Introduction Methods Gene Organisms
Introduction
DNA degradation (which results in a smear pattern) occurs with some bacterial strains during pulsed-field gel electrophoresis (PFGE), like Streptomyces lividans 1326. The DNA degradation (Dnd) phenotype is also frequently determinated by PCR with activated TAE buffer.
Fig. 1. DNA degradation (Dnd) phenotype under normal agarose gel electrophoresis. Lane 1, 6, 7 and 8 display the intact DNA after treatment with the activated TAE buffer, whereas Lane 2, 3, 4, 5 and 9 show the Dnd phenotype after treatment.
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Methods
Protocol for the Dnd phenotype determination with activated TAE buffer, in the MS Word file (.doc) or in the Adobe PDF document (.pdf).
Protocol of pulsed-field gel electrophoresis (PFGE) at protocol-online.
A liquid chromatography-coupled tandem quadrupole mass spectrometry approach was descriped in the paper of Wang, et al. (2011).
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Analysis of dndABCDE genes responsible for The DNA degradation (Dnd) system in Streptomyces lividans 1326
Mutations in dndA ,dndC, dndD and dndE in wide-type Streptomyces lividans 1326 all abolished the Dnd phenotype while mutation in dndB only aggravates the Dnd phenotype.
Fig. 2. Streptomyces lividans 1326 and its dnd mutants. [Xu et al., BMC Microbiol. 2009 Feb 20;9(1)]
Fig. 3. (A) All of the DNA samples were proven to be stable in normal agarose gel electrophoresis buffer with added thiourea. (B) Genomic DNA from wide-type Streptomyces lividans 1326 and its dndB mutant XTG2 both undergo degradation (streaking in the lane) during gel electrophoresis in Tris-containing buffer. [Xu et al., BMC Microbiol. 2009 Feb 20;9(1)]
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Reported organisms with Dnd phenotype under agarose gel electrophoresis
The file containing NCBI taxonomy IDs: NCBI_Taxon_ID_170624_388.txt
iTOL can generate the phylogenetic tree based on NCBI taxonomy IDs provided.

No. Organism Description Dnd phenotype Reference
1Clostridium botulinum [NCBI taxonomy]21 Clostridium botulinum (non-proteolytic) group II strains.Dnd phenotype by PFGE, 20 strains.Hielm, S., Bjorkroth, J., Hyytia, E. and Korkeala, H. (1998) Genomic analysis of Clostridium botulinum group II by pulsed-field gel electrophoresis. Appl Environ Microbiol, 64, 703-708.  [Abstract]
2Clostridium difficile [NCBI taxonomy]pathogen, antibiotic-associated diarrhea and pseudomembranous colitis in hospitalized patients.Dnd phenotype using PFGE, 25 out of 30 isolates collected from three different hospitals.Klaassen, C.H., van Haren, H.A. and Horrevorts, A.M. (2002) Molecular fingerprinting of Clostridium difficile isolates: pulsed-field gel electrophoresis versus amplified fragment length polymorphism. J Clin Microbiol, 40, 101-104.  [Abstract]
3Clostridium difficile [NCBI taxonomy]46 strains of Clostridium difficile, including 16 nosocomial isolates from one ward (outbreak ward) plus 17 other nosocomial isolates and 13 community-acquired isolatesDnd phenotype using PFGE, one isolate from the outbreak ward and two other nosocomial isolatesKristjansson, M., Samore, M.H., Gerding, D.N., DeGirolami, P.C., Bettin, K.M., Karchmer, A.W. and Arbeit, R.D. (1994) Comparison of restriction endonuclease analysis, ribotyping, and pulsed-field gel electrophoresis for molecular differentiation of Clostridium difficile strains. J Clin Microbiol, 32, 1963-1969.  [Abstract]
4Clostridium difficile [NCBI taxonomy]Clostridium difficile PCR ribotype 1 strainsDnd phenotype using PFGE, five Clostridium difficile PCR ribotype 1 strainsCorkill, J.E., Graham, R., Hart, C.A. and Stubbs, S. (2000) Pulsed-field gel electrophoresis of degradation-sensitive DNAs from Clostridium difficile PCR ribotype 1 strains. J Clin Microbiol, 38, 2791-2792.  [Abstract]
5Enterobacter cloacae [NCBI taxonomy]-Dnd phenotype using PFGE, 1 Enterobacter cloacae strainSilbert, S., Boyken, L., Hollis, R.J. and Pfaller, M.A. (2003) Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea. Diagn Microbiol Infect Dis, 47, 619-621.  [Abstract]
6Escherichia coli [NCBI taxonomy]-Dnd phenotype using PFGE, 21 Escherichia coliSilbert, S., Boyken, L., Hollis, R.J. and Pfaller, M.A. (2003) Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea. Diagn Microbiol Infect Dis, 47, 619-621.  [Abstract]
7Escherichia coli B7A [NCBI taxonomy]The enterotoxigenic (ETEC) Escherichia coli strain B7A (O148:H28:CS6:LT+:ST+) was isolated from an American soldier who had diarrhea in Viet Nam. Dnd phenotype using PFGE. The E. coli B7A dnd cluster was shown to mediate the incorporation of sulphur into the DNA backbone via a sequence-selective, stereo-specific phosphorothioate modification [Wang et al. (2007). Nature Chem. Bio., 3, 709-710]. This is the first report of natural modification of the DNA backbone itself and sets it apart from well-documented DNA methylation and other changes to DNA bases.Wang, LR; Chen, S; Xu, TG; Taghizadeh, K; Wishnok, JS; Zhou, XF; You, DL; Deng, ZX; Dedon, PC (2007). Phosphorothioation of DNA in bacteria by dnd genes. NATURE CHEMICAL BIOLOGY, 3:709-710.   [Abstract]
8Escherichia coli non-O157:H7 [NCBI taxonomy]enterohemorrhagic Escherichia coli (non-O157) strainsDnd phenotype using PFGE, two enterohemorrhagic Escherichia coli (non-O157) strainsKoort, J.M., Lukinmaa, S., Rantala, M., Unkila, E. and Siitonen, A. (2002) Technical improvement to prevent DNA degradation of enteric pathogens in pulsed-field gel electrophoresis. J Clin Microbiol, 40, 3497-3498.  [Abstract]
9Escherichia coli O157:H7 [NCBI taxonomy]825 enterohemorrhagic Escherichia coli (EHEC) O157:H7 isolates, most of which were from 19 outbreaks and 608 sporadic cases in Japan, mainly in May to August 1996.Dnd phenotype using PFGE, 25 out of 825 isolates.Izumiya, H., Terajima, J., Wada, A., Inagaki, Y., Itoh, K.I., Tamura, K. and Watanabe, H. (1997) Molecular typing of enterohemorrhagic Escherichia coli O157:H7 isolates in Japan by using pulsed-field gel electrophoresis. J Clin Microbiol, 35, 1675-1680.  [Abstract]
10Klebsiella pneumoniae [NCBI taxonomy]-Dnd phenotype using PFGE, 4 Klebsiella pneumoniae strainsSilbert, S., Boyken, L., Hollis, R.J. and Pfaller, M.A. (2003) Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea. Diagn Microbiol Infect Dis, 47, 619-621.  [Abstract]
11Mycobacterium abscessus [NCBI taxonomy]Mycobacterium abscessus most commonly causes wound infections, abscess formation, and chronic pulmonary disease. Dnd phenotype using PFGE, sixty-nine clinical M. abscessus isolates.Zhang, Y., Yakrus, M.A., Graviss, E.A., Williams-Bouyer, N., Turenne, C., Kabani, A. and Wallace, R.J., Jr. (2004) Pulsed-field gel electrophoresis study of Mycobacterium abscessus isolates previously affected by DNA degradation. J Clin Microbiol, 42, 5582-5587.  [Abstract]
12Pseudomonas aeruginosa [NCBI taxonomy]-Dnd phenotype using PFGE, 17 Pseudomonas aeruginosa strainsSilbert, S., Boyken, L., Hollis, R.J. and Pfaller, M.A. (2003) Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea. Diagn Microbiol Infect Dis, 47, 619-621.  [Abstract]
13Pseudomonas aeruginosa [NCBI taxonomy]isolates from patients, the clinical environment and aquatic habitats.Dnd phenotype using PFGE, 50 Pseudomonas aeruginosa strains.Romling, U. and Tummler, B. (2000) Achieving 100% typeability of Pseudomonas aeruginosa by pulsed-field gel electrophoresis. J Clin Microbiol, 38, 464-465.  [Abstract]
14Pseudomonas fluorescens PfO-1 [NCBI taxonomy]A nonpathogenic saprophyte which inhabits soil, water and plant surface environments.Dnd phenotype using PFGE.Zhou, XF; He, XY; Liang, JD; Li, AY; Xu, TG; Kieser, T; Helmann, JD; Deng, ZX (2005). A novel DNA modification by sulphur. MOLECULAR MICROBIOLOGY, 57:1428-1438.  [Abstract]
15Ralstonia sp. CDC group IV c-2 [NCBI taxonomy]The opportunistic pathogenic CDC group IV c-2, an environmental gram-negative bacillus, isolated in several human infections.Eight C IV-2 clinical isolates showed Dnd phenotype during PFGE. Conversely, none of the four type strains exhibited Dnd phenotype.Moissenet, D., Goujon, C.P., Garbarg-Chenon, A. and Vu-Thien, H. (1999) CDC group IV c-2: a new Ralstonia species close to Ralstonia eutropha. J Clin Microbiol, 37, 1777-1781.  [Abstract]
16Salmonella enterica serovar Cerro [NCBI taxonomy]isolates from a commercial egg-producing fram.Dnd phenotype using PFGE, 7 out of 47 S. enterica serovar Cerro isolates collected.Murase, T., Nagato, M., Shirota, K., Katoh, H. and Otsuki, K. (2004) Pulsed-field gel electrophoresis-based subtyping of DNA degradation-sensitive Salmonella enterica subsp. enterica serovar Livingstone and serovar Cerro isolates obtained from a chicken layer farm. Vet Microbiol, 99, 139-143.  [Abstract]
17Salmonella enterica serovar Livingstone [NCBI taxonomy]isolates from a commercial egg-producing fram.Dnd phenotype using PFGE, all the 53 S. enterica serovar Livingstone isolates collected.Murase, T., Nagato, M., Shirota, K., Katoh, H. and Otsuki, K. (2004) Pulsed-field gel electrophoresis-based subtyping of DNA degradation-sensitive Salmonella enterica subsp. enterica serovar Livingstone and serovar Cerro isolates obtained from a chicken layer farm. Vet Microbiol, 99, 139-143.  [Abstract]
18Salmonella enterica serovar Ohio [NCBI taxonomy]-Dnd phenotype using PFGE, nine Salmonella enterica subsp. enterica serovar OhioKoort, J.M., Lukinmaa, S., Rantala, M., Unkila, E. and Siitonen, A. (2002) Technical improvement to prevent DNA degradation of enteric pathogens in pulsed-field gel electrophoresis. J Clin Microbiol, 40, 3497-3498.  [Abstract]
19Salmonella serovar Newport [NCBI taxonomy]-Dnd phenotype using PFGE, seven Salmonella serovar NewportKoort, J.M., Lukinmaa, S., Rantala, M., Unkila, E. and Siitonen, A. (2002) Technical improvement to prevent DNA degradation of enteric pathogens in pulsed-field gel electrophoresis. J Clin Microbiol, 40, 3497-3498.  [Abstract]
20Salmonella spp. [NCBI taxonomy]-Dnd phenotype using PFGE, 4 Salmonella spp.Silbert, S., Boyken, L., Hollis, R.J. and Pfaller, M.A. (2003) Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea. Diagn Microbiol Infect Dis, 47, 619-621.  [Abstract]
21Serratia marcescens [NCBI taxonomy]-Dnd phenotype using PFGE, 12 Serratia marcescens strainSilbert, S., Boyken, L., Hollis, R.J. and Pfaller, M.A. (2003) Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea. Diagn Microbiol Infect Dis, 47, 619-621.  [Abstract]
22Streptomyces avermitilis [NCBI taxonomy]-Dnd phenotype using PFGE, Streptomyces avermitilis DNA samples.Evans, M., Kaczmarek, F.S., Stutzman-Engwall, K. and Dyson, P. (1994) Characterization of a Streptomyces-lividans-type site-specific DNA modification system in the avermectin-producer Streptomyces avermitilis permits investigation of two novel giant linear plasmids, pSA1 and pSA2. Microbiology, 140 ( Pt 6), 1367-1371.  [Abstract]
23Streptomyces lividans 1326 [NCBI taxonomy]Streptomyces lividans 1326 commonly used as the host strain for gene cloning in Streptomyces, closely related to S. coelicolor A3(2).The five-gene dnd cluster in Streptomyces lividans 1326 responsible for Dnd phenotype was described in the paper, X. Zhou, X. He, J. Liang., T. Xu, A. Li, T. Kieser, J. D. Helmann and Z. Deng (2005). A novel DNA modification by sulphur. Molecular Microbiology, 57(5): 1428-1438 Zhou, X; Deng, Z; Firmin, J L; Hopwood, D A; Kieser, T (1988). Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminate. NUCLEIC ACIDS RESEARCH, 16:4341-4352  [Abstract]
24Vibrio parahaemolyticus [NCBI taxonomy]38 isolates from patients, 16 isolates from environmental sources collected during the outbreak of Vibrio parahaemolyticus gastroenteritis on Canada’s west coast in 1997. Six other human V. parahaemolyticus isolates from sporadic cases of gastroenteritis. A total of 60 isolates were characterized. Dnd phenotype using PFGE, 14 out of 60 (23%) isolates.Marshall, S., Clark, C.G., Wang, G., Mulvey, M., Kelly, M.T. and Johnson, W.M. (1999) Comparison of molecular methods for typing Vibrio parahaemolyticus. J Clin Microbiol, 37, 2473-2478.  [Abstract]
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