The microarray data related to YmdB overexpression Linsitinib mouse were compared with the tiling array data for an RNase III mutant , in which 592 genes were affected by the absence of RNase III. Of 127 coding genes from the tiling array data, 47 are known RNase III targets and, of these, 37
were similarly regulated by YmdB and the RNase III mutant (Additional file 1: Table S3). This suggests that YmdB modulates these genes by down-regulating RNase III activity. However, 80 genes that were not previously regarded as RNase III targets also appeared to be modulated via an as yet uncharacterized YmdB function(s). When the 80 genes were classified according to the biological process in which they are involved, we Pevonedistat solubility dmso identified ten different cellular processes that were modulated by YmdB induction (Table 1). Therefore, the data indicate that YmdB, either as an RNase III regulator or by itself, participates in the regulation of multiple cellular processes within E. coli. Table 1 Classification of up- or down-regulated 80 genes when PD0332991 clinical trial YmdB was overexpressed Functions Gene No. of gene Go term ID Transport dppA, emrA, exbB, exuT, fdx, fecI, gutM, icd, mntH,
nrfA 2 , proP, srlA 2 , srlB 2 , srlE 2 , srlR, sucA 2 , sucC 2 , sucD 2 , tdcC, tolB, tolR, yhbE, ynfM 23 GO:0006810 GO:0006811 GO:0006855 GO:0006865 GO:0006099 GO:0009401 GO:0015031 GO:0015992 GO:0017038 GO:0022900 GO:0043213
GO:0055085 Transcription/replication cspB, cspG, fecI, gutM, lacI, mprA, mukF, mqsR 3 , pspB 1,2 , pspC 1,3 , relE 3 , rpoA, rpoB, rpoC, rplD, rpoE 3 , rseB, srlR, yoeB, ygiT 3 20 GO:0006260 GO:0006351 GO:0006352 GO:0006355 GO:0045892 GO:0055072 Cellular responses cspB, cspG, emrA, mprA, nusA, pspB 1,3 , pspC 1,3 , pspD 1,3 , 13 GO:0006950 GO:0009266 Methocarbamol GO:0009271 relE 3 , rplD, rpoE 3 , rseA 3 , sseA GO:0009408 GO:0009409 GO:0046677 Modification csdA, iscA, iscU, mqsR 3 , pheT, 11 GO:0006432 GO:0016226 relE 3 , srlB 2 , srlE 2 GO:0016310 GO:0090305 ydaL 3 , yfhJ, ygdK Translation mqsR 3 , pheT, rplC, rplD, rpsA, rpsJ, yhbC, relE 3 8 GO:0006412 GO:0017148 Metabolic process fabD, lacI, srlA 2 , srlB 2 , srlD 2 , srlE 2 , sucA 2 , ycjM 8 GO:0008152 Oxidation-reduction ahpC 3 , nrfA 2 , srlD 2 , sucA 2 , torZ, ygjR 6 GO:0055114 Biosynthesis fabD 1 GO:0006633 GO:0006654 GO:0008610 Cell cycle mukF 1 GO:0007049 GO:0051301 Nucleotide binding yeeZ 3 1 GO:0000166 GO:0005524 Genes 1up- (>3-fold) or 2down-(<0.5-fold) regulated by YmdB overexpression were indicated. Detailed quantitative data are shown in Additional file 1: Table S3. 3Gene is related to biofilm formation in literature, even though GO term analysis (http://www.ecocyc.org) did not classify it as such.