Biochemical Characterization and Substrate Degradation Mode of a

Aug 18, 2017 - AgWH50B exhibited good enzymatic properties with high specific activity and catalytic efficiency (1523.2 U/mg and a Vmax of 1700 μmol/...
1 downloads 14 Views 1MB Size
Subscriber access provided by UNIVERSITY OF ADELAIDE LIBRARIES

Article

Biochemical Characterization and Substrate Degradation Mode of a Novel Exo-type #-agarase from Agarivorans gilvus WH0801 Yunxiao Liang, Xiaoqing Ma, Lujia Zhang, Fuli Li, Zhen Liu, and Xiangzhao Mao J. Agric. Food Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jafc.7b01533 • Publication Date (Web): 18 Aug 2017 Downloaded from http://pubs.acs.org on August 18, 2017

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

Journal of Agricultural and Food Chemistry is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

Page 1 of 27

Journal of Agricultural and Food Chemistry

1

Biochemical Characterization and Substrate Degradation Mode of a Novel Exo-type

2

β-agarase from Agarivorans gilvus WH0801

3

Yunxiao Liang1, #, Xiaoqing Ma2, #, Lujia Zhang1, 3, Fuli Li2, Zhen Liu1, Xiangzhao Mao1, * 1

4 2

5

College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China

Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China

6 3

7

School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China

8 9 10

#

11

*

12

Address: College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China

13

Tel.: +86-532-82032660

14

Fax: +86-532-82032272

15

E-mail: [email protected]

LY and MX contributed equally to this work

Corresponding author: Xiangzhao Mao

16

1

ACS Paragon Plus Environment

Journal of Agricultural and Food Chemistry

17

Page 2 of 27

Abstract

18

Agarases are important hydrolytic enzymes for the biodegradation of agar. Understanding the

19

degradation mode and hydrolysis products of agarases is essential for their utilization in oligosaccharide

20

preparations. Herein, we cloned and expressed AgWH50B, a novel neoagarotetraose-forming β-agarase

21

from Agarivorans gilvus WH0801 that has high specific activity and a fast reaction rate. AgWH50B

22

consists of a C-terminal glycoside hydrolase family 50 catalytic domain with two tandem noncatalytic

23

carbohydrate-binding modules (CBMs) in the N-terminus (residues 45-214 and 236-442). AgWH50B

24

exhibited good enzymatic properties with high specific activity and catalytic efficiency (1523.2 U/mg

25

and a Vmax of 1700 µmol/min/mg) under optimal hydrolysis conditions of pH 7.0 and 40 °C. Analysis of

26

the hydrolysis products revealed that this enzyme is an exo-type β-agarase and that the dominant product

27

of agarose or oligosaccharide degradation was neoagarotetraose. These findings suggest that AgWH50B

28

could be utilized to yield abundant neoagarotetraose.

29

Keywords: Agarase; GH50 family; Agarivorans gilvus; Degradation mode

2

ACS Paragon Plus Environment

Page 3 of 27

30

Journal of Agricultural and Food Chemistry

INTRODUCTION

31

Agar, a type of hydrophilic polysaccharide, is obtained from the cell walls of red macroalgae,

32

including Gelidium, Gracilaria, and Pterocladia, and consists of agarose and agaropectin.1, 2 Agarose is

33

a linear chain composed of alternating monosaccharide residues of 3-O-linked β-D-galactose and

34

4-O-linked 3,6-anhydro-α-L-galactose (L-AHG).1 As the main component of agar, agarose can be

35

biologically degraded into agaro-oligosaccharides, which have been reported to have functional

36

activities, such as being anti-inflammatory,3 antioxidative,4, 5 and effective as a prebiotic and as having a

37

whitening effect on melanoma cells,6, 7 and have been widely applied in the food and medical industries.

38

Agarases, which catalyze the hydrolysis of agarose, can cleave the α-1,3 linkages of agarose to

39

produce agaro-oligosaccharides (AOS) (α-agarase; EC 3.2.1.158), or they can hydrolyze the β-1,4

40

linkages to neoagaro-oligosaccharides (NAOS) (β-agarase; EC 3.2.1.81).8,

41

successfully used in biotechnology applications such as protoplast preparation from seaweed and DNA

42

gel recovery.10, 11 Until now, most of the reported agarases have been isolated from marine microbes.12

43

Only two α-agarases classified as glycoside hydrolase (GH) 96 have been characterized according to the

44

CAZy database (http://www.cazy.org/GH96_characterized.html) and literature,13,

45

enzymes are β-agarases that were isolated from marine bacteria such as Agarivorans,15,

46

Catenovulum,17 Flammeovirga,18 Streptomyces,19 and Vibrio.11, 20 Based on their amino acid sequence

47

similarities, β-agarases are usually distributed into four GH families: GH16, GH50, GH86 and GH118.

48

To date, several β-agarases of the GH50 family have been identified with either an endo- or exo-mode of

49

action, and the main final products are neoagarotetraoses (NA4)15, 20, 21 or neoagarobioses (NA2),19, 22, 23

50

respectively. The Aga50D enzyme from Saccharophagus degradans 2-40, which cleaves agarose 3

ACS Paragon Plus Environment

9

Agarases have been

14

while the other 16

Journal of Agricultural and Food Chemistry

Page 4 of 27

51

oligomers into NA2, is the first and only β-agarase from the GH50 family to have been characterized

52

biochemically and structurally.24, 25 Aga50D has a complex structure with two domains: a β-sandwich

53

module at the N-terminus and an (α/β)8-barrel catalytic domain at the C-terminus.24 The catalytic domain

54

and part of the β-sandwich CBM-like domain forms an active site tunnel that is plugged at one end,

55

suggesting an exo-mode of action, and the substrate-binding site residues are present in both the

56

catalytic domain and β-sandwich domain. Two catalytic residues (Glu534 and Glu695) situated in the

57

active site channel indicate a retaining catalytic mechanism.24 Another β-agarase, AgaO from

58

Flammeovirga sp. strain MY04, has been proven to produce NA2 via an exo-lytic pattern.9 However, the

59

substrate degradation pattern from the production of NA4, another main enzymatic hydrolysis product of

60

agarose, is still unclear.

61

Agarivorans gilvus WH0801 is an agarase-producing and non-endospore-forming bacterium that

62

was isolated from the surface of seaweed samples.26 The β-agarase AgWH50C from A. gilvus WH0801,

63

which is able to hydrolyze agarose into NA2, was previously cloned and characterized.22 In this study,

64

we successfully cloned and expressed the novel NA4-forming-β-agarase AgWH50B, which has two

65

tandem β-sandwich domains, using the genome sequence of A. gilvus WH0801 (GenBank accession no.

66

CP013021).27 The biochemical characterization and degradation mode of AgWH50B with different

67

substrates is discussed. To the best of our knowledge, this is the first time that the degradation pattern of

68

an NA4-forming β-agarase in the GH50 family has been investigated.

69

MATERIALS AND METHODS

70

Bacterial strains and culture conditions. A. gilvus WH0801 was cultivated at 28 °C in 2216E

71

medium composed of (w/v) 0.5% tryptone, 0.1% yeast extract and 0.001% ferric citrate with clean 4

ACS Paragon Plus Environment

Page 5 of 27

Journal of Agricultural and Food Chemistry

72

seawater as the solvent.26 The yeast extract and tryptone used for the lysogeny broth medium were

73

purchased from Oxoid (Basingstoke, England). The Escherichia coli strains were grown in LB medium

74

(1% tryptone, 0.5% yeast extract and 1% NaCl) at 37 °C with 100 µg/mL ampicillin (Solarbio, China)

75

when required. Other analytical reagents, unless otherwise indicated, were from Sigma (USA).

76

Sequence analysis. Using the gene sequence of agWH50B, the protein sequence of AgWH50B was

77

obtained with DNAMAN software (Lynnon, USA). Function prediction and homology analysis of

78

AgWH50B were performed using the NCBI (National Center for Biotechnology Information, USA)

79

database (http://www.ncbi.nlm.nih.gov/). The structure of the protein and its signal peptide were

80

predicted using SWISS-MODEL (http://www.swissmodel.expasy.org/interactive) and SignalP 3.0 Server

81

(http://www.cbs.dtu.dk/services/SignalP-3.0/), respectively. Phylogenetic analysis was performed with

82

MEGA version 5.0.

83

Cloning, expression and purification of recombinant AgWH50B. Genomic DNA was extracted

84

from A. gilvus WH0801 using a TIANamp Bacteria DNA Kit (Tiangen Biotech, Beijing, China). The

85

primers

86

(5’-TTTTTTGTAACGCAGATTATATAGATCACGGTTG-3’) were designed for amplification of the

87

agWH50B gene without its signal peptide sequence. All of the primers were synthesized by BGI Tech

88

(Beijing, China). The agWH50B PCR product was cloned into the pEASY-E2 expression vector, which

89

contains a 6×His tag, according to the instructions of the manufacturer (TransGen Biotech, China). The

90

nucleotide sequence of the inserted gene fragment was confirmed by sequencing (BGI, Beijing, China).

91

The recombinant expression vector was then transformed into E. coli BL21 (DE3) chemically competent

92

cells (Tiangen Biotech, China), which were grown on solid LB medium with 100 µg/mL ampicillin.

AgWH50B-F

(5’-GCCGCCGGTGAACAAGTAG-3’)

5

ACS Paragon Plus Environment

and

AgWH50B-R

Journal of Agricultural and Food Chemistry

Page 6 of 27

93

Transformants were selected and screened by PCR to ensure the correctness of the sequence. The

94

transformants were grown in auto-induction medium, ZYP-5052 (1% tryptone, 0.5% yeast extract, 0.2%

95

MgSO4, 1.25% glycerin, 0.125% glucose and 10% α-galactose), with shaking (220 rpm) for 48 h at

96

20 °C after which the cells were collected by centrifugation at 8000×g for 15 min at 4 °C, resuspended

97

in binding buffer (50 mM Tris-HCl and 200 mM NaCl, pH 8.0), and then disrupted by sonication. The

98

supernatant was collected by centrifugation at 10,000×g for 20 min at 4 °C. The crude extract was

99

filtered and purified with Ni2+-NTA resin in accordance with the manufacturer’s instructions (TransGen

100

Biotech, China). Finally, the purified protein was analyzed by SDS-PAGE, and its concentration was

101

determined using a BCA Protein Assay Kit (Thermo Scientific, USA) with bovine serum album (BSA)

102

as the standard. The purified enzyme was then used for further enzyme activity assay and biochemical

103

characterization.

104

Enzyme activity assay. Enzyme activity assays were performed as previously described using the

105

3,5-dinitrosalicylic acid (DNS) method with some modifications.28 Each reaction of 200 µL contained 20

106

mM Tris-HCl buffer (pH 7.0), 0.2% low-melting point agarose and 25 µL purified enzyme solution (91.7

107

U). After incubation at the optimum temperature for 30 min, the reaction solution was mixed with 300

108

µL of DNS reagent, boiled immediately for 5 min and then cooled in a cold water bath. Samples were

109

subsequently diluted with water, and the absorbance was determined at 540 nm. Heat-inactivated

110

enzyme was used as a control. One unit of enzymatic activity (U) was defined as the amount of enzyme

111

that produced 1 µmol of reducing sugar per min by hydrolyzing agarose under the assay conditions.

112

Biochemical characterization of AgWH50B. The optimum pH was determined at different pH

113

values using 20 mM sodium citrate buffer (pH 4.0 to 6.0), 20 mM Tris-HCl buffer (pH 7.0 to 8.0) and 20 6

ACS Paragon Plus Environment

Page 7 of 27

Journal of Agricultural and Food Chemistry

114

mM glycine-NaOH buffer (pH 9.0 to 10.0) at 40 °C for 30 min. The optimal temperature was

115

determined in 20 mM Tris-HCl (pH 7.0) in a temperature range of 10-70 °C. For the thermal stability

116

assay, aliquots of enzyme were incubated at various temperatures for 1 h and renatured for 2 h at 4 °C.

117

Then, the residual enzyme activity was determined according to the standard method. To examine the

118

effects of metal ions (Fe3+, Ni2+, Ca2+, Zn2+, Co2+, Cu2+, Mg2+) and a series of chemicals (Na2EDTA,

119

SDS) on the activity of the enzyme, various chemical reagents were added to the reaction mixture at a

120

final concentration of 10 mM.

121

Determination of the kinetic parameters of AgWH50B. The kinetic parameters of recombinant

122

AgWH50B were determined under standard conditions. The enzyme was mixed with substrates at

123

concentrations ranging from 1 mg/mL to 12 mg/mL. The Km, Vmax and kcat were calculated using

124

GraphPad Prism 5 (GraphPad Software, Inc. USA).

125

Degradation pattern analysis of AgWH50B. The degradation products were analyzed by thin

126

layer chromatography (TLC). Purified AgWH50B was incubated with 0.3% agarose in Tris–HCl buffer

127

at the optimal temperature for 24 h. Aliquots of the reaction product were loaded on silica gel 60 TLC

128

plates (Merck, Germany). The plates were developed in a developing solvent composed of

129

n-butanol/acetic acid/water (2:1:1 by volume). Then, the spots were visualized by soaking in an ethanol

130

solution containing 10% (v/v) H2SO4, followed by heating at 95 °C for 5 min, and each oligosaccharide

131

was preliminarily ascertained by colored spots on the TLC plates. NAOS standards (Qingdao BZ Oligo

132

Biotech, China) dissolved into the same buffer were used as oligosaccharide markers. To determine the

133

sugar content at certain reaction times, both the samples and standards were analyzed by HPLC using a

134

Sugar-Pak I column (Waters, USA) under the following conditions: the mobile phase was EDTA calcium 7

ACS Paragon Plus Environment

Journal of Agricultural and Food Chemistry

Page 8 of 27

135

disodium (50 mg/mL), the column temperature was 75 °C, the flow velocity was 0.5 mL/min, and the

136

detector was a refractive index detector (RID).

137

To estimate the substrate with the lowest DP, highly purified NAOS solutions including NA4,

138

neoagarohexaose (NA6) and neoagarooctaose (NA8), were incubated with the enzyme individually.

139

After incubation at 40 °C for 12 h, the reaction was stopped by boiling, and the product was analyzed

140

using both TLC and HPLC.

141

RESULTS AND DISCUSSION

142

Sequence analysis of the β-agarase gene. The opening reading frame (ORF) of agWH50B

143

encodes a 955 amino acid protein (GenBank accession no. KY417136), the molecular mass and

144

isoelectric point of which were predicted to be 105 kDa and 4.42, respectively. The signal peptide

145

predicted by SignalP 3.0 Server includes 32 amino acid residues located in the N-terminus of the

146

putative protein. Based on sequence alignment, AgWH50B shares its highest sequence identity of 73%

147

with two GH50 β-agarases, NA4-producing enzyme HZ2 from Agarivorans sp. HZ105 (GenBank

148

accession no. ADY17919.1) and AgD02 from Agarivorans sp. QM38 (GenBank accession no.

149

ABM90422.1). However, phylogenetic analysis indicated that AgWH50B clusters with a different

150

branch of the GH50 family (Fig. 1). According to homology modeling and amino acid alignment,

151

AgWH50B contains two tandem β-sandwich CBM-like domains in its N-terminus (residues 45-214 and

152

236-442) and a catalytic domain (residues 472-955) in its C-terminus (Fig. 2A), different from two

153

reported NA2-producing GH50 β-agarases, AgWH50C and Aga50D, both of which consist of one

154

N-terminal CBM and a C-terminal catalytic domain.22, 25 These features suggested that AgWH50B is a

155

novel β-agarase from Agarivorans sp. 8

ACS Paragon Plus Environment

Page 9 of 27

Journal of Agricultural and Food Chemistry

156

Cloning and expression of AgWH50B. The full length AgWH50B gene was cloned and

157

successfully expressed in E. coli BL21 (DE3) with a C-terminal His tag. The recombinant protein was

158

purified and detected by SDS-PAGE, which showed one evident band corresponding to 105 kDa (Fig.

159

2B). This result indicated that the purified recombinant protein was appropriate for analyzing the

160

properties of the enzyme.

161

The specific activity of purified AgWH50B under standard conditions (40 °C, pH 7.0, 20 mM

162

Tris-HCl) was 1523.2 U/mg, and it had a Vmax of 1700 µmol/min/mg for agarose, which are significantly

163

higher than other β-agarases, including AgaA (349.3 U/mg and 901.9 µmol/min/mg) and AgaB34 (242

164

U/mg and 50 µmol/min/mg).16, 29 AgWH50B also showed a distinct advantage over the other GH50

165

agarases Aga50D (17.9 U/mg), rHZ2 (235 U/mg) and AgaA34 (25.54 U/mg) in terms of its Vmax value,12,

166

15, 25

167

which suggests that AgWH50B has huge potential for industrial applications. Effects of temperature and pH on the activity of AgWH50B. Using 0.2% of agarose as substrate,

168

the optimal temperature and pH of AgWH50B were determined to be 40 °C and 7.0, respectively (Fig.

169

3A and B). The enzyme was quite stable at 40 °C, retaining more than 90% of its activity after

170

incubation for 1 h (Fig. 3A); however, inactivation of AgWH50B occurred above 50 °C. Meanwhile,

171

AgWH50B retained more than 80% of its activity in a pH range from 6.0 to 10.0 (Fig. 3C). These results

172

indicate that AgWH50B could degrade agarose in a wide pH range similar to a recently reported GH16

173

family thermostable and pH-stable β-agarase from the deep-sea bacterium Flammeovirga sp. OC4.30 In

174

terms of the optimal temperature and pH, AgWH50B was similar to the β-agarases HZ2 from

175

Agarivorans sp. HZ105 and AgaG1 from Alteromonas sp. GNUM1.15,

176

AgWH50B has excellent hydrolytic ability in high temperature environments. 9

ACS Paragon Plus Environment

31

The results suggest that

Journal of Agricultural and Food Chemistry

Page 10 of 27

177

Effects of chemicals on agarase activities. The activity of recombinant AgWH50B was evidently

178

disabled by some heavy metal ions such as Fe3+, Zn2+ and Cu2+ and was mildly inhibited by Ni2+,

179

Co2+and Mg2+ at a concentration of 10 mM (Fig. 3D). For the other chemicals investigated, the enzyme

180

was completely inhibited by Na2EDTA. These inhibitory effects may occur because divalent metal ions

181

as well as EDTA have affinity interactions with the SH, CO and NH functional groups of the enzyme,

182

which causes structural changes in the catalytic moieties and thus decreases activity.32, 33 SDS strongly

183

reduced the enzyme activity of AgWH50B to less than 30%, which has been found with other

184

β-agarases,17, 34 indicating that this enzyme is not resistant to such a surfactant.

185

Agarose degradation pattern analysis. The hydrolysis products detected by TLC showed that

186

NA4 was produced at the beginning of the reaction, and then a small amount of NA2 as well as larger

187

NAOS such as NA6 and NA8 were observed gradually after incubation with agarose for 10 min. After

188

24 h, the hydrolysis of agarose with AgWH50B led to the production of NA4 and NA2 with a small

189

amount of NAOS larger than NA4 (Fig. 4A). These preliminary results suggested that the final products

190

of AgWH50B may be both NA4 and NA2.

191

To further confirm the final products, the hydrolyzed samples and NAOS standard oligosaccharide

192

markers (NA2, NA4, NA6 and NA8) were analyzed by HPLC. As shown in Fig. 4B, during agarose

193

degradation by AgWH50B, only one peak with a retention time corresponding to NA4 was observed

194

after 1 min. The production of NA6 and NA2 was subsequently detected after 10 min. After 24 h, peaks

195

corresponding to NA2, NA4 and NA6 still remained in the degradation products (Fig. 4B). The contents

196

of NA2, NA4 and NA6 were also calculated by quantitative analysis. After one minute of reaction, the

197

content of the NA4 product was 302.49 mg/L with no trace amounts of NA6 (0.00 mg/L) or NA2 (0.00 10

ACS Paragon Plus Environment

Page 11 of 27

Journal of Agricultural and Food Chemistry

198

mg/L). After hydrolysis for 24 h, the content of NA4 reached 900.98 mg/L, which was much higher than

199

those of NA2 (53.26 mg/L) and NA6 (139.74 mg/L). These results suggested that the reaction products

200

are NA2, NA6 and NA8, with NA4 being the dominant product and that AgWH50B is an exo-lytic

201

NA4-producing β-agarase.

202

AgWH50B is one of the few reported GH50 family agarases that can produce NA4. Thus far,

203

several agarases have been reported to have this activity, such as HZ2 from Agarivorans sp. HZ105 and

204

Aga41A from Vibrio sp. CN41, which shares the sequence identity of 73% and 50% with AgWH50B,

205

respectively.15, 20 Both HZ2 and Aga41A are endo-lytic β-agarases that randomly depolymerize agarose

206

into product with a logarithmic decrease in its average molecular weight during the reaction.35 However,

207

in the AgWH50B reaction system, NA4 was produced initially and continued to increase gradually,

208

suggesting that AgWH50B can cleave the four-sugar unit processively from the non-reducing end of

209

long-chain agarose. Thus, we infer that AgWH50B is an exo-type NA4-producing β-agarase. To the best

210

of our knowledge, AgWH50B is the first exo-lytic β-agarase to be reported, which cleaves one

211

four-sugar unit at a time.

212

TLC and HPLC analysis of the oligosaccharide degradation products. To further investigate

213

the cleavage patterns of AgWH50B and to determine its smallest substrate, NAOS with different lengths

214

were used as substrates. The NAOS were dissolved individually in deionized water and incubated with

215

AgWH50B at 40 °C for 12 h. The samples were then analyzed by TLC and HPLC (Fig. 5). TLC analysis

216

showed that with NA4 as the substrate, no new product was detected even after 12 h (Fig. 5A), which

217

indicated that AgWH50B cannot hydrolyze NA4 into NA2. However, NA6 and NA8 were degraded into

218

NA4, with NA2 as an accompanying product when NA6 was the substrate (Fig. 5B and 5C). HPLC 11

ACS Paragon Plus Environment

Journal of Agricultural and Food Chemistry

Page 12 of 27

219

quantitative analysis further confirmed the TLC results (Fig. 5D and 5E) that NA2 was produced only

220

when NA6 was the substrate. NA4 could not be degraded further, and NA8 could only be hydrolyzed

221

into NA4 (Fig. 5F). Combined with the product analysis of agarose hydrolysis, the production of NA2

222

from agarose degradation was suggested to result from the further hydrolysis of NA6 but not NA4.

223

Therefore, the smallest oligosaccharide substrate of AgWH50B is NA6, and the main hydrolysis product

224

is NA4.

225

Neoagaro-oligosaccharides have been reported to have potential application values because of their

226

high biological activity, which is connected to their degree of polymerization. In our previous research,

227

we demonstrated that NA4 has the potential to alleviate intense exercise-induced fatigue by modulating

228

the structure and function of the gut microbiome.36 This finding shows that neoagaro-oligosaccharides

229

have huge application prospects in the food industry, including as antioxidative functional ingredients in

230

food products. In addition, NA4 or NA2 can be further degraded by an α-neoagarobiose hydrolase into

231

D-galactose and 3, 6-anhydro-L-galactose (L-AHG).37 L-AHG is also valuable due to its

232

anti-inflammatory activity and skin whitening function.7 The TLC and HPLC assays demonstrated that

233

AgWH50B is an exo-lytic β-agarase that yields NA4 as its main product during agarose degradation. So

234

far, several β-agarases have been reported to produce NA4 by degrading agarose. Except AgWH50A,

235

which was reported to show both exo- and endo-lytic features,21 all the other NA4-forming agarases

236

were endo-lytic enzymes, including rHZ2 and AgaA41 from GH50 family as well as AgaAc and AgaA

237

from GH16 family.15, 16, 20, 38 The glucoside hydrolase exo-mode of action has distinct advantages in

238

terms of oligosaccharide purity compared to the endo-mode of action because endo-type agarases

239

usually produce two or more main neoagaro-oligosaccharides, which increases the complexity of 12

ACS Paragon Plus Environment

Page 13 of 27

Journal of Agricultural and Food Chemistry

240

oligosaccharide purification and decreases the monomer yield. In addition, as an NA4-producing

241

β-agarase, AgWH50B showed a significant advantage in reaction rate. Compared to other

242

NA4-producing agarases such as AgaB34,29 AgaA,38 and rHZ2,15 the specific activity of AgWH50B

243

exhibited more than 5, 3 and 6 times higher, respectively. Therefore, the GH50 family β-agarase

244

AgWH50B is a key tool for NA4 preparation, and the study of its biochemical characteristics will be of

245

great significance.

246

In conclusion, AgWH50B is a novel NA4-producing β-agarase isolated from A. gilvus WH0801

247

that belongs to the GH50 family and has good enzyme characteristics, including a high specific activity

248

and

249

neoagaro-oligosaccharides by an exo-lytic pattern to yield abundant NA4, which can be utilized in

250

functional food applications.

251

ABBREVIATIONS

fast

reaction

rate.

The

enzyme

can

effectively

hydrolyze

agarose

as

well

as

252

GH: glycoside hydrolase; AOS: agaro-oligosaccharides, NAOS: neoagaro-oligosaccharides;

253

L-AHG: 3, 6-anhydro-L-galactose; DP: degree of polymerization; DNA, deoxyribonucleic acid; ORF:

254

open reading frame; MEGA: molecular evolutionary genetics analysis; LB: Luria-Bertani; NTA:

255

nitrilotriacetic acid; SDS, sodium dodecyl sulfate; PAGE, polyacrylamide gel electrophoresis; DNS,

256

3,5-dinitrosalicylic acid; EDTA: ethylene diamine tetraacetic; TLC: thin layer chromatography; HPLC:

257

high-performance liquid chromatography; NA2: neoagarobiose; NA4: neoagarotetraose; NA6:

258

neoagarohexaose; NA8: neoagarooctaose.

259

FUNDING

260

This work was supported by the National Natural Science Foundation of China (31471607 and 13

ACS Paragon Plus Environment

Journal of Agricultural and Food Chemistry

261

31271923) and the China Postdoctoral Science Foundation (2016M590661).

262

Notes

263

The authors declare that they have no competing interests.

264

14

ACS Paragon Plus Environment

Page 14 of 27

Page 15 of 27

Journal of Agricultural and Food Chemistry

265

REFERENCES

266

(1)Rees, D. A., Structure, Conformation, and Mechanism in the Formation of Polysaccharide Gels and

267

Networks. Adv. Carbohyd. Chem. Biochem. 1969, 24, 267-332.

268

(2)Yun, E. J.; Kim, H. T.; Cho, K. M.; Yu, S.; Kim, S.; Choi, I. G.; Kim, K. H., Pretreatment and

269

saccharification of red macroalgae to produce fermentable sugars. Bioresour. Technol. 2016, 199,

270

311-8.

271

(3)Enoki, T.; Okuda, S.; Kudo, Y.; Takashima, F.; Sagawa, H.; Kato, I., Oligosaccharides from agar

272

inhibit pro-inflammatory mediator release by inducing heme oxygenase 1. Biosci. Biotechnol.

273

Biochem. 2010, 74, 766-70.

274 275

(4)Wang, J.; Jiang, X.; Mou, H.; Guan, H., Anti-oxidation of agar oligosaccharides produced by agarase from a marine bacterium. J. Appl. Phycol. 2004, 16, 333-340.

276

(5)Kang, O. L.; Ghani, M.; Hassan, O.; Rahmati, S.; Ramli, N., Novel agaro-oligosaccharide production

277

through enzymatic hydrolysis: Physicochemical properties and antioxidant activities. Food

278

Hydrocoll. 2014, 42, 304-308.

279 280

(6)Hu, B.; Gong, Q.; Wang, Y.; Ma, Y.; Li, J.; Yu, W., Prebiotic effects of neoagaro-oligosaccharides prepared by enzymatic hydrolysis of agarose. Anaerobe. 2006, 12, 260-6.

281

(7)Yun, E. J.; Lee, S.; Kim, J. H.; Kim, B. B.; Kim, H. T.; Lee, S. H.; Pelton, J. G.; Kang, N. J.; Choi, I.

282

G.; Kim, K. H., Enzymatic production of 3,6-anhydro-L-galactose from agarose and its

283

purification and in vitro skin whitening and anti-inflammatory activities. Appl. Microbiol.

284

Biotechnol. 2013, 97, 2961-70.

285

(8)Flament, D.; Barbeyron, T.; Jam, M.; Potin, P.; Czjzek, M.; Kloareg, B.; Michel, G., Alpha-agarases 15

ACS Paragon Plus Environment

Journal of Agricultural and Food Chemistry

Page 16 of 27

286

define a new family of glycoside hydrolases, distinct from beta-agarase families. Appl. Environ.

287

Microbiol. 2007, 73, 4691-4.

288

(9)Han, W.; Cheng, Y.; Wang, D.; Wang, S.; Liu, H.; Gu, J.; Wu, Z.; Li, F., Biochemical Characteristics

289

and

290

Polysaccharide-Degrading Marine Bacterium Flammeovirga sp. Strain MY04. Appl. Environ.

291

Microbiol. 2016, 82, 4944-54.

292 293

Substrate Degradation

Pattern

of a

Novel

Exo-Type beta-Agarase from

the

(10)Yeong, H.-Y.; Khalid, N.; Phang, S.-M., Protoplast isolation and regeneration from Gracilaria changii (Gracilariales, Rhodophyta). J. Appl. Phycol. 2007, 20, 641-651.

294

(11)Sugano, Y.; Terada, I.; Arita, M.; Noma, M.; Matsumoto, T., Purification and characterization of a

295

new agarase from a marine bacterium, Vibrio sp. strain JT0107. Appl. Environ. Microbiol. 1993,

296

59, 1549-54.

297 298

(12)Fu, X. T.; Lin, H.; Kim, S. M., Purification and characterization of a novel beta-agarase, AgaA34, from Agarivorans albus YKW-34. Appl. Microbiol. Biotechnol. 2008, 78, 265-73.

299

(13)Potin, P.; Richard, C.; Rochas, C.; Kloareg, B., Purification and characterization of the α-agarase

300

from Alteromonas agarlyticus (Cataldi) comb. nov., strain GJ1B. Eur. J. Biochem. 1993, 214,

301

599-607.

302 303

(14)Hatada, Y.; Ohta, Y.; Horikoshi, K., Hyperproduction and application of alpha-agarase to enzymatic enhancement of antioxidant activity of porphyran. J. Agric. Food Chem. 2006, 54, 9895-900.

304

(15)Lin, B.; Lu, G.; Zheng, Y.; Xie, W.; Li, S.; Hu, Z., Gene cloning, expression and characterization of a

305

neoagarotetraose-producing beta-agarase from the marine bacterium Agarivorans sp. HZ105.

306

World J. Microbiol. Biotechnol. 2012, 28, 1691-7. 16

ACS Paragon Plus Environment

Page 17 of 27

307 308

Journal of Agricultural and Food Chemistry

(16)Long, M.; Yu, Z.; Xu, X., A novel beta-agarase with high pH stability from marine Agarivorans sp. LQ48. Mar. Biotechnol. 2010, 12, 62-9.

309

(17)Xie, W.; Lin, B.; Zhou, Z.; Lu, G.; Lun, J.; Xia, C.; Li, S.; Hu, Z., Characterization of a novel

310

beta-agarase from an agar-degrading bacterium Catenovulum sp. X3. Appl. Microbiol.

311

Biotechnol. 2013, 97, 4907-15.

312

(18)Yang, J. I.; Chen, L. C.; Shih, Y. Y.; Hsieh, C.; Chen, C. Y.; Chen, W. M.; Chen, C. C., Cloning and

313

characterization of beta-agarase AgaYT from Flammeovirga yaeyamensis strain YT. J. Biosci.

314

Bioeng. 2011, 112, 225-32.

315

(19)Temuujin, U.; Chi, W. J.; Chang, Y. K.; Hong, S. K., Identification and biochemical characterization

316

of Sco3487 from Streptomyces coelicolor A3(2), an exo- and endo-type beta-agarase-producing

317

neoagarobiose. J. Bacteriol. 2012, 194, 142-9.

318

(20)Liao, L.; Xu, X. W.; Jiang, X. W.; Cao, Y.; Yi, N.; Huo, Y. Y.; Wu, Y. H.; Zhu, X. F.; Zhang, X. Q.;

319

Wu, M., Cloning, expression, and characterization of a new beta-agarase from Vibrio sp. strain

320

CN41. Appl. Environ. Microbiol. 2011, 77, 7077-9.

321

(21)Liu, N.; Mao, X.; Du, Z.; Mu, B.; Wei, D., Cloning and characterisation of a novel

322

neoagarotetraose-forming-beta-agarase,

323

Carbohydr. Res. 2014, 388, 147-51.

AgWH50A from

Agarivorans

gilvus

WH0801.

324

(22)Liu, N.; Mao, X.; Yang, M.; Mu, B.; Wei, D., Gene cloning, expression and characterisation of a

325

new beta-agarase, AgWH50C, producing neoagarobiose from Agarivorans gilvus WH0801.

326

World J. Microbiol. Biotechnol. 2014, 30, 1691-8.

327

(23)Liang, S. S.; Chen, Y. P.; Chen, Y. H.; Chiu, S. H.; Liaw, L. L., Characterization and overexpression 17

ACS Paragon Plus Environment

Journal of Agricultural and Food Chemistry

328

Page 18 of 27

of a novel beta-agarase from Thalassomonas agarivorans. J. Appl. Microbiol. 2014, 116, 563-72.

329

(24)Pluvinage, B.; Hehemann, J. H.; Boraston, A. B., Substrate recognition and hydrolysis by a family

330

50 exo-beta-agarase, Aga50D, from the marine bacterium Saccharophagus degradans. J. Biol.

331

Chem. 2013, 288, 28078-88.

332

(25)Kim, H. T.; Lee, S.; Lee, D.; Kim, H. S.; Bang, W. G.; Kim, K. H.; Choi, I. G., Overexpression and

333

molecular characterization of Aga50D from Saccharophagus degradans 2-40: an exo-type

334

beta-agarase producing neoagarobiose. Appl. Microbiol. Biotechnol. 2010, 86, 227-34.

335 336

(26)Du, Z. J.; Lv, G. Q.; Rooney, A. P.; Miao, T. T.; Xu, Q. Q.; Chen, G. J., Agarivorans gilvus sp. nov. isolated from seaweed. Int. J. Syst. Evol. Microbiol. 2011, 61, 493-6.

337

(27)Zhang, P.; Rui, J.; Du, Z.; Xue, C.; Li, X.; Mao, X., Complete genome sequence of Agarivorans

338

gilvus WH0801(T), an agarase-producing bacterium isolated from seaweed. J. Biotechnol. 2016,

339

219, 22-3.

340 341

(28)Naidu, G. S. N.; Panda, T., Studies on pH and thermal deactivation of pectolytic enzymes from Aspergillus niger. Biochem. Eng. J. 2003, 16, 57-67.

342

(29)Fu, X. T.; Pan, C.; Lin, H.; Kim, S. M., Gene Cloning, Expression, and Characterization of a

343

β-Agarase, AgaB34, from Agarivorans albus YKW-34. J. Microbiol. Biotechnol. 2009, 19,

344

257-264.

345

(30)Chen, X. L.; Hou, Y. P.; Jin, M.; Zeng, R. Y.; Lin, H. T., Expression and Characterization of a Novel

346

Thermostable and pH-Stable beta-Agarase from Deep-Sea Bacterium Flammeovirga Sp. OC4. J.

347

Agric. Food Chem. 2016, 64, 7251-8.

348

(31)Seo, Y. B.; Lu, Y.; Chi, W.-J.; Park, H. R.; Jeong, K. J.; Hong, S.-K.; Chang, Y. K., Heterologous 18

ACS Paragon Plus Environment

Page 19 of 27

Journal of Agricultural and Food Chemistry

349

expression of a newly screened β-agarase from Alteromonas sp. GNUM1 in Escherichia coli and

350

its application for agarose degradation. Process Biochem. 2014, 49, 430-436.

351

(32)Gupta, V.; Trivedi, N.; Kumar, M.; Reddy, C. R. K.; Jha, B., Purification and characterization of

352

exo-β-agarase from an endophytic marine bacterium and its catalytic potential in bioconversion

353

of red algal cell wall polysaccharides into galactans. Biomass Bioenerg. 2013, 49, 290-298.

354

(33)Ohta, Y.; Hatada, Y.; Ito, S.; Horikoshi, K., High-level expression of a neoagarobiose-producing

355

β-agarase gene from Agarivorans sp. JAMB-A11 in Bacillus subtilis and enzymic properties of

356

the recombinant enzyme. Biotechnol. Appl. Biochem. 2005, 41.

357 358 359 360

(34)Boraston, A. B.; Bolam, D. N.; Gilbert, H. J.; Davies, G. J., Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem. J. 2004, 382, 769-781. (35)Suzuki, H.; Sawai, Y.; Suzuki, T.; Kawai, K., Purification and characterization of an extracellular β-agarase from Bacillus sp. MK03. J. Biosci. Bioeng. 2003, 95, 328-334.

361

(36)Zhang, N.; Mao, X.; Li, R. W.; Hou, E.; Wang, Y.; Xue, C.; Tang, Q., Neoagarotetraose protects

362

mice against intense exercise induced fatigue damage by modulating gut microbial composition

363

and function. Mol. Nutr. Food Res. 2017, 1600585-n/a.

364

(37)Ha, S. C.; Lee, S.; Lee, J.; Kim, H. T.; Ko, H. J.; Kim, K. H.; Choi, I. G., Crystal structure of a key

365

enzyme in the agarolytic pathway, alpha-neoagarobiose hydrolase from Saccharophagus

366

degradans 2-40. Biochem. Biophys. Res. Commun. 2011, 412, 238-44.

367

(38)Jam, M.; Flament, D.; Allouch, J.; Potin, P.; Thion, L.; Kloareg, B., The endo- beta -agarases AgaA

368

and AgaB from the marine bacterium Zobellia galactanivorans: two paralogue enzymes with

369

differentmolecular organizations and catalytic behaviours. Biochem. J. 2005, 385, 703-13. 19

ACS Paragon Plus Environment

Journal of Agricultural and Food Chemistry

Page 20 of 27

370

Figure captions

371

Figure 1 Phylogenetic analysis of AgWH50B with other characterized GH50 agarases. The

372

neighbor-joining tree was obtained using MEGA version 5.0 software. The numbers on the

373

branches indicate the bootstrap confidence values from 1,000 replicates. The scale bar indicates 0.1

374

substitutions per site.

375

Figure 2 Sequence characterization of AgWH50B. A. The module structure of AgWH50B. The

376

protein contains an N-terminal signal peptide (residues 1-32, in black), two tandem CBM-like

377

domains (residues 45-214 and 236-442, in dark gray and light gray, respectively) and a C-terminal

378

catalytic domain (residues 472-955, in pink). B. SDS-PAGE analysis of purified AgWH50B. Lane

379

M, protein molecular mass marker, and Lane 1, purified AgWH50B.

380

Figure 3 Biochemical characteristics of AgWH50B. A. Effects of temperature on the activity and

381

thermostability of rAgWH50B. B. Effects of pH on the activity of AgWH50B; pH 4.0 to 6.0, citric

382

acid-Na buffer; pH 7.0 to 8.0, Tris-HCl buffer; and pH 9.0 to 10.0, glycine-NaOH buffer. C. Effects

383

of pH on the stability of AgWH50B. The protein was treated at different pH values, and the residual

384

activity was analyzed at standard conditions. D. Effects of cations, anions, and other chemicals on

385

the enzyme activity of AgWH50B.

386

Figure 4 Agarose degradation patterns of AgWH50B. A. TLC analysis of the agarose degradation

387

products of AgWH50B. The reactions were performed at 40 °C for 24 h in 20 mM Tris-HCl buffer

388

(pH 7.0) containing 0.3% agarose. M: standard oligosaccharide markers and (-): negative control. B.

389

HPLC analysis of the agarose degradation products of AgWH50B. The retention times of the

390

standard NAOS are indicated by arrows. 20

ACS Paragon Plus Environment

Page 21 of 27

391

Journal of Agricultural and Food Chemistry

Figure 5 Oligosaccharide degradation products of AgWH50B. TLC analysis of the final products

392

from NA4 (A), NA6 (B) and NA8 (C) hydrolysis by AgWH50B. M: standard oligosaccharide

393

markers and (-): the negative control in which boiled AgWH50B was used. HPLC analysis of the

394

final degradation products from NA4 (D), NA6 (E) and NA8 (F) hydrolysis by AgWH50B.

21

ACS Paragon Plus Environment

Journal of Agricultural and Food Chemistry

Figures

Figure 1 Phylogenetic analysis of AgWH50B with other characterized GH50 agarases.

22

ACS Paragon Plus Environment

Page 22 of 27

Page 23 of 27

Journal of Agricultural and Food Chemistry

Figure 2 Sequence characterization of AgWH50B.

23

ACS Paragon Plus Environment

Journal of Agricultural and Food Chemistry

Figure 3 Biochemical characteristics of AgWH50B.

24

ACS Paragon Plus Environment

Page 24 of 27

Page 25 of 27

Journal of Agricultural and Food Chemistry

Figure 4 Agarose degradation patterns of AgWH50B.

25

ACS Paragon Plus Environment

Journal of Agricultural and Food Chemistry

Figure 5 Oligosaccharide degradation products of AgWH50B.

26

ACS Paragon Plus Environment

Page 26 of 27

Page 27 of 27

Journal of Agricultural and Food Chemistry

TOC Graphic

27

ACS Paragon Plus Environment