. 2019 Jul 17;10:1649. doi: 10.3389/fmicb.2019.01649

Table 3.

Genes regulated by Thi2p in GX stage and their effects on xylose utilization.

Category	Strains	Gene annotation	Log₂(fold changes)^a	$r_{xylose}^{b}$ (g g⁻¹ DCW h⁻¹)
	Control (BSGX001)			0.061 ± 0.001
OVEREXPRESSION THE UP-REGULATED GENES
RP-related genes	RPS25B	Protein component of the small (40S) ribosomal subunit	1.379	0.053 ± 0.001^*
	MRPL15	Mitochondrial ribosomal protein of the large subunit	1.157	0.035 ± 0.003^*
	RPL38	Ribosomal 60S subunit protein L38	1.048	0.022 ± 0.001^*
	MAK16	Constituent of 66S pre-ribosomal particles	1.802	0.052 ± 0.001^*
	RPPO	Conserved ribosomal protein P0 of the ribosomal stalk	1.345	0.054 ± 0.001^*
	RPS28B	Protein component of the small (40S) ribosomal subunit	1.113	0.060 ± 0.000^*
	DBP9	A putative ATP-dependent RNA helicase involved in 60S-ribosomal-subunit biogenesis	1.380	0.060 ± 0.000^*
	POP5	Subunit of both RNase MRP and nuclear RNase P	1.616	0.050 ± 0.001^*
	RBG1	Translating ribosomes	1.275	0.060 ± 0.001^*
Signal transducer genes	GPB2	Multistep regulator of cAMP-PKA signaling	1.146	0.039 ± 0.003^*
	MID2	Acts as a sensor for cell wall integrity signaling	1.053	0.089 ± 0.003^*
	CDC42	Establishment and maintenance of cell polarity	1.241	0.069 ± 0.002^*
	PEX22	Required for import of peroxisomal proteins	1.422	0.049 ± 0.001^*
	FAR10	Protein involved in recovery from arrest in response to pheromone	1.051	0.060 ± 0.001^*
Generation of precursor Metabolites and energy	PIG1	Glycogen synthesis	1.412	0.045 ± 0.001^*
	RGI2	Involved in energy metabolism under respiratory conditions	1.136	0.086 ± 0.001^*
Response to starvation	ECM22	Sterol regulatory element binding protein	1.268	0.068 ± 0.002^*
ATPase activity	MCM5	An active ATP-dependent helicase	1.334	0.022 ± 0.000^*
	SFH1	Component of the RSC chromatin remodeling complex	1.075	0.000 ± 0.000^*
GTPase activity	GPN3	Biogenesis of RNA pol II and polIII	1.252	0.069 ± 0.001^*
Oxidoreductase activity	BDH2	Putative medium-chain alcohol dehydrogenase	1.241	0.077 ± 0.001^*
Transcription factor activity, protein binding	TFC3	Subunit of RNA polymerase III Transcription initiation factor complex	1.014	0.087 ± 0.000^*
Cofactor metabolic process	COQ11	Putative oxidoreductase, subunit of Coenzyme Q biosynthetic complexes	1.069	0.064 ± 0.000
	BOL1	Mitochondrial matrix protein involved in Fe-S cluster biogenesis	1.014	0.060 ± 0.002
Lipid metabolic process	STT4	Phosphatidylinositol-4-kinase	1.282	0.091 ± 0.001^*
	ARV1	Involved in intracellular sterol and sphingolipid transport	1.374	0.055 ± 0.003^*
	ECI1	Essential for the beta-oxidation of unsaturated fatty acids	1.306	0.057 ± 0.000^*
Transmembrane Transporter activity	CSC1	May be involved in detoxification	1.071	0.069 ± 0.002^*
	THI7	Responsible for the uptake of thiamine	1.233	0.020 ± 0.001^*
Phosphatase activity	PHO11	One of three repressible acid phosphatases	1.492	0.034 ± 0.002^*
Protein modification	UBC12	Related to E2 ubiquitin-conjugating enzymes	1.696	0.046 ± 0.002^*
Function unknown	BOP2	Protein of unknown function	1.882	0.068 ± 0.001^*
DELETION THE DOWN-REGULATED GENES
Cellular amino acid metabolic or transport	hom3Δ	Cytoplasmic enzyme that catalyzes the first step in the common pathway for methionine and threonine biosynthesis	−1.071	0.000 ± 0.000^*
Amino acid transport	btn2Δ	Modulates arginine uptake	−1.038	0.030 ± 0.001^*
Cell cycle related genes	cip1Δ	Cyclin-dependent kinase inhibitor	–1.035	0.077 ± 0.002^*
	yor338wΔ	Putative protein of unknown function	−1.455	0.039 ± 0.002^*
Response to chemical	Ixr1Δ	Transcriptional repressor that regulates hypoxic genes during normoxia	–1.044	0.083 ± 0.003^*
DNA binding	mga1Δ	Protein similar to heat shock transcription factor	−1.055	0.039 ± 0.002^*
	dal3Δ	Ureidoglycolate lyase	−1.108	0.037 ± 0.001^*
Molecular function Unknown	prm7Δ	Pheromone-regulated protein	−1.294	0.048 ± 0.001^*
	ydr246w-AΔ	Unknown function	–1.070	0.071 ± 0.001^*
	rrt5 Δ	Unknown function	−1.004	0.051 ± 0.002^*
	ygl015cΔ	Null mutants accumulate cargo in the Golgi	–1.121	0.070 ± 0.005^*
	Bsc1	Null mutant has increased glycogen accumulation	−1.397	0.056 ± 0.004^*

Cells were cultured at 30°C in a shake flask and agitated at 200 rpm. All the data are the mean value ± standard deviation of independent triplicate tests. The bold gene names and values refers to the operations brought the positive effect in xylose utilization in the GX stage.

p <0.05.

The THI2 deletion strain compared to the parent strain BSGX001, up-regulate represents genes with higher expression in THI2 deletion strain compared to the parent strain BSGX001, down-regulate represents the reverse operation.

^bThe specific consumption/production rates of xylose/ethanol (r_xylose/r_ethanol) were calculated from the data on the xylose consumption phase in the GX stage.