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. 2016 Mar 22;17:253. doi: 10.1186/s12864-016-2387-x

Table 3.

Top-35 upregulated genes under free-living TSB conditions in the ∆fabR mutant versus the wildtype

Rankinga IDb Nameb Functionb Folda Processb
1 STM2378 fabB 3-Oxoacyl-[acyl-carrier-protein] synthase I 3.14 Fatty acid metabolism
6 STM3982 fadA β-subunit of the fatty acid-oxidizing multi-enzyme complex 2.26
8 STM3983 fadB α-subunit of the fatty acid-oxidizing multi-enzyme complex 2.16
19 STM0309 yafH/fadE Acyl-CoA dehydrogenase 1.71
34 STM0454 ybaW/fadM Long-chain acyl-CoA thioesterase III 1.49
35 STM1067 fabA D-3-hydroxydecanoyl-(acyl carrier-protein) 1.48
2 STM3049 yqfA Putative hemolysin 2.73 Membrane-related
31 STM1254 Putative lipoprotein 1.51
3 STM4078 yneB/lsrF Putative fructose 1-6-phosphate aldolase 2.60 AI-2 metabolism
5 STM4079 yneC/lsrG Isomerase for processing of phospho-AI-2 2.49
7 STM4080 lsrE Putative ribulose-5-phosphate 3-epimerase 2.24
10 STM4077 yneA/lsrB ABC transport protein, solute-binding component 2.13
12 STM4071 Hypothetical protein 2.02
13 STM4072 ydeV/lsrK Sugar kinase 1.87
17 STM4076 ydeZ/lsrD ABC transporter, membrane component 1.75
21 STM4074 ego/lsrA ABC transporter ATP-binding protein 1.66
23 STM4075 ydeY/lsrC ABC transporter permease protein 1.64
4 STM4184 aceA Isocitrate lyase 2.50 Glyoxylate metabolism
11 STM4183 aceB Malate synthase A 2.07
14 STM4185 aceK Isocitrate dehydrogenase kinase/phosphatase 1.86
9 STM3195 ribB 3,4-Dihydroxy-2-butanone 4-phosphate synthase 2.14 Riboflavin metabolism
15 STM2935 cysD ATP sulphurylase (ATP:sulphate adenyltransferase) 1.79 Sulphur metabolism
16 STM3304 rplU 50S ribosomal subunit protein L21 1.78 Ribosomal protein synthesis and modification
22 STM3303 rpmA 50S ribosomal subunit protein L27 1.65
26 STM3209 rpsU 30S ribosomal subunit protein S21 1.62
27 STM3345 rplM 50S ribosomal subunit protein L13 1.61
30 STM3429 rplX 50S ribosomal subunit protein L24 1.51
18 STM2970 sdaC Putative serine transporter 1.72 Transport processes
20 STM1530 Putative outer membrane protein (truncation) 1.68
28 STM2444 cysP Thiosulphate-binding protein precursor 1.55
32 STM1473 ompN Outer membrane protein 1.51
33 STM1452 ydgR Putative proton/oligopeptide symporter 1.49
24 STM0307 Putative secreted protein 1.64 Pathogenicity
25 STM0447 tig Trigger factor 1.63 Protein folding
29 STM4459 pyrI Aspartate carbamoyltransferase regulatory subunit 1.52 Pyrimidine metabolism

aRank (#) depends on the fold change with 1 being the gene with the greatest fold induction and 35 the one with the 35th fold induction. Fold change represents the differential expression of the gene in the isogenic fabR deletion mutant (CMPG5624) according to the wildtype under free-living TSB conditions, as detected by t-test with multiple testing correction. b STM numbers, gene names and gene functions are taken from the fully annotated S. Typhimurium LT2 genome (NCBI Refseq NC_003197) [86] and adapted according to recent literature (e.g. functions of the lsr genes were taken from [36, 87]). Results are sorted according to the functional classes (process) they belong to and with descending fold change in each class