Inter- and Intraspecific Genetic Analysis of the Genus Saccharomonospora with 16S to 23S Ribosomal DNA (rDNA) and 23S to 5S rDNA Internally Transcribed Spacer Sequences

Abstract

In order to clarify interspecific relationships and to investigate the intraspecific phylogenetic structure of the genus Saccharomonospora, 16s to 23s ribosomal DNA (16s-23s) and 23s to 5s ribosomal DNA (23s-5s) internally transcribed spacers (ITSs) were used for sequence analyses. The 16s-23s and 23s-5s ITSs from 22 Saccharomonospora strains were amplified by PCR and directly sequenced. The average levels of nucleotide similarity of the 16s-23s and 23s-5s ITSs for the four valid species were 87.6% f 3.9% and 83% +-2.2%, respectively. For the most part, intraspecific sequence differences were not found in the two ITSs; the only exception was Saccharomonospora ghuca K194, which differed from other S. ghuca strains by 1 bp in the 23s-5s ITS. The Sacchuromonospora viridis strains had a smaller 16s-23s ITS region than the other strains, which may be useful for differentiating these organisms from other Saccharomonospora species. The characteristics of the two ITS regions make them more useful than 16s rRNA sequences as a tool for defining and identifying Saccharomonospora strains. However, Sacchuromonospora azurea K161T had two types of 23s-5s ITSs; rrnB, separated by XhoI digestion, had two additional nucleotides inserted between positions 52 and 55. Most of the 16s-23s and 23s-5s ITS sequences of S. azurea K161T and strains of "Saccharomonospora caesia" were identical; the only exception was rrnB in S. azurea K161T. The lengths and levels of sequence divergence of the two ITSs of Saccharomonospora sp. strain KlSO were different from the lengths and levels of sequence divergence of the ITSs of other species. These findings suggest that a taxonomic revision of the genus Saccharomonospora is necessary. Two trees based on 16s-23s and 23s-5s ITS sequences revealed distinct interspecific relationships in the genus Saccharomonospora.The genus Saccharomonospora was proposed by Nonomura and Ohara (20) for monosporic actinomycetes containing meso-diaminopimelic acid, arabinose, and galactose in the cell wall peptidoglycan (wall chemotype IV sensu Lechevalier and Lechevalier [ 181). Representatives of this genus form nonfragmenting, branched mycelia and develop aerial hyphae that bear single spores. The additional physical and chemical markers that characterize the genus have been described elsewhere The original type species of the genus is Saccharomonospora viridis (20). In addition to S. viridis, three Saccharomonospora species, Saccharomonospora azurea (24), Saccharomonospora cyanea (25), and Saccharomonospora glauca (7), have been validly described. Although "Saccharomonospora caesia" was proposed by Greiner-Mai et al. (8) as a fifth taxon for strains previously classified as Micropolyspora caesia (9, 13), this organism was not included on the Approved Lists of Bacterial Names (28) and has not been validly published on subsequent Approved Lists or Validation Lists. The results of recent numerical phenetic studies (11) and results obtained by nucleic acid techniques (12,(39)(40)(41) suggest that the strains of "S. caesi...

Phylogenetic relationships of Xylella fastidiosa strains from different hosts, based on 16S rDNA and 16S-23S intergenic spacer sequences.

“…It has been proposed that sequencing of the 16S-23S intergenic spacer region could overcome this problem because of its higher variation in length and sequence. Indeed, analysis of this region has successfully differentiated strains of many groups of bacteria, and sequences of the 16S-23S regions of many species have become available for comparison (Leblond-Bourget et al, 1996 ;Yoon et al, 1997).…”

Note

“…Saccharomonospora sp. strain K180 exhibited levels of DNA-DNA relatedness of 32, 37, 23 and 15 % to S. azurea KCTC 9475T, S. cyanea KCTC 947gT, S. glauca KCTC 9479T and S. viridis KCTC 9 1 1 5T, respectively.The high possibility of strain K180 being a new species of the genus Saccharomonospora has already been shown (Kim et al, 1995;Yoon et al, 1997) and its description as a new species will be published elsewhere. S .…”

“…The high possibility of strain K180 being a new species of the genus Saccharomonospora has already been shown (Kim et al, 1995;Yoon et al, 1997) and its description as a new species will be published elsewhere. S .…”

“…The additional phenotypic characteristics and phylogenetic analysis of this genus have been described elsewhere (Kim et al, 1995;Yoon et al, 1996Yoon et al, , 1997. There are currently four validly described Saccharomonospora species, namely, Saccharomonospora azurea (Runmao, 1987), Saccharomonospora cyanea (Runmao et al, 1988), Saccharomonospora glauca (Greiner-Mai et al, 1988) and Saccharomonospora viridis (Nonomura & Ohara, 1971), the type species of the genus. '…”

“…S. azurea and ' S . caesia' have identical sequences in 5s rRNA (unpublished), in 16s-23s rDNA ITS (internally transcribed spacer) region (Yoon et al, 1997) and in approximately 340 bp of RNase P RNA gene (Cho et al, 1998). The 23s-5s ITS sequences of S. azurea, except for one rRNA allele which has two inserted 00864 0 1999 IUMS J.-H. Yoon and others nucleotides, also were identical to 23s-5s ITS sequences of 'S.…”