High-purity cellulose from paper pulp can be obtained after appropriate treatments involving pure xylanases and cellulases/endoglucanases. This study investigated the efficacy of using crude xylanase and cellulase instead of commercial ones to improve process economics. Kraft paper grade pulp produced from veneer waste, hardwood, and non-wood sources was utilized as a more sustainable option. Crude xylanase and cellulase from isolated soil bacteria Bacillus pumilus 3GAH and Bacillus subtilis PJK6 were used for process optimization. The correlation between Fock reactivity, chain scission, and crystallinity after crude-cellulase treatment was established through chemical, FTIR, and XRD analyses. Pentosans in kraft pulp were reduced from an initial 18.7% to 4.9% through sequential treatments with crude xylanase and alkali. Subsequent crude-cellulase treatment, even at 8 U/g o.d. pulp, improved Fock reactivity from 28.2% to 61.2%, fulfilling a major criterion for viscose. Thus, crude enzymes can be effectively used for the efficient and economical upgrading of paper pulp to dissolving pulp.
{"title":"Prospects of crude enzymes in replacing pure enzymes for dissolving pulp production","authors":"Prabhjot Kaur, Jitender Sharma, Nishi Kant Bhardwaj, Shubhang Bhardwaj, Daljeet Kaur, Amarjit Singh, Ashish Kumar","doi":"10.1007/s13205-024-04080-w","DOIUrl":"https://doi.org/10.1007/s13205-024-04080-w","url":null,"abstract":"<p>High-purity cellulose from paper pulp can be obtained after appropriate treatments involving pure xylanases and cellulases/endoglucanases. This study investigated the efficacy of using crude xylanase and cellulase instead of commercial ones to improve process economics. Kraft paper grade pulp produced from veneer waste, hardwood, and non-wood sources was utilized as a more sustainable option. Crude xylanase and cellulase from isolated soil bacteria <i>Bacillus pumilus</i> 3GAH and <i>Bacillus subtilis</i> PJK6 were used for process optimization. The correlation between Fock reactivity, chain scission, and crystallinity after crude-cellulase treatment was established through chemical, FTIR, and XRD analyses. Pentosans in kraft pulp were reduced from an initial 18.7% to 4.9% through sequential treatments with crude xylanase and alkali. Subsequent crude-cellulase treatment, even at 8 U/g o.d. pulp, improved Fock reactivity from 28.2% to 61.2%, fulfilling a major criterion for viscose. Thus, crude enzymes can be effectively used for the efficient and economical upgrading of paper pulp to dissolving pulp.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"68 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Endophytic fungal molecules have the potential to be a cost-effective chemical source for developing eco-friendly disease-controlling pharmaceuticals that target mosquito-borne illnesses. The primary aims of the study were to identify the fungus Fusarium begoniae larvicidal ability against Aedes aegypti, Culex quinquefasciatus, and Anopheles stephensi. The ethyl acetate extract demonstrated lethal concentrations that kill 50% of exposed larvae (LC50) and 90% of exposed larvae (LC90) for the 1st to 4th instar larvae of An. stephensi (LC50 = 54.821, 66.525, 68.250, and 73.614; LC90 = 104.56, 138.205, 150.415, and 159.466 μg/mL), Cx. quinquefasciatus (LC50 = 64.981, 36.505, 42.230, and 36.514; LC90 = 180.46, 157.105, 140.318, and 153.366 μg/ mL), and Ae. aegypti (LC50 = 74.890, 33.607, 52.173, and 26.974; LC90 = 202.56, 162.205, 130.518, and 163.286 μg/mL). Mycelium metabolites were evaluated for their pupicidal activity towards Ae. aegypti (LC50 = 80.669, LC90 = 119.904), Cx. quinquefasciatus (LC50 = 70.569, LC90 = 109.840), and An. stephensi (LC50 = 73.269, LC90 = 110.590 μg/mL). The highest larvicidal activity was recorded at 300 µg/mL, with 100% mortality against first and second-instar larvae of Cx. quinquefasciatus. Metabolite exposure to larvae exhibited several abnormal behavioral changes. The exposure to F. begoniae metabolite, key esterases such as acetylcholinesterase, α-and-β-carboxylesterase, and acid and alkaline phosphatase activity significantly decreased compared to control larvae. The outcomes of the histology analysis revealed that the mycelium metabolites-treated targeted larvae had a disorganized abdominal mid and hindgut epithelial cells. The is first-hand information on study of ethyl-acetate-derived metabolites from F. begoniae tested against larvae and pupae of Ae. aegypti, Cx. quinquefasciatus and An. stephensi. Bio-indicator toxicity findings demonstrate that A. nauplii displayed no mortality.
{"title":"Fusarium begoniae metabolites: a promising larvicidal, pupicidal potential, histopathological alterations and detoxifications enzyme profiles of medically important mosquito vector Aedes aegypti, Culex quinquefasciatus and Anopheles stephensi","authors":"Chinnasamy Ragavendran, Annadurai Govindaraj, Chinnaperumal Kamaraj, Devarajan Natarajan, Guilherme Malafaia, Abdulwahed Fahad Alrefaei, Mikhlid H. Almutairi","doi":"10.1007/s13205-024-04061-z","DOIUrl":"https://doi.org/10.1007/s13205-024-04061-z","url":null,"abstract":"<p>Endophytic fungal molecules have the potential to be a cost-effective chemical source for developing eco-friendly disease-controlling pharmaceuticals that target mosquito-borne illnesses. The primary aims of the study were to identify the fungus <i>Fusarium begoniae</i> larvicidal ability against <i>Aedes aegypti</i>, <i>Culex quinquefasciatus,</i> and <i>Anopheles stephensi.</i> The ethyl acetate extract demonstrated lethal concentrations that kill 50% of exposed larvae (LC<sub>50</sub>) and 90% of exposed larvae (LC<sub>90</sub>) for the 1st to 4th instar larvae of <i>An. stephensi</i> (LC<sub>50</sub> = 54.821, 66.525, 68.250, and 73.614; LC<sub>90</sub> = 104.56, 138.205, 150.415, and 159.466 μg/mL), <i>Cx. quinquefasciatus</i> (LC<sub>50</sub> = 64.981, 36.505, 42.230, and 36.514; LC<sub>90</sub> = 180.46, 157.105, 140.318, and 153.366 μg/ mL), and <i>Ae. aegypti</i> (LC<sub>50</sub> = 74.890, 33.607, 52.173, and 26.974; LC<sub>90</sub> = 202.56, 162.205, 130.518, and 163.286 μg/mL). Mycelium metabolites were evaluated for their pupicidal activity towards <i>Ae. aegypti</i> (LC<sub>50</sub> = 80.669, LC<sub>90</sub> = 119.904), <i>Cx. quinquefasciatus</i> (LC<sub>50</sub> = 70.569, LC<sub>90</sub> = 109.840), and <i>An. stephensi</i> (LC<sub>50</sub> = 73.269, LC<sub>90</sub> = 110.590 μg/mL). The highest larvicidal activity was recorded at 300 µg/mL, with 100% mortality against first and second-instar larvae of <i>Cx. quinquefasciatus</i>. Metabolite exposure to larvae exhibited several abnormal behavioral changes. The exposure to <i>F. begoniae</i> metabolite, key esterases such as acetylcholinesterase, α-and-β-carboxylesterase, and acid and alkaline phosphatase activity significantly decreased compared to control larvae. The outcomes of the histology analysis revealed that the mycelium metabolites-treated targeted larvae had a disorganized abdominal mid and hindgut epithelial cells. The is first-hand information on study of ethyl-acetate-derived metabolites from <i>F. begoniae</i> tested against larvae and pupae of <i>Ae. aegypti, Cx. quinquefasciatus</i> and <i>An. stephensi</i>. Bio-indicator toxicity findings demonstrate that <i>A. nauplii</i> displayed no mortality.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"126 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-08-24DOI: 10.1007/s13205-024-04040-4
C Shanmugaraj, Deeba Kamil, R Parimalan, Praveen Kumar Singh, P R Shashank, M A Iquebal, Zakir Hussain, Amrita Das, Robin Gogoi, K Nishmitha
Biological control agents are preferred over chemicals for managing plant diseases, with Trichoderma species being particularly effective against soil-borne pathogens. This study examines the use of a highly antagonistic strain, Trichoderma asperellum A10, and a virulent strain, Sclerotium rolfsii Sr38, identified and confirmed through ITS, β-tubulin (T. asperellum), TEF 1α, and RPB2 (S. rolfsii) sequences. In vitro and in planta experiments compared the antagonistic potential of A10 with other antagonistic fungi and fungicides against S. rolfsii. A10 achieved 94.66% inhibition of S. rolfsii in dual culture assays. In greenhouse trials with tomato variety Pusa Ruby, A10 showed significant pre- and post-inoculation effectiveness, with disease inhibition of 86.17 and 80.60%, respectively, outperforming T. harzianum, Propiconazole, and Carbendazim. Additionally, microbial priming with A10 was explored to enhance plant defense responses. Pre-treatment of tomato plants with T. asperellum A10 led to significant upregulation of several defense-related genes, including PR1, PR2, PR3, PR5, PR12, thioredoxin peroxidase, catalase, polyphenol oxidase, phenylalanine ammonia lyase, isochorismate synthase, laccase, prosystemin, multicystatin, WRKY31, MYC2, lipoxygenase A, lipoxygenase C, proteinase inhibitor I, proteinase inhibitor II, and ethylene response 1 associated with various signaling pathways such as salicylic acid (SA)-mediated and jasmonic acid/ethylene (JA/ET)-mediated responses. This upregulation was particularly evident at 48 h post-inoculation in A10-primed plants challenged with S. rolfsii, inducing resistance against collar rot disease. This study underscores the effectiveness of T. asperellum A10 in controlling collar rot and highlights its potential for inducing resistance in plants through microbial priming, providing valuable insights into sustainable disease management strategies.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04040-4.
在管理植物病害方面,生物防治剂比化学药剂更受青睐,其中毛霉菌种对土壤传播的病原体尤其有效。本研究考察了高度拮抗菌株毛霉 A10 和毒株 Sclerotium rolfsii Sr38 的使用情况,通过 ITS、β-微管蛋白(T. asperellum)、TEF 1α 和 RPB2(S. rolfsii)序列进行了鉴定和确认。体外和植物实验比较了 A10 与其他拮抗真菌和杀真菌剂对 S. rolfsii 的拮抗潜力。在双重培养试验中,A10 对 S. rolfsii 的抑制率达到 94.66%。在番茄品种 Pusa Ruby 的温室试验中,A10 在接种前和接种后都显示出显著的效果,病害抑制率分别为 86.17% 和 80.60%,优于 T. harzianum、丙环唑和多菌灵。此外,还探索了用 A10 进行微生物预处理以增强植物防御反应的方法。用 T. asperellum A10 对番茄植株进行预处理,可提高植株的防御能力。Asperellum A10 可显著上调多个防御相关基因,包括 PR1、PR2、PR3、PR5、PR12、硫氧还蛋白过氧化物酶、过氧化氢酶、多酚氧化酶、苯丙氨酸氨化酶、异喋脲酸合成酶、漆酶、原系统蛋白、多囊蛋白、WRKY31、MYC2、脂氧合酶 A、脂氧合酶 C、蛋白酶抑制剂 I、蛋白酶抑制剂 II 和乙烯反应 1 与水杨酸(SA)介导的反应和茉莉酸/乙烯(JA/ET)介导的反应等各种信号途径有关。在接种后 48 小时,这种上调在以 A10 为诱导剂、受到 S. rolfsii 挑战的植株中尤为明显,从而诱导植株产生抗领腐病的能力。这项研究强调了T. asperellum A10在控制领腐病方面的有效性,并突出了其通过微生物引诱诱导植物产生抗性的潜力,为可持续病害管理策略提供了宝贵的见解:在线版本包含补充材料,可查阅 10.1007/s13205-024-04040-4。
{"title":"Deciphering the defense response in tomato against <i>Sclerotium rolfsii</i> by <i>Trichoderma asperellum</i> strain A10 through gene expression analysis.","authors":"C Shanmugaraj, Deeba Kamil, R Parimalan, Praveen Kumar Singh, P R Shashank, M A Iquebal, Zakir Hussain, Amrita Das, Robin Gogoi, K Nishmitha","doi":"10.1007/s13205-024-04040-4","DOIUrl":"10.1007/s13205-024-04040-4","url":null,"abstract":"<p><p>Biological control agents are preferred over chemicals for managing plant diseases, with <i>Trichoderma</i> species being particularly effective against soil-borne pathogens. This study examines the use of a highly antagonistic strain, <i>Trichoderma asperellum</i> A10, and a virulent strain, <i>Sclerotium rolfsii</i> Sr38, identified and confirmed through ITS, β-tubulin (<i>T. asperellum</i>), TEF 1α, and RPB2 (<i>S. rolfsii</i>) sequences. In vitro and in planta experiments compared the antagonistic potential of A10 with other antagonistic fungi and fungicides against <i>S. rolfsii</i>. A10 achieved 94.66% inhibition of <i>S. rolfsii</i> in dual culture assays. In greenhouse trials with tomato variety Pusa Ruby, A10 showed significant pre- and post-inoculation effectiveness, with disease inhibition of 86.17 and 80.60%, respectively, outperforming <i>T. harzianum</i>, Propiconazole, and Carbendazim. Additionally, microbial priming with A10 was explored to enhance plant defense responses. Pre-treatment of tomato plants with <i>T. asperellum</i> A10 led to significant upregulation of several defense-related genes, including PR1, PR2, PR3, PR5, PR12, thioredoxin peroxidase, catalase, polyphenol oxidase, phenylalanine ammonia lyase, isochorismate synthase, laccase, prosystemin, multicystatin, WRKY31, MYC2, lipoxygenase A, lipoxygenase C, proteinase inhibitor I, proteinase inhibitor II, and ethylene response 1 associated with various signaling pathways such as salicylic acid (SA)-mediated and jasmonic acid/ethylene (JA/ET)-mediated responses. This upregulation was particularly evident at 48 h post-inoculation in A10-primed plants challenged with <i>S. rolfsii</i>, inducing resistance against collar rot disease. This study underscores the effectiveness of <i>T. asperellum</i> A10 in controlling collar rot and highlights its potential for inducing resistance in plants through microbial priming, providing valuable insights into sustainable disease management strategies.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04040-4.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"210"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11344752/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-08-30DOI: 10.1007/s13205-024-04056-w
Asma Hatami
Medicinal plants, renowned for their antibacterial phytocompounds and secondary metabolites, hold significant promise in addressing antibiotic-resistant bacterial strains. This study aimed to conduct phytochemical profiling of the methanolic and dichloromethane extracts of Ziziphora tenuior root using the GC-MS technique. These extracts' antioxidant potential was assessed via DPPH assay and their antibacterial activity was evaluated against S. aureus, E. coli, and VRE bacterial strains. Furthermore, the drug-ligand interactions between the extracts' biocompounds and d-alanyl-d-lactate ligase (VanA) protein of vancomycin-resistant enterococci strains (VRE) were analyzed using molecular docking. Based on the results, 74% of methanolic extract consisted of (3methyl, 24S)-stigmast-5-en-3-ol (which is a β-sitosterol), followed by Tetrasiloxane, decamethyl (15.5%), and 1-methyl-4-phenyl-5-thioxo-1,2,4-triazolidin-3-one (10.5%). Also, the only predominant compound identified in the dichloromethane extract was Benzo[h]quinoline, 2,4-dimethyl-. Both extracts showed antioxidant activity, while the antioxidant activity of the methanolic extract (IC50 = 95.33 μg/ml) was significantly higher than that of the dichloromethane extract (IC50 = 934.23 μg/ml). Also, both extracts displayed substantial antibacterial efficacy against the tested pathogens, particularly against VRE. Moreover, the in silico analysis revealed that (3methyl, 24S)-stigmast-5-en-3-ol and Benzo[h]quinoline,2,4-dimethyl- exhibited notable interactions with VanA through docking energy values of - 9.0 and - 9.1 kcal/mol, respectively. Furthermore, these compounds formed 2 and 1 hydrogen bonds with VanA, respectively, highlighting their potential as effective interactants. These findings provide valuable visions into the therapeutic potentials of these plant-derived biocompounds in combating antibiotic-resistant bacterial infections.
{"title":"Phytochemical profiling and antibacterial activities of <i>Ziziphora tenuior</i> root extracts: a molecular docking against VanA of vancomycin-resistant enterococci.","authors":"Asma Hatami","doi":"10.1007/s13205-024-04056-w","DOIUrl":"10.1007/s13205-024-04056-w","url":null,"abstract":"<p><p>Medicinal plants, renowned for their antibacterial phytocompounds and secondary metabolites, hold significant promise in addressing antibiotic-resistant bacterial strains. This study aimed to conduct phytochemical profiling of the methanolic and dichloromethane extracts of <i>Ziziphora tenuior</i> root using the GC-MS technique. These extracts' antioxidant potential was assessed via DPPH assay and their antibacterial activity was evaluated against <i>S. aureus</i>, <i>E. coli</i>, and VRE bacterial strains. Furthermore, the drug-ligand interactions between the extracts' biocompounds and d-alanyl-d-lactate ligase (VanA) protein of vancomycin-resistant enterococci strains (VRE) were analyzed using molecular docking. Based on the results, 74% of methanolic extract consisted of (3methyl, 24S)-stigmast-5-en-3-ol (which is a β-sitosterol), followed by Tetrasiloxane, decamethyl (15.5%), and 1-methyl-4-phenyl-5-thioxo-1,2,4-triazolidin-3-one (10.5%). Also, the only predominant compound identified in the dichloromethane extract was Benzo[h]quinoline, 2,4-dimethyl-. Both extracts showed antioxidant activity, while the antioxidant activity of the methanolic extract (IC<sub>50</sub> = 95.33 μg/ml) was significantly higher than that of the dichloromethane extract (IC<sub>50</sub> = 934.23 μg/ml). Also, both extracts displayed substantial antibacterial efficacy against the tested pathogens, particularly against VRE. Moreover, the in silico analysis revealed that (3methyl, 24S)-stigmast-5-en-3-ol and Benzo[h]quinoline,2,4-dimethyl- exhibited notable interactions with VanA through docking energy values of - 9.0 and - 9.1 kcal/mol, respectively. Furthermore, these compounds formed 2 and 1 hydrogen bonds with VanA, respectively, highlighting their potential as effective interactants. These findings provide valuable visions into the therapeutic potentials of these plant-derived biocompounds in combating antibiotic-resistant bacterial infections.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"217"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11362404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The biocatalytic degradation of poly(ethylene terephthalate) (PET) through enzymatic methods has garnered considerable attention due to its environmentally friendly and non-polluting nature, as well as its high specificity. While previous efforts in enhancing IsPETase performance have focused on amino acid substitutions in protein engineering, we introduced an amino acid insertion strategy in this work. By inserting a negatively charged acidic amino acid, Glu, at the right-angle bend of IsPETase, the binding capability between the enzyme's active pocket and PET was improved. The resulted mutant IsPETase9394insE exhibited enhanced hydrolytic activity towards PET at various temperatures ranging from 30 to 45 ℃ compared with the wild-type IsPETase. Notably, a 10.04-fold increase was observed at 45 ℃. To further enhance PET hydrolysis, different carbohydrate-binding modules (CBMs) were incorporated at the C-terminus of IsPETase9394insE. Among these, the fusion of CBM from Verrucosispora sioxanthis exhibited the highest enhancement, resulting in a 1.82-fold increase in PET hydrolytic activity at 37 ℃ compared with the IsPETase9394insE. Finally, the engineered variant was successfully employed for the degradation of polyester filter cloth, demonstrating its promising hydrolytic capacity. In conclusion, this research presents an alternative enzyme engineering strategy for modifying PETases and enriches the pool of potential candidates for industrial PET degradation.
通过酶法生物催化降解聚对苯二甲酸乙二酯(PET)因其环境友好、无污染以及高特异性而备受关注。以往提高 IsPET 酶性能的方法主要是在蛋白质工程中进行氨基酸置换,而我们在这项工作中引入了氨基酸插入策略。通过在 IsPETase 的直角弯曲处插入一个带负电荷的酸性氨基酸 Glu,提高了酶的活性口袋与 PET 之间的结合能力。与野生型 IsPETase 相比,得到的突变体 IsPETase9394insE 在 30 至 45 ℃ 的不同温度下对 PET 的水解活性都有所提高。值得注意的是,在 45 ℃ 时,活性提高了 10.04 倍。为了进一步加强 PET 的水解,在 IsPETase9394insE 的 C 端加入了不同的碳水化合物结合模块(CBM)。其中,融合来自 Verrucosispora sioxanthis 的 CBM 的效果最好,与 IsPETase9394insE 相比,37 ℃ 下的 PET 水解活性提高了 1.82 倍。最后,该工程变体被成功用于降解聚酯滤布,证明其具有良好的水解能力。总之,这项研究为改造 PET 酶提供了另一种酶工程策略,并丰富了工业 PET 降解的潜在候选酶库。
{"title":"Enhancement of the degradation capacity of <i>Is</i>PETase by acidic amino acids insertion and carbohydrate-binding module fusion.","authors":"Chuang Li, Qingqing Zheng, Wei Liu, Quanyu Zhao, Ling Jiang","doi":"10.1007/s13205-024-04041-3","DOIUrl":"10.1007/s13205-024-04041-3","url":null,"abstract":"<p><p>The biocatalytic degradation of poly(ethylene terephthalate) (PET) through enzymatic methods has garnered considerable attention due to its environmentally friendly and non-polluting nature, as well as its high specificity. While previous efforts in enhancing <i>Is</i>PETase performance have focused on amino acid substitutions in protein engineering, we introduced an amino acid insertion strategy in this work. By inserting a negatively charged acidic amino acid, Glu, at the right-angle bend of <i>Is</i>PETase, the binding capability between the enzyme's active pocket and PET was improved. The resulted mutant <i>Is</i>PETase<sup>9394insE</sup> exhibited enhanced hydrolytic activity towards PET at various temperatures ranging from 30 to 45 ℃ compared with the wild-type <i>Is</i>PETase. Notably, a 10.04-fold increase was observed at 45 ℃. To further enhance PET hydrolysis, different carbohydrate-binding modules (CBMs) were incorporated at the C-terminus of <i>Is</i>PETase<sup>9394insE</sup>. Among these, the fusion of CBM from <i>Verrucosispora sioxanthis</i> exhibited the highest enhancement, resulting in a 1.82-fold increase in PET hydrolytic activity at 37 ℃ compared with the <i>Is</i>PETase<sup>9394insE</sup>. Finally, the engineered variant was successfully employed for the degradation of polyester filter cloth, demonstrating its promising hydrolytic capacity. In conclusion, this research presents an alternative enzyme engineering strategy for modifying PETases and enriches the pool of potential candidates for industrial PET degradation.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"195"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11306670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-08-18DOI: 10.1007/s13205-024-04052-0
Jun Xu, Shuangwei Liu, Yueming Ren, Yang You, Zhifang Wang, Yongqiang Zhang, Xinjie Zhu, Ping Hu
Heat shock protein 90 (HSP90) is important for many organisms, including plants. Based on the whole genome information, the gene number, gene structure, evolutionary relationship, protein structure, and active site of the HSP90 gene family in Rosa chinensis and Rubus idaeus were determined, and the expression of the HSP90 gene under salt, and drought stresses in two rose varieties Wangxifeng and Sweet Avalanche were analyzed. Six and eight HSP90 genes were identified from R. chinensis and Ru. idaeus, respectively. Phylogenetic analysis revealed that the analyzed genes were divided into two Groups and four subgroups (Classes 1a, 1b, 2a, and 2b). Although members within the same classes displayed highly similar gene structures, while the gene structures and conserved domains of Group 1 (Class 1a and 1b) and the Group 2 (Class 2a and 2b) are different. Tandem and segmental duplication genes were found in Ru. idaeus, but not in R. chinensis, perhaps explaining the difference in HSP90 gene quantity in the two analyzed species. Analysis of cis-acting elements revealed abundant abiotic stress, photolight-response, and hormone-response elements in R. chinensis HSP90s. qRT-PCR analysis suggested that RcHSP90-1-1, RcHSP90-5-1 and RcHSP90-6-1 in Sweet Avalanche and Wangxifeng varieties played important regulatory roles under salt and drought stress. The analysis of protein structure and active sites indicate that the potential different roles of RcHSP90-1-1, RcHSP90-5-1, and RcHSP90-6-1 in salt and drought stresses may come from the differences of corresponding protein structures and activation sites. These data will provide information for the breeding of rose varieties with high stress resistance.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04052-0.
{"title":"Genome-wide identification of <i>HSP90</i> gene family in <i>Rosa chinensis</i> and its response to salt and drought stresses.","authors":"Jun Xu, Shuangwei Liu, Yueming Ren, Yang You, Zhifang Wang, Yongqiang Zhang, Xinjie Zhu, Ping Hu","doi":"10.1007/s13205-024-04052-0","DOIUrl":"10.1007/s13205-024-04052-0","url":null,"abstract":"<p><p>Heat shock protein 90 (HSP90) is important for many organisms, including plants. Based on the whole genome information, the gene number, gene structure, evolutionary relationship, protein structure, and active site of the HSP90 gene family in <i>Rosa chinensis</i> and <i>Rubus idaeus</i> were determined, and the expression of the <i>HSP90</i> gene under salt, and drought stresses in two rose varieties Wangxifeng and Sweet Avalanche were analyzed. Six and eight <i>HSP90</i> genes were identified from <i>R. chinensis</i> and <i>Ru. idaeus</i>, respectively. Phylogenetic analysis revealed that the analyzed genes were divided into two Groups and four subgroups (Classes 1a, 1b, 2a, and 2b). Although members within the same classes displayed highly similar gene structures, while the gene structures and conserved domains of Group 1 (Class 1a and 1b) and the Group 2 (Class 2a and 2b) are different. Tandem and segmental duplication genes were found in <i>Ru. idaeus</i>, but not in <i>R. chinensis</i>, perhaps explaining the difference in <i>HSP90</i> gene quantity in the two analyzed species. Analysis of cis-acting elements revealed abundant abiotic stress, photolight-response, and hormone-response elements in <i>R. chinensis</i> HSP90s. qRT-PCR analysis suggested that <i>RcHSP90-1-1</i>, <i>RcHSP90-5-1</i> and <i>RcHSP90-6-1</i> in Sweet Avalanche and Wangxifeng varieties played important regulatory roles under salt and drought stress. The analysis of protein structure and active sites indicate that the potential different roles of <i>RcHSP90-1-1</i>, <i>RcHSP90-5-1</i>, and <i>RcHSP90-6-1</i> in salt and drought stresses may come from the differences of corresponding protein structures and activation sites. These data will provide information for the breeding of rose varieties with high stress resistance.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04052-0.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"204"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11330952/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-08-23DOI: 10.1007/s13205-024-04044-0
Nguyen Huy Thuan, Quach Thi Thu Huong, Bui Dinh Lam, Ho Thanh Tam, Pham The Thu, Nguyen Xuan Canh, Vinay Bharadwaj Tatipamula
Currently, numerous glycosides have been synthesized and used in clinical applications, neutraceuticals, cosmetics, and food processing. Structurally, a glycoside is composed of aglycone attaching to one or several sugar moieties so-called glycone. It is found that biochemical or biopharmaceutical properties of glycoside are mainly determined by its sugar part and thereby alternation of this glycone resulting in novel structure and characteristics as well. The use of traditional production methods of glycosides such as direct extraction and purification from plants, animals, or microorganisms is very challenging (laborious, time-consuming, technique, high price, low yield, etc.). Alternatively, the use of enzymatic methods for the biosynthesis of glycosides has become a highly promising tool. Particularly, the diverse structure of glycosides can be obtained using the promiscuous catalytic activity of glycosyltransferases (GT) mined from bioresources (plants, fungi, microorganisms, etc.). In addition, the exploration of GT catalytic promiscuity toward diverse aglycones, and glycones has indeed been interesting and played a key role in the production of novel glycosides. This review described the recent advances in glycosyltransferase-mediated glycodiversification of small molecules (flavonoids, steroids, terpenoids, etc.). Mostly, references were collected from 2014 to 2023.
{"title":"Advances in glycosyltransferase-mediated glycodiversification of small molecules.","authors":"Nguyen Huy Thuan, Quach Thi Thu Huong, Bui Dinh Lam, Ho Thanh Tam, Pham The Thu, Nguyen Xuan Canh, Vinay Bharadwaj Tatipamula","doi":"10.1007/s13205-024-04044-0","DOIUrl":"10.1007/s13205-024-04044-0","url":null,"abstract":"<p><p>Currently, numerous glycosides have been synthesized and used in clinical applications, neutraceuticals, cosmetics, and food processing. Structurally, a glycoside is composed of aglycone attaching to one or several sugar moieties so-called glycone. It is found that biochemical or biopharmaceutical properties of glycoside are mainly determined by its sugar part and thereby alternation of this glycone resulting in novel structure and characteristics as well. The use of traditional production methods of glycosides such as direct extraction and purification from plants, animals, or microorganisms is very challenging (laborious, time-consuming, technique, high price, low yield, etc.). Alternatively, the use of enzymatic methods for the biosynthesis of glycosides has become a highly promising tool. Particularly, the diverse structure of glycosides can be obtained using the promiscuous catalytic activity of glycosyltransferases (GT) mined from bioresources (plants, fungi, microorganisms, etc.). In addition, the exploration of GT catalytic promiscuity toward diverse aglycones, and glycones has indeed been interesting and played a key role in the production of novel glycosides. This review described the recent advances in glycosyltransferase-mediated glycodiversification of small molecules (flavonoids, steroids, terpenoids, etc.). Mostly, references were collected from 2014 to 2023.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"209"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11343957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-08-07DOI: 10.1007/s13205-024-04030-6
A S Rahul Dev, S Harish, G Karthikeyan, M Nivedha, C Sangeetha
In the present study, Streptomyces spp. were isolated, characterized, and the efficacy was tested against Groundnut bud necrosis orthotospovirus (GBNV) in tomato. Among the three inoculation methods viz., pre-, post-, and simultaneous inoculation, tested for antiviral efficacy, pre-inoculation spray of the three Streptomyces spp. viz., Streptomyces mutabilis, Streptomyces rochei, and Streptomyces chrestomyceticus (SAT1, SAT4, and STR2) recorded the least disease severity index (DSI) of GBNV in tomato. In the pot culture, seed treatment of liquid consortium of three Streptomyces spp. @ 2 ml/g of seeds along with seedling dip at 10 ml/lit followed by soil drenching at 10 ml/lit on 7 days after transplanting (DAT) and foliar application at 0.5% on 15 DAT, 30 DAT, and 45 DAT recorded the least GBNV infection of 15% DSI and 16.67% DSI in trial I and II respectively. Besides, under field conditions, the disease incidence was reduced to 14.44% recording a higher yield of 76.67 t/ha in the treated plants against 63.99 t/ha in control. Upregulation of defense genes viz., PR1, PR2, PR6, WRKY, MAPKK, and NPR1 during tripartite interaction between tomato, Streptomyces, and GBNV was analyzed by qRTPCR, indicating that the consortia could decrease the virus severity through induced systemic resistance pathways. Thus, it is concluded that Streptomyces spp. can be used for the management of GBNV in tomato.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04030-6.
{"title":"Consortia of <i>Streptomyces</i> spp. triggers defense/PAMP genes during the interaction of <i>Groundnut bud</i> <i>necrosis</i> <i>orthotospovirus</i> in tomato.","authors":"A S Rahul Dev, S Harish, G Karthikeyan, M Nivedha, C Sangeetha","doi":"10.1007/s13205-024-04030-6","DOIUrl":"10.1007/s13205-024-04030-6","url":null,"abstract":"<p><p>In the present study, <i>Streptomyces</i> spp. were isolated, characterized, and the efficacy was tested against <i>Groundnut bud necrosis orthotospovirus</i> (GBNV) in tomato. Among the three inoculation methods viz., pre-, post-, and simultaneous inoculation, tested for antiviral efficacy, pre-inoculation spray of the three <i>Streptomyces</i> spp. viz., <i>Streptomyces mutabilis, Streptomyces rochei,</i> and <i>Streptomyces chrestomyceticus</i> (SAT1, SAT4, and STR2) recorded the least disease severity index (DSI) of GBNV in tomato. In the pot culture, seed treatment of liquid consortium of three <i>Streptomyces</i> spp. @ 2 ml/g of seeds along with seedling dip at 10 ml/lit followed by soil drenching at 10 ml/lit on 7 days after transplanting (DAT) and foliar application at 0.5% on 15 DAT, 30 DAT, and 45 DAT recorded the least GBNV infection of 15% DSI and 16.67% DSI in trial I and II respectively. Besides, under field conditions, the disease incidence was reduced to 14.44% recording a higher yield of 76.67 t/ha in the treated plants against 63.99 t/ha in control. Upregulation of defense genes viz., PR1, PR2, PR6, WRKY, MAPKK, and NPR1 during tripartite interaction between tomato, <i>Streptomyces</i>, and GBNV was analyzed by qRTPCR, indicating that the consortia could decrease the virus severity through induced systemic resistance pathways. Thus, it is concluded that <i>Streptomyces</i> spp. can be used for the management of GBNV in tomato.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04030-6.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"196"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11306705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-08-15DOI: 10.1007/s13205-024-04037-z
Hui Xu, Hong-Ye Zheng, Chang-Hong Liu
Synthetic dyes pose a significant environmental threat due to their complex structures and resistance to microbial degradation. S. commune 15R-5-F01 exhibited over 96% degradation efficiency of Methyl Red in a medium with 100 mg L-1 Methyl Red within 3 h. The fungus demonstrated adaptability to various environmental conditions, including different pH levels, temperatures, oxygen concentrations, salinity, and heavy metals. S. commune 15R-5-F01 is capable of achieving repeated cycles of Methyl Red reduction with sustained degradation duration minimum of 6 cycles. It showed a maximum Methyl Red biodegradation capacity of at least 558 mg g-1 dry mycelia and a bioadsorption capacity of 57 mg g-1. Gas chromatography-mass spectrometry analysis confirmed the azo reduction of Methyl Red into N,N-dimethyl-p-phenylenediamine and 2-aminobenzoic acid. Enzymatic activity assays indicated the involvement of lignin peroxidases, laccases, and manganese peroxidase in the biodegradation process. Phytotoxicity tests on Triticum eastivum, Oryza sativa, and Vigna umbellata seeds revealed reduced toxicity of the degradation products compared to Methyl Red. This study identifies S. commune 15R-5-F01 as a viable candidate for the sustainable degradation of synthetic dyes in industrial wastewater.
合成染料因其复杂的结构和对微生物降解的抗性而对环境构成严重威胁。在含有 100 mg L-1 甲基红的培养基中,S. commune 15R-5-F01 真菌在 3 小时内对甲基红的降解效率超过 96%。该真菌表现出对各种环境条件的适应性,包括不同的 pH 值、温度、氧气浓度、盐度和重金属。S. commune 15R-5-F01 能够反复循环还原甲基红,持续降解时间最少为 6 个循环。它的最大甲基红生物降解能力至少为 558 毫克 g-1 干菌丝体,生物吸附能力为 57 毫克 g-1。气相色谱-质谱分析证实,甲基红被还原成 N,N-二甲基对苯二胺和 2-氨基苯甲酸。酶活性测定表明,木质素过氧化物酶、木质素酶和锰过氧化物酶参与了生物降解过程。对东亚小麦、大米和伞形木葡萄种子进行的植物毒性测试表明,与甲基红相比,降解产物的毒性有所降低。这项研究将 S. commune 15R-5-F01 确定为可持续降解工业废水中合成染料的可行候选物。
{"title":"Methyl Red degradation by a subseafloor fungus <i>Schizophyllum commune</i> 15R-5-F01: efficiency, pathway, and product toxicity.","authors":"Hui Xu, Hong-Ye Zheng, Chang-Hong Liu","doi":"10.1007/s13205-024-04037-z","DOIUrl":"10.1007/s13205-024-04037-z","url":null,"abstract":"<p><p>Synthetic dyes pose a significant environmental threat due to their complex structures and resistance to microbial degradation. <i>S. commune</i> 15R-5-F01 exhibited over 96% degradation efficiency of Methyl Red in a medium with 100 mg L<sup>-1</sup> Methyl Red within 3 h. The fungus demonstrated adaptability to various environmental conditions, including different pH levels, temperatures, oxygen concentrations, salinity, and heavy metals. <i>S. commune</i> 15R-5-F01 is capable of achieving repeated cycles of Methyl Red reduction with sustained degradation duration minimum of 6 cycles. It showed a maximum Methyl Red biodegradation capacity of at least 558 mg g<sup>-1</sup> dry mycelia and a bioadsorption capacity of 57 mg g<sup>-1</sup>. Gas chromatography-mass spectrometry analysis confirmed the azo reduction of Methyl Red into N,N-dimethyl-p-phenylenediamine and 2-aminobenzoic acid. Enzymatic activity assays indicated the involvement of lignin peroxidases, laccases, and manganese peroxidase in the biodegradation process. Phytotoxicity tests on <i>Triticum eastivum</i>, <i>Oryza sativa</i>, and <i>Vigna umbellata</i> seeds revealed reduced toxicity of the degradation products compared to Methyl Red. This study identifies <i>S. commune</i> 15R-5-F01 as a viable candidate for the sustainable degradation of synthetic dyes in industrial wastewater.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"202"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11327228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-08-24DOI: 10.1007/s13205-024-04057-9
Chandra Devi, Prashant Ranjan, Sonam Raj, Parimal Das
We analyzed the impact of nine previously identified missense PKD1 variants from our studies, including c.6928G > A p.G2310R, c.8809G > A p.E2937K, c.2899 T > C p.W967R, c.6284A > G p.D2095G, c.6644G > A p.R2215Q, c.7810G > A p.D2604N, c.11249G > C p.R3750P, c.1001C > T p.T334M, and c.3101A > G p.N1034S on RNA structures and PC1 protein structure dynamics utilizing computational tools. RNA structure analysis was done using short RNA snippets of 41 nucleotides with the variant position at the 21st nucleotide, ensuring 20 bases on both sides. The secondary structures of these RNA snippets were predicted using RNAstructure. Structural changes of the mutants compared to the wild type were analyzed using the MutaRNA webserver. Molecular dynamics (MD) simulation of PC1 wild-type and mutant protein regions were performed using GROMACS 2018 (GROMOS96 54a7 force field). Findings revealed that five variants including c.8809G > A (p.E2937K), c.11249G > C (p.R3750P), c.3101A > G (p.N1034S), c.6928G > A (p.G2310R), c.6644G > A (p.R2215Q) exhibited major alterations in RNA structures and thereby their interactions with other proteins or RNAs affecting protein structure dynamics. While certain variants have minimal impact on RNA conformations, their observed alterations in MD simulations indicate impact on protein structure dynamics highlighting the importance of evaluating the functional consequences of genetic variants by considering both RNA and protein levels. The study also emphasizes that each missense variant exerts a unique impact on RNA stability, and protein structure dynamics, potentially contributing to the heterogeneous clinical manifestations and progression observed in Autosomal Dominant Polycystic Kidney Disease (ADPKD) patients offering a novel perspective in this direction. Thus, the utility of studying the structure dynamics through computational tools can help in prioritizing the variants for their functional implications, understanding the molecular mechanisms underlying variability in ADPKD presentation and developing targeted therapeutic interventions.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04057-9.
我们分析了之前研究中发现的 9 个 PKD1 错义变异的影响,包括 c.6928G > A p.G2310R、c.8809G > A p.E2937K、c.2899 T > C p.W967R、c.6284A > G p.D2095G、c.6644G > A p.R2215Q、c.7810G > A p.D2604N、c.11249G > C p.R3750P、c.1001C > T p.T334M,以及 c.3101A > G p.N1034S。RNA 结构分析使用的是 41 个核苷酸的短 RNA 片段,变异位置位于第 21 个核苷酸,确保两侧各有 20 个碱基。使用 RNAstructure 预测了这些 RNA 片段的二级结构。利用 MutaRNA 网络服务器分析了突变体与野生型相比的结构变化。使用 GROMACS 2018(GROMOS96 54a7 力场)对 PC1 野生型和突变体蛋白质区域进行了分子动力学(MD)模拟。研究结果显示,包括 c.8809G > A (p.E2937K), c.11249G > C (p.R3750P), c.3101A > G (p.N1034S), c.6928G > A (p.G2310R), c.6644G > A (p.R2215Q) 在内的五个变异体的 RNA 结构发生了重大改变,从而影响了它们与其他蛋白质或 RNA 的相互作用,进而影响了蛋白质结构动力学。虽然某些变体对 RNA 构象的影响微乎其微,但在 MD 模拟中观察到的变化表明它们对蛋白质结构动态产生了影响,这突出了通过考虑 RNA 和蛋白质水平来评估基因变体功能后果的重要性。该研究还强调,每种错义变体都对 RNA 稳定性和蛋白质结构动态产生独特的影响,这可能是导致常染色体显性多囊肾(ADPKD)患者出现不同临床表现和病情进展的原因之一,为研究提供了一个新的视角。因此,通过计算工具研究结构动态有助于确定变异的优先次序,了解ADPKD表现变异的分子机制,并开发有针对性的治疗干预措施:在线版本包含补充材料,可查阅 10.1007/s13205-024-04057-9。
{"title":"Computational exploration of protein structure dynamics and RNA structural consequences of <i>PKD1</i> missense variants: implications in ADPKD pathogenesis.","authors":"Chandra Devi, Prashant Ranjan, Sonam Raj, Parimal Das","doi":"10.1007/s13205-024-04057-9","DOIUrl":"10.1007/s13205-024-04057-9","url":null,"abstract":"<p><p>We analyzed the impact of nine previously identified missense <i>PKD1</i> variants from our studies, including c.6928G > A p.G2310R, c.8809G > A p.E2937K, c.2899 T > C p.W967R, c.6284A > G p.D2095G, c.6644G > A p.R2215Q, c.7810G > A p.D2604N, c.11249G > C p.R3750P, c.1001C > T p.T334M, and c.3101A > G p.N1034S on RNA structures and PC1 protein structure dynamics utilizing computational tools. RNA structure analysis was done using short RNA snippets of 41 nucleotides with the variant position at the 21st nucleotide, ensuring 20 bases on both sides. The secondary structures of these RNA snippets were predicted using RNAstructure. Structural changes of the mutants compared to the wild type were analyzed using the MutaRNA webserver. Molecular dynamics (MD) simulation of PC1 wild-type and mutant protein regions were performed using GROMACS 2018 (GROMOS96 54a7 force field). Findings revealed that five variants including c.8809G > A (p.E2937K), c.11249G > C (p.R3750P), c.3101A > G (p.N1034S), c.6928G > A (p.G2310R), c.6644G > A (p.R2215Q) exhibited major alterations in RNA structures and thereby their interactions with other proteins or RNAs affecting protein structure dynamics. While certain variants have minimal impact on RNA conformations, their observed alterations in MD simulations indicate impact on protein structure dynamics highlighting the importance of evaluating the functional consequences of genetic variants by considering both RNA and protein levels. The study also emphasizes that each missense variant exerts a unique impact on RNA stability, and protein structure dynamics, potentially contributing to the heterogeneous clinical manifestations and progression observed in Autosomal Dominant Polycystic Kidney Disease (ADPKD) patients offering a novel perspective in this direction. Thus, the utility of studying the structure dynamics through computational tools can help in prioritizing the variants for their functional implications, understanding the molecular mechanisms underlying variability in ADPKD presentation and developing targeted therapeutic interventions.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04057-9.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"211"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11344749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}