16S-23S and 23S-5S intergenic spacer regions of Streptococcus thermophilus and Streptococcus salivarius, primary and secondary structure

Nour, Mohamed; Naimi, Afaf; Beck, G; Branlant, Christiane

doi:10.1007/bf00314579

Cited by 28 publications

(28 citation statements)

References 30 publications

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“…The phylogenetic relationship based on tRNA Ile (GAU)-tDNA Ala (UGC) sequences found in L-ISR was readily comparable to current bacterial taxonomy based on 16S rDNA sequence data. The majority of LAB, including members of the genera Lactococcus, Streptococcus, and Leuconostoc, have one type of rrn operon with a tRNA Ala gene which is similar to the M-ISR of Carnobacterium species (21,33,44). Staphylococcus aureus (12) has three types of rrn operons with structures identical to those of Carnobacterium species.…”

Section: Discussionmentioning

confidence: 99%

Differentiation of Closely Related Carnobacterium Food Isolates Based on 16S-23S Ribosomal DNA Intergenic Spacer Region Polymorphism

Hristova

Dousset

Cam

et al. 2002

Appl Environ Microbiol

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A novel strategy for identification of Carnobacterium food isolates based on restriction fragment length polymorphism (RFLP) of PCR-amplified 16S-23S ribosomal intergenic spacer regions (ISRs) was developed. PCR amplification from all Carnobacterium strains studied always yielded three ISR amplicons, which were designated the small ISR (S-ISR), the medium ISR (M-ISR), and the large ISR (L-ISR). The lengths of theseLactic acid bacteria (LAB) have been the focus of extensive research due to their value in the food-processing industry (14,27). One of the most recent taxonomic additions to the LAB group is the genus Carnobacterium. Members of this genus are widespread in nature, and the habitats of these organisms range from foods, such as poultry, meat, cheese, and seafood, to fish intestines and anoxic Antarctic lake water (2,10,16,26,29). The four species of Carnobacterium isolated from food are Carnobacterium divergens, C. piscicola, C. gallinarum, and C. mobile (6). Most research on the genus Carnobacterium has been focused on the production of bacteriocins and the regulation of metabolic enzymes (9, 28). In the last few years, many ways to differentiate Carnobacterium species have been developed. The phylogenetic interrelationships of species in the genus Carnobacterium have been investigated by using numerical taxonomic matrices and sequencing of the 16S rrn segments encoding mature rRNAs (19,41). The Carnobacterium species form a phylogenetically coherent group, which is quite distinct from all other LAB. However, the number of polymorphic sites in the 16S rRNA of Carnobacterium species is rather low, since some species have the same sequence (the sequences of C. piscicola and C. gallinarum are 98% identical) and other species exhibit very high degrees of sequence similarity (the sequences of C. divergens and C. mobile are 96% similar) (41). Thus, it is difficult to define specific 16S RNA rrn sequences that can be used for differentiation of these closely related species. Carnobacteria have been identified at the genus level by nucleic acid hybridization by using 16S rRNA-targeted genus-specific probes (32). Species-specific primers have been designed by using the domains that exhibit low homology in the 16S ribosomal DNA (rDNA) sequences of species of Carnobacterium (1, 4). However, the PCR primers used in these studies were not specific enough to differentiate Carnobacterium spp. from other genera of LAB. Data obtained with the randomly amplified polymorphic DNA PCR technique enable only C. divergens to be differentiated from other Carnobacterium species (20).In view of this, a study of the more variable sequences in the rRNA operon of phylogenetically closely related Carnobacterium species could be useful. In most prokaryotes, the ribosomal genes form an operon with the order 5Ј-16S-23S-5S-3Ј, and the genes are separated by two intergenic spacer regions (ISRs). ISRs, especially those located between the 16S and 23S rDNAs, are thought to be under less evolutionary pressure and, therefore, to provide great...

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Section: Discussionmentioning

confidence: 99%

Differentiation of Closely Related Carnobacterium Food Isolates Based on 16S-23S Ribosomal DNA Intergenic Spacer Region Polymorphism

Hristova

Dousset

Cam

et al. 2002

Appl Environ Microbiol

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“…Until now, such a feature had been found only in streptococci (Bacot & Reeves, 1991 ;Chiaruttini & Milet, 1993;Nour et al, 1995), lactobacilli (Pittet & Hottinger, 1989) and some archaeobacteria (reviewed by Bacot & Reeves, 1991 …”

Section: Discussionmentioning

confidence: 99%

“…4). The nucleotide sequence of the stem containing the putative dsPS2 site is highly conserved in the five enterococcal species (Figs 2,3 and 4) and shows a strong sequence conservation when compared to the L. lactis (Chiaruttini & Milet, 1993), S. thermophilus and S. salivarius (Nour et al, 1995) dsPS2 stem (Fig. 4b).…”

Section: Figmentioning

confidence: 99%

“…Although only a limited number of rrn spacer regions have been characterized (reviewed by Gurtler & Stanisich, 1996), the presence of long double-stranded regions that close the 16s and 23s rRNA sequences and contain the primary processing sites seem to be a general feature of bacterial prerRNAs, they are not always found in archaeobacteria (Potter et al, 1995). A model of the interaction between spacer regions 1 and 2 that is supported by results of S1 nuclease digestion was proposed for L. factis (Chiaruttini & Milet, 1993), and we recently proposed a model of interaction for the spacer regions 1 and 2 of S. thermophilus and S. saliuarius (Nour et al, 1995). T o establish a model of interaction between spacer regions 1 and 2 for the third genus of streptococci, namely Enterococcus, the nucleotide sequence of a spacer region 2 from enterococci had to be determined.…”

Section: Introductionmentioning

confidence: 95%

“…Elution was according to the methods of Sambrook et al (1989). The complete sequences of the amplified fragments were determined on both strands as described by Nour et al (1995). Oligonucleotides 514, 554, 601 and 667 were used as primers for sequence analysis.…”

Section: Introductionmentioning

confidence: 99%

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Primary and secondary structures of rRNA spacer regions in enterococci

Naimi¹,

Beck²,

Branlant³

1997

Microbiology

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The 165-235 and 235-55 rRNA spacer DNA regions (spacer regions 1 and 2, respectively) from Enterococcus faecalis, Enterococcus faecium, Enterncoccus hirae, Enterococcus durans and Enterncoccus mundtii were amplified by PCR. Their nucleotide sequences were established and a secondary structure model showing the interaction between the two spacer regions was built. Whereas lactococci and Streptococcus sensu stricto are characterized by a single type of spacer region 1 , the enterococci show a high degree of variability in this region; thus the spacer regions 1 with and without tRNAAia were characterized. However, as shown for lactococci and Streptococcus sensu stricto, the tRNAAia gene does not encode the 3'4erminal CCA trinucleotide. A putative antitermination signal is found downstream from the tRNAAia gene. Based on comparison with Lactococcus lactis and Streptococcus thermophilus, a doublestranded processing stem is proposed. In €. hirae, one of the three different types of spacer region 1 contains no tRNAAia, but displays a 107 nt insertion that forms a long stem-loop structure. A similar insertion (1 15 nt in length) was found in E. faecium and base compensatory mutations preserve the ability to form the long stem-loop structure. Such insertions may correspond to mobile intervening sequences, as found in the 235 rRNA coding sequences of some Gram-negative bacteria. The spacer regions 1 and 2 from the three subgroups of streptococci were compared, and except for the tRNAAia gene and the double-stranded processing sites, little similarity was found, which opens large possibilities for future development of DNA-based typing methods.

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The D1-A2 and D2-A2 Pairs of Splice Sites from Human Immunodeficiency Virus Type 1 Are Highly Efficientin Vitro,in Spite of an Unusual Branch Site

Damier

Domenjoud

Branlant

1997

Biochemical and Biophysical Research Communications

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16S-23S and 23S-5S intergenic spacer regions of Streptococcus thermophilus and Streptococcus salivarius, primary and secondary structure

Cited by 28 publications

References 30 publications

Differentiation of Closely Related Carnobacterium Food Isolates Based on 16S-23S Ribosomal DNA Intergenic Spacer Region Polymorphism

Differentiation of Closely Related Carnobacterium Food Isolates Based on 16S-23S Ribosomal DNA Intergenic Spacer Region Polymorphism

Primary and secondary structures of rRNA spacer regions in enterococci

The D1-A2 and D2-A2 Pairs of Splice Sites from Human Immunodeficiency Virus Type 1 Are Highly Efficientin Vitro,in Spite of an Unusual Branch Site

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