Abstract
The aim of this study was to evaluate the inter-and intraspecific as well as intragenomic variability of Geobacillus 16S–23S rRNA internal transcribed spacers without tRNA genes and to compare these sequences with sequences bearing tRNA genes. In this study the structural analysis was performed in a unique way because the length and the sequence of the structural blocks were adjusted to fit the structure of 16S–23S rRNA internal transcribed spacers of five different Geobacillus species. Our study demonstrated the mosaic-like structure of 16S–23S rRNA internal transcribed spacers in Geobacillus. Some characteristics of these spacers of geobacilli were not previously reported for other bacteria: unusually short conserved sequence in the 5′ end region, some identical conserved blocks in both 5′ and 3′ regions of 16S–23S rRNA internal transcribed spacers, the same sequence blocks in both 16S–23S and 23S–5S rRNA intergenic spacers. Our study demonstrated quite uniform arrangement of the sequence blocks in Geobacillus thermodenitrificans. This species diverged early in the phylogenetic tree of the genus Geobacillus. For the phylogenetically recent species Geobacillus kaustophilus and Geobacillus lituanicus the low inter-and intraspecific, but high intragenomic variability, as a consequence of recent phylogenetic events, was established.
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Cherif A., Borin S., Rizzi A., Ouzari H., Boudabous A., Daffonchio D., Bacillus anthracis diverges from related clades of the Bacillus cereus group in 16S-23S ribosomal DNA intergenic transcribed spacers containing tRNA genes, Appl. Environ. Microbiol., 2003, 69, 33–40
Carr L.E., Gürtler V., Seviour R.J., Variation of 16S-23S rRNA intergenic spacer regions (ISRs) in Acinetobacter baylyi (strain B2) isolated from activated sludge, Syst. Appl. Microbiol., 2004, 27, 478–491
Osorio C.R., Collins M.D., Romalde J.L., Toranzo A.E., Variation in 16S-23S rRNA intergenic spacer regions in Photobacterium damselae: a mosaiclike structure, Appl. Environ. Microbiol., 2005, 71, 636–645
Privitera A., Rappazzo G., Sangari P., Gianninò V., Licciardello L., Stefani S., Cloning and sequencing of a 16S/23S ribosomal spacer from Haemophilus parainfluenzae reveals an invariant, mosaic-like organization of sequence blocks, FEMS Microbiol. Lett., 1998, 164, 289–294
Sadeghifard N., Gürtler V., Beer M., Seviour R.J., The mosaic nature of intergenic 16S-23S rRNA spacer regions suggests rRNA operon copy number variation in Clostridium difficile strains, Appl. Environ. Microbiol., 2006, 72, 7311–7323
Wenner T., Roth V., Decaris B., Leblond P., Intragenomic and intraspecific polymorphism of the 16S-23S rDNA internally transcribed sequences of Streptomyces ambofaciens, Microbiology, 2002, 148, 633–642
Chun J., Huq A., Colwell R.R., Analysis of 16S-23S rRNA intergenic spacer regions of Vibrio cholerae and Vibrio mimicus, Appl. Environ. Microbiol., 1999, 65, 2202–2208
Gürtler V., Barrie H.D., Typing of Staphylococcus aureus strains by PCR-amplification of variablelength 16S-23S rDNA spacer regions: characterization of spacer sequences, Microbiology, 1995, 141, 1255–1265
Perez-Luz S., Fernandez J., Rodriguez-Valera F., Pascual L., Moreno C., Amo A., et al., Sequence diversity of the internal transcribed spacer (ITS) region of the rRNA operons among different serogroups of Legionella pneumophila isolates, Syst. Appl. Microbiol., 2002, 25, 212–219
Kuisiene N., Raugalas J., Stuknyte M., Chitavichius D., Identification of the genus Geobacillus using genus-specific primers, based on the 16S-23S rRNA internal transcribed spacer, FEMS Microbiol. Lett., 2007, 277, 165–172
Kuisiene N., Raugalas J., Chitavichius D., Comparative sequence analysis of 16S–23S rRNA internal transcribed spacers of the genus Geobacillus, Biologija, 2008, 54, 1–6
Kumar S., Tamura K., Nei M., MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment, Brief. Bioinform., 2004, 5, 150–163
Xu D., Côte J.-C., Phylogenetic relatioships between Bacillus species and related genera inferred from comparison of 3′ end 16S rDNA and 5′ end 16S–23S ITS nucleotide sequences, Int. J. Syst. Evol. Microbiol., 2003, 53, 695–704
Gürtler V., The role of recombination and mutation in 16S–23S rDNA spacer rearrangements, Gene, 1999, 238, 241–252
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Kuisiene, N., Raugalas, J. & Chitavichius, D. Unusual intragenomic and interspecific variability of Geobacillus 16S-23S rRNA internal transcribed spacers. cent.eur.j.biol. 3, 396–406 (2008). https://doi.org/10.2478/s11535-008-0043-4
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DOI: https://doi.org/10.2478/s11535-008-0043-4