A possible mechanism for lincomycin induction of secondary metabolism in Streptomyces coelicolor A3(2)

Abstract

Lincomycin forms cross-links within the peptidyl transferase loop region of the 23S ribosomal RNA (rRNA) of the 50S subunit of the bacterial ribosome, which is the site of peptide bond formation, thereby inhibiting protein synthesis. We have previously reported that lincomycin at concentrations below the minimum inhibitory concentration potentiates the production of secondary metabolites in actinomycete strains, suggesting that activation of these strains by utilizing the dose-dependent response of lincomycin could be used to effectively induce the production of cryptic secondary metabolites. Here, we aimed to elucidate the fundamental mechanisms underlying lincomycin induction of secondary metabolism in actinomycetes. In the present study, the dose-dependent response of lincomycin on gene expression of the model actinomycete Streptomyces coelicolor A3(2) and possible relationships to secondary metabolism were investigated. RNA sequencing analysis indicated that lincomycin produced enormous changes in gene expression profiles. Moreover, reverse transcription PCR and/or comparative proteome analysis revealed that in S. coelicolor A3(2), lincomycin, which was used at concentrations for markedly increased blue-pigmented antibiotic actinorhodin production, rapidly enhanced expression of the gene encoding the lincomycin-efflux ABC transporter, the 23S rRNA methyltransferase, and the ribosome-splitting factor to boost the intrinsic lincomycin resistance mechanisms and to reconstruct the probably stalled 70S ribosomes with lincomycin; and in contrast temporarily but dramatically reduced mRNA levels of housekeeping genes, such as those encoding FF ATP synthase, RNA polymerase, ribosomal proteins, and transcription and translation factors, with an increase in intracellular NTPs. A possible mechanism for lincomycin induction of secondary metabolism in S. coelicolor A3(2) is discussed on the basis of these results.

The metabolic switch can be activated in a recombinant strain of Streptomyces lividans by a low oxygen transfer rate in shake flasks

“…RED production started when oxygen was limited in NF; in contrast, there was no significant oxygen limitation in BF and CF, so RED production was detected at a much later time point and at lower concentrations. In addition to the previously published data regarding the metabolic switch triggered by phosphate [ 2 , 5 , 18 , 19 ] or glucose depletion [ 53 ], we provide evidence in this study that oxygen limitation can also influence the metabolic switch from primary to secondary metabolism in Streptomyces sp.…”

“…The secondary metabolites formed depend on the primary metabolites, such as glucose-6-phosphate, glyceraldehyde-3-phosphate, acetyl-CoA, α-ketoglutarate, and oxaloacetate, that serve as biosynthesis precursors and are generated during central carbon metabolism [ 17 ]. Furthermore, this metabolic switch has been associated with depletion of carbon, nitrogen, and phosphate sources in conventional shake flask cultures of S. coelicolor [ 2 , 5 , 18 , 19 ]. During the metabolic switch, genes related to ribosomal proteins, protein biosynthesis, and nitrogen metabolism are downregulated, while those related to antibiotic biosynthesis (actinorhodin [ACT] and undecylprodigiosins [REDs]), as well as those related to the biosynthesis of several amino acids, are upregulated [ 3 ].…”

Beyond Self-Resistance: ABCF ATPase LmrC Is a Signal-Transducing Component of an Antibiotic-Driven Signaling Cascade Accelerating the Onset of Lincomycin Biosynthesis

“…The induction of specialized metabolism by antibiotics targeting the 50S subunit of the ribosome has been described previously ( 6 , 7 , 52 ), but this is the first time the mechanism of antibiotic sensing and signal transduction has been revealed. The detection of antibiotics by a ribosome via a 5′UTR attenuator upstream of the ABCF-encoding gene differs fundamentally from known antibiotic signaling cascades, in which antibiotic or biosynthetic intermediates are detected regardless of their mode of action, typically by direct binding to a transcription factor or its cognate receptor ( 53 ).…”

Regulation of Antibiotic Production by Signaling Molecules in Streptomyces

“…For example, lincomycin at a sub-inhibitory concentration resulted in an elevated expression of the CSR activator gene actII-ORF4, and therefore increased ACT overproduction in S. coelicolor (Imai et al, 2015). A recent study suggests that lincomycin produced profound changes in gene expression profiles of S. coelicolor (Ishizuka et al, 2018). In another example, a sub-inhibitory concentration of JdB (the angucycline from S. venezuelae) induced early RED production and premature differentiation (formation of sporulating aerial mycelium) in S. coelicolor.…”