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Hunashal Y, Kumar GS, Choy MS, D'Andréa ÉD, Da Silva Santiago A, Schoenle MV, Desbonnet C, Arthur M, Rice LB, Page R, Peti W. Molecular basis of β-lactam antibiotic resistance of ESKAPE bacterium E. faecium Penicillin Binding Protein PBP5. Nat Commun 2023; 14:4268. [PMID: 37460557 DOI: 10.1038/s41467-023-39966-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
Penicillin-binding proteins (PBPs) are essential for the formation of the bacterial cell wall. They are also the targets of β-lactam antibiotics. In Enterococcus faecium, high levels of resistance to β-lactams are associated with the expression of PBP5, with higher levels of resistance associated with distinct PBP5 variants. To define the molecular mechanism of PBP5-mediated resistance we leveraged biomolecular NMR spectroscopy of PBP5 - due to its size (>70 kDa) a challenging NMR target. Our data show that resistant PBP5 variants show significantly increased dynamics either alone or upon formation of the acyl-enzyme inhibitor complex. Furthermore, these variants also exhibit increased acyl-enzyme hydrolysis. Thus, reducing sidechain bulkiness and expanding surface loops results in increased dynamics that facilitates acyl-enzyme hydrolysis and, via increased β-lactam antibiotic turnover, facilitates β-lactam resistance. Together, these data provide the molecular basis of resistance of clinical E. faecium PBP5 variants, results that are likely applicable to the PBP family.
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Affiliation(s)
- Yamanappa Hunashal
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Ganesan Senthil Kumar
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
- National Institute of Immunology, New Delhi, India
| | - Meng S Choy
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Éverton D D'Andréa
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | | | - Marta V Schoenle
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Charlene Desbonnet
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Michel Arthur
- INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Louis B Rice
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA.
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Sargun A, Johnstone TC, Zhi H, Raffatellu M, Nolan EM. Enterobactin- and salmochelin-β-lactam conjugates induce cell morphologies consistent with inhibition of penicillin-binding proteins in uropathogenic Escherichia coli CFT073. Chem Sci 2021; 12:4041-4056. [PMID: 34163675 PMCID: PMC8179508 DOI: 10.1039/d0sc04337k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/31/2020] [Indexed: 12/15/2022] Open
Abstract
The design and synthesis of narrow-spectrum antibiotics that target a specific bacterial strain, species, or group of species is a promising strategy for treating bacterial infections when the causative agent is known. In this work, we report the synthesis and evaluation of four new siderophore-β-lactam conjugates where the broad-spectrum β-lactam antibiotics cephalexin (Lex) and meropenem (Mem) are covalently attached to either enterobactin (Ent) or diglucosylated Ent (DGE) via a stable polyethylene glycol (PEG3) linker. These siderophore-β-lactam conjugates showed enhanced minimum inhibitory concentrations against Escherichia coli compared to the parent antibiotics. Uptake studies with uropathogenic E. coli CFT073 demonstrated that the DGE-β-lactams target the pathogen-associated catecholate siderophore receptor IroN. A comparative analysis of siderophore-β-lactams harboring ampicillin (Amp), Lex and Mem indicated that the DGE-Mem conjugate is advantageous because it targets IroN and exhibits low minimum inhibitory concentrations, fast time-kill kinetics, and enhanced stability to serine β-lactamases. Phase-contrast and fluorescence imaging of E. coli treated with the siderophore-β-lactam conjugates revealed cellular morphologies consistent with the inhibition of penicillin-binding proteins PBP3 (Ent/DGE-Amp/Lex) and PBP2 (Ent/DGE-Mem). Overall, this work illuminates the uptake and cell-killing activity of Ent- and DGE-β-lactam conjugates against E. coli and supports that native siderophore scaffolds provide the opportunity for narrowing the activity spectrum of antibiotics in clinical use and targeting pathogenicity.
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Affiliation(s)
- Artur Sargun
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA +1-617-452-2495
| | - Timothy C Johnstone
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA +1-617-452-2495
| | - Hui Zhi
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego La Jolla CA 92093 USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego La Jolla CA 92093 USA
- Center for Microbiome Innovation, University of California San Diego La Jolla CA 92093 USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines La Jolla CA 92093 USA
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA +1-617-452-2495
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3
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Pachiadaki MG, Rédou V, Beaudoin DJ, Burgaud G, Edgcomb VP. Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy. Front Microbiol 2016; 7:846. [PMID: 27375571 PMCID: PMC4899926 DOI: 10.3389/fmicb.2016.00846] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/22/2016] [Indexed: 11/13/2022] Open
Abstract
The deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis, and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere.
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Affiliation(s)
- Maria G Pachiadaki
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Vanessa Rédou
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, EA 3882, ESIAB, Technopôle de Brest Iroise, Université de Brest Plouzané, France
| | - David J Beaudoin
- Department of Biology, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Gaëtan Burgaud
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, EA 3882, ESIAB, Technopôle de Brest Iroise, Université de Brest Plouzané, France
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution Woods Hole, MA, USA
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4
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Affiliation(s)
- R. F. Pratt
- Department
of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, United States
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Ogawara H. Self-resistance in Streptomyces, with Special Reference to β-Lactam Antibiotics. Molecules 2016; 21:E605. [PMID: 27171072 PMCID: PMC6273383 DOI: 10.3390/molecules21050605] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/26/2016] [Accepted: 04/29/2016] [Indexed: 11/30/2022] Open
Abstract
Antibiotic resistance is one of the most serious public health problems. Among bacterial resistance, β-lactam antibiotic resistance is the most prevailing and threatening area. Antibiotic resistance is thought to originate in antibiotic-producing bacteria such as Streptomyces. In this review, β-lactamases and penicillin-binding proteins (PBPs) in Streptomyces are explored mainly by phylogenetic analyses from the viewpoint of self-resistance. Although PBPs are more important than β-lactamases in self-resistance, phylogenetically diverse β-lactamases exist in Streptomyces. While class A β-lactamases are mostly detected in their enzyme activity, over two to five times more classes B and C β-lactamase genes are identified at the whole genomic level. These genes can subsequently be transferred to pathogenic bacteria. As for PBPs, two pairs of low affinity PBPs protect Streptomyces from the attack of self-producing and other environmental β-lactam antibiotics. PBPs with PASTA domains are detectable only in class A PBPs in Actinobacteria with the exception of Streptomyces. None of the Streptomyces has PBPs with PASTA domains. However, one of class B PBPs without PASTA domain and a serine/threonine protein kinase with four PASTA domains are located in adjacent positions in most Streptomyces. These class B type PBPs are involved in the spore wall synthesizing complex and probably in self-resistance. Lastly, this paper emphasizes that the resistance mechanisms in Streptomyces are very hard to deal with, despite great efforts in finding new antibiotics.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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6
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Targeting metallo-carbapenemases via modulation of electronic properties of cephalosporins. Biochem J 2015; 464:271-9. [PMID: 25220027 DOI: 10.1042/bj20140364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The global proliferation of metallo-carbapenemase-producing Enterobacteriaceae has created an unmet need for inhibitors of these enzymes. The rational design of metallo-carbapenemase inhibitors requires detailed knowledge of their catalytic mechanisms. Nine cephalosporins, structurally identical except for the systematic substitution of electron-donating and withdrawing groups in the para position of the styrylbenzene ring, were synthesized and utilized to probe the catalytic mechanism of New Delhi metallo-β-lactamase (NDM-1). Under steady-state conditions, K(m) values were all in the micromolar range (1.5-8.1 μM), whereas k(cat) values varied widely (17-220 s(-1)). There were large solvent deuterium isotope effects for all substrates under saturating conditions, suggesting a proton transfer is involved in the rate-limiting step. Pre-steady-state UV-visible scans demonstrated the formation of short-lived intermediates for all compounds. Hammett plots yielded reaction constants (ρ) of -0.34 ± 0.02 and -1.15 ± 0.08 for intermediate formation and breakdown, respectively. Temperature-dependence experiments yielded ΔG(‡) values that were consistent with the Hammett results. These results establish the commonality of the formation of an azanide intermediate in the NDM-1-catalysed hydrolysis of a range cephalosporins with differing electronic properties. This intermediate is a promising target for judiciously designed β-lactam antibiotics that are poor NDM-1 substrates and inhibitors with enhanced active-site residence times.
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7
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Erdem SS, Khan S, Palanisami A, Hasan T. Rapid, low-cost fluorescent assay of β-lactamase-derived antibiotic resistance and related antibiotic susceptibility. JOURNAL OF BIOMEDICAL OPTICS 2014; 19:105007. [PMID: 25321396 PMCID: PMC4193078 DOI: 10.1117/1.jbo.19.10.105007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/25/2014] [Accepted: 07/03/2014] [Indexed: 06/04/2023]
Abstract
Antibiotic resistance (AR) is increasingly prevalent in low and middle income countries (LMICs), but the extent of the problem is poorly understood. This lack of knowledge is a critical deficiency, leaving local health authorities essentially blind to AR outbreaks and crippling their ability to provide effective treatment guidelines. The crux of the problem is the lack of microbiology laboratory capacity available in LMICs. To address this unmet need, we demonstrate a rapid and simple test of β -lactamase resistance (the most common form of AR) that uses a modified β -lactam structure decorated with two fluorophores quenched due to their close proximity. When the β -lactam core is cleaved by β -lactamase, the fluorophores dequench, allowing assay speeds of 20 min to be obtained with a simple, streamlined protocol. Furthermore, by testing in competition with antibiotics, the β -lactamase-associated antibiotic susceptibility can also be extracted. This assay can be easily implemented into standard lab work flows to provide near real-time information of β -lactamase resistance, both for epidemiological purposes as well as individualized patient care.
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Affiliation(s)
- S. Sibel Erdem
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Shazia Khan
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Akilan Palanisami
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Tayyaba Hasan
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
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Valegård K, Iqbal A, Kershaw NJ, Ivison D, Généreux C, Dubus A, Blikstad C, Demetriades M, Hopkinson RJ, Lloyd AJ, Roper DI, Schofield CJ, Andersson I, McDonough MA. Structural and mechanistic studies of the orf12 gene product from the clavulanic acid biosynthesis pathway. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1567-79. [PMID: 23897479 DOI: 10.1107/s0907444913011013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/23/2013] [Indexed: 11/10/2022]
Abstract
Structural and biochemical studies of the orf12 gene product (ORF12) from the clavulanic acid (CA) biosynthesis gene cluster are described. Sequence and crystallographic analyses reveal two domains: a C-terminal penicillin-binding protein (PBP)/β-lactamase-type fold with highest structural similarity to the class A β-lactamases fused to an N-terminal domain with a fold similar to steroid isomerases and polyketide cyclases. The C-terminal domain of ORF12 did not show β-lactamase or PBP activity for the substrates tested, but did show low-level esterase activity towards 3'-O-acetyl cephalosporins and a thioester substrate. Mutagenesis studies imply that Ser173, which is present in a conserved SXXK motif, acts as a nucleophile in catalysis, consistent with studies of related esterases, β-lactamases and D-Ala carboxypeptidases. Structures of wild-type ORF12 and of catalytic residue variants were obtained in complex with and in the absence of clavulanic acid. The role of ORF12 in clavulanic acid biosynthesis is unknown, but it may be involved in the epimerization of (3S,5S)-clavaminic acid to (3R,5R)-clavulanic acid.
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Affiliation(s)
- Karin Valegård
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, S-751 24 Uppsala, Sweden
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9
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Braga PAC, Tata A, Gonçalves dos Santos V, Barreiro JR, Schwab NV, Veiga dos Santos M, Eberlin MN, Ferreira CR. Bacterial identification: from the agar plate to the mass spectrometer. RSC Adv 2013. [DOI: 10.1039/c2ra22063f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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10
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry-based functional assay for rapid detection of resistance against β-lactam antibiotics. J Clin Microbiol 2012; 50:927-37. [PMID: 22205812 DOI: 10.1128/jcm.05737-11] [Citation(s) in RCA: 228] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Resistance against β-lactam antibiotics is a growing challenge for managing severe bacterial infections. The rapid and cost-efficient determination of β-lactam resistance is an important prerequisite for the choice of an adequate antibiotic therapy. β-Lactam resistance is based mainly on the expression/overexpression of β-lactamases, which destroy the central β-lactam ring of these drugs by hydrolysis. Hydrolysis corresponds to a mass shift of +18 Da, which can be easily detected by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Therefore, a MALDI-TOF MS-based assay was set up to investigate different enterobacteria for resistance against different β-lactam antibiotics: ampicillin, piperacillin, cefotaxime, ceftazidime, ertapenem, imipenem, and meropenem. β-Lactamases are enzymes that have a high turnover rate. Therefore, hydrolysis can be detected by MALDI-TOF MS already after a few hours of incubation of the bacteria to be tested with the given antibiotic. The comparison of the MS-derived data with the data from the routine procedure revealed identical classification of the bacteria according to sensitivity and resistance. The MALDI-TOF MS-based assay delivers the results on the same day. The approved routine procedures require at least an additional overnight incubation.
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Zafón C. [Evolutionary endocrinology: a pending matter]. ACTA ACUST UNITED AC 2011; 59:62-8. [PMID: 22113050 DOI: 10.1016/j.endonu.2011.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 08/05/2011] [Accepted: 09/01/2011] [Indexed: 12/22/2022]
Abstract
Twenty years have passed since the foundational article of what is now known as evolutionary medicine (EM) was published. This young medical discipline examines, following Darwinian principles, susceptibility to certain diseases and how we react to them. In short, EM analyzes the final cause of the disease from a historical perspective. Over the years, EM has been introduced in various medical areas in very different ways. While it has found a role in some fields such as infectious diseases and oncology, its contribution in other areas has been quite limited. In endocrinology, EM has only gained prominence as a basis for the so-called "diseases of civilization", including diabetes mellitus and obesity. However, many experts suggest that it may have a much higher potential. The aim of this paper is to provide a view about what evolutionary medicine is. Some examples of how EM may contribute to progress of our specialty are also given. There is no doubt that evolution enriches medicine, but medicine also offers knowledge to evolution.
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Affiliation(s)
- Carles Zafón
- Servicio de Endocrinología y Nutrición, Hospital Universitari Vall d'Hebron, Barcelona, España.
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12
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Toth M, Smith C, Frase H, Mobashery S, Vakulenko S. An antibiotic-resistance enzyme from a deep-sea bacterium. J Am Chem Soc 2010; 132:816-23. [PMID: 20000704 PMCID: PMC2826318 DOI: 10.1021/ja908850p] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe herein a highly proficient class A beta-lactamase OIH-1 from the bacterium Oceanobacillus iheyensis, whose habitat is the sediment at a depth of 1050 m in the Pacific Ocean. The OIH-1 structure was solved by molecular replacement and refined at 1.25 A resolution. OIH-1 has evolved to be an extremely halotolerant beta-lactamase capable of hydrolyzing its substrates in the presence of NaCl at saturating concentration. Not only is this the most highly halotolerant bacterial enzyme structure known to date, it is also the highest resolution halophilic protein structure yet determined. Evolution of OIH-1 in the salinity of the ocean has resulted in a molecular surface that is coated with acidic residues, a marked difference from beta-lactamases of terrestrial sources. OIH-1 is the first example of an antibiotic-resistance enzyme that has evolved in the depths of the ocean in isolation from clinical selection and gives us an extraordinary glimpse into protein evolution under extreme conditions. It represents evidence for the existence of a reservoir of antibiotic-resistance enzymes in nature among microbial populations from deep oceanic sources.
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Affiliation(s)
- Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Clyde Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025
| | - Hilary Frase
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Sergei Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
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Tripathi LP, Sowdhamini R. Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes. BMC Genomics 2008; 9:549. [PMID: 19019219 PMCID: PMC2605481 DOI: 10.1186/1471-2164-9-549] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2008] [Accepted: 11/19/2008] [Indexed: 12/29/2022] Open
Abstract
Background Serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. While studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. Current analysis is aimed at understanding the distribution and probable biological functions of the select serine proteases encoded in representative prokaryotic organisms. Results A total of 966 putative serine proteases, belonging to five families, were identified in the 91 prokaryotic genomes using various sensitive sequence search techniques. Phylogenetic analysis reveals several species-specific clusters of serine proteases suggesting their possible involvement in organism-specific functions. Atypical phylogenetic associations suggest an important role for lateral gene transfer events in facilitating the widespread distribution of the serine proteases in the prokaryotes. Domain organisations of the gene products were analysed, employing sensitive sequence search methods, to infer their probable biological functions. Trypsin, subtilisin and Lon protease families account for a significant proportion of the multi-domain representatives, while the D-Ala-D-Ala carboxypeptidase and the Clp protease families are mostly single-domain polypeptides in prokaryotes. Regulatory domains for protein interaction, signalling, pathogenesis, cell adhesion etc. were found tethered to the serine protease domains. Some domain combinations (such as S1-PDZ; LON-AAA-S16 etc.) were found to be widespread in the prokaryotic lineages suggesting a critical role in prokaryotes. Conclusion Domain architectures of many serine proteases and their homologues identified in prokaryotes are very different from those observed in eukaryotes, suggesting distinct roles for serine proteases in prokaryotes. Many domain combinations were found unique to specific prokaryotic species, suggesting functional specialisation in various cellular and physiological processes.
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Affiliation(s)
- Lokesh P Tripathi
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore-560065, India.
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14
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Abstract
Key enzymes that assemble the bacterial cell wall are also the target of the Beta-lactam class of antibiotics. The covalent binding of labeled penicillin to these proteins has been used in numerous studies in drug discovery, antibiotic mechanisms of action and resistance, and cell wall physiology. Methods to label and measure penicillin binding proteins in two prototypical organisms, a Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus), are described. The methods discussed include identifying penicillin-binding proteins in both intact cells (in vivo measurements) and isolated cell membranes.
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15
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Identification of a novel multidrug efflux pump of Mycobacterium tuberculosis. Antimicrob Agents Chemother 2008; 52:2503-11. [PMID: 18458127 DOI: 10.1128/aac.00298-08] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The impermeability of the outer membrane in combination with drug efflux are major determinants of the natural drug resistance of mycobacteria. beta-Lactams are the most widely used antibiotics for treatment of bacterial infections. However, it is unknown how beta-lactams enter Mycobacterium tuberculosis and whether efflux pumps exist that can export these drugs out of the cell. To identify the molecular mechanisms of M. tuberculosis resistance to beta-lactams, a library of 7,500 transposon mutants was generated in the model organism Mycobacterium bovis BCG. Thirty-three unique insertion sites were determined that conferred medium or high-level (> or =2,000 microg/ml) resistance to ampicillin. Three mutants in sulfolipid synthesis or transport were highly resistant to ampicillin, indicating an indirect effect of the lipid composition on the outer membrane permeability of M. bovis BCG to ampicillin. Mutants with insertions in genes encoding surface molecules such as PPE proteins or lipoarabinomannan were also completely resistant to ampicillin, thus suggesting a lack of transport across the outer membrane. Insertion of the transposon in front of bcg0231 increased transcription of the gene and concomitantly the resistance of M. bovis BCG to ampicillin, streptomycin, and chloramphenicol by 32- to 64-fold. Resistance to vancomycin and tetracycline was increased four- to eightfold. Bcg0231 and Rv0194 are almost identical ATP-binding cassette transporters. Expression of rv0194 significantly reduced accumulation of ethidium bromide and conferred multidrug resistance to Mycobacterium smegmatis. Both effects were abrogated in the presence of the efflux pump inhibitor reserpine. These results demonstrate that Rv0194 is a novel multidrug efflux pump of M. tuberculosis.
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16
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Kumar I, Josephine HR, Pratt R. Reactions of peptidoglycan-mimetic beta-lactams with penicillin-binding proteins in vivo and in membranes. ACS Chem Biol 2007; 2:620-4. [PMID: 17894439 PMCID: PMC2536641 DOI: 10.1021/cb7001347] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The membrane-bound bacterial D-alanyl- D-alanine peptidases or penicillin-binding proteins (PBPs) catalyze the final transpeptidation reaction of bacterial cell wall biosynthesis and are the targets of beta-lactam antibiotics. Rather surprisingly, the substrate specificity of these enzymes is not well understood. In this paper, we present measurements of the reactivity of typical examples of these enzymes with peptidoglycan-mimetic beta-lactams under in vivo conditions. The minimum inhibitory concentrations of beta-lactams with Escherichia coli-specific side chains were determined against E. coli cells. Analogous measurements were made with Streptococcus pneumoniae R6. The reactivity of the relevant beta-lactams with E. coli PBPs in membrane preparations was also determined. The results show that under none of the above protocols were beta-lactams with peptidoglycan-mimetic side chains more reactive than generic analogues. This suggests that in vivo, as in vitro, these enzymes do not specifically recognize elements of peptidoglycan structure local to the reaction center. Substrate recognition must thus involve extended structure.
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Affiliation(s)
| | | | - R.F. Pratt
- To whom correspondence should be addressed.
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Adediran SA, Cabaret D, Lohier JF, Wakselman M, Pratt RF. Benzopyranones with retro-amide side chains as (inhibitory) beta-lactamase substrates. Bioorg Med Chem Lett 2005; 14:5117-20. [PMID: 15380211 DOI: 10.1016/j.bmcl.2004.07.067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2004] [Revised: 07/27/2004] [Accepted: 07/28/2004] [Indexed: 10/26/2022]
Abstract
3-(N-Benzylcarbamoyl)-7-carboxy-3, 4-dihydro-2H-1-benzo-pyran-2-one and its 8-carboxy analogue have been synthesized and evaluated as potential (inhibitory) substrates of beta-lactam-recognizing enzymes. These compounds are bicyclic delta-lactones with retro-amide (with respect to classical beta-lactams) side chains. They were found to be comparably effective as substrates of typical class A, C and D beta-lactamases as analogous benzopyranones bearing 'normal' amide side chains. The new 8-carboxy derivative, however, formed a much more (1000-fold) tightly-bound acyl-enzyme with a class C beta-lactamase than did its 'normal' analogue, and thus provides a structural lead to new inhibitors of this class of beta-lactamase.
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Affiliation(s)
- S A Adediran
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
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18
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Silvaggi NR, Josephine HR, Kuzin AP, Nagarajan R, Pratt RF, Kelly JA. Crystal Structures of Complexes between the R61 DD-peptidase and Peptidoglycan-mimetic β-Lactams: A Non-covalent Complex with a “Perfect Penicillin”. J Mol Biol 2005; 345:521-33. [PMID: 15581896 DOI: 10.1016/j.jmb.2004.10.076] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2004] [Revised: 10/18/2004] [Accepted: 10/22/2004] [Indexed: 11/30/2022]
Abstract
The bacterial D-alanyl-D-alanine transpeptidases (DD-peptidases) are the killing targets of beta-lactams, the most important clinical defense against bacterial infections. However, due to the constant development of antibiotic-resistance mechanisms by bacteria, there is an ever-present need for new, more effective antimicrobial drugs. While enormous numbers of beta-lactam compounds have been tested for antibiotic activity in over 50 years of research, the success of a beta-lactam structure in terms of antibiotic activity remains unpredictable. Tipper and Strominger suggested long ago that beta-lactams inhibit DD-peptidases because they mimic the D-alanyl-D-alanine motif of the peptidoglycan substrate of these enzymes. They also predicted that beta-lactams having a peptidoglycan-mimetic side-chain might be better antibiotics than their non-specific counterparts, but decades of research have not provided any evidence for this. We have recently described two such novel beta-lactams. The first is a penicillin having the glycyl-L-alpha-amino-epsilon-pimelyl side-chain of Streptomyces strain R61 peptidoglycan, making it the "perfect penicillin" for this organism. The other is a cephalosporin with the same side-chain. Here, we describe the X-ray crystal structures of the perfect penicillin in non-covalent and covalent complexes with the Streptomyces R61 DD-peptidase. The structure of the non-covalent enzyme-inhibitor complex is the first such complex to be trapped crystallographically with a DD-peptidase. In addition, the covalent complex of the peptidyl-cephalosporin with the R61 DD-peptidase is described. Finally, two covalent complexes with the traditional beta-lactams benzylpenicillin and cephalosporin C were determined for comparison with the peptidyl beta-lactams. These structures, together with relevant kinetics data, support Tipper and Strominger's assertion that peptidoglycan-mimetic side-chains should improve beta-lactams as inhibitors of DD-peptidases.
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Affiliation(s)
- Nicholas R Silvaggi
- Department of Molecular and Cell Biology and Institute for Materials Science, University of Connecticut, Storrs, CT 06269-3125, USA
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19
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Reid CW, Blackburn NT, Clarke AJ. The effect of NAGâthiazoline on morphology and surface hydrophobicity ofEscherichia coli. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09553.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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20
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Pong A, Bradley JS. Clinical challenges of nosocomial infections caused by antibiotic-resistant pathogens in pediatrics. ACTA ACUST UNITED AC 2004; 15:21-9. [PMID: 15175992 DOI: 10.1053/j.spid.2004.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antibiotic resistance in nosocomial infections is an ever-increasing problem as health care institutions provide care for children with more complicated medical and surgical problems. Several mechanisms of antibiotic resistance are reviewed for both gram-negative and gram-positive nosocomial pathogens. These adaptive resistance mechanisms allow organisms to survive in an environment of extensive antibiotic use and result in clinically significant infections. Mobile genetic elements have facilitated the rapid spread of antibiotic resistance within and among species. The clinical challenge faced by many practitioners is to understand these mechanisms of antibiotic resistance and to develop strategies for successfully treating infection caused by resistant pathogens. Nosocomial outbreaks caused by resistant organisms are described, and an approach to empiric therapy based on presumed pathogens, site of infection, and local resistance patterns is discussed.
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Affiliation(s)
- Alice Pong
- Division of Infectious Diseases, Children's Hospital and Health Center, San Diego, CA 92123, USA
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21
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Abstract
Through billions of years of evolution, microbes have developed myriad defense mechanisms designed to ensure their survival. This protection is readily transferred to their fellow life forms via transposable elements. Despite very early warnings, humans have chosen to abuse the gift of antibiotics and have created a situation where all microorganisms are resistant to some antibiotics and some microorganisms are resistant to all antibiotics. When antibiotics are used, six events may occur with only one being beneficial: when the antibiotic aids the host defenses to gain control and eliminate the infection. Alternatively, the antibiotic may cause toxicity or allergy, initiate a superinfection with resistant bacteria, promote microbial chromosomal mutations to resistance, encourage resistance gene transfer to susceptible species, or promote the expression of dormant resistance genes.
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Affiliation(s)
- Thomas J Pallasch
- School of Dentistry, University of Southern California, Los Angeles, CA, USA.
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22
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Abstract
When Bacteria, Archaea, and Eucarya separated from each other, a great deal of evolution had taken place. Only then did extensive diversity arise. The bacteria split off with the new property that they had a sacculus that protected them from their own turgor pressure. The saccular wall of murein (or peptidoglycan) was an effective solution to the osmotic pressure problem, but it then was a target for other life-forms, which created lysoymes and beta-lactams. The beta-lactams, with their four-member strained rings, are effective agents in nature and became the first antibiotic in human medicine. But that is by no means the end of the story. Over evolutionary time, bacteria challenged by beta-lactams evolved countermeasures such as beta-lactamases, and the producing organisms evolved variant beta-lactams. The biology of both classes became evident as the pharmaceutical industry isolated, modified, and produced new chemotherapeutic agents and as the properties of beta-lactams and beta-lactamases were examined by molecular techniques. This review attempts to fit the wall biology of current microbes and their clinical context into the way organisms developed on this planet as well as the changes arising since the work done by Fleming. It also outlines the scientific advances in our understanding of this broad area of biology.
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Affiliation(s)
- Arthur L Koch
- Biology Department, Indiana University, Bloomington, Indiana 47405-6801, USA.
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McDonough MA, Anderson JW, Silvaggi NR, Pratt RF, Knox JR, Kelly JA. Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins. J Mol Biol 2002; 322:111-22. [PMID: 12215418 DOI: 10.1016/s0022-2836(02)00742-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Penicillin-binding proteins (PBPs), the target enzymes of beta-lactam antibiotics such as penicillins and cephalosporins, catalyze the final peptidoglycan cross-linking step of bacterial cell-wall biosynthesis. beta-Lactams inhibit this reaction because they mimic the D-alanyl-D-alanine peptide precursors of cell-wall structure. Prior crystallographic studies have described the site of beta-lactam binding and inhibition, but they have failed to show the binding of D-Ala-D-Ala substrates. We present here the first high-resolution crystallographic structures of a PBP, D-Ala-D-Ala-peptidase of Streptomyces sp. strain R61, non-covalently complexed with a highly specific fragment (glycyl-L-alpha-amino-epsilon-pimelyl-D-Ala-D-Ala) of the cell-wall precursor in both enzyme-substrate and enzyme-product forms. The 1.9A resolution structure of the enzyme-substrate Henri-Michaelis complex was achieved by using inactivated enzyme, which was formed by cross-linking two catalytically important residues Tyr159 and Lys65. The second structure at 1.25A resolution of the uncross-linked, active form of the DD-peptidase shows the non-covalent binding of the two products of the carboxypeptidase reaction. The well-defined substrate-binding site in the two crystallographic structures shows a subsite that is complementary to a portion of the natural cell-wall substrate that varies among bacterial species. In addition, the structures show the displacement of 11 water molecules from the active site, the location of residues responsible for substrate binding, and clearly demonstrate the necessity of Lys65 and or Tyr159 for the acylation step with the donor peptide. Comparison of the complexed structures described here with the structures of other known PBPs suggests the design of species-targeted antibiotics as a counter-strategy towards beta-lactamase-elicited bacterial resistance.
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Affiliation(s)
- Michael A McDonough
- Department of Molecular and Cell Biology and Institute for Materials Science, University of Connecticut, Storrs 06269-3125, USA
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Chesnel L, Zapun A, Mouz N, Dideberg O, Vernet T. Increase of the deacylation rate of PBP2x from Streptococcus pneumoniae by single point mutations mimicking the class A beta-lactamases. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:1678-83. [PMID: 11895438 DOI: 10.1046/j.1432-1327.2002.02815.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The class A beta-lactamases and the transpeptidase domain of the penicillin-binding proteins (PBPs) share the same topology and conserved active-site residues. They both react with beta-lactams to form acylenzymes. The stability of the PBP acylenzymes results in the inhibition of the transpeptidase function and the antibiotic activity of the beta-lactams. In contrast, the deacylation of the beta-lactamases is extremely fast, resulting in a high turnover of beta-lactam hydrolysis, which confers resistance to these antibiotics. In TEM-1 beta-lactamase from Escherichia coli, Glu166 is required for the fast deacylation and occupies the same spatial location as Phe450 in PBP2x from Streptococcus pneumoniae. To gain insight into the deacylation mechanism of both enzymes, Phe450 of PBP2x was replaced by various residues. The introduction of ionizable side chains increased the deacylation rate, in a pH-dependent manner, for the acidic residues. The aspartic acid-containing variant had a 110-fold faster deacylation at pH 8. The magnitude of this effect is similar to that observed in a naturally occurring variant of PBP2x, which confers increased resistance to cephalosporins.
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Affiliation(s)
- Laurent Chesnel
- Laboratoire d'Ingénierie des Macromolécules and Laboratoire de Cristallographie Macromoléculaire, Institut de Biologie Structurale J.-P. Ebel, Grenoble, France
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Abstract
The need for strategic planning for antimicrobial use has reached a critical point. The rise in resistant nosocomial and community gram-positive bacteria mandates appropriate antibiotic selection and dosing. The development of new compounds is not the answer, because many are based off existing structures to which bacteria have already developed resistance. New antimicrobial agents are falling to the resistant mechanisms developed by the bacteria, after only limited clinical exposure. Judicious use of antimicrobial agents and applying pharmacokinetic principles when dosing can help slow the rate of resistance.
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Affiliation(s)
- Jaye S Weston
- Department of Pharmacy, East Texas Medical Center, Tyler 75711, USA.
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Pucci MJ, Dougherty TJ. Direct quantitation of the numbers of individual penicillin-binding proteins per cell in Staphylococcus aureus. J Bacteriol 2002; 184:588-91. [PMID: 11751840 PMCID: PMC139569 DOI: 10.1128/jb.184.2.588-591.2002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2001] [Accepted: 10/04/2001] [Indexed: 11/20/2022] Open
Abstract
The penicillin-binding proteins (PBPs) are a set of enzymes that participate in bacterial peptidoglycan assembly. The absolute numbers of each PBP were determined by direct measurement and have been reported for two Staphylococcus aureus strains, RN4220 (methicillin-sensitive S. aureus) and RN450M (methicillin-resistant S. aureus). From the specific activity of the labeled penicillin and the absolute number of disintegrations per minute, and from the number of CFU per milliliter calculated from proteins and optical density, a determination of the number of PBPs per cell was made. These numbers ranged from approximately 150 to 825 PBPs/cell and represent the first direct determination of absolute numbers of PBPs in S. aureus.
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Affiliation(s)
- Michael J Pucci
- Department of Microbiology, Bristol-Myers Squibb Pharmaceutical Research Institute, Wallingford, Connecticut 06492, USA.
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