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Scientia Agricola

On-line version ISSN 1678-992X

Sci. agric. vol.57 n.3 Piracicaba July/Sept. 2000 


A simple method for DNA isolation from Xanthomonas spp.


Luiz Humberto Gomes1*; Keila Maria Roncato Duarte1,2; Felipe Gabriel Andrino1,2; Flavio Cesar Almeida Tavares1
1Depto. de Genética - USP/ESALQ, C.P. 83 - CEP: 13418-900 - Piracicaba, SP.
2Fellow FAPESP.
*Corresponding author <>



ABSTRACT: A simple DNA isolation method was developed with routine chemicals that yields high quality and integrity preparations when compared to some of the most well known protocols. The method described does not require the use of lysing enzymes, water bath and the DNA was obtained within 40 minutes The amount of nucleic acid extracted (measured in terms of absorbancy at 260 nm) from strains of Xanthomonas spp., Pseudomonas spp. and Erwinia spp. was two to five times higher than that of the most commonly used method.
Key words: DNA, Xanthomonas, RAPD


Método simplificado de isolamento de DNA de Xanthomonas spp.

RESUMO: Foi desenvolvido um método simplificado de isolamento de DNA utilizando substâncias de uso rotineiro facilitando a metodologia e obtendo-se DNA de alta qualidade e integridade quando comparado com os métodos tradicionais. O método descrito não utiliza enzimas líticas, nem banho-maria, e o DNA é obtido em 40 minutos. As quantificações dos DNAs extraídos (medido em D.O. a 260 nm) das dez linhagens de Xanthomonas spp., uma de Pseudomonas spp. e outra de Erwinia spp. mostraram-se de duas a cinco vezes maiores que os métodos conhecidos e suas integridades, testadas em RAPD, apresentaram-se satisfatórias.
Palavras-chave: DNA, Xanthomonas, RAPD




Several procedures are described for Xanthomonas DNA isolation (Alvarez et al., 1996; Hartung & Civerolo, 1987), as well as for Pseudomonas spp. and Erwinia spp., where the bacteria are grown in Wilbrink's agar plates for 72h and, cells are treated with egg white lysozyme for 30 min on ice. The lysis solution (0.5% SDS, 50 mmol L-1 Tris-HCl, pH 7.5, 400 mmol L-1 EDTA, 1 mg pronase) is added to cell suspension and incubated at 50oC in water bath for 3-5 h and then deproteination is carried out.

Pan et al. (1997) used a simpler method where bacterial cells are grown in 1.5 ml of XAS broth, centrifuged for 8 min at 1,500 x g , washed in 0.5 ml of STE buffer (100 mmol L-1 NaCl, 10 mmol L-1 tris, pH 8.0, 1 mmol L-1 EDTA) and lysed in 400 ml of lysing buffer (20 ml of 1 mol L-1 Tris, pH 8.0, 40 ml of 0.5 mol L-1 EDTA, 120 ml of 10% SDS, 4 ml of 2-mercaptoethanol and 216 ml of H2O. The lysate mix is incubated at 65oC for 2 h and deproteinated. The method described by Ausubel et al. (1992) has been widely used (Lopes et al., 1998; Louws et al.,1994) and cells after and centrifuged for 2 min at 13,000 x g, the pellet is resuspended in 567 ml of TE buffer, 30 ml of 10% SDS and 3 ml of proteinase K (20 mg mL-1) and incubated at 37oC for 1.5 h. Then 100 ul of 5 mol L-1 NaCl and 80 ml of CTAB buffer (10 g CTAB, 4.1 g NaCl in 100 ml of water) are added, incubated 10 min. in a 65oC water bath. Deproteination is done and isopropanol is used to precipitated the DNA. Other similar methods are cited by Boucher et al. (1985) in the work of Restrepo & Verdier (1997) and other procedures (Cupples & Morris, 1990; Kuflu & Cupples, 1997).

All the protocols cited are able to give large amounts of high quality DNA.



The strains used came from the Tropical Culture Collection (CCT - Fundação Tropical de Pesquisas e Tecnologia "André Tosello"- Campinas, SP) (Xanthomonas campestris pv. manihotis; X. campestris pv. vesicatoria; X. campestris pv. campestris; X. maltophilia) and from our laboratories (Erwinia spp., Pseudomonas spp.; X. albilineans and X. axonopodis pv. phaseoli).

The cultures were grown in 5 ml nutrient broth (Difco) with 10% glycerol v/v (suggested by Maringoni et al. (1988) to avoid xanthan formation) for 72h at 27oC. One tube of 1.5 ml was used to centrifuged the cells at 13,000 x g for 5 min and the pellet was suspended in 200 ml Tris 0.1 mol L-1 and added with 200 ml of lysis solution (NaOH 0.2 N and 1% SDS), mixed and deproteinazed with 700 ml of phenol/chloroform/isoamyl alcohol (25:24:1 v/v/v), homogenized and centrifuged 10 min at 13,000 x g .To precipitate DNA, 700 ml of cold 95% ethanol was added and spinned, washed in 70% ethanol and centrifuged. Precipitated DNA is dried at room temperature and suspended in 100 ul of water. The method described by Ausubel et al. (1992) was performed comparing twelve strains. The samples from the both methods were electrophoresed on 0.8% agarose gels, stained with ethidium bromide and photographed under UV light . The RAPD was performed according to Williams et al. (1990) using primer OPL 11 (Operon Technologies, USA).



DNA samples were quantified in spectrophotometer at 260/280 nm and the results can be seen in Table 1. The integrity of the samples are shown in Figure 1 and 2, and the quality can be observed in the RAPD shown on Figure 3 and 4, for both methods where in Figure 3 a higher number of polymorphic bands are shown than in Figure 4, using the same primer.








This work presents a simpler high performance and short time consuming procedure for Xanthomonas DNA isolation and for the two other bacteria, Pseudomonas spp. and Erwinia spp.. Samples 260/280 nm ratio was approximately 1.7 to 2.0 in both methods but the quantity and quality seen in agarose gel electrophoresis is higher in the first method.

All mentioned methods employ chemicals such as egg white lysosyme, pronase, proteinase K and require periods of water bath incubation. In addition, the method using pronase (Alvarez et al., 1996; Hartung & Civerolo, 1987) takes from 4 to 6 hours, the method described by Pan et al. (1997) is simpler but requires water bath and takes about three hours to DNA isolation the DNA. The last described protocol (Ausubel et al., 1992; Lopes et al., 1998; Louws et al., 1994) which was used in comparison to our method requires proteinase K, water bath and three hours for DNA isolation. The presented method has no need of lysis reagents other than NaOH and SDS and takes about 30 to 40 minutes to total DNA isolation showing that simple reagents can provide good results in DNA isolation, quality and quantity-wise for Xanthomonas species.



To Vera Maria Quecini for revising the text and FAPESP for the financial support of this work.



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Received November 16, 1999

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