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Bon CG, Grigg JC, Lee J, Robb CS, Caveney NA, Eltis LD, Strynadka NCJ. Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1. J Struct Biol 2024; 216:108086. [PMID: 38527711 DOI: 10.1016/j.jsb.2024.108086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/02/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/27/2024]
Abstract
Staphylococcus aureus, an ESKAPE pathogen, is a major clinical concern due to its pathogenicity and manifold antimicrobial resistance mechanisms. The commonly used β-lactam antibiotics target bacterial penicillin-binding proteins (PBPs) and inhibit crosslinking of peptidoglycan strands that comprise the bacterial cell wall mesh, initiating a cascade of effects leading to bacterial cell death. S. aureus PBP1 is involved in synthesis of the bacterial cell wall during division and its presence is essential for survival of both antibiotic susceptible and resistant S. aureus strains. Here, we present X-ray crystallographic data for S. aureus PBP1 in its apo form as well as acyl-enzyme structures with distinct classes of β-lactam antibiotics representing the penicillins, carbapenems, and cephalosporins, respectively: oxacillin, ertapenem and cephalexin. Our structural data suggest that the PBP1 active site is readily accessible for substrate, with little conformational change in key structural elements required for its covalent acylation of β-lactam inhibitors. Stopped-flow kinetic analysis and gel-based competition assays support the structural observations, with even the weakest performing β-lactams still having comparatively high acylation rates and affinities for PBP1. Our structural and kinetic analysis sheds insight into the ligand-PBP interactions that drive antibiotic efficacy against these historically useful antimicrobial targets and expands on current knowledge for future drug design and treatment of S. aureus infections.
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Affiliation(s)
- Christopher G Bon
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jason C Grigg
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Craig S Robb
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nathanael A Caveney
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Wolf ME, Lalande AT, Newman BL, Bleem AC, Palumbo CT, Beckham GT, Eltis LD. The catabolism of lignin-derived p-methoxylated aromatic compounds by Rhodococcus jostii RHA1. Appl Environ Microbiol 2024; 90:e0215523. [PMID: 38380926 PMCID: PMC10952524 DOI: 10.1128/aem.02155-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Emergent strategies to valorize lignin, an abundant but underutilized aromatic biopolymer, include tandem processes that integrate chemical depolymerization and biological catalysis. To date, aromatic monomers from C-O bond cleavage of lignin have been converted to bioproducts, but the presence of recalcitrant C-C bonds in lignin limits the product yield. A promising chemocatalytic strategy that overcomes this limitation involves phenol methyl protection and autoxidation. Incorporating this into a tandem process requires microbial cell factories able to transform the p-methoxylated products in the resulting methylated lignin stream. In this study, we assessed the ability of Rhodococcus jostii RHA1 to catabolize the major aromatic products in a methylated lignin stream and elucidated the pathways responsible for this catabolism. RHA1 grew on a methylated pine lignin stream, catabolizing the major aromatic monomers: p-methoxybenzoate (p-MBA), veratrate, and veratraldehyde. Bioinformatic analyses suggested that a cytochrome P450, PbdA, and its cognate reductase, PbdB, are involved in p-MBA catabolism. Gene deletion studies established that both pbdA and pbdB are essential for growth on p-MBA and several derivatives. Furthermore, a deletion mutant of a candidate p-hydroxybenzoate (p-HBA) hydroxylase, ΔpobA, did not grow on p-HBA. Veratraldehyde and veratrate catabolism required both vanillin dehydrogenase (Vdh) and vanillate O-demethylase (VanAB), revealing previously unknown roles of these enzymes. Finally, a ΔpcaL strain grew on neither p-MBA nor veratrate, indicating they are catabolized through the β-ketoadipate pathway. This study expands our understanding of the bacterial catabolism of aromatic compounds and facilitates the development of biocatalysts for lignin valorization.IMPORTANCELignin, an abundant aromatic polymer found in plant biomass, is a promising renewable replacement for fossil fuels as a feedstock for the chemical industry. Strategies for upgrading lignin include processes that couple the catalytic fractionation of biomass and biocatalytic transformation of the resulting aromatic compounds with a microbial cell factory. Engineering microbial cell factories for this biocatalysis requires characterization of bacterial pathways involved in catabolizing lignin-derived aromatic compounds. This study identifies new pathways for lignin-derived aromatic degradation in Rhodococcus, a genus of bacteria well suited for biocatalysis. Additionally, we describe previously unknown activities of characterized enzymes on lignin-derived compounds, expanding their utility. This work advances the development of strategies to replace fossil fuel-based feedstocks with sustainable alternatives.
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Affiliation(s)
- Megan E. Wolf
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Anne T. Lalande
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Brianne L. Newman
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Alissa C. Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Chad T. Palumbo
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
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Brown KL, Krekhno JMC, Xing S, Huan T, Eltis LD. Cholesterol-Mediated Coenzyme A Depletion in Catabolic Mutants of Mycobacteria Leads to Toxicity. ACS Infect Dis 2024; 10:107-119. [PMID: 38054469 DOI: 10.1021/acsinfecdis.3c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Cholesterol is a critical growth substrate for Mycobacterium tuberculosis (Mtb) during infection, and the cholesterol catabolic pathway has been targeted for the development of new antimycobacterial agents. A key metabolite in cholesterol catabolism is 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP). Many of the HIP metabolites are acyl-coenzyme A (CoA) thioesters, whose accumulation in deletion mutants can cause cholesterol-mediated toxicity. We used LC-MS/MS analysis to demonstrate that deletion of genes involved in HIP catabolism leads to acyl-CoA accumulation with concomitant depletion of free CoASH, leading to dysregulation of central metabolic pathways. CoASH and acyl-CoAs inhibited PanK, the enzyme that catalyzes the first step in the transformation of pantothenate to CoASH. Inhibition was competitive with respect to ATP with Kic values ranging from 9 μM for CoASH to 57 μM for small acyl-CoAs and 180 ± 30 μM for cholesterol-derived acyl-CoA. These findings link two critical metabolic pathways and suggest that therapeutics targeting cholesterol catabolic enzymes could both prevent the utilization of an important growth substrate and simultaneously sequester CoA from essential cellular processes, leading to bacterial toxicity.
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Affiliation(s)
- Kirstin L Brown
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Jessica M C Krekhno
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Shipei Xing
- Department of Chemistry, The University of British Columbia, Vancouver V6T 1Z1, Canada
| | - Tao Huan
- Department of Chemistry, The University of British Columbia, Vancouver V6T 1Z1, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
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4
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Grigg JC, Copp JN, Krekhno JMC, Liu J, Ibrahimova A, Eltis LD. Deciphering the biosynthesis of a novel lipid in Mycobacterium tuberculosis expands the known roles of the nitroreductase superfamily. J Biol Chem 2023; 299:104924. [PMID: 37328106 PMCID: PMC10404671 DOI: 10.1016/j.jbc.2023.104924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Mycobacterium tuberculosis's (Mtb) success as a pathogen is due in part to its sophisticated lipid metabolic programs, both catabolic and biosynthetic. Several of Mtb lipids have specific roles in pathogenesis, but the identity and roles of many are unknown. Here, we demonstrated that the tyz gene cluster in Mtb, previously implicated in resistance to oxidative stress and survival in macrophages, encodes the biosynthesis of acyl-oxazolones. Heterologous expression of tyzA (Rv2336), tyzB (Rv2338c) and tyzC (Rv2337c) resulted in the biosynthesis of C12:0-tyrazolone as the predominant compound, and the C12:0-tyrazolone was identified in Mtb lipid extracts. TyzA catalyzed the N-acylation of l-amino acids, with highest specificity for l-Tyr and l-Phe and lauroyl-CoA (kcat/KM = 5.9 ± 0.8 × 103 M-1s-1). In cell extracts, TyzC, a flavin-dependent oxidase (FDO) of the nitroreductase (NTR) superfamily, catalyzed the O2-dependent desaturation of the N-acyl-L-Tyr produced by TyzA, while TyzB, a ThiF homolog, catalyzed its ATP-dependent cyclization. The substrate preference of TyzB and TyzC appear to determine the identity of the acyl-oxazolone. Phylogenetic analyses revealed that the NTR superfamily includes a large number of broadly distributed FDOs, including five in Mtb that likely catalyze the desaturation of lipid species. Finally, TCA1, a molecule with activity against drug-resistant and persistent tuberculosis, failed to inhibit the cyclization activity of TyzB, the proposed secondary target of TCA1. Overall, this study identifies a novel class of Mtb lipids, clarifies the role of a potential drug target, and expands our understanding of the NTR superfamily.
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Affiliation(s)
- Jason C Grigg
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Janine N Copp
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessica M C Krekhno
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jie Liu
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Aygun Ibrahimova
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lindsay D Eltis
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada.
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5
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Abstract
In 2014, Linger et al. presented a tandem process for lignin valorization by integrating chemical and biological catalysis. Chemical pretreatment of corn stover generated mixed lignocellulose-derived monomers that were converted to a single product, polyhydroxyalkanoates, by Pseudomonas putida. Tandem processes have since been developed for diverse feedstocks to support the bioeconomy.
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Affiliation(s)
- Allison Z Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA.
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada.
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6
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Navas LE, Zahn M, Bajwa H, Grigg JC, Wolf ME, Chan ACK, Murphy MEP, McGeehan JE, Eltis LD. Characterization of a phylogenetically distinct extradiol dioxygenase involved in the bacterial catabolism of lignin-derived aromatic compounds. J Biol Chem 2022; 298:101871. [PMID: 35346686 PMCID: PMC9062432 DOI: 10.1016/j.jbc.2022.101871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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] [Received: 02/12/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 10/28/2022] Open
Abstract
The actinobacterium Rhodococcus jostii RHA1 grows on a remarkable variety of aromatic compounds and has been studied for applications ranging from the degradation of polychlorinated biphenyls to the valorization of lignin, an underutilized component of biomass. In RHA1, the catabolism of two classes of lignin-derived compounds, alkylphenols and alkylguaiacols, involves a phylogenetically distinct extradiol dioxygenase, AphC, previously misannotated as BphC, an enzyme involved in biphenyl catabolism. To better understand the role of AphC in RHA1 catabolism, we first showed that purified AphC had highest apparent specificity for 4-propylcatechol (kcat/KM ∼106 M-1 s-1), and its apparent specificity for 4-alkylated substrates followed the trend for alkylguaiacols: propyl > ethyl > methyl > phenyl > unsubstituted. We also show AphC only poorly cleaved 3-phenylcatechol, the preferred substrate of BphC. Moreover, AphC and BphC cleaved 3-phenylcatechol and 4-phenylcatechol with different regiospecificities, likely due to the substrates' binding mode. A crystallographic structure of the AphC·4-ethylcatechol binary complex to 1.59 Å resolution revealed that the catechol is bound to the active site iron in a bidentate manner and that the substrate's alkyl side chain is accommodated by a hydrophobic pocket. Finally, we show RHA1 grows on a mixture of 4-ethylguaiacol and guaiacol, simultaneously catabolizing these substrates through meta-cleavage and ortho-cleavage pathways, respectively, suggesting that the specificity of AphC helps to prevent the routing of catechol through the Aph pathway. Overall, this study contributes to our understanding of the bacterial catabolism of aromatic compounds derived from lignin, and the determinants of specificity in extradiol dioxygenases.
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Affiliation(s)
- Laura E Navas
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Michael Zahn
- Centre for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Harbir Bajwa
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Jason C Grigg
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Megan E Wolf
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Anson C K Chan
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - John E McGeehan
- Centre for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada.
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7
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Mahto JK, Neetu N, Waghmode B, Kuatsjah E, Sharma M, Sircar D, Sharma AK, Tomar S, Eltis LD, Kumar P. Molecular insights into substrate recognition and catalysis by phthalate dioxygenase from Comamonas testosteroni. J Biol Chem 2021; 297:101416. [PMID: 34800435 PMCID: PMC8649396 DOI: 10.1016/j.jbc.2021.101416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Phthalate, a plasticizer, endocrine disruptor, and potential carcinogen, is degraded by a variety of bacteria. This degradation is initiated by phthalate dioxygenase (PDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of phthalate to a dihydrodiol. PDO has long served as a model for understanding ROs despite a lack of structural data. Here we purified PDOKF1 from Comamonas testosteroni KF1 and found that it had an apparent kcat/Km for phthalate of 0.58 ± 0.09 μM-1s-1, over 25-fold greater than for terephthalate. The crystal structure of the enzyme at 2.1 Å resolution revealed that it is a hexamer comprising two stacked α3 trimers, a configuration not previously observed in RO crystal structures. We show that within each trimer, the protomers adopt a head-to-tail configuration typical of ROs. The stacking of the trimers is stabilized by two extended helices, which make the catalytic domain of PDOKF1 larger than that of other characterized ROs. Complexes of PDOKF1 with phthalate and terephthalate revealed that Arg207 and Arg244, two residues on one face of the active site, position these substrates for regiospecific hydroxylation. Consistent with their roles as determinants of substrate specificity, substitution of either residue with alanine yielded variants that did not detectably turnover phthalate. Together, these results provide critical insights into a pollutant-degrading enzyme that has served as a paradigm for ROs and facilitate the engineering of this enzyme for bioremediation and biocatalytic applications.
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Affiliation(s)
- Jai Krishna Mahto
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Neetu Neetu
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | | | - Eugene Kuatsjah
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Monica Sharma
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | | | - Shailly Tomar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Lindsay D Eltis
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India.
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8
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Lien KA, Dinshaw K, Nichols RJ, Cassidy-Amstutz C, Knight M, Singh R, Eltis LD, Savage DF, Stanley SA. A nanocompartment system contributes to defense against oxidative stress in Mycobacterium tuberculosis. eLife 2021; 10:e74358. [PMID: 34751132 PMCID: PMC8635971 DOI: 10.7554/elife.74358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/06/2021] [Indexed: 01/18/2023] Open
Abstract
Encapsulin nanocompartments are an emerging class of prokaryotic protein-based organelle consisting of an encapsulin protein shell that encloses a protein cargo. Genes encoding nanocompartments are widespread in bacteria and archaea, and recent works have characterized the biochemical function of several cargo enzymes. However, the importance of these organelles to host physiology is poorly understood. Here, we report that the human pathogen Mycobacterium tuberculosis (Mtb) produces a nanocompartment that contains the dye-decolorizing peroxidase DyP. We show that this nanocompartment is important for the ability of Mtb to resist oxidative stress in low pH environments, including during infection of host cells and upon treatment with a clinically relevant antibiotic. Our findings are the first to implicate a nanocompartment in bacterial pathogenesis and reveal a new mechanism that Mtb uses to combat oxidative stress.
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Affiliation(s)
- Katie A Lien
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
| | - Kayla Dinshaw
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
| | - Robert J Nichols
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Caleb Cassidy-Amstutz
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Matthew Knight
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Rahul Singh
- Department of Microbiology and Immunology, The University of British ColumbiaVancouverCanada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, The University of British ColumbiaVancouverCanada
| | - David F Savage
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Sarah A Stanley
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, BerkeleyBerkeleyUnited States
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9
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Vuong TV, Singh R, Eltis LD, Master ER. The Comparative Abilities of a Small Laccase and a Dye-Decoloring Peroxidase From the Same Bacterium to Transform Natural and Technical Lignins. Front Microbiol 2021; 12:723524. [PMID: 34733245 PMCID: PMC8559727 DOI: 10.3389/fmicb.2021.723524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Received: 06/10/2021] [Accepted: 09/23/2021] [Indexed: 11/29/2022] Open
Abstract
The relative ability of the small laccase (sLac) and dye-decoloring peroxidase (DyP2) from Amycolatopsis sp. 75iv2 to transform a variety of lignins was investigated using time-of-flight secondary ion mass spectrometry (ToF-SIMS). The enzymes modified organosolv hardwood lignin to different extents even in the absence of an added mediator. More particularly, sLac decreased the lignin modification metric S (S-lignin)/Ar (total aromatics) by 58% over 16h, while DyP2 lowered this ratio by 31% in the absence of exogenous H2O2. When used on their own, both sLac and DyP2 also modified native lignin present in aspen wood powder, albeit to lesser extents than in the organosolv lignin. The addition of ABTS for sLac and Mn2+ as well as H2O2 for DyP2 led to increased lignin modification in aspen wood powder as reflected by a decrease in the G/Ar metric by up to a further 13%. This highlights the importance of exogenous mediators for transforming lignin within its native matrix. Furthermore, the addition of ABTS reduced the selectivity of sLac for S-lignin over G-lignin, indicating that the mediator also altered the product profiles. Finally, when sLac was included in reactions containing DyP2, in part to generate H2O2in situ, the relative abundance of lignin products differed from individual enzymatic treatments. Overall, these results identify possible routes to tuning lignin modification or delignification through choice of enzyme and mediator. Moreover, the current study expands the application of ToF-SIMS to evaluating enzyme action on technical lignins, which can accelerate the discovery and engineering of industrially relevant enzymes for lignin valorization.
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Affiliation(s)
- Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Rahul Singh
- Department of Microbiology and Immunology, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada.,Genome British Columbia, Vancouver, BC, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.,Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
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10
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Navas LE, Dexter G, Liu J, Levy-Booth D, Cho M, Jang SK, Mansfield SD, Renneckar S, Mohn WW, Eltis LD. Bacterial Transformation of Aromatic Monomers in Softwood Black Liquor. Front Microbiol 2021; 12:735000. [PMID: 34566938 PMCID: PMC8461187 DOI: 10.3389/fmicb.2021.735000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Received: 07/01/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
The valorization of lignin, a major component of plant-derived biomass, is essential to sustainable biorefining. We identified the major monoaromatic compounds present in black liquor, a lignin-rich stream generated in the kraft pulping process, and investigated their bacterial transformation. Among tested solvents, acetone extracted the greatest amount of monoaromatic compounds from softwood black liquor, with guaiacol, vanillin, and acetovanillone, in an approximately 4:3:2 ratio, constituting ~90% of the total extracted monoaromatic content. 4-Ethanol guaiacol, vanillate, and 4-propanol guaiacol were also present. Bacterial strains that grew on minimal media supplemented with the BL extracts at 1mM total aromatic compounds included Pseudomonas putida KT2442, Sphingobium sp. SYK-6, and Rhodococcus rhodochrous EP4. By contrast, the extracts inhibited the growth of Rhodococcus jostii RHA1 and Rhodococcus opacus PD630, strains extensively studied for lignin valorization. Of the strains that grew on the extracts, only R. rhodochrous GD01 and GD02, isolated for their ability to grow on acetovanillone, depleted the major extracted monoaromatics. Genomic analyses revealed that EP4, GD01, and GD02 share an average nucleotide identity (ANI) of 98% and that GD01 and GD02 harbor a predicted three-component carboxylase not present in EP4. A representative carboxylase gene was upregulated ~100-fold during growth of GD02 on a mixture of the BL monoaromatics, consistent with the involvement of the enzyme in acetovanillone catabolism. More generally, quantitative RT-PCR indicated that GD02 catabolizes the BL compounds in a convergent manner via the β-ketoadipate pathway. Overall, these studies help define the catabolic capabilities of potential biocatalytic strains, describe new isolates able to catabolize the major monoaromatic components of BL, including acetovanillone, and facilitate the design of biocatalysts to valorize under-utilized components of industrial lignin streams.
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Affiliation(s)
- Laura E Navas
- Department of Microbiology and Immunology, Life Sciences Institute, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Gara Dexter
- Department of Microbiology and Immunology, Life Sciences Institute, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Jie Liu
- Department of Microbiology and Immunology, Life Sciences Institute, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
| | - David Levy-Booth
- Department of Microbiology and Immunology, Life Sciences Institute, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
| | - MiJung Cho
- Department of Wood Science, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Soo-Kyeong Jang
- Department of Wood Science, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Shawn D Mansfield
- Department of Wood Science, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Scott Renneckar
- Department of Wood Science, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
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11
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Abstract
The development of microbial cell factories requires robust synthetic biology tools to reduce design uncertainty and accelerate the design-build-test-learn process. Herein, we developed a suite of integrative genetic tools to facilitate the engineering of Rhodococcus, a genus of bacteria with considerable biocatalytic potential. We first created pRIME, a modular, copy-controlled integrative-vector, to provide a robust platform for strain engineering and characterizing genetic parts. This vector was then employed to benchmark a series of strong promoters. We found PM6 to be the strongest constitutive rhodococcal promoter, 2.5- to 3-fold stronger than the next in our study, while overall promoter activities ranged 23-fold between the weakest and strongest promoters during exponential growth. Next, we used an optimized variant of PM6 to develop hybrid-promoters and integrative vectors to allow for tetracycline-inducible gene expression in Rhodococcus. The best of the resulting hybrid-promoters maintained a maximal activity of ∼50% of PM6 and displayed an induction factor of ∼40-fold. Finally, we developed and implemented a uLoop-derived Golden Gate assembly strategy for high-throughput DNA assembly in Rhodococcus. To demonstrate the utility of our approaches, pRIME was used to engineer Rhodococcus jostii RHA1 to grow on vanillin at concentrations 10-fold higher than what the wild-type strain tolerated. Overall, this study provides a suite of tools that will accelerate the engineering of Rhodococcus for various biocatalytic applications, including the sustainable production of chemicals from lignin-derived aromatics.
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Affiliation(s)
- James W. Round
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Logan D. Robeck
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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12
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Kuatsjah E, Chan ACK, Katahira R, Haugen SJ, Beckham GT, Murphy MEP, Eltis LD. Structural and functional analysis of lignostilbene dioxygenases from Sphingobium sp. SYK-6. J Biol Chem 2021; 296:100758. [PMID: 33965373 PMCID: PMC8191317 DOI: 10.1016/j.jbc.2021.100758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 11/27/2022] Open
Abstract
Lignostilbene-α,β-dioxygenases (LSDs) are iron-dependent oxygenases involved in the catabolism of lignin-derived stilbenes. Sphingobium sp. SYK-6 contains eight LSD homologs with undetermined physiological roles. To investigate which homologs are involved in the catabolism of dehydrodiconiferyl alcohol (DCA), derived from β-5 linked lignin subunits, we heterologously produced the enzymes and screened their activities in lysates. The seven soluble enzymes all cleaved lignostilbene, but only LSD2, LSD3, and LSD4 exhibited high specific activity for 3-(4-hydroxy-3-(4-hydroxy-3-methoxystyryl)-5-methoxyphenyl) acrylate (DCA-S) relative to lignostilbene. LSD4 catalyzed the cleavage of DCA-S to 5-formylferulate and vanillin and cleaved lignostilbene and DCA-S (∼106 M−1 s−1) with tenfold greater specificity than pterostilbene and resveratrol. X-ray crystal structures of native LSD4 and the catalytically inactive cobalt-substituted Co-LSD4 at 1.45 Å resolution revealed the same fold, metal ion coordination, and edge-to-edge dimeric structure as observed in related enzymes. Key catalytic residues, Phe-59, Tyr-101, and Lys-134, were also conserved. Structures of Co-LSD4·vanillin, Co-LSD4·lignostilbene, and Co-LSD4·DCA-S complexes revealed that Ser-283 forms a hydrogen bond with the hydroxyl group of the ferulyl portion of DCA-S. This residue is conserved in LSD2 and LSD4 but is alanine in LSD3. Substitution of Ser-283 with Ala minimally affected the specificity of LSD4 for either lignostilbene or DCA-S. By contrast, substitution with phenylalanine, as occurs in LSD5 and LSD6, reduced the specificity of the enzyme for both substrates by an order of magnitude. This study expands our understanding of an LSD critical to DCA catabolism as well as the physiological roles of other LSDs and their determinants of substrate specificity.
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Affiliation(s)
- Eugene Kuatsjah
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada; Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge Tennessee, USA
| | - Anson C K Chan
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Rui Katahira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Stefan J Haugen
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge Tennessee, USA
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada; BioProducts Institute, The University of British Columbia, Vancouver, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada; BioProducts Institute, The University of British Columbia, Vancouver, Canada.
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13
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Affiliation(s)
- Ruben Shrestha
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Kaimin Jia
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Samiksha Khadka
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ping Li
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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14
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Notonier S, Werner AZ, Kuatsjah E, Dumalo L, Abraham PE, Hatmaker EA, Hoyt CB, Amore A, Ramirez KJ, Woodworth SP, Klingeman DM, Giannone RJ, Guss AM, Hettich RL, Eltis LD, Johnson CW, Beckham GT. Metabolism of syringyl lignin-derived compounds in Pseudomonas putida enables convergent production of 2-pyrone-4,6-dicarboxylic acid. Metab Eng 2021; 65:111-122. [PMID: 33741529 DOI: 10.1016/j.ymben.2021.02.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [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: 11/15/2020] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022]
Abstract
Valorization of lignin, an abundant component of plant cell walls, is critical to enabling the lignocellulosic bioeconomy. Biological funneling using microbial biocatalysts has emerged as an attractive approach to convert complex mixtures of lignin depolymerization products to value-added compounds. Ideally, biocatalysts would convert aromatic compounds derived from the three canonical types of lignin: syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H). Pseudomonas putida KT2440 (hereafter KT2440) has been developed as a biocatalyst owing in part to its native catabolic capabilities but is not known to catabolize S-type lignin-derived compounds. Here, we demonstrate that syringate, a common S-type lignin-derived compound, is utilized by KT2440 only in the presence of another energy source or when vanAB was overexpressed, as syringate was found to be O-demethylated to gallate by VanAB, a two-component monooxygenase, and further catabolized via extradiol cleavage. Unexpectedly, the specificity (kcat/KM) of VanAB for syringate was within 25% that for vanillate and O-demethylation of both substrates was well-coupled to O2 consumption. However, the native KT2440 gallate-cleaving dioxygenase, GalA, was potently inactivated by 3-O-methylgallate. To engineer a biocatalyst to simultaneously convert S-, G-, and H-type monomers, we therefore employed VanAB from Pseudomonas sp. HR199, which has lower activity for 3MGA, and LigAB, an extradiol dioxygenase able to cleave protocatechuate and 3-O-methylgallate. This strain converted 93% of a mixture of lignin monomers to 2-pyrone-4,6-dicarboxylate, a promising bio-based chemical. Overall, this study elucidates a native pathway in KT2440 for catabolizing S-type lignin-derived compounds and demonstrates the potential of this robust chassis for lignin valorization.
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Affiliation(s)
- Sandra Notonier
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Allison Z Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Eugene Kuatsjah
- Department of Microbiology and Immunology, BioProducts Institute, and the Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Linda Dumalo
- Department of Microbiology and Immunology, BioProducts Institute, and the Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Paul E Abraham
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - E Anne Hatmaker
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Caroline B Hoyt
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Antonella Amore
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Kelsey J Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Sean P Woodworth
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Dawn M Klingeman
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Richard J Giannone
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Adam M Guss
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Robert L Hettich
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, BioProducts Institute, and the Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
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15
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Gadbery JE, Round JW, Yuan T, Wipperman MF, Story KT, Crowe AM, Casabon I, Liu J, Yang X, Eltis LD, Sampson NS. IpdE1-IpdE2 Is a Heterotetrameric Acyl Coenzyme A Dehydrogenase That Is Widely Distributed in Steroid-Degrading Bacteria. Biochemistry 2020; 59:1113-1123. [PMID: 32101684 PMCID: PMC7081610 DOI: 10.1021/acs.biochem.0c00005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Steroid-degrading bacteria, including Mycobacterium tuberculosis (Mtb), utilize an architecturally distinct subfamily of acyl coenzyme A dehydrogenases (ACADs) for steroid catabolism. These ACADs are α2β2 heterotetramers that are usually encoded by adjacent fadE-like genes. In mycobacteria, ipdE1 and ipdE2 (formerly fadE30 and fadE33) occur in divergently transcribed operons associated with the catabolism of 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP), a steroid metabolite. In Mycobacterium smegmatis, ΔipdE1 and ΔipdE2 mutants had similar phenotypes, showing impaired growth on cholesterol and accumulating 5-OH HIP in the culture supernatant. Bioinformatic analyses revealed that IpdE1 and IpdE2 share many of the features of the α- and β-subunits, respectively, of heterotetrameric ACADs that are encoded by adjacent genes in many steroid-degrading proteobacteria. When coproduced in a rhodococcal strain, IpdE1 and IpdE2 of Mtb formed a complex that catalyzed the dehydrogenation of 5OH-HIP coenzyme A (5OH-HIP-CoA) to 5OH-3aα-H-4α(3'-prop-1-enoate)-7aβ-methylhexa-hydro-1,5-indanedione coenzyme A ((E)-5OH-HIPE-CoA). This corresponds to the initial step in the pathway that leads to degradation of steroid C and D rings via β-oxidation. Small-angle X-ray scattering revealed that the IpdE1-IpdE2 complex was an α2β2 heterotetramer typical of other ACADs involved in steroid catabolism. These results provide insight into an important class of steroid catabolic enzymes and a potential virulence determinant in Mtb.
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Affiliation(s)
- John E Gadbery
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - James W Round
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Tianao Yuan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Matthew F Wipperman
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States.,Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.,Clinical & Translational Science Center, Weill Cornell Medicine, New York, New York 10065, United States
| | - Keith T Story
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Adam M Crowe
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Israel Casabon
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jie Liu
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Xinxin Yang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nicole S Sampson
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
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16
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Levy-Booth DJ, Fetherolf MM, Stewart GR, Liu J, Eltis LD, Mohn WW. Catabolism of Alkylphenols in Rhodococcus via a Meta-Cleavage Pathway Associated With Genomic Islands. Front Microbiol 2019; 10:1862. [PMID: 31481940 PMCID: PMC6710988 DOI: 10.3389/fmicb.2019.01862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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] [Received: 06/19/2019] [Accepted: 07/29/2019] [Indexed: 01/01/2023] Open
Abstract
The bacterial catabolism of aromatic compounds has considerable promise to convert lignin depolymerization products to commercial chemicals. Alkylphenols are a key class of depolymerization products whose catabolism is not well-elucidated. We isolated Rhodococcus rhodochrous EP4 on 4-ethylphenol and applied genomic and transcriptomic approaches to elucidate alkylphenol catabolism in EP4 and Rhodococcus jostii RHA1. RNA-Seq and RT-qPCR revealed a pathway encoded by the aphABCDEFGHIQRS genes that degrades 4-ethylphenol via the meta-cleavage of 4-ethylcatechol. This process was initiated by a two-component alkylphenol hydroxylase, encoded by the aphAB genes, which were upregulated ~3,000-fold. Purified AphAB from EP4 had highest specific activity for 4-ethylphenol and 4-propylphenol (~2,000 U/mg) but did not detectably transform phenol. Nevertheless, a ΔaphA mutant in RHA1 grew on 4-ethylphenol by compensatory upregulation of phenol hydroxylase genes (pheA1-3). Deletion of aphC, encoding an extradiol dioxygenase, prevented growth on 4-alkylphenols but not phenol. Disruption of pcaL in the β-ketoadipate pathway prevented growth on phenol but not 4-alkylphenols. Thus, 4-alkylphenols are catabolized exclusively via meta-cleavage in rhodococci while phenol is subject to ortho-cleavage. A putative genomic island encoding aph genes was identified in EP4 and several other rhodococci. Overall, this study identifies a 4-alkylphenol pathway in rhodococci, demonstrates key enzymes involved, and presents evidence that the pathway is encoded in a genomic island. These advances are of particular importance for wide-ranging industrial applications of rhodococci, including upgrading of lignocellulose biomass.
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Affiliation(s)
- David J Levy-Booth
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Morgan M Fetherolf
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Gordon R Stewart
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Jie Liu
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
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17
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Kuatsjah E, Verstraete MM, Kobylarz MJ, Liu AKN, Murphy MEP, Eltis LD. Identification of functionally important residues and structural features in a bacterial lignostilbene dioxygenase. J Biol Chem 2019; 294:12911-12920. [PMID: 31292192 DOI: 10.1074/jbc.ra119.009428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 05/27/2019] [Revised: 07/03/2019] [Indexed: 01/21/2023] Open
Abstract
Lignostilbene-α,β-dioxygenase A (LsdA) from the bacterium Sphingomonas paucimobilis TMY1009 is a nonheme iron oxygenase that catalyzes the cleavage of lignostilbene, a compound arising in lignin transformation, to two vanillin molecules. To examine LsdA's substrate specificity, we heterologously produced the dimeric enzyme with the help of chaperones. When tested on several substituted stilbenes, LsdA exhibited the greatest specificity for lignostilbene (k cat app = 1.00 ± 0.04 × 106 m-1 s-1). These experiments further indicated that the substrate's 4-hydroxy moiety is required for catalysis and that this moiety cannot be replaced with a methoxy group. Phenylazophenol inhibited the LsdA-catalyzed cleavage of lignostilbene in a reversible, mixed fashion (Kic = 6 ± 1 μm, Kiu = 24 ± 4 μm). An X-ray crystal structure of LsdA at 2.3 Å resolution revealed a seven-bladed β-propeller fold with an iron cofactor coordinated by four histidines, in agreement with previous observations on related carotenoid cleavage oxygenases. We noted that residues at the dimer interface are also present in LsdB, another lignostilbene dioxygenase in S. paucimobilis TMY1009, rationalizing LsdA and LsdB homo- and heterodimerization in vivo A structure of an LsdA·phenylazophenol complex identified Phe59, Tyr101, and Lys134 as contacting the 4-hydroxyphenyl moiety of the inhibitor. Phe59 and Tyr101 substitutions with His and Phe, respectively, reduced LsdA activity (k cat app) ∼15- and 10-fold. The K134M variant did not detectably cleave lignostilbene, indicating that Lys134 plays a key catalytic role. This study expands our mechanistic understanding of LsdA and related stilbene-cleaving dioxygenases.
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Affiliation(s)
- Eugene Kuatsjah
- Genome Science and Technology Program, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Meghan M Verstraete
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Marek J Kobylarz
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Alvin K N Liu
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Lindsay D Eltis
- Genome Science and Technology Program, The University of British Columbia, Vancouver V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver V6T 1Z3, Canada.
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18
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Navas LE, Martínez FD, Taverna ME, Fetherolf MM, Eltis LD, Nicolau V, Estenoz D, Campos E, Benintende GB, Berretta MF. A thermostable laccase from Thermus sp. 2.9 and its potential for delignification of Eucalyptus biomass. AMB Express 2019; 9:24. [PMID: 30756202 PMCID: PMC6372703 DOI: 10.1186/s13568-019-0748-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/04/2019] [Indexed: 11/25/2022] Open
Abstract
Laccases are multicopper oxidases that are being studied for their potential application in pretreatment strategies of lignocellulosic feedstocks for bioethanol production. Here, we report the expression and characterization of a predicted laccase (LAC_2.9) from the thermophilic bacterial strain Thermus sp. 2.9 and investigate its capacity to delignify lignocellulosic biomass. The purified enzyme displayed a blue color typical of laccases, showed strict copper dependence and retained 80% of its activity after 16 h at 70 °C. At 60 °C, the enzyme oxidized 2,2′-azino-di-(3-ethylbenzthiazoline sulfonate) (ABTS) and 2,6-dimethoxyphenol (DMP) at optimal pH of 5 and 6, respectively. LAC_2.9 had higher substrate specificity (kcat/KM) for DMP with a calculated value that accounts for one of the highest reported for laccases. Further, the enzyme oxidized a phenolic lignin model dimer. The incubation of steam-exploded eucalyptus biomass with LAC_2.9 and 1-hydroxybenzotriazole (HBT) as mediator changed the structural properties of the lignocellulose as evidenced by Fourier transform infrared (FTIR) spectroscopy and thermo-gravimetric analysis (TGA). However, this did not increase the yield of sugars released by enzymatic saccharification. In conclusion, LAC_2.9 is a thermostable laccase with potential application in the delignification of lignocellulosic biomass.
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19
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Kuatsjah E, Chan ACK, Hurst TE, Snieckus V, Murphy MEP, Eltis LD. Metal- and Serine-Dependent Meta-Cleavage Product Hydrolases Utilize Similar Nucleophile-Activation Strategies. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02955] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - Timothy E. Hurst
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Victor Snieckus
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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20
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Alexander JAN, Chatterjee SS, Hamilton SM, Eltis LD, Chambers HF, Strynadka NCJ. Structural and kinetic analyses of penicillin-binding protein 4 (PBP4)-mediated antibiotic resistance in Staphylococcus aureus. J Biol Chem 2018; 293:19854-19865. [PMID: 30366985 DOI: 10.1074/jbc.ra118.004952] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 07/19/2018] [Revised: 10/24/2018] [Indexed: 01/08/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) causes serious community-acquired and nosocomial infections worldwide. MRSA strains are resistant to a variety of antibiotics, including the classic penicillin and cephalosporin classes of β-lactams, making them intractable to treatment. Although β-lactam resistance in MRSA has been ascribed to the acquisition and activity of penicillin-binding protein 2a (PBP2a, encoded by mecA), it has recently been observed that resistance can also be mediated by penicillin-binding protein 4 (PBP4). Previously, we have shown that broad-spectrum β-lactam resistance can arise following serial passaging of a mecA-negative COL strain of S. aureus, creating the CRB strain. This strain has two missense mutations in pbp4 and a mutation in the pbp4 promoter, both of which play an instrumental role in β-lactam resistance. To better understand PBP4's role in resistance, here we have characterized its kinetics and structure with clinically relevant β-lactam antibiotics. We present the first crystallographic PBP4 structures of apo and acyl-enzyme intermediate forms complexed with three late-generation β-lactam antibiotics: ceftobiprole, ceftaroline, and nafcillin. In parallel, we characterized the structural and kinetic effects of the PBP4 mutations present in the CRB strain. Localized within the transpeptidase active-site cleft, the two substitutions appear to have different effects depending on the drug. With ceftobiprole, the missense mutations impaired the Km value 150-fold, decreasing the proportion of inhibited PBP4. However, ceftaroline resistance appeared to be mediated by other factors, possibly including mutation of the pbp4 promoter. Our findings provide evidence that S. aureus CRB has at least two PBP4-mediated resistance mechanisms.
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Affiliation(s)
- J Andrew N Alexander
- From the Department of Biochemistry and Molecular Biology.,the Centre for Blood Research, and
| | - Som S Chatterjee
- the Division of Infectious Disease, Department of Medicine, San Francisco General Hospital, San Francisco, California 94110
| | - Stephanie M Hamilton
- the Division of Infectious Disease, Department of Medicine, San Francisco General Hospital, San Francisco, California 94110
| | - Lindsay D Eltis
- From the Department of Biochemistry and Molecular Biology.,the Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada and
| | - Henry F Chambers
- the Division of Infectious Disease, Department of Medicine, San Francisco General Hospital, San Francisco, California 94110
| | - Natalie C J Strynadka
- From the Department of Biochemistry and Molecular Biology, .,the Centre for Blood Research, and
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21
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Wilhelm RC, Singh R, Eltis LD, Mohn WW. Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing. ISME J 2018; 13:413-429. [PMID: 30258172 PMCID: PMC6331573 DOI: 10.1038/s41396-018-0279-6] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/20/2018] [Accepted: 08/11/2018] [Indexed: 11/19/2022]
Abstract
Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin, cellulose and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of 13C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated 13C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.
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Affiliation(s)
- Roland C Wilhelm
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Rahul Singh
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - William W Mohn
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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22
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Nerdinger S, Kuatsjah E, Hurst TE, Schlapp-Hackl I, Kahlenberg V, Wurst K, Eltis LD, Snieckus V. Bacterial Catabolism of Biphenyls: Synthesis and Evaluation of Analogues. Chembiochem 2018; 19:1771-1778. [PMID: 29905982 DOI: 10.1002/cbic.201800231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 05/01/2018] [Indexed: 12/31/2022]
Abstract
A series of alkylated 2,3-dihydroxybiphenyls has been prepared on the gram scale by using an effective Directed ortho Metalation-Suzuki-Miyaura cross-coupling strategy. These compounds have been used to investigate the substrate specificity of the meta-cleavage dioxygenase BphC, a key enzyme in the microbial catabolism of biphenyl. Isolation and characterization of the meta-cleavage products will allow further study of related processes, including the catabolism of lignin-derived biphenyls.
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Affiliation(s)
- Sven Nerdinger
- Global Commercial Operations, Sandoz GmbH, Biochemiestrasse 10, 6250, Kundl, Austria
| | - Eugene Kuatsjah
- Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Timothy E Hurst
- Department of Chemistry, Queen's University, Chernoff Hall, Kingston, ON, K7L 3N6, Canada
| | - Inge Schlapp-Hackl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Center for Chemistry and Biomedicine, Innrain 80-82, 6020, Innsbruck, Austria
| | - Volker Kahlenberg
- Institute of Mineralogy and Petrography, University of Innsbruck, Innrain 52, 6020, Innsbruck, Austria
| | - Klaus Wurst
- Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Lindsay D Eltis
- Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Victor Snieckus
- Department of Chemistry, Queen's University, Chernoff Hall, Kingston, ON, K7L 3N6, Canada
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23
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Abstract
Enzymes that catalyze hydroxylation of unactivated carbons normally contain heme and nonheme iron cofactors. By contrast, how a pyridoxal phosphate (PLP)-dependent enzyme could catalyze such a hydroxylation was unknown. Here, we investigate RohP, a PLP-dependent enzyme that converts l-arginine to ( S)-4-hydroxy-2-ketoarginine. We determine that the RohP reaction consumes oxygen with stoichiometric release of H2O2. To understand this unusual chemistry, we obtain ∼1.5 Å resolution structures that capture intermediates along the catalytic cycle. Our data suggest that RohP carries out a four-electron oxidation and a stereospecific alkene hydration to give the ( S)-configured product. Together with our earlier studies on an O2, PLP-dependent l-arginine oxidase, our work suggests that there is a shared pathway leading to both oxidized and hydroxylated products from l-arginine.
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Affiliation(s)
| | | | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
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24
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Hedges JB, Kuatsjah E, Du Y, Eltis LD, Ryan KS. Snapshots of the catalytic cycle of an O
2
, pyridoxal phosphate‐dependent hydroxylase. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.796.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jason B. Hedges
- Department of ChemistryUniversity of British ColumbiaVancouverBCCanada
| | - Eugene Kuatsjah
- Genome Science and Technology ProgramUniversity of British ColumbiaVancouverBCCanada
- Department of Microbiology and ImmunologyUniversity of British ColumbiaVancouverBCCanada
| | - Yi‐Ling Du
- Institute of Pharmaceutical BiotechnologyCollege of Pharmaceutical SciencesZhejiang UniversityHangzhouPeople's Republic of China
| | - Lindsay D. Eltis
- Department of Microbiology and ImmunologyUniversity of British ColumbiaVancouverBCCanada
| | - Katherine S. Ryan
- Department of ChemistryUniversity of British ColumbiaVancouverBCCanada
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25
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Eltis LD, Singh R. Chapter 11. Biological Funneling as a Means of Transforming Lignin-derived Aromatic Compounds into Value-added Chemicals. Energy and Environment Series 2018. [DOI: 10.1039/9781788010351-00290] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Bowden CFM, Chan ACK, Li EJW, Arrieta AL, Eltis LD, Murphy MEP. Structure-function analyses reveal key features in Staphylococcus aureus IsdB-associated unfolding of the heme-binding pocket of human hemoglobin. J Biol Chem 2017; 293:177-190. [PMID: 29109153 DOI: 10.1074/jbc.m117.806562] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 07/12/2017] [Revised: 10/19/2017] [Indexed: 11/06/2022] Open
Abstract
IsdB is a receptor on the surface of the bacterial pathogen Staphylococcus aureus that extracts heme from hemoglobin (Hb) to enable growth on Hb as a sole iron source. IsdB is critically important both for in vitro growth on Hb and in infection models and is also highly up-regulated in blood, serum, and tissue infection models, indicating a key role of this receptor in bacterial virulence. However, structural information for IsdB is limited. We present here a crystal structure of a complex between human Hb and IsdB. In this complex, the α subunits of Hb are refolded with the heme displaced to the interface with IsdB. We also observe that atypical residues of Hb, His58 and His89 of αHb, coordinate to the heme iron, which is poised for transfer into the heme-binding pocket of IsdB. Moreover, the porphyrin ring interacts with IsdB residues Tyr440 and Tyr444 Previously, Tyr440 was observed to coordinate heme iron in an IsdB·heme complex structure. A Y440F/Y444F IsdB variant we produced was defective in heme transfer yet formed a stable complex with Hb (Kd = 6 ± 2 μm) in solution with spectroscopic features of the bis-His species observed in the crystal structure. Haptoglobin binds to a distinct site on Hb to inhibit heme transfer to IsdB and growth of S. aureus, and a ternary complex of IsdB·Hb·Hp was observed. We propose a model for IsdB heme transfer from Hb that involves unfolding of Hb and heme iron ligand exchange.
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Affiliation(s)
- Catherine F M Bowden
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Anson C K Chan
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Emily J W Li
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Angelé L Arrieta
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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27
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Kuatsjah E, Chan ACK, Kobylarz MJ, Murphy MEP, Eltis LD. The bacterial meta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the α/β-hydrolase superfamily. J Biol Chem 2017; 292:18290-18302. [PMID: 28935670 DOI: 10.1074/jbc.m117.797696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 05/25/2017] [Revised: 09/15/2017] [Indexed: 01/27/2023] Open
Abstract
Strain SYK-6 of the bacterium Sphingobium sp. catabolizes lignin-derived biphenyl via a meta-cleavage pathway. In this pathway, LigY is proposed to catalyze the hydrolysis of the meta-cleavage product (MCP) 4,11-dicarboxy-8-hydroxy-9-methoxy-2-hydroxy-6-oxo-6-phenyl-hexa-2,4-dienoate. Here, we validated this reaction by identifying 5-carboxyvanillate and 4-carboxy-2-hydroxypenta-2,4-dienoate as the products and determined the kcat and kcat/Km values as 9.3 ± 0.6 s-1 and 2.5 ± 0.2 × 107 m-1 s-1, respectively. Sequence analyses and a 1.9 Å resolution crystal structure established that LigY belongs to the amidohydrolase superfamily, unlike previously characterized MCP hydrolases, which are serine-dependent enzymes of the α/β-hydrolase superfamily. The active-site architecture of LigY resembled that of α-amino-β-carboxymuconic-ϵ-semialdehyde decarboxylase, a class III amidohydrolase, with a single zinc ion coordinated by His-6, His-8, His-179, and Glu-282. Interestingly, we found that LigY lacks the acidic residue proposed to activate water for hydrolysis in other class III amidohydrolases. Moreover, substitution of His-223, a conserved residue proposed to activate water in other amidohydrolases, reduced the kcat to a much lesser extent than what has been reported for other amidohydrolases, suggesting that His-223 has a different role in LigY. Substitution of Arg-72, Tyr-190, Arg-234, or Glu-282 reduced LigY activity over 100-fold. On the basis of these results, we propose a catalytic mechanism involving substrate tautomerization, substrate-assisted activation of water for hydrolysis, and formation of a gem-diol intermediate. This last step diverges from what occurs in serine-dependent MCP hydrolases. This study provides insight into C-C-hydrolyzing enzymes and expands the known range of reactions catalyzed by the amidohydrolase superfamily.
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Affiliation(s)
| | - Anson C K Chan
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Marek J Kobylarz
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E P Murphy
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- From the Genome Science and Technology Program and .,the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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28
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Kuatsjah E, Chen HM, Withers SG, Eltis LD. Characterization of an extradiol dioxygenase involved in the catabolism of lignin-derived biphenyl. FEBS Lett 2017; 591:1001-1009. [DOI: 10.1002/1873-3468.12611] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 02/22/2017] [Accepted: 02/23/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Eugene Kuatsjah
- Genome Science and Technology Program; The University of British Columbia; Vancouver BC Canada
| | - Hong-Ming Chen
- Department of Chemistry; The University of British Columbia; Vancouver BC Canada
| | - Stephen G. Withers
- Genome Science and Technology Program; The University of British Columbia; Vancouver BC Canada
- Department of Chemistry; The University of British Columbia; Vancouver BC Canada
- Department of Biochemistry; Life Sciences Institute; The University of British Columbia; Vancouver BC Canada
| | - Lindsay D. Eltis
- Genome Science and Technology Program; The University of British Columbia; Vancouver BC Canada
- Department of Biochemistry; Life Sciences Institute; The University of British Columbia; Vancouver BC Canada
- Department of Microbiology and Immunology; Life Sciences Institute; The University of British Columbia; Vancouver BC Canada
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29
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Amara S, Seghezzi N, Otani H, Diaz-Salazar C, Liu J, Eltis LD. Characterization of key triacylglycerol biosynthesis processes in rhodococci. Sci Rep 2016; 6:24985. [PMID: 27126051 PMCID: PMC4850399 DOI: 10.1038/srep24985] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/01/2016] [Indexed: 11/09/2022] Open
Abstract
Oleaginous microorganisms have considerable potential for biofuel and commodity chemical production. Under nitrogen-limitation, Rhodococcus jostii RHA1 grown on benzoate, an analog of lignin depolymerization products, accumulated triacylglycerols (TAGs) to 55% of its dry weight during transition to stationary phase, with the predominant fatty acids being C16:0 and C17:0. Transcriptomic analyses of RHA1 grown under conditions of N-limitation and N-excess revealed 1,826 dysregulated genes. Genes whose transcripts were more abundant under N-limitation included those involved in ammonium assimilation, benzoate catabolism, fatty acid biosynthesis and the methylmalonyl-CoA pathway. Of the 16 atf genes potentially encoding diacylglycerol O-acyltransferases, atf8 transcripts were the most abundant during N-limitation (~50-fold more abundant than during N-excess). Consistent with Atf8 being a physiological determinant of TAG accumulation, a Δatf8 mutant accumulated 70% less TAG than wild-type RHA1 while atf8 overexpression increased TAG accumulation 20%. Genes encoding type-2 phosphatidic acid phosphatases were not significantly expressed. By contrast, three genes potentially encoding phosphatases of the haloacid dehalogenase superfamily and that cluster with, or are fused with other Kennedy pathway genes were dysregulated. Overall, these findings advance our understanding of TAG metabolism in mycolic acid-containing bacteria and provide a framework to engineer strains for increased TAG production.
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Affiliation(s)
- Sawsan Amara
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Nicolas Seghezzi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Hiroshi Otani
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Carlos Diaz-Salazar
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jie Liu
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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30
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Ho NAT, Dawes SS, Crowe AM, Casabon I, Gao C, Kendall SL, Baker EN, Eltis LD, Lott JS. The Structure of the Transcriptional Repressor KstR in Complex with CoA Thioester Cholesterol Metabolites Sheds Light on the Regulation of Cholesterol Catabolism in Mycobacterium tuberculosis. J Biol Chem 2016; 291:7256-66. [PMID: 26858250 DOI: 10.1074/jbc.m115.707760] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 12/01/2015] [Indexed: 12/19/2022] Open
Abstract
Cholesterol can be a major carbon source forMycobacterium tuberculosisduring infection, both at an early stage in the macrophage phagosome and later within the necrotic granuloma. KstR is a highly conserved TetR family transcriptional repressor that regulates a large set of genes responsible for cholesterol catabolism. Many genes in this regulon, includingkstR, are either induced during infection or are essential for survival ofM. tuberculosis in vivo In this study, we identified two ligands for KstR, both of which are CoA thioester cholesterol metabolites with four intact steroid rings. A metabolite in which one of the rings was cleaved was not a ligand. We confirmed the ligand-protein interactions using intrinsic tryptophan fluorescence and showed that ligand binding strongly inhibited KstR-DNA binding using surface plasmon resonance (IC50for ligand = 25 nm). Crystal structures of the ligand-free form of KstR show variability in the position of the DNA-binding domain. In contrast, structures of KstR·ligand complexes are highly similar to each other and demonstrate a position of the DNA-binding domain that is unfavorable for DNA binding. Comparison of ligand-bound and ligand-free structures identifies residues involved in ligand specificity and reveals a distinctive mechanism by which the ligand-induced conformational change mediates DNA release.
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Affiliation(s)
- Ngoc Anh Thu Ho
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| | - Stephanie S Dawes
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| | - Adam M Crowe
- the Departments of Biochemistry and Molecular Biology and
| | - Israël Casabon
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand, Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Chen Gao
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| | - Sharon L Kendall
- the Department of Pathology and Pathogen Biology The Royal Veterinary College, Royal College Street, London NW1 0TU, United Kingdom, and
| | - Edward N Baker
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand
| | - Lindsay D Eltis
- the Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - J Shaun Lott
- From the School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3a Symonds Street, Auckland 1142, New Zealand,
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31
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Du YL, Singh R, Alkhalaf LM, Kuatsjah E, He HY, Eltis LD, Ryan KS. A pyridoxal phosphate–dependent enzyme that oxidizes an unactivated carbon-carbon bond. Nat Chem Biol 2016; 12:194-9. [DOI: 10.1038/nchembio.2009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/02/2015] [Indexed: 11/09/2022]
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32
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Otani H, Stogios PJ, Xu X, Nocek B, Li SN, Savchenko A, Eltis LD. The activity of CouR, a MarR family transcriptional regulator, is modulated through a novel molecular mechanism. Nucleic Acids Res 2015; 44:595-607. [PMID: 26400178 PMCID: PMC4737184 DOI: 10.1093/nar/gkv955] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/11/2015] [Indexed: 12/21/2022] Open
Abstract
CouR, a MarR-type transcriptional repressor, regulates the cou genes, encoding p-hydroxycinnamate catabolism in the soil bacterium Rhodococcus jostii RHA1. The CouR dimer bound two molecules of the catabolite p-coumaroyl-CoA (Kd = 11 ± 1 μM). The presence of p-coumaroyl-CoA, but neither p-coumarate nor CoASH, abrogated CouR's binding to its operator DNA in vitro. The crystal structures of ligand-free CouR and its p-coumaroyl-CoA-bound form showed no significant conformational differences, in contrast to other MarR regulators. The CouR-p-coumaroyl-CoA structure revealed two ligand molecules bound to the CouR dimer with their phenolic moieties occupying equivalent hydrophobic pockets in each protomer and their CoA moieties adopting non-equivalent positions to mask the regulator's predicted DNA-binding surface. More specifically, the CoA phosphates formed salt bridges with predicted DNA-binding residues Arg36 and Arg38, changing the overall charge of the DNA-binding surface. The substitution of either arginine with alanine completely abrogated the ability of CouR to bind DNA. By contrast, the R36A/R38A double variant retained a relatively high affinity for p-coumaroyl-CoA (Kd = 89 ± 6 μM). Together, our data point to a novel mechanism of action in which the ligand abrogates the repressor's ability to bind DNA by steric occlusion of key DNA-binding residues and charge repulsion of the DNA backbone.
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Affiliation(s)
- Hiroshi Otani
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Boguslaw Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory and the Midwest Center for Structural Genomics, Lemont, IL 60439, USA
| | - Shu-Nan Li
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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33
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Crowe AM, Stogios PJ, Casabon I, Evdokimova E, Savchenko A, Eltis LD. Structural and functional characterization of a ketosteroid transcriptional regulator of Mycobacterium tuberculosis. J Biol Chem 2014; 290:872-82. [PMID: 25406313 DOI: 10.1074/jbc.m114.607481] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catabolism of host cholesterol is critical to the virulence of Mycobacterium tuberculosis and is a potential target for novel therapeutics. KstR2, a TetR family repressor (TFR), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (HIP). Binding of KstR2 to its operator sequences is relieved upon binding of HIP-CoA. A 1.6-Å resolution crystal structure of the KstR2(Mtb)·HIP-CoA complex reveals that the KstR2(Mtb) dimer accommodates two molecules of HIP-CoA. Each ligand binds in an elongated cleft spanning the dimerization interface such that the HIP and CoA moieties interact with different KstR2(Mtb) protomers. In isothermal titration calorimetry studies, the dimer bound 2 eq of HIP-CoA with high affinity (K(d) = 80 ± 10 nm) but bound neither HIP nor CoASH. Substitution of Arg-162 or Trp-166, residues that interact, respectively, with the diphosphate and HIP moieties of HIP-CoA, dramatically decreased the affinity of KstR2(Mtb) for HIP-CoA but not for its operator sequence. The variant of R162M that decreased the affinity for HIP-CoA (ΔΔG = 13 kJ mol(-1)) is consistent with the loss of three hydrogen bonds as indicated in the structural data. A 24-bp operator sequence bound two dimers of KstR2. Structural comparisons with a ligand-free rhodococcal homologue and a DNA-bound homologue suggest that HIP-CoA induces conformational changes of the DNA-binding domains of the dimer that preclude their proper positioning in the major groove of DNA. The results provide insight into KstR2-mediated regulation of expression of steroid catabolic genes and the determinants of ligand binding in TFRs.
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Affiliation(s)
- Adam M Crowe
- From the Departments of Biochemistry and Molecular Biology and
| | - Peter J Stogios
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and
| | - Israël Casabon
- Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Elena Evdokimova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and The Midwest Center for Structural Genomics (MCSG), Argonne National Laboratory, Argonne, Illinois 60439
| | - Alexei Savchenko
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and The Midwest Center for Structural Genomics (MCSG), Argonne National Laboratory, Argonne, Illinois 60439
| | - Lindsay D Eltis
- From the Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada,
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34
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Zhu SH, Reuther J, Liu J, Crocker FH, Indest KJ, Eltis LD, Mohn WW. The essential role of nitrogen limitation in expression of xplA and degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in Gordonia sp. strain KTR9. Appl Microbiol Biotechnol 2014; 99:459-67. [PMID: 25142696 DOI: 10.1007/s00253-014-6013-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 08/01/2014] [Accepted: 08/04/2014] [Indexed: 10/24/2022]
Abstract
Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a widely used explosive and a major soil and groundwater contaminant. Organisms such as Gordonia sp. KTR9, capable of degrading RDX and using it as an N source, may prove useful for bioremediation of contaminated sites. XplA is a cytochrome P450 monooxygenase responsible for RDX degradation. Expression of xplA in KTR9 was not induced by RDX but was strongly induced (50-fold) during N-limited growth. When glnR, encoding a regulatory protein affecting N assimilation in diverse Actinobacteria, was deleted from KTR9, the bacterium lost the ability to use nitrate, nitrite, and RDX as N sources. Deletion of glnR also abolished the inhibition of xplA expression by nitrite. Our results confirm the essential role of GlnR in regulating assimilation of nitrite, but there was no evidence for a direct role of GlnR in regulating XplA expression. Rather, the general availability of nitrogen repressed XplA expression. We conclude that the inability of the glnR mutant to use RDX as an N source was due to its inability to assimilate nitrite, an intermediate in the assimilation of nitrogen from RDX. Regulation of XplA does not seem adaptive for KTR9, but it is important for RDX bioremediation with KTR9 or similar bacteria.
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Affiliation(s)
- Song-Hua Zhu
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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35
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Penfield JS, Worrall LJ, Strynadka NC, Eltis LD. Substrate specificities and conformational flexibility of 3-ketosteroid 9α-hydroxylases. J Biol Chem 2014; 289:25523-36. [PMID: 25049233 DOI: 10.1074/jbc.m114.575886] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
KshA is the oxygenase component of 3-ketosteroid 9α-hydroxylase, a Rieske oxygenase involved in the bacterial degradation of steroids. Consistent with its role in bile acid catabolism, KshA1 from Rhodococcus rhodochrous DSM43269 had the highest apparent specificity (kcat/Km) for steroids with an isopropyl side chain at C17, such as 3-oxo-23,24-bisnorcholesta-1,4-diene-22-oate (1,4-BNC). By contrast, the KshA5 homolog had the highest apparent specificity for substrates with no C17 side chain (kcat/Km >10(5) s(-1) M(-1) for 4-estrendione, 5α-androstandione, and testosterone). Unexpectedly, substrates such as 4-androstene-3,17-dione (ADD) and 4-BNC displayed strong substrate inhibition (Ki S ∼100 μM). By comparison, the cholesterol-degrading KshAMtb from Mycobacterium tuberculosis had the highest specificity for CoA-thioesterified substrates. These specificities are consistent with differences in the catabolism of cholesterol and bile acids, respectively, in actinobacteria. X-ray crystallographic structures of the KshAMtb·ADD, KshA1·1,4-BNC-CoA, KshA5·ADD, and KshA5·1,4-BNC-CoA complexes revealed that the enzymes have very similar steroid-binding pockets with the substrate's C17 oriented toward the active site opening. Comparisons suggest Tyr-245 and Phe-297 are determinants of KshA1 specificity. All enzymes have a flexible 16-residue "mouth loop," which in some structures completely occluded the substrate-binding pocket from the bulk solvent. Remarkably, the catalytic iron and α-helices harboring its ligands were displaced up to 4.4 Å in the KshA5·substrate complexes as compared with substrate-free KshA, suggesting that Rieske oxygenases may have a dynamic nature similar to cytochrome P450.
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Affiliation(s)
| | - Liam J Worrall
- From the Departments of Biochemistry and Molecular Biology and
| | | | - Lindsay D Eltis
- From the Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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36
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Bowden CFM, Verstraete MM, Eltis LD, Murphy MEP. Hemoglobin binding and catalytic heme extraction by IsdB near iron transporter domains. Biochemistry 2014; 53:2286-94. [PMID: 24645787 DOI: 10.1021/bi500230f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Isd (iron-regulated surface determinant) system is a multiprotein transporter that allows bacterium Staphylococcus aureus to take up iron from hemoglobin (Hb) during human infection. In this system, IsdB is a cell wall-anchored surface protein that contains two near iron transporter (NEAT) domains, one of which binds heme. IsdB rapidly extracts heme from Hb and transfers it to IsdA for relay into the bacterial cell. Using a series of recombinant IsdB constructs that included at least one NEAT domain, we demonstrated that both domains are required to bind Hb with high affinity (KD = 0.42 ± 0.05 μM) and to extract heme from Hb. Moreover, IsdB extracted heme only from oxidized metHb, although it also bound oxyHb and the Hb-CO complex. In a reconstituted model of the biological heme relay pathway, IsdB catalyzed the transfer of heme from metHb to IsdA with a Km for metHb of 0.75 ± 0.07 μN and a kcat of 0.22 ± 0.01 s(-1). The latter is consistent with the transfer of heme from metHb to IsdB being the rate-limiting step. With both NEAT domains and the linker region present in a single contiguous polypeptide, high-affinity Hb binding was achieved, rapid heme uptake was observed, and multiple turnovers of heme extraction from metHb and transfer to IsdA were conducted, representing all known Hb-heme uptake functions of the full-length IsdB protein.
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Affiliation(s)
- Catherine F M Bowden
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia , Vancouver, BC, Canada V6T 1Z3
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37
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Barrientos Á, Merino E, Casabon I, Rodríguez J, Crowe AM, Holert J, Philipp B, Eltis LD, Olivera ER, Luengo JM. Functional analyses of three acyl-CoA synthetases involved in bile acid degradation in Pseudomonas putida DOC21. Environ Microbiol 2014; 17:47-63. [PMID: 24428272 DOI: 10.1111/1462-2920.12395] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/30/2013] [Accepted: 01/04/2014] [Indexed: 12/15/2022]
Abstract
Pseudomonas putida DOC21, a soil-dwelling proteobacterium, catabolizes a variety of steroids and bile acids. Transposon mutagenesis and bioinformatics analyses identified four clusters of steroid degradation (std) genes encoding a single catabolic pathway. The latter includes three predicted acyl-CoA synthetases encoded by stdA1, stdA2 and stdA3 respectively. The ΔstdA1 and ΔstdA2 deletion mutants were unable to assimilate cholate or other bile acids but grew well on testosterone or 4-androstene-3,17-dione (AD). In contrast, a ΔstdA3 mutant grew poorly in media containing either testosterone or AD. When cells were grown with succinate in the presence of cholate, ΔstdA1 accumulated Δ(1/4) -3-ketocholate and Δ(1,4) -3-ketocholate, whereas ΔstdA2 only accumulated 7α,12α-dihydroxy-3-oxopregna-1,4-diene-20-carboxylate (DHOPDC). When incubated with testosterone or bile acids, ΔstdA3 accumulated 3aα-H-4α(3'propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP) or the corresponding hydroxylated derivative. Biochemical analyses revealed that StdA1 converted cholate, 3-ketocholate, Δ(1/4) -3-ketocholate, and Δ(1,4) -3-ketocholate to their CoA thioesters, while StdA2 transformed DHOPDC to DHOPDC-CoA. In contrast, purified StdA3 catalysed the CoA thioesterification of HIP and its hydroxylated derivatives. Overall, StdA1, StdA2 and StdA3 are acyl-CoA synthetases required for the complete degradation of bile acids: StdA1 and StdA2 are involved in degrading the C-17 acyl chain, whereas StdA3 initiates degradation of the last two steroid rings. The study highlights differences in steroid catabolism between Proteobacteria and Actinobacteria.
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Affiliation(s)
- Álvaro Barrientos
- Departmento de Biología Molecular, Facultad de Veterinaria, Universidad de León, León, Spain
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38
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Sainsbury PD, Hardiman EM, Ahmad M, Otani H, Seghezzi N, Eltis LD, Bugg TDH. Breaking down lignin to high-value chemicals: the conversion of lignocellulose to vanillin in a gene deletion mutant of Rhodococcus jostii RHA1. ACS Chem Biol 2013; 8:2151-6. [PMID: 23898824 DOI: 10.1021/cb400505a] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The aromatic polymer lignin represents a possible renewable source of aromatic chemicals, if biocatalytic routes for lignin breakdown can be developed. The availability of a genome sequence for Rhodococcus jostii RHA1, a bacterium that breaks down lignin, has allowed the application of a targeted pathway engineering strategy to lignin breakdown to produce vanillin, a valuable food/flavor chemical. A gene deletion strain of R. jostii RHA1 in which the vanillin dehydrogenase gene had been deleted, when grown on minimal medium containing 2.5% wheat straw lignocellulose and 0.05% glucose, was found to accumulate vanillin with yields of up to 96 mg/L after 144 h, together with smaller amounts of ferulic acid and 4-hydroxybenzaldehyde.
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Affiliation(s)
- Paul D. Sainsbury
- Department of Chemistry, University
of Warwick, Coventry CV4 7AL, U.K
| | | | - Mark Ahmad
- Department of Chemistry, University
of Warwick, Coventry CV4 7AL, U.K
| | - Hiroshi Otani
- Department of Microbiology and Immunology, University of British
Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T
1Z3, Canada
| | - Nicolas Seghezzi
- Department of Microbiology and Immunology, University of British
Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T
1Z3, Canada
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, University of British
Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T
1Z3, Canada
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39
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Ramón-García S, Ng C, Jensen PR, Dosanjh M, Burian J, Morris RP, Folcher M, Eltis LD, Grzesiek S, Nguyen L, Thompson CJ. WhiB7, an Fe-S-dependent transcription factor that activates species-specific repertoires of drug resistance determinants in actinobacteria. J Biol Chem 2013; 288:34514-28. [PMID: 24126912 DOI: 10.1074/jbc.m113.516385] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
WhiB-like (Wbl) proteins are well known for their diverse roles in actinobacterial morphogenesis, cell division, virulence, primary and secondary metabolism, and intrinsic antibiotic resistance. Gene disruption experiments showed that three different Actinobacteria (Mycobacterium smegmatis, Streptomyces lividans, and Rhodococcus jostii) each exhibited a different whiB7-dependent resistance profile. Heterologous expression of whiB7 genes showed these resistance profiles reflected the host's repertoire of endogenous whiB7-dependent genes. Transcriptional activation of two resistance genes in the whiB7 regulon, tap (a multidrug transporter) and erm(37) (a ribosomal methyltransferase), required interaction of WhiB7 with their promoters. Furthermore, heterologous expression of tap genes isolated from Mycobacterium species demonstrated that divergencies in drug specificity of homologous structural proteins contribute to the variation of WhiB7-dependent drug resistance. WhiB7 has a specific tryptophan/glycine-rich region and four conserved cysteine residues; it also has a peptide sequence (AT-hook) at its C terminus that binds AT-rich DNA sequence motifs upstream of the promoters it activates. Targeted mutagenesis showed that these motifs were required to provide antibiotic resistance in vivo. Anaerobically purified WhiB7 from S. lividans was dimeric and contained 2.1 ± 0.3 and 2.2 ± 0.3 mol of iron and sulfur, respectively, per protomer (consistent with the presence of a 2Fe-2S cluster). However, the properties of the dimer's absorption spectrum were most consistent with the presence of an oxygen-labile 4Fe-4S cluster, suggesting 50% occupancy. These data provide the first insights into WhiB7 iron-sulfur clusters as they exist in vivo, a major unresolved issue in studies of Wbl proteins.
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Affiliation(s)
- Santiago Ramón-García
- From the Department of Microbiology and Immunology, Centre for Tuberculosis Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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40
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Ruzzini AC, Bhowmik S, Ghosh S, Yam KC, Bolin JT, Eltis LD. A substrate-assisted mechanism of nucleophile activation in a Ser-His-Asp containing C-C bond hydrolase. Biochemistry 2013; 52:7428-38. [PMID: 24067021 DOI: 10.1021/bi401156a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The meta-cleavage product (MCP) hydrolases utilize a Ser-His-Asp triad to hydrolyze a carbon-carbon bond. Hydrolysis of the MCP substrate has been proposed to proceed via an enol-to-keto tautomerization followed by a nucleophilic mechanism of catalysis. Ketonization involves an intermediate, ES(red), which possesses a remarkable bathochromically shifted absorption spectrum. We investigated the catalytic mechanism of the MCP hydrolases using DxnB2 from Sphingomonas wittichii RW1. Pre-steady-state kinetic and LC ESI/MS evaluation of the DxnB2-mediated hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid to 2-hydroxy-2,4-pentadienoic acid and benzoate support a nucleophilic mechanism catalysis. In DxnB2, the rate of ES(red) decay and product formation showed a solvent kinetic isotope effect of 2.5, indicating that a proton transfer reaction, assigned here to substrate ketonization, limits the rate of acylation. For a series of substituted MCPs, this rate was linearly dependent on MCP pKa2 (βnuc ∼ 1). Structural characterization of DxnB2 S105A:MCP complexes revealed that the catalytic histidine is displaced upon substrate-binding. The results provide evidence for enzyme-catalyzed ketonization in which the catalytic His-Asp pair does not play an essential role. The data further suggest that ES(red) represents a dianionic intermediate that acts as a general base to activate the serine nucleophile. This substrate-assisted mechanism of nucleophilic catalysis distinguishes MCP hydrolases from other serine hydrolases.
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Affiliation(s)
- Antonio C Ruzzini
- Departments of †Biochemistry & Molecular Biology and ‡Microbiology & Immunology, The University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
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41
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Ruzzini AC, Bhowmik S, Yam KC, Ghosh S, Bolin JT, Eltis LD. The lid domain of the MCP hydrolase DxnB2 contributes to the reactivity toward recalcitrant PCB metabolites. Biochemistry 2013; 52:5685-5695. [PMID: 23879719 PMCID: PMC3903462 DOI: 10.1021/bi400774m] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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: 11/28/2022]
Abstract
DxnB2 and BphD are meta-cleavage product (MCP) hydrolases that catalyze C-C bond hydrolysis of the biphenyl metabolite 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA). BphD is a bottleneck in the bacterial degradation of polychlorinated biphenyls (PCBs) by the Bph catabolic pathway due in part to inhibition by 3-Cl HOPDAs. By contrast, DxnB2 from Sphingomonas wittichii RW1 catalyzes the hydrolysis of 3-Cl HOPDAs more efficiently. X-ray crystallographic studies of the catalytically inactive S105A variant of DxnB2 complexed with 3-Cl HOPDA revealed a binding mode in which C1 through C6 of the dienoate are coplanar. The chlorine substituent is accommodated by a hydrophobic pocket that is larger than the homologous site in BphDLB400 from Burkholderia xenovorans LB400. The planar binding mode observed in the crystalline complex was consistent with the hyper- and hypsochromically shifted absorption spectra of 3-Cl and 3,9,11-triCl HOPDA, respectively, bound to S105A in solution. Moreover, ES(red), an intermediate possessing a bathochromically shifted spectrum observed in the turnover of HOPDA, was not detected, suggesting that substrate destabilization was rate-limiting in the turnover of these PCB metabolites. Interestingly, electron density for the first α-helix of the lid domain was poorly defined in the dimeric DxnB2 structures, unlike in the tetrameric BphDLB400. Structural comparison of MCP hydrolases identified the NC-loop, connecting the lid to the α/β-hydrolase core domain, as a determinant in the oligomeric state and suggests its involvement in catalysis. Finally, an increased mobility of the DxnB2 lid may contribute to the enzyme's ability to hydrolyze PCB metabolites, highlighting how lid architecture contributes to substrate specificity in α/β-hydrolases.
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Affiliation(s)
- Antonio C. Ruzzini
- Department of Biochemistry and Molecular Biology, University of British Columbia, BC, Canada
| | - Shiva Bhowmik
- Purdue Cancer Research Center and Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Katherine C. Yam
- Department of Biochemistry and Molecular Biology, University of British Columbia, BC, Canada
| | - Subhangi Ghosh
- Purdue Cancer Research Center and Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Jeffrey T. Bolin
- Purdue Cancer Research Center and Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Lindsay D. Eltis
- Department of Biochemistry and Molecular Biology, University of British Columbia, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, BC, Canada
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42
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Casabon I, Zhu SH, Otani H, Liu J, Mohn WW, Eltis LD. Regulation of the KstR2 regulon of Mycobacterium tuberculosis by a cholesterol catabolite. Mol Microbiol 2013; 89:1201-12. [PMID: 23879670 DOI: 10.1111/mmi.12340] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2013] [Indexed: 11/28/2022]
Abstract
Cholesterol catabolism is widespread in actinobacteria and is critical for Mycobacterium tuberculosis (Mtb) virulence. Catabolism of steroid nucleus rings C and D is poorly understood: it is initiated by the CoA thioesterification of 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP) by FadD3, whose gene is part of the KstR2 regulon. In Mtb, genes of this regulon were upregulated up to 30- and 22-fold during growth on cholesterol and HIP, respectively, versus another minimal medium. In contrast, genes involved in degrading the cholesterol side-chain and nucleus rings A and B were only upregulated during growth on cholesterol. Similar results were obtained in Rhodococcus jostii RHA1. Moreover, the regulon was not upregulated in a ΔfadD3 mutant unable to produce HIP-CoA. In electrophoretic mobility shift assays, HIP-CoA relieved the binding of KstR2(Mtb) to each of three KstR2 boxes: CoASH, HIP and a related CoA thioester did not. Inspection of the structure of KstR2(RHA1) revealed no obvious HIP-CoA binding pocket. The results establish that Mtb can catabolize the entire cholesterol molecule and that HIP-CoA is an effector of KstR2. They further indicate that KstR2 specifically represses the expression of the HIP degradation genes in actinobacteria, which encode a lower pathway involved in the catabolism of multiple steroids.
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Affiliation(s)
- Israël Casabon
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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43
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Bocedi A, Fabrini R, Farrotti A, Stella L, Ketterman AJ, Pedersen JZ, Allocati N, Lau PCK, Grosse S, Eltis LD, Ruzzini A, Edwards TE, Morici L, Del Grosso E, Guidoni L, Bovi D, Lo Bello M, Federici G, Parker MW, Board PG, Ricci G. The impact of nitric oxide toxicity on the evolution of the glutathione transferase superfamily: a proposal for an evolutionary driving force. J Biol Chem 2013; 288:24936-47. [PMID: 23828197 DOI: 10.1074/jbc.m113.476135] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glutathione transferases (GSTs) are protection enzymes capable of conjugating glutathione (GSH) to toxic compounds. During evolution an important catalytic cysteine residue involved in GSH activation was replaced by serine or, more recently, by tyrosine. The utility of these replacements represents an enigma because they yield no improvements in the affinity toward GSH or in its reactivity. Here we show that these changes better protect the cell from nitric oxide (NO) insults. In fact the dinitrosyl·diglutathionyl·iron complex (DNDGIC), which is formed spontaneously when NO enters the cell, is highly toxic when free in solution but completely harmless when bound to GSTs. By examining 42 different GSTs we discovered that only the more recently evolved Tyr-based GSTs display enough affinity for DNDGIC (KD < 10(-9) M) to sequester the complex efficiently. Ser-based GSTs and Cys-based GSTs show affinities 10(2)-10(4) times lower, not sufficient for this purpose. The NO sensitivity of bacteria that express only Cys-based GSTs could be related to the low or null affinity of their GSTs for DNDGIC. GSTs with the highest affinity (Tyr-based GSTs) are also over-represented in the perinuclear region of mammalian cells, possibly for nucleus protection. On the basis of these results we propose that GST evolution in higher organisms could be linked to the defense against NO.
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Affiliation(s)
- Alessio Bocedi
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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44
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Singh R, Grigg JC, Qin W, Kadla JF, Murphy MEP, Eltis LD. Improved manganese-oxidizing activity of DypB, a peroxidase from a lignolytic bacterium. ACS Chem Biol 2013; 8:700-6. [PMID: 23305326 DOI: 10.1021/cb300608x] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DypB, a dye-decolorizing peroxidase from the lignolytic soil bacterium Rhodococcus jostii RHA1, catalyzes the peroxide-dependent oxidation of divalent manganese (Mn(2+)), albeit less efficiently than fungal manganese peroxidases. Substitution of Asn246, a distal heme residue, with alanine increased the enzyme's apparent k(cat) and k(cat)/K(m) values for Mn(2+) by 80- and 15-fold, respectively. A 2.2 Å resolution X-ray crystal structure of the N246A variant revealed the Mn(2+) to be bound within a pocket of acidic residues at the heme edge, reminiscent of the binding site in fungal manganese peroxidase and very different from that of another bacterial Mn(2+)-oxidizing peroxidase. The first coordination sphere was entirely composed of solvent, consistent with the variant's high K(m) for Mn(2+) (17 ± 2 mM). N246A catalyzed the manganese-dependent transformation of hard wood kraft lignin and its solvent-extracted fractions. Two of the major degradation products were identified as 2,6-dimethoxybenzoquinone and 4-hydroxy-3,5-dimethoxybenzaldehyde, respectively. These results highlight the potential of bacterial enzymes as biocatalysts to transform lignin.
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Affiliation(s)
- Rahul Singh
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
| | - Jason C. Grigg
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
| | - Wei Qin
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
| | - John F. Kadla
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
| | - Michael E. P. Murphy
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
| | - Lindsay D. Eltis
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
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45
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Haußmann U, Wolters DA, Fränzel B, Eltis LD, Poetsch A. Physiological adaptation of the Rhodococcus jostii RHA1 membrane proteome to steroids as growth substrates. J Proteome Res 2013; 12:1188-98. [PMID: 23360181 DOI: 10.1021/pr300816n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodococcus jostii RHA1 is a catabolically versatile soil actinomycete that can utilize a wide range of organic compounds as growth substrates including steroids. To globally assess the adaptation of the protein composition in the membrane fraction to steroids, the membrane proteomes of RHA1 grown on each of cholesterol and cholate were compared to pyruvate-grown cells using gel-free SIMPLE-MudPIT technology. Label-free quantification by spectral counting revealed 59 significantly regulated proteins, many of them present only during growth on steroids. Cholesterol and cholate induced distinct sets of steroid-degrading enzymes encoded by paralogous gene clusters, consistent with transcriptomic studies. CamM and CamABCD, two systems that take up cholate metabolites, were found exclusively in cholate-grown cells. Similarly, 9 of the 10 Mce4 proteins of the cholesterol uptake system were found uniquely in cholesterol-grown cells. Bioinformatic tools were used to construct a model of Mce4 transporter within the RHA1 cell envelope. Finally, comparison of the membrane and cytoplasm proteomes indicated that several steroid-degrading enzymes are membrane-associated. The implications for the degradation of steroids by actinomycetes, including cholesterol by the pathogen Mycobacterium tuberculosis , are discussed.
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Affiliation(s)
- Ute Haußmann
- Lehrstuhl fuer Biochemie der Pflanzen, Ruhr Universitaet Bochum, Bochum, Germany
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46
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Colbert CL, Agar NYR, Kumar P, Chakko MN, Sinha SC, Powlowski JB, Eltis LD, Bolin JT. Structural characterization of Pandoraea pnomenusa B-356 biphenyl dioxygenase reveals features of potent polychlorinated biphenyl-degrading enzymes. PLoS One 2013; 8:e52550. [PMID: 23308114 PMCID: PMC3536784 DOI: 10.1371/journal.pone.0052550] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 11/19/2012] [Indexed: 11/19/2022] Open
Abstract
The oxidative degradation of biphenyl and polychlorinated biphenyls (PCBs) is initiated in Pandoraea pnomenusa B-356 by biphenyl dioxygenase (BPDO(B356)). BPDO(B356), a heterohexameric (αβ)(3) Rieske oxygenase (RO), catalyzes the insertion of dioxygen with stereo- and regioselectivity at the 2,3-carbons of biphenyl, and can transform a broad spectrum of PCB congeners. Here we present the X-ray crystal structures of BPDO(B356) with and without its substrate biphenyl 1.6-Å resolution for both structures. In both cases, the Fe(II) has five ligands in a square pyramidal configuration: H233 Nε2, H239 Nε2, D386 Oδ1 and Oδ2, and a single water molecule. Analysis of the active sites of BPDO(B356) and related ROs revealed structural features that likely contribute to the superior PCB-degrading ability of certain BPDOs. First, the active site cavity readily accommodates biphenyl with minimal conformational rearrangement. Second, M231 was predicted to sterically interfere with binding of some PCBs, and substitution of this residue yielded variants that transform 2,2'-dichlorobiphenyl more effectively. Third, in addition to the volume and shape of the active site, residues at the active site entrance also apparently influence substrate preference. Finally, comparison of the conformation of the active site entrance loop among ROs provides a basis for a structure-based classification consistent with a phylogeny derived from amino acid sequence alignments.
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Affiliation(s)
- Christopher L Colbert
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA.
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Casabon I, Crowe AM, Liu J, Eltis LD. FadD3 is an acyl-CoA synthetase that initiates catabolism of cholesterol rings C and D in actinobacteria. Mol Microbiol 2012; 87:269-83. [PMID: 23146019 DOI: 10.1111/mmi.12095] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2012] [Indexed: 01/28/2023]
Abstract
The cholesterol catabolic pathway occurs in most mycolic acid-containing actinobacteria, such as Rhodococcus jostii RHA1, and is critical for Mycobacterium tuberculosis (Mtb) during infection. FadD3 is one of four predicted acyl-CoA synthetases potentially involved in cholesterol catabolism. A ΔfadD3 mutant of RHA1 grew on cholesterol to half the yield of wild-type and accumulated 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP), consistent with the catabolism of half the steroid molecule. This phenotype was rescued by fadD3 of Mtb. Moreover, RHA1 but not ΔfadD3 grew on HIP. Purified FadD3(Mtb) catalysed the ATP-dependent CoA thioesterification of HIP and its hydroxylated analogues, 5α-OH HIP and 1β-OH HIP. The apparent specificity constant (k(cat) /K(m) ) of FadD3(Mtb) for HIP was 7.3 ± 0.3 × 10(5) M(-1) s(-1) , 165 times higher than for 5α-OH HIP, while the apparent K(m) for CoASH was 110 ± 10 μM. In contrast to enzymes involved in the catabolism of rings A and B, FadD3(Mtb) did not detectably transform a metabolite with a partially degraded C17 side-chain. Overall, these results indicate that FadD3 is a HIP-CoA synthetase that initiates catabolism of steroid rings C and D after side-chain degradation is complete. These findings are consistent with the actinobacterial kstR2 regulon encoding ring C/D degradation enzymes.
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Affiliation(s)
- Israël Casabon
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver V6T 1Z3, Canada
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Ruzzini AC, Horsman GP, Eltis LD. The Catalytic Serine of meta-Cleavage Product Hydrolases Is Activated Differently for C–O Bond Cleavage Than for C–C Bond Cleavage. Biochemistry 2012; 51:5831-40. [DOI: 10.1021/bi300663r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antonio C. Ruzzini
- Department of Biochemistry
and Molecular Biology and
Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver,
British Columbia V6T 1Z3, Canada
| | - Geoff P. Horsman
- Department of Biochemistry
and Molecular Biology and
Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver,
British Columbia V6T 1Z3, Canada
| | - Lindsay D. Eltis
- Department of Biochemistry
and Molecular Biology and
Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver,
British Columbia V6T 1Z3, Canada
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Ruzzini AC, Ghosh S, Horsman GP, Foster LJ, Bolin JT, Eltis LD. Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad. J Am Chem Soc 2012; 134:4615-24. [DOI: 10.1021/ja208544g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Antonio C. Ruzzini
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Subhangi Ghosh
- Purdue Cancer Research Center
and Markey Center for Structural Biology, Department of Biological
Sciences, Purdue University, West Lafayette,
Indiana 47907, United States
| | - Geoff P. Horsman
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Leonard J. Foster
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Jeffrey T. Bolin
- Purdue Cancer Research Center
and Markey Center for Structural Biology, Department of Biological
Sciences, Purdue University, West Lafayette,
Indiana 47907, United States
| | - Lindsay D. Eltis
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
- Department of Microbiology and
Immunology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
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50
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Singh R, Grigg JC, Armstrong Z, Murphy MEP, Eltis LD. Distal heme pocket residues of B-type dye-decolorizing peroxidase: arginine but not aspartate is essential for peroxidase activity. J Biol Chem 2012; 287:10623-10630. [PMID: 22308037 DOI: 10.1074/jbc.m111.332171] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DypB from Rhodococcus jostii RHA1 is a bacterial dye-decolorizing peroxidase (DyP) that oxidizes lignin and Mn(II). Three residues interact with the iron-bound solvent species in ferric DypB: Asn-246 and the conserved Asp-153 and Arg-244. Substitution of either Asp-153 or Asn-246 with alanine minimally affected the second order rate constant for Compound I formation (k(1) ∼ 10(5) M(-1)s(-1)) and the specificity constant (k(cat)/K(m)) for H(2)O(2). Even in the D153A/N246A double variant, these values were reduced less than 30-fold. However, these substitutions dramatically reduced the stability of Compound I (t(1/2) ∼ 0.13 s) as compared with the wild-type enzyme (540 s). By contrast, substitution of Arg-244 with leucine abolished the peroxidase activity, and heme iron of the variant showed a pH-dependent transition from high spin (pH 5) to low spin (pH 8.5). Two variants were designed to mimic the plant peroxidase active site: D153H, which was more than an order of magnitude less reactive with H(2)O(2), and N246H, which had no detectable peroxidase activity. X-ray crystallographic studies revealed that structural changes in the variants are confined to the distal heme environment. The data establish an essential role for Arg-244 in Compound I formation in DypB, possibly through charge stabilization and proton transfer. The principle roles of Asp-153 and Asn-246 appear to be in modulating the subsequent reactivity of Compound I. These results expand the range of residues known to catalyze Compound I formation in heme peroxidases.
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Affiliation(s)
- Rahul Singh
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jason C Grigg
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Zachary Armstrong
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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