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. 2007 Jan 12;189(7):2873–2885. doi: 10.1128/JB.01615-06

TABLE 3.

Transcripts reduced or enhanced more than twofold between J2670 (whiI+) and J2676 (ΔwhiI) at 48 h and/or 72 h of growth

Open reading framea,f Genea Producta Time of growth (h)b Normalized intensity ratioc
Transcriptional ratiod
J2670 (whiI+) J2671 (D27A) J2673 (D69E) J2676 (ΔwhiI) J2670/ J2676 J2670/ J2671
Gene expression reduced only in whiI null mutantd
    SCO0323* Unknown 48 4.3 4.0 6.8 0.8 5.4 1.1
    SCO2718* rdlA Secreted protein 48 5.5 7.1 11.2 1.3 4.2 0.8
    SCO0834 Unknown 72 2.1 1.5 2.2 1.0 2.1 1.4
    SCO6375* Secreted protein 72 1.6 1.1 3.2 0.6 2.7 1.4
    SCO6744 Unknown 72 1.4 1.2 1.5 0.6 2.3 1.2
Gene expression reduced in both whiI null and D27A mutantsd
    SCO4104 Integral membrane protein 48 2.0 1.3 1.5 1.0 2.0 1.5
    SCO4393 Phosphoheptose isomerase 48 3.6 2.0 2.5 1.6 2.3 1.8
    SCO4761 groES 10-kDa chaperonin Cpn10 48 3.9 2.3 2.5 1.8 2.2 1.7
    SCO5315* whiE Polyketide cyclase 48 2.2 1.0 3.0 0.7 3.1 2.2
    SCO6197 Secreted protein 48 1.2 0.6 1.1 0.6 2.0 2.0
    SCO0681 Ferredoxin/ferredoxin-NADP reductase 72 3.7 2.4 2.2 1.5 2.5 1.5
    SCO0682 Unknown 72 3.6 2.2 2.7 1.6 2.3 1.6
    SCO1366* PadR-like transcriptional regulator 72 7.2 3.2 3.5 2.4 3.0 2.3
    SCO1367 ABC transport system ATP-binding protein 72 2.6 1.2 2.7 0.7 3.7 2.2
    SCO2008* Branched-chain amino acid binding protein 72 6.4 2.4 4.4 2.1 3.0 2.7
    SCO2009 Branched-chain amino acid transport permease 72 1.7 1.0 1.3 0.8 2.1 1.7
    SCO2162 Quinolinate synthetase 72 2.5 0.7 1.8 0.8 3.1 3.6
    SCO3899 myo-Inositol-1-phosphate synthase 72 3.0 1.0 1.8 1.3 2.3 3.0
    SCO3900 Conserved hypothetical protein 72 4.0 1.4 2.7 1.7 2.4 2.9
    SCO7510 cypH Peptidyl-prolyl cis-trans isomerase 72 3.6 1.7 4.2 1.5 2.4 2.1
    SCO7511 gap-2 Glyceraldehyde 3-phosphate dehydrogenase 72 3.6 1.7 4.3 1.7 2.1 2.1
Gene expression reduced in whiI null mutant, with indeterminate response to other whiI allelese
    SCO4172* Membrane protein 48 1.7 0.7 0.7 0.4 4.3 2.4
    SCO4174* Integral membrane protein 48 1.3 0.4 0.7 0.3 4.3 3.3
Gene expression enhanced only in whiI null mutantd
    SCO4187 Membrane protein 48 1.0 1.1 1.2 2.0 2.0 1.8
    SCO5583 amtB Ammonium transporter 48 1.3 0.8 0.8 3.2 2.5 4.0
    SCO5584 glnK Nitrogen regulatory protein P-II 48 1.2 0.9 0.8 3.6 3.0 4.0
    SCO3299 rtcB Unknown 72 0.6 0.5 0.6 1.3 2.2 2.6
    SCO4002* Secreted protein 72 1.2 2.5 2.0 4.5 3.8 1.8
    SCO5189* Unknown 72 6.3 10.2 6.9 20.5 3.3 2.0
    SCO5190* wblC DNA-binding protein 72 3.8 4.6 3.7 10.9 2.9 2.4
    SCO5191 Unknown 72 6.9 10.0 5.5 23.5 3.4 2.4
    SCO7211 Secreted glycosyl hydrolase 72 0.6 1.0 1.0 1.7 2.8 1.7
Gene expression enhanced in both whiI null and D27A mutants
    SCO5249* Cyclic nucleotide-binding protein 48 2.0 2.9 2.0 4.4 2.2 1.5
    SCO0140* MerR family transcriptional regulator 72 0.5 1.3 0.6 1.9 3.8 1.5
    SCO1648 arc AAA ATPase 72 2.5 5.2 3.0 5.0 2.0 1.0
    SCO2922 Membrane protein 72 1.2 3.4 0.8 2.4 2.0 0.7
    SCO3123 prsA2 Ribose-phosphate pyrophosphokinase 72 1.0 1.4 1.2 2.1 2.1 1.5
    SCO3660 Integrase/recombinase 72 0.5 0.8 0.5 1.0 2.0 1.3
    SCO4602 nuoH2 NADH dehydrogenase subunit 72 1.0 2.2 1.2 2.6 2.6 1.2
    SCO4605 nuoK2 NADH dehydrogenase subunit 72 2.4 4.8 3.1 7.0 2.9 1.5
    SCO5124* Hypothetical protein 72 2.6 6.5 2.8 6.9 2.6 1.1
    SCO5125 Chitinase promoter binding protein 1 72 1.8 3.7 2.0 3.7 2.1 1.0
    SCO5269 Unknown 72 0.9 1.9 0.9 1.8 2.0 0.9
    SCO5576* acy Acylphosphatase 72 1.6 4.8 2.0 4.5 2.8 0.9
Gene expression enhanced in whiI null mutant, with indeterminate response to other whiI allelese
    SCO1201 Reductase 72 1.0 1.7 1.5 2.0 2.0 1.2
a

The SCO numbers were taken from EMBL database accession no. AL645882. The possible function of each product was either known from previous work or was based on the genome annotation and further information given in the ScoDB database (http://streptomyces.org.uk). Genes in bold are also represented in Streptomyces avermitilis, based on reciprocal hits in BLAST searches.

b

Earliest culture age showing whiI influence.

c

The normalization process was performed by the per spot and per chip intensity-dependent (Lowess) normalization method, which performs an intensity-dependent (Lowess) normalization and divides the signal channel (Cy3 channel for cDNA) by the control channel (Cy5 channel for genomic DNA). The values in the table were averaged from all the biological and experimental replicates.

d

A J2670/J2676 ratio of >2 was the threshold for reduced expression in the whiI null mutant. If the J2670/J2671 ratio was <1.5, then the effect was considered whiI null specific. A J2676/J2670 ratio of >2 was the threshold for enhanced expression in the whiI null mutant, and if the J2676/J2671 ratio was >1.5, then the effect was considered whiI null specific.

e

For SCO4172 and -4174, expression in J2673 was not consistent with that in J2670 (wild type); for SCO1201, expression in both J2671 and J2673 was intermediate between that in J2670 and J2676.

f

Genes indicated with asterisks passed all filters during the screen for changes in expression by GeneSpring, whereas the others had differences in at least four of five comparisons (five wild-type replicates, including replicate cultures and experiments, compared with three null mutant individual samples).