M13 phage DNA as a universal marker for DNA fingerprinting of animals, plants and microorganisms

Ryskov, A. P.; Jincharadze, A.G.; Prosnyak, M. I.; Иванов, П. Л.; Limborska, Svetlana A.

doi:10.1016/0014-5793(88)80467-8

Cited by 149 publications

(40 citation statements)

References 6 publications

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“…When necessary, rifampin was added to a final concentration of 100 ,ug/ml, tetracycline was added to 5 V.g/ml, spectinomycin was added were shown to hybridize under low-stringency conditions to eucaryotic as well as to bacterial DNA fragments (20,28).…”

Section: Methodsmentioning

confidence: 99%

Identification and characterization of a functional nodD gene in Azorhizobium caulinodans ORS571

Goethals¹,

Eeede²,

Montagu³

et al. 1990

J Bacteriol

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Azorhizobium caulinodans ORS571, a bacterium capable of nodulating roots and stems of the tropical legume Sesbania rostrata, has been shown to have no nodD-like gene located immediately upstream from its common nodABC locus. A clone carrying a functional nodD gene of strain ORS571 has now been isolated from a pLAFR1 gene library by screening for naringenin-induced expression of the common nod genes in an Agrobacterium background. TnS mutagenesis of the cloned insert DNA delimited the inducing activity to a ±0.8-kilobase-pair fragment. One of the Tn5 insertions in the activator locus was homogenotized in the ORS571 genome. This resulted in a mutant strain (ORS571-3) that was unable to induce common nod gene expression in the presence of host plant exudate or the flavanone naringenin and that had lost the capacity to nodulate the roots and stems of S. rostrata. Complementation of both mutant phenotypes was achieved upon introduction of the cloned nodD gene. Sequencing of the nodD locus indicated the presence of a single, 942-base-pair-long open reading frame (ORFD) with significant homology to the nodD genes of (brady)rhizobia. The level of homology, however, is the lowest thus far reported for this kind of gene. ORFD most likely initiates translation with a TTG start codon. Upstream from ORFD, a divergently oriented nod box-like sequence is present, the function of which remains to be determined.The interaction between leguminous plant species and soil bacteria belonging to the genera Bradyrhizobium and Rhizobium can lead to the development of nodules on the roots of the host plant. In these new plant organs, differentiated bacteria (bacteroids) encounter favorable conditions for symbiotic nitrogen fixation. Several bacterial and plant genes involved in the establishment of this symbiosis have been studied extensively during the last few years (for reviews, see references 23 and 26).More recently, Azorhizobium caulinodans ORS571 has been described as the archetypical species of a new genus of soil bacteria which, apart from being diazotrophic in freeliving conditions, is also able to nodulate effectively the tropical legume Sesbania rostrata (11). A unique feature of the host plant is the occurrence of dormant root primordia in vertical rows all along the stem. Upon infection by A. caulinodans, these primordia develop into N2-fixing aerial or stem nodules (9).To understand the factors that contribute to the formation of these N2-fixing aerial nodules, we started identifying and characterizing Azorhizobium genes involved in the nodulation process. In previous reports, we described the identification and characterization of common nodABC-related genes (14, 34) that are essential for the interaction with the host plant and are highly conserved among rhizobia, bradyrhizobia, and, to a lesser extent, the genus Azorhizobium.In (brady)rhizobia, the common nod genes are organized in an operon that is coregulated with other nod operons by a positive, regulatory function encoded by the nodD gene. The NodD proteins typicall...

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Section: Methodsmentioning

confidence: 99%

Identification and characterization of a functional nodD gene in Azorhizobium caulinodans ORS571

Goethals¹,

Eeede²,

Montagu³

et al. 1990

J Bacteriol

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“…Ryskov et al (1988) first proposed the use of the M13 phage as a universal marker because it can be used to rapidly generate a DNA fingerprint from organisms belonging to distinct taxonomic groups (Degen et al, 1995). This technique has been called M13 fingerprinting (Ulrich et al, 2009), M13 random amplified polymorphic DNA (RAPD) analysis (Rossetti and Giraff, 2005) and M13 minisatellite analysis (Zamponi et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Distribution of mating-type alleles and M13 PCR markers in the black leaf spot fungus Mycosphaerella fijiensis of bananas in Brazil

Queiroz

Miranda²,

Hanada³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. The fungus Mycosphaerella fijiensis is the causative agent of black sigatoka, which is one of the most destructive diseases of banana plants. Infection with this pathogen results in underdeveloped fruit, with no commercial value. We analyzed the distribution of the M. fijiensis mating-type system and its genetic variability using M13 phage DNA markers. We found a 1:1 distribution of mating-type alleles, indicating MAT1-1 and MAT1-2 idiomorphs. A polymorphism analysis using three different primers for M13 markers showed that only the M13 minisatellite primers generated polymorphic products. We then utilized this polymorphism to characterize 40 isolates from various Brazilian states. The largest genetic distances were found between isolates from the same location and between isolates from different parts of the country. Therefore, there was no correlation between the genetic similarity and the geographic origin of the isolates. The M13 marker was used to generate genetic fingerprints for five isolates; these fingerprints were compared with the band profiles obtained from inter-simple sequence repeat (UBC861) and inter-retrotransposon amplified polymorphism analyses. We found that the M13 marker was more effective than the other two markers for differentiating these isolates.

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“…In the late 1980s, hybridizationbased DNA fingerprinting was applied to investigate fungal genomes (e.g., [2, 31. In general, three types of DNA probes have been used for hybridization-based DNA fingerprinting: (i) anonymous repetitive DNA probes derived from the fungal genome under investiga-tion (e.g., [3-71; (ii) minisatellite probes, most of which originated from human or wild-type M13 phage genome (e.g., [2,8,91; and (iii) synthetic oligonucleotide probes that are complementary to simple repetitive sequences (e.g., .…”

Section: Introductionmentioning

confidence: 99%

Polymerase chain reaction fingerprinting in fungi using single primers specific to minisatellites and simple repetitive DNA sequences: Strain variation in Cryptococcus neoformans

1995

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Minisatellites and simple repetitive DNA sequence motifs are used as conventional oligonucleotide probes in DNA-hybridization-based fingerprinting. The same oligonucleotides can be used as single primers in the polymerase chain reaction (PCR) to generate individual PCR fingerprints. In this study, the simple repetitive sequences, (CA)8, (CT)8, (CAC)5, (GTG)5, (GACA)4 and (GATA)4, and a minisatellite core sequence derived from the wild-type phage M13 (5' GAGGGTGGCGGTTCT 3') were used as specific, single primers to amplify hypervariable repetitive DNA sequences during PCR analysis. The potential applications of this techniques are demonstrated with clinical isolates of the human pathogenic yeast, Cryptococcus neoformans. PCR fingerprint patterns have remained stable after long-term in vitro passage ( > 2 1/2 years to date). Hybridization of the primers to blots of electrophorectically separated chromosomes demonstrated that the target sequences recognized by most of the primers are dispersed through the entire yeast genome. Sequence analysis of the cloned bands obtained by PCR fingerprinting indicated that if the same or extremely similar, inversely oriented tandem repeats are located close to each other, when only one repeat-specific primer is used in the PCR, the region between these repeats is amplified. PCR fingerprinting has a wide range of current and potential applications to fungi, such as clarifying taxonomic questions, facilitating epidemiological studies and improving the diagnosis of mycotic diseases.

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M13 phage DNA as a universal marker for DNA fingerprinting of animals, plants and microorganisms

Cited by 149 publications

References 6 publications

Identification and characterization of a functional nodD gene in Azorhizobium caulinodans ORS571

Identification and characterization of a functional nodD gene in Azorhizobium caulinodans ORS571

Distribution of mating-type alleles and M13 PCR markers in the black leaf spot fungus Mycosphaerella fijiensis of bananas in Brazil

Polymerase chain reaction fingerprinting in fungi using single primers specific to minisatellites and simple repetitive DNA sequences: Strain variation in Cryptococcus neoformans

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