1
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Amaeze NJ, Akinbobola AB, Kean R, Ramage G, Williams C, Mackay W. Transfer of micro-organisms from dry surface biofilms and the influence of long survival under conditions of poor nutrition and moisture on the virulence of Staphylococcusaureus. J Hosp Infect 2024; 150:34-39. [PMID: 38823646 DOI: 10.1016/j.jhin.2024.03.023] [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: 01/30/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Biofilms on dry hospital surfaces can enhance the persistence of micro-organisms on dry harsh clinical surfaces and can potentially act as reservoirs of infectious agents on contaminated surfaces. AIM This study was conducted to quantify the transfer of viable Staphylococcus aureus cells from dry biofilms through touching and to investigate the impact of nutrient and moisture deprivation on virulence levels in S. aureus. METHODS Dry biofilms of S. aureus ATCC 25923 and a defective biofilm-forming ability mutant, S. aureus 1132, were formed in 24-well plates under optimized conditions mimicking dry biofilm formation on clinical surfaces. Microbial cell transfer was induced through the touching of the dry biofilms, which were quantified on nutrient agar. To investigate the impact of nutrient and moisture deprivation on virulence levels, dry and standard biofilms as well as planktonic cells of S. aureus ATCC 25923 were inoculated into Galleria mellonella and their kill rates compared. FINDINGS Results of this study showed that viable cells from dry biofilms of S. aureus ATCC 25923 were significantly more virulent and readily transferrable from dry biofilms through a touch test, therefore representing a greater risk of infection. The biofilm-forming capability of S. aureus strains had no significant impact on their transferability with more cells transferring when biofilm surfaces were wet. CONCLUSIONS These findings indicate that dry biofilms on hospital surfaces may serve as a reservoir for the dissemination of pathogenic micro-organisms in hospitals, thus highlighting the importance of regular cleaning and adequate disinfection of hospital surfaces.
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Affiliation(s)
- N J Amaeze
- School of Health and Life Sciences, University of West of Scotland, Lanarkshire Campus, South Lanarkshire, UK
| | - A B Akinbobola
- Department of Microbiology, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - R Kean
- School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
| | - G Ramage
- School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
| | - C Williams
- University Hospitals of Morecambe NHS Foundation Trust, Kendal, UK
| | - W Mackay
- School of Health and Life Sciences, University of West of Scotland, Lanarkshire Campus, South Lanarkshire, UK.
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2
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Amacher JF, Antos JM. Sortases: structure, mechanism, and implications for protein engineering. Trends Biochem Sci 2024; 49:596-610. [PMID: 38692993 DOI: 10.1016/j.tibs.2024.04.003] [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: 11/06/2023] [Revised: 03/22/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
Sortase enzymes are critical cysteine transpeptidases on the surface of bacteria that attach proteins to the cell wall and are involved in the construction of bacterial pili. Due to their ability to recognize specific substrates and covalently ligate a range of reaction partners, sortases are widely used in protein engineering applications via sortase-mediated ligation (SML) strategies. In this review, we discuss recent structural studies elucidating key aspects of sortase specificity and the catalytic mechanism. We also highlight select recent applications of SML, including examples where fundamental studies of sortase structure and function have informed the continued development of these enzymes as tools for protein engineering.
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Affiliation(s)
- Jeanine F Amacher
- Department of Chemistry, Western Washington University, Bellingham, WA 98225, USA.
| | - John M Antos
- Department of Chemistry, Western Washington University, Bellingham, WA 98225, USA.
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3
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Liu Y, Lu Z, Wu P, Liang Z, Yu Z, Ni K, Ma L. The Transpeptidase Sortase A Binds Nucleic Acids and Mediates Mammalian Cell Labeling. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305605. [PMID: 38581131 DOI: 10.1002/advs.202305605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/10/2024] [Indexed: 04/08/2024]
Abstract
Wild-type sortase A is an important virulence factor displaying a diverse array of proteins on the surface of bacteria. This protein display relies on the transpeptidase activity of sortase A, which is widely engineered to allow protein ligation and protein engineering based on the interaction between sortase A and peptides. Here an unknown interaction is found between sortase A from Staphylococcus aureus and nucleic acids, in which exogenously expressed engineered sortase A binds oligonucleotides in vitro and is independent of its canonical transpeptidase activity. When incubated with mammalian cells, engineered sortase A further mediates oligonucleotide labeling to the cell surface, where sortase A attaches itself and is part of the labeled moiety. The labeling reaction can also be mediated by many classes of wild-type sortases as well. Cell surface GAG appears involved in sortase-mediated oligonucleotide cell labeling, as demonstrated by CRISPR screening. This interaction property is utilized to develop a technique called CellID to facilitate sample multiplexing for scRNA-seq and shows the potential of using sortases to label cells with diverse oligonucleotides. Together, the binding between sortase A and nucleic acids opens a new avenue to understanding the virulence of wild-type sortases and exploring the application of sortases in biotechnology.
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Affiliation(s)
- Yingzheng Liu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Zhike Lu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Panfeng Wu
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Zhaohui Liang
- AIdit Therapeutics, 1 Yunmeng Road, Building 1, Hangzhou, 310024, China
| | - Zhenxing Yu
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Ke Ni
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
- AIdit Therapeutics, 1 Yunmeng Road, Building 1, Hangzhou, 310024, China
| | - Lijia Ma
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
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4
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Vogel BA, Blount JM, Kodama HM, Goodwin-Rice NJ, Andaluz DJ, Jackson SN, Antos JM, Amacher JF. A unique binding mode of P1' Leu-containing target sequences for Streptococcus pyogenes sortase A results in alternative cleavage. RSC Chem Biol 2024; 5:30-40. [PMID: 38179192 PMCID: PMC10763551 DOI: 10.1039/d3cb00129f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/26/2023] [Indexed: 01/06/2024] Open
Abstract
Sortase enzymes are cysteine transpeptidases that attach environmental sensors, toxins, and other proteins to the cell surface in Gram-positive bacteria. The recognition motif for many sortases is the cell wall sorting signal (CWSS), LPXTG, where X = any amino acid. Recent work from ourselves and others has described recognition of additional amino acids at a number of positions in the CWSS, specifically at the Thr (or P1) and Gly (or P1') positions. In addition, although standard cleavage occurs between these two residues (P1/P1'), we previously observed that the SrtA enzyme from Streptococcus pneumoniae will cleave after the P1' position when its identity is a Leu or Phe. The stereochemical basis of this alternative cleavage is not known, although homologs, e.g., SrtA from Listeria monocytogenes or Staphylococcus aureus do not show alternative cleavage to a significant extent. Here, we use protein biochemistry, structural biology, and computational biochemistry to predict an alternative binding mode that facilitates alternative cleavage. We use Streptococcus pyogenes SrtA (spySrtA) as our model enzyme, first confirming that it shows similar standard/alternative cleavage ratios for LPATL, LPATF, and LPATY sequences. Molecular dynamics simulations suggest that when P1' is Leu, this amino acid binds in the canonical S1 pocket, pushing the P1 Thr towards solvent. The P4 Leu (L̲PATL) binds as it does in standard binding, resulting in a puckered binding conformation. We use P1 Glu-containing peptides to support our hypotheses, and present the complex structure of spySrtA-LPALA to confirm favorable accommodation of Leu in the S1 pocket. Overall, we structurally characterize an alternative binding mode for spySrtA and specific target sequences, expanding the potential protein engineering possibilities in sortase-mediated ligation applications.
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Affiliation(s)
- Brandon A Vogel
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Jadon M Blount
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Hanna M Kodama
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Noah J Goodwin-Rice
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Devin J Andaluz
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Sophie N Jackson
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - John M Antos
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Jeanine F Amacher
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
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5
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Chen F, Di H, Wang Y, Peng C, Chen R, Pan H, Yang CG, Liang H, Lan L. The enzyme activity of sortase A is regulated by phosphorylation in Staphylococcus aureus. Virulence 2023; 14:2171641. [PMID: 36694285 PMCID: PMC9928477 DOI: 10.1080/21505594.2023.2171641] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In many Gram-positive bacteria, the transpeptidase enzyme sortase A (SrtA) anchors surface proteins to cell wall and plays a critical role in the bacterial pathogenesis. Here, we show that in Staphylococcus aureus, an important human pathogen, the SrtA is phosphorylated by serine/threonine protein kinase Stk1. S. aureus SrtA can also be phosphorylated by small-molecule phosphodonor acetyl phosphate (AcP) in vitro. We determined that various amino acid residues of S. aureus SrtA are subject to phosphorylation, primarily on its catalytic site residue cysteine-184 in the context of a bacterial cell lysate. Both Stk1 and AcP-mediated phosphorylation inhibited the enzyme activity of SrtA in vitro. Consequently, deletion of gene (i.e. stp1) encoding serine/threonine phosphatase Stp1, the corresponding phosphatase of Stk1, caused an increase in the phosphorylation level of SrtA. The stp1 deletion mutant mimicked the phenotypic traits of srtA deletion mutant (i.e. attenuated growth where either haemoglobin or haem as a sole iron source and reduced liver infections in a mouse model of systemic infection). Importantly, the phenotypic defects of the stp1 deletion mutant can be alleviated by overexpressing srtA. Taken together, our finding suggests that phosphorylation plays an important role in modulating the activity of SrtA in S. aureus.
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Affiliation(s)
- Feifei Chen
- College of Life Science, Northwest University, Xi’an, China,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Hongxia Di
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yanhui Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,University of Chinese Academy of Sciences, Beijing, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Rongrong Chen
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China,University of Chinese Academy of Sciences, Beijing, China
| | - Huiwen Pan
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China,University of Chinese Academy of Sciences, Beijing, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China,University of Chinese Academy of Sciences, Beijing, China
| | - Haihua Liang
- College of Life Science, Northwest University, Xi’an, China,School of Medicine, Southern University of Science and Technology, Shenzhen, China,Haihua Liang School of Medicine Southern University of Science and Technology, Shenzhen, China
| | - Lefu Lan
- College of Life Science, Northwest University, Xi’an, China,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China,University of Chinese Academy of Sciences, Beijing, China,CONTACT Lefu Lan
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6
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Obeng EM, Steer DL, Fulcher A, Wagstaff KM. Steric-Deficient Oligoglycine Surrogates Facilitate Multivalent and Bifunctional Nanobody Synthesis via Combined Sortase A Transpeptidation and Click Chemistry. Bioconjug Chem 2023; 34:1667-1678. [PMID: 37534819 DOI: 10.1021/acs.bioconjchem.3c00319] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Conferring multifunctional properties to proteins via enzymatic approaches has greatly facilitated recent progress in protein nanotechnology. In this regard, sortase (Srt) A transpeptidation has facilitated many of these developments due to its exceptional specificity, mild reaction conditions, and complementation with other bioorthogonal techniques, such as click chemistry. In most of these developments, Srt A is used to seamlessly tether oligoglycine-containing molecules to a protein of interest that is equipped with the enzyme's recognition sequence, LPXTG. However, the dependence on oligoglycine attacking nucleophiles and the associated cost of certain derivatives (e.g., cyclooctyne) limit the utility of this approach to lab-scale applications only. Thus, the quest to identify appropriate alternatives and understand their effectiveness remains an important area of research. This study identifies that steric and nucleophilicity-associated effects influence Srt A transpeptidation when two oligoglycine surrogates were examined. The approach was further used in complementation with click chemistry to synthesize bivalent and bifunctional nanobody conjugates for application in epithelial growth factor receptor targeting. The overall technique and tools developed here may facilitate the advancement of future nanotechnologies.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - David L Steer
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton 3800, Victoria, Australia
| | - Alex Fulcher
- Monash Micro Imaging, Monash University, Clayton 3800, Victoria, Australia
| | - Kylie M Wagstaff
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
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7
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Obeng EM, Fulcher AJ, Wagstaff KM. Harnessing sortase A transpeptidation for advanced targeted therapeutics and vaccine engineering. Biotechnol Adv 2023; 64:108108. [PMID: 36740026 DOI: 10.1016/j.biotechadv.2023.108108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
The engineering of potent prophylactic and therapeutic complexes has always required careful protein modification techniques with seamless capabilities. In this light, methods that favor unobstructed multivalent targeting and correct antigen presentations remain essential and very demanding. Sortase A (SrtA) transpeptidation has exhibited these attributes in various settings over the years. However, its applications for engineering avidity-inspired therapeutics and potent vaccines have yet to be significantly noticed, especially in this era where active targeting and multivalent nanomedications are in great demand. This review briefly presents the SrtA enzyme and its associated transpeptidation activity and describes interesting sortase-mediated protein engineering and chemistry approaches for achieving multivalent therapeutic and antigenic responses. The review further highlights advanced applications in targeted delivery systems, multivalent therapeutics, adoptive cellular therapy, and vaccine engineering. These innovations show the potential of sortase-mediated techniques in facilitating the development of simple plug-and-play nanomedicine technologies against recalcitrant diseases and pandemics such as cancer and viral infections.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Kylie M Wagstaff
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
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8
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Maciag JJ, Chantraine C, Mills KB, Yadav R, Yarawsky AE, Chaton CT, Vinod D, Fitzkee NC, Mathelié-Guinlet M, Dufrêne YF, Fey PD, Horswill AR, Herr AB. Mechanistic basis of staphylococcal interspecies competition for skin colonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525635. [PMID: 36747832 PMCID: PMC9900903 DOI: 10.1101/2023.01.26.525635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Staphylococci, whether beneficial commensals or pathogens, often colonize human skin, potentially leading to competition for the same niche. In this multidisciplinary study we investigate the structure, binding specificity, and mechanism of adhesion of the Aap lectin domain required for Staphylococcus epidermidis skin colonization and compare its characteristics to the lectin domain from the orthologous Staphylococcus aureus adhesin SasG. The Aap structure reveals a legume lectin-like fold with atypical architecture, showing specificity for N-acetyllactosamine and sialyllactosamine. Bacterial adhesion assays using human corneocytes confirmed the biological relevance of these Aap-glycan interactions. Single-cell force spectroscopy experiments measured individual binding events between Aap and corneocytes, revealing an extraordinarily tight adhesion force of nearly 900 nN and a high density of receptors at the corneocyte surface. The SasG lectin domain shares similar structural features, glycan specificity, and corneocyte adhesion behavior. We observe cross-inhibition of Aap-and SasG-mediated staphylococcal adhesion to corneocytes. Together, these data provide insights into staphylococcal interspecies competition for skin colonization and suggest potential avenues for inhibition of S. aureus colonization.
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Affiliation(s)
- Joseph J. Maciag
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Constance Chantraine
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Krista B. Mills
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
| | - Rahul Yadav
- Department of Chemistry, Mississippi State University, Mississippi State, MS
| | - Alexander E. Yarawsky
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Catherine T. Chaton
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Divya Vinod
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Medical Sciences Undergraduate Program, University of Cincinnati, Cincinnati, OH
| | - Nicholas C. Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS
| | - Marion Mathelié-Guinlet
- Institut de Chimie et Biologie des Membranes et des Nano-Objets, CNRS UMR 5248, University of Bordeaux, Pessac, France
| | - Yves F. Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Alexander R. Horswill
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
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9
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Vorasin O, Momphanao K, Katrun P, Kuhakarn C, Jiarpinitnun C. Antibacterial activity evaluation of vinyl sulfones against global predominant methicillin-resistant Staphylococcus aureus USA300. Bioorg Med Chem Lett 2022; 63:128652. [PMID: 35245662 DOI: 10.1016/j.bmcl.2022.128652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/18/2022] [Accepted: 02/27/2022] [Indexed: 11/27/2022]
Abstract
The electrophilic potential of vinyl sulfone permits the rapid capture of cysteine-containing proteins under physiological conditions. These cysteine proteinases play vital roles in bacterial survival and pathogenesis of Staphylococcus aureus (S. aureus) and the global health threat methicillin resistant S. aureus (MRSA). Here in, total of 28 vinyl sulfones were synthesized and subjected to susceptibility testing of pathogenic bacteria, including global epidemic MRSA PFGE strain type USA300 (SF8300). Number of antibacterial vinyl sulfone derivatives were discovered. Among these, nitrile-substituted vinyl phenyl sulfones showed potent antibacterial activity. (E)-3-((4-methoxyphenyl)sulfonyl)acrylonitrile exhibited the strongest potency with MIC of 1.875 µg/mL against methicillin susceptible S. aureus and 3.75 µg/mL against MRSA USA300. Based on the structure-activity relationship analysis, the antibacterial activity of these compounds may involve sulfhydryl conjugation. In addition, the nitrile-substituted vinyl phenyl sulfone could also impair host cell adhesion. With their promising antibacterial activities, these vinyl sulfones have potential for S. aureus and MRSA therapeutics.
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Affiliation(s)
- Onanong Vorasin
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
| | - Khanchyd Momphanao
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
| | - Praewpan Katrun
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chutima Kuhakarn
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
| | - Chutima Jiarpinitnun
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand.
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10
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Scutellarin potentiates vancomycin against lethal pneumonia caused by methicillin-resistant Staphylococcus aureus through dual inhibition of sortase A and caseinolytic peptidase P. Biochem Pharmacol 2022; 199:114982. [PMID: 35247333 DOI: 10.1016/j.bcp.2022.114982] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/12/2022] [Accepted: 02/22/2022] [Indexed: 01/09/2023]
Abstract
The strategy of targeting virulence factor has received great attention as it barely develops bacterial resistance. Sortase A (SrtA) and caseinolytic peptidase P (ClpP), as important virulence factors, are considered to be ideal pharmacological targets for methicillin-resistant Staphylococcus aureus (MRSA) infection. Through screening hundreds of compounds, we found scutellarin, a natural flavonoid, markedly inhibited SrtA and ClpP activities of MRSA strain USA300 with an IC50 of 53.64 μg/mL and 107.00 μg/mL, respectively. Subsequently, we observed that scutellarin could inhibit the SrtA-related virulence of MRSA. To demonstrate whether scutellarin directly binding to SrtA, fluorescence quenching assay and molecular docking were performed and the results indicated that scutellarin directly bonded to SrtA molecule with a KA value of 7.58 × 104 L/mol. In addition to direct SrtA inhibition, scutellarin could also inhibit hemolytic activity of S. aureus by inhibiting the expression of Hla in a SrtA-independent manner. Further assays confirmed that scutellarin inhibited hemolysis by inhibiting ClpP. The combination of scutellarin and vancomycin showed enhancing inhibition of USA300 in vitro and in vivo, evidenced by decreased MIC from 3 μg/mL to 0.5 μg/mL and increased survival and improvement of lung pathology in pneumonia mice. Taken together, these results suggest that scutellarin exhibited di-inhibitory effects on SrtA and ClpP of USA300. The di-inhibition of virulence factors by scutellarin combined with vancomycin to prevent MRSA invasion of A549 cells and pneumonia in mice, indicating that scutellarin is expected to be a potential adjuvant against MRSA in the future.
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11
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Gao M, Johnson DA, Piper IM, Kodama HM, Svendsen JE, Tahti E, Longshore‐Neate F, Vogel B, Antos JM, Amacher JF. Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes. Protein Sci 2022; 31:701-715. [PMID: 34939250 PMCID: PMC8862441 DOI: 10.1002/pro.4266] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 01/22/2023]
Abstract
Sequence variation in related proteins is an important characteristic that modulates activity and selectivity. An example of a protein family with a large degree of sequence variation is that of bacterial sortases, which are cysteine transpeptidases on the surface of gram-positive bacteria. Class A sortases are responsible for attachment of diverse proteins to the cell wall to facilitate environmental adaption and interaction. These enzymes are also used in protein engineering applications for sortase-mediated ligations (SML) or sortagging of protein targets. We previously investigated SrtA from Streptococcus pneumoniae, identifying a number of putative β7-β8 loop-mediated interactions that affected in vitro enzyme function. We identified residues that contributed to the ability of S. pneumoniae SrtA to recognize several amino acids at the P1' position of the substrate motif, underlined in LPXTG, in contrast to the strict P1' Gly recognition of SrtA from Staphylococcus aureus. However, motivated by the lack of a structural model for the active, monomeric form of S. pneumoniae SrtA, here, we expanded our studies to other Streptococcus SrtA proteins. We solved the first monomeric structure of S. agalactiae SrtA which includes the C-terminus, and three others of β7-β8 loop chimeras from S. pyogenes and S. agalactiae SrtA. These structures and accompanying biochemical data support our previously identified β7-β8 loop-mediated interactions and provide additional insight into their role in Class A sortase substrate selectivity. A greater understanding of individual SrtA sequence and structural determinants of target selectivity may also facilitate the design or discovery of improved sortagging tools.
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Affiliation(s)
- Melody Gao
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - D. Alex Johnson
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Isabel M. Piper
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Hanna M. Kodama
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Justin E. Svendsen
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Elise Tahti
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | | | - Brandon Vogel
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - John M. Antos
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Jeanine F. Amacher
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
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12
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Lieser RM, Hartzell EJ, Yur D, Sullivan MO, Chen W. EGFR Ligand Clustering on E2 Bionanoparticles for Targeted Delivery of Chemotherapeutics to Breast Cancer Cells. Bioconjug Chem 2022; 33:452-462. [PMID: 35167278 DOI: 10.1021/acs.bioconjchem.1c00579] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Naturally occurring protein nanocages are promising drug carriers because of their uniform size and biocompatibility. Engineering efforts have enhanced the delivery properties of nanocages, but cell specificity and high drug loading remain major challenges. Herein, we fused the SpyTag peptide to the surface of engineered E2 nanocages to enable tunable nanocage decoration and effective E2 cell targeting using a variety of SpyCatcher (SC) fusion proteins. Additionally, the core of the E2 nanocage incorporated four phenylalanine mutations previously shown to allow hydrophobic loading of doxorubicin and pH-responsive release in acidic environments. We functionalized the surface of the nanocage with a highly cell-specific epidermal growth factor receptor (EGFR)-targeting protein conjugate, 4GE11-mCherry-SC, developed previously in our laboratories by employing unnatural amino acid (UAA) protein engineering chemistries. Herein, we demonstrated the benefits of this engineered protein nanocage construct for efficient drug loading, with a straightforward method for removal of the unloaded drug through elastin-like polypeptide-mediated inverse transition cycling. Additionally, we demonstrated approximately 3-fold higher doxorubicin internalization in inflammatory breast cancer cells compared to healthy breast epithelial cells, leading to targeted cell death at concentrations below the IC50 of free doxorubicin. Collectively, these results demonstrated the versatility of our UAA-based EGFR-targeting protein construct to deliver a variety of cargoes efficiently, including engineered E2 nanocages capable of site-specific functionalization and doxorubicin loading.
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Affiliation(s)
- Rachel M Lieser
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Emily J Hartzell
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Daniel Yur
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
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13
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Barthels F, Meyr J, Hammerschmidt SJ, Marciniak T, Räder HJ, Ziebuhr W, Engels B, Schirmeister T. 2-Sulfonylpyrimidines as Privileged Warheads for the Development of S. aureus Sortase A Inhibitors. Front Mol Biosci 2022; 8:804970. [PMID: 35047562 PMCID: PMC8763382 DOI: 10.3389/fmolb.2021.804970] [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: 10/29/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022] Open
Abstract
Staphylococcus aureus is one of the most frequent causes of nosocomial and community-acquired infections, with emerging multiresistant isolates causing a significant burden to public health systems. We identified 2-sulfonylpyrimidines as a new class of potent inhibitors against S. aureus sortase A acting by covalent modification of the active site cysteine 184. Series of derivatives were synthesized to derive structure-activity relationship (SAR) with the most potent compounds displaying low micromolar KI values. Studies on the inhibition selectivity of homologous cysteine proteases showed that 2-sulfonylpyrimidines reacted efficiently with protonated cysteine residues as found in sortase A, though surprisingly, no reaction occurred with the more nucleophilic cysteine residue from imidazolinium-thiolate dyads of cathepsin-like proteases. By means of enzymatic and chemical kinetics as well as quantum chemical calculations, it could be rationalized that the SNAr reaction between protonated cysteine residues and 2-sulfonylpyrimidines proceeds in a concerted fashion, and the mechanism involves a ternary transition state with a conjugated base. Molecular docking and enzyme inhibition at variable pH values allowed us to hypothesize that in sortase A this base is represented by the catalytic histidine 120, which could be substantiated by QM model calculation with 4-methylimidazole as histidine analog.
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Affiliation(s)
- Fabian Barthels
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Jessica Meyr
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Würzburg, Würzburg, Germany
| | - Stefan J Hammerschmidt
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Tessa Marciniak
- Institute for Molecular Infection Biology, Julius-Maximilians-University of Würzburg, Würzburg, Germany
| | | | - Wilma Ziebuhr
- Institute for Molecular Infection Biology, Julius-Maximilians-University of Würzburg, Würzburg, Germany
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Würzburg, Würzburg, Germany
| | - Tanja Schirmeister
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
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14
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Malik A, Subramaniyam S, Kim CB, Manavalan B. SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information. Comput Struct Biotechnol J 2021; 20:165-174. [PMID: 34976319 PMCID: PMC8703055 DOI: 10.1016/j.csbj.2021.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
Sortase enzymes are cysteine transpeptidases that embellish the surface of Gram-positive bacteria with various proteins thereby allowing these microorganisms to interact with their neighboring environment. It is known that several of their substrates can cause pathological implications, so researchers have focused on the development of sortase inhibitors. Currently, six different classes of sortases (A-F) are recognized. However, with the extensive application of bacterial genome sequencing projects, the number of potential sortases in the public databases has exploded, presenting considerable challenges in annotating these sequences. It is very laborious and time-consuming to characterize these sortase classes experimentally. Therefore, this study developed the first machine-learning-based two-layer predictor called SortPred, where the first layer predicts the sortase from the given sequence and the second layer predicts their class from the predicted sortase. To develop SortPred, we constructed an original benchmarking dataset and investigated 31 feature descriptors, primarily on five feature encoding algorithms. Afterward, each of these descriptors were trained using a random forest classifier and their robustness was evaluated with an independent dataset. Finally, we selected the final model independently for both layers depending on the performance consistency between cross-validation and independent evaluation. SortPred is expected to be an effective tool for identifying bacterial sortases, which in turn may aid in designing sortase inhibitors and exploring their functions. The SortPred webserver and a standalone version are freely accessible at: https://procarb.org/sortpred.
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Affiliation(s)
- Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul 03016, Republic of Korea
| | | | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Republic of Korea
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15
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Discovery of Sortase A covalent inhibitors with benzofuranene cyanide structures as potential antibacterial agents against Staphylococcus aureus. Eur J Med Chem 2021; 229:114032. [PMID: 34954590 DOI: 10.1016/j.ejmech.2021.114032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/19/2021] [Accepted: 11/28/2021] [Indexed: 11/19/2022]
Abstract
Sortase A (SrtA) is a cysteine transpeptidase of most gram-positive bacteria that is responsible for the anchoring of many surface protein virulence factors to the cell wall. SrtA ablation has demonstrated to alleviate the infection without affecting the viability of bacteria. Herein, a series of benzofuran cyanide derivatives were synthesized and evaluated. Several compounds exhibited excellent inhibitory activity against SrtA with IC50 values from 3.3 μM to 21.8 μM compared with the known SrtA inhibitor pHMB (IC50 = 130 μM). Ⅲ-1, Ⅲ-15, Ⅲ-34 and V-1 showed potent inhibitory effects on biofilm formation with IC50 values from 2.1 μM to 54.2 μM. Invasion assays showed the four compounds caused a decrease of 4%-24.0% in the uptake of the S. aureus strain by 293T cells. Further assay showed that compound Ⅲ-15 decreased the amount of cell wall-associated protein A by 26.5%. Structure-activity relationship and docking studies demonstrated that the acrylonitrile moiety of the compounds played an important role in enhancing the activity. When the double bond of acrylonitrile changed to single bond, the activity was decreased significantly. This indicates that acrylonitrile, which is a Michael receptor, can inhibit the activity of SrtA by covalent binding effectively to the thiol group of Cys184.
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16
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Yang MH, Hu CC, Wong CH, Liang JJ, Ko HY, He MH, Lin YL, Lin NS, Hsu YH. Convenient Auto-Processing Vector Based on Bamboo Mosaic Virus for Presentation of Antigens Through Enzymatic Coupling. Front Immunol 2021; 12:739837. [PMID: 34721406 PMCID: PMC8551676 DOI: 10.3389/fimmu.2021.739837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/28/2021] [Indexed: 11/25/2022] Open
Abstract
We have developed a new binary epitope-presenting CVP platform based on bamboo mosaic virus (BaMV) by using the sortase A (SrtA)-mediated ligation technology. The reconstructed BaMV genome harbors two modifications: 1) a coat protein (CP) with N-terminal extension of the tobacco etch virus (TEV) protease recognition site plus 4 extra glycine (G) residues as the SrtA acceptor; and 2) a TEV protease coding region replacing that of the triple-gene-block proteins. Inoculation of such construct, pKB5G, on Nicotiana benthamiana resulted in the efficient production of filamentous CVPs ready for SrtA-mediated ligation with desired proteins. The second part of the binary platform includes an expression vector for the bacterial production of donor proteins. We demonstrated the applicability of the platform by using the recombinant envelope protein domain III (rEDIII) of Japanese encephalitis virus (JEV) as the antigen. Up to 40% of the BaMV CP subunits in each CVP were loaded with rEDIII proteins in 1 min. The rEDIII-presenting BaMV CVPs (BJLPET5G) could be purified using affinity chromatography. Immunization assays confirmed that BJLPET5G could induce the production of neutralizing antibodies against JEV infections. The binary platform could be adapted as a useful alternative for the development and mass production of vaccine candidates.
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MESH Headings
- Aminoacyltransferases/genetics
- Aminoacyltransferases/metabolism
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antigens, Viral/administration & dosage
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Cell Line
- Cysteine Endopeptidases/genetics
- Cysteine Endopeptidases/metabolism
- Disease Models, Animal
- Encephalitis Virus, Japanese/genetics
- Encephalitis Virus, Japanese/immunology
- Encephalitis, Japanese/blood
- Encephalitis, Japanese/immunology
- Encephalitis, Japanese/prevention & control
- Encephalitis, Japanese/virology
- Endopeptidases/genetics
- Endopeptidases/metabolism
- Escherichia coli/genetics
- Escherichia coli/immunology
- Escherichia coli/metabolism
- Female
- Genetic Vectors
- Immunogenicity, Vaccine
- Japanese Encephalitis Vaccines/administration & dosage
- Japanese Encephalitis Vaccines/genetics
- Japanese Encephalitis Vaccines/immunology
- Mice, Inbred BALB C
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/immunology
- Plants, Genetically Modified/metabolism
- Potexvirus/enzymology
- Potexvirus/genetics
- Potexvirus/immunology
- Nicotiana/genetics
- Nicotiana/immunology
- Nicotiana/metabolism
- Virion/enzymology
- Virion/genetics
- Virion/immunology
- Mice
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Affiliation(s)
- Ming-Hao Yang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chi-Hzeng Wong
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hui-Ying Ko
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Meng-Hsun He
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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17
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Sapra R, Rajora AK, Kumar P, Maurya GP, Pant N, Haridas V. Chemical Biology of Sortase A Inhibition: A Gateway to Anti-infective Therapeutic Agents. J Med Chem 2021; 64:13097-13130. [PMID: 34516107 DOI: 10.1021/acs.jmedchem.1c00386] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Staphylococcus aureus is the leading cause of hospital-acquired infections. The enzyme sortase A, present on the cell surface of S. aureus, plays a key role in bacterial virulence without affecting the bacterial viability. Inhibition of sortase A activity offers a powerful but clinically less explored therapeutic strategy, as it offers the possibility of not inducing any selective pressure on the bacteria to evolve drug-resistant strains. In this Perspective, we offer a chemical space narrative for the design of sortase A inhibitors, as delineated into three broad domains: peptidomimetics, natural products, and synthetic small molecules. This provides immense opportunities for medicinal chemists to alleviate the ever-growing crisis of antibiotic resistance.
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Affiliation(s)
- Rachit Sapra
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Amit K Rajora
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Pushpendra Kumar
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Govind P Maurya
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Nalin Pant
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
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18
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Sequence variation in the β7-β8 loop of bacterial class A sortase enzymes alters substrate selectivity. J Biol Chem 2021; 297:100981. [PMID: 34302812 PMCID: PMC8361268 DOI: 10.1016/j.jbc.2021.100981] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 01/03/2023] Open
Abstract
Gram-positive bacteria contain sortase enzymes on their cell surfaces that catalyze transpeptidation reactions critical for proper cellular function. In vitro, sortases are used in sortase-mediated ligation (SML) reactions for a variety of protein engineering applications. Historically, sortase A from Staphylococcus aureus (saSrtA) has been the enzyme of choice to catalyze SML reactions. However, the stringent specificity of saSrtA for the LPXTG sequence motif limits its uses. Here, we describe the impact on substrate selectivity of a structurally conserved loop with a high degree of sequence variability in all classes of sortases. We investigate the contribution of this β7–β8 loop by designing and testing chimeric sortase enzymes. Our chimeras utilize natural sequence variation of class A sortases from eight species engineered into the SrtA sequence from Streptococcus pneumoniae. While some of these chimeric enzymes mimic the activity and selectivity of the WT protein from which the loop sequence was derived (e.g., that of saSrtA), others results in chimeric Streptococcus pneumoniae SrtA enzymes that are able to accommodate a range of residues in the final position of the substrate motif (LPXTX). Using mutagenesis, structural comparisons, and sequence analyses, we identify three interactions facilitated by β7–β8 loop residues that appear to be broadly conserved or converged upon in class A sortase enzymes. These studies provide the foundation for a deeper understanding of sortase target selectivity and can expand the sortase toolbox for future SML applications.
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19
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Anchoring surface proteins to the bacterial cell wall by sortase enzymes: how it started and what we know now. Curr Opin Microbiol 2021; 60:73-79. [PMID: 33611145 DOI: 10.1016/j.mib.2021.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 11/20/2022]
Abstract
In Gram-positive bacteria, the peptidoglycan serves as a placeholder for surface display of a unique class of monomeric and polymeric proteins, or pili - the precursors of which harbor a cell wall sorting signal with LPXTG motif that is recognized by a conserved transpeptidase enzyme called sortase. Since this original discovery over two decades ago, extensive genetic, biochemical and structural studies have illuminated the basic mechanisms of sortase-mediated cell wall anchoring of surface proteins and pili. We now know how LPXTG-containing surface proteins are folded post-translocationally, how sortase enzymes recognize substrates, and how a remnant of the cell wall sorting signal modulates intramembrane signaling. In this review, we will highlight new findings from a few model experimental paradigms and present future prospects for the field.
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20
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Use of molecular homology model to identify inhibitors of Staphylococcus pseudintermedius sortase A. RESULTS IN CHEMISTRY 2021. [DOI: 10.1016/j.rechem.2021.100185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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21
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Yang T, Zhang T, Guan XN, Dong Z, Lan L, Yang S, Yang CG. Tideglusib and Its Analogues As Inhibitors of Staphylococcus aureus SrtA. J Med Chem 2020; 63:8442-8457. [PMID: 32639734 DOI: 10.1021/acs.jmedchem.0c00803] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Sortase A (SrtA) anchors surface proteins to the cell wall envelope, and it has attracted increasing interesting as a potential antivirulence target. Several small-molecule inhibitors for SrtA have been developed, but target validation remains largely underexplored. Herein, we report a new class of SrtA inhibitors that supports antivirulence therapy through small-molecule targeting of SrtA. Tideglusib (TD), a drug candidate for myotonic dystrophy, was outstanding in high-throughput screening. A concise synthetic route quickly provided TD analogues, and the structure-activity relationships for SrtA inhibition have been established from those analogues. Several compounds largely retained the in vitro potency and exhibited a better solubility than TD. Additionally, TD attenuated virulence-related phenotypes in vitro and protected mice against lethal S. aureus USA300 bacteremia. Our study indicates that TD and its analogues could be new candidates as SrtA inhibitors with potential in the development of new antivirulence agents.
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Affiliation(s)
- Teng Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guizhou 550025, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tao Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiang-Na Guan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ze Dong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lefu Lan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of the Chinese Academy of Sciences, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guizhou 550025, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of the Chinese Academy of Sciences, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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22
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Ramirez NA, Das A, Ton-That H. New Paradigms of Pilus Assembly Mechanisms in Gram-Positive Actinobacteria. Trends Microbiol 2020; 28:999-1009. [PMID: 32499101 DOI: 10.1016/j.tim.2020.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023]
Abstract
Adhesive pili in Gram-positive bacteria represent a variety of extracellular multiprotein polymers that mediate bacterial colonization of specific host tissues and associated pathogenesis. Pili are assembled in two distinct but coupled steps, an orderly crosslinking of pilin monomers and subsequent anchoring of the polymer to peptidoglycan, catalyzed by two transpeptidase enzymes - the pilus-specific sortase and the housekeeping sortase. Here, we review this biphasic assembly mechanism based on studies of two prototypical models, the heterotrimeric pili in Corynebacterium diphtheriae and the heterodimeric pili in Actinomyces oris, highlighting some newly emerged basic paradigms. The disparate mechanisms of protein ligation mediated by the pilus-specific sortase and the spatial positioning of adhesive pili on the cell surface modulated by the housekeeping sortase are among the notable highlights.
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Affiliation(s)
- Nicholas A Ramirez
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Asis Das
- Department of Medicine, Neag Comprehensive Cancer Center, University of Connecticut Health Center, Farmington, CT, USA
| | - Hung Ton-That
- Molecular Biology Institute, University of California, Los Angeles, CA, USA; Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, CA, USA.
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23
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Kang CY, Huang IH, Chou CC, Wu TY, Chang JC, Hsiao YY, Cheng CH, Tsai WJ, Hsu KC, Wang S. Functional analysis of Clostridium difficile sortase B reveals key residues for catalytic activity and substrate specificity. J Biol Chem 2020; 295:3734-3745. [PMID: 32005667 PMCID: PMC7076211 DOI: 10.1074/jbc.ra119.011322] [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: 10/02/2019] [Revised: 01/31/2020] [Indexed: 01/07/2023] Open
Abstract
Most of Gram-positive bacteria anchor surface proteins to the peptidoglycan cell wall by sortase, a cysteine transpeptidase that targets proteins displaying a cell wall sorting signal. Unlike other bacteria, Clostridium difficile, the major human pathogen responsible for antibiotic-associated diarrhea, has only a single functional sortase (SrtB). Sortase's vital importance in bacterial virulence has been long recognized, and C. difficile sortase B (Cd-SrtB) has become an attractive therapeutic target for managing C. difficile infection. A better understanding of the molecular activity of Cd-SrtB may help spur the development of effective agents against C. difficile infection. In this study, using site-directed mutagenesis, biochemical and biophysical tools, LC-MS/MS, and crystallographic analyses, we identified key residues essential for Cd-SrtB catalysis and substrate recognition. To the best of our knowledge, we report the first evidence that a conserved serine residue near the active site participates in the catalytic activity of Cd-SrtB and also SrtB from Staphylococcus aureus The serine residue indispensable for SrtB activity may be involved in stabilizing a thioacyl-enzyme intermediate because it is neither a nucleophilic residue nor a substrate-interacting residue, based on the LC-MS/MS data and available structural models of SrtB-substrate complexes. Furthermore, we also demonstrated that residues 163-168 located on the β6/β7 loop of Cd-SrtB dominate specific recognition of the peptide substrate PPKTG. The results of this work reveal key residues with roles in catalysis and substrate specificity of Cd-SrtB.
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Affiliation(s)
- Chia-Yu Kang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
| | - I-Hsiu Huang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi-Chi Chou
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Tsai-Yu Wu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
| | - Jyun-Cyuan Chang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
| | - Yu-Yuan Hsiao
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan,Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Cheng-Hsuan Cheng
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan,Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Wei-Jiun Tsai
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan,Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Shuying Wang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan,Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, To whom correspondence should be addressed:
Dept. of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan. Tel.:
886-6-2353535, Ext. 5634; Fax:
886-6-2082705; E-mail:
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24
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Malik A, Kim YR, Jang IH, Hwang S, Oh DC, Kim SB. Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium. BMC Genomics 2020; 21:118. [PMID: 32013859 PMCID: PMC6998099 DOI: 10.1186/s12864-020-6468-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment. RESULTS A high quality draft genome (7.8 Mb) of S. yeochonensis CN732 was obtained with a G + C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites. CONCLUSIONS This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.
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Affiliation(s)
- Adeel Malik
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Yu Ri Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - In Hee Jang
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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25
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Structural studies of Staphylococcus aureus Sortase inhibiton via Conus venom peptides. Arch Biochem Biophys 2019; 671:87-102. [DOI: 10.1016/j.abb.2019.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/13/2022]
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26
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Anderl A, Ferlemann C, Muth M, Henkel-Gupalo A, Ebenig A, Brenner-Weiß G, Kolmar H, Fuchsbauer HL. Biochemical study of sortase E2 from Streptomyces mobaraensis and determination of transglutaminase cross-linking sites. FEBS Lett 2019; 593:1944-1956. [PMID: 31155711 DOI: 10.1002/1873-3468.13466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/27/2019] [Accepted: 05/29/2019] [Indexed: 12/15/2022]
Abstract
Distinct streptomycetes such as Streptomyces mobaraensis produce the protein cross-linking enzyme transglutaminase. Bioinformatic analysis predicted the occurrence of seven sortases exerting transpeptidation reactions similarly to transglutaminase. Here, we report the production and characterization of sortase E2 (Sm-SrtE2) solubilized by removal of its membrane anchor domain. Sm-SrtE2 activity was measured using pentapeptides predicted to be cell wall sorting signals of putative sortase substrate proteins. Preferred linkage to Gly3 by Sm-SrtE2 was in the order LAETG>>LAHTG>>LAQTG~LANTG>LARTG. Chaplin 1 from S. mobaraensis was further demonstrated to be an excellent substrate of both the intrinsic Sm-SrtE2 and transglutaminase. The unexpected discovery showing Gln-62 and Gln-65 of Δ1-50 -Sm-SrtE2 as transglutaminase cross-linking sites suggests that low enzyme stability might be due to anchor domain truncation and a disordered N terminus.
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Affiliation(s)
- Anita Anderl
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany.,Department of Chemistry, Technische Universität Darmstadt, Germany
| | - Cathrin Ferlemann
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
| | - Marius Muth
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany.,Bioengineering and Biosystems, Institute of Functional Interfaces, Karlsruhe Institute of Technology, Germany
| | - Antonina Henkel-Gupalo
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
| | - Aileen Ebenig
- Department of Chemistry, Technische Universität Darmstadt, Germany
| | - Gerald Brenner-Weiß
- Bioengineering and Biosystems, Institute of Functional Interfaces, Karlsruhe Institute of Technology, Germany
| | - Harald Kolmar
- Department of Chemistry, Technische Universität Darmstadt, Germany
| | - Hans-Lothar Fuchsbauer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
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27
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A comprehensive in silico analysis of sortase superfamily. J Microbiol 2019; 57:431-443. [DOI: 10.1007/s12275-019-8545-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 12/22/2022]
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28
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Characterization of the housekeeping sortase from the human pathogen Propionibacterium acnes: first investigation of a class F sortase. Biochem J 2019; 476:665-682. [PMID: 30670573 DOI: 10.1042/bcj20180885] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/17/2022]
Abstract
Sortase enzymes play an important role in Gram-positive bacteria. They are responsible for the covalent attachment of proteins to the surface of the bacteria and perform this task via a highly sequence-specific transpeptidation reaction. Since these immobilized proteins are often involved in pathogenicity of Gram-positive bacteria, characterization of this type of enzyme is also of medical relevance. Different classes of sortases (A-F) have been found, which recognize characteristic recognition sequences present in substrate proteins. Up to date, sortase A from Staphylococcus aureus, a housekeeping class A sortase, is the most thoroughly studied representative of the sortase family of enzymes. Here we report the in-depth characterization of the class F sortase from Propionibacterium acnes, a class of sortases that has not been investigated before. As Sortase F is the only transpeptidase found in the P. acnes genome, it is the housekeeping sortase of this organism. Sortase F from P. acnes shows a behavior similar to sortases from class A in terms of pH dependence, recognition sequence and catalytic activity; furthermore, its activity is independent of bivalent ions, which contrasts to sortase A from S. aureus We demonstrate that sortase F is useful for protein engineering applications, by producing a site-specifically conjugated homogenous antibody-drug conjugate with a potency similar to that of a conjugate prepared with sortase A. Thus, the detailed characterization presented here will not only enable the development of anti-virulence agents targeting P. acnes but also provides a powerful alternative to sortase A for protein engineering applications.
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29
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Schneewind O, Missiakas D. Sortases, Surface Proteins, and Their Roles in Staphylococcus aureus Disease and Vaccine Development. Microbiol Spectr 2019; 7:10.1128/microbiolspec.PSIB-0004-2018. [PMID: 30737913 PMCID: PMC6386163 DOI: 10.1128/microbiolspec.psib-0004-2018] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Indexed: 12/27/2022] Open
Abstract
Sortases cleave short peptide motif sequences at the C-terminal end of secreted surface protein precursors and either attach these polypeptides to the peptidoglycan of Gram-positive bacteria or promote their assembly into pilus structures that are also attached to peptidoglycan. Sortase A, the enzyme first identified in the human pathogen Staphylococcus aureus, binds LPXTG motif sorting signals, cleaves between threonine (T) and glycine (G) residues, and forms an acyl enzyme between its active-site cysteine thiol and the carboxyl group of threonine (T). Sortase A acyl enzyme is relieved by the nucleophilic attack of the cross bridge amino group within lipid II, thereby generating surface protein linked to peptidoglycan precursor. Such products are subsequently incorporated into the cell wall envelope by enzymes of the peptidoglycan synthesis pathway. Surface proteins linked to peptidoglycan may be released from the bacterial envelope to diffuse into host tissues and fulfill specific biological functions. S. aureus sortase A is essential for host colonization and for the pathogenesis of invasive diseases. Staphylococcal sortase-anchored surface proteins fulfill key functions during the infectious process, and vaccine-induced antibodies targeting surface proteins may provide protection against S. aureus. Alternatively, small-molecule inhibitors of sortase may be useful agents for the prevention of S. aureus colonization and invasive disease.
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Affiliation(s)
- Olaf Schneewind
- Department of Microbiology, University of Chicago, Chicago, IL 60637
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30
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Pohlschroder M, Pfeiffer F, Schulze S, Abdul Halim MF. Archaeal cell surface biogenesis. FEMS Microbiol Rev 2018; 42:694-717. [PMID: 29912330 PMCID: PMC6098224 DOI: 10.1093/femsre/fuy027] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Cell surfaces are critical for diverse functions across all domains of life, from cell-cell communication and nutrient uptake to cell stability and surface attachment. While certain aspects of the mechanisms supporting the biosynthesis of the archaeal cell surface are unique, likely due to important differences in cell surface compositions between domains, others are shared with bacteria or eukaryotes or both. Based on recent studies completed on a phylogenetically diverse array of archaea, from a wide variety of habitats, here we discuss advances in the characterization of mechanisms underpinning archaeal cell surface biogenesis. These include those facilitating co- and post-translational protein targeting to the cell surface, transport into and across the archaeal lipid membrane, and protein anchoring strategies. We also discuss, in some detail, the assembly of specific cell surface structures, such as the archaeal S-layer and the type IV pili. We will highlight the importance of post-translational protein modifications, such as lipid attachment and glycosylation, in the biosynthesis as well as the regulation of the functions of these cell surface structures and present the differences and similarities in the biogenesis of type IV pili across prokaryotic domains.
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Affiliation(s)
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Stefan Schulze
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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31
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Wang J, Song M, Pan J, Shen X, Liu W, Zhang X, Li H, Deng X. Quercetin impairs Streptococcus pneumoniae biofilm formation by inhibiting sortase A activity. J Cell Mol Med 2018; 22:6228-6237. [PMID: 30334338 PMCID: PMC6237587 DOI: 10.1111/jcmm.13910] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/20/2018] [Indexed: 02/03/2023] Open
Abstract
Biofilm formation mediated by sortase A (srtA) is important for bacterial colonisation and resistance to antibiotics. Thus, the inhibitor of SrtA may represent a promising agent for bacterial infection. The structure of Streptococcus pneumoniae D39 srtA has been characterised by crystallisation. Site‐directed mutagenesis was used for the determination of the key residues for the activity of S. pneumoniae D39 srtA. An effective srtA inhibitor, quercetin, and its mechanism was further identified using srtA activity inhibition assay and molecular modelling. In this study, the crystal structure of S. pneumoniae D39 srtA has been solved and shown to contain a unique domain B. Additionally, its transpeptidase activity was evaluated in vitro. Based on the structure, we identified Cys207 as the catalytic residue, with His141 and Arg215 serving as binding sites for the peptide substrate. We found that quercetin can specifically compete with the natural substrate, leading to a significant decrease in the catalytic activity of this enzyme. In cells co‐cultured with this small molecule inhibitor, NanA cannot anchor to the cell wall effectively, and biofilm formation and biomass decrease significantly. Interestingly, when we supplemented cultures with sialic acid, a crucial signal for pneumococcal coloniation and the invasion of the host in the co‐culture system, biofilm loss did not occur. This result indicates that quercetin inhibits biofilm formation by affecting sialic acid production. In conclusion, the inhibition of pneumococcal srtA by the small molecule quercetin offers a novel strategy for pneumococcal preventative therapy.
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Affiliation(s)
- Jianfeng Wang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Meng Song
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Juan Pan
- Tianjin International Travel Healthcare Center, Tianjin, China
| | - Xue Shen
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wentao Liu
- Heilongjiang Veterinary Drug and Feed Super Vision Institute, Haerbin, China
| | - Xueke Zhang
- Heilongjiang Veterinary Drug and Feed Super Vision Institute, Haerbin, China
| | - Hongen Li
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuming Deng
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
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32
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Yoo J, Louis JM, Gopich IV, Chung HS. Three-Color Single-Molecule FRET and Fluorescence Lifetime Analysis of Fast Protein Folding. J Phys Chem B 2018; 122:11702-11720. [PMID: 30230835 DOI: 10.1021/acs.jpcb.8b07768] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the theory, experiment, and analysis of three-color Förster resonance energy transfer (FRET) spectroscopy for probing conformational dynamics of a fast-folding protein, α3D. In three-color FRET, site-specific labeling of fluorophores is required to avoid ambiguity resulting from various species with different combinations of labeling positions. To this end, we first attached two dyes to a cysteine residue and an unnatural amino acid and then appended a cysteine residue to the C-terminus of the protein by the sortase-mediated ligation for attaching the third dye. To determine all three FRET efficiencies, we used alternating excitation of the donor and acceptor 1 with two picosecond-pulsed lasers. Since the folded and unfolded states are not distinguishable in binned fluorescence trajectories due to fast-folding on a millisecond time scale, we used a maximum likelihood method that analyzes photon trajectories without binning the data. The extracted kinetic parameters agree very well with the previously measured parameters for the same protein with two-color FRET, suggesting that the addition of the third fluorophore does not affect the folding dynamics of the protein. From the extracted fractions of acceptor photon counts, the FRET efficiencies for all three dye pairs were calculated after various corrections. They were compared with the FRET efficiencies obtained from the global analysis of two-color segments collected in the same experiment. The FRET efficiencies of the folded state from the three-color segments agree with those from the two-color segments, whereas the three-color and two-color FRET efficiencies of the unfolded state are different. This happens because fluctuations of all three interdye distances contribute to the FRET efficiency measured in three-color FRET. We show that this difference can be accounted for by using the Gaussian chain model for the unfolded state with the parameters obtained from the analysis of two-color segments. This result shows that three-color FRET provides additional information on the flexibility of molecules that cannot be obtained from a combination of two-color FRET experiments with three dye pairs. Using the delay times of photons from the laser pulse, fluorescence lifetimes were determined using the maximum likelihood analysis. The correlation between FRET efficiencies and lifetimes of the donor, acceptor 1, and acceptor 2 was visualized in two-dimensional FRET efficiency-lifetime histograms. These histograms can be used to demonstrate the presence of conformational dynamics in a protein.
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Affiliation(s)
- Janghyun Yoo
- Laboratory of Chemical Physics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
| | - John M Louis
- Laboratory of Chemical Physics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
| | - Irina V Gopich
- Laboratory of Chemical Physics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
| | - Hoi Sung Chung
- Laboratory of Chemical Physics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
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33
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Erianin against Staphylococcus aureus Infection via Inhibiting Sortase A. Toxins (Basel) 2018; 10:toxins10100385. [PMID: 30249042 PMCID: PMC6215257 DOI: 10.3390/toxins10100385] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/08/2018] [Accepted: 09/20/2018] [Indexed: 02/04/2023] Open
Abstract
With continuous emergence and widespread of multidrug-resistant Staphylococcus aureus infections, common antibiotics have become ineffective in treating these infections in the clinical setting. Anti-virulence strategies could be novel, effective therapeutic strategies against drug-resistant bacterial infections. Sortase A (srtA), a transpeptidase in gram-positive bacteria, can anchor surface proteins that play a vital role in pathogenesis of these bacteria. SrtA is known as a potential antivirulent drug target to treat bacterial infections. In this study, we found that erianin, a natural bibenzyl compound, could inhibit the activity of srtA in vitro (half maximal inhibitory concentration-IC50 = 20.91 ± 2.31 μg/mL, 65.7 ± 7.2 μM) at subminimum inhibitory concentrations (minimum inhibitory concentrations-MIC = 512 μg/mL against S. aureus). The molecular mechanism underlying the inhibition of srtA by erianin was identified using molecular dynamics simulation: erianin binds to srtA residues Ile182, Val193, Trp194, Arg197, and Ile199, forming a stable bond via hydrophobic interactions. In addition, the activities of S. aureus binding to fibronectin and biofilm formation were inhibited by erianin, when co-culture with S. aureus. In vivo, erianin could improve the survival in mice that infected with S. aureus by tail vein injection. Experimental results showed that erianin is a potential novel therapeutic compound against S. aureus infections via affecting srtA.
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34
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Abdul Halim MF, Rodriguez R, Stoltzfus JD, Duggin IG, Pohlschroder M. Conserved residues are critical for Haloferax volcanii archaeosortase catalytic activity: Implications for convergent evolution of the catalytic mechanisms of non-homologous sortases from archaea and bacteria. Mol Microbiol 2018; 108:276-287. [PMID: 29465796 DOI: 10.1111/mmi.13935] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2018] [Indexed: 11/29/2022]
Abstract
Proper protein anchoring is key to the biogenesis of prokaryotic cell surfaces, dynamic, resilient structures that play crucial roles in various cell processes. A novel surface protein anchoring mechanism in Haloferax volcanii depends upon the peptidase archaeosortase A (ArtA) processing C-termini of substrates containing C-terminal tripartite structures and anchoring mature substrates to the cell membrane via intercalation of lipid-modified C-terminal amino acid residues. While this membrane protein lacks clear homology to soluble sortase transpeptidases of Gram-positive bacteria, which also process C-termini of substrates whose C-terminal tripartite structures resemble those of ArtA substrates, archaeosortases do contain conserved cysteine, arginine and arginine/histidine/asparagine residues, reminiscent of His-Cys-Arg residues of sortase catalytic sites. The study presented here shows that ArtAWT -GFP expressed in trans complements ΔartA growth and motility phenotypes, while alanine substitution mutants, Cys173 (C173A), Arg214 (R214A) or Arg253 (R253A), and the serine substitution mutant for Cys173 (C173S), fail to complement these phenotypes. Consistent with sortase active site replacement mutants, ArtAC173A -GFP, ArtAC173S -GFP and ArtAR214A -GFP cannot process substrates, while replacement of the third residue, ArtAR253A -GFP retains some processing activity. These findings support the view that similarities between certain aspects of the structures and functions of the sortases and archaeosortases are the result of convergent evolution.
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Affiliation(s)
| | - Ronald Rodriguez
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Iain G Duggin
- The ithree Institute, University of Technology Sydney, Sydney, NSW, 2007, Australia
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35
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Nikghalb KD, Horvath NM, Prelesnik JL, Banks OGB, Filipov PA, Row RD, Roark TJ, Antos JM. Expanding the Scope of Sortase-Mediated Ligations by Using Sortase Homologues. Chembiochem 2017; 19:185-195. [PMID: 29124839 DOI: 10.1002/cbic.201700517] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 02/04/2023]
Abstract
Sortase-catalyzed transacylation reactions are widely used for the construction of non-natural protein derivatives. However, the most commonly used enzyme for these strategies (sortase A from Staphylococcus aureus) is limited by its narrow substrate scope. To expand the range of substrates compatible with sortase-mediated reactions, we characterized the in vitro substrate preferences of eight sortase A homologues. From these studies, we identified sortase A enzymes that recognize multiple substrates that are unreactive toward sortase A from S. aureus. We further exploited the ability of sortase A from Streptococcus pneumoniae to recognize an LPATS substrate to perform a site-specific modification of the N-terminal serine residue in the naturally occurring antimicrobial peptide DCD-1L. Finally, we unexpectedly observed that certain substrates (LPATXG, X=Nle, Leu, Phe, Tyr) were susceptible to transacylation at alternative sites within the substrate motif, and sortase A from S. pneumoniae was capable of forming oligomers. Overall, this work provides a foundation for the further development of sortase enzymes for use in protein modification.
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Affiliation(s)
- Keyvan D Nikghalb
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - Nicholas M Horvath
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - Jesse L Prelesnik
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - Orion G B Banks
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - Pavel A Filipov
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - R David Row
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - Travis J Roark
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - John M Antos
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
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36
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Suliman M, Santosh V, Seegar TCM, Dalton AC, Schultz KM, Klug CS, Barton WA. Directed evolution provides insight into conformational substrate sampling by SrtA. PLoS One 2017; 12:e0184271. [PMID: 28859178 PMCID: PMC5578623 DOI: 10.1371/journal.pone.0184271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/21/2017] [Indexed: 11/19/2022] Open
Abstract
The Sortase family of transpeptidases are found in numerous gram-positive bacteria and involved in divergent physiological processes including anchoring of surface proteins to the cell wall as well as pili assembly. As essential proteins, sortase enzymes have been the focus of considerable interest for the development of novel anti-microbials, however, more recently their function as unique transpeptidases has been exploited for the synthesis of novel bio-conjugates. Yet, for synthetic purposes, SrtA-mediated conjugation suffers from the enzyme's inherently poor catalytic efficiency. Therefore, to identify SrtA variants with improved catalytic efficiency, we used directed evolution to select a catalytically enhanced SrtA enzyme. An analysis of improved SrtA variants in the context of sequence conservation, NMR and x-ray crystal structures, and kinetic data suggests a novel mechanism for catalysis involving large conformational changes that delivers substrate to the active site pocket. Indeed, using DEER-EPR spectroscopy, we reveal that upon substrate binding, SrtA undergoes a large scissors-like conformational change that simultaneously translates the sort-tag substrate to the active site in addition to repositioning key catalytic residues for esterification. A better understanding of Sortase dynamics will significantly enhance future engineering and drug discovery efforts.
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Affiliation(s)
- Muna Suliman
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Vishaka Santosh
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Tom C. M. Seegar
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Annamarie C. Dalton
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Kathryn M. Schultz
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Candice S. Klug
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - William A. Barton
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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Anchoring of LPXTG-Like Proteins to the Gram-Positive Cell Wall Envelope. Curr Top Microbiol Immunol 2017; 404:159-175. [PMID: 27097813 DOI: 10.1007/82_2016_8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In Gram-positive bacteria, protein precursors with a signal peptide and a cell wall sorting signal (CWSS)-which begins with an LPXTG motif, followed by a hydrophobic domain and a tail of positively charged residues-are targeted to the cell envelope by a transpeptidase enzyme call sortase. Evolution and selective pressure gave rise to six classes of sortase, i.e., SrtA-F. Only class C sortases are capable of polymerizing substrates harboring the pilin motif and CWSS into protein polymers known as pili or fimbriae, whereas the others perform cell wall anchoring functions. Regardless of the products generated from these sortases, the basic principle of sortase-catalyzed transpeptidation is the same. It begins with the cleavage of the LPXTG motif, followed by the cross-linking of this cleaved product at the threonine residue to a nucleophile, i.e., an active amino group of the peptidoglycan stem peptide or the lysine residue of the pilin motif. This chapter will summarize the efforts to identify and characterize sortases and their associated pathways with emphasis on the cell wall anchoring function.
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Fargašová A, Balzerová A, Prucek R, Sedláková MH, Bogdanová K, Gallo J, Kolář M, Ranc V, Zbořil R. Detection of Prosthetic Joint Infection Based on Magnetically Assisted Surface Enhanced Raman Spectroscopy. Anal Chem 2017; 89:6598-6607. [DOI: 10.1021/acs.analchem.7b00759] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ariana Fargašová
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, Šlechtitelů
27, 783 71 Olomouc, Czech Republic
| | - Anna Balzerová
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, Šlechtitelů
27, 783 71 Olomouc, Czech Republic
| | - Robert Prucek
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, Šlechtitelů
27, 783 71 Olomouc, Czech Republic
| | - Miroslava Htoutou Sedláková
- Department
of Microbiology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 3, 775 15 Olomouc, Czech Republic
| | - Kateřina Bogdanová
- Department
of Microbiology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 3, 775 15 Olomouc, Czech Republic
| | - Jiří Gallo
- Department
of Orthopaedics, Faculty of Medicine and Dentistry, Palacký University Olomouc, I. P. Pavlova 6, 77520 Olomouc, Czech Republic
| | - Milan Kolář
- Department
of Microbiology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 3, 775 15 Olomouc, Czech Republic
| | - Václav Ranc
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, Šlechtitelů
27, 783 71 Olomouc, Czech Republic
| | - Radek Zbořil
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, Šlechtitelů
27, 783 71 Olomouc, Czech Republic
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Jacobitz AW, Kattke MD, Wereszczynski J, Clubb RT. Sortase Transpeptidases: Structural Biology and Catalytic Mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 109:223-264. [PMID: 28683919 DOI: 10.1016/bs.apcsb.2017.04.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Gram-positive bacteria use sortase cysteine transpeptidase enzymes to covalently attach proteins to their cell wall and to assemble pili. In pathogenic bacteria sortases are potential drug targets, as many of the proteins that they display on the microbial surface play key roles in the infection process. Moreover, the Staphylococcus aureus Sortase A (SaSrtA) enzyme has been developed into a valuable biochemical reagent because of its ability to ligate biomolecules together in vitro via a covalent peptide bond. Here we review what is known about the structures and catalytic mechanism of sortase enzymes. Based on their primary sequences, most sortase homologs can be classified into six distinct subfamilies, called class A-F enzymes. Atomic structures reveal unique, class-specific variations that support alternate substrate specificities, while structures of sortase enzymes bound to sorting signal mimics shed light onto the molecular basis of substrate recognition. The results of computational studies are reviewed that provide insight into how key reaction intermediates are stabilized during catalysis, as well as the mechanism and dynamics of substrate recognition. Lastly, the reported in vitro activities of sortases are compared, revealing that the transpeptidation activity of SaSrtA is at least 20-fold faster than other sortases that have thus far been characterized. Together, the results of the structural, computational, and biochemical studies discussed in this review begin to reveal how sortases decorate the microbial surface with proteins and pili, and may facilitate ongoing efforts to discover therapeutically useful small molecule inhibitors.
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Affiliation(s)
- Alex W Jacobitz
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States
| | - Michele D Kattke
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States
| | - Jeff Wereszczynski
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States
| | - Robert T Clubb
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States.
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40
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High yield synthesis of cyclic analogues of antibacterial peptides P-113 by Sortase A-mediated ligation and their conformation studies. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2016.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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41
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Siegel SD, Liu J, Ton-That H. Biogenesis of the Gram-positive bacterial cell envelope. Curr Opin Microbiol 2016; 34:31-37. [PMID: 27497053 PMCID: PMC5164837 DOI: 10.1016/j.mib.2016.07.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 07/19/2016] [Indexed: 01/29/2023]
Abstract
The Gram-positive cell envelope serves as a molecular platform for surface display of capsular polysaccharides, wall teichoic acids (WTAs), lipoteichoic acids (LTAs), lipoproteins, surface proteins and pili. WTAs, LTAs, and sortase-assembled pili are a few features that make the Gram-positive cell envelope distinct from the Gram-negative counterpart. Interestingly, a set of LytR-CpsA-Psr family proteins, found in all Gram-positives but limited to a minority of Gram-negative organisms, plays divergent functions, while decorating the cell envelope with glycans. Furthermore, a phylum of Gram-positive bacteria, the actinobacteria, appear to employ oxidative protein folding as the major folding mechanism, typically occurring in an oxidizing environment of the Gram-negative periplasm. These distinctive features will be highlighted, along with recent findings in the cell envelope biogenesis.
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Affiliation(s)
- Sara D Siegel
- Department of Microbiology & Molecular Genetics, University of Texas McGovern Medical School, Houston, TX, USA
| | - Jun Liu
- Department of Pathology & Laboratory Medicine, University of Texas McGovern Medical School, Houston, TX, USA
| | - Hung Ton-That
- Department of Microbiology & Molecular Genetics, University of Texas McGovern Medical School, Houston, TX, USA.
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Chen JL, Wang X, Yang F, Cao C, Otting G, Su XC. 3D Structure Determination of an Unstable Transient Enzyme Intermediate by Paramagnetic NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:13744-13748. [DOI: 10.1002/anie.201606223] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/15/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Chan Cao
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Gottfried Otting
- Research School of Chemistry; Australian National University; Canberra ACT 2601 Australia
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
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43
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Chen JL, Wang X, Yang F, Cao C, Otting G, Su XC. 3D Structure Determination of an Unstable Transient Enzyme Intermediate by Paramagnetic NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Chan Cao
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Gottfried Otting
- Research School of Chemistry; Australian National University; Canberra ACT 2601 Australia
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
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44
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Schatte M, Bocola M, Roth T, Martinez R, Kopetzki E, Schwaneberg U, Bönitz-Dulat M. Reporter Immobilization Assay (REIA) for Bioconjugating Reactions. Bioconjug Chem 2016; 27:1484-92. [DOI: 10.1021/acs.bioconjchem.6b00111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin Schatte
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52074 Aachen, Germany
| | - Marco Bocola
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52074 Aachen, Germany
| | | | - Ronny Martinez
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52074 Aachen, Germany
| | | | - Ulrich Schwaneberg
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52074 Aachen, Germany
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45
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Si L, Li P, Liu X, Luo L. Chinese herb medicine against Sortase A catalyzed transformations, a key role in gram-positive bacterial infection progress. J Enzyme Inhib Med Chem 2016; 31:184-196. [PMID: 27162091 DOI: 10.1080/14756366.2016.1178639] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Many Gram-positive bacteria can anchor their surface proteins to the cell wall peptidoglycan covalently by a common mechanism with Sortase A (SrtA), thus escaping from the host's identification of immune cells. SrtA can complete this anchoring process by cleaving LPXTG motif conserved among these surface proteins and thus these proteins anchor on the cell wall. Moreover, those SrtA mutants lose this capability to anchor these relative proteins, with these bacteria no longer infectious. Therefore, SrtA inhibitors can be promising anti-infective agents to cure bacterial infections. Chinese herb medicines (CHMs) (chosen from Science Citation Index) have exhibited inhibition on SrtA of Gram-positive pathogens irreversibly or reversibly. In general, CHMs are likely to have important long-term impact as new antibacterial compounds and sought after by academia and the pharmaceutical industry. This review mainly focuses on SrtA inhibitors from CHMs and the potential inhibiting mechanism related to chemical structures of compounds in CHMs.
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Affiliation(s)
- Lifang Si
- a School of Bioscience & Bioengineering, South China University of Technology, Guangzhou University Town , Panyu , Guangzhou , China
| | - Pan Li
- a School of Bioscience & Bioengineering, South China University of Technology, Guangzhou University Town , Panyu , Guangzhou , China
| | - Xiong Liu
- a School of Bioscience & Bioengineering, South China University of Technology, Guangzhou University Town , Panyu , Guangzhou , China
| | - Lixin Luo
- a School of Bioscience & Bioengineering, South China University of Technology, Guangzhou University Town , Panyu , Guangzhou , China
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46
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Williams FP, Milbradt AG, Embrey KJ, Bobby R. Segmental Isotope Labelling of an Individual Bromodomain of a Tandem Domain BRD4 Using Sortase A. PLoS One 2016; 11:e0154607. [PMID: 27128490 PMCID: PMC4851411 DOI: 10.1371/journal.pone.0154607] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/17/2016] [Indexed: 11/19/2022] Open
Abstract
Bromodomain and extra-terminal (BET) family of proteins are one of the major readers of epigenetic marks and an important target class in oncology and other disease areas. The importance of the BET family of proteins is manifested by the explosion in the number of inhibitors against these targets that have successfully entered clinical trials. One important BET family member is bromodomain containing protein 4 (BRD4). Structural and biophysical studies of BRD4 are complicated by its tertiary-structure consisting of two bromodomains connected by a flexible inter-domain linker of approximately 180 amino acids. A detailed understanding of the interplay of these bromodomains will be key to rational drug design in BRD4, yet there are no reported three-dimensional structures of the multi-domain BRD4 and NMR studies of the tandem domain are hampered by the size of the protein. Here, we present a method for rapid Sortase A-mediated segmental labelling of the individual bromodomains of BRD4 that provides a powerful strategy that will enable NMR studies of ligand-bromodomain interactions with atomic detail. In our labelling strategy, we have used U-[2H,15N]-isotope labelling on the C-terminal bromodomain with selective introduction of 13CH3 methyl groups on Ile (δ1), Val and Leu, whereas the N-terminal bromodomain remained unlabelled. This labelling scheme resulted in significantly simplified NMR spectra and will allow for high-resolution interaction, structure and dynamics studies in the presence of ligands.
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Affiliation(s)
- Felix P. Williams
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Alderley Park, Macclesfield SK10 4TF, United Kingdom
| | - Alexander G. Milbradt
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Alderley Park, Macclesfield SK10 4TF, United Kingdom
| | - Kevin J. Embrey
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Alderley Park, Macclesfield SK10 4TF, United Kingdom
- * E-mail: (KJE); (RB)
| | - Romel Bobby
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Alderley Park, Macclesfield SK10 4TF, United Kingdom
- * E-mail: (KJE); (RB)
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Shrestha P, Wereszczynski J. Discerning the catalytic mechanism of Staphylococcus aureus sortase A with QM/MM free energy calculations. J Mol Graph Model 2016; 67:33-43. [PMID: 27172839 DOI: 10.1016/j.jmgm.2016.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/08/2016] [Accepted: 04/09/2016] [Indexed: 10/21/2022]
Abstract
Sortases are key virulence factors in Gram-positive bacteria. These enzymes embed surface proteins in the cell wall through a transpeptidation reaction that involves recognizing a penta-peptide "sorting signal" in a target protein, cleaving it, and covalently attaching it to a second substrate that is later inserted into the cell wall. Although well studied, several aspects of the mechanism by which sortases perform these functions remains unclear. In particular, experiments have revealed two potential sorting signal binding motifs: a "Threonine-Out" (Thr-Out) structure in which the catalytically critical threonine residues protrudes into solution, and a "Threonine-In" (Thr-In) configuration in which this residue inserts into the binding site. To determine which of these is the biologically relevant state, we have performed a series of conventional and hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations of the Staphylococcus aureus sortase A (SrtA) enzyme bound to a sorting signal substrate. Through the use of multi-dimensional metadynamics, our simulations were able to both map the acylation mechanism of SrtA in the Thr-In and Thr-Out states, as well as determine the free energy minima and barriers along these reactions. Results indicate that in both states the catalytic mechanisms are similar, however the free energy barriers are lower in the Thr-In configuration, suggesting that Thr-In is the catalytically relevant state. This has important implications for advancing our understanding of the mechanisms of sortase enzymes, as well we for future structure based drug design efforts aimed at inhibiting sortase function in vivo.
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Affiliation(s)
- Pooja Shrestha
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, 3440 S Dearborn St., Chicago, IL 60616, USA
| | - Jeff Wereszczynski
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, 3440 S Dearborn St., Chicago, IL 60616, USA.
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48
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Wallock-Richards DJ, Marles-Wright J, Clarke DJ, Maitra A, Dodds M, Hanley B, Campopiano DJ. Molecular basis of Streptococcus mutans sortase A inhibition by the flavonoid natural product trans-chalcone. Chem Commun (Camb) 2016; 51:10483-5. [PMID: 26029850 DOI: 10.1039/c5cc01816a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sortase A (SrtA) from Gram positive pathogens is an attractive target for inhibitors due to its role in the attachment of surface proteins to the cell wall. We found that the plant natural product trans-chalcone inhibits Streptococcus mutans SrtA in vitro and also inhibited S. mutans biofilm formation. Mass spectrometry revealed that the trans-chalcone forms a Michael addition adduct with the active site cysteine. The X-ray crystal structure of the SrtA H139A mutant provided new insights into substrate recognition by the sortase family. Our study suggests that chalcone flavonoids have potential as sortase-specific oral biofilm inhibitors.
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Affiliation(s)
- Daynea J Wallock-Richards
- EastChem School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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49
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Li H, Chen Y, Zhang B, Niu X, Song M, Luo Z, Lu G, Liu B, Zhao X, Wang J, Deng X. Inhibition of sortase A by chalcone prevents Listeria monocytogenes infection. Biochem Pharmacol 2016; 106:19-29. [PMID: 26826492 DOI: 10.1016/j.bcp.2016.01.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/26/2016] [Indexed: 12/22/2022]
Abstract
The critical role of sortase A in gram-positive bacterial pathogenicity makes this protein a good potential target for antimicrobial therapy. In this study, we report for the first time the crystal structure of Listeria monocytogenes sortase A and identify the active sites that mediate its transpeptidase activity. We also used a sortase A (SrtA) enzyme activity inhibition assay, simulation, and isothermal titration calorimetry analysis to discover that chalcone, an agent with little anti-L. monocytogenes activity, could significantly inhibit sortase A activity with an IC50 of 28.41 ± 5.34 μM by occupying the active site of SrtA. The addition of chalcone to a co-culture of L. monocytogenes and Caco-2 cells significantly inhibited bacterial entry into the cells and L. monocytogenes-mediated cytotoxicity. Additionally, chalcone treatment decreased the mortality of infected mice, the bacterial burden in target organs, and the pathological damage to L. monocytogenes-infected mice. In conclusion, these findings suggest that chalcone is a promising candidate for the development of treatment against L. monocytogenes infection.
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Affiliation(s)
- Hongen Li
- Key Laboratory of Zoonosis, Ministry of Education, Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yutao Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhang
- Key Laboratory of Zoonosis, Ministry of Education, Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xiaodi Niu
- Key Laboratory of Zoonosis, Ministry of Education, Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Meng Song
- Key Laboratory of Zoonosis, Ministry of Education, Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhaoqing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Gejin Lu
- Key Laboratory of Zoonosis, Ministry of Education, Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Bowen Liu
- Key Laboratory of Zoonosis, Ministry of Education, Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xiaoran Zhao
- Key Laboratory of Zoonosis, Ministry of Education, Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jianfeng Wang
- Key Laboratory of Zoonosis, Ministry of Education, Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China.
| | - Xuming Deng
- Key Laboratory of Zoonosis, Ministry of Education, Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China.
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50
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Mann S, Sharma A, Biswas S, Gupta RK. Identification and molecular docking analysis of active ingredients with medicinal properties from edible Baccaurea sapida. Bioinformation 2015; 11:437-43. [PMID: 26527853 PMCID: PMC4620621 DOI: 10.6026/97320630011437] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/26/2015] [Accepted: 06/26/2015] [Indexed: 11/26/2022] Open
Abstract
Underutilized plant species has started changing the conception of plants by expanding the use well beyond from foods and fibers to rich source of medicinally important secondary metabolites. Bioactive compounds from natural sources are gaining importance as potential drug candidates towards many inflammatory conditions like Rheumatoid Arthritis (RA). The focus of the present study has been centred to reveal the anti-inflammatory potential of an underutilized fruits of B. sapida. Further efforts towards its medicinal significance may provide relieve from symptoms of RA by reducing the side effects that are observed in available medications. Total 10 compounds in fruit crude methanol extract were identified and quantified by LC-MS/MS analysis followed by the agar well diffusion method for their anti microbial activity. Among all studied micro organism S. aureus was found to surmount the inflammation in RA through domain B of surface protein A (Staphylococcal surface protein A). Identified compounds (having anti-inflammatory properties) were scrutinized for their toxicity and quantitative structure-activity relationship (QSAR) using lazer toxicity and Molinspiration servers respectively. Further, docking studies have been carried out between domain B and studied compounds using AutoDock. Out of 6 anti-inflammtory compounds, quercetin has been identified as the most potent compound in reference to its inhibitory constant (47.01) and binding energy (-5.90 kcal/mol) to bacterial protein. Our data suggest that methanol extract of B. sapida fruit posses medicinally significant anti-inflammatory compounds and thus justifies the use of this fruit as folklore medicine for preventing inflammation related diseases.
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Affiliation(s)
- Sonia Mann
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi - 110078, India
| | - Ankita Sharma
- CSIRInstitute of Genomics & Integrative Biology, Mall Road, Delhi-110007, India
| | - Sagarika Biswas
- CSIRInstitute of Genomics & Integrative Biology, Mall Road, Delhi-110007, India
| | - Rajinder K Gupta
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi - 110078, India
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