechnology Martin Luther University Halle-WittenbergHalle/SaaleGermany Microbiology Department University of TennesseeKnoxvilleTNUSA Present address:Institute of Biochemistry and Biotechnology Martin Luther University Halle-WittenbergHalle/SaaleGermany School of Oceanography University of WashingtonSeattleWAUSA

Photosystem I(PSI)is one of two photosystems involved in oxygenic *** of cyanobacteria exists in monomeric,trimeric,and tetrameric forms,in contrast to the strictly monomeric form of PSI in plants and *** tetrameric organization raises questions about its structural,physiological,and evolutionary *** we report the3.72 A˚resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic,unicellular cyanobacterium Chroococcidiopsis *** structure resolves 44 subunits and 448 cofactor *** conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers *** localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent *** analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric *** PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms.

关键词： cryo-EM photosystem I non-heterocyst-forming cyanobacteria Chroococcidiopsis evolution of chloroplast high light adaptation

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Genome-wide analysis of detoxification genes conferring diamide insecticide resistance in Spodoptera exigua identifies CYP9A40

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Chemosphere 2024年 367卷 143623页

作者： Han, Changhee Rahman, Md-Mafizur Kim, Juil Lueke, Bettina Nauen, Ralf Interdisciplinary Graduate Program in Smart Agriculture Kangwon National University Chuncheon24341 Korea Republic of Department Biotechnology and Genetic Engineering Faculty of Biological Science Islamic University Kushtia7003 Bangladesh Agriculture and Life Science Research Institute Kangwon National University Chuncheon24341 Korea Republic of Bayer AG Crop Science Division R&D Monheim40789 Germany

For over a decade, diamide insecticides have been effective against lepidopteran pests like beet armyworm, Spodoptera exigua (Hübner, 1808). However, the evolution of resistance poses a challenge to their sustainable use. We identified an I4790 M mutation in the S. exigua ryanodine receptor (RyR) gene, but its correlation with resistance varied across the field-collected Korean populations of S. exigua. RNA sequencing and differential gene expression analysis were performed to investigate other resistance mechanisms. Diamide-resistant and susceptible strains and F1 hybrids were compared by mapping RNA-seq reads to the S. exigua reference genome. CYP9A40 was identified as a critical gene in diamide resistance due to its high expression in the resistant strains. Synergist bioassays with piperonyl butoxide supported the role of P450s in diamide metabolic resistance in S. exigua. A strong positive correlation between CYP9A40 over-expression levels (up to 80-fold) and diamide LC50 values was obtained for field-collected populations uniformly showing a 100% frequency of the RyR I4790 M target-site resistance allele. To validate the function of CYP9A40 in diamide detoxification, we recombinantly expressed the gene and tested its ability to bind and degrade chlorantraniliprole as a substrate. The results confirmed its catalytic role in diamide metabolism. CYP9A40 has been identified and validated to confer metabolic resistance in Korean S. exigua populations. It works alongside the RyR target-site I4790 M mutation to enhance diamide resistance. These mechanisms offer insights for resistance monitoring and support insecticide resistance management programs to improve control strategies for S. exigua. © 2024 The Author(s)

关键词： Spodoptera exigua Diamide P450 CYP9A40 Heterologous expression RNA-Seq

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Metabolic Engineering of Yarrowia lipolytica for Enhanced Production of Naringenin-Derived Flavonoids: Apigenin and Acacetin

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Journal of agricultural and food chemistry 2025年第23期73卷 2025 May 29页

作者： Nahye Park Yangsub Ham Seungwoo Cha Byeongseon Jang Gyeongmin Kim Seung-Ho Baek Ji-Sook Hahn Interdisciplinary Program for Biochemical Engineering and Biotechnology Seoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea. Department of Chemical and Biological Engineering Institute of Chemical Processes Seoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea. Center for Bio-Based Chemistry Korea Research Institute of Chemical Technology (KRICT) Ulsan 44429 Republic of Korea.

Apigenin and acacetin are flavonoids with potent antioxidant, anti-inflammatory, and anticancer activities, making them attractive for pharmaceutical and nutraceutical applications. However, their low natural abundance presents a challenge to large-scale production. In this study, we engineered for the biosynthesis of apigenin and acacetin from naringenin. To enhance naringenin production from l-tyrosine, we introduced four heterologous genes, optimized the flux through the l-tyrosine pathway, and eliminated the competing homogentisate pathway. Malonyl-CoA availability was increased by downregulating (fatty acid synthase 1), while erythrose-4-phosphate levels were elevated through overexpression of (transketolase 1). Additionally, genes encoding flavone synthase and flavonoid 4'-O-methyltransferase were integrated to convert naringenin into apigenin, and subsequently apigenin into acacetin. Under fed-batch fermentation with an optimized carbon-to-nitrogen ratio, acacetin production reached 1.10 g/L─the highest titer reported to date in a microbial system. These results highlight as a promising chassis for scalable flavonoid biosynthesis.

关键词： Yarrowia lipolytica acacetin apigenin flavonoids naringenin

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Synthesis and Structure-Activity Relationship of Covalent Inhibitors of Sars-Cov-2 Papain-Like Protease with Antiviral Potency

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SSRN 2024年

作者： Rouch, Catherine C. Chatterjee, Arnab K. McCarty, Connor Song, Lirui Chu, Alan Johnson, Kristen Heacock, Mina Riva, Laura McNamara, Case W. Wolff, Karen C. Greene-Cramer, Rebecca De Falco, Anna Montelione, Gaetano T. Grabovyi, Gennadii A. Calibr-Skaggs Institute for Innovative Medicines a Division of Scripps Research La Jolla CA92037 United States Department of Chemistry and Chemical Biology Center for Biotechnology and Interdisciplinary Sciences Rensselaer Polytechnic Institute TroyNY12180 United States The Scripps Research Institute United States Immunity and Pathogenesis Program Department of Biochemistry and Molecular Biology

The papain-like protease (PLpro) is a highly conserved domain encoded by the coronavirus (CoV) genome and it plays an essential role in the replication and maturation of the virus in addition to weakening host immune response. Due to the virus’s reliance on PLpro for survival and propagation, small-molecule inhibitors of PLpro serve as an attractive model for direct-acting antiviral therapeutic agents against SARS-CoV-2. Building upon existing work aimed at designing covalent inhibitors against PLpro, we report the synthesis and structure-activity relationship of analogs based on the known covalent inhibitor 1 (Sanders, et al. 2023). To evaluate the efficacy of synthesized derivatives, we conducted enzymatic inhibition assays, SARS-CoV-2/HeLa-ACE2 cellular potency and toxicity assays, and profiled the most promising analogs via in vitro ADME and in vivo pharmacokinetic studies. Additionally, we describe computational docking of profiled compounds bound to PLpro to elucidate the structure-activity relationship of compounds based on 1 and offer suggestions for optimizing the potency and selectivity of the electrophilic warhead and improving ADME and PK properties for this chemotype. Relative to the parent compound, new designs demonstrate comparable potency and target selectivity for PLpro. Accomplished SAR campaign provides novel insight for future development of antivirals against SARS-CoV-2. © 2024, The Authors. All rights reserved.

关键词： Papain

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Cultivation of Chlorella sp. HS2 using wastewater from soy sauce factory

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Chemosphere 2023年 342卷 140162页

作者： Kim, Minsik Lee, Sang-Ah Yun, Jin-Ho Ko, So-Ra Cho, Dae-Hyun Kim, Hee Su Oh, Hee-Mock Kim, Hee-Sik Ahn, Chi-Yong Daejeon34141 Korea Republic of Dept. of Biological Engineering Inha University Incheon22212 Korea Republic of Faculty of Biotechnology College of Applied Life Sciences Jeju National University Jeju63243 Korea Republic of Interdisciplinary Graduate Program in Advance Convergence Technology and Science Jeju National University Jeju63243 Korea Republic of Department of Integrative Biotechnology Sungkyunkwan University Gyeonggi-do Suwon16419 Korea Republic of FarmHannong Chungcheongnam-do Nonsan33010 Korea Republic of

Incorporation of wastewater from industrial sectors into the design of microalgal biorefineries has significant potential for advancing the practical application of this emerging industry. This study tested various food industrial wastewaters to assess their suitability for microalgal cultivation. Among these wastewaters, defective soy sauce (DSS) and soy sauce wastewater (SWW) were chosen but DSS exhibited the highest nutrient content with 13,500 ppm total nitrogen and 3051 ppm total phosphorus. After diluting DSS by a factor of 50, small-scale cultivation of microalgae was conducted to optimize culture conditions. SWW exhibited optimal growth at 25–30 °C and 300–500 μE m−2 s−1, while DSS showed optimal growth at 30–35 °C. Based on a 100-mL lab-scale and 3-L outdoor cultivation with an extended cultivation period, DSS outperformed SWW, exhibiting higher final biomass productivity. Additionally, nutrient-concentrated nature of DSS is advantageous for transportation at an industrial scale, leading us to select it as the most promising feedstock for microalgal cultivation. With further optimization, DSS has the potential to serve as an effective microalgal cultivation feedstock for large-scale biomass production. © 2023 The Authors

关键词： Microalgae

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Genome-Wide Analysis of Detoxification Genes Conferring Diamide Insecticide Resistance in Spodoptera Exigua Identifies Cyp9a40

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SSRN 2024年

作者： Kim, Juil Han, Changhee Rahman, Md-Mafizur Lueke, Bettina Nauen, Ralf Interdisciplinary Graduate Program in Smart Agriculture Kangwon National University Chuncheon24341 Korea Republic of Department Biotechnology and Genetic Engineering Faculty of Biological Science Islamic University Kushtia7003 Bangladesh Agriculture and Life Science Research Institute Kangwon National University Chuncheon24341 Korea Republic of Bayer AG Crop Science Division Monheim40789 Germany

For over a decade, diamide insecticides have been effective against lepidopteran pests like beet armyworm, Spodoptera exigua (Hübner, 1808). However, the evolution of resistance poses a challenge to their sustainable use. We identified an I4790M mutation in the S. exigua ryanodine receptor (RyR) gene, but its correlation with resistance varied across the field-collected Korean populations of S. exigua. RNA sequencing and differential gene expression analysis were performed to investigate other resistance mechanisms. Diamide-resistant and susceptible strains and F1 hybrids were compared by mapping RNA-seq reads to the S. exigua reference genome. CYP9A40 was identified as a critical gene in diamide resistance due to its high expression in the resistant strains. Synergist bioassays with piperonyl butoxide supported the role of P450s in diamide metabolic resistance in S. exigua. A strong positive correlation between CYP9A40 over-expression levels (up to 80-fold) and diamide LC50 values was obtained for field-collected populations uniformly showing a 100% frequency of the RyR I4790M target-site resistance allele. To validate the function of CYP9A40 in diamide detoxification, we recombinantly expressed the gene and tested its ability to bind and degrade chlorantraniliprole as a substrate. The results confirmed its catalytic role in diamide metabolism. CYP9A40 has been identified and validated to confer metabolic resistance in Korean S. exigua populations. It works alongside the RyR target-site I4790M mutation to enhance diamide resistance. These mechanisms offer insights for resistance monitoring and support insecticide resistance management programs to improve control strategies for S. exigua. © 2024, The Authors. All rights reserved.

关键词： RNA

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Directional Sewage Sludge Transformation Using Acidic Hydrothermal Carbonization for Enhanced Alkaline Extraction of Phosphorus

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SSRN 2024年

作者： Tiwari, Satya Brat Veksha, Andrei Chan, Wei Ping Fei, Xunchang Liu, Wen Lisak, Grzegorz Lim, Teik-Thye School of Civil and Environmental Engineering Nanyang Technological University 50 Nanyang Avenue 639798 Singapore Nanyang Environment and Water Research Institute Nanyang Technological University 1 Cleantech Loop CleanTech One 637141 Singapore Interdisciplinary Graduate Program Nanyang Technological University Singapore School of Chemistry Chemical Engineering and Biotechnology Nanyang Technological University 62 Nanyang Drive 637459 Singapore

This study presents a two-stage process to recover phosphorus (P) from sewage sludge (SS) hydrochar, aimed at reducing trace element (TE) contamination. SS, mixed with Al-rich alum sludge (AS), underwent acidic HTC to convert Ca-P to Al-P. Alkaline extraction of hydrochar produced a P-rich, TE-deficient extract, as Al-P dissolves at high pH (> 12), leaving TEs insoluble. Optimal conditions for maximum P recovery were high temperature (~240°C), Al/P molar ratio (APMR) of ~4, and feedstock pH of ~3 – 4. This design process achieved 82% alkaline P recovery, 34% higher than the reference process. Overall P recovery ranged from 59 – 75% in the design process, compared to 30 – 37% in the reference process. Solid-state NMR revealed the Al-P association in hydrochar through surface complexation. TEs were mainly concentrated in the hydrochar, not the alkaline extract. This method offers a potentially cost-effective, and energy-efficient solution for P recovery. © 2024, The Authors. All rights reserved.

关键词： Heavy metals

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Pseudomonas aeruginosa-derived DnaJ induces TLR2 expression through TLR10-mediated activation of the PI3K-SGK1 pathway in macrophages

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Microbes and Infection 2025年第4期27卷 105481页

作者： Lee, Jaehoo Jin, Yongxin Wu, Weihui Lee, Yeji Ha, Un-Hwan Department of Biotechnology and Bioinformatics Korea University Sejong 30019 South Korea Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology Korea University Sejong 30019 South Korea State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education Department of Microbiology Nankai University Tianjin 300071 China

TLR2 is a key component of the innate immune system, responsible for recognizing Gram-positive bacterial components and initiating inflammatory signaling cascades that activate defense responses. However, little is known about the regulatory effects of Pseudomonas aeruginosa (P. aeruginosa) on TLR2 expression. In this study, we investigated the potential link between P. aeruginosa-derived DnaJ and TLR2 expression in macrophages, as well as the activation of downstream signaling pathways. Our findings revealed that DnaJ significantly induced TLR2 expression in a dose- and time-dependent manner, predominantly affecting TLR2 with minimal impact on other TLRs, such as TLR4 and TLR5, which detect bacterial PAMPs. The DnaJ-mediated TLR2 induction was driven by activation of the PI3K-SGK1 signaling pathway, with TLR10 playing a crucial role in facilitating these effects. This increase in TLR2 expression led to enhanced production of inflammatory cytokines in response to secondary Staphylococcus aureus infections, indicating a role in boosting host defense mechanisms. In conclusion, these findings suggest that P. aeruginosa-derived DnaJ promotes TLR2 expression via TLR10-mediated activation of the PI3K-SGK1 pathway, thereby enhancing host immune responses against Gram-positive bacterial infections. © 2025 Institut Pasteur

关键词： DnaJ Pseudomonas aeruginosa SGK1 TLR10 TLR2

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Structure-Based Optimization of Tead Inhibitors: Exploring a Novel Subpocket Near Glu347 for the Treatment of Nf2-Mutant Cancer

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SSRN 2024年

作者： Kim, Jin Kwan Kim, Jinhyuk Kim, Hadong Jin, Haiyan Yoo, Youngki Fei, Xiang Maeng, Han-Joo Seo, Seung-Yong Han, Gyoonhee No, Kyoung Tai Baobab AiBIO Co. Ltd. Incheon21983 Korea Republic of Gachon Institute of Pharmaceutical Sciences College of Pharmacy Gachon University Incheon21936 Korea Republic of Department of Integrative Biotechnology Yonsei University Incheon21983 Korea Republic of Incheon21983 Korea Republic of Department of Pharmacy College of Pharmacy Yonsei University Incheon21983 Korea Republic of Institute of Convergence Science and Technology Yonsei University Incheon21983 Korea Republic of Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine Korea Republic of

The Hippo pathway is a signaling pathway implicated in various diseases, including cancer, that regulates the levels of yes-associated protein (YAP) and PDZ-binding motif (TAZ) proteins. These proteins bind to transcriptional enhanced associate domain (TEAD) proteins and function as transcription factors in the nucleus, producing oncogenic target genes such as CTGF and CYR61. TEAD proteins require palmitoylation via a covalent bond with cysteine in the central pocket to bind YAP/TAZ. Therefore, competitive inhibition that prevents palmitoylation could serve as an effective anticancer strategy. In this study, we analyzed the crystal structures of known inhibitors to identify new binding spots that were previously unexplored, with the aim of discovering more potent compounds using structure-based drug design. Consequently, we identified a novel hydrogen-bonding site and discovered Compound 2, which effectively binds to this site, as confirmed by X-ray crystallography. Furthermore, Compound 2 exhibited stable pharmacokinetic properties and demonstrated impressive efficacy in a mouse xenograft model. © 2024, The Authors. All rights reserved.

关键词： Transcription

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Granular nanocellulose derived from sugarcane bagasse and corn stover: Production, characterization, and its potential for lipid hydrolysis reduction

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Carbohydrate Polymer Technologies and Applications 2025年 10卷

作者： Chumchoochart, Warathorn Ketvaraporn, Tullawat Chandet, Nopakarn Saenjum, Chalermpong Tinoi, Jidapha Interdisciplinary Program in Biotechnology Multidisciplinary and Interdisciplinary School Chiang Mai University Chiang Mai 50200 Thailand Department of Chemistry Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand Research Center for Innovation in Analytical Science and Technology for Biodiversity-based Economic and Society (I-ANALY-S-T_B.BES-CMU) Chiang Mai University Chiang Mai 50200 Thailand Department of Pharmaceutical Sciences Faculty of Pharmacy Chiang Mai University Chiang Mai 50200 Thailand

Nanocellulose is an emerging biomaterial with diverse applications, including its potential use in food systems. Granular nanocellulose (GNC), a unique form of nanocellulose, has limited studies in terms of its production and effects on lipid hydrolysis. This work aimed to develop GNC from sugarcane bagasse and corn stover cellulose fibers, characterize their physicochemical properties and assess their impact on lipid digestion. Cellulose fibers were extracted via alkaline treatment and bleaching, achieving a purity of 92.5–94.2 %. GNC was subsequently produced using enzymatic and oxalic acid hydrolysis. Enzymatic hydrolysis yielded 25–32 % GNC-E (295–342 nm) with good dispersibility (-49.0 mV zeta potential), moderate homogeneity (PDI ∼0.4), and low crystallinity (CrI 29–32 %). Oxalic acid hydrolysis generated smaller GNC[sbnd]Ox (∼200 nm) with 21–36 % yields, lower crystallinity (CrI 20–24 %), and high dispersibility (-36.2 to -39.7 mV). At 0.02 % (w/v), all GNC significantly inhibited lipase activity and olive oil hydrolysis (relative activity: 60 – 77 %). GNC[sbnd]Ox reduced lipase activity to 60 % via physical adsorption, while GNC-E from sugarcane bagasse exhibited the greatest inhibition of lipid hydrolysis (53 %) through steric hindrance. These findings suggest that GNC can be effectively produced and have potential applications as food additives to regulate lipid digestion. © 2025 The Authors

关键词： Cellulose Food additive Granular nanocellulose Lipase activity Lipid hydrolysis Nanocellulose

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