Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives

Francois, Jean Marie; Alkim, Ceren; Morin, Nicolas

doi:10.1186/s13068-020-01744-6

Biotechnology for Biofuels and Bioproducts

Table 1 Description of enzymes and corresponding genes implicated in microbial assimilation of lignocellulosic sugars

From: Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives

Pathway	Enzyme name	Enzyme abbreviation	Gene name	Specific constant kcat/Km (s⁻¹ M⁻¹) [substrat]	Microbial origin	Reference
Pentose oxido-reductive pathway	d-Xylose reductase	XR	XYL1 xyrA	na na	P. stipitis A. niger	[32]
	Xylitol dehydrogenase	XDH	xdh1 XYL2	na na	Filamentous fungi S. cerevisiae	[136] [137]
	d-Xylulokinase	XK	xylB	879 10³ [xylulose]	E. coli	[138]
	d-Xylulokinase	XK	XKS1 xkiA XYL3	na	S. cerevisiae Aspergillus niger Pichia stipitis	[139] [140] [141]
	l-Arabinose reductase	AR	XYL1 larA	na na	T. reesei Aspergilus niger	[32] [142]
	l-Arabitol 4-dehydrogenase	ARDH	ladA	na	Filamentous fungi*	[33, 143]
	l-Xylulose reductase (NADPH) l-Xylulose reductase (NADH)	lXR	lrx3 lxrA ALX1	712 [l-xylulose] 47,10³ [l-xylulose] na	T. reesei Aspergillus niger Ambrosiozyma monospora	[144] [145] [146]
	d-Arabinitol 2-dehydrogenase/ribulose reductase	RIR	ARD	na	Pichia stipitis Candida tropicalis	[33] [147]
	d-Ribulokinase	RIK	YDR109c	80 10³ [D-ribulose]	S.cerevisiae,	[148]
Isomerase pathway	Xylose isomerase	XI	xylA	na	E. coli	[149]
	d-Xylulokinase	XK	xylB	879 10³ [xylulose]	E. coli	[138]
	l-Arabinose isomerasz	AI	araA	na	E. coli	[150]
	l-Ribulokinase	RKI	araB	na	E. coli	[151, 152]
	l-Xylulokinase	XKI	xylK	na	E. coli	[108]
	l-Ribulose-5-P 3-epimerase	UlaE	ulaE	na	E. coli	[153]
	l-Ribulose 5-P 4-epimerase	RPE	araD	na	E. coli	[154]
Non-phosphorylative pathway	d-Xylose dehydrogenase	XylDH	xylB xylB HVO_B0028	10⁴ [D-Xylose] 157,10³ [xylose]	Caulobacter crescenti S.solfataricus H. vulcanii	[46, 48, 155, 156]
	d-Xylonate lactonase	XAL	xylC	na na	C.crescenti H.volcanii	[48, 81]
	d-Xylonate dehydratase	XAD	xylD HVO B0038A yagE/yjhG	40 10³ [D-xylonate) 4 10³ (D-Xylonate)	C. crescenti H.volcanii Escherichia coli	[48, 70, 155]
	l-Arabinose 1-dehydrogenase	AraDH	araA	32.3 10³[l-arabinose]	B. multivorans	[81]
	l-Arabinolactonase	AraL	araL	na	B. multivorans, S. solfataricus	[81]
	l-Arabinonate dehydratase	AraD	araC	83 [l-arabinonate]	B.multivorans S. solfataricus	[81] [156]
	2-Keto-3-deoxy-d-xylonate dehydratase	KdxD	xylX	260 [2-keto-3-deoxy-D-pentanoate] 530 [2-keto-3-deoxy-D-pentanoate]	C. crescenti B. xenovorans	[80, 81]
	2-Keto-3-deoxy-l-arabinonate dehydratase	KdaD	araD	23 [2-keto-3-deoxy-l-arabinonate]	B. xenovorans	[81]
	2-Ketoglutarate semialdehyde dehydrogenase	KGSADH	xylA ycbD HV0_B0039	4.6 10⁵ [α-ketoglutaric semialdehyde]	A. brasilense C. crescenti S. solfataricus H. valcanii	[48, 155,156,157]
	2-Keto-3-deoxy-D/l-pentanoate aldolase	KDPA	kdxA yagE/yjhH	450 [2-keto-3-deoxy-D-pentanoate] 7000 [pyruvate]	S. solfataricus Escherichia coli	[47, 62]

na: Not accessible

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