1
|
Iacovelli R, Bovenberg RAL, Driessen AJM. Nonribosomal peptide synthetases and their biotechnological potential in Penicillium rubens. J Ind Microbiol Biotechnol 2021; 48:6324005. [PMID: 34279620 PMCID: PMC8788816 DOI: 10.1093/jimb/kuab045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/12/2021] [Indexed: 01/23/2023]
Abstract
Nonribosomal peptide synthetases (NRPS) are large multimodular enzymes that synthesize a diverse variety of peptides. Many of these are currently used as pharmaceuticals, thanks to their activity as antimicrobials (penicillin, vancomycin, daptomycin, echinocandin), immunosuppressant (cyclosporin) and anticancer compounds (bleomycin). Because of their biotechnological potential, NRPSs have been extensively studied in the past decades. In this review, we provide an overview of the main structural and functional features of these enzymes, and we consider the challenges and prospects of engineering NRPSs for the synthesis of novel compounds. Furthermore, we discuss secondary metabolism and NRP synthesis in the filamentous fungus Penicillium rubens and examine its potential for the production of novel and modified β-lactam antibiotics.
Collapse
Affiliation(s)
- Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands.,DSM Biotechnology Centre, 2613 AX Delft, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| |
Collapse
|
2
|
Klimacek M, Sigg A, Nidetzky B. On the donor substrate dependence of group-transfer reactions by hydrolytic enzymes: Insight from kinetic analysis of sucrose phosphorylase-catalyzed transglycosylation. Biotechnol Bioeng 2020; 117:2933-2943. [PMID: 32573774 PMCID: PMC7540478 DOI: 10.1002/bit.27471] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/15/2020] [Accepted: 06/21/2020] [Indexed: 12/30/2022]
Abstract
Chemical group-transfer reactions by hydrolytic enzymes have considerable importance in biocatalytic synthesis and are exploited broadly in commercial-scale chemical production. Mechanistically, these reactions have in common the involvement of a covalent enzyme intermediate which is formed upon enzyme reaction with the donor substrate and is subsequently intercepted by a suitable acceptor. Here, we studied the glycosylation of glycerol from sucrose by sucrose phosphorylase (SucP) to clarify a peculiar, yet generally important characteristic of this reaction: partitioning between glycosylation of glycerol and hydrolysis depends on the type and the concentration of the donor substrate used (here: sucrose, α-d-glucose 1-phosphate (G1P)). We develop a kinetic framework to analyze the effect and provide evidence that, when G1P is used as donor substrate, hydrolysis occurs not only from the β-glucosyl-enzyme intermediate (E-Glc), but additionally from a noncovalent complex of E-Glc and substrate which unlike E-Glc is unreactive to glycerol. Depending on the relative rates of hydrolysis of free and substrate-bound E-Glc, inhibition (Leuconostoc mesenteroides SucP) or apparent activation (Bifidobacterium adolescentis SucP) is observed at high donor substrate concentration. At a G1P concentration that excludes the substrate-bound E-Glc, the transfer/hydrolysis ratio changes to a value consistent with reaction exclusively through E-Glc, independent of the donor substrate used. Collectively, these results give explanation for a kinetic behavior of SucP not previously accounted for, provide essential basis for design and optimization of the synthetic reaction, and establish a theoretical framework for the analysis of kinetically analogous group-transfer reactions by hydrolytic enzymes.
Collapse
Affiliation(s)
- Mario Klimacek
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Alexander Sigg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria.,Austrian Centre of Industrial Biotechnology (acib), Graz, Austria
| |
Collapse
|
3
|
Jha RK, Strauss CEM. Smart Microbial Cells Couple Catalysis and Sensing to Provide High-Throughput Selection of an Organophosphate Hydrolase. ACS Synth Biol 2020; 9:1234-1239. [PMID: 32369698 DOI: 10.1021/acssynbio.0c00025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Enzyme engineering for gain of function requires navigating a large combinatorial sequence space efficiently. Typically, many mutations are needed to get significant improvements, while a single "bad" mutation can inactivate the enzyme. To establish high-throughput screening and achieve enhanced resolution between two variants, genetic libraries of the organophosphate hydrolase enzyme paraoxonase 1 (PON1) were rapidly screened via an engineered positive-feedback circuit: a p-nitrophenol (PNP)-specific transcription factor (TF) regulated expression of PON1, which catalyzed paraoxon breakdown and PNP production. Rare active mutant colonies, picked by simple visual fluorescence of a PON1-green fluorescent protein (GFP) fusion, were characterized. In a single screening round, high (library-scale) throughput enabled the discovery of enhanced paraoxon degradation activity in PON1, including structurally unexpected mutations.
Collapse
Affiliation(s)
- Ramesh K. Jha
- Bioscience Division, Los Alamos National Laboratory, MS M888, P.O. Box 1663, Los Alamos, New Mexico 87545, United States
| | - Charlie E. M. Strauss
- Bioscience Division, Los Alamos National Laboratory, MS M888, P.O. Box 1663, Los Alamos, New Mexico 87545, United States
| |
Collapse
|
4
|
Efficient synthesis of β-lactam antibiotics with in situ product removal by a newly isolated penicillin G acylase. Bioorg Chem 2020; 99:103765. [DOI: 10.1016/j.bioorg.2020.103765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/13/2020] [Accepted: 03/14/2020] [Indexed: 12/17/2022]
|
5
|
Fitting replacement of signal peptide for highly efficient expression of three penicillin G acylases in E. coli. Appl Microbiol Biotechnol 2018; 102:7455-7464. [DOI: 10.1007/s00253-018-9163-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/05/2018] [Accepted: 06/05/2018] [Indexed: 02/06/2023]
|
6
|
Huang X, Xue J, Zhu Y. Computational design of cephradine synthase in a new scaffold identified from structural databases. Chem Commun (Camb) 2018. [PMID: 28639649 DOI: 10.1039/c7cc02270k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational enzyme design exhibits excellent performance for identifying potential scaffolds from structural databases and creating new enzymatic catalysts from naught. Using the active site-matching algorithm ProdaMatch, we identified a new scaffold cocaine esterase from Rhodococcus sp. that showed modest activity (kcat/Km = 0.018 M-1 s-1) towards the hydrolysis of β-lactam antibiotic cephradine. The identified cocaine esterase scaffold afforded low sequence identity (<30%) with the known β-lactam synthases, such as penicillin G acylase or α-amino acid ester hydrolase, and was able to catalyze the condensation reaction between d-dihydrophenylglycine methyl ester and 7-aminodesacetoxycephalosporanic acid to produce cephradine via a kinetically controlled synthesis. By virtue of the computational enzyme design protocol, hundreds of sequences were predicted in the cocaine esterase scaffold to promote the catalytic activity towards the hydrolytic reaction of cephradine. Moreover, a single mutant (F261T) was experimentally confirmed to have improved the catalytic efficiency by ten times (kcat/Km = 0.193 M-1 s-1), indicating that the novel scaffold cocaine esterase may be potentially redesigned to become an industrially useful cephradine synthase.
Collapse
Affiliation(s)
- Xiaoqiang Huang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China.
| | | | | |
Collapse
|
7
|
Efficient synthesis of β-lactam antibiotics with very low product hydrolysis by a mutant Providencia rettgeri penicillin G acylase. Appl Microbiol Biotechnol 2018; 102:1749-1758. [PMID: 29306966 DOI: 10.1007/s00253-017-8692-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/30/2017] [Accepted: 12/02/2017] [Indexed: 10/18/2022]
Abstract
Penicillin G acylase (PGA) was isolated from Providencia rettgeri PX04 (PrPGApx04) and utilized for the kinetically controlled synthesis of β-lactam antibiotics. Site-directed mutagenesis was performed to increase the process efficiency. Molecular docking was carried out to speculate the key mutant positions corresponding with synthetic activity, which resulted in the achievement of an efficient mutant, βF24G. It yielded higher conversions than the wild-type enzyme in the synthesis of amoxicillin (95 versus 17.2%) and cefadroxil (95.4 versus 43.2%). The reaction time for achieving the maximum conversion decreased from 14 to 16 h to 2-2.5 h. Furthermore, the secondary hydrolysis of produced antibiotics was hardly observed. Kinetic analysis showed that the (kcat/Km)AD value for the activated acyl donor D-hydroxyphenylglycine methyl ester (D-HPGME) increased up to 41 times. In contrast, the (kcat/Km)Ps values for the products amoxicillin and cefadroxil decreased 6.5 and 21 times, respectively. Consequently, the α value (kcat/Km)Ps/(kcat/Km)AD, which reflected the relative hydrolytic specificity of PGA for produced antibiotics with respect to the activated acyl donor, were only 0.028 and 0.043, respectively. The extremely low hydrolytic activity for the products of the βF24G mutant enabled greater product accumulation to occur during synthesis, which made it a promising enzyme for industrial applications.
Collapse
|
8
|
Utari PD, Vogel J, Quax WJ. Deciphering Physiological Functions of AHL Quorum Quenching Acylases. Front Microbiol 2017; 8:1123. [PMID: 28674525 PMCID: PMC5474475 DOI: 10.3389/fmicb.2017.01123] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/01/2017] [Indexed: 11/13/2022] Open
Abstract
N-Acylhomoserine lactone (AHL)-acylase (also known as amidase or amidohydrolase) is a class of enzyme that belongs to the Ntn-hydrolase superfamily. As the name implies, AHL-acylases are capable of hydrolysing AHLs, the most studied signaling molecules for quorum sensing in Gram-negative bacteria. Enzymatic degradation of AHLs can be beneficial in attenuating bacterial virulence, which can be exploited as a novel approach to fight infection of human pathogens, phytopathogens or aquaculture-related contaminations. Numerous acylases from both prokaryotic and eukaryotic sources have been characterized and tested for the interference of quorum sensing-regulated functions. The existence of AHL-acylases in a multitude of organisms from various ecological niches, raises the question of what the physiological roles of AHL-acylases actually are. In this review, we attempt to bring together recent studies to extend our understanding of the biological functions of these enzymes in nature.
Collapse
Affiliation(s)
- Putri D Utari
- Chemical and Pharmaceutical Biology Department, University of GroningenGroningen, Netherlands
| | - Jan Vogel
- Chemical and Pharmaceutical Biology Department, University of GroningenGroningen, Netherlands
| | - Wim J Quax
- Chemical and Pharmaceutical Biology Department, University of GroningenGroningen, Netherlands
| |
Collapse
|
9
|
Protein-based inverse opals: A novel support for enzyme immobilization. Enzyme Microb Technol 2017; 96:42-46. [DOI: 10.1016/j.enzmictec.2016.08.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 08/23/2016] [Accepted: 08/30/2016] [Indexed: 01/19/2023]
|
10
|
Grulich M, Brezovský J, ŠtĿpánek V, Palyzová A, Kyslíková E, Kyslík P. Resolution of α/β-amino acids by enantioselective penicillin G acylase from Achromobacter sp . ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
11
|
Ramanathan M, Muthuramalingam R, Lakshmanan R. The Mathematical Theory of Diffusion and Reaction in Enzymes Immoblized Artificial Membrane. The Theory of the Non-Steady State. J Membr Biol 2015; 248:1127-35. [PMID: 26265446 DOI: 10.1007/s00232-015-9829-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
Abstract
In this paper, mathematical model pertaining to the decomposition of enzyme-substrate complex in an artificial membrane is discussed. Here the transport through liquid membrane phases is considered. The model involves the system of non-linear reaction diffusion equations. The non-linear terms in this model are related to Michaelis-Menten reaction scheme. Approximate analytical expressions for the concentrations of substrate and product have been derived by solving the system of non-linear reaction diffusion equations using new approach of homotopy perturbation method for all values of Michaelis-Menten constant, diffusion coefficient, and rate constant. Approximate flux expression for substrate and product for non-steady-state conditions are also reported. A comparison of the analytical approximation and numerical simulation is also presented. The results obtained in this work are valid for the entire solution domain.
Collapse
Affiliation(s)
- Malinidevi Ramanathan
- Department of Mathematics, The Standard Fireworks Rajaratnam College for Women, Sivakasi, Tamil Nadu, 626 123, India.
| | - Rasi Muthuramalingam
- Department of Mathematics, Sethu Institute of Technology, Kariapatti, Tamil Nadu, 626 115, India.
| | - Rajendran Lakshmanan
- Department of Mathematics, Sethu Institute of Technology, Kariapatti, Tamil Nadu, 626 115, India.
| |
Collapse
|
12
|
Ma X, Deng S, Su E, Wei D. One-pot enzymatic production of deacetyl-7-aminocephalosporanic acid from cephalosporin C via immobilized cephalosporin C acylase and deacetylase. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
13
|
Eş I, Vieira JDG, Amaral AC. Principles, techniques, and applications of biocatalyst immobilization for industrial application. Appl Microbiol Biotechnol 2015; 99:2065-82. [DOI: 10.1007/s00253-015-6390-y] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/06/2015] [Accepted: 01/07/2015] [Indexed: 11/28/2022]
|
14
|
Avinash VS, Pundle AV, Ramasamy S, Suresh CG. Penicillin acylases revisited: importance beyond their industrial utility. Crit Rev Biotechnol 2014; 36:303-16. [PMID: 25430891 DOI: 10.3109/07388551.2014.960359] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
It is of great importance to study the physiological roles of enzymes in nature; however, in some cases, it is not easily apparent. Penicillin acylases are pharmaceutically important enzymes that cleave the acyl side chains of penicillins, thus paving the way for production of newer semi-synthetic antibiotics. They are classified according to the type of penicillin (G or V) that they preferentially hydrolyze. Penicillin acylases are also used in the resolution of racemic mixtures and peptide synthesis. However, it is rather unfortunate that the focus on the use of penicillin acylases for industrial applications has stolen the spotlight from the study of the importance of these enzymes in natural metabolism. The penicillin acylases, so far characterized from different organisms, show differences in their structural nature and substrate spectrum. These enzymes are also closely related to the bacterial signalling phenomenon, quorum sensing, as detailed in this review. This review details studies on biochemical and structural characteristics of recently discovered penicillin acylases. We also attempt to organize the available insights into the possible in vivo role of penicillin acylases and related enzymes and emphasize the need to refocus research efforts in this direction.
Collapse
Affiliation(s)
- Vellore Sunder Avinash
- a Division of Biochemical Sciences, CSIR-National , National Chemical Laboratory , Pune , India
| | - Archana Vishnu Pundle
- a Division of Biochemical Sciences, CSIR-National , National Chemical Laboratory , Pune , India
| | - Sureshkumar Ramasamy
- a Division of Biochemical Sciences, CSIR-National , National Chemical Laboratory , Pune , India
| | | |
Collapse
|
15
|
Current state and perspectives of penicillin G acylase-based biocatalyses. Appl Microbiol Biotechnol 2014; 98:2867-79. [DOI: 10.1007/s00253-013-5492-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/20/2013] [Accepted: 12/22/2013] [Indexed: 10/25/2022]
|
16
|
Grulich M, Štěpánek V, Kyslík P. Perspectives and industrial potential of PGA selectivity and promiscuity. Biotechnol Adv 2013; 31:1458-72. [DOI: 10.1016/j.biotechadv.2013.07.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 07/02/2013] [Accepted: 07/06/2013] [Indexed: 11/26/2022]
|
17
|
Wahjudi M, Murugappan S, van Merkerk R, Eissens AC, Visser MR, Hinrichs WL, Quax WJ. Development of a dry, stable and inhalable acyl–homoserine–lactone–acylase powder formulation for the treatment of pulmonary Pseudomonas aeruginosa infections. Eur J Pharm Sci 2013; 48:637-43. [DOI: 10.1016/j.ejps.2012.12.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 11/01/2012] [Accepted: 12/20/2012] [Indexed: 02/02/2023]
|
18
|
Hamed RB, Gomez-Castellanos JR, Henry L, Ducho C, McDonough MA, Schofield CJ. The enzymes of β-lactam biosynthesis. Nat Prod Rep 2013; 30:21-107. [DOI: 10.1039/c2np20065a] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
19
|
Buller AR, Labonte JW, Freeman MF, Wright NT, Schildbach JF, Townsend CA. Autoproteolytic activation of ThnT results in structural reorganization necessary for substrate binding and catalysis. J Mol Biol 2012; 422:508-18. [PMID: 22706025 PMCID: PMC3428426 DOI: 10.1016/j.jmb.2012.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 06/02/2012] [Accepted: 06/08/2012] [Indexed: 11/01/2022]
Abstract
cis-Autoproteolysis is a post-translational modification necessary for the function of ThnT, an enzyme involved in the biosynthesis of the β-lactam antibiotic thienamycin. This modification generates an N-terminal threonine nucleophile that is used to hydrolyze the pantetheinyl moiety of its natural substrate. We determined the crystal structure of autoactivated ThnT to 1.8Å through X-ray crystallography. Comparison to a mutationally inactivated precursor structure revealed several large conformational rearrangements near the active site. To probe the relevance of these transitions, we designed a pantetheine-like chloromethyl ketone inactivator and co-crystallized it with ThnT. Although this class of inhibitor has been in use for several decades, the mode of inactivation had not been determined for an enzyme that uses an N-terminal nucleophile. The co-crystal structure revealed the chloromethyl ketone bound to the N-terminal nucleophile of ThnT through an ether linkage, and analysis suggests inactivation through a direct displacement mechanism. More importantly, this inactivated complex shows that three regions of ThnT that are critical to the formation of the substrate binding pocket undergo rearrangement upon autoproteolysis. Comparison of ThnT with other autoproteolytic enzymes of disparate evolutionary lineage revealed a high degree of similarity within the proenzyme active site, reflecting shared chemical constraints. However, after autoproteolysis, many enzymes, like ThnT, are observed to rearrange in order to accommodate their specific substrate. We propose that this is a general phenomenon, whereby autoprocessing systems with shared chemistry may possess similar structural features that dissipate upon rearrangement into a mature state.
Collapse
Affiliation(s)
- Andrew R. Buller
- Department of Biophysics, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jason W. Labonte
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael F. Freeman
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nathan T. Wright
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Joel F. Schildbach
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Craig A. Townsend
- Department of Biophysics, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
20
|
Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJT, Gallaher J, Pianowski Z, Helgeson RC, Grjasnow A, Xiao R, Seetharaman J, Su M, Vorobiev S, Lew S, Forouhar F, Kornhaber GJ, Hunt JF, Montelione GT, Tong L, Houk KN, Hilvert D, Baker D. Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. J Am Chem Soc 2012; 134:16197-206. [PMID: 22871159 DOI: 10.1021/ja3037367] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleophilic catalysis is a general strategy for accelerating ester and amide hydrolysis. In natural active sites, nucleophilic elements such as catalytic dyads and triads are usually paired with oxyanion holes for substrate activation, but it is difficult to parse out the independent contributions of these elements or to understand how they emerged in the course of evolution. Here we explore the minimal requirements for esterase activity by computationally designing artificial catalysts using catalytic dyads and oxyanion holes. We found much higher success rates using designed oxyanion holes formed by backbone NH groups rather than by side chains or bridging water molecules and obtained four active designs in different scaffolds by combining this motif with a Cys-His dyad. Following active site optimization, the most active of the variants exhibited a catalytic efficiency (k(cat)/K(M)) of 400 M(-1) s(-1) for the cleavage of a p-nitrophenyl ester. Kinetic experiments indicate that the active site cysteines are rapidly acylated as programmed by design, but the subsequent slow hydrolysis of the acyl-enzyme intermediate limits overall catalytic efficiency. Moreover, the Cys-His dyads are not properly formed in crystal structures of the designed enzymes. These results highlight the challenges that computational design must overcome to achieve high levels of activity.
Collapse
Affiliation(s)
- Florian Richter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Van Den Berg M, Gidijala L, Kiela J, Bovenberg R, Vander Keli I. Biosynthesis of active pharmaceuticals: β-lactam biosynthesis in filamentous fungi. Biotechnol Genet Eng Rev 2011; 27:1-32. [PMID: 21415891 DOI: 10.1080/02648725.2010.10648143] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
β-lactam antibiotics (e.g. penicillins, cephalosporins) are of major clinical importance and contribute to over 40% of the total antibiotic market. These compounds are produced as secondary metabolites by certain actinomycetes and filamentous fungi (e.g. Penicillium, Aspergillus and Acremonium species). The industrial producer of penicillin is the fungus Penicillium chrysogenum. The enzymes of the penicillin biosynthetic pathway are well characterized and most of them are encoded by genes that are organized in a cluster in the genome. Remarkably, the penicillin biosynthetic pathway is compartmentalized: the initial steps of penicillin biosynthesis are catalyzed by cytosolic enzymes, whereas the two final steps involve peroxisomal enzymes. Here, we describe the biochemical properties of the enzymes of β-lactam biosynthesis in P. chrysogenum and the role of peroxisomes in this process. An overview is given on strain improvement programs via classical mutagenesis and, more recently, genetic engineering, leading to more productive strains. Also, the potential of using heterologous hosts for the development of novel ß-lactam antibiotics and non-ribosomal peptide synthetase-based peptides is discussed.
Collapse
Affiliation(s)
- Marco Van Den Berg
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Kluyver Center for Genomics of Industrial Fermentation, University of Groningen, The Netherlands.
| | | | | | | | | |
Collapse
|
22
|
Wahjudi M, Papaioannou E, Hendrawati O, van Assen AHG, van Merkerk R, Cool RH, Poelarends GJ, Quax WJ. PA0305 of Pseudomonas aeruginosa is a quorum quenching acylhomoserine lactone acylase belonging to the Ntn hydrolase superfamily. MICROBIOLOGY-SGM 2011; 157:2042-2055. [PMID: 21372094 DOI: 10.1099/mic.0.043935-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Pseudomonas aeruginosa PAO1 genome has at least two genes, pvdQ and quiP, encoding acylhomoserine lactone (AHL) acylases. Two additional genes, pa1893 and pa0305, have been predicted to encode penicillin acylase proteins, but have not been characterized. Initial studies on a pa0305 transposon insertion mutant suggested that the gene is not related to the AHL growth phenotype of P. aeruginosa. The close similarity (67 %) of pa0305 to HacB, an AHL acylase of Pseudomonas syringae, prompted us to investigate whether the PA0305 protein might also function as an AHL acylase. The pa0305 gene has been cloned and the protein (PA0305) has been overproduced, purified and subjected to functional characterization. Analysis of the purified protein showed that, like β-lactam acylases, PA0305 undergoes post-translational processing resulting in α- and β-subunits, with the catalytic serine as the first amino acid of the β-subunit, strongly suggesting that PA0305 is a member of the N-terminal nucleophile hydrolase superfamily. Using a biosensor assay, PA0305his was shown to degrade AHLs with acyl side chains ranging in length from 6 to 14 carbons. Kinetics studies using N-octanoyl-L-homoserine lactone (C(8)-HSL) and N-(3-oxo-dodecanoyl)-L-homoserine lactone (3-oxo-C(12)-HSL) as substrates showed that the enzyme has a robust activity towards these two AHLs, with apparent K(cat)/K(m) values of 0.14 × 10(4) M(-1) s(-1) towards C(8)-HSL and 7.8 × 10(4) M(-1 )s(-1) towards 3-oxo-C(12)-HSL. Overexpression of the pa0305 gene in P. aeruginosa showed significant reductions in both accumulation of 3-oxo-C(12)-HSL and expression of virulence factors. A mutant P. aeruginosa strain with a deleted pa0305 gene showed a slightly increased capacity to kill Caenorhabditis elegans compared with the P. aeruginosa PAO1 wild-type strain and the PAO1 strain carrying a plasmid overexpressing pa0305. The harmful effects of the Δpa0305 strain on the animals were most visible at 5 days post-exposure and the mortality rate of the animals fed on the Δpa0305 strain was faster than for the animals fed on either the wild-type strain or the strain overexpressing pa0305. In conclusion, the pa0305 gene encodes an efficient acylase with activity towards long-chain homoserine lactones, including 3-oxo-C(12)-HSL, the natural quorum sensing signal molecule in P. aeruginosa, and we propose to name this acylase HacB.
Collapse
Affiliation(s)
- Mariana Wahjudi
- Faculty of Technobiology, University of Surabaya, Indonesia.,Department of Pharmaceutical Biology, University of Groningen, 9713AV Groningen, The Netherlands
| | - Evelina Papaioannou
- Department of Pharmaceutical Biology, University of Groningen, 9713AV Groningen, The Netherlands
| | - Oktavia Hendrawati
- Department of Pharmaceutical Biology, University of Groningen, 9713AV Groningen, The Netherlands
| | - Aart H G van Assen
- Department of Pharmaceutical Biology, University of Groningen, 9713AV Groningen, The Netherlands
| | - Ronald van Merkerk
- Department of Pharmaceutical Biology, University of Groningen, 9713AV Groningen, The Netherlands
| | - Robbert H Cool
- Department of Pharmaceutical Biology, University of Groningen, 9713AV Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Pharmaceutical Biology, University of Groningen, 9713AV Groningen, The Netherlands
| | - Wim J Quax
- Department of Pharmaceutical Biology, University of Groningen, 9713AV Groningen, The Netherlands
| |
Collapse
|
23
|
Zhao J, Wang Y, Luo G, Zhu S. Immobilization of penicillin G acylase on macro-mesoporous silica spheres. BIORESOURCE TECHNOLOGY 2011; 102:529-535. [PMID: 20965720 DOI: 10.1016/j.biortech.2010.09.076] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 09/18/2010] [Accepted: 09/20/2010] [Indexed: 05/30/2023]
Abstract
In this study, macro-mesoporous silica spheres were prepared with a micro-device and used as the support for the immobilization of penicillin G acylase (PGA). To measure the enzymatic activity, the silica spheres with immobilized PGA were placed into a packed-bed reactor, in which the hydrolysis of penicillin G was carried out. The influences of the residence time, the initial concentration of the substrate, the accumulation of the target product 6-aminopenicillanic acid, and the enzyme loading amount on the performance of the immobilized PGA were investigated. The introduction of macropores increased the enzyme loading amount and decreased the internal mass transfer resistance, and the results showed that the enzyme loading amount reached 895 mg/g (dry support), and the apparent enzymatic activity achieved up to 1033 U/g (dry support). In addition, the immobilized PGA was found to have great stability.
Collapse
Affiliation(s)
- Junqi Zhao
- The State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | | | | | | |
Collapse
|
24
|
van der Sloot AM, Quax WJ. Computational design of TNF ligand-based protein therapeutics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 691:521-34. [PMID: 21153357 DOI: 10.1007/978-1-4419-6612-4_54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Almer M van der Sloot
- EMBL-CRG Systems Biology Program, Design of Biological Systems, Centre de Regulació Genòmica, Dr Aiguader 88, 08003, Barcelona, Spain
| | | |
Collapse
|
25
|
Ali Khan A, Alzohairy MA. Recent Advances and Applications of Immobilized Enzyme Technologies: A Review. ACTA ACUST UNITED AC 2010. [DOI: 10.3923/rjbsci.2010.565.575] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
26
|
Bernardino SM, Fernandes P, Fonseca LP. Improved specific productivity in cephalexin synthesis by immobilized PGA in silica magnetic micro-particles. Biotechnol Bioeng 2010; 107:753-62. [DOI: 10.1002/bit.22867] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
27
|
Bolivar JM, López-Gallego F, Godoy C, Rodrigues DS, Rodrigues RC, Batalla P, Rocha-Martín J, Mateo C, Giordano RL, Guisán JM. The presence of thiolated compounds allows the immobilization of enzymes on glyoxyl agarose at mild pH values: New strategies of stabilization by multipoint covalent attachment. Enzyme Microb Technol 2009. [DOI: 10.1016/j.enzmictec.2009.09.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
28
|
Kumar A, Gowda NM, Gaikwad S, Pundle A. Rhodotorula aurantiaca penicillin V acylase: active site characterization and fluorometric studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 97:109-16. [PMID: 19819716 DOI: 10.1016/j.jphotobiol.2009.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 08/05/2009] [Accepted: 08/18/2009] [Indexed: 11/27/2022]
Abstract
Penicillin V acylase (PVA), a member of newly evolved Ntn-hydrolase superfamily, is a pharmaceutically important enzyme to produce 6-aminopenicillanic acid. Active site characterization of recently purified monomeric PVA from Rhodotorula aurantiaca (Ra-PVA), the yeast source, showed the involvement of serine and tryptophan in the enzyme activity. Modification of the protein with serine and tryptophan specific reagents such as PMSF and NBS showed partial loss of PVA activity and substrate protection. Ra-PVA was found to be a multi-tryptophan protein exhibiting one tryptophan, in native and, four in its denatured condition. Various solute quenchers and substrate were used to probe the microenvironment of the putative reactive tryptophan through fluorescence quenching. The results obtained indicate that the tryptophan residues of Ra-PVA were largely buried in hydrophobic core of the protein matrix. Quenching of the fluorescence by acrylamide was collisional. Acrylamide was the most effective quencher amongst all the used quenchers, which quenched 71.6% of the total intrinsic fluorescence of the protein, at a very less final concentration of 0.1M. Surface tryptophan residues were found to have predominantly more electropositively charged amino acids around them, however differentially accessible for ionic quenchers. Denaturation led to shift in lambda(max) from 336, in native state, to 357 nm and more exposed to the solvent, consequently increase in fluorescence quenching with all quenchers. This is an attempt towards the conformational studies of Ra-PVA.
Collapse
Affiliation(s)
- Atul Kumar
- Division of Biochemical Sciences, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | | | | | | |
Collapse
|
29
|
Jimenez PN, Koch G, Papaioannou E, Wahjudi M, Krzeslak J, Coenye T, Cool RH, Quax WJ. Role of PvdQ in Pseudomonas aeruginosa virulence under iron-limiting conditions. MICROBIOLOGY-SGM 2009; 156:49-59. [PMID: 19778968 DOI: 10.1099/mic.0.030973-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
PvdQ, an acylase from Pseudomonas aeruginosa PAO1, has been shown to have at least two functions. It can act as a quorum quencher due to its ability to degrade long-chain N-acylhomoserine lactones (AHLs), e.g. 3-oxo-C12-HSL, leading to a decrease in virulence factors. In addition, PvdQ is involved in iron homeostasis by playing a role in the biosynthesis of pyoverdine, the major siderophore of P. aeruginosa. In accordance with earlier studies on RNA level, we could show at the protein level that PvdQ is only expressed when iron is present at very low concentrations. We therefore set out to investigate the two functions of PvdQ under iron-limiting conditions. Gene deletion of pvdQ does not affect growth of P. aeruginosa but abrogates pyoverdine production, and results in an accumulation of 3-oxo-C12-HSL. Phenotypic analyses of our DeltapvdQ mutant at low iron concentrations revealed that this mutant is impaired in swarming motility and biofilm formation. Additionally, a plant and a Caenorhabditis elegans infection model demonstrated that the deletion of pvdQ resulted in reduced virulence. None of the phenotypes in the present study could be linked to the presence or absence of AHLs. These results clearly indicate that under iron-limiting conditions PvdQ plays a major role in swarming motility, in biofilm development and in infection that is more likely to be linked to the pyoverdine pathway rather than the LasI/LasR/3-oxo-C12-HSL quorum-sensing circuit.
Collapse
Affiliation(s)
- Pol Nadal Jimenez
- Department of Pharmaceutical Biology, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Gudrun Koch
- Department of Pharmaceutical Biology, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Evelina Papaioannou
- Department of Pharmaceutical Biology, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Mariana Wahjudi
- Faculty of Pharmacy and Faculty of Technobiology, University of Surabaya, Indonesia.,Department of Pharmaceutical Biology, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Joanna Krzeslak
- Department of Pharmaceutical Biology, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Tom Coenye
- Laboratory for Pharmaceutical Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Robbert H Cool
- Department of Pharmaceutical Biology, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Wim J Quax
- Department of Pharmaceutical Biology, University of Groningen, 9713 AV Groningen, The Netherlands
| |
Collapse
|
30
|
Heterologous production of Escherichia coli penicillin G acylase in Pseudomonas aeruginosa. J Biotechnol 2009; 142:250-8. [DOI: 10.1016/j.jbiotec.2009.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 05/18/2009] [Accepted: 05/19/2009] [Indexed: 11/22/2022]
|
31
|
Bolivar JM, Mateo C, Godoy C, Pessela BC, Rodrigues DS, Giordano RL, Fernandez-Lafuente R, Guisan JM. The co-operative effect of physical and covalent protein adsorption on heterofunctional supports. Process Biochem 2009. [DOI: 10.1016/j.procbio.2009.03.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
32
|
Romero O, Vergara J, Fernández-Lafuente R, Guisán JM, Illanes A, Wilson L. Simple strategy of reactivation of a partially inactivated penicillin g acylase biocatalyst in organic solvent and its impact on the synthesis of β-lactam antibiotics. Biotechnol Bioeng 2009; 103:472-9. [DOI: 10.1002/bit.22264] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
33
|
Serra I, Cecchini DA, Ubiali D, Manazza EM, Albertini AM, Terreni M. Coupling of Site-Directed Mutagenesis and Immobilization for the Rational Design of More Efficient Biocatalysts: The Case of Immobilized 3G3K PGA fromE.coli. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801204] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
34
|
Sonawane VC. Enzymatic Modifications of Cephalosporins by Cephalosporin Acylase and Other Enzymes. Crit Rev Biotechnol 2008; 26:95-120. [PMID: 16809100 DOI: 10.1080/07388550600718630] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Semisynthetic cephalosporins are important antibacterials in clinical practice. Semisynthetic cephalosporins are manufactured by derivatizing 7-aminocephalosporanic acid (7-ACA) and its desacetylated form. Microbial enzymes such as D-amino acid oxidase, glutaryl-7-ACA acylase and cephalosporin esterase are being used as biocatalysts for the conversion of cephalosporin C (CEPH-C) to 7-ACA and its desacetylated derivatives. Recent developments in the field of enzymatic modifications of cephalosporin with special emphasis on group of enzymes called as cephalosporin acylase is discussed in this review. Aspects related to screening methods, isolation and purification, immobilization, molecular cloning, gene structure and expression and protein engineering of cephalosporin acylases have been covered. Topics pertaining to enzymatic modifications of cephalosporin by D-amino acid oxidase, cephalosporin methoxylase and beta-lactamase are also covered.
Collapse
|
35
|
Kumar A, Prabhune A, Suresh C, Pundle A. Characterization of smallest active monomeric penicillin V acylase from new source: A yeast, Rhodotorula aurantiaca (NCIM 3425). Process Biochem 2008. [DOI: 10.1016/j.procbio.2008.04.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
36
|
|
37
|
López-Gallego F, Betancor L, Sio C, Reis C, Jimenez PN, Guisan J, Quax W, Fernandez-Lafuente R. Evaluation of Different Glutaryl Acylase Mutants to Improve the Hydolysis of Cephalosporin C in the Absence of Hydrogen Peroxide. Adv Synth Catal 2008. [DOI: 10.1002/adsc.200700320] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
38
|
Wang A, Wang H, Zhu S, Zhou C, Du Z, Shen S. An efficient immobilizing technique of penicillin acylase with combining mesocellular silica foams support and p-benzoquinone cross linker. Bioprocess Biosyst Eng 2008; 31:509-17. [DOI: 10.1007/s00449-007-0189-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Accepted: 12/13/2007] [Indexed: 11/30/2022]
|
39
|
WANG A, WANG H, ZHOU C, DU Z, ZHU S, SHEN S. Ag-induced Efficient Immobilization of Papain on Silica Spheres. Chin J Chem Eng 2008. [DOI: 10.1016/s1004-9541(08)60129-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
40
|
Cecchini DA, Serra I, Ubiali D, Terreni M, Albertini AM. New active site oriented glyoxyl-agarose derivatives of Escherichia coli penicillin G acylase. BMC Biotechnol 2007; 7:54. [PMID: 17845725 PMCID: PMC2045090 DOI: 10.1186/1472-6750-7-54] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 09/10/2007] [Indexed: 11/10/2022] Open
Abstract
Background Immobilized Penicillin G Acylase (PGA) derivatives are biocatalysts that are industrially used for the hydrolysis of Penicillin G by fermentation and for the kinetically controlled synthesis of semi-synthetic β-lactam antibiotics. One of the most used supports for immobilization is glyoxyl-activated agarose, which binds the protein by reacting through its superficial Lys residues. Since in E. coli PGA Lys are also present near the active site, an immobilization that occurs through these residues may negatively affect the performance of the biocatalyst due to the difficult diffusion of the substrate into the active site. A preferential orientation of the enzyme with the active site far from the support surface would be desirable to avoid this problem. Results Here we report how it is possible to induce a preferential orientation of the protein during the binding process on aldehyde activated supports. A superficial region of PGA, which is located on the opposite side of the active site, is enriched in its Lys content. The binding of the enzyme onto the support is consequently forced through the Lys rich region, thus leaving the active site fully accessible to the substrate. Different mutants with an increasing number of Lys have been designed and, when active, immobilized onto glyoxyl agarose. The synthetic performances of these new catalysts were compared with those of the immobilized wild-type (wt) PGA. Our results show that, while the synthetic performance of the wt PGA sensitively decreases after immobilization, the Lys enriched mutants have similar performances to the free enzyme even after immobilization. We also report the observations made with other mutants which were unable to undergo a successful maturation process for the production of active enzymes or which resulted toxic for the host cell. Conclusion The desired orientation of immobilized PGA with the active site freely accessible can be obtained by increasing the density of Lys residues on a predetermined region of the enzyme. The newly designed biocatalysts display improved synthetic performances and are able to maintain a similar activity to the free enzymes. Finally, we found that the activity of the immobilized enzyme proportionally improves with the number of introduced Lys.
Collapse
Affiliation(s)
- Davide A Cecchini
- Dipartimento di Genetica e Microbiologia, via Ferrata 1, Università degli Studi di Pavia, 27100 Pavia, Italy
| | - Immacolata Serra
- Dipartimento di Chimica Farmaceutica, Pharmaceutical Biocatalysis Laboratories, via Taramelli 12, Università degli Studi di Pavia, 27100 Pavia, Italy
| | - Daniela Ubiali
- Dipartimento di Chimica Farmaceutica, Pharmaceutical Biocatalysis Laboratories, via Taramelli 12, Università degli Studi di Pavia, 27100 Pavia, Italy
| | - Marco Terreni
- Dipartimento di Chimica Farmaceutica, Pharmaceutical Biocatalysis Laboratories, via Taramelli 12, Università degli Studi di Pavia, 27100 Pavia, Italy
| | - Alessandra M Albertini
- Dipartimento di Genetica e Microbiologia, via Ferrata 1, Università degli Studi di Pavia, 27100 Pavia, Italy
| |
Collapse
|
41
|
A tryptophan residue is identified in the substrate binding of penicillin G acylase from Kluyvera citrophila. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.10.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
42
|
Jager SA, Jekel PA, Janssen DB. Hybrid penicillin acylases with improved properties for synthesis of β-lactam antibiotics. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.10.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
43
|
Zhang D, Koreishi M, Imanaka H, Imamura K, Nakanishi K. Cloning and characterization of penicillin V acylase from Streptomyces mobaraensis. J Biotechnol 2007; 128:788-800. [PMID: 17289203 DOI: 10.1016/j.jbiotec.2006.12.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 12/14/2006] [Accepted: 12/22/2006] [Indexed: 11/24/2022]
Abstract
We report on the molecular cloning and characterization of penicillin V acylase (PVA) from an actinomycete, Streptomyces mobaraensis (Sm-PVA), which was originally isolated as an acylase that efficiently hydrolyzes the amide bond of various N-fatty-acyl-l-amino acids and N-fatty-acyl-peptides as well as capsaicin (8-methyl-N-vanillyl-6-nonenamide). In addition, the purified Sm-PVA hydrolyzed penicillin V with the highest activity (k(cat)) among the PVAs so far reported, penicillin G, and 2-nitro-5-phenoxyacetamide benzoic acid. The BLAST search revealed that the Sm-PVA precursor is composed of a polypeptide that is characteristic of enzymes belonging to the beta-lactam acylase family with four distinct segments; a signal sequence (43 amino acids), an alpha subunit (173 amino acids), a linker peptide (28 amino acids), and a beta subunit (570 amino acids). The mature, active Sm-PVA is a heterodimeric protein with alpha and beta subunits, in contrast to PVAs isolated from Bacillus sphaericus and B. subtilis, which have a homotetrameric structure. The amino acid sequence of Sm-PVA showed identities to PVA from S. lavendulae, N-acylhomoserine lactone-degrading acylase from Streptomyces sp., cyclic lipopeptide acylase from Streptomyces sp., and aculeacin A acylase from Actinoplanes utahensis with 68, 67, 67, and 41% identities, respectively.
Collapse
Affiliation(s)
- Demin Zhang
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, 3-1-1, Tsushima-Naka, Okayama 700-8530, Japan
| | | | | | | | | |
Collapse
|
44
|
Montes T, Grazú V, López-Gallego F, Hermoso JA, García JL, Manso I, Galán B, González R, Fernández-Lafuente R, Guisán JM. Genetic modification of the penicillin G acylase surface to improve its reversible immobilization on ionic exchangers. Appl Environ Microbiol 2007; 73:312-9. [PMID: 17098917 PMCID: PMC1797127 DOI: 10.1128/aem.02107-06] [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] [Received: 09/06/2006] [Accepted: 10/29/2006] [Indexed: 11/20/2022] Open
Abstract
A new mutant of the industrial enzyme penicillin G acylase (PGA) from Escherichia coli has been designed to improve its reversible immobilization on anionic exchangers (DEAE- or polyethyleneimine [PEI]-coated agarose) by assembling eight new glutamic residues distributed homogeneously through the enzyme surface via site-directed mutagenesis. The mutant PGA is produced and processed in vivo as is the native enzyme. Moreover, it has a similar specific activity to and shows the same pH activity profile as native PGA; however, its isoelectric point decreased from 6.4 to 4.3. Although the new enzyme is adsorbed on both supports, the adsorption was even stronger when supports were coated with PEI, allowing us to improve the enzyme stability in organic cosolvents. The use of restrictive conditions during the enzyme adsorption on anionic exchangers (pH 5 and high ionic strength) permitted us to still further increase the strength of adsorption and the enzyme stability in the presence of organic solvents, suggesting that these conditions allow the penetration of the enzyme inside the polymeric beds, thus becoming fully covered with the polymer. After the enzyme inactivation, it can be desorbed to reuse the support. The possibility to improve the immobilization properties on an enzyme by site-directed mutagenesis of its surface opens a promising new scenario for enzyme engineering.
Collapse
Affiliation(s)
- Tamara Montes
- Instituto de Catálisis, CSIC, Campus Universidad Autónoma, 28049 Madrid, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Montes T, Grazu V, López-Gallego F, Hermoso JA, Guisan JM, Fernandez-Lafuente R. Chemical Modification of Protein Surfaces To Improve Their Reversible Enzyme Immobilization on Ionic Exchangers. Biomacromolecules 2006; 7:3052-8. [PMID: 17096531 DOI: 10.1021/bm060527p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme penicillin G acylase (PGA) is not adsorbed at pH 7 on DEAE- or PEI-coated supports, neither is it adsorbed on carboxymethyl (CM)- or dextran sulfate (DS)-coated supports. The surface of the enzyme was chemically modified under controlled conditions: chemical amination of the protein surface of carboxylic groups (using soluble carbodiimide and ethylendiamine) and chemical succinylation (using succinic anhydride) of amino groups. The full chemical modification produced some negative effects on enzyme stability and activity, although partial modification (mainly succinylation) presented negligible effects on both enzyme features. The chemical amination of the protein surface permitted the immobilization of the enzyme on CM- and DS-coated support, while the chemical succinylation permitted the enzyme immobilization on DEAE- and PEI-coated supports. Immobilization was very strong on these supports, mainly in the polymeric ones, and dependent on the degree of modification, although the enzymes still can be desorbed after inactivation by incubation under drastic conditions. Moreover, the immobilization on ionic polymeric beds allowed a significant increase in enzyme stability against the inactivation and inhibitory effects of organic solvents, very likely by the promotion of a certain partition of the organic solvent out of the enzyme environment. These results suggest that the enrichment of the surface of proteins with ionic groups may be a good strategy to take advantage of the immobilization of industrial enzymes via ionic exchange on ionic polymeric beds.
Collapse
Affiliation(s)
- Tamara Montes
- Departamento de Biocatalisis, Instituto de Catalisis, CSIC, Campus Universidad Autonoma, Cantoblanco, 28049 Madrid, Spain
| | | | | | | | | | | |
Collapse
|
46
|
Sio CF, Otten LG, Cool RH, Diggle SP, Braun PG, Bos R, Daykin M, Cámara M, Williams P, Quax WJ. Quorum quenching by an N-acyl-homoserine lactone acylase from Pseudomonas aeruginosa PAO1. Infect Immun 2006; 74:1673-82. [PMID: 16495538 PMCID: PMC1418629 DOI: 10.1128/iai.74.3.1673-1682.2006] [Citation(s) in RCA: 217] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The virulence of the opportunistic human pathogen Pseudomonas aeruginosa PAO1 is controlled by an N-acyl-homoserine lactone (AHL)-dependent quorum-sensing system. During functional analysis of putative acylase genes in the P. aeruginosa PAO1 genome, the PA2385 gene was found to encode an acylase that removes the fatty acid side chain from the homoserine lactone (HSL) nucleus of AHL-dependent quorum-sensing signal molecules. Analysis showed that the posttranslational processing of the acylase and the hydrolysis reaction type are similar to those of the beta-lactam acylases, strongly suggesting that the PA2385 protein is a member of the N-terminal nucleophile hydrolase superfamily. In a bioassay, the purified acylase was shown to degrade AHLs with side chains ranging in length from 11 to 14 carbons at physiologically relevant low concentrations. The substituent at the 3' position of the side chain did not affect activity, indicating broad-range AHL quorum-quenching activity. Of the two main AHL signal molecules of P. aeruginosa PAO1, N-butanoyl-l-homoserine lactone (C4-HSL) and N-(3-oxododecanoyl)-l-homoserine lactone (3-oxo-C12-HSL), only 3-oxo-C12-HSL is degraded by the enzyme. Addition of the purified protein to P. aeruginosa PAO1 cultures completely inhibited accumulation of 3-oxo-C12-HSL and production of the signal molecule 2-heptyl-3-hydroxy-4(1H)-quinolone and reduced production of the virulence factors elastase and pyocyanin. Similar results were obtained when the PA2385 gene was overexpressed in P. aeruginosa. These results demonstrate that the protein has in situ quorum-quenching activity. The quorum-quenching AHL acylase may enable P. aeruginosa PAO1 to modulate its own quorum-sensing-dependent pathogenic potential and, moreover, offers possibilities for novel antipseudomonal therapies.
Collapse
Affiliation(s)
- Charles F Sio
- Pharmaceutical Biology, University Centre for Pharmacy, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Glyoxyl agarose: A fully inert and hydrophilic support for immobilization and high stabilization of proteins. Enzyme Microb Technol 2006. [DOI: 10.1016/j.enzmictec.2005.10.014] [Citation(s) in RCA: 316] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
48
|
Liljeblad A, Kanerva LT. Biocatalysis as a profound tool in the preparation of highly enantiopure β-amino acids. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.03.109] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
49
|
Polizzi KM, Chaparro-Riggers JF, Vazquez-Figueroa E, Bommarius AS. Structure-guided consensus approach to create a more thermostable penicillin G acylase. Biotechnol J 2006; 1:531-6. [PMID: 16892288 DOI: 10.1002/biot.200600029] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The thermostabilization of penicillin G acylase (PGA) is a difficult problem due to the large size of the protein and its complex maturation process. We developed a data-driven protein design method that requires fewer homologous sequences than the traditional consensus approach and utilizes structural information to limit the number of variants created. Approximately 50% of our 21 single-point mutants were found experimentally to be more thermostable than the wild-type PGA, two had almost threefold longer half-life at 50 degrees C, with very little effect on activity. An analysis of four programs that predict the thermostability conferred by point mutations shows little agreement between the programs and with the experimental data, emphasizing that the chosen stabilizing mutations are very difficult to predict, but that our data-driven design method should prove useful.
Collapse
Affiliation(s)
- Karen M Polizzi
- School of Chemical & Biomolecular Engineering, Parker H. Petit Institute of Bioengineering and Bioscience, Atlanta, GA 30332-0363, USA
| | | | | | | |
Collapse
|
50
|
Senerovic L, Stankovic N, Spizzo P, Basso A, Gardossi L, Vasiljevic B, Ljubijankic G, Tisminetzky S, Degrassi G. High-level production and covalent immobilization ofProvidencia rettgeri penicillin G acylase (PAC) from recombinantPichia pastoris for the development of a novel and stable biocatalyst of industrial applicability. Biotechnol Bioeng 2006; 93:344-54. [PMID: 16259000 DOI: 10.1002/bit.20728] [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: 11/07/2022]
Abstract
A complete, integrated process for the production of an innovative formulation of penicillin G acylase from Providencia rettgeri(rPAC(P.rett))of industrial applicability is reported. In order to improve the yield of rPAC, the clone LN5.5, carrying four copies of pac gene integrated into the genome of Pichia pastoris, was constructed. The proteinase activity of the recombinant strain was reduced by knockout of the PEP4 gene encoding for proteinase A, resulting in an increased rPAC(P.rett) activity of approximately 40% (3.8 U/mL vs. 2.7 U/mL produced by LN5.5 in flask). A high cell density fermentation process was established with a 5-day methanol induction phase and a final PAC activity of up to 27 U/mL. A single step rPAC(P.rett) purification was also developed with an enzyme activity yield of approximately 95%. The novel features of the rPAC(P.rett) expressed in P.pastoris were fully exploited and emphasized through the covalent immobilization of rPAC(P.rett). The enzyme was immobilized on a series of structurally correlated methacrylic polymers, specifically designed and produced for optimizing rPAC(P.rett) performances in both hydrolytic and synthetic processes. Polymers presenting aminic functionalities were the most efficient, leading to formulations with higher activity and stability (half time stability >3 years and specific activity ranging from 237 to 477 U/g (dry) based on benzylpenicillin hydrolysis). The efficiency of the immobilized rPAC(P.rett) was finally evaluated by studying the kinetically controlled synthesis of beta-lactam antibiotics (cephalexin) and estimating the synthesis/hydrolysis ratio (S/H), which is a crucial parameter for the feasibility of the process.
Collapse
Affiliation(s)
- Lidija Senerovic
- Institute of Molecular Genetics and Genetic Engineering, Vojvode Stepe 444a, Belgrade, Serbia and Montenegro
| | | | | | | | | | | | | | | | | |
Collapse
|