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Lu K, Wang X, Zhou Y, Zhu Q. Genomic characterization and probiotic potential assessment of an exopolysaccharide-producing strain Pediococcus pentosaceus LL-07 isolated from fermented meat. BMC Microbiol 2024; 24:142. [PMID: 38664612 PMCID: PMC11044368 DOI: 10.1186/s12866-024-03304-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND The genomic information available for Pediococcus pentosaceus is primarily derived from fermented fruits and vegetables, with less information available from fermented meat. P. pentosaceus LL-07, a strain isolated from fermented meat, has the capability of producing exopolysaccharides (EPS). To assess the probiotic attributes of P. pentosaceus LL-07, we conducted whole-genome sequencing (WGS) using the PacBio SequelIIe and Illumina MiSeq platforms, followed by in vitro experiments to explore its probiotic potential. RESULTS The genome size of P. pentosaceus LL-07 is 1,782,685 bp, comprising a circular chromosome and a circular plasmid. Our investigation revealed the absence of a CRISPR/Cas system. Sugar fermentation experiments demonstrated the characteristics of carbohydrate metabolism. P. pentosaceus LL-07 contains an EPS synthesis gene cluster consisting of 13 genes, which is different from the currently known gene cluster structure. NO genes associated with hemolysis or toxin synthesis were detected. Additionally, eighty-six genes related to antibiotic resistance were identified but not present in the prophage, transposon or plasmid. In vitro experiments demonstrated that P. pentosaceus LL-07 was comparable to the reference strain P. pentosaceus ATCC25745 in terms of tolerance to artificial digestive juice and bile, autoaggregation and antioxidation, and provided corresponding genomic evidence. CONCLUSION This study confirmed the safety and probiotic properties of P. pentosaceus LL-07 via complete genome and phenotype analysis, supporting its characterization as a potential probiotic candidate.
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Affiliation(s)
- Kuan Lu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guizhou Province, Guiyang, 550025, China
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China
| | - Xueya Wang
- Chili Pepper Research Institute, Guizhou Provincial Academy of Agricultural Sciences, Guizhou, Guiyang, 550006, China
| | - Ying Zhou
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China
| | - Qiujin Zhu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guizhou Province, Guiyang, 550025, China.
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China.
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2
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Priyodip P, Balaji S. Characterization of a putative metal-dependent PTP-like phosphatase from Lactobacillus helveticus 2126. Int Microbiol 2024; 27:37-47. [PMID: 37365352 PMCID: PMC10830716 DOI: 10.1007/s10123-023-00390-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: 06/17/2022] [Revised: 04/01/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023]
Abstract
To date, there are very limited reports on sequence analysis and structure-based molecular modeling of phosphatases produced by probiotic bacteria. Therefore, a novel protein tyrosine-like phosphatase was characterized from L. helveticus 2126 in this study. The purified bacterial phosphatase was subjected to mass spectrometric analysis, and the identity of constructed sequence was analyzed using peptide mass fingerprint. The 3-D structure of protein was elucidated using homology modeling, while its stability was assessed using Ramachandran plot, VERIFY 3D, and PROCHECK. The bacterium produced an extracellular phosphatase of zone diameter 15 ± 0.8 mm on screening medium within 24 h of incubation. This bacterial phosphatase was highly specific towards sodium phytate as it yielded the lowest Km value of 299.50 ± 4.95 μM compared to other phosphorylated substrates. The activity was effectively stimulated in the presence of zinc, magnesium, and manganese ions thereby showing its PTP-like behavior. The phosphatase showed a molecular mass of 43 kDa, and the corresponding M/Z ratio data yielded 46% query coverage to Bacillus subtilis (3QY7). This showed a 61.1% sequence similarity to Ligilactobacillus ruminis (WP_046923835.1). The final sequence construct based on these bacteria showed a conserved motif "HCHILPGIDD" in their active site. In addition, homology modeling showed a distorted Tim barrel structure with a trinuclear metal center. The final model after energy minimization showed 90.9% of the residues in the favorable region of Ramachandran's plot. This structural information can be used in genetic engineering for improving the overall stability and catalytic efficiency of probiotic bacterial phosphatases.
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Affiliation(s)
- Paul Priyodip
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, -576104, Manipal, Karnataka, India
| | - Seetharaman Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, -576104, Manipal, Karnataka, India.
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3
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Aberuagba A, Joel EB, Bello AJ, Igunnu A, Malomo SO, Olorunniji FJ. Thermophilic PHP Protein Tyrosine Phosphatases (Cap8C and Wzb) from Mesophilic Bacteria. Int J Mol Sci 2024; 25:1262. [PMID: 38279261 PMCID: PMC10816263 DOI: 10.3390/ijms25021262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Protein tyrosine phosphatases (PTPs) of the polymerase and histidinol phosphatase (PHP) superfamily with characteristic phosphatase activity dependent on divalent metal ions are found in many Gram-positive bacteria. Although members of this family are co-purified with metal ions, they still require the exogenous supply of metal ions for full activation. However, the specific roles these metal ions play during catalysis are yet to be well understood. Here, we report the metal ion requirement for phosphatase activities of S. aureus Cap8C and L. rhamnosus Wzb. AlphaFold-predicted structures of the two PTPs suggest that they are members of the PHP family. Like other PHP phosphatases, the two enzymes have a catalytic preference for Mn2+, Co2+ and Ni2+ ions. Cap8C and Wzb show an unusual thermophilic property with optimum activities over 75 °C. Consistent with this model, the activity-temperature profiles of the two enzymes are dependent on the divalent metal ion activating the enzyme.
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Affiliation(s)
- Adepeju Aberuagba
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
| | - Enoch B. Joel
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos 930003, Nigeria
| | - Adebayo J. Bello
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
| | - Adedoyin Igunnu
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin 234031, Nigeria; (A.I.); (S.O.M.)
| | - Sylvia O. Malomo
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin 234031, Nigeria; (A.I.); (S.O.M.)
| | - Femi J. Olorunniji
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
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4
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Shukla S, Rawat P, Sharma P, Trivedi P, Ghous F, Bishnoi A. Spectroscopic characterization, molecular docking and machine learning studies of sulphur containing hydrazide derivatives. Phys Chem Chem Phys 2023; 25:27677-27693. [PMID: 37812135 DOI: 10.1039/d3cp01133j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Machine learning applied in chemistry is a growing field of research. For assessing structure-property variations, this paper describes in silico studies of the hydrazide derivatives of thiosemicarbazide (TSCZ) and thiocarbohydrazide (TCHZ). The structures of TSCZ and TCHZ have been elucidated using modern spectroscopic techniques. The UV-vis spectra showed strong charge transfer transitions (π-π*) for TSCZ and TCHZ with high extinction coefficients. The NBO analysis showed orbital overlap between lp1 (N2) and σ* (C3-S4) in TSCZ and TCHZ due to intramolecular charge transfer. The first hyperpolarizabilities (β0) for TSCZ and TCHZ were found to be 0.7155 and 2.1615 × 10-30 esu, respectively, indicating their greater suitability for NLO applications as compared to standard reference urea. The strong electrophilic behaviour of TSCZ and TCHZ has been indicated by their global elecrophilicity index. The electrophilic reactivity descriptor analysis indicated that the investigated molecules could serve as precursors for the targeted synthesis of new heterocyclic derivatives. The docking studies showed appreciable binding energies with target proteins having PDB IDs 2WJE and 6CLU of Gram-positive bacteria, namely, Streptococcus pneumoniae phosphatase (PTP-CPS4B) and Staphylococcus aureus dihydropteroate synthase (saDHPS), respectively, for TSCZ and TCHZ, predicting good antimicrobial activity.
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Affiliation(s)
- Soni Shukla
- Department of Chemistry, University of Lucknow, Lucknow-226007, Uttar Pradesh, India.
| | - Poonam Rawat
- Department of Chemistry, University of Lucknow, Lucknow-226007, Uttar Pradesh, India.
| | - Pulkit Sharma
- Department of Chemistry, University of Lucknow, Lucknow-226007, Uttar Pradesh, India.
| | - Prince Trivedi
- Department of Chemistry, University of Lucknow, Lucknow-226007, Uttar Pradesh, India.
| | - Faraz Ghous
- Department of Chemistry, University of Lucknow, Lucknow-226007, Uttar Pradesh, India.
| | - Abha Bishnoi
- Department of Chemistry, University of Lucknow, Lucknow-226007, Uttar Pradesh, India.
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5
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Edison LK, Kudva IT, Kariyawasam S. Comparative Transcriptome Analysis of Shiga Toxin-Producing Escherichia coli O157:H7 on Bovine Rectoanal Junction Cells and Human Colonic Epithelial Cells during Initial Adherence. Microorganisms 2023; 11:2562. [PMID: 37894220 PMCID: PMC10609592 DOI: 10.3390/microorganisms11102562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are notorious foodborne pathogens, capable of causing severe diarrhea and life-threatening complications in humans. Cattle, acting as both primary reservoirs and asymptomatic carriers of STEC, predominantly harbor the pathogen in their rectoanal junction (RAJ), facilitating its transmission to humans through contaminated food sources. Despite the central role of cattle in STEC transmission, the molecular mechanisms governing STEC's adaptation in the RAJ of the asymptomatic reservoir host and its subsequent infection of human colonic epithelial cells, resulting in diarrhea, remain largely unexplored. This study aims to uncover these complicated dynamics by focusing on the STEC O157:H7 serotype within two distinct host environments, bovine RAJ cells and human colonic epithelial cells, during initial colonization. We employed comparative transcriptomics analysis to investigate differential gene expression profiles of STEC O157:H7 during interactions with these cell types. STEC O157:H7 was cultured either with bovine RAJ cells or the human colonic epithelial cell line CCD CoN 841 to simulate STEC-epithelial cell interactions within these two host species. High-throughput RNA sequencing revealed 829 and 1939 bacterial genes expressed in RAJ and CCD CoN 841, respectively. After gene filtering, 221 E. coli O157:H7 genes were upregulated during initial adherence to CCD CoN cells and 436 with RAJ cells. Furthermore, 22 genes were uniquely expressed with human cells and 155 genes with bovine cells. Our findings revealed distinct expression patterns of STEC O157:H7 genes involved in virulence, including adherence, metal iron homeostasis, and stress response during its initial adherence (i.e., six hours post-infection) to bovine RAJ cells, as opposed to human colonic epithelial cells. Additionally, the comparative analysis highlighted the potential role of some genes in host adaptation and tissue-specific pathogenicity. These findings shed new light on the potential mechanisms of STEC O157:H7 contributing to colonize the intestinal epithelium during the first six hours of infection, leading to survival and persistence in the bovine reservoir and causing disease in humans.
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Affiliation(s)
- Lekshmi K. Edison
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Indira T. Kudva
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, IA 50010, USA;
| | - Subhashinie Kariyawasam
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA;
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6
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El-Shall FN, Fahim AM, Dacrory S. Making a new bromo-containing cellulosic dye with antibacterial properties for use on various fabrics using computational research. Sci Rep 2023; 13:10066. [PMID: 37344546 DOI: 10.1038/s41598-023-36688-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023] Open
Abstract
The reaction of cyanoethyl cellulose with para-bromo diazonium chloride resulted in the creation of a novel bromo-containing cellulosic (MCPT). The dispersion stability of MCPT has been improved by its dispersion into 1% waterborne polyurethane acrylate (WPUA). TEM, particle size, and zeta potential were used to track the dispersion stability of aqueous MCPT and MCPT in 1% WPUA and particle size. The prepared MCPT has been utilized as a unique green colorant (dye) for the printing of cotton, polyester, and cotton/polyester blend fabrics using a silkscreen printing technique through a single printing step and one color system. Color improvement has been achieved by printing different fabrics with a printing paste of MCPT dispersed in 1% WPUA. The MCPT and MCPT in 1% WPUA printed fabrics were evaluated for rubbing, light, washing, and perspiration fastness, UV blocking activity, and antibacterial activity. These findings were established through structural optimization at the DFT/B3LYP/6-31 (G) level and simulations involving several proteins.
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Affiliation(s)
- Fatma N El-Shall
- Dyeing, Printing and Textile Auxiliaries Department, National Research Centre, P.O. Box 12622, Dokki, Cairo, Egypt
| | - Asmaa M Fahim
- Green Chemistry Department, National Research Center, P.O. Box 12622, Dokki, Cairo, Egypt.
| | - Sawsan Dacrory
- Cellulose and Paper Department, National Research Centre, Giza, 12622, Egypt
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7
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Tang J, Guo M, Chen M, Xu B, Ran T, Wang W, Ma Z, Lin H, Fan H. A link between STK signalling and capsular polysaccharide synthesis in Streptococcus suis. Nat Commun 2023; 14:2480. [PMID: 37120581 PMCID: PMC10148854 DOI: 10.1038/s41467-023-38210-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 04/20/2023] [Indexed: 05/01/2023] Open
Abstract
Synthesis of capsular polysaccharide (CPS), an important virulence factor of pathogenic bacteria, is modulated by the CpsBCD phosphoregulatory system in Streptococcus. Serine/threonine kinases (STKs, e.g. Stk1) can also regulate CPS synthesis, but the underlying mechanisms are unclear. Here, we identify a protein (CcpS) that is phosphorylated by Stk1 and modulates the activity of phosphatase CpsB in Streptococcus suis, thus linking Stk1 to CPS synthesis. The crystal structure of CcpS shows an intrinsically disordered region at its N-terminus, including two threonine residues that are phosphorylated by Stk1. The activity of phosphatase CpsB is inhibited when bound to non-phosphorylated CcpS. Thus, CcpS modulates the activity of phosphatase CpsB thereby altering CpsD phosphorylation, which in turn modulates the expression of the Wzx-Wzy pathway and thus CPS production.
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Affiliation(s)
- Jinsheng Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengru Guo
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bin Xu
- National Research Center of Veterinary Biologicals Engineering and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210000, China
| | - Tingting Ran
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiwu Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhe Ma
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Huixing Lin
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Hongjie Fan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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8
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Synthesis, spectral investigation, biological activities and docking stimulation of novel metal complexes of Trifluoro phenylthiazol derivative with computational studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Synthesis, characterization, antibacterial activities, molecular docking, and computational investigation of novel imine-linked covalent organic framework. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Synthesis of novel antipyrine-azole-S-alkyl derivatives antimicrobial activity, molecular docking, and computational studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Synthesis, X-ray crystal structure, Hirshfeld analysis and computational investigation of bis(methylthio)acrylonitrile with antimicrobial and docking evaluation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Alphonse S, Djemil I, Piserchio A, Ghose R. Structural basis for the recognition of the bacterial tyrosine kinase Wzc by its cognate tyrosine phosphatase Wzb. Proc Natl Acad Sci U S A 2022; 119:e2201800119. [PMID: 35737836 PMCID: PMC9245664 DOI: 10.1073/pnas.2201800119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/07/2022] [Indexed: 12/25/2022] Open
Abstract
Bacterial tyrosine kinases (BY-kinases) comprise a family of protein tyrosine kinases that are structurally distinct from their functional counterparts in eukaryotes and are highly conserved across the bacterial kingdom. BY-kinases act in concert with their counteracting phosphatases to regulate a variety of cellular processes, most notably the synthesis and export of polysaccharides involved in biofilm and capsule biogenesis. Biochemical data suggest that BY-kinase function involves the cyclic assembly and disassembly of oligomeric states coupled to the overall phosphorylation levels of a C-terminal tyrosine cluster. This process is driven by the opposing effects of intermolecular autophosphorylation, and dephosphorylation catalyzed by tyrosine phosphatases. In the absence of structural insight into the interactions between a BY-kinase and its phosphatase partner in atomic detail, the precise mechanism of this regulatory process has remained poorly defined. To address this gap in knowledge, we have determined the structure of the transiently assembled complex between the catalytic core of the Escherichia coli (K-12) BY-kinase Wzc and its counteracting low-molecular weight protein tyrosine phosphatase (LMW-PTP) Wzb using solution NMR techniques. Unambiguous distance restraints from paramagnetic relaxation effects were supplemented with ambiguous interaction restraints from static spectral perturbations and transient chemical shift changes inferred from relaxation dispersion measurements and used in a computational docking protocol for structure determination. This structurepresents an atomic picture of the mode of interaction between an LMW-PTP and its BY-kinase substrate, and provides mechanistic insight into the phosphorylation-coupled assembly/disassembly process proposed to drive BY-kinase function.
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Affiliation(s)
- Sébastien Alphonse
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031
| | - Imane Djemil
- PhD Program in Biochemistry, The Graduate Center of The City University of New York (CUNY), New York, NY 10016
| | - Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031
- PhD Program in Biochemistry, The Graduate Center of The City University of New York (CUNY), New York, NY 10016
- PhD Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016
- PhD Program in Physics, The Graduate Center of CUNY, New York, NY 10016
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13
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Kay EJ, Mauri M, Willcocks SJ, Scott TA, Cuccui J, Wren BW. Engineering a suite of E. coli strains for enhanced expression of bacterial polysaccharides and glycoconjugate vaccines. Microb Cell Fact 2022; 21:66. [PMID: 35449016 PMCID: PMC9026721 DOI: 10.1186/s12934-022-01792-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycoengineering, in the biotechnology workhorse bacterium, Escherichia coli, is a rapidly evolving field, particularly for the production of glycoconjugate vaccine candidates (bioconjugation). Efficient production of glycoconjugates requires the coordinated expression within the bacterial cell of three components: a carrier protein, a glycan antigen and a coupling enzyme, in a timely fashion. Thus, the choice of a suitable E. coli host cell is of paramount importance. Microbial chassis engineering has long been used to improve yields of chemicals and biopolymers, but its application to vaccine production is sparse. RESULTS In this study we have engineered a family of 11 E. coli strains by the removal and/or addition of components rationally selected for enhanced expression of Streptococcus pneumoniae capsular polysaccharides with the scope of increasing yield of pneumococcal conjugate vaccines. Importantly, all strains express a detoxified version of endotoxin, a concerning contaminant of therapeutics produced in bacterial cells. The genomic background of each strain was altered using CRISPR in an iterative fashion to generate strains without antibiotic markers or scar sequences. CONCLUSIONS Amongst the 11 modified strains generated in this study, E. coli Falcon, Peregrine and Sparrowhawk all showed increased production of S. pneumoniae serotype 4 capsule. Eagle (a strain without enterobacterial common antigen, containing a GalNAc epimerase and PglB expressed from the chromosome) and Sparrowhawk (a strain without enterobacterial common antigen, O-antigen ligase and chain length determinant, containing a GalNAc epimerase and chain length regulators from Streptococcus pneumoniae) respectively produced an AcrA-SP4 conjugate with 4 × and 14 × more glycan than that produced in the base strain, W3110. Beyond their application to the production of pneumococcal vaccine candidates, the bank of 11 new strains will be an invaluable resource for the glycoengineering community.
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Affiliation(s)
- Emily J Kay
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Marta Mauri
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Sam J Willcocks
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Timothy A Scott
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jon Cuccui
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
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14
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Ren L, Shen D, Liu C, Ding Y. Protein Tyrosine and Serine/Threonine Phosphorylation in Oral Bacterial Dysbiosis and Bacteria-Host Interaction. Front Cell Infect Microbiol 2022; 11:814659. [PMID: 35087767 PMCID: PMC8787120 DOI: 10.3389/fcimb.2021.814659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/13/2021] [Indexed: 02/05/2023] Open
Abstract
The human oral cavity harbors approximately 1,000 microbial species, and dysbiosis of the microflora and imbalanced microbiota-host interactions drive many oral diseases, such as dental caries and periodontal disease. Oral microbiota homeostasis is critical for systemic health. Over the last two decades, bacterial protein phosphorylation systems have been extensively studied, providing mounting evidence of the pivotal role of tyrosine and serine/threonine phosphorylation in oral bacterial dysbiosis and bacteria-host interactions. Ongoing investigations aim to discover novel kinases and phosphatases and to understand the mechanism by which these phosphorylation events regulate the pathogenicity of oral bacteria. Here, we summarize the structures of bacterial tyrosine and serine/threonine kinases and phosphatases and discuss the roles of tyrosine and serine/threonine phosphorylation systems in Porphyromonas gingivalis and Streptococcus mutans, emphasizing their involvement in bacterial metabolism and virulence, community development, and bacteria-host interactions.
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Affiliation(s)
- Liang Ren
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Daonan Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yi Ding
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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15
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Sande C, Whitfield C. Capsules and Extracellular Polysaccharides in Escherichia coli and Salmonella. EcoSal Plus 2021; 9:eESP00332020. [PMID: 34910576 PMCID: PMC11163842 DOI: 10.1128/ecosalplus.esp-0033-2020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 10/26/2021] [Indexed: 12/16/2022]
Abstract
Escherichia coli and Salmonella isolates produce a range of different polysaccharide structures that play important roles in their biology. E. coli isolates often possess capsular polysaccharides (K antigens), which form a surface structural layer. These possess a wide range of repeat-unit structures. In contrast, only one capsular polymer (Vi antigen) is found in Salmonella, and it is confined to typhoidal serovars. In both genera, capsules are vital virulence determinants and are associated with the avoidance of host immune defenses. Some isolates of these species also produce a largely secreted exopolysaccharide called colanic acid as part of their complex Rcs-regulated phenotypes, but the precise function of this polysaccharide in microbial cell biology is not fully understood. E. coli isolates produce two additional secreted polysaccharides, bacterial cellulose and poly-N-acetylglucosamine, which play important roles in biofilm formation. Cellulose is also produced by Salmonella isolates, but the genes for poly-N-acetylglucosamine synthesis appear to have been lost during its evolution toward enhanced virulence. Here, we discuss the structures, functions, relationships, and sophisticated assembly mechanisms for these important biopolymers.
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Affiliation(s)
- Caitlin Sande
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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16
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Enhancement of Molecular imprinted polymer as organic fillers on bagasse cellulose fibers with biological evaluation and computational calculations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130660] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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17
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Yang Y, Liu J, Clarke BR, Seidel L, Bolla JR, Ward PN, Zhang P, Robinson CV, Whitfield C, Naismith JH. The molecular basis of regulation of bacterial capsule assembly by Wzc. Nat Commun 2021; 12:4349. [PMID: 34272394 PMCID: PMC8285477 DOI: 10.1038/s41467-021-24652-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/29/2021] [Indexed: 01/06/2023] Open
Abstract
Bacterial extracellular polysaccharides (EPSs) play critical roles in virulence. Many bacteria assemble EPSs via a multi-protein "Wzx-Wzy" system, involving glycan polymerization at the outer face of the cytoplasmic/inner membrane. Gram-negative species couple polymerization with translocation across the periplasm and outer membrane and the master regulator of the system is the tyrosine autokinase, Wzc. This near atomic cryo-EM structure of dephosphorylated Wzc from E. coli shows an octameric assembly with a large central cavity formed by transmembrane helices. The tyrosine autokinase domain forms the cytoplasm region, while the periplasmic region contains small folded motifs and helical bundles. The helical bundles are essential for function, most likely through interaction with the outer membrane translocon, Wza. Autophosphorylation of the tyrosine-rich C-terminus of Wzc results in disassembly of the octamer into multiply phosphorylated monomers. We propose that the cycling between phosphorylated monomer and dephosphorylated octamer regulates glycan polymerization and translocation.
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Affiliation(s)
- Yun Yang
- Rosalind Franklin Institute, Harwell Campus, Harwell, UK.,Division of Structural Biology, The University of Oxford, Oxford, UK.,The Research Complex at Harwell, Harwell Campus, Harwell, UK
| | - Jiwei Liu
- Rosalind Franklin Institute, Harwell Campus, Harwell, UK.,Division of Structural Biology, The University of Oxford, Oxford, UK
| | - Bradley R Clarke
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, ON, Canada
| | - Laura Seidel
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, ON, Canada
| | - Jani R Bolla
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, South Parks Road, The University of Oxford, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Philip N Ward
- Rosalind Franklin Institute, Harwell Campus, Harwell, UK.,Division of Structural Biology, The University of Oxford, Oxford, UK.,The Research Complex at Harwell, Harwell Campus, Harwell, UK
| | - Peijun Zhang
- Division of Structural Biology, The University of Oxford, Oxford, UK.,Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Harwell, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, South Parks Road, The University of Oxford, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, ON, Canada.
| | - James H Naismith
- Rosalind Franklin Institute, Harwell Campus, Harwell, UK. .,Division of Structural Biology, The University of Oxford, Oxford, UK. .,The Research Complex at Harwell, Harwell Campus, Harwell, UK.
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18
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Cellular Mn/Zn Ratio Influences Phosphoglucomutase Activity and Capsule Production in Streptococcus pneumoniae D39. J Bacteriol 2021; 203:e0060220. [PMID: 33875543 PMCID: PMC8316032 DOI: 10.1128/jb.00602-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Capsular polysaccharide (CPS) is a major virulence determinant for many human-pathogenic bacteria. Although the essential functional roles for CPS in bacterial virulence have been established, knowledge of how CPS production is regulated remains limited. Streptococcus pneumoniae (pneumococcus) CPS expression levels and overall thickness change in response to available oxygen and carbohydrate. These nutrients in addition to transition metal ions can vary significantly between host environmental niches and infection stage. Since the pneumococcus must modulate CPS expression among various host niches during disease progression, we examined the impact of the nutritional transition metal availability of manganese (Mn) and zinc (Zn) on CPS production. We demonstrate that increased Mn/Zn ratios increase CPS production via Mn-dependent activation of the phosphoglucomutase Pgm, an enzyme that functions at the branch point between glycolysis and the CPS biosynthetic pathway in a transcription-independent manner. Furthermore, we find that the downstream CPS protein CpsB, an Mn-dependent phosphatase, does not promote aberrant dephosphorylation of its target capsule-tyrosine kinase CpsD during Mn stress. Together, these data reveal a direct role for cellular Mn/Zn ratios in the regulation of CPS biosynthesis via the direct activation of Pgm. We propose a multilayer mechanism used by the pneumococcus in regulating CPS levels across various host niches. IMPORTANCE Evolving evidence strongly indicates that maintenance of metal homeostasis is essential for establishing colonization and continued growth of bacterial pathogens in the vertebrate host. In this study, we demonstrate the impact of cellular manganese/zinc (Mn/Zn) ratios on bacterial capsular polysaccharide (CPS) production, an important virulence determinant of many human-pathogenic bacteria, including Streptococcus pneumoniae. We show that higher Mn/Zn ratios increase CPS production via the Mn-dependent activation of the phosphoglucomutase Pgm, an enzyme that functions at the branch point between glycolysis and the CPS biosynthetic pathway. The findings provide a direct role for Mn/Zn homeostasis in the regulation of CPS expression levels and further support the ability of metal cations to act as important cellular signaling mediators in bacteria.
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19
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Synthesis, antimicrobial and antiproliferative activities, molecular docking, and computational studies of novel heterocycles. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2021. [DOI: 10.1007/s13738-021-02251-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Performance efficiency of MIPOH polymers as organic filler on cellulose pulp waste to form cellulosic paper sheets with biological evaluation and computational studies. Polym Bull (Berl) 2021. [DOI: 10.1007/s00289-021-03685-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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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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22
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Niu T, Guo L, Luo Q, Zhou K, Yu W, Chen Y, Huang C, Xiao Y. Wza gene knockout decreases Acinetobacter baumannii virulence and affects Wzy-dependent capsular polysaccharide synthesis. Virulence 2021; 11:1-13. [PMID: 31878839 PMCID: PMC6961727 DOI: 10.1080/21505594.2019.1700659] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
To investigate the virulence of capsular polysaccharide export protein (Wza) in carbapenem-resistant Acinetobacter baumannii and its effect on capsule formation. wza gene knockout and complementation strains were constructed, and changes in bacterial virulence were observed using in vitro adhesion, antiserum complement killing, anti-oxidation experiments, and infections in Galleria mellonella and mice. The effect of wza knockout on the genes wzb and wzc and wzi were assessed by RT-PCR. We successfully constructed wza knockout and complementation strains. Compared with wild-type (WT) strains, wza knockout strains displayed lower adhesion to A549 cells (p = 0.044), lower antiserum complement killing ability (p = 0.001), and lower mortality of G. mellonella (p = 0.010) and mice (p = 0.033). Expression levels of wzb, wzc and wzi were decreased in wza knockout strains. The antioxidant capacity of Wza knockout bacteria was only slightly decreased. Complementation of the wza gene returned the adhesion ability, antiserum complement killing ability, and mortality of G. mellonella and mice to WT levels. Expression of wzb, wzc and wzi was also returned to WT levels following wza complementation. The results clearly demonstrate that Wza is toxic. Wza affects the expression of other proteins of the Wzy capsule polysaccharide synthesis pathway, which affects the assembly, export, and extracellular fixation of capsular polysaccharide, resulting in synergistic effects that decrease bacterial virulence.
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Affiliation(s)
- Tianshui Niu
- Collaborative Initiative Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, the First Affiliated Hospital, college of Medicine, Zhejiang University, Hangzhou, China.,Hangzhou Red Cross Hospital/Zhe Jiang Chinese Medcine and Western Medcine Integrated Hospital, Hangzhou, China
| | - Lihua Guo
- Collaborative Initiative Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, the First Affiliated Hospital, college of Medicine, Zhejiang University, Hangzhou, China
| | - Qixia Luo
- Collaborative Initiative Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, the First Affiliated Hospital, college of Medicine, Zhejiang University, Hangzhou, China
| | - Kai Zhou
- Collaborative Initiative Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, the First Affiliated Hospital, college of Medicine, Zhejiang University, Hangzhou, China
| | - Wei Yu
- Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yunbo Chen
- Collaborative Initiative Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, the First Affiliated Hospital, college of Medicine, Zhejiang University, Hangzhou, China
| | - Chen Huang
- Collaborative Initiative Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, the First Affiliated Hospital, college of Medicine, Zhejiang University, Hangzhou, China
| | - Yonghong Xiao
- Collaborative Initiative Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, the First Affiliated Hospital, college of Medicine, Zhejiang University, Hangzhou, China
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23
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Sierra-López F, Baylón-Pacheco L, Vanegas-Villa SC, Rosales-Encina JL. Characterization of low molecular weight protein tyrosine phosphatases of Entamoeba histolytica. Biochimie 2021; 180:43-53. [PMID: 33122104 DOI: 10.1016/j.biochi.2020.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/20/2020] [Accepted: 10/24/2020] [Indexed: 12/12/2022]
Abstract
Entamoeba histolytica is an intestinal protozoan parasite of humans and is endemic in developing countries. E. histolytica has two low molecular weight protein tyrosine phosphatase (LMW-PTP) genes, EhLMW-PTP1 and EhLMW-PTP2, which are expressed in cultured trophozoites, clinical isolates, and cysts. The amino acid sequences of proteins EhLMW-PTP1 and EhLMW-PTP2 showed only one amino acid difference between them at position A85V, respectively. Both genes are expressed in cultured trophozoites, mainly EhLMW-PTP2, and in trophozoites recovered from amoebic liver abscess, the expression of EhLMW-PTP1 is downregulated. We cloned the two genes and purified the corresponding recombinant (rEhLMW-PTPs) proteins. Antibodies anti-rEhLMW-PTP2 showed that during red blood cells uptake by E. histolytica, the EhLMW-PTPs were found in the phagocytic cups based on analysis of fluorescence signals. On the other hand, rEhLMW-PTPs showed an optimum phosphatase activity at pH 6.0 with p-nitrophenyl phosphate as the substrate. They dephosphorylate phosphotyrosine and 3-O-methylfluorescein phosphate, but not phosphoserine or phosphothreonine, and the enzymatic activity is inhibited by orthovanadate. rEhLMW-PTP1 and rEhLMW-PTP2 exhibited optimum temperatures of activities at 60 °C and 58 °C, respectively, with high thermal stability at 50 °C. Also, the rEhLMW-PTPs showed high specific activities and specific km value with pNPP or OMFP as the substrates at the physiological temperature (37 °C).
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Affiliation(s)
- Francisco Sierra-López
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., Ciudad de México, Mexico.
| | - Lidia Baylón-Pacheco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., Ciudad de México, Mexico.
| | - Sonia Cynthia Vanegas-Villa
- Programa de Doctorado en Ciencias Biomédicas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de, Mexico.
| | - José Luis Rosales-Encina
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., Ciudad de México, Mexico.
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24
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Su T, Nakamoto R, Chun YY, Chua WZ, Chen JH, Zik JJ, Sham LT. Decoding capsule synthesis in Streptococcus pneumoniae. FEMS Microbiol Rev 2020; 45:6041728. [PMID: 33338218 DOI: 10.1093/femsre/fuaa067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pneumoniae synthesizes more than one hundred types of capsular polysaccharides (CPS). While the diversity of the enzymes and transporters involved is enormous, it is not limitless. In this review, we summarized the recent progress on elucidating the structure-function relationships of CPS, the mechanisms by which they are synthesized, how their synthesis is regulated, the host immune response against them, and the development of novel pneumococcal vaccines. Based on the genetic and structural information available, we generated provisional models of the CPS repeating units that remain unsolved. In addition, to facilitate cross-species comparisons and assignment of glycosyltransferases, we illustrated the biosynthetic pathways of the known CPS in a standardized format. Studying the intricate steps of pneumococcal CPS assembly promises to provide novel insights for drug and vaccine development as well as improve our understanding of related pathways in other species.
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Affiliation(s)
- Tong Su
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Rei Nakamoto
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Ye Yu Chun
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Wan Zhen Chua
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Jia Hui Chen
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Justin J Zik
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
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25
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Zaman Z, Khan S, Nouroz F, Farooq U, Urooj A. Targeting protein tyrosine phosphatase to unravel possible inhibitors for Streptococcus pneumoniae using molecular docking, molecular dynamics simulations coupled with free energy calculations. Life Sci 2020; 264:118621. [PMID: 33164832 DOI: 10.1016/j.lfs.2020.118621] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 10/03/2020] [Accepted: 10/12/2020] [Indexed: 01/27/2023]
Abstract
AIMS Protein tyrosine phosphatase (PTP-CPS4B) is a signaling enzyme that is essential for a wide range of cellular processes, like metabolism, proliferation, survival and motility. Studies suggest that PTPs are vital for the production of Wzy-dependent capsule in bacteria, making it a valuable target for the discovery of pneumonia associated anti-virulence antibacterial agents. Present study aims at identifying the potential drug candidates to be exploited in inhibiting the growth of Streptococcus pneumonia targeting PTP-CPS4B. MATERIALS AND METHODS The present study exploits the molecular docking potential coupled with molecular dynamic simulation as well as free energy calculations to identify potential inhibitors of PTP-CPS4B. Libraries of known and unknown compounds were docked into the active site of PTP-CPS4B using MOE. The compounds with best binding affinity and orientation were subjected to MD simulations and free energy calculations. FINDINGS Top three compounds based on their binding energy and well composed interaction pattern obtained from molecular docking study were subjected to MD simulations and were compared to reported antibiotic drugs. MD Simulation studies have shown that the presence of an inhibitor inside the active site reduces protein flexibility as evident from RMSD, RMSF and Principal component analyses. MD simulations identified a transition from extended to bended motional shift in loop α6 of the PTP-CPS4B in ligand bound state. This flexibility was reported in the RMSF analysis and verified by the visual investigation of the loop α6 at different time intervals during the simulation. Free energy of binding affinity (computed using MMPBSA &MMGBSA approach) and the interaction patterns obtained from MD trajectory indicate that compound ZN1 (-31.50 Kcal/mol), ZN2 (-33.14 Kcal/mol) and ZN3 (-26.60 Kcal/mol) are potential drug candidates against PTP-CPS4B. Residue wise decomposition study helped in identifying the role of individual amino acid towards the overall inhibition behavior of the compounds. PCA analysis has led to the conclusion that the behavior of PTP-CPS4B inhibitors causes conformational dynamics that can be used to describe the protein inhibition mechanism. SIGNIFICANCE The outcome reveals that this study provide enough evidences for the consideration of ZN1, ZN2, ZN3 as potential PTP-CPS4B inhibitors and further in vitro and in vivo studies may prove their therapeutic potential.
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Affiliation(s)
- Zainab Zaman
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Sara Khan
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan.
| | - Faisal Nouroz
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Umar Farooq
- Department of Chemistry, COMSATS University, Abbottabad 22060, Pakistan
| | - Akasha Urooj
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
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26
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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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27
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Whitfield C, Wear SS, Sande C. Assembly of Bacterial Capsular Polysaccharides and Exopolysaccharides. Annu Rev Microbiol 2020; 74:521-543. [PMID: 32680453 DOI: 10.1146/annurev-micro-011420-075607] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polysaccharides are dominant features of most bacterial surfaces and are displayed in different formats. Many bacteria produce abundant long-chain capsular polysaccharides, which can maintain a strong association and form a capsule structure enveloping the cell and/or take the form of exopolysaccharides that are mostly secreted into the immediate environment. These polymers afford the producing bacteria protection from a wide range of physical, chemical, and biological stresses, support biofilms, and play critical roles in interactions between bacteria and their immediate environments. Their biological and physical properties also drive a variety of industrial and biomedical applications. Despite the immense variation in capsular polysaccharide and exopolysaccharide structures, patterns are evident in strategies used for their assembly and export. This review describes recent advances in understanding those strategies, based on a wealth of biochemical investigations of select prototypes, supported by complementary insight from expanding structural biology initiatives. This provides a framework to identify and distinguish new systems emanating from genomic studies.
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Affiliation(s)
- Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada;
| | - Samantha S Wear
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada;
| | - Caitlin Sande
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada;
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Sánchez-Rodríguez R, González GM, Becerril-García MA, Treviño-Rangel RDJ, Marcos-Vilchis A, González-Pedrajo B, Valvano MA, Andrade A. The BPtpA protein from Burkholderia cenocepacia belongs to a new subclass of low molecular weight protein tyrosine phosphatases. Arch Biochem Biophys 2020; 681:108277. [PMID: 31978399 DOI: 10.1016/j.abb.2020.108277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 11/24/2022]
Abstract
Low molecular weight protein tyrosine phosphatases (LMW-PTP) are ubiquitous enzymes found across a spectrum of genera from prokaryotes to higher eukaryotes. LMW-PTP belong to the Cys-based PTP class II protein family. Here, we show that LMW-PTP can be categorized into two different groups, referred as class II subdivision I (class II.I) and subdivision II (class II.II). Using BPtpA from the opportunistic pathogen Burkholderia cenocepacia, as a representative member of the LMW-PTP class II.I, we demonstrated that four conserved residues (W47, H48, D80, and F81) are required for enzyme function. Guided by an in silico model of BPtpA, we show that the conserved residues at α3-helix (D80 and F81) contribute to protein stability, while the other conserved residues in the W-loop (W47 and H48) likely play a role in substrate recognition. Overall, our results provide new information on LMW-PTP protein family and establish B. cenocepacia as a suitable model to investigate how substrates are recognized and sorted by these proteins.
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Affiliation(s)
- Rebeca Sánchez-Rodríguez
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología. Monterrey, Nuevo León, 64460, Mexico
| | - Gloria M González
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología. Monterrey, Nuevo León, 64460, Mexico
| | - Miguel A Becerril-García
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología. Monterrey, Nuevo León, 64460, Mexico
| | - Rogelio de J Treviño-Rangel
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología. Monterrey, Nuevo León, 64460, Mexico
| | - Arely Marcos-Vilchis
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 70-243, Mexico
| | - Bertha González-Pedrajo
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 70-243, Mexico
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, United Kingdom
| | - Angel Andrade
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología. Monterrey, Nuevo León, 64460, Mexico.
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29
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Synthesis, antimicrobial evaluation, molecular docking and theoretical calculations of novel pyrazolo[1,5-a]pyrimidine derivatives. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127025] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Jung YJ, Miller DP, Perpich JD, Fitzsimonds ZR, Shen D, Ohshima J, Lamont RJ. Porphyromonas gingivalis Tyrosine Phosphatase Php1 Promotes Community Development and Pathogenicity. mBio 2019; 10:e02004-19. [PMID: 31551334 PMCID: PMC6759763 DOI: 10.1128/mbio.02004-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/23/2019] [Indexed: 01/17/2023] Open
Abstract
Protein-tyrosine phosphorylation in bacteria plays a significant role in multiple cellular functions, including those related to community development and virulence. Metal-dependent protein tyrosine phosphatases that belong to the polymerase and histindinol phosphatase (PHP) family are widespread in Gram-positive bacteria. Here, we show that Porphyromonas gingivalis, a Gram-negative periodontal pathogen, expresses a PHP protein, Php1, with divalent metal ion-dependent tyrosine phosphatase activity. Php1 tyrosine phosphatase activity was attenuated by mutation of conserved histidine residues that are important for the coordination of metal ions and by mutation of a conserved arginine residue, a key residue for catalysis in other bacterial PHPs. The php1 gene is located immediately downstream of the gene encoding the bacterial tyrosine (BY) kinase Ptk1, which was a substrate for Php1 in vitro Php1 rapidly caused the conversion of Ptk1 to a state of low tyrosine phosphorylation in the absence of discernible intermediate phosphoforms. Active Php1 was required for P. gingivalis exopolysaccharide production and for community development with the antecedent oral biofilm constituent Streptococcus gordonii under nutrient-depleted conditions. In contrast, the absence of Php1 had no effect on the ability of P. gingivalis to form monospecies biofilms. In vitro, Php1 enzymatic activity was resistant to the effects of the streptococcal secreted metabolites pABA and H2O2, which inhibited Ltp1, an enzyme in the low-molecular-weight (LMW) phosphotyrosine phosphatase family. Ptk1 reciprocally phosphorylated Php1 on tyrosine residues 159 and 161, which independently impacted phosphatase activity. Loss of Php1 rendered P. gingivalis nonvirulent in an animal model of periodontal disease. Collectively, these results demonstrate that P. gingivalis possesses active PHP and LMW tyrosine phosphatases, a unique configuration in Gram-negatives which may allow P. gingivalis to maintain phosphorylation/dephosphorylation homeostasis in multispecies communities. Moreover, Php1 contributes to the pathogenic potential of the organism.IMPORTANCE Periodontal diseases are among the most common infections of humans and are also associated with systemic inflammatory conditions. Colonization and pathogenicity of P. gingivalis are regulated by signal transduction pathways based on protein tyrosine phosphorylation and dephosphorylation. Here, we identify and characterize a novel component of the tyrosine (de)phosphorylation axis: a polymerase and histindinol phosphatase (PHP) family enzyme. This tyrosine phosphatase, designated Php1, was required for P. gingivalis community development with other oral bacteria, and in the absence of Php1 activity P. gingivalis was unable to cause disease in a mouse model of periodontitis. This work provides significant insights into the protein tyrosine (de)phosphorylation network in P. gingivalis, its adaptation to heterotypic communities, and its contribution to colonization and virulence.
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Affiliation(s)
- Young-Jung Jung
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Daniel P Miller
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - John D Perpich
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Zackary R Fitzsimonds
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Daonan Shen
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Jun Ohshima
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
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31
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Pereira SB, Santos M, Leite JP, Flores C, Eisfeld C, Büttel Z, Mota R, Rossi F, De Philippis R, Gales L, Morais‐Cabral JH, Tamagnini P. The role of the tyrosine kinase Wzc (Sll0923) and the phosphatase Wzb (Slr0328) in the production of extracellular polymeric substances (EPS) by Synechocystis PCC 6803. Microbiologyopen 2019; 8:e00753. [PMID: 30675753 PMCID: PMC6562117 DOI: 10.1002/mbo3.753] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/10/2022] Open
Abstract
Many cyanobacteria produce extracellular polymeric substances (EPS) mainly composed of heteropolysaccharides with unique characteristics that make them suitable for biotechnological applications. However, manipulation/optimization of EPS biosynthesis/characteristics is hindered by a poor understanding of the production pathways and the differences between bacterial species. In this work, genes putatively related to different pathways of cyanobacterial EPS polymerization, assembly, and export were targeted for deletion or truncation in the unicellular Synechocystis sp. PCC 6803. No evident phenotypic changes were observed for some mutants in genes occurring in multiple copies in Synechocystis genome, namely ∆wzy (∆sll0737), ∆wzx (∆sll5049), ∆kpsM (∆slr2107), and ∆kpsM∆wzy (∆slr2107∆sll0737), strongly suggesting functional redundancy. In contrast, Δwzc (Δsll0923) and Δwzb (Δslr0328) influenced both the amount and composition of the EPS, establishing that Wzc participates in the production of capsular (CPS) and released (RPS) polysaccharides, and Wzb affects RPS production. The structure of Wzb was solved (2.28 Å), revealing structural differences relative to other phosphatases involved in EPS production and suggesting a different substrate recognition mechanism. In addition, Wzc showed the ATPase and autokinase activities typical of bacterial tyrosine kinases. Most importantly, Wzb was able to dephosphorylate Wzc in vitro, suggesting that tyrosine phosphorylation/dephosphorylation plays a role in cyanobacterial EPS production.
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Affiliation(s)
- Sara B. Pereira
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Marina Santos
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - José P. Leite
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - Carlos Flores
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - Carina Eisfeld
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Present address:
Department of Water ManagementDelft University of TechnologyDelftThe Netherlands
| | - Zsófia Büttel
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Present address:
Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Rita Mota
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Federico Rossi
- Department of Agrifood Production and Environmental SciencesUniversity of FlorenceFlorenceItaly
| | - Roberto De Philippis
- Department of Agrifood Production and Environmental SciencesUniversity of FlorenceFlorenceItaly
| | - Luís Gales
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - João H. Morais‐Cabral
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Paula Tamagnini
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Faculdade de Ciências, Departamento de BiologiaUniversidade do PortoPortoPortugal
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32
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Chatterjee S, Nath S, Ghosh B, Sen U. Vibrio cholerae LMWPTP-2 display unique surface charge and grooves around the active site: Indicative of distinctive substrate specificity and scope to design specific inhibitor. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:114-124. [PMID: 30447286 DOI: 10.1016/j.bbapap.2018.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/08/2018] [Accepted: 11/13/2018] [Indexed: 11/25/2022]
Abstract
Low molecular weight protein tyrosine phosphatases (LMWPTPs) are ubiquitously found as small cytoplasmic enzymes which act on phospho-tyrosine containing proteins that are engaged in various cellular functions. Vibrio cholerae O395 contains two LMWPTPs having widely different sequence. Phylogenetic analysis based on a non redundant set of 124 LMWPTP sequences, designate that LMWPTP-2 from Vibrio choleraeO395 (VcLMWPTP-2) is a single taxon. We have determined the crystal structure of VcLMWPTP-2 at 2.6 Å with MOPS bound in the active site. Tertiary structure analysis indicates that VcLMWPTP-2 forms dimer. Studies in solution state also confirm exclusive presence of a dimeric form. Kinetic studies demonstrate that VcLMWPTP-2 dimer is catalytically active while inactivation through oligomerisation was reported as one of the regulatory mechanism in case of mammalian LMWPTP viz., Bos taurus LMWPTP, BPTP. Kinetic studies using p-nitrophenyl phosphate (p-NPP) as a substrate demonstrate active participation of both the P-loop cysteine in catalysis. Vicinal Cys17, in addition plays a role of protecting the catalytic Cys12 under oxidative stress. Structural analysis and MD simulations allowed us to propose the role of several conserved residues around the active site. Distribution of surface charges and grooves around the active site delineates unique features of VcLMWPTP-2 which could be utilized to design specific inhibitor.
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Affiliation(s)
- Shramana Chatterjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India
| | - Seema Nath
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India
| | - Biplab Ghosh
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Udayaditya Sen
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India.
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Monteiro Pedroso M, Selleck C, Bilyj J, Harmer JR, Gahan LR, Mitić N, Standish AJ, Tierney DL, Larrabee JA, Schenk G. Reaction mechanism of the metallohydrolase CpsB from Streptococcus pneumoniae, a promising target for novel antimicrobial agents. Dalton Trans 2018; 46:13194-13201. [PMID: 28573276 DOI: 10.1039/c7dt01350g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
CpsB is a metal ion-dependent hydrolase involved in the biosynthesis of capsular polysaccharides in bacterial organisms. The enzyme has been proposed as a promising target for novel chemotherapeutics to combat antibiotic resistance. The crystal structure of CpsB indicated the presence of as many as three closely spaced metal ions, modelled as Mn2+, in the active site. While the preferred metal ion composition in vivo is obscure Mn2+ and Co2+ have been demonstrated to be most effective in reconstituting activity. Using isothermal titration calorimetry (ITC) we have demonstrated that, in contrast to the crystal structure, only two Mn2+ or Co2+ ions bind to a monomer of CpsB. This observation is in agreement with magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) data that indicate the presence of two weakly ferromagnetically coupled Co2+ ions in the active site of catalytically active CpsB. While CpsB is known to be a phosphoesterase we have also been able to demonstrate that this enzyme is efficient in hydrolyzing the β-lactam substrate nitrocefin. Steady-state and stopped-flow kinetics measurements further indicated that phosphoesters and nitrocefin undergo catalysis in a conserved manner with a metal ion-bridging hydroxide acting as a nucleophile. Thus, the combined physicochemical studies demonstrate that CpsB is a novel member of the dinuclear metallohydrolase family.
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Affiliation(s)
- Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia.
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Sachdeva S, Palur RV, Sudhakar KU, Rathinavelan T. E. coli Group 1 Capsular Polysaccharide Exportation Nanomachinary as a Plausible Antivirulence Target in the Perspective of Emerging Antimicrobial Resistance. Front Microbiol 2017; 8:70. [PMID: 28217109 PMCID: PMC5290995 DOI: 10.3389/fmicb.2017.00070] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/11/2017] [Indexed: 02/02/2023] Open
Abstract
Bacteria evolving resistance against the action of multiple drugs and its ability to disseminate the multidrug resistance trait(s) across various strains of the same bacteria or different bacterial species impose serious threat to public health. Evolution of such multidrug resistance is due to the fact that, most of the antibiotics target bacterial survival mechanisms which exert selective pressure on the bacteria and aids them to escape from the action of antibiotics. Nonetheless, targeting bacterial virulence strategies such as bacterial surface associated polysaccharides biosynthesis and their surface accumulation mechanisms may be an attractive strategy, as they impose less selective pressure on the bacteria. Capsular polysaccharide (CPS) or K-antigen that is located on the bacterial surface armors bacteria from host immune response. Thus, unencapsulating bacteria would be a good strategy for drug design, besides CPS itself being a good vaccine target, by interfering with CPS biosynthesis and surface assembly pathway. Gram-negative Escherichia coli uses Wzy-polymerase dependent (Groups 1 and 4) and ATP dependent (Groups 1 and 3) pathways for CPS production. Considering E. coli as a case in point, this review explains the structure and functional roles of proteins involved in Group 1 Wzy dependent CPS biosynthesis, surface expression and anchorage in relevance to drug and vaccine developments.
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Affiliation(s)
- Shivangi Sachdeva
- Department of Biotechnology, Indian Institute of Technology Hyderabad Kandi, India
| | - Raghuvamsi V Palur
- Department of Biotechnology, Indian Institute of Technology Hyderabad Kandi, India
| | - Karpagam U Sudhakar
- Department of Biotechnology, Indian Institute of Technology Hyderabad Kandi, India
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35
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Salomone-Stagni M, Musiani F, Benini S. Characterization and 1.57 Å resolution structure of the key fire blight phosphatase AmsI from Erwinia amylovora. Acta Crystallogr F Struct Biol Commun 2016; 72:903-910. [PMID: 27917839 PMCID: PMC5137468 DOI: 10.1107/s2053230x16018781] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/23/2016] [Indexed: 11/10/2022] Open
Abstract
AmsI is a low-molecular-weight protein tyrosine phosphatase that regulates the production of amylovoran in the Gram-negative bacterium Erwinia amylovora, a specific pathogen of rosaceous plants such as apple, pear and quince. Amylovoran is an exopolysaccharide that is necessary for successful infection. In order to shed light on AmsI, its structure was solved at 1.57 Å resolution at the same pH as its highest measured activity (pH 5.5). In the active site, a water molecule, bridging between the catalytic Arg15 and the reaction-product analogue sulfate, might be representative of the water molecule attacking the phospho-cysteine intermediate in the second step of the reaction mechanism.
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Affiliation(s)
- Marco Salomone-Stagni
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 5, 39100 Bolzano, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Stefano Benini
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 5, 39100 Bolzano, Italy
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Kay EJ, Yates LE, Terra VS, Cuccui J, Wren BW. Recombinant expression of Streptococcus pneumoniae capsular polysaccharides in Escherichia coli. Open Biol 2016; 6:150243. [PMID: 27110302 PMCID: PMC4838161 DOI: 10.1098/rsob.150243] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/15/2016] [Indexed: 12/13/2022] Open
Abstract
Currently, Streptococcus pneumoniae is responsible for over 14 million cases of pneumonia worldwide annually, and over 1 million deaths, the majority of them children. The major determinant for pathogenesis is a polysaccharide capsule that is variable and is used to distinguish strains based on their serotype. The capsule forms the basis of the pneumococcal polysaccharide vaccine (PPV23) that contains purified capsular polysaccharide from 23 serotypes, and the pneumococcal conjugate vaccine (PCV13), containing 13 common serotypes conjugated to CRM197 (mutant diphtheria toxin). Purified capsule from S. pneumoniae is required for pneumococcal conjugate vaccine production, and costs can be prohibitively high, limiting accessibility of the vaccine in low-income countries. In this study, we demonstrate the recombinant expression of the capsule-encoding locus from four different serotypes of S. pneumoniae within Escherichia coli. Furthermore, we attempt to identify the minimum set of genes necessary to reliably and efficiently express these capsules heterologously. These E. coli strains could be used to produce a supply of S. pneumoniae serotype-specific capsules without the need to culture pathogenic bacteria. Additionally, these strains could be applied to synthetic glycobiological applications: recombinant vaccine production using E. coli outer membrane vesicles or coupling to proteins using protein glycan coupling technology.
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Affiliation(s)
- Emily J Kay
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT , UK
| | - Laura E Yates
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT , UK
| | - Vanessa S Terra
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT , UK
| | - Jon Cuccui
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT , UK
| | - Brendan W Wren
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT , UK
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Sajid A, Arora G, Singhal A, Kalia VC, Singh Y. Protein Phosphatases of Pathogenic Bacteria: Role in Physiology and Virulence. Annu Rev Microbiol 2015; 69:527-47. [DOI: 10.1146/annurev-micro-020415-111342] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andaleeb Sajid
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi 110007, India;
| | - Gunjan Arora
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi 110007, India;
| | - Anshika Singhal
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi 110007, India;
| | - Vipin C. Kalia
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi 110007, India;
| | - Yogendra Singh
- Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi 110007, India;
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38
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Toniolo C, Balducci E, Romano MR, Proietti D, Ferlenghi I, Grandi G, Berti F, Ros IMY, Janulczyk R. Streptococcus agalactiae capsule polymer length and attachment is determined by the proteins CpsABCD. J Biol Chem 2015; 290:9521-32. [PMID: 25666613 DOI: 10.1074/jbc.m114.631499] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Indexed: 11/06/2022] Open
Abstract
The production of capsular polysaccharides (CPS) or secreted exopolysaccharides is ubiquitous in bacteria, and the Wzy pathway constitutes a prototypical mechanism to produce these structures. Despite the differences in polysaccharide composition among species, a group of proteins involved in this pathway is well conserved. Streptococcus agalactiae (group B Streptococcus; GBS) produces a CPS that represents the main virulence factor of the bacterium and is a prime target in current vaccine development. We used this human pathogen to investigate the roles and potential interdependencies of the conserved proteins CpsABCD encoded in the cps operon, by developing knock-out and functional mutant strains. The mutant strains were examined for CPS quantity, size, and attachment to the cell surface as well as CpsD phosphorylation. We observed that CpsB, -C, and -D compose a phosphoregulatory system where the CpsD autokinase phosphorylates its C-terminal tyrosines in a CpsC-dependent manner. These Tyr residues are also the target of the cognate CpsB phosphatase. An interaction between CpsD and CpsC was observed, and the phosphorylation state of CpsD influenced the subsequent action of CpsC. The CpsC extracellular domain appeared necessary for the production of high molecular weight polysaccharides by influencing CpsA-mediated attachment of the CPS to the bacterial cell surface. In conclusion, although having no impact on cps transcription or the synthesis of the basal repeating unit, we suggest that these proteins are fine-tuning the last steps of CPS biosynthesis (i.e. the balance between polymerization and attachment to the cell wall).
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Affiliation(s)
- Chiara Toniolo
- From Novartis Vaccines and Diagnostics, Research Center, Via Fiorentina 1, 53100 Siena, Italy
| | - Evita Balducci
- From Novartis Vaccines and Diagnostics, Research Center, Via Fiorentina 1, 53100 Siena, Italy
| | - Maria Rosaria Romano
- From Novartis Vaccines and Diagnostics, Research Center, Via Fiorentina 1, 53100 Siena, Italy
| | - Daniela Proietti
- From Novartis Vaccines and Diagnostics, Research Center, Via Fiorentina 1, 53100 Siena, Italy
| | - Ilaria Ferlenghi
- From Novartis Vaccines and Diagnostics, Research Center, Via Fiorentina 1, 53100 Siena, Italy
| | - Guido Grandi
- From Novartis Vaccines and Diagnostics, Research Center, Via Fiorentina 1, 53100 Siena, Italy
| | - Francesco Berti
- From Novartis Vaccines and Diagnostics, Research Center, Via Fiorentina 1, 53100 Siena, Italy
| | | | - Robert Janulczyk
- From Novartis Vaccines and Diagnostics, Research Center, Via Fiorentina 1, 53100 Siena, Italy
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39
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Taylor VL, Huszczynski SM, Lam JS. Membrane Translocation and Assembly of Sugar Polymer Precursors. Curr Top Microbiol Immunol 2015; 404:95-128. [PMID: 26853690 DOI: 10.1007/82_2015_5014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial polysaccharides play an essential role in cell viability, virulence, and evasion of host defenses. Although the polysaccharides themselves are highly diverse, the pathways by which bacteria synthesize these essential polymers are conserved in both Gram-negative and Gram-positive organisms. By utilizing a lipid linker, a series of glycosyltransferases and integral membrane proteins act in concert to synthesize capsular polysaccharide, teichoic acid, and teichuronic acid. The pathways used to produce these molecules are the Wzx/Wzy-dependent, the ABC-transporter-dependent, and the synthase-dependent pathways. This chapter will cover the initiation, synthesis of the various polysaccharides on the cytoplasmic face of the membrane using nucleotide sugar precursors, and export of the nascent chain from the cytoplasm to the extracellular milieu. As microbial glycobiology is an emerging field in Gram-positive bacteria research, parallels will be drawn to the more widely studied polysaccharide biosynthesis systems in Gram-negative species in order to provide greater understanding of these biologically significant molecules.
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Affiliation(s)
- Véronique L Taylor
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Steven M Huszczynski
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Joseph S Lam
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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40
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Benini S, Caputi L, Cianci M. Cloning, purification, crystallization and 1.57 Å resolution X-ray data analysis of AmsI, the tyrosine phosphatase controlling amylovoran biosynthesis in the plant pathogen Erwinia amylovora. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:1693-6. [PMID: 25484228 DOI: 10.1107/s2053230x14024947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 11/13/2014] [Indexed: 02/02/2023]
Abstract
The Gram-negative bacterium Erwinia amylovora is a destructive pathogen of plants belonging to the Rosaceae family. Amongst its pathogenicity factors, E. amylovora produces the exopolysaccharide amylovoran, which contributes to the occlusion of plant vessels, causing wilting of shoots and eventually resulting in plant death. Amylovoran biosynthesis requires the presence of 12 genes (from amsA to amsL) clustered in the ams region of the E. amylovora genome. They mostly encode glycosyl transferases (AmsG, AmsB, AmsD, AmsE, AmsJ and AmsK), proteins involved in amylovoran translocation and assembly (AmsH, AmsL and AmsC), and also a tyrosine kinase (AmsA) and a tyrosine phosphatase (AmsI), which are both involved in the regulation of amylovoran biosynthesis. The low-molecular-weight protein tyrosine phosphatase AmsI was overexpressed as a His6-tagged protein in Escherichia coli, purified and crystallized. X-ray diffraction data were collected to a maximum resolution of 1.57 Å in space group P3121.
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Affiliation(s)
- Stefano Benini
- Laboratory of Bioorganic Chemistry and Bio-Crystallography (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100 Bolzano, Italy
| | - Lorenzo Caputi
- Biological Chemistry Department, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, England
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41
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Nath S, Banerjee R, Sen U. Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family. Biochem Biophys Res Commun 2014; 450:390-5. [PMID: 24909685 DOI: 10.1016/j.bbrc.2014.05.129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 05/27/2014] [Indexed: 10/25/2022]
Abstract
Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which follows a common mechanism involving active site residues leading to an enzymatically inactive species. Here we report a novel form of dimerization in a LMWPTP from Vibrio cholera 0395 (VcLMWPTP-1). Studies in solution reveal the existence of the dimer in solution while kinetic study depicts the active form of the enzyme. This indicates that the mode of dimerization in VcLMWPTP-1 is different from others where active site residues are not involved in the process. A high resolution (1.45Å) crystal structure of VcLMWPTP-1 confirms a different mode of dimerization where the active site is catalytically accessible as evident by a tightly bound substrate mimicking ligand, MOPS at the active site pocket. Although being a member of a prokaryotic protein family, VcLMWPTP-1 structure resembles very closely to LMWPTP from a eukaryote, Entamoeba histolytica. It also delineates the diverse surface properties around the active site of the enzyme.
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Affiliation(s)
- Seema Nath
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India
| | - Ramanuj Banerjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India
| | - Udayaditya Sen
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India.
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42
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Standish AJ, Morona R. The role of bacterial protein tyrosine phosphatases in the regulation of the biosynthesis of secreted polysaccharides. Antioxid Redox Signal 2014; 20:2274-89. [PMID: 24295407 PMCID: PMC3995119 DOI: 10.1089/ars.2013.5726] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SIGNIFICANCE Tyrosine phosphorylation and associated protein tyrosine phosphatases are gaining prominence as critical mechanisms in the regulation of fundamental processes in a wide variety of bacteria. In particular, these phosphatases have been associated with the control of the biosynthesis of capsular polysaccharides and extracellular polysaccharides, critically important virulence factors for bacteria. RECENT ADVANCES Deletion and overexpression of the phosphatases result in altered polysaccharide biosynthesis in a range of bacteria. The recent structures of associated auto-phosphorylating tyrosine kinases have suggested that the phosphatases may be critical for the cycling of the kinases between monomers and higher order oligomers. CRITICAL ISSUES Additional substrates of the phosphatases apart from cognate kinases are currently being identified. These are likely to be critical to our understanding of the mechanism by which polysaccharide biosynthesis is regulated. FUTURE DIRECTIONS Ultimately, these protein tyrosine phosphatases are an attractive target for the development of novel antimicrobials. This is particularly the case for the polymerase and histidinol phosphatase family, which is predominantly found in bacteria. Furthermore, the determination of bacterial tyrosine phosphoproteomes will likely help to uncover the fundamental roles, mechanism, and critical importance of these phosphatases in a wide range of bacteria.
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Affiliation(s)
- Alistair J Standish
- School of Molecular and Biomedical Science, University of Adelaide , Adelaide, Australia
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Streptococcus pneumoniae phosphotyrosine phosphatase CpsB and alterations in capsule production resulting from changes in oxygen availability. J Bacteriol 2014; 196:1992-2003. [PMID: 24659769 DOI: 10.1128/jb.01545-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Streptococcus pneumoniae produces a protective capsular polysaccharide whose production must be modulated for bacterial survival within various host niches. Capsule production is affected in part by a phosphoregulatory system comprised of CpsB, CpsC, and CpsD. Here, we found that growth of serotype 2 strain D39 under conditions of increased oxygen availability resulted in decreased capsule levels concurrent with an ∼5-fold increase in Cps2B-mediated phosphatase activity. The change in Cps2B phosphatase activity did not result from alterations in the levels of either the cps2B transcript or the Cps2B protein. Recombinant Cps2B expressed in Escherichia coli similarly exhibited increased phosphatase activity under conditions of high-oxygen growth. S. pneumoniae D39 derivatives with defined deletion or point mutations in cps2B demonstrated reduced phosphatase activity with corresponding increases in levels of Cps2D tyrosine phosphorylation. There was, however, no correlation between these phenotypes and the level of capsule production. During growth under reduced-oxygen conditions, the Cps2B protein was essential for parental levels of capsule, but phosphatase activity alone could be eliminated without an effect on capsule. Under increased-oxygen conditions, deletion of cps2B did not affect capsule levels. These results indicate that neither Cps2B phosphatase activity nor Cps2D phosphorylation levels per se are determinants of capsule levels, whereas the Cps2B protein is important for capsule production during growth under conditions of reduced but not enhanced oxygen availability. Roles for factors outside the capsule locus, possible interactions between capsule regulatory proteins, and links to other cellular processes are also suggested by the results described in this study.
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Cummings JA, Vetting M, Ghodge SV, Xu C, Hillerich B, Seidel RD, Almo SC, Raushel FM. Prospecting for unannotated enzymes: discovery of a 3',5'-nucleotide bisphosphate phosphatase within the amidohydrolase superfamily. Biochemistry 2014; 53:591-600. [PMID: 24401123 PMCID: PMC3985815 DOI: 10.1021/bi401640r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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In
bacteria, 3′,5′-adenosine bisphosphate (pAp) is
generated from 3′-phosphoadenosine 5′-phosphosulfate
in the sulfate assimilation pathway, and from coenzyme A by the transfer
of the phosphopantetheine group to the acyl-carrier protein. pAp is
subsequently hydrolyzed to 5′-AMP and orthophosphate, and this
reaction has been shown to be important for superoxide stress tolerance.
Herein, we report the discovery of the first instance of an enzyme
from the amidohydrolase superfamily that is capable of hydrolyzing
pAp. Crystal structures of Cv1693 from Chromobacterium violaceum have been determined to a resolution of 1.9 Å with AMP and
orthophosphate bound in the active site. The enzyme has a trinuclear
metal center in the active site with three Mn2+ ions. This
enzyme (Cv1693) belongs to the Cluster of Orthologous Groups cog0613
from the polymerase and histidinol phosphatase family of enzymes.
The values of kcat and kcat/Km for the hydrolysis
of pAp are 22 s–1 and 1.4 × 106 M–1 s–1, respectively. The enzyme is
promiscuous and is able to hydrolyze other 3′,5′-bisphosphonucleotides
(pGp, pCp, pUp, and pIp) and 2′-deoxynucleotides with comparable
catalytic efficiency. The enzyme is capable of hydrolyzing short oligonucleotides
(pdA)5, albeit at rates much lower than that of pAp. Enzymes
from two other enzyme families have previously been found to hydrolyze
pAp at physiologically significant rates. These enzymes include CysQ
from Escherichia coli (cog1218) and YtqI/NrnA from Bacillus subtilis (cog0618). Identification of the functional
homologues to the experimentally verified pAp phosphatases from cog0613,
cog1218, and cog0618 suggests that there is relatively little overlap
of enzymes with this function in sequenced bacterial genomes.
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Affiliation(s)
- Jennifer A Cummings
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
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Bushell S, Mainprize I, Wear M, Lou H, Whitfield C, Naismith J. Wzi is an outer membrane lectin that underpins group 1 capsule assembly in Escherichia coli. Structure 2013; 21:844-53. [PMID: 23623732 PMCID: PMC3791409 DOI: 10.1016/j.str.2013.03.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/19/2013] [Accepted: 03/20/2013] [Indexed: 12/12/2022]
Abstract
Many pathogenic bacteria encase themselves in a polysaccharide capsule that provides a barrier to the physical and immunological challenges of the host. The mechanism by which the capsule assembles around the bacterial cell is unknown. Wzi, an integral outer-membrane protein from Escherichia coli, has been implicated in the formation of group 1 capsules. The 2.6 Å resolution structure of Wzi reveals an 18-stranded β-barrel fold with a novel arrangement of long extracellular loops that blocks the extracellular entrance and a helical bundle that plugs the periplasmic end. Mutagenesis shows that specific extracellular loops are required for in vivo capsule assembly. The data show that Wzi binds the K30 carbohydrate polymer and, crucially, that mutants functionally deficient in vivo show no binding to K30 polymer in vitro. We conclude that Wzi is a novel outer-membrane lectin that assists in the formation of the bacterial capsule via direct interaction with capsular polysaccharides.
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Affiliation(s)
- Simon R. Bushell
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Iain L. Mainprize
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Martin A. Wear
- School of Chemistry, King’s Buildings, University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Hubing Lou
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Chris Whitfield
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
- Corresponding author
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46
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Cefalo AD, Broadbent JR, Welker DL. The Streptococcus thermophilus protein Wzh functions as a phosphotyrosine phosphatase. Can J Microbiol 2013; 59:391-8. [PMID: 23750953 DOI: 10.1139/cjm-2013-0094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Amino acid residues that are important for metal binding and catalysis in Gram-positive phosphotyrosine phosphatases were identified in the Wzh protein of Streptococcus thermophilus MR-1C by using sequence comparisons. A His-tagged fusion Wzh protein was purified from Escherichia coli cultures and tested for phosphatase activity against synthetic phosphotyrosine and phosphoserine-threonine peptides. Purified Wzh released 2316.5 ± 138.7 pmol PO4·min(-1)·μg(-1) from phosphotyrosine peptide-1 and 2345.7 ± 135.2 pmol PO4·min(-1)·μg(-1) from phosphotyrosine peptide-2. The presence of the phosphotyrosine phosphatase inhibitor sodium vanadate decreased purified Wzh activity by 45%-50% at 1 mmol·L(-1), 74%-84% at 5 mmol·L(-1), and by at least 88% at 10 mmol·L(-1). Purified Wzh had no detectable activity against the phosphoserine-threonine peptide. These results clearly establish that S. thermophilus MR-1C Wzh functions as a phosphotyrosine phosphatase that could function to remove phosphate groups from proteins involved in exopolysaccharide biosynthesis, including the protein tyrosine kinase Wze and priming glycosyltransferase.
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Affiliation(s)
- Angela D Cefalo
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA.
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47
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Yuan B, Cheng A, Wang M. Polysaccharide export outer membrane proteins in Gram-negative bacteria. Future Microbiol 2013; 8:525-35. [DOI: 10.2217/fmb.13.13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Polysaccharide export outer membrane proteins of Gram-negative bacteria are involved in the export of polysaccharides across the outer membrane. The mechanisms of polysaccharide export across the outer membrane in Gram-negative bacteria are not yet completely clear. However, the mechanisms of polysaccharide assembly in Escherichia coli have been intensively investigated. Here, we mainly review the current understanding of the assembly mechanisms of group 1 capsular polysaccharide, group 2 capsular polysaccharide and lipopolysaccharide of E. coli, and the current structures and interactions of some polysaccharide export outer membrane proteins with other proteins involved in polysaccharide export in Gram-negative bacteria. In addition, LptD may be targeted by peptidomimetic antibiotics in Gram-negative bacteria. We also give insights into the directions of future research regarding the mechanisms of polysaccharide export.
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Affiliation(s)
- Biao Yuan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, China.
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, 46 Xinkang Road, Ya’an, Sichuan 625014, China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu city, Sichuan 611130, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, 46 Xinkang Road, Ya’an, Sichuan 625014, China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu city, Sichuan 611130, China
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48
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Temel DB, Dutta K, Alphonse S, Nourikyan J, Grangeasse C, Ghose R. Regulatory interactions between a bacterial tyrosine kinase and its cognate phosphatase. J Biol Chem 2013; 288:15212-28. [PMID: 23543749 DOI: 10.1074/jbc.m113.457804] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cyclic process of autophosphorylation of the C-terminal tyrosine cluster (YC) of a bacterial tyrosine kinase and its subsequent dephosphorylation following interactions with a counteracting tyrosine phosphatase regulates diverse physiological processes, including the biosynthesis and export of polysaccharides responsible for the formation of biofilms or virulence-determining capsules. We provide here the first detailed insight into this hitherto uncharacterized regulatory interaction at residue-specific resolution using Escherichia coli Wzc, a canonical bacterial tyrosine kinase, and its opposing tyrosine phosphatase, Wzb. The phosphatase Wzb utilizes a surface distal to the catalytic elements of the kinase, Wzc, to dock onto its catalytic domain (WzcCD). WzcCD binds in a largely YC-independent fashion near the Wzb catalytic site, inducing allosteric changes therein. YC dephosphorylation is proximity-mediated and reliant on the elevated concentration of phosphorylated YC near the Wzb active site resulting from WzcCD docking. Wzb principally recognizes the phosphate of its phosphotyrosine substrate and further stabilizes the tyrosine moiety through ring stacking interactions with a conserved active site tyrosine.
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Affiliation(s)
- Deniz B Temel
- Department of Chemistry, City College of New York, New York, New York 10031, USA
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Böhmer F, Szedlacsek S, Tabernero L, Ostman A, den Hertog J. Protein tyrosine phosphatase structure-function relationships in regulation and pathogenesis. FEBS J 2013; 280:413-31. [PMID: 22682070 DOI: 10.1111/j.1742-4658.2012.08655.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein phosphorylation on tyrosine residues is tightly controlled by protein tyrosine phosphatases (PTPs) at multiple levels: spatio-temporal expression, subcellular localization and post-translational modification. Structural and functional analysis of the PTP domains has provided insight into catalysis and regulatory mechanisms that control the enzymatic activity. Understanding the molecular basis of PTP regulation is of fundamental importance to dissect the pleiotropic effect of these enzymes in both health and disease. Here, we review recent insights into the regulation of receptor-like PTPs by extracellular ligands and into regulation by reversible oxidation that impairs catalysis directly. The physiological roles of PTPs are essential in homeostasis in eukaryotic cells and pertubation of their functional attributes causes different disease states. As an example, we discuss recent findings indicating how inappropriate oxidation of PTPs in cancer cells may contribute to cell transformation. On the other hand, PTPs from many pathogens are key virulence factors and manipulate signalling pathways in the host cells to promote invasion and survival of the microorganisms. This research area has received relatively little attention but has advanced remarkably. We review the structural features of pathogenic PTPs, their similarities and differences with eukaryotic PTPs, and the possible exploitation of this knowledge for therapeutic intervention.
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Affiliation(s)
- Frank Böhmer
- Center for Molecular Biomedicine, Jena University Hospital, Jena, Germany
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50
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Standish AJ, Salim AA, Capon RJ, Morona R. Dual inhibition of DNA polymerase PolC and protein tyrosine phosphatase CpsB uncovers a novel antibiotic target. Biochem Biophys Res Commun 2012. [PMID: 23194664 DOI: 10.1016/j.bbrc.2012.11.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Increasing antibiotic resistance is making the identification of novel antimicrobial targets critical. Recently, we discovered an inhibitor of protein tyrosine phosphatase CpsB, fascioquinol E (FQE), which unexpectedly inhibited the growth of Gram-positive pathogens. CpsB is a member of the polymerase and histidinol phosphate phosphatase (PHP) domain family. Another member of this family found in a variety of Gram-positive pathogens is DNA polymerase PolC. We purified the PHP domain from PolC (PolC(PHP)), and showed that this competes away FQE inhibition of CpsB phosphatase activity. Furthermore, we showed that this domain hydrolyses the 5'-p-nitrophenyl ester of thymidine-5'-monophosphate (pNP-TMP), which has been used as a measure of exonuclease activity. Finally, we showed that FQE not only inhibits the phosphatase activity of CpsB, but also ability of PolC(PHP) to catalyse the hydrolysis of pNP-TMP. This suggests that PolC may be the essential target of FQE, and that the PHP domain may represent an as yet untapped target for the development of novel antibiotics.
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Affiliation(s)
- Alistair J Standish
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia.
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