Genome rearrangements of Streptomyces albus J1074 lead to the carotenoid gene cluster activation

Myronovskyi M, Tokovenko B, Brötz E, Rückert C, Kalinowski J, Luzhetskyy A. Genome rearrangements of Streptomyces albus J1074 lead to the carotenoid gene cluster activation. Applied microbiology and biotechnology. 2014;98(2):795-806.Streptomyces albus J1074 is a derivative of the S. albus G1 strain defective in SalG1 restriction-modification system. Genome sequencing of S. albus J1074 revealed that the size of its chromosome is 6.8 Mb with unusually short terminal arms of only 0.3 and 0.4 Mb. Here we present our attempts to evaluate the dispensability of subtelomeric regions of the S. albus J1074 chromosome. A number of large site-directed genomic deletions led to circularization of the S. albus J1074 chromosome and to the overall genome reduction by 307 kb. Two spontaneous mutants with an activated carotenoid cluster were obtained. Genome sequencing and transcriptome analysis indicated that phenotypes of these mutants resulted from the right terminal 0.42 Mb chromosomal region deletion, followed by the carotenoid cluster amplification. Our results indicate that the right terminal 0.42 Mb fragment is dispensable under laboratory conditions. In contrast, the left terminal arm of the S. albus J1074 chromosome contains essential genes and only 42 kb terminal region is proved to be dispensable. We identified overexpressed carotenoid compounds and determined fitness costs of the large genomic rearrangements

The Family Streptomycetaceae

The family Streptomycetaceae comprises the genera Streptomyces, Kitasatospora, and Streptacidiphilus that are very difficult to differentiate both with genotypic and phenotypic characteristics. A separate generic status for Kitasatospora and Streptacidiphilus is questionable. Members of the family can be characterized as non-acid-alcohol-fast actinomycetes that generate most often an extensively branched substrate mycelium that rarely fragments. At maturity, the aerial mycelium forms chains of few to many spores. A large variety of pigments is produced, responsible for the color of the substrate and aerial mycelium. The organisms are chemoorganotrophic with an oxidative type of metabolism and grow within different pH ranges. Streptomyces are notable for their complex developmental cycle and production of bioactive secondary metabolites, producing more than a third of commercially available antibiotics. Antibacterial, antifungal, antiparasitic, and immunosuppressant compounds have been identified as products of Streptomyces secondary metabolism. Streptomyces can be distinguished from other filamentous actinomycetes on the basis of morphological characteristics, in particular by vegetative mycelium, aerial mycelium, and arthrospores. The genus comprises at the time of writing more than 600 species with validated names. 16S rRNA gene sequence-based analysis for species delineation within the Streptomycetaceae is of limited value. The variations within the 16S rRNA genes—even in the variable regions—are too small to resolve problems of species differentiation and to establish a taxonomic structure within the genus. Comprehensive comparative studies including protein-coding gene sequences with higher phylogenetic resolution and genome-based studies are needed to clarify the species delineation within the Streptomycetaceae