In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria

Motwalli, Olaa; Essack, Magbubah; Jankovic, Boris R.; Ji, Boyang; Liu, Xinyao; Ansari, Hifzur Rahman; Hoehndorf, Robert; Gao, Xin; Arold, Stefan T.; Mineta, Katsuhiko; Archer, John A. C.; Gojobori, Takashi; Mijakovic, Ivan; Bajic, Vladimir B.

doi:10.1186/s12864-016-3389-4

BMC Genomics

Table 1 List of 49 OGs relevant for FFA production

From: In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria

KEGG Orthology	Definition	Effects	Method	Organism	Ref.
rOGs
K00873 pyk	pyruvate kinase	Carbohydrate metabolism		cyan.	[11, 34]
K01007 pps	pyruvate, water dikinase
K00161 pdhA	pyruvate dehydrogenase E1 component alpha subunit
K00162 pdhB	pyruvate dehydrogenase E1 component beta subunit
K00627 pdhC	pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase)
K00382 phdD (ipdA)	dihydrolipoamide dehydrogenase
K00648 fabH	3-oxoacyl-[acyl-carrier-protein] synthase III	Lipid metabolism
K00645 fabD	[acyl-carrier-protein] S-malonyltransferase
K09458 fabF	3-oxoacyl-[acyl-carrier-protein] synthase II
K02372 fabZ	3-hydroxyacyl-[acyl-carrier-protein] dehydratase
K00208 fabI	enoyl-[acyl-carrier protein] reductase I
K01046 E3.1.1.3	triacylglycerol lipase	Increase chance of strain to secrete FA	secretion & extraction		[15]
pOGs
K01962 accA	acetyl-CoA carboxylase carboxyl transferase subunit alpha	Enhance FFA production (Increase supply of desired substrate)	secretion	cyan.	[12, 14, 34, 44]
K01963 accD	acetyl-CoA carboxylase carboxyl transferase subunit beta
K01961 accC	acetyl-CoA carboxylase, biotin carboxylase subunit
K02160 accB	acetyl-CoA carboxylase biotin carboxyl carrier protein
K00432 gpx	glutathione peroxidase	Reduce the toxic effect of FFA production and improve cell growth, physiology and FFA production	secretion	cyan.	[13]
K04564 SOD2	superoxide dismutase, Fe-Mn family
K06198 coiA	competence protein CoiA
K03782 katG	catalase-peroxidase
K03621 plsX	glycerol-3-phosphate acyltransferase PlsX	Lead to higher lipid levels		plant	[11, 35]
K08591 plsY	glycerol-3-phosphate acyltransferase PlsY
K00655 plsC	1-acyl-sn-glycerol-3-phosphate acyltransferase
virNOG10454 PDAT1	IQ-domain	Enhancing FA synthesis and diverting FA from membrane lipid to Triacylglycerol	accu.		[36]
virNOG19439 OLEO1	oleosin 1				[36]
K14457 MGAT2	2-acylglycerol O-acyltransferase 2	Enhance acyl-CoA-dependent triacylglycerol TAG			[39]
virNOG24576 LCIA	Anion transporter	Help regulate CO2 intake and increase biomass		algae	[32, 37]
virNOG22763 LCIB	Low-CO2 inducible protein	Help regulate CO2 intake and increase biomass		algae	[32, 37]
K00006 GPD1	glycerol-3-phosphate dehydrogenase (NAD+)	Increase glycerol and neutral lipid content (16- and 18-carbon monounsaturated FA significantly increased)		diatom	[38]
K01601 rbcL	ribulose-bisphosphate carboxylase large chain	Improve FFA production		cyan.	[14, 88]
K01602 rbcS	ribulose-bisphosphate carboxylase small chain	Improve FFA production		cyan.	[14, 88]
K01648 ACLY	ATP citrate (pro-S)-lyase	Enhance biofuel precursor production		yeast	[40]
K10804 tesA	acyl-CoA thioesterase I	Remove feedback inhibition and increase production of FFA	secretion	cyan.	[12, 14, 17, 34, 43, 44]
K10781 FATB	fatty acyl-ACP thioesterase B (Plant thioesterase)	Modify the chain length of FFAs for better fuel quality			[11, 12]
K10782 FATA	fatty acyl-ACP thioesterase A	Release FFA			[88]
K14075 PLRP2	pancreatic lipase-related protein 2	Degrade the membrane lipids into FFA with collapse of cell	extraction		[15]
nOGs
K01595 ppc	phosphoenolpyruvate carboxylase	Increase the lipid content		cyan.	[11]
K01897 aas(fadD)	long-chain acyl-CoA synthetase	Channel needed substrates for synthesis of FFA into divergent or reverse pathways and preventing degradation of desired product	secretion	cyan.	[11–14, 17, 34]
K00059 fabG	3-oxoacyl-[acyl-carrier protein] reductase	Divert energy into production of substantial by-products that would compete with production of FFA			[12]
K00626 E2.3.1.9	acetyl-CoA C-acetyltransferase
K11003 hlyD	hemolysin D	Enhance secretion of FFA by weakening cell walls
cyaNOG01264 (PBP2)	penicillin-binding protein	Enhance secretion of FFA by weakening peptidoglycan layer
K13788 pta	phosphate acetyltransferase	“Channel needed substrates for synthesis of FFA into divergent or reverse pathways and preventing degradation of desired product”
K13282 cphB	cyanophycinase	“Divert energy into production of substantial by-products that would compete with production of FFA”
K03802 cphA	cyanophycin synthetase
cyaNOG01069 porin protein	Carbohydrate-selective porin OprB	Enhanced extracellular FFA concentration			[13]
K13535 CLD1	cardiolipin-specific phospholipase	Increase lipid yields without affecting growth or biomass	accu.	diatom	[41]
K00030 IDH3	isocitrate dehydrogenase (NAD+)	Increase intracellular citrate level which enhance biofuel precursor production	accu.	yeast	[40]
K03603 fadR	GntR family transcriptional regulator, negative regulator for fad regulon and positive regulator of fabA	Fatty acid biosynthesis is feadback-inhibited at the transcriptional level by fadR		bacterium	[11, 42]

Abbreviations: rOGs required OGs, pOGs, OGs that positively impact FFA production, nOGs, OGs that negatively impact FFA production, FFA Free Fatty Acid, accu. Accumulation, cyan. Cyanobactia
Classification: nOG (based on reported knockout or knockdown) and pOGs (based on reported inserted or overexpressed) during genetic engineering experiments on that organism in order to secretion, extraction, or accumulation fatty acid

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ISSN: 1471-2164

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