Pub Date : 2024-12-01Epub Date: 2024-01-08DOI: 10.1007/s00253-023-12867-9
Xingyi Zhang, Yinghui Feng, Yuanzhe Hua, Chuanxi Zhang, Bohuan Fang, Xiang Long, Yue Pan, Bei Gao, John Z H Zhang, Lijun Li, Hui Ni, Lujia Zhang
The flavonoid naringenin is abundantly present in pomelo peels, and the unprocessed naringenin in wastes is not friendly for the environment once discarded directly. Fortunately, the hydroxylated product of eriodictyol from naringenin exhibits remarkable antioxidant and anticancer properties. The P450s was suggested promising for the bioconversion of the flavonoids, but less naturally existed P450s show hydroxylation activity to C3' of the naringenin. By well analyzing the catalytic mechanism and the conformations of the naringenin in P450, we proposed that the intermediate Cmpd I ((porphyrin)Fe = O) is more reasonable as key conformation for the hydrolyzation, and the distance between C3'/C5' of naringenin to the O atom of CmpdI determines the hydroxylating activity for the naringenin. Thus, the "flying kite model" that gradually drags the C-H bond of the substrate to the O atom of CmpdI was put forward for rational design. With ab initio design, we successfully endowed the self-sufficient P450-BM3 hydroxylic activity to naringenin and obtained mutant M5-5, with kcat, Km, and kcat/Km values of 230.45 min-1, 310.48 µM, and 0.742 min-1 µM-1, respectively. Furthermore, the mutant M4186 was screened with kcat/Km of 4.28-fold highly improved than the reported M13. The M4186 also exhibited 62.57% yield of eriodictyol, more suitable for the industrial application. This study provided a theoretical guide for the rational design of P450s to the nonnative compounds. KEY POINTS: •The compound I is proposed as the starting point for the rational design of the P450BM3 •"Flying kite model" is proposed based on the distance between O of Cmpd I and C3'/C5' of naringenin •Mutant M15-5 with 1.6-fold of activity than M13 was obtained by ab initio modification.
柚皮中含有丰富的黄酮类化合物柚皮苷,废弃物中未经加工的柚皮苷直接丢弃对环境不利。幸运的是,从柚皮苷中提取的羟基化产物二碘酪醇(eriodictyol)具有显著的抗氧化和抗癌特性。P450s 被认为有望用于黄酮类化合物的生物转化,但天然存在的 P450s 对柚皮苷的 C3'具有羟化活性的较少。通过深入分析催化机理和柚皮苷在 P450 中的构象,我们提出中间体 Cmpd I((卟啉)Fe = O)作为水解的关键构象更为合理,而柚皮苷的 C3'/C5' 与 CmpdI 的 O 原子之间的距离决定了柚皮苷的羟化活性。因此,我们提出了将底物的 C-H 键逐渐拖向 CmpdI 的 O 原子的 "放飞风筝模型 "来进行合理设计。通过ab initio设计,我们成功地赋予了柚皮苷自给自足的P450-BM3羟化活性,得到了突变体M5-5,其kcat、Km和kcat/Km值分别为230.45 min-1、310.48 µM和0.742 min-1 µM-1。此外,还筛选出了突变体 M4186,其 kcat/Km 比已报道的 M13 提高了 4.28 倍。M4186 还显示出 62.57% 的二碘tyol 收率,更适合工业应用。这项研究为合理设计 P450s 非原生化合物提供了理论指导。关键点-根据 Cmpd I 的 O 与柚皮苷的 C3'/C5' 之间的距离,提出了 "飞鸢模型"--通过 ab initio 修饰得到了比 M13 活性高 1.6 倍的突变体 M15-5。
{"title":"Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylation.","authors":"Xingyi Zhang, Yinghui Feng, Yuanzhe Hua, Chuanxi Zhang, Bohuan Fang, Xiang Long, Yue Pan, Bei Gao, John Z H Zhang, Lijun Li, Hui Ni, Lujia Zhang","doi":"10.1007/s00253-023-12867-9","DOIUrl":"10.1007/s00253-023-12867-9","url":null,"abstract":"<p><p>The flavonoid naringenin is abundantly present in pomelo peels, and the unprocessed naringenin in wastes is not friendly for the environment once discarded directly. Fortunately, the hydroxylated product of eriodictyol from naringenin exhibits remarkable antioxidant and anticancer properties. The P450s was suggested promising for the bioconversion of the flavonoids, but less naturally existed P450s show hydroxylation activity to C3' of the naringenin. By well analyzing the catalytic mechanism and the conformations of the naringenin in P450, we proposed that the intermediate Cmpd I ((porphyrin)Fe = O) is more reasonable as key conformation for the hydrolyzation, and the distance between C3'/C5' of naringenin to the O atom of CmpdI determines the hydroxylating activity for the naringenin. Thus, the \"flying kite model\" that gradually drags the C-H bond of the substrate to the O atom of CmpdI was put forward for rational design. With ab initio design, we successfully endowed the self-sufficient P450-BM3 hydroxylic activity to naringenin and obtained mutant M5-5, with k<sub>cat</sub>, K<sub>m</sub>, and k<sub>cat</sub>/K<sub>m</sub> values of 230.45 min<sup>-1</sup>, 310.48 µM, and 0.742 min<sup>-1</sup> µM<sup>-1</sup>, respectively. Furthermore, the mutant M4186 was screened with k<sub>cat</sub>/K<sub>m</sub> of 4.28-fold highly improved than the reported M13. The M4186 also exhibited 62.57% yield of eriodictyol, more suitable for the industrial application. This study provided a theoretical guide for the rational design of P450s to the nonnative compounds. KEY POINTS: •The compound I is proposed as the starting point for the rational design of the P450BM3 •\"Flying kite model\" is proposed based on the distance between O of Cmpd I and C3'/C5' of naringenin •Mutant M15-5 with 1.6-fold of activity than M13 was obtained by ab initio modification.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139377150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-01Epub Date: 2024-01-08DOI: 10.1007/s00253-023-12907-4
Elisabeth Tamayo, Basant Nada, Isabell Hafermann, J Philipp Benz
Filamentous fungi like Neurospora crassa are able to take up and metabolize important sugars present, for example, in agricultural and human food wastes. However, only a fraction of all putative sugar transporters in filamentous fungi has been characterized to date, and for many sugar substrates, the corresponding transporters are unknown. In N. crassa, only 14 out of the 42 putative major facilitator superfamily (MFS)-type sugar transporters have been characterized so far. To uncover this hidden potential for biotechnology, it is therefore necessary to find new strategies. By correlation of the uptake profile of sugars of interest after different induction conditions with the expression profiles of all 44 genes encoding predicted sugar transporters in N. crassa, together with an exhaustive phylogenetic analysis using sequences of characterized fungal sugar transporters, we aimed to identify transporter candidates for the tested sugars. Following this approach, we found a high correlation of uptake rates and expression strengths for many sugars with dedicated transporters, like galacturonic acid and arabinose, while the correlation is loose for sugars that are transported by several transporters due to functional redundancy. Nevertheless, this combinatorial approach allowed us to elucidate the uptake system for the disaccharide lactose, a by-product of the dairy industry, which consists of the two main cellodextrin transporters CDT-1 and CDT-2 with a minor contribution of the related transporter NCU00809. Moreover, a non-MFS transporter involved in glycerol transport was also identified. Deorphanization of sugar transporters or identification of transporters for orphan sugar substrates by correlation of uptake kinetics with transporter expression and phylogenetic information can thus provide a way to optimize the reuse of food industry by-products and agricultural wastes by filamentous fungi in order to create economic value and reduce their environmental impact. KEY POINTS: • The Neurospora crassa genome contains 30 uncharacterized putative sugar transporter genes. • Correlation of transporter expression and sugar uptake profiles can help to identify transporters for orphan sugar substrates. • CDT-1, CDT-2, and NCU00809 are key players in the transport of the dairy by-product lactose in N. crassa.
{"title":"Correlating sugar transporter expression and activities to identify transporters for an orphan sugar substrate.","authors":"Elisabeth Tamayo, Basant Nada, Isabell Hafermann, J Philipp Benz","doi":"10.1007/s00253-023-12907-4","DOIUrl":"10.1007/s00253-023-12907-4","url":null,"abstract":"<p><p>Filamentous fungi like Neurospora crassa are able to take up and metabolize important sugars present, for example, in agricultural and human food wastes. However, only a fraction of all putative sugar transporters in filamentous fungi has been characterized to date, and for many sugar substrates, the corresponding transporters are unknown. In N. crassa, only 14 out of the 42 putative major facilitator superfamily (MFS)-type sugar transporters have been characterized so far. To uncover this hidden potential for biotechnology, it is therefore necessary to find new strategies. By correlation of the uptake profile of sugars of interest after different induction conditions with the expression profiles of all 44 genes encoding predicted sugar transporters in N. crassa, together with an exhaustive phylogenetic analysis using sequences of characterized fungal sugar transporters, we aimed to identify transporter candidates for the tested sugars. Following this approach, we found a high correlation of uptake rates and expression strengths for many sugars with dedicated transporters, like galacturonic acid and arabinose, while the correlation is loose for sugars that are transported by several transporters due to functional redundancy. Nevertheless, this combinatorial approach allowed us to elucidate the uptake system for the disaccharide lactose, a by-product of the dairy industry, which consists of the two main cellodextrin transporters CDT-1 and CDT-2 with a minor contribution of the related transporter NCU00809. Moreover, a non-MFS transporter involved in glycerol transport was also identified. Deorphanization of sugar transporters or identification of transporters for orphan sugar substrates by correlation of uptake kinetics with transporter expression and phylogenetic information can thus provide a way to optimize the reuse of food industry by-products and agricultural wastes by filamentous fungi in order to create economic value and reduce their environmental impact. KEY POINTS: • The Neurospora crassa genome contains 30 uncharacterized putative sugar transporter genes. • Correlation of transporter expression and sugar uptake profiles can help to identify transporters for orphan sugar substrates. • CDT-1, CDT-2, and NCU00809 are key players in the transport of the dairy by-product lactose in N. crassa.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10774165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139377158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 : 2024-12-01Epub Date: 2024-01-09DOI: 10.1007/s00253-023-12974-7
Minseok Cha, Jung Kon Kim, Won-Heong Lee, Hyoungwoon Song, Tae-Gi Lee, Sun-Ki Kim, Soo-Jung Kim
Hydrogen is an alternative fuel for transportation vehicles because it is clean, sustainable, and highly flammable. However, the production of hydrogen from lignocellulosic biomass by microorganisms presents challenges. This microbial process involves multiple complex steps, including thermal, chemical, and mechanical treatment of biomass to remove hemicellulose and lignin, as well as enzymatic hydrolysis to solubilize the plant cell walls. These steps not only incur costs but also result in the production of toxic hydrolysates, which inhibit microbial growth. A hyper-thermophilic bacterium of Caldicellulosiruptor bescii can produce hydrogen by decomposing and fermenting plant biomass without the need for conventional pretreatment. It is considered as a consolidated bioprocessing (CBP) microorganism. This review summarizes the basic scientific knowledge and hydrogen-producing capacity of C. bescii. Its genetic system and metabolic engineering strategies to improve hydrogen production are also discussed. KEY POINTS: • Hydrogen is an alternative and eco-friendly fuel. • Caldicellulosiruptor bescii produces hydrogen with a high yield in nature. • Metabolic engineering can make C. bescii to improve hydrogen production.
氢气是运输车辆的替代燃料,因为它清洁、可持续且高度易燃。然而,利用微生物从木质纤维素生物质中制氢却面临着挑战。这种微生物工艺涉及多个复杂步骤,包括对生物质进行热处理、化学处理和机械处理以去除半纤维素和木质素,以及酶水解以溶解植物细胞壁。这些步骤不仅会产生成本,还会产生有毒的水解物,抑制微生物的生长。一种超嗜热细菌 Caldicellulosiruptor bescii 可以通过分解和发酵植物生物质产生氢气,而无需进行传统的预处理。它被认为是一种综合生物加工(CBP)微生物。本综述总结了 C. bescii 的基础科学知识和制氢能力。还讨论了其基因系统和代谢工程策略,以提高制氢能力。要点:- 氢是一种替代性环保燃料。- 在自然界中,Caldicellulosiruptor bescii 能高产氢气。- 代谢工程可使 C. bescii 提高氢气产量。
{"title":"Metabolic engineering of Caldicellulosiruptor bescii for hydrogen production.","authors":"Minseok Cha, Jung Kon Kim, Won-Heong Lee, Hyoungwoon Song, Tae-Gi Lee, Sun-Ki Kim, Soo-Jung Kim","doi":"10.1007/s00253-023-12974-7","DOIUrl":"10.1007/s00253-023-12974-7","url":null,"abstract":"<p><p>Hydrogen is an alternative fuel for transportation vehicles because it is clean, sustainable, and highly flammable. However, the production of hydrogen from lignocellulosic biomass by microorganisms presents challenges. This microbial process involves multiple complex steps, including thermal, chemical, and mechanical treatment of biomass to remove hemicellulose and lignin, as well as enzymatic hydrolysis to solubilize the plant cell walls. These steps not only incur costs but also result in the production of toxic hydrolysates, which inhibit microbial growth. A hyper-thermophilic bacterium of Caldicellulosiruptor bescii can produce hydrogen by decomposing and fermenting plant biomass without the need for conventional pretreatment. It is considered as a consolidated bioprocessing (CBP) microorganism. This review summarizes the basic scientific knowledge and hydrogen-producing capacity of C. bescii. Its genetic system and metabolic engineering strategies to improve hydrogen production are also discussed. KEY POINTS: • Hydrogen is an alternative and eco-friendly fuel. • Caldicellulosiruptor bescii produces hydrogen with a high yield in nature. • Metabolic engineering can make C. bescii to improve hydrogen production.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10776719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139401546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 : 2024-12-01Epub Date: 2024-01-09DOI: 10.1007/s00253-023-12958-7
Justinas Babinskas, Jerica Sabotič, Inga Matijošytė
Biocatalysis is one of the greatest tools for implementing the 12 principles of Green chemistry. Biocatalysts are bio-based, highly efficient and selective, operate at moderate conditions, and can be reused multiple times. However, the wider application of biocatalysts is plagued by a plethora of drawbacks, such as poor stability at operating conditions, inadequate efficiency of catalytic systems, a small number of commercially available biocatalysts, and a lack of substrates or methods for their discovery and development. In this work, we address the lack of suitable substrates for high-throughput screening of laccase by synthesising and investigating a newly developed phenazine-type substrate - Ferbamine. Investigation of Ferbamine pH and thermal stability indicated that its long-term stability in an aqueous medium is superior to that of commercially available substrates and does not require organic solvents. Ferbamine displayed convincing performance in detecting laccase activity on Ferbamine-agar plates in commercial laccase products and the collection of extracts from wild terrestrial fungi (42 species, 65 extracts), of which 26 species have not been described to have laccase activity prior to this work. Incubation of microorganisms on Ferbamine-agar plates showed its compatibility with live colonies. Ferbamine proved to be an easy-to-use substrate, which could be a great addition to the toolbox of methods for the functional analysis of laccases.
{"title":"Synthesis and application of a phenazine class substrate for high-throughput screening of laccase activity.","authors":"Justinas Babinskas, Jerica Sabotič, Inga Matijošytė","doi":"10.1007/s00253-023-12958-7","DOIUrl":"10.1007/s00253-023-12958-7","url":null,"abstract":"<p><p>Biocatalysis is one of the greatest tools for implementing the 12 principles of Green chemistry. Biocatalysts are bio-based, highly efficient and selective, operate at moderate conditions, and can be reused multiple times. However, the wider application of biocatalysts is plagued by a plethora of drawbacks, such as poor stability at operating conditions, inadequate efficiency of catalytic systems, a small number of commercially available biocatalysts, and a lack of substrates or methods for their discovery and development. In this work, we address the lack of suitable substrates for high-throughput screening of laccase by synthesising and investigating a newly developed phenazine-type substrate - Ferbamine. Investigation of Ferbamine pH and thermal stability indicated that its long-term stability in an aqueous medium is superior to that of commercially available substrates and does not require organic solvents. Ferbamine displayed convincing performance in detecting laccase activity on Ferbamine-agar plates in commercial laccase products and the collection of extracts from wild terrestrial fungi (42 species, 65 extracts), of which 26 species have not been described to have laccase activity prior to this work. Incubation of microorganisms on Ferbamine-agar plates showed its compatibility with live colonies. Ferbamine proved to be an easy-to-use substrate, which could be a great addition to the toolbox of methods for the functional analysis of laccases.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10776486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139401551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 : 2024-12-01Epub Date: 2024-01-11DOI: 10.1007/s00253-023-12872-y
Stefano Serra, Stefano Marzorati, Ewa Szczepańska, Tomasz Strzała, Filip Boratyński
Substituted benzaldehydes are the most commonly used natural-occurring flavours in the world. The consumer's preference for 'natural or organic' aromas has increased the request for flavours possessing the 'natural' status. The resulting shortage of aromatic aldehydes of extractive origin, such as vanillin, veratraldehyde and piperonal, can be offset by developing a new biotechnological synthesis method. Here, we report a study on the microbiological reduction of five natural benzoic acid derivatives, namely p-anisic, vanillic, veratric, piperonylic and eudesmic acids, to produce the corresponding fragrant aldehydes. We found that different Basidiomycota strains can efficiently perform this transformation, with good chemical selectivity and tolerance to the toxicity of substrates and products. Besides confirming the carboxylic acid reductase activity of the already studied fungi Pycnoporus cinnabarinus, we discovered that other species such as Pleurotus eryngii, Pleurotus sapidus and Laetiporus sulphureus as well as the non-ligninolytic fungi Lepista nuda are valuable microorganisms for the synthesis of anisaldehyde, vanillin, veratraldehyde, piperonal and 3,4,5-trimethoxybenzaldehyde from the corresponding acids. According to our findings, we propose a reliable process for the preparation of the above-mentioned aldehydes, in natural form. KEY POINTS: • Fragrant benzaldehydes were obtained by biotransformation. • Basidiomycota strains reduced substituted benzoic acid to the corresponding aldehydes. • Anisaldehyde, vanillin, veratraldehyde, piperonal and 3,4,5-trimethoxybenzaldehyde were prepared in natural form.
{"title":"Basidiomycota strains as whole-cell biocatalysts for the synthesis of high-value natural benzaldehydes.","authors":"Stefano Serra, Stefano Marzorati, Ewa Szczepańska, Tomasz Strzała, Filip Boratyński","doi":"10.1007/s00253-023-12872-y","DOIUrl":"10.1007/s00253-023-12872-y","url":null,"abstract":"<p><p>Substituted benzaldehydes are the most commonly used natural-occurring flavours in the world. The consumer's preference for 'natural or organic' aromas has increased the request for flavours possessing the 'natural' status. The resulting shortage of aromatic aldehydes of extractive origin, such as vanillin, veratraldehyde and piperonal, can be offset by developing a new biotechnological synthesis method. Here, we report a study on the microbiological reduction of five natural benzoic acid derivatives, namely p-anisic, vanillic, veratric, piperonylic and eudesmic acids, to produce the corresponding fragrant aldehydes. We found that different Basidiomycota strains can efficiently perform this transformation, with good chemical selectivity and tolerance to the toxicity of substrates and products. Besides confirming the carboxylic acid reductase activity of the already studied fungi Pycnoporus cinnabarinus, we discovered that other species such as Pleurotus eryngii, Pleurotus sapidus and Laetiporus sulphureus as well as the non-ligninolytic fungi Lepista nuda are valuable microorganisms for the synthesis of anisaldehyde, vanillin, veratraldehyde, piperonal and 3,4,5-trimethoxybenzaldehyde from the corresponding acids. According to our findings, we propose a reliable process for the preparation of the above-mentioned aldehydes, in natural form. KEY POINTS: • Fragrant benzaldehydes were obtained by biotransformation. • Basidiomycota strains reduced substituted benzoic acid to the corresponding aldehydes. • Anisaldehyde, vanillin, veratraldehyde, piperonal and 3,4,5-trimethoxybenzaldehyde were prepared in natural form.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10784365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139429057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Livestock farms are major reservoirs of antibiotic resistance genes (ARGs) that are discharged into the environment. However, the abundance, diversity, and transmission of ARGs in duck farms and its impact on surrounding environments remain to be further explored. Therefore, the characteristics of ARGs and their bacterial hosts from duck farms and surrounding environment were investigated by using metagenomic sequencing. Eighteen ARG types which consist of 823 subtypes were identified and the majority conferred resistance to multidrug, tetracyclines, aminoglycosides, chloramphenicols, MLS, and sulfonamides. The floR gene was the most abundant subtype, followed by sul1, tetM, sul2, and tetL. ARG abundance in fecal sample was significantly higher than soil and water sample. Our results also lead to a hypothesis that Shandong province have been the most contaminated by ARGs from duck farm compared with other four provinces. PcoA results showed that the composition of ARG subtypes in water and soil samples was similar, but there were significant differences between water and feces samples. However, the composition of ARG subtypes were similar between samples from five provinces. Bacterial hosts of ARG subtypes were taxonomically assigned to eight phyla that were dominated by the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. In addition, some human bacterial pathogens could be enriched in duck feces, including Enterococcus faecium, Acinetobacter baumannii, and Staphylococcus aureus, and even serve as the carrier of ARGs. The combined results indicate that a comprehensive overview of the diversity and abundance of ARGs, and strong association between ARGs and bacterial community shift proposed, and benefit effective measures to improve safety of antibiotics use in livestock and poultry farming. KEY POINTS: • ARG distribution was widespread in the duck farms and surroundings environment • ARG abundance on the duck farms was significantly higher than in soil and water • Human bacterial pathogens may serve as the vectors for ARGs.
{"title":"Distribution of antibiotic resistance genes and their pathogen hosts in duck farm environments in south-east coastal China.","authors":"Kaidi Liu, Minge Wang, Yin Zhang, Chang Fang, Rongmin Zhang, Liangxing Fang, Jian Sun, Yahong Liu, Xiaoping Liao","doi":"10.1007/s00253-023-12842-4","DOIUrl":"10.1007/s00253-023-12842-4","url":null,"abstract":"<p><p>Livestock farms are major reservoirs of antibiotic resistance genes (ARGs) that are discharged into the environment. However, the abundance, diversity, and transmission of ARGs in duck farms and its impact on surrounding environments remain to be further explored. Therefore, the characteristics of ARGs and their bacterial hosts from duck farms and surrounding environment were investigated by using metagenomic sequencing. Eighteen ARG types which consist of 823 subtypes were identified and the majority conferred resistance to multidrug, tetracyclines, aminoglycosides, chloramphenicols, MLS, and sulfonamides. The floR gene was the most abundant subtype, followed by sul1, tetM, sul2, and tetL. ARG abundance in fecal sample was significantly higher than soil and water sample. Our results also lead to a hypothesis that Shandong province have been the most contaminated by ARGs from duck farm compared with other four provinces. PcoA results showed that the composition of ARG subtypes in water and soil samples was similar, but there were significant differences between water and feces samples. However, the composition of ARG subtypes were similar between samples from five provinces. Bacterial hosts of ARG subtypes were taxonomically assigned to eight phyla that were dominated by the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. In addition, some human bacterial pathogens could be enriched in duck feces, including Enterococcus faecium, Acinetobacter baumannii, and Staphylococcus aureus, and even serve as the carrier of ARGs. The combined results indicate that a comprehensive overview of the diversity and abundance of ARGs, and strong association between ARGs and bacterial community shift proposed, and benefit effective measures to improve safety of antibiotics use in livestock and poultry farming. KEY POINTS: • ARG distribution was widespread in the duck farms and surroundings environment • ARG abundance on the duck farms was significantly higher than in soil and water • Human bacterial pathogens may serve as the vectors for ARGs.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10789667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139477525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 : 2024-12-01Epub Date: 2024-05-11DOI: 10.1080/21691401.2024.2350475
Ki-Kwang Oh, Sang-Jun Yoon, Seol Hee Song, Jeong Ha Park, Jeong Su Kim, Dong Joon Kim, Ki-Tae Suk
Type 2 diabetes mellitus (T2DM), nonalcoholic fatty liver disease (NAFLD), obesity (OB) and hypertension (HT) are categorized as metabolic disorders (MDs), which develop independently without distinct borders. Herein, we examined the gut microbiota (GM) and Saururus chinensis (SC) to confirm their therapeutic effects via integrated pharmacology. The overlapping targets from the four diseases were determined to be key protein coding genes. The protein-protein interaction (PPI) networks, and the SC, GM, signalling pathway, target and metabolite (SGSTM) networks were analysed via RPackage. Additionally, molecular docking tests (MDTs) and density functional theory (DFT) analysis were conducted to determine the affinity and stability of the conformer(s). TNF was the main target in the PPI analysis, and equol derived from Lactobacillus paracasei JS1 was the most effective agent for the formation of the TNF complex. The SC agonism (PPAR signalling pathway), and antagonism (neurotrophin signalling pathway) by SC were identified as agonistic bioactives (aromadendrane, stigmasta-5,22-dien-3-ol, 3,6,6-trimethyl-3,4,5,7,8,9-hexahydro-1H-2-benzoxepine, 4α-5α-epoxycholestane and kinic acid), and antagonistic bioactives (STK734327 and piclamilast), respectively, via MDT. Finally, STK734327-MAPK1 was the most favourable conformer according to DFT. Overall, the seven bioactives from SC and equol that can be produced by Lactobacillus paracasei JS1 can exert synergistic effects on these four diseases.
{"title":"The synchronized feature of <i>Saururus chinensis</i> and gut microbiota against T2DM, NAFLD, obesity and hypertension via integrated pharmacology.","authors":"Ki-Kwang Oh, Sang-Jun Yoon, Seol Hee Song, Jeong Ha Park, Jeong Su Kim, Dong Joon Kim, Ki-Tae Suk","doi":"10.1080/21691401.2024.2350475","DOIUrl":"https://doi.org/10.1080/21691401.2024.2350475","url":null,"abstract":"<p><p>Type 2 diabetes mellitus (T2DM), nonalcoholic fatty liver disease (NAFLD), obesity (OB) and hypertension (HT) are categorized as metabolic disorders (MDs), which develop independently without distinct borders. Herein, we examined the gut microbiota (GM) and <i>Saururus chinensis</i> (SC) to confirm their therapeutic effects via integrated pharmacology. The overlapping targets from the four diseases were determined to be key protein coding genes. The protein-protein interaction (PPI) networks, and the SC, GM, signalling pathway, target and metabolite (SGSTM) networks were analysed via RPackage. Additionally, molecular docking tests (MDTs) and density functional theory (DFT) analysis were conducted to determine the affinity and stability of the conformer(s). TNF was the main target in the PPI analysis, and equol derived from <i>Lactobacillus paracasei JS1</i> was the most effective agent for the formation of the TNF complex. The SC agonism (PPAR signalling pathway), and antagonism (neurotrophin signalling pathway) by SC were identified as agonistic bioactives (aromadendrane, stigmasta-5,22-dien-3-ol, 3,6,6-trimethyl-3,4,5,7,8,9-hexahydro-1H-2-benzoxepine, 4α-5α-epoxycholestane and kinic acid), and antagonistic bioactives (STK734327 and piclamilast), respectively, via MDT. Finally, STK734327-MAPK1 was the most favourable conformer according to DFT. Overall, the seven bioactives from SC and equol that can be produced by <i>Lactobacillus paracasei JS1</i> can exert synergistic effects on these four diseases.</p>","PeriodicalId":8736,"journal":{"name":"Artificial Cells, Nanomedicine, and Biotechnology","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140908025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-01Epub Date: 2023-11-23DOI: 10.1080/21691401.2023.2276768
Yingcan Xu, Kehui Zhu, Jiakang Wu, Shifan Zheng, Rui Zhong, Wentao Zhou, Ye Cao, Jiaxin Liu, Hong Wang
Radiotherapy (RT) is a highly valuable method in cancer therapy, but its therapeutic efficacy is limited by its side effects and tumour radiation resistance. The resistance is mainly induced by hypoxia in the tumour microenvironment (TME). As a nano-oxygen carrier, Haemoglobin-based oxygen carriers (HBOCs) administration is a promising strategy to alleviate tumour hypoxia which may remodel TME to ameliorate radiation resistance and enable RT more effective. In this study, we administered fractionated RT combined with HBOC to treat Miapaca-2 cell and Hela cell xenografts on nude mice. The study found that HBOC relieved hypoxic environment and down-regulate expression of hypoxia-inducible factor-1α (Hif-1α) both in regular (100 mm3) and large (360/400 mm3) tumours. The proliferation and metastasis of tumour tissue also decreased after HBOC application. Nevertheless, in vivo RT combined with HBOC performed more effectively to suppress tumour growth in large tumours than in regular tumours. This is due to more severe hypoxic regions exist in the large solid tumours compared to the regular counterparts, and HBOC administration may be more effective in alleviating hypoxia in large tumours. Thus, HBOC sensitization therapy is more suitable for large solid tumours.
{"title":"HBOC alleviated tumour hypoxia during radiotherapy more intensely in large solid tumours than regular ones.","authors":"Yingcan Xu, Kehui Zhu, Jiakang Wu, Shifan Zheng, Rui Zhong, Wentao Zhou, Ye Cao, Jiaxin Liu, Hong Wang","doi":"10.1080/21691401.2023.2276768","DOIUrl":"10.1080/21691401.2023.2276768","url":null,"abstract":"<p><p>Radiotherapy (RT) is a highly valuable method in cancer therapy, but its therapeutic efficacy is limited by its side effects and tumour radiation resistance. The resistance is mainly induced by hypoxia in the tumour microenvironment (TME). As a nano-oxygen carrier, Haemoglobin-based oxygen carriers (HBOCs) administration is a promising strategy to alleviate tumour hypoxia which may remodel TME to ameliorate radiation resistance and enable RT more effective. In this study, we administered fractionated RT combined with HBOC to treat Miapaca-2 cell and Hela cell xenografts on nude mice. The study found that HBOC relieved hypoxic environment and down-regulate expression of hypoxia-inducible factor-1α (Hif-1α) both in regular (100 mm<sup>3</sup>) and large (360/400 mm<sup>3</sup>) tumours. The proliferation and metastasis of tumour tissue also decreased after HBOC application. Nevertheless, <i>in vivo</i> RT combined with HBOC performed more effectively to suppress tumour growth in large tumours than in regular tumours. This is due to more severe hypoxic regions exist in the large solid tumours compared to the regular counterparts, and HBOC administration may be more effective in alleviating hypoxia in large tumours. Thus, HBOC sensitization therapy is more suitable for large solid tumours.</p>","PeriodicalId":8736,"journal":{"name":"Artificial Cells, Nanomedicine, and Biotechnology","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138294567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lung cancer is a dangerous disease that is lacking in an ideal therapy. Here, we evaluated the anti-lung cancer effect in nude mice of a fully human single-chain antibody (scFv) against the associated antigen 7 transmembrane receptor (Ts7TMR), which is also called G protein-coupled receptor, between A549 cells and Trichinella spiralis (T. spiralis). Our data showed that anti-Ts7TMR scFv could inhibit lung cancer growth in a dose-dependent manner, with a tumour inhibition rate of 59.1%. HE staining did not reveal any obvious tissue damage. Mechanistically, immunohistochemical staining revealed that the scFv down-regulated the expression of PCNA and VEGF in tumour tissues. Overall, this study found that anti-Ts7TMR scFv could inhibit A549 lung cancer growth by suppressing cell proliferation and angiogenesis, which may provide a new strategy for treating lung cancer.
{"title":"The effects of anti-lung cancer in nude mice by a fully human single-chain antibody against associated antigen Ts7TMR between A549 cells and <i>Trichinella spiralis</i>.","authors":"Taotao Yue, Jinpeng Wang, Fang Liu, Pengtao Gong, Jianhua Li, Xichen Zhang, Nan Zhang","doi":"10.1080/21691401.2024.2347377","DOIUrl":"https://doi.org/10.1080/21691401.2024.2347377","url":null,"abstract":"<p><p>Lung cancer is a dangerous disease that is lacking in an ideal therapy. Here, we evaluated the anti-lung cancer effect in nude mice of a fully human single-chain antibody (scFv) against the associated antigen 7 transmembrane receptor (Ts7TMR), which is also called G protein-coupled receptor, between A549 cells and <i>Trichinella spiralis</i> (<i>T. spiralis</i>). Our data showed that anti-Ts7TMR scFv could inhibit lung cancer growth in a dose-dependent manner, with a tumour inhibition rate of 59.1%. HE staining did not reveal any obvious tissue damage. Mechanistically, immunohistochemical staining revealed that the scFv down-regulated the expression of PCNA and VEGF in tumour tissues. Overall, this study found that anti-Ts7TMR scFv could inhibit A549 lung cancer growth by suppressing cell proliferation and angiogenesis, which may provide a new strategy for treating lung cancer.</p>","PeriodicalId":8736,"journal":{"name":"Artificial Cells, Nanomedicine, and Biotechnology","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140955546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-01Epub Date: 2024-05-11DOI: 10.1080/21691401.2024.2352003
Sean Dowd, Catherine Sharo, Osheiza Abdulmalik, Jacob Elmer
Haemorrhagic shock is a leading cause of death worldwide. Blood transfusions can be used to treat patients suffering severe blood loss but donated red blood cells (RBCs) have several limitations that limit their availability and use. To solve the problems associated with donated RBCs, several acellular haemoglobin-based oxygen carriers (HBOCs) have been developed to restore the most important function of blood: oxygen transport. One promising HBOC is the naturally extracellular haemoglobin (i.e. erythrocruorin) of Lumbricus terrestris (LtEc). The goal of this study was to maximise the portability of LtEc by lyophilising it and then testing its stability at elevated temperatures. To prevent oxidation, several cryoprotectants were screened to determine the optimum formulation for lyophilisation that could minimise oxidation of the haem iron and maximise recovery. Furthermore, samples were also deoxygenated prior to storage to decrease auto-oxidation, while resuspension in a solution containing ascorbic acid was shown to partially reduce LtEc that had oxidised during storage (e.g. from 42% Fe3+ to 11% Fe3+). Analysis of the oxygen equilibria and size of the resuspended LtEc showed that the lyophilisation, storage, and resuspension processes did not affect the oxygen transport properties or the structure of the LtEc, even after 6 months of storage at 40 °C. Altogether, these efforts have yielded a shelf-stable LtEc powder that can be stored for long periods at high temperatures, but future animal studies will be necessary to prove that the resuspended product is a safe and effective oxygen transporter in vivo.
{"title":"Optimizing the lyophilization of <i>Lumbricus terrestris</i> erythrocruorin.","authors":"Sean Dowd, Catherine Sharo, Osheiza Abdulmalik, Jacob Elmer","doi":"10.1080/21691401.2024.2352003","DOIUrl":"10.1080/21691401.2024.2352003","url":null,"abstract":"<p><p>Haemorrhagic shock is a leading cause of death worldwide. Blood transfusions can be used to treat patients suffering severe blood loss but donated red blood cells (RBCs) have several limitations that limit their availability and use. To solve the problems associated with donated RBCs, several acellular haemoglobin-based oxygen carriers (HBOCs) have been developed to restore the most important function of blood: oxygen transport. One promising HBOC is the naturally extracellular haemoglobin (i.e. erythrocruorin) of <i>Lumbricus terrestris</i> (LtEc). The goal of this study was to maximise the portability of LtEc by lyophilising it and then testing its stability at elevated temperatures. To prevent oxidation, several cryoprotectants were screened to determine the optimum formulation for lyophilisation that could minimise oxidation of the haem iron and maximise recovery. Furthermore, samples were also deoxygenated prior to storage to decrease auto-oxidation, while resuspension in a solution containing ascorbic acid was shown to partially reduce LtEc that had oxidised during storage (e.g. from 42% Fe<sup>3+</sup> to 11% Fe<sup>3+</sup>). Analysis of the oxygen equilibria and size of the resuspended LtEc showed that the lyophilisation, storage, and resuspension processes did not affect the oxygen transport properties or the structure of the LtEc, even after 6 months of storage at 40 °C. Altogether, these efforts have yielded a shelf-stable LtEc powder that can be stored for long periods at high temperatures, but future animal studies will be necessary to prove that the resuspended product is a safe and effective oxygen transporter <i>in vivo</i>.</p>","PeriodicalId":8736,"journal":{"name":"Artificial Cells, Nanomedicine, and Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11218865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140908023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}