Journal
JOURNAL OF PROTEOMICS
Volume 269, Issue -, Pages -Publisher
ELSEVIER
DOI: 10.1016/j.jprot.2022.104719
Keywords
Streptomyces; Escherichia; Phosphoproteomics; Zirconium(IV)-IMAC; LC-MS/MS
Categories
Funding
- EU Marie Sk ? [RTI2018-093978-B-I00]
- Ministerio de Ciencia, Innovacion Universidades/Agencia Estatal de Investigacion/Fondo Europeo de Desarrollo Regional [RTI2018-093978-B-I00, PID2021-122911OB-I00]
- Consejeria de Empleo, Industria y Turismo del Principado de Asturias [SV-PA-21-AYUD/2021/51399]
- Universidad de Oviedo
- Severo Ochoa predoctoral grant [PA-20-PF-BP19-006]
- Consejeria de Ciencia, Innovacion y Universidad del Principado de Asturias
- FEMS (Federation of European Microbiological Societies) Research and Training (RTG)
- EU [722171]
- VILLUM Foundation
- PRO-MS, Danish National Mass Spectrometry Platform for Functional Proteomics
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This article describes the expansion of the Streptomyces phosphoproteome using optimized immobilized zirconium (IV) affinity chromatography and mass spectrometry, resulting in the identification of many novel phosphoproteins. The study enhances our understanding of Streptomyces development and secondary metabolism regulation.
Streptomycetes are multicellular gram-positive bacteria that produce many bioactive compounds, including antibiotics, antitumorals and immunosuppressors. The Streptomyces phosphoproteome remains largely uncharted even though protein phosphorylation at Ser/Thr/Tyr is known to modulate morphological differentiation and specialized metabolic processes. We here expand the S. coelicolor phosphoproteome by optimised immobilized zirconium (IV) affinity chromatography and mass spectrometry to identify phosphoproteins at the vegetative and sporulating stages. We mapped 361 phosphorylation sites (41% pSer, 56.2% pThr, 2.8% pTyr) and discovered four novel Thr phosphorylation motifs ( Kxxxx(pT)xxxxK , DxE(pT) , D(pT) and Exxxxx (pT) ) in 351 phosphopeptides derived from 187 phosphoproteins. We identified 154 novel phosphoproteins, thereby almost doubling the number of experimentally verified Streptomyces phosphoproteins. Novel phos-phoproteins included cell division proteins (FtsK, CrgA) and specialized metabolism regulators (ArgR, AfsR, CutR and HrcA) that were differentially phosphorylated in the vegetative and in the antibiotic producing sporulating stages. Phosphoproteins involved in primary metabolism included 27 novel ribosomal proteins that were phosphorylated during the vegetative stage. Phosphorylation of these proteins likely participate in the intricate and incompletely understood regulation of Streptomyces development and secondary metabolism. We conclude that Zr(IV)-IMAC is an efficient and sensitive method to study protein phosphorylation and regulation in bacteria and enhance our understanding of bacterial signalling. Significance: Two thirds of the secondary metabolites used in clinic, especially antibiotics, were discovered in Streptomyces strains. Antibiotic resistance became one of the major challenges in clinic, and new antibiotics are urgently required in clinic. Next-generation sequencing analyses revealed that streptomycetes harbour many cryptic secondary metabolite pathways, i.e. pathways not expressed in the laboratory. Secondary metabolism is tightly connected with hypha differentiation and sporulation, and understanding Streptomyces differentiation is one of the main challenges in industrial microbiology, in order to activate the expression of cryptic pathways in the laboratory. Protein phosphorylation at Ser/Thr/Tyr modulates development and secondary metabolism, but the Streptomyces phosphoproteome is still largely uncharted. Previous S. coelicolor phosphoproteomic studies used TiO2 affinity enrichment and LC-MS/MS identifying a total of 184 Streptomyces phosphoproteins. Here, we used by first time zirconium (IV) affinity chromatography and mass spectrometry, identifying 186 S. coelicolor phosphoproteins. Most of these phosphoproteins (154) were not identified in previous phosphoproteomic studies using TiO2 af-finity enrichment. Thereby we almost doubling the number of experimentally verified Streptomyces
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