Comparative sequence analyses of the ribonuclease P (RNase P) RNA genes from LL-2,6-diaminopimelic acid-containing actinomycetes.

Abstract

Ribonuclease P (RNase P) RNA genes of LL-2,6-diaminopimelic acid (LL-A 2 pm)-containing actinomycetes, except Streptomyces species, were sequenced after PCR-amplification and cloning. By using the sequence data, the relationships between species within genera and the relationships between taxa above genus level were investigated and the usefulness of the RNase P RNA gene as another phylogenetic marker was evaluated. RNase P RNA gene sequences of all strains used in this study contained relatively conserved regions along with highly variable regions. The mean RNase P RNA gene similarity value was approximately 82O18 % and the mean RNase P RNA gene similarity value when gaps were included was approximately 76O24 %. The nucleotide similarities between the RNase P RNA genes of different strains were mostly fewer than the 16S rDNA similarities. The RNase P RNA gene was more useful than 16S rDNA for clearly differentiating the relationships between species belonging to a genus and the relationships between some genera. However, nucleotide sequences of RNase P RNA genes were not necessarily appropriate for comparisons at all taxonomic levels (such as those between species, between genera and between families).Keywords : RNase P RNA gene, -2,6-diaminopimelic acid, actinomycetes, phylogeny INTRODUCTIONThe best means of investigating the genetic relationship between organisms is to compare their total genomic sequences. However, this approach is not likely to be possible without innovation in the existing molecular biological and analytical techniques. In the meantime, DNA-DNA hybridization and some useful gene fragments are used for elucidating genetic relationships or in phylogenetic studies. Such gene fragments include genes for rRNAs (Woese, 1987), the β-subunit of ATPsynthase (Amann et al., 1988), tRNA (Hofle, 1990), glutamine synthetase (Brown et al., 1994), elongation factor Tu (Kamla et al., 1996), a 65 kDa heat-shock protein (hsp65) (Swanson et al., 1997) and a histonelike protein (hbb) (Valsangiacomo et al., 1997 The GenBank accession numbers for the sequences of the RNase P RNA genes determined in this study are listed in Table 1. these, 16S rRNA or 16S rDNA have been extensively studied and have become important as target genes in the phylogeny and classification of prokaryotic organisms (Woese & Fox, 1977 ;Woese, 1987 ;Stackebrandt et al., 1997). Nevertheless, there is a general consensus that 16S rRNA gene sequences may be inappropriate for elucidating the relationships between closely related organisms and may be insufficient to guarantee species identity (Fox et al., 1992). DNA-DNA relatedness is generally recognized as being very important for defining species in current bacterial systematics (Wayne et al., 1987 ;Stackebrandt & Goebel, 1994). However, despite the fact that it provides a decisive criterion in species definition, DNA-DNA reassociation also has some experimental problems, being affected by various factors such as DNA concentration, DNA purity, size of DNA fragments, incubation temperature,...

Conserved and variable domains within divergent rnase P RNA gene sequences of Prochlorococcus strains.

“…Thus, rnpB-based phylogenies might be of potential interest because of the high level of variability within the coding region. Phylogenetic trees have previously been inferred successfully from the comparison of RNase P RNA sequences of various species (Cho et al, 1998 ;Herrmann et al, 1996Herrmann et al, , 2000Yoon & Park, 2000). The sequence identity between the different rnpB sequences is 74-99 %.…”

“…Previous comparative analyses of rnpB sequences from natural samples provided important information on the diversity of natural microbial populations (Brown et al, 1996). Sequences and structures of RNase P RNAs were suggested as distinctive markers within Saccharomonospora, the Chlamydiales and actinomycetes and allowed the inference of evolutionary relationships (Cho et al, 1998 ;Herrmann et al, 2000 ;Yoon & Park, 2000). In addition, information about the existing variants of RNase P RNAs provided clues towards the functional relevance of the different domains for the function of the catalytic core (Brown et al, 1996).…”

Diversity and distribution of the bioactive actinobacterial genus Salinispora from sponges along the Great Barrier Reef

“…Previous work has found RNase P RNA to be a suitable phylogenetic marker in actinomycetes when comparing species within the same genus. There have been previous investigations using RNase P RNA for the phylogenetic analysis of actinomycetes Saccharomonospora (Cho et al 1998) and LL-2,6-diaminopimelic acid-containing actinomycetes (Yoon and Park 2000).…”

Comparative analysis of ribonuclease P RNA of the planctomycetes

“…A third intermediate type, type C, has been observed in the green nonsulfur bacteria (Haas & Brown, 1998). RNase P RNA has proven useful for phylogenetic analysis of the Chlamydiales (Herrmann et al, 2000), Prochlorococcus (Schön et al, 2002), the LL-2,6-diaminopimelic acid-containing actinomycetes (Yoon & Park, 2000), Bartonella (Pitulle et al, 2002) and Vibrio core species (Maeda et al, 2001), among others.…”

“…A third intermediate type, type C, has been observed in the green nonsulfur bacteria (Haas & Brown, 1998). RNase P RNA has proven useful for phylogenetic analysis of the Chlamydiales (Herrmann et al, 2000), Prochlorococcus (Schön et al, 2002), the LL-2,6-diaminopimelic acid-containing actinomycetes (Yoon & Park, 2000), Bartonella (Pitulle et al, 2002) and Vibrio core species (Maeda et al, 2001), among others.The phylum Planctomycetes (Garrity et al, 2001) comprises a distinct group of the domain Bacteria on the basis of 16S rRNA analyses (Embley et al, 1994;Fuerst, 1995;Hugenholtz et al, 1998;Liesack et al, 1992;Schlesner & Stackebrandt, 1986;Woese et al, 1985). They may be one of the most deeply branching lineages within the domain Bacteria (Brochier & Philippe, 2002;Di Giulio, 2003).…”