Biotechnology Letters最新文献

{"title":"High-yield magnetosome production of Magnetospirillum magneticum strain AMB-1 in flask fermentation through simplified processing and optimized iron supplementation.","authors":"Yu Wang, Zhengyi Liu, Wenjun Li, Hongli Cui, Yandi Huang, Song Qin","doi":"10.1007/s10529-024-03507-x","DOIUrl":"10.1007/s10529-024-03507-x","url":null,"abstract":"<p><strong>Objectives: </strong>Developing a simplified flask fermentation strategy utilizing magnetotactic bacterium AMB-1 and optimized iron supplementation for high-yield magnetosome production to address the challenges associated with magnetosome acquisition.</p><p><strong>Results: </strong>A reliable processing for the pure culture of AMB-1 was established using standard laboratory consumables and equipment. Subsequently, the medium and iron supplementation were optimized to enhance the yield of AMB-1 magnetosomes. The mSLM supported higher biomass accumulation in flask fermentation, reaching an OD₅₆₅ of ~ 0.7. The premixed solution of ferric quinate and EDTA-Fe (at a ratio of 0.5:0.5 and a concentration of 0.4 mmol/L) stabilized Fe³⁺ and significantly increased the reductase activity of AMB-1. Flask fermentations with an initial volume of 15 L were then conducted employing the optimized fermentation strategy. After two rounds of iron and nutrient supplementation, the magnetosome yield reached 185.7 ± 9.5 mg/batch (approximately 12 mg/L), representing the highest AMB-1 flask fermentation yield to our knowledge.</p><p><strong>Conclusion: </strong>A flask fermentation strategy for high-yield magnetsome production was developed, eliminating the need for bioreactors and greatly simplifying the process of magnetosome acquisition.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"1069-1083"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141730993","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}

{"title":"A key component Rxt3 in the Rpd3L histone deacetylase complex regulates development, stress tolerance, amylase production and kojic acid synthesis in Aspergillus oryzae.","authors":"Chaofeng Chang, Herui Wang, Yiling Liu, Yiting Xie, Dingxiang Xue, Feng Zhang","doi":"10.1007/s10529-024-03515-x","DOIUrl":"10.1007/s10529-024-03515-x","url":null,"abstract":"<p><p>Rpd3L is a highly conserved histone deacetylase complex in eukaryotic cells and participates in various cellular processes. However, the roles of the Rpd3L component in filamentous fungi remain to be delineated ultimately. In this study, we constructed two knockout mutants of Rpd3L's Rxt3 subunit and characterized their biological functions in A. oryzae. Phenotypic analysis showed that AoRxt3 played a positive role in hyphal growth and conidia formation. Deletion of Aorxt3 resulted in augmented tolerance to multiple stresses, including cell wall stress, cell membrane stress, endoplasmic reticulum stress, osmotic stress and oxidative stress. Noteworthily, we found that Aorxt3-deleting mutants showed a higher kojic acid production than the control strain. However, the loss of Aorxt3 led to a significant decrease in amylase synthesis. Our findings lay the foundation for further exploring the role of other Rpd3L subunits and provide a new strategy to improve kojic acid production in A. oryzae.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"1121-1131"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854652","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}

{"title":"Efficient genome engineering in Mycolicibacterium neoaurum using Cas9 from Streptococcus thermophilus.","authors":"Gedan Xiang, Tao Liu, Lekai Li, Guihong Lin, Ke Liu, Fengqing Wang","doi":"10.1007/s10529-024-03519-7","DOIUrl":"10.1007/s10529-024-03519-7","url":null,"abstract":"<p><p>Non-pathogenic mycobacteria, including Mycolicibacterium neoaurum, can directly utilize phytosterols for large-scale industrial production of steroid medicine intermediates due to their natural steroid metabolism pathway. The targeted genetic modification of M. neoaurum is conducive to the selection of high-yield engineering bacteria with high-value-added product, such as Pregnadien-20-carboxylic acid (PDC), which is an important precursor for synthesizing some corticosteroids. Based on heterologous type II CRISPR/sth1Cas9 system, a simple strategy was developed to genetic engineer M. neoaurum genome. Here, a customizable plasmid tool pMSC9 was constructed from pMV261 with integration of sth1Cas9 protein and corresponding sgRNA scaffold. Subsequently, the pMSC9 was inserted with spacer sequences corresponding to different targeted genes, generating editing plasmids, and then transformed into M. neoaurum. As a result, the targeted genes were introduced with DNA double stand breaks (DSBs) by CRISPR/sth1Cas9 system and then repaired by innate non-homologous end-joining (NHEJ) mechanism. Finally, editing plasmids were cured from correctly edited M. neoaurum mutants by means of no resistance cultivation, and the resulting mutant deleting the one target gene was used as the host to which another target gene could be deleted via the same process. This study demonstrated that the CRISPR/sth1Cas9 tool allowed M. neoaurum strains to be rapidly edited. And the editing mode of CRISPR/sth1Cas9 system indicated that this tool was an important supplement to the gene editing toolbox of M. neoaurum.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"1319-1332"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854653","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}

{"title":"Multilevel metabolic engineering for enhanced synthesis of S-adenosylmethionine by Bacillus amyloliquefaciens.","authors":"Cong Jiang, Dian Zou, Liying Ruan, Wenyuan Han, Xuetuan Wei","doi":"10.1007/s10529-024-03523-x","DOIUrl":"10.1007/s10529-024-03523-x","url":null,"abstract":"<p><strong>Objectives: </strong>To enhance the de novo synthesis of SAM, the effects of several key genes on SAM synthesis were examined based on modular strategy, and the key genes were manipulated to obtain an engineered strain with high SAM production.</p><p><strong>Results: </strong>In Bacillus amyloliquefaciens HSAM6, the deletion of argG gene to block aspartic acid branching degradation increased SAM titer to 254.78 ± 15.91 mg/L, up 18% from HSAM6. Subsequently, deleting the moaA gene to boost the supply of 5-methyltetrahydrofolate led to the stunted growth and the plummeting yield of SAM. Further improvement of strain growth by overexpression of the citA gene, while SAM synthesis was not significantly enhanced. Finally, the maximum SAM titer (452.89 ± 13.42 mg/L) was obtained by overexpression SAM2 gene using the multicopy plasmid.</p><p><strong>Conclusions: </strong>The deletion of argG gene and the overexpression of SAM2 gene significantly improved SAM synthesis in B. amyloliquefaciens.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"1155-1162"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003512","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}

{"title":"Gallic acid as biofilm inhibitor can improve transformation efficiency of Ruminiclostridium papyrosolvens.","authors":"Duodong Wang, Na Liu, Mingqiang Qiao, Chenggang Xu","doi":"10.1007/s10529-024-03522-y","DOIUrl":"10.1007/s10529-024-03522-y","url":null,"abstract":"<p><p>Ruminiclostridium papyrosolvens is an anaerobic, mesophilic, and cellulolytic clostridia, promising consolidated bioprocessing (CBP) candidate for producing renewable green chemicals from cellulose, but its genetic transformation has been severely impeded by extracellular biofilm. Here, we analyzed the effects of five different inhibitors with gradient concentrations on R. papyrosolvens growth and biofilm formation. Gallic acid was proved to be a potent inhibitor of biofilm synthesis of R. papyrosolvens. Furthermore, the transformation efficiency of R. papyrosolvens was significantly increased when the cells were treated by the gallic acid, and the mutant strain was successfully obtained by the improved transformation method. Thus, inhibition of biofilm formation of R. papyrosolvens by using gallic acid will contribute to its genetic transformation and efficient metabolic engineering.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"1143-1153"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003566","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}

{"title":"Amyloidogenesis of SARS-CoV-2 delta plus and omicron variants receptor-binding domain (RBD): impact of SUMO fusion tag.","authors":"Sadegh Zargan, Hasan Jalili, Bahareh Dabirmanesh, Saba Mesdaghinia, Khosro Khajeh","doi":"10.1007/s10529-024-03525-9","DOIUrl":"10.1007/s10529-024-03525-9","url":null,"abstract":"<p><strong>Purpose: </strong>The RBD of SARS-CoV-2 mediates viral entry into host cells by binding to the host receptor ACE2. SARS-CoV-2 infection is linked to various health issues resembling amyloid-related problems, persuading us to investigate the amyloidogenicity of the SARS-CoV-2 spike RBD.</p><p><strong>Methods: </strong>The FoldAmyloid program was used to assess the amyloidogenic propensities in the RBD of Delta Plus and RBD of the Omicron variant, with and without the SUMO tag. After the expression of RBDs, purification, and dialysis steps were performed, subsequently the ThT assay, FTIR, and TEM were employed to check the RBD ability to form fibrils.</p><p><strong>Results: </strong>The ThT assay, TEM, and FTIR revealed the ability of RBD to self-assemble into β-sheet-rich aggregates (48.4% β-sheet content). Additionally, the presence of the SUMO tag reduced the formation of RBD amyloid-like fibrils. The amyloidogenic potential of Omicron RBD was higher than Delta Plus, according to both in silico and experimental analyses.</p><p><strong>Conclusions: </strong>The SARS-CoV-2 RBD can assemble itself by forming aggregates containing amyloid-like fibrils and the presence of a SUMO tag can significantly decrease the formation of RBD amyloid-like fibrils. In silico analysis suggested that variation in the ThT fluorescence intensity of amyloid accumulations in the two SARS-CoV-2 strains arises from specific mutations in their RBD regions.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"1037-1048"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054858","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}

{"title":"Recombinant expression, downstream optimization, and therapeutic evaluation of recombinant human interleukin-37 for cancer therapy.","authors":"Zaheer Abbas, Samia Afzal, Nao Akusa Fujimura, Muhammad Akram, Saad Tahir, Kausar Malik, Nadeem Ahmed","doi":"10.1007/s10529-024-03539-3","DOIUrl":"10.1007/s10529-024-03539-3","url":null,"abstract":"<p><p>Interleukin-37 is a cytokine with potent immunosuppressive properties that has been shown to have potential to treat autoimmune and chronic inflammatory diseases, as well as certain types of cancer. IL-37 is a 19 kDa protein which interacts with proteins in receptor-dependent and receptor-independent pathways. The expression of the IL-37 protein cloned into the pET-28a vector was optimized in Rosetta 2(DE3) after comparing its expression with Rosetta-gami 2(DE3) and Rosetta 2(DE3) pLysS, which was then used for the large-scale production of IL-37. IMAC purification of IL-37 yielded > 97% pure 0.9 mg/mL protein from auto-induced fermentation. The IC₅₀ value of IL-37 was < 1 µM, which was similar to that of doxorubicin, and proliferation of > 80% of all cancer cells was inhibited by 100 µg/mL of IL-37 protein. IL-37 may be a promising theragnostic target for cancer due to its comparable IC₅₀ value with that of doxorubicin.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"1269-1291"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457170","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}

{"title":"Breaking resistance: in silico subtractive and comparative genomics approaches for drug targeting in Bacteroides fragilis.","authors":"Tehreem Zia, Kanwal Khan, Saltanat Aghayeva, Reaz Uddin","doi":"10.1007/s10529-024-03537-5","DOIUrl":"10.1007/s10529-024-03537-5","url":null,"abstract":"<p><p>The purpose of this study was to identify potential novel drug targets for Bacteroides fragilis infections using bioinformatics techniques, such as subtractive and comparative genomics. Bacteroides fragilis is a frequently isolated anaerobic pathogen, particularly in the human digestive tract, where its pathogenesis and persistence are influenced by various virulence factors. By understanding these factors, the study aims to explore alternative therapeutic strategies and provide insights for the development of treatments against B. fragilis infections, particularly as alternatives to antibiotic therapy. A comparative subtractive genomic analysis was performed against the B. fragilis (strain CL07T12C05) to identify unique drug targets. The analysis includes the identification of non-paralogous, non-homologous, essential, and drug target like proteins. Moreover, a comprehensive structural analysis of the protein was conducted utilizing structure modeling and validation techniques, along with network topology analysis. Furthermore, a library comprising approximately 9000 FDA-approved compounds accessible in the DrugBank database was employed to conduct virtual screenings for compounds effective against the designated drug target. The top shortlisted compounds were further studied by employing MD simulations using GROMACS. This approach was chosen due to the established safety, efficacy, pharmacokinetics, and toxicity profiles of these compounds. As a result, B. fragilis (strain CL07T12C05) was found to possess 4595 proteins. Among these, 3518 were identified as non-homologous, 1508 deemed essential for bacterial viability, 348 exhibited drug-like properties, 203 were implicated in virulence, and 135 displayed antibiotic resistance. Following an extensive literature review, the protein Sialic acid O-acetyltransferase was chosen through a hierarchical shortlisting process as a potential therapeutic target. The ongoing research facilitated the repurposing of drug compounds: DB12411, DB02112, DB03591, and DB00192, as cost-effective medications against B. fragilis related infections. MD simulations analysis showed that DB12411 may be a potential drug candidate against Sialic acid O-acetyltransferase from B. fragilis. Through subtractive and comparative genomic analysis, Sialic acid O-acetyltransferase was identified as a promising drug target against Bacteroides fragilis. The findings indicate that compounds targeting this protein could potentially be effective in treating B. fragilis infections. However, further experimental validation is required to conclusively confirm their efficacy.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"1249-1268"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457168","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}

{"title":"Completely noninvasive multi-analyte monitoring system for cell culture processes.","authors":"Vida Rahmatnejad, Michael Tolosa, Xudong Ge, Govind Rao","doi":"10.1007/s10529-024-03521-z","DOIUrl":"10.1007/s10529-024-03521-z","url":null,"abstract":"<p><p>Although online monitoring of dissolved O₂, pH, and dissolved CO₂ is critical in bioprocesses, nearly all existing technologies require some level of direct contact with the cell culture environment, posing risks of contamination. This study addresses the need for an accurate, and completely noninvasive technique for simultaneous measurement of these analytes. A \"non-contact\" technique for simultaneous monitoring of dissolved O_2, pH, and dissolved CO₂ was developed. Instead of direct contact with the culture media, the measurements were made through permeable membranes via either a sampling port in the culture vessel wall or a flow cell. The efficacy of the \"non-contact\" technique was validated in Escherichia coli (E.coli), Chinese hamster ovary (CHO) culture processes, and dynamic environments created by sparging gases in cell culture medium. The measurements obtained through the developed techniques were comparable to those obtained through control methods. The noninvasive monitoring system can offer accurate, and contamination-minimized monitoring of critical process parameters including dissolved O₂, pH, and dissolved CO₂. These advancements will enhance the control and optimization of cell culture processes, promising improved cell culture performance.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"983-996"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11550249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003565","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}

{"title":"Synthesis of di-rhamnolipids by the avirulent, mono-rhamnolipid producing strain Pseudomonas aeruginosa ATCC 9027.","authors":"Abigail González-Valdez, Paola G Vázquez-Bueno, Jessica Hernández-Pineda, Gloria Soberón-Chávez","doi":"10.1007/s10529-024-03527-7","DOIUrl":"10.1007/s10529-024-03527-7","url":null,"abstract":"<p><p>To construct a derivative of the avirulent Pseudomonas aeruginosa ATCC 9027 that produces high levels of di-rhamnolipid, that has better physico-chemical characteristics for biotechnological applications than mono-rhamnolipid, which is the sole type produced by ATCC 9027. We used plasmids expressing the rhlC gene, which encodes for rhamnosyl transferase II that transforms mono- to di-rhamnolipids under different promoters and in combination with the gene coding for the RhlR quorum sensing regulator, or the mono-rhamnolipid biosynthetic rhlAB operon. The plasmids tested carrying the rhlC gene under the lac promoter were plasmid prhlC and prhlRC, while prhlAB-R-C expressed this gene from the rhlA promoter, forming part of the artificially constructed rhlAB-R-C operon. We measured rhamnolipds concentrations using the orcinol method and determined the proportion of mono-rhamnolipids and di-rhamnolipids by UPLC/MS/MS. We found that the expression of rhlC in P. aeruginosa ATCC 9027 caused the production of di-rhamnolipids and that the derivative carrying plasmid prhlAB-R-C gives the best results considering total rhamnolipids and a higher proportion of di-rhamnolipids. A P. aeruginosa ATCC 9027 derivative with increased di-rhamnolipids production was developed by expressing plasmid prhlAB-R-C, that produces similar rhamnolipids levels as PAO1 type-strain and presented a higher proportion of di-rhamnolipids than this type-strain.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"1163-1170"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11550238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118916","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}