title: Recognition of individual genes in diverse microorganisms by cycling primed in situ amplification.
abstract: Cycling primed in situ amplification-fluorescent in situ hybridization (CPRINS-FISH) was developed to recognize individual genes in a single bacterial cell. In CPRINS, the amplicon was long single-stranded DNA and thus retained within the permeabilized microbial cells. FISH with a multiply labeled fluorescent probe set enabled significant reduction in nonspecific background while maintaining high fluorescence signals of target bacteria. The ampicillin resistance gene in Escherichia coli, chloramphenicol acetyltransferase gene in different gram-negative strains, and RNA polymerase sigma factor (rpoD) gene in Aeromonas spp. could be detected under identical permeabilization conditions. After concentration of environmental freshwater samples onto polycarbonate filters and subsequent coating of filters in gelatin, no decrease in bacterial cell numbers was observed with extensive permeabilization. The detection rates of bacterioplankton in river and pond water samples by CPRINS-FISH with a universal 16S rRNA gene primer and probe set ranged from 65 to 76% of total cell counts (mean, 71%). The concentrations of cells detected by CPRINS-FISH targeting of the rpoD genes of Aeromonas sobria and A. hydrophila in the water samples varied between 2.1 x 10(3) and 9.0 x 10(3) cells ml(-1) and between undetectable and 5.1 x 10(2) cells ml(-1), respectively. These results demonstrate that CPRINS-FISH provides a high sensitivity for microscopic detection of bacteria carrying a specific gene in natural aquatic samples.
authors.affiliation: Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka 565-0871, Japan.
authors.forename: Takehiko
authors.initials: T
authors.lastname: Kenzaka
authors.forename: Shigeru
authors.initials: S
authors.lastname: Tamaki
authors.forename: Nobuyasu
authors.initials: N
authors.lastname: Yamaguchi
authors.forename: Katsuji
authors.initials: K
authors.lastname: Tani
authors.forename: Masao
authors.initials: M
authors.lastname: Nasu
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D004277:DNA, Single-Stranded / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D005618:Fresh Water / Q000382:microbiology*; D006090:Gram-Negative Bacteria / Q000145:classification* / Q000166:cytology / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D020401:Primed In Situ Labeling / Q000379:methods*; D012808:Sigma Factor / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases