Complete genome sequence of the rifamycin SV-producing Amycolatopsis mediterranei U32 revealed its genetic characteristics in phylogeny and metabolism

Abstract

Amycolatopsis mediterranei is used for industry-scale production of rifamycin, which plays a vital role in antimycobacterial therapy. As the first sequenced genome of the genus Amycolatopsis, the chromosome of strain U32 comprising 10 236 715 base pairs, is one of the largest prokaryotic genomes ever sequenced so far. Unlike the linear topology found in streptomycetes, this chromosome is circular, particularly similar to that of Saccharopolyspora erythraea and Nocardia farcinica, representing their close relationship in phylogeny and taxonomy. Although the predicted 9 228 protein-coding genes in the A. mediterranei genome shared the greatest number of orthologs with those of S. erythraea, it was unexpectedly followed by Streptomyces coelicolor rather than N. farcinica, indicating the distinct metabolic characteristics evolved via adaptation to diverse ecological niches. Besides a core region analogous to that common in streptomycetes, a novel 'quasi-core' with typical core characteristics is defined within the non-core region, where 21 out of the total 26 gene clusters for secondary metabolite production are located. The rifamycin biosynthesis gene cluster located in the core encodes a cytochrome P450 enzyme essential for the conversion of rifamycin SV to B, revealed by comparing to the highly homologous cluster of the rifamycin B-producing strain S699 and further confirmed by genetic complementation. The genomic information of A. mediterranei demonstrates a metabolic network orchestrated not only for extensive utilization of various carbon sources and inorganic nitrogen compounds but also for effective funneling of metabolic intermediates into the secondary antibiotic synthesis process under the control of a seemingly complex regulatory mechanism.

Genetics and Genomics of the Genus Amycolatopsis

“…Transposable element induced genomic rearrangement was assumed to be responsible for the transfer of this quasi-core from the core into the non-core forming an integration hotspot. The ancestral core contained most of the essential genes that extended unequally on both side of the replication origin (oriC) [13]. By the time when genome sequence was released, the biosynthetic gene cluster for rifamycin was already characterized [31].…”

“…In an attempt to further analyze these strains, genomes of some of these strains have been sequenced: U32 [13], S699 [11,12], RB (unpublished), DSM 46096 [20], DSM 40773 [21] and HP-130 [5]. ND no data available…”

“…It was obtained through mutagenesis and is an important industrial strain for the production of rifamycin SV. The complete genome was sequenced and annotated in 2010 [13] and formed the basis for the phylogeny/taxonomy relationship comparative study of different genera viz. Streptomyces and Amycolatopsis of the order Actinomycetales.…”

“…While the genomes of Streptomyces spp. have been extensively studied, Amycolatopsis genomes appear to have been sequenced only recently [11][12][13]. The information on the secondary metabolome based on genomic analysis of species belonging to the genera Streptomyces, Saccharopolyspora, Salinispora, Frankia and Rhodococcus have already been reviewed [14], the analysis of recently sequenced genomes of Amycolatopsis has not been carried out.…”

RifZ (AMED_0655) Is a Pathway-Specific Regulator for Rifamycin Biosynthesis in Amycolatopsis mediterranei

“…Due to their ability to tightly bind to prokaryotic RNA polymerases, rifamycins kill bacteria by blocking the transcription elongation (4,5). In the past 2 decades, most processes in rifamycin biosynthesis have been characterized, and the nearly 90-kb rifamycin biosynthetic gene cluster (rif cluster) from several A. mediterranei strains has been sequenced (6)(7)(8)(9); it starts with AMED_0613 (rifS) and ends with AMED_0655 (the last gene in the rif cluster, thus named rifZ) in A. mediterranei U32 (Fig. 1).…”