. Author manuscript; available in PMC: 2018 Mar 26.

Published in final edited form as: J Ind Microbiol Biotechnol. 2015 Feb 27;42(5):745–757. doi: 10.1007/s10295-015-1599-4

Table 5.

Genes differentially expressed in the presence of Sudan III

Function and locus tag	Gene name	COG category^a	Description of gene product	p value	Putative location	Fold change
Message storage and processing
SAUSA300_0334		K	Transcriptional regulator, MarR family	0.0402	Unknown	1.55
SAUSA300_1200	glnR	K	Glutamine synthetase repressor	0.0456	Cytoplasmic	1.73
SAUSA300_1793		L	Conserved hypothetical protein	0.0379	Cytoplasmic	1.51
Cellular processes and signaling
SAUSA300_1855	sgtB	M	Monofunctional glycosyltransferase	0.0325	Cytoplasmic membrane	1.53
SAUSA300_2314		M	Conserved hypothetical protein	0.0345	Unknown	1.51
SAUSA300_1512	pbp3	M	Penicillin-binding protein 3	0.0195	Cytoplasmic membrane	1.94
SAUSA300_0394		MG	FAD/NAD(P)-binding Rossmann fold Superfamily	0.0185	Cytoplasmic	−1.98
SAUSA300_0867	spsA	U	Signal peptidase IA	0.0117	Cell wall	1.65
SAUSA300_1317	msrA	O	Methionine-S-sulfoxide reductase	0.0347	Unknown	−1.55
Metabolism
SAUSA300_0170		C	Aldehyde dehydrogenase	0.0329	Cytoplasmic	1.88
SAUSA300_1731	pckA	C	Phosphoenolpyruvate carboxykinase (ATP)	0.0392	Cytoplasmic	2.31
SAUSA300_2329	gltT	C	Proton/sodium-glutamate symport protein	0.0412	Cytoplasmic membrane	1.67
SAUSA300_2449		G	Putative transporter	0.0347	Cytoplasmic membrane	1.53
SAUSA300_1454	zwf	G	Glucose-6-phosphate 1-dehydrogenase	0.0309	Cytoplasmic	1.52
SAUSA300_2105	mtlF	G	PTS system, mannitol specific IIBC component	0.0238	Cytoplasmic membrane	1.67
SAUSA300_0337	glpT	G	Glycerol-3-phosphate transporter	0.0458	Cytoplasmic membrane	1.90
SAUSA300_2385		E	Putative membrane protein	0.0175	Cytoplasmic membrane	2.20
SAUSA300_1231		E	Gamma-aminobutyrate permease	0.0241	Cytoplasmic membrane	1.56
SAUSA300_0864	argG	E	Argininosuccinate synthase	0.0075	Cytoplasmic	3.14
SAUSA300_2538		E	Amino acid permease family protein	0.0103	Cytoplasmic membrane	1.91
SAUSA300_1808		E	Amino acid ABC transporter,	0.0332	Cytoplasmic membrane	2.45
SAUSA300_1916		E	Aminotransferase	0.0224	Cytoplasmic	1.51
SAUSA300_0914		E	Sodium:alanine symporter family protein	0.0058	Cytoplasmic membrane	2.33
SAUSA300_2006	ilvD	EG	Dihydroxy-acid dehydratase	0.0263	Cytoplasmic	2.06
SAUSA300_1102	gmk	F	Guanylate kinase	0.0317	Cytoplasmic	2.23
SAUSA300_1476	accB	I	Acetyl-CoA carboxylase, biotin carboxyl carrier	0.0277	Cytoplasmic	2.20
SAUSA300_0229		I	Putative acyl-CoA transferase FadX	0.0003	Unknown	2.17
SAUSA300_1679	acsA	I	Acetyl-coenzyme A synthetase	0.0072	Cytoplasmic	2.18
SAUSA300_1673		I	1-acyl-sn-glycerol-3-phosphate acyl-transferases	0.0334	Cytoplasmic	1.51
SAUSA300_2176		P	ABC transporter, ATP-binding protein	0.0267	Cytoplasmic membrane	1.52
SAUSA300_1005		P	Mn²⁺/Fe²⁺ transporter, NRAMP family	0.0338	Cytoplasmic membrane	1.67
SAUSA300_1897		P	Sodium-dependent transporter	0.0399	Cytoplasmic membrane	2.16
SAUSA300_0619		P	ABC transporter, permease protein	0.0416	Cytoplasmic membrane	2.45
SAUSA300_1899		Q	Conserved hypothetical protein	0.0246	Cytoplasmic	1.52
Poorly characterized
SAUSA300_1700		R	Polysaccharide biosynthesis protein	0.0085	Cytoplasmic membrane	1.77
SAUSA300_2268		R	Sodium/bile acid symporter family	0.0351	Cytoplasmic membrane	1.61
SAUSA300_1229		R	Hydrolase, haloacid dehalogenase-like family	0.0439	Cytoplasmic	1.53
SAUSA300_1685		R	Conserved hypothetical protein	0.0459	Cytoplasmic	−1.55
SAUSA300_1364	engA	R	GTP-binding protein EngA	0.0126	Cytoplasmic membrane	2.05
SAUSA300_0013		S	Putative membrane protein	0	Cytoplasmic membrane	1.62
SAUSA300_0733		S	degV family protein	0.047	Cytoplasmic	1.67
SAUSA300_2418		S	Conserved hypothetical protein	0.0019	Cytoplasmic	−1.53
SAUSA300_0330		S	Putative transport protein SgaT	0.0309	Cytoplasmic membrane	1.84
SAUSA300_2031		S	Conserved hypothetical protein	0.0086	Cytoplasmic membrane	1.59
SAUSA300_1284		S	Conserved hypothetical protein	0.0136	Cytoplasmic	1.59
Not in COGs
SAUSA300_pUSA010001		–	Replication protein	0.0346	Cytoplasmic	1.95
SAUSA300_pUSA030001	repA	–	Replication initiator protein	0.0459	Cytoplasmic	1.87
SAUSA300_pUSA030007	ermC	–	rRNA adenine N-6-methyltransferase	0.0234	Cytoplasmic	2.02
SAUSA300_0661		–	Conserved hypothetical protein	0.0107	Cytoplasmic membrane	1.67
SAUSA300_0642		–	Conserved hypothetical protein	0.0334	Cytoplasmic membrane	1.58
SAUSA300_0681		–	Conserved hypothetical protein	0.0182	Unknown	1.61
SAUSA300_1011		–	Conserved hypothetical protein	0.034	Unknown	1.64
SAUSA300_2355		–	Putative lipoprotein	0.0158	Unknown	2.09
SAUSA300_1680	acuA	–	Acetoin utilization protein AcuA	0.0027	Cytoplasmic	2.13
SAUSA300_1461		–	Conserved hypothetical protein	0.0167	Cytoplasmic membrane	1.98
SAUSA300_1053		–	Conserved hypothetical protein	0.0061	Unknown	−1.81
SAUSA300_1055	efb	–	Fibrinogen-binding protein	0.0211	Extracellular	−1.58

– Not in COGs

The COGs functional categories are shown as follows: message and storage and processing [includes transcription (K), replication, recombination and repair (L)]. Cellular processes and signaling [includes cell wall/membrane/envelope biogenesis (M), intracellular trafficking, secretion and vesicular transport (U), post-translational modification, protein turnover, chaperones (O)]. Metabolism [includes energy production and conversion (C), carbohydrate transport and metabolism (G), amino acid transport and metabolism (E), nucleotide transport and metabolism (F), lipid transport and metabolism (I), inorganic ion transport and metabolism (P), secondary metabolites biosynthesis, transport and catabolism (Q)]. Poorly characterized (includes general function prediction only (R), function unknown (S))