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Table 3 Genes directly adjacent to peaks identified in ChIP-chip analysis

From: Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes

Gene ID

S. coelicolor homologue

Annotation

Fold change in Transcript level at T30 in glnR strain

MEME-Identifed GlnR concensus sites

Sven_1863

SCO2198

GSI

-1.2

TT AAC TTCGACG AAAC

GT CA TGCTTGAG AAA T

Sven_1874

SCO2210

GSII

-291.6

GT AAC ACGGGGTT CAC

G CAAC CGACGGG AAA T

Sven_7046

n/a

NRPS cluster

1.1

G AAAC ACGGGCG AAAC

Sven_5517

SCO5842

Putative acetyltransferase

1.4

n/a

Sven_6731

SCO5931

Xylanase

-1.5

G AAAC ATCTTCG AAAC

Sven_5279

SCO5583

AmtB

-624.7

GT CAC GGCTCCG AAAC TT CAC GGTCGCGT AAC

Sven_4770

n/a

Unknown

-1.1

TT AAC GCGCAGG CAAC

Sven_3917/3918

SCO4159/4160

GlnR/putative hydrolase

(n/a)/30.7

TT CA TCCATCCGT AAC

Sven_6152/6153

n/a

ATP-cassette/cytochrome P450

1.0/-1.2

GT TAC CCCCACGT AAC

GT TAC CGTCGGGT CAC

GT AAC CGGTCGGT AA G

GT GAC CCGACGGT AAC

Sven_6199/6200

n/a

NRPS cluster

1.7/3.2

TT CAC TCCGGCG AAAC

GT GAC CGCTGAGT AGC

TT GA TCTCCTGGT AA A

Sven_2720

SCO2958

Fused RR/uroporphrinogen III synthase

-13.7

n/a

Sven_2830

n/a

β-glucan synthesis

-1.4

n/a

Sven_0629/0630

SCO6598/0545

LacI family repressor/secreted protein

2.5/1.5

G ATAC AGGGGGG AAAC

Sven_0867

SCO1293

N-acetyl glutamate synthase

-9.1

TT AAC CCGTCAGT CAC

Sven_1634

SCO2008

Branched chain amino acid binding protein

-1.3

AT AAC AAGACAGTCAC

Sven_1677

SCO2026

Glutamate synthase

-1.1

GT AAC CTGCACG AAA T

Sven_5967

SCO3051

FadE acetyl CoA dehydrogenase

-1.3

G ACAC CCCGAGTT AAC

Sven_6632

SCO5685

Putative sugar hydrolase

1.4

GT TA AGTGAACGT CAC

Sven_0035

 

Secreted protein

-1.2

GT GAC GCCGAGGT TAC

Sven_2895

SCO3092

Fragment of NADH dehydrogenase

1

TT CAC AAGGGGTGAAC

Sven_2285

SCO4892

Transcriptional regulator

1.1

G AAAC ACCCTGGT AAC

Sven_6163

n/a

Unknown

-1.6

n/a

Sven_2694

SCO2937

Transcriptional regulator

-1.4

n/a

Sven_0835

SCO1236

UreA

-2.5

TT AAC GAGCCGG AAA A

Sven_1338/1339

SCO1721/n/a

Probable serine/threonine protein kinase

1.6/-1.4

G ATAC ACGGGTGT CAC

Sven_1860

SCO2195

Unknown

-4.5

GT CAC GCCCTGGT AAC

Sven_6307

SCO6473

Crotonyl-CoA reductase

-1.7

n/a

Sven_5972/5973

n/a

JadR2/JadR1 (and small orf inbetween)

1.1/-1.7

TT AA TGGCGGCGT CAC TT GAC CACTTCTT GAC TT GAC ACGGAGTT GAC GT CA ACTCCGTGT CA A

   Sven_0812

SCO2423

Secreted protein

1.3

GT TTC CCGCAAGT AAC

Sven_1894/1895

SCO2231/2232

Maltose binding protein/transcriptional repressor

1.1/1.2

G ACAC GCGGATGT AAC

   Sven_3785

SCO4034

RNA polymerase sigma factor N

-1

n/a

   Sven_4759

n/a

Putative peptide transport system secreted peptide-binding protein

1.6

n/a

   Sven_1354

SCO1735

Probable secreted lipase

1.3

TT TAC CGACGCGT AAC GT CAC GCCTTCAT GAC

Sven_6299/6300

n/a/SCO6803

Epimerase/acetyl transferase

1.9/-6.1

TT CAC GTGCCCG AAAC

   Sven_7354

SCO7012

Putative binding protein dependent transport protein permease

-3.7

n/a

   Sven_7089

n/a

Assimilatory nitrate reductase

-1.8

GT GAC ACAGGTGT AAC

  1. Peaks were called as present when two or more consecutive probe signals were greater than 2.5 standard deviations above the mean. Duplicate biological experiments were performed for each time point, with independent hybridisations. Peaks listed were present in at least two independent samples. Sections of sequences in bold and underlined are those that match the proposed GlnR consensus sequence.
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BMC Genomics

ISSN: 1471-2164

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