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Thornbury M, Sicheri J, Slaine P, Getz LJ, Finlayson-Trick E, Cook J, Guinard C, Boudreau N, Jakeman D, Rohde J, McCormick C. Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics. PLoS One 2019; 14:e0209221. [PMID: 30601862 PMCID: PMC6314593 DOI: 10.1371/journal.pone.0209221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
Plant cell walls are composed of cellulose, hemicellulose, and lignin, collectively known as lignocellulose. Microorganisms degrade lignocellulose to liberate sugars to meet metabolic demands. Using a metagenomic sequencing approach, we previously demonstrated that the microbiome of the North American porcupine (Erethizon dorsatum) is replete with genes that could encode lignocellulose-degrading enzymes. Here, we report the identification, synthesis and partial characterization of four novel genes from the porcupine microbiome encoding putative lignocellulose-degrading enzymes: β-glucosidase, α-L-arabinofuranosidase, β-xylosidase, and endo-1,4-β-xylanase. These genes were identified via conserved catalytic domains associated with cellulose- and hemicellulose-degradation. Phylogenetic trees were created for each of these putative enzymes to depict genetic relatedness to known enzymes. Candidate genes were synthesized and cloned into plasmid expression vectors for inducible protein expression and secretion. The putative β-glucosidase fusion protein was efficiently secreted but did not permit Escherichia coli (E. coli) to use cellobiose as a sole carbon source, nor did the affinity purified enzyme cleave p-Nitrophenyl β-D-glucopyranoside (p-NPG) substrate in vitro over a range of physiological pH levels (pH 5–7). The putative hemicellulose-degrading β-xylosidase and α-L-arabinofuranosidase enzymes also lacked in vitro enzyme activity, but the affinity purified endo-1,4-β-xylanase protein cleaved a 6-chloro-4-methylumbelliferyl xylobioside substrate in acidic and neutral conditions, with maximal activity at pH 7. At this optimal pH, KM, Vmax, and kcat were determined to be 32.005 ± 4.72 μM, 1.16x10-5 ± 3.55x10-7 M/s, and 94.72 s-1, respectively. Thus, our pipeline enabled successful identification and characterization of a novel hemicellulose-degrading enzyme from the porcupine microbiome. Progress towards the goal of introducing a complete lignocellulose-degradation pathway into E. coli will be accelerated by combining synthetic metagenomic approaches with functional metagenomic library screening, which can identify novel enzymes unrelated to those found in available databases.
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Affiliation(s)
- Mackenzie Thornbury
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jacob Sicheri
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Patrick Slaine
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Landon J. Getz
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Emma Finlayson-Trick
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jamie Cook
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Caroline Guinard
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Nicholas Boudreau
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David Jakeman
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John Rohde
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Craig McCormick
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
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Ducatti DRB, Carroll MA, Jakeman DL. On the phosphorylase activity of GH3 enzymes: A β-N-acetylglucosaminidase from Herbaspirillum seropedicae SmR1 and a glucosidase from Saccharopolyspora erythraea. Carbohydr Res 2016; 435:106-112. [PMID: 27744113 DOI: 10.1016/j.carres.2016.09.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/21/2016] [Accepted: 09/21/2016] [Indexed: 10/21/2022]
Abstract
A phosphorolytic activity has been reported for beta-N-acetylglucosaminidases from glycoside hydrolase family 3 (GH3) giving an interesting explanation for an unusual histidine as catalytic acid/base residue and suggesting that members from this family may be phosphorylases [J. Biol. Chem. 2015, 290, 4887]. Here, we describe the characterization of Hsero1941, a GH3 beta-N-acetylglucosaminidase from the endophytic nitrogen-fixing bacterium Herbaspirillum seropedicae SmR1. The enzyme has significantly higher activity against pNP-beta-D-GlcNAcp (Km = 0.24 mM, kcat = 1.2 s-1, kcat/Km = 5.0 mM-1s-1) than pNP-beta-D-Glcp (Km = 33 mM, kcat = 3.3 × 10-3 s-1, kcat/Km = 9 × 10-4 mM-1s-1). The presence of phosphate failed to significantly modify the kinetic parameters of the reaction. The enzyme showed a broad aglycone site specificity, being able to hydrolyze sugar phosphates beta-D-GlcNAc 1P and beta-D-Glc 1P, albeit at a fraction of the rate of hydrolysis of aryl glycosides. GH3 beta-glucosidase EryBI, that does not have a histidine as the general acid/base residue, also hydrolyzed beta-D-Glc 1P, at comparable rates to Hsero1941. These data indicate that Hsero1941 functions primarily as a hydrolase and that phosphorolytic activity is likely adventitious. The prevalence of histidine as a general acid/base residue is not predictive, nor correlative, with GH3 beta-N-acetylglucosaminidases having phosphorolytic activity.
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Affiliation(s)
- Diogo R B Ducatti
- College of Pharmacy, Dalhousie University, 5968 College Street, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada; Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Centro Politécnico, CEP 81-531-990, P.O. Box 19046, Curitiba, Paraná, Brazil
| | - Madison A Carroll
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada
| | - David L Jakeman
- College of Pharmacy, Dalhousie University, 5968 College Street, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada; Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada.
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3
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Robertson AW, Forget SM, Martinez-Farina CF, McCormick NE, Syvitski RT, Jakeman DL. JadX is a Disparate Natural Product Binding Protein. J Am Chem Soc 2016; 138:2200-8. [PMID: 26814718 DOI: 10.1021/jacs.5b11286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We report that JadX, a protein of previously undetermined function coded for in the jadomycin biosynthetic gene cluster of Streptomyces venezuelae ISP5230, affects both chloramphenicol and jadomycin production levels in blocked mutants. Characterization of recombinant JadX through protein-ligand interactions by chemical shift perturbation and WaterLOGSY NMR spectroscopy resulted in the observation of binding between JadX and a series of jadomycins and between JadX and chloramphenicol, another natural product produced by S. venezuelae ISP5230. These results suggest JadX to be an unusual class of natural product binding protein involved in binding structurally disparate natural products. The ability for JadX to bind two different natural products in vitro and the ability to affect production of these secondary metabolites in vivo suggest a potential role in regulation or signaling. This is the first example of functional characterization of these JadX-like proteins, and provides insight into a previously unobserved regulatory process.
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Affiliation(s)
| | | | | | | | - Raymond T Syvitski
- Institute for Marine Biosciences, National Research Council of Canada , Halifax, Nova Scotia B3H 3Z1, Canada
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Martinez-Farina CF, McCormick N, Robertson AW, Clement H, Jee A, Ampaw A, Chan NL, Syvitski RT, Jakeman DL. Investigations into the binding of jadomycin DS to human topoisomerase IIβ by WaterLOGSY NMR spectroscopy. Org Biomol Chem 2015; 13:10324-7. [DOI: 10.1039/c5ob01508a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
First evidence that jadomycins bind human topoisomerase IIβ.
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Affiliation(s)
| | | | | | - Helen Clement
- College of Pharmacy
- Dalhousie University
- Halifax
- Canada
| | - Alison Jee
- College of Pharmacy
- Dalhousie University
- Halifax
- Canada
| | - Anna Ampaw
- Department of Chemistry
- Dalhousie University
- Halifax
- Canada
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology
- College Medicine
- National Taiwan University
- Taipei City 100
- Taiwan
| | - Ray T. Syvitski
- Department of Chemistry
- Dalhousie University
- Halifax
- Canada
- Institute of Marine Biosciences
| | - David L. Jakeman
- Department of Chemistry
- Dalhousie University
- Halifax
- Canada
- College of Pharmacy
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Beaton SA, Jiang PM, Melong JC, Loranger MW, Mohamady S, Veinot TI, Jakeman DL. The effect of bisphosphonate acidity on the activity of a thymidylyltransferase. Org Biomol Chem 2014; 11:5473-80. [PMID: 23857455 DOI: 10.1039/c3ob41017j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Thymidylyltransferases (thymidine diphospho pyrophosphorylases) are nucleotidylyltransferases that play key roles in the biosynthesis of carbohydrate components within bacterial cell walls and in the biosynthesis of glycosylated natural products. They catalyze the formation of sugar nucleotides concomitant with the release of pyrophosphate. Protein engineering of thymidylyltransferases has been an approach for the production of a variety of non-physiological sugar nucleotides. In this work, we have explored chemical approaches towards modifying the activity of the thymidylyltransferase (Cps2L) cloned from S. pneumoniae, through the use of chemically synthesized 'activated' nucleoside triphosphates with enhanced leaving groups, or by switching the metal ion co-factor specificity. Within a series of phosphonate-containing nucleoside triphosphate analogues, thymidylyltransferase activity is enhanced based on the acidity of the leaving group and a Brønsted-type analysis indicated that leaving group departure is rate limiting. We have also determined IC50 values for a series of bisphosphonates as inhibitors of thymidylyltransferases. No correlation between the acidity of the inhibitors (pKa) and the magnitude of enzyme inhibition was found.
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Affiliation(s)
- Stephen A Beaton
- Department of Chemistry, Dalhousie University, 1459 Oxford St., Halifax, Nova Scotia B3H 4R2, Canada
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Zmudka MW, Thoden JB, Holden HM. The structure of DesR from Streptomyces venezuelae, a β-glucosidase involved in macrolide activation. Protein Sci 2013; 22:883-92. [PMID: 23225731 DOI: 10.1002/pro.2204] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 11/26/2012] [Indexed: 11/11/2022]
Abstract
Antibiotics have, indeed, altered the course of human history as is evidenced by the increase in human life expectancy since the 1940s. Many of these natural compounds are produced by bacteria that, by necessity, must have efficient self-resistance mechanisms. The methymycin/pikromycin producing species Streptomyces venezuelae, for example, utilizes β-glucosylation of its macrolide products to neutralize their effects within the confines of the cell. Once released into the environment, these compounds are activated by the removal of the glucose moiety. In S. venezuelae, the enzyme responsible for removal of the sugar from the parent compound is encoded by the desR gene and referred to as DesR. It is a secreted enzyme containing 828 amino acid residues, and it is known to be a retaining glycosidase. Here, we describe the structure of the DesR/D-glucose complex determined to 1.4-Å resolution. The overall architecture of the enzyme can be envisioned in terms of three regions: a catalytic core and two auxiliary domains. The catalytic core harbors the binding platform for the glucose ligand. The first auxiliary domain adopts a "PA14 fold," whereas the second auxiliary domain contains an immunoglobulin-like fold. Asp 273 and Glu 578 are in the proper orientation to function as the catalytic base and proton donor, respectively, required for catalysis. The overall fold of the core region places DesR into the GH3 glycoside hydrolase family of enzymes. Comparison of the DesR structure with the β-glucosidase from Kluyveromyces marxianus shows that their PA14 domains assume remarkably different orientations.
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Affiliation(s)
- Matthew W Zmudka
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Jakeman DL, Sadeghi-Khomami A. A β-(1,2)-Glycosynthase and an Attempted Selection Method for the Directed Evolution of Glycosynthases. Biochemistry 2011; 50:10359-66. [DOI: 10.1021/bi201438q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David L. Jakeman
- College of Pharmacy, Dalhousie University, 5968 College Street, P.O. Box
15000, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, 6274 Coberg Road, P.O. Box 15000,
Halifax, Nova Scotia B3H 4R2, Canada
| | - Ali Sadeghi-Khomami
- College of Pharmacy, Dalhousie University, 5968 College Street, P.O. Box
15000, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, 6274 Coberg Road, P.O. Box 15000,
Halifax, Nova Scotia B3H 4R2, Canada
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