101
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Coordinated and distinct functions of velvet proteins in Fusarium verticillioides. EUKARYOTIC CELL 2014; 13:909-18. [PMID: 24792348 DOI: 10.1128/ec.00022-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Velvet-domain-containing proteins are broadly distributed within the fungal kingdom. In the corn pathogen Fusarium verticillioides, previous studies showed that the velvet protein F. verticillioides VE1 (FvVE1) is critical for morphological development, colony hydrophobicity, toxin production, and pathogenicity. In this study, tandem affinity purification of FvVE1 revealed that FvVE1 can form a complex with the velvet proteins F. verticillioides VelB (FvVelB) and FvVelC. Phenotypic characterization of gene knockout mutants showed that, as in the case of FvVE1, FvVelB regulated conidial size, hyphal hydrophobicity, fumonisin production, and oxidant resistance, while FvVelC was dispensable for these biological processes. Comparative transcriptional analysis of eight genes involved in the ROS (reactive oxygen species) removal system revealed that both FvVE1 and FvVelB positively regulated the transcription of a catalase-encoding gene, F. verticillioides CAT2 (FvCAT2). Deletion of FvCAT2 resulted in reduced oxidant resistance, providing further explanation of the regulation of oxidant resistance by velvet proteins in the fungal kingdom.
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102
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Sulfonylurea resistance reconstitution as a novel strategy for ILV2-specific integration in Magnaporthe oryzae. Fungal Genet Biol 2014; 68:71-6. [PMID: 24769367 DOI: 10.1016/j.fgb.2014.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 11/23/2022]
Abstract
A sulfonylurea-resistant allele of the ILV2 gene encoding an acetolactate synthase from the rice-blast fungus Magnaporthe oryzae has been extensively used in fungal transformation as a dominant selectable marker that confers resistance to chlorimuron ethyl. We devised a novel strategy for site-specific integration of foreign DNA via sulfonylurea resistance reconstitution (SRR) by replacing the native ILV2 with the sulfonylurea-resistant ILV2(SUR) variant. In contrast to random ectopic integration, SRR-based targeted incorporation at a defined locus eliminates position/orientation effects, unnecessary mutations and/or variation in gene expression. Independent transformants derived from the same SRR construct showed consistent and reproducible fluorescent signal in M. oryzae. Furthermore, the high frequency (>95%) of ILV2-specific targeted integration via SRR circumvents the need for a deficiency in non-homologous end joining (NHEJ) pathway in the recipient strain. Unlike the split-marker technique, which is particularly suitable for targeted gene replacement, the SRR strategy should prove useful for promoter analyses, gene tagging and/or complementation analyses in filamentous fungi.
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103
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Gold SE. Let's get physical!: Comment on "Physical methods for genetic transformation of fungi and yeast" by Ana L. Rivera, Denis Magaña-Ortíz, Miguel Gómez-Lim, Francisco Fernández and Achim M. Loske. Phys Life Rev 2014; 11:215-6. [PMID: 24721713 DOI: 10.1016/j.plrev.2014.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 11/15/2022]
Affiliation(s)
- Scott E Gold
- Toxicology and Mycotoxin Research Unit, Russell Research Center, USDA Agricultural Research Service, Athens, GA 30605, USA
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104
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Shao Y, Lei M, Mao Z, Zhou Y, Chen F. Insights into Monascus biology at the genetic level. Appl Microbiol Biotechnol 2014; 98:3911-22. [PMID: 24633442 DOI: 10.1007/s00253-014-5608-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/10/2014] [Accepted: 02/10/2014] [Indexed: 12/24/2022]
Abstract
The genus of Monascus was nominated by van Tieghem in 1884, but its fermented product-red mold rice (RMR), namely red yeast rice, has been used as folk medicines, food colorants, and fermentation starters for more than thousands of years in oriental countries. Nowadays, RMR is widely developed as food supplements around the world due to its functional compounds such as monacolin K (MK, also called lovastatin) and γ-aminobutyric acid. But the usage of RMR also incurs controversy resulting from contamination of citrinin (a kind of mycotoxin) produced by some Monascus strains. In the past decade, it has made great progress to Monascus spp. at the genetic level with the application of molecular biology techniques to restrain the citrinin production and increase the yields of MK and pigment in RMR, as well as aid Monascus classification and phylogenesis. Up to now, hundreds of papers about Monascus molecular biology (MMB) have been published in the international primary journals. However, to our knowledge, there is no MMB review issued until now. In this review, current understanding of Monascus spp. from the view of molecular biology will be covered and insights into research areas that need to be further investigated will also be discussed.
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Affiliation(s)
- Yanchun Shao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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105
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Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius. Int J Food Microbiol 2014; 179:10-7. [PMID: 24699234 DOI: 10.1016/j.ijfoodmicro.2014.03.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/03/2014] [Accepted: 03/10/2014] [Indexed: 11/24/2022]
Abstract
Ochratoxin A (OTA) is a potent mycotoxin produced by Aspergillus and Penicillium species and is a common contaminant of a wide variety of food commodities, with Aspergillus carbonarius being the main producer of OTA contamination in grapes and wine. The molecular structure of OTA comprises a dihydroisocoumarin ring linked to phenylalanine and, as shown in different producing fungal species, a polyketide synthase (PKS) is a component of the OTA biosynthetic pathway. Similar to observations in other filamentous ascomycetes, the genome sequence of A. carbonarius contains a large number of genes predicted to encode PKSs. In this work a pks gene identified within the putative OTA cluster of A. carbonarius, designated as AcOTApks, was inactivated and the resulting mutant strain was unable to produce OTA, confirming the role of AcOTApks in this biosynthetic pathway. AcOTApks protein is characteristic of the highly reduced (HR)-PKS family, and also contains a putative methyltransferase domain likely responsible for the addition of the methyl group to the OTA polyketide structure. AcOTApks is different from the ACpks protein that we previously described in A. carbonarius, which showed an expression profile compatible with OTA production. We performed phylogenetic analyses of the β-ketosynthase and acyl-transferase domains of the OTA PKSs that had been identified and characterized in different OTA producing fungal species. The phylogenetic results were similar for both domains analyzed and showed that OTA PKS of A. carbonarius, Aspergillus niger and Aspergillus ochraceus clustered in a monophyletic group with 100% bootstrap support suggesting a common origin, while the other OTA PKSs analyzed were phylogenetically distant. A quantitative RT-PCR assay monitored AcOTApks expression during fungal growth and concomitant production of OTA by A. carbonarius in synthetic grape medium. A clear correlation between the expression profile of AcOTApks and kinetics of OTA production was observed, with AcOTApks reaching its maximum level of transcription before OTA accumulation in mycelium reached its highest level, confirming the fact that gene transcription always precedes phenotypic production.
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106
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Koh CMJ, Liu Y, Moehninsi, Du M, Ji L. Molecular characterization of KU70 and KU80 homologues and exploitation of a KU70-deficient mutant for improving gene deletion frequency in Rhodosporidium toruloides. BMC Microbiol 2014; 14:50. [PMID: 25188820 PMCID: PMC4101874 DOI: 10.1186/1471-2180-14-50] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 02/21/2014] [Indexed: 01/19/2023] Open
Abstract
Background Rhodosporidium toruloides is a β-carotenoid accumulating, oleaginous yeast that has great biotechnological potential. The lack of reliable and efficient genetic manipulation tools have been a major hurdle blocking its adoption as a biotechnology platform. Results We report for the first time the development of a highly efficient targeted gene deletion method in R. toruloides ATCC 10657 via Agrobacterium tumefaciens-mediated transformation. To further improve targeting frequency, the KU70 and KU80 homologs in R. toruloides were isolated and characterized in detail. A KU70-deficient mutant (∆ku70e) generated with the hygromycin selection cassette removed by the Cre-loxP recombination system showed a dramatically improved targeted gene deletion frequency, with over 90% of the transformants being true knockouts when homology sequence length of at least 1 kb was used. Successful gene targeting could be made with homologous flanking sequences as short as 100 bp in the ∆ku70e strain. KU70 deficiency did not perturb cell growth although an elevated sensitivity to DNA mutagenic agents was observed. Compared to the other well-known oleaginous yeast, Yarrowia lipolytica, R. toruloides KU70/KU80 genes contain much higher density of introns and are the most GC-rich KU70/KU80 genes reported. Conclusions The KU70-deficient mutant generated herein was effective in improving gene deletion frequency and allowed shorter homology sequences to be used for gene targeting. It retained the key oleaginous and fast growing features of R. toruloides. The strain should facilitate both fundamental and applied studies in this important yeast, with the approaches taken here likely to be applicable in other species in subphylum Pucciniomycotina.
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107
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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]
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108
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109
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Bloemendal S, Löper D, Terfehr D, Kopke K, Kluge J, Teichert I, Kück U. Tools for advanced and targeted genetic manipulation of the β-lactam antibiotic producer Acremonium chrysogenum. J Biotechnol 2014; 169:51-62. [DOI: 10.1016/j.jbiotec.2013.10.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/22/2013] [Accepted: 10/25/2013] [Indexed: 11/30/2022]
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110
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Blatzer M, Gsaller F, Abt B, Schrettl M, Specht T, Haas H. An endogenous promoter for conditional gene expression in Acremonium chrysogenum: the xylan and xylose inducible promoter xyl1(P.). J Biotechnol 2013; 169:82-6. [PMID: 24246269 DOI: 10.1016/j.jbiotec.2013.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 10/31/2013] [Accepted: 11/06/2013] [Indexed: 11/28/2022]
Abstract
Acremonium chrysogenum is the natural producer of the beta-lactam antibiotic cephalosporin C and therefore of significant biotechnological importance. Here we identified and characterized the xylanase-encoding xyl1 gene and demonstrate that its promoter, xyl1(P), is suitable for conditional expression of heterologous genes in A. chrysogenum. This was shown by xylose and xylan-inducible xyl1(P)-driven expression of genes encoding green fluorescence protein and phleomycin resistance. Moreover, we demonstrate the potential of the xyl1(P) promoter for selection marker recycling. Taken together, these finding will help to overcome the limitation in genetic tools in this important filamentous fungus.
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Affiliation(s)
- Michael Blatzer
- Christian Doppler Laboratory for Fungal Biotechnology, Division of Molecular Biology/Biocenter, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Fabio Gsaller
- Christian Doppler Laboratory for Fungal Biotechnology, Division of Molecular Biology/Biocenter, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Beate Abt
- Christian Doppler Laboratory for Fungal Biotechnology, Division of Molecular Biology/Biocenter, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Markus Schrettl
- Christian Doppler Laboratory for Fungal Biotechnology, Division of Molecular Biology/Biocenter, Innrain 80-82, A-6020 Innsbruck, Austria; Sandoz GmbH, Biochemiestraße 10, 6250 Kundl, Austria
| | - Thomas Specht
- Sandoz GmbH, Biochemiestraße 10, 6250 Kundl, Austria
| | - Hubertus Haas
- Christian Doppler Laboratory for Fungal Biotechnology, Division of Molecular Biology/Biocenter, Innrain 80-82, A-6020 Innsbruck, Austria.
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111
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Bidirectional-genetics platform, a dual-purpose mutagenesis strategy for filamentous fungi. EUKARYOTIC CELL 2013; 12:1547-53. [PMID: 24058171 DOI: 10.1128/ec.00234-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Rapidly increasing fungal genome sequences call for efficient ways of generating mutants to translate quickly gene sequences into their functions. A reverse genetic strategy via targeted gene replacement (TGR) has been inefficient for many filamentous fungi due to dominant production of undesirable ectopic transformants. Although large-scale random insertional mutagenesis via transformation (i.e., forward genetics) facilitates high-throughput uncovering of novel genes of interest, generating a huge number of transformants, which is necessary to ensure the likelihood of mutagenizing most genes, is time-consuming. We propose a new strategy, entitled the Bidirectional-Genetics (BiG) platform, which combines both forward and reverse genetic strategies by recycling ectopic transformants derived from TGR as a source for random insertional mutants. The BiG platform was evaluated using the rice blast fungus Magnaporthe oryzae as a model. Over 10% of >1,000 M. oryzae ectopic transformants, generated during disruption of specific genes, displayed abnormality in vegetative growth, pigmentation, and/or asexual reproduction. In this pool of putative mutants, we isolated insertional mutants with mutations in three genes involved in histidine biosynthesis (MoHIS5), vegetative growth (MoVPS74), or conidiophore formation (MoFRQ) (where "Mo" indicates "M. oryzae"), supporting the utility of this platform for systematic gene function studies.
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112
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Molecular tools for functional genomics in filamentous fungi: recent advances and new strategies. Biotechnol Adv 2013; 31:1562-74. [PMID: 23988676 DOI: 10.1016/j.biotechadv.2013.08.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 07/06/2013] [Accepted: 08/05/2013] [Indexed: 11/22/2022]
Abstract
Advances in genetic transformation techniques have made important contributions to molecular genetics. Various molecular tools and strategies have been developed for functional genomic analysis of filamentous fungi since the first DNA transformation was successfully achieved in Neurospora crassa in 1973. Increasing amounts of genomic data regarding filamentous fungi are continuously reported and large-scale functional studies have become common in a wide range of fungal species. In this review, various molecular tools used in filamentous fungi are compared and discussed, including methods for genetic transformation (e.g., protoplast transformation, electroporation, and microinjection), the construction of random mutant libraries (e.g., restriction enzyme mediated integration, transposon arrayed gene knockout, and Agrobacterium tumefaciens mediated transformation), and the analysis of gene function (e.g., RNA interference and transcription activator-like effector nucleases). We also focused on practical strategies that could enhance the efficiency of genetic manipulation in filamentous fungi, such as choosing a proper screening system and marker genes, assembling target-cassettes or vectors effectively, and transforming into strains that are deficient in the nonhomologous end joining pathway. In summary, we present an up-to-date review on the different molecular tools and latest strategies that have been successfully used in functional genomics in filamentous fungi.
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113
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Wang S, Xing M, Tian S, Gou D, Huang B, Liu G. Establishment of an efficient RNA silencing system in Trichoderma koningii using DsRed as a reporter. Folia Microbiol (Praha) 2013; 58:601-6. [PMID: 23588496 DOI: 10.1007/s12223-013-0246-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 03/19/2013] [Indexed: 02/02/2023]
Abstract
We aimed to establish an efficient RNA interference (RNAi) system in the industrially important filamentous fungus Trichoderma koningii using the DsRed protein as a reporter of the silencing process. To accomplish this, a DsRed expression cassette was transformed into T. koningii, and a recombinant strain that stably expressed DsRed was obtained. Next, a vector-directing expression of a DsRed hairpin RNA was constructed and transformed into the T. koningii recipient strain. Approximately 79 % of transformants displayed a decrease in DsRed fluorescence, and expression of DsRed in some transformants appeared to be fully suppressed. Characterization of randomly selected transformants by genomic DNA PCR analysis, real-time PCR quantification, and western blot confirmed downregulation of gene expression at different levels. The RNA silencing approach described here for T. koningii is effective, and the DsRed reporter gene provides a convenient tool for identification of silenced fungal transformants by their DsRed fluorescence compared to the control strain. The results of this study demonstrate the power of RNAi in T. koningii, which supports the use of this technology for strain development programs and functional genomics studies in industrial fungal strains.
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Affiliation(s)
- Shaowen Wang
- School of Life Sciences, Northeast Normal University, Changchun, 130024, China
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114
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He Y, Liu Q, Shao Y, Chen F. Ku70 and ku80 null mutants improve the gene targeting frequency in Monascus ruber M7. Appl Microbiol Biotechnol 2013; 97:4965-76. [PMID: 23546425 DOI: 10.1007/s00253-013-4851-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 03/10/2013] [Accepted: 03/11/2013] [Indexed: 01/25/2023]
Abstract
Normally, gene targeting by homologous recombination occurs rarely during a transformation process since non-homologous recombination is predominant in filamentous fungi. In our previous researches, the average gene replacement frequency (GRF) in Monascus ruber M7 was as low as 15 %. To develop a highly efficient gene targeting system for M. ruber M7, two M. ruber M7 null mutants of ku70 (MrΔku70) and ku80 (MrΔku80) were constructed which had no apparent defects in the development including vegetative growth, colony phenotype, microscopic morphology and spore yield compared with M. ruber M7. In addition, the production of some significant secondary metabolites such as pigments and citrinin had no differences between the two disruptants and the wild-type strain. Further results revealed that the GRFs of triA (encoding a putative acetyltransferase) were 42.2 % and 61.5 % in the MrΔku70 and MrΔku80 strains, respectively, while it was only about 20 % in M. ruber M7. Furthermore, GRFs of these two disruptants at other loci (the pigE, fmdS genes in MrΔku70 and the ku70 gene in MrΔku80) were investigated, and the results indicated that GRFs in the MrΔku70 strain and the MrΔku80 strain were doubled and tripled compared with that in M. ruber M7, respectively. Therefore, the ku70 and ku80 null mutants of M. ruber M7, especially the ku80-deleted strain, will be excellent hosts for efficient gene targeting.
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Affiliation(s)
- Yi He
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
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115
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Recent advances in the biosynthesis of penicillins, cephalosporins and clavams and its regulation. Biotechnol Adv 2013; 31:287-311. [DOI: 10.1016/j.biotechadv.2012.12.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 11/30/2012] [Accepted: 12/01/2012] [Indexed: 11/23/2022]
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116
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Sexual reproduction and mating-type-mediated strain development in the penicillin-producing fungus Penicillium chrysogenum. Proc Natl Acad Sci U S A 2013; 110:1476-81. [PMID: 23307807 DOI: 10.1073/pnas.1217943110] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Penicillium chrysogenum is a filamentous fungus of major medical and historical importance, being the original and present-day industrial source of the antibiotic penicillin. The species has been considered asexual for more than 100 y, and despite concerted efforts, it has not been possible to induce sexual reproduction, which has prevented sexual crosses being used for strain improvement. However, using knowledge of mating-type (MAT) gene organization, we now describe conditions under which a sexual cycle can be induced leading to production of meiotic ascospores. Evidence of recombination was obtained using both molecular and phenotypic markers. The identified heterothallic sexual cycle was used for strain development purposes, generating offspring with novel combinations of traits relevant to penicillin production. Furthermore, the MAT1-1-1 mating-type gene, known primarily for a role in governing sexual identity, was also found to control transcription of a wide range of genes with biotechnological relevance including those regulating penicillin production, hyphal morphology, and conidial formation. These discoveries of a sexual cycle and MAT gene function are likely to be of broad relevance for manipulation of other asexual fungi of economic importance.
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117
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The first promoter for conditional gene expression in Acremonium chrysogenum: Iron starvation-inducible mir1P. J Biotechnol 2013; 163:77-80. [DOI: 10.1016/j.jbiotec.2012.10.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 10/10/2012] [Accepted: 10/12/2012] [Indexed: 11/20/2022]
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118
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Efficient sequential repetitive gene deletions in Neurospora crassa employing a self-excising β-recombinase/six cassette. J Microbiol Methods 2012; 92:236-43. [PMID: 23246910 DOI: 10.1016/j.mimet.2012.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 12/07/2012] [Accepted: 12/07/2012] [Indexed: 11/20/2022]
Abstract
Despite its long-standing history as a model organism, Neurospora crassa has limited tools for repetitive gene deletions utilizing recyclable self-excising marker systems. Here we describe, for the first time, the functionality of a bacterial recombination system employing β-recombinase acting on six recognition sequences (β-rec/six) in N. crassa, which allowed repetitive site-specific gene deletion and marker recycling. We report generating the mus-51 deletion strain using this system, recycling the marker cassette, and subsequently deleting the global transcriptional regulator gene cre-1.
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119
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Liu H, Zheng Z, Wang P, Gong G, Wang L, Zhao G. Morphological changes induced by class III chitin synthase gene silencing could enhance penicillin production of Penicillium chrysogenum. Appl Microbiol Biotechnol 2012. [PMID: 23179625 DOI: 10.1007/s00253-012-4581-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chitin synthases catalyze the formation of β-(1,4)-glycosidic bonds between N-acetylglucosamine residues to form the unbranched polysaccharide chitin, which is the major component of cell walls in most filamentous fungi. Several studies have shown that chitin synthases are structurally and functionally divergent and play crucial roles in the growth and morphogenesis of the genus Aspergillus although little research on this topic has been done in Penicillium chrysogenum. We used BLAST to find the genes encoding chitin synthases in P. chrysogenum related to chitin synthase genes in Aspergillus nidulans. Three homologous sequences coding for a class III chitin synthase CHS4 and two hypothetical proteins in P. chrysogenum were found. The gene which product showed the highest identity and encoded the class III chitin synthase CHS4 was studied in detail. To investigate the role of CHS4 in P. chrysogenum morphogenesis, we developed an RNA interference system to silence the class III chitin synthase gene chs4. After transformation, mutants exhibited a slow growth rate and shorter and more branched hyphae, which were distinct from those of the original strain. The results also showed that the conidiation efficiency of all transformants was reduced sharply and indicated that chs4 is essential in conidia development. The morphologies of all transformants and the original strain in penicillin production were investigated by light microscopy, which showed that changes in chs4 expression led to a completely different morphology during fermentation and eventually caused distinct penicillin yields, especially in the transformants PcRNAi1-17 and PcRNAi2-1 where penicillin production rose by 27 % and 41 %, respectively.
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Affiliation(s)
- Hui Liu
- Key Lab of Ion Beam Bioengineering, Chinese Academy of Science, Hefei, Anhui 230031, People's Republic of China
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120
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Gibbons JG, Rokas A. The function and evolution of the Aspergillus genome. Trends Microbiol 2012; 21:14-22. [PMID: 23084572 DOI: 10.1016/j.tim.2012.09.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Revised: 09/20/2012] [Accepted: 09/24/2012] [Indexed: 10/27/2022]
Abstract
Species in the filamentous fungal genus Aspergillus display a wide diversity of lifestyles and are of great importance to humans. The decoding of genome sequences from a dozen species that vary widely in their degree of evolutionary affinity has galvanized studies of the function and evolution of the Aspergillus genome in clinical, industrial, and agricultural environments. Here, we synthesize recent key findings that shed light on the architecture of the Aspergillus genome, on the molecular foundations of the genus' astounding dexterity and diversity in secondary metabolism, and on the genetic underpinnings of virulence in Aspergillus fumigatus, one of the most lethal fungal pathogens. Many of these insights dramatically expand our knowledge of fungal and microbial eukaryote genome evolution and function and argue that Aspergillus constitutes a superb model clade for the study of functional and comparative genomics.
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Affiliation(s)
- John G Gibbons
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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121
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Sivagurunathan S, Schnittker RR, Nandini S, Plamann MD, King SJ. A mouse neurodegenerative dynein heavy chain mutation alters dynein motility and localization in Neurospora crassa. Cytoskeleton (Hoboken) 2012; 69:613-24. [PMID: 22991199 DOI: 10.1002/cm.21049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 06/27/2012] [Indexed: 01/08/2023]
Abstract
Cytoplasmic dynein is responsible for the transport and delivery of cargoes in organisms ranging from humans to fungi. Dysfunction of dynein motor machinery due to mutations in dynein or its activating complex dynactin can result in one of several neurological diseases in mammals. The mouse Legs at odd angles (Loa) mutation in the tail domain of the dynein heavy chain has been shown to lead to progressive neurodegeneration in mice. The mechanism by which the Loa mutation affects dynein function is just beginning to be understood. In this work, we generated the dynein tail mutation observed in Loa mice into the Neurospora crassa genome and utilized cell biological and complementing biochemical approaches to characterize how that tail mutation affected dynein function. We determined that the Loa mutation exhibits several subtle defects upon dynein function in N. crassa that were not seen in mice, including alterations in dynein localization, impaired velocity of vesicle transport, and in the biochemical properties of purified motors. Our work provides new information on the role of the tail domain on dynein function and points out areas of future research that will be of interest to pursue in mammalian systems.
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Olson DG, McBride JE, Joe Shaw A, Lynd LR. Recent progress in consolidated bioprocessing. Curr Opin Biotechnol 2012; 23:396-405. [DOI: 10.1016/j.copbio.2011.11.026] [Citation(s) in RCA: 370] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/08/2011] [Accepted: 11/23/2011] [Indexed: 12/30/2022]
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Predominance of a versatile-peroxidase-encoding gene, mnp4, as demonstrated by gene replacement via a gene targeting system for Pleurotus ostreatus. Appl Environ Microbiol 2012; 78:5341-52. [PMID: 22636004 DOI: 10.1128/aem.01234-12] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pleurotus ostreatus (the oyster mushroom) and other white rot filamentous basidiomycetes are key players in the global carbon cycle. P. ostreatus is also a commercially important edible fungus with medicinal properties and is important for biotechnological and environmental applications. Efficient gene targeting via homologous recombination (HR) is a fundamental tool for facilitating comprehensive gene function studies. Since the natural HR frequency in Pleurotus transformations is low (2.3%), transformed DNA is predominantly integrated ectopically. To overcome this limitation, a general gene targeting system was developed by producing a P. ostreatus PC9 homokaryon Δku80 strain, using carboxin resistance complemented by the development of a protocol for hygromycin B resistance protoplast-based DNA transformation and homokaryon isolation. The Δku80 strain exhibited exclusive (100%) HR in the integration of transforming DNA, providing a high efficiency of gene targeting. Furthermore, the Δku80 strains produced showed a phenotype similar to that of the wild-type PC9 strain, with similar growth fitness, ligninolytic functionality, and capability of mating with the incompatible strain PC15 to produce a dikaryon which retained its resistance to the corresponding selection and was capable of producing typical fruiting bodies. The applicability of this system is demonstrated by inactivation of the versatile peroxidase (VP) encoded by mnp4. This enzyme is part of the ligninolytic system of P. ostreatus, being one of the nine members of the manganese-peroxidase (MnP) gene family, and is the predominantly expressed VP in Mn(2+)-deficient media. mnp4 inactivation provided a direct proof that mnp4 encodes a key VP responsible for the Mn(2+)-dependent and Mn(2+)-independent peroxidase activity under Mn(2+)-deficient culture conditions.
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124
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Segato F, Damásio ARL, Gonçalves TA, de Lucas RC, Squina FM, Decker SR, Prade RA. High-yield secretion of multiple client proteins in Aspergillus. Enzyme Microb Technol 2012; 51:100-6. [PMID: 22664194 DOI: 10.1016/j.enzmictec.2012.04.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 03/27/2012] [Accepted: 04/24/2012] [Indexed: 10/28/2022]
Abstract
Production of pure and high-yield client proteins is an important technology that addresses the need for industrial applications of enzymes as well as scientific experiments in protein chemistry and crystallization. Fungi are utilized in industrial protein production because of their ability to secrete large quantities of proteins. In this study, we engineered a high-expression-secretion vector, pEXPYR that directs proteins towards the extracellular medium in two Aspergillii host strains, examine the effect of maltose-induced over-expression and protein secretion as well as time and pH-dependent protein stability in the medium. We describe five client proteins representing a core set of hemicellulose degrading enzymes that accumulated up to 50-100 mg/L of protein. Using a recyclable genetic marker that allows serial insertion of multiple genes, simultaneous hyper-secretion of three client proteins in a single host strain was accomplished.
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Affiliation(s)
- Fernando Segato
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
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125
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Zain M, Bahkali A, Al-Othman MR. Effect of chemical compounds on amino acid content of some Fusarium species and its significance to fungal chemotaxonomy. JOURNAL OF SAUDI CHEMICAL SOCIETY 2012. [DOI: 10.1016/j.jscs.2011.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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126
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Fernandez EQ, Moyer DL, Maiyuran S, Labaro A, Brody H. Vector-initiated transitive RNA interference in the filamentous fungus Aspergillus oryzae. Fungal Genet Biol 2012; 49:294-301. [PMID: 22366516 DOI: 10.1016/j.fgb.2012.01.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 01/20/2012] [Accepted: 01/30/2012] [Indexed: 10/28/2022]
Abstract
RNA interference (RNAi), modulates gene expression via cleavage of double-stranded RNA (dsRNA) by Dicer, producing 21-25 nucleotide silence-inducing RNAs (siRNAs). In association with Argonaute containing complexes, these siRNAs target sequence-specific degradation of the homologous single-stranded messenger RNA. In the majority of eukaryotes, degradation occurs within the boundaries of the dsRNA target. In Arabidopsis thaliana and Caenorhabditis elegans, gene silencing can also take place transitively, impacting transcripts from coding sequences that are adjacent to the intended target gene. Here we demonstrate effective transitive RNAi in the ascomycete Aspergillus oryzae. Fragments of 174 bp and 499 bp derived from the A. oryzae wA gene involved in spore color development, were inserted immediately upstream of an inverted repeat derived from the Escherichia coli gene encoding for Hygromycin Phosphotransferase B (hph), which provided a double-stranded hph RNAi trigger. Introduction of this construct into A. oryzae host cells produced transformants with spores that were lighter in color than those of wild type. Real-time RT-qPCR analysis demonstrated a direct correspondence of steady-state wA mRNA level to spore color. An A. oryzae strain deficient in RNA-dependent RNA Polymerase (RdRP) produced exclusively wild type colored spores when transformed with a wA transitive RNAi construct. Conversely, increased expression of RdRP enhanced the incidence of wA gene silencing via transitive RNAi.
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127
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Arentshorst M, Ram AFJ, Meyer V. Using non-homologous end-joining-deficient strains for functional gene analyses in filamentous fungi. Methods Mol Biol 2012; 835:133-150. [PMID: 22183652 DOI: 10.1007/978-1-61779-501-5_9] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Fungal strains deficient in the non-homologous end-joining (NHEJ) pathway are excellent recipient strains for gene targeting approaches. In addition, NHEJ-deficiency can facilitate the formation of heterokaryons which allows rapid identification of essential genes. However, the use of NHEJ-deficient strains can also pose some limitations for gene function analyses. For example, lack of the NHEJ pathway can interfere with phenotypic analyses and complicate complementation studies. Moreover, heterokaryons are difficult to propagate and re-transform. We describe here strategies and methods to circumvent these problems and to better exploit the power of NHEJ-deficient strains. We provide methods for the establishment of transiently deficient NHEJ strains, for improved complementation analyses using AMA1-based vectors and for fast identification and propagation of heterokaryons. The methods described are applicable for a wide range of filamentous fungi.
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Affiliation(s)
- Mark Arentshorst
- Department Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
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128
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Ridenour JB, Hirsch RL, Bluhm BH. Identifying genes in Fusarium verticillioides through forward and reverse genetics. Methods Mol Biol 2012; 835:457-479. [PMID: 22183671 DOI: 10.1007/978-1-61779-501-5_28] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The increasing availability of sequenced genomes for plant pathogenic fungi has revolutionized molecular plant pathology in recent years. However, the genetic regulatory networks underlying many important components of pathogenesis remain poorly defined. Although the protocols outlined in this chapter can be utilized to identify genes regulating a wide range of biological processes in many filamentous fungi, we focus on describing how to identify genes through forward and reverse genetics, using the plant pathogenic fungus Fusarium verticillioides as a model for the protocol. Specifically, this chapter explains how to create a collection of insertional mutants via Restriction Enzyme Mediated Integration (REMI) and how to screen mutants with a high-throughput method to visualize defects in amylolysis. Next, techniques are described to define the genomic lesions in REMI mutants with genome-walker PCR in order to identify candidate genes. Finally, protocols are presented describing a reverse-genetic approach to disrupt candidate genes in the wild-type strain with a split-marker strategy to confirm the phenotype observed in the REMI mutant.
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Affiliation(s)
- J B Ridenour
- Division of Agriculture, Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
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129
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Zhong S, Leng Y, Bolton MD. Construction of hairpin RNA-expressing vectors for RNA-mediated gene silencing in fungi. Methods Mol Biol 2012; 835:623-633. [PMID: 22183683 DOI: 10.1007/978-1-61779-501-5_40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RNA-mediated gene silencing is one of the major tools for functional genomics in fungi and can be achieved by transformation with constructs that express hairpin (hp) RNA with sequences homologous to the target gene(s). To make an hpRNA expression construct, a portion of the target gene can be amplified by PCR and cloned into a vector as an inverted repeat. The generic gene-silencing vectors such as the pSilent1 and pSGate1 have been developed and are available for RNA-mediated gene-silencing studies. In this protocol, we describe construction of hpRNA-expressing constructs using both pSilent1 and pSGate1. With pSilent1, the PCR products of the target gene are inserted into the vector by conventional cloning (i.e., restriction enzyme digestion and ligation). For pSGate1, the PCR products of the target gene are inserted into the vector through the Gateway-directed recombination system. In this chapter, we describe the construction of RNAi vectors for RNA-mediated gene silencing using both pSilent1 and pSGate1.
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Affiliation(s)
- Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA.
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130
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Vetukuri RR, Tian Z, Avrova AO, Savenkov EI, Dixelius C, Whisson SC. Silencing of the PiAvr3a effector-encoding gene from Phytophthora infestans by transcriptional fusion to a short interspersed element. Fungal Biol 2011; 115:1225-33. [DOI: 10.1016/j.funbio.2011.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/31/2011] [Indexed: 11/25/2022]
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131
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Hu YJ, Zhu BQ. [Research progress on strain improvement of Acremonium chrysogenum by genetic engineering]. YI CHUAN = HEREDITAS 2011; 33:1079-1086. [PMID: 21993282 DOI: 10.3724/sp.j.1005.2011.01079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Acremonium chrysogenum, cephalosporin C (CPC) producing strain, is an important industrial microorganism. CPC is used to produce 7-ACA, a major intermediate for manufacturing of many first-line anti-infectious cephalosporin-antibiotics. The fermentation level of CPC determines the production, quality and cost of its downstream products. Therefore, it is necessary to develop the strains of A. chrysogenum. Along with the development of molecular biology, genetic manipulation technique is becoming more and more important in the field of molecular breeding. This paper reviews the latest research progresses on CPC biosynthesis and its regulation. Genetic manipulations of A. chrysogenum were summarized and concluded. We suggested that strain improvement of A. chrysogenum by means of induction and expression of biosynthetic and regulatory genes, as well as exogenous genes, and further optimization could be applied to different aspects including CPC production enhancement and metabolic pathway elongation, etc. Future direction of this field is also proposed. We believed that incorporation of comparative proteomics and genomic shuffling with molecular breeding could lead the achievements close to industry promptly.
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Affiliation(s)
- You-Jia Hu
- Shanghai Institute of Pharmaceutical Industry, Shanghai, China.
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132
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Rodriguez-Caban J, Gonzalez-Velazquez W, Perez-Sanchez L, Gonzalez-Mendez R, Rodriguez-del Valle N. Calcium/calmodulin kinase1 and its relation to thermotolerance and HSP90 in Sporothrix schenckii: an RNAi and yeast two-hybrid study. BMC Microbiol 2011; 11:162. [PMID: 21745372 PMCID: PMC3146815 DOI: 10.1186/1471-2180-11-162] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 07/11/2011] [Indexed: 11/10/2022] Open
Abstract
Background Sporothrix schenckii is a pathogenic dimorphic fungus of worldwide distribution. It grows in the saprophytic form with hyaline, regularly septated hyphae and pyriform conidia at 25°C and as the yeast or parasitic form at 35°C. Previously, we characterized a calcium/calmodulin kinase in this fungus. Inhibitors of this kinase were observed to inhibit the yeast cell cycle in S. schenckii. Results The presence of RNA interference (RNAi) mechanism in this fungus was confirmed by the identification of a Dicer-1 homologue in S. schenckii DNA. RNAi technology was used to corroborate the role of calcium/calmodulin kinase I in S. schenckii dimorphism. Yeast cells were transformed with the pSilent-Dual2G (pSD2G) plasmid w/wo inserts of the coding region of the calcium/calmodulin kinase I (sscmk1) gene. Transformants were selected at 35°C using resistance to geneticin. Following transfer to liquid medium at 35°C, RNAi transformants developed as abnormal mycelium clumps and not as yeast cells as would be expected. The level of sscmk1 gene expression in RNAi transformants at 35°C was less than that of cells transformed with the empty pSD2G at this same temperature. Yeast two-hybrid analysis of proteins that interact with SSCMK1 identified a homologue of heat shock protein 90 (HSP90) as interacting with this kinase. Growth of the fungus similar to that of the RNAi transformants was observed in medium with geldanamycin (GdA, 10 μM), an inhibitor of HSP90. Conclusions Using the RNAi technology we silenced the expression of sscmk1 gene in this fungus. RNAi transformants were unable to grow as yeast cells at 35°C showing decreased tolerance to this temperature. The interaction of SSCMK1 with HSP90, observed using the yeast two-hybrid assay suggests that this kinase is involved in thermotolerance through its interaction with HSP90. SSCMK1 interacted with the C terminal domain of HSP90 where effector proteins and co-chaperones interact. These results confirmed SSCMK1 as an important enzyme involved in the dimorphism of S. schenckii, necessary for the development of the yeast phase of this fungus. Also this study constitutes the first report of the transformation of S. schenckii and the use of RNAi to study gene function in this fungus.
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Affiliation(s)
- Jorge Rodriguez-Caban
- Department of Microbiology and Medical Zoology, Medical Sciences Campus, University of Puerto Rico, PO Box 365067, San Juan, PR 00936-5067.
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133
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Nakazawa T, Ando Y, Kitaaki K, Nakahori K, Kamada T. Efficient gene targeting in ΔCc.ku70 or ΔCc.lig4 mutants of the agaricomycete Coprinopsis cinerea. Fungal Genet Biol 2011; 48:939-46. [PMID: 21704178 DOI: 10.1016/j.fgb.2011.06.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 05/30/2011] [Accepted: 06/02/2011] [Indexed: 12/25/2022]
Abstract
Coprinopsis cinerea is a model for studies of sexual development in agaricomycetes (homobasidiomycetes). Efficient gene targeting should facilitate such studies, especially because increasing genome and transcriptome information is now available in C. cinerea. To estimate the frequency of gene disruption by homologous integration in this fungus, we tried to disrupt Cc.wc-2, which encodes a WC-2 homolog, a partner of the fungal blue-light photoreceptor, WC-1. Disruption of Cc.wc-2 did not occur when recipients (protoplasts) of the disrupting construct were prepared from asexual spores, oidia, from the wild type, 326, while it occurred when protoplasts were prepared from mycelial cells from the same strain, albeit at a low frequency (3%). Double-stranded RNA-mediated silencing of a ku70 homolog, named Cc.ku70, or the lig4 homolog Cc.lig4 more or less increased the frequency of Cc.wc-2 targeting. On the basis of these results, we disrupted Cc.ku70 using a Cc.lig4-silenced strain. We then disrupted Cc.lig4 using the Cc.ku70 disruptant. We found that the disruption of Cc.ku70 or Cc.lig4 greatly enhanced gene targeting. In addition, this study demonstrates that Cc.wc-2 is involved in blue light perception in this fungus.
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Affiliation(s)
- Takehito Nakazawa
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Okayama, Japan
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134
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Visser H, Joosten V, Punt PJ, Gusakov AV, Olson PT, Joosten R, Bartels J, Visser J, Sinitsyn AP, Emalfarb MA, Verdoes JC, Wery J. RESEARCH: Development of a mature fungal technology and production platform for industrial enzymes based on a Myceliophthora thermophila isolate, previously known as Chrysosporium lucknowense C1. Ind Biotechnol (New Rochelle N Y) 2011. [DOI: 10.1089/ind.2011.7.214] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hans Visser
- Dyadic Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Vivi Joosten
- Dyadic Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Peter J. Punt
- TNO Microbiology and Systems Biology, PO Box 360, 3700 AJ Zeist, The Netherlands
- University Leiden, Molecular Microbiology and Biotechnology. Sylviusweg 72, 2333 BE Leiden. The Netherlands
| | - Alexander V. Gusakov
- Department of Chemistry, M.V Lomonosov Moscow State University, Vorobyovy Gory 1/11, Moscow 119991, Russia
| | - Phil T. Olson
- Bio-Technical Resources, 1035 S. Seventh St., Manitowoc, Wisconsin 54220, USA
| | - Rob Joosten
- Dyadic Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Jeffrey Bartels
- Dyadic Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Jaap Visser
- Fungal Genetics and Technology Consultancy, PO Box 396, 6700 AJ Wageningen, The Netherlands
| | - Arkady P. Sinitsyn
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect, 33-2, Moscow 119071, Russia
| | - Mark A. Emalfarb
- Dyadic International, Inc., 140 Intracoastal Pointe Drive, Jupiter, Florida 33477-5094, USA
| | - Jan C. Verdoes
- Dyadic Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
- This manuscript is dedicated to the memory of Jan C. Verdoes, who passed away too early on November 26, 2007, and whom we thank for many of the results described herein
| | - Jan Wery
- Dyadic Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
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135
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Leng Y, Wu C, Liu Z, Friesen TL, Rasmussen JB, Zhong S. RNA-mediated gene silencing in the cereal fungal pathogen Cochliobolus sativus. MOLECULAR PLANT PATHOLOGY 2011; 12:289-98. [PMID: 21356000 PMCID: PMC6640516 DOI: 10.1111/j.1364-3703.2010.00666.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A high-throughput RNA-mediated gene silencing system was developed for Cochliobolus sativus (anamorph: Bipolaris sorokiniana), the causal agent of spot blotch, common root rot and black point in barley and wheat. The green fluorescent protein gene (GFP) and the proteinaceous host-selective toxin gene (ToxA) were first introduced into C. sativus via the polyethylene glycol (PEG)-mediated transformation method. Transformants with a high level of expression of GFP or ToxA were generated. A silencing vector (pSGate1) based on the Gateway cloning system was developed and used to construct RNA interference (RNAi) vectors. Silencing of GFP and ToxA in the transformants was demonstrated by transformation with the RNAi construct expressing hairpin RNA (hpRNA) of the target gene. The polyketide synthase gene (CsPKS1), involved in melanin biosynthesis pathways in C. sativus, was also targeted by transformation with the RNAi vector (pSGate1-CsPKS1) encoding hpRNA of the CsPKS1 gene. The transformants with pSGate1-CsPKS1 exhibited an albino phenotype or reduced melanization, suggesting effective silencing of the endogenous CsPKS1 in C. sativus. Sectors exhibiting the wild-type phenotype of the fungus appeared in some of the CsPKS1-silenced transformants after subcultures as a result of inactivation or deletions of the RNAi transgene. The gene silencing system established provides a useful tool for functional genomics studies in C. sativus and other filamentous fungi.
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Affiliation(s)
- Yueqiang Leng
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, USA
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136
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Kües U, Rühl M. Multiple multi-copper oxidase gene families in basidiomycetes - what for? Curr Genomics 2011; 12:72-94. [PMID: 21966246 PMCID: PMC3129051 DOI: 10.2174/138920211795564377] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 03/11/2011] [Accepted: 03/14/2011] [Indexed: 11/22/2022] Open
Abstract
Genome analyses revealed in various basidiomycetes the existence of multiple genes for blue multi-copper oxidases (MCOs). Whole genomes are now available from saprotrophs, white rot and brown rot species, plant and animal pathogens and ectomycorrhizal species. Total numbers (from 1 to 17) and types of mco genes differ between analyzed species with no easy to recognize connection of gene distribution to fungal life styles. Types of mco genes might be present in one and absent in another fungus. Distinct types of genes have been multiplied at speciation in different organisms. Phylogenetic analysis defined different subfamilies of laccases sensu stricto (specific to Agaricomycetes), classical Fe2+-oxidizing Fet3-like ferroxidases, potential ferroxidases/laccases exhibiting either one or both of these enzymatic functions, enzymes clustering with pigment MCOs and putative ascorbate oxidases. Biochemically best described are laccases sensu stricto due to their proposed roles in degradation of wood, straw and plant litter and due to the large interest in these enzymes in biotechnology. However, biological functions of laccases and other MCOs are generally little addressed. Functions in substrate degradation, symbiontic and pathogenic intercations, development, pigmentation and copper homeostasis have been put forward. Evidences for biological functions are in most instances rather circumstantial by correlations of expression. Multiple factors impede research on biological functions such as difficulties of defining suitable biological systems for molecular research, the broad and overlapping substrate spectrum multi-copper oxidases usually possess, the low existent knowledge on their natural substrates, difficulties imposed by low expression or expression of multiple enzymes, and difficulties in expressing enzymes heterologously.
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Affiliation(s)
- Ursula Kües
- University of Goettingen, Büsgen-Institute, Division of Molecular Wood Biotechnology and Technical Mycology, Büsgenweg 2, 37077 Goettingen, Germany
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137
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Meyer V, Wu B, Ram AFJ. Aspergillus as a multi-purpose cell factory: current status and perspectives. Biotechnol Lett 2011; 33:469-76. [PMID: 21088867 PMCID: PMC3040820 DOI: 10.1007/s10529-010-0473-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 10/29/2010] [Indexed: 01/10/2023]
Abstract
Aspergilli have a long history in biotechnology as expression platforms for the production of food ingredients, pharmaceuticals and enzymes. The achievements made during the last years, however, have the potential to revolutionize Aspergillus biotechnology and to assure Aspergillus a dominant place among microbial cell factories. This mini-review will highlight most recent breakthroughs in fundamental and applied Aspergillus research with a focus on new molecular tools, techniques and products. New trends and concepts related to Aspergillus genomics and systems biology will be discussed as well as the challenges that have to be met to integrate omics data with metabolic engineering attempts.
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Affiliation(s)
- Vera Meyer
- Department of Molecular Microbiology and Biotechnology, Leiden University, Institute of Biology Leiden, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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138
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Multifactorial induction of an orphan PKS-NRPS gene cluster in Aspergillus terreus. ACTA ACUST UNITED AC 2011; 18:198-209. [PMID: 21236704 DOI: 10.1016/j.chembiol.2010.12.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 11/16/2010] [Accepted: 12/13/2010] [Indexed: 12/26/2022]
Abstract
Mining the genome of the pathogenic fungus Aspergillus terreus revealed the presence of an orphan polyketide-nonribosomal-peptide synthetase (PKS-NRPS) gene cluster. Induced expression of the transcriptional activator gene adjacent to the PKS-NRPS gene was not sufficient for the activation of the silent pathway. Monitoring gene expression, metabolic profiling, and using a lacZ reporter strain allowed for the systematic investigation of physiological conditions that eventually led to the discovery of isoflavipucine and dihydroisoflavipucine. Phytotoxin formation is only activated in the presence of certain amino acids, stimulated at alkaline pH, but strictly repressed in the presence of glucose. Global carbon catabolite repression by CreA cannot be abolished by positive-acting factors such as PacC and overrides the pathway activator. Gene inactivation and stable isotope labeling experiments unveiled the molecular basis for flavipucine/fruit rot toxin biosynthesis.
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139
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Wang NY, Yang SL, Lin CH, Chung KR. Gene inactivation in the citrus pathogenic fungus Alternaria alternata defect at the Ku70 locus associated with non-homologous end joining. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0640-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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140
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Transformation system for Hypocrea jecorina (Trichoderma reesei) that favors homologous integration and employs reusable bidirectionally selectable markers. Appl Environ Microbiol 2010; 77:114-21. [PMID: 21075888 DOI: 10.1128/aem.02100-10] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hypocrea jecorina is an industrially important filamentous fungus due to its effective production of hydrolytic enzymes. It has received increasing interest because of its ability to convert lignocellulosic biomass to monomeric sugars, which can be converted into biofuels or platform chemicals. Genetic engineering of strains is a highly important means of meeting the requirements of tailor-made applications. Therefore, we report the development of a transformation system that allows highly efficient gene targeting by using a tmus53 (human LIG4 homolog) deletion strain. Moreover, it permits the unlimited reuse of the same marker by employing a Cre/loxP-based excision system. Both marker insertion and marker excision can be positively selected for by combining resistance to hygromycin B and loss of sensitivity to fluoroacetamide. Finally, the marker pyr4, also positively selectable for insertion and loss, can be used to remove the cre gene.
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Salame TM, Ziv C, Hadar Y, Yarden O. RNAi as a potential tool for biotechnological applications in fungi. Appl Microbiol Biotechnol 2010; 89:501-12. [DOI: 10.1007/s00253-010-2928-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 09/29/2010] [Accepted: 09/29/2010] [Indexed: 12/28/2022]
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142
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Engh I, Nowrousian M, Kück U. Sordaria macrospora, a model organism to study fungal cellular development. Eur J Cell Biol 2010; 89:864-72. [PMID: 20739093 DOI: 10.1016/j.ejcb.2010.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During the development of multicellular eukaryotes, the processes of cellular growth and organogenesis are tightly coordinated. Since the 1940s, filamentous fungi have served as genetic model organisms to decipher basic mechanisms underlying eukaryotic cell differentiation. Here, we focus on Sordaria macrospora, a homothallic ascomycete and important model organism for developmental biology. During its sexual life cycle, S. macrospora forms three-dimensional fruiting bodies, a complex process involving the formation of different cell types. S. macrospora can be used for genetic, biochemical and cellular experimental approaches since diverse tools, including fluorescence microscopy, a marker recycling system and gene libraries, are available. Moreover, the genome of S. macrospora has been sequenced and allows functional genomics analyses. Over the past years, our group has generated and analysed a number of developmental mutants which has greatly enhanced our fundamental understanding about fungal morphogenesis. In addition, our recent research activities have established a link between developmental proteins and conserved signalling cascades, ultimately leading to a regulatory network controlling differentiation processes in a eukaryotic model organism. This review summarizes the results of our recent findings, thus advancing current knowledge of the general principles and paradigms underpinning eukaryotic cell differentiation and development.
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Affiliation(s)
- Ines Engh
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany
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143
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Application of the Saccharomyces cerevisiae FLP/FRT recombination system in filamentous fungi for marker recycling and construction of knockout strains devoid of heterologous genes. Appl Environ Microbiol 2010; 76:4664-74. [PMID: 20472720 DOI: 10.1128/aem.00670-10] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To overcome the limited availability of antibiotic resistance markers in filamentous fungi, we adapted the FLP/FRT recombination system from the yeast Saccharomyces cerevisiae for marker recycling. We tested this system in the penicillin producer Penicillium chrysogenum using different experimental approaches. In a two-step application, we first integrated ectopically a nourseothricin resistance cassette flanked by the FRT sequences in direct repeat orientation (FRT-nat1 cassette) into a P. chrysogenum recipient. In the second step, the gene for the native yeast FLP recombinase, and in parallel, a codon-optimized P. chrysogenum flp (Pcflp) recombinase gene, were transferred into the P. chrysogenum strain carrying the FRT-nat1 cassette. The corresponding transformants were analyzed by PCR, growth tests, and sequencing to verify successful recombination events. Our analysis of several single- and multicopy transformants showed that only when the codon-optimized recombinase was present could a fully functional recombination system be generated in P. chrysogenum. As a proof of application of this system, we constructed a DeltaPcku70 knockout strain devoid of any heterologous genes. To further improve the FLP/FRT system, we produced a flipper cassette carrying the FRT sites as well as the Pcflp gene together with a resistance marker. This cassette allows the controlled expression of the recombinase gene for one-step marker excision. Moreover, the applicability of the optimized FLP/FRT recombination system in other fungi was further demonstrated by marker recycling in the ascomycete Sordaria macrospora. Here, we discuss the application of the optimized FLP/FRT recombination system as a molecular tool for the genetic manipulation of filamentous fungi.
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Carvalho NDSP, Arentshorst M, Jin Kwon M, Meyer V, Ram AFJ. Expanding the ku70 toolbox for filamentous fungi: establishment of complementation vectors and recipient strains for advanced gene analyses. Appl Microbiol Biotechnol 2010; 87:1463-73. [PMID: 20422182 PMCID: PMC2892608 DOI: 10.1007/s00253-010-2588-1] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 03/22/2010] [Accepted: 03/25/2010] [Indexed: 11/28/2022]
Abstract
Mutants with a defective non-homologous-end-joining (NHEJ) pathway have boosted functional genomics in filamentous fungi as they are very efficient recipient strains for gene-targeting approaches, achieving homologous recombination frequencies up to 100%. For example, deletion of the ku70 homologous gene kusA in Aspergillus niger resulted in a recipient strain in which deletions of essential or non-essential genes can efficiently be obtained. To verify that the mutant phenotype observed is the result of a gene deletion, a complementation approach has to be performed. Here, an intact copy of the gene is transformed back to the mutant, where it should integrate ectopically into the genome. However, ectopic complementation is difficult in NHEJ-deficient strains, and the gene will preferably integrate via homologous recombination at its endogenous locus. To circumvent that problem, we have constructed autonomously replicating vectors useful for many filamentous fungi which contain either the pyrG allele or a hygromycin resistance gene as selectable markers. Under selective conditions, the plasmids are maintained, allowing complementation analyses; once the selective pressure is removed, the plasmid becomes lost and the mutant phenotype prevails. Another disadvantage of NHEJ-defective strains is their increased sensitivity towards DNA damaging conditions such as radiation. Thus, mutant analyses in these genetic backgrounds are limited and can even be obscured by pleiotropic effects. The use of sexual crossings for the restoration of the NHEJ pathway is, however, impossible in imperfect filamentous fungi such as A. niger. We have therefore established a transiently disrupted kusA strain as recipient strain for gene-targeting approaches.
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Affiliation(s)
- Neuza D S P Carvalho
- Department Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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