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Co-Evolution of HAD Phosphatase and Hotdog-Fold Thioesterase

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Co-Evolution of HAD Phosphatase and Hotdog-Fold Thioesterase FEBS Letters 587 (2013) 2851–2859 journal homepage: www.FEBSLetters.org Co-evolution of HAD phosphatase and hotdog-fold thioesterase domain function in the menaquinone-pathway fusion proteins BF1314 and PG1653 ⇑ ⇑ Min Wang a, Feng Song a,1, Rui Wu b,2, Karen N. Allen b, , Patrick S. Mariano a, Debra Dunaway-Mariano a, a Department of Chemistry & Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA b Department of Chemistry, Boston University, Boston, MA 02215, USA article info abstract Article history: The function of a Bacteroidetes menaquinone biosynthetic pathway fusion protein comprised of an Received 8 June 2013 N-terminal haloacid dehalogenase (HAD) family domain and a C-terminal hotdog-fold family Accepted 2 July 2013 domain is described. Whereas the thioesterase domain efficiently catalyzes 1,4-dihydroxy- Available online 10 July 2013 napthoyl-CoA hydrolysis, an intermediate step in the menaquinone pathway, the HAD domain is devoid of catalytic activity. In some Bacteroidetes a homologous, catalytically active 1,4-dihydroxy- Edited by Athel Cornish-Bowden napthoyl-CoA thioesterase replaces the fusion protein. Following the gene fusion event, sequence divergence resulted in a HAD domain that functions solely as the oligomerization domain of an otherwise inactive thioesterase domain. Keywords: Haloacid dehalogenase Ó 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. 14-Dihroxynapthoyl-coenzyme A Enzyme evolution Enzyme superfamily Bacteroides fragilis Porphyromonas gingivalis 1. Introduction Historically, the Escherichia coli menaquinone pathway and the structures and mechanisms of the pathway enzymes have been the Menaquinone-7, also known as vitamin K2, is a lipid-soluble focus of investigation [15–25]. Nevertheless the menaquinone molecule that, in humans, plays a crucial role in blood coagulation, pathways of other bacteria have been characterized [26–28], some bone metabolism, and calcification of arteries [1–6]. Bacteria of the of which employ different biosynthetic strategies [29]. In the first large intestine synthesize menaquinone-7 (hereafter simplified to step of the upper pathway (Fig. 1a), chorismate, derived from the ‘‘menaquinone’’) for use as an electron transporter in anaerobic shikimate pathway, is converted to isochorismate by MenF, an respiration [7,8]. Humans do not synthesize menaquinone but ac- isochorismate synthase. In the second step 2-succinyl-5-eno- quire it from their diet and intestinal flora [9]. Because the menqui- lpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate is formed by none biosynthetic pathway is restricted to bacteria, the enzymes the action of the thiamine-dependent enzyme MenD. MenH, a that function in this pathway are potential targets for the develop- member of the a,b-fold hydrolase family, has recently been shown ment of novel antibiotics [10–14]. Thus, the elucidation of the to catalyze the elimination of the pyruvyl-substituent from this chemical steps of the menaquinone pathway and the catalytic intermediate. The product 2-succinyl-6-hydroxy-2,4-cyclohexadi- mechanisms of the enzyme catalysts are important objectives. ene-1-carboxylate, is converted through the elimination of H2O to 2-succinylbenzoate as catalyzed by MenC, a member of the enolase superfamily. The succinyl side chain of 2-succinylbenzoate is acti- Abbreviations: CoA, coenzyme A; HAD, haloacid dehalogenase; IPTG, isopropyl- vated for cyclization through the action of the ligase MenE that cat- 1-thio-b-D-galactopyranoside; MES, 2-(N-morpholino)ethanesulfonate; HEPES, N- (2-hydroxyethyl)piperazine-N0-2-ethanesulfonate alyzes the transformation of the carboxylate group to the coenzyme ⇑ Corresponding authors. Fax: +1 617 353 6466 (K.N. Allen), fax: +1 505 277 2609 A (CoA) thioester. The naphthoquinol skeleton of 1,4-dihydroxy- (D. Dunaway-Mariano). napthoyl-CoA is generated via a cyclization reaction catalyzed by E-mail addresses: [email protected] (K.N. Allen), [email protected] (D. Dunaway- 1,4-dihydroxynaphthoyl-CoA synthase, MenB, a member of the Mariano). crotonase family. The genes encoding these six enzymes in E. coli are 1 Present address: 3054 E Cornwallis Road, Syngenta Crop Protection, LLC, Research Triangle Park, NC 27709, USA. co-located (Fig. 1B). The 1,4-dihydroxynapthoyl-CoA is then hydro- 2 Present address: Immunogen. Inc., 830 Winter St, Waltham, MA 02451, USA. lyzed by a thioesterase of the hotdog-fold family [30–32]. In the 0014-5793/$36.00 Ó 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.febslet.2013.07.009 2852 M. Wang et al. / FEBS Letters 587 (2013) 2851–2859 Fig. 1. A: The chemical steps of the E. coli menaquinone biosynthetic pathway. B: The menaquinone biosynthetic pathway gene cluster in E. coli K-12 and in B. fragilis. The E. coli genes menf, mend, menh, menb, menc, and mene encode isochorismate synthase, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, 2- succinyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, 2-succinylbenzoate synthase, 2-succinylbenzoate:CoA ligase, and napthoate synthase, respectively. The B. fragilis gene cluster is annotated based on the sequence homology to the E. coli K-12 genes. The two ‘‘extra genes’’ BF1314 and BF1317 encode the fusion protein and a hypothetical protein, respectfully. lower pathway, menaquinone is generated from 1,4-dihydroxy- phosphatase domain as an oligomerization domain. In addition, napthoate in two steps. First, the polyprenyl unit from octaprenyl- through comprehensive bioinformatic analysis we track the two pyrophosphate is added in a reaction catalyzed by MenA [33]. domains throughout Bacteroidetes to provide insight into the path- Second, the napthyl ring is methylated by reaction with S-adeno- way for evolution of the fusion protein. sylmethionine as catalyzed by MenG [34]. Our interest in the biochemical basis for adaptation by bacteria 2. Materials and methods that colonize the human internal cavity lead us to a comparative analysis of the meniquinone gene clusters among the genomes of 2.1. Materials Bacteroidetes species. These species constitute a large fraction of the human gut bacterial community. Homologs to all E. coli upper Unless otherwise stated, all chemicals were obtained from Sig- pathway genes were found in these species with the exception of ma–Aldrich. Primers, T4 DNA ligase, and restriction enzymes were MenH. Most significant was the discovery of an additional gene purchased from Invitrogen, Pfu and Pfu Turbo polymerases were that co-locates with the meniquinone gene cluster in a large num- from Stratagene, the pET-14a, and pET23a, pET28a and pET28b vec- ber of the Bacteroidetes species (Fig. 1B). This gene encodes a fu- tor kits were from Novagen, and the Geneclean Spin and the Qiaprep sion protein consisting of an N-terminal domain that is Spin Miniprep kits were from Qiagen. Genomic DNA from Bacteroi- homologous to the class C2B haloacid dehalogenase (HAD) enzyme des thetaiotaomicron VPI-5482 (ATCC-29148D), Porphyromonas superfamily phosphatases and a C-terminal domain that is homol- gingivalis W83, Bacteroides fragilis and Bacteroides vulgatus were ogous to type AB thioesterases of the hotdog-fold enzyme super- from ATCC. DEAE Sepharose was from Amersham Biosciences. family. Our first objective was to demonstrate that the hotdog- Butyryl-CoA, isobutyryl-CoA, hexanoyl-CoA, octanoyl-CoA, deca- fold domain catalyzes the hydrolysis of the menaquinone pathway noyl-CoA, myristoryl-CoA and benzoyl-CoA were purchased from 1,4-dihydroxynapthoyl-CoA to 1,4-dihydroxynapthoate, and by Sigma–Aldrich. The phosphate esters and anhydrides were pur- doing so complete the set of pathway catalysts. Our second objec- chased from Sigma–Aldrich. The 4-hydroxybenzoyl-CoA and 3- tive was to determine the function of the appended HAD domain hydroxyphenylacetyl-CoA were synthesized according to published and its relationship to the menaquinone pathway. Our approach procedures [37–40]. Napthoyl-CoA and 1,4-dihydroxynapthoyl- to this problem represents the merging of the kinetic analyses en- CoA were synthesized as detailed in Supporting Information. abled by Michaelis and Menton [35] (see [36] for a translation) 100 years ago and the bioinformatic methods that have become 2.2. Gene cloning and expression and protein purification available in the genomic era. Herein, we provide the results from steady-state kinetic analy- The genes encoding the BT4699 (NCBI accession NP_813610, ses of the targeted gene product derived from two different Bacter- UniProt accession Q89YN2), PG1653 (NCBI accession NP_905773, oidetes species, which establish the identity of the menaquinone UniProt accession Q7MU91), BF1314 (NCBI accession YP_098598, pathway thioesterase and which define the role of the HAD UniProt accession Q5LFS7) and BVU2420 (NCBI accession M. Wang et al. / FEBS Letters 587 (2013) 2851–2859 2853 YP_001299701, UniProt accession A6L315) were amplified from was calibrated using the gel-filtration low molecular weight and the genomic DNA derived from B. thetaiotaomicron, P. gingivalis high molecular weight calibration kits from Amersham W83, B. fragilis and B. vulgatus, respectively, using PCR techniques Biosciences. in combination with commercial primers that contain the endo- nuclease cleavage sites Nde I and Xho I. The PCR products were 2.5. Steady-state kinetic assays purified and then subcloned into a pET-28a vector, which adds a His6 tag to the N-terminus of each protein. Plasmid DNA was puri- The rate of enzyme-catalyzed hydrolysis of p-nitrophenyl phos- fied using a Qiaprep Spin Miniprep Kit. The identity of the sub- phate (PNPP) was determined at 25 or 37 °C by monitoring the in- cloned genes was demonstrated by full-length DNA sequencing crease in solution absorbance at 410 nm (De = 18.4 mMÀ1 cmÀ1). (University of New Mexico). The 0.5 ml assay mixtures contained 50 mM HEPES (pH 7.0) and Transformed E. coli BL21 (DE3) competent cells were grown at 5 mM MgCl2. Hydrolysis reactions of all other phosphate esters 37 °C for 6 h in 3 L of LB media containing 50 lg/ml of kanamycin were monitored using the Enzcheck phosphate assay kit (Invitro- with shaking at 220 rpm.
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