A Taxonomic Study of the Genus Streptomyces by Analysis of Ribosomal Protein AT-L30

Abstract

The ribosomal AT-I30 proteins from 81 species of the genus Streptomyces as listed by Williams et al. in Bergey's Manual of Systematic Bacteriology were analyzed. My results provided further evidence that the genus Streptomyces is well circumscribed. On the basis of levels of AT-L30 N-terminal amino acid sequence homology, the strains were classified into four groups (groups I to IV) and a nongrouped category, whose members contained amino acid sequences characteristic of each species. A phylogenetic tree constructed on the basis of the levels of similarity of the amino acid sequences revealed the existence of six clusters within the genus. The first cluster contains the members of groups I and I1 together with several other species; the second cluster contains the members of groups I11 and IV and several other species; the third cluster contains Streptomyces ramulosus and Streptomyces ochraceiscleroticus; the fourth cluster contains only Streptomyces rimosus; the fifth cluster contains Streptomyces aurantiacus and Streptomyces tubercidicus; and the sixth cluster contains Streptomyces albus and Streptomyces sulphureus. Considerable agreement between the results of the AT-L30 analyses and the results of numerical phenetic classification was found, although there were numerous disagreements in details. For example, four groups (groups I to IV) defined by the AT-L30 analysis data did not correlate with the aggregate groups defined by numerical classification. In general, but not always, the species classified in a particular cluster in the numerical classification system had the same or similar AT-L30 terminal amino acid sequences. The AT-UO analysis data were more consistent with the 16s rRNA analysis data than with the numerical classification data, indicating that there was a good correlation between the four groups defined by AT-L30 analysis data and the aggregate groups defined by 16s rRNA analysis data. I stress that discrepancies between results of phenetic analyses and results of phylogenetic analyses should be taxonomically significant and can be resolved by other taxonomic approaches, such as DNA relatedness analysis.The genus Streptomyces of the family Streptomycetaceae contains the largest number of species among the genera of the Actinornycetales and can be separated from other actinomycete genera with wall chemotype I by using a combination of chemical and morphological properties (reviewed in references 2, 10, and 33). Traditionally, streptomycete systematics has been based mainly on morphology, pigmentation, and physiological properties, but increasing weight is now given to chemical and genetic features (2,3,9,11,15,28), especially for generic circumspection. As mentioned by O'Donnell (27), analysis of quantitative data by appropriate cluster analysis techniques may be essential for the characterization of streptomycetes at the subgeneric level. Because of importance of the genus Streptomyces as a source of novel antibiotics, the number of proposed streptomycete species, including those only cited i...

Analysis of Thermophilic Clades within the Genus Streptomyces by 16S Ribosomal DNA Sequence Comparisons

“…Goodfellow et al 1987 (12). AT-L30 ribosomal protein analyses also revealed that Streptomyces thermonitrificans, Streptomyces thermoviolaceus, and Streptomyces thermovulgaris are closely related (27). DNA-DNA relatedness studies are needed to resolve the finer taxonomic relationships among Streptomyces thermonitrificans, Streptomyces thermoviolaceus, and Streptomyces thermovulgaris.…”

Streptomyces malaysiensis sp. nov., a new streptomycete species with rugose, ornamented spores

“…Streptomycetes with rugose spores were assigned to a single taxon, cluster 32, in the numerical phenetic survey of Williams et al (1983). However, this cluster was subsequently shown to be heterogeneous on the basis of both DNA relatedness (Labeda & Lyons,199 1) and extensive numerical taxonomic (Kampfer et al,199 1) data, although the type strains of Streptomyces hygroscopicus and Streptomyces violaceusniger share an identical ribosomal AT-L30 protein sequence (Ochi, 1995).…”

Phylogenetic Analysis of Mycolic Acid-Containing Wall-Chemotype IV Actinomycetes and Allied Taxa by Partial Sequencing of Ribosomal Protein AT-L30

“…This ap-* Phone: proach is based on analysis of ribosomal AT-L30 proteins (homologous to Escherichia coli L30 protein); i.e., the electrophoretic mobilities of the AT-L30 proteins and their N-terminal amino acid sequences are determined. The efficacy of this approach has been demonstrated in studies of the phylogeny of actinomycete genera such as Streptomyces, Streptoverticillium, Streptosporangium, Actinomadura , Microbispora , Microtetraspora , and Thermoactinomyces, in addition to the genera belonging to the family Pseudonocardiaceae (31,34,36,(38)(39)(40)(41)(42). This approach has also proven to be effective for studying the phylogeny of bacteria other than actinomycetes, including the genera Bacillus, Staphylococcus, Escherichia, and Pseudomonas and allied taxa (33,35).…”