Intragenomic heterogeneity of the 16S rRNA–23S rRNA internal transcribed spacer amongPseudomonas syringaeandPseudomonas fluorescensstrains

Abstract

The 16S-23S rRNA internal transcribed spacer regions (ITS1) from 14 strains of Pseudomonas syringae and P. fluorescens were sequenced. ITS1 exhibited significant sequence variability among different operons within a single genome. From 1 to 4 types of ITS1 were found in individual genomes of the P. syringae and P. fluorescens strains. A total of eight ITS1 types were identified among strains studied. The ITS1 nucleotide sequences consisted of conserved blocks including, among others, a stem-forming region of box B, tRNAIle and tRNAAla genes and several variable blocks. The differences in the variable regions were mostly due to insertions and/or deletions of nucleotide blocks. The intragenomic heterogeneity of ITS1 was brought about by different combinations of variable blocks, which possibly have resulted from recombination and horizontal transfer.

Microbial Diversity in Milled Rice as Revealed by Riosomal Intergenic Spacer Analysis

“…The locations of the amplicons derived from both the E. coli and F. graminearum contaminants in these profiles were confirmed by comparison with the RISA profiles of DNA directly prepared from these microbes (data not shown). The multiple fragments derived from E. coli most likely reflect the intragenomic variation in ribosomal rRNA gene operons, as reported for several bacteria including E. coli 35) .…”

Intercistronic heterogeneity of the 16S–23S rRNA spacer region among Pseudomonas strains isolated from subterranean seeds of hog peanut (Amphicarpa bracteata)

“…ITS1 varies considerably among different operons (Naimi et al, 1997;Gurtler, 1999;Iteman et al, 2000) without a remarkable length difference. In the genus Pseudomonas, intercistronic heterogeneity of the ITS1 reported to date is primarily due to insertions and/or deletions of nucleotide blocks outside the tRNA genes (Milyutina et al, 2004;Natalini & Scortichini, 2007). Milyutina et al (2004) identified eight ITS1 types among 14 strains of P. syringae and P. fluorescens with similar sequence lengths except for one strain exhibiting about 8 % length difference among its copies.…”

“…Smith et al (1999) demonstrated the presence of two different ITS1 types in Pseudomonas fluorescens strain F113, and Pseudomonas putida strain KT2440 was reported to have seven rRNA operons with non-identical ITS1 sequences (Nelson et al, 2002). One to four types of ITS1 were found in individual genomes of Pseudomonas syringae and P. fluorescens strains (Milyutina et al, 2004). However, none of the reported intercistronic heterogeneity of ITS1 among Pseudomonas strains was due to excessive deletions within the tRNA Ile and tRNA Ala regions; in most cases it appeared to be due to recombination and horizontal transfer of variable nucleotide blocks outside the tRNA genes.…”

“…Restriction fragment length polymorphism analysis (Cho & Tiedje, 2000) and PCR-based cloning followed by DNA sequencing (Smith et al, 1999;Milyutina et al, 2004) indicated the existence of more than one type of ITS1 within a single genome of Pseudomonas strains. Real-time PCR has been increasingly used for accurate detection and identification of specific bacteria in soil samples but has apparently not been employed to study intercistronic heterogeneity.…”

Soil microbial community analysis in the environmental risk assessment of transgenic plants

“…As one of the potential biases in RISA, Milyutina et al (2004) have demonstrated in their previous report that intragenomic differences in the IGS in some cases exceed the differences in these sequences among strains. This could bias the interpretation of both the quantitative and qualitative interpretation of the data obtained by RISA.…”