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Introduction of large DNA inserts into the barley pathogenic fungus, Ustilago hordei, via recombined binary BAC vectors and Agrobacterium-mediated transformation. Curr Genet 2010; 57:63-73. [PMID: 20936474 DOI: 10.1007/s00294-010-0324-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 09/17/2010] [Accepted: 09/21/2010] [Indexed: 10/19/2022]
Abstract
Genetic transformation of organisms with large genome fragments containing complete genes, with regulatory elements or clusters of genes, can contribute to the functional analysis of such genes. However, large inserts, such as those found on bacterial artificial chromosome (BAC) clones, are often not easy to transfer. We exploited an existing technique to convert BAC clones, containing genomic DNA fragments from the barley-covered smut fungus Ustilago hordei to binary BACs (BIBACs) to make them transferable by the Agrobacterium tumefaciens T-DNA transfer machinery. Genetic transformation of U. hordei with BAC clones using polyethylene glycol or electroporation is difficult. As a proof of concept, two BAC clones were successfully converted into BIBAC vectors and transferred by A. tumefaciens into U. hordei and U. maydis, the related corn smut fungi. Molecular analysis of the transformants showed that the T-DNA containing the BAC clones with their inserts was stably integrated into the U. hordei genome. A transformation frequency of approximately 10⁻⁴ was achieved both for U. hordei sporidia and protoplasts; the efficiencies were 25-30 times higher for U. maydis. The combination of in vivo recombineering technology for BAC clones and A. tumefaciens-mediated transformation of Ustilago species should pave the way for functional genomics studies.
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Linning R, Lin D, Lee N, Abdennadher M, Gaudet D, Thomas P, Mills D, Kronstad JW, Bakkeren G. Marker-based cloning of the region containing the UhAvr1 avirulence gene from the basidiomycete barley pathogen Ustilago hordei. Genetics 2004; 166:99-111. [PMID: 15020410 PMCID: PMC1470683 DOI: 10.1534/genetics.166.1.99] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Race-cultivar specialization during the interaction of the basidiomycete smut pathogen Ustilago hordei with its barley host was described in the 1940s. Subsequent genetic analyses revealed the presence of dominant avirulence genes in the pathogen that conform to the gene-for-gene theory. This pathosystem therefore presents an opportunity for the molecular genetic characterization of fungal genes controlling avirulence. We performed a cross between U. hordei strains to obtain 54 progeny segregating for three dominant avirulence genes on three differential barley cultivars. Bulked segregant analysis was used to identify RAPD and AFLP markers tightly linked to the avirulence gene UhAvr1. The UhAvr1 gene is located in an area containing repetitive DNA and this region is undetectable in cosmid libraries prepared from the avirulent parental strain. PCR and hybridization probes developed from the linked markers were therefore used to identify cosmid clones from the virulent (Uhavr1) parent. By walking on Uhavr1-linked cosmid clones, a nonrepetitive, nearby probe was found that recognized five overlapping BAC clones spanning 170 kb from the UhAvr1 parent. A contig of the clones in the UhAvr1 region was constructed and selected probes were used for RFLP analysis of the segregating population. This approach genetically defined an approximately 80-kb region that carries the UhAvr1 gene and provided cloned sequences for subsequent genetic analysis. UhAvr1 represents the first avirulence gene cloned from a basidiomycete plant pathogen.
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Affiliation(s)
- R Linning
- Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia V0H 1Z0, Canada
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Frangeul L, Nelson KE, Buchrieser C, Danchin A, Glaser P, Kunst F. Cloning and assembly strategies in microbial genome projects. MICROBIOLOGY (READING, ENGLAND) 1999; 145 ( Pt 10):2625-34. [PMID: 10537184 DOI: 10.1099/00221287-145-10-2625] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- L Frangeul
- Laboratoire de Génomique des Microorganismes Pathogènes, Institut Pasteur, Paris, France
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4
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Simons G, Groenendijk J, Wijbrandi J, Reijans M, Groenen J, Diergaarde P, Van der Lee T, Bleeker M, Onstenk J, de Both M, Haring M, Mes J, Cornelissen B, Zabeau M, Vos P. Dissection of the fusarium I2 gene cluster in tomato reveals six homologs and one active gene copy. THE PLANT CELL 1998. [PMID: 9634592 DOI: 10.1105/tpc.10.6.105510.2307/3870690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The I2 locus in tomato confers resistance to race 2 of the soil-borne fungus Fusarium oxysporum f sp lycopersici. The selective restriction fragment amplification (AFLP) positional cloning strategy was used to identify I2 in the tomato genome. A yeast artificial chromosome (YAC) clone covering approximately 750 kb encompassing the I2 locus was isolated, and the AFLP technique was used to derive tightly linked AFLP markers from this YAC clone. Genetic complementation analysis in transgenic R1 plants using a set of overlapping cosmids covering the I2 locus revealed three cosmids giving full resistance to F. o. lycopersici race 2. These cosmids shared a 7-kb DNA fragment containing an open reading frame encoding a protein with similarity to the nucleotide binding site leucine-rich repeat family of resistance genes. At the I2 locus, we identified six additional homologs that included the recently identified I2C-1 and I2C-2 genes. However, cosmids containing the I2C-1 or I2C-2 gene could not confer resistance to plants, indicating that these members are not the functional resistance genes. Alignments between the various members of the I2 gene family revealed two significant variable regions within the leucine-rich repeat region. They consisted of deletions or duplications of one or more leucine-rich repeats. We propose that one or both of these leucine-rich repeats are involved in Fusarium wilt resistance with I2 specificity.
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Affiliation(s)
- G Simons
- Keygene N.V., Agro Business Park 90, P.O. Box 216, 6700 AE Wageningen, The Netherlands.
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Simons G, Groenendijk J, Wijbrandi J, Reijans M, Groenen J, Diergaarde P, Van der Lee T, Bleeker M, Onstenk J, de Both M, Haring M, Mes J, Cornelissen B, Zabeau M, Vos P. Dissection of the fusarium I2 gene cluster in tomato reveals six homologs and one active gene copy. THE PLANT CELL 1998; 10:1055-68. [PMID: 9634592 PMCID: PMC144031 DOI: 10.1105/tpc.10.6.1055] [Citation(s) in RCA: 182] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The I2 locus in tomato confers resistance to race 2 of the soil-borne fungus Fusarium oxysporum f sp lycopersici. The selective restriction fragment amplification (AFLP) positional cloning strategy was used to identify I2 in the tomato genome. A yeast artificial chromosome (YAC) clone covering approximately 750 kb encompassing the I2 locus was isolated, and the AFLP technique was used to derive tightly linked AFLP markers from this YAC clone. Genetic complementation analysis in transgenic R1 plants using a set of overlapping cosmids covering the I2 locus revealed three cosmids giving full resistance to F. o. lycopersici race 2. These cosmids shared a 7-kb DNA fragment containing an open reading frame encoding a protein with similarity to the nucleotide binding site leucine-rich repeat family of resistance genes. At the I2 locus, we identified six additional homologs that included the recently identified I2C-1 and I2C-2 genes. However, cosmids containing the I2C-1 or I2C-2 gene could not confer resistance to plants, indicating that these members are not the functional resistance genes. Alignments between the various members of the I2 gene family revealed two significant variable regions within the leucine-rich repeat region. They consisted of deletions or duplications of one or more leucine-rich repeats. We propose that one or both of these leucine-rich repeats are involved in Fusarium wilt resistance with I2 specificity.
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Affiliation(s)
- G Simons
- Keygene N.V., Agro Business Park 90, P.O. Box 216, 6700 AE Wageningen, The Netherlands.
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Zabarovsky ER, Klein G, Winberg G. Lambda SK diphasmids: phage lambda vectors for genomic, jumping, linking and cDNA libraries. Gene X 1993; 127:1-14. [PMID: 8486275 DOI: 10.1016/0378-1119(93)90610-f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Fifteen new phage lambda vectors are discussed: lambda SK4, lambda SK6, lambda SK10, lambda SK16, lambda SK17, lambda SK20, lambda SK21, lambda SK22, lambda SK23, lambda SK24, lambda SK25, lambda SK27, lambda SK28, lambda SK40 and lambda SK41. Their structural and functional features facilitate the implementation of a number of new strategies and cloning procedures which simplify, economize and vastly improve the utility and efficiency of library construction in lambda vectors. Such improved strategies and examples of their application, with particular reference to jumping and linking libraries, are presented.
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Affiliation(s)
- E R Zabarovsky
- Department of Tumor Biology, Karolinska Institutet, Stockholm, Sweden
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Stauffer JK, Ciejek-Baez E. Autonomous activity of the alternate aldolase A muscle promoter is maintained by a sequestering mechanism. Nucleic Acids Res 1992; 20:327-36. [PMID: 1741258 PMCID: PMC310374 DOI: 10.1093/nar/20.2.327] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The mouse aldolase A gene contains two closely-spaced alternate promoter/first exons. The more distal of the two, the M promoter, is muscle-specific while the 3' promoter, the H promoter, is expressed constitutively. Various segments from these promoter regions were linked to a reporter gene and used to transfect the myogenic cell line C2C12 and the hepatoma cell line BWTG3. A muscle-specific enhancer, MEN1, responsible for 80% of promoter M activity and containing 4 consensus MyoD binding sites was localized between -2578 to -2723 of the M promoter. Another muscle-specific enhancer and a restrictive element, MEN2/MSE, were found in the interval -1100 to -350. The MSE restrictive element was found to prohibit inappropriate up-regulation of the M promoter by selectively sequestering it from H promoter elements in both myoblasts and myotubes. Among the H promoter elements was found an enhancer, HEN, situated between -533 and -200 which did not function in myotubes. These studies also show that H promoter elements can act synergistically with a non-specific element, MAE, located between -350 and -130 of the M cap site greatly stimulating M promoter transcription in all cell types when the MSE restrictive element was absent. Through the analysis of interactions between these elements and the aldolase A and HSV-TK promoters we showed that neither the enhancers nor the promoter proximal sequences by themselves contain adequate information to reproduce the native pattern of aldolase A promoter modulation. Rather, the sequestering of the M promoter by the MSE restrictive element and the relative positioning and context of promoters M and H appear critical to the regulated expression of aldolase A.
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Affiliation(s)
- J K Stauffer
- Department of Biochemistry, University of Rochester School of Medicine and Dentistry, NY 14642
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Young JR, Morzaria SP. Agarose entrapment method for the production of SfiI linking library for Theileria parva. GENETIC ANALYSIS, TECHNIQUES AND APPLICATIONS 1991; 8:148-50. [PMID: 1931184 DOI: 10.1016/1050-3862(91)90023-k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have developed a simple method for isolation of SfiI linking clones from a eukaryotic genomic DNA. The method involves the physical separation of the small proportion of plasmids in a plasmid genomic library that are linearized by SfiI digestion, from the bulk of molecules that remain circular, by ordinary electrophoresis through high-percentage gels of SeaPlaque agarose. Following the isolation of linearized molecules, their recircularization, and introduction into Escherichia coli, 55% of recovered plasmids contained inserts of the expected size, and 73% of these had SfiI sites. This represented a 25-fold enrichment of linking clones expected to be present at a frequency of 1/60 in the original library of 4- 6-kb fragments of genomic DNA of the protozoan parasite Theileria parva. This approach is rapid and obviates the need for introduction of a selectable marker. It is uniquely appropriate for linking clones spanning SfiI sites as this enzyme leaves degenerate 3' overhanging ends that preclude the direct ligation into vector sites required by most alternative strategies, but that favor the recircularization reactions used here.
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Affiliation(s)
- J R Young
- International Laboratory for Research on Animal Diseases, Nairobi, Kenya
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Bellemare G, Potvin C. Classification of type-II restriction endonucleases and cloning of non-identical cohesive-end fragments without self-polymerization using nonpalindromic oligodeoxyribonucleotide adapters. Gene 1991; 101:67-74. [PMID: 1676386 DOI: 10.1016/0378-1119(91)90225-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Enzymatic partial filling-in of recessed 3'-end sequences, left after digestion of DNA by the restriction endonucleases (ENases) Sau3A and SalI, with the Klenow fragment of E. coli DNA polymerase I allows the forced ligation of the resulting fragments; this technology is already used for subcloning and for genomic bank construction. To simplify and generalize its utilization, class-II ENases have been arranged into 16 different families according to the composition of the 5'-protruding sequences present after cleavage. Moreover, this system was extended to allow the joining of noncompatible ends by the use of nonpalindromic complementary oligodeoxyribonucleotides (NPCOs) containing two nucleotides protruding at each 5' end. The use of these synthetic adapters maintains all the advantages of the initial gap-filling cloning technique: only one insert can be cloned per vector molecule and no self-ligation or -polymerization can occur with any of the DNA molecules involved. Only 22 such oligodeoxyribonucleotides are needed to generate the 60 NPCO pairs necessary to ligate to each other any member of twelve ENase families when the regeneration of ENase recognition sites is not required.
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Affiliation(s)
- G Bellemare
- Département de Biochimie, Faculté des Sciences et de Génie, Université Laval, Ste-Foy, Québec, Canada
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Kieser T, Hopwood DA. Genetic manipulation of Streptomyces: integrating vectors and gene replacement. Methods Enzymol 1991; 204:430-58. [PMID: 1943784 DOI: 10.1016/0076-6879(91)04023-h] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Levin HL, Boeke JD. The absence of adenine methylation increases the ligation efficiency of partially filled staggered DNA ends. Nucleic Acids Res 1990; 18:6146. [PMID: 2235512 PMCID: PMC332435 DOI: 10.1093/nar/18.20.6146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- H L Levin
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205
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12
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Kessler C, Manta V. Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3). Gene 1990; 92:1-248. [PMID: 2172084 DOI: 10.1016/0378-1119(90)90486-b] [Citation(s) in RCA: 128] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The properties and sources of all known class-I, class-II and class-III restriction endonucleases (ENases) and DNA modification methyltransferases (MTases) are listed and newly subclassified according to their sequence specificity. In addition, the enzymes are distinguished in a novel manner according to sequence specificity, cleavage position and methylation sensitivity. Furthermore, new nomenclature rules are proposed for unambiguously defined enzyme names. In the various Tables, the enzymes are cross-indexed alphabetically according to their names (Table I), classified according to their recognition sequence homologies (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the DNA of the bacteriophages lambda, phi X174, and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328, and the microorganisms from which they originate. Other tabulated properties of the ENases include relaxed specificities (integrated within Table II), the structure of the generated fragment ends (Table III), interconversion of restriction sites (Table IV) and the sensitivity to different kinds of DNA methylation (Table V). Table VI shows the influence of class-II MTases on the activity of class-II ENases with at least partially overlapping recognition sequences. Table VII lists all class-II restriction endonucleases and MTases which are commercially available. The information given in Table V focuses on the influence of methylation of the recognition sequences on the activity of ENases. This information might be useful for the design of cloning experiments especially in Escherichia coli containing M.EcodamI and M.EcodcmI [H16, M21, U3] or for studying the level and distribution of site-specific methylation in cellular DNA, e.g., 5'- (M)CpG-3' in mammals, 5'-(M)CpNpG-3' in plants or 5'-GpA(M)pTpC-3' in enterobacteria [B29, E4, M30, V4, V13, W24]. In Table IV a cross index for the interconversion of two- and four-nt 5'-protruding ends into new recognition sequences is complied. This was obtained by the fill-in reaction with the Klenow (large) fragment of the E. coli DNA polymerase I (PolIk), or additional nuclease S1 treatment followed by ligation of the modified fragment termini [P3]. Interconversion of restriction sites generates novel cloning sites without the need of linkers. This should improve the flexibility of genetic engineering experiments [K56, P3].(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- C Kessler
- Boehringer Mannheim GmbH, Biochemical Research Center, Penzberg, F.R.G
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Zabarovsky ER, Turina OV, Allikmets RL, Nurbekov MK, Filippov SA, Dobrynin VN, Kisselev LL. Lambda SK3 and lambda SK5, vectors for constructing genomic libraries derived from lambda EMBL3 and lambda EMBL4 by insertion of lac gene. Nucleic Acids Res 1989; 17:3310. [PMID: 2524723 PMCID: PMC317749 DOI: 10.1093/nar/17.8.3310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- E R Zabarovsky
- Engelhardt Institute of Molecular Biology, Acad. Sci. USSR, Moscow
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Zabarovsky ER, Turina OV, Nurbekov MK, Kisselev LL. SK18 diphasmid for constructing genomic libraries with blue/white selection, multiple cloning sites, and with the M13 and lambda ori. Nucleic Acids Res 1989; 17:3309. [PMID: 2726473 PMCID: PMC317748 DOI: 10.1093/nar/17.8.3309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- E R Zabarovsky
- Engelhardt Institute of Molecular Biology, Acad. Sci. USSR, Moscow
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