Microbial Biotechnology最新文献_第9页

Entrapment of antimicrobial compounds in a metal matrix for crop protection 金属基质中的抗菌化合物用于作物保护

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-13 DOI: 10.1111/1751-7915.70005

Aya Brill, Barak Menagen, Einav Malach, Einat Zelinger, David Avnir, Saul Burdman, Zvi Hayouka

{"title":"Entrapment of antimicrobial compounds in a metal matrix for crop protection","authors":"Aya Brill, Barak Menagen, Einav Malach, Einat Zelinger, David Avnir, Saul Burdman, Zvi Hayouka","doi":"10.1111/1751-7915.70005","DOIUrl":"https://doi.org/10.1111/1751-7915.70005","url":null,"abstract":"Agricultural yields are often limited by damage caused by pathogenic microorganisms, including plant-pathogenic bacteria. The chemical control options to cope with bacterial diseases in agriculture are limited, predominantly relying on copper-based products. These compounds, however, possess limited efficacy. Therefore, there is an urgent need to develop novel technologies to manage bacterial plant diseases and reduce food loss. In this study, a new antimicrobial agent was developed using a doping method that entraps small bioactive organic molecules inside copper as the metal matrix. The food preservative agent lauroyl arginate ethyl ester (ethyl lauroyl arginate; LAE) was chosen as the doped organic compound. The new composites were termed LAE@[Cu]. Bactericidal assays against Acidovorax citrulli, a severe plant pathogen, revealed that LAE and copper in the composites possess a synergistic interaction as compared with each component individually. LAE@[Cu] composites were further characterised in terms of chemical properties and in planta assays demonstrated their potential for further development as crop protection agents.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142231041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bacterioruberin extract from Haloarchaea Haloferax marinum: Component identification, antioxidant activity and anti-atrophy effect in LPS-treated C2C12 myotubes 从海洋卤虫（Haloarchaea Haloferax marinum）中提取的细菌黄素：LPS 处理的 C2C12 肌细胞中的成分鉴定、抗氧化活性和抗萎缩作用

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-12 DOI: 10.1111/1751-7915.70009

Hyeju Lee, Eui-Sang Cho, Chi Young Hwang, Lei Cao, Mi-Bo Kim, Sang Gil Lee, Myung-Ji Seo

{"title":"Bacterioruberin extract from Haloarchaea Haloferax marinum: Component identification, antioxidant activity and anti-atrophy effect in LPS-treated C2C12 myotubes","authors":"Hyeju Lee, Eui-Sang Cho, Chi Young Hwang, Lei Cao, Mi-Bo Kim, Sang Gil Lee, Myung-Ji Seo","doi":"10.1111/1751-7915.70009","DOIUrl":"https://doi.org/10.1111/1751-7915.70009","url":null,"abstract":"Carotenoids are natural pigments utilized as colourants and antioxidants across food, pharmaceutical and cosmetic industries. They exist in carbon chain lengths of C30, C40, C45 and C50, with C40 variants being the most common. Bacterioruberin (BR) and its derivatives are part of the less common C50 carotenoid group, synthesized primarily by halophilic archaea. This study analysed the compositional characteristics of BR extract (BRE) isolated from ‘Haloferax marinum’ MBLA0078, a halophilic archaeon isolated from seawater near Yeoungheungdo Island in the Republic of Korea, and investigated its antioxidant activity and protective effect on lipopolysaccharide (LPS)-induced C2C12 myotube atrophy. The main components of BRE included all-trans-BR, monoanhydrobacterioruberin, 2-isopentenyl-3,4-dehydrorhodopin and all-trans-bisanhydrobacterioruberin. BRE exhibited higher antioxidant activity and DNA nicking protection activity than other well-known C40 carotenoids, such as β-carotene, lycopene and astaxanthin. In C2C12 myotubes, LPS treatment led to a reduction in myotube diameter and number, as well as the hypertranscription of the muscle-specific ubiquitin ligase MAFbx and MuRF1. BRE mitigated these changes by activating the Akt/mTOR pathway. Furthermore, BRE abolished the elevated cellular reactive oxygen species levels and the inflammation response induced by LPS. This study demonstrated that ‘Hfx. marinum’ is an excellent source of natural microbial C50 carotenoids with strong antioxidant capacity and may offer potential protective effects against muscle atrophy.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142174196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bacterioruberin extract from Haloarchaea Haloferax marinum: Component identification, antioxidant activity and anti-atrophy effect in LPS-treated C2C12 myotubes 从海洋卤虫（Haloarchaea Haloferax marinum）中提取的细菌黄素：LPS 处理的 C2C12 肌细胞中的成分鉴定、抗氧化活性和抗萎缩作用

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-12 DOI: 10.1111/1751-7915.70009

Hyeju Lee, Eui-Sang Cho, Chi Young Hwang, Lei Cao, Mi-Bo Kim, Sang Gil Lee, Myung-Ji Seo

{"title":"Bacterioruberin extract from Haloarchaea Haloferax marinum: Component identification, antioxidant activity and anti-atrophy effect in LPS-treated C2C12 myotubes","authors":"Hyeju Lee, Eui-Sang Cho, Chi Young Hwang, Lei Cao, Mi-Bo Kim, Sang Gil Lee, Myung-Ji Seo","doi":"10.1111/1751-7915.70009","DOIUrl":"https://doi.org/10.1111/1751-7915.70009","url":null,"abstract":"Carotenoids are natural pigments utilized as colourants and antioxidants across food, pharmaceutical and cosmetic industries. They exist in carbon chain lengths of C30, C40, C45 and C50, with C40 variants being the most common. Bacterioruberin (BR) and its derivatives are part of the less common C50 carotenoid group, synthesized primarily by halophilic archaea. This study analysed the compositional characteristics of BR extract (BRE) isolated from ‘Haloferax marinum’ MBLA0078, a halophilic archaeon isolated from seawater near Yeoungheungdo Island in the Republic of Korea, and investigated its antioxidant activity and protective effect on lipopolysaccharide (LPS)-induced C2C12 myotube atrophy. The main components of BRE included all-trans-BR, monoanhydrobacterioruberin, 2-isopentenyl-3,4-dehydrorhodopin and all-trans-bisanhydrobacterioruberin. BRE exhibited higher antioxidant activity and DNA nicking protection activity than other well-known C40 carotenoids, such as β-carotene, lycopene and astaxanthin. In C2C12 myotubes, LPS treatment led to a reduction in myotube diameter and number, as well as the hypertranscription of the muscle-specific ubiquitin ligase MAFbx and MuRF1. BRE mitigated these changes by activating the Akt/mTOR pathway. Furthermore, BRE abolished the elevated cellular reactive oxygen species levels and the inflammation response induced by LPS. This study demonstrated that ‘Hfx. marinum’ is an excellent source of natural microbial C50 carotenoids with strong antioxidant capacity and may offer potential protective effects against muscle atrophy.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142174195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Contribution of machine learning for subspecies identification from Mycobacterium abscessus with MALDI-TOF MS in solid and liquid media 在固体和液体培养基中利用 MALDI-TOF MS 进行脓肿分枝杆菌亚种鉴定的机器学习贡献

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-10 DOI: 10.1111/1751-7915.14545

Alexandre Godmer, Lise Bigey, Quentin Giai-Gianetto, Gautier Pierrat, Noshine Mohammad, Faiza Mougari, Renaud Piarroux, Nicolas Veziris, Alexandra Aubry

{"title":"Contribution of machine learning for subspecies identification from Mycobacterium abscessus with MALDI-TOF MS in solid and liquid media","authors":"Alexandre Godmer, Lise Bigey, Quentin Giai-Gianetto, Gautier Pierrat, Noshine Mohammad, Faiza Mougari, Renaud Piarroux, Nicolas Veziris, Alexandra Aubry","doi":"10.1111/1751-7915.14545","DOIUrl":"https://doi.org/10.1111/1751-7915.14545","url":null,"abstract":"Mycobacterium abscessus (MABS) displays differential subspecies susceptibility to macrolides. Thus, identifying MABS's subspecies (M. abscessus, M. bolletii and M. massiliense) is a clinical necessity for guiding treatment decisions. We aimed to assess the potential of Machine Learning (ML)-based classifiers coupled to Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) MS to identify MABS subspecies. Two spectral databases were created by using 40 confirmed MABS strains. Spectra were obtained by using MALDI-TOF MS from strains cultivated on solid (Columbia Blood Agar, CBA) or liquid (MGIT®) media for 1 to 13 days. Each database was divided into a dataset for ML-based pipeline development and a dataset to assess the performance. An in-house programme was developed to identify discriminant peaks specific to each subspecies. The peak-based approach successfully distinguished M. massiliense from the other subspecies for strains grown on CBA. The ML approach achieved 100% accuracy for subspecies identification on CBA, falling to 77.5% on MGIT®. This study validates the usefulness of ML, in particular the Random Forest algorithm, to discriminate MABS subspecies by MALDI-TOF MS. However, identification in MGIT®, a medium largely used in mycobacteriology laboratories, is not yet reliable and should be a development priority.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.14545","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142170091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Contribution of machine learning for subspecies identification from Mycobacterium abscessus with MALDI-TOF MS in solid and liquid media 在固体和液体培养基中利用 MALDI-TOF MS 进行脓肿分枝杆菌亚种鉴定的机器学习贡献

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-10 DOI: 10.1111/1751-7915.14545

Alexandre Godmer, Lise Bigey, Quentin Giai-Gianetto, Gautier Pierrat, Noshine Mohammad, Faiza Mougari, Renaud Piarroux, Nicolas Veziris, Alexandra Aubry

{"title":"Contribution of machine learning for subspecies identification from Mycobacterium abscessus with MALDI-TOF MS in solid and liquid media","authors":"Alexandre Godmer, Lise Bigey, Quentin Giai-Gianetto, Gautier Pierrat, Noshine Mohammad, Faiza Mougari, Renaud Piarroux, Nicolas Veziris, Alexandra Aubry","doi":"10.1111/1751-7915.14545","DOIUrl":"https://doi.org/10.1111/1751-7915.14545","url":null,"abstract":"Mycobacterium abscessus (MABS) displays differential subspecies susceptibility to macrolides. Thus, identifying MABS's subspecies (M. abscessus, M. bolletii and M. massiliense) is a clinical necessity for guiding treatment decisions. We aimed to assess the potential of Machine Learning (ML)-based classifiers coupled to Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) MS to identify MABS subspecies. Two spectral databases were created by using 40 confirmed MABS strains. Spectra were obtained by using MALDI-TOF MS from strains cultivated on solid (Columbia Blood Agar, CBA) or liquid (MGIT®) media for 1 to 13 days. Each database was divided into a dataset for ML-based pipeline development and a dataset to assess the performance. An in-house programme was developed to identify discriminant peaks specific to each subspecies. The peak-based approach successfully distinguished M. massiliense from the other subspecies for strains grown on CBA. The ML approach achieved 100% accuracy for subspecies identification on CBA, falling to 77.5% on MGIT®. This study validates the usefulness of ML, in particular the Random Forest algorithm, to discriminate MABS subspecies by MALDI-TOF MS. However, identification in MGIT®, a medium largely used in mycobacteriology laboratories, is not yet reliable and should be a development priority.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.14545","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142170062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic characterization and identification of candidate genes for putative podophyllotoxin biosynthesis pathway in Penicillium herquei HGN12.1C Genomic characterization and identification of candidate genes for putative podophyllotoxin biosynthesis pathway in Penicillium herquei HGN12.1C.

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-05 DOI: 10.1111/1751-7915.70007

Duong Huy Nguyen, Quang Ho Tran, Lam Tung Le, Ha Hong Thi Nguyen, Hoa Thi Tran, Thuy Phuong Do, Anh Ngoc Ho, Quang Hong Tran, Hien Thi Nguyen Thu, Van Ngoc Bui, Hoang Ha Chu, Ngoc Bich Pham

{"title":"Genomic characterization and identification of candidate genes for putative podophyllotoxin biosynthesis pathway in Penicillium herquei HGN12.1C","authors":"Duong Huy Nguyen, Quang Ho Tran, Lam Tung Le, Ha Hong Thi Nguyen, Hoa Thi Tran, Thuy Phuong Do, Anh Ngoc Ho, Quang Hong Tran, Hien Thi Nguyen Thu, Van Ngoc Bui, Hoang Ha Chu, Ngoc Bich Pham","doi":"10.1111/1751-7915.70007","DOIUrl":"10.1111/1751-7915.70007","url":null,"abstract":"Previous studies have reported the functional role, biochemical features and synthesis pathway of podophyllotoxin (PTOX) in plants. In this study, we employed combined morphological and molecular techniques to identify an endophytic fungus and extract PTOX derivatives. Based on the analysis of ITS sequences and the phylogenetic tree, the isolate was classified as Penicillium herquei HGN12.1C, with a sequence identity of 98.58%. Morphologically, the HGN12.1C strain exhibits white colonies, short-branched mycelia and densely packed hyphae. Using PacBio sequencing at an average read depth of 195×, we obtained a high-quality genome for the HGN12.1C strain, which is 34.9 Mb in size, containing eight chromosomes, one mitochondrial genome and a GC content of 46.5%. Genome analysis revealed 10 genes potentially involved in PTOX biosynthesis. These genes include VdtD, Pinoresinollariciresinol reductase (PLR), Secoisolariciresinol dehydrogenase (SDH), CYP719A23, CYP71BE54, O-methyltransferase 1 (OMT1), O-methyltransferase 3 (OMT3), 2-ODD, CYP71CU and CYP82D61. Notably, the VdtD gene in fungi shares functional similarities with the DIR gene found in plants. Additionally, we identified peltatin, a PTOX derivative, in the HGN12.1C extract. Docking analysis suggests a potential role for the 2-ODD enzyme in converting yatein to deoxypodophyllotoxin. These findings offer invaluable insights into the synthesis mechanism of PTOX in fungi, shedding light on the relationship between host plants and endophytes.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11376216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Feedstock variability impacts the bioconversion of sugar and lignin streams derived from corn stover by Clostridium tyrobutyricum and engineered Pseudomonas putida 原料变化影响酪酸梭菌和工程假单胞菌对玉米秸秆产生的糖和木质素流的生物转化。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-05 DOI: 10.1111/1751-7915.70006

Ilona A. Ruhl, Robert S. Nelson, Rui Katahira, Jacob S. Kruger, Xiaowen Chen, Stefan J. Haugen, Morgan A. Ingraham, Sean P. Woodworth, Hannah Alt, Kelsey J. Ramirez, Darren J. Peterson, Ling Ding, Philip D. Laible, Jeffrey G. Linger, Davinia Salvachúa

{"title":"Feedstock variability impacts the bioconversion of sugar and lignin streams derived from corn stover by Clostridium tyrobutyricum and engineered Pseudomonas putida","authors":"Ilona A. Ruhl, Robert S. Nelson, Rui Katahira, Jacob S. Kruger, Xiaowen Chen, Stefan J. Haugen, Morgan A. Ingraham, Sean P. Woodworth, Hannah Alt, Kelsey J. Ramirez, Darren J. Peterson, Ling Ding, Philip D. Laible, Jeffrey G. Linger, Davinia Salvachúa","doi":"10.1111/1751-7915.70006","DOIUrl":"10.1111/1751-7915.70006","url":null,"abstract":"Feedstock variability represents a challenge in lignocellulosic biorefineries, as it can influence both lignocellulose deconstruction and microbial conversion processes for biofuels and biochemicals production. The impact of feedstock variability on microbial performance remains underexplored, and predictive tools for microbial behaviour are needed to mitigate risks in biorefinery scale-up. Here, twelve batches of corn stover were deconstructed via deacetylation, mechanical refining, and enzymatic hydrolysis to generate lignin-rich and sugar streams. These batches and their derived streams were characterised to identify their chemical components, and the streams were used as substrates for producing muconate and butyrate by engineered Pseudomonas putida and wildtype Clostridium tyrobutyricum, respectively. Bacterial performance (growth, product titers, yields, and productivities) differed among the batches, but no strong correlations were identified between feedstock composition and performance. To provide metabolic insights into the origin of these differences, we evaluated the effect of twenty-three isolated chemical components on these microbes, including three components in relevant bioprocess settings in bioreactors, and we found that growth-inhibitory concentrations were outside the ranges observed in the streams. Overall, this study generates a foundational dataset on P. putida and C. tyrobutyricum performance to enable future predictive models and underscores their resilience in effectively converting fluctuating lignocellulose-derived streams into bioproducts.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11376215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Concepts and criteria defining emerging microbiome applications 定义新兴微生物组应用的概念和标准。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-05 DOI: 10.1111/1751-7915.14550

Tanja Kostic, Michael Schloter, Paulo Arruda, Gabriele Berg, Trevor C. Charles, Paul D. Cotter, George Seghal Kiran, Lene Lange, Emmanuelle Maguin, Annelein Meisner, Leo van Overbeek, Yolanda Sanz, Inga Sarand, Joseph Selvin, Effie Tsakalidou, Hauke Smidt, Martin Wagner, Angela Sessitsch

{"title":"Concepts and criteria defining emerging microbiome applications","authors":"Tanja Kostic, Michael Schloter, Paulo Arruda, Gabriele Berg, Trevor C. Charles, Paul D. Cotter, George Seghal Kiran, Lene Lange, Emmanuelle Maguin, Annelein Meisner, Leo van Overbeek, Yolanda Sanz, Inga Sarand, Joseph Selvin, Effie Tsakalidou, Hauke Smidt, Martin Wagner, Angela Sessitsch","doi":"10.1111/1751-7915.14550","DOIUrl":"10.1111/1751-7915.14550","url":null,"abstract":"In recent years, microbiomes and their potential applications for human, animal or plant health, food production and environmental management came into the spotlight of major national and international policies and strategies. This has been accompanied by substantial R&D investments in both public and private sectors, with an increasing number of products entering the market. Despite widespread agreement on the potential of microbiomes and their uses across disciplines, stakeholders and countries, there is no consensus on what defines a microbiome application. This often results in non-comprehensive communication or insufficient documentation making commercialisation and acceptance of the novel products challenging. To showcase the complexity of this issue we discuss two selected, well-established applications and propose criteria defining a microbiome application and their conditions of use for clear communication, facilitating suitable regulatory frameworks and building trust among stakeholders.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11376781/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142138819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Strangers in a foreign land: ‘Yeastizing’ plant enzymes 异国他乡的陌生人："酵母化 "植物酶。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-09-02 DOI: 10.1111/1751-7915.14525

Kristen Van Gelder, Steffen N. Lindner, Andrew D. Hanson, Juannan Zhou

{"title":"Strangers in a foreign land: ‘Yeastizing’ plant enzymes","authors":"Kristen Van Gelder, Steffen N. Lindner, Andrew D. Hanson, Juannan Zhou","doi":"10.1111/1751-7915.14525","DOIUrl":"10.1111/1751-7915.14525","url":null,"abstract":"Expressing plant metabolic pathways in microbial platforms is an efficient, cost-effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour-intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In response to this challenge, we propose the development of a cost-effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data-driven machine learning framework designed to extract ‘yeastizing’ rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design-build-test cycle.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 9","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.14525","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improving the odds: Artificial intelligence and the great plate count anomaly 提高胜算：人工智能与盘数大反常

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2024-08-30 DOI: 10.1111/1751-7915.70004

Detmer Sipkema

引用次数: 0