Table 1

Genes differentially expressed in S. lividans adpA mutant at early stationary phase in YEME mediuma
S. coelicolor geneb S. lividans genec Other gene namesd Annotated functionb Fce Class or metabolismf
SCO0382 SLI0340 UDP-glucose/GDP-mannose family dehydrogenase 0.491 Secondary (s. m.)
SCO0383 SLI0341 Hypothetical protein SCF62.09 0.527 Secondary (s. m.)
SCO0384 SLI0342 Putative membrane protein 0.611 Secondary (s. m.)
SCO0391 SLI0349 Putative transferase 0.613 Secondary (s. m.)
SCO0392 SLI0350 Putative methyltransferase 0.606 Secondary (s. m.)
SCO0394 SLI0352 Hypothetical protein SCF62.20 0.518 Secondary (s. m.)
SCO0396 SLI0354 Hypothetical protein SCF62.22 0.454 Secondary (s. m.)
SCO0397 SLI0355 Putative integral membrane protein 0.312 Secondary (s. m.)
SCO0399 SLI0357 Putative membrane protein 0.532 Secondary (s. m.)
SCO0494 SLI0454 cchF Putative iron-siderophore binding lipoprotein 0.615 Secondary (s. m.)
SCO0496 SLI0456 cchD Putative iron-siderophore permease transmembrane protein 0.505 Secondary (s. m.)
SCO0497 SLI0457 cchC Putative iron-siderophore permease transmembrane protein 0.492 Secondary (s. m.)
SCO0498 SLI0458* cchB Putative peptide monooxygenase 0.336 Secondary (s. m.)
SCO0499 SLI0459* cchA Putative formyltransferase 0.374 Secondary (s. m.)
SCO0762 SLI0743 sti1, sgiA Protease inhibitor precursor 0.124 (m. m.)
SCO0773 SLI0754 soyB2 Putative ferredoxin, Fdx4 0.098 Electron transport (s. m.)
SCO0774 SLI0755* Putative cytochrome P450, CYP105D5 0.075 Electron transport (s. m.)
SCO0775 SLI0756* Conserved hypothetical protein 0.424 Unknown function
SCO1630-28 SLI1934-32 rarABC, cvnABC9 Putative integral membrane protein ± 0.43 Cell envelope
SCO1674 SLI1979 chpC Putative secreted protein 0.564 Cell envelope
SCO1675 SLI1980 chpH Putative small membrane protein 0.237 Cell envelope
SCO1800 SLI2108 chpE Putative small secreted protein 0.256 Cell envelope
SCO2780 SLI3127 desE Putative secreted protein 1.757 Cell envelope
SCO2792 SLI3139 bldH, adpA araC-family transcriptional regulator 0.383 Regulation
SCO2793 SLI3140 ornA Oligoribonuclease 1.966 (m. m.)
SCO3202 SLI3556 hrdD RNA polymerase principal sigma factor 2.499 Regulation
SCO3323 SLI3667 bldN, adsA Putative RNA polymerase sigma factor 0.389 Regulation
SCO3579 SLI3822 wblA Putative regulatory protein 0.310 Regulation
SCO3945 SLI4193 cydA Putative cytochrome oxidase subunit I 3.386 Electron transport (s. m.)
SCO3946 SLI4194 cydB Putative cytochrome oxidase subunit II 3.594 Electron transport (s. m.)
SCO4114 SLI4345 Sporulation associated protein 0.487 Cell envelope
SCO5240 SLI5531 wblE Hypothetical protein 2.246 Unknown function
SCO5862-63 SLI6134-35 cutRS Two-component regulator/sensor ± 1.82 Regulation
SCO6197 SLI6586* Putative secreted protein 0.147 Cell envelope
SCO6198 SLI6587* Putative secreted protein 0.618 Cell envelope
SCO6685 SLI7029* ramR, amfR Putative two-component system response regulator 0.624 Regulation
SCO7400-398 SLI7619-17 cdtCBA Putative ABC-transport protein ± 1.75 Cell process
SCO7657 SLI7885* hyaS Putative secreted protein 0.033 Cell envelope
SCO7658 detected Hypothetical protein SC10F4.31 0.103 Unknown function

aGene expression in the S. lividans adpA mutant was compared to that in the wild-type, using S. coelicolor microarrays. Table 1 shows a selected subset of the genes (see Additional file 2: Table S2 for the complete list). The genes presented here were further studied or are discussed in the text because of their role in Streptomyces primary or secondary metabolism [1,6,17].

bGene names for S. coelicolor (SCO) and S. lividans (SLI) and annotated function are from the StrepDB database [7].

cS. coelicolor microarrays were used for transcriptome analysis of the S. lividans adpA mutant (the complete microarray data set is presented in Additional file 2: Table S2). The S. lividans genome sequence was recently made available [24] and SLI ortholog gene numbers were identified as SCO gene orthologs with StrepDB database [7]. The expression of genes shown in bold was analysed by qRT-PCR. Intergenic DNA regions between genes labelled with asterisks were analyzed by EMSA (Figure 2). A SCO7658-orthologous sequence (98% nucleotide identity according to BLAST) was detected in S. lividans, downstream from hyaS, but it was not annotated as a S. lividans coding DNA sequence (CDS). However our microarray data suggest that this sequence is indeed a CDS or alternatively that the S. lividans hyaS CDS is longer than annotated.

dSCO genes and their S. griseus orthologs studied and described under another name found on StrepDB database [7] or see “References”.

eFold change (Fc) in gene expression in the S. lividans adpA mutant with respect to the parental strain with P-value < 0.05, as calculated by Student’s t-test applying the Benjamini and Hochberg multiple testing correction. ± indicates average Fc of some gene operons (see Additional file 2: Table S2 for details).

fFrom a protein classification scheme for the S. coelicolor genome available from the Welcome Trust Sanger Institute database [37]: macromolecule metabolism (m. m.), small molecule metabolism (s. m.).

Guyet et al.

Guyet et al. BMC Microbiology 2014 14:81   doi:10.1186/1471-2180-14-81

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