Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions

Abstract

Little is known about the role of global phosphorylation events in the control of prokaryote metabolism. By performing a detailed analysis of all protein phosphorylation events previously reported in Escherichia coli, dynamic changes in protein phosphorylation were elucidated under three different culture conditions. Using scheduled reaction monitoring, the phosphorylation ratios of 82 peptides corresponding to 71 proteins were quantified to establish whether serine (S), threonine (T) and tyrosine (Y) phosphorylation events displayed a dynamic profile under changing culture conditions. The ratio of phosphorylation for 23 enzymes from central carbon metabolism was found to be dynamic. The data presented contributes to our understanding of the global role of phosphorylation in bacterial metabolism and highlight that phosphorylation is an important, yet poorly understood, regulatory mechanism of metabolism control in bacteria. Biological significanceThe findings in this manuscript provide novel scientific knowledge about protein phosphorylation in dynamic regulation of the central carbon metabolism of E. coli. Evidence has accumulated confirming that phosphorylation is prevalently present in bacteria and has important regulatory roles of control of the central carbon metabolism. This investigation goes beyond data collections and shows that protein phosphorylation is quantitatively significant and varies under changing culture conditions.

Identification and Biochemical Characterization of a Novel Protein Phosphatase 2C-Like Ser/Thr Phosphatase in Escherichia coli

“…In prokaryotes, signaling phosphorylation has been thought to occur largely on histidine and aspartate residues, mediated by histidine kinases of two-component systems (2). However, mass spectrometry-based phosphoproteomic analyses over the past decade have identified numerous Ser/Thr/Tyrphosphorylated proteins in many bacteria (3-5), including Escherichia coli (6)(7)(8)(9). Some of these phosphoproteins and the specific phosphosites are conserved in divergent species (7), suggesting that this regulation may be physiologically relevant.…”

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

“…Hundreds of potentially functional PTM sites have been identified in bacteria (10). While some may be spurious and low-stoichiometry chemical modifications (11), many are high stoichiometry and likely to regulate bacterial metabolism (12)(13)(14)(15)(16). However, it remains difficult to unravel the physiological roles of the PTMs in a high-throughput manner.…”

Identification and biochemical characterization of a novel PP2C-like Ser/Thr phosphatase inE. coli

“…These so-called eukaryotic-like Ser/Thr kinases and their partner PP2C-like Ser/Thr phosphatases have extensive structural and biochemical similarity with their eukaryotic counterparts (5). In E. coli , extensive Ser/Thr phosphorylation has been observed, with several studies reporting >75 proteins (6–9). However, the kinases and phosphatases responsible for making or removing these modifications are not known.…”

“…In prokaryotes, signaling phosphorylation has been thought to occur largely on histidine and aspartate residues mediated by histidine kinases of two-component systems (2). However, mass spectrometry based-phosphoproteomic analyses over past decade have identified numerous Ser/Thr/Tyr phosphorylated proteins in many bacteria (3–5), including Escherichia coli (6–9). Some of these phosphoproteins and the specific phosphosites are conserved in divergent species (7) suggesting that this regulation may be physiologically relevant.…”