US20190264216A1

US20190264216A1 - Fungal artificial chromosomes, compositions, methods and uses therefor

Info

Publication number: US20190264216A1
Application number: US16/409,586
Authority: US
Inventors: Chengcang Charles Wu
Original assignee: Intact Genomics Inc
Current assignee: Intact Genomics Inc
Priority date: 2016-01-25
Filing date: 2019-05-10
Publication date: 2019-08-29
Also published as: CN107574178A; US20170211077A1; CN107574178B; US10337019B2

Abstract

Fungal artificial chromosome (FAC) vectors are disclosed. A vector can be replicated in a bacterial or a fungal host, and can comprise an insert of heterologous DNA up to about 500 kilobases. A vector can be used for cloning and expressing a secondary metabolite (SM) gene cluster. An insert sequence can be modified by homologous recombination. A vector can be a plasmid comprising bacterial and fungal origins of replication, as well as bacterial and fungal selection marker genes. Also disclosed are vectors that can be integrated into a fungal genome, and dual function vectors which can be replicated in a bacterial or a fungal host and can also be integrated into a fungal genome. Also disclosed are methods of generating plasmid libraries including vectors comprising intact SM gene clusters.

Description

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 15/143,493, filed Apr. 29, 2016, which claims the benefit of and priority to U.S. Provisional Application No. 62/286,542, filed Jan. 25, 2016, the entire disclosure of each is hereby incorporated by reference in its entirety.

GOVERNMENT SUPPORT

This invention was made with government support under R43/44AI094885 awarded by the National Institutes of Health. The government has certain rights in the invention.

REFERENCE TO A SEQUENCE LISTING

The Sequence Listing, which is a part of the present disclosure, includes text file 0749sequence_ST25.txt, an 86 kilobyte file created on Apr. 29, 2016. This file comprises primer nucleotide and/or amino acid sequences of the present invention. The subject matter of the Sequence Listing is incorporated herein by reference in its entirety.

INTRODUCTION

Fungi contain an extensive but unexplored biosynthetic capacity, and can serve as reservoirs for novel bioactive compounds (Kobayashi, A., et al., Agric. Biol. Chem., 1988, 52, 3119-3123.; Kuno, F., et al., J. Antibiot. (Tokyo), 1996, 49, 742-747; Kumar, C. G., et al, Lett. Appl. Microbiol., 2011, 53, 350-358; Wu, M. C., et al., Curr. Opin. Biotechnol., 2012, 23, 931-940; Du, L., et al., Angew. Chem. Int. Ed. Engl., 2014, 53, 804-809; Fang, S. M., et al., Mar. Drugs, 2014, 12, 1788-1814; Leitão, A. L. and Enguita, F. J., Microbiol. Res., 2014, 169, 652-665).
Filamentous fungi produce secondary metabolites (SMs) which have historically been a rich source of lead compounds for the pharmaceutical industry. Fungi produce 45% of bioactive molecules from all microbial sources (Bérdy, J., J. Antibiot. (Tokyo), 2012, 65, 385-395). These compounds, derived from terpene, polyketide, and non-ribosomal peptide pathways (Keller, N. P., et al., Nat Rev Microbiol. 2005, 3: 937-947), display a broad range of useful antibiotic and pharmaceutical activities. A recent literature survey of fungal metabolites covering 1500 compounds that were isolated and characterized between 1993 and 2001, showed that more than half of the molecules had antibacterial, antifungal or antitumor activity (Pelaez, F., Handbook of Industrial Mycology (ed. An, Z.) 49-92 (Marcel Dekker, New York. 2005). Examples of fungal natural products having therapeutic or economic significance include the antibiotic penicillin from Penicillium chrysogenum, the immunosuppressant cyclosporine (a cyclic peptide) from Tolypocladium inflatum, and the cholesterol-lowering mevinolin (a.k.a. lovastatin, a polyketide) from Aspergillus terreus.
Fungal genomes can harbor 50 or more different SM gene clusters ranging from 20 to greater than 100 kb in size (Nordberg, H. et al., Nucleic Acids Res., 2014, 42(Database issue), D26-31). Conservative estimates suggest that there are more than 5 million fungal species (Blackwell, M., Am. J. Bot., 2011, 98, 426-438), of which fewer than 5% have been described and less than 1% are available in the world's culture collections (Colwell, R. R., Microbial biodiversity and biotechnology. Washington, D.C.: Joseph Henry Press; p. 279-88, 1997). In addition, because each of these fungal genomes may harbor 50 or more different SM gene clusters ranging from 20 kb to greater than 100 kb in size (Nordberg, H. et al., Nucleic Acids Res., 2014, 42(Database issue), D26-31), the number of undiscovered SMs is presumably extremely large.
Several approaches to induce expression of SM clusters have been successful. These include overexpressing cluster-specific transcription factors or enzymatic genes, deleting or overexpressing chromatin-modifying genes, overexpressing trans-acting activators and deleting trans-acting inhibitors (Palmer, J. M. and Keller, N. P., Curr. Opin. Microbiol. 2010, 13: 431-436; Brakhage, A. A. and Schroeckh, V., Fungal Genet. Biol., 2011, 48, 15-22; Strauss, J. and Reyes-Dominguez, Y., Fungal Genet. Biol., 2011, 48, 62-69; Hong, S. Y., et al., Toxins (Basel) 2013, 5, 683-702). expression of heterologous SM genes (Itoh, T. et al., Methods Mol Biol 2012, 944, 175-182; Chiang, Y. M., et al., J. Am. Chem. Soc., 2013, 135, 7720-7731; Nielsen, M. T., et al., PLoS ONE 2013, 8: e72871; Tsunematsu, Y., et al., Nat Prod Rep 2013, 30: 1139-1149; Yin, W. B., et al. ACS Synth Biol 2013, 2: 629-634).
Expression of heterologous clusters in fungi is one approach to identify SM compounds, biosynthetic SM proteins and genes. Recently, this approach has been reported for synthesis of the A. terreus-encoded compounds geodin and asperfuranone in A. nidulans (Chiang, Y. M., et al., J. Am. Chem. Soc., 2013, 135, 7720-7731; Nielsen, M. T., et al., PLoS ONE, 2013, 8, e72871). A. nidulans was also used to heterologously express a dermatophyte-derived gene cluster responsible for the synthesis of neosartoricin B (Yin, W. B., et al., ACS Synth. Biol., 2013, 2, 629-634). These studies utilized a shuttle vector that included a ColE1 origin of replication, a yeast centromere sequence and an autonomously replicating sequence. This vector was used to create a single full length cluster in A. nidulans. These technologies require considerable time and effort to express just one heterologous cluster. These technologies are also only compatible with inserts smaller than about 20 kilobases (kb).
Large insert DNA cloning vectors are well established in a variety of systems, including: yeast artificial chromosome (YAC, Burke, D., et al., Science, 1987, 236, 806-812), bacterial artificial chromosome (BAC, Shizuya, H., et al., Proc. Natl. Acad. Sci. USA., 1992, 89, 8794-8797), P1-derived artificial chromosome (PAC, Ioannou, P. A., et al., Nat. Genet., 1994, 6, 84-89), E. coli-plant shuttle BAC, also called binary BAC (BIBAC, Hamilton, C. M., Gene, 1997, 200, 107-116), E. coli-Streptomyces artificial chromosome (ESAC, Sosio, M., et al., Nat. Biotechnol., 2000, 18, 343-345). However these plasmid systems are not compatible with fungi. A previously reported E. coli-fungus shuttle plasmid vector can neither accommodate nor maintain 100 kb or larger DNA fragments (Yin, W. B., et al., ACS Synth. Biol., 2013, 2, 629-634).
A. nidulans AMA1 is a fungal replication element that has been used in an E. coli-fungus shuttle vector for small plasmids (Gems, D., et al., Gene, 1991, 98, 61-67; Aleksenko, A. and Clutterbuck, A., J. Fungal Genet. Biol., 1997, 21, 373-387; Kubodera, T. et al., Biosci. Biotechnol. Biochem., 2000, 64, 1416-1426). There were also fungal shuttle plasmids or vectors reported for integration (Tiburn, J., et al., Gene. 1983, 26:205-221; Golduran, G. H. and Morris, N. R., Methods in Molecular Genetics 1995, 6, 48-65 Microbial Gene Techniques Edited by Kenneth W. Adolph; Kubodera, T., et al., Biosci. Biotechnol. Biochem., 2000, 64, 1416-1426; Arentshorst, M., et al., Fungal Biology and Biotechnology, 2015, 2, 2), autonomous replication or extra-chromosomal maintenance (Gems, D., et al., Gene, 1991, 98, 61 -67; Golduran, G. H. and Morris, N. R., Methods in Molecular Genetics 1995, 6, 48-65 Microbial Gene Techniques Edited by Kenneth W. Adolph; Kubodera, T. et al., Biosci. Biotechnol. Biochem., 2000, 64, 1416-1426). However, these shuttle plasmids or vectors cannot be used to clone and transform very large DNA (such as 20 kb or larger). A previous attempt to introduce up to 75 Kb of fungal DNA into Fusarium oxysporum and A. awamori using an Agrobacterium tumefaciens transformation system yielded few transformants with large DNA inserts. Furthermore, no attempts to examine stability of heterologous DNA, let alone expression, were made (Takken, F. L., et al., Curr. Genet., 2004, 45, 242-248).
Bacterial artificial chromosomes (BACs) have been widely used for genomic DNA sequencing, positional cloning, and mapping in prokaryotes and eukaryotes including filamentous fungi (Zhu, H., et al., Fungal Genet. Biol., 1997, 21, 337-347; Nishimura, M., et al., Biosci. Biotechnol. Biochem., 1998, 62, 1515-1521; Adler, H. et al., Rev. Med. Virol., 2003, 13, 111-121; Diener, S. E., et al., Fungal Genet. Biol., 2004, 41, 1077-1087; Srivastava, S. K., et al., PLoS One 2014, 9: e81832). Although large-insert DNA systems have also been applied for heterologous expression of microbial natural product biosynthetic pathways and metagenomic studies, there has been limited success reported (Béjà, O., Curr. Opin. Biotechnol., 2004, 15, 187-190; Lorenz, P. and Eck, J., Nat. Rev. Microbiol., 2005, 3, 510-516; Ongley, S. E., et al., Nat. Prod. Rep., 2013, 30, 1121-1138). Challenges with these systems include: 1) DNA cloning bias; 2) small DNA insert size; 3) lack of advanced heterologous expression hosts and 4) insufficient high-resolution chemical and data analysis pipelines. One reason for these challenges is that to date almost all BAC libraries are produced using partial restriction digestion (Wu, C. C., et al., Encyclopedia of Molecular Cell Biology and Molecular Medicine Volume 3 (2nd Edition), Edited by Meyers R. A., Wiley-VCH Verlag GmbH: Weinheim, Germany 2004, pp 385-425 2004; Zhang, M., et al., Nat. Protoc., 2012, 7, 467-478). Partial restriction digestion can be biased because the occurrence of restriction sites is highly variable and non-random in any genome including fungal genomes. Certain genomic regions can contain an excess of the restriction sites or lack them altogether, for example in regions of genomic DNA that contain highly repetitive sequences, such as centromeres and telomeres (Godiska, R., et al., Bias-Free Cloning of ‘Unclonable’ DNA for Simplified Genomic Finishing. In DNA Sequencing III: Dealing with Difficult Templates. Sudbury, M A: Jones and Bartlett Publishers: 2008). As a result, some sequences can be difficult or impossible to determine, even with multiple biased partial digestion libraries and up to 50× coverage.
Additionally, DNA fragments from rare or frequent cutting genomic regions can be either too large or too small for DNA fragment fractionation and can be excluded from cloning. Fragmentation of high molecular weight (HMW) genomic DNA by mechanical shearing, such as sonication, nebulization and hydroshearing, can generate small DNA fragments (10 kb or smaller). These methods can be unsuitable for preparing fragments ranging from 100 kb-300 kb. Freeze-thaw cycles have been reported to result in large DNA fragmentation, but these methods are not efficient enough for routine use (Osoegawa, K., et al., Genomics., 2007, 89, 291-299).
Red/ET (Red alpha/beta or RecE/T) tools have been developed for efficient large DNA or BAC-based recombinant engineering (Copeland, N. G., et al., Nat. Rev. Genet. 2001, 2: 769-779; Muyrers, J. P. P. et al., Trends in Bioch. Sci., 2001, 26, 325-331). Engineered large DNA or BACs have been routinely used for generating transgenic animals, such as mice, and for the functional study of large genes or pathways in mammals, such as humans (Johnson, S. J. and Wade-Martins, R. A., Biochem. Soc. Trans. 2011, 39, 862-867).
BAC-based large gene expression in animal models (Johnson, S. J. and Wade-Martins, R. A., Biochem. Soc. Trans. 2011, 39, 862-867) cannot be directly applied to study fungal SM pathways or discovery of natural products (NPs).
There is thus an unmet need for new methods and compositions for cloning large stretches of fungal DNA, such as entire clusters of genes involved in biosynthesis of secondary metabolites.

SUMMARY

Because of an unmet need for new tools to study fungal genes, the present inventor has developed vectors and methods for generating libraries of SM gene clusters that can be propagated and expressed in a fungal host.
In some embodiments, the present teachings include a fungal artificial chromosome (FAC). In various aspects, a fungal artificial chromosome can comprise at least one bacterial origin of replication, a bacterial selectable marker gene, a fungal selectable marker gene and a fungal autonomous replicating element. In various aspects, a FAC can be a shuttle vector or plasmid that can replicate in a bacterial host such as, for example, and without limitation E. coli as well as a fungal host, such as, for example and without limitation a filamentous fungus such as an Aspergillus. In some configurations, the Aspergillus can be Aspergillus nidulans.
In some configurations, a fungal artificial chromosome of the present teachings can be a dual-function fungal artificial chromosome (FACdual). In various configurations, a FACdual can comprise at least one bacterial origin of replication, a bacterial selectable marker gene, a fungal autonomous replicating element, an integration site for recombination with a host, an integrase gene, and a fungal selectable marker gene. In some configurations, the integration site can be, without limitation, an attP site. In some configurations, the integrase gene can be, without limitation, a fungal codon-optimized phi31 integrase gene. In some configurations, a FACdual can further comprise a fungal-operative promoter such as a fungal inducible promoter. In various configurations, the fungal-operative promoter can be operably linked to the integrase gene. In various aspects, a fungal inducible promoter can be an alcA(p) (Romero, B., et al., Fungal Genet. Biol. 2003 40, 103-114). In various aspects, a fungal inducible promoter can be a glaA(p) (Smith, T. L., et al., Gene, 1990, 88, 259-262). In various aspects, a fungal inducible promoter can be a sucA promoter (Roth, A. H., et al., Appl Microbiol Biotechnol., 2010, 86, 659-670).
In various configurations, a fungal autonomous replicating element can be any fungal autonomous replicating element, such as, without limitation, an AMA1 autonomous replicating element.
In some embodiments, the present teachings include a fungal artificial chromosome integration vector (FACint). In various configurations, a fungal artificial chromosome integration vector can comprise at least one bacterial origin of replication, a bacterial selectable marker gene, two fungal DNA sequences in the same orientation, and a fungal selectable marker gene. In various configurations, the two fungal sequences can be sequences homologous to a host fungal DNA. In various configurations, two fungal homologous DNA sequences can be, for example and without limitation, Aspergillus 1,007-bp 5′trpC and 1,000-bp 3′trpC homologous sequences. In various aspects, a FACint can replicate in a prokaryotic host such as, without limitation, an E. coli. In various aspects, a FACint can integrate into the genome of a fungal host such as, without limitation, an Aspergillus fungus such as an Aspergillus nidulans. In various aspects, a FACint can serve as a shuttle vector or plasmid. In various aspects, the bacterial selectable marker gene can be any bacterial selectable marker gene known to skilled artisans, such as, but not limited to a kanamycin-resistance gene (kanR).
In various configurations, a vector of the present teachings, i.e., a FAC, a FACdual or a FACint of the present teachings, can further comprise a cloning site comprising a plurality of recognition sites for endonucleases that bind and cut DNA at specific sequences. Endonuclease recognition sequences include recognition sequences of restriction endonucleases from prokaryotes and homing endonucleases from eukaryotes (as used herein, “restriction enzymes”). In some configurations, a cloning site can comprise a plurality of recognition sites for restriction enzymes that generate incompatible (i.e., non-complementary or non-palindromic) single-stranded overhangs upon digestion of the FAC. In some aspects, a cloning site can include recognition sequences for one or more restriction enzymes such as, without limitation, Bsr I, I-CeuI, BstXI, I-SceI or a combination thereof. In some aspects, a recognition sequence can be a recognition sequence of a restriction enzyme such as, without limitation, BstXI, I-SceI or a combination thereof. In some aspects, a cloning site can include a pair of restriction enzyme recognition sites in a tandem orientation. In some aspects, a cloning site can include a pair of restriction enzyme recognition sites in an opposing, “head-to-head” orientation. In some aspects a cloning site can include, in order, recognition sites for I-SceI, BstXI, BstXI, and I-SceI. In some aspects, the I-SceI sites can be in a head-to-head orientation with each other. In some aspects, the BstXI sites can be in a head-to-head orientation with each other. In some configurations, a cloning site can further comprise one or more recognition sites for other restriction enzymes such as, for example, Bam HI, Hind III, Eco RI, or NotI.
In various configurations, a vector of the present teachings can be maintained and can replicate in a prokaryotic host such as, without limitation, an E. coli, or in a eukaryotic fungal host such as, without limitation, an Aspergillus such as A. nidulans.
In some configurations, a vector of the present teachings can include a low-copy number bacterial origin of replication, an inducible high-copy number bacterial origin of replication, or a combination thereof, i.e., both a low-copy number and an inducible high-copy number bacterial origins of replication. In various aspects, a low-copy number bacterial origin of replication can be, for example and without limitation, an oriS. In various aspects, an inducible high-copy number bacterial origin of replication can be, for example and without limitation, an oriV. In various configurations, the high copy number origin of replication can be controlled by a replication initiation protein gene encoded in the E. coli host genome or a plasmid. In various configurations, the replication initiation protein gene can be TrfA. In various configurations, an inducible promoter can be operably linked to the replication initiation protein gene. In various configurations, the inducible promoter can be any bacterial inducible promoter, such as, without limitation, an arabinose-inducible promoter, a lac promoter, an IPTG-inducible T3 promoter, an IPTG-inducible T5 promoter or a rhamnose-inducible (rhaBAD) promoter.
In some configurations, a vector of the present teachings can include one or more genes for selectable markers for bacteria such as E. coli, such as, without limitation, a chloramphenicol resistance gene (camR or CAT), kanR, ampR, genR, tetA, strepR, galK or a combination thereof. In various aspects, a selectable marker can be used for positive selection (e.g., selecting for the presence of ampicillin resistance or galK (galactokinase) activity) or negative selection (e.g., selecting for the absence of galK activity (Warming, S., et al., Nucleic Acids Res. 2005, Vol. 33, No. 4 e36)).
In some configurations, a vector of the present teachings can include a fungal selectable marker gene, such as, without limitation, pyrG, ptrA, trpC or a combination thereof. In some aspects, a fungal selection marker gene can be a pyrG gene.
In some configurations, a vector of the present teachings can include an insertion of DNA from an exogenous source. In various configurations, a DNA insert can be an insertion at the cloning site. In various configurations, a DNA insert can be from any source, such as a virus, a prokaryotic microorganism, a eukaryotic microorganism, a plant, an animal, a human, or a cDNA generated from an RNA. In some configurations, a source of DNA can be the genome of a eukaryotic microorganism, such as a yeast or a filamentous fungus. In some configurations, a source of DNA can be an Aspergillus fungus, including any Aspergillus species. In some configurations, a source of DNA can be an Aspergillus fungus other than Aspergillus nidulans. In some configurations, a source of a DNA insert can be an Aspergillus fungus such as, without limitation, A. acidus, A. aculeatinus, A. aculeatus, A. aeneus, A. affinis, A. alabamensis, A. alliaceus, A. amazonicus, A. ambiguus, A. amoenus, A. amstelodami, A. amyloliquefaciens, A. amylovorus, A. anomalus, A. anthodesmis, A. apicalis, A. appendiculatus, A. arachidicola, A. arenarius, A. arvii, A. asperescens, A. assulatus, A. astellatus, A. aurantiobrunneus, A. aureofulgens, A. aureolatus, A. aureoterreus, A. aureus, A. auricomus, A. australensis, A. austroafricanus, A. avenaceus, A. awamori, A. baeticus, A. bahamensis, A. biplanus, A. bisporus, A. bombycis, A. brasiliensis, A. brevipes, A. brevistipitatus, A. bridgeri, A. brunneo-uniseriatus, A. brunneoviolaceu, A. caelatus, A. caesiellus, A. caespitosus, A. calidoustus, A. campestris, A. candidus, A. capensis, A. carbonarius, A. carneus, A. cavernicola, A. cavernicola, A. cervinus, A. chevalieri, A. chungii, A. cibarius, A. clavatoflavus, A. clavatonanicus, A. clavatus, A. conicus, A. conjunctus, A. conversis, A. coreanus, A. coremiiformis, A. costaricensis, A. costiformis, A. creber, A. cretensis, A. cristatus, A. crustosus, A. crystallinus, A. cvjetkovicii, A. deflectus, A. delacroixii, A. delicatus, A. densus, A. dentatulus, A. depauperatus, A. dessyi, A. digitatus, A. dimorphicus, A. diplocystis, A. discophorus, A. disjunctus, A. diversus, A. dorothicus, A. dubius, A. dubius, A. duricaulis, A. dybowskii, A. eburneocremeus, A. eburneus, A. echinosporus, A. echinulatus, A. ecuadorensis, A. effusus, A. egyptiacus, A. elatior, A. elegans, A. ellipsoideus, A. ellipticus, A. elongatus, A. equitis, A. erythrocephalus, A. falconensis, A. fasciculatus, A. fennelliae, A. ferrugineus, A. ferrugineus, A. ficuum, A. fiemonthi, A. filifera, A. fimetarius, A. fimeti, A. fischeri, A. fischerianus, A. flaschentraegeri, A. flavescens, A. flavidus, A. flavipes, A. flavofurcatus, A. flavoviridescens, A. flavus, A. flocculosus, A. floriformis, A. foeniculicola, A. foetidus, A. fonsecaeus, A. foutoynontii, A. foveolatus, A. fresenii, A. fruticans, A. fruticulosus, A. fujiokensis, A. fuliginosus, A. fulvus, A. fumaricus, A. fumigatiaffinis, A. fumigatoides, A. fumigatus, A. fumisynnematus, A. fungoides, A. funiculosus, A. fuscus, A. galeritus, A. giganteus, A. gigantosulphureus, A. gigas, A. glaber, A. glaucoaffinis, A. glauconiveus, A. glaucus, A. globosus, A. godfrini, A. gorakhpurensis, A. gracilis, A. granulatus, A. granulosus, A. gratioti, A. greconis, A. griseus, A. guttifer, A. gymnosardae, A. halophilicus, A. halophilus, A. helicothrix, A. hennebergii, A. herbariorum, A. heterocaryoticus, A. heteromorphus, A. heterothallicus, A. heyangensis, A. hiratsukae, A. hollandicus, A. homomorphus, A. hortae, A. humicola, A. humus, A. ibericus, A. igneus, A. iizukae, A. implicatus, A. incrassatus, A. indicus, A. indohii, A. ingratus, A. insecticola, A. insuetus, A. insulicola, A. intermedius, A. inuii, A. itaconicus, A. ivoriensis, A. Janus, A. japonicus, A. Jeanselmei, A. kambarensis, A. kanagawaensis, A. kassunensis, A. katsuobushi, A. keveii, A. koningii, A. laciniosus, A. lacticoffeatus, A. laneus, A. lanosus, A. laokiashanensis, A. lateralis, A. lentulus, A. lepidophyton, A. leporis, A. leucocarpus, A. lignieresii, A. longivesica, A. longobasidia, A. luchensi, A. luchuensis, A. lucknowensis, A. luteoniger, A. luteovirescens, A. lutescens, A. luteus, A. macfiei, A. macrosporus, A. malignus, A. malodoratus, A. malvaceus, A. mandshuricus, A. manginii, A. mannitosus, A. maritimus, A. mattletii, A. maximus, A. medius, A. melitensis, A. melleus, A. meffinus, A. mencieri, A. michelii, A. microcephalus, A. microcysticus, A. microsporus, A. microthecius, A. micro viridicitrinus, A. minimus, A. minisclerotigenes, A. minor, A. minutus, A. miyajii, A. miyakoensis, A. mollis, A. montenegroi, A. montevidensis, A. mucoroides, A. mucoroideus, A. muelleri, A. multicolor, A. multiplicatus, A. muricatus, A. muscivora, A. mutabilis, A. mycetomi-villabruzzii, A. mycobanche, A. nakazawae, A. nantae, A. nanus, A. navahoensis, A. neobridgeri, A. neocarnoyi, A. neoeffipticus, A. neoglaber, A. nidulellus, A. niger, A. nigrescens, A. nigricans, A. nishimurae, A. niveoglaucus, A. niveus, A. noelting, A. nominus, A. nomius, A. novofumigatus, A. novus, A. ochraceopetaliformis, A. ochraceoroseus, A. ochraceoruber, A. ochraceus, A. okazakii, A. olivaceofuscus, A. olivaceus, A. olivascens, A. olivicola, A. omanensis, A. onikii, A. oosporus, A. ornatulus, A. ornatus, A. oryzae, A. ostianus, A. otanii, A. ovalispermus, A. paleaceus, A. pallidus, A. panamensis, A. paradoxus, A. parasiticus, A. parrulus, A. parvathecius, A. parvisclerotigenus, A. parviverruculosus, A. parvulu, A. paulistensi, A. penicillatus, A. peniciffiformis, A. peniciffioides, A. peniciffioideum, A. penicillopsis, A. periconioides, A. perniciosus, A. persii, A. petrakii, A. peyronelii, A. phaeocephalus, A. phialiseptatus, A. phoenicis, A. pidoplichknovii, A. piperis, A. polychromus, A. pouchetii, A. primulinus, A. profusus, A. proliferans, A. protuberus, A. pseudocaelatus, A. pseudocarbonarius, A. pseudocitricus, A. pseudoclavatus, A. pseudodeflectus, A. pseudoelatior, A. pseudoelegans, A. pseudoflavus, A. pseudoglaucus, A. pseudoheteromorphus, A. pseudoniger, A. pseudoniger, A. pseudonomius, A. pseudotamarii, A. pulchellus, A. pulmonum-hominis, A. pulverulentus, A. pulvinus, A. puniceus, A. purpureofuscus, A. purpureus, A. pusillus, A. pyramidus, A. pyri, A. qinqixianii, A. qizutongii, A. quadricinctus, A. quadricingens, A. quadrifidus, A. quadrilineatus, A. quercinus, A. quininae, A. quitensis, A. racemosus, A. raianus, A. rambellii, A. ramosus, A. raperi, A. recurvatus, A. rehmii, A. repandus, A. repens, A. reptans, A. restrictus, A. rhizopodus, A. robustus, A. roseoglobosus, A. roseoglobulosus, A. roseovelutinus, A. roseus, A. roseus, A. ruber, A. rubrobrunneus, A. rubrum, A. rufescens, A. rugulosus, A. rugulovalvus, A. rutilans, A. sacchari, A. saitoi, A. salviicola, A. sartoryi, A. scheelei, A. schiemanniae, A. sclerogenus, A. sclerotficarbonarius, A. sclerotioniger, A. sclerotiorum, A. sejunctus, A. septatus, A. sepultus, A. silvaticus, A. simplex, A. sojae, A. sparsus, A. spathulatus, A. spectabilis, A. spelunceus, A. spiculosus, A. spinosus, A. spinulosus, A. spiralis, A. stella-maris, A. stellatus, A. stellifer, A. stercoreus, A. sterigmatophorus, A. steynii, A. stramenius, A. striatulus, A. striatus, A. stromatoides, A. strychni, A. subfuscus, A. subgriseus, A. sublatus, A. sublevisporus, A. subolivaceus, A. subsessilis, A. subunguis, A. sulphureus, A. sulphureus, A. sunderbanii, A. sydowii, A. sylvaticus, A. syncephalis, A. tabacinus, A. taichungensis, A. takakii, A. taklimakanensis, A. tamari, A. tapirirae, A. tardus, A. tatenoi, A. terrestris, A. terreus, A. terricola, A. testaceocolorans, A. tetrazonus, A. thermomutatus, A. thomi, A. tiraboschii, A. togoensis, A. tokelau, A. tonophilus, A. toxicarius, A. tritici, A. tsurutae, A. tuberculatus, A. tubingensis, A. tunetanus, A. udagawae, A. umbrinus, A. umbrosus, A. undulatus, A. unguis, A. unilateralis, A. usamii, A. ustilago, A. ustus, A. uvarum, A. vadensis, A. vancampenhoutii, A. varanasensis, A. variabilis, A. varians, A. variecolor, A. variegatus, A. velutinus, A. venezuelensis, A. versicolor, A. vinosobubalinus, A. violaceobrunneus, A. violaceofuscus, A. violaceus, A. virens, A. viridigriseus, A. viridinutans, A. vitellinus, A. vitis, A. vitricola, A. wangduanlii, A. warcupii, A. wehmeri, A. welwitschiae, A. wentii, A. westendorpii, A. westerdijkiae, A. xerophilus, A. yezoensis, A. zhaoqingensis or A. zonatus.
In various configurations, a vector of the present teachings (i.e., a FAC, a FACdual or a FACint of the present teachings) can include an insert which can be at least 10 kb in length, at least 20 kb in length, at least 30 kb in length, at least 40 kb in length, at least 50 kb in length, at least 60 kb in length, at least 70 kb in length, at least 80 kb in length, at least 90 kb in length, at least 100 kb in length, at least 110 kb in length, or at least 120 kb in length. In various configurations, an insert can be up to 500 kb in length, up to 400 kb in length, up to 300 kb in length, up to 200 kb in length, or up to 150 kb in length. Thus, in various configurations, a vector of the present teachings can include an insert ranging, for example and without limitation, from 30 kb up to 500 kb, from 40 kb up to 400 kb, from 50 kb up to 300 kb, or from 100 kb to 500 kb.
In various configurations, a vector of the present teachings can include an insert which can comprise, consist essentially of, or consist of at least one secondary metabolite (SM) gene cluster. In various configurations, a vector of the present teachings can include an insert which can comprise, consist essentially of, or consist of at least one secondary metabolite (SM) gene cluster and all genes of this gene cluster encoding a final metabolite product from a fungus. In various aspect, the SM gene cluster can be from a fungal species heterologous to a host fungal species of a vector of the present teachings. In various aspects, the SM gene cluster can be from a fungal species other than A. nidulans, and the host fungal species can be A. nidulans. In various configurations, an insert comprising an SM gene cluster can be up to 500 kb in length, up to 400 kb in length, up to 300 kb in length, up to 200 kb in length, or up to 150 kb in length. Thus, in various configurations, a vector of the present teachings can include an SM gene cluster ranging, for example and without limitation, from 30 kb up to 500 kb, from 40 kb up to 400 kb, from 50 kb up to 300 kb, from 100 kb to 500 kb, from 100 kb to 400 kb, or from 100 kb to 300 kb. In various configurations, an SM gene cluster comprised by a vector of the present teachings can be a complete gene cluster. In some aspects, expression of an SM gene cluster in a heterologous fungal host can be used to recreate a biosynthetic pathway of a secondary metabolite.
In various configurations, the present teachings include a host fungus comprising a vector of the present teachings (i.e., a FAC, a FACdual, or a FACint). In various aspects, the host fungus can be a filamentous fungus, such as, without limitation, an Aspergillus fungus. In various aspects, the fungus can be an Aspergillus nidulans fungus. In various configurations, a host fungus comprising a vector of the present teachings comprising an SM gene cluster can express genes of the cluster. Because the genes of an SM gene cluster comprised by a vector of the present teachings are in a fungal environment, naturally occurring gene expression, post-transcriptional and post-translational regulation and modifications, as well as synthesis of secondary metabolites, can be duplicated or closely approximated. In some aspects, one or more genes of an SM gene cluster can be modified to effect an increase or a decrease in expression levels, or to alter protein structure.
In various configurations, a secondary metabolite (SM) gene cluster comprised by vector of the present teachings can be modified with one or more targeted insertions, one or more targeted deletions, or a combination thereof. In various aspects, a modification can lead to enhanced expression of one or more genes comprised by an SM gene cluster. In various aspects, a modification can lead to reduced expression of one or more genes comprised by an SM gene cluster. In various aspects, a modification can lead to activation of a cryptic gene. In various aspects, a modification can be a targeted insertion into a specific site in an SM gene cluster. In various aspects, a modification can be a targeted deletion of a portion of an SM gene cluster. In some aspects, the vector can be a FAC, a FACdual a FACint of the present teachings.
In some embodiments, the present teachings include methods of inserting a DNA sequence into a targeted location in a secondary metabolite (SM) gene cluster. In various configurations, these methods can comprise providing a vector of the present teachings (i.e., a FAC, a FACdual or a FACint of the present teachings) comprising a secondary metabolite (SM) gene cluster; providing an insertion DNA comprising, consisting essentially of, or consisting of a) a first sequence homologous to a sequence flanking a first side of the targeted location, b) a sequence to be inserted, c) a second sequence homologous to a sequence flanking a second side of the targeted location and d) a bacterial selectable marker; transforming the vector and the insertion DNA into an E. coli strain that expresses Red/ET recombinase enzymes; and selecting a transformed E. coli cell that comprises the bacterial selectable marker. Without being limited by theory, it is believed that insertion of a sequence at a targeted location can be achieved through homologous recombination between the insertion DNA and the SM gene cluster comprised by the vector. In some configurations, the bacterial selectable marker of the insertion DNA can be a marker other than a bacterial selectable marker comprised by the vector prior to the transformation. In various configurations, the bacterial selectable marker can be a positive selection marker or a negative selection marker. In some aspects, the vector can be a FAC.
In some embodiments, the present teachings include methods of deleting a targeted DNA sequence from a secondary metabolite (SM) gene cluster. In various configurations, these methods can comprise providing a vector of the present teachings (i.e., a FAC, a FACdual or a FACint of the present teachings) comprising a secondary metabolite (SM) gene cluster; providing a deletion DNA comprising a) a first sequence homologous to a sequence flanking a first side of the targeted DNA sequence, b) a second sequence homologous to a sequence flanking a second side of the targeted DNA sequence, and c) a bacterial selectable marker; transforming the vector and the insertion DNA into an E. coli strain that expresses Red/ET recombinase enzymes; and selecting a transformed E. coli cell that comprises the bacterial selectable marker. Without being limited by theory, it is believed that deletion of a targeted sequence can be achieved through homologous recombination between the deletion DNA and the SM gene cluster comprised by the vector. In some configurations, the bacterial selectable marker of the deletion DNA can be a marker other than a bacterial selectable marker comprised by the vector prior to the transformation. In various configurations, the bacterial selectable marker can be a positive selection marker or a negative selection marker. In some aspects, the vector can be a FAC of the present teachings.
In some embodiments, the present teachings include methods of constructing unbiased libraries in a vector of the present teachings. In various configurations, these methods can comprise providing high molecular weight (HMW) genomic DNA from a source of DNA such as a fungus; mechanically shearing the HMW genomic DNA into fragments of 100 kb-300 kb in length; generating blunt ends on the DNA fragments; ligating restriction enzyme linkers such as BstXI linkers to the blunt ends, thereby generating linker-ligated DNA fragments; purifying the linker-ligated DNA fragments by pulse field gel electrophoresis; and ligating the purified and linker-ligated DNA fragments into a restriction enzyme-cut vector such as a BstXI-cut vector of the present teachings. In various aspects, the methods can further comprise transforming a host microorganism with the ligated, restriction enzyme-cut vector. In various configurations, the host microorganism can be an E. coli or a second fungus such as, for example, an A. nidulans. In various configurations, the restriction enzyme can be BstXI. In various configurations, the vector can be a FAC of the present teachings. In various aspects, the source of the DNA can be a filamentous fungus such as, without limitation, an Aspergillus fungus, such as an Aspergillus other than A. nidulans. In some aspects, the host microorganism can be an Aspergillus fungus such as A. nidulans. In various aspects, the source of high molecular weight genomic DNA can be a fungal species other than the host fungal species. In various aspects, the HMW genomic DNA can be fungal genomic DNA heterologous to the host fungal species. In various aspects, the HMW genomic DNA can be fungal genomic DNA comprising a secondary metabolite gene cluster.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-C illustrate diagrams of FAC vectors of the present teachings.

FIG. 2A-B illustrate preparation of HMW genomic DNA from Aspergillus wentii and random shear FAC cloning results.

FIG. 3A-C CHEFF gels showing that E. coli-Aspergillus shuttle BACs or FACs are successfully transferred from transformed strains of A. nidulans back into E. coli.

FIG. 4A-B Illustrate schematic overview of one-step precise FAC modification and molecular confirmation of successful fusion PCR.

FIG. 5 A CHEFF gel shows five precise gene deletions of AtFAC9J20 (FAC20).

FIG. 6 A schematic diagram of assembling a synthetic SM gene cluster by the FAC system in A. nidulans.

DETAILED DESCRIPTION

The present teachings provide vectors and methods for the production of unbiased large-insert genomic libraries, for capturing complete sets of large intact SM gene pathways from a fungus. The vectors can be used to shuttle large intact SM gene clusters between a fungal host and a bacterial host. A. nidulans can be used as a host for heterologous expression of SM gene clusters. In addition, vectors of the present teaching allow targeted modification of SM gene clusters with insertions and deletions using homologous recombination.
The present inventor has constructed unbiased fungal shuttle BAC (FAC) libraries with average insert sizes of 100 kb or larger from six sequenced fungi: Aspergillus aculeatus, A. wentii, A. terreus, Fusarium solani, Penicillium expansum, and P. marneffei. The average insert size in each library is such that an individual vector can contain a complete SM pathway, or a fungal secondary metabolite gene cluster which can range from 20 kb to over 80 kb. In some configurations, one vector can comprise all the genes of a SM biosynthetic pathway.
The new FAC libraries were created using randomly sheared DNA and without restriction partial digestion, another milestone in the field, removing bias and thus improving the quality of the library. With the FAC libraries, the present inventor has successfully captured 263 of 271 intact SM gene clusters or pathways predicted from the 6 sequenced fungi as individual FAC clones (Table 1).
The present inventor has demonstrated that large vectors such as vectors comprising intact SM gene clusters can be shuttled into a fungal host for stable plasmid maintenance. In addition, heterologous expression in an A. nidulans host of large SM gene clusters that are at least 150 kb has been achieved. In some configurations, A vector of the present teachings can contain a full-length SM gene cluster that can be regulated by the regulatory elements of a fungal host.
In some aspects, a vector comprising an intact SM gene cluster (such as a vector comprising an insert of about 100 kb) can be modified by a Red/ET technique, for fungal functional SM study. The present teachings include methods for the precise modification of fungal intact SM gene clusters at any selected DNA sequence position. The methods can be used, for example and without limitation, for activating cryptic, silent and or low-expression SM gene clusters, characterizing a gene or genetic element within a fungal SM gene cluster, and natural product (NP) discovery. Examples of modifications of 55 SM gene clusters or pathways are listed in Table 2.
In some configurations, an antibiotic resistance gene (for example, but without limitation a resistance gene for kanamycin, ampicillin or carbenicillin, erythromycin, tetracycline, gentamicin sulfate, penicillin, streptomycin, spectromycin, or chloramphenicol), can be used to select bacterial colonies harboring a vector comprising a modified SM gene cluster. Such vectors can be grown in E. coli on LB media with antibiotics appropriate for the both the vector and RED/ET selection markers. In some aspects, a selected colony can be grown within one day.
In some configurations, the present teachings include a fusion PCR approach which combines a selectable marker (e.g. KanR or galK gene) and a promoter (such as, but without limitation, gpdA(p), alcA(p), glaA(p), or pkiA(A)) as one PCR product for modifying a SM gene cluster (e.g. FIGS. 4A-B and 5).
In some configurations, the present teachings include methods for expressing a toxic SM compound, without the need to coexpress a resistance gene that can transport a toxic SM compound out of the cell. These methods use a vector comprising an inducible strong promoter such as alcA(p). In these methods, cells are initially grown without an inducing agent. When the cells reach a sufficient density, an inducing agent is added, and the cells express the genes of a secondary metabolite pathway. This approach can be used for the production of a toxic SM compound.
In some configurations, vectors of the present teaching provide tools for assembling synthetic SM gene clusters in A. nidulan by fungal homologous recombination (FIG. 6). Individual genes (for example Gene1, Gene2, and Gene3, or more, total ˜100 kb in size) can be either completely synthesized according to bioinformatics designs or cloned and fused with an inducible strong promoter (such as, but without limitation alcA(p)) and flanking homologous sequences (about 1 kb, H1, H2, H3, H4 and more). These genes and the cloning ready vectors (pFAC or pFACdual) containing the flanking homologous sequences of the synthetic SM gene cluster (e.g. H1, and H4) can be simultaneously transformed into A. nidulans to assemble the synthetic SM gene cluster by homologous recombination. Fungal selection markers such as AfpyroA and AfriboB (Szewczyk, E, et al., Nat. Protoc., 2006, 1, 3111-3120) can be used for the selection of a vector with a synthetic SM gene cluster. Unlike the previous genomic integration reported in the art (Szewczyk, E., et al., Nat. Protoc., 2006, 1, 3111-3120; Chiang, Y. M., et al., J. Am. Chem. Soc., 2013, 135, 7720-7731), a synthetic SM gene cluster-FAC of the present teachings can be isolated from A. nidulans and then shuttled back into E. coli. In some configurations, a FAC can be further modified, for example by adding regulatory elements or genes in E. coli or in vitro.
In some configurations, the present teachings include methods for assembly of novel synthetic SM gene clusters in A. nidulan by fungal homologous recombination (FIG. 6)
The present teachings disclose three types of vectors for the cloning of large inserts. These vectors can be used for replication and maintenance of large inserts as artificial chromosomes or for integration of large inserts into the host fungal genome. In various configurations, a plasmid that can be used as a fungal artificial chromosome can be a P1-based vector, a BAC-based vector, or a shuttle BAC vector that can be used to replicate large inserts in E. coli and fungal hosts.
In various configurations a vector of the present teachings can contain features for replication and maintenance of the plasmid in E. coli. A vector can comprise an origin of replication for E. coli, such as low-copy number origin, for example but without limitation an origin derived from an F plasmid. A low-copy number origin of replication can include, without limitation, an oriS. A vector can also comprise an origin of replication for E. coli that can be an inducible high-copy replication origin, such as, but without limitation, an oriV. A vector can also include an E. coli selection marker gene, such as a gene that confers resistance to an antibiotic such as, but without limitation: chloramphenicol, kanamycin, ampicillin or carbenicillin, erythromycin, tetracycline, gentamicin sulfate, penicillin, streptomycin, or spectromycin. In some configurations, a vector can also comprise at least one cloning site, which can be a multiple cloning site. In some aspects, a cloning site can comprise a pair of restriction sites wherein digestion with a restriction enzyme generates non-complementary single-stranded overhangs that can be ligated to specific linkers. Suitable enzymes include enzymes that can produce non-complementary single-stranded overhangs, such as non-palindromic overhangs such as overhangs resulting from digestion with an enzyme such as, without limitation, BstXI, BseYI, I-CeuI, I-SceI, PI-PspI, PI-SceI, AIwNI, BgII, BsII, BstAPI, DrdI, MwoI, PfIMI, or SfiI. In some configuraitons, a second cloning site can comprise a pair restriction sites which flank the first cloning site enzyme cut sites wherein digestion with a second enzyme targeting these sites generates non-complementary single-stranded overhangs. Suitable enzymes include rare cutters that can create non-complementary single-stranded overhangs such as, but without limitation I-SceI, PI-PspI, and I-CeuI. Without being limited by theory, the combination of these two restriction enzyme site pairs can facilitate clean excision of the cloned large DNA fragment and exchange with other FAC plasmids, such as FAC integration plasmids. In various configurations, the high-copy number origin of replication can be regulated by a replication initiation protein that can be integrated into a host E. coli cell's genome on an inducible promoter, such as but without limitation an arabinose inducible promoter, a T5 promoter, a T7 promoter, a rhaBAD promoter or a β-galactosidase promoter. The replication initiation protein can be, for example and without limitation, TrfA.
In some configurations, a FAC vector can contain features for their replication in fungal cells. These include a fungal origin of replication, such as, but without limitation autonomous maintenance in Aspergillus (AMA1, SEQ ID NO: 8). A FAC vector can also contain a fungal selection marker gene, such as but without limitation, orotidine-5′-phosphate decarboxylase gene (pyrG, originated from A. parasiticus, SEQ ID NO: 9 and SEQ ID NO: 10), ptrA, or trpC.
In some configurations, the present teachings include a FAC dual-function vector that can be maintained in E. coli as a fungal artificial chromosome, can be induced to integrate into the fungal genome, and can be used as a E. coli-fungus shuttle BAC vector. A dual function vector has the same features as a regular FAC vector as described supra, and an additional gene cassette: an attP site and an integrase gene, such as but without limitation a phi31 integrase gene, under the control of fungal inducible promoter, such as but without limitation, alcA promoter or glaA(p). In various configurations, the integrase gene can be codon optimized for fungal expression.
In various configuration, a FAC system of the present teachings can be used in a wide variety of fungi, such as and without limitation Aspergillus aculeatus, A. terreus, A. wentii, Fusarium solani, Penicillium expansum, P. marneffei, Neurospora crassa, and fungi belonging to the phylum Ascomycetes.

Definitions

Various terms are used herein to refer to aspects of the present teachings. To aid in the clarification of description of the components of these teachings, the following definitions are included.
The term “fungus” as used herein refers to is any member of the group of eukaryotic organisms that includes unicellular microorganisms such as, without limitation, yeasts and molds, as well as multicellular fungi that produce familiar fruiting forms known as mushrooms. More particularly they are filamentous fungi or molds, such as, and without limitation, Aspergillus aculeatus, A. terreus, A. wentii, Fusarium solani, Penicillium expansum, and P. marneffei.
“Secondary metabolite (SM)” as used herein refers to a chemical compound that is not involved in primary metabolism, and therefore differs from the more prevalent macromolecules such as proteins and nucleic acids. Thousands of SMs have been described from various eukaryotic organisms including fungi (Donadio, S., et al., Nat. Prod. Rep., 2007, 24, 1073-1109).
“SM gene cluster or pathway” as used herein refers to a set of biosynthetic genes that comprise polynucleotide sequences encoding the proteins, such as but without limitation an enzyme, required for synthesis and activity of a secondary metabolite. SM gene clusters or pathways implement the conversion of a starting compound, such as but without limitation a substrate, into a final compound or NP.
The term “intact or full-length SM gene cluster or pathway” used herein refers to a SM gene cluster or pathway contains a complete set of biosynthetic genes and regulatory elements. Each fungal genome may harbor 50 or more different intact SM gene clusters ranging from 20 to more than 100 kb in size (Nordberg, H. et al., Nucleic Acids Res., 2014, 42(Database issue), D26-31). Fungal SM clusters usually comprise one or more backbone gene(s) such as polyketide synthases (PKSs), nonribosomal peptide synthetases (NRPSs), dimethylallyl tryptophan synthases (DMATs), and terpene cyclases (TCs), surrounded by genes for modifying enzymes including, but not limited to, oxidoreductases, oxygenases, dehydrogenases, reductases, and transferases (Keller, N. P. and Hohn, T. M., Fungal Genet. Biol. 1997, 21, 17-29; Walton, J. D., Fungal Genet. Biol., 2000, 30, 167-171).
“Regulatory element” as used herein refers to a nucleic acid sequence element that controls or influences the expression of a gene, such as a gene within a large polynucleotide insert from a gene cassette, genetic construct or a FAC vector. A regulatory element can be, for example and without limitation, a promoter, an enhancer, a transcription factor or control sequence, a translation control sequence, a temporal or tissue-specific regulatory element, a polyadenylation signal sequence, a 5′ or 3′ UTR, a repressor or a terminator. Regulatory elements can be homologous or heterologous to the large polynucleotide insert or intact SM gene cluster to be expressed from a FAC construct or vector as described herein. When a FAC vector as described herein is present in a cell such as a heterologous A. nidulans cell, a regulatory element can be naturally occurring, endogenous, exogenous, and/or engineered with respect to the cell.
“Compatible” as used herein refers to two nucleic acid ends may mean that the ends are either both blunt or contain complementary single strand overhangs, such as that created by mechanically shearing DNA followed by DNA end repair, DNA linker ligation, or after digestion with a restriction endonuclease. At least one of the ends may contain a 5′ phosphate group, which can allow ligation of the ends by a double-stranded DNA ligase.
“BstXI Linker” (Klickstein, L. B. and Neve, R. L., Current Protocols in Molecular Biology, John Wiley & Sons, Inc. 1991, 5.6.1-5.6.10) as used herein refers to two partially complementary strands of DNA that are annealed to one another to produce a double-strand DNA molecule with an overhang complementary to one end of the BstXI cutting sequences as above. An example of a BstXI linker for ligation of the blunt ends of large DNA fragments is the following:

(SEQ ID NO: 5)

	BstXI Linker Top	5′-CTGGAAAG-3′

(SEQ ID NO: 6)

BstXI Linker Bottom

5′-CTTTCCAGCACA-3′

The blunt ends of the BstXI linker can be designed to be complementary to large DNA fragments. For example, the target large DNA fragments may be mechanically sheared DNA which is polished and made blunt by DNA end repairing enzyme mixture (Intact Genomics, St. Louis, Mo.). The blunt DNA can also be modified by non-template mediated addition of a single A nucleotide to each end of the target large DNA by Taq polymerase. In this case, the above linker can be modified with an additional single T nucleotide to the 3′ of BstXI Linker Top strand.
“Shuttle bacterial artificial chromosome (BAC) vector” means a BAC vector that can be used for the transfer and the maintenance of genetic information from one (or more) donor bacterial species or strain(s) to one or more host organism(s) or strain(s) or species.
“FAC vector” as used herein refers to a fungal artificial chromosome vector, or a shuttle BAC vector between E. coli and A. nidulans.
“Library” as used herein refers to a plurality of clones each comprising an insert sequence and a vector.

Methods

Methods and compositions described herein utilize laboratory techniques well known to skilled artisans, and can be found in laboratory manuals such as Sambrook, J., et al., Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2001; Spector, D. L. et al., Cells: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1998; Nagy, A., Manipulating the Mouse Embryo: A Laboratory Manual (Third Edition), Cold Spring Harbor, N.Y., 2003 and Harlow, E., Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1999. As used in the present description and any appended claims, the singular forms “a”, “an” and “the” are intended to include the plural forms as well, unless the context indicates otherwise.
The following materials and methods are also used in various aspects of the present teachings.
The present teachings provide for the preparation of ultra-high quality of high molecular weight (HMW) genomic DNA from a fungus and the generation of an unbiased large insert FAC library by randomly shearing with average insert size 100 kb or larger. The large DNA population of a library includes not only fragments of all biosynthetic loci in the fungal genome with minimal bias, but also each DNA molecule is large enough (100 kb or larger) to cover at least one of the intact SM gene clusters.
High molecular weight (HMW) genomic DNA can be derived from any cultured, isolated, purified or mixed fungi, including fungi with published genome sequences. The HMW genomic DNA can be prepared directly from a population of uncultured fungi in their natural habitat, environment, or biomass without the need of fungal isolation and cultivation.
The techniques of HMW genomic DNA preparation for BAC cloning have been documented (Wu, C. C., et al, Encyclopedia of Molecular Cell Biology and Molecular Medicine Volume 3 (2nd Edition), Edited by Meyers R. A., Wiley-VCH Verlag GmbH: Weinheim, Germany 2004, pp 385-425; Zhang, M., et al., Nat. Protoc., 2012, 7: 467-478). In some configurations, HMW genomic DNA can include intact chromosomes or can be megabases in size.
For preparation of HMW genomic DNA, fungal cells, such as, but without limitation, spores, germinated spores, protoplasts, or nuclei can be collected and directly embedded in low-melting agarose plugs. The low-melt agarose plugs can be from about 0.4% to about 1% in concentration and can have a final concentration of about 0.5%. HMW genomic DNA can be purified by treatment with lauryl sarcosine and proteinase K in 0.5 M EDTA, pH 9.0. HMW genomic DNA can be prepared by preparing fungal protoplasts (Bok, J. W. and Keller, N. P., Methods Mol. Biol., 2012, 944, 163-174) and then embedding the fungal protoplasts in low melt agarose plugs.
HMW genomic DNA can be used to generate unbiased large insert recombinant DNA libraries to cover large intact SM gene clusters wherein one clone contains an intact SM gene cluster or pathway. The present teachings provide for preparation of liquid HMW genomic DNA by either electroelution or Gelase digestion of the agarose DNA plugs. The liquid HMW genomic DNA can then be mechanically sheared by hydroshearing, repeated pipetting, low-speed vortexing or a combination thereof. Conditions for a given fungal genome can be determined by running sheared HMW genomic DNA on a CHEFF gel with the size range of about 100 kb to about 300 kb.
The E. coli-fungal shuttle BAC vectors or FAC (FIG. 1) vectors disclosed herein (see Example 1) can be used for BAC/FAC library construction with average inserts 100 kb or larger. The present inventor has demonstrated that the large-insert FACs (at least 150 kb) can be shuttled into the heterologous A. nidulans host for stable maintenance and NP discovery (FIG. 3, Bok, J. W., et al., BMC Genomics, 2015, 16, 343).

Random Shear BAC Cloning Method for Construction of Unbiased FAC Libraries.

HMW genomic DNA was sheared as described in Methods. To 400 μl of sheared HMW genomic DNA (100˜300 kb), 5 μl of DNA end repairing enzyme mixture (Intact Genomics, St. Louis Mo.), 100 μl of 5× DNA end repairing buffer to a total of 500 μl. The sample is mixed well by gently pipetting with a wide-bore tip and the reaction is incubated at room temperature for 30 min. The DNA end repairing enzymes are heat killed by incubating the large DNA end repair reaction at 70° C. for 15 min. 20 μl each of 100 μM BstXI linker TOP and Bottom (10{circumflex over ( )}6˜10{circumflex over ( )}7-fold more molar rate excess linkers than the large DNA molecules), 61 μl of 10× T4 ligation buffer with ATP and 10 μl of large DNA T4 ligase (intactgenomics) are added immediately and then the reaction is mixed well by gently pipetting with a wide-bored tip. The linker ligation reaction is set at room temperature for 3-8 hours. The linker-ligated large DNA fragments are fractionated and excess BstXI linkers are removed by 1% agarose CHEFF gel electrophoresis at 0.5× TBE, 6V/cm, 90 s/90 s for 16 hours and 4V/cm, 5 s/5 s for additional 8 hours. Lambda DNA ladder marker (Intact Genomics) is used as a control to recover 100˜150, 150˜210, 210˜300 kb large DNA fractions as gel slices, and then the gel slices are placed into dialysis tubes and the DNA is electreluted, and then the purified linker-ligated large DNA fragments are dialyzed against 100 ml of ice-cold and autoclaved ultra-pure water at least 3 times, for one hour each. The cloning-ready BstXI-FAC vectors (20 ng/μl, Intact Genomics) are mixed with the gel-purified BstXI-linker ligated DNA (2˜3 ng/μl) at 1:3 molar rate, and the ligation reaction is set at 16° C. for overnight. For example, 200 ul large DNA (3 ng/μl) is mixed with 10 ul of the FAC vector (20 ng/μl), 60 μl of 5× T4 ligation buffer, 30 μl of BAC cloning T4 ligase (intactgenomics), ligation reaction is set at 16° C. for overnight, preferably 12˜18 hours.

Large-Insert FAC Library Construction.

The large DNA fragments of the library are cloned into FAC vector(s) and serve as a screening library for covering the fungal SM gene clusters or pathways in E. coli. Preferably, the large-insert FAC library has average insert size 100 kb or larger, therefore it is sufficient to contain at least one intact SM gene cluster in an individual FAC clone. Furthermore, the large-insert FAC library is unbiased and a FAC library with only 10×, or even 5× genome coverage can be enough to capture an entire set of intact SM gene clusters from a sequenced fungal genome or a fungal sample. Using the methods described herein, the inventor can capture a complete set of intact SM gene clusters with 4˜5 384-well plates of FAC clones (average about 100 kb, 4˜5× genome coverage) from all 6 fungi studied (Table 1; Bok, J. W., et al., BMC Genomics, 2015, 16, 343).
Because the FAC system is a shuttle BAC system, vectors of the present teachings can be in the BAC/fosmid library screening techniques known in the art. To identify intact SM gene cluster-containing FAC clones, sequence-based approaches can be used for FAC library screening such as PCR or colony hybridization (Zhang, H. B. and Wu, C. C., Plant Physiol. Biochem., 2001, 39, 1-15; Kang, H. S. and Brady, S. F., Angew. Chem. Int. Ed. Engl., 2013, 52, 11063-11067). One application of sequence-based approaches involves the design of DNA probes or primers which are derived from conserved regions of already known genes or protein families, for example but without limitation, pooled FAC DNAs from each arrayed library are screened using degenerate primers designed to amplify the conserved domains/regions of PKS or NRPS (Kang, H. S. and Brady, S. F., Angew. Chem. Int. Ed. Engl., 2013, 52, 11063-11067). Positive FAC clones can be recovered from libraries by PCR screening of the respective pools, followed by screening of their plates, columns, and rows from which they are identified. Another sequence based approach is to use high throughput next generation sequencing of pooled FAC libraries by plate-column-row with multiplex barcodes. This strategy will reduce sequence complexity from whole fungal genomes into FAC pool-level (plate-column-row), therefore enabling the complete assembly of pooled FAC clones (each 100 kb or larger). The intact SM gene clusters will be identified by annotation of completely sequenced and assembled FAC clones. The individual SM gene cluster-containing FAC clones will then be de-convoluted by barcodes and plate-column-row coordinates. The advantage of these sequence-based approaches is to identify SM gene clusters and their FACs from fungi without the precondition of genome sequence or even metagenomes of unculturable fungal community. In the present teachings, another sequence-based approach is used to sequence the FAC clone ends by the traditional Sanger sequencing method, then identify the entire set of intact SM gene cluster-containing FACs by aligning the FAC end sequences onto the fungal reference genome sequences. Similarly a next-generation sequence method may be used for this purpose with FAC DNA pooling and barcoding to reduce the sequencing cost.

Microbial Strains and Culture Conditions.

The parental strain RJW256 (pyrG89, pyroA4, Anku70::argB, ΔST::afpyrG, veA1) was obtained by a sexual cross between LO4641 (riboB2, pyroA4, ΔST::AfpyrG, ΔAN7909::afpyrG, Δnku70::argB, veA1) and RJW113.5 (ΔveA::argB, pyrG89). RJW256 was transformed with FAC plasmids to produce FAC recombinant strains. AST::AfpyrG indicates that the entire endogenous sterigmatocystin gene cluster was removed from A. nidulans.
For antimicrobial activity tests, we used A. nidulans RDIT9.32, A. fumigatus 293, Candida albicans, Pseudomonas aeroginosa PAO1, Bacillus cereus U85, and Micrococcus luteus strains. All of the fungal and bacterial strains were maintained as frozen glycerol stocks at −80° C. Fungal strains were grown at 37° C. on glucose minimal medium (GMM, Bok, J. W. and Keller, N. P., Eukaryot. Cell, 2004, 3, 527-535) and bacterial strains were cultured on tryptic soy broth medium.
A. nidulans Transformation and the Recovery of SM Cluster-Containing FACs
A modified PEG-calcium based transformation method was applied to improve transformation. The described method (Bok, J. W. and Keller, N. P., Eukaryot. Cell, 2004, 3, 527-535) was modified as follows: 200 μL containing 107 A. nidulans RJW256 protoplasts mixed with 2 μg FAC DNA were gently placed over 200 μL of 30% PEG 4,000 with 50 mM CaCl₂in a 1.5 mL centrifuge tube. The centrifuge tube with protoplasts was incubated 30 min on ice. After centrifuging the incubated mixture for 5 min at 250×g, the solution was gently mixed using an autopipette. This mixture was then incubated for 10 minutes at room temperature before 1 mL of sorbitol-Tris-HCl-CaCl₂(STC: 1.2M sorbitol, 10 mM Tris-HCl, 10 mM CaCl₂pH 7.5) buffer was added and gently mixed into the solution. After transferring the mixture into a 13 mL tube, an additional 5 mL of STC was added into the tube and gently mixed. One mL of this final solution was distributed onto regeneration media to obtain transformants.
A. nidulans FAC transformants were maintained on culture plates for three generations for phenotype and chemical screening. For FAC recovery, we prepared ˜0.3 mL of 106/mL protoplasts from A. nidulans FAC strains and FAC DNA was isolated by the common alkali lysis method, and resuspended in 10 μL of TE. One microliter of recovered DNA was re-transformed back into E. coli cells (BAC cells, Intact Genomics).

Fungal Genomic DNA Extraction

Fungal DNA was extracted from lyophilized mycelia using previously described techniques (Bok, J. W. and Keller, N. P., Methods Mol. Biol., 2012, 944, 163-174) to perform PCR reaction.

Antimicrobial Screening

A disc-diffusion method (Bauer 1966) was used for antibiotic activity-guided screening. One plate of each A. nidulans FAC strain was inoculated on solid GMM and incubated for seven days at 37° C. Subsequently, the entire contents of the plates were collected and lyophilized for 48 hours. Samples were then pulverized with mortar and pestle prior to the addition of 10 mL of methanol. Air-dried methanol extracts were dissolved in 150 μL methanol for activity testing. Media preparation for antibacterial assays were performed as previously described (Bok, J. W. and Keller, N. P., Eukaryot. Cell, 2004, 3, 527-535). For antifungal assays, 106 spores mentioned in the section above were embedded in 5 mL soft GMM agar (0.75% agar) and overlaid on solid GMM. 10 μL out of the 150 μL methanol extract above was loaded on a 1 cm diameter paper disc for each assay. Assay plates were incubated for 24 to 48 hour at 37° C. and observed for antimicrobial activity.

LC-HRMS Analysis

Five plates of A. nidulans FAC strain, for example and without limitation, AtFAC6J7 were inoculated on solid GMM and incubated for seven days at 37° C. Subsequently, the entire contents of the plates were collected and lyophilized for 48 hours. Samples were then pulverized with mortar and pestle prior to the addition of 10 mL of methanol. Air-dried methanol extracts were then further extracted with organic solvent (chloroform:methanol:ethylacetate=8:1:1). Organic extracts were evaporated to dryness and stored at −20° C. until analysis.
Organic extracts obtained were resuspended in methanol to a final concentration of 2 μg/μL. For each analysis, 40 μg of sample was loaded onto a LUNA® C18 column (150 mm×2 mm; 3 μm particle size) (Phenomenex, Torrance, Calif.). Chromatography was performed using an AGILENT® 1150 LC system (Agilent, Santa Clara, Calif.) at a flow rate of 200 μL/min. The following gradient was employed (Buffer A: water with 0.1% formic acid, Buffer B: acetonitrile with 0.1% formic acid): time 0 min, 2% B; 35 min, 70% B; 54 min, 98% B. A 1:7 split was employed post-column, resulting in a flow rate of 25 μL/min being directed to the mass spectrometer. A Q-EXACTIVE™ mass spectrometer (Thermo Fisher Scientific, Waltham, Mass.) was used for MS analysis with the following settings: capillary temperature 275° C., sheath gas 4 (arbitrary units), spray voltage 4.2 kV. Full MS spectra were acquired at 35,000 resolution for the mass range m/z 200 to 1500 for all samples. Following each full MS scan, the top 5 most intense ions were selected for a dependent MS2 scan. MS2 was conducted using higher-energy collisional dissociation (HCD) with a normalized collision energy of 30%. Three biological replicates of AtFAC6J7 extracts were prepared and analyzed in technical duplicate, followed by the data workup described below.

Data Analysis, Informatics, and Software

The SIEVE software suite (Thermo Fisher Scientific, Waltham, Mass.) was used for component detection and relative quantification of ions produced by electrospray during small molecule LC-HRMS. Component detection was performed using a mass tolerance of 10 part-per-million (ppm) and a retention time window of 2.5 min. A minimum intensity of 5×10⁶was selected as the threshold for defining a peak as a component. For each component, a selected ion chromatogram was created and the integrated intensity of the peak was calculated. Peak areas were normalized based on total ion current. To increase statistical power and confidence of the final analysis, the procedure adopted here involved a decoy approach to multiple hypothesis testing. Specifically, the replicate data AtFAC6J7 was subjected to a uniqueness filter against processed LC-HRMS data generated from a control group of strains containing empty vectors, as well as 13 other strains containing a variety of other FACs with unique genetic content. For dereplication, all components were initially searched against a targeted accurate mass database consisting of known fungal metabolites produced by A. nidulans using a mass tolerance of 3 ppm. A dozen of these known compounds were present at consistent levels in nearly all samples, and were monitored to rapidly identify highly perturbed systems. All components were also searched against a comprehensive accurate mass database consisting of over 13,000 known fungal secondary metabolites. This fungal database was prepared using Antibase (2011), Dictionary of Natural Products (2013), as well as additional fungal natural products found in the literature (Caboche et al. 2008; Andersen et al. 2013).

Vector General Descriptions.

The BstXI Linker overhang is not complementary to itself, nor is the BstXI-cut vector (above). Upon ligation of the linker-ligated large DNA fragments and vector, the preferred ligation reaction product can be a circle containing one vector joined to one large DNA fragment via a single adapter at each end. This molecule may be transformed into host cells to produce a clone.

EXAMPLES

The present teachings including descriptions provided in the Examples that are not intended to limit the scope of any claim or aspect. Unless specifically presented in the past tense, an example can be a prophetic or an actual example. The following non-limiting examples are provided to further illustrate the present teachings. Those of skill in the art, in light of the present disclosure, will appreciate that many changes can be made in the specific embodiments that are disclosed and still obtain a like or similar result without departing from the spirit and scope of the present teachings.

Example 1

This example describes pFAC plasmid, a vector of the present teachings that maintains extra-chromosomes in A. nidulans.
In the present teachings, a FAC vector (pFAC, FIG. 1A, SEQ ID NO: 7) is a BAC-based shuttle vector that can shuttle large DNA between E. coli and A. nidulans hosts. Several features are required for maintaining the plasmid in E. coli, including two E. coli origins of replication: oriS and oriV. The first replication origin, oriS, is derived from a low-copy F plasmid for BAC-based large DNA cloning and library construction. The second replication origin, oriV, is an inducible high-copy replication origin oriV, which can produce higher yield of large inserts when grown in E. coli containing a TrfA gene under the control of an arabinose promoter when they are grown on arabinose containing media. pFAC also contains a chloramphenicol-resistance gene (cat) for plasmid selection. For cloning purposes, the plasmid contains a large DNA cloning site comprising pair of BstXI sites designed next to each other in oppose orientations. When digested with BstXI, this configuration produces a pair of identical BstXI overhangs, that are not self-complimentary, but are complimentary to unique BstXI linkers. Therefore, the digested vector will not religate itself, nor will the linkers concatermerize easily. Two I-SceI homing restriction sites were inserted flanking the BstXI cloning site in reverse orientations. These sites facilitate clean excision of the cloned large DNA fragment and exchange with pFACint cloning vector (see example 2).
pFAC also contains features required for use in A. nidulans. These include a third replication origin, AMA1, the autonomous maintenance in Aspergillus (AMA1, SEQ ID NO: 8). This sequence is required for maintaining large intact SM pathways as extra-chromosomal elements, or FACs. pFAC also contains a fungal selection marker gene, the orotidine-5′-phosphate decarboxylase gene (pyrG from A. parasiticus, SEQ ID NO: 9 & 10).

Example 2

This example describes pFACint, a FAC integration vector.
FAC integration vector (pFACint, FIG. 1B, SEQ ID NO: 11) is a BAC-based shuttle BAC vector that can shuttle large DNA between E. coli and A. nidulans hosts. Several features are required for maintaining the plasmid in E. coli, including two E. coli origins of replication: oriS and oriV. The first replication origin, oriS, is derived from a low-copy F plasmid for BAC-based large DNA cloning and library construction. The second replication origin, oriV, is an inducible high-copy replication origin oriV, which can produce higher yield of large inserts when grown in E. coli containing a TrfA gene under the control of an arabinose promoter when they are grown on arabinose containing media. pFACint carries kanamycin-resistance gene (kan) as a selection marker gene or cloning purposes, the plasmid contains a large DNA cloning site comprising pair of BstXI sites designed next to each other in oppose orientations. When digested with BstXI, this configuration produces a pair of identical BstXI overhangs, that are not self-complimentary, but are complimentary to unique BstXI linkers. Therefore, the digested vector will not religate itself, nor will the linkers concatermerize easily. Two I-SceI homing restriction sites were inserted flanking the BstXI cloning site in reverse orientations. These sites facilitate clean excision of the cloned large DNA fragment and exchange with pFAC cloning vector. The I-Sce-I homing restriction sites also facilitate clean excision of the large intact SM gene pathways from the genomic integration site of the heterologous host A. nidulans.
pFACint also contains features integrating the plasmid into the A. nidulans genome: 1,000-bp 3′trpC (SEQ ID NO: 12) and 1,007-bp 5′trpC (SEQ ID NO: 13) homologous sequences, which were inserted flanking the I-Sce I restriction sites in the same orientations, thus enabling fungal site-specific integration of large pFACint clones into the A. nidulans trpC gene, which encodes a polypeptide homologous to polyketide. The plasmid also contains a fungal selection marker gene, the orotidine-5′-phosphate decarboxylase gene (pyrG, from A. parasiticus).

Example 3

This example describes the vector pFACdual.
pFACdual plasmid, which also substantially corresponds pFAC plasmid except that it includes an additional gene cassette: an attP site and a fungal codon-optimized phi31 integrase gene under the control of fungal inducible promoter, such as alcA(p). Therefore, the large DNA pFACdual clones are usually maintaining as FAC and also be able integrated into the fungal genome with an attB site whenever it is needed.
pFACdual vector is a fungal dual-function vector (pFACdual, FIG. 1C, SEQ ID NO: 14), and can act as both a fungal artificial chromosome and an inducible fungal genomic integration vector, or it can be used as an E. coli-A. nidulans shuttle BAC vector. pFACdual has similar features as pFAC (see Example 1), but pFAC dual has an additional gene cassette: an attP site and a fungal codon-optimized phi31 integrase gene (SEQ ID NO: 16 and SEQ ID NO: 17) under the control of the inducible alcA fungal promoter (alcA(p), SEQ ID NO: 15). Therefore, the large DNA pFACdual clones are usually maintained as a FAC but can be induced to integratd into the fungal genome with an attB site.

Example 4

This example illustrates the preparation of high molecular weight A. wentii DNA.
Aspergillus wentii strain DTO 134E9 was used as a proof of concept. Different fungal species/strain starting materials were compared to test for quality of high molecular weight (HMW) genomic DNA: spores, germinated spores, protoplasts, or nuclei obtained from protoplasts. The protoplast preparation method was performed as previously described (Bok, J. W. and Keller, N. P., Eukaryot. Cell, 2004, 3: 527-535). To isolate nuclei, protoplasts were lysed with 0.5% Triton X-100 in HMW DNA preparation buffer (0.5 M Sucrose, 80 mM KCl, 10 mM Tris, 10 mM EDTA, 1 mM sperm idine, 1 mM spermine, pH 9.4). The protoplasts in buffer were gently mixed, incubated on ice for 30 minutes, and the resulting nuclei pelleted at 1,800×g for 20 minutes. To prepare low melting agarose plugs of HMW DNA, the pellet (˜5×10⁸)—of nuclei, protoplasts, germinated spores, or spores—was resuspended with the HMW DNA preparation buffer to a total volume of 0.6 mL, and an equal volume of 1% low melting agarose was then added to the buffer to a total volume of 1.2 mL at 45° C. This was sufficient to make 10 plugs (about 100 μL per plug) which solidified at 4° C. The plugs were then incubated at 50° C. for 48 hours in 1 mL lysis buffer/plug: 0.5 M EDTA, pH 9.0, 1% lauryl sarcosine, 1 mg/mL proteinase K. Finally, the plugs were extensively washed in 10-20 volumes of the following buffers for one hour for each wash: once with buffer 1 (0.5 M EDTA, pH 9.0-9.3 at 50° C.), once with buffer 2 (0.05 M EDTA, pH 8.0 on ice), three times with buffer 3 (ice cold TE plus 0.1 mM phenylmethyl sulfonyl fluoride (PMSF) on ice), three times with buffer 4 (ice cold TE on ice) and finally all plugs were stored in TE at 4° C. In order to estimate the size and yield of the extracted DNA, plugs were assessed using pulsed field gel electrophoresis (PFGE) (Bio-Rad CHEF Mapper, Hercules, Calif.). The final quality check conditions for the HMW genomic DNA were 6 V/cm, 10 sec to 1 min switch time for 12-16 hours at 14° C. by PFGE, along with appropriate HMW size markers (Zhang, M. et al., Nat. Protoc., 2012, 7, 467-478). The highest quality and quantity of HMW genomic DNA was obtained from the protoplast preparation (FIG. 2A). FIG. 2A shows a CHEF gel that contains A. wentii HMW genomic DNA ranging from greater than 50 kb but mainly Mb sizes of DNA fragments.

Example 5

This example illustrates the construction of unbiased shuttle BAC library of A. wentii DNA.
The HMW genomic DNA obtained from the protoplast preparation in Example 2 ranged from 50˜>1,000 kb (mainly megabase sized fragments). The HMW DNA from three plugs was end-repaired with the DNA end repair enzyme kit (Intact Genomics) in a total volume of 500 μL with 10 μL of the end repair enzymes which were then heat inactivated (70° C., 15 min). The resulting DNA was ligated with BstXI adaptors (10 μL of 100 μM each) and 10 μL ligase (2 U/μL, Intact Genomics) in a total volume of 700 μL. Gel-fractionated DNA fragments ranging from 100 to 200 kb were purified by PFGE. Purified large DNA fragments (about 100 μL 1-3 ng/μL) were ligated into the cloning ready BAC BstXI shuttle vector (pFAC) at 16° C. for ˜18 hours. Next, the ligated DNA mixture was electroporated into electroporation competent E. coli cells (BAC cells, Intact Genomics). Small-scale ligations and transformations (1 μL DNA per 20 μL cells) were used to judge the cloning efficiency. The insert sizes of about 50 BAC clones were determined and confirmed to include inserts of about 100 kb using CHEF gel electrophoresis and NotI digestion of random selected BAC clones in pFAC vector. FIG. 2B illustrates that the average insert size was estimated at ˜100 kb (M, Lambda ladder Marker). Once the suitability of the ligated DNA was confirmed, large-scale ligations and transformations were conducted to achieve at least 7,680 clones for colony picking (20×384-well plates) for the unbiased shuttle BAC library.

Example 6

This example illustrates BAC/FAC end sequencing, and select SM cluster-containing candidate FAC clones.
BAC-end sequences of 1,536 clones from the unbiased Random Shear FAC library of A. wentii were completed by the Sanger BigDye sequencing method. The software Phred was used for base calling and sequence trimming. Vector masking was achieved using the DNAStar SeqMan Pro software package. The BAC end sequences were aligned against the A. wentii reference genome sequence by BLAST Assembled Genomes (NCBI). All 47 SM clusters-containing candidate FAC clones were successfully identified based on the FAC end sequence flanking one end of a SM cluster and the other FAC end sequence flanking the other end of the same SM cluster.

Example 7

This example illustrates construction of unbiased shuttle BAC library of A. wentii DNA and heterologous expression of SM clusters as FACs in A. nidulans.
A. wentii was used as an example for shuttle BAC DNA library construction, and it has a fully sequenced genome containing 47 annotated SM gene clusters (Cerqueira, G. C., et al., Nucleic Acids Res., 2013, 42(Database issue), D705-D710). High molecular weight genomic DNA was prepared from A. wentii (see Example 4) and construction of the unbiased FAC library (see Example 5) resulted in ˜20× genome coverage of the A. wentii genome, or a total of 7,680 FAC clones with an average insert size of 100 kb (FIG. 2A-B). The FAC library was arrayed into 384-well plates and both ends of 1,536 FAC clones were sequenced. Sequence alignment of these end sequences with the A. wentii reference genome was used to identify SM-BAC clones or candidate FACs containing all 47 SM gene clusters (Table 1). In addition, at least 10 of 56 SM clusters of A. terreus are located near telomeres and some telomeric sequences are still not complete in the whole genome sequence database. These data illustrate that these methods successfully overcome the potential bias against telomeric sequences in conventional BAC library construction through the introduction of randomly sheared genomic DNA into the FAC vectors.

Example 8

This example illustrates the validation of shuttle functions of FACs.
To date hundreds of FACs (ranging from 70 to 150 kb in size) were used for heterologous expression and analysis through transformation into A. nidulans. To validate the shuttle function of FACs, we also extracted five of the 15 FAC DNAs from transformed A. nidulans strains and successfully transformed FAC DNA back into E. coli (FIG. 3). A. nidulans was transformed with different FAC clones as determined by return of prototropy on medium without uracil and uridine. Forty or more colonies of E. coli each were then assessed from the recovery of the FACs in FIG. 3A-C respectively. The results show the recovery of FAC examples from all 3 A. nidulans transformants: AtFAC9O3 (˜100 kb), AtFAC9A23 (˜80 kb), and AtFAC7A10 (˜90 kb) respectively. The 2nd and 3rd (D) lane(s) on the left hand side of the gels is the control FAC used to transform A. nidulans. All recovered FACs were digested with NotI, there is no obvious large mutation observed. M, Lambda ladder Marker. This was the first demonstration of the capability of AMA1 in supporting autonomous replication (FAC) of large DNA constructs at least 150 kb in A. nidulans. The present inventor and his collaborators the first to demonstrate that the FAC system allows for extrachromosomal replication of at least 150 kb in A. nidulans (Bok, J. W., et al. BMC Genomics, 2015, 16, 343).

Example 9

This example illustrates LC-HRMS linked FAC SM discovery.
For the initial identification and structure elucidation of SM compounds through FACs, A. nidulans AtFAC9D19 strain samples were prepared as described in the Methods section. A. nidulans AtFAC9D19 was found to produce the insecticide compounds: alantrypinone, serantrypinone, alantrypinene B, alantryleunone. A. nidulans AtFAC6J7 strain was also selected for initial proof-of-concept experiments, as it contained a cluster highly homologous to the recently characterized hexadehydroastechrome cluster in A. fumigatus (Yin, W. B., et al., ACS Synth. Biol., 2013, 2, 629-634,). AtFAC6J7 contains seven out of the eight genes found in the corresponding A. fumigatus cluster. The gene not present in this A. terreus cluster, hasG, encodes for an FAD binding protein responsible for converting a prenyl to a methylbutadienyl side chain to produce hexadehydroastechrome from astechrome. AtFAC6J7 metabolites were identified by analyzing organic extracts of the A. nidulans AtFAC6J7 transformant and control A. nidulans using LC-HRMS. Following data acquisition, Sieve software was used for component detection and relative quantitation (see Methods). When comparing AtFAC6J7 extracts to control sample extracts (wild type and other FAC strains), a compound that was present only in the AtFAC6J7 extract was identified as terezine D by both accurate mass (0.3 part-per-million error) and tandem mass spectrometry (MS/MS or MS2). Terezine D is a stable intermediate of astechrome biosynthesis (Watanabe, T., et al., Bioorg. Med. Chem., 2009, 17, 94-111; Bok, J. W., et al. BMC Genomics, 2015, 16, 343).

Example 10

This example illustrates an antibiotic activity test against FAC clones.
An antibiotic activity test was performed 14 FAC clones. Ten pl out of 150 μl methanol extract from FAC transformants cultured on GMM plate for 7 days at 37° C. were loaded on small disc (diameter: 1 cm) for antimicrobial activity test against Aspergillus spp., Candida albicans, Bacillus cereus, Micrococcus luteus and Pseudomonas aeruginosa. Antibiotic activity was observed against Bacillus cereus with two FAC extracts (Bok, J. W., et al. BMC Genomics, 2015, 16, 343).

Example 11

This example illustrates FAC recombineering and activating silent SM gene clusters.
Red/ET tools were used to elucidate the biosynthesis of benzomalvins from A. terreus FAC AtFAC9J20. Two smaller-size constructs (33.372 kb AtFAC9J20Δ#1 and 68.988 kb AtFAC9J20Δ#2) were created from the FAC clone AtFAC9J20 (102.715 kb) using the NIH BAC recombineering tool with the Red/ET homologous recombination. We also deleted 5 genes (AtFAC9J20ΔMtase, AtFAC9J20ΔNRPS1, AtFAC9J20ΔNRPS2, AtFAC9J20ΔNRPS3, and AtFAC9J20ΔPKS) in the benzomalvin cluster to obtain 5 additional FAC mutation constructs that helped to precisely elucidate biosynthetic pathway benzomalvin efficiently and effectively.
To activate a weakly expressed SM gene cluster in FAC AtFAC7O19, we have successfully inserted the fungal strong promoter gpdAp in front of the start codon ‘ATG’ of the transcription factor (TF) gene in this cluster. FAC recombineering was performed as a two step process. The inventor inserted the galK gene and selected Gal+ colonies on minimal media plus chloramphenicol and galactose and then replaced galK with the gpdA promoter by counter-selecting galK− colonies on minimal media plus chloramphicol, 2-deoxy-galactose, and glycerol. Eight out of eight trials produced FAC mutation constructs.
Fusion PCR was performed (FIG. 4A) to combine the selectable marker (e.g. KanR or galK gene) and a promoter (gpdA(p) or any genetic element) as one PCR product for FAC recombineering. The strong fungal promoter gpdAp was inserted in front of the ATG start codon of SM cluster genes in FAC AtFAC7O19 with a kanamycin resistance gene. The Fusion PCR reactions are shown schematically in FIG. 4A (H1 and H2, homology sequences 1 and 2, respectively; cat, chloramphenicol acetyl transferase gene; FAC, origins of replication). For construction of the fusion PCR product of Kan gene and gpdA promoter, the primers used were: 38TF-Kan-leftendF (5′-TGGGACTTTGTCGCTCACGATTCGCCGAGTTGTATGGGCTGACCAGTGACcgacctgcagcctgttga-3′, SEQ ID NO: 1) and Kan-leftendR (5′-GGTGCCCCAAGCCTTGGATCCGTCGAGGCTGATCAGCGAgctc-3′, SEQ ID NO: 2); gpdA-rightendF (5′-TCGCTGATCAGCCTCGACGGATCCAAGGCTTGGGGCACCtgcgtt-3′, SEQ ID NO: 3) and 38TF-gpdA-rightendR (5′-TCCTCATGAATTAGATGGTTAGATGGACCTACCATCAGGATAGGTTCCATtgtgatgtctgctcaagcggg-3′, SEQ ID NO: 4). The result of the one-step targeting event is the insertion of constitutively active Kan-resistance gene next to gpdAp into a defined position on the FAC by selection on LB media with kanamycin and chloramphenicol for the maintenance of the engineered FAC. The fusion PCR insertions were confirmed with PCR followed by Notl restriction analysis of FAC DNA from 7 clones after the insertion of the kan-gpdAp selection cassettes, as shown in the gels in FIG. 4B. The first lane is unmodified FAC AtFAC7O19 DNA, which was included as a control. All tested clones show the same pattern, had the intended insertion but no obvious mutation on the pulse field gel. M, Lambda ladder Marker. The bacteria are now phenotypically Kan+.
An example of recombineering using the modified RED/ET tools includes the deletion of 5 genes of AtFAC9J20 individually with the galK selection cassette. FIG. 5 shows the NotI restriction analysis of FAC miniprep DNA from 4 clones each were confirmed by PCR (M, Lambda ladder Marker). The second to last lane contains unmodified AtFAC9J20 DNA, which was included as a control. AtFAC9J20 contains 2 SM gene clusters. The five genes, all members of the same cluster, are 1.239-kb Mtase (dimethylallyltryptophan N-methyltransferase) gene, 3.334-kb NRPS1, 7.284-kb NRPS2, 7.815-kb NRPS3, and 7.741-kb PKS genes. Each set of 4 tested clones show the same pattern, and therefore had the intended deletion. No obvious mutations were detected by PCR, sequencing, or on the pulse field gel.
All engineered FACs were successfully transformed back into the A. nidulans host strain. Initially, heterologous expression of the intact FAC AtFAC9J20 identified a group of methylated NRPS products, which we successfully identified as belonging to benzomalvins family (benzomalvin A and benzomalvin E). Benzomalvin A is an indoleamine 2,3-dioxygenase (IDO) inhibitor with the potential of immune-therapy for cancer. With current FAC recombineering, we then observed a parallel 10,000-fold drop in signal of the NRPS products in the gene deletion mutants AtFAC9J20ΔNRPS1 and AtFAC9J20ΔNRPS2, which supports that these two NRPS are involved in the biosynthesis directly. We also observed accumulation of the expected biosynthetic precursors in our deletion mutants. In addition, accumulation of unmethylated intermediates in AtFAC9J20ΔMtase demonstrates identification of the methyl-transferase responsible for NRPS tailoring. In conclusion, we have established the biosynthesis of a known NRPS that has long eluded the field using the FAC technology and FAC deletants. These deletants not only allow us to see loss of their corresponding gene products, but also accumulation of biosynthetic precursors.
All cited references are incorporated by reference, each in its entirety. Applicant reserves the right to challenge any conclusions presented by the authors of any reference.

Claims

What is claimed is:

1. A fungal artificial chromosome (FAC) comprising a bacterial artificial chromosome (BAC) backbone comprising:

at least one bacterial origin of replication;

a bacterial selectable marker gene;

a fungal selectable marker gene; and

a fungal autonomous replicating element.

2. The fungal artificial chromosome of claim 1, wherein the at least one bacterial origin of replication is selected from the group consisting of a low-copy number bacterial origin of replication, an inducible high-copy number bacterial origin of replication, and a combination thereof.

3. The fungal artificial chromosome of claim 2, wherein the low-copy number bacterial origin of replication is an oriS and the inducible high-copy number bacterial origin of replication is an oriV.

4. The fungal artificial chromosome of claim 1, wherein the bacterial selectable marker gene is selected from the group consisting of a chloramphenicol resistance gene (camR), kanR, ampR, genR, tetA, strepR, galK, and a combination thereof.

5. The fungal artificial chromosome of claim 1, wherein the fungal selectable marker gene is selected from the group consisting of pyrG, ptrA, trpC, and a combination thereof.

6. The fungal artificial chromosome of claim 1, wherein the fungal autonomous replicating element is an AMA1 autonomous replicating element.

7. The fungal artificial chromosome of claim 1, wherein the FAC is a plasmid.

8. The fungal artificial chromosome of claim 7, wherein the plasmid replicates extrachromosomally in a bacterial host and in a fungal host.

9. The fungal artificial chromosome of claim 8, wherein the bacterial host is E. coli and the fungal host is Aspergillus.

10. The fungal artificial chromosome of claim 1, further comprising a pair of recognition sites in a head-to-head orientation for a restriction enzyme that generates non-complementary single-stranded overhangs upon digestion of the FAC.

11. The fungal artificial chromosome of claim 10, wherein the restriction enzyme that generates non-complementary single-stranded overhangs upon digestion of the FAC is selected from the group consisting of BstXI, I-SceI, BsrI, and I-CeuI.

12. A fungal artificial chromosome in accordance with claim 10, further comprising an insert of up to about 500 kb.

13. The fungal artificial chromosome of claim 1, further comprising an integration site and an integrase gene.

14. The fungal artificial chromosome of claim 13, wherein the integration site is an attP site and the integrase gene is a fungal codon-optimized phi31 integrase gene.

15. The fungal artificial chromosome of claim 1, further comprising two fungal sequences in the same orientation.

16. The fungal artificial chromosome of claim 15, wherein the two fungal sequences are 5′trpC and 3′trpC.