Aberrant expression of gene is driven by its promoter methylation and is the key molecular basis of carcinogenic processes. This study aimed at identifying a risk signature of methylation-driven (MD) genes and evaluating its prognostic value for colon cancer (CC) patients. The expression profiles of methylation and mRNA in CC samples were obtained from the TCGA database, and the MethylMix algorithm was used to identify MD genes. The relationships between their expression levels and overall survival (OS) of CC patients were analyzed, and a prognostic signature of MD genes was established. The risk score of gene signature was calculated, and the median was used to divide all patients into high (H) and low (L) risk groups. The prognostic value of gene signature was tested by the TCGA cohort and an independent validation cohort (GSE17538 dataset). In total, 69 MD genes were identified, and 7 were associated with OS of CC patients. Ultimately, 4 (TWIST1, LDOC1, EPHX3, and STC2) were screened out to establish a risk signature. The H-risk patients (>0.923) had a worse OS than L-risk patients (≤0.923) in both the TCGA (5-year cumulative survival: 52.9% vs 72.0%, P=0.005) and GSE17538 cohort (49.4% vs 69.3%, P=0.004). The AUC values of MD genes signature for the prediction of 3- and 5-year OS were 0.648 and 0.643 in the TCGA dataset and 0.634 and 0.624 in the GSE17538 dataset, respectively. The risk signature of four MD genes was identified as an independent predictor of OS for CC patients (HR for TCGA dataset: 2.071, 95% CI=1.196-3.586, P=0.009; HR for GSE17538 dataset: 2.021, 95% CI=1.290-3.166, P=0.002). The risk signature of four MD genes might be a useful prognostic tool and help doctors improve the clinical management of CC patients.
{"title":"Identifying a Risk Signature of Methylation-Driven Genes as a Predictor of Survival Outcome for Colon Cancer Patients.","authors":"Bochao Zhao, Jingchao Wang, Guannan Sheng, Yiming Wang, Tao Yang, Kewei Meng","doi":"10.1007/s12010-023-04751-z","DOIUrl":"10.1007/s12010-023-04751-z","url":null,"abstract":"<p><p>Aberrant expression of gene is driven by its promoter methylation and is the key molecular basis of carcinogenic processes. This study aimed at identifying a risk signature of methylation-driven (MD) genes and evaluating its prognostic value for colon cancer (CC) patients. The expression profiles of methylation and mRNA in CC samples were obtained from the TCGA database, and the MethylMix algorithm was used to identify MD genes. The relationships between their expression levels and overall survival (OS) of CC patients were analyzed, and a prognostic signature of MD genes was established. The risk score of gene signature was calculated, and the median was used to divide all patients into high (H) and low (L) risk groups. The prognostic value of gene signature was tested by the TCGA cohort and an independent validation cohort (GSE17538 dataset). In total, 69 MD genes were identified, and 7 were associated with OS of CC patients. Ultimately, 4 (TWIST1, LDOC1, EPHX3, and STC2) were screened out to establish a risk signature. The H-risk patients (>0.923) had a worse OS than L-risk patients (≤0.923) in both the TCGA (5-year cumulative survival: 52.9% vs 72.0%, P=0.005) and GSE17538 cohort (49.4% vs 69.3%, P=0.004). The AUC values of MD genes signature for the prediction of 3- and 5-year OS were 0.648 and 0.643 in the TCGA dataset and 0.634 and 0.624 in the GSE17538 dataset, respectively. The risk signature of four MD genes was identified as an independent predictor of OS for CC patients (HR for TCGA dataset: 2.071, 95% CI=1.196-3.586, P=0.009; HR for GSE17538 dataset: 2.021, 95% CI=1.290-3.166, P=0.002). The risk signature of four MD genes might be a useful prognostic tool and help doctors improve the clinical management of CC patients.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71419428","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 : 2024-07-01Epub Date: 2023-11-03DOI: 10.1007/s12010-023-04762-w
Noor Nabilah Talik Sisin, Aaron Raphael Kong, Hisham Atan Edinur, Noor Izani Noor Jamil, Nor Fazila Che Mat
E6 and E7 human papillomavirus (HPV) oncoproteins play a significant role in the malignant transformation of infected cervical cancer cells via suppression of tumour suppressor pathways by targeting p53 and pRb, respectively. This study aimed to investigate the anticancer effects of Oroxylum indicum (OI) leaves' methanol extract on SiHa cervical cancer cells. Expression of apoptosis-related proteins (Bcl-2, caspase (cas)-3, and cas-9), viral oncoproteins (E6 and E7), and tumour suppressor proteins (p53 and pRb) were evaluated using western blot analysis before and after E6/E7 small interfering RNAs (siRNAs) transfection. In addition, the E6/E7 mRNA expression levels were assessed with real-time (RT)-PCR. The present study showed that the OI extract effectively hindered the proliferation of SiHa cells and instigated increments of cas-3 and cas-9 expressions but decreased the Bcl-2 expressions. The OI extract inhibited E6/E7 viral oncoproteins, leading to upregulation of p53 and pRb tumour suppressor genes in SiHa cells. Additionally, combinatorial treatment of OI extract and gossypin flavonoid induced restorations of p53 and pRb. Treatment with OI extract in siRNA-transfected cells also further suppressed E6/E7 expression levels and further upregulations of p53 and pRb proteins. In conclusion, OI extract treatment on siRNAs-transfected SiHa cells can additively and effectively block E6- and E7-dependent p53 and pRb degradations. All these data suggest that OI could be explored for its chemotherapeutic potential in cervical cancer cells with HPV-integrated genomes.
{"title":"Silencing E6/E7 Oncoproteins in SiHa Cells Treated with siRNAs and Oroxylum indicum Extracts Induced Apoptosis by Upregulating p53/pRb Pathways.","authors":"Noor Nabilah Talik Sisin, Aaron Raphael Kong, Hisham Atan Edinur, Noor Izani Noor Jamil, Nor Fazila Che Mat","doi":"10.1007/s12010-023-04762-w","DOIUrl":"10.1007/s12010-023-04762-w","url":null,"abstract":"<p><p>E6 and E7 human papillomavirus (HPV) oncoproteins play a significant role in the malignant transformation of infected cervical cancer cells via suppression of tumour suppressor pathways by targeting p53 and pRb, respectively. This study aimed to investigate the anticancer effects of Oroxylum indicum (OI) leaves' methanol extract on SiHa cervical cancer cells. Expression of apoptosis-related proteins (Bcl-2, caspase (cas)-3, and cas-9), viral oncoproteins (E6 and E7), and tumour suppressor proteins (p53 and pRb) were evaluated using western blot analysis before and after E6/E7 small interfering RNAs (siRNAs) transfection. In addition, the E6/E7 mRNA expression levels were assessed with real-time (RT)-PCR. The present study showed that the OI extract effectively hindered the proliferation of SiHa cells and instigated increments of cas-3 and cas-9 expressions but decreased the Bcl-2 expressions. The OI extract inhibited E6/E7 viral oncoproteins, leading to upregulation of p53 and pRb tumour suppressor genes in SiHa cells. Additionally, combinatorial treatment of OI extract and gossypin flavonoid induced restorations of p53 and pRb. Treatment with OI extract in siRNA-transfected cells also further suppressed E6/E7 expression levels and further upregulations of p53 and pRb proteins. In conclusion, OI extract treatment on siRNAs-transfected SiHa cells can additively and effectively block E6- and E7-dependent p53 and pRb degradations. All these data suggest that OI could be explored for its chemotherapeutic potential in cervical cancer cells with HPV-integrated genomes.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71433797","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}
The continued spread of SARS-CoV-2 has presented unprecedented obstacles to the worldwide public health system. Especially, individuals with chronic obstructive pulmonary disease (COPD) are at a heightened risk of contracting SARS-CoV-2 infection due to their pre-existing respiratory symptoms that are not well-managed. However, the viral mechanism of affecting the expression of host genes, COPD progression, and prognosis is not clear yet.This study integrated the differential expression information of COPD patients and then calculated the correlation between mRNAs and miRNAs to construct a COPD-specific ceRNA network. The DEGs of individuals with SARS-CoV-2 infection and anticipated miRNAs and their targets were analyzed in 9 SARS-CoV-2 sequences from different geographic locations. Furthermore, combining the experimentally validated miRNAs and genes, the regulatory miRNA-mRNA relationships were identified. All the regulatory relationships were integrated into the COPD-specific network and the network modules were explored to get insight into the functional mechanism of SARS-CoV-2 infection in COPD patients.A higher proportion of DEGs compete with the same miRNA suggesting a higher expression of genes in the COPD-specific ceRNA network. Hsa-miR-21-3p is the largest connected point in the network, but the proportion of genes upregulated by hsa-miR-21-3p is low (P = 0.1406). This indicates that the regulatory relationship of competitive inhibition has little effect on has-miR-21, and the high expression pattern is a poor prognostic factor in COPD. Hsa-miR-15a-5p is the most significant miRNA with the highest proportion of DEGs. And ANXA2P3 is the only gene in the COPD ceRNA network that interferes with hsa-miR-15a-5p. In addition, we found that has-miR-1184- and has-miR-99-cored modules were significant, and genes ZDHHC18, PCGF3, and KIAA0319L interacting with them were all associated with COPD prognosis, and high expression of these genes could lead to poor prognosis in COPD.The key regulators such as miR-21, miR-15a, ANXA2P3, ZDHHC18, PCGF3, and KIAA0319L can be used as prognostic biomarkers for early intervention in COPD with SARS-CoV-2 infection.
{"title":"ceRNA Network Analysis Reveals Potential Key miRNAs and Target Genes in COVID-19-Related Chronic Obstructive Pulmonary Disease.","authors":"Lihai Zhang, Xiaodong Jia, Zhipeng Zhang, Tong Yu, Zhangyan Geng, Lindong Yuan","doi":"10.1007/s12010-023-04773-7","DOIUrl":"10.1007/s12010-023-04773-7","url":null,"abstract":"<p><p>The continued spread of SARS-CoV-2 has presented unprecedented obstacles to the worldwide public health system. Especially, individuals with chronic obstructive pulmonary disease (COPD) are at a heightened risk of contracting SARS-CoV-2 infection due to their pre-existing respiratory symptoms that are not well-managed. However, the viral mechanism of affecting the expression of host genes, COPD progression, and prognosis is not clear yet.This study integrated the differential expression information of COPD patients and then calculated the correlation between mRNAs and miRNAs to construct a COPD-specific ceRNA network. The DEGs of individuals with SARS-CoV-2 infection and anticipated miRNAs and their targets were analyzed in 9 SARS-CoV-2 sequences from different geographic locations. Furthermore, combining the experimentally validated miRNAs and genes, the regulatory miRNA-mRNA relationships were identified. All the regulatory relationships were integrated into the COPD-specific network and the network modules were explored to get insight into the functional mechanism of SARS-CoV-2 infection in COPD patients.A higher proportion of DEGs compete with the same miRNA suggesting a higher expression of genes in the COPD-specific ceRNA network. Hsa-miR-21-3p is the largest connected point in the network, but the proportion of genes upregulated by hsa-miR-21-3p is low (P = 0.1406). This indicates that the regulatory relationship of competitive inhibition has little effect on has-miR-21, and the high expression pattern is a poor prognostic factor in COPD. Hsa-miR-15a-5p is the most significant miRNA with the highest proportion of DEGs. And ANXA2P3 is the only gene in the COPD ceRNA network that interferes with hsa-miR-15a-5p. In addition, we found that has-miR-1184- and has-miR-99-cored modules were significant, and genes ZDHHC18, PCGF3, and KIAA0319L interacting with them were all associated with COPD prognosis, and high expression of these genes could lead to poor prognosis in COPD.The key regulators such as miR-21, miR-15a, ANXA2P3, ZDHHC18, PCGF3, and KIAA0319L can be used as prognostic biomarkers for early intervention in COPD with SARS-CoV-2 infection.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72012955","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 : 2024-06-28DOI: 10.1007/s12010-024-04994-4
Renu Wadhwa, Mangala Hegde, Huayue Zhang, Ashish Kaul, Jia Wang, Yoshiyuki Ishida, Keiji Terao, Ajaikumar B Kunnumakkara, Sunil C Kaul
Chronic stress has been linked to a large number of pathologies, including cancer, premature aging, and neurodegenerative diseases. The accumulation of molecular waste resulting from oxidative and heavy metal-induced stress has been ascribed as a major factor contributing to these diseases. With this in mind, we started by screening 13 small molecules to determine their antistress potential in heavy metal stress-exposed C6 glioblastoma and found that alpha-lipoic acid (ALA) (a natural antioxidant abundantly present in yeast, spinach, broccoli, and meat) was the most effective candidate. We then conducted molecular analyses to validate its mechanism of action. Dose-dependent toxicity assays of cells treated with two ALA enantiomers, R-ALA and S-ALA, showed that they are nontoxic and can be tolerated at relatively high doses. Cells exposed to heavy metal, heat, and oxidative stress showed better recovery when cultured in R-ALA-/S-ALA-supplemented medium, supported by reduction of reactive oxygen species (ROS), aggregated proteins, and mitochondrial and deoxyribonucleic acid (DNA) damage. Molecular analyses revealed protection against stress-induced apoptosis and induction of autophagy in R-ALA- and S-ALA-treated C6/U2OS cells. Consistent with these findings, normal human fibroblasts showed lifespan extension. Taken together, this study demonstrates that lipoic acid has antiaging and antistress potential and warrants further attention in laboratory and clinical studies.
{"title":"Antistress and Antiaging Potentials of Alpha-Lipoic Acid: Insights from Cell Culture-Based Experiments.","authors":"Renu Wadhwa, Mangala Hegde, Huayue Zhang, Ashish Kaul, Jia Wang, Yoshiyuki Ishida, Keiji Terao, Ajaikumar B Kunnumakkara, Sunil C Kaul","doi":"10.1007/s12010-024-04994-4","DOIUrl":"https://doi.org/10.1007/s12010-024-04994-4","url":null,"abstract":"<p><p>Chronic stress has been linked to a large number of pathologies, including cancer, premature aging, and neurodegenerative diseases. The accumulation of molecular waste resulting from oxidative and heavy metal-induced stress has been ascribed as a major factor contributing to these diseases. With this in mind, we started by screening 13 small molecules to determine their antistress potential in heavy metal stress-exposed C6 glioblastoma and found that alpha-lipoic acid (ALA) (a natural antioxidant abundantly present in yeast, spinach, broccoli, and meat) was the most effective candidate. We then conducted molecular analyses to validate its mechanism of action. Dose-dependent toxicity assays of cells treated with two ALA enantiomers, R-ALA and S-ALA, showed that they are nontoxic and can be tolerated at relatively high doses. Cells exposed to heavy metal, heat, and oxidative stress showed better recovery when cultured in R-ALA-/S-ALA-supplemented medium, supported by reduction of reactive oxygen species (ROS), aggregated proteins, and mitochondrial and deoxyribonucleic acid (DNA) damage. Molecular analyses revealed protection against stress-induced apoptosis and induction of autophagy in R-ALA- and S-ALA-treated C6/U2OS cells. Consistent with these findings, normal human fibroblasts showed lifespan extension. Taken together, this study demonstrates that lipoic acid has antiaging and antistress potential and warrants further attention in laboratory and clinical studies.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465338","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}
Plumbagin is a naphthoquinone from the roots of the Plumbago species and exhibits anticancer activity. Translational usage of plumbagin in biomedical sciences is restricted due to its poor solubility and bioavailability. Therefore, pH-responsive plumbagin-loaded vaginal nanoformulations with polylactic acid (PLA)-chitosan polymeric coat were fabricated by inotropic gelation technique. Among the four (F1, F2, F3, F4) nanoformulations prepared, F3 exhibited good interaction of polymers with plumbagin as evidenced by FTIR, XRD, and thermal analysis. The positive zeta potential (48.4 ± 5.57 mV), optimal size (694 ± 65.76 nm), low PDI (0.157), and good encapsulation efficiency (77.8 ± 3.62%) of F3 were significant. The indirect method of drug loading (58.35 ± 5.00%) confirmed the drug content of about 495.44 ± 5.00 µg of plumbagin in 1 mg of F3. The drug loading pattern was confirmed by TEM analysis, and the spherical morphology of the nanocomposite was confirmed by SEM analysis. F3 formulation showed 46% and 25.2% of drug release in 24 h in simulated vaginal fluid at pH 4.5 and 7 respectively with sustained release and hydrolyses of lactic acid from PLA. Among all the nanoformulations evaluated, nanoformulation F3 with promising physicochemical properties showed good antifungal and antibacterial activity against various fungal and bacterial strains. F3 exhibited potent cytotoxicity with an IC50 of 3.6 ± 0.12 µg/ml for HeLa and an IC50 of 0.81 ± 0.01 µg/ml for SiHa cells. Altogether, the nanoformulation F3 exhibited potent antimicrobial activity against vaginal infections and cytotoxicity against cervical cancer cell lines.
{"title":"Antibacterial, Antifungal, and Cytotoxic Potential of PlumbaginLoaded pH-Responsive Vaginal Nanoformulations.","authors":"Tamil Mani Subi, Nandhakumar Selvasudha, Sivakumar Priyadharshini, Pradeep Kumar, Rakesh Singh, Hannah Rachel Vasanthi","doi":"10.1007/s12010-024-04987-3","DOIUrl":"https://doi.org/10.1007/s12010-024-04987-3","url":null,"abstract":"<p><p>Plumbagin is a naphthoquinone from the roots of the Plumbago species and exhibits anticancer activity. Translational usage of plumbagin in biomedical sciences is restricted due to its poor solubility and bioavailability. Therefore, pH-responsive plumbagin-loaded vaginal nanoformulations with polylactic acid (PLA)-chitosan polymeric coat were fabricated by inotropic gelation technique. Among the four (F1, F2, F3, F4) nanoformulations prepared, F3 exhibited good interaction of polymers with plumbagin as evidenced by FTIR, XRD, and thermal analysis. The positive zeta potential (48.4 ± 5.57 mV), optimal size (694 ± 65.76 nm), low PDI (0.157), and good encapsulation efficiency (77.8 ± 3.62%) of F3 were significant. The indirect method of drug loading (58.35 ± 5.00%) confirmed the drug content of about 495.44 ± 5.00 µg of plumbagin in 1 mg of F3. The drug loading pattern was confirmed by TEM analysis, and the spherical morphology of the nanocomposite was confirmed by SEM analysis. F3 formulation showed 46% and 25.2% of drug release in 24 h in simulated vaginal fluid at pH 4.5 and 7 respectively with sustained release and hydrolyses of lactic acid from PLA. Among all the nanoformulations evaluated, nanoformulation F3 with promising physicochemical properties showed good antifungal and antibacterial activity against various fungal and bacterial strains. F3 exhibited potent cytotoxicity with an IC50 of 3.6 ± 0.12 µg/ml for HeLa and an IC50 of 0.81 ± 0.01 µg/ml for SiHa cells. Altogether, the nanoformulation F3 exhibited potent antimicrobial activity against vaginal infections and cytotoxicity against cervical cancer cell lines.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454425","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 : 2024-06-26DOI: 10.1007/s12010-024-04995-3
Lu Liu, Weihe Rong, Xiang Du, Qianqian Yuan, Zhaoyu Xu, Chang Yu, Hongzhong Lu, Yanfei Wang, Yan Zhu, Zhijia Liu, Guokun Wang
Microbial proteins represent a promising solution to address the escalating global demand for protein, particularly in regions with limited arable land. Yeasts, such as Saccharomyces cerevisiae, are robust and safe protein-producing strains. However, the utilization of non-conventional yeast strains for microbial protein production has been hindered, partly due to a lack of comprehensive understanding of protein production traits. In this study, we conducted experimental analyses focusing on the growth, protein content, and amino acid composition of nine yeast strains, including one S. cerevisiae strain, three Yarrowia lipolytica strains, and five Pichia spp. strains. We identified that, though Y. lipolytica and Pichia spp. strains consumed glucose at a slower rate compared to S. cerevisiae, Pichia spp. strains showed a higher cellular protein content, and Y. lipolytica strains showed a higher glucose-to-biomass/protein yield and methionine content. We further applied computational approaches to explain that metabolism economy was the main underlying factor for the limited amount of scarce/carbon-inefficient amino acids (such as methionine) within yeast cell proteins. We additionally verified that the specialized metabolism was a key reason for the high methionine content in Y. lipolytica strains, and proposed Y. lipolytica strain as a potential producer of high-quality single-cell protein rich in scarce amino acids. Through experimental evaluation, we identified Pichia jadinii CICC 1258 as a potential strain for high-quality protein production under unfavorable pH/temperature conditions. Our work suggests a promising avenue for optimizing microbial protein production, identifying the factors influencing amino acid composition, and paving the way for the use of unconventional yeast strains to meet the growing protein demands.
微生物蛋白质是一种很有前景的解决方案,可满足全球日益增长的蛋白质需求,尤其是在耕地有限的地区。酵母(如酿酒酵母)是稳健安全的蛋白质生产菌株。然而,利用非常规酵母菌株生产微生物蛋白质一直受到阻碍,部分原因是缺乏对蛋白质生产性状的全面了解。在本研究中,我们对九种酵母菌株的生长、蛋白质含量和氨基酸组成进行了实验分析,其中包括一种 S. cerevisiae 菌株、三种 Yarrowia lipolytica 菌株和五种 Pichia spp.我们发现,虽然与 S. cerevisiae 相比,Y. lipolytica 和 Pichia spp.菌株消耗葡萄糖的速度较慢,但 Pichia spp.菌株的细胞蛋白质含量较高,而 Y. lipolytica 菌株的葡萄糖-生物质/蛋白质产量和蛋氨酸含量较高。我们进一步应用计算方法解释了代谢经济是酵母细胞蛋白质中稀缺/碳效率氨基酸(如蛋氨酸)数量有限的主要根本原因。此外,我们还验证了特殊代谢是脂肪溶解酵母菌株蛋氨酸含量高的关键原因,并提出脂肪溶解酵母菌株是富含稀缺氨基酸的高质量单细胞蛋白质的潜在生产者。通过实验评估,我们发现 Pichia jadinii CICC 1258 是在不利的 pH 值/温度条件下生产优质蛋白质的潜在菌株。我们的工作为优化微生物蛋白质生产、确定影响氨基酸组成的因素提供了一条前景广阔的途径,并为使用非常规酵母菌株满足日益增长的蛋白质需求铺平了道路。
{"title":"Integrating Experimental and Computational Analyses of Yeast Protein Profiles for Optimizing the Production of High-Quality Microbial Proteins.","authors":"Lu Liu, Weihe Rong, Xiang Du, Qianqian Yuan, Zhaoyu Xu, Chang Yu, Hongzhong Lu, Yanfei Wang, Yan Zhu, Zhijia Liu, Guokun Wang","doi":"10.1007/s12010-024-04995-3","DOIUrl":"https://doi.org/10.1007/s12010-024-04995-3","url":null,"abstract":"<p><p>Microbial proteins represent a promising solution to address the escalating global demand for protein, particularly in regions with limited arable land. Yeasts, such as Saccharomyces cerevisiae, are robust and safe protein-producing strains. However, the utilization of non-conventional yeast strains for microbial protein production has been hindered, partly due to a lack of comprehensive understanding of protein production traits. In this study, we conducted experimental analyses focusing on the growth, protein content, and amino acid composition of nine yeast strains, including one S. cerevisiae strain, three Yarrowia lipolytica strains, and five Pichia spp. strains. We identified that, though Y. lipolytica and Pichia spp. strains consumed glucose at a slower rate compared to S. cerevisiae, Pichia spp. strains showed a higher cellular protein content, and Y. lipolytica strains showed a higher glucose-to-biomass/protein yield and methionine content. We further applied computational approaches to explain that metabolism economy was the main underlying factor for the limited amount of scarce/carbon-inefficient amino acids (such as methionine) within yeast cell proteins. We additionally verified that the specialized metabolism was a key reason for the high methionine content in Y. lipolytica strains, and proposed Y. lipolytica strain as a potential producer of high-quality single-cell protein rich in scarce amino acids. Through experimental evaluation, we identified Pichia jadinii CICC 1258 as a potential strain for high-quality protein production under unfavorable pH/temperature conditions. Our work suggests a promising avenue for optimizing microbial protein production, identifying the factors influencing amino acid composition, and paving the way for the use of unconventional yeast strains to meet the growing protein demands.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141449296","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 : 2024-06-22DOI: 10.1007/s12010-024-04973-9
Jing Zhao, Hao Chen, Jian Sun
Lung adenocarcinoma (LUAD) is the most frequent type of lung cancer with a high mortality rate. Here, we aim to explore novel immune-related biomarkers for LUAD patients. Datasets, mRNA expression profiles, and clinical data concerned with LUAD were obtained from Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA), respectively. Differential expression analysis was performed to obtain differentially expressed genes (DEGs). Based on DEGs, we conducted functional enrichment analyses. Subsequently, Kaplan‑Meier (KM) was performed to analyze survival differences among different groups. Furthermore, immune cell infiltration proportion was calculated by CIBERSORT and TIMER. The relationship between gene and immune response was analyzed using Tumor Immune System Interactions (TISIDB) database. Finally, Pearson correlation analysis was performed between CD1C and six immune checkpoints. We identified dendritic cells (DCs)-related expression profiles from four LUAD samples. DCs' immune marker CD1C in LUAD was selected by univariate Cox regression analysis. Low CD1C expression patients had a poor prognosis. A total of 332 DEGs were identified in high and low CD1C expression groups, which primarily enriched in 348 GO terms and 30 KEGG pathways. There were significant differences in the infiltration proportion of 17 immune cells between high and low CD1C expression groups. Most immunomodulators, chemokines, and chemokine receptors were positively associated with CD1C expression. Six immune checkpoints were also positively correlated with CD1C expression. DCs related immunomarker CD1C probably plays a pivotal part in prognosis and immunotherapy of LUAD via a joint analysis of single-cell and bulk sequencing data.
{"title":"Dendritic Cell-Related Immune Marker CD1C for Predicting Prognosis and Immunotherapy Opportunities of Lung Adenocarcinoma Patients.","authors":"Jing Zhao, Hao Chen, Jian Sun","doi":"10.1007/s12010-024-04973-9","DOIUrl":"https://doi.org/10.1007/s12010-024-04973-9","url":null,"abstract":"<p><p>Lung adenocarcinoma (LUAD) is the most frequent type of lung cancer with a high mortality rate. Here, we aim to explore novel immune-related biomarkers for LUAD patients. Datasets, mRNA expression profiles, and clinical data concerned with LUAD were obtained from Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA), respectively. Differential expression analysis was performed to obtain differentially expressed genes (DEGs). Based on DEGs, we conducted functional enrichment analyses. Subsequently, Kaplan‑Meier (KM) was performed to analyze survival differences among different groups. Furthermore, immune cell infiltration proportion was calculated by CIBERSORT and TIMER. The relationship between gene and immune response was analyzed using Tumor Immune System Interactions (TISIDB) database. Finally, Pearson correlation analysis was performed between CD1C and six immune checkpoints. We identified dendritic cells (DCs)-related expression profiles from four LUAD samples. DCs' immune marker CD1C in LUAD was selected by univariate Cox regression analysis. Low CD1C expression patients had a poor prognosis. A total of 332 DEGs were identified in high and low CD1C expression groups, which primarily enriched in 348 GO terms and 30 KEGG pathways. There were significant differences in the infiltration proportion of 17 immune cells between high and low CD1C expression groups. Most immunomodulators, chemokines, and chemokine receptors were positively associated with CD1C expression. Six immune checkpoints were also positively correlated with CD1C expression. DCs related immunomarker CD1C probably plays a pivotal part in prognosis and immunotherapy of LUAD via a joint analysis of single-cell and bulk sequencing data.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141439975","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 : 2024-06-21DOI: 10.1007/s12010-024-04990-8
Yao Wen, Jiawen Chen
The ultrasonic-assisted deep eutectic solvent method was used to extract the polysaccharides of Pericarpium Citri Reticulatae (PCRP), and the ultrasound-assisted DES extraction process was optimized by Box-Behnken response surface test using the extraction rate of the PCRP as an index; the in vitro activities of purified the PCRP(PCRPs-1) were investigated by determining the scavenging rate of DPPH• and ABTS•+ as well as by enzyme inhibition assay. The monosaccharide composition was analyzed by HPLC. The best process conditions for response surface optimization were a material-liquid ratio of 1:37 g/mL, water content of 44%, time of 89 min, and power of 320 W. The polysaccharide extraction rate was measured to be 5.41%, which was well optimized when compared with that of the ordinary aqueous extraction method of 3.92%. By α-glucosidase and α-amylase inhibition activity test, it showed that the PCRPs-1 had hypoglycemic activity. The DPPH radical scavenging activity test and ABTS + scavenging activity test indicated that the PCRPs-1 had good biological activity. Analysis of the monosaccharide fractions showed that the PCRPs-1 consisted of mannose, rhamnose, glucuronic acid, galacturonic acid, glucose, galactose, xylose, and arabinose, with molar ratios of 1:39.24:4.41:8.91:7.83:86.00:1.02:9.17. The activity studies showed that PCRPs-1 possessed certain hypoglycaemic and antioxidant activities.
{"title":"Optimization of Ultrasound-Assisted Deep Eutectic Solvent Extraction, Characterization, and Bioactivities of Polysaccharide from Pericarpium Citri Reticulatae.","authors":"Yao Wen, Jiawen Chen","doi":"10.1007/s12010-024-04990-8","DOIUrl":"https://doi.org/10.1007/s12010-024-04990-8","url":null,"abstract":"<p><p>The ultrasonic-assisted deep eutectic solvent method was used to extract the polysaccharides of Pericarpium Citri Reticulatae (PCRP), and the ultrasound-assisted DES extraction process was optimized by Box-Behnken response surface test using the extraction rate of the PCRP as an index; the in vitro activities of purified the PCRP(PCRPs-1) were investigated by determining the scavenging rate of DPPH• and ABTS•<sup>+</sup> as well as by enzyme inhibition assay. The monosaccharide composition was analyzed by HPLC. The best process conditions for response surface optimization were a material-liquid ratio of 1:37 g/mL, water content of 44%, time of 89 min, and power of 320 W. The polysaccharide extraction rate was measured to be 5.41%, which was well optimized when compared with that of the ordinary aqueous extraction method of 3.92%. By α-glucosidase and α-amylase inhibition activity test, it showed that the PCRPs-1 had hypoglycemic activity. The DPPH radical scavenging activity test and ABTS <sup>+</sup> scavenging activity test indicated that the PCRPs-1 had good biological activity. Analysis of the monosaccharide fractions showed that the PCRPs-1 consisted of mannose, rhamnose, glucuronic acid, galacturonic acid, glucose, galactose, xylose, and arabinose, with molar ratios of 1:39.24:4.41:8.91:7.83:86.00:1.02:9.17. The activity studies showed that PCRPs-1 possessed certain hypoglycaemic and antioxidant activities.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141431001","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 : 2024-06-20DOI: 10.1007/s12010-024-04982-8
Yucheng Fan, Zijia Wei, Yuhua Zhang, Xuguo Duan
L-asparaginase synthetase, an ATP-dependent enzyme, necessitates ATP for its catalytic activity. However, the integration of L-asparaginase synthetase into industrial processes is curtailed by the prohibitive cost of ATP. To address this limitation, this study explores the construction of an efficient ATP regeneration system using the glucose metabolism of Escherichia coli, synergistically coupled with L-asparaginase synthetase catalysis. The optimal conditions for L-asparagine yield were determined in shake flasks. A total of 2.7 g/L was the highest yield achieved under specific parameters, including 0.1 mol/L of substrate, 0.2 mol/L glucose, 0.01 mol/L MgCl2 at pH 7.5, a temperature of 37 °C, and agitation at 300 r/min over 12 h. The process was then scaled to a 3-L fermenter, optimizing the addition rates of the substrate and magnesium chloride, and employing a constant glucose feed of 10 g/L/h. The scale-up process led to a significant enhancement in the production of L-asparagine. The yield of L-asparagine was increased to 38.49 g/L after 20 h of conversion, and the molar conversion rate reached 29.16%. This strategy has proven to be effective in improving the efficiency of L-asparagine production. When compared to in vitro ATP regeneration methods, this in vivo approach showcased superior efficiency and reduced costs. These findings furnish pivotal insights that may propel the enzymatic synthesis of L-asparagine toward viable industrial application.
L-天冬酰胺酶合成酶是一种依赖 ATP 的酶,其催化活性需要 ATP。然而,由于 ATP 的成本过高,L-天冬酰胺酶合成酶在工业生产过程中的应用受到限制。为解决这一局限性,本研究利用大肠杆菌的葡萄糖代谢与 L-天冬酰胺酶合成酶催化协同作用,探索构建高效的 ATP 再生系统。在摇瓶中确定了 L-天冬酰胺产量的最佳条件。在特定参数(包括 0.1 摩尔/升底物、0.2 摩尔/升葡萄糖、0.01 摩尔/升氯化镁,pH 值为 7.5,温度为 37 °C,搅拌速度为 300 r/min,持续 12 小时)下,L-天冬酰胺的最高产量为 2.7 克/升。放大工艺显著提高了 L-天冬酰胺的产量。经过 20 小时的转化,L-天冬酰胺的产量增加到 38.49 克/升,摩尔转化率达到 29.16%。事实证明,这种策略能有效提高 L-天冬酰胺的生产效率。与体外 ATP 再生方法相比,这种体内方法效率更高,成本更低。这些发现为酶法合成 L-天冬酰胺的工业应用提供了重要启示。
{"title":"Enhancing L-asparagine Production Through In Vivo ATP Regeneration System Utilizing Glucose Metabolism of Escherichia coli.","authors":"Yucheng Fan, Zijia Wei, Yuhua Zhang, Xuguo Duan","doi":"10.1007/s12010-024-04982-8","DOIUrl":"https://doi.org/10.1007/s12010-024-04982-8","url":null,"abstract":"<p><p>L-asparaginase synthetase, an ATP-dependent enzyme, necessitates ATP for its catalytic activity. However, the integration of L-asparaginase synthetase into industrial processes is curtailed by the prohibitive cost of ATP. To address this limitation, this study explores the construction of an efficient ATP regeneration system using the glucose metabolism of Escherichia coli, synergistically coupled with L-asparaginase synthetase catalysis. The optimal conditions for L-asparagine yield were determined in shake flasks. A total of 2.7 g/L was the highest yield achieved under specific parameters, including 0.1 mol/L of substrate, 0.2 mol/L glucose, 0.01 mol/L MgCl<sub>2</sub> at pH 7.5, a temperature of 37 °C, and agitation at 300 r/min over 12 h. The process was then scaled to a 3-L fermenter, optimizing the addition rates of the substrate and magnesium chloride, and employing a constant glucose feed of 10 g/L/h. The scale-up process led to a significant enhancement in the production of L-asparagine. The yield of L-asparagine was increased to 38.49 g/L after 20 h of conversion, and the molar conversion rate reached 29.16%. This strategy has proven to be effective in improving the efficiency of L-asparagine production. When compared to in vitro ATP regeneration methods, this in vivo approach showcased superior efficiency and reduced costs. These findings furnish pivotal insights that may propel the enzymatic synthesis of L-asparagine toward viable industrial application.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426005","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}
Biodegradation effectiveness of S. maltophilia DHHJ is determined by its ability to attach to the hydrolyzed feather keratin monomers. This binding capacity can be influenced by many components in the culture medium. Keratin monomers from feathers or those produced by gene overexpression can induce keratinase production in S. maltophilia DHHJ, and several proteases lack the ability to degrade keratin fragments and cysteines. In this study, we co-incubated FITC-labelled keratin monomers with S. maltophilia DHHJ cells in the presence of BSA, DNA, ATP, and several metal ions, and measured fluorescence values and keratinase activity. BSA was found to compete with keratins for cell binding sites, resulting in less keratinase production. DNA did not interfere with cellular binding to keratins revealing unchanged keratinase level. ATP, along with metal ions, enhanced the cellular binding capacity to keratins and increased the production of keratinase by S. maltophilia DHHJ. Fragments of keratin monomers degraded by proteases reduced the ability of cells to bind to keratin and affected enzyme production. Cysteine, a characteristic amino acid of feather keratin, did not have an effect on cellular binding to keratin monomer or on keratinase production. This study will facilitate the tweaking of catalytic parameters to improve feather biodegradation by S. maltophilia DHHJ.
{"title":"Effects of various substances on the binding of keratin monomers to S. maltophilia DHHJ cells for the induction of keratinase production.","authors":"Kai Xue, XiaoXiao Song, Wei Zhang, YunLong Zhang, ZhangJun Cao, XingQun Zhang, ZhongGe Zhang","doi":"10.1007/s12010-024-04991-7","DOIUrl":"https://doi.org/10.1007/s12010-024-04991-7","url":null,"abstract":"<p><p>Biodegradation effectiveness of S. maltophilia DHHJ is determined by its ability to attach to the hydrolyzed feather keratin monomers. This binding capacity can be influenced by many components in the culture medium. Keratin monomers from feathers or those produced by gene overexpression can induce keratinase production in S. maltophilia DHHJ, and several proteases lack the ability to degrade keratin fragments and cysteines. In this study, we co-incubated FITC-labelled keratin monomers with S. maltophilia DHHJ cells in the presence of BSA, DNA, ATP, and several metal ions, and measured fluorescence values and keratinase activity. BSA was found to compete with keratins for cell binding sites, resulting in less keratinase production. DNA did not interfere with cellular binding to keratins revealing unchanged keratinase level. ATP, along with metal ions, enhanced the cellular binding capacity to keratins and increased the production of keratinase by S. maltophilia DHHJ. Fragments of keratin monomers degraded by proteases reduced the ability of cells to bind to keratin and affected enzyme production. Cysteine, a characteristic amino acid of feather keratin, did not have an effect on cellular binding to keratin monomer or on keratinase production. This study will facilitate the tweaking of catalytic parameters to improve feather biodegradation by S. maltophilia DHHJ.</p>","PeriodicalId":465,"journal":{"name":"Applied Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417028","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}