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Schastnaya E, Raguz Nakic Z, Gruber CH, Doubleday PF, Krishnan A, Johns NI, Park J, Wang HH, Sauer U. Extensive regulation of enzyme activity by phosphorylation in Escherichia coli. Nat Commun 2021; 12:5650. [PMID: 34561442 PMCID: PMC8463566 DOI: 10.1038/s41467-021-25988-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/03/2021] [Indexed: 02/08/2023] Open
Abstract
Protein serine/threonine/tyrosine (S/T/Y) phosphorylation is an essential and frequent post-translational modification in eukaryotes, but historically has been considered less prevalent in bacteria because fewer proteins were found to be phosphorylated and most proteins were modified to a lower degree. Recent proteomics studies greatly expanded the phosphoproteome of Escherichia coli to more than 2000 phosphorylation sites (phosphosites), yet mechanisms of action were proposed for only six phosphosites and fitness effects were described for 38 phosphosites upon perturbation. By systematically characterizing functional relevance of S/T/Y phosphorylation in E. coli metabolism, we found 44 of the 52 mutated phosphosites to be functional based on growth phenotypes and intracellular metabolome profiles. By effectively doubling the number of known functional phosphosites, we provide evidence that protein phosphorylation is a major regulation process in bacterial metabolism. Combining in vitro and in vivo experiments, we demonstrate how single phosphosites modulate enzymatic activity and regulate metabolic fluxes in glycolysis, methylglyoxal bypass, acetate metabolism and the split between pentose phosphate and Entner-Doudoroff pathways through mechanisms that include shielding the substrate binding site, limiting structural dynamics, and disrupting interactions relevant for activity in vivo.
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Affiliation(s)
- Evgeniya Schastnaya
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Zrinka Raguz Nakic
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
- Institute of Chemistry and Biotechnology, ZHAW Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Christoph H Gruber
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | | | - Aarti Krishnan
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Nathan I Johns
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Jimin Park
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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Rajagopalan K, Dworkin J. Escherichia coli YegI is a novel Ser/Thr kinase lacking conserved motifs that localizes to the inner membrane. FEBS Lett 2020; 594:3530-3541. [PMID: 32888201 DOI: 10.1002/1873-3468.13920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
Abstract
In bacteria, signaling phosphorylation is thought to occur primarily on His and Asp residues. However, phosphoproteomic surveys in phylogenetically diverse bacteria over the past decade have identified numerous proteins that are phosphorylated on Ser and/or Thr residues. Consistently, genes encoding Ser/Thr kinases are present in many bacterial genomes such as in the Escherichia coli genome, which encodes at least three Ser/Thr kinases. Here, we identify a previously uncharacterized ORF, yegI, and demonstrate that it encodes a novel Ser/Thr kinase. YegI lacks several conserved motifs including residues important for Mg2+ binding seen in other bacterial Ser/Thr kinases, suggesting that the consensus may be too stringent. We further find that YegI is a two-pass membrane protein with both N- and C termini located intracellularly.
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Affiliation(s)
- Krithika Rajagopalan
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jonathan Dworkin
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
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Yu D, Wang Z, Cupp-Sutton KA, Liu X, Wu S. Deep Intact Proteoform Characterization in Human Cell Lysate Using High-pH and Low-pH Reversed-Phase Liquid Chromatography. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2502-2513. [PMID: 31755044 PMCID: PMC7539543 DOI: 10.1007/s13361-019-02315-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 08/10/2019] [Accepted: 08/10/2019] [Indexed: 05/26/2023]
Abstract
Post-translational modifications (PTMs) play critical roles in biological processes and have significant effects on the structures and dynamics of proteins. Top-down proteomics methods were developed for and applied to the study of intact proteins and their PTMs in human samples. However, the large dynamic range and complexity of human samples makes the study of human proteins challenging. To address these challenges, we developed a 2D pH RP/RPLC-MS/MS technique that fuses high-resolution separation and intact protein characterization to study the human proteins in HeLa cell lysate. Our results provide a deep coverage of soluble proteins in human cancer cells. Compared to 225 proteoforms from 124 proteins identified when 1D separation was used, 2778 proteoforms from 628 proteins were detected and characterized using our 2D separation method. Many proteoforms with critically functional PTMs including phosphorylation were characterized. Additionally, we present the first detection of intact human GcvH proteoforms with rare modifications such as octanoylation and lipoylation. Overall, the increase in the number of proteoforms identified using 2DLC separation is largely due to the reduction in sample complexity through improved separation resolution, which enables the detection of low-abundance PTM-modified proteoforms. We demonstrate here that 2D pH RP/RPLC is an effective technique to analyze complex protein samples using top-down proteomics.
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Affiliation(s)
- Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019-5251, USA
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019-5251, USA
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019-5251, USA
| | - Xiaowen Liu
- School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019-5251, USA.
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Identification and Biochemical Characterization of a Novel Protein Phosphatase 2C-Like Ser/Thr Phosphatase in Escherichia coli. J Bacteriol 2018; 200:JB.00225-18. [PMID: 29967116 DOI: 10.1128/jb.00225-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/21/2018] [Indexed: 02/02/2023] Open
Abstract
In bacteria, signaling phosphorylation is thought to occur primarily on His and Asp residues. However, phosphoproteomic surveys over the past decade in phylogenetically diverse bacteria have identified numerous proteins that are phosphorylated on Ser and/or Thr residues. Consistently, genes encoding Ser/Thr kinases are present in many bacterial genomes, such as that of Escherichia coli, which encodes at least three Ser/Thr kinases. Since Ser/Thr phosphorylation is a stable modification, a dedicated phosphatase is necessary to allow reversible regulation. Ser/Thr phosphatases belonging to several conserved families are found in bacteria. One family of particular interest are Ser/Thr phosphatases, which have extensive sequence and structural homology to eukaryotic Ser/Thr protein phosphatase 2C (PP2C) phosphatases. These proteins, called eukaryote-like Ser/Thr phosphatases (eSTPs), have been identified in a number of bacteria but not in E. coli Here, we describe a previously unknown eSTP encoded by an E. coli open reading frame (ORF), yegK, and characterize its biochemical properties, including its kinetics, substrate specificity, and sensitivity to known phosphatase inhibitors. We investigate differences in the activity of this protein in closely related E. coli strains. Finally, we demonstrate that this eSTP acts to dephosphorylate a novel Ser/Thr kinase that is encoded in the same operon.IMPORTANCE Regulatory protein phosphorylation is a conserved mechanism of signaling in all biological systems. Recent phosphoproteomic analyses of phylogenetically diverse bacteria, including the model Gram-negative bacterium Escherichia coli, demonstrate that many proteins are phosphorylated on serine or threonine residues. In contrast to phosphorylation on histidine or aspartate residues, phosphorylation of serine and threonine residues is stable and requires the action of a partner Ser/Thr phosphatase to remove the modification. Although a number of Ser/Thr kinases have been reported in E. coli, no partner Ser/Thr phosphatases have been identified. Here, we biochemically characterize a novel Ser/Thr phosphatase that acts to dephosphorylate a Ser/Thr kinase that is encoded in the same operon.
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Herrera Y, Contreras S, Hernández M, Álvarez L, Mora Y, Encarnación-Guevara S. Displacers improve the selectivity of phosphopeptide enrichment by metal oxide affinity chromatography. BOLETIN MEDICO DEL HOSPITAL INFANTIL DE MEXICO 2018; 74:200-207. [PMID: 29382487 DOI: 10.1016/j.bmhimx.2017.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 03/17/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND A key process in cell regulation is protein phosphorylation, which is catalyzed by protein kinases and phosphatases. However, phosphoproteomics studies are difficult because of the complexity of protein phosphorylation and the number of phosphorylation sites. METHODS We describe an efficient approach analyzing phosphopeptides in single, separated protein by two-dimensional gel electrophoresis. In this method, a titanium oxide (TiO2)-packed NuTip is used as a phosphopeptide trap, together with displacers as lactic acid in the loading buffer to increase the efficiency of the interaction between TiO2 and phosphorylated peptides. RESULTS The results were obtained from the comparison of mass spectra of proteolytic peptides of proteins with a matrix-assisted laser desorption-ionization-time of flight (MALDI-TOF) instrument. CONCLUSIONS This method has been applied to identifying phosphoproteins involved in the symbiosis Rhizobium etli-Phaseolus vulgaris.
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Affiliation(s)
- Yesenia Herrera
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Sandra Contreras
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Magdalena Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Laura Álvarez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Yolanda Mora
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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A novel mass spectrometric strategy "BEMAP" reveals Extensive O-linked protein glycosylation in Enterotoxigenic Escherichia coli. Sci Rep 2016; 6:32016. [PMID: 27562176 PMCID: PMC5000012 DOI: 10.1038/srep32016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/01/2016] [Indexed: 11/24/2022] Open
Abstract
The attachment of sugars to proteins via side-chain oxygen atoms (O-linked glycosylation) is seen in all three domains of life. However, a lack of widely-applicable analytical tools has restricted the study of this process, particularly in bacteria. In E. coli, only four O-linked glycoproteins have previously been characterized. Here we present a glycoproteomics technique, termed BEMAP, which is based on the beta-elimination of O-linked glycans followed by Michael-addition of a phosphonic acid derivative, and subsequent titanium dioxide enrichment. This strategy allows site-specific mass-spectrometric identification of proteins with O-linked glycan modifications in a complex biological sample. Using BEMAP we identified cell surface-associated and membrane vesicle glycoproteins from Enterotoxigenic E. coli (ETEC) and non-pathogenic E. coli K-12. We identified 618 glycosylated Serine and Threonine residues mapping to 140 proteins in ETEC, including several known virulence factors, and 34 in E. coli K-12. The two strains had 32 glycoproteins in common. Remarkably, the majority of the ETEC glycoproteins were conserved in both strains but nevertheless were only glycosylated in the pathogen. Therefore, bacterial O-linked glycosylation is much more extensive than previously thought, and is especially important to the pathogen.
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Soares NC, Blackburn JM. Mass Spectrometry Targeted Assays as a Tool to Improve Our Understanding of Post-translational Modifications in Pathogenic Bacteria. Front Microbiol 2016; 7:1216. [PMID: 27540373 PMCID: PMC4972818 DOI: 10.3389/fmicb.2016.01216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/21/2016] [Indexed: 01/03/2023] Open
Affiliation(s)
- Nelson C. Soares
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape TownCape Town, South Africa
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Lin MH, Sugiyama N, Ishihama Y. Systematic profiling of the bacterial phosphoproteome reveals bacterium-specific features of phosphorylation. Sci Signal 2015; 8:rs10. [DOI: 10.1126/scisignal.aaa3117] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Dworkin J. Ser/Thr phosphorylation as a regulatory mechanism in bacteria. Curr Opin Microbiol 2015; 24:47-52. [PMID: 25625314 DOI: 10.1016/j.mib.2015.01.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/31/2014] [Accepted: 01/10/2015] [Indexed: 11/30/2022]
Abstract
This review will discuss some recent work describing the role of Ser/Thr phosphorylation as a post-translational mechanism of regulation in bacteria. I will discuss the interaction between bacterial eukaryotic-like Ser/Thr kinases (eSTKs) and two-component systems as well as hints as to physiological function of eSTKs and their cognate eukaryotic-like phosphatases (eSTPs). In particular, I will highlight the role of eSTKs and eSTPs in the regulation of peptidoglycan metabolism and protein synthesis. In addition, I will discuss how data from phosphoproteomic surveys suggest that Ser/Thr phosphorylation plays a much more significant physiological role than would be predicted simply based on in vivo and in vitro analyses of individual kinases.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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