TABLE 1.

Selected upregulated genes under cadmium stress^a

Gene function and N. europaea locus tag	Gene name	Description	Fold change	P value (<0.05)
Mercury resistance pathway
NE0838	merD*	Bacterial regulatory protein (MerR family)	107.4	1.9 × 10−5
NE0839	merA*	Mercuric reductase	296.7	9.1 × 10−6
NE0840	merC*	Putative mercury transport protein	171.8	9.2 × 10−5
NE0841	merP*	Mercury scavenger protein	438.6	9.6 × 10−7
NE0842	merT*	Mercuric transport protein	370.3	4.8 × 10−5
Inorganic ion transport mechanism, NE0852	yvgQ	Nitrite and sulfite reductase	2.0	2.1 × 10−3
Efflux pump, NE1640	czcC	Outer membrane efflux protein	2.4	1.4 × 10−3
Oxidative stress, NE1034	trxA	Thioredoxin domain-containing protein	2.1	2.6 × 10−2
ABC transporter, NE1899*		ATPase component ABC-type transport system	2.4	2.5 × 10−3
Coenzyme metabolism
NE0856		Flavin adenine dinucleotide biosynthesis	2.0	4.9 × 10−3
NE0634	cobO	Cobalamine biosynthesis	2.7	2.8 × 10−4
NE0636		Outer membrane cobalamin receptor protein	2.0	2.6 × 10−4
Posttranslational modification, protein turnover, chaperones
NE0221		Organic radical activating enzymes	2.1	3.3 × 10−4
NE2206	ppiD	Peptidyl-prolyl isomerase	2.0	8.0 × 10−3
Cell envelope biosynthesis
NE0378		Sugar transferases involved in lipopolysaccharide synthesis	2.1	4.7 × 10−4
NE2279	yccZ	Periplasmic protein involved in polysaccharide export	2.0	2.6 × 10−4
Translation, ribosomal structure, biogenesis
NE2072	gatA	Amidase:glutamyl-tRNA (Gln), amidotransferase A subunit	2.9	3.0 × 10−4
NE2073	gatB	GatB:glutamyl-tRNA(Gln) amidotransferase, B subunit	2.1	4.7 × 10−4
NE0389	rnpA*	RNase P protein component	2.4	2.6 × 10−4
NE1457		Ribonucleases G and E	2.4	9.2 × 10−5
NE2363	glnS	Glutamyl- and glutaminyl-tRNA synthetases	2.1	3.3 × 10−4
DNA replication, recombination, repair
NE0835	tnpA	Transposase and inactivated derivatives TnpA family	25.5	9.1 × 10−6
NE0836	tnpR	Site-specific recombinase DNA	36.7	3.0 × 10−6
NE0837*		Domain of unknown function 2	157.7	1.4 × 10−5
NE2207	hupB	Bacterial histone-like DNA binding protein	2.1	2.5 × 10−5
Transcription
NE2324	rnc	Double-stranded-RNA-specific RNase	2.4	1.4 × 10−4
NE1035		Transcription termination factor	2.6	2.5 × 10−3
NE0854	cysB	Transcriptional regulator	2.2	5.0 × 10−3
NE0951		Predicted transcriptional regulators (MerR family)	2.0	1.2 × 10−3
Amino acid transport and metabolism
NE1005	argB	Acetylglutamate kinase	2.7	3.4 × 10−4
NE0872	hisD	Histidinol dehydrogenase	2.1	5.0 × 10−3
Nucleotide transport and metabolism, NE0277		XTP pyrophosphatase	2.2	1.4 × 10−3
Carbohydrate transport and metabolism, NE1691		Phosphogluconolactonase/glucosamine-6-phosphate isomerase/deaminase	3.8	6.2 × 10−4
Fatty acid biosynthesis, NE1646		Fatty acid synthesis	2.1	3.1 × 10−4
Signal transduction mechanism, NE0848		Phosphoglycerate mutase family	2.1	3.1 × 10−4
Others
NE1176*		Peptidoglycan binding	2.6	3.0 × 10−4
NE0090		Predicted ATPase	2.0	2.6 × 10−4
NE2325		Transmembrane protein	2.4	5.1 × 10−5
NE2326	lepB	Signal peptidase I	2.0	3.0 × 10−4
NE0218	tolB	Periplasmic component of the Tol biopolymer transport system	2.0	5.3 × 10−4

^aCommonly upregulated genes under Cd²⁺ and Zn²⁺ treatment are indicated by an asterisk.