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John-White M, Gardiner J, Johanesen P, Lyras D, Dumsday G. β-Aminopeptidases: Insight into Enzymes without a Known Natural Substrate. Appl Environ Microbiol 2019; 85:e00318-19. [PMID: 31126950 PMCID: PMC6643246 DOI: 10.1128/aem.00318-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/08/2019] [Indexed: 02/05/2023] Open
Abstract
β-Aminopeptidases have the unique capability to hydrolyze N-terminal β-amino acids, with varied preferences for the nature of β-amino acid side chains. This unique capability makes them useful as biocatalysts for synthesis of β-peptides and to kinetically resolve β-peptides and amides for the production of enantiopure β-amino acids. To date, six β-aminopeptidases have been discovered and functionally characterized, five from Gram-negative bacteria and one from a fungus, Aspergillus Here we report on the purification and characterization of an additional four β-aminopeptidases, one from a Gram-positive bacterium, Mycolicibacterium smegmatis (BapAMs), one from a yeast, Yarrowia lipolytica (BapAYlip), and two from Gram-negative bacteria isolated from activated sludge identified as Burkholderia spp. (BapABcA5 and BapABcC1). The genes encoding β-aminopeptidases were cloned, expressed in Escherichia coli, and purified. The β-aminopeptidases were produced as inactive preproteins that underwent self-cleavage to form active enzymes comprised of two different subunits. The subunits, designated α and β, appeared to be tightly associated, as the active enzyme was recovered after immobilized-metal affinity chromatography (IMAC) purification, even though only the α-subunit was 6-histidine tagged. The enzymes were shown to hydrolyze chromogenic substrates with the N-terminal l-configurations β-homo-Gly (βhGly) and β3-homo-Leu (β3hLeu) with high activities. These enzymes displayed higher activity with H-βhGly-p-nitroanilide (H-βhGly-pNA) than previously characterized enzymes from other microorganisms. These data indicate that the new β-aminopeptidases are fully functional, adding to the toolbox of enzymes that could be used to produce β-peptides. Overexpression studies in Pseudomonas aeruginosa also showed that the β-aminopeptidases may play a role in some cellular functions.IMPORTANCE β-Aminopeptidases are unique enzymes found in a diverse range of microorganisms that can utilize synthetic β-peptides as a sole carbon source. Six β-aminopeptidases have been previously characterized with preferences for different β-amino acid substrates and have demonstrated the capability to catalyze not only the degradation of synthetic β-peptides but also the synthesis of short β-peptides. Identification of other β-aminopeptidases adds to this toolbox of enzymes with differing β-amino acid substrate preferences and kinetics. These enzymes have the potential to be utilized in the sustainable manufacture of β-amino acid derivatives and β-peptides for use in biomedical and biomaterial applications. This is important, because β-amino acids and β-peptides confer increased proteolytic resistance to bioactive compounds and form novel structures as well as structures similar to α-peptides. The discovery of new enzymes will also provide insight into the biological importance of these enzymes in nature.
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Affiliation(s)
- Marietta John-White
- CSIRO Manufacturing, Clayton, Victoria, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | | | - Priscilla Johanesen
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
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Simon AH, Liebscher S, Aumüller TH, Treblow D, Bordusa F. Application of a Dual Internally Quenched Fluorogenic Substrate in Screening for D-Arginine Specific Proteases. Front Microbiol 2019; 10:711. [PMID: 31001242 PMCID: PMC6456654 DOI: 10.3389/fmicb.2019.00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 03/21/2019] [Indexed: 11/13/2022] Open
Abstract
The application of D-stereospecific proteases (DSPs) in resolution of racemic amino acids and in the semisynthesis of proteins has been a successful strategy. The main limitation for a broader application is, however, the accessibility of suitable DSPs covering multiple substrate specificities. To identify DSPs with novel primary substrate preferences, a fast specificity screening method using the easily accessible internally quenched fluorogenic substrate aminobenzoyl-D-arginyl-D-alanyl-p-nitroanilide was developed. By monitoring both UV/vis-absorbance and fluorescence signals at the same time it allows to detect two distinct D-amino acid substrate specificities simultaneously and separately with respect to the individual specificities. In order to identify novel DSP specificities for synthesis applications, DSPs specific for D-arginine were of special interest due to their potential ability as catalysts for substrate mimetics-mediated peptide and protein ligations. D-alanine in the substrate served as positive control and reference based on its known acceptance by numerous DSPs. In silico analysis suggested that DSPs are predominantly present in gram-positive microorganisms, therefore this study focused on the bacilli strains Bacillus thuringiensis and Bacillus subtilis as potential hosts of D-Arg-specific DSPs. While protease activities toward D-alanine were found in both organisms, a novel and so far unknown D-arginine specific DSP was detected within the culture supernatant of B. thuringiensis. Enrichment of this activity via cation exchange and size exclusion chromatography allowed isolation and further characterization of this novel enzyme consisting of a molecular mass of 37.7 kDa and an enzymatic activity of 8.3 U mg-1 for cleaving the D-Arg|D-Ala bond in the detecting substrate. Independent experiments also showed that the identified enzyme shows similarities to the class of penicillin binding proteins. In future applications this enzyme will be a promising starting point for the development of novel strategies for the semisynthesis of all-L-proteins.
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Affiliation(s)
- Andreas H Simon
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Sandra Liebscher
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Tobias H Aumüller
- Max Planck Research Unit for Enzymology of Protein Folding, Halle, Germany
| | - Dennis Treblow
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Frank Bordusa
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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John-White M, Dumsday GJ, Johanesen P, Lyras D, Drinkwater N, McGowan S. Crystal structure of a β-aminopeptidase from an Australian Burkholderia sp. Acta Crystallogr F Struct Biol Commun 2017; 73:386-392. [PMID: 28695846 PMCID: PMC5505242 DOI: 10.1107/s2053230x17007737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/24/2017] [Indexed: 11/11/2022] Open
Abstract
β-Aminopeptidases are a unique group of enzymes that have the unusual capability to hydrolyze N-terminal β-amino acids from synthetic β-peptides. β-Peptides can form secondary structures mimicking α-peptide-like structures that are resistant to degradation by most known proteases and peptidases. These characteristics of β-peptides give them great potential as peptidomimetics. Here, the X-ray crystal structure of BcA5-BapA, a β-aminopeptidase from a Gram-negative Burkholderia sp. that was isolated from activated sludge from a wastewater-treatment plant in Australia, is reported. The crystal structure of BcA5-BapA was determined to a resolution of 2.0 Å and showed a tetrameric assembly typical of the β-aminopeptidases. Each monomer consists of an α-subunit (residues 1-238) and a β-subunit (residues 239-367). Comparison of the structure of BcA5-BapA with those of other known β-aminopeptidases shows a highly conserved structure and suggests a similar proteolytic mechanism of action.
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Affiliation(s)
- Marietta John-White
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Melbourne, VIC 3800, Australia
- Manufacturing, CSIRO, Clayton, Melbourne, VIC 3800, Australia
| | | | - Priscilla Johanesen
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Dena Lyras
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Nyssa Drinkwater
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Melbourne, VIC 3800, Australia
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The Staphylococcus aureus Methicillin Resistance Factor FmtA Is a d-Amino Esterase That Acts on Teichoic Acids. mBio 2016; 7:e02070-15. [PMID: 26861022 PMCID: PMC4752606 DOI: 10.1128/mbio.02070-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED The methicillin resistance factor encoded by fmtA is a core member of the Staphylococcus aureus cell wall stimulon, but its function has remained elusive for the past two decades. First identified as a factor that affects methicillin resistance in S. aureus strains, FmtA was later shown to interact with teichoic acids and to localize to the cell division septum. We have made a breakthrough in understanding FmtA function. We show that FmtA hydrolyzes the ester bond between d-Ala and the backbone of teichoic acids, which are polyglycerol-phosphate or polyribitol-phosphate polymers found in the S. aureus cell envelope. FmtA contains two conserved motifs found in serine active-site penicillin-binding proteins (PBPs) and β-lactamases. The conserved SXXK motif was found to be important for the d-amino esterase activity of FmtA. Moreover, we show that deletion of fmtA (ΔfmtA) led to higher levels of d-Ala in teichoic acids, and this effect was reversed by complementation of ΔfmtA with fmtA. The positive charge on d-Ala partially masks the negative charge of the polyol-phosphate backbone of teichoic acids; hence, a change in the d-Ala content will result in modulation of their charge. Cell division, biofilm formation, autolysis, and colonization are among the many processes in S. aureus affected by the d-Ala content and overall charge of the cell surface teichoic acids. The esterase activity of FmtA and the regulation of fmtA suggest that FmtA functions as a modulator of teichoic acid charge, thus FmtA may be involved in S. aureus cell division, biofilm formation, autolysis, and colonization. IMPORTANCE Teichoic acids are involved in cell division, cell wall synthesis, biofilm formation, attachment of bacteria to artificial surfaces, and colonization. However, the function of teichoic acids is not fully understood. Modification by glycosylation and/or d-alanylation of the polyol-phosphate backbone of teichoic acids is important in the above cell processes. The intrinsic negative charge of teichoic acid backbone plays a role in the charge and/or pH of the bacterial surface, and d-alanylation represents a means through which bacteria modulate the charge or the pH of their surfaces. We discovered that FmtA removes d-Ala from teichoic acids. We propose FmtA may provide a temporal and spatial regulation of the bacterial cell surface charge in two ways, by removing the d-Ala from LTA to make it available to wall teichoic acid (WTA) in response to certain conditions and by removing it from WTA to allow the cell to reset its surface charge to a previous condition.
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Matsushita-Morita M, Nakagawa H, Tada S, Marui J, Hattori R, Suzuki S, Yamagata Y, Amano H, Ishida H, Takeuchi M, Kusumoto KI. Characterization of a (D)-stereoselective aminopeptidase (DamA) exhibiting aminolytic activity and halophilicity from Aspergillus oryzae. Appl Biochem Biotechnol 2013; 171:145-64. [PMID: 23821291 DOI: 10.1007/s12010-013-0330-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/14/2013] [Indexed: 11/28/2022]
Abstract
β-Aminopeptidases exhibit both hydrolytic and aminolytic (peptide bond formation) activities and have only been reported in bacteria. We identified a gene encoding the β-aminopeptidase homolog from a genome database of the filamentous fungus Aspergillus oryzae. The gene was overexpressed in A. oryzae, and the resulting recombinant enzyme was purified. Apart from bacterial homologs [β-Ala-para-nitroanilide (pNA)], the enzyme preferred D-Leu-pNA and D-Phe-pNA as substrates. Therefore, we designated this gene as d-stereoselective aminopeptidase A (damA). The purified recombinant DamA was estimated to be a hexamer and was composed of two subunits with molecular masses of 29.5 and 11.5 kDa, respectively. Optimal hydrolytic activity of DamA toward D-Leu-pNA was observed at 50 °C and pH 8.0. The enzyme was stable up to 60 °C and from pH 4.0-11.0. DamA also exhibited aminolytic activity, producing D-Leu-D-Leu-NH2 from D-Leu-NH2 as a substrate. In the presence of 3.0 M NaCl, the amount of pNA liberated from D-Leu-pNA by DamA was 3.1-fold higher than that in the absence of NaCl. Thus, DamA is a halophilic enzyme. The enzyme was utilized to synthesize several hetero-dipeptides containing a D-amino acid at the N-terminus as well as physiologically active peptides.
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Affiliation(s)
- Mayumi Matsushita-Morita
- National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
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Autoproteolytic and Catalytic Mechanisms for the β-Aminopeptidase BapA—A Member of the Ntn Hydrolase Family. Structure 2012; 20:1850-60. [DOI: 10.1016/j.str.2012.07.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/14/2012] [Accepted: 07/15/2012] [Indexed: 11/23/2022]
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Eryngase: a Pleurotus eryngii aminopeptidase exhibiting peptide bond formation activity. Appl Microbiol Biotechnol 2010; 87:1791-801. [DOI: 10.1007/s00253-010-2663-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 04/28/2010] [Accepted: 04/29/2010] [Indexed: 11/30/2022]
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Simple method for transformation of Ochrobactrum anthropi. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-008-9716-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Graham RLJ, Sharma MK, Ternan NG, Weatherly DB, Tarleton RL, McMullan G. A semi-quantitative GeLC-MS analysis of temporal proteome expression in the emerging nosocomial pathogen Ochrobactrum anthropi. Genome Biol 2008; 8:R110. [PMID: 17567905 PMCID: PMC2394761 DOI: 10.1186/gb-2007-8-6-r110] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Revised: 05/10/2007] [Accepted: 06/13/2007] [Indexed: 11/10/2022] Open
Abstract
A semi-quantitative gel-based analysis identifies distinct proteomic profiles associated with specific growth points for the nosocomial pathogen Ochrobactrum anthropi. Background The α-Proteobacteria are capable of interaction with eukaryotic cells, with some members, such as Ochrobactrum anthropi, capable of acting as human pathogens. O. anthropi has been the cause of a growing number of hospital-acquired infections; however, little is known about its growth, physiology and metabolism. We used proteomics to investigate how protein expression of this organism changes with time during growth. Results This first gel-based liquid chromatography-mass spectrometry (GeLC-MS) temporal proteomic analysis of O. anthropi led to the positive identification of 131 proteins. These were functionally classified and physiochemically characterized. Utilizing the emPAI protocol to estimate protein abundance, we assigned molar concentrations to all proteins, and thus were able to identify 19 with significant changes in their expression. Pathway reconstruction led to the identification of a variety of central metabolic pathways, including nucleotide biosynthesis, fatty acid anabolism, glycolysis, TCA cycle and amino acid metabolism. In late phase growth we identified a number of gene products under the control of the oxyR regulon, which is induced in response to oxidative stress and whose protein products have been linked with pathogen survival in response to host immunity reactions. Conclusion This study identified distinct proteomic profiles associated with specific growth points for O. anthropi, while the use of emPAI allowed semi-quantitative analyses of protein expression. It was possible to reconstruct central metabolic pathways and infer unique functional and adaptive processes associated with specific growth phases, thereby resulting in a deeper understanding of the physiology and metabolism of this emerging pathogenic bacterium.
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Affiliation(s)
| | - Mohit K Sharma
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry BT52 1SA, UK
| | - Nigel G Ternan
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry BT52 1SA, UK
| | - D Brent Weatherly
- The Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30605, USA
| | - Rick L Tarleton
- The Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30605, USA
| | - Geoff McMullan
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry BT52 1SA, UK
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Heck T, Kohler HPE, Limbach M, Flögel O, Seebach D, Geueke B. Enzyme-Catalyzed Formation ofβ-Peptides:β-Peptidyl Aminopeptidases BapA and DmpA Acting asβ-Peptide-Synthesizing Enzymes. Chem Biodivers 2007; 4:2016-30. [PMID: 17886858 DOI: 10.1002/cbdv.200790168] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In recent studies, we discovered that the three beta-peptidyl aminopeptidases, BapA from Sphingosinicella xenopeptidilytica 3-2W4, BapA from S. microcystinivorans Y2, and DmpA from Ochrobactrum anthropi LMG7991, possess the unique feature of cleaving N-terminal beta-amino acid residues from beta- and alpha/beta-peptides. Herein, we investigated the use of the same three enzymes for the reverse reaction catalyzing the oligomerization of beta-amino acids and the synthesis of mixed peptides with N-terminal beta-amino acid residues. As substrates, we employed the beta-homoamino acid derivatives H-beta hGly-pNA, H-beta3 hAla-pNA, H-(R)-beta3 hAla-pNA, H-beta3 hPhe-pNA, H-(R)-beta3 hPhe-pNA, and H-beta3 hLeu-pNA. All three enzymes were capable of coupling the six beta-amino acids to oligomers with chain lengths of up to eight amino acid residues. With the enzyme DmpA as the catalyst, we observed very high conversion rates, which correspond to dimer yields of up to 76%. The beta-dipeptide H-beta3 hAla-beta3 hLeu-OH and the beta/alpha-dipeptide H-beta hGly-His-OH (carnosine) were formed with almost 50% conversion, when a five-fold excess of beta3-homoleucine or histidine was incubated with H-beta3 hAla-pNA and H-beta hGly-pNA, respectively, in the presence of the enzyme BapA from S. microcystinivorans Y2. BapA from S. xenopeptidilytica 3-2W4 turned out to be a versatile catalyst capable of coupling various beta-amino acid residues to the free N-termini of beta- and alpha-amino acids and even to an alpha-tripeptide. Thus, these aminopeptidases might be useful to introduce a beta-amino acid residue as an N-terminal protecting group into a 'natural' alpha-peptide, thereby stabilizing the peptide against degradation by other proteolytic enzymes.
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Affiliation(s)
- Tobias Heck
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf
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Geueke B, Kohler HPE. Bacterial β-peptidyl aminopeptidases: on the hydrolytic degradation of β-peptides. Appl Microbiol Biotechnol 2007; 74:1197-204. [PMID: 17318535 DOI: 10.1007/s00253-007-0872-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 01/26/2007] [Accepted: 01/30/2007] [Indexed: 10/23/2022]
Abstract
The special chemical and biological features of beta-peptides have been investigated intensively during recent years. Many studies emphasize the restricted biodegradability and the high metabolic stability of this class of compounds. beta-Peptidyl aminopeptidases form the first family of enzymes that hydrolyze a variety of short beta-peptides and beta-amino-acid-containing peptides. All representatives of this family were isolated from Gram-negative bacteria. The substrate specificities of the peptidases vary greatly, but the enzymes have common structural properties, and a similar reaction mechanism can be expected. This review gives an overview on the beta-peptidyl aminopeptidases with emphasis on their biochemical and structural properties. Their possible physiological function is discussed. Functionally and structurally related enzymes are compared to the beta-peptidyl aminopeptidases.
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Affiliation(s)
- B Geueke
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Ueberlandstrasse 133, 8600 Dübendorf, Switzerland.
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12
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Heck T, Limbach M, Geueke B, Zacharias M, Gardiner J, Kohler HPE, Seebach D. Enzymatic degradation of beta- and mixed alpha,beta-oligopeptides. Chem Biodivers 2007; 3:1325-48. [PMID: 17193247 DOI: 10.1002/cbdv.200690136] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
One of the main and most astonishing characteristics of peptides comprised of beta-amino acids with proteinogenic side chains is their extraordinarily high stability towards enzymatic degradation. So far, only certain microbial enzymes have been shown to cleave N-terminal beta(3)-homoamino acid residues from peptides. In this work, the L-aminopeptidase-D-amidase/esterase (DmpA) from Ochrobactrum anthropi LMG7991 is compared to two closely related beta-peptidyl aminopeptidases (BapA), which originate from Sphingosinicella strains, and to microsomal leucine aminopeptidase (LAP) as a reference. All four enzymes are aminopeptidases cleaving N-terminal amino acids from small peptides. Degradation experiments reveal that DmpA and both BapA enzymes exhibit unique, but clearly distinct substrate specificities and preferences. DmpA also cleaves beta- and mixed alpha,beta-peptides and amides, but a short side chain of the N-terminal beta-amino acid residue seems to be a prerequisite, since only peptides carrying N-terminal betahGly and beta(3)hAla are hydrolyzed with good efficiencies. Both beta-peptidyl aminopeptidases cleave beta-amino acids from a variety of beta-peptides and mixed alpha,beta-peptides, but they do not accept alpha-amino acids in the N-terminal position. Astonishingly, DmpA exhibited much higher catalytical rates for the mixed dipeptide carnosine (H-betahGly-His-OH) than for any other substrate described until now.
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Affiliation(s)
- Tobias Heck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf
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Graham RLJ, Pollock CE, O'Loughlin SN, Ternan NG, Weatherly DB, Jackson PJ, Tarleton RL, McMullan G. Multidimensional proteomic analysis of the soluble subproteome of the emerging nosocomial pathogen Ochrobactrum anthropi. J Proteome Res 2007; 5:3145-53. [PMID: 17081066 DOI: 10.1021/pr060293g] [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
We report the first large-scale gel-free proteomic analysis of the soluble subproteome of the emerging pathogen Ochrobactrum anthropi. Utilizing our robust offline multidimensional protein identification protocol, a total of 57 280 peptides were initially identified utilizing automated MS/MS analysis software. We describe our investigation of the heuristic protein validation tool PROVALT and demonstrate its ability to increase the speed and accuracy of the curation process of large-scale proteomic datasets. PROVALT reduced our peptide list to 8517 identified peptides and further manual curation of these peptides led to a final list of 984 uniquely identified peptides that resulted in the positive identification of 249 proteins. These identified proteins were functionally classified and physiochemically characterized. A variety of typical "housekeeping" functions identified within the proteome included nucleic acid, amino and fatty acid anabolism and catabolism, glycolysis, TCA cycle, and pyruvate and selenoamino acid metabolism. In addition, a number of potential virulence factors of relevance to both plant and human disease were identified.
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Affiliation(s)
- Robert Leslie James Graham
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry, BT52 1SA, United Kingdom.
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Seleem M, Ali M, Abd Al-Azeem MW, Boyle SM, Sriranganathan N. High-level heterologous gene expression in Ochrobactrum anthropi using an A-rich UP element. Appl Microbiol Biotechnol 2007; 73:1123-7. [PMID: 16944128 DOI: 10.1007/s00253-006-0555-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Revised: 06/08/2006] [Accepted: 06/15/2006] [Indexed: 10/24/2022]
Abstract
DNA regions that flank a gene's promoter play an important role in determining transcription efficiency by interacting with the carboxy-terminal domain of RNA polymerase alpha-subunit. We placed an adenine-rich upstream element (UP) between -38 and -59 of the core trc promoter to enhance gene expression in Ochrobactrum anthropi up to 66-fold. The high level of expression achieved by the UP element and the N-terminus fusion of a 6xHis epitope tag facilitated detection and purification of heterologous proteins directly from O. anthropi.
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Affiliation(s)
- Mohamed Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, 1410 Prices Fork Rd, Blacksburg, VA 24061-0342, USA
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Sonke T, Ernste S, Tandler RF, Kaptein B, Peeters WPH, van Assema FBJ, Wubbolts MG, Schoemaker HE. L-selective amidase with extremely broad substrate specificity from Ochrobactrum anthropi NCIMB 40321. Appl Environ Microbiol 2006; 71:7961-73. [PMID: 16332774 PMCID: PMC1317364 DOI: 10.1128/aem.71.12.7961-7973.2005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An industrially attractive L-specific amidase was purified to homogeneity from Ochrobactrum anthropi NCIMB 40321 wild-type cells. The purified amidase displayed maximum initial activity between pH 6 and 8.5 and was fully stable for at least 1 h up to 60 degrees C. The purified enzyme was strongly inhibited by the metal-chelating compounds EDTA and 1,10-phenanthroline. The activity of the EDTA-treated enzyme could be restored by the addition of Zn2+ (to 80%), Mn2+ (to 400%), and Mg2+ (to 560%). Serine and cysteine protease inhibitors did not influence the purified amidase. This enzyme displayed activity toward a broad range of substrates consisting of alpha-hydrogen- and (bulky) alpha,alpha-disubstituted alpha-amino acid amides, alpha-hydroxy acid amides, and alpha-N-hydroxyamino acid amides. In all cases, only the L-enantiomer was hydrolyzed, resulting in E values of more than 150. Simple aliphatic amides, beta-amino and beta-hydroxy acid amides, and dipeptides were not converted. The gene encoding this L-amidase was cloned via reverse genetics. It encodes a polypeptide of 314 amino acids with a calculated molecular weight of 33,870. Since the native enzyme has a molecular mass of about 66 kDa, it most likely has a homodimeric structure. The deduced amino acid sequence showed homology to a few other stereoselective amidases and the acetamidase/formamidase family of proteins (Pfam FmdA_AmdA). Subcloning of the gene in expression vector pTrc99A enabled efficient heterologous expression in Escherichia coli. Altogether, this amidase has a unique set of properties for application in the fine-chemicals industry.
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Affiliation(s)
- Theo Sonke
- DSM Pharma Chemicals-Advanced Synthesis, Catalysis and Development, P.O. Box 18, 6160 MD Geleen, The Netherlands.
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Delmarcelle M, Boursoit MC, Filée P, Baurin SL, Frère JM, Joris B. Specificity inversion of Ochrobactrum anthropi D-aminopeptidase to a D,D-carboxypeptidase with new penicillin binding activity by directed mutagenesis. Protein Sci 2006; 14:2296-303. [PMID: 16131658 PMCID: PMC2253486 DOI: 10.1110/ps.051475305] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The serine penicillin-recognizing proteins have been extensively studied. They show a wide range of substrate specificities accompanied by multidomain features. Their adaptation capacity has resulted in the emergence of pathogenic bacteria resistant to beta-lactam antibiotics. The most divergent enzymatic activities in this protein family are those of the Ochrobactrum anthropi D-aminopeptidase and of the Streptomyces R61 D,D-carboxypeptidase/transpeptidase. With the help of structural data, we have attempted to identify the factors responsible for this opposite specificity. A loop deletion mutant of the Ochrobactrum anthropi D-aminopeptidase lost its original activity in favor of a new penicillin-binding activity. D-aminopeptidase activity of the deletion mutant can be restored by complementation with another deletion mutant corresponding to the noncatalytic domain of the wild-type enzyme. By a second step site-directed mutagenesis, the specificity of the Ochrobactrum anthropi D-aminopeptidase was inverted to a D,D-carboxypeptidase specificity. These results imply a core enzyme with high diversity potential surrounded by specificity modulators. It is the first example of drastic specificity change in the serine penicillin-recognizing proteins. These results open new perspectives in the conception of new enzymes with nonnatural specificities. The structure/specificity relationship in the serine penicillin-recognizing proteins are discussed.
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Affiliation(s)
- Michaël Delmarcelle
- Centre d'Ingénierie des Protéines, Institut de Chimie, B6a, Universitéde Liège, Sart-Tilman, B- 4000 Liège, Belgium
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17
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Asano Y, Lübbehüsen TL. Enzymes acting on peptides containing D-amino acid. J Biosci Bioeng 2005; 89:295-306. [PMID: 16232749 DOI: 10.1016/s1389-1723(00)88949-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2000] [Accepted: 02/21/2000] [Indexed: 11/17/2022]
Abstract
Mainly microorganisms but only a few higher organisms are presently known to express enzymes that hydrolyze peptides containing D-amino acids. These enzymes can be involved in proceedings at the bacterial cell wall, in either assembly or modification, and thus cause resistance to glycopeptide antibiotics, or mediate resistance against beta-lactam antibiotics. In other cases the in vivo function is still unknown. New enzymes screened from nature, such as D-aminopeptidase, D-amino acid amidase, alkaline D-peptidase or D-aminoacylase, offer potential application in the production of D-amino acids, the synthesis of D-amino acid oligomers by promoting the reversed reaction under appropriate conditions, or in the field of semi-synthetic antibiotics.
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Affiliation(s)
- Y Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Kosugi, Toyama 939-0398, Japan
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Komeda H, Asano Y. A DmpA-homologous protein from Pseudomonas sp. is a dipeptidase specific for beta-alanyl dipeptides. FEBS J 2005; 272:3075-84. [PMID: 15955066 DOI: 10.1111/j.1742-4658.2005.04721.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have determined the nucleotide sequence of a DNA fragment covering the flanking region of the R-stereoselective amidase gene, ramA, from the Pseudomonas sp. MCI3434 genome and found an additional gene, bapA, coding for a protein showing sequence similarity to DmpA aminopeptidase from Ochrobactrum anthropi LMG7991 (43% identity). The DmpA (called L-aminopeptidase D-Ala-esterase/amidase) hydrolyzes alanine-p-nitroanilide, alaninamide, and alanine methylester with a preference for the D-configuration of the alanine, whereas the enzyme acts as an L-stereoselective aminopeptidase on a tripeptide Ala-(Gly)2, indicating a reverse stereoselectivity [Fanuel L, Goffin C, Cheggour A, Devreese B, Van Driessche G, Joris B, Van Beeumen J & Frère J-M (1999) Biochem J341, 147-155]. A recombinant BapA exhibiting hydrolytic activity toward D-alanine-p-nitroanilide was purified from the cell-free extract of an Escherichia coli transformant overexpressing the bapA gene and characterized. The purified enzyme contained two polypeptides corresponding to residues 1-238 (alpha-peptide) and 239-366 (beta-peptide) of the precursor as observed for DmpA. On gel-filtration chromatography, BapA in the native form appeared to be a tetramer. It had maximal activity at 60 degrees C and pH 9.0-10.0, and was inactivated in the presence of p-chloromercuribenzoate, N-ethylmaleimide, dithiothreitol, Zn2+, Ag+, Cd2+ or Hg2+. The enzyme hydrolyzed D-alanine-p-nitroanilide more efficiently than L-alanine-p-nitroanilide the same as DmpA. Furthermore, BapA was found to hydrolyze peptide bonds of beta-alanyl dipeptides including beta-Ala-L-Ala, beta-Ala-Gly, beta-Ala-L-His (carnosine), beta-Ala-L-Leu, and (beta-Ala)2 with high efficiency compared to D-alanine-p-nitroanilide. Beta-alaninamide was also efficiently hydrolyzed, but the enzyme did not act on the peptides containing proteinogenic amino acids or their D-counterparts for N-terminal residues. Based on its unique substrate specificity, the enzyme should not be called L-aminopeptidase D-Ala-esterase/amidase but beta-Ala-Xaa dipeptidase.
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Affiliation(s)
- Hidenobu Komeda
- Biotechnology Research Center, Toyama Prefectural University, Kosugi, Toyama, Japan
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Bompard-Gilles C, Remaut H, Villeret V, Prangé T, Fanuel L, Delmarcelle M, Joris B, Frère J, Van Beeumen J. Crystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family. Structure 2000; 8:971-80. [PMID: 10986464 DOI: 10.1016/s0969-2126(00)00188-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND beta-Lactam compounds are the most widely used antibiotics. They inactivate bacterial DD-transpeptidases, also called penicillin-binding proteins (PBPs), involved in cell-wall biosynthesis. The most common bacterial resistance mechanism against beta-lactam compounds is the synthesis of beta-lactamases that hydrolyse beta-lactam rings. These enzymes are believed to have evolved from cell-wall DD-peptidases. Understanding the biochemical and mechanistic features of the beta-lactam targets is crucial because of the increasing number of resistant bacteria. DAP is a D-aminopeptidase produced by Ochrobactrum anthropi. It is inhibited by various beta-lactam compounds and shares approximately 25% sequence identity with the R61 DD-carboxypeptidase and the class C beta-lactamases. RESULTS The crystal structure of DAP has been determined to 1.9 A resolution using the multiple isomorphous replacement (MIR) method. The enzyme folds into three domains, A, B and C. Domain A, which contains conserved catalytic residues, has the classical fold of serine beta-lactamases, whereas domains B and C are both antiparallel eight-stranded beta barrels. A loop of domain C protrudes into the substrate-binding site of the enzyme. CONCLUSIONS Comparison of the biochemical properties and the structure of DAP with PBPs and serine beta-lactamases shows that although the catalytic site of the enzyme is very similar to that of beta-lactamases, its substrate and inhibitor specificity rests on residues of domain C. DAP is a new member of the family of penicillin-recognizing proteins (PRPs) and, at the present time, its enzymatic specificity is clearly unique.
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Affiliation(s)
- C Bompard-Gilles
- Laboratorium voor Eiwitbiochemie en Eiwitengineering, Rijksuniversiteit-Gent, K.L. Ledeganckstraat, 35, B-9000, Gent, Belgium
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Bompard-Gilles C, Villeret V, Davies GJ, Fanuel L, Joris B, Frère JM, Van Beeumen J. A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi. Structure 2000; 8:153-62. [PMID: 10673442 DOI: 10.1016/s0969-2126(00)00091-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND The L-aminopeptidase D-Ala-esterase/amidase from Ochrobactrum anthropi (DmpA) releases the N-terminal L and/or D-Ala residues from peptide substrates. This is the only known enzyme to liberate N-terminal amino acids with both D and L stereospecificity. The DmpA active form is an alphabeta heterodimer, which results from a putative autocatalytic cleavage of an inactive precursor polypeptide. RESULTS The crystal structure of the enzyme has been determined to 1.82 A resolution using the multiple isomorphous replacement method. The heterodimer folds into a single domain organised as an alphabetabetaalpha sandwich in which two mixed beta sheets are flanked on both sides by two alpha helices. CONCLUSIONS DmpA shows no similarity to other known aminopeptidases in either fold or catalytic mechanism, and thus represents the first example of a novel family of aminopeptidases. The protein fold of DmpA does, however, show structural homology to members of the N-terminal nucleophile (Ntn) hydrolase superfamily. DmpA presents functionally equivalent residues in the catalytic centre when compared with other Ntn hydrolases, and is therefore likely to use the same catalytic mechanism. In spite of this homology, the direction and connectivity of the secondary structure elements differ significantly from the consensus Ntn hydrolase topology. The DmpA structure thus characterises a new subfamily, but supports the common catalytic mechanism for these enzymes suggesting an evolutionary relationship.
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Affiliation(s)
- C Bompard-Gilles
- Laboratorium voor Eiwitbiochemie en Eiwitengineering, Rijksuniversiteit-Gent, Gent, B-9000, Belgium
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