Báo cáo khoa học: Characterization of a b-N-acetylhexosaminidase and a b-N-acetylglucosaminidase/b-glucosidase from Cellulomonas fimi potx

Characterization of a b-N-acetylhexosaminidase and a b-N-acetylglucosaminidase/b-glucosidase from Cellulomonas fimi Christoph Mayer 1,2,3 , David J. Vocadlo 1, *, Melanie Mah 2 , Karen Rupitz 1 , Dominik Stoll 2 , R. A. J. Warren 2 and Stephen G. Withers 1 1 Department of Chemistry, University of British Columbia, Vancouver, Canada 2 Department of Microbiology & Immunology, University of British Columbia, Vancouver, Canada 3 Department of Biology, University of Konstanz, Germany Most enzymes catalyzing the hydrolysis of terminal b-N-acetylglucosaminide linkages belong to families 3 and 20 of the glycoside hydrolases ([1,2] and the glyco- side hydrolases database at URL http://afmb.cnrs-mrs. fr/CAZY/). Members of the two families greatly differ in structure, enzyme mechanism, substrate specificity, and physiologic function (for a review see [3] and references cited therein). The enzymes in family 20 are designated as N-acetylhexosaminidases (EC 3.2.1.52) because they hydrolyze b-N-acetylgalactosaminides and b-N-acetylglucosaminides, with about a four-fold greater activity on the latter ([1] , and references cited therein). b-N-Acetylglucosaminidases (EC 3.2.1.52) in family 3 are much more specific for the gluco-configuration, Keywords bifunctional glycosidase; cell wall recycling; chitin metabolism; murein; peptidoglycan Correspondence C. Mayer, Department of Biology, University of Konstanz, 78457 Konstanz, Germany Fax: +49 7531 88 3356 Tel: +49 7531 88 4854 E-mail: ch.mayer@uni-konstanz.de *Present address Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada Database The nucleotide sequences listed in this paper have been submitted to the DDBJ ⁄ EMBL ⁄ GenBank database under the accession numbers AF478459 and AF478460 (Received 22 February 2006, revised 3 May 2006, accepted 4 May 2006) doi:10.1111/j.1742-4658.2006.05308.x The Gram-positive soil bacterium Cellulomonas fimi is shown to produce at least two intracellular b-N-acetylglucosaminidases, a family 20 b-N-acetyl- hexosaminidase (Hex20), and a novel family 3-b-N-acetylglucosamini- dase ⁄ b-glucosidase (Nag3), through screening of a genomic expression library, cloning of genes and analysis of their sequences. Nag3 exhibits broad substrate specificity for substituents at the C2 position of the gly- cone: k cat ⁄ K m values at 25 °C were 0.066 s )1 Æmm )1 and 0.076 s )1 Æmm )1 for 4¢-nitrophenyl b-N-acetyl-d-glucosaminide and 4¢-nitrophenyl b-d-glu- coside, respectively. The first glycosidase with this broad specificity to be described, Nag3, suggests an interesting evolutionary link between b-N-ace- tylglucosaminidases and b-glucosidases of family 3. Reaction by a double- displacement mechanism was confirmed for Nag3 through the identification of a glycosyl–enzyme species trapped with the slow substrate 2¢,4¢-dinitro- phenyl 2-deoxy-2-fluoro-b-d-glucopyranoside. Hex20 requires the acetami- do group at C2 of the substrate, being unable to cleave b-glucosides, since its mechanism involves an oxazolinium ion intermediate. However, it is broad in its specificity for the d-glucosyl ⁄ d-galactosyl configuration of the glycone: K m and k cat values were 53 lm and 482.3 s )1 for 4¢-nitrophenyl b-N-acetyl-d-glucosaminide and 66 lm and 129.1 s )1 for 4¢-nitrophenyl b-N-acetyl-d-galactosaminide. Abbreviations DNP-2FGlc, 2¢,4¢-dinitrophenyl 2-deoxy-2-fluoro-b- D-glucopyranoside; Dp, degree of polarization; IPTG, isopropyl thiogalactopyranoside; 4MU-GlcNAc, 4¢-methylumbelliferyl b-N-acetyl- D-glucosaminide; pNP, 4-nitrophenol; pNP-Glc, 4¢-nitrophenyl b-D-glucopyranoside; pNP-GlcNAc, 4¢-nitrophenyl b -N-acetyl- D-glucosaminide; pNP-GalNAc, 4¢-nitrophenyl b-N-acetyl-D-galactosaminide; PVDF, polyvininylidene difluoride. FEBS Journal 273 (2006) 2929–2941 ª 2006 The Authors Journal compilation ª 2006 FEBS 2929 exhibiting little if any activity on galactosyl substrates [1,4–6]. Family 3 primarily comprises b-glucosidases (EC 3.2.1.21) and exo-b-glucanases (EC 3.2.1.58 and 3.2.1.74). However, b-N-acetylglucosaminidases form a subgroup within family 3, characterized by the sequence pattern K-H-(FI)-P-G-(HL)-G-x(4)-D-(ST)-H, which is believed to be involved in binding of the N-acetyl group [1,7]. The b-N-acetylglucosaminidases and hexosaminidases in families 3 and 20 are both retaining enzymes, yet they have different mechanisms [8]. The family 20 enzymes do not form covalent glycosyl–enzyme inter- mediates because they lack a nucleophilic carboxylate; hydrolysis involves the anchimeric assistance of the acetamido group of the substrate [8–11]. By contrast, family 3 enzymes do contain a nucleophilic carboxylate and catalyze hydrolysis by a double-displacement mechanism via a covalent glycosyl–enzyme intermedi- ate [7,13–15]. This mechanism is found in most retain- ing glycosidases, e.g. in lysozyme, an enzyme that catalyzes an endo-type cleavage of the N-acetylglucosa- mine-containing bacterial cell wall peptidoglycan [12]. The mechanism of family 3 exoglucanase ExoI from Hordeum vulgare is understood in some detail [16]. The enzyme consists of two modules, one an (a ⁄ b) 8 -barrel, and the second a six-stranded b-sandwich [17,18]. The substrate binds to a pocket formed between the two modules, with Asp285 of the first domain being the catalytic nucleophile and Glu491 of the second domain the acid–base catalyst, which accelerates the departure of the aglycon by protonation of the glycosidic oxygen [19]. The catalytic nucleophile of a family 3 b-N-acetyl- glucosaminidase (ExoII) from Vibrio furnissii was identified using the slow substrate N-acetyl-5-fluoro- a-l-idopyranosaminyl fluoride [7]. This residue is con- served throughout family 3. An amino acid acting as an acid–base catalyst in this enzyme is apparently missing, since ExoII and other family 3 b-N-acetyl- glucosaminidases of Gram-negative bacteria comprise only a single (a ⁄ b) 8 -barrel module. Generally, they have molecular masses of about 35 kDa and are pre- dicted to be cytoplasmic: the b-N-acetylglucosamini- dase of Escherichia coli (NagZ) is a cytoplasmic enzyme involved in peptidoglycan recycling [20,21]. Similar enzymes in other Gram-negative bacteria may have the same function. To date, only one family 3 b-N-acetylglucosaminidase-encoding gene (nagA) has been cloned from a Gram-positive bacterium, namely Streptomyces thermoviolaceus [6]. This enzyme, like most putative family 3 b-N-acetylglucosaminidases of Gram-positive bacteria, has a molecular mass of about 60 kDa and comprises two modules. It is extracellular and thought to be involved in chitin degradation. Chitin is degraded by the concerted action of chi- tinase(s) (EC 3.2.1.14) and b-N-acetylhexosamini- dase(s), which may involve other proteins [22–27]. As part of an analysis of the mechanisms and func- tions of N-acetylglucosaminidases of Gram-positive bacteria, this article reports the cloning and sequencing of two genes from the Gram-positive soil bacterium Cellulomonas fimi that encode enzymes acting on ter- minal b-N-acetylglucosamine residues: a family 20 b-N-acetylhexosaminidase (Hex20) and a novel family 3 b-N-acetylglucosaminidase ⁄ b-glucosidase (Nag3). Nag3 is the first b-glycosylase to be described that lacks specificity for substituents at C-2. Results Detection of b-N-acetylglucosaminidase activity in Cellulomonas fimi cell extracts Cellulomonas fimi grows on minimal medium supple- mented with 0.2% (w ⁄ v) chitin as the sole source of carbon and it secretes a chitinase (C. Mayer, unpub- lished results). However, b-N-acetylglucosaminidase activity assayed with chromogenic substrates could only be detected in the soluble cell fraction; a specific activity of 0.20 ± 0.05 UnitsÆmg )1 with 4¢-methylum- belliferyl b-N-acetyl-d-glucosaminide (4MU-GlcNAc) was determined within the soluble cell extract. The intracellular b-N-acetylglucosaminidase(s) of Cellulo- monas fimi could not be induced by addition of chitin or chitosan (0.2% w ⁄ v) to the growth medium. How- ever, significantly higher b-N-acetylglucosaminidase activity (0.34 ± 0.05 UÆmg )1 ) was measured when 0.05% (w ⁄ v) N-acetylglucosamine was added to the growth medium. Glucose in the culture medium had no catabolic repression effect. To identify and clone the gene(s) encoding for intracellular b-N-acetylglu- cosaminidase(s), a Cellulomonas fimi genomic expres- sion library was screened. Screening of a Cellulomonas fimi genomic library A Cellulomonas fimi genomic library was prepared pre- viously by inserting genomic DNA fragments (2– 5 kbp) into the EcoRI site of the multiple cloning site of lambda ZAPII (Stratagene [28,29]). This created fusions of the genomic inserts with the first 36 amino acids of the E. coli b-galactosidase coding sequence transcribed from the lacZ promoter. E. coli XLOLR cells transformed with the excised phagemid library were screened for isopropyl thiogalactopyranoside (IPTG)-inducible expression of b-N-acetylglucosamini- dase activity using 4MU-GlcNAc. Five positive clones Cellulomonas fimi b-N-acetylglucosaminidases C. Mayer et al. 2930 FEBS Journal 273 (2006) 2929–2941 ª 2006 The Authors Journal compilation ª 2006 FEBS were isolated from two independent screenings. Three clones (designated CF2, 3 and 10) produced intensely fluorescent halos, whereas the other two colonies (CF5 and 13) produced weakly fluorescent haloes. Restric- tion endonuclease digestion showed that the plasmids in the clones carried inserts of the following sizes: 2.8 kb (pCF5), 2.2 kb (pCF2 and pCF3), 2.0 kb (pCF10), and 1.7 kb (pCF13). By restriction mapping, pCF2 and pCF3 were found to contain an identical 2.2 kb insert, which contained the 2.0 kb insert of pCF10. DNA sequencing of the inserts revealed the 2.0 kb insert to be an incomplete ORF missing 20 bp at the 5¢ end and a 200 bp portion at the 3¢ end. Plas- mid pCF5 carried a 2.8 kb insert containing the com- plete insert (1.7 kb) in pCF13. Sequence alignment and classification to family 20 glycoside hydrolases The 2.2 kb Cellulomonas fimi genomic DNA fragment of pCF2 carries a 1491 kb ORF with a G ⁄ C content of 73.3% that starts with a GTG codon and ends with a TGA stop codon. A putative ribosome-binding site (Shine–Dalgarno sequence) was found six bases upstream of the start codon. The deduced amino acid sequence of the encoded protein, designated Hex20, had high similarity (38% overall sequence identity according to the blast sequence alignment tool) to a b-N-acetylhexosaminidase from Streptomyces plicatus (UniProt database identifier O85361) as well as other family 20 glycoside hydrolases. Recently, the crystal structure of Streptomyces plicatus b-N-acetylhexosa- minidase was determined ([9]; structure identifier 1HP4): the catalytic C-terminal module forms a (b ⁄ a) 8 -barrel-type (TIM-barrel) structure, first elucida- ted for the Serratia marcescens chitobiase [30], and the N-terminal module forms a a + b sandwich structure. A multiple sequence alignment of the b-N-acetylhexos- aminidases from Cellulomonas fimi, Streptomyces plica- tus and Streptomyces thermoviolaceus (NagB, Q9RHV6 [31]), as well as a highly similar putative enzyme from Streptomyces coelicolor (Q9L068), along with the sec- ondary structural elements of 1HP4, are given in Fig. 1. Regions within Hex20 that differ strongly from comparable regions within the Streptomyces plicatus enzyme are found in the N-terminal module of unknown function and within the following regions of the catalytic module: a-helix 4 and the loops after b-strands 4 and 6. These parts of the catalytic (ba) 8 - barrel are believed to constitute the aglycon-binding site of the enzymes. However, we do not know if these differences in sequence lead to distinct aglycon specifi- cities of the enzymes. Sequence alignment and classification to family 3 glycoside hydrolases The 2.8 kb Cellulomonas fimi genomic DNA fragment of pCF4 (¼ pCF13) contained a 1695 bp open reading frame (ORF) with a G ⁄ C content of 70.3%, starting with an ATG codon and ending with a TGA stop codon. A putative ribosome-binding site (Shine–Dalg- arno sequence) was found upstream of the start codon. The deduced amino acid sequence of the protein, enco- ded by the 1695 bp ORF, designated Nag3, had some 25% overall sequence identity to b-N-acetylglucosa- minidase NagA from Steptomyces thermoviolaceus (O82840) and similarity to other members of the b-N-acetylglucosaminidase subfamily of family 3 glyco- side hydrolases (Figs 2,3). Nag3 may be part of an operon; there are putative ORFs upstream and down- stream of the 1695 bp ORF. The upstream ORF showed similarities to ABC transport proteins and the downstream ORF showed similarities to haloacid deh- alogenase-like hydrolases (HAD superfamily). The stop codon (TGA) of the putative upstream ORF overlaps the start codon of the 1695 bp ORF. Subcloning, overexpression and N-terminal protein sequencing The genes hex20 and nag3 were subcloned into the expression vector pET29b, which allowed heterologous overexpression of the Cellulomonas fimi enzymes in E. coli BL21(DE3) cells. Typically, about 100 mg of pure His6-tag fusion proteins (Hex20 and Nag3) were obtainable from 1 L of LB culture. Overexpression of Nag3 was enhanced by growth of E. coli cells at reduced temperature (25 °C) after induction with IPTG. The N-terminal amino acid sequences of the purified proteins were identical to those deduced from the nuc- leotide sequences (italics in Figs 1 and 2). It should be noted that the GTG start codon obtained for hex20 was exchanged with ATG for expression in E. coli (Fig. 1). Characterization of the purified enzymes Purified Hex20 and Nag3 His6-fusion proteins were active on 4MU-GlcNAc, which is the fluorogenic sub- strate used for the screening. In addition, they released 4-nitrophenol (pNP) from the chromogenic substrate 4¢-nitrophenyl b-N-acetyl-d-glucosaminide (pNP-Glc- NAc). The huge differences in activity already observed throughout the screening were confirmed with purified protein. The kinetic parameters of Hex20 and Nag3 for pNP-glycosides are presented in Table 1. Hex20 was highly active on both b-N-acetylglucosaminide C. Mayer et al. Cellulomonas fimi b-N-acetylglucosaminidases FEBS Journal 273 (2006) 2929–2941 ª 2006 The Authors Journal compilation ª 2006 FEBS 2931 and b-N-acetylgalactosaminide (Fig. 4A): K m and k cat values were 53 lm and 482.3 s )1 for pNP-GlcNAc, and 66 lm and 129.1 s )1 for p-nitrophenyl b-N-acetyl- galactosaminide (pNP-GalNAc) at 25 °C. An activity ratio (pNP-GlcNAc ⁄ pNP-GalNAc) of 3.7 was deter- mined, a value in the range commonly observed for hydrolysis of these substrates by family 20 b-N-acetyl- hexosaminidases [1]. A high K m value and a low k cat value were deter- mined for Nag3 with pNP-GlcNAc: the K m value was 2.7 mm and the k cat value at 25 °C was 0.18 s )1 . These values are in the range observed for other fam- ily 3 N-acetylglucosaminidases [4,6], which generally have very low specific activity. Nag3 was also found to be active on 4¢-nitrophenyl b-d-glucopyranoside (pNP-Glc) (Fig. 4B). However, there was a linear rela- tionship of enzyme velocity with pNP-Glc concen- tration up to 24 mm, the limit of solubility of the substrate, so the K m and k cat values could not be deter- mined for pNP-Glc. Interestingly, the values reflecting Fig. 2. Multiple amino acid sequence alignment of Nag3 of Cellulomonas fimi (Q7WUL4_CELFI) and selected family 3 b-N-acetylglucosami- nidases: NagA of Streptomyces thermoviolaceus (Q82840_STRTH) and HexA from Alteromonas sp. (P48823_ALTSO) and the sequences of three putative b-N-acetylglucosaminidases from Bacillus subtilis (P40406_BACSU), Streptomyces colicolor (Q9RDG9_STRCO) and Clostridium perfringens (HEXA_CLOPE). The conserved catalytic nucleophile residue (r) identified in ExoII from Vibrio furnissii (31) and the sequence identifier (16) of the N-acetylglucosaminidase subgroup of family 3 glycoside hydrolases (*, bold letters) are indicated. For definitions see also legend to Fig. 1. Fig. 1. Multiple amino acid sequence align- ment of Hex20 of Cellulomonas fimi (Q7WUL4_CELFI) and selected family 20 b-N-acetylhexosaminidases: NagB of Strep- tomyces thermoviolaceus (Q9RHV6_STRTL), Hex of Streptomyces plicatus (O85361_ STRPL), and a putative b-N-acetylhexos- aminidase of Streptomyces coelicolor (Q9L068_STRCO). The abbreviations used reference the accession numbers of the UniProt database and the organism codes. Dark shading indicates highly conserved res- idues, and light shading indicates conserved similar residues. Alignment was generated using CLUSTALW [46], and shading was per- formed with version 3.21 of BOXSHADE (by K. Hofmann and M. Baron). The N-terminal amino acid sequence of Hex20 from Cellulo- monas fimi that was confirmed by sequen- cing is shown in italics; the GTG start codon obtained for the native hex20 was exchanged with ATG for expression in Escherichia coli. Underlined are the (puta- tive) cleavage sites of the signal sequences. Secondary structural elements of the Strep- tomyces plicatus enzyme [9] are indicated: b-sheet (¼), a-helix (//) and the structural elements of the N-terminal catalytic (ab) 8 - barrel. The conserved catalytic acid ⁄ base residue (r) and the cysteine residues form- ing an intramolecular disulfide bridge in the b-N-acetylglucosaminidase of Streptomyces plicatus (*) are indicated. Cellulomonas fimi b-N-acetylglucosaminidases C. Mayer et al. 2932 FEBS Journal 273 (2006) 2929–2941 ª 2006 The Authors Journal compilation ª 2006 FEBS C. Mayer et al. Cellulomonas fimi b-N-acetylglucosaminidases FEBS Journal 273 (2006) 2929–2941 ª 2006 The Authors Journal compilation ª 2006 FEBS 2933 the catalytic efficiency (k cat ⁄ K m ) determined for pNP- GlcNAc and pNP-Glc were about the same for Nag3 (Table 1). Hex20 hydrolyzed N-acetylchitooligomers (degree of polarization (Dp) 2–6) at about the same rate, as ana- lyzed by TLC (supplementary Fig. S1). However, Nag3 did not release GlcNAc from chitobiose ⁄ N-ace- tylchitooligomers and Glc from cellobiose ⁄ b-glucan-ol- igomers (data not shown). Stability and pH effect Hex20 was stable at pH 6.0–9.5, retaining its activity for several months when stored in the elution buffer used for nickel chelate chromatography (20 mm sodium phosphate ⁄ 80 mm imidazole pH 7.5 and 300 mm NaCl) at 4 °C. However, the enzyme was rapidly inactivated above pH 9.5. Nag3 precipitated below pH 6.0; it was resonably stable between pH 6.8 0.1 Q9XEI3/EXOI HORVU P33363/BGLX ECOLI Q9P8F4/BGLA ASPNG P96157/EXOII VIBFU P75949/NAGZ ECOLI P48823/HEXA ALTSO P40406/YBBD BACSU 082840/NAGA STRTL Q9RDG9 STRCO Q8XP12 CLOPE Q7WUL3/NAG3 CELFI Q8W012/ARAI HORVU Q8W011/XYLA HORVU Q42835/EXOII HORVU Fig. 3. Cladogram showing the evolutionary relationship of Nag3 of Cellulomonas fimi (Q7WUL3 ⁄ NAG3_CELFI) and selected members of family 3 of glycoside hydrolases. The abbreviations used reference the accession numbers of the UniProt database and the organism codes: NagA of Streptomyces thermoviolaceus (Q82840 ⁄ NAGA_STRTH) and HexA from Alteromonas sp. (P48823 ⁄ HEXA_ALTSO) and the sequences of three putative b-N-acetylglucosaminidases from Bacillus subtilis (P40406 ⁄ YBBD_BACSU), Streptomyces colicolor (Q9RDG9_STRCO) and Clostridium perfringens (HEXA_CLOPE) (see Fig. 3); the b-N-acetylglucosaminidases of two Gram-negative bacteria, NagZ of Escherichia coli (P75949 ⁄ NAGZ_ECOLI) and ExoII of Vibrio furnisii (P96157 ⁄ EXOII_VIBFU); members of the b-glucosidase subfamily, b-glucosidase X of Escherichia coli (P33363 ⁄ BGLX_ECOLI) and b-glucosidase A of Aspergillus niger (Q9P8F4 ⁄ BGLA_ASPNG), the two exoglucanases ExoI and ExoII of Hordeum vulgare (Q9XEI3 ⁄ EXOI_HORVU and Q42835 ⁄ EXOII_HORVU), and a b-xylosidase and an a- L-arabi- ofuranosidase ⁄ b-xylosidase of Hordeum vulgare (Q8W011 ⁄ XYLA_HORVU and (QW012 ⁄ ARAI_HORVU).Nag3 and the putative family 3 N-acetylglucosaminidase of Clostridium perfringens (Q8XP12) form an intermediate branch between b-glucosidases and b-N-acetylglucosami- nidases of family 3. The phylogenetic tree was created with the program TREEVIEW (by R. D .M. Page). Table 1. Kinetic parameters for the reactions of Cellulomonas fimi b-N-acetylhexosaminidase (Hex20) and b-N-acetylglucosaminidases (Nag3) with pNP glycosides. The enzymic reaction was carried out in 50 m M sodium phosphate buffer (pH 7.08) at 25 °C. The molar extinction coef- ficient ( M )1 Æcm )1 ) at 400 nm for pNP was 7280. Standard errors for the values of K m and k cat measured here were less than 5%, except where standard error values are indicated. a Not determined due to a reaction being too slow to be detected. b Not determined due to the linear relationship of enzyme velocity with substrate concentration. pNP-GlcNAc, 4¢-nitrophenyl b-N-acetyl- D-glucosaminide; pNP-GalNAc, 4¢-nitrophenyl b-N-acetyl- D-galactosaminide; pNP-Glc, 4¢-nitrophenyl b-D-glucopyranoside. Substrate Hex20 Nag3 K m (lM) k cat (s )1 ) k cat ⁄ K m (s )1 ÆlM )1 ) K m (lM) k cat (s )1 ) k cat ⁄ K m (s )1 ÆlM )1 ) pNP-GlcNAc 53 482 9.09 2.7 ± 0.2 0.18 0.067 pNP-GalNAc 66 129 1.95 ND a ND a ND a pNP-Glc ND a ND a *ND a *ND b ND b 0.076 Cellulomonas fimi b-N-acetylglucosaminidases C. Mayer et al. 2934 FEBS Journal 273 (2006) 2929–2941 ª 2006 The Authors Journal compilation ª 2006 FEBS and 8.4; however, it lost its catalytic activity in diluted buffers within a day at 4 °C. The half-life of Nag3 at room temperature was only a few hours. Addition of sodium chloride (0.5 m), dithiothreitol (0.1 and 1 mm), BSA (0.5 mgÆmL )1 ), sucrose and trehalose (20%) had no huge effect on Hex3 stability (Table 2). However, adding glycerol and ⁄ or phosphate stabilized the enzymes, and Nag3 retained its activity for several 0.00 0.05 0.10 A 400 / min 1/v (A 400 / min) –1 0.15 0.20 0.00 0.25 0.50 0.75 1.00 1.25 [S] (m M ) -20 0 20 40 60 80 100 120 140 160 25 50 75 100 1 / [S] (m M ) -1 A A 400 / min 1/v (A 400 / min) –1 [S] (m M ) 1 / [S] (m M ) -1 02468 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 -101234 50 100 150 B Fig. 4. Michaelis–Menten plot of initial rates of hydrolysis of (A) 4¢-nitrophenyl b-N-acetyl- D-glucosaminide (pNP-GlcNAc) (d)and4¢-nitrophe- nyl b-N-acetyl- D-galactosaminide (pNP-GalNAc) (s)byCellulomonas fimi Hex20 (5.59 · 10 )5 mg ⁄ mL) at 25.2 °C and pH 7.08 and (B) pNP- GlcNAc (n) and pNP-Glc (h)byCellulomonas fimi Nag3 (3.09 · 10 )3 mg ⁄ mL) at 25.2 °C and pH 7.08. Inset: graphical analysis of K m and k cat by Lineweaver–Burk linearization. Table 2. Effects of various reagents on the stability of Cellulomonas fimi Nag3 dithiothreitol. Reagents Concentration % Remaining relative activity a (18 h incubation) b Remaining relative activity a (90 h incubation) b NaCl 500 mM 10 0 Dithiothreitol 0.1 m M 35 0 Dithiothreitol and glycerol 0.1 m M and 20% 100 90 BSA 5% 35 0 Sucrose 20% 66 25 Trehalose 20% 0 0 Tris pH 7.3 330 m M 80 Phosphate pH 7.3 330 m M 100 90 Glycerol 20% 80 60 Glycerol 20% 95 95 60 m M imidazol pH 7.5 Glycerol c 20% 100 mM phosphate pH 7.3 100 100 a The enzymic reaction was carried out in 20 mM Tris ⁄ HCl buffer (pH 7.3) at 25 °C with 4¢-nitrophenyl b-N-acetyl-D-glucosaminide (pNP-Glc- NAc) (6.5 m M). b Before assaying, Nag3 was incubated for 18 and 90 h with the indicated supplement; c the activity measured after incubation for the indicated time with the supplement shown in bold was set at 100%. C. Mayer et al. Cellulomonas fimi b-N-acetylglucosaminidases FEBS Journal 273 (2006) 2929–2941 ª 2006 The Authors Journal compilation ª 2006 FEBS 2935 months when stored in glycerol (20% final concentra- tion) and phosphate buffer at pH 7.3 and ) 20 °C. Ex- oII, a family 3 N-acetylglucosaminidase from Vibrio furnissi, is activated by 400–700 mm sodium chloride [4]. However, sodium chloride up to 700 mm had no effect on Hex3; there was a 10% decrease in activity with 1 m NaCl. The pH dependence of Hex20 and Nag3 was investi- gated using pNP-GlcNAc and pNP-Glc, respectively, over a pH range of 6.2–9.2 and 6.8–8.5, respectively. Hex20 showed a broad, bell-shaped pH optimum curve with a maximum between pH 7.3 and 8.7 with pNP- GlcNAc and half-maximal rate at about pH 7 and 9 (Fig. 5A). By contrast, the family 20 b-N-acetylhexosa- minidase from Streptomyces plicatus has a pH optimum of 5 on pNP-GlcNAc [11]. The k cat ⁄ K m for Hex20 was dependent on two ionizable groups with pK a values of 6.9 and 8.8 (Fig. 6B). Nag3 gave a com- plex pH profile on pNP-Glc, with a narrow maximal rate at pH 7.3 and half-maximal rates at about pH 6.8 and 8.0 (Fig. 5). This is consistent with the pH opti- mum determined for the b-N-acetylglucosaminidase (ExoII) from Vibrio furnissii [4]. The pK a of the lower ionization constant was 6.7; however, a value for an upper ionization could not be determined from the data (Fig. 5B). MS and labeling The mass of purified Hex20 was 54 186 Da, as ana- lyzed by ESI ⁄ MS, which is in perfect agreement with 0.00 0.02 0.04 0 2500 5000 7500 A k ca t /K m (s –1 m M –1 ) p(K cat /K m ) 6.5 7.0 7.5 8.0 8.5 9.0 9.5 -1 0 1 2 3 -4 -3 -2 -1 B pH Fig. 5. pH dependence of k cat ⁄ K m for the Nag3- and Hex20-cata- lyzed reaction. (A) The pH profiles of Nag3 (d, left scale) and Hex20 (s, right scale) were determined using pNP-Glc and 4¢-nitro- phenyl b-N-acetyl- D-glucosaminide (pNP-GlcNAc), respectively, at 25 °C. The reaction buffers were 100 m M sodium citrate ⁄ phos- phate (pH 6.0–7.3), 100 m M sodium phosphate (pH 7.0–8.2) and 100 m M glycine ⁄ HCl (pH 7.8–10). (B) Shows the same data used to fit Eqn (1); the lines represent the best fit of the equation to the pk cat ⁄ K m data (Nag3, pK a1 ¼ 6.70 ± 0.33; pK a2 could not be deter- mined from the data; Hex20, pK a1 ¼ 6.91 ± 0.10; pK a2 ¼ 8.79 ± 0.12). 100 A B C 60971.0 61126.0 61135.0 60000 61000 mass (Da) 62000 50 0 20 10 0 20 10 0 relative intensity (%) Fig. 6. Transform of the electrospray mass spectrum of (A) Nag3, and (B) and (C) Nag3 incubated at room temperature with 10 m M 2¢,4¢-dinitrophenyl-2-deoxy-2-fluoro-b-glucose for 4 h and 20 h, respectively. The mass shifts (157 and 166) of peaks shown in (B) and (C) compared to the peak shown in (A) correspond to a 2-de- oxy-2-fluoro-b-glucosyl residue (162 Da) covalently bound to Nag3. Cellulomonas fimi b-N-acetylglucosaminidases C. Mayer et al. 2936 FEBS Journal 273 (2006) 2929–2941 ª 2006 The Authors Journal compilation ª 2006 FEBS the theoretical mass of the cloned enzyme (54 186 Da). The mass of the purified Nag3 protein was determined by ESI ⁄ MS to be 60 971 Da, close to the theoretical mass of the cloned enzyme (60 945 Da). After incuba- tion with 2¢,4¢-dinitrophenyl 2-deoxy-2-fluoro-b- d-glucopyranoside (DNP-2FGlc), two species are observed: the native, unlabeled enzyme, and another species with a mass of 61 126–61 135 Da (Fig. 6). The mass difference observed between the native and inhib- ited enzyme is 164 Da, a value that is consistent, within error, with the addition of a single 2-deoxy-2- fluoroglucosyl label (162 Da). The rate of the labeling was consistent with the expectation of slow inactiva- tion by the inhibitor when the low apparent k cat values for Nag3 with chromogenic glucosides are kept in mind. Prolonged incubation of the enzyme with the inhibitor leads to almost complete inactivation of the native enzyme. The observation of a covalent glycosyl intermediate provides strong evidence for a mechanism involving an enzymic nucleophile, as shown previously for two family 3 glycoside hydrolases: the single domain b-N-acetylglucosaminidase from V. furnissii [7] and the two domain b-glucosidases from Aspergillus niger [13]. Sequence alignment using the clustal w algorithm revealed a conserved aspartate residue within the sequence GLVVS DS to be the putative cat- alytic nucleophile. By contrast, the hydrolytic mechan- ism of retaining family 20 b-N-acetylhexosaminidases involves the assistance of the acetamido group of the substrate [8,9,11]. Discussion Cellulomonas fimi is strongly cellulolytic, producing a complex cellulose degradative system. The system, comprising mostly extracellular enzymes, is understood in considerable detail (e.g. [29,32–38]). Cellulomonas fimi also degrades chitin (C. Mayer, unpublished observation), a homopolymer of GlcNAc similar to cellulose, but nothing is known of its chitinolytic sys- tem. Recently, a chitinase was isolated from culture supernatant of Cellulomonas flavigena [39] and a chi- tinase-encoding gene was cloned from Cellulomonas uda [40]. Cellulomonas fimi also secretes one (or more) chitinase(s) (C. Mayer, unpublished observation), but N-acetylglucosaminidase activity is present only in the soluble cell extract. Of the two enzymes described here, only Hex20 degrades N-acetylchitooligomers and may be involved in chitin degradation. The function of Nag3 is unclear. It has low catalytic activity relative to Hex20 on chromogenic substrates: the catalytic effi- ciency (k cat ⁄ K m value) for hydrolysis of pNP-GlcNAc by the two enzymes differs by a factor of 10 5 (Table 1). In this respect, Nag3 resembles family 3 N-acetylglucosaminidases of Gram-negative bacteria, which are involved in cell wall (peptidoglycan) recyc- ling [1,7,20,21,41]. However, Nag3 is unusual in that it acts on b-N-acetyl-d-glucosaminides and b-d-gluco- sides, so it should be referred to as a b-N-acetyl-d-glu- cosaminidase ⁄ b-d-glucosidase. The catalytic efficiencies against pNP-Glc and pNP-GlcNAc were similar, seem- ingly a consequence of much higher apparent values for both k cat and K m for the b-glucoside. Unfortu- nately, the exact kinetic parameters for hydrolysis of pNP-Glc by Nag3 could not be determined because the enzyme was not saturated with the substrate within the limits of its solubility. Although a family 3 enzyme from barley was characterized that was referred to as a ‘bifunctional’ a-l-arabinofuranosidase ⁄ b-d-xylopyra- nosidase [42], there is, to our knowledge, no previous report on an enzyme with equivalent b-glucosidase and b-N-acetylglucosaminidase activity. Glycosyl hydrolases of family 3 form two distinct subgroups: a b-glucosidase subfamily and a b-N-acetyl- glucosaminidase subfamily (Fig. 3). Being a ‘bifunc- tional’ b-N-acetyl-d-glucosaminidase ⁄ b-d-glucosidase, Nag3 of Cellulomonas fimi represents an interesting link between the b-N-acetylglucosaminidase and the b-glucosidase branch of family 3 of glycoside hydrolas- es. A conserved sequence motif in the b-N-acetylglu- cosaminidase subgroup within family 3 may represent the N-acetyl group-binding site [1,7]. Interest- ingly, Nag3, as well as the uncharacterized family 3 enzyme (Q8XP12) within the genome of the recently sequenced bacterium Clostridium perfringens [43], show a significant alteration within this motif: the K-H- (FI)-P-G-( HL)-G-x(4)-D-(ST)-H motif is changed to K-H-(FI)-P-G- D-G-x(4)-D-Q-H (Fig. 2). It can be spe- culated that changes within this motif (underlined) are responsible for the broad substrate specificity of Cellu- lomonas fimi Nag3 for substitution of the C2 position, and further studies in order to confirm this thesis are under way. A hint for a possible function of Nag3 comes from a gene neighbor analysis of a putative b-N-acetylglucosaminidase of Clostridium perfringens using the European Molecular Biology Laboratory Search Tool for the Retrieval of Interacting Genes ⁄ Proteins (string). Analysis revealed that the encoding gene is connected to a cluster of genes similar to known genes involved in the uptake and metabolism of glucuronides. We speculate that the putative N-ace- tylglucosaminidase of Clostridium perfringens and poss- ibly also Nag3 of Cellulomonas fimi might be involved in the degradation of glucuronic acid-containing gly- cosaminoglycans such as hyaluronic acid. Preliminary experiments, however, could not confirm this hypothesis; C. Mayer et al. Cellulomonas fimi b-N-acetylglucosaminidases FEBS Journal 273 (2006) 2929–2941 ª 2006 The Authors Journal compilation ª 2006 FEBS 2937 hydrolysis of hyaluronic acid by Nag3 could not be detected by TLC analysis. b-N-Acetylglucosaminidases involved in hyaluronic acid degradation have been placed into family 84 of glycoside hydrolases rather than family 3 [44]. N-Acetylglucosaminidases in family 84, like family 20 enzymes, use a catalytic mechanism involving anchimeric assistance of the 2-acetamido group of the substrate. However, N-acetylglucosami- nidases in family 3 are retaining enzymes that use a double-displacement mechanism involving the partici- pation of a catalytic nucleophilic group in the enzyme active site [7,13]. Our data confirm that Cellulomonas fimi Nag3 acts by participation of a catalytic nucleo- phile: incubation of Nag3 with DNP-2FGlc permits the observation by ESI ⁄ MS of a high steady-state population of a 2-deoxy-2-fluoroglucosyl–enzyme inter- mediate. The identification of a bifunctional b-N-ace- tyl-d-glucosaminidase ⁄ b-d-glucosidase is an interesting example of divergent evolution towards new substrate specificity within family 3 of glycoside hydrolases. Fur- ther structural and mutational studies are required to elucidate the basis of substrate specificity in this family of glycoside hydrolases. Experimental procedures Materials Chemicals, reagents and materials were purchased as fol- lows: growth media components from Difco (Sparks, ML); DNA purification kits from Qiagen (Hilden, Germany); restriction endonucleases, DNA ligase and DNA poly- merase from New England Biolabs (Beverly, MA) and Roche-Boehringer Mannheim (Germany); and His-bind metal chelation resin from Novagen (Madison, WI). Oligo- nucleotides were synthesized, and DNA and protein sequences determined by the Nucleic Acids and Peptide Service (NAPS) Unit of the Biotechnology Laboratory at the University of British Columbia. N-Acetylchitooligosac- charides (Dp 2–6) were from Seikagaku America (Fal- mouth, MA, USA). Chromogenic substrates and hyaluronic acid were from Sigma. 4MU-GlcNAc and DNP- 2FGlc were synthesized by standard procedures. Bacterial strains, plasmids and phages E. coli strain BL21(DE3) and pET29b were from Novagen (Madison, WI). E. coli XLOLR and the library (2–5 kbp fragment length) of genomic DNA from Cellulomonas fimi in k zapii (18, 19) were from Stratagene (La Jolla, CA). Cultures were grown in LB medium supplemented with 50 mgÆL )1 ampicillin, or TYP medium (tryptone 16 gÆL )1 , yeast extract 16 gÆL )1 , NaCl 5 gÆL )1 ,K 2 HPO 4 2.5 gÆL )1 ) containing 50 mgÆL )1 kanamycin. Screening and isolation of Cellulomonas fimi genes encoding N-acetylglucosaminidases Plasmid isolations, restriction enzyme digests, ligations and transformations were performed using standard techniques. Phagemids (pBluescript SK) were excised from the k ZAPII library using a helper phage and transferred to E. coli XLOLR according to the supplier’s protocol. Sufficient cells to yield about 500 colonies per plate were spread on LB ampicillin agar. After incubation for two days at 37 °C, colonies were replicated on LB ampicillin agar supplemen- ted with 4MU-GlcNAc (200 mgÆL )1 ) and isopropyl thiogal- actopyranoside (IPTG; 1 mm). It was necessary to screen replicas because the 4-methylumbelliferone product released by enzyme action appeared to be toxic to the cells. Colonies were screened for fluorescence at 366 nm using a UV trans- illuminator. Nucleotide sequences of inserts were deter- mined by primer walking and confirmed by sequencing the complementary strand. The nucleotide sequences of hex20A and nag3A have been submitted to the DDBJ ⁄ EMBL ⁄ GenBank databases under the accession numbers AF478459 and AF478460. The UniProt database accession numbers are Q7WUL4 and Q7WUL3, repectively. The GenBank and SWISS-PROT databases were used for nuc- leotide and amino acid sequence searches using the basic local alignment search tool (blast). Construction of pETcfnag3 and pETcfhex20 The putative N-acetylglucosaminidase genes within the inserts in pCF2 and pCF5 were amplified by PCR using oligonucleotide primers based on the ORF sequences (under- lined are the restriction sites NdeI, NotI and XhoI introduced by the primer): CF2NdeI 5¢-CC CAT ATG CCC GAC GTC GCC GTC ATC C-3¢; CF2NotI 5¢-TT GCG GCC GCG CCC GGC GCG GAA CCC-3¢; CF5NdeI 5¢-AA CAT ATG ATC GAC CTG ACC GCA GCC-3¢; CF5XhoI 5¢-AA CTC GAG GTG GGT GTC CCA CTG GCC-3 ¢. PCR mixtures contained 10 lm primers, 1 mm each deoxyri- bonucleoside triphosphate, $ 50 ng of phagemid DNA, 5 U of Pwo polymerase and 4% DMSO in 100 lL of DNA polymerase buffer. Thirty PCR cycles (45 s at 94 °C, 45 s at 63 °C, and 120 s at 72 °C) were performed in a thermal cycler (Perkin Elmer Applied Biosystems, Boston, MA, USA, GeneAmp PCR System 2400). The amplified frag- ments were cloned into pET29b according to a protocol des- cribed previously [45]. Production, purification and N-terminal sequencing of recombinant proteins E. coli BL21(DE3) carrying pET29cfnag3 or pET29cfhex20 was grown at 37 °C in TYP kanamycin to a D 600 nm value of 0.6–0.8, IPTG was added to a concentration of 1 mm, and incubation was continued for a further 12 h at 28 °C. Cellulomonas fimi b-N-acetylglucosaminidases C. Mayer et al. 2938 FEBS Journal 273 (2006) 2929–2941 ª 2006 The Authors Journal compilation ª 2006 FEBS [...]... Bifunctional family 3 glycoside hydrolases from barley with a- 1-arabinofuranosidase and b-d-xylosidase activity Characterization, primary structures, and COOH-terminal processing J Biol Chem 278, 5377–5387 Shimizu T, Ohtani K, Hirakawa H, Ohshima K, Yamashita A, Shiba T, Ogasawara N, Hattori M, Kuhara S & Hayashi H (2002) Complete genome sequence of Clostridium perfringens, an anaerobic flesheater Proc Natl Acad... 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EXOII_HORVU), and a b-xylosidase and an a- L-arabi- ofuranosidase ⁄ b-xylosidase of Hordeum vulgare (Q8W011 ⁄ XYLA_HORVU and (QW012 ⁄ ARAI_HORVU).Nag3 and the putative family 3 N-acetylglucosaminidase of. Characterization of a b-N-acetylhexosaminidase and a b-N-acetylglucosaminidase/b-glucosidase from Cellulomonas fimi Christoph Mayer 1,2,3 , David J. Vocadlo 1, *, Melanie Mah 2 , Karen Rupitz 1 ,. H, Hatano N, Mikami T, Izumizawa Y, Miya- moto K & Inamori Y (1998) Cloning, characterization and expression of b-N-acetylglucosaminidase gene from Cellulomonas fimi b-N-acetylglucosaminidases