Table 3.

Selected differentially downregulated genes in the transcriptome

Genea	Description	Expression ratio	Log2 ratio
DET0114	ABC transporter, substrate-binding protein, putative	−2.4	−1.3
DET0115	ABC transporter, permease protein, putative	−2.3	−1.2
DET0183	ATP-dependent RNA helicase, DEAD DEAH-box family	−3.4	−1.8
DET0370	Membrane-associated zinc metalloprotease, putative	−2.3	−1.2
DET0371	1-Deoxy-d-xylulose 5-phosphate reductoisomerase	−2.0	−1.0
DET0372	Phosphatidate cytidylyltransferase	−2.1	−1.1
DET0417	Amino acid ABC transporter, ATP-binding protein	−2.2	−1.1
DET0418	Amino acid ABC transporter, permease protein, His Glu Gln Arg opine family	−2.1	−1.1
DET0608	Ribosomal protein-alanine acetyltransferase	−2.3	−1.2
DET0654	Cobalamin biosynthesis protein CobDb	−2.1	−1.0
DET0655	Histidinol-phosphate aminotransferase, putativeb	−2.0	−1.0
DET0716	Tyrosine recombinase XerC	−2.3	−1.2
DET0770	Transcription elongation factor GreA	−2.1	−1.1
DET0784	V-type H(+)-translocating pyrophosphatase	−2.0	−1.0
DET0838	Phosphoribosylamine-glycine ligase	−2.3	−1.2
DET0840	Adenylosuccinate lyase	−2.2	−1.1
DET0841	Phosphoribosylaminoimidazole-succinocarboxamide synthase	−2.6	−1.4
DET0844	Histidinol dehydrogenase	−2.0	−1.0
DET0964	Single-stranded-DNA-specific exonuclease RecJ	−2.4	−1.3
DET1173	FwdE family protein	−5.2	−2.4
DET1174	Fec-type ABC transporter, periplasmic iron-binding protein	−4.4	−2.1
DET1175	Fec-type ABC transporter, permease protein	−4.0	−2.0
DET1176	Fec-type ABC transporter, ATP-binding protein	−3.0	−1.6
DET1192	Signal peptidase I	−3.0	−1.6
DET1193	Orotate phosphoribosyltransferase	−2.3	−1.2
DET1194	Conserved hypothetical protein	−2.8	−1.5
DET1196	ATP-dependent DNA helicase PcrA	−2.5	−1.3
DET1199	Aspartate carbamoyltransferase	−2.3	−1.2
DET1200	Dihydroorotase, multifunctional complex type	−2.2	−1.1
DET1202	Carbamoyl-phosphate synthase, large subunit	−2.3	−1.2
DET1203	Dihydroorotate dehydrogenase, electron transfer subunit	−2.8	−1.5
DET1258	Acetylornithine aminotransferase	−2.1	−1.0
DET1259	Hypothetical protein	−3.8	−1.9
DET1389	Formamidopyrimidine-DNA glycosylase	−2.0	−1.0
DET1422	Phosphoglycerate mutase family protein	−2.2	−1.1
DET1434	Hydrogenase expression formation protein HypD	−2.1	−1.1
DET1435	Hydrogenase expression formation protein HypE	−2.6	−1.4
DET1461	Lipoprotein, putative	−3.0	−1.6
DET1462	DNA repair protein, RadC family	−2.2	−1.2
DET1490	Peptide ABC transporter, ATP-binding protein	−2.5	−1.3
DET1491	Peptide ABC transporter, ATP-binding protein	−3.3	−1.7
DET1492	Peptide ABC transporter, permease protein	−3.1	−1.6
DET1493	Peptide ABC transporter, permease protein	−2.5	−1.3
DET1494	Peptide ABC transporter, periplasmic peptide-binding protein	−3.4	−1.8
DET1495	Conserved hypothetical protein	−2.8	−1.5
DET1502	Major facilitator family protein	−2.4	−1.3
DET1515	Conserved hypothetical protein	−2.7	−1.4
DET1557	Lipoprotein, putativec	−2.8	−1.5
DET1558	Reductive dehalogenase-anchoring protein, putativec	−2.0	−1.0
DET1568	Hypothetical protein	−5.5	−2.5

^aSelected genes with an FDR of <1% and with an expression level changed by 2-fold or greater are reported. Expression ratios were calculated by using averages from biological triplicates, and negative values indicate downregulation during FNL.

^bGene is duplicated in the genome.

^cGene is within integrated elements.