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Zhao X, Cebrián R, Fu Y, Rink R, Bosma T, Moll GN, Kuipers OP. High-Throughput Screening for Substrate Specificity-Adapted Mutants of the Nisin Dehydratase NisB. ACS Synth Biol 2020; 9:1468-1478. [PMID: 32374981 PMCID: PMC7309312 DOI: 10.1021/acssynbio.0c00130] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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Microbial
lanthipeptides are formed by a two-step enzymatic introduction
of (methyl)lanthionine rings. A dehydratase catalyzes the dehydration
of serine and threonine residues, yielding dehydroalanine and dehydrobutyrine,
respectively. Cyclase-catalyzed coupling of the formed dehydroresidues
to cysteines forms (methyl)lanthionine rings in a peptide. Lanthipeptide
biosynthetic systems allow discovery of target-specific, lanthionine-stabilized
therapeutic peptides. However, the substrate specificity of existing
modification enzymes impose limitations on installing lanthionines
in non-natural substrates. The goal of the present study was to obtain
a lanthipeptide dehydratase with the capacity to dehydrate substrates
that are unsuitable for the nisin dehydratase NisB. We report high-throughput
screening for tailored specificity of intracellular, genetically encoded
NisB dehydratases. The principle is based on the screening of bacterially
displayed lanthionine-constrained streptavidin ligands, which have
a much higher affinity for streptavidin than linear ligands. The designed
NisC-cyclizable high-affinity ligands can be formed via mutant NisB-catalyzed
dehydration but less effectively via wild-type NisB activity. In Lactococcus lactis, a cell surface display precursor was
designed comprising DSHPQFC. The Asp residue preceding the serine
in this sequence disfavors its dehydration by wild-type NisB. The
cell surface display vector was coexpressed with a mutant NisB library
and NisTC. Subsequently, mutant NisB-containing bacteria that display
cyclized strep ligands on the cell surface were selected via panning
rounds with streptavidin-coupled magnetic beads. In this way, a NisB
variant with a tailored capacity of dehydration was obtained, which
was further evaluated with respect to its capacity to dehydrate nisin
mutants. These results demonstrate a powerful method for selecting
lanthipeptide modification enzymes with adapted substrate specificity.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Yuxin Fu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Rick Rink
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Tjibbe Bosma
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Gert N. Moll
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
- Lanthio Pharma, Rozenburglaan 13 B, Groningen 9727 DL, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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2
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Abstract
Many therapeutic peptides can still be improved with respect to target specificity, target affinity, resistance to peptidases/proteases, physical stability, and capacity to pass through membranes required for oral delivery. Several modifications can improve the peptides' properties, in particular those that impose (a) conformational constraint(s). Screening of constrained peptides and the identification of hits is greatly facilitated by the generation of genetically encoded libraries. Recent breakthrough bacterial, phage, and yeast display screening systems of ribosomally synthesized post-translationally constrained peptides, particularly those of lanthipeptides, are earning special attention. Here we provide an overview of display systems for constrained, genetically encoded peptides and indicate prospects of constrained peptide-displaying phage and bacterial systems as such in vivo.
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Affiliation(s)
- Tjibbe Bosma
- Lanthio Pharma, a MorphoSys AG Company, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands
| | - Rick Rink
- Lanthio Pharma, a MorphoSys AG Company, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands
| | | | - Gert N Moll
- Lanthio Pharma, a MorphoSys AG Company, Rozenburglaan 13B, 9727 DL, Groningen, The Netherlands.,Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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3
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Kuipers A, de Vries L, de Vries MP, Rink R, Bosma T, Moll GN. Semi-microbiological synthesis of an active lysinoalanine-bridged analog of glucagon-like-peptide-1. Peptides 2017; 91:33-39. [PMID: 28300673 DOI: 10.1016/j.peptides.2017.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 03/03/2017] [Accepted: 03/07/2017] [Indexed: 10/20/2022]
Abstract
Some modified glucagon-like-peptide-1 (GLP-1) analogs are highly important for treating type 2 diabetes. Here we investigated whether GLP-1 analogs expressed in Lactococcus lactis could be substrates for modification and export by the nisin dehydratase and transporter enzyme. Subsequently we introduced a lysinoalanine by coupling a formed dehydroalanine with a lysine and investigated the structure and activity of the formed lysinoalanine-bridged GLP-1 analog. Our data show: (i) GLP-1 fused to the nisin leader peptide is very well exported via the nisin transporter NisT, (ii) production of leader-GLP-1 via NisT is higher than via the SEC system, (iii) leader-GLP-1 exported via NisT was more efficiently dehydrated by the nisin dehydratase NisB than when exported via the SEC system, (iv) individual serines and threonines in GLP-1 are dehydrated by NisB to a significantly different extent, (v) an introduced Ser30 is well dehydrated and can be coupled to Lys34 to form a lysinoalanine-bridged GLP-1 analog, (vi) a lysinoalanine(30-34) variant's conformation shifts in the presence of 25% trifluoroethanol towards a higher alpha helix content than observed for wild type GLP-1 under identical condition, (vii) a lysinoalanine(30-34) GLP-1 variant has retained significant activity. Taken together the data extend knowledge on the substrate specificities of NisT and NisB and their combined activity relative to export via the Sec system, and demonstrate that introducing a lysinoalanine bridge is an option for modifying therapeutic peptides.
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Affiliation(s)
- Anneke Kuipers
- Lanthio Pharma, a MorphoSys AG company, 9727 DL Groningen, The Netherlands
| | - Louwe de Vries
- Lanthio Pharma, a MorphoSys AG company, 9727 DL Groningen, The Netherlands
| | - Marcel P de Vries
- Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands; Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Rick Rink
- Lanthio Pharma, a MorphoSys AG company, 9727 DL Groningen, The Netherlands
| | - Tjibbe Bosma
- Lanthio Pharma, a MorphoSys AG company, 9727 DL Groningen, The Netherlands
| | - Gert N Moll
- Lanthio Pharma, a MorphoSys AG company, 9727 DL Groningen, The Netherlands; Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands.
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4
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van den Berg S, Bonarius HPJ, van Kessel KPM, Elsinga GS, Kooi N, Westra H, Bosma T, van der Kooi-Pol MM, Koedijk DGAM, Groen H, van Dijl JM, Buist G, Bakker-Woudenberg IAJM. A human monoclonal antibody targeting the conserved staphylococcal antigen IsaA protects mice against Staphylococcus aureus bacteremia. Int J Med Microbiol 2014; 305:55-64. [PMID: 25466204 DOI: 10.1016/j.ijmm.2014.11.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 10/29/2014] [Accepted: 11/04/2014] [Indexed: 10/24/2022] Open
Abstract
Due to substantial therapy failure and the emergence of antibiotic-resistant Staphylococcus aureus strains, alternatives for antibiotic treatment of S. aureus infections are urgently needed. Passive immunization using S. aureus-specific monoclonal antibodies (mAb) could be such an alternative to prevent and treat severe S. aureus infections. The invariantly expressed immunodominant staphylococcal antigen A (IsaA) is a promising target for passive immunization. Here we report the development of the human anti-IsaA IgG1 mAb 1D9, which was shown to bind to all 26 S. aureus isolates tested. These included both methicillin-susceptible and methicillin-resistant S. aureus (MSSA and MRSA, respectively). Immune complexes consisting of IsaA and 1D9 stimulated human as well as murine neutrophils to generate an oxidative burst. In a murine bacteremia model, the prophylactic treatment with a single dose of 5 mg/kg 1D9 improved the survival of mice challenged with S. aureus isolate P (MSSA) significantly, while therapeutic treatment with the same dose did not influence animal survival. Neither prophylactic nor therapeutic treatment with 5 mg/kg 1D9 resulted in improved survival of mice with S. aureus USA300 (MRSA) bacteremia. Importantly, our studies show that healthy S. aureus carriers elicit an immune response which is sufficient to generate protective mAbs against invariant staphylococcal surface antigens. Human mAb 1D9, possibly conjugated to for example another antibody, antibiotics, cytokines or chemokines, may be valuable to fight S. aureus infections in patients.
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Affiliation(s)
- Sanne van den Berg
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | | | - Kok P M van Kessel
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | | | - Magdalena M van der Kooi-Pol
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Danny G A M Koedijk
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Girbe Buist
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Irma A J M Bakker-Woudenberg
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
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5
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van den Berg S, Bowden MG, Bosma T, Buist G, van Dijl JM, van Wamel WJ, de Vogel CP, van Belkum A, Bakker-Woudenberg IAJM. A multiplex assay for the quantification of antibody responses in Staphylococcus aureus infections in mice. J Immunol Methods 2010; 365:142-8. [PMID: 21185300 DOI: 10.1016/j.jim.2010.12.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 11/06/2010] [Accepted: 12/15/2010] [Indexed: 01/16/2023]
Abstract
Staphylococcus aureus causes a variety of infections. Knowledge about the physiological role of most S. aureus antigens in colonization and infection is only limited. This can be studied by measuring antigen-specific antibody responses. In this study, we optimized the multiplex microsphere bead-based flow cytometry technique for mouse serum samples. We analysed immunoglobulin G (IgG) levels directed against 26 S. aureus proteins in a single small-volume mouse serum sample. We assessed possible cross reactivity. Furthermore, we analysed serum samples from mice with different types of S. aureus infections caused by different S. aureus strains. The results show that cross reactivity between proteins on microspheres and serum antibodies towards other proteins was limited. We found that lung-infected mice had a higher and broader IgG response than skin-infected mice. Clearly, the site of infection influences the IgG profile. Next, we compared sera from mice with intravenously-induced bacteraemia caused by different S. aureus strains. We showed different IgG responses depending on the causing S. aureus strain. It is concluded that the bead-based multiplex S. aureus antibody assay can be successfully applied to determine the immunogenicity of different S. aureus proteins in relation to the site of infection and the S. aureus strain causing the infection.
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Affiliation(s)
- Sanne van den Berg
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, 3015 CE Rotterdam, The Netherlands.
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Moll G, Kuipers A, de Vries L, Bosma T, Rink R. A biological stabilization technology for peptide drugs: enzymatic introduction of thioether-bridges. Drug Discov Today Technol 2009; 6:e1-e40. [PMID: 24128987 DOI: 10.1016/j.ddtec.2009.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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van Roosmalen ML, Kanninga R, El Khattabi M, Neef J, Audouy S, Bosma T, Kuipers A, Post E, Steen A, Kok J, Buist G, Kuipers OP, Robillard G, Leenhouts K. Mucosal vaccine delivery of antigens tightly bound to an adjuvant particle made from food-grade bacteria. Methods 2006; 38:144-9. [PMID: 16414272 DOI: 10.1016/j.ymeth.2005.09.015] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Accepted: 09/22/2005] [Indexed: 10/25/2022] Open
Abstract
Mucosal immunization with subunit vaccines requires new types of antigen delivery vehicles and adjuvants for optimal immune responses. We have developed a non-living and non-genetically modified gram-positive bacterial delivery particle (GEM) that has built-in adjuvant activity and a high loading capacity for externally added heterologous antigens that are fused to a high affinity binding domain. This binding domain, the protein anchor (PA), is derived from the Lactococcus lactis AcmA cell-wall hydrolase, and contains three repeats of a LysM-type cell-wall binding motif. Antigens are produced as antigen-PA fusions by recombinant expression systems that secrete the hybrid proteins into the culture growth medium. GEM particles are then used as affinity beads to isolate the antigen-PA fusions from the complex growth media in a one step procedure after removal of the recombinant producer cells. This procedure is also highly suitable for making multivalent vaccines. The resulting vaccines are stable at room temperature, lack recombinant DNA, and mimic pathogens by their bacterial size, surface display of antigens and adjuvant activity of the bacterial components in the GEM particles. The GEM-based vaccines do not require additional adjuvant for eliciting high levels of specific antibodies in mucosal and systemic compartments.
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Bosma T, Kanninga R, Neef J, Audouy SAL, van Roosmalen ML, Steen A, Buist G, Kok J, Kuipers OP, Robillard G, Leenhouts K. Novel surface display system for proteins on non-genetically modified gram-positive bacteria. Appl Environ Microbiol 2006; 72:880-9. [PMID: 16391130 PMCID: PMC1352190 DOI: 10.1128/aem.72.1.880-889.2006] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel display system is described that allows highly efficient immobilization of heterologous proteins on bacterial surfaces in applications for which the use of genetically modified bacteria is less desirable. This system is based on nonliving and non-genetically modified gram-positive bacterial cells, designated gram-positive enhancer matrix (GEM) particles, which are used as substrates to bind externally added heterologous proteins by means of a high-affinity binding domain. This binding domain, the protein anchor (PA), was derived from the Lactococcus lactis peptidoglycan hydrolase AcmA. GEM particles were typically prepared from the innocuous bacterium L. lactis, and various parameters for the optimal preparation of GEM particles and binding of PA fusion proteins were determined. The versatility and flexibility of the display and delivery technology were demonstrated by investigating enzyme immobilization and nasal vaccine applications.
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Affiliation(s)
- Tjibbe Bosma
- BiOMaDe Technology, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Bosma T, Pikkemaat MG, Kingma J, Dijk J, Janssen DB. Steady-state and pre-steady-state kinetic analysis of halopropane conversion by a rhodococcus haloalkane dehalogenase. Biochemistry 2003; 42:8047-53. [PMID: 12834356 DOI: 10.1021/bi026907m] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Haloalkane dehalogenase from Rhodococcus rhodochrous NCIMB 13064 (DhaA) catalyzes the hydrolysis of carbon-halogen bonds in a wide range of haloalkanes. We examined the steady-state and pre-steady-state kinetics of halopropane conversion by DhaA to illuminate mechanistic details of the dehalogenation pathway. Steady-state kinetic analysis of DhaA with a range of halopropanes showed that bromopropanes had higher k(cat) and lower K(M) values than the chlorinated analogues. The kinetic mechanism of dehalogenation was further studied using rapid-quench-flow analysis of 1,3-dibromopropane conversion. This provided a direct measurement of the chemical steps in the reaction mechanism, i.e., cleavage of the carbon-halogen bond and hydrolysis of the covalent alkyl-enzyme intermediate. The results lead to a minimal mechanism consisting of four main steps. The occurrence of a pre-steady-state burst, both for bromide and 3-bromo-1-propanol, suggests that product release is rate-limiting under steady-state conditions. Combining pre-steady-state burst and single-turnover experiments indicated that the rate of carbon-bromine bond cleavage was indeed more than 100-fold higher than the steady-state k(cat). Product release occurred with a rate constant of 3.9 s(-1), a value close to the experimental k(cat) of 2.7 s(-1). Comparing the kinetic mechanism of DhaA with that of the corresponding enzyme from Xanthobacter autotrophicus GJ10 (DhlA) shows that the overall mechanisms are similar. However, whereas in DhlA the rate of halide release represents the slowest step in the catalytic cycle, our results suggest that in DhaA the release of 3-bromo-1-propanol is the slowest step during 1,3-dibromopropane conversion.
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Affiliation(s)
- Tjibbe Bosma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Egelhaaf SU, van Swieten E, Bosma T, de Boef E, van Dijk AA, Robillard GT. Size and shape of the repetitive domain of high molecular weight wheat gluten proteins. I. Small-angle neutron scattering. Biopolymers 2003; 69:311-24. [PMID: 12833258 DOI: 10.1002/bip.10370] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The solution structure of the central repetitive domain of high molecular weight (HMW) wheat gluten proteins has been investigated for a range of concentrations and temperatures using mainly small-angle neutron scattering. A representative part of the repetitive domain (dB1) was studied as well as an "oligomer" basically consisting of four dB1 units, which has a length similar to the complete central domain. The scattering data over the entire angular range of both proteins are in quantitative agreement with a structural model based on a worm-like chain, a model frequently used in polymer theory. This model describes the "supersecondary structure" of dB1 and dB4 as a semiflexible cylinder with a length of about 235 and 900 A, respectively, and a cross-sectional diameter of about 15 A. The flexibility of both proteins is characterized by a persistence length of about 13 A. Their structures are thus quantitatively identical, which implies that the central HMW domain can be elongated while retaining its structural characteristics. It seems conceivable that the flexible cylinder results from a helical structure, which resembles the beta-spiral observed in earlier studies on gluten proteins and elastin. However, compared to the previously proposed structure of a (stiff) rod, our experiments clearly indicate flexibility of the cylinder.
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Affiliation(s)
- Stefan U Egelhaaf
- University of Edinburgh, Department of Physics and Astronomy, James Clerk Maxwell Building, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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Bosma T, Damborský J, Stucki G, Janssen DB. Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene. Appl Environ Microbiol 2002; 68:3582-7. [PMID: 12089046 PMCID: PMC126774 DOI: 10.1128/aem.68.7.3582-3587.2002] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2002] [Accepted: 04/24/2002] [Indexed: 11/20/2022] Open
Abstract
Using a combined strategy of random mutagenesis of haloalkane dehalogenase and genetic engineering of a chloropropanol-utilizing bacterium, we constructed an organism that is capable of growth on 1,2,3-trichloropropane (TCP). This highly toxic and recalcitrant compound is a waste product generated from the manufacture of the industrial chemical epichlorohydrin. Attempts to select and enrich bacterial cultures that can degrade TCP from environmental samples have repeatedly been unsuccessful, prohibiting the development of a biological process for groundwater treatment. The critical step in the aerobic degradation of TCP is the initial dehalogenation to 2,3-dichloro-1-propanol. We used random mutagenesis and screening on eosin-methylene blue agar plates to improve the activity on TCP of the haloalkane dehalogenase from Rhodococcus sp. m15-3 (DhaA). A second-generation mutant containing two amino acid substitutions, Cys176Tyr and Tyr273Phe, was nearly eight times more efficient in dehalogenating TCP than wild-type dehalogenase. Molecular modeling of the mutant dehalogenase indicated that the Cys176Tyr mutation has a global effect on the active-site structure, allowing a more productive binding of TCP within the active site, which was further fine tuned by Tyr273Phe. The evolved haloalkane dehalogenase was expressed under control of a constitutive promoter in the 2,3-dichloro-1-propanol-utilizing bacterium Agrobacterium radiobacter AD1, and the resulting strain was able to utilize TCP as the sole carbon and energy source. These results demonstrated that directed evolution of a key catabolic enzyme and its subsequent recruitment by a suitable host organism can be used for the construction of bacteria for the degradation of a toxic and environmentally recalcitrant chemical.
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Affiliation(s)
- Tjibbe Bosma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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12
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van Hylckama Vlieg JE, Tang L, Lutje Spelberg JH, Smilda T, Poelarends GJ, Bosma T, van Merode AE, Fraaije MW, Janssen DB. Halohydrin dehalogenases are structurally and mechanistically related to short-chain dehydrogenases/reductases. J Bacteriol 2001; 183:5058-66. [PMID: 11489858 PMCID: PMC95381 DOI: 10.1128/jb.183.17.5058-5066.2001] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halohydrin dehalogenases, also known as haloalcohol dehalogenases or halohydrin hydrogen-halide lyases, catalyze the nucleophilic displacement of a halogen by a vicinal hydroxyl function in halohydrins to yield epoxides. Three novel bacterial genes encoding halohydrin dehalogenases were cloned and expressed in Escherichia coli, and the enzymes were shown to display remarkable differences in substrate specificity. The halohydrin dehalogenase of Agrobacterium radiobacter strain AD1, designated HheC, was purified to homogeneity. The k(cat) and K(m) values of this 28-kDa protein with 1,3-dichloro-2-propanol were 37 s(-1) and 0.010 mM, respectively. A sequence homology search as well as secondary and tertiary structure predictions indicated that the halohydrin dehalogenases are structurally similar to proteins belonging to the family of short-chain dehydrogenases/reductases (SDRs). Moreover, catalytically important serine and tyrosine residues that are highly conserved in the SDR family are also present in HheC and other halohydrin dehalogenases. The third essential catalytic residue in the SDR family, a lysine, is replaced by an arginine in halohydrin dehalogenases. A site-directed mutagenesis study, with HheC as a model enzyme, supports a mechanism for halohydrin dehalogenases in which the conserved Tyr145 acts as a catalytic base and Ser132 is involved in substrate binding. The primary role of Arg149 may be lowering of the pK(a) of Tyr145, which abstracts a proton from the substrate hydroxyl group to increase its nucleophilicity for displacement of the neighboring halide. The proposed mechanism is fundamentally different from that of the well-studied hydrolytic dehalogenases, since it does not involve a covalent enzyme-substrate intermediate.
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Affiliation(s)
- J E van Hylckama Vlieg
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, NL-9747 AG Groningen, The Netherlands
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Lu XX, Tao S, Bosma T, Gerritse J. Characteristic hydrogen concentrations for various redox processes in batch study. J Environ Sci Health A Tox Hazard Subst Environ Eng 2001; 36:1725-1734. [PMID: 11688686 DOI: 10.1081/ese-100106254] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The dissolved hydrogen concentrations under various redox processes were investigated based on batch experiments. Chloroethenes including tetrachloroethene (PCE), cis-dichloroethene (cis-DCE) and vinylchloride (VC) were respectively used as culture substrates. For each chloroethene, a series of bottles were prepared with the additions of different electron acceptors or donors such as nitrate, manganese oxide, ferrous iron, sulfate, carbondioxide and volatile fatty acids. Hydrogen concentrations as well as redox species were measured over time to ensure the achievements of characteristic hydrogen levels in various enrichment batches. The results showed that redox processes with nitrate, manganese oxide and ferric iron as the electron acceptors exhibited hydrogen threshold values close to PCE/TCE dechlorination, whereas cis-DCE and VC dechlorinations exhibited hydrogen threshold values in the range of sulfate reduction and methanogenesis, respectively. Characteristic hydrogen concentrations for various redox processes were as follows (nM): denitrification, 0.1-0.4; manganese reduction, 0.1-2.0; iron reduction, 0.1-0.4; sulfate reduction, 1.5-4.5; methanogenesis, 2.5-24; PCE/TCE dechlorination, 0.6-0.9; eis-DCE dechlorination, 0.1-2.5; and VC dechlorination, 2-24.
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Affiliation(s)
- X X Lu
- Peking University, Beijing, PR China.
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14
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Poelarends GJ, Zandstra M, Bosma T, Kulakov LA, Larkin MJ, Marchesi JR, Weightman AJ, Janssen DB. Haloalkane-utilizing Rhodococcus strains isolated from geographically distinct locations possess a highly conserved gene cluster encoding haloalkane catabolism. J Bacteriol 2000; 182:2725-31. [PMID: 10781539 PMCID: PMC101978 DOI: 10.1128/jb.182.10.2725-2731.2000] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sequences of the 16S rRNA and haloalkane dehalogenase (dhaA) genes of five gram-positive haloalkane-utilizing bacteria isolated from contaminated sites in Europe, Japan, and the United States and of the archetypal haloalkane-degrading bacterium Rhodococcus sp. strain NCIMB13064 were compared. The 16S rRNA gene sequences showed less than 1% sequence divergence, and all haloalkane degraders clearly belonged to the genus Rhodococcus. All strains shared a completely conserved dhaA gene, suggesting that the dhaA genes were recently derived from a common ancestor. The genetic organization of the dhaA gene region in each of the haloalkane degraders was examined by hybridization analysis and DNA sequencing. Three different groups could be defined on the basis of the extent of the conserved dhaA segment. The minimal structure present in all strains consisted of a conserved region of 12.5 kb, which included the haloalkane-degradative gene cluster that was previously found in strain NCIMB13064. Plasmids of different sizes were found in all strains. Southern hybridization analysis with a dhaA gene probe suggested that all haloalkane degraders carry the dhaA gene region both on the chromosome and on a plasmid (70 to 100 kb). This suggests that an ancestral plasmid was transferred between these Rhodococcus strains and subsequently has undergone insertions or deletions. In addition, transposition events and/or plasmid integration may be responsible for positioning the dhaA gene region on the chromosome. The data suggest that the haloalkane dehalogenase gene regions of these gram-positive haloalkane-utilizing bacteria are composed of a single catabolic gene cluster that was recently distributed worldwide.
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Affiliation(s)
- G J Poelarends
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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Bosma T, Kruizinga E, de Bruin EJ, Poelarends GJ, Janssen DB. Utilization of trihalogenated propanes by Agrobacterium radiobacter AD1 through heterologous expression of the haloalkane dehalogenase from Rhodococcus sp. strain M15-3. Appl Environ Microbiol 1999; 65:4575-81. [PMID: 10508091 PMCID: PMC91609 DOI: 10.1128/aem.65.10.4575-4581.1999] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/1999] [Accepted: 07/30/1999] [Indexed: 11/20/2022] Open
Abstract
Trihalogenated propanes are toxic and recalcitrant organic compounds. Attempts to obtain pure bacterial cultures able to use these compounds as sole carbon and energy sources were unsuccessful. Both the haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 (DhlA) and that from Rhodococcus sp. strain m15-3 (DhaA) were found to dehalogenate trihalopropanes to 2,3-dihalogenated propanols, but the kinetic properties of the latter enzyme are much better. Broad-host-range dehalogenase expression plasmids, based on RSF1010 derivatives, were constructed with the haloalkane dehalogenase from Rhodococcus sp. strain m15-3 under the control of the heterologous promoters P(lac), P(dhlA), and P(trc). The resulting plasmids yielded functional expression in several gram-negative bacteria. A catabolic pathway for trihalopropanes was designed by introducing these broad-host-range dehalogenase expression plasmids into Agrobacterium radiobacter AD1, which has the ability to utilize dihalogenated propanols for growth. The recombinant strain AD1(pTB3), expressing the haloalkane dehalogenase gene under the control of the dhlA promoter, was able to utilize both 1,2,3-tribromopropane and 1,2-dibromo-3-chloropropane as sole carbon sources. Moreover, increased expression of the haloalkane dehalogenase resulted in elevated resistance to trihalopropanes.
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Affiliation(s)
- T Bosma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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Lutje Spelberg JH, van Hylckama Vlieg JE, Bosma T, Kellogg RM, Janssen DB. A tandem enzyme reaction to produce optically active halohydrins, epoxides and diols. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0957-4166(99)00308-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Johnstone P, Whitby JE, Bosma T, Best JM, Sanders PG. Sequence variation in 5' termini of rubella virus genomes: changes affecting structure of the 5' proximal stem-loop. Arch Virol 1998; 141:2471-7. [PMID: 9526551 DOI: 10.1007/bf01718645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Variation within a 523 nucleotide region proximal to the 5' terminus of seven rubella virus strains has been analysed. Compared to the Therien strain twenty sites of nucleotide variation have been identified, three of which are in the 5' untranslated region. Individual strains have between three and nine nucleotide differences, only three of which result in amino acid substitutions. TO-336 has a serine for threonine at amino acid (aa) 42 and CM arginine for histidine at aa 159. RA27/3 has arginine for lysine at aa 3 and serine for threonine at aa 42. Nucleotide differences which affect a stem-loop structure reported to be important for binding of host cell proteins have been identified.
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Affiliation(s)
- P Johnstone
- Molecular Microbiology Group, School of Biological Sciences, University of Surrey, Guildford, U.K
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Elferink MG, Bosma T, Lolkema JS, Gleiszner M, Driessen AJ, Konings WN. Thermostability of respiratory terminal oxidases in the lipid environment. Biochim Biophys Acta 1995; 1230:31-7. [PMID: 7612641 DOI: 10.1016/0005-2728(95)00028-h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The effect of the lipid environment on the thermostability of three respiratory terminal oxidases was determined. Cytochrome-c oxidase from beef heart and Bacillus stearothermophilus were used as representative proteins from mesophilic and thermophilic origin, respectively. Quinol oxidase from the archaeon Sulfolobus acidocaldarius represented the model for a extreme thermoacidophilic enzyme. All three integral membrane proteins were tested for their thermal inactivation in detergent and after reconstitution in liposomes composed of phospholipids of Escherichia coli or tetraether lipids from S. acidocaldarius. When preincubated at 0 degrees C, all three enzymes exhibited biphasic thermal inactivation curves. Data could be analysed according to a two-state model that defines two conformations of the enzyme, differing in their thermostability. Monophasic inactivation curves were observed when the enzymes were preincubated at higher temperatures prior to thermal inactivation. Lipids rendered the beef-heart cytochrome-c oxidase and S. acidocaldarius quinol oxidase more thermostable as compared to detergent solution. In contrast, the B. stearothermophilus oxidase, an intrinsically thermostable enzyme, was as thermostable in detergent as in the reconstituted state. These data suggest that the lipid environment can be an important factor in the thermostability of membrane proteins.
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Affiliation(s)
- M G Elferink
- Department of Microbiology, University of Groningen, Haren, The Netherlands
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Tashjian AH, Voelkel EF, Lazzaro M, Goad D, Bosma T, Levine L. Tumor necrosis factor-alpha (cachectin) stimulates bone resorption in mouse calvaria via a prostaglandin-mediated mechanism. Endocrinology 1987; 120:2029-36. [PMID: 3106013 DOI: 10.1210/endo-120-5-2029] [Citation(s) in RCA: 178] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Recombinant human (h) and murine (m) tumor necrosis factor (TNF)-alpha stimulated bone resorption and the production of prostaglandin (PG) E2 in neonatal mouse calvaria in organ culture. In experiments of 72-h duration, the effect on bone resorption was of large magnitude (an average increase in medium calcium of 3.3 mg/dl above control values in 11 separate experiments) and occurred over a concentration range of 0.1-20 ng/ml mTNF and 0.5-50 ng/ml hTNF. Accompanying the TNF-enhanced release of bone calcium there was enhanced accumulation of PGE2 in the culture medium. The increases in medium calcium and PGE2 were both inhibited completely by nontoxic concentrations of 4 different PG cyclooxygenase inhibitors (indomethacin, piroxicam, ibuprofen, and acetylsalicylic acid) but not by the noncyclooxygenase inhibitor salicylic acid. The magnitude of the PGE2 response, but not the calcium release, was less for bones treated with TNF than for those treated with equipotent doses of epidermal growth factor or human transforming growth factors-alpha or -beta, suggesting that the local site of production of PGE2 in bone may be different for TNF than for the other factors. Repeated sc injections of hTNF to intact mice for a 48-h period produced a statistically significant elevation of the plasma calcium concentration. Because TNF is produced by cells of the monocyte/macrophage lineage in response to invasive stimuli such as the presence of tumor, our findings indicate that a host factor produced in response to malignant cells can cause enhanced bone resorption. Thus, the concept of the humoral hypercalcemias of malignancy must be expanded to include mediators not produced by the tumor cells themselves.
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