TABLE 1.

Differentially expressed genes in B. velezensis GA1 after HGLM perception

Locus tag	Name			Conservation in related speciesa				Category	Information
		Fold change at:		B. amyloliquefaciens DSM 7		B. subtilis 168
		5 h	8 h	QC (%)	ID (%)	QC (%)	ID (%)
GL331_00010	floT (yuaG)		−3.048	100	93.2	97	81.46	Stress	Inner membrane protein, flotillin-like protein
GL331_00015	yuaF	−3.016		99	93.4	94	68.97	Stress	Involved in the control of membrane fluidity
GL331_00985	yusU	−3.072		100	95.12	99	76.37	Unknown	Unknown
GL331_01085	liaH		−4.878	100	93.95	100	77.21	Stress	lia operon expression modulator, similar to phage shock protein, resistance against oxidative stress, and cell wall antibiotics
GL331_01090	liaI		−3.846	100	93.96	100	69.71		Resistance against oxidative stress and cell wall antibiotics
GL331_01180	fhuD	−3.176		100	95.1	99	77.31	Transport	Hydroxamate siderophore ABC transporter
GL331_01520	opuCA		3.066	100	95.61	99	82.35	Transport	Glycine betaine/carnitine/choline/arsenobetaine/arsenocholine ABC transporter
GL331_02210	hpf	−4.636		100	97	100	83.71	Stress	General stress protein, required for ribosome dimerization in the stationary phase, protects essential ribosomal proteins
GL331_02265	flgN	−3.608		100	96.48	76	76.55	Motility	Flagellar filament assembly protein
GL331_02270	flgM	−4.334		100	98.5	100	77.15		Negative regulator of flagellin synthesis, anti-sigD
GL331_02275	yvyF	−4.562		100	95.71	100	78.38		Unknown
GL331_02335	tuaF		−5.05	100	92.51	100	70.91	Cell wall	Teichuronic acid biosynthesis protein
GL331_02355	tuaB		−3.262	100	94.41	100	73.25	Cell wall	Polymer export
GL331_03100	maeA		−3.69	100	97.29	100	82.88	Metabolism	Malate utilization
GL331_03645	ywcE		−3.516	100	96.93	89	85.04	Sporulation	Holin, spore morphogenesis and germination protein
GL331_03950	cydB	−5.742	−3.506	100	95.38	100	79.45	Metabolism	Cytochrome d ubiquinol oxidase subunit 2
GL331_03955	cydA	−4.792		100	96.52	100	82.3		Cytochrome d ubiquinol oxidase subunit 1
GL331_04110			−3.374					Unknown	Hypothetical protein
GL331_04120	wapA		−4.134			92	77.81	Cell wall	Cell wall-associated protein precursor
GL331_04135	yxiE	−3.784		100	95.53	98	78.25	Stress	Universal stress protein
GL331_04235		−3.672		100	94.18	89	75.79	Transport	Hydroxamate siderophore ABC transporter
GL331_04550			3.198	99	96.39			Transport	Transport protein (putative quinolone resistance)
GL331_04560	thiF		3.138					Metabolism	Thiazole biosynthesis adenylyltransferase
GL331_04675			−3.768	100	92.69			Unknown	PIG-L family deacetylase
GL331_05550	ctsR	−3.034		100	96.77	100	86.45	Regulation	Transcriptional repressor, protein synthesis, modification and degradation
GL331_06040	btr	−3.352		100	91.23	72	68.27	Regulation	Transcriptional activator, regulation of iron acquisition
GL331_06530	yceF		−3.108	100	96.77	100	82.43	Stress	General stress protein, manganese resistance protein
GL331_06540	yceH		−3.104	100	95.22	98	83.68		Similar to toxic anion resistance protein
GL331_06585		−3.342		100	94.65	97	81.42	Metabolism	l-Lactate dehydrogenase
GL331_07095	yczJ		−4.126	100	95.64	99	74.38	Unknown	Unknown
GL331_07100			−3.124
GL331_07310	gsiB	−3.068		100	96.6	93	89.97	Stress	General stress protein, response to glucose starvation or to water deficits
GL331_08210	pspA		−3.664	100	93.74	96	74.52	Stress	Phage shock protein A homolog, paralogous to liaH
GL331_08215	ydjG		−3.246	99	94.43	99	75.05		Unknown
GL331_08225	ydjI		−3.014	99	97.01	98	77.93		Unknown
GL331_09875	nhaX	−3.04		99	92.59	99	74.9	Stress	Universal stress protein
GL331_10225	yhzC	−3.306		100	94.87	100	85.04	Unknown	Unknown
GL331_10530	argJ		3.852	99	94.82	99	77.23	Metabolism	Biosynthesis of arginine
GL331_10535	argB		5.39	100	91.51	100	71.5
GL331_10540	argD		4.64	100	93.96	96	74.62
GL331_10545	carA		5.726	100	93.48	100	73.46
GL331_10715	cwlQ	−3.67		100	92.43	75	77.02	Cell wall	Bifunctional cell wall hydrolase
GL331_14205	iseA	−5.102		100	93.19	100	72	Cell wall	Cell wall endopeptidases and cell separation inhibitor
GL331_15495	sigX		−3.024	100	97.44	99	87.18	Sigma factor	RNA polymerase sigma factor
GL331_15575	ribH		3.352	100	95.91	100	81.29	Metabolism	Riboflavin biosynthesis
GL331_15580	ribA		3.946	100	94.57	100	78.11
GL331_15585	ribE		3.896	100	94.29	100	74.88
GL331_15590	ribD		4.102	100	94.44	99	76.73
GL331_15930	loaP	−3.848						Regulation	Antiterminator involved in regulation of polyketide synthesis
GL331_16515	pstBB		−5.384	99	92.7	93	73.36	Metabolism, transport	High-affinity phosphate uptake, phosphate ABC transporter
GL331_16520	pstBA		−4.924	100	92.32	89	77
GL331_16525	pstA		−4.038	100	94.8	99	79.07
GL331_17335			−5.61	100	89.17	48	75.86	Unknown	Unknown
GL331_17345	safA		−4.26	99	89.73	42	76.04	Sporulation	Major organizer of the inner spore coat
GL331_17895	pftB	−3.294		100	95.03	100	81.73	Metabolism, transport	Pyruvate transporter
GL331_17900	pftA	−3.958		100	97.28	83	79.89
GL331_18085	ytzJ	−3.29		100	98.96	100	84.38	Unknown	Unknown
GL331_18115	argH		5.002	100	95.06	99	83.98	Metabolism	Biosynthesis of arginine
GL331_18120	argG		5.144	100	95.3	100	81.77

^aQC, query cover; ID, identity.