Streptomyces venezuelae NRRL B-65442: genome sequence of a model strain used to study morphological differentiation in filamentous actinobacteria

Abstract

For over a decade, Streptomyces venezuelae has been used to study the molecular mechanisms that control morphological development in streptomycetes and it is now a well-established model strain. Its rapid growth and ability to sporulate in a near-synchronised manner in liquid culture, unusual among streptomycetes, greatly facilitates the application of modern molecular techniques such as ChIP-seq and RNA-seq, as well as fluorescence time-lapse imaging of the complete Streptomyces life cycle. Here we describe a high-quality genome sequence of our isolate of the strain (NRRL B-65442) consisting of an 8.2 Mb chromosome and a 158 kb plasmid, pSVJI1, which had not been reported previously. Surprisingly, while NRRL B-65442 yields green spores on MYM agar, the ATCC type strain 10712 (from which NRRL B-65442 was derived) produces grey spores. While comparison of the genome sequences of the two isolates revealed almost total identity, it did reveal a single nucleotide substitution in a gene, vnz_33525, likely to be involved in spore pigment biosynthesis. Replacement of the vnz_33525 allele of ATCC 10712 with that of NRRL B-65442 resulted in green spores, explaining the discrepancy in spore pigmentation. We also applied CRISPR-Cas9 to delete the essential parB of pSVJI1 to cure the plasmid from the strain without obvious phenotypic consequences.

Genome-wide identification of the LexA-mediated DNA damage response inStreptomyces venezuelae

“…In this work we confirm the existence of the SOS response in Streptomyces venezuelae , one of the key model organisms for this genus (7, 10), and demonstrate that RecA and LexA are important for survival during DNA damaging growth conditions. By combining global transcriptomic profiling and ChIP-seq analysis, we identify the LexA regulon and the core set of SOS genes involved in DNA repair.…”

“…In this way, we were able to identify 175 LexA binding sites that were associated with differentially expressed transcriptional units upon treatment with MMC (adjusted p- value p <0.05, |log2-fold change|>1) (Figure 3C and Supplementary Table 3). Of these, 97 transcriptional units were upregulated, including one putative LexA-target of unknown function located on the S. venezuelae plasmid pSVIJ1 and 78 transcriptional units were downregulated following MMC treatment (10). Although LexA generally functions as transcriptional repressor (13–15), the MMC-induced downregulation of genes associated with a LexA binding site is indicative of a direct or indirect positive regulation of these genes by LexA.…”

Genome-Wide Identification of the LexA-Mediated DNA Damage Response in Streptomyces venezuelae

“…In this work, we confirm the existence of the SOS response in Streptomyces venezuelae , one of the key model organisms for this genus ( 7 , 10 ), and demonstrate that RecA and LexA are important for survival under DNA-damaging growth conditions. By combining global transcriptomic profiling and chromatin immunoprecipitation sequencing (ChIP-seq) analysis, we identified the LexA regulon and the core set of SOS genes involved in DNA repair.…”

Bilateral symmetry of linear streptomycete chromosomes

“…A total of 20.14% of parS sites lie to the left of oriC and 79.86% to the right (Table S4), meaning that during DNA replication and partitioning it is likely that the right replichore carries a greater abundance of ParB/ parS nucleoprotein complexes with potential implications for chromosome segregation and connection of the chromosome to the hyphal tip. We did not include Streptomyces venezuelae in our analysis as the telomeres of its chromosome have not yet been established [ 61 ]; although, the possession of tap and tpg suggests that they resemble the archetypal telomeres of S. coelicolor M145. However, ChIP-seq analysis confirmed the formation of large nucleoprotein ParB complexes located at 16 parS sites in S. venezuelae 10712 [ 62 ] and, recently, the role of ParB in promoting chromosome inter-arm contact was reported [ 63 ].…”