Multifunctional properties of glycoside hydrolase family 43 from Paenibacillus curdlanolyticus strain B-6 including exo-β-xylosidase, endo-xylanase, and α-L-arabinofuranosidase activities

Wongratpanya, K., Imjongjairak, S., Waeonukul, R., Sornyotha, S., Phitsuwan, P., Pason, P., Nimchua, T., Tachaapaikoon, C., and Ratanakhanokchai, K. (2015). "Multifunctional properties of glycoside hydrolase family 43 from Paenibacillus curdlanolyticus strain B-6 including exo-β-xylosidase, endo-xylanase, and α-L-arabinofuranosidase activities," BioRes. 10(2), 2492-2505.

Abstract

The glycoside hydrolase family 43 from Paenibacillus curdlanolyticus strain B-6 (GH43B6) exhibited multifunctional properties, including exo-β-xylosidase, endo-xylanase, and α-L-arabinofuranosidase enzymatic activities. GH43B6 released xylose as a hydrolysis product from the successive reduction of xylooligosaccharides as a result of exo-β-xylosidase activity. Moreover, GH43B6 also predominantly released xylose from low-substituted xylan derived from birchwood. However, when the highly substituted rye flour arabinoxylan was used as a substrate, exo-β-xylosidase activity changed to endo-xylanase activity, indicating that the enzymatic property of GH43B6 is influenced by the substituted side groups of xylan. For α-L-arabinofuranosidase, arabinose was released from short-chain substrates including p-nitrophenyl-α-L-arabinofuranoside and α-L-Araf-(1→2)-[α-L-Araf-(1→3)]-β-D-Xylp. This study reports the novel trifunctional properties of GH43B6 containing exo- and endo-activity together with xylanolytic debranching enzymatic activity, which increases its potential for application in lignocellulose-based biorefineries.

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Multifunctional Properties of Glycoside Hydrolase Family 43 from Paenibacillus curdlanolyticus Strain B-6 Including Exo-β-xylosidase, Endo-xylanase, and α-L-Arabinofuranosidase Activities

Kanok Wongratpanya,^a Siriluck Imjongjairak,^a Rattiya Waeonukul,^b Somphit Sornyotha,^c Paripok Phitsuwan,^a Patthra Pason,^b Thidarat Nimchua,^d Chakrit Tachaapaikoon,^b and Khanok Ratanakhanokchai ^a,*

Keywords: Exo-β-xylosidase/endo-xylanase/α-L-arabinofuranosidase activities; Glycoside hydrolase family 43; Multifunctional enzyme; Paenibacillus curdlanolyticus; Xylanolytic enzyme

Contact information: a: School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bangkuntien Campus), Bangkok 10150, Thailand; b: Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bangkuntien Campus), Bangkok 10150, Thailand; c: Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand; d: Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani 12120, Thailand;

* Corresponding author: khanok.rat @kmutt.ac.th

INTRODUCTION

Plant biomass contains a variety of polysaccharides as structural and storage compounds, and the most prominent are cellulose and hemicelluloses (Schwarz 2001). Xylans are the major components of hemicelluloses. Xylan from hardwoods is mainly composed of glucuronoxylan, in which some xylose units within the linear β-(1,4)-D-xylopyranose backbone are decorated with acetyl groups and 4-O-methylglucuronic acids (Alén 2000). Meanwhile, arabinoglucuronoxylan was identified in softwoods and grasses. The structure of arabinoglucuronoxylan consists of a linear β-(1,4)-D-xylopyranose backbone decorated with 4-O-methyl-α-D-glucopyranosyluronic acid and α-L-arabinofuranosyl linked by α-(1,2) and α-(1,3) glycosidic bonds. Nonetheless, arabinose decoration of xylan from grasses was higher than it was from softwoods (Gírio et al. 2010). However, the type and degree of the substituted side chains on xylan vary with the botanical origin (Biely 1985). Due to the complicated architecture of xylans, the hydrolysis of xylan requires the action of a complex enzyme system of xylanolytic enzymes that act synergistically to depolymerise xylan to its sugar constituents. Xylanolytic enzymes are usually composed of non-debranching enzymes (endo-xylanase and -xylosidase) and debranching enzymes (-arabinofuranosidase, -glucuronidase, acetyl xylan esterase, and phenolic acid esterase) (Biely 1985).

Glycoside hydrolase family 43 (GH43) is a group of enzymes with broad similarity and a variety of enzymatic functions (Cantarel et al. 2009) encompassing monofunctional enzymes such as α-L-arabinofuranosidase (EC 3.2.1.55), β-xylosidase (EC 3.2.1.37), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), galactan 1,3-β-galactosidase (EC 3.2.1.145), α-1,2-L-arabinofuranosidase (EC 3.2.1.-), exo-α-1,5-L-arabinofuranosidase (EC 3.2.1.-), exo-α-1,5-L-arabinanase (EC 3.2.1.-), and β-1,3-xylosidase (EC 3.2.1-). Moreover, multifunctional enzymes from several origins have been reported in GH43 such as β-xylosidase/α-L-arabinofuranosidase (Kim and Yoon 2010), β-xylosidase/exo-xylanase (GenBank ID: ABD48561.1), and β-1,4-xylosidase/α-1,5-arabinofur(pyr)anosidase/β-1,4-lactase/α-1,6-raffinase/α-1,6-stachyase/β-galactosidase/α-1,4-glucosidase (Ferrer et al. 2012). Recently, Viborg et al. (2013) classified 92 characterised GH43 enzymes based on sequence similarity and functions to five distinct substrate specificity groups. GH43 enzymes contribute to xylan degradation by releasing substituted side groups from xylan, which allows endo-xylanases to act efficiently for complete hydrolysis (Lagaert et al. 2014). This issue is of great interest for biomass utilisation in the biorefinery and bioenergy areas.

We found one open reading frame (ORF) from the Paenibacillus curdlanolyticus strain B-6 encoding a protein belonging to GH family 43, which comprises a broad variety of enzyme specificities and similarities. As a result, we speculated that GH43 from strain B-6 (GH43B6) may exhibit enzymatic properties that differ from other GH43 enzymes. P. curdlanolyticus strain B-6 is a true cellulolytic/xylanolytic bacterium that produces a unique extracellular xylanolytic-cellulolytic multienzyme complex-like structure capable of degrading insoluble substrates (Pason et al. 2006). Therefore, this study was conducted to elucidate the enzymatic properties of GH43 from P. curdlanolyticus strain B-6. The results are important in determining how the enzymatic properties of GH43B6 cooperate with endo-xylanases to depolymerise xylans.

EXPERIMENTAL

Strains and Plasmid

P. curdlanolyticus B-6 was isolated from an anaerobic digester, fed with pineapple waste (Pason et al.2006), and deposited in the BIOTEC Culture Collection of the National Center for Genetic Engineering and Biotechnology, Thailand, with the accession number BCC no. 11175. All cloning strategies were performed in Escherichia coli DH5α (New England Biolabs, Ipswich, MA, USA). Escherichia coli BL21 (DE3) (Novagen, Darmstadt, Germany) was used as the host for the derivative of pET28b(+) (Novagen).

Gene Manipulation

Genomic DNA was extracted from P. curdlanolyticus B-6 by using a chromosomal DNA extraction kit (Viogene, New Taipei City, Taiwan) and subjected to GH43B6 amplification. The oligonucleotide primers were forward primer 5′ CGGGATCCCGATGGA CAACAAACCGGTAAA 3′ and reverse primer 5′ CCGCTCGAGCGGTTTCAATTTGCTA TAATCGAGC 3′; they were designed based on a genomic library of strain B-6 and constructed using a CopyControl Fosmid Library Production Kit (Epicenter, Madison, WI), which has been described previously (Sudo et al. 2010). The suitable BamHI and XhoI recognition sites for cloning were added to the forward and reverse primers, respectively (underlined sequences). The PCR product was introduced into pET28b(+) at the same restriction sites to yield pGH43B6.

Expression, Purification, and Optimum Conditions of GH43B6

Plasmid pGH43B6 was transformed into E. coli BL21 (DE3). A transformant harbouring pGH43B6was grown on Luria Bertani medium, supplemented with kanamycin (30 µg/mL final concentration). The culture was incubated at 37°C and 200 rpm until the OD₆₀₀ reached 0.6. Protein expression was induced with a 1 mM final concentration of isopropyl β-D-1-thiogalactopyranoside, and the culture was further incubated at 16°C for 16 h. The cells were harvested and disrupted. Cell-free extracts were applied to HisTrap^TM FF columns (GE healthcare, Little Chalfont, UK) for affinity purification. The purity of purified proteins was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) (Laemmli 1970). α-L-Arabinofuranosidase was used for monitoring the target protein. The optimum pH of GH43B6 for hydrolysis was determined at a pH ranging from 3.0 to 10.0 (pH 3.0 to 6.0, acetate buffer; pH 6.0 to 8.0, phosphate buffer; pH 8.0 to 9.0, Tris-HCl buffer; pH 9.0 to 10.0, carbonate buffer) for 30 min at 50 °C. The optimum temperature was determined in the range of 30 to 90 °C for 30 min at the optimum pH.

Enzyme Assays and Protein Determination

The following substrates—p-nitrophenyl-α-L-arabinofuranoside (pNPA), p-nitro-phenyl-β-D-xylopyranoside (pNPX), p-nitrophenyl acetate, p-nitrophenyl-β-D-glucopyran-oside (pNPG), p-nitrophenyl-β-D-galactopyranoside (pNPGal), and p-nitrophenyl-β-D-cellobioside (all from Sigma-Aldrich, St. Louis, MO, USA)—were used for assaying α-L-arabinofuranosidase, β-xylosidase, acetyl esterase, β-glucosidase, galactan 1,3-β-galactosidase, and cellobiohydrolase activities, respectively. Enzyme aliquots were incubated with 100 µL of 0.9 mM substrate in 50 mM sodium phosphate buffer (SPB) (pH 7.0) at 50 °C for 30 min, and the reaction was stopped by adding 1 mL of 1 M Na₂CO₃. Liberation of p-nitrophenol was measured by absorbance at 410 nm. One unit (U) of enzyme activity was defined as the amount of enzyme required for liberating 1 µmol of p-nitrophenol per min.Xylanase activity was assayed on 1% xylan from birchwood (Sigma-Aldrich) in 50 mM SPB (pH 7.0) at 50 °C for 10 min. Liberated reducing sugars were analysed by the Nelson-Somogyi method (Nelson 1944). One unit (U) of xylanase activity was defined as the amount of enzyme used for liberating 1 µmol of xylose per minute. Protein concentration was determined as described by Lowry et al. (1951).

Determination of the Hydrolysis Action of GH43B6

The hydrolysis action of purified GH43B6 was elucidated on various types of substrates. To assess β-xylosidase action, 0.025% (w/v) of xylohexaose and xylobiose (Megazyme International, Wicklow, Ireland), were used as substrates. The action of xylanase was determined on 1% (w/v) xylans from birchwood, oat spelt (Sigma-Aldrich), wheat flour arabinoxylan (Megazyme), and rye flour arabinoxylan (Megazyme). The α-L-arabinofuranosidase action was determined on 1% (w/v) rye flour arabinoxylan, oat spelt xylan, and 0.025% (w/v) α-L-Araf-(1→2)-[α-L-Araf-(1→3)]-β-D-Xylp (A-X-A). Aliquots of 0.1 U of α-L-arabinofuranosidase, β-xylosidase, or xylanase from GH43B6 were mixed with their substrate in 50 mM SPB buffer pH 7.0 and incubated at 50 °C. The hydrolysis reaction was stopped by boiling for 15 min.

Preparation of A-X-A

Rye flour arabinoxylan (1%) in 50 mM SPB pH 7.0 was hydrolysed by 0.1 U of xylanase Xyn10C from P. curdlanolyticus strain B-6 (Imjongjairak et al. in press) at 50 °C for 16 h. The hydrolysis products were separated by thin layer chromatography (TLC) as described by Sornyotha et al. (2007). The A-X-A was cut out from the TLC plate at the same position as the standard A-X-A that had been prepared in the laboratory as described by Imjongjairak et al. (in press); it was verified by electrospray ionization mass spectrometry and enzymatic analysis using Bacillus licheniformis α-L-arabinofuranosidase Axh43A (Sakka et al. 2012), suspended in deionised water, and then sonicated. Silica was removed by centrifugation at 9,200 x g for 1 min. The supernatant was collected and dried in a speed vacuum (Univapro 100 ECH, UniEquip, Planegg, Germany).

Analysis of Hydrolysis Products

Hydrolysis samples from the xylans were centrifuged at 9,200 x g for 1 min, and the supernatants were collected. The analyses of the hydrolysis products from xylohexaose and xylans were carried out by TLC. The xylobiose hydrolysis products were analysed by high performance liquid chromatography (HPLC) (Shimadzu, Kyoto, Japan) with a reflective index detector (Shimadzu RID-10A) on BP-100 Pb⁺⁺ carbohydrate columns (Benson polymeric, Sparks, NV, USA) operated at 85 °C with deionised water at a flow rate of 0.6 mL/min.

RESULTS AND DISCUSSION

The gene encoding glycoside hydrolase family 43 from P. curdlanolyticus B6 (GH43B6) was cloned in this study. GH43B6 (accession No. KM272280) was annotated to encode an enzyme belonging to GH43 based on amino acid sequence similarity. It contains an ORF of 990 nucleotides corresponding to 330 amino acids with a predicted molecular mass of 37.5 kDa. GH43B6 amino acid sequencepositions 11 through 321 were confidently predicted by SMART software (Letunic et al. 2014) to be a glycoside hydrolase family 43 catalytic domain, while two unknown regions were also identified at positions 1 through 10 and 322 through 330, respectively. Signal peptide prediction by the SignalP 4.0 server (Petersen et al. 2011) suggested the absence of a signal peptide in GH43B6. BlastP analysis of GH43B6 revealed high similarity to uncharacterised GH43 mono- and bi-functional enzymes such as α-L-arabinofuranosidase, β-xylosidase, and bifunctional β-xylosidase/α-L-arabinofuranosidase, with the highest identity (84%) to α-L-arabinofuranosidases from Paenibacillus sp. J14 (GenBank ID: WP_028537372.1) and Paenibacillus sp. oral taxon 786 (WP_009224277.1). Comparison of GH43B6 with GH43 α-L-arabinofuranosidases from P. lactis (GenBank ID: WP_007127515.1), P. vortex (WP_006211951.1), and P. curdlanolyticus (WP_006040336.1) showed sequence identities of 81%, 77%, and 72%, respectively. Moreover, comparisons with GH43 xylosidase/arabinofuranosidase from Clostridium saccharoperbutylacetonicum N1-4(HMT) (YP_007457878.1) and β-xylosidases from Thermobacillus composti KWC4 (YP_007212002.1) and Aspergillus terreus (ADF63137.1) showed sequence identities of 77% 76%, and 64%, respectively. Subsequently, almost all the catalytic domain of GH34B6 was subjected to multiple sequence alignment with other GH43 members (Fig. 1).

Multiple conserved regions were identified, especially aspartic acids (positions 69, 81, 145, 151, 153, 186, 201, 211, and 285) and glutamic acids (positions 196, 202, 218, and 302). A phylogenetic tree of GH43B6 with characterised GH43 representatives was constructed based on categories described by Viborg et al. (2013). Representatives were chosen by the criteria of enzymatic function and sequence similarity compared with GH43B6. The results indicated that GH43B6 belongs to group III, which consists of α-L-arabinofuranosidase, -xylosidase, endo-xylanase, and -xylosidase/α-L-arabinofuranosidase (Fig. 2). However, AAD30363.1 bifunctional endo-xylanase/α-L-arabinofuranosidase from Caldicellulosiruptor sp. Tok7B.1, which has been classified to group III by Viborg et al. (2013), was individually separated due to low sequence similarity with GH43B6 (22.54%).

GH43B6 HGEVLHMKD—-VPWVSKQMWAPDCAFK-NNTYYLYFPARDKDGIFRIGVATSSRPEGP 115

C. saccharoperbutylacetonicum HGEALHLKD—-IPWASKQLWAPDAVYK-NGTYYLFFPARDKDEIFRIGVATSSNPAGP 57

C. papyrosolvens NGEALHMKD—-VPWVSKQMWAPDAAFK-NNTYYLYFPARDKDGIFRIGVASSSSPAGP 65

P. lactis HGEVLHVKD—-VPWAQKQMWAPDAAFK-NDTYYLYFPARDHEGIFRIGVATSSSPSGP 115

P. vortex HGQALHVKD—-VPWAKKQMWAPDAAYK-NDTYYLYFPARDHNDIFRLGVATSSSPSGP 57

P. curdlanolyticus HGQALHVKD—-VPWASKQMWAPDAAFK-NDTYYLFFPARDHDDIFRIGVATSPSPAGP 57

T. composti HGEALHVRD—-VPWASKQMWAPDAAFK-NGKYYLYFPARDLEGNFRIGVAVSDKPAGP 111

C. japonicus CGVALHVKD—-VPWAERQMWAPDAITK-DGKYYLYFPARARDGLFKIGVAIGDQPEGP 58

GH43B6 FKAEPNYIEGSYSIDPAVFVDEDNRAYMYFGGLWGGQLEKWQTGEFLGDVTEGPAADAPA 175

C. saccharoperbutylacetonicumFKAEENYIPGSFSIDPAVLMDDDNRSYVYFGGLWGGQLEKWQTGTFKADA-EGPAVTAPA 116

C. papyrosolvensFTAQKEPIPGSFSIDPAVLVDDDNRAYIYFGGLWGGQLEKWQTGSFSPDA-EGPDVSAPA 124

P. lactis FTPEPNYIPGSFSIDPAVFVDDDNRAYMYFGGLWGGQLEKWQTGTFVPDA-EGPAADAPA 174

P. vortex FTPEPDYIPGSYSIDPAVFVDDDNRAYIYFGGLWGGQLEQWQTGSHIPDG-EGPAADAPA 116

P. curdlanolyticusFEPQPEYIPGSFSIDPAVFVDEDDRAYMYFGGLWGGQLEKWQTDAYVAEP-AEIEPDQPA 116

T. composti FKPEPNYIPGSFSIDPAVLVDDDGEAYMYFGGLWGGQLEKWQTGTFNPEG-KEPAPDAPA 170

C. japonicus FVAEPEPIAGSYSIDPAVFGDDDGEFYLYFGGIWGGQLQKYRDNTYSEIH-EEPTADQPA 117

GH43B6 IGPRVAELSDDMLSIKGEVKEISIVDENGNPIVAGDEDRRYFEGPWMHKYNGYYYLSYST 235

C. saccharoperbutylacetonicumLGPRVAELNEDMLTFKESPEEISIVDEDGNPLLAGDEDRRYFEGPWVHKYNGNYYLSYST 176

C. papyrosolvensIGPRVAELSDDMLTFKEAPEEISIVDEEGNPILAGDEDRRYFEGPWMHKYNGNYYLSYST 184

P. lactisLGPRVAELSDDMLTFKAAPQEISIVDENGKPIPAGDEDRRYFEGPWMHKYNGTYYLSYST 234

P. vortexIGPRVAELSDDMLTFKDTPQEISIIDENGSPITAGDEERRYFEGPWVHKYNGTYYLSYST 176

P. curdlanolyticusLGPRVAELSEDMLTFRERPVEIAIVDEQGNALLAGDEERRYFEGPWMHKYKGKYYLSYST 176

T. compostiLGPRVARLSGDMLTFAETPREVQILDENGEPIKAGDEDRRYFEGPWMHKYNGKYYLSYST 230

C. japonicusLGARVARLSADMKSFVEASREVVILDEQGQPLLAGDNSRRYFEGPWMHKYQGKYYLSYST 177

GH43B6 GSTHKLVYAMSKNPEGPFVFKGTILTP—————VIGWTTHHSIVEFQGKWY 280

C. saccharoperbutylacetonicum GSTHYIVYAMSKNPKGPYTFKGKILDP—————VIGWTTHHSIVQFQDKWY 221

C. papyrosolvens GTTHTIVYAVGNNPKGPFVFKGKILTP—————VVGWTTHHSIVQYQDKWY 229

P. lactis GSTHKIVYATSQSPTGPFEYKGTILTP—————VLGWTTHHSIVEFKNKWY 279

P. vortex GSTHQIVYGTSQSPTGPFEFKGTILTP—————VIGWTTHHSIVQFQDKWY 221

P. curdlanolyticus GSTHQIVYGTSQSPTGPFEFKGTILTP—————VIGWTTHHSIVQFQDKWY 221

T. composti GTTHKLVYAIGDNPYGPFTYKGVILTP—————VIGWTTHHSIVEFRGKWY 275

C. japonicus GDTHFLCYATSDNPYGPFTYQGQILTP—————VVGWTTHHSICEFEGKWY 222

GH43B6 LFYHDSSLSGGVNHKRCVKYTEIKYNEDGTI 311

C. saccharoperbutylacetonicum LFYHDSSLSGGSDNKRCVKFTELKYNEDGTI 252

C. papyrosolvens LFYHDSSLSGGRDNKRCVKFTELKYNEDGTI 260

P. lactis LFYHDSSLSGGADNKRSVKFTELKYNEDGTI 310

P. vortex LFYHDSSLSGGADNKRSVKFTELKYNADGTI 252

P. curdlanolyticus LFYHDSSLSGGADNKRSVKFTELEYNEDGTI 252

T. composti LFYHDASLSGGVNHLRCVKYTELHYNPDGTI 306

C. japonicus LFYHDSVLSEGVTHLRSVKVTELHYEADGKI 253

Fig. 1. Amino acid sequence alignment of the catalytic domain of GH43B6 compared with uncharacterised β-xylosidase/α-L-arabinofuranosidase from Clostridium saccharoperbutylacetonicum (YP_007457878.1) and Cellvibrio japonicus Ueda107 (YP_00198 1807.1), α-L-arabinofuranosidases from C. papyrosolvens (EPR10382.1), Paenibacillus lactis (WP_007 127515.1), P. vortex(WP_006211951.1) and P. curdlanolyticus (WP_006040336.1), and β-xylosidase from Thermobacillus composti KWC4 (YP_007212002.1). Conserved regions are highlighted; conserved aspartic acid (D) and glutamic acid (E) are marked with asterisks.

Fig. 2. Phylogenetic tree constructed based on Viborg et al. (2013) category by the Neighbor-Joining method of GH43B6 and representatives of the GH family 43. Five distinct groups represent a different specificity: group I consists of galactan 1,3-β-galactosidase; group II consists of α-L-arabinofurano-sidase; group III was divided into a cluster of α-L-arabinofuranosidase, -xylosidase, endo-xylanase, and -xylosidase/α-L-arabinofuranosidase and another individual branch of endo-xylanase/α-L-arabinofuranosidase; group IV consists of α-L-arabinofuranosidase, -xylosidase, endo-xylanase, -xylosidase/α-L-arabinofuranosidase, and -1,3-xylosidase; and group V consists exclusively of endo-arabinanase. Sequences were designed with the GenBank protein accession number.

Recombinant expression of GH43B6 yielded 71.77% purified protein and a 16.72-fold purification. The purified protein showed a single band of approximately 39 kDa by SDS-PAGE (Fig. 3). The histidyl tag from the pET28b(+) system contributed an extra mass to that which was predicted for the recombinant protein. The GH43B6, which fused with histidyl tag at the C-terminus, retained the enzymatic function indicated that histidyl tag did not interfere the function of GH43B6. The presence of the histidyl tag had no significant effect on protein structure (Carson et al. 2007). Thus, biochemical characterization of GH43B6 could be conducted without cleaving of histidyl tag. Determination of the enzymatic activities of GH43B6 showed α-L-arabinofuranosidase, β-xylosidase, and xylanase (Table 1). Furthermore, xylanase activity of GH43B6 on various structural types of xylan exhibited the highest xylanase activity of 2.86 U/mg on xylan from birchwood, and 1.46 U/mg on xylan from oat spelt. Meanwhile, low xylanase activity was observed (0.03 and 0.005 U/mg, respectively) on the highly substituted wheat flour arabinoxylan and rye flour arabinoxylan. The reduced xylanase activity on oat spelt xylan, wheat flour arabinoxylan, and rye flour arabinoxylan may be due to xylooligosaccharides, which exhibit less reducing power than xylose according to the Nelson-Somogyi method. Determination of the optimum pH and temperature for enzyme activities revealed that all enzymatic activities of GH43B6 showed the same optimum hydrolysis condition at pH 6.0 and 50 °C.

Table 1. Substrate Specificity of the Purified GH43B6

Fig. 3. SDS-PAGE of GH43B6 purified via Ni-NTA columns. Lanes M, 1, and 2 represent a molecular mass marker, a cell free extract, and purified GH43B6, respectively.

Elucidation of GH43B6 hydrolysis action was performed on xylohexaose (X₆), xylobiose (X₂), and xylans. GH43B6 predominantly produced xylose as a hydrolysis product from X₆ (Fig. 4a). The GH43B6 immediately converted X₆ to xylopentaose (X₅), and X₅ was suddenly reduced to xylotetraose (X₄). Successive reduction of X₆to X₄ revealed the continuous accumulation of xylose. However, trace amounts of xylotriose (X₃) and X₂ were observed, while X₆, X₅, and X₄ still remained after the reaction had been processed for 1 h (Fig. 4a, lane 11). Although reduction of X₂to xyloseoccurred slowly, xylose was obviously detected after a 16-h hydrolysis, while small amounts of X₂remained (Fig. 4b). Predominant and continuous increasing of xylose from X₆hydrolysis indicated the exo-acting activity of β-xylosidase. GH43B6 cleaved one xylose from the end of a long chain substrate, such as X₆ and X_5, faster than from a short chain substrate (X₂). Generally, true β-xylosidases prefer xylobiose (Wong et al. 1988) and the affinity of the enzyme toward xylooligosaccharides decreases with increasing degrees of polymerisation (Bajpai 1997). In contrast to common β-xylosidases, exo-β-xylosidase of GH43B6 showed weak activity against xylobiose and preferably hydrolysed xylooligomers with a degree of polymerisation higher than four. However, the existence of GH43 with a broad xylooligosaccharide specificity toward X₂-X₆ has been reported (Lagaert et al. 2011).

Fig. 4. Chromatograms of the hydrolysis products of xylohexaose (a) and xylobiose (b) by GH43B6. Standard xylose and xylooligosaccharides, X2-X6 are marked by M; lanes 1 through 6 represent hydrolysis products from 0 to 5 min; lanes 7 through 10 represent hydrolysis products from 10, 15, 20, and 30 min; lane 11 represents hydrolysis products at 1 h. Hydrolysis products of xylobiose were analysed via HPLC.

The hydrolysis action of GH43B6 was further elucidated when low branching xylan from birchwood (Fig. 5a) showed that xylose was detected in the early stage of hydrolysis and continuously accumulated, which also indicated the action of exo-β-xylosidase. After 10 min of hydrolysis, xylooligosaccharides were observed between X₄ and X₅ (Fig. 5a, lanes 5 through 7), which implied the presence of an endo-acting mode of GH43B6. Based on xylan structure, xylan from birchwood had the simplest structure, containing trace numbers of substitution (Adams et al. 2004). This may suggest that exo-β-xylosidase continuously cleaved one xylose from the end of the xylan chain, and its function was changed to endo-xylanase when GH43B6 was obstructed by the substituted side chain. Based on this evidence, the substituted side groups of xylan may have influenced the enzymatic functions of GH43B6. In addition, 16-h hydrolyses of various structural types of xylans showed that birchwood xylan yielded predominantly xylose and xylooligosaccharides larger than X₅ (Fig. 5b, lane 1), while hydrolysis products from oat spelt xylan resulted in xylose and xylooligosaccharides of sizes between those of X₂ to X₅ (Fig. 5b, lane 2).

Detection of xylooligosaccharides and xylose from oat spelt xylan hydrolysis indicated that GH43B6 exhibited endo-xylanase and β-xylosidase activities. This may result from the structure of oat spelt xylan, which contains more substitution than xylan from birchwood (Puls et al. 1987); this makes it difficult for GH43B6 to attack near the substituted end and facilitates its move to the inner chain. Thus, the dominant function of GH43B6 was endo-xylanase activity. Moreover, predominant hydrolysis products resulting from the highly substituted xylan, rye flour arabinoxylan that contains both α-1,3 and α-1,2 monosubstitutions and O2, O3 disubstituted α-L-arabinofuranosides were xylooligosaccharides larger than X₅ (Pitkänen et al. 2009) (Fig. 5b, lane 3) and trace amounts of xylose. This also reinforced the mode of action of GH43B6 as mainly that of an endo-xylanase. The arabinose/xylose ratio of rye flour arabinoxylan is 38/62 (Megazyme). As a result of a high degree of side chain decoration, a substituted side group of xylan could limit the exo-β-xylosidase activity of GH43B6, thereby allowing for its endo-xylanase function. These results revealed that the type and frequency of substituted side chains on xylan might influence GH43B6 function.

Fig. 5. Chromatograms of xylans and A-X-A hydrolysed by GH43B6. Monitoring of xylan from birchwood hydrolysis products are shown in panel (a). Standard xylooligosaccharides, X1 to X6 are marked by M; lanes 1 through 4 represent hydrolysis products at 0, 1, 2, and 4 min, respectively; lanes 5 through 6 represent hydrolysis products at 10 and 15 min; and lane 7 represents hydrolysis products at 1 h. The 16-h hydrolysis products from xylans are shown in panel (b), birchwood (lane 1), oat spelt (lane 2), and rye flour arabinoxylan (lane 3). α-L-Arabinofuranosidase was determined (c), A-X-A hydrolysis products at 16 h (lane 1) were compared with those of standard A-X-A (lane 2). Standard arabinose is marked by A.

Determination of α-L-arabinofuranosidase activity of GH43B6 showed that there was no arabinose released from the hydrolysis of arabinoxylans from oat spelt and rye flour. Conversely after a 16-h hydrolysis, GH43B6 could partially hydrolyse A-X-A to arabinose and AX (Fig. 5C, lane 1), whereas GH43B6 could release arabinose from aryl-arabinoside, pNPA, within 30 min. This suggested that arabinose liberation depends on the chain length of the substrate. GH43B6 preferred only short-chain substrates, which differed from the long chains preferred by GH43 α-L-arabinofuranosidase from Bacillus licheniformis SVD1 (Sakka et al. 2012) and the broad chain lengths preferred by GH43 α-L-arabinofuranosidase from a compost starter mixture (Wagschal et al. 2009). A comparison between A-X-A and aryl-arabinoside revealed that GH43B6 could release arabinose from aryl-arabinoside faster than from A-X-A. This result suggested that the orientation and/or types of backbones forming between arabinosyl and an aromatic ring or xylose might have different effects on GH43B6 arabinofuranosidase activity. In addition, aryl-arabinoside containing an α-1,4 glycosidic linked arabinoside on the aromatic ring might be more easily hydrolysed than the α-1,2 and 1,3 disubstitution on xylose of A-X-A. However, the specificity of the arabinosyl position on AX was not examined. Arabinofuranosidases are categorised by the specificity of the arabinosyl positions, which are specific on α-1,2 and 1,3 monosubstitution (Bourgois et al. 2007; Lagaert et al. 2010), and only on α-1,3 of diarabinosyl substitution (van den Broek et al. 2005, Sørensen et al. 2007).

Even though multiple sequence alignment indicated a low similarity between the amino acid sequence of GH43B6 and other GH43 enzymes, conserved residues (aspartate and glutamate in particular) were identified. The catalytic action of GH43 proceeds via an inverting mechanism with two aspartates playing a role as the general base and pK_a modulator, respectively, and one glutamate playing a role as a general acid (Pitson et al. 1996). Nurizzo et al. (2002) established that aspartates 38 and 158, and glutamate 221 are involved in the catalytic mechanism of GH43 α-L-arabinofuranosidase from Cellvibrio japonicus. Furthermore, Shallom et al. (2005) found that aspartate 14 and glutamate 187 were general bases and general acid catalytic residues of GH43 β-D-xylosidase from Geobacillus stearothermophilus T-6, respectively. Moreover, both catalytic actions of bifunctional β-xylosidase/α-L-arabinofuranosidase from Cel. japonicus Ueda 107 were also driven by aspartates and glutamate. (Cartmell et al. 2011) These results revealed that the monofunctional and bifunctional activities of GH43 are driven by the same catalytic residues. Hence, analysis of the sequence homology with known structures GH43 was further conducted. GH43B6 was compared in terms of the amino acid sequence homology via SWISS-MODEL automated protein structure homology-modelling server (Bordoli et al. 2008). GH43B6 showed the highest identity at 53.48% homologue with β-xylosidase RS223 from an uncultured organism (PDB code: 4mlg) and 40% identity homologue with bifunctional β-xylosidase/α-L-arabinofuranosidase from Cel. japonicus Ueda107 (CJA_3018) (PDB code: 3qed) (DeBoy et al. 2008). Nevertheless, GH43B6 exhibits multi-enzymatic functions; therefore, we selected β-xylosidase/α-L-arabinofuranosidase CJA_3018 (CjAbf43A) to study the comparative analysis. The study of CJA_3018 indicated that Asp41, Asp168, and Glu215 exhibit a significant role in catalytic residues. Moreover, Trp103, Ile167, His267, and Arg295 were shown to play a role in substrate binding sites (Cartmell et al. 2011). The comparative analysis of amino acid sequences of GH43B6 and CJA_3018 revealed that although GH43B6 showed low sequence homology with CJA_3018, all key catalytic residues (Asp41, Asp168, and Glu215) and amino acids in substrate binding sites (Trp103, Ile167, His267, and Arg295) were conserved (Fig. 6). Moreover, GH43B6 contains only one GH43 catalytic domain and the optimal conditions of all enzymatic activities of GH43B6 were the same. Additionally, Ferrer et al. (2012) suggested that although the catalytic action of GH43 from a fiber-adherent microbial community from a dairy cow rumen was achieved via the same key residues as other GH43, promiscuous enzymatic activities occurred by the atypical folding of the active site. Atypical folding of the active site enhanced the flexibility of the active site for binding with various types of substrates such as, pNPA, p-NP-α-arabinopyranoside, pNPX, pNPGal, pNPG, p-NP-α-D-maltoside, 1,4-β-xylooligosac-charides (X₁-X₆), 1,5-α-L-arabinooligosaccharides (A₂-A₄), maltooligosaccharides (M₂-M₇), lactose, raffinose, and stachyose. These evidences lead to the logical conclusion that multifunctional properties of GH43B6 were driven by one active site. The significant difference in amino acid sequences contributes to the promiscuous characteristics of GH43B6, which may be caused by atypical folding of the binding site within the active site, compared to other GH43 enzymes.

CJA_3018 MTTSLNSRRLWLHRLCALLLGTGSALVQAENPIFTDVFTADPAALVHKGRVYLYAGRDEA 60

GH43B6 ———————MDNKPVKPNQPLVTHIYTADPSAHVFEGKIYIYPSHDID 39

.. *:.::*:.*.::****:* *.:*::*:*..:*

CJA_3018 P—–DNTTFFVMNEWLVYSSDDMAN-WEAHGPGLRAKDFTWAKGDAWASQVIERNGKF 114

GH43B6 HDGPDNDNGDQYKMEDYHVLSLDDFNSPCVDHGEVLHMKDVPWVSKQMWAPDCAFKNNTY 99

** : *::: * * **: . ** *: **..*.. : **.: :*..:

CJA_3018 YWYVTVRHDDTKPGFAIGVAVGDSPIGPFKDALGKALITNDMTTDTPIDWDDIDPSVFID 174

GH43B6 YLYFPARDKD–GIFRIGVATSSRPEGPFKAEP–NYIEGSYS———IDPAVFVD 146

* *…*..* * ****… * **** * .. : ***:**:*

CJA_3018 DDGQAYLFWG—————————-NTRPRYAKLKKNMVELDGPIRA 206

GH43B6 EDNRAYMYFGGLWGGQLEKWQTGEFLGDVTEGPAADAPAIGPRVAELSDDMLSIKGEVKE 206

:*.:**:::* ** *:*..:*:.:.* ::

CJA_3018 IEGLP————-EFTEAIWVHKYQDNYYLSYAMGFPEKIGYAMGKSIKGPWVYK 253

GH43B6 ISIVDENGNPIVAGDEDRRYFEGPWMHKYNGYYYLSYSTGSTHKLVYAMSKNPEGPFVFK 266

*. : .: *. *:***:. *****: * ..*: ***.*. :**:*:*

CJA_3018 G-ILNEVAGNTPTNHQAIIEFNNKHYFIYHTGAGRPDGGQYRRSVSIDELFYNPDGTIKR 312

GH43B6 GTILTPVIG–WTTHHSIVEFQGKWYLFYHDSS-LSGGVNHKRCVKYTEIKYNEDGTIQM 323

* **. * * *.*::*:**:.* *::** .: ..* :::*.*. *: ** ****:

CJA_3018 IVMTTEGVAPNKSPERVKKAAK 334

GH43B6 LDYDKLK————— 330

: .

Fig. 6. Comparative analysis of amino acid sequence of GH43B6 with the bifunctional β-xylosidase/α-L-arabinofuranosidase from Cel. japonicus Ueda107 (CJA_3018, GenBank ID ACE83886.1) accomplished with ClustalW2 (Larkin et al. 2007). The conserve catalytic residues were indicated in box and amino acids in substrate binding sites were shaded in gray.

In summary, this study is the first report of GH43 exhibiting a new combination of exo- and endo-activity together with the side chain removing activity of exo-β-xylosidase/endo-xylanase/α-L-arabinofuranosidase. The different mode of action of GH43B6 from the endo-xylanases suggests that GH43B6 may be a good accessory enzyme in xylanolytic enzyme cocktails to boost the hydrolysis efficiency for the bioconversion of biomass.

CONCLUSIONS

Glycoside hydrolase family 43 from P. curdlanolyticus strain B-6 (GH43B6) exhibited multifunctional properties including a combination of exo- and endo-acting enzymatic activity together with xylanolytic debranching enzymes.
GH43B6 showed an exo-acting function toward xylooligosaccharides and low-substituted xylan.
Substituted side chains of xylan influenced the change in the mode from exo- to endo-action of GH43B6.
α-L-Arabinofuranosidase of GH43B6 could release arabinose from short-chain substrates, α-L-araf-(1→2)-[α-L-araf-(1→3)]-β-D-xylp and p-nitrophenyl-α-L-arabinofuranoside.

ACKNOWLEDGMENTS

This work was financially supported in part by King Mongkut’s University of Technology Thonburi, Thailand (under the Higher Education Research Promotion and National Research University Project of Thailand, Office of the Higher Education Commission), the Japan Society for the Promotion of Science and the National Research Council of Thailand, and Thailand Graduate Institute of Science and Technology.

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Article submitted: October 29, 2014; Peer review completed: February 9, 2015; Revised version received and accepted: February 25, 2015; Published: March 3, 2015.

DOI: 10.15376/biores.10.2.2492-2505