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Asghar A, Tan YC, Shahid M, Yow YY, Lahiri C. Metabolite Profiling of Malaysian Gracilaria edulis Reveals Eplerenone as Novel Antibacterial Compound for Drug Repurposing Against MDR Bacteria. Front Microbiol 2021; 12:653562. [PMID: 34276590 PMCID: PMC8279767 DOI: 10.3389/fmicb.2021.653562] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
With a continuous threat of antimicrobial resistance on human health worldwide, efforts for new alternatives are ongoing for the management of bacterial infectious diseases. Natural products of land and sea, being conceived to be having fewer side effects, pose themselves as a welcome relief. In this respect, we have taken a scaffolded approach to unearthing the almost unexplored chemical constituents of Malaysian red seaweed, Gracilaria edulis. Essentially, a preliminary evaluation of the ethyl acetate and acetone solvent extracts, among a series of six such, revealed potential antibacterial activity against six MDR species namely, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella enterica, methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pyogenes, and Bacillus subtilis. Detailed analyses of the inlying chemical constituents, through LC-MS and GC-MS chromatographic separation, revealed a library of metabolic compounds. These were led for further virtual screening against selected key role playing proteins in the virulence of the aforesaid bacteria. To this end, detailed predictive pharmacological analyses added up to reinforce Eplerenone as a natural alternative from the plethora of plausible bioactives. Our work adds the ongoing effort to re-discover and repurpose biochemical compounds to combat the antimicrobial resistance offered by the Gram-positive and the -negative bacterial species.
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Affiliation(s)
- Ali Asghar
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Yong-Chiang Tan
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Muhammad Shahid
- Department of Food Sciences, Universiti Kebangsaan, Bangi, Malaysia
| | - Yoon-Yen Yow
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Chandrajit Lahiri
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
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2
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Da Costa M, Gevaert O, Van Overtveldt S, Lange J, Joosten HJ, Desmet T, Beerens K. Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering. Biotechnol Adv 2021; 48:107705. [PMID: 33571638 DOI: 10.1016/j.biotechadv.2021.107705] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/18/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
Short-chain Dehydrogenase/Reductase enzymes that are active on nucleotide sugars (abbreviated as NS-SDR) are of paramount importance in the biosynthesis of rare sugars and glycosides. Some family members have already been extensively characterized due to their direct implication in metabolic disorders or in the biosynthesis of virulence factors. In this review, we combine the knowledge gathered from studies that typically focused only on one NS-SDR activity with an in-depth analysis and overview of all of the different NS-SDR families (169,076 enzyme sequences). Through this structure-based multiple sequence alignment of NS-SDRs retrieved from public databases, we could identify clear patterns in conservation and correlation of crucial residues. Supported by this analysis, we suggest updating and extending the UDP-galactose 4-epimerase "hexagonal box model" to an "heptagonal box model" for all NS-SDR enzymes. This specificity model consists of seven conserved regions surrounding the NDP-sugar substrate that serve as fingerprint for each specificity. The specificity fingerprints highlighted in this review will be beneficial for functional annotation of the large group of NS-SDR enzymes and form a guide for future enzyme engineering efforts focused on the biosynthesis of rare and specialty carbohydrates.
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Affiliation(s)
- Matthieu Da Costa
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Ophelia Gevaert
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Stevie Van Overtveldt
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Joanna Lange
- Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511, AA, Nijmegen, the Netherlands
| | - Henk-Jan Joosten
- Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511, AA, Nijmegen, the Netherlands
| | - Tom Desmet
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - Koen Beerens
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
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3
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Rodríguez-Rojas A, Nath A, El Shazely B, Santi G, Kim JJ, Weise C, Kuropka B, Rolff J. Antimicrobial Peptide Induced-Stress Renders Staphylococcus aureus Susceptible to Toxic Nucleoside Analogs. Front Immunol 2020; 11:1686. [PMID: 33133056 PMCID: PMC7550632 DOI: 10.3389/fimmu.2020.01686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
Cationic antimicrobial peptides (AMPs) are active immune effectors of multicellular organisms and are also considered as new antimicrobial drug candidates. One of the problems encountered when developing AMPs as drugs is the difficulty of reaching sufficient killing concentrations under physiological conditions. Here, using pexiganan, a cationic peptide derived from a host defense peptide of the African clawed frog and the first AMP developed into an antibacterial drug, we studied whether sub-lethal effects of AMPs can be harnessed to devise treatment combinations. We studied the pexiganan stress response of Staphylococcus aureus at sub-lethal concentrations using quantitative proteomics. Several proteins involved in nucleotide metabolism were elevated, suggesting a metabolic demand. We then show that Staphylococcus aureus is highly susceptible to antimetabolite nucleoside analogs when exposed to pexiganan, even at sub-inhibitory concentrations. These findings could be used to enhance pexiganan potency while decreasing the risk of resistance emergence, and our findings can likely be extended to other antimicrobial peptides.
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Affiliation(s)
| | - Arpita Nath
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
| | - Baydaa El Shazely
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
- Zoology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Greta Santi
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
| | - Joshua Jay Kim
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
| | - Christoph Weise
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jens Rolff
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
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4
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The sps Genes Encode an Original Legionaminic Acid Pathway Required for Crust Assembly in Bacillus subtilis. mBio 2020; 11:mBio.01153-20. [PMID: 32817102 PMCID: PMC7439481 DOI: 10.1128/mbio.01153-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The crust is the outermost spore layer of most Bacillus strains devoid of an exosporium. This outermost layer, composed of both proteins and carbohydrates, plays a major role in the adhesion and spreading of spores into the environment. Recent studies have identified several crust proteins and have provided insights about their organization at the spore surface. However, although carbohydrates are known to participate in adhesion, little is known about their composition, structure, and localization. In this study, we showed that the spore surface of Bacillus subtilis is covered with legionaminic acid (Leg), a nine-carbon backbone nonulosonic acid known to decorate the flagellin of the human pathogens Helicobacter pylori and Campylobacter jejuni We demonstrated that the spsC, spsD, spsE, spsG, and spsM genes of Bacillus subtilis are required for Leg biosynthesis during sporulation, while the spsF gene is required for Leg transfer from the mother cell to the surface of the forespore. We also characterized the activity of SpsM and highlighted an original Leg biosynthesis pathway in B. subtilis Finally, we demonstrated that Leg is required for the assembly of the crust around the spores, and we showed that in the absence of Leg, spores were more adherent to stainless steel probably because of their reduced hydrophilicity and charge.IMPORTANCE Bacillus species are a major economic and food safety concern of the food industry because of their food spoilage-causing capability and persistence. Their persistence is mainly due to their ability to form highly resistant spores adhering to the surfaces of industrial equipment. Spores of the Bacillus subtilis group are surrounded by the crust, a superficial layer which plays a key role in their adhesion properties. However, knowledge of the composition and structure of this layer remains incomplete. Here, for the first time, we identified a nonulosonic acid (Leg) at the surfaces of bacterial spores (B. subtilis). We uncovered a novel Leg biosynthesis pathway, and we demonstrated that Leg is required for proper crust assembly. This work contributes to the description of the structure and composition of Bacillus spores which has been under way for decades, and it provides keys to understanding the importance of carbohydrates in Bacillus adhesion and persistence in the food industry.
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Ferek JD, Thoden JB, Holden HM. Biochemical analysis of a sugar 4,6-dehydratase from Acanthamoeba polyphaga Mimivirus. Protein Sci 2020; 29:1148-1159. [PMID: 32083779 DOI: 10.1002/pro.3843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
Abstract
The exciting discovery of the giant DNA Mimivirus in 2003 challenged the conventional description of viruses in a radical way, and since then, dozens of additional giant viruses have been identified. It has now been demonstrated that the Mimivirus genome encodes for the two enzymes required for the production of the unusual sugar 4-amino-4,6-dideoxy-d-glucose, namely a 4,6-dehydratase and an aminotransferase. In light of our long-standing interest in the bacterial 4,6-dehydratases and in unusual sugars in general, we conducted a combined structural and functional analysis of the Mimivirus 4,6-dehydratase referred to as R141. For this investigation, the three-dimensional X-ray structure of R141 was determined to 2.05 Å resolution and refined to an R-factor of 18.3%. The overall fold of R141 places it into the short-chain dehydrogenase/reductase (SDR) superfamily of proteins. Whereas its molecular architecture is similar to that observed for the bacterial 4,6-dehydratases, there are two key regions where the polypeptide chain adopts different conformations. In particular, the conserved tyrosine that has been implicated as a catalytic acid or base in SDR superfamily members is splayed away from the active site by nearly 12 Å, thereby suggesting that a major conformational change must occur upon substrate binding. In addition to the structural analysis, the kinetic parameters for R141 using either dTDP-d-glucose or UDP-d-glucose as substrates were determined. Contrary to a previous report, R141 demonstrates nearly identical catalytic efficiency with either nucleotide-linked sugar. The data presented herein represent the first three-dimensional model for a viral 4,6-dehydratase and thus expands our understanding of these fascinating enzymes.
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Affiliation(s)
- Justin D Ferek
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States
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Mohamed N, Timofeyeva Y, Jamrozy D, Rojas E, Hao L, Silmon de Monerri NC, Hawkins J, Singh G, Cai B, Liberator P, Sebastian S, Donald RGK, Scully IL, Jones CH, Creech CB, Thomsen I, Parkhill J, Peacock SJ, Jansen KU, Holden MTG, Anderson AS. Molecular epidemiology and expression of capsular polysaccharides in Staphylococcus aureus clinical isolates in the United States. PLoS One 2019; 14:e0208356. [PMID: 30641545 PMCID: PMC6331205 DOI: 10.1371/journal.pone.0208356] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus capsular polysaccharides (CP) are important virulence factors under evaluation as vaccine antigens. Clinical S. aureus isolates have the biosynthetic capability to express either CP5 or CP8 and an understanding of the relationship between CP genotype/phenotype and S. aureus epidemiology is valuable. Using whole genome sequencing, the clonal relatedness and CP genotype were evaluated for disease-associated S. aureus isolates selected from the Tigecycline Evaluation and Surveillance Trial (T.E.S.T) to represent different geographic regions in the United States (US) during 2004 and 2009–10. Thirteen prominent clonal complexes (CC) were identified, with CC5, 8, 30 and 45 representing >80% of disease isolates. CC5 and CC8 isolates were CP type 5 and, CC30 and CC45 isolates were CP type 8. Representative isolates from prevalent CC were susceptible to in vitro opsonophagocytic killing elicited by anti-CP antibodies, demonstrating that susceptibility to opsonic killing is not linked to the genetic lineage. However, as not all S. aureus isolates may express CP, isolates representing the diversity of disease isolates were assessed for CP production. While approximately 35% of isolates (primarily CC8) did not express CP in vitro, CP expression could be clearly demonstrated in vivo for 77% of a subset of these isolates (n = 20) despite the presence of mutations within the capsule operon. CP expression in vivo was also confirmed indirectly by measuring an increase in CP specific antibodies in mice infected with CP5 or CP8 isolates. Detection of antigen expression in vivo in relevant disease states is important to support the inclusion of these antigens in vaccines. Our findings confirm the validity of CP as vaccine targets and the potential of CP-based vaccines to contribute to S. aureus disease prevention.
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Affiliation(s)
- Naglaa Mohamed
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Yekaterina Timofeyeva
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Dorota Jamrozy
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Eduardo Rojas
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Li Hao
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | | | - Julio Hawkins
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Guy Singh
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Bing Cai
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Paul Liberator
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Shite Sebastian
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Robert G. K. Donald
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Ingrid L. Scully
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - C. Hal Jones
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - C. Buddy Creech
- Vanderbilt Vaccine Research Program, Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Isaac Thomsen
- Vanderbilt Vaccine Research Program, Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Sharon J. Peacock
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kathrin U. Jansen
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | | | - Annaliesa S. Anderson
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
- * E-mail:
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7
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Kaundinya CR, Savithri HS, Krishnamurthy Rao K, Balaji PV. In vitro characterization of N-terminal truncated EpsC from Bacillus subtilis 168, a UDP-N-acetylglucosamine 4,6-dehydratase. Arch Biochem Biophys 2018; 657:78-88. [PMID: 30222950 DOI: 10.1016/j.abb.2018.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 12/16/2022]
Abstract
Bacillus subtilis 168 EpsC is annotated as "Probable polysaccharide biosynthesis protein" in the SwissProt database. epsC is part of the eps operon, thought to be involved in the biosynthesis of exopolymeric substances (EPS). The present study was undertaken to determine the molecular function of EpsC. Sequence analysis of EpsC suggested the presence of a transmembrane domain. Two N-terminal deletion mutants in which residues 1-89 (EpsC89) and 1-115 (EpsC115) are deleted were cloned and overexpressed. Enzyme activity and substrate preferences were investigated by reverse phase HPLC, surface plasmon resonance (SPR) spectroscopy and absorption spectroscopy. These data show that EpsC has UDP-GlcNAc 4,6-dehydratase activity in vitro. Purified recombinant proteins were found to utilise UDP-Glc and TDP-Glc also as substrates. In addition, EpsC115 could utilise UDP-Gal and UDP-GalNAc as substrates whereas EpsC89 could only bind these two sugar nucleotides. These results show that deletion of a longer N-terminal region broadens substrate specificity. These broadened specificity is perhaps an outcome of the deletion of the putative transmembrane domain and may not be present in vivo. EpsC, together with the aminotransferase EpsN (Kaundinya CR et al., Glycobiology, 2018) and acetyltransferase EpsM (unpublished data), appears to be involved in the biosynthesis of N,N'-diacetylbacillosamine.
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Affiliation(s)
- Chinmayi R Kaundinya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Handanahal S Savithri
- Department of Biochemistry, Indian Institute of Science, CV Raman Road, Bengaluru, 560012, India
| | - K Krishnamurthy Rao
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Petety V Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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8
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Shah BS, Ashwood HE, Harrop SJ, Farrugia DN, Paulsen IT, Mabbutt BC. Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii. PLoS One 2018; 13:e0191610. [PMID: 29352301 PMCID: PMC5774825 DOI: 10.1371/journal.pone.0191610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 01/08/2018] [Indexed: 11/29/2022] Open
Abstract
With new strains of Acinetobacter baumannii undergoing genomic analysis, it has been possible to define regions of genomic plasticity (RGPs), encoding specific adaptive elements. For a selected RGP from a community-derived isolate of A. baumannii, we outline sequences compatible with biosynthetic machinery of surface polysaccharides, specifically enzymes utilized in the dehydration and conversion of UDP-N-acetyl-D-glucosamine (UDP-D-GlcNAc). We have determined the crystal structure of one of these, the epimerase Ab-WbjB. This dehydratase belongs to the ‘extended’ short-chain dehydrogenase/reductase (SDR) family, related in fold to previously characterised enzymes CapE and FlaA1. Our 2.65Å resolution structure of Ab-WbjB shows a hexamer, organised into a trimer of chain pairs, with coenzyme NADP+ occupying each chain. Specific active-site interactions between each coenzyme and a lysine quaternary group of a neighbouring chain interconnect adjacent dimers, so stabilising the hexameric form. We show UDP-GlcNAc to be a specific substrate for Ab-WbjB, with binding evident by ITC (Ka = 0.23 μmol-1). The sequence of Ab-WbjB shows variation from the consensus active-site motifs of many SDR enzymes, demonstrating a likely catalytic role for a specific threonine sidechain (as an alternative to tyrosine) in the canonical active site chemistry of these epimerases.
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Affiliation(s)
- Bhumika S. Shah
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Heather E. Ashwood
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Stephen J. Harrop
- School of Physics, The University of New South Wales, Sydney, Australia
| | - Daniel N. Farrugia
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Bridget C. Mabbutt
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- * E-mail:
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9
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Riegert AS, Thoden JB, Schoenhofen IC, Watson DC, Young NM, Tipton PA, Holden HM. Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily. Biochemistry 2017; 56:6030-6040. [PMID: 29053280 DOI: 10.1021/acs.biochem.7b00910] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Within recent years it has become apparent that protein glycosylation is not limited to eukaryotes. Indeed, in Campylobacter jejuni, a Gram-negative bacterium, more than 60 of its proteins are known to be glycosylated. One of the sugars found in such glycosylated proteins is 2,4-diacetamido-2,4,6-trideoxy-α-d-glucopyranose, hereafter referred to as QuiNAc4NAc. The pathway for its biosynthesis, initiating with UDP-GlcNAc, requires three enzymes referred to as PglF, PglE, and PlgD. The focus of this investigation is on PglF, an NAD+-dependent sugar 4,6-dehydratase known to belong to the short chain dehydrogenase/reductase (SDR) superfamily. Specifically, PglF catalyzes the first step in the pathway, namely, the dehydration of UDP-GlcNAc to UDP-2-acetamido-2,6-dideoxy-α-d-xylo-hexos-4-ulose. Most members of the SDR superfamily contain a characteristic signature sequence of YXXXK where the conserved tyrosine functions as a catalytic acid or a base. Strikingly, in PglF, this residue is a methionine. Here we describe a detailed structural and functional investigation of PglF from C. jejuni. For this investigation five X-ray structures were determined to resolutions of 2.0 Å or better. In addition, kinetic analyses of the wild-type and site-directed variants were performed. On the basis of the data reported herein, a new catalytic mechanism for a SDR superfamily member is proposed that does not require the typically conserved tyrosine residue.
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Affiliation(s)
- Alexander S Riegert
- Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Ian C Schoenhofen
- National Research Council Canada, Human Health Therapeutics , Ottawa, Ontario K1A 0R6, Canada
| | - David C Watson
- National Research Council Canada, Human Health Therapeutics , Ottawa, Ontario K1A 0R6, Canada
| | - N Martin Young
- National Research Council Canada, Human Health Therapeutics , Ottawa, Ontario K1A 0R6, Canada
| | - Peter A Tipton
- Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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10
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Vasu D, Kumar PS, Prasad UV, Swarupa V, Yeswanth S, Srikanth L, Sunitha MM, Choudhary A, Sarma PVGK. Phosphorylation of Staphylococcus aureus Protein-Tyrosine Kinase Affects the Function of Glucokinase and Biofilm Formation. IRANIAN BIOMEDICAL JOURNAL 2016; 21:94-105. [PMID: 27695030 PMCID: PMC5274716 DOI: 10.18869/acadpub.ibj.21.2.94] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background: When Staphylococcus aureus is grown in the presence of high concentration of external glucose, this sugar is phosphorylated by glucokinase (glkA) to form glucose-6-phosphate. This product subsequently enters into anabolic phase, which favors biofilm formation. The presence of ROK (repressor protein, open reading frame, sugar kinase) motif, phosphate-1 and -2 sites, and tyrosine kinase sites in glkA of S. aureus indicates that phosphorylation must regulate the glkA activity. The aim of the present study was to identify the effect of phosphorylation on the function of S. aureusglkA and biofilm formation. Methods: Pure glkA and protein-tyrosine kinase (BYK) of S. aureus ATCC 12600 were obtained by fractionating the cytosolic fractions of glkA1 and BYK-1 expressing recombinant clones through nickel metal chelate column. The pure glkA was used as a substrate for BYK, and the phosphorylation of glkA was confirmed by treating with reagent A and resolving in SDS-PAGE, as well as staining with reagent A. The kinetic parameters of glkA and phosphorylated glkA were determined spectrophotometrically, and in silico tools were used for validation. S. aureus was grown in brain heart infusion broth, which was supplemented with glucose, and then biofilm units were calculated. Results: Fourfold elevated glkA activity was observed upon the phosphorylation by BYK. Protein-protein docking analysis revealed that glkA structure docked close to the adenosine triphosphate-binding site of BYK structure corroborating the kinetic results. Further, S. aureus grown in the presence of elevated glucose concentration exhibited an increase in the rate of biofilm formation. Conclusion: The elevated function of glkA is an essential requirement for increased biofilm units in S. aureus, a key pathogenic factor that helps its survival and the progress of infection.
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Affiliation(s)
- Dudipeta Vasu
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - Pasupuleti Santhosh Kumar
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - Uppu Venkateswara Prasad
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - Vimjam Swarupa
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - Sthanikam Yeswanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - Lokanathan Srikanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - Manne Mudhu Sunitha
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
| | - Abhijith Choudhary
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517 507, Andhra Pradesh, India
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11
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Nakano K, Chigira T, Miyafusa T, Nagatoishi S, Caaveiro JMM, Tsumoto K. Discovery and characterization of natural tropolones as inhibitors of the antibacterial target CapF from Staphylococcus aureus. Sci Rep 2015; 5:15337. [PMID: 26471247 PMCID: PMC5393024 DOI: 10.1038/srep15337] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/23/2015] [Indexed: 01/01/2023] Open
Abstract
The rapid spread of antibiotic-resistance among pathogenic bacteria poses a serious risk for public health. The search for novel therapeutic strategies and antimicrobial compounds is needed to ameliorate this menace. The bifunctional metalloenzyme CapF is an antibacterial target produced by certain pathogenic bacteria essential in the biosynthetic route of capsular polysaccharide, a mucous layer on the surface of bacterium that facilitates immune evasion and infection. We report the first inhibitor of CapF from Staphylococcus aureus, which was identified by employing fragment-based methodologies. The hit compound 3-isopropenyl-tropolone inhibits the first reaction catalyzed by CapF, disrupting the synthesis of a key precursor of capsular polysaccharide. Isothermal titration calorimetry demonstrates that 3-isopropenyl-tropolone binds tightly (KD = 27 ± 7 μM) to the cupin domain of CapF. In addition, the crystal structure of the enzyme-inhibitor complex shows that the compound engages the essential Zn2+ ion necessary for the first reaction catalyzed by the enzyme, explaining its inhibitory effect. Moreover, the tropolone compound alters the coordination sphere of the metal, leading to the overall destabilization of the enzyme. We propose 3-isopropenyl-tropolone as a precursor to develop stronger inhibitors for this family of enzymes to impair the synthesis of capsular polysaccharide in Staphylococcus aureus.
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Affiliation(s)
- Koichiro Nakano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Takeru Chigira
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takamitsu Miyafusa
- Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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12
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Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10. J Virol 2015; 89:11975-89. [PMID: 26378169 PMCID: PMC4645341 DOI: 10.1128/jvi.01793-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/10/2015] [Indexed: 12/16/2022] Open
Abstract
The 4E10 antibody recognizes the membrane-proximal external region (MPER) of the HIV-1 Env glycoprotein gp41 transmembrane subunit, exhibiting one of the broadest neutralizing activities known to date. The neutralizing activity of 4E10 requires solvent-exposed hydrophobic residues at the apex of the complementarity-determining region (CDR) H3 loop, but the molecular basis for this requirement has not been clarified. Here, we report the cocrystal structures and the energetic parameters of binding of a peptide bearing the 4E10-epitope sequence (4E10ep) to nonneutralizing versions of the 4E10 Fab. Nonneutralizing Fabs were obtained by shortening and decreasing the hydrophobicity of the CDR-H3 loop (termed ΔLoop) or by substituting the two tryptophan residues of the CDR-H3 apex with Asp residues (termed WDWD), which also decreases hydrophobicity but preserves the length of the loop. The analysis was complemented by the first crystal structure of the 4E10 Fab in its ligand-free state. Collectively, the data ruled out major conformational changes of CDR-H3 at any stage during the binding process (equilibrium or transition state). Although these mutations did not impact the affinity of wild-type Fab for the 4E10ep in solution, the two nonneutralizing versions of 4E10 were deficient in binding to MPER inserted in the plasma membrane (mimicking the environment faced by the antibody in vivo). The conclusions of our structure-function analysis strengthen the idea that to exert effective neutralization, the hydrophobic apex of the solvent-exposed CDR-H3 loop must recognize an antigenic structure more complex than just the linear α-helical epitope and likely constrained by the viral membrane lipids. IMPORTANCE The broadly neutralizing anti-HIV-1 4E10 antibody blocks infection caused by nearly all viral strains and isolates examined thus far. However, 4E10 (or 4E10-like) antibodies are rarely found in HIV-1-infected individuals or elicited through vaccination. Impediments to the design of successful 4E10 immunogens are partly attributed to an incomplete understanding of the structural and binding characteristics of this class of antibodies. Since the broadly neutralizing activity of 4E10 is abrogated by mutations of the tip of the CDR-H3, we investigated their impact on binding of the MPER-epitope at the atomic and energetic levels. We conclude that the difference between neutralizing and nonneutralizing antibodies of 4E10 is neither structural nor energetic but is related to the capacity to recognize the HIV-1 gp41 epitope inserted in biological membranes. Our findings strengthen the idea that to elicit similar neutralizing antibodies, the suitable MPER vaccine must be “delivered” in a membrane environment.
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Taylor VL, Huszczynski SM, Lam JS. Membrane Translocation and Assembly of Sugar Polymer Precursors. Curr Top Microbiol Immunol 2015; 404:95-128. [PMID: 26853690 DOI: 10.1007/82_2015_5014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial polysaccharides play an essential role in cell viability, virulence, and evasion of host defenses. Although the polysaccharides themselves are highly diverse, the pathways by which bacteria synthesize these essential polymers are conserved in both Gram-negative and Gram-positive organisms. By utilizing a lipid linker, a series of glycosyltransferases and integral membrane proteins act in concert to synthesize capsular polysaccharide, teichoic acid, and teichuronic acid. The pathways used to produce these molecules are the Wzx/Wzy-dependent, the ABC-transporter-dependent, and the synthase-dependent pathways. This chapter will cover the initiation, synthesis of the various polysaccharides on the cytoplasmic face of the membrane using nucleotide sugar precursors, and export of the nascent chain from the cytoplasm to the extracellular milieu. As microbial glycobiology is an emerging field in Gram-positive bacteria research, parallels will be drawn to the more widely studied polysaccharide biosynthesis systems in Gram-negative species in order to provide greater understanding of these biologically significant molecules.
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Affiliation(s)
- Véronique L Taylor
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Steven M Huszczynski
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Joseph S Lam
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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14
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Analysis of the Staphylococcus aureus capsule biosynthesis pathway in vitro: Characterization of the UDP-GlcNAc C6 dehydratases CapD and CapE and identification of enzyme inhibitors. Int J Med Microbiol 2014; 304:958-69. [DOI: 10.1016/j.ijmm.2014.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/30/2014] [Accepted: 06/01/2014] [Indexed: 12/25/2022] Open
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15
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Piacente F, De Castro C, Jeudy S, Molinaro A, Salis A, Damonte G, Bernardi C, Abergel C, Tonetti MG. Giant virus Megavirus chilensis encodes the biosynthetic pathway for uncommon acetamido sugars. J Biol Chem 2014; 289:24428-39. [PMID: 25035429 DOI: 10.1074/jbc.m114.588947] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Giant viruses mimicking microbes, by the sizes of their particles and the heavily glycosylated fibrils surrounding their capsids, infect Acanthamoeba sp., which are ubiquitous unicellular eukaryotes. The glycans on fibrils are produced by virally encoded enzymes, organized in gene clusters. Like Mimivirus, Megavirus glycans are mainly composed of virally synthesized N-acetylglucosamine (GlcNAc). They also contain N-acetylrhamnosamine (RhaNAc), a rare sugar; the enzymes involved in its synthesis are encoded by a gene cluster specific to Megavirus close relatives. We combined activity assays on two enzymes of the pathway with mass spectrometry and NMR studies to characterize their specificities. Mg534 is a 4,6-dehydratase 5-epimerase; its three-dimensional structure suggests that it belongs to a third subfamily of inverting dehydratases. Mg535, next in the pathway, is a bifunctional 3-epimerase 4-reductase. The sequential activity of the two enzymes leads to the formation of UDP-l-RhaNAc. This study is another example of giant viruses performing their glycan synthesis using enzymes different from their cellular counterparts, raising again the question of the origin of these pathways.
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Affiliation(s)
- Francesco Piacente
- From the Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV,1 16132 Genova, Italy
| | - Cristina De Castro
- the Department of Chemical Sciences, University of Napoli "Federico II", Via Cintia 4, Italy
| | - Sandra Jeudy
- the Structural and Genomic Information Laboratory, CNRS, Aix-Marseille Université UMR7256, IMM, Parc Scientifique de Luminy, FR-13288 Marseille, France, and
| | - Antonio Molinaro
- the Department of Chemical Sciences, University of Napoli "Federico II", Via Cintia 4, Italy
| | - Annalisa Salis
- From the Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV,1 16132 Genova, Italy, the Department of Hearth Environmental and Life Science (DISTAV), University of Genova, Corso Europa 26, 16132 Genova, Italy
| | - Gianluca Damonte
- From the Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV,1 16132 Genova, Italy
| | - Cinzia Bernardi
- From the Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV,1 16132 Genova, Italy
| | - Chantal Abergel
- the Structural and Genomic Information Laboratory, CNRS, Aix-Marseille Université UMR7256, IMM, Parc Scientifique de Luminy, FR-13288 Marseille, France, and
| | - Michela G Tonetti
- From the Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV,1 16132 Genova, Italy,
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