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Table 1 Genes differentially expressed in S. lividans adpA mutant at early stationary phase in YEME medium a

From: Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism

S. coelicolorgeneb

S. lividansgenec

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

  1. 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].
  2. bGene names for S. coelicolor (SCO) and S. lividans (SLI) and annotated function are from the StrepDB database [7].
  3. c S. 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.
  4. dSCO genes and their S. griseus orthologs studied and described under another name found on StrepDB database [7] or see “References”.
  5. 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).
  6. 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.).