In organisms other than higher plants, family 19 chitinase was first discovered in Streptomyces griseus HUT6037, and later, the general occurrence of this enzyme in Streptomyces species was demonstrated. In the present study, the distribution of family 19 chitinases in the class Actinobacteria and the phylogenetic relationship of Actinobacteria family 19 chitinases with family 19 chitinases of other organisms were investigated. Forty-nine strains were chosen to cover almost all the suborders of the class Actinobacteria, and chitinase production was examined. Of the 49 strains, 22 formed cleared zones on agar plates containing colloidal chitin and thus appeared to produce chitinases. These 22 chitinase-positive strains were subjected to Southern hybridization analysis by using a labeled DNA fragment corresponding to the catalytic domain of ChiC, and the presence of genes similar to chiC of S. griseus HUT6037 in at least 13 strains was suggested by the results. PCR amplification and sequencing of the DNA fragments corresponding to the major part of the catalytic domains of the family 19 chitinase genes confirmed the presence of family 19 chitinase genes in these 13 strains. The strains possessing family 19 chitinase genes belong to 6 of the 10 suborders in the order Actinomycetales, which account for the greatest part of the Actinobacteria: Phylogenetic analysis suggested that there is a close evolutionary relationship between family 19 chitinases found in Actinobacteria and plant class IV chitinases. The general occurrence of family 19 chitinase genes in Streptomycineae and the high sequence similarity among the genes found in Actinobacteria suggest that the family 19 chitinase gene was first acquired by an ancestor of the Streptomycineae and spread among the Actinobacteria through horizontal gene transfer.

The family Streptosporangiaceae (suborder Streptosporangineae) comprises 13 genera and 100 species with validly published names. In a recent study, gyrB gene sequences were obtained for members of the family Streptosporangiaceae and the GyrB amino acid sequences were analysed for molecular signatures. In this study, recA gene sequences (895nt) were determined for the type strains of members of the family Streptosporangiaceae. The sequences used represent 81% of the full-length recA gene of Streptosporangium roseum DSM 43021(T). The recA gene sequences were used for phylogenetic analyses and the trees were compared to the corresponding 16S-rRNA and gyrB gene trees. RecA amino acid alignments (298 amino acids) were generated and inspected for unique amino acid signatures to distinguish the genera in the family from each other. As was observed for the gyrB gene trees, the recA gene trees generally supported the division of the members of the family Streptosporangiaceae into 13 genera. The genus Nonomuraea was not monophyletic in any of the recA gene trees, while the genera Planomonospora and Streptosporangium were not monophyletic in the maximum likelihood and maximum parsimony trees. The gyrB-recA concatenated-gene tree was more robust than the recA gene tree, with 63 nodes in the gyrB-recA tree having bootstrap values ?95%. The only insertions in the recA gene sequences were inteins identified in the type strains of Acrocarpospora phusangensis, Acrocarpospora pleiomorpha and Microbispora mesophila. Examination of the RecA sequence alignments for genus-specific amino acid sequences showed that the genera Herbidospora, Planobispora, Planomonospora and Streptosporangium contain unique amino acid sequences that distinguish these genera from all other genera in the family Streptosporangiaceae. The results of this investigation extend the results of the GyrB study and will be useful in future taxonomic studies in the family Streptosporangiaceae by providing additional genus-specific molecular signatures.

Higher order taxonomic assignments (family level and above) in the phylum Actinobacteria are currently based only on 16S-rRNA gene sequence analyses. Additional molecular markers need to be identified to increase the number of reference points for defining actinobacterial families and other higher taxa. Furthermore, since most novel actinobacterial taxa are defined at the level of species and genera, it is necessary to define molecular signatures at the genus level to enhance the robustness of genus descriptions. The current use of chemotaxonomic markers to define genera could be improved by the identification of genus-specific molecular signatures. In this study, GyrB amino acid sequences for members of the family Streptosporangiaceae were analysed for molecular signatures. Phylogenetic analyses showed that the gyrB gene tree supported the composition of the currently recognised genera in this family. The catalytically important amino acids were identified in the GyrB sequences, as were the GHKL superfamily motifs. Examination of GyrB protein sequence alignments revealed that there are genus-specific sequences for most of the multi-species genera and genus-defining amino acid insertions for the genera Herbidospora and Microbispora. Furthermore, there are GyrB signature amino acids which distinguish the family Streptosporangiaceae from the family Nocardiopsaceae.