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1 The Korean Journal of Microbiology, Vol. 43, No. 3, September 2007, p Copyright 2007, The Microbiological Society of Korea Nested PCR DNA Enzyme-Linked Immunosorbent Assay w Ralstonia solanacearum š Á y 1 * v w œw polymerase chain reaction (PCR)» DNA enzyme-linked immunosorbent assay (DNA ELISA)» w m ü ³ Ralstonia solanacearum wš w. m l R. solanacearum DNA w» w ƒ sƒw» DNA w Guanidin isothiocyanate Chelex-100 resin w m ü w w w R. solanacearum š w PCR w w z. R. solanacearum p w» w flic p primer w. p ùkü set primer RsolfliC (forward; 5-GAACGCCAACGGTGCGAACT-3 and reverse; 5-GGCGG CCTTCAGGGAGGTC-3, designed by J. Schönfeld et al.) RS_247 (forward; 5-GGCGGTCTGTCGGCRG-3 and reverse; 5-CGGTCGCGTTGGCAAC-3, designed by this study) w nested PCR ww š w. Nested PCR primer biotin t w š nested PCR ü p w probe w PCR DNA-EIA y w w. Primary PCR nested PCR» y w, nested PCR 10 2 ùkü š DNA-EIA 10 2 ~10 3 g y. Key words ý DNA enzyme immunoassay, Ralstonia solanacearum Ralstonia solanacearum»z sww 450 t w ³ (9). p š w y ƒ ƒ j vw öeš (13), w û w š (26) ü t ù û t š. š m m l t, ƒ š (1). R. solanacearum r w d x w z r ù ƒ t w (27, 28). w m wš 5 ƒ w 30 cm dm tmd w w» ƒ w (3). š y w»ù» m l R. solanacearum y w w (21). R. solanacearum w» w PCR» *To whom correspondence should be addressed. Tel: , Fax: hbcho@skuniv.ac.kr rrna sw w (2, 7, 18, 25, 29), PCR-ribotyping RFLP ww R. solanacearum ww» w (17). ù, R. solanacearum 16S rrna ƒ 98%» R. picketti ³ ùkû (23). z 16S rrna wì endoglucanase, hrpb (19)» w x w R. solanacearum strain 1 w» w (IS)ü p sw w š (15). Schfeld (21) flagellin (flic) target w Southern blot hybridization m ü w R. solanacearum w. flic œm š ³ p y ù m DNA z PCR û z š. m l w DNA z z wš, primer š w PCR p w wr DNA enzyme-linked immunosorbent assay (DNA ELISA) w m ü w R. solanacearum z w» wš w. 179
2 180 Young-Jin Ko and Hong-Bum Cho Kor. J. Microbiol ³ w Ralstonia solanacearum strain Escherichia coli, Pseudomonas aeruginosa, Burkholderia glumae. Xanthomonas xonopodis x w ³ Table 1 w. R. solanacearum ³ CPG (casamino acid 1 g/l, peptone 10 g/l, glucose 5 g/l) 1.8% w, 0.05% 2,3,5- triphenyltetrazolium chloride (TTC)ƒ sw TZC š s q 28 C o š,»k ³ Luria 9 broth -3¾ 34 C o. m 1g 1 10 w R. solanacearum w š ³ Haemacytometer (Marienfeld, Germany) w w. z R. solanacearum m l DNA w x w š ³ ƒ m w. DNA m l R. solanacearum DNA w. 1 ml w cell pellet š phosphate buffer saline (PBS, 0.01 M phosphate beffer, M potassium chloride, M sodium chloride; ph 7.4) 3z w 200 µl PBS xk g. m 500 µl v w. DNAzol (MRC, USA) 1 ml ƒw š, z DNAzol w w. DNAzol z DNA pellet 200 µl chelex-100 resin 5% ƒw 10 ò wš 5µl w PCR DNA Table 1. Strains used in this study x w. Primer, probe PCR x primer probe Table 2 ùkü. Primer probe Primer3 v (Whitehead Institude, MT center for Genome research) mw. RsolfliC forward reverse primer flic ü 400 bp PCR š RS_247 forward reverse nested PCR mw 247 bp. Probe nested PCR. PCR AmplitronII mw w. Primary PCR 10 PCR buffer 10 mm datp, dgtp, dctp, dutp 0.5 µl 10 pmol primer set 1 U Taq wz 5µl x DNA w.» 94 o C 5 z, 94 o C 1, 61 o C 1, 72 o C 1 40 cycles z 72 o C 5. Primary PCR nested PCR x DNA nested PCR w, 94 o C 30, 55 o C 40, 72 o C cycles. PCR 2.5% agarose» y w. DNA enzyme immunoassay DNA Enzyme-linked immunosorbent assay (DNA ELISA) nested PCR probe w. DEIA ww» w plate w» w, 1- Ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDAC, Sigma E-7750, USA) probe bovine serum albumin (BSA, Sigma, USA) š jš 96-well plate Species Strain Biovar Host plant Geographic origin Source of reference a R. solanacearum DSM Tomato United States KCCM R. solanacearum KACC Tomato Korea KACC R. solanacearum KACC Potato Korea KACC R. solanacearum KACC Potato Korea KACC R. solanacearum KACC Potato Korea KACC R. solanacearum KACC Tomato Korea KACC R. solanacearum KACC Pepper Korea KACC R. solanacearum KACC Potato Korea KACC R. solanacearum KACC10815 ND b Potato Egypt KACC R. solanacearum KACC Potato Fidji KACC E. coli KCCM11234 KCCM P. aeruginosa KCCM11328 KCCM B. glumae Seoul National Univ. X. xonopodis Seoul National Univ. a KCCM, Korean Culture Center of Microorganisms; KACC, Korean Agricultural Culture Collection b ND, not determined
3 Vol. 43, No. 3 Ralstonia solanacearum DNA enzyme-linked immunosorbent assay 181 Table 2. Characteristics of primers and probe used to detect R. solanacearum Primer or probe a Sequence (5' 3') Length Modification 5' end RsolfliC b -F GAA CGC CAA CGG TGC GAA CT 20 RsolfliC b -R GGC GGC CTT CAG GGA GGT C 19 RS_247-F GGC GGT CTG TCG GCR c G 16 RS_247-R CGG TCG CGT TGG CAA C 16 Biotin RS_200-F CAA CTA CAA CGG CAA CAA GC 20 RS_200-R TCA GGG AGG TCA GAT CGG TA 20 RS_250-R CCG TAC TGG AAG GTC GTC G 19 RS_122-F TTC GAC GAC CTT CCA GTA 18 RS_122-R CGG TCG CGT TGG CAA C 16 RS_fliC-P GTC ACC AAC GTC GAC ATG TC 20 Amine a F, forward; R,Greverse; P,Gprobe b primer RsolfliC from Schönfeld et al. c R, A or G (F96 well plate, Nunc) 0.2 pmol/µl 100 µl w 18 g. z Tween20 s w PBS (PBST, 0.1% Tween in PBS) 3z wš 0.5% BSAƒ sw PBS blocking w ww. Nested PCR 95 C 10 jš o 96-well plate ƒ 60 C w o w. z PBST wš streptavidin-peroxidase (1:2000, Sigma S-5512, USA) 100 µl ƒw 37 C w k z wš o 3,3',5,5'-tetramethyl-benzidine (TMB, Sigma T0440, USA) 100 µl ƒw streptavidin-peroxidase 15 g. 2 M H 2 SO 4 50 µl z jš ELISA plate reader (Molecular Device, USA) 450 nm Ÿ d w. dutp Uracil nucleosidic glycosylase w» w x dutp-uracil-n-glycosidase (UNG) w, PCR w dutpƒ ƒ dntp yw w dutpƒ ƒ w. 10 U UNG ƒwš» 37 C 30 ww o UNG w w. In vivo pot assay š j R. solanacearum y w» w in vivo pot assay ww. 10 cm sp f m(w z ) 180 g š š q w 25~35 C w o w. 4»ƒ üš R. solanacearum xk 30 ml (10 CFU/ml) w 7 w. z y wš l R. solanacearum w, ³ genomic DNA z w PCR DNA EIA x DNA w. DNA m l R. solanacearum genomic DNA w» w SDS w, STET ò, resin ƒ w ò DNAzol w ƒƒ w w x ww. w l ƒ mw genomic DNA wš 16S rdna flic sw» PCR w. DNAzol w DNA w w PCR s z ƒ w, w z w j, d w g e j ƒ» ù š rw. z x w chelex-100 resin š ò m ü w PCR w w z (Fig. 1). PCR mw R. solanacearum DSM9544 KACC 9 R. solanacearum RsolfliC primer w w s 400 bp PCR y w. ³ B. glumae, X. xonopodis, E. coli P. aeruginosa s. z primary PCR x w nested PCR ww 247 bp PCR y w (Fig. 2), x R. solanacearum flic ƒ œm w y w.,
4 182 Young-Jin Ko and Hong-Bum Cho Kor. J. Microbiol primary PCR ƒ û š, nested PCR primary PCR w 2. Fig. 1. Results of agarose gel electrophoresis of amplified genomic DNA of R. solanacearum extracted by each method. Lane 1, genomic DNA extracted by SDS lysis method; 2, STET method; 3, boiling with chelex X-100 resin method; 4, DNAzol method; 5, DNAzol treatment and boiling with chelex X-100 resin; L, ladder; N, negative control. DNA enzyme immunoassay Nested PCR primer biotin t š, probe amine t. 5' amine t probe EDAC MES mw BSA w z 96-well plate gq. DNA ELISA biotin t primer s nested PCR 96-well plate gq probe w. Probe nested PCR streptavidin-peroxidase w š z streptavidin-peroxidase» TMB ƒw z w d w (Table 3). wš d w ƒ ƒ, w ù 96-well plate gqw probe š wù ww. Probe 5~10 pmol/microwell, 60 C ƒ š o ùkü. Fig. 2. Nested PCR products of R. solanacearum strains studied. Lanes 1 to 10, reference strains DSM9544, KACC 10698, 10699, 10702, 10706, 10708, 10711, 10722, 10815, 10816, respectively. L, ladder; N, negative control. x ww 4 cell/g ¾ 400 bp» y w 3 cell/g ¾ 247 bp y w (Fig. 3). m 400 bp 5, 247 bp 3 cell/g ¾ y w (Fig. 4). x m w In vivo pot assay t l R. solanacearum wš genomic DNA w PCR DNA EIA mw w š w. 4» R. solanacearum wš z w, z 2 ü t l R. solanacearum x w PCR y w (Fig. 5). š x primary PCR mw swš w flic R. solanacearum GMI e w x R. solanacearum flic 400 bp PCR y w R. Fig. 3. Threshold of detection for R. solanacearum in culture broth by PCR. Results of agarose gel electrophoresis of amplified DNA from tenfold serial dilutions of cell concentration. Lanes 1 to 10, cell concentration of R. solanacearum diluted 8 to -1, respectively. (A) Amplification of 400 bp PCR fragment by primary PCR; (B) Amplification of 247 bp PCR fragment by nested PCR. L, ladder; N, negative control.
5 의 DNA enzyme-linked immunosorbent assay Vol. 43, No. 3 Ralstonia solanacearum 183 Threshold of detection for R. solanacearum in soil by PCR. Results of agarose gel electrophoresis of amplified DNA from tenfold serial dilutions of cell concentration. Lanes 1 to 10, cell concentration of R. solanacearum diluted to, respectively. (A) Amplification of 400 bp PCR fragment by primary PCR; (B) Amplification of 247 bp PCR fragment by nested PCR. L, ladder; N, negative control. Fig Symptom of R. solanacearum infection in pepper plants and results of nested PCR. (A) Agroinoculated wild-type pepper plant; (B) Agroinoculated pepper plant infected by R. solanacearum (C) Amplification of 247 bp PCR fragment by nested PCR from wild-type and R. solanacearum infected plants in vivo assay; 1, (A); 2, (B); L, ladder; N, negative control. Fig. 5. 과 유사한 토양내의 이종 세균에서는 검출되지 않 았다 유전자 내의 위치는 3종류의 biovar를 포함하는 6종류 의 아종 - DSM9544와 K60 (biovar 1), 1609와 1737과 267 (biovar 2), GMI1000 (biovar 3) -의 유전자 서열을 비교하였을 때, flic의 가장 중앙에 위치하고 있었으며 종간의 유전적 다양성도 가장 심하였다. flic 유전자는 편모 단백질의 비기능적 위치를 담고 있기 때문에 병원성을 좌우하는 부분도 아니며 유전자의 수평적 이동도 발견되지 않는다(30). 즉 flic 유 전자는 종내와 아종간의 연관성이 깊기 때문에 R. solanacearum 의 검출을 위한 유전자 지표로서 매우 유효함을 확인할 수 있었 다. 토양으로부터 직접 추출한 DNA로부터 분자생물학적 기법을 수행하는 데 있어서는 humic acid와 같은 반응 저해물질로 인한 solanacearum. flic R. solanacearum 어려움이 많다. 이들이 포함되어진 PCR 혼합 용액 내에서는 Thermus aquticus의 DNA 중합효소, Amplitaq Gold 뿐만 아니라 다른 다양한 종류의 내열성 DNA 중합효소 모두가 활성에 저해 를 받는 것으로 알려져 있으며(16), 본 연구의 수행과정에서도 R. solanacearum의 액체 배양액과 토양 시료에서 PCR 반응을 저해하는 또 다른 물질이 존재한다는 것도 알 수 있었다. 이에 본 연구에서는 일반적으로 사용되는 DNA 회수 방법을 개선하여 토양으로부터 빠르고 단순하면서도 PCR 저해물질을 효과적으로 제거할 수 있는 방법을 고안하였다. Chelex-100 resin을 넣고 끓 이는 방법은 기존의 guanidine thiocyanate 분해법이나 킬레이트 물질을 첨가하여 독성을 갖거나 인체에 유해한 시약을 사용하는 방법들과 비교하였을 때 알코올 침전 반응을 거치지 않고도 PCR에 바로 사용할 수 있는 순수한 DNA를 얻을 수 있었다. Absorbance values of DNA ELISA from amplified DNA according to tenfold serial dilutions of R. solanacearum Cell density of R. solanacearum PCR product of R. solanacearum from Culture broth Soil Table
6 184 Young-Jin Ko and Hong-Bum Cho Kor. J. Microbiol Enzyme Immunoassay (ELISA)», q ³ w» w p w p ³ ù w w rp d w» w š (24). R. solanacearum» w DNA ELISA» ELISA DNA w» (4, 5, 6, 8, 12).» s 96-well plate ƒw l š z. w z d d ƒ w,» w w zw (14). DNAzol chelex-100 resin w m l PCR w wš DNA š z w, RsolfliC primer w DNA ELISA» R. solanacearum y. (11) RT-PCR m w m l R. eutropha l ww, ww DNA ELISA p» RT-PCR ww»ƒ ¼ R. solanacearum k m l l ƒ w q. š x 1. w» w. 2. Boudazin, G., A.C. Le Roux, K. Josi, P. Labarre, and B. Jouan Design of division specific primers of Ralstonia solanacearum and application to the identification of European isolates. Eur. J. Plant Pathol. 105, Brian, E.G. and R.S. Todd The viable but nonculturable state of Ralstonia solanacearum may be involved in long-term survival and plant infection. Appl. Environ. Microbiol. 67, Buck, G.E Detection of Bordetella pertussis by rapid-cycle PCR and colorimetric microwell hybridization. J. Clin. Microbiol. 34, Chevrier, D., M.Y. Popoff, M.P. Dion, and D. Hermant Rapid detection of Salmonella subspecies I by PCR combined with non-radioactive hybridisation using covalently immobilised oligonucleotide on a microplate. FEMS Immunol. Med. Microbiol. 10, Cho, S.-N., G.M.E. van der Vliet, S. Park, S.-H. Baik, S.-K. Kim, Y. Chong, A.H.J. Kolk, P.R. Klatser, and J.-D. Kim Colorimetric microwell plate hybridization assay for detection of amplified Mycobacterium tuberculosis DNA from sputum samples. J. Clin. Microbiol. 33, Fegan, M., M. Taghavi, L.I. Sly, and A.C. Hayward Phylogeny, diversity and molecular diagnostics of Ralstonia solanacearum, p In P. Prior, C. Allen, and J.G. Elphinstone (ed.), Bacterial wilt disease-molecular and ecological aspects. Springer- Verlag, Berlin, Germany. 8. Fujita, S.-I., B.A. Lasker, T.J. Lott, E. Reiss, and C.J. Morrison Microtitration plate enzyme immunoassay to detect PCRamplified DNA from Candida species in blood. J. Clin. Microbiol. 33, Hayward, H.C Biology and epidemiology of bacterial wilt caused by Pseudomonas solanacearum. Annu. Rev. Phytopathol. 29, Holben, W.E Isolation and purification of bacterial DNA from soil, p In R.W. Weaver, S. Angle, P. Bottomley, D. Bezdicek, S. Smith, A. Tabatabai, and A. Wollum (ed.), Methods of soil analysis, part 2. Microbiological and biochemical properties. Soil Science Society of America, Inc., Madison, Wis., USA. 11. Jung, K.-J., B.-H. Kim, E. Kim, J.-S. So, and S.-C. Koh Monitoring expression of bphc gene from Ralstonia eutropha H850 induced by plant terpenes in soil. Kor. J. Microbiol. 42, Katz, J.B., A.D. Alstad, G.A. Gustafson, and K.M. Moser Sensitive identification of bluetongue virus serogroup by a colorimetric dual oligonucleotide sorbent assay of amplified viral nucleic acid. J. Clin. Microbiol. 31, Kelman, A One hundred and one years of research on bacterial wilt, p In P. Prior, C. Allen, and J. Elphinstone (ed.), Bacterial wilt disease. Molecular and ecological aspects. Springer- Verlag, Heidelberg, Germany. 14. Lebech, A.-M., K. Hansen, F. Brandrup, O. Clemmensen, and L. Halkier-Sorensen Diagnostic value of PCR for detection of Borrelia burgdorferi DNA in clinical specimens from patients with erythema migrans and Lyme neuroborreliosis. Mol. Diagn. 5, Lee, Y.-A., S.-C. Fan, L.-Y. Chiu, and K.-C. Hsia Isolation of an insertion sequence from Ralstonia solanacearum race 1 and its potential use for strain characterization and detection. Appl. Environ. Microbiol. 67, Miller, D.N., J.E. Bryant, E.L. Madsen, and W.C. Ghiorse Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65, Moissenet, D., P. Bidet, A. Garbarg-Chenon, G. Arlet, and H. Vu- Thien Ralstonia paucula (formerly CDC group IV c-2): unsuccessful strain differentiation with PCR-based methods, study of the 16S-23S spacer of the rrna operon, and comparison with other Ralstonia Species (R. eutropha, R. pickettii, R. gilardii, and R. solanacearum). J. Clin. Microbiol. 39, Pastrik, K.H. and E. Maiss Detection of Ralstonia solanacearum in potato tubers by polymerase chain reaction. J. Phytopathol. 148, Poussier, S., P. Prior, J. Luisetti, C. Hayward, and M. Fegan Partial sequencing of the hrpb and endoglucanase genes confirms and expands the known diversity within the Ralstonia solanacearum species complex. Syst. Appl. Microbiol. 23, Sambrook, J., E.F. Fritsch, and T. Maniatis Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA. 21. Schfeld, J., H. Heuer, J.D. van Elsas, and K. Smalla Specific and sensitive detection of Ralstonia solanacearum in soil on the basis of PCR amplification of flic fragments. Appl. Environ. Microbiol. 69, Seal, S.E., L.A. Jackson, J.P. Young, and M.J. Daniels Differentiation of Pseudomonas solanacearum, Pseudomonas syzygii, Pseudomonas pickettii, and the blood disease bacterium by partial 16S rrna sequencing: construction of oligonucleotide primers for sensitive detection by polymerase chain reaction. J. Gen. Microbiol. 139, Taghavi, M., C. Hayward, L.I. Sly, and M. Fegan Analysis
7 Vol. 43, No. 3 Ralstonia solanacearum DNA enzyme-linked immunosorbent assay 185 of the phylogenetic relationships of strains of Burkholderia solanacearum, Pseudomonas syzygii, and the blood disease bacterium of banana based on 16S rrna gene sequences. Int. J. Syst. Bacteriol. 46, Tanyuksel, M., C. Guney, E. Araz, M.A. Saracli, and L. Doganci Performance of the immunoglobulin G avidity and enzyme immunoassay IgG/IgM screening tests for differentiation of the clinical spectrum of toxoplasmosis. Kor. J. Microbiol. 40, Van der Wolf, J.M., S.G.C. Vriend, P. Kastelein, E.H. Nijhuis, P.J. van Bekkum, and J.W.L. van Vuurde Immunofluorescence colony-staining (IFC) for detection and quantification of Ralstonia (Pseudomonas) solanacearum biovar 2 (race 3) in soil and verification of positive results by PCR and dilution plating. Eur. J. Plant Pathol. 106, Van Elsas, J.D., P. Kastelein, P. van Bekkum, J.M. van der Wolf, P.M. de Vries, and L.S. van Overbeek Survival of Ralstonia solanacearum biovar 2, the causative agent of potato brown rot, in field and microcosm soils in temperate climates. Phytopathology 90, Vasse, J., P. Frey, and A. Trigalet Microscopic studies of intercellular infection and protoxylem invasion of tomato roots by Pseudomonas solanacearum. Mol. Plant-Microbe Interact. 8, Wallis, F.M. and S.J. Truter Histopathology of tomato plants infected with Pseudomonas solanacearum, with emphasis on ultrastructure. Physiol. Plant Pathol. 13, Weller, S.A., J.G. Elphinstone, N.C. Smith, N. Boonham, and D.E. Stead Detection of Ralstonia solanacearum strains with a quantitative, multiplex, real-time, fluorogenic PCR (TaqMan) assay. Appl. Environ. Microbiol. 66, Winstanley, C. and J.A.W. Morgan The bacterial flagellin gene as a biomarker for detection, population genetics and epidemiological analysis. Microbiology 143, (Received June 7, 2007/Accepted August 27, 2007) ABSTRACT : Detection of Ralstonia solanacearum with Nested PCR and DNA Enzyme-Linked Immunosorbent Assay Young-Jin Ko and Hong-Bum Cho 1 * (Department of diagnosis, Diaprobe Lab., 1 Department of Biotechnology, Seokyeong University, Seoul , Korea) In this study, we used the method of guanidin isothiocyanate and boiling with Chelex-100 resin to extract genomic DNA of Ralstonia solanacearum from soil. It is more efficient than general protocols to remove inhibitory compounds in soil and R. solanacearum own. Then, we applied polymerase chain reaction and DNA enzyme-linked immunosorbent assay (ELISA) to identify and detect pathogen. The flic gene of R. solanacearum was selected for specific detection of pathogen and primer sets were designed. Among the primer sets, two specific and sensitive primer sets, RsolfliC (forward; 5-GAACGCCAACGGTGCGAACT-3 and reverse; 5- GGCGGCCTTCAGGGAGGTC-3, designed by J. Schönfeld et al.) and RS_247 (forward; 5-GGCGGTCT- GTCGGCRG-3 and reverse; 5-CGGTCGCGTTGGCAAC-3 designed by this study), were designed to perform nested PCR. Nested PCR primer was labeled with biotin for hybridization between nested PCR product and probe to analyze with DNA ELISA.
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