Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens

Eva Pinatel,Adelfia Talà,Fabrizio Damiano,Antonio Pennetta,Giuseppe Egidio De Benedetto,Gianluca De Bellis,Pietro Alifano,Clelia Peano,Luisa Siculella,Matteo Calcagnile

doi:10.3390/antibiotics10080947

Abstract

While in recent years the key role of non-coding RNAs (ncRNAs) in the regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: (i) the wild-type strain; (ii) an isogenic pirA-defective mutant with central carbon metabolism imbalance, “relaxed” phenotype, and repression of antibiotic production; and (iii) a pirA-derivative strain harboring a “stringent” RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that the expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response.

Highlights

IntroductionIntroduction published maps and institutional affilIn recent years, the key role that small non-coding RNAs (ncRNAs) play in the regulation of gene expression in bacteria is becoming increasingly evident. ncRNA-mediated gene regulation involving riboswitches, trans-encoded small RNAs ( referred to as sRNAs), or cis-encoded antisense RNAs ( referred to as asRNAs) modulates many essential physiological and stress responses [1,2,3,4]
Introduction published maps and institutional affilIn recent years, the key role that small non-coding RNAs play in the regulation of gene expression in bacteria is becoming increasingly evident. ncRNA-mediated gene regulation involving riboswitches, trans-encoded small RNAs, or cis-encoded antisense RNAs modulates many essential physiological and stress responses [1,2,3,4]
The transcriptome of S. ambofaciens ATCC 23877 linear chromosome was redefined from RNAseq data of bacteria growing in YS broth at different time points (48 h, 72 h, 96 h, and 120 h) based on Rockhopper software [38,39,40] predictions

Summary

Introduction

Introduction published maps and institutional affilIn recent years, the key role that small non-coding RNAs (ncRNAs) play in the regulation of gene expression in bacteria is becoming increasingly evident. ncRNA-mediated gene regulation involving riboswitches, trans-encoded small RNAs ( referred to as sRNAs), or cis-encoded antisense RNAs ( referred to as asRNAs) modulates many essential physiological and stress responses [1,2,3,4]. The key role that small non-coding RNAs (ncRNAs) play in the regulation of gene expression in bacteria is becoming increasingly evident. Among ncRNAs, sRNAs and asRNAs mostly act on target mRNAs via base-pairing leading to positive or negative modulation of the target gene expression, providing the bacterial cell with a very simple, cheap and effective gene regulation mechanism that is alternative to more complex and expensive mechanisms based on protein-nucleic acid interactions [5,6]. SRNAs are encoded elsewhere in the genome with respect to gene coding for their target mRNAs and are usually able to act on multiple targets with a limited base pairing that often requires RNA chaperone proteins [5,6,7]. One must be very cautious before excluding the biological relevance of a particular asRNA, especially if the asRNA was preserved during evolution

Objectives

Methods

Results

Conclusion