1
|
Sato Y, Kondo H, Suzuki N. Argonaute-independent, Dicer-dependent antiviral defense against RNA viruses. Proc Natl Acad Sci U S A 2024; 121:e2322765121. [PMID: 38865263 PMCID: PMC11194562 DOI: 10.1073/pnas.2322765121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024] Open
Abstract
Antiviral RNA interference (RNAi) is conserved from yeasts to mammals. Dicer recognizes and cleaves virus-derived double-stranded RNA (dsRNA) and/or structured single-stranded RNA (ssRNA) into small-interfering RNAs, which guide effector Argonaute to homologous viral RNAs for digestion and inhibit virus replication. Thus, Argonaute is believed to be essential for antiviral RNAi. Here, we show Argonaute-independent, Dicer-dependent antiviral defense against dsRNA viruses using Cryphonectria parasitica (chestnut blight fungus), which is a model filamentous ascomycetous fungus and hosts a variety of viruses. The fungus has two dicer-like genes (dcl1 and dcl2) and four argonaute-like genes (agl1 to agl4). We prepared a suite of single to quadruple agl knockout mutants with or without dcl disruption. We tested these mutants for antiviral activities against diverse dsRNA viruses and ssRNA viruses. Although both DCL2 and AGL2 worked as antiviral players against some RNA viruses, DCL2 without argonaute was sufficient to block the replication of other RNA viruses. Overall, these results indicate the existence of a Dicer-alone defense and different degrees of susceptibility to it among RNA viruses. We discuss what determines the great difference in susceptibility to the Dicer-only defense.
Collapse
Affiliation(s)
- Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| |
Collapse
|
2
|
Roth MG, Westrick NM, Baldwin TT. Fungal biotechnology: From yesterday to tomorrow. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1135263. [PMID: 37746125 PMCID: PMC10512358 DOI: 10.3389/ffunb.2023.1135263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/07/2023] [Indexed: 09/26/2023]
Abstract
Fungi have been used to better the lives of everyday people and unravel the mysteries of higher eukaryotic organisms for decades. However, comparing progress and development stemming from fungal research to that of human, plant, and bacterial research, fungi remain largely understudied and underutilized. Recent commercial ventures have begun to gain popularity in society, providing a new surge of interest in fungi, mycelia, and potential new applications of these organisms to various aspects of research. Biotechnological advancements in fungal research cannot occur without intensive amounts of time, investments, and research tool development. In this review, we highlight past breakthroughs in fungal biotechnology, discuss requirements to advance fungal biotechnology even further, and touch on the horizon of new breakthroughs with the highest potential to positively impact both research and society.
Collapse
Affiliation(s)
- Mitchell G. Roth
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
| | - Nathaniel M. Westrick
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas T. Baldwin
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| |
Collapse
|
3
|
Malcı K, Watts E, Roberts TM, Auxillos JY, Nowrouzi B, Boll HO, Nascimento CZSD, Andreou A, Vegh P, Donovan S, Fragkoudis R, Panke S, Wallace E, Elfick A, Rios-Solis L. Standardization of Synthetic Biology Tools and Assembly Methods for Saccharomyces cerevisiae and Emerging Yeast Species. ACS Synth Biol 2022; 11:2527-2547. [PMID: 35939789 PMCID: PMC9396660 DOI: 10.1021/acssynbio.1c00442] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
As redesigning organisms using engineering principles
is one of
the purposes of synthetic biology (SynBio), the standardization of
experimental methods and DNA parts is becoming increasingly a necessity.
The synthetic biology community focusing on the engineering of Saccharomyces cerevisiae has been in the foreground in this
area, conceiving several well-characterized SynBio toolkits widely
adopted by the community. In this review, the molecular methods and
toolkits developed for S. cerevisiae are discussed
in terms of their contributions to the required standardization efforts.
In addition, the toolkits designed for emerging nonconventional yeast
species including Yarrowia lipolytica, Komagataella
phaffii, and Kluyveromyces marxianus are
also reviewed. Without a doubt, the characterized DNA parts combined
with the standardized assembly strategies highlighted in these toolkits
have greatly contributed to the rapid development of many metabolic
engineering and diagnostics applications among others. Despite the
growing capacity in deploying synthetic biology for common yeast genome
engineering works, the yeast community has a long journey to go to
exploit it in more sophisticated and delicate applications like bioautomation.
Collapse
Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Emma Watts
- School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3JW Edinburgh, United Kingdom
| | | | - Jamie Yam Auxillos
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Heloísa Oss Boll
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília, Federal District 70910-900, Brazil
| | | | - Andreas Andreou
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Peter Vegh
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sophie Donovan
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Rennos Fragkoudis
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Edward Wallace
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Alistair Elfick
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| |
Collapse
|
4
|
St. Leger RJ. From the Lab to the Last Mile: Deploying Transgenic Approaches Against Mosquitoes. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.804066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ingenious exploitation of transgenic approaches to produce malaria resistant or sterile mosquitoes, or hypervirulent mosquito pathogens, has produced many potential solutions to vector borne diseases. However, in spite of technological feasibility, it has not been determined how well these new methods will work, and how they should be tested and regulated. Some self-limiting transgenic fungal pathogens and mosquitoes are almost field ready, and may be easier to regulate than self-sustaining strategies. However, they require repeat sales and so must show business viability; low-cost mass production is just one of a number of technical constraints that are sometimes treated as an afterthought in technology deployment. No transgenic self-sustaining approach to anopheline control has ever been deployed because of unresolved ethical, social and regulatory issues. These overlapping issues include: 1) the transparency challenge, which requires public discourse, particularly in Africa where releases are proposed, to determine what society is willing to risk given the potential benefits; 2) the transboundary challenge, self-sustaining mosquitoes or pathogens are potentially capable of crossing national boundaries and irreversibly altering ecosystems, and 3) the risk assessment challenge. The polarized debate as to whether these technologies will ever be used to save lives is ongoing; they will founder without a political answer as to how do we interpret the precautionary principle, as exemplified in the Cartagena protocol, in the global context of technological changes.
Collapse
|
5
|
Schmitz L, Kronstad JW, Heimel K. Conditional gene expression reveals stage-specific functions of the unfolded protein response in the Ustilago maydis-maize pathosystem. MOLECULAR PLANT PATHOLOGY 2020; 21:258-271. [PMID: 31802604 PMCID: PMC6988420 DOI: 10.1111/mpp.12893] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Ustilago maydis is a model organism for the study of biotrophic plant-pathogen interactions. The sexual and pathogenic development of the fungus are tightly connected since fusion of compatible haploid sporidia is prerequisite for infection of the host plant, maize (Zea mays). After plant penetration, the unfolded protein response (UPR) is activated and required for biotrophic growth. The UPR is continuously active throughout all stages of pathogenic development in planta. However, since development of UPR deletion mutants stops directly after plant penetration, the role of an active UPR at later stages of development remained to be determined. Here, we established a gene expression system for U. maydis that uses endogenous, conditionally active promoters to either induce or repress expression of a gene of interest during different stages of plant infection. Integration of the expression constructs into the native genomic locus and removal of resistance cassettes were required to obtain a wild-type-like expression pattern. This indicates that genomic localization and chromatin structure are important for correct promoter activity and gene expression. By conditional expression of the central UPR regulator, Cib1, in U. maydis, we show that a functional UPR is required for continuous plant defence suppression after host infection and that U. maydis relies on a robust control system to prevent deleterious UPR hyperactivation.
Collapse
Affiliation(s)
- Lara Schmitz
- Institute for Microbiology and GeneticsDepartment of Molecular Microbiology and GeneticsGöttingen Center for Molecular Biosciences (GZMB)University of GöttingenGrisebachstr. 8D‐37077GöttingenGermany
- International Research Training Group 2172 PRoTECTGöttingen, VancouverGermany
| | - James W. Kronstad
- International Research Training Group 2172 PRoTECTGöttingen, VancouverGermany
- Michael Smith LaboratoriesDepartment of Microbiology and ImmunologyUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Kai Heimel
- Institute for Microbiology and GeneticsDepartment of Molecular Microbiology and GeneticsGöttingen Center for Molecular Biosciences (GZMB)University of GöttingenGrisebachstr. 8D‐37077GöttingenGermany
- International Research Training Group 2172 PRoTECTGöttingen, VancouverGermany
| |
Collapse
|
6
|
Liu Q, Zhang Y, Li F, Li J, Sun W, Tian C. Upgrading of efficient and scalable CRISPR-Cas-mediated technology for genetic engineering in thermophilic fungus Myceliophthora thermophila. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:293. [PMID: 31890021 PMCID: PMC6927189 DOI: 10.1186/s13068-019-1637-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/12/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Thermophilic filamentous fungus Myceliophthora thermophila has great capacity for biomass degradation and is an attractive system for direct production of enzymes and chemicals from plant biomass. Its industrial importance inspired us to develop genome editing tools to speed up the genetic engineering of this fungus. First-generation CRISPR-Cas9 technology was developed in 2017 and, since then, some progress has been made in thermophilic fungi genetic engineering, but a number of limitations remain. They include the need for complex independent expression cassettes for targeting multiplex genomic loci and the limited number of available selectable marker genes. RESULTS In this study, we developed an Acidaminococcus sp. Cas12a-based CRISPR system for efficient multiplex genome editing, using a single-array approach in M. thermophila. These CRISPR-Cas12a cassettes worked well for simultaneous multiple gene deletions/insertions. We also developed a new simple approach for marker recycling that relied on the novel cleavage activity of the CRISPR-Cas12a system to make DNA breaks in selected markers. We demonstrated its performance by targeting nine genes involved in the cellulase production pathway in M. thermophila via three transformation rounds, using two selectable markers neo and bar. We obtained the nonuple mutant M9 in which protein productivity and lignocellulase activity were 9.0- and 18.5-fold higher than in the wild type. We conducted a parallel investigation using our transient CRISPR-Cas9 system and found the two technologies were complementary. Together we called them CRISPR-Cas-assisted marker recycling technology (Camr technology). CONCLUSIONS Our study described new approaches (Camr technology) that allow easy and efficient marker recycling and iterative stacking of traits in the same thermophilic fungus strain either, using the newly established CRISPR-Cas12a system or the established CRISPR-Cas9 system. This Camr technology will be a versatile and efficient tool for engineering, theoretically, an unlimited number of genes in fungi. We expect this advance to accelerate biotechnology-oriented engineering processes in fungi.
Collapse
Affiliation(s)
- Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yongli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fangya Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| |
Collapse
|
7
|
Chen H, Zhu C, Zhu M, Xiong J, Ma H, Zhuo M, Li S. High production of valencene in Saccharomyces cerevisiae through metabolic engineering. Microb Cell Fact 2019; 18:195. [PMID: 31699116 PMCID: PMC6839068 DOI: 10.1186/s12934-019-1246-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/29/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The biological synthesis of high value compounds in industry through metabolically engineered microorganism factories has received increasing attention in recent years. Valencene is a high value ingredient in the flavor and fragrance industry, but the low concentration in nature and high cost of extraction limits its application. Saccharomyces cerevisiae, generally recognized as safe, is one of the most commonly used gene expression hosts. Construction of S. cerevisiae cell factory to achieve high production of valencene will be attractive. RESULTS Valencene was successfully biosynthesized after introducing valencene synthase into S. cerevisiae BJ5464. A significant increase in valencene yield was observed after down-regulation or knock-out of squalene synthesis and other inhibiting factors (such as erg9, rox1) in mevalonate (MVA) pathway using a recyclable CRISPR/Cas9 system constructed in this study through the introduction of Cre/loxP. To increase the supplement of the precursor farnesyl pyrophosphate (FPP), all the genes of FPP upstream in MVA pathway were overexpressed in yeast genome. Furthermore, valencene expression cassettes containing different promoters and terminators were compared, and PHXT7-VS-TTPI1 was found to have excellent performance in valencene production. Finally, after fed-batch fermentation in 3 L bioreactor, valencene production titer reached 539.3 mg/L with about 160-fold improvement compared to the initial titer, which is the highest reported valencene yield. CONCLUSIONS This study achieved high production of valencene in S. cerevisiae through metabolic engineering and optimization of expression cassette, providing good example of microbial overproduction of valuable chemical products. The construction of recyclable plasmid was useful for multiple gene editing as well.
Collapse
Affiliation(s)
- Hefeng Chen
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China
| | - Chaoyi Zhu
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China
| | - Muzi Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Jinghui Xiong
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China
| | - Hao Ma
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China
| | - Min Zhuo
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Higher Education Mega Center, Guangzhou, 510006, China.
| |
Collapse
|
8
|
Strategies for gene disruption and expression in filamentous fungi. Appl Microbiol Biotechnol 2019; 103:6041-6059. [DOI: 10.1007/s00253-019-09953-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 02/02/2023]
|
9
|
Twaruschek K, Spörhase P, Michlmayr H, Wiesenberger G, Adam G. New Plasmids for Fusarium Transformation Allowing Positive-Negative Selection and Efficient Cre- loxP Mediated Marker Recycling. Front Microbiol 2018; 9:1954. [PMID: 30258410 PMCID: PMC6143793 DOI: 10.3389/fmicb.2018.01954] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/02/2018] [Indexed: 11/14/2022] Open
Abstract
In filamentous fungi such as Fusarium graminearum, disruption of multiple genes of interest in the same strain (e.g., to test for redundant gene function) is a difficult task due to the limited availability of reliable selection markers. We have created a series of transformation vectors that allow antibiotic-based selection of transformants and subsequent negative selection for marker removal using thymidine kinase fusions combined with the Cre-loxP system. The fusion genes contain commonly used C-terminal drug resistance markers, either nptII (G418), nat1 (nourseothricin), or hph (hygromycin B). These resistance genes are fused to the sequence encoding Herpes simplex virus thymidine kinase (HSVtk). Despite the presence of the 1 kb HSVtk gene (about ∼30% increase in total marker size), there is only a slight reduction in transformation efficiency on a molar basis. The fusion genes expressed under the Trichoderma pyruvate kinase (PKI) promoter also confer antibiotic resistance in Escherichia coli, allowing straightforward construction of disruption plasmids. For removal of the loxP flanked resistance cassettes, protoplasts of transformants are directly treated with purified Cre recombinase protein. Loss of the HSVtk containing cassette is selected by restoration of resistance to 5-fluoro-2-deoxyuridine (FdU). As a proof of principle, we demonstrated the efficiency of the HSVtk-based marker removal in Fusarium by reversing the disruption phenotype of the gene responsible for production of the red pigment aurofusarin. We first disrupted the FgPKS12 gene via integration of the loxP-flanked HSVtk-nptII cassette into the promoter or the first intron, thereby generating transformants with a white mycelium phenotype. Using Cre recombinase and FdU, the selection marker was subsequently removed, and the resulting transformants regained red pigmentation despite the remaining loxP site. We also found that it is possible to remove several unselected loxP-flanked cassettes with a single Cre protein treatment, as long as one of them contains a negative selectable HSVtk cassette. The negative selection system can also be used to introduce allele swaps into strains without leaving marker sequences, by first disrupting the gene of interest and then complementing the deletion in situ with genomic DNA containing a different allele.
Collapse
Affiliation(s)
| | | | | | - Gerlinde Wiesenberger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | |
Collapse
|
10
|
Lovett B, St Leger RJ. Genetically engineering better fungal biopesticides. PEST MANAGEMENT SCIENCE 2018; 74:781-789. [PMID: 28905488 DOI: 10.1002/ps.4734] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 09/08/2017] [Indexed: 06/07/2023]
Abstract
Microbial insect pathogens offer an alternative means of pest control with the potential to wean us off our heavy reliance on chemical pesticides. Insect pathogenic fungi play an important natural role in controlling disease vectors and agricultural pests. Most commercial products employ Ascomycetes in the genera Metarhizium and Beauveria. However, their utilization has been limited by inconsistent field results as a consequence of sensitivity to abiotic stresses and naturally low virulence. Other naturally occurring biocontrol agents also face these hurdles to successful application, but the availability of complete genomes and recombinant DNA technologies have facilitated design of multiple fungal pathogens with enhanced virulence and stress resistance. Many natural and synthetic genes have been inserted into entomopathogen genomes. Some of the biggest gains in virulence have been obtained using genes encoding neurotoxic peptides, peptides that manipulate host physiology and proteases and chitinases that degrade the insect cuticle. Prokaryotes, particularly extremophiles, are useful sources of genes for improving entomopathogen resistance to ultraviolet (UV) radiation. These biological insecticides are environmentally friendly and cost-effective insect pest control options. © 2017 Society of Chemical Industry.
Collapse
Affiliation(s)
- Brian Lovett
- Department of Entomology, University of Maryland, College Park, MD, USA
| | | |
Collapse
|
11
|
Jiang B, Zhang R, Feng D, Wang F, Liu K, Jiang Y, Niu K, Yuan Q, Wang M, Wang H, Zhang Y, Fang X. A Tet-on and Cre-loxP Based Genetic Engineering System for Convenient Recycling of Selection Markers in Penicillium oxalicum. Front Microbiol 2016; 7:485. [PMID: 27148179 PMCID: PMC4828452 DOI: 10.3389/fmicb.2016.00485] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 03/23/2016] [Indexed: 01/15/2023] Open
Abstract
The lack of selective markers has been a key problem preventing multistep genetic engineering in filamentous fungi, particularly for industrial species such as the lignocellulose degrading Penicillium oxalicum JUA10-1(formerly named as Penicillium decumbens). To resolve this problem, we constructed a genetic manipulation system taking advantage of two established genetic systems: the Cre-loxP system and Tet-on system in P. oxalicum JUA10-1. This system is efficient and convenient. The expression of Cre recombinase was activated by doxycycline since it was controlled by Tet-on system. Using this system, two genes, ligD and bglI, were sequentially disrupted by loxP flanked ptrA. The successful application of this procedure will provide a useful tool for genetic engineering in filamentous fungi. This system will also play an important role in improving the productivity of interesting products and minimizing by-product when fermented by filamentous fungi.
Collapse
Affiliation(s)
- Baojie Jiang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Ruiqin Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Dan Feng
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Fangzhong Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Kuimei Liu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Yi Jiang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Quanquan Yuan
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China; State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong UniversityJinan, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China; State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong UniversityJinan, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| |
Collapse
|
12
|
Zhao H, Lovett B, Fang W. Genetically Engineering Entomopathogenic Fungi. ADVANCES IN GENETICS 2016; 94:137-63. [PMID: 27131325 DOI: 10.1016/bs.adgen.2015.11.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Entomopathogenic fungi have been developed as environmentally friendly alternatives to chemical insecticides in biocontrol programs for agricultural pests and vectors of disease. However, mycoinsecticides currently have a small market share due to low virulence and inconsistencies in their performance. Genetic engineering has made it possible to significantly improve the virulence of fungi and their tolerance to adverse conditions. Virulence enhancement has been achieved by engineering fungi to express insect proteins and insecticidal proteins/peptides from insect predators and other insect pathogens, or by overexpressing the pathogen's own genes. Importantly, protein engineering can be used to mix and match functional domains from diverse genes sourced from entomopathogenic fungi and other organisms, producing insecticidal proteins with novel characteristics. Fungal tolerance to abiotic stresses, especially UV radiation, has been greatly improved by introducing into entomopathogens a photoreactivation system from an archaean and pigment synthesis pathways from nonentomopathogenic fungi. Conversely, gene knockout strategies have produced strains with reduced ecological fitness as recipients for genetic engineering to improve virulence; the resulting strains are hypervirulent, but will not persist in the environment. Coupled with their natural insect specificity, safety concerns can also be mitigated by using safe effector proteins with selection marker genes removed after transformation. With the increasing public concern over the continued use of synthetic chemical insecticides and growing public acceptance of genetically modified organisms, new types of biological insecticides produced by genetic engineering offer a range of environmentally friendly options for cost-effective control of insect pests.
Collapse
Affiliation(s)
- H Zhao
- Zhejiang University, Hangzhou, Zhejiang, China
| | - B Lovett
- University of Maryland, College Park, MD, United States
| | - W Fang
- Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
13
|
Engineering super mycovirus donor strains of chestnut blight fungus by systematic disruption of multilocus vic genes. Proc Natl Acad Sci U S A 2016; 113:2062-7. [PMID: 26858412 DOI: 10.1073/pnas.1522219113] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transmission of mycoviruses that attenuate virulence (hypovirulence) of pathogenic fungi is restricted by allorecognition systems operating in their fungal hosts. We report the use of systematic molecular gene disruption and classical genetics for engineering fungal hosts with superior virus transmission capabilities. Four of five diallelic virus-restricting allorecognition [vegetative incompatibility (vic)] loci were disrupted in the chestnut blight fungus Cryphonectria parasitica using an adapted Cre-loxP recombination system that allowed excision and recycling of selectable marker genes (SMGs). SMG-free, quadruple vic mutant strains representing both allelic backgrounds of the remaining vic locus were then produced through mating. In combination, these super donor strains were able to transmit hypoviruses to strains that were heteroallelic at one or all of the virus-restricting vic loci. These results demonstrate the feasibility of modulating allorecognition to engineer pathogenic fungi for more efficient transmission of virulence-attenuating mycoviruses and enhanced biological control potential.
Collapse
|
14
|
Eusebio-Cope A, Suzuki N. Mycoreovirus genome rearrangements associated with RNA silencing deficiency. Nucleic Acids Res 2015; 43:3802-13. [PMID: 25800742 PMCID: PMC4402544 DOI: 10.1093/nar/gkv239] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 03/06/2015] [Indexed: 01/31/2023] Open
Abstract
Mycoreovirus 1 (MyRV1) has 11 double-stranded RNA genome segments (S1 to S11) and confers hypovirulence to the chestnut blight fungus, Cryphonectria parasitica. MyRV1 genome rearrangements are frequently generated by a multifunctional protein, p29, encoded by a positive-strand RNA virus, Cryphonectria hypovirus 1. One of its functional roles is RNA silencing suppression. Here, we explored a possible link between MyRV1 genome rearrangements and the host RNA silencing pathway using wild-type (WT) and mutant strains of both MyRV1 and the host fungus. Host strains included deletion mutants of RNA silencing components such as dicer-like (dcl) and argonaute-like (agl) genes, while virus strains included an S4 internal deletion mutant MyRV1/S4ss. Consequently, intragenic rearrangements with nearly complete duplication of the three largest segments, i.e. S1, S2 and S3, were observed even more frequently in the RNA silencing-deficient strains Δdcl2 and Δagl2 infected with MyRV1/S4ss, but not with any other viral/host strain combinations. An interesting difference was noted between genome rearrangement events in the two host strains, i.e. generation of the rearrangement required prolonged culture for Δagl2 in comparison with Δdcl2. These results suggest a role for RNA silencing that suppresses genome rearrangements of a dsRNA virus.
Collapse
Affiliation(s)
- Ana Eusebio-Cope
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Nobuhiro Suzuki
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| |
Collapse
|
15
|
Vlaardingerbroek I, Beerens B, Shahi S, Rep M. Fluorescence Assisted Selection of Transformants (FAST): Using flow cytometry to select fungal transformants. Fungal Genet Biol 2015; 76:104-9. [DOI: 10.1016/j.fgb.2015.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 12/11/2022]
|
16
|
Eusebio-Cope A, Sun L, Tanaka T, Chiba S, Kasahara S, Suzuki N. The chestnut blight fungus for studies on virus/host and virus/virus interactions: From a natural to a model host. Virology 2015; 477:164-175. [DOI: 10.1016/j.virol.2014.09.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 09/15/2014] [Accepted: 09/26/2014] [Indexed: 01/03/2023]
|
17
|
|
18
|
Rao G, Sui J, Zeng Y, He C, Duan A, Zhang J. De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana. PLoS One 2014; 9:e109122. [PMID: 25275458 PMCID: PMC4183547 DOI: 10.1371/journal.pone.0109122] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 09/08/2014] [Indexed: 01/04/2023] Open
Abstract
Salix matsudana Koidz. is a deciduous, rapidly growing, and drought resistant tree and is one of the most widely distributed and commonly cultivated willow species in China. Currently little transcriptomic and small RNAomic data are available to reveal the genes involve in the stress resistant in S. matsudana. Here, we report the RNA-seq analysis results of both transcriptome and small RNAome data using Illumina deep sequencing of shoot tips from two willow variants(Salix. matsudana and Salix matsudana Koidz. cultivar 'Tortuosa'). De novo gene assembly was used to generate the consensus transcriptome and small RNAome, which contained 106,403 unique transcripts with an average length of 944 bp and a total length of 100.45 MB, and 166 known miRNAs representing 35 miRNA families. Comparison of transcriptomes and small RNAomes combined with quantitative real-time PCR from the two Salix libraries revealed a total of 292 different expressed genes(DEGs) and 36 different expressed miRNAs (DEMs). Among the DEGs and DEMs, 196 genes and 24 miRNAs were up regulated, 96 genes and 12 miRNA were down regulated in S. matsudana. Functional analysis of DEGs and miRNA targets showed that many genes were involved in stress resistance in S. matsudana. Our global gene expression profiling presents a comprehensive view of the transcriptome and small RNAome which provide valuable information and sequence resources for uncovering the stress response genes in S. matsudana. Moreover the transcriptome and small RNAome data provide a basis for future study of genetic resistance in Salix.
Collapse
Affiliation(s)
- Guodong Rao
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China
| | - Jinkai Sui
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China
| | - Yanfei Zeng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China
| | - Caiyun He
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China
| | - Aiguo Duan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China
| |
Collapse
|
19
|
Zhang DX, Spiering MJ, Nuss DL. Characterizing the roles of Cryphonectria parasitica RNA-dependent RNA polymerase-like genes in antiviral defense, viral recombination and transposon transcript accumulation. PLoS One 2014; 9:e108653. [PMID: 25268858 PMCID: PMC4182546 DOI: 10.1371/journal.pone.0108653] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/03/2014] [Indexed: 01/24/2023] Open
Abstract
An inducible RNA-silencing pathway, involving a single Dicer protein, DCL2, and a single Argonaute protein, AGL2, was recently shown to serve as an effective antiviral defense response in the chestnut blight fungus Cryphonectria parasitica. Eukaryotic RNA-dependent RNA polymerases (RdRPs) are frequently involved in transcriptional and posttranscriptional gene silencing and antiviral defense. We report here the identification and characterization of four RdRP genes (rdr1–4) in the C. parasitica genome. Sequence relationships with other eukaryotic RdRPs indicated that RDR1 and RDR2 were closely related to QDE-1, an RdRP involved in RNA silencing (“quelling”) in Neurospora crassa, whereas RDR3 was more closely related to the meiotic silencing gene SAD-1 in N. crassa. The RdRP domain of RDR4, related to N. crassa RRP-3 of unknown function, was truncated and showed evidence of alternative splicing. Similar to reports for dcl2 and agl2, the expression levels for rdr3 and rdr4 increased after hypovirus CHV-1/EP713 infection, while expression levels of rdr1 and rdr2 were unchanged. The virus-responsive induction patterns for rdr3 and rdr4 were altered in the Δdcl2 and Δagl2 strains, suggesting some level of interaction between rdr3 and rdr4 and the dcl2/agl2 silencing pathway. Single rdr gene knockouts Δrdr1–4, double knockouts Δrdr1/2, Δrdr2/3, Δrdr1/3, and a triple knockout, Δrdr1/2/3, were generated and evaluated for effects on fungal phenotype, the antiviral defense response, viral RNA recombination activity and transposon expression. None of the single or multiple rdr knockout strains displayed any phenotypic differences from the parental strains with or without viral infection or any significant changes in viral RNA accumulation or recombination activity or transposon RNA accumulation, indicating no detectable contribution by the C. parasitica rdr genes to these processes.
Collapse
Affiliation(s)
- Dong-Xiu Zhang
- Institute for Bioscience and Biotechnology Research and Department of Cell Biology and Molecular Genetics, University of Maryland, Rockville, Maryland, United States of America
| | - Martin J. Spiering
- Institute for Bioscience and Biotechnology Research and Department of Cell Biology and Molecular Genetics, University of Maryland, Rockville, Maryland, United States of America
| | - Donald L. Nuss
- Institute for Bioscience and Biotechnology Research and Department of Cell Biology and Molecular Genetics, University of Maryland, Rockville, Maryland, United States of America
- * E-mail:
| |
Collapse
|
20
|
Vegetative incompatibility loci with dedicated roles in allorecognition restrict mycovirus transmission in chestnut blight fungus. Genetics 2014; 197:701-14. [PMID: 24690544 DOI: 10.1534/genetics.114.164574] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vegetative incompatibility (vic), a form of nonself allorecognition, operates widely in filamentous fungi and restricts transmission of virulence-attenuating hypoviruses in the chestnut blight fungus Cryphonectria parasitica. We report here the use of a polymorphism-based comparative genomics approach to complete the molecular identification of the genetically defined C. parasitica vic loci with the identification of vic1 and vic3. The vic1 locus in the C. parasitica reference strain EP155 consists of a polymorphic HET-domain-containing 771-aa ORF designated vic1a-2, which shares 91% identity with the corresponding vic1a-1 allele, and a small (172 aa) idiomorphic DUF1909-domain-containing ORF designated vic1b-2 that is absent at the vic1-1 locus. Gene disruption of either vic1a-2 or vic1b-2 in strain EP155 eliminated restrictions on virus transmission when paired with a vic1 heteroallelic strain; however, only disruption of vic1a-2 abolished the incompatible programmed cell death (PCD) reaction. The vic3 locus of strain EP155 contains two polymorphic ORFs of 599 aa (vic3a-1) and 102 aa (vic3b-1) that shared 46 and 85% aa identity with the corresponding vic3a-2 and vic3b-2 alleles, respectively. Disruption of either vic3a-1 or vic3b-1 resulted in increased virus transmission. However, elimination of PCD required disruption of both vic3a and vic3b. Additional allelic heterogeneity included a sequence inversion and a 8.5-kb insertion containing a LTR retrotransposon sequence and an adjacent HET-domain gene at the vic1 locus and a 7.7-kb sequence deletion associated with a nonfunctional, pseudo vic locus. Combined gene disruption studies formally confirmed restriction of mycovirus transmission by five C. parasitica vic loci and suggested dedicated roles in allorecognition. The relevance of these results to the acquisition and maintenance of vic genes and the potential for manipulation of vic alleles for enhanced mycovirus transmission are discussed.
Collapse
|
21
|
Genetic surgery in fungi: employing site-specific recombinases for genome manipulation. Appl Microbiol Biotechnol 2014; 98:1971-82. [DOI: 10.1007/s00253-013-5480-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 12/21/2022]
|
22
|
Suzuki N. [Cryphonectria parasitica as a host of fungal viruses: a tool useful to unravel the mycovirus world]. Uirusu 2014; 64:11-24. [PMID: 25765976 DOI: 10.2222/jsv.64.11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
There appear to be over a million of fungal species including those that have been unidentified and unreported, where a variety of viruses make a world as well. Studies on a very small number of them conducted during the last two decades demonstrated the infectivity of fungal viruses that had previously been assumed to be inheritable, indigenus and non-infectious. Also, great technical advances were achieved. The chest blight fungus (Cryphonectria parasitica), a phytopathogenic ascomycetous fungus, has emerged as a model filamentous fungus for fungal virology. The genome sequence with annotations, albeit not thorough, many useful research tools, and gene manipulation technologies are available for this fungus. Importantly, C. parasitica can support replication of homologous viruses naturally infecting it, in addition to heterologous viruses infecting another plant pathogenic fungus, Rosellinia necatrix taxonomically belonging to a different order. In this article, I overview general properties of fungal viruses and advantages of the chestnut blight fungus as a mycovirus host. Furthermore, I introduce two recent studies carried out using this fungal host:''Defective interfering RNA and RNA silencing that regulate the replication of a partitivirus'' and'' RNA silencing and RNA recombination''.
Collapse
Affiliation(s)
- Nobuhiro Suzuki
- Agrivirology Laboratory, Group of Plant/Microbe Interactions, Institute of Plant Science and Resources, Okayama University
| |
Collapse
|