1
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Bhattacharjee P, Wang D, Anderson D, Buckler JN, de Geus E, Yan F, Polekhina G, Schittenhelm R, Creek DJ, Harris LD, Sadler AJ. The immune response to RNA suppresses nucleic acid synthesis by limiting ribose 5-phosphate. EMBO J 2024; 43:2636-2660. [PMID: 38778156 PMCID: PMC11217295 DOI: 10.1038/s44318-024-00100-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/29/2024] [Accepted: 03/19/2024] [Indexed: 05/25/2024] Open
Abstract
During infection viruses hijack host cell metabolism to promote their replication. Here, analysis of metabolite alterations in macrophages exposed to poly I:C recognises that the antiviral effector Protein Kinase RNA-activated (PKR) suppresses glucose breakdown within the pentose phosphate pathway (PPP). This pathway runs parallel to central glycolysis and is critical to producing NADPH and pentose precursors for nucleotides. Changes in metabolite levels between wild-type and PKR-ablated macrophages show that PKR controls the generation of ribose 5-phosphate, in a manner distinct from its established function in gene expression but dependent on its kinase activity. PKR phosphorylates and inhibits the Ribose 5-Phosphate Isomerase A (RPIA), thereby preventing interconversion of ribulose- to ribose 5-phosphate. This activity preserves redox control but decreases production of ribose 5-phosphate for nucleotide biosynthesis. Accordingly, the PKR-mediated immune response to RNA suppresses nucleic acid production. In line, pharmacological targeting of the PPP during infection decreases the replication of the Herpes simplex virus. These results identify an immune response-mediated control of host cell metabolism and suggest targeting the RPIA as a potential innovative antiviral treatment.
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Affiliation(s)
- Pushpak Bhattacharjee
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Die Wang
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Dovile Anderson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Joshua N Buckler
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, 5010, New Zealand
| | - Eveline de Geus
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Feng Yan
- Australian Centre for Blood Diseases, Department of Clinical Hematology, Monash University, Clayton, VIC, 3004, Australia
| | - Galina Polekhina
- Department of Epidemiology & Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Ralf Schittenhelm
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Lawrence D Harris
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, 5010, New Zealand
| | - Anthony J Sadler
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia.
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2
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Royzenblat SK, Freddolino L. Spatio-temporal organization of the E. coli chromosome from base to cellular length scales. EcoSal Plus 2024:eesp00012022. [PMID: 38864557 DOI: 10.1128/ecosalplus.esp-0001-2022] [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: 05/19/2023] [Accepted: 04/17/2024] [Indexed: 06/13/2024]
Abstract
Escherichia coli has been a vital model organism for studying chromosomal structure, thanks, in part, to its small and circular genome (4.6 million base pairs) and well-characterized biochemical pathways. Over the last several decades, we have made considerable progress in understanding the intricacies of the structure and subsequent function of the E. coli nucleoid. At the smallest scale, DNA, with no physical constraints, takes on a shape reminiscent of a randomly twisted cable, forming mostly random coils but partly affected by its stiffness. This ball-of-spaghetti-like shape forms a structure several times too large to fit into the cell. Once the physiological constraints of the cell are added, the DNA takes on overtwisted (negatively supercoiled) structures, which are shaped by an intricate interplay of many proteins carrying out essential biological processes. At shorter length scales (up to about 1 kb), nucleoid-associated proteins organize and condense the chromosome by inducing loops, bends, and forming bridges. Zooming out further and including cellular processes, topological domains are formed, which are flanked by supercoiling barriers. At the megabase-scale both large, highly self-interacting regions (macrodomains) and strong contacts between distant but co-regulated genes have been observed. At the largest scale, the nucleoid forms a helical ellipsoid. In this review, we will explore the history and recent advances that pave the way for a better understanding of E. coli chromosome organization and structure, discussing the cellular processes that drive changes in DNA shape, and what contributes to compaction and formation of dynamic structures, and in turn how bacterial chromatin affects key processes such as transcription and replication.
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Affiliation(s)
- Sonya K Royzenblat
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lydia Freddolino
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
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3
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Keskin B, Chen CS, Tsai PS, Du PX, Santos JHM, Syu GD. Reverse-Phase Protein Microarrays for Overexpressed Escherichia coli Lysates Reveal a Novel Tyrosine Kinase. Anal Chem 2024; 96:8721-8729. [PMID: 38683735 PMCID: PMC11140677 DOI: 10.1021/acs.analchem.4c00965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Tyrosine phosphorylation is one of the most important posttranslational modifications in bacteria, linked to regulating growth, migration, virulence, secondary metabolites, biofilm formation, and capsule production. Only two tyrosine kinases (yccC (etk) and wzc) have been identified in Escherichia coli. The investigation by similarity has not revealed any novel BY-kinases in silico so far, most probably due to their sequence and structural variability. Here we developed a reverse-phase protein array from 4126 overexpressed E. coli clones, lysed, and printed on coated glass slides. These high-density E. coli lysate arrays (ECLAs) were quality controlled by the reproducibility and immobilization of total lysate proteins and specific overexpressed proteins. ECLAs were used to interrogate the relationship between protein overexpression and tyrosine phosphorylation in the total lysate. We identified 6 protein candidates, including etk and wzc, with elevated phosphotyrosine signals in the total lysates. Among them, we identified a novel kinase nrdD with autophosphorylation and transphosphorylation activities in the lysates. Moreover, the overexpression of nrdD induced biofilm formation. Since nrdD is a novel kinase, we used E. coli proteome microarrays (purified 4,126 E. coli proteins) to perform an in vitro kinase assay and identified 33 potential substrates. Together, this study established a new ECLA platform for interrogating posttranslational modifications and identified a novel kinase that is important in biofilm formation, which will shed some light on bacteria biochemistry and new ways to impede drug resistance.
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Affiliation(s)
- Batuhan
Birol Keskin
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Chien-Sheng Chen
- Department
of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Institute
of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Pei-Shan Tsai
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Pin-Xian Du
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - John Harvey M. Santos
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Centre
for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Guan-Da Syu
- Department
of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
- International
Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan 701, Taiwan
- Medical Device
Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
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4
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Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
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Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
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5
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Li L, Yang B, Wang J, Wei Y, Xiang B, Liu Y, Wu P, Li W, Wang Y, Zhao X, Qin J, Liu M, Liu R, Ma G, Fu T, Wang M, Liu B. CobB-mediated deacetylation of the chaperone CesA regulates Escherichia coli O157:H7 virulence. Gut Microbes 2024; 16:2331435. [PMID: 38502202 PMCID: PMC10956630 DOI: 10.1080/19490976.2024.2331435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/13/2024] [Indexed: 03/21/2024] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a common food-borne pathogen that can cause acute diseases. Lysine acetylation is a post-translational modification (PTM) that occurs in various prokaryotes and is regulated by CobB, the only deacetylase found in bacteria. Here, we demonstrated that CobB plays an important role in the virulence of EHEC O157:H7 and that deletion of cobB significantly decreased the intestinal colonization ability of bacteria. Using acetylation proteomic studies, we systematically identified several proteins that could be regulated by CobB in EHEC O157:H7. Among these CobB substrates, we found that acetylation at the K44 site of CesA, a chaperone for the type-III secretion system (T3SS) translocator protein EspA, weakens its binding to EspA, thereby reducing the stability of this virulence factor; this PTM ultimately attenuating the virulence of EHEC O157:H7. Furthermore, we showed that deacetylation of the K44 site, which is deacetylated by CobB, promotes the interaction between CesA and EspA, thereby increasing bacterial virulence in vitro and in animal experiments. In summary, we showed that acetylation influences the virulence of EHEC O157:H7, and uncovered the mechanism by which CobB contributes to bacterial virulence based on the regulation of CesA deacetylation.
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Affiliation(s)
- Linxing Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Bin Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Jing Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Yi Wei
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Binbin Xiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Yutao Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Pan Wu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Wanwu Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Yanling Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Xinyu Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Jingliang Qin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Miaomiao Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Ruiying Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Guozhen Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Tian Fu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Min Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, China
- Nankai International Advanced Research Institute, Nankai University, Shenzhen, China
| | - Bin Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, China
- Nankai International Advanced Research Institute, Nankai University, Shenzhen, China
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6
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Norris V, Kayser C, Muskhelishvili G, Konto-Ghiorghi Y. The roles of nucleoid-associated proteins and topoisomerases in chromosome structure, strand segregation, and the generation of phenotypic heterogeneity in bacteria. FEMS Microbiol Rev 2023; 47:fuac049. [PMID: 36549664 DOI: 10.1093/femsre/fuac049] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
How to adapt to a changing environment is a fundamental, recurrent problem confronting cells. One solution is for cells to organize their constituents into a limited number of spatially extended, functionally relevant, macromolecular assemblies or hyperstructures, and then to segregate these hyperstructures asymmetrically into daughter cells. This asymmetric segregation becomes a particularly powerful way of generating a coherent phenotypic diversity when the segregation of certain hyperstructures is with only one of the parental DNA strands and when this pattern of segregation continues over successive generations. Candidate hyperstructures for such asymmetric segregation in prokaryotes include those containing the nucleoid-associated proteins (NAPs) and the topoisomerases. Another solution to the problem of creating a coherent phenotypic diversity is by creating a growth-environment-dependent gradient of supercoiling generated along the replication origin-to-terminus axis of the bacterial chromosome. This gradient is modulated by transcription, NAPs, and topoisomerases. Here, we focus primarily on two topoisomerases, TopoIV and DNA gyrase in Escherichia coli, on three of its NAPs (H-NS, HU, and IHF), and on the single-stranded binding protein, SSB. We propose that the combination of supercoiling-gradient-dependent and strand-segregation-dependent topoisomerase activities result in significant differences in the supercoiling of daughter chromosomes, and hence in the phenotypes of daughter cells.
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Affiliation(s)
- Vic Norris
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Clara Kayser
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Georgi Muskhelishvili
- Agricultural University of Georgia, School of Natural Sciences, 0159 Tbilisi, Georgia
| | - Yoan Konto-Ghiorghi
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
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7
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Lamont RJ, Miller DP. Tyrosine Kinases and Phosphatases: Enablers of the Porphyromonas gingivalis Lifestyle. FRONTIERS IN ORAL HEALTH 2022; 3:835586. [PMID: 35224543 PMCID: PMC8863745 DOI: 10.3389/froh.2022.835586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/17/2022] [Indexed: 11/17/2022] Open
Abstract
Tyrosine phosphorylation modifies the functionality of bacterial proteins and forms the basis of a versatile and tunable signal transduction system. The integrated action of tyrosine kinases and phosphatases controls bacterial processes important for metabolism and virulence. Porphyromonas gingivalis, a keystone pathogen in periodontal disease, possesses an extensive phosphotyrosine signaling network. The phosphorylation reaction is catalyzed by a bacterial tyrosine (BY) kinase, Ptk1, and a Ubiquitous bacterial Kinase UbK1. Dephosphorylation is mediated by a low-molecular-weight phosphatase, Ltp1 and a polymerase and histidinol phosphatase, Php1. Phosphotyrosine signaling controls exopolysaccharide production, gingipain activity, oxidative stress responses and synergistic community development with Streptococcus gordonii. Additionally, Ltp1 is secreted extracellularly and can be delivered inside gingival epithelial cells where it can override host cell signaling and readjust cellular physiology. The landscape of coordinated tyrosine kinase and phosphatase activity thus underlies the adaptive responses of P. gingivalis to both the polymicrobial environment of bacterial communities and the intracellular environment of gingival epithelial cells.
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Affiliation(s)
- Richard J. Lamont
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States
- *Correspondence: Richard J. Lamont
| | - Daniel P. Miller
- Department of Microbiology and Immunology, Virginia Commonwealth University Richmond, Richmond, VA, United States
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8
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Qi C, Sun F, Wei Q, Xu J, Li R, Zhang L, Lu F, Jiang X, Fu H, Zhang C, Li L. Quantitative phosphoproteomics reveals the effect of baeSR and acrB genes on protein phosphorylation in Salmonella enterica serovar Typhimurium. Res Microbiol 2021; 173:103886. [PMID: 34715324 DOI: 10.1016/j.resmic.2021.103886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/26/2021] [Accepted: 10/10/2021] [Indexed: 10/20/2022]
Abstract
The BaeSR two-component system and the AcrB efflux pump are closely associated with Salmonella resistance to antibiotics. However, the relationship between the two-component system, efflux pumps and protein phosphorylation of Salmonella is poorly understood. In this study, S. typhimurium ciprofloxacin-resistant strain CR, baeSR gene deletion strain CRΔbaeSR, acrB gene deletion strain CRΔacrB, and double gene deletion strain CRΔbaeSRΔacrB were used to explore phosphorylated proteins with significant difference, based on non-marker, quantitative phosphorylation modified proteomics technique. Consequently, 363 phosphosites of 213 phosphoproteins were identified in the four strains. More than 70% of the phosphosites were serine phosphorylation. In the CRΔbaeSR/CR, CRΔacrB/CR and CRΔbaeSRΔacrB/CR comparison groups, 36, 37 and 49 phosphosites were significantly altered, respectively. Bioinformatic analysis revealed that the main enrichment pathways of these differentially phosphorylated proteins were metabolic pathways, biosynthesis of antibiotics, phosphotransferase system (PTS), ABC transporters, and lipopolysaccharide biosynthesis. Furthermore, 21 differentially phosphorylated proteins were identified to be associated with antibiotic resistance. These results suggest that the BaeSR two-component system and the AcrB efflux pump affect the phosphorylation of proteins in S. typhimurium and may influence the drug resistance and virulence of S. typhimurium by affecting protein phosphorylation, providing a new idea to explore the mechanism of drug resistance in Salmonella.
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Affiliation(s)
- Caili Qi
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Feifei Sun
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China; Anhui Province Key Lab of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China
| | - Qiling Wei
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Jun Xu
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Rui Li
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Lin Zhang
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Fang Lu
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Xidi Jiang
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Hengfeng Fu
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Chunxiao Zhang
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Lin Li
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China; Anhui Province Key Lab of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.
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9
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Yadav M, Srinivasan M, Tulsian NK, Liu YX, Lin Q, Rosenshine I, Sivaraman J. Binding specificity of type three secretion system effector NleH2 to multi-cargo chaperone CesT and their phosphorylation. Protein Sci 2021; 30:2433-2444. [PMID: 34662450 DOI: 10.1002/pro.4210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/08/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
Gram-negative pathogens like Enteropathogenic Escherichia coli (EPEC) utilize the type three secretion system (T3SS) to translocate various effector proteins that are needed to "hijack" the host system for pathogenic survival. Specialized T3SS chaperones inside bacterial cells stabilize these effector proteins and facilitate their translocation. CesT is a unique multi-cargo chaperone that interacts with and translocates ~10 different effector proteins. Here, we report the specific interaction between CesT and its key effector, NleH2, and explore the potential role of NleH2 as a kinase for CesT phosphorylation. First, we identified the chaperone-binding domain (CBD; 19-97aa) of NleH2, and mapped the specific interaction sites for both CesT and NleH2. The N- and C-terminal residues of the CBD interact with the dimeric interface of CesT. Further, we compared the CesT binding to NleH2, to that of another key effector Tir and with the global carbon regulator CsrA. Notably, the effectors have the binding regions at the β-sheet core and dimer interface of CesT, whereas the CsrA regulator interacts predominantly through the C-terminal region, which is found ~17 Å away from the effectors-binding sites. Next, we showed that NleH2 remains an active kinase even as a complex with CesT and is responsible for its autophosphorylation as well as phosphorylation of CesT at Tyr153. Collectively, our findings enhance the understanding of the role of multi-cargo chaperone CesT in orchestrating effector translocation through T3SS.
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Affiliation(s)
- Manisha Yadav
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Nikhil K Tulsian
- Department of Biological Sciences, National University of Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore
| | - Yu Xuan Liu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore
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10
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Luu LDW, Zhong L, Kaur S, Raftery MJ, Lan R. Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence. Front Cell Infect Microbiol 2021; 11:660280. [PMID: 33928046 PMCID: PMC8076611 DOI: 10.3389/fcimb.2021.660280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/17/2021] [Indexed: 11/13/2022] Open
Abstract
The Bordetella genus is divided into two groups: classical and non-classical. Bordetella pertussis, Bordetella bronchiseptica and Bordetella parapertussis are known as classical bordetellae, a group of important human pathogens causing whooping cough or whooping cough-like disease and hypothesized to have evolved from environmental non-classical bordetellae. Bordetella infections have increased globally driving the need to better understand these pathogens for the development of new treatments and vaccines. One unexplored component in Bordetella is the role of serine, threonine and tyrosine phosphorylation. Therefore, this study characterized the phosphoproteome of classical bordetellae and examined its potential role in Bordetella biology and virulence. Applying strict identification of localization criteria, this study identified 70 unique phosphorylated proteins in the classical bordetellae group with a high degree of conservation. Phosphorylation was a key regulator of Bordetella metabolism with proteins involved in gluconeogenesis, TCA cycle, amino acid and nucleotide synthesis significantly enriched. Three key virulence pathways were also phosphorylated including type III secretion system, alcaligin synthesis and the BvgAS master transcriptional regulatory system for virulence genes in Bordetella. Seven new phosphosites were identified in BvgA with 6 located in the DNA binding domain. Of the 7, 4 were not present in non-classical bordetellae. This suggests that serine/threonine phosphorylation may play an important role in stabilizing/destabilizing BvgA binding to DNA for fine-tuning of virulence gene expression and that BvgA phosphorylation may be an important factor separating classical from non-classical bordetellae. This study provides the first insight into the phosphoproteome of classical Bordetella species and the role that Ser/Thr/Tyr phosphorylation may play in Bordetella biology and virulence.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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11
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Sultan A, Jers C, Ganief TA, Shi L, Senissar M, Køhler JB, Macek B, Mijakovic I. Phosphoproteome Study of Escherichia coli Devoid of Ser/Thr Kinase YeaG During the Metabolic Shift From Glucose to Malate. Front Microbiol 2021; 12:657562. [PMID: 33889145 PMCID: PMC8055822 DOI: 10.3389/fmicb.2021.657562] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/15/2021] [Indexed: 12/30/2022] Open
Abstract
Understanding phosphorylation-mediated regulation of metabolic enzymes, pathways, and cell phenotypes under metabolic shifts represents a major challenge. The kinases associated with most phosphorylation sites and the link between phosphorylation and enzyme activity remain unknown. In this study, we performed stable isotope labeling by amino acids in cell culture (SILAC)-based proteome and phosphoproteome analysis of Escherichia coli ΔyeaG, a strain lacking a poorly characterized serine/threonine kinase YeaG, to decipher kinase-substrate interactions and the effects on metabolic phenotype during shifts from glucose to malate. The starting point of our analysis was the identification of physiological conditions under which ΔyeaG exhibits a clear phenotype. By metabolic profiling, we discovered that ΔyeaG strain has a significantly shorter lag phase than the wild type during metabolic shift from glucose to malate. Under those conditions, our SILAC analysis revealed several proteins that were differentially phosphorylated in the ΔyeaG strain. By focusing on metabolic enzymes potentially involved in central carbon metabolism, we narrowed down our search for putative YeaG substrates and identified isocitrate lyase AceA as the direct substrate of YeaG. YeaG was capable of phosphorylating AceA in vitro only in the presence of malate, suggesting that this phosphorylation event is indeed relevant for glucose to malate shift. There is currently not enough evidence to firmly establish the exact mechanism of this newly observed regulatory phenomenon. However, our study clearly exemplifies the usefulness of SILAC-based approaches in identifying proteins kinase substrates, when applied in physiological conditions relevant for the activity of the protein kinase in question.
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Affiliation(s)
- Abida Sultan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tariq A Ganief
- Quantitative Proteomics and Proteome Center Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Meriem Senissar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julie Bonne Køhler
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Boris Macek
- Quantitative Proteomics and Proteome Center Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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12
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Wang X, Ma Q. Wzb of Vibrio vulnificus represents a new group of low-molecular-weight protein tyrosine phosphatases with a unique insertion in the W-loop. J Biol Chem 2021; 296:100280. [PMID: 33450227 PMCID: PMC7948962 DOI: 10.1016/j.jbc.2021.100280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/28/2020] [Accepted: 01/08/2021] [Indexed: 12/23/2022] Open
Abstract
Protein tyrosine phosphorylation regulates the production of capsular polysaccharide, an essential virulence factor of the deadly pathogen Vibrio vulnificus. The process requires the protein tyrosine kinase Wzc and its cognate phosphatase Wzb, both of which are largely uncharacterized. Herein, we report the structures of Wzb of V. vulnificus (VvWzb) in free and ligand-bound forms. VvWzb belongs to the low-molecular-weight protein tyrosine phosphatase (LMWPTP) family. Interestingly, it contains an extra four-residue insertion in the W-loop, distinct from all known LMWPTPs. The W-loop of VvWzb protrudes from the protein body in the free structure, but undergoes significant conformational changes to fold toward the active site upon ligand binding. Deleting the four-residue insertion from the W-loop severely impaired the enzymatic activity of VvWzb, indicating its importance for optimal catalysis. However, mutating individual residues or even substituting the whole insertion with four alanine residues only modestly decreased the enzymatic activity, suggesting that the contribution of the insertion to catalysis is not determined by the sequence specificity. Furthermore, inserting the four residues into Escherichia coli Wzb at the corresponding position enhanced its activity as well, indicating that the four-residue insertion in the W-loop can act as a general activity enhancing element for other LMWPTPs. The novel W-loop type and phylogenetic analysis suggested that VvWzb and its homologs should be classified into a new group of LMWPTPs. Our study sheds new insight into the catalytic mechanism and structural diversity of the LMWPTP family and promotes the understanding of the protein tyrosine phosphorylation system in prokaryotes.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qingjun Ma
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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13
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Tyrosine phosphorylation-dependent localization of TmaR that controls activity of a major bacterial sugar regulator by polar sequestration. Proc Natl Acad Sci U S A 2021; 118:2016017118. [PMID: 33376208 DOI: 10.1073/pnas.2016017118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The poles of Escherichia coli cells are emerging as hubs for major sensory systems, but the polar determinants that allocate their components to the pole are largely unknown. Here, we describe the discovery of a previously unannotated protein, TmaR, which localizes to the E. coli cell pole when phosphorylated on a tyrosine residue. TmaR is shown here to control the subcellular localization and activity of the general PTS protein Enzyme I (EI) by binding and polar sequestration of EI, thus regulating sugar uptake and metabolism. Depletion or overexpression of TmaR results in EI release from the pole or enhanced recruitment to the pole, which leads to increasing or decreasing the rate of sugar consumption, respectively. Notably, phosphorylation of TmaR is required to release EI and enable its activity. Like TmaR, the ability of EI to be recruited to the pole depends on phosphorylation of one of its tyrosines. In addition to hyperactivity in sugar consumption, the absence of TmaR also leads to detrimental effects on the ability of cells to survive in mild acidic conditions. Our results suggest that this survival defect, which is sugar- and EI-dependent, reflects the difficulty of cells lacking TmaR to enter stationary phase. Our study identifies TmaR as the first, to our knowledge, E. coli protein reported to localize in a tyrosine-dependent manner and to control the activity of other proteins by their polar sequestration and release.
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14
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Fostier CR, Monlezun L, Ousalem F, Singh S, Hunt JF, Boël G. ABC-F translation factors: from antibiotic resistance to immune response. FEBS Lett 2020; 595:675-706. [PMID: 33135152 DOI: 10.1002/1873-3468.13984] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Energy-dependent translational throttle A (EttA) from Escherichia coli is a paradigmatic ABC-F protein that controls the first step in polypeptide elongation on the ribosome according to the cellular energy status. Biochemical and structural studies have established that ABC-F proteins generally function as translation factors that modulate the conformation of the peptidyl transferase center upon binding to the ribosomal tRNA exit site. These factors, present in both prokaryotes and eukaryotes but not in archaea, use related molecular mechanisms to modulate protein synthesis for heterogenous purposes, ranging from antibiotic resistance and rescue of stalled ribosomes to modulation of the mammalian immune response. Here, we review the canonical studies characterizing the phylogeny, regulation, ribosome interactions, and mechanisms of action of the bacterial ABC-F proteins, and discuss the implications of these studies for the molecular function of eukaryotic ABC-F proteins, including the three human family members.
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Affiliation(s)
- Corentin R Fostier
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Laura Monlezun
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Shikha Singh
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - John F Hunt
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
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15
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Forrest S, Welch M. Arming the troops: Post-translational modification of extracellular bacterial proteins. Sci Prog 2020; 103:36850420964317. [PMID: 33148128 PMCID: PMC10450907 DOI: 10.1177/0036850420964317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein secretion is almost universally employed by bacteria. Some proteins are retained on the cell surface, whereas others are released into the extracellular milieu, often playing a key role in virulence. In this review, we discuss the diverse types and potential functions of post-translational modifications (PTMs) occurring to extracellular bacterial proteins.
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Affiliation(s)
- Suzanne Forrest
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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16
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Schwechheimer C, Hebert K, Tripathi S, Singh PK, Floyd KA, Brown ER, Porcella ME, Osorio J, Kiblen JTM, Pagliai FA, Drescher K, Rubin SM, Yildiz FH. A tyrosine phosphoregulatory system controls exopolysaccharide biosynthesis and biofilm formation in Vibrio cholerae. PLoS Pathog 2020; 16:e1008745. [PMID: 32841296 PMCID: PMC7485978 DOI: 10.1371/journal.ppat.1008745] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 09/11/2020] [Accepted: 06/25/2020] [Indexed: 11/19/2022] Open
Abstract
Production of an extracellular matrix is essential for biofilm formation, as this matrix both secures and protects the cells it encases. Mechanisms underlying production and assembly of matrices are poorly understood. Vibrio cholerae, relies heavily on biofilm formation for survival, infectivity, and transmission. Biofilm formation requires Vibrio polysaccharide (VPS), which is produced by vps gene-products, yet the function of these products remains unknown. Here, we demonstrate that the vps gene-products vpsO and vpsU encode respectively for a tyrosine kinase and a cognate tyrosine phosphatase. Collectively, VpsO and VpsU act as a tyrosine phosphoregulatory system to modulate VPS production. We present structures of VpsU and the kinase domain of VpsO, and we report observed autocatalytic tyrosine phosphorylation of the VpsO C-terminal tail. The position and amount of tyrosine phosphorylation in the VpsO C-terminal tail represses VPS production and biofilm formation through a mechanism involving the modulation of VpsO oligomerization. We found that tyrosine phosphorylation enhances stability of VpsO. Regulation of VpsO phosphorylation by the phosphatase VpsU is vital for maintaining native VPS levels. This study provides new insights into the mechanism and regulation of VPS production and establishes general principles of biofilm matrix production and its inhibition. The biofilm life style protects microbes from a plethora of harm, to increase their survival and pathogenicity. Exopolysaccharides are the essential glue of the microbial biofilm matrix, and loss of this glue negates biofilm formation and renders cells more sensitive to antimicrobial agents. Here, we show that a tyrosine phosphoregulatory system controls the biosynthesis and abundance of Vibrio exopolysaccharide (VPS), an essential biofilm component of the pathogen Vibrio cholerae. The phosphorylation state of the tyrosine autokinase VpsO, mediated by the tyrosine phosphatase VpsU, directly modulates VPS production and also affects the kinase’s own degradation, to regulate VPS production. This study provides new insights into the mechanisms of V. cholerae biofilm formation and consequently ways to combat pathogens more broadly, due to conservation of tyrosine phosphoregulatory systems among exopolysaccharide producing bacteria.
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Affiliation(s)
- Carmen Schwechheimer
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Kassidy Hebert
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Praveen K. Singh
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kyle A. Floyd
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Elise R. Brown
- Department of Chemistry and Biochemistry, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Monique E. Porcella
- Department of Chemistry and Biochemistry, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Jacqueline Osorio
- Department of Chemistry and Biochemistry, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Joseph T. M. Kiblen
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Fernando A. Pagliai
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Seth M. Rubin
- Department of Chemistry and Biochemistry, University of California—Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (SMR), (FHY)
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (SMR), (FHY)
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17
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Bonne Køhler J, Jers C, Senissar M, Shi L, Derouiche A, Mijakovic I. Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis. FEBS Lett 2020; 594:2339-2369. [PMID: 32337704 DOI: 10.1002/1873-3468.13797] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation regulates a large variety of biological processes in all living cells. In pathogenic bacteria, the study of serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation has shed light on the course of infectious diseases, from adherence to host cells to pathogen virulence, replication, and persistence. Mass spectrometry (MS)-based phosphoproteomics has provided global maps of Ser/Thr/Tyr phosphosites in bacterial pathogens. Despite recent developments, a quantitative and dynamic view of phosphorylation events that occur during bacterial pathogenesis is currently lacking. Temporal, spatial, and subpopulation resolution of phosphorylation data is required to identify key regulatory nodes underlying bacterial pathogenesis. Herein, we discuss how technological improvements in sample handling, MS instrumentation, data processing, and machine learning should improve bacterial phosphoproteomic datasets and the information extracted from them. Such information is expected to significantly extend the current knowledge of Ser/Thr/Tyr phosphorylation in pathogenic bacteria and should ultimately contribute to the design of novel strategies to combat bacterial infections.
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Affiliation(s)
- Julie Bonne Køhler
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mériem Senissar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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18
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Deb B, George IA, Sharma J, Kumar P. Phosphoproteomics Profiling to Identify Altered Signaling Pathways and Kinase-Targeted Cancer Therapies. Methods Mol Biol 2020; 2051:241-264. [PMID: 31552632 DOI: 10.1007/978-1-4939-9744-2_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phosphorylation is one of the most extensively studied posttranslational modifications (PTM), which regulates cellular functions like cell growth, differentiation, apoptosis, and cell signaling. Kinase families cover a wide number of oncoproteins and are strongly associated with cancer. Identification of driver kinases is an intense area of cancer research. Thus, kinases serve as the potential target to improve the efficacy of targeted therapies. Mass spectrometry-based phosphoproteomic approach has paved the way to the identification of a large number of altered phosphorylation events in proteins and signaling cascades that may lead to oncogenic processes in a cell. Alterations in signaling pathways result in the activation of oncogenic processes predominantly regulated by kinases and phosphatases. Therefore, drugs such as kinase inhibitors, which target dysregulated pathways, represent a promising area for cancer therapy.
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Affiliation(s)
- Barnali Deb
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Irene A George
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India. .,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India.
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19
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Qin L, Erkelens AM, Ben Bdira F, Dame RT. The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins. Open Biol 2019; 9:190223. [PMID: 31795918 PMCID: PMC6936261 DOI: 10.1098/rsob.190223] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/08/2019] [Indexed: 12/15/2022] Open
Abstract
Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns- phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes.
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Affiliation(s)
- L. Qin
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - A. M. Erkelens
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - F. Ben Bdira
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - R. T. Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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20
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Ma Y, Ding S, Fei Y, Liu G, Jang H, Fang J. Antimicrobial activity of anthocyanins and catechins against foodborne pathogens Escherichia coli and Salmonella. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.106712] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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21
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Abstract
Phosphorylation events modify bacterial and archaeal proteomes, imparting cells with rapid and reversible responses to specific environmental stimuli or niches. Phosphorylated proteins are generally modified at one or more serine, threonine, or tyrosine residues. Within the last ten years, increasing numbers of global phosphoproteomic surveys of prokaryote species have revealed an abundance of tyrosine-phosphorylated proteins. In some cases, novel phosphorylation-dependent regulatory paradigms for cell division, gene transcription, and protein translation have been identified, suggesting that a wide scope of prokaryotic physiology remains to be characterized. Recent observations of bacterial proteins with putative phosphotyrosine binding pockets or Src homology 2 (SH2)-like domains suggest the presence of phosphotyrosine-dependent protein interaction networks. Here in this minireview, we focus on protein tyrosine phosphorylation, a posttranslational modification once thought to be rare in prokaryotes but which has emerged as an important regulatory facet in microbial biology.
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22
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Hu L, Kong W, Yang D, Han Q, Guo L, Shi Y. Threonine Phosphorylation Fine-Tunes the Regulatory Activity of Histone-Like Nucleoid Structuring Protein in Salmonella Transcription. Front Microbiol 2019; 10:1515. [PMID: 31333620 PMCID: PMC6616471 DOI: 10.3389/fmicb.2019.01515] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 06/18/2019] [Indexed: 12/30/2022] Open
Abstract
Histone-like nucleoid structuring protein (H-NS) in enterobacteria plays an important role in facilitating chromosome organization and functions as a crucial transcriptional regulator for global gene regulation. Here, we presented an observation that H-NS of Salmonella enterica serovar Typhimurium could undergo protein phosphorylation at threonine 13 residue (T13). Analysis of the H-NS wild-type protein and its T13E phosphomimetic substitute suggested that T13 phosphorylation lead to alterations of H-NS structure, thus reducing its dimerization to weaken its DNA binding affinity. Proteomic analysis revealed that H-NS phosphorylation exerts regulatory effects on a wide range of genetic loci including the PhoP/PhoQ-regulated genes. In this study, we investigated an effect of T13 phosphorylation of H-NS that rendered transcription upregulation of the PhoP/PhoQ-activated genes. A lower promoter binding of the T13 phosphorylated H-NS protein was correlated with a stronger interaction of the PhoP protein, i.e., a transcription activator and also a competitor of H-NS, to the PhoP/PhoQ-dependent promoters. Unlike depletion of H-NS which dramatically activated the PhoP/PhoQ-dependent transcription even in a PhoP/PhoQ-repressing condition, mimicking of H-NS phosphorylation caused a moderate upregulation. Wild-type H-NS protein produced heterogeneously could rescue the phenotype of T13E mutant and fully restored the PhoP/PhoQ-dependent transcription enhanced by T13 phosphorylation of H-NS to wild-type levels. Therefore, our findings uncover a strategy in S. typhimurium to fine-tune the regulatory activity of H-NS through specific protein phosphorylation and highlight a regulatory mechanism for the PhoP/PhoQ-dependent transcription via this post-translational modification.
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Affiliation(s)
- Lizhi Hu
- The State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.,School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Wei Kong
- The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Dezhi Yang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Qiangqiang Han
- The State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lin Guo
- The State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yixin Shi
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,The Biodesign Institute, Arizona State University, Tempe, AZ, United States
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23
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Pagano GJ, Arsenault RJ. Advances, challenges and tools in characterizing bacterial serine, threonine and tyrosine kinases and phosphorylation target sites. Expert Rev Proteomics 2019; 16:431-441. [DOI: 10.1080/14789450.2019.1601015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Giovanni J. Pagano
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, USA
| | - Ryan J. Arsenault
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, USA
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24
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Lubner JM, Balsbaugh JL, Church GM, Chou MF, Schwartz D. Characterizing Protein Kinase Substrate Specificity Using the Proteomic Peptide Library (ProPeL) Approach. ACTA ACUST UNITED AC 2019; 10:e38. [PMID: 29927115 DOI: 10.1002/cpch.38] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Characterizing protein kinase substrate specificity motifs represents a powerful step in elucidating kinase-signaling cascades. The protocol described here uses a bacterial system to evaluate kinase specificity motifs in vivo, without the need for radioactive ATP. The human kinase of interest is cloned into a heterologous bacterial expression vector and allowed to phosphorylate E. coli proteins in vivo, consistent with its endogenous substrate preferences. The cells are lysed, and the bacterial proteins are digested into peptides and phosphoenriched using bulk TiO2 . The pooled phosphopeptides are identified by tandem mass spectrometry, and bioinformatically analyzed using the pLogo visualization tool. The ProPeL approach allows for detailed characterization of wildtype kinase specificity motifs, identification of specificity drift due to kinase mutations, and evaluation of kinase residue structure-function relationships. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Joshua M Lubner
- University of Connecticut, Department of Physiology and Neurobiology, Storrs, Connecticut
| | - Jeremy L Balsbaugh
- University of Connecticut, Proteomics & Metabolomics Facility, Center for Open Research Resources & Equipment, Storrs, Connecticut
| | - George M Church
- Harvard Medical School, Department of Genetics, Boston, Massachusetts and Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts
| | - Michael F Chou
- Harvard Medical School, Department of Genetics, Boston, Massachusetts and Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts
| | - Daniel Schwartz
- University of Connecticut, Department of Physiology and Neurobiology, Storrs, Connecticut
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25
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Abstract
Bacterial signal transduction systems are responsible for sensing environmental cues and adjusting the cellular behaviour and/or metabolism in response to these cues. They also monitor the intracellular conditions and the status of the cell envelope and the cytoplasmic membrane and trigger various stress responses to counteract adverse changes. This surveillance involves several classes of sensor proteins: histidine kinases; chemoreceptors; membrane components of the sugar phosphotransferase system; adenylate, diadenylate and diguanylate cyclases and certain cAMP, c-di-AMP and c-di-GMP phosphodiesterases; extracytoplasmic function sigma factors and Ser/Thr/Tyr protein kinases and phosphoprotein phosphatases. We have compiled a detailed listing of sensor proteins that are encoded in the genomes of Escherichia coli, Bacillus subtilis and 10 widespread pathogens: Chlamydia trachomatis, Haemophilus influenzae, Helicobacter pylori, Mycobacterium tuberculosis, Mycoplasma pneumoniae, Neisseria gonorrhoeae, Porphyromonas gingivalis, Rickettsia typhi, Streptococcus pyogenes and Treponema pallidum, and checked what, if anything, is known about their functions. This listing shows significant gaps in the understanding of which environmental and intracellular cues are perceived by these bacteria and which cellular responses are triggered by the changes in the respective parameters. A better understanding of bacterial preferences may suggest new ways to modulate the expression of virulence factors and therefore decrease the reliance on antibiotics to fight infection.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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26
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Choi E, Hwang J. The GTPase BipA expressed at low temperature in Escherichia coli assists ribosome assembly and has chaperone-like activity. J Biol Chem 2018; 293:18404-18419. [PMID: 30305394 DOI: 10.1074/jbc.ra118.002295] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 09/27/2018] [Indexed: 12/29/2022] Open
Abstract
BPI-inducible protein A (BipA) is a conserved ribosome-associated GTPase in bacteria that is structurally similar to other GTPases associated with protein translation, including IF2, EF-Tu, and EF-G. Its binding site on the ribosome appears to overlap those of these translational GTPases. Mutations in the bipA gene cause a variety of phenotypes, including cold and antibiotics sensitivities and decreased pathogenicity, implying that BipA may participate in diverse cellular processes by regulating translation. According to recent studies, a bipA-deletion strain of Escherichia coli displays a ribosome assembly defect at low temperature, suggesting that BipA might be involved in ribosome assembly. To further investigate BipA's role in ribosome biogenesis, here, we compared and analyzed the ribosomal protein compositions of MG1655 WT and bipA-deletion strains at 20 °C. Aberrant 50S ribosomal subunits (i.e. 44S particles) accumulated in the bipA-deletion strain at 20 °C, and the ribosomal protein L6 was absent in these 44S particles. Furthermore, bipA expression was significantly stimulated at 20 °C, suggesting that it encodes a cold shock-inducible GTPase. Moreover, the transcriptional regulator cAMP receptor protein (CRP) positively promoted bipA expression only at 20 °C. Importantly, GFP and α-glucosidase refolding assays revealed that BipA has chaperone activity. Our findings indicate that BipA is a cold shock-inducible GTPase that participates in 50S ribosomal subunit assembly by incorporating the L6 ribosomal protein into the 44S particle during the assembly.
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Affiliation(s)
- Eunsil Choi
- From the Department of Microbiology, Pusan National University, Busan 46241, Korea
| | - Jihwan Hwang
- From the Department of Microbiology, Pusan National University, Busan 46241, Korea.
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27
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Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proc Natl Acad Sci U S A 2018; 115:11096-11101. [PMID: 30301795 DOI: 10.1073/pnas.1811971115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Understanding the complex interactions of protein posttranslational modifications (PTMs) represents a major challenge in metabolic engineering, synthetic biology, and the biomedical sciences. Here, we present a workflow that integrates multiplex automated genome editing (MAGE), genome-scale metabolic modeling, and atomistic molecular dynamics to study the effects of PTMs on metabolic enzymes and microbial fitness. This workflow incorporates complementary approaches across scientific disciplines; provides molecular insight into how PTMs influence cellular fitness during nutrient shifts; and demonstrates how mechanistic details of PTMs can be explored at different biological scales. As a proof of concept, we present a global analysis of PTMs on enzymes in the metabolic network of Escherichia coli Based on our workflow results, we conduct a more detailed, mechanistic analysis of the PTMs in three proteins: enolase, serine hydroxymethyltransferase, and transaldolase. Application of this workflow identified the roles of specific PTMs in observed experimental phenomena and demonstrated how individual PTMs regulate enzymes, pathways, and, ultimately, cell phenotypes.
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28
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Post-translational modification of nucleoid-associated proteins: an extra layer of functional modulation in bacteria? Biochem Soc Trans 2018; 46:1381-1392. [PMID: 30287510 DOI: 10.1042/bst20180488] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/31/2018] [Accepted: 09/04/2018] [Indexed: 01/08/2023]
Abstract
Post-translational modification (PTM) of histones has been investigated in eukaryotes for years, revealing its widespread occurrence and functional importance. Many PTMs affect chromatin folding and gene activity. Only recently the occurrence of such modifications has been recognized in bacteria. However, it is unclear whether PTM of the bacterial counterparts of eukaryotic histones, nucleoid-associated proteins (NAPs), bears a comparable significance. Here, we scrutinize proteome mass spectrometry data for PTMs of the four most abundantly present NAPs in Escherichia coli (H-NS, HU, IHF and FIS). This approach allowed us to identify a total of 101 unique PTMs in the 11 independent proteomic studies covered in this review. Combined with structural and genetic information on these proteins, we describe potential effects of these modifications (perturbed DNA-binding, structural integrity or interaction with other proteins) on their function.
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29
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Molecular basis for CesT recognition of type III secretion effectors in enteropathogenic Escherichia coli. PLoS Pathog 2018; 14:e1007224. [PMID: 30118511 PMCID: PMC6114900 DOI: 10.1371/journal.ppat.1007224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/29/2018] [Accepted: 07/17/2018] [Indexed: 11/19/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) use a needle-like injection apparatus known as the type III secretion system (T3SS) to deliver protein effectors into host cells. Effector translocation is highly stratified in EPEC with the translocated intimin receptor (Tir) being the first effector delivered into the host. CesT is a multi-cargo chaperone that is required for the secretion of Tir and at least 9 other effectors. However, the structural and mechanistic basis for differential effector recognition by CesT remains unclear. Here, we delineated the minimal CesT-binding region on Tir to residues 35–77 and determined the 2.74 Å structure of CesT bound to an N-terminal fragment of Tir. Our structure revealed that the CesT-binding region in the N-terminus of Tir contains an additional conserved sequence, distinct from the known chaperone-binding β-motif, that we termed the CesT-extension motif because it extends the β-sheet core of CesT. This motif is also present in the C-terminus of Tir that we confirmed to be a unique second CesT-binding region. Point mutations that disrupt CesT-binding to the N- or C-terminus of Tir revealed that the newly identified carboxy-terminal CesT-binding region was required for efficient Tir translocation into HeLa cells and pedestal formation. Furthermore, the CesT-extension motif was identified in the N-terminal region of NleH1, NleH2, and EspZ, and mutations that disrupt this motif reduced translocation of these effectors, and in some cases, overall effector stability, thus validating the universality of this CesT-extension motif. The presence of two CesT-binding regions in Tir, along with the presence of the CesT-extension motif in other highly translocated effectors, may contribute to differential cargo recognition by CesT. Enteropathogenic Escherichia coli injects effector proteins into host cells using a type III secretion system (T3SS). The translocated intimin receptor (Tir) is the first effector delivered into host cells and imparts efficient secretion of other effectors. However, the mechanism for Tir-dependent modulation of the T3SS is poorly understood. We provide evidence that the multi-cargo chaperone CesT binds to two regions in Tir at the N- and C-terminus through a specific recognition motif, and show that CesT binding to the Tir C-terminus is important for host translocation. Furthermore we show that the CesT-specific motif is conserved in a subset of highly translocated effectors. This study highlights the multi-faceted role that T3SS chaperones play in effector secretion dynamics.
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30
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Runte CS, Jain U, Getz LJ, Secord S, Kuwae A, Abe A, LeBlanc JJ, Stadnyk AW, Kaper JB, Hansen AM, Thomas NA. Tandem tyrosine phosphosites in the Enteropathogenic Escherichia coli chaperone CesT are required for differential type III effector translocation and virulence. Mol Microbiol 2018; 108:536-550. [PMID: 29509331 DOI: 10.1111/mmi.13948] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2018] [Indexed: 11/29/2022]
Abstract
Enteropathogenic Escherichia coli (EPEC) use a type 3 secretion system (T3SS) for injection of effectors into host cells and intestinal colonization. Here, we demonstrate that the multicargo chaperone CesT has two strictly conserved tyrosine phosphosites, Y152 and Y153 that regulate differential effector secretion in EPEC. Conservative substitution of both tyrosine residues to phenylalanine strongly attenuated EPEC type 3 effector injection into host cells, and limited Tir effector mediated intimate adherence during infection. EPEC expressing a CesT Y152F variant were deficient for NleA effector expression and exhibited significantly reduced translocation of NleA into host cells during infection. Other effectors were observed to be dependent on CesT Y152 for maximal translocation efficiency. Unexpectedly, EPEC expressing a CesT Y153F variant exhibited significantly enhanced effector translocation of many CesT-interacting effectors, further implicating phosphosites Y152 and Y153 in CesT functionality. A mouse infection model of intestinal disease using Citrobacter rodentium revealed that CesT tyrosine substitution variants displayed delayed colonization and were more rapidly cleared from the intestine. These data demonstrate genetically separable functions for tandem tyrosine phosphosites within CesT. Therefore, CesT via its C-terminal tyrosine phosphosites, has relevant roles beyond typical type III secretion chaperones that interact and stabilize effector proteins.
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Affiliation(s)
- Cameron S Runte
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Umang Jain
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Landon J Getz
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sabrina Secord
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Asaomi Kuwae
- Laboratory of Bacterial Infection, Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Akio Abe
- Laboratory of Bacterial Infection, Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Jason J LeBlanc
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Medicine, Division of Infectious Diseases, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew W Stadnyk
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - James B Kaper
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Anne-Marie Hansen
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nikhil A Thomas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Medicine, Division of Infectious Diseases, Dalhousie University, Halifax, Nova Scotia, Canada
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31
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Abstract
Enteric pathogens with low infectious doses rely on the ability to orchestrate the expression of virulence and metabolism-associated genes in response to environmental cues for successful infection. Accordingly, the human pathogen enterohemorrhagic Escherichia coli (EHEC) employs a complex multifaceted regulatory network to link the expression of type III secretion system (T3SS) components to nutrient availability. While phosphorylation of histidine and aspartate residues on two-component system response regulators is recognized as an integral part of bacterial signaling, the involvement of phosphotyrosine-mediated control is minimally explored in Gram-negative pathogens. Our recent phosphotyrosine profiling study of E. coli identified 342 phosphorylated proteins, indicating that phosphotyrosine modifications in bacteria are more prevalent than previously anticipated. The present study demonstrates that tyrosine phosphorylation of a metabolite-responsive LacI/GalR family regulator, Cra, negatively affects T3SS expression under glycolytic conditions that are typical for the colonic lumen environment where production of the T3SS is unnecessary. Our data suggest that Cra phosphorylation affects T3SS expression by modulating the expression of ler, which encodes the major activator of EHEC virulence gene expression. Phosphorylation of the Cra Y47 residue diminishes DNA binding to fine-tune the expression of virulence-associated genes, including those of the locus of enterocyte effacement pathogenicity island that encode the T3SS, and thereby negatively affects the formation of attaching and effacing lesions. Our data indicate that tyrosine phosphorylation provides an additional mechanism to control the DNA binding of Cra and other LacI/GalR family regulators, including LacI and PurR. This study describes an initial effort to unravel the role of global phosphotyrosine signaling in the control of EHEC virulence potential. Enterohemorrhagic Escherichia coli (EHEC) causes outbreaks of hemorrhagic colitis and the potentially fatal hemolytic-uremic syndrome. Successful host colonization by EHEC relies on the ability to coordinate the expression of virulence factors in response to environmental cues. A complex network that integrates environmental signals at multiple regulatory levels tightly controls virulence gene expression. We demonstrate that EHEC utilizes a previously uncharacterized phosphotyrosine signaling pathway through Cra to fine-tune the expression of virulence-associated genes to effectively control T3SS production. This study demonstrates that tyrosine phosphorylation negatively affects the DNA-binding capacity of Cra, which affects the expression of genes related to virulence and metabolism. We demonstrate for the first time that phosphotyrosine-mediated control affects global transcription in EHEC. Our data provide insight into a hitherto unexplored regulatory level of the global network controlling EHEC virulence gene expression.
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32
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Dai Y, Shortreed MR, Scalf M, Frey BL, Cesnik AJ, Solntsev S, Schaffer LV, Smith LM. Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. J Proteome Res 2017; 16:4156-4165. [PMID: 28968100 PMCID: PMC5679780 DOI: 10.1021/acs.jproteome.7b00516] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A proteoform family is a group of related molecular forms of a protein (proteoforms) derived from the same gene. We have previously described a strategy to identify proteoforms and elucidate proteoform families in complex mixtures of intact proteins. The strategy is based upon measurements of two properties for each proteoform: (i) the accurate proteoform intact-mass, measured by liquid chromatography/mass spectrometry (LC-MS), and (ii) the number of lysine residues in each proteoform, determined using an isotopic labeling approach. These measured properties are then compared with those extracted from a catalog of theoretical proteoforms containing protein sequences and localized post-translational modifications (PTMs) for the organism under study. A match between the measured properties and those in the catalog constitutes an identification of the proteoform. In the present study, this strategy is extended by utilizing a global PTM discovery database and is applied to the widely studied model organism Escherichia coli, providing the most comprehensive elucidation of E. coli proteoforms and proteoform families to date.
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Affiliation(s)
- Yunxiang Dai
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael R. Shortreed
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Brian L. Frey
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Anthony J. Cesnik
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Stefan Solntsev
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Leah V. Schaffer
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin, 425G Henry Mall, Room 3420, Madison, Wisconsin 53706, United States
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33
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Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO. Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions. BMC Genomics 2017; 18:301. [PMID: 28412930 PMCID: PMC5392934 DOI: 10.1186/s12864-017-3676-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 03/31/2017] [Indexed: 01/24/2023] Open
Abstract
Background Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which have only recently been recognized and studied in depth. It is increasingly apparent that a deep sampling of abundance across a wide range of environmental stresses, growth conditions, and PTM types, rather than simply cataloging targets for a handful of modifications, is critical to understanding the complex pathways that govern PTM deposition and downstream effects. Results We utilized a deeply-sampled dataset of MS/MS proteomic analysis covering 9 timepoints spanning the Escherichia coli growth cycle and an unbiased PTM search strategy to construct a temporal map of abundance for all PTMs within a 400 Da window of mass shifts. Using this map, we are able to identify novel targets and temporal patterns for N-terminal N α acetylation, C-terminal glutamylation, and asparagine deamidation. Furthermore, we identify a possible relationship between N-terminal N α acetylation and regulation of protein degradation in stationary phase, pointing to a previously unrecognized biological function for this poorly-understood PTM. Conclusions Unbiased detection of PTM in MS/MS proteomics data facilitates the discovery of novel modification types and previously unobserved dynamic changes in modification across growth timepoints. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3676-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colin W Brown
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Viswanadham Sridhara
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, USA
| | - Daniel R Boutz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Maria D Person
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
| | - Edward M Marcotte
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Jeffrey E Barrick
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Claus O Wilke
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA. .,Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, USA. .,Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA.
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34
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Grabowski B, Schmidt MA, Rüter C. Immunomodulatory Yersinia outer proteins (Yops)-useful tools for bacteria and humans alike. Virulence 2017; 8:1124-1147. [PMID: 28296562 DOI: 10.1080/21505594.2017.1303588] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human-pathogenic Yersinia produce plasmid-encoded Yersinia outer proteins (Yops), which are necessary to down-regulate anti-bacterial responses that constrict bacterial survival in the host. These Yops are effectively translocated directly from the bacterial into the target cell cytosol by the type III secretion system (T3SS). Cell-penetrating peptides (CPPs) in contrast are characterized by their ability to autonomously cross cell membranes and to transport cargo - independent of additional translocation systems. The recent discovery of bacterial cell-penetrating effector proteins (CPEs) - with the prototype being the T3SS effector protein YopM - established a new class of autonomously translocating immunomodulatory proteins. CPEs represent a vast source of potential self-delivering, anti-inflammatory therapeutics. In this review, we give an update on the characteristic features of the plasmid-encoded Yops and, based on recent findings, propose the further development of these proteins for potential therapeutic applications as natural or artificial cell-penetrating forms of Yops might be of value as bacteria-derived biologics.
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Affiliation(s)
- Benjamin Grabowski
- a Institute of Infectiology - Centre for Molecular Biology of Inflammation (ZMBE), University of Münster , Münster , Germany
| | - M Alexander Schmidt
- a Institute of Infectiology - Centre for Molecular Biology of Inflammation (ZMBE), University of Münster , Münster , Germany
| | - Christian Rüter
- a Institute of Infectiology - Centre for Molecular Biology of Inflammation (ZMBE), University of Münster , Münster , Germany
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35
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Vitrac H, MacLean DM, Karlstaedt A, Taegtmeyer H, Jayaraman V, Bogdanov M, Dowhan W. Dynamic Lipid-dependent Modulation of Protein Topology by Post-translational Phosphorylation. J Biol Chem 2016; 292:1613-1624. [PMID: 27974465 DOI: 10.1074/jbc.m116.765719] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/13/2016] [Indexed: 01/01/2023] Open
Abstract
Membrane protein topology and folding are governed by structural principles and topogenic signals that are recognized and decoded by the protein insertion and translocation machineries at the time of initial membrane insertion and folding. We previously demonstrated that the lipid environment is also a determinant of initial protein topology, which is dynamically responsive to post-assembly changes in membrane lipid composition. However, the effect on protein topology of post-assembly phosphorylation of amino acids localized within initially cytoplasmically oriented extramembrane domains has never been investigated. Here, we show in a controlled in vitro system that phosphorylation of a membrane protein can trigger a change in topological arrangement. The rate of change occurred on a scale of seconds, comparable with the rates observed upon changes in the protein lipid environment. The rate and extent of topological rearrangement were dependent on the charges of extramembrane domains and the lipid bilayer surface. Using model membranes mimicking the lipid compositions of eukaryotic organelles, we determined that anionic lipids, cholesterol, sphingomyelin, and membrane fluidity play critical roles in these processes. Our results demonstrate how post-translational modifications may influence membrane protein topology in a lipid-dependent manner, both along the organelle trafficking pathway and at their final destination. The results provide further evidence that membrane protein topology is dynamic, integrating for the first time the effect of changes in lipid composition and regulators of cellular processes. The discovery of a new topology regulatory mechanism opens additional avenues for understanding unexplored structure-function relationships and the development of optimized topology prediction tools.
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Affiliation(s)
- Heidi Vitrac
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030.
| | - David M MacLean
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Anja Karlstaedt
- the Department of Internal Medicine, Division of Cardiology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Heinrich Taegtmeyer
- the Department of Internal Medicine, Division of Cardiology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Vasanthi Jayaraman
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - Mikhail Bogdanov
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030
| | - William Dowhan
- From the Department of Biochemistry and Molecular Biology and Center for Membrane Biology, University of Texas McGovern Medical School, Houston, Texas 77030.
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36
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H-NS, Its Family Members and Their Regulation of Virulence Genes in Shigella Species. Genes (Basel) 2016; 7:genes7120112. [PMID: 27916940 PMCID: PMC5192488 DOI: 10.3390/genes7120112] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 12/04/2022] Open
Abstract
The histone-like nucleoid structuring protein (H-NS) has played a key role in shaping the evolution of Shigella spp., and provides the backdrop to the regulatory cascade that controls virulence by silencing many genes found on the large virulence plasmid. H-NS and its paralogue StpA are present in all four Shigella spp., but a second H-NS paralogue, Sfh, is found in the Shigella flexneri type strain 2457T, which is routinely used in studies of Shigella pathogenesis. While StpA and Sfh have been proposed to serve as “molecular backups” for H-NS, the apparent redundancy of these proteins is questioned by in vitro studies and work done in Escherichia coli. In this review, we describe the current understanding of the regulatory activities of the H-NS family members, the challenges associated with studying these proteins and their role in the regulation of virulence genes in Shigella.
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37
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Izumigawa M, Hasegawa Y, Ikai R, Horie T, Inomata M, Into T, Kitai N, Yoshimura F, Murakami Y. Separation of novel phosphoproteins of Porphyromonas gingivalis using phosphate-affinity chromatography. Microbiol Immunol 2016; 60:702-707. [PMID: 27663267 DOI: 10.1111/1348-0421.12441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/06/2016] [Accepted: 09/19/2016] [Indexed: 11/28/2022]
Abstract
Phosphorylation of serine, threonine and tyrosine is a central mechanism for regulating the structure and function of proteins in both eukaryotes and prokaryotes. However, the action of phosphorylated proteins present in Porphyromonas gingivalis, a major periodontopathogen, is not fully understood. Here, six novel phosphoproteins that possess metabolic activities were identified, namely PGN_0004, PGN_0375, PGN_0500, PGN_0724, PGN_0733 and PGN_0880, having been separated by phosphate-affinity chromatography. The identified proteins were detectable by immunoblotting specific to phosphorylated Ser (P-Ser), P-Thr, and/or P-Tyr. These results imply that novel phosphorylated proteins might play an important role for regulation of metabolism in P. gingivalis.
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Affiliation(s)
- Masashi Izumigawa
- Department of Oral Microbiology, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu 501-0296, Japan
| | - Yoshiaki Hasegawa
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Aichi, Japan.
| | - Ryota Ikai
- Department of Community Oral Health, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu 501-0296, Japan
| | - Toshi Horie
- Department of Oral Microbiology, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu 501-0296, Japan
| | - Megumi Inomata
- Department of Oral Microbiology, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu 501-0296, Japan
| | - Takeshi Into
- Department of Oral Microbiology, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu 501-0296, Japan
| | - Noriyuki Kitai
- Department of Orthodontic, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu 501-0296, Japan
| | - Fuminobu Yoshimura
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Aichi, Japan
| | - Yukitaka Murakami
- Department of Oral Microbiology, Asahi University School of Dentistry, 1851-1 Hozumi, Mizuho, Gifu 501-0296, Japan
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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: 17] [Impact Index Per Article: 2.1] [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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NADPH oxidase-derived H2O2 subverts pathogen signaling by oxidative phosphotyrosine conversion to PB-DOPA. Proc Natl Acad Sci U S A 2016; 113:10406-11. [PMID: 27562167 DOI: 10.1073/pnas.1605443113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Strengthening the host immune system to fully exploit its potential as antimicrobial defense is vital in countering antibiotic resistance. Chemical compounds released during bidirectional host-pathogen cross-talk, which follows a sensing-response paradigm, can serve as protective mediators. A potent, diffusible messenger is hydrogen peroxide (H2O2), but its consequences on extracellular pathogens are unknown. Here we show that H2O2, released by the host on pathogen contact, subverts the tyrosine signaling network of a number of bacteria accustomed to low-oxygen environments. This defense mechanism uses heme-containing bacterial enzymes with peroxidase-like activity to facilitate phosphotyrosine (p-Tyr) oxidation. An intrabacterial reaction converts p-Tyr to protein-bound dopa (PB-DOPA) via a tyrosinyl radical intermediate, thereby altering antioxidant defense and inactivating enzymes involved in polysaccharide biosynthesis and metabolism. Disruption of bacterial signaling by DOPA modification reveals an infection containment strategy that weakens bacterial fitness and could be a blueprint for antivirulence approaches.
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Standish AJ, Teh MY, Tran ENH, Doyle MT, Baker PJ, Morona R. Unprecedented Abundance of Protein Tyrosine Phosphorylation Modulates Shigella flexneri Virulence. J Mol Biol 2016; 428:4197-4208. [PMID: 27380737 DOI: 10.1016/j.jmb.2016.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/06/2016] [Accepted: 06/23/2016] [Indexed: 01/09/2023]
Abstract
Evidence is accumulating that protein tyrosine phosphorylation plays a crucial role in the ability of important human bacterial pathogens to cause disease. While most works have concentrated on its role in the regulation of a major bacterial virulence factor, the polysaccharide capsule, recent studies have suggested a much broader role for this post-translational modification. This prompted us to investigate protein tyrosine phosphorylation in the human pathogen Shigella flexneri. We first completed a tyrosine phosphoproteome, identifying 905 unique tyrosine phosphorylation sites on at least 573 proteins (approximately 15% of all proteins). This is the most tyrosine-phosphorylated sites and proteins in a single bacterium identified to date, substantially more than the level seen in eukaryotic cells. Most had not previously been identified and included proteins encoded by the virulence plasmid, which is essential for S. flexneri to invade cells and cause disease. In order to investigate the function of these phosphorylation sites in important virulence factors, phosphomimetic and ablative mutations were constructed in the type 3 secretion system ATPase Spa47 and the master virulence regulator VirB. This revealed that tyrosine residues phosphorylated in our study are critical for Spa47 and VirB activity, and tyrosine phosphorylation likely regulates their functional activity and subsequently the virulence of this major human pathogen. This study suggests that tyrosine phosphorylation plays a critical role in regulating a wide variety of virulence factors in the human pathogen S. flexneri and serves as a base for future studies defining its complete role.
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Affiliation(s)
- Alistair James Standish
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Min Yan Teh
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Elizabeth Ngoc Hoa Tran
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew Thomas Doyle
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Paul J Baker
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Renato Morona
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
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Ouidir T, Jouenne T, Hardouin J. Post-translational modifications in Pseudomonas aeruginosa revolutionized by proteomic analysis. Biochimie 2016; 125:66-74. [PMID: 26952777 DOI: 10.1016/j.biochi.2016.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 03/01/2016] [Indexed: 11/25/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes severe infections in vulnerable individuals. It is known that post-translational modifications (PTMs) play a key role in bacterial physiology. Their characterization is still challenging and the recent advances in proteomics allow large-scale and high-throughput analyses of PTMs. Here, we provide an overview of proteomic data about the modified proteins in P. aeruginosa. We emphasize the significant contribution of proteomics in knowledge enhancement of PTMs (phosphorylation, N-acetylation and glycosylation) and we discuss their importance in P. aeruginosa physiology.
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Affiliation(s)
- Tassadit Ouidir
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France.
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Garcia-Garcia T, Poncet S, Derouiche A, Shi L, Mijakovic I, Noirot-Gros MF. Role of Protein Phosphorylation in the Regulation of Cell Cycle and DNA-Related Processes in Bacteria. Front Microbiol 2016; 7:184. [PMID: 26909079 PMCID: PMC4754617 DOI: 10.3389/fmicb.2016.00184] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/02/2016] [Indexed: 11/26/2022] Open
Abstract
In all living organisms, the phosphorylation of proteins modulates various aspects of their functionalities. In eukaryotes, protein phosphorylation plays a key role in cell signaling, gene expression, and differentiation. Protein phosphorylation is also involved in the global control of DNA replication during the cell cycle, as well as in the mechanisms that cope with stress-induced replication blocks. Similar to eukaryotes, bacteria use Hanks-type kinases and phosphatases for signal transduction, and protein phosphorylation is involved in numerous cellular processes. However, it remains unclear whether protein phosphorylation in bacteria can also regulate the activity of proteins involved in DNA-mediated processes such as DNA replication or repair. Accumulating evidence supported by functional and biochemical studies suggests that phospho-regulatory mechanisms also take place during the bacterial cell cycle. Recent phosphoproteomics and interactomics studies identified numerous phosphoproteins involved in various aspect of DNA metabolism strongly supporting the existence of such level of regulation in bacteria. Similar to eukaryotes, bacterial scaffolding-like proteins emerged as platforms for kinase activation and signaling. This review reports the current knowledge on the phosphorylation of proteins involved in the maintenance of genome integrity and the regulation of cell cycle in bacteria that reveals surprising similarities to eukaryotes.
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Affiliation(s)
| | - Sandrine Poncet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
| | - Abderahmane Derouiche
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | - Lei Shi
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | - Ivan Mijakovic
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of TechnologyGothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
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Egan M, Ramirez J, Xander C, Upreti C, Bhatt S. Lambda Red-mediated Recombineering in the Attaching and Effacing Pathogen Escherichia albertii. Biol Proced Online 2016; 18:3. [PMID: 26843851 PMCID: PMC4739404 DOI: 10.1186/s12575-015-0032-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/29/2015] [Indexed: 02/06/2023] Open
Abstract
Background The ability to introduce site-specific mutations in bacterial pathogens is essential towards understanding their molecular mechanisms of pathogenicity. This has been greatly facilitated by the genetic engineering technique of recombineering. In recombineering, linear double- or single-stranded DNA molecules with two terminal homology arms are electroporated into hyperrecombinogenic bacteria that express a phage-encoded recombinase. The recombinase catalyzes the replacement of the endogenous allele with the exogenous allele to generate selectable or screenable recombinants. In particular, lambda red recombinase has been instrumental in engineering mutations to characterize the virulence arsenal of the attaching and effacing (A/E) pathogens enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC), and Citrobacter rodentium. Escherichia albertii is another member of this taxon; however, the virulence of E. albertii remains cryptic despite accumulating evidence that E. albertii is an emerging pathogen. Multiple retrospective studies have reported that a substantial number of EPEC and EHEC isolates (~15 %) that were previously incriminated in human outbreaks actually belong to the E. albertii lineage. Thus, there is increased urgency to reliably identify and rapidly engineer mutations in E. albertii to systematically characterize its virulence determinants. To the best of our knowledge not a single chromosomal gene has been altered by targeted mutagenesis in E. albertii since it was first isolated almost 25 years ago. This is disconcerting because an E. albertii outbreak could cause significant morbidity and mortality owing to our inadequate understanding of its virulence program. Results In this report we describe a modified lambda red recombineering protocol to mutagenize E. albertii. As proof of principle, we successfully deleted three distinct virulence-associated genetic loci – ler, grlRA, and hfq – and replaced each wild type allele by a mutant allele with an encodable drug resistance cassette bracketed by FRT sites. Subsequently, the FRT-site flanked drug resistance marker was evicted by FLP-dependent site-specific recombination to generate excisants containing a solitary FRT site. Conclusions Our protocol will enable researchers to construct marked and unmarked genome-wide mutations in E. albertii, which, in turn, will illuminate its molecular mechanisms of pathogenicity and aid in developing appropriate preventative and therapeutic approaches to combat E. albertii outbreaks.
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Affiliation(s)
- Marisa Egan
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131 USA ; Department of Mathematics, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131 USA
| | - Jasmine Ramirez
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131 USA ; Present address: Microbiology Department, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, 221 Johnson Pavilion, Philadelphia, PA 19104 USA
| | - Christian Xander
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131 USA ; Present address: Bluemle Life Sciences Building, Thomas Jefferson University, 233 South Tenth Street, Philadelphia, PA 19107 USA
| | - Chirag Upreti
- Howard Hughes Medical Institute, Columbia University Medical Center, Columbia, USA ; Columbia University Medical Center, 1051 Riverside Drive, New York, NY 10032 USA
| | - Shantanu Bhatt
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131 USA
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Tyrosine Phosphorylation and Dephosphorylation in Burkholderia cenocepacia Affect Biofilm Formation, Growth under Nutritional Deprivation, and Pathogenicity. Appl Environ Microbiol 2015; 82:843-56. [PMID: 26590274 DOI: 10.1128/aem.03513-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/14/2015] [Indexed: 11/20/2022] Open
Abstract
Burkholderia cenocepacia, a member of the B. cepacia complex (Bcc), is an opportunistic pathogen causing serious chronic infections in patients with cystic fibrosis. Tyrosine phosphorylation has emerged as an important posttranslational modification modulating the physiology and pathogenicity of Bcc bacteria. Here, we investigated the predicted bacterial tyrosine kinases BCAM1331 and BceF and the low-molecular-weight protein tyrosine phosphatases BCAM0208, BceD, and BCAL2200 of B. cenocepacia K56-2. We show that BCAM1331, BceF, BCAM0208, and BceD contribute to biofilm formation, while BCAL2200 is required for growth under nutrient-limited conditions. Multiple deletions of either tyrosine kinase or low-molecular-weight protein tyrosine phosphatase genes resulted in the attenuation of B. cenocepacia intramacrophage survival and reduced pathogenicity in the Galleria mellonella larval infection model. Experimental evidence indicates that BCAM1331 displays reduced tyrosine autophosphorylation activity compared to that of BceF. With the artificial substrate p-nitrophenyl phosphate, the phosphatase activities of the three low-molecular-weight protein tyrosine phosphatases demonstrated similar kinetic parameters. However, only BCAM0208 and BceD could dephosphorylate BceF. Further, BCAL2200 became tyrosine phosphorylated in vivo and catalyzed its autodephosphorylation. Together, our data suggest that despite having similar biochemical activities, low-molecular-weight protein tyrosine phosphatases and tyrosine kinases have both overlapping and specific roles in the physiology of B. cenocepacia.
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Ravikumar V, Jers C, Mijakovic I. Elucidating Host-Pathogen Interactions Based on Post-Translational Modifications Using Proteomics Approaches. Front Microbiol 2015; 6:1313. [PMID: 26635773 PMCID: PMC4653285 DOI: 10.3389/fmicb.2015.01312] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 11/09/2015] [Indexed: 11/13/2022] Open
Abstract
Microbes with the capability to survive in the host tissue and efficiently subvert its innate immune responses can cause various health hazards. There is an inherent need to understand microbial infection patterns and mechanisms in order to develop efficient therapeutics. Microbial pathogens display host specificity through a complex network of molecular interactions that aid their survival and propagation. Co-infection states further lead to complications by increasing the microbial burden and risk factors. Quantitative proteomics based approaches and post-translational modification analysis can be efficiently applied to gain an insight into the molecular mechanisms involved. The measurement of the proteome and post-translationally modified proteome dynamics using mass spectrometry, results in a wide array of information, such as significant changes in protein expression, protein abundance, the modification status, the site occupancy level, interactors, functional significance of key players, potential drug targets, etc. This mini review discusses the potential of proteomics to investigate the involvement of post-translational modifications in bacterial pathogenesis and host-pathogen interactions.
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Affiliation(s)
- Vaishnavi Ravikumar
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology , Gothenburg, Sweden
| | - Carsten Jers
- Department of Systems Biology, Technical University of Denmark , Lyngby, Denmark
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology , Gothenburg, Sweden ; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Hørsholm, Denmark
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Rosenberg A, Soufi B, Ravikumar V, Soares NC, Krug K, Smith Y, Macek B, Ben-Yehuda S. Phosphoproteome dynamics mediate revival of bacterial spores. BMC Biol 2015; 13:76. [PMID: 26381121 PMCID: PMC4574613 DOI: 10.1186/s12915-015-0184-7] [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: 03/02/2015] [Accepted: 08/27/2015] [Indexed: 12/19/2022] Open
Abstract
Background Bacterial spores can remain dormant for decades, yet harbor the exceptional capacity to rapidly resume metabolic activity and recommence life. Although germinants and their corresponding receptors have been known for more than 30 years, the molecular events underlying this remarkable cellular transition from dormancy to full metabolic activity are only partially defined. Results Here, we examined whether protein phospho-modifications occur during germination, the first step of exiting dormancy, thereby facilitating spore revival. Utilizing Bacillus subtilis as a model organism, we performed phosphoproteomic analysis to define the Ser/Thr/Tyr phosphoproteome of a reviving spore. The phosphoproteome was found to chiefly comprise newly identified phosphorylation sites located within proteins involved in basic biological functions, such as transcription, translation, carbon metabolism, and spore-specific determinants. Quantitative comparison of dormant and germinating spore phosphoproteomes revealed phosphorylation dynamics, indicating that phospho-modifications could modulate protein activity during this cellular transition. Furthermore, by mutating select phosphorylation sites located within proteins representative of key biological processes, we established a functional connection between phosphorylation and the progression of spore revival. Conclusions Herein, we provide, for the first time, a phosphoproteomic view of a germinating bacterial spore. We further show that the spore phosphoproteome is dynamic and present evidence that phosphorylation events play an integral role in facilitating spore revival. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0184-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alex Rosenberg
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, POB 12272, 91120, Jerusalem, Israel
| | - Boumediene Soufi
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany
| | - Vaishnavi Ravikumar
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany
| | - Nelson C Soares
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany
| | - Karsten Krug
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University - Hadassah Medical School, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Boris Macek
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany.
| | - Sigal Ben-Yehuda
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, POB 12272, 91120, Jerusalem, Israel.
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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: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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48
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Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions. J Proteomics 2015; 126:24-33. [DOI: 10.1016/j.jprot.2015.05.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/13/2015] [Accepted: 05/20/2015] [Indexed: 12/25/2022]
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Abstract
PURPOSE OF REVIEW Colonization of the host epithelia by pathogenic Escherichia coli is influenced by the ability of the bacteria to interact with host surfaces. Because the initial step of an E. coli infection is to adhere, invade, and persist within host cells, some strategies used by intestinal and extraintestinal E. coli to infect host cell are presented. RECENT FINDINGS This review highlights recent progress understanding how extraintestinal pathogenic E. coli strains express specific adhesins or invasins that allow colonization of the urinary tract or the meninges, while intestinal E. coli strains are able to colonize different regions of the intestinal tract using other specialized adhesins or invasins. Finally, evaluation of different diets and environmental conditions regulating the colonization of these pathogens is discussed. SUMMARY Discovery of new interactions between pathogenic E. coli and the host epithelial cells unravels the need for more mechanistic studies that can provide new clues regarding how to combat these infections.
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Pisithkul T, Patel NM, Amador-Noguez D. Post-translational modifications as key regulators of bacterial metabolic fluxes. Curr Opin Microbiol 2015; 24:29-37. [PMID: 25597444 DOI: 10.1016/j.mib.2014.12.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/22/2014] [Accepted: 12/30/2014] [Indexed: 01/05/2023]
Abstract
In order to survive and compete in natural settings, bacteria must excel at quickly adapting their metabolism to fluctuations in nutrient availability and other environmental variables. This necessitates fast-acting post-translational regulatory mechanisms, that is, allostery or covalent modification, to control metabolic flux. While allosteric regulation has long been a well-established strategy for regulating metabolic enzyme activity in bacteria, covalent post-translational modes of regulation, such as phosphorylation or acetylation, have previously been regarded as regulatory mechanisms employed primarily by eukaryotic organisms. Recent findings, however, have shifted this perception and point to a widespread role for covalent posttranslational modification in the regulation of metabolic enzymes and fluxes in bacteria. This review provides an outline of the exciting recent advances in this area.
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Affiliation(s)
- Tippapha Pisithkul
- Cellular and Molecular Biology, University of Wisconsin-Madison, United States; Department of Bacteriology, University of Wisconsin-Madison, United States
| | - Nishaben M Patel
- Department of Bacteriology, University of Wisconsin-Madison, United States
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