Investigation of the Synergetic Effect of Xylose Metabolic Pathways on

Sep 25, 2017 - BiotecEra Inc., Athens, Georgia 30602, United States. ∥ College of Engineering, The University of Georgia, Athens, Georgia 30602, Uni...
0 downloads 10 Views 907KB Size
Subscriber access provided by UNIVERSITY OF ADELAIDE LIBRARIES

Letter

Investigation of the synergetic effect of xylose metabolic pathways on the production of glutaric acid Jia Wang, Xiaolin Shen, Yuheng Lin, Zhenya Chen, Yaping Yang, Qipeng Yuan, and Yajun Yan ACS Synth. Biol., Just Accepted Manuscript • DOI: 10.1021/acssynbio.7b00271 • Publication Date (Web): 25 Sep 2017 Downloaded from http://pubs.acs.org on September 26, 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.

ACS Synthetic Biology 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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Synthetic Biology

1

Investigation of the synergetic effect of xylose metabolic pathways on the production of

2

glutaric acid

3 4

Jia Wang a,b, Xiaolin Shena,b, Yuheng Linc, Zhenya Chen a,b, Yaping Yangd,

5

Qipeng Yuana,b,*, Yajun Yand,*

6 7

a

8

Technology, Beijing 100029, China

State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical

9 10

b

11

University of Chemical Technology, Beijing 100029, China

Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing

12 13

c

BiotecEra Inc., Athens, GA 30602, USA

d

College of Engineering, The University of Georgia, Athens, GA 30602, USA

14 15 16 17

* Corresponding authors:

18

Qipeng Yuan

19

15 Beisanhuan East Road, Chaoyang District, Beijing 100029, China

20

E-mail: [email protected]; telephone: +86-10-64437610

21

Yajun Yan

22

146 Riverbend Research Lab South, The University of Georgia, Athens, GA 30602, USA

23

E-mail: [email protected]; telephone: +1-706-542-8293

1 ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

24

Abstract

25

Efficient utilization of lignocellulose is pivotal for economically converting renewable

26

feedstocks into value-added products. Xylose is the second most abundant sugar in

27

lignocellulose, but it is quite challenging to ferment xylose as efficiently as glucose by

28

microorganisms. Here, we investigated the metabolic potential of three xylose catabolic

29

pathways (isomerase, Weimberg and Dahms pathways) and illustrated the synergetic effect

30

between isomerase pathway and Weimberg pathway for the synthesis of chemicals derived from

31

2-ketoglutarate and acetyl-CoA. When using glutaric acid as the target product, employment of

32

such synergetic pathways in combination resulted in an increased glutaric acid titer (602 mg/L)

33

compared with using each pathway alone (104 or 209 mg/L) and this titer even outcompetes that

34

obtained from glucose catabolic pathway for glutaric acid synthesis (420 mg/L). This work

35

validates a novel and powerful strategy for xylose metabolic utilization to overcome the

36

inefficiency of using single xylose metabolic pathway for the synthesis of TCA cycle derived

37

chemicals.

38 39

Keywords: Lignocellulose, Xylose Metabolism, Synergetic Pathways, Glutaric Acid

2 ACS Paragon Plus Environment

Page 2 of 27

Page 3 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Synthetic Biology

40

Lignocellulose is an attractive renewable feedstock for the production of chemicals owing to its

41

low cost and abundance 1. Xylose, as the second most abundant sugar in lignocellulose,

42

constitutes as much as 30% of the total sugar in lignocellulosic hydrolysates 2. However,

43

utilization of xylose as efficiently as glucose by microorganisms is still quite challenging so far.

44

Thus, development of efficient metabolic pathways and rational optimization strategies for the

45

conversion of xylose into desired products is very crucial for complete utilization of

46

lignocellulose.

47 48

There are at least three pathways for assimilation of xylose into the tricarboxylic acid (TCA)

49

cycle in nature (Fig 1). The isomerase pathway is the native xylose metabolic pathway in wild

50

type E. coli. Xylose is first isomerized and phosphorylated into xylulose-5P. Xylulose-5P is then

51

diverted into the pentose phosphate pathway to generate fructose-6P and glyceraldehyde-3P,

52

which are further processed through the Embden-Meyerhof-Parness pathway to enter the TCA

53

cycle (Fig 1).

54

enzymatic steps to reach 2-ketoglutarate (2-KG), a key intermediate in TCA cycle, with a

55

theoretical molar yield of 83%. The Weimberg pathway is another xylose metabolic pathway

56

where the xylose is oxidized into xylonic acid. Xylonic acid is then dehydrated two water

57

molecules to form 2-keto-glutarate semialdehyde, which is subsequently converted into 2-KG 3.

58

This pathway is nonphosphorylative and more straightforward to generate 2-KG with five

59

enzymatic steps and a 100% theoretical molar yield (Fig 1). The third xylose metabolic pathway

60

is Dahms pathway, which starts as the Weimberg pathway but cleaves the intermediate 2-keto-3-

61

deoxy-xylonate into glycolaldehyde and pyruvate 4, the latter is decarboxylated into acetyl-CoA

62

to enter the TCA cycle (Fig 1). Each of the three pathways has been successfully engineered to

This pathway produces a lot of intermediates and requires more than ten

3 ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 4 of 27

63

produce many high value compounds in E. coli, including muconic acid 5, 1,4-butanediol 6, 7, 3,4-

64

dihydroxybutyric acid 8, mesaconate 9, poly(lactate-co-glycolate)

65

glycol

66

production of TCA cycle-derived products so far.

11

10

, glycolic acid and ethylene

. However, no one has investigated which pathway is the most favorable route for the

67 68

Frequently, a desired product can be synthesized through more than one metabolic route.

69

Synergetic effect among these pathways may be formed when intermediate employment,

70

cofactor demand and ATP requirement are complementary to each other. In this case,

71

combination of such pathways may result in improved product titer and yield compared with

72

utilization of each single pathway along

73

pathway are co-utilized to divert xylose into the TCA cycle. However, this metabolism contains

74

multiple reaction steps and suffers complicated regulations, which limit the production titer and

75

yield. In order to overcome those issues, novel and efficient xylose metabolic utilization

76

strategies need to be developed.

12

. Traditionally, glycolysis and pentose phosphate

77 78

In this work, we investigated the metabolic potential and illustrated the synergetic effect among

79

abovementioned three xylose catabolic pathways for producing the compounds derived from

80

TCA cycle. We chose glutaric acid as our target product for the following reasons. First, glutaric

81

acid is an important dicarboxylic acid with a wide range of applications in polymer industry for

82

the synthesis of polyamides and polyesters 13. It is of great industrial significance to pursue high-

83

level biosynthesis of glutaric acid. Second, we previously established a novel glutaric acid

84

biosynthetic pathway using glucose as the carbon source, yielding 420 mg/L glutaric acid by

85

employment of a carbon chain elongation pathway from acetyl-CoA and 2-KG 14, which are two

4 ACS Paragon Plus Environment

Page 5 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Synthetic Biology

86

intermediates produced by glycolysis and TCA cycle, respectively (Fig. 1). The high-level

87

production of glutaric acid requires sufficient amounts of both acetyl-CoA and 2-KG. Those

88

reasons render glutaric acid as an ideal product for demonstration of the synergetic effect

89

between different xylose metabolic pathways.

90 91

In order to test the production potential of xylose catabolic pathways for glutaric acid

92

biosynthesis, E. coli native xylose isomerase pathway was first investigated independently. We

93

calculated its maximum theoretical molar yield (See the supporting information). The xylose

94

isomerase pathway has the potential to produce 0.556 mol glutaric acid per mol xylose. The

95

reason for the poor yield of this pathway is that generation of acetyl-CoA and 2-KG causes

96

carbon loss due to the pyruvate decarboxylation reaction. Then, to test the glutaric acid

97

production in vivo, the plasmids pJW87 carrying kivD and gabD with pZE-HCS-HA-HICDH

98

were introduced into E. coli BW25113 (F’), generating strain JW11. The resulting strain was

99

cultivated in LB medium containing 10 g/L xylose. As shown in Fig. 2A, JW11 produced 104

100

mg/L glutaric acid with an OD600 value of 2.11 at 60 hours. This is the first time to achieve

101

biosynthesis of glutaric acid using xylose as the carbon source. However, the low titer obtained

102

in xylose isomerase pathway indicated that the E. coli native xylose metabolic pathway is less

103

efficient for the production of compounds derived from TCA cycle due to lengthy enzymatic

104

steps and complex regulations involved in this pathway.

105 106

Compared with xylose isomerase pathway, Weimberg pathway is a promising alternative

107

metabolic pathway that can generate 2-KG with only 5 enzymatic steps in a nonphosphorylated

108

and carbon-conserved manner. It has been reported that introduction of Weimberg pathway to

5 ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 6 of 27

109

generate a 2-KG pool, coupled with over-expression of downstream mesaconate biosynthetic

110

pathway yielded 12.5 g/L mesaconate from xylose [9], demonstrating the high efficiency of

111

Weimberg pathway for the production of 2-KG derived compounds. We speculated that

112

employment of Weimberg pathway would enhance the 2-KG availability thereby to improve the

113

glutaric acid titer. However, we believe that Weimberg pathway alone could not provide enough

114

acetyl-CoA to support the high-level glutaric acid production since no intermediate could be

115

directly used for acetyl-CoA supply in this pathway. Branching off from Weimberg pathway,

116

Dahms

117

glycolaldehyde and pyruvate, the latter is the direct precursor for acetyl-CoA formation.

118

Therefore, simultaneous use of Weimberg pathway and Dahms pathway was conducted so that

119

the former mainly generates 2-KG and the latter offers acetyl-CoA via decarboxylation of

120

pyruvate. As calculated in the supporting information, the maximum theoretical molar yield of

121

glutaric acid using this strategy is only 0.5 mol per mol xylose. The lower theoretical yield

122

obtained in this way is caused by the by-product formation, glycoaldehyde was produced as 0.5

123

mol per mol xylose. In order to verify our hypothesis, strain JW271 was constructed by deletion

124

of xylA gene encoding xylose isomerase to block the pentose phosphate pathway. The plasmids

125

pJW88 carrying xylD, kivD and gabD and pJW31 carrying HCS, HA, HICDH, xylB, xylC, xylX,

126

xylA were introduced into JW271 to generate strain JW12. As we expected, the glutaric acid titer

127

was increased by 2-fold compared with JW11 and reached 209 mg/L with a comparable OD600

128

value of 2.03 at 60 hours (Fig. 2B), which indicates the superiority of Weimberg pathway for the

129

production of 2-KG derived glutaric acid. However, this titer is still far from our previous

130

feeding experiment which produced 600 mg/L glutaric acid by feeding 4 g/L 2-KG

131

noticed that there is a trade-off relationship between acetyl-CoA formation and 2-KG generation

pathway

cleavages

the

common

intermediate

6 ACS Paragon Plus Environment

2-keto-3-deoxy-xylonate

14

into

. We

Page 7 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Synthetic Biology

132

in Weimberg-Dahms pathway since Dahms pathway is branching off from Weimberg pathway.

133

In this condition, the production of the acetyl-CoA is at the expense of 2-KG formation. Thus,

134

though the Weimberg pathway could supply more 2-KG, the Dahms pathway is not an ideal

135

route to provide enough acetyl-CoA. More efficient optimization strategies need to be developed

136

to overcome this issue.

137 138

In some cases, complementary characteristics of different pathways may result in synergetic

139

effect when producing one desired product, which improves the production titer and yield. For

140

instance, both E. coli native threonine pathway and heterologous citramalate pathway are able to

141

produce 1-propanol. Those two pathways are complementary to each other in redox demands.

142

Utilization of the dual pathway for 1-propanol production achieved higher productivity and yield

143

than individual pathway alone

144

TCA cycle and glyoxylate shunt for the succinic acid synthesis has also been revealed

145

previously15. Utilization of the synergetic pathways in combination led to increased succinic acid

146

titer. In our case, the isomerase pathway is inefficient for 2-KG generation but provides

147

sufficient amount of acetyl-CoA, While Weimberg pathway or Weimberg-Dahms pathway are

148

more straightforward for the synthesis of 2-KG but less efficient for the production of acetyl-

149

CoA. The complementary precursors supply between xylose isomerase pathway and Weimberg

150

pathway or Weimberg-Dahms pathway may lead to a synergetic effect for the production of

151

chemicals derived from acetyl-CoA and 2-KG. In order to verify our hypothesis, we first

152

combined xylose isomerase pathway with Weimberg-Dahms pathway to explore the synergetic

153

effect between those pathways for the de novo production of glutaric acid. All of the three xylose

154

metabolic pathways were co-expressed in E. coli. The maximum theoretical molar yield of

12

. Similarly, the synergetic effect between oxidative branch of

7 ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 8 of 27

155

glutaric acid using this strategy is increased to 0.528 mol per mol xylose (Supporting

156

information). To experimentally verify it, plasmids pJW88 and pJW31 were co-introduced into

157

BW25113 (F’) to generate JW13 which carries xylose Weimberg, Dahms, isomerase pathway

158

and downstream glutaric acid biosynthetic pathway together. Remarkably, glutaric acid titer was

159

further improved to 484 mg/L with a comparable OD600 value of 2.24 after 60 hours (Fig. 3).

160

Although this titer is still lower than that of the direct feeding of 2-KG as the precursor, it is

161

higher than our previously constructed glutaric acid de novo biosynthetic pathway which

162

produced 420 mg/L glutaric acid using 20 g/L glucose as the substrate

163

that combination of those three pathways increased glutaric acid titer by 380% to 130%

164

compared with utilization of isomerase pathway or Weimberg-Dahms pathway alone, which

165

demonstrates the synergetic effect between xylose isomerase and Weimberg-Dahms pathway in

166

glutaric acid biosynthesis.

14

. It is exciting to note

167 168

Next, we hypothesized that Dahms pathway is not essential for maintaining of such a synergetic

169

effect, because: 1) the supply of acetyl-CoA could be achieved by expression of xylose

170

isomerase pathway alone; and 2) The trade-off relationship between acetyl-CoA formation and

171

2-KG generation in Dahms pathway reduced the 2-KG generation efficiency in Weimberg

172

pathway. Thus, we speculated that deletion of Dahms pathway would keep the synergetic effect

173

and furthermore can conserve more 2-KG to support the improvement of glutaric acid titer. We

174

also calculated the maximum theoretical molar yield of glutaric acid after deletion of Dahms

175

pathway. Co-utilization of xylose isomerase pathway and Weimberg pathway has the potential to

176

produce 0.611 mol glutaric acid per mol xylose (Supporting information). In order to verify our

177

hypothesis, Dahms pathway was blocked in BW25113 (F’) by deletion of yagE and yjhH which

8 ACS Paragon Plus Environment

Page 9 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Synthetic Biology

178

encoding aldolase, generating strain JW285. Plasmids pJW88 and pJW31 were co-introduced

179

into JW285 to yield strain JW14. Remarkably, the glutaric acid titer was enhanced to 602 mg/L

180

with a higher OD600 value of 3.09 (Fig. 4A). This titer was improved by 480% and 188%

181

compared with utilization of isomerase pathway or Weimberg-Dahms pathway alone, which

182

revealed that the synergetic effect still exists when only co-utilization of xylose isomerase

183

pathway and Weimberg pathway. Furthermore, the increased titer compared with using all of

184

three pathways demonstrated that deletion of Dahms pathway led to more pronounced synergetic

185

effect due to conserved 2-KG availability. Therefore, we concluded that xylose isomerase

186

pathway and Weimberg pathway are synergetic pathways for glutaric acid synthesis. It is worth

187

noting that this titer is comparable with our previous feeding experiment (600 mg/L) and higher

188

than the de novo production titer (420 mg/L) that obtained by using glucose as the substrate

189

coupled with down-regulation of 2-KG dehydrogenase (SucAB), which indicated the efficiency

190

of the constructed xylose synergetic pathways outcompetes the glucose metabolic pathway for

191

glutaric acid synthesis. In addition, we are wondering that whether the synergetic effect could be

192

further enhanced by inactivation of the citrate synthase (encoded by gltA), which is responsible

193

for diverting acetyl-CoA into the TCA cycle. By doing so, the xylose isomerase pathway

194

conserves more acetyl-CoA and no longer offers 2-KG and Weimberg pathway is the sole

195

pathway to produce 2-KG. As we calculated, the maximum theoretical molar yield of glutaric

196

acid is increased to 0.625 mol per mol xylose in this condition (Supporting information). To

197

experimentally verify it, strain JW287 was constructed by deletion of gltA in strain JW285 to

198

create a ∆yjhH ∆yagE∆gltA triple knockout strain. Plasmids pJW88 and pJW31 were co-

199

introduced into JW287 to yield strain JW15. As shown in Fig. 4B, the glutaric acid titer

200

decreased to 250 mg/L and the OD600 value reach to 1.62 reduced by nearly 50% compared with

9 ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 10 of 27

201

JW14. We concluded that deletion of gltA impairs the synergetic effect between xylose

202

isomerase pathway and Weimberg pathway, probably due to reduced growth caused by the

203

disruption of the TCA cycle (∆gltA).

204 205

In summary, we investigated the biosynthesis potential of different xylose metabolic pathways

206

and illustrated a novel synergetic effect between the xylose isomerase pathway and Weimberg

207

pathway for glutaric acid synthesis in E. coli. The two pathways are complementary with each

208

other in precursors supply. The host strain with the dual pathways for glutaric acid production

209

yielded higher titer than utilization of each pathway alone. The efficiency of the constructed

210

xylose synergetic pathways is even higher than that of glutaric acid biosynthesis from glucose.

211

We believe that the glutaric acid titer could be further improved by increase of the acetyl-CoA

212

supply. The recently developed genome-scale models are promising to predict the gene over-

213

expression or deletion targets to enhance the acetyl-CoA availability16,

214

pathway efficiency could also be improved by precisely controlling the carbon flux distribution

215

between the xylose isomerase and Weimberg pathway to maximize the glutaric acid titer via the

216

library-based combinatorial pathway optimization18, 19.

17

. Additionally, the

217 218

This work presented here provides a novel and powerful strategy for xylose metabolic utilization

219

to overcome the inefficiency of single xylose metabolic pathway. Besides glutaric acid, acetyl-

220

CoA and 2-KG are the precursors for biosynthesis of many other high-value chemicals, such as

221

1,4-BDO

222

poly(D-lactate-co-glycolate-co-D-2-hydroxybutyrate)

20

, five-, six and seven carbon lactams

21

, nylon-6 10, 23

22

, poly(lactate-co-glycolate) and

. Therefore, the applicability of our

10 ACS Paragon Plus Environment

Page 11 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Synthetic Biology

223

constructed xylose synergetic pathways can be expanded to synthesize other value-added

224

compounds to achieve production improvement.

11 ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 12 of 27

225

Methods

226

Media, Strains and Plasmids

227

Luria-Bertani (LB) medium containing 10 g/L tryptone, 5 g/L yeast extract and 10 g/L NaCl was

228

used for cell inoculation and plasmid propagation. The modified LB medium (LB medium added

229

with 10 g/L of xylose) was used for de novo biosynthesis of glutaric acid. The antibiotics

230

Ampicillin (100 µg/mL) and kanamycin (50 µg/mL) were supplemented into the medium if

231

necessary. E. coli BW25113 (F’) was used as the host for glutaric acid production and E. coli

232

strain XL1-Blue for DNA manipulation experiments. Knock-out strains of E. coli BW25113 (F’)

233

were generated by disrupting target gene(s) using P1 transduction 24. The high-copy number and

234

medium-copy number plasmids pZE12-luc and pCS-27 were used for pathway construction. All

235

of used strains and plasmids in this study were listed in Table 1.

236 237

DNA manipulations

238

Genes kivD from L. lactis and gabD from P. putida were cloned into the backbone of pCS27 to

239

create pJW87 by amplifying kivD-gabD from pZE-kivD-gabD and inserting into pCS27 between

240

AvrII and XhoI. Genes xylD from Caulobacter crescentus, kivD and gabD were cloned into the

241

backbone of pZE12-luc using Acc65I, PstI, sphI and XbaI to create pJW77. To create pJW88,

242

the fragment xylD-kivD-gabD was amplified from pJW77 and inserting into pCS27 between

243

AvrII and XhoI. Genes xylB, xylC, xylX and xylA from C. crescentus were cloned into the

244

backbone of pZE12-luc using Acc65I, BamHI, NdeI, HindIII and XbaI to create pJW19. To

245

create pJW31, fragment xylB-xylC-xylX-xylA was amplified from pJW19 and inserting into pZE-

246

HCS-HA-HICDH between SpeI and SacI.

247

12 ACS Paragon Plus Environment

Page 13 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Synthetic Biology

248

De novo biosynthesis of glutaric acid

249

Shake flask experiments were conducted using LB medium supplemented with 10 g/L xylose.

250

Production colonies were inoculated in 3 ml LB medium (37ºC, 270 rpm) for overnight. 200 µL

251

of the pre-inoculum along with appropriate antibiotics was added into screw cap bottles (125 mL)

252

consisting of 20 mL LB xylose medium and grown for 3 hours (37ºC, 270 rpm). Then 0.5 mM

253

IPTG were added to the cultures and the cultures were grown till 60 hours at 30ºC, 270 rpm. 1

254

mL samples were collected every 12 hours for HPLC analysis.

255 256

Analytical procedures

257

Genesys 10S UV-Vis Spectrophotometer (Thermo Scientific, Waltham, MA) was used to

258

measure the optical density at 600 nm. To analyze the samples, 1 mL samples were collected

259

every 12 hours during the shake flask experiments and centrifuged at 13,000 rpm for 10 min,

260

following which the supernatant was filtered and analyzed by HPLC-RID (Shimadzu) equipped

261

with a Coregel-64H column (Transgenomic). The eluent used was 4 mN H2SO4 with a flow rate

262

of 0.6 mL/min. The column temperature was set at 55ºC.

13 ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

263

AUTHOR INFORMATION

264

Corresponding Authors

265

*E-mails: [email protected] (Q. Yuan), [email protected] (Y. Yan).

Page 14 of 27

266 267

Author Contributions

268

JW conceived the study and wrote the manuscript. JW and XS performed the experiments. QY

269

and YYan directed the research. JW, YL, XS and YYan revised the manuscript. ZC and YYang

270

participated the research.

271 272

Notes

273

The authors declare no competing financial interest.

274 275

ACKNOWLEDGMENTS

276

This work was supported by National Natural Science Foundation of China (21376017,

277

21406010, 21636001), the Program of Introducing Talents of Discipline to Universities (“111”

278

project, B13005), the Program for Changjiang Scholars and Innovative Research Team in

279

Universities in China (No. IRT13045), the National High Technology Research and

280

Development Program of China (863 Program, No. NO.2015AA021001). We would also like to

281

thank the College of Engineering, The University of Georgia, Athens.

282 283

14 ACS Paragon Plus Environment

Page 15 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

284 285

ACS Synthetic Biology

Table 1. List of strains and plasmids used in this study. Strain

Genotype

Reference

E. coli BW25113 (F’)

rrnBT14 ∆lacZWJ16 hsdR514 ∆araBADAH33

25

∆rhaBADLD78 F‫[ ׳‬traD36 proAB lacIqZ∆M15 Tn10(Tetr)] E. coli XL1-Blue

recA1 endA1gyrA96thi-1hsdR17supE44relA1lac

Stratagene

[F’ proAB lacIqZDM15Tn10 (TetR)] JW3537-1

BW25113 ∆xylA::kan

Yale CGSC

JW5775-2

BW25113 ∆yjhH::kan

Yale CGSC

JW0261-1

BW25113 ∆yagE::kan

Yale CGSC

JW271

BW25113 (F’) ∆xylA

This study

JW285

BW25113 (F’) ∆yjhH ∆yagE

This study

JW287

BW25113 (F’) ∆yjhH ∆yagE∆gltA

This study

JW11

BW25113 (F’) harboring pJW87 and pZE-HCS-

This study

HA-HICDH JW12

JW271 harboring pJW88 and pJW31

This study

JW13

BW25113 (F’) harboring pJW88 and pJW31

This study

JW14

JW285 harboring pJW88 and pJW31

This study

JW15

JW287 harboring pJW88 and pJW31

This study

Plasmid

Description

Reference

pZE12- luc

pLlacO-1; luc; ColE1 ori; AmpR

26

pCS27

pLlacO-1; p15A ori; KanR

27

kivD from Lactococcus lactis and gabD from

15 ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 16 of 27

pZE-kivD-gabD

Pseudomonas putida cloned into pZE12-luc

14

pJW87

kivD from Lactococcus lactis and gabD from

This study

Pseudomonas putida cloned into pCS27 pZE-HCS-HA-HICDH

HCS, HA and HICDH from Saccharomyces

14

cerevisiae cloned into pZE12-luc pJW77

xylD from Caulobacter crescentuss, kivD from

This study

Lactococcus lactis and gabD from Pseudomonas putida cloned into pZE12-luc pJW88

xylD from Caulobacter crescentus, kivD from

This study

Lactococcus lactis and gabD from Pseudomonas putida cloned into pCS27 pJW19

xylB, xylC, xylX and xylA from C. crescentus

This study

cloned into pZE12-luc pJW31

HCS, HA, HICDH and xylB, xylC, xylX, xylA from C. crescentus cloned into pZE12-luc

286

16 ACS Paragon Plus Environment

This study

Page 17 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

287

ACS Synthetic Biology

Figure Legends

288 289

Fig. 1. Schematic representation of three different xylose metabolic pathways and glutaric acid

290

biosynthetic pathway. GA: Glycolaldehyde. Genes: EcxylA: encoding xylose isomerase; CcxylB:

291

encoding xylose dehydrogenase; CcxylC: encoding xylonolactonase; CcxylD: encoding xylonate

292

dehydratase; CcxylX: encoding 2-keto-3-deoxy-xylonate dehydratase; CcxylA: encoding 2-

293

ketoglutarate semialdehyde dehydrogenase; yagE or yjhH: encoding aldolase; gltA: encoding

294

citrate synthase; HCS: encoding homocitrate synthase; HA: encoding homoaconitase; HICDH:

295

encoding homoisocitrate dehydrogenase; kivD: encoding alpha-ketoisovalerate decarboxylase;

296

gabD: encoding succinate semialdehyde dehydrogenase.

297 298

Fig. 2. Results of shake flask studies for glutaric acid production from two different xylose

299

metabolic pathways. (A) Glutaric acid produced from xylose isomerase pathway; (B) Glutaric

300

acid produced from xylose Weimberg-Dahms pathway. The data were generated from three

301

independent experiments (n=3; s.d. represented by ±).

302 303

Fig. 3. Results of shake flask studies for glutaric acid production from xylose synergetic

304

pathways by utilization of xylose isomerase pathway and Weimberg-Dahms pathway in

305

combination. The data were generated from three independent experiments (n=3; s.d. represented

306

by ±).

307 308

Fig. 4. Results of shake flask studies for glutaric acid production from re-constructed xylose

309

synergetic pathways. (A) Glutaric acid produced from xylose synergetic pathways by utilization

17 ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

310

of xylose isomerase pathway and Weimberg pathway in combination; (B) Glutaric acid produced

311

from xylose synergetic pathways by utilization of xylose isomerase pathway and Weimberg

312

pathway in combination, but the TCA cycle was disrupted by deletion of gltA in this case. The

313

data were generated from three independent experiments (n=3; s.d. represented by ±).

18 ACS Paragon Plus Environment

Page 18 of 27

Page 19 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

314

ACS Synthetic Biology

Supporting Information

315 316

The maximum theoretical molar yields of glutaric acid from different xylose metabolic pathways

317

19 ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

318

Page 20 of 27

References

319 320

(1) Gall, D. L., Ralph, J., Donohue, T. J., and Noguera, D. R. (2017) Biochemical transformation

321

of lignin for deriving valued commodities from lignocellulose, Curr. Opin. Biotechnol.

322

45, 120-126.

323

(2) López-Linares, J. C., Romero, I., Cara, C., and Castro, E. (2016) Bioconversion of rapeseed

324

straw: enzymatic hydrolysis of whole slurry and cofermentation by an ethanologenic

325

Escherichia coli, Energy Fuels 30, 9532-9539.

326

(3) Weimberg, R. (1961) Pentose oxidation by Pseudomonas fragi, J. Biol. Chem. 236, 629-635.

327

(4) Dahms, A. S. (1974) 3-Deoxy-D-pentulosonic acid aldolase and its role in a new pathway of

328

D-xylose degradation, Biochem. Biophys. Res. Commun. 60, 1433-1439.

329

(5) Zhang, H., Pereira, B., Li, Z., and Stephanopoulos, G. (2015) Engineering Escherichia coli

330

coculture systems for the production of biochemical products, Proc. Natl. Acad. Sci.

331

U.S.A. 112, 8266-8271.

332

(6) Tai, Y.-S., Xiong, M., Jambunathan, P., Wang, J., Wang, J., Stapleton, C., and Zhang, K.

333

(2016) Engineering nonphosphorylative metabolism to generate lignocellulose-derived

334

products, Nat. Chem. Biol. 12.

335

(7) Wang, J., Jain, R., Shen, X., Sun, X., Cheng, M., Liao, J. C., Yuan, Q., and Yan, Y. (2017)

336

Rational engineering of diol dehydratase enables 1, 4-butanediol biosynthesis from

337

xylose, Metab. Eng. 40, 148-156.

338

(8) Wang, J., Shen, X., Jain, R., Wang, J., Yuan, Q., and Yan, Y. (2017) Establishing a novel

339

biosynthetic pathway for the production of 3, 4-dihydroxybutyric acid from xylose in

340

Escherichia coli, Metab. Eng. 41, 39-45.

341

(9) Bai, W., Tai, Y.-S., Wang, J., Wang, J., Jambunathan, P., Fox, K. J., and Zhang, K. (2016)

342

Engineering

nonphosphorylative

metabolism

to

synthesize

343

lignocellulosic sugars in Escherichia coli, Metab. Eng. 38, 285-292.

mesaconate

from

344

(10) Choi, S. Y., Park, S. J., Kim, W. J., Yang, J. E., Lee, H., Shin, J., and Lee, S. Y. (2016)

345

One-step fermentative production of poly (lactate-co-glycolate) from carbohydrates in

346

Escherichia coli, Nat. Biotechnol. 34, 435-440.

20 ACS Paragon Plus Environment

Page 21 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Synthetic Biology

347

(11) Pereira, B., Li, Z.-J., De Mey, M., Lim, C. G., Zhang, H., Hoeltgen, C., and

348

Stephanopoulos, G. (2016) Efficient utilization of pentoses for bioproduction of the

349

renewable two-carbon compounds ethylene glycol and glycolate, Metab. Eng. 34, 80-87.

350 351

(12) Shen, C. R., and Liao, J. C. (2013) Synergy as design principle for metabolic engineering of 1-propanol production in Escherichia coli, Metab. Eng. 17, 12-22.

352

(13) Park, S. J., Kim, E. Y., Noh, W., Park, H. M., Oh, Y. H., Lee, S. H., Song, B. K., Jegal, J.,

353

and Lee, S. Y. (2013) Metabolic engineering of Escherichia coli for the production of 5-

354

aminovalerate and glutarate as C5 platform chemicals, Metab. Eng. 16, 42-47.

355

(14) Wang, J., Wu, Y., Sun, X., Yuan, Q., and Yan, Y. (2017) De novo biosynthesis of glutarate

356

via α-keto acid carbon chain extension and decarboxylation pathway in Escherichia coli,

357

ACS Synth. Biol.

358

(15) Lin, H., Bennett, G. N., and San, K.-Y. (2005) Metabolic engineering of aerobic succinate

359

production systems in Escherichia coli to improve process productivity and achieve the

360

maximum theoretical succinate yield, Metab. Eng. 7, 116-127.

361

(16) Xu, P., Ranganathan, S., Fowler, Z. L., Maranas, C. D., and Koffas, M. A. (2011) Genome-

362

scale metabolic network modeling results in minimal interventions that cooperatively

363

force carbon flux towards malonyl-CoA, Metab. Eng. 13, 578-587.

364

(17) Bhan, N., Xu, P., Khalidi, O., and Koffas, M. A. (2013) Redirecting carbon flux into

365

malonyl-CoA to improve resveratrol titers: proof of concept for genetic interventions

366

predicted by OptForce computational framework, Chem. Eng. Sci. 103, 109-114.

367

(18) Xu, P., Rizzoni, E. A., Sul, S.-Y., and Stephanopoulos, G. (2016) Improving metabolic

368

pathway efficiency by statistical model-based multivariate regulatory metabolic

369

engineering, ACS Synth. Biol. 6, 148-158.

370

(19) Xu, P., Gu, Q., Wang, W., Wong, L., Bower, A. G., Collins, C. H., and Koffas, M. A.

371

(2013) Modular optimization of multi-gene pathways for fatty acids production in E. coli,

372

Nat. Commun. 4, 1409.

373

(20) Yim, H., Haselbeck, R., Niu, W., Pujol-Baxley, C., Burgard, A., Boldt, J., Khandurina, J.,

374

Trawick, J. D., Osterhout, R. E., and Stephen, R. (2011) Metabolic engineering of

375

Escherichia coli for direct production of 1, 4-butanediol, Nat. Chem. Biol. 7, 445-452.

21 ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 22 of 27

376

(21) Chae, T. U., Ko, Y.-S., Hwang, K.-S., and Lee, S. Y. (2017) Metabolic engineering of

377

Escherichia coli for the production of four-, five-and six-carbon lactams, Metab. Eng. 41,

378

82-91.

379

(22) Turk, S. C., Kloosterman, W. P., Ninaber, D. K., Kolen, K. P., Knutova, J., Suir, E.,

380

Schürmann, M., Raemakers-Franken, P. C., Müller, M., and De Wildeman, S. M. (2015)

381

Metabolic engineering toward sustainable production of nylon-6, ACS Synth. Biol. 5, 65-

382

73.

383

(23) Choi, S. Y., Kim, W. J., Yu, S. J., Park, S. J., Im, S. G., and Lee, S. Y. (2017) Engineering

384

the xylose‐catabolizing Dahms pathway for production of poly (d‐lactate‐co‐

385

glycolate)

386

Escherichia coli, Microb. Biotechnol.

387 388

and

poly

(d‐lactate‐co‐glycolate‐co‐d‐2‐hydroxybutyrate)

in

(24) Thomason, L. C., Costantino, N., and Court, D. L. (2007) E. coli genome manipulation by P1 transduction, Curr. Protoc. Mol. Biol., 1.17. 11-11.17. 18.

389

(25) Atsumi, S., Cann, A. F., Connor, M. R., Shen, C. R., Smith, K. M., Brynildsen, M. P., Chou,

390

K. J., Hanai, T., and Liao, J. C. (2008) Metabolic engineering of Escherichia coli for 1-

391

butanol production, Metab. Eng. 10, 305-311.

392

(26) Lutz, R., and Bujard, H. (1997) Independent and tight regulation of transcriptional units in

393

Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements, Nucleic

394

Acids Res. 25, 1203-1210.

395 396

(27) Shen, C. R., and Liao, J. C. (2008) Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways, Metab. Eng. 10, 312-320.

397

22 ACS Paragon Plus Environment

Page 23 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Synthetic Biology

57x32mm (300 x 300 DPI)

ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Schematic representation of three different xylose metabolic pathways and glutaric acid biosynthetic pathway. GA: Glycolaldehyde. Genes: EcxylA: encoding xylose isomerase; CcxylB: encoding xylose dehydrogenase; CcxylC: encoding xylonolactonase; CcxylD: encoding xylonate dehydratase; CcxylX: encoding 2-keto-3-deoxy-xylonate dehydratase; CcxylA: encoding 2-ketoglutarate semialdehyde dehydrogenase; yagE or yjhH: encoding aldolase; gltA: encoding citrate synthase; HCS: encoding homocitrate synthase; HA: encoding homoaconitase; HICDH: encoding homoisocitrate dehydrogenase; kivD: encoding alpha-ketoisovalerate decarboxylase; gabD: encoding succinate semialdehyde dehydrogenase. 84x67mm (300 x 300 DPI)

ACS Paragon Plus Environment

Page 24 of 27

Page 25 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Synthetic Biology

Results of shake flask studies for glutaric acid production from two different xylose metabolic pathways. (A) Glutaric acid produced from xylose isomerase pathway; (B) Glutaric acid produced from xylose WeimbergDahms pathway. The data were generated from three independent experiments (n=3; s.d. represented by ±). 143x49mm (300 x 300 DPI)

ACS Paragon Plus Environment

ACS Synthetic Biology

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Results of shake flask studies for glutaric acid production from xylose synergetic pathways by utilization of xylose isomerase pathway and Weimberg-Dahms pathway in combination. The data were generated from three independent experiments (n=3; s.d. represented by ±). 70x49mm (300 x 300 DPI)

ACS Paragon Plus Environment

Page 26 of 27

Page 27 of 27

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Synthetic Biology

Results of shake flask studies for glutaric acid production from re-constructed xylose synergetic pathways. (A) Glutaric acid produced from xylose synergetic pathways by utilization of xylose isomerase pathway and Weimberg pathway in combination; (B) Glutaric acid produced from xylose synergetic pathways by utilization of xylose isomerase pathway and Weimberg pathway in combination, but the TCA cycle was disrupted by deletion of gltA in this case. The data were generated from three independent experiments (n=3; s.d. represented by ±). 140x49mm (300 x 300 DPI)

ACS Paragon Plus Environment