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Table 1 Genes differentially expressed in the transcriptome data as a result of bldA mutation1

From: New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures

Gene2 Annotated function3 P-value4 Mean pfp value5 Up/down in bldA6 Potential reason for absence in proteomic data7
SCO0072 possible secreted protein N/A 0.055* down Secreted
SCO0247 conserved hypothetical protein 3.29E-06 N/A down Predicted 1 transmembrane domain
SCO0248 hypothetical protein 1.76E-05 N/A down Predicted pI = 11.6
SCO0297 secreted protein 8.25E-05 0.033 down Secreted
SCO0472 possible secreted protein N/A 0.076* down Secreted
SCO0499 possible formyltransferase 9.76E-04 N/A down  
SCO0759 hypothetical protein 0.000976 N/A down Predicted 1 transmembrane domain
SCO0760 probable methyltransferase 0.000796 0.083 down Predicted pI = 10.9
SCO0762 protease inhibitor precursor 0.0262 0.012 down Secreted
SCO0990 integral membrane protein 7.72E-03 N/A down Predicted 7 transmembrane domains
SCO0991 conserved hypothetical protein 0.00772 N/A down Predicted transmembrane domain
SCO0994 integral membrane protein 0.0317 N/A down Predicted 9 transmembrane domains
SCO0995 probable methyltransferase 9.76E-04 N/A down Predicted 2 transmembrane domains
SCO1089 unknown N/A 0* up None
SCO1815 probable 3-oxacyl-(acyl-carrier-protein) reductase N/A 0.084* down Predicted 2 transmembrane domains
SCO1845 possible low-affinity phosphate transport protein N/A 0* up Predicted 10 transmembrane domains
SCO1968 probable secreted hydrolase N/A 0* down Secreted
SCO2435 hypothetical protein 0.00589 N/A down None
SCO3088 hypothetical protein 0.000415 N/A up Predicted pI = 9.7, mwt = 8377 Da
SCO3285 large gly/ala rich protein 7.72E-03 N/A up  
SCO3286 secreted protein 0.00772 0.05 up Secreted
SCO3428 50S ribosomal protein N/A 0.082* down Predicted pI = 10.8, mwt = 6416 Da
SCO3608 hypothetical protein N/A 0.1* up Predicted 3 transmembrane domains
SCO3717 probable cation transport system component N/A 0.068 up Predicted 7 transmembrane domains
SCO3718 probable cation transport system component N/A 0 up Predicted 11 transmembrane domains
SCO4131 integral membrane protein 0.0389 N/A down Predicted 2 transmembrane domains
SCO4173 unknown N/A 0.088* down Predicted 1 transmembrane domains
SCO4174 possible integral membrane protein N/A 0.088* down Predicted 1 transmembrane domains; predicted pI = 11.0
SCO4187 putative membrane protein 0.0404 0.1 down Predicted pI = 9.5, mwt = 6268 Da
SCO4246 hypothetical protein 5.89E-03 N/A down Predicted pI = 9.7
SCO4252 hypothetical protein 3.29E-06 0.017 down  
SCO4253 conserved hypothetical protein 5.93E-05 5.66E-03 down  
SCO4256 possible hydrolytic protein 0.00772 N/A down None
SCO4262 hypothetical protein 0.000976 0.083 down Predicted pI = 11.7, mwt = 12884 Da
SCO4295 Cold shock protein scoF4 0.00126 0.053 down Predicted mwt = 7387 Da
SCO4442 hypothetical protein 0.00608 0.09* down Predicted mwt = 6484 Da
SCO4653 50S ribosomal protein N/A 0.097* down None
SCO4661 elongation factor G N/A 0.088* down None
SCO4677 possible regulatory protein N/A 0.038* down  
SCO4703 50S ribosomal protein N/A 0.076* down Predicted pI = 10.0
SCO4704 50S ribosomal protein N/A 0.044* down Predicted pI = 10.6
SCO4705 50S ribosomal protein N/A 0.087* down Predicted pI = 11.3
SCO4706 30S ribosomal protein N/A 0.095* down Predicted pI = 10.8
SCO4707 50S ribosomal protein N/A 0.091* down Predicted pI = 10.2
SCO4712 50S ribosomal protein N/A 0.087* down Predicted pI = 10.2
SCO4713 50S ribosomal protein N/A 0.076* down Predicted pI = 10.3
SCO4714 50S ribosomal protein N/A 0.088* down Predicted pI = 9.6
SCO4716 30S ribosomal protein N/A 0.077* down Predicted pI = 9.6
SCO4717 50S ribosomal protein N/A 0.043* down Predicted pI = 9.8
SCO4718 50S ribosomal protein N/A 0.074* down Predicted pI = 10.6
SCO4719 30S ribosomal protein N/A 0.071* down Predicted pI = 10.1
SCO4994 hypothetical protein 0.0136 N/A down Predicted 1 transmembrane domain
SCO5013 secreted protein 0.0479 N/A down Secreted
SCO5073 possible oxidoreductase 4.79E-02 0* down  
SCO5074 possible dehydratase N/A 0* down Predicted pI = 8.6; secreted
SCO5079 conserved hypothetical protein N/A 0* down  
SCO5123 membrane protein 0.000415 N/A down Predicted pI = 8.2, mwt = 6622 Da
SCO5124 hypothetical protein 0.00512 N/A down Predicted pI = 7.12, mwt = 7054 Da
SCO5125 hypothetical protein 0.000788 N/A down None
SCO5166 putative helicase 5.12E-03 N/A up Predicted pI = 9.5
SCO5225 ribonucleotide-diphosphate reductase small chain N/A 0.007* up Predicted 2 transmembrane domains
SCO5624 30S ribosomal protein S2 N/A 0.089* down None
SCO5649 unknown N/A 0.1* down None
SCO6197 secreted protein 3.29E-06 0.063 down Secreted
SCO6198 secreted protein 8.09E-03 N/A down Secreted
SCO6346 hypothetical protein 6.08E-03 N/A down None
SCO6362 Probable two-component sensor 0.00589 N/A down Predicted 6 transmembrane domains; pI = 10.43
SCO6637 hypothetical protein 0.000788 N/A down  
SCO6638 hypothetical protein 0.000415 N/A down  
SCO6808 possible ArsR-family regulator 0.00219 N/A down Predicted mwt = 13271 Da
SCO6958 putative membrane protein 0.036 N/A up Predicted 3 transmembrane domains; pI= 8.7; mwt = 11304 Da
SCO7510 peptidyl-prolyl cis-trans isomerase N/A 0.01* up None
SCO7511 glyceraldehyde 3-phosphate dehydrogenase N/A 0* up  
SCO7657 secreted protein 1.76E-05 0.066* down Secreted
  1. 1 presented in more detail in Additional File 8.
  2. 2 genes in bold were also found to be different in the proteome analysis detailed in Additional File 5. Underlined genes were more highly expressed during all stages of growth in M600 relative to the bldA mutant. Q-RT-PCR was performed with the 16 RNA samples from replicate 3 time courses, using specific primers and probes covering 50–150 bp, for each of the following genes: SCO4295, SCO5013, SCO6808, and SCO7657; five genes up-regulated in the bldA mutant – SCO3088, SCO3285, SCO3286, SCO5166, SCO6958; the TTA-containing gene SCO6638; and the ribosomal protein genes SCO4648, SCO4702, SCO4705, SCO4717. See Additional File 2 for these results.
  3. 3from ScoDB [55]
  4. 4 from a Welch t-test applying the Benjamini and Hochberg multiple testing correction
  5. 5 average pfp (Probability of False Prediction) values from time-point comparisons outputted from Rank Product Analysis. * denotes those genes found differentially expressed at one time point only.
  6. 6determined from a visual inspection of expression profiles in Additional File 1
  7. 7 pI and Mwt values from ScoDB [55]: transmembrane domain predictions from TmPred [56]