Subtraction of bacterial genomes
SSH method has been adapted for comparison of bacterial genomes (Akopyants et al., 1998). Genes that are present in certain isolates of a given bacterial species and absent or substantially different in others can be of great interest biologically. Some may determine strain-specific traits such as drug resistance, bacterial surface structure, or restriction-modification. Of special importance in infectious disease are the "pathogenicity islands" (PAIs), multigene segments of virulent strains that tend to be absent from avirulent members of the same species and that help determine the nature and severity of disease.
To select strain-specific genes in bacterial genomes using SSH, pools of digested genomic DNA from the strain of interest (tester) are deprived of sequences also present in the reference strain (driver) by judicious use of hybridization and PCR. The remaining tester-enriched DNA fragments are then cloned for further analysis.
References
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Akopyants NS, Fradkov A, Diatchenko L, Hill JE, Siebert PD, Lukyanov SA, Sverdlov ED, Berg DE. (1998) PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori. Proc Natl Acad Sci U S A 95(22):13108-13113. /PMID:9789049
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Diachenko L, Lau YF, Campbell AP, Chenchik A, Mogadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert D. (1996) Suppression Subtracive Hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93(12): 6025-6030. / PMID:8650213
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Gurskaya NG, Diachenko L, Chenchik A, Siebert PD, Khaspekov GL, Lukyanov K, Vagner LL, Ermolaeva OD, Lukyanov S, Sverdlov ED. (1996) The Equalizing cDNA Subtraction Based on Selective Suppression of Polymerase Chain Reaction: Cloning of the Jurkat Cells' Transcripts Induced by Phytohemaglutinin and Phorbol 12-myristate 13-acetate. Anal. Biochem. 240(1): 90-97. / PMID:8811883
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Lukyanov SA, Gurskaya NG, Lukyanov KA, Tarabykin VS and Sverdlov ED (1994) Highly efficient subtractive hybridisation of cDNA. Russian Journal of Bioorganic Chemistry, 20 (6):701-704.
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Rebrikov DV, Britanova OV, Gurskaya NG, Lukyanov KA, Tarabykin VS and Lukyanov SA (2000) Mirror orientation selection (MOS) – a method for eliminating false positive clones from libraries generated by suppression subtractive hybridization. Nucleic Acid Research 28 (20): e90. / PMID:11024192