Fungal Biology and Biotechnology最新文献

{"title":"Evaluation of synthetic formaldehyde and methanol assimilation pathways in <i>Yarrowia lipolytica</i>.","authors":"Eija Vartiainen,&nbsp;Peter Blomberg,&nbsp;Marja Ilmén,&nbsp;Martina Andberg,&nbsp;Mervi Toivari,&nbsp;Merja Penttilä","doi":"10.1186/s40694-019-0090-9","DOIUrl":"https://doi.org/10.1186/s40694-019-0090-9","url":null,"abstract":"<p><strong>Background: </strong>Crude glycerol coming from biodiesel production is an attractive carbon source for biological production of chemicals. The major impurity in preparations of crude glycerol is methanol, which is toxic for most microbes. Development of microbes, which would not only tolerate the methanol, but also use it as co-substrate, would increase the feasibility of bioprocesses using crude glycerol as substrate.</p><p><strong>Results: </strong>To prevent methanol conversion to CO₂ via formaldehyde and formate, the formaldehyde dehydrogenase (FLD) gene was identified in and deleted from <i>Yarrowia lipolytica.</i> The deletion strain was able to convert methanol to formaldehyde without expression of heterologous methanol dehydrogenases. Further, it was shown that expression of heterologous formaldehyde assimilating enzymes could complement the deletion of FLD. The expression of either 3-hexulose-6-phosphate synthase (HPS) enzyme of ribulose monosphosphate pathway or dihydroxyacetone synthase (DHAS) enzyme of xylulose monosphosphate pathway restored the formaldehyde tolerance of the formaldehyde sensitive Δ<i>fld1</i> strain.</p><p><strong>Conclusions: </strong>In silico, the expression of heterologous formaldehyde assimilation pathways enable <i>Y. lipolytica</i> to use methanol as substrate for growth and metabolite production. In vivo, methanol was shown to be converted to formaldehyde and the enzymes of formaldehyde assimilation were actively expressed in this yeast. However, further development is required to enable <i>Y. lipolytica</i> to efficiently use methanol as co-substrate with glycerol.</p>","PeriodicalId":52292,"journal":{"name":"Fungal Biology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40694-019-0090-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37501808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in <i>Aspergillus niger</i> submerged culture.","authors":"Timothy C Cairns,&nbsp;Claudia Feurstein,&nbsp;Xiaomei Zheng,&nbsp;Li Hui Zhang,&nbsp;Ping Zheng,&nbsp;Jibin Sun,&nbsp;Vera Meyer","doi":"10.1186/s40694-019-0087-4","DOIUrl":"https://doi.org/10.1186/s40694-019-0087-4","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1186/s40694-019-0081-x.].</p>","PeriodicalId":52292,"journal":{"name":"Fungal Biology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40694-019-0087-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37502273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new vector system for targeted integration and overexpression of genes in the crop pathogen <i>Fusarium solani</i>.","authors":"Mikkel Rank Nielsen,&nbsp;Anna Karolina Rilana Holzwarth,&nbsp;Emmett Brew,&nbsp;Natalia Chrapkova,&nbsp;Samba Evelyne Kabemba Kaniki,&nbsp;Kenneth Kastaniegaard,&nbsp;Trine Sørensen,&nbsp;Klaus Ringsborg Westphal,&nbsp;Reinhard Wimmer,&nbsp;Teis Esben Sondergaard,&nbsp;Jens Laurids Sørensen","doi":"10.1186/s40694-019-0089-2","DOIUrl":"https://doi.org/10.1186/s40694-019-0089-2","url":null,"abstract":"<p><strong>Background: </strong>Besides their ability to produce several interesting bioactive secondary metabolites, members of the <i>Fusarium solani</i> species complex comprise important pathogens of plants and humans. One of the major obstacles in understanding the biology of this species complex is the lack of efficient molecular tools for genetic manipulation.</p><p><strong>Results: </strong>To remove this obstacle we here report the development of a reliable system where the vectors are generated through yeast recombinational cloning and inserted into a specific site in <i>F. solani</i> through <i>Agrobacterium tumefaciens</i>-mediated transformation. As proof-of-concept, the enhanced yellow fluorescent protein (eYFP) was inserted in a non-coding genomic position of <i>F. solani</i> and subsequent analyses showed that the resulting transformants were fluorescent on all tested media. In addition, we cloned and overexpressed the Zn(II)₂Cys₆ transcriptional factor <i>fsr6</i> controlling mycelial pigmentation. A transformant displayed deep red/purple pigmentation stemming from bostrycoidin and javanicin.</p><p><strong>Conclusion: </strong>By creating streamlined plasmid construction and fungal transformation systems, we are now able to express genes in the crop pathogen <i>F. solani</i> in a reliable and fast manner. As a case study, we targeted and activated the fusarubin (<i>PKS3</i>: <i>fsr</i>) gene cluster, which is the first case study of secondary metabolites being directly associated with the responsible gene cluster in <i>F. solani</i> via targeted activation. The system provides an approach that in the future can be used by the community to understand the biochemistry and genetics of the <i>Fusarium solani</i> species complex, and is obtainable from Addgene catalog #133094.</p><p><strong>Graphic abstract: </strong></p>","PeriodicalId":52292,"journal":{"name":"Fungal Biology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40694-019-0089-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37501807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bidirectional histone-gene promoters in <i>Aspergillus</i>: characterization and application for multi-gene expression.","authors":"Jakob K H Rendsvig, Christopher T Workman, Jakob B Hoof","doi":"10.1186/s40694-019-0088-3","DOIUrl":"10.1186/s40694-019-0088-3","url":null,"abstract":"<p><strong>Background: </strong>Filamentous fungi are important producers of enzymes and bioactive secondary metabolites and are exploited for industrial purposes. Expression and characterization of biosynthetic pathways requires stable expression of multiple genes in the production host. Fungal promoters are indispensable for the accomplishment of this task, and libraries of promoters that show functionality across diverse fungal species facilitate synthetic biology approaches, pathway expression, and cell-factory construction.</p><p><strong>Results: </strong>In this study, we characterized the intergenic region between the genes encoding histones H4.1 and H3, from five phylogenetically diverse species of <i>Aspergillus</i>, as bidirectional promoters (P<i>h4h3</i>). By expression of the genes encoding fluorescent proteins mRFP1 and mCitrine, we show at the translational and transcriptional level that this region from diverse species is applicable as strong and constitutive bidirectional promoters in <i>Aspergillus nidulans</i>. Bioinformatic analysis showed that the divergent gene orientation of <i>h4.1</i> and <i>h3</i> appears maintained among fungi, and that the P<i>h4h3</i> display conserved DNA motifs among the investigated 85 Aspergilli. Two of the heterologous P<i>h4h3</i>s were utilized for single-locus expression of four genes from the putative malformin producing pathway from <i>Aspergillus brasiliensis</i> in <i>A. nidulans</i>. Strikingly, heterologous expression of <i>mlfA</i> encoding the non-ribosomal peptide synthetase is sufficient for biosynthesis of malformins in <i>A. nidulans</i>, which indicates an iterative use of one adenylation domain in the enzyme. However, this resulted in highly stressed colonies, which was reverted to a healthy phenotype by co-expressing the residual four genes from the putative biosynthetic gene cluster.</p><p><strong>Conclusions: </strong>Our study has documented that P<i>h4h3</i> is a strong constitutive bidirectional promoter and a valuable new addition to the genetic toolbox of at least the genus <i>Aspergillus</i>.</p>","PeriodicalId":52292,"journal":{"name":"Fungal Biology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6900853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37483253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On mycohuman performances: fungi in current artistic research.","authors":"Regine Rapp","doi":"10.1186/s40694-019-0085-6","DOIUrl":"https://doi.org/10.1186/s40694-019-0085-6","url":null,"abstract":"<p><p>This review reflects several artists and their artistic research in the field of hybrid art, bio art, or science art, working with Fungi as both subject matter and medium. The work of Saša Spačal, Tarsh Bates and Theresa Schubert is not representational in the manner of traditional fine art, but works rather through performative, multidisciplinary and research-based strategies to produce artwork through fungal material as such. My research results are based on the series \"Nonhuman subjectivities\" and \"Nonhuman agents\" that Christian de Lutz and I conceived and realized at Art Laboratory Berlin (2016-18) in various formats-exhibitions, workshops, lectures and a conference. The work of Saša Spačal and her colleagues involves creating interactive situations of symbiosis between the fungal and the human. An example of this is <i>Myconnect</i>, in which a biofeedback loop is related between the human participant and Oyster mushroom mycelia through a special encounter, which is mediated by non-linguistic forms of awareness and exchange-sonic, electronic and metabolic. Tarsh Bates' work with <i>Candida albicans</i> and <i>Candida parapsilosis</i> refers to a complex and intimate relation between the human and yeasts that form part of the human microbiome. Bates considers the relationship between humans and yeast as \"CandidaHomo Ecologies\" and sees both partners as equals. She explores this relationship through her work <i>The Surface dynamics of adhesion,</i> examines it from historical and metabolic levels through an installation that includes the live yeast growing on agar mixed with the artist's own blood. Theresa Schubert's installations and site-specific interventions treat living organisms, especially Fungi, as collaborators and co-creators. Her work <i>Growing Geometries</i>-<i>Tattooing Mushrooms</i> follows the morphological development of fungal fruiting bodies through the intervention of a tattoo. Her performative forest walks, especially the <i>Forestal Psyche</i> and also new actions for the \"Mind the Fungi\" project, engage the public in an intimate and multi sensory encounter with Fungi and their surrounding environment.</p>","PeriodicalId":52292,"journal":{"name":"Fungal Biology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40694-019-0085-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37449280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interaction between arbuscular mycorrhizal fungi and Bacillus spp. in soil enhancing growth of crop plants","authors":"Anuroopa Nanjundappa, D. Bagyaraj, A. Saxena, Murugan Kumar, H. Chakdar","doi":"10.1186/s40694-019-0086-5","DOIUrl":"https://doi.org/10.1186/s40694-019-0086-5","url":null,"abstract":"","PeriodicalId":52292,"journal":{"name":"Fungal Biology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40694-019-0086-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49438391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of novel citramalate biosynthesis pathways in <i>Aspergillus niger</i>.","authors":"Abeer H Hossain,&nbsp;Aiko Hendrikx,&nbsp;Peter J Punt","doi":"10.1186/s40694-019-0084-7","DOIUrl":"https://doi.org/10.1186/s40694-019-0084-7","url":null,"abstract":"<p><strong>Background: </strong>The filamentous fungus <i>Aspergillus niger</i> is frequently used for industrial production of fermentative products such as enzymes, proteins and biochemicals. Notable examples of industrially produced <i>A. niger</i> fermentation products are glucoamylase and citric acid. Most notably, the industrial production of citric acid achieves high titers, yield and productivities, a feat that has prompted researchers to propose <i>A. niger</i> to serve as heterologous production host for the industrial production of itaconic acid (IA), a promising sustainable chemical building-block for the fabrication of various synthetic resins, coatings, and polymers. Heterologous production of IA in <i>A. niger</i> has resulted in unexpected levels of metabolic rewiring that has led us to the identification of IA biodegradation pathway in <i>A. niger</i>. In this study we have attempted to identify the final product of the IA biodegradation pathway and analyzed the effect of metabolic rewiring on the bioproduction of 9 industrially relevant organic acids.</p><p><strong>Results: </strong>IA biodegradation manifests in diminishing titers of IA and the occurrence of an unidentified compound in the HPLC profile. Based on published results on the IA biodegradation pathway, we hypothesized that the final product of IA biodegradation in <i>A. niger</i> may be citramalic acid (CM). Based on detailed HPLC analysis, we concluded that the unidentified compound is indeed CM. Furthermore, by transcriptome analysis we explored the effect of metabolic rewiring on the production of 9 industrially relevant organic acids by transcriptome analysis of IA producing and WT <i>A. niger</i> strains. Interestingly, this analysis led to the identification of a previously unknown biosynthetic cluster that is proposed to be involved in the biosynthesis of CM. Upon overexpression of the putative citramalate synthase and a genomically clustered organic acid transporter, we have observed CM bioproduction by <i>A. niger</i>.</p><p><strong>Conclusion: </strong>In this study, we have shown that the end product of IA biodegradation pathway in <i>A. niger</i> is CM. Knock-out of the IA biodegradation pathway results in the cessation of CM production. Furthermore, in this study we have identified a citramalate biosynthesis pathway, which upon overexpression drives citramalate bioproduction in <i>A. niger</i>.</p>","PeriodicalId":52292,"journal":{"name":"Fungal Biology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40694-019-0084-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37449279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Practical guidance for the implementation of the CRISPR genome editing tool in filamentous fungi","authors":"M. Kwon, Tabea Schütze, Sebastian Spohner, S. Haefner, V. Meyer","doi":"10.1186/s40694-019-0082-9","DOIUrl":"https://doi.org/10.1186/s40694-019-0082-9","url":null,"abstract":"","PeriodicalId":52292,"journal":{"name":"Fungal Biology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40694-019-0082-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44994763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dissecting cellobiose metabolic pathway and its application in biorefinery through consolidated bioprocessing in Myceliophthora thermophila","authors":"Jingen Li, Shuying Gu, Zhen Zhao, Bingchen Chen, Qian Liu, T. Sun, Wenliang Sun, Chaoguang Tian","doi":"10.1186/s40694-019-0083-8","DOIUrl":"https://doi.org/10.1186/s40694-019-0083-8","url":null,"abstract":"","PeriodicalId":52292,"journal":{"name":"Fungal Biology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40694-019-0083-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43165069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in <i>Aspergillus niger</i> submerged culture.","authors":"Timothy C Cairns, Claudia Feurstein, Xiaomei Zheng, Li Hui Zhang, Ping Zheng, Jibin Sun, Vera Meyer","doi":"10.1186/s40694-019-0081-x","DOIUrl":"10.1186/s40694-019-0081-x","url":null,"abstract":"<p><strong>Background: </strong>Filamentous fungal cell factories are used to produce numerous proteins, enzymes, and organic acids. Protein secretion and filamentous growth are tightly coupled at the hyphal tip. Additionally, both these processes require ATP and amino acid precursors derived from the citric acid cycle. Despite this interconnection of organic acid production and protein secretion/filamentous growth, few studies in fungi have identified genes which may concomitantly impact all three processes.</p><p><strong>Results: </strong>We applied a novel screen of a global co-expression network in the cell factory <i>Aspergillus niger</i> to identify candidate genes which may concomitantly impact macromorphology, and protein/organic acid fermentation. This identified genes predicted to encode the Golgi localized ArfA GTPase activating protein (GAP, AgeB), and ArfA guanine nucleotide exchange factors (GEFs SecG and GeaB) to be co-expressed with citric acid cycle genes. Consequently, we used CRISPR-based genome editing to place the titratable Tet-on expression system upstream of <i>ageB</i>, <i>secG</i>, and <i>geaB</i> in <i>A. niger</i>. Functional analysis revealed that <i>ageB</i> and <i>geaB</i> are essential whereas <i>secG</i> was dispensable for early filamentous growth. Next, gene expression was titrated during submerged cultivations under conditions for either protein or organic acid production. ArfA regulators played varied and culture-dependent roles on pellet formation. Notably, <i>ageB</i> or <i>geaB</i> expression levels had major impacts on protein secretion, whereas <i>secG</i> was dispensable. In contrast, reduced expression of each predicted ArfA regulator resulted in an absence of citric acid in growth media. Finally, titrated expression of either GEFs resulted in an increase in oxaloacetic acid concentrations in supernatants.</p><p><strong>Conclusion: </strong>Our data suggest that the Golgi may play an underappreciated role in modulating organic acid titres during industrial applications, and that this is SecG, GeaB and AgeB dependent in <i>A. niger</i>. These data may lead to novel avenues for strain optimization in filamentous fungi for improved protein and organic acid titres.</p>","PeriodicalId":52292,"journal":{"name":"Fungal Biology and Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49478643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}