library_construction_protocol: For total RNA extraction (transcriptome analysis), bacterial cultures were treated with RNA protect bacteria reagent ( Qiagen #76506) and incubated for 10 min at room temperature. Cultures were centrifuged and the pellets were stored at -80°C. Pellets from 15 ml of bacterial cultures were resuspended in 200 µl of lysozyme dissolved in TE buffer at a concentration of 0.015 g per ml and incubated at room temperature for 15 min. 600 µl of RNeasy Lysis Buffer (RLT buffer, Qiagen #79216) containing 10 µl / ml β-mercaptoethanol was added and the mixture mixed by vortex mixer then transferred to a 2 ml microfuge tube containing 5 mm stainless steel beads (Qiagen #69989) and placed in a Tissuelyser LT (Qiagen #85600) for efficient mechanical cell disruption / homogenisation for 2 min at 30 rpm. The suspension was then centrifuged at 16,627 RCF for 2 min, the supernatant was recovered and its volume estimated. One volume of acid pH 4.5 phenol:chloroform:isoamyl alcohol (125:24:1, Fisher #AM9720) was added and the mixture mixed by vortex mixer for 30 seconds, then centrifuged at 4°C for 5 min at 16,627 RCF. The upper phase containing the nucleic acids was removed and retained leaving behind the proteins in the interface, and the phenol/chloroform extraction repeated twice more. Then one volume of chloroform was added, the mixture mixed by vortex mixer then centrifuged at 4°C for 2 min at 16,627 RCF, and the upper phase was again transferred to a fresh RNase-free microfuge tube. From this point onward the standard manufacturer's instructions were followed for the miRNAeasy RNA extraction kit (Qiagen #217004). The total RNA was eluted in 30 µl of nuclease free water and stored at -80°C. Genomic DNA was removed using the Turbo DNA free kit (Invitrogen AM1907). For the Riboseq protocol the protocol followed was based on that described in Jeong et al. Nature Communications 2016. Briefly, the mycelium was ground in lysis buffer and stored at -80°C as described in the treatment protocol. The ground mycelium was defrosted in ice and centrifuged at 20,000 RCF at 4°C. The supernatant was recovered and the RNA concentration was determined by NanoDrop spectrophotometer or Qubit fluorometer. 50 µg of cell lysate was incubated with 400 U of MNase for 2 h at 37°C. The digestion was stopped by adding 2.5 µl of EGTA 0.5M. The monosomes were isolated through Sephacryl S400 Microspin columns (GE cat 27-5140-01) in Recovery buffer (50mM Tris-HCl (pH8); 1% Triton X100; 50mM MgCl2; 25mM EGTA; 250mM NaCl) and the purified ribosomes were stored at -80°C. The ribosome protected RNA was isolated by column purification using the miRNeasy kit (Qiagen #217004) according to manufacturer's protocol, and RNA between 15 and 45 nt was size selected by electrophoresis in 15% acrylamide gel in TBE. RNA was extracted from the gel in 500 µl of gel extraction buffer (0.25% SDS, 0.3M NaOAc pH 5.5, 1 mM EDTA) and precipitated by adding 16 µl of 5M NaCl, 45 µl 3M NaOAc, 4 µl glycoblue (15 mg / ml, Fisher #10391565) and 1.2 ml absolute ethanol and incubating at -80°C for 1 h. The RNA was centrifuged for 30 min at 20,000 RCF at 4°C. The RNA pellet was washed twice with ice cold 70% ethanol and air dried before resuspension in 9 - 11 µl of RNAse free water. The RNA was subsequently rRNA depleted using NEBNext Core Reagent Set (NEB #E7865) with custom DNA probes designed to cover Streptomyces specific rRNA and tRNA sequences. The RNA was subsequently treated with Polynucleotide Kinase for 1h at 37°C and the RNA was purified from the enzyme and the buffer using miRNeasy mini columns. The RNA was eluted in 30 µl of RNase free water, dehydrated and resuspended in 6 µl of nuclease-free water and used for library construction using the NEB NEBNext Small RNA Library Prep Set for Illumina (cat E7330S) following the manufacturer instructions. Total RNA were depleted of rRNA by using the NEBNext Core Reagent Set (NEB #E7865) with custom DNA probes designed to cover Streptomyces specific rRNA and tRNA sequences and library constructions were carried out using the NEB directional RNAseq kit (NEB #E7760) and NEB NEBNext Small RNA Library Prep Set for Illumina (NEB #E7330S) following the manufacturer instructions. directional RNA-seq for total RNA and miRNAseq library prep for the ribosome protected RNAs