Phylogenetic analysis of the genera Streptomyces and Kitasatospora based on partial RNA polymerase {beta}-subunit gene (rpoB) sequences

This study evaluated the RNA polymerase beta-subunit gene (rpoB) as a phylogenetic marker for classifying Streptomyces and Kitasatospora species. Researchers sequenced partial rpoB genes from 67 Streptomyces strains (57 species), five Kitasatospora strains, and Micromonospora echinospora. Within-species rpoB similarity was 99.7-100%, while between-species similarity ranged from 90.2-99.3% among streptomycetes. The phylogenetic tree topology based on rpoB sequences resembled those derived from 16S rDNA analysis. Kitasatospora strains formed a distinct monophyletic clade separate from all Streptomyces species, supporting the proposal to recognize Kitasatospora as a separate genus. The study identified signature nucleotides specific to Kitasatospora that could enable development of genus-specific primers. Seven Streptomyces strains carried a codon variant (Asn442) associated with natural rifampicin resistance in other bacteria. Results showed good agreement with numerical phenetic classification. The authors conclude that rpoB analysis complements 16S rDNA and phenetic methods for polyphasic taxonomy of these actinomycetes and enables species-level differentiation of unknown isolates.

Key findings

• rpoB sequences showed 99.7-100% intraspecific similarity and 90.2-99.3% interspecific variation in Streptomyces, enabling reliable species differentiation
• Kitasatospora formed a stable monophyletic clade distinct from Streptomyces, supporting genus recognition and revival
• rpoB-based phylogenetic topology agreed with 16S rDNA analysis and numerical phenetic classification
• Signature nucleotide ACG at codon 430 is specific to Kitasatospora strains and could enable development of genus-specific molecular markers
• Seven Streptomyces strains carried Asn(AAC)442 codon variant potentially associated with natural rifampicin resistance