Complex Intra-Operonic Dynamics Mediated by a Small RNA in Streptomyces coelicolor

Abstract

Streptomyces are predominantly soil-dwelling bacteria that are best known for their multicellular life cycle and their prodigious metabolic capabilities. They are also renowned for their regulatory capacity and flexibility, with each species encoding >60 sigma factors, a multitude of transcription factors, and an increasing number of small regulatory RNAs. Here, we describe our characterization of a conserved small RNA (sRNA), scr4677. In the model species Streptomyces coelicolor, this sRNA is located in the intergenic region separating SCO4677 (an anti-sigma factor-encoding gene) and SCO4676 (a putative regulatory protein-encoding gene), close to the SCO4676 translation start site in an antisense orientation. There appears to be considerable genetic interplay between these different gene products, with wild type expression of scr4677 requiring function of the anti-sigma factor SCO4677, and scr4677 in turn influencing the abundance of SCO4676-associated transcripts. The scr4677-mediated effects were independent of RNase III (a double stranded RNA-specific nuclease), with RNase III having an unexpectedly positive influence on the level of SCO4676-associated transcripts. We have shown that both SCO4676 and SCO4677 affect the production of the blue-pigmented antibiotic actinorhodin under specific growth conditions, and that this activity appears to be independent of scr4677.

sRNA scr5239 Involved in Feedback Loop Regulation of Streptomyces coelicolor Central Metabolism

“…In contrast, only a few sRNAs in streptomycetes have been experimentally characterized so that their function is known. Examples include scr4677, which is thought to impact the actinorhodin production under specific growth conditions (Hindra et al, 2014) and scr3097, which in combination with a riboswitch influences rpf A expression post-transcriptionally (St-Onge and Elliot, 2017). Furthermore, there are the antisense RNA cnc2198.1 that regulates glutamine synthase glnA (D'Alia et al, 2010) and scr5239.…”

Transcriptional response ofStreptomyces coelicolorto rapid chromosome relaxation or long-term supercoiling imbalance

“…The cluster also encompasses genes 384 whose products may contribute to DNA/RNA transactions, including: putative DNA helicase 385 (sco4685), transposase (sco4698), and a homolog of E. coli Rhs protein (rearrangement hotspot 386 protein), which putatively contains the C-terminal toxin domain and is involved in bacterial 387 intercellular competition (Koskiniemi et al, 2013). When we compared the genes in this region to 388 other Streptomyces species, we found the synteny was not strong, perhaps suggesting that some of 389 these genes may have been acquired through horizontal transfer (Hindra et al, 2014). This 390 hypothesis is supported by the notion that mobile elements tend to be sensitive to changes in 391 chromosome topology (Lodge and Berg, 1990).…”

Recent advances in understanding Streptomyces

“…There is growing evidence of complex crosstalk interactions among the even larger number of anti-sigma and anti-anti-sigma factors for this class of σ factor, and it has been suggested that the signal input to regulate these interactions may involve some of the variable, but always multiple, collection of whiJ -like gene sets present in Streptomyces genomes: the clusters include anti-sigma genes of this type and have been implicated in development and antibiotic production 51, 59 . In one such cluster, which is known to influence antibiotic production and differentiation, a small RNA antisense to the Sco4676–4677 intergenic region has been found to have complicated regulatory effects on Sco4676–4677 expression 60 .…”