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. 2022 Oct 26;7(5):e0019922.
doi: 10.1128/msystems.00199-22. Epub 2022 Sep 12.

Phosphoproteome Dynamics of Streptomyces rimosus during Submerged Growth and Antibiotic Production

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Phosphoproteome Dynamics of Streptomyces rimosus during Submerged Growth and Antibiotic Production

Ela Šarić et al. mSystems. .

Abstract

Streptomyces rimosus is an industrial streptomycete, best known as a producer of oxytetracycline, one of the most widely used antibiotics. Despite the significant contribution of Streptomyces species to the pharmaceutical industry, most omics analyses have only been conducted on the model organism Streptomyces coelicolor. In recent years, protein phosphorylation on serine, threonine, and tyrosine (Ser, Thr, and Tyr, respectively) has been shown to play a crucial role in the regulation of numerous cellular processes, including metabolic changes leading to antibiotic production and morphological changes. In this study, we performed a comprehensive quantitative (phospho)proteomic analysis during the growth of S. rimosus under conditions of oxytetracycline production and pellet fragmentation. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis combined with phosphopeptide enrichment detected a total of 3,725 proteins, corresponding to 45.6% of the proteome and 417 phosphorylation sites from 230 phosphoproteins. Significant changes in abundance during three distinct growth phases were determined for 494 proteins and 98 phosphorylation sites. Functional analysis revealed changes in phosphorylation events of proteins involved in important cellular processes, including regulatory mechanisms, primary and secondary metabolism, cell division, and stress response. About 80% of the phosphoproteins detected during submerged growth of S. rimosus have not yet been reported in streptomycetes, and 55 phosphoproteins were not reported in any prokaryote studied so far. This enabled the creation of a unique resource that provides novel insights into the dynamics of (phospho)proteins and reveals many potential regulatory events during antibiotic production in liquid culture of an industrially important bacterium. IMPORTANCE Streptomyces rimosus is best known as a primary source of oxytetracycline (OTC). The significant global market value of OTC highlights the need for a better understanding of the regulatory mechanisms that lead to production of this antibiotic. Our study provides, for the first time, a detailed insight into the dynamics of (phospho)proteomic profiles during growth and antibiotic production in liquid culture of S. rimosus. Significant changes in protein synthesis and phosphorylation have been revealed for a number of important cellular proteins during the growth stages that coincide with OTC production and morphological changes of this industrially important bacterium. Most of these proteins have not been detected in previous studies. Therefore, our results significantly expand the insight into phosphorylation events associated with important cellular processes and antibiotic production; they also greatly increase the phosphoproteome of streptomycetes and contribute with newly discovered phosphoproteins to the database of prokaryotic phosphoproteomes. This can consequently lead to the design of novel research directions in elucidation of the complex regulatory network in Streptomyces.

Keywords: Streptomyces rimosus; oxytetracycline; oxytetracycline production; pellet fragmentation; peptide dimethylation labeling; phosphoproteome; proteome.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIG 1
FIG 1
Growth and mycelial fragmentation of S. rimosus G7 in submerged culture, from early exponential to late stationary phase. (A) Growth curve based on dry weight accumulation (sampling time of biomass is indicated by arrows; error bars indicate standard deviations). This figure also shows increase in OTC (red) and decrease in glucose (green). (B) Mycelial fragmentation at various time points was followed by confocal fluorescence microscopy after SYTO 9 and PI staining (green and red hyphae represent live and dead cells, respectively, while arrows point to the fragments embedded in the extracellular matrix).
FIG 2
FIG 2
Distribution of (phospho)proteins into functional subcategories. Percentages of various subcategories obtained for S. rimosus proteome (3,448 proteins) and phosphoproteome (206 phosphoproteins) are shown by solid (proteome) and dashed bars (phosphoproteome). Note that only proteins assigned to one functional subcategory were used for this analysis (i.e., 93% of the proteome and, i.e., 90% of the phosphoproteome).
FIG 3
FIG 3
Distribution of differentially expressed proteins during S. rimosus growth. The y axis (−log10 P value) represents the level of significance of each protein, while the x axis (log2 fold change) represents the difference in protein ratios between the two different growth phases derived from two replicates (A, SII/SI; B, SIII/SII; C, SIII/SII). Significantly upregulated proteins in a given ratio are represented by red circles, and downregulated proteins are represented by blue circles. Proteins described in detail below are marker with corresponding name (if possible) or with the number of SRIM locus tag.
FIG 4
FIG 4
Clusters of proteins with similar temporal abundance profiles and their functional enrichment analysis. (A) Proteins with significant changes in their abundances determined by t test (P < 0.05) during the S. rimosus growth (SI, SII, and SIII) are grouped into five clusters according to their Z-scored normalized log2-transformed proteins ratios. (B) Functional annotation terms from KEGG, eggNOG, and EC are enriched in different clusters using Fisher’s exact test (see Table S1 in the supplemental material).
FIG 5
FIG 5
Distribution and dynamics of proteins with upregulated phosphorylation sites during S. rimosus growth. (A) Number of all and unique upregulated phosphoproteins/phosphorylation sites by growth stages (dark blue, all proteins; light blue, unique proteins; dark green, all phosphorylation sites; light green, unique phosphorylation sites) (B and C) Venn diagrams represent phosphoproteins (B) and phosphorylation sites (C) shared between growth phases. (D) Dynamics of proteins with upregulated phosphorylated sites throughout growth phases (the y axis shows log2 transformed ratios of phosphorylation sites in each growth stage shown on the x axis; phosphoproteins marked in bold are reported here for the first time, streptomycetes are in gray, and any other prokaryote are in black).
FIG 6
FIG 6
Phylogenetic tree of STPK sequences from S. rimosus G7 and S. coelicolor M145. Experimentally detected S. rimosus kinases are shown in bold. Phosphorylated kinases were marked by a red P, and information regarding growth phase (SI, SII, or SIII) was added if available. Phosphorylated S. coelicolor kinases found by the Manteca group (16, 17) were marked similarly using MI (12 h or 16 h), MII (24 h or 30 h), and MIII (65 h or 72 h) for growth stages. Kinases found by Parker et al. (15) were marked with asterisks. M. tuberculosis kinases (PDB IDs 6I2P and 3OUV) were used as outgroups. aLRT values are shown for main branches.
FIG 7
FIG 7
S. rimosus phosphorylated orthologs shared with other Gram-positive and Gram-negative bacteria and archaea.

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