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Table 1 GlnR binding regions identified by ChIP-seq and corresponding gene expression fold change (wild type vs glnR deletion strain) in M. smegmatis during nitrogen limitation

From: Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis

Peak no.a Coordinatesb Peak intensityc Adjacent gene (s)d Fold change in gene expressione Gene annotation
1 501431-501471 8.4 MSMEG0427* 76.4 nirB Nitrite reductase, large subunit
2 508651-508691 42.9 MSMEG0432* 18.3 nnaR Transcriptional regulator
3 510091-510131 8.4 MSMEG0433 24.6 narK3 Nitrate extrusion protein
4 647871-647911 27.1 MSMEG0572* 263.4 Putative uncharacterised protein
5 864391-864431 6.1 MSMEG0780L* 23.0 Phosphotransferase enzyme family protein
    MSMEG0781R 8.4 Amino acid permease
6 1121631-1121671 54.3 MSMEG1052 6.3 Amino acid carrier protein
7 1142851-1142891 6.5 MSMEG1078L -3.8 Hydrolase
    MSMEG1079R* 3.4 Putative uncharacterised protein
8 1146711-1146751 71.9 MSMEG1082 277.4 Putative response regulator, LuxR family
9 1238491-1238531 19.3 MSMEG1177L 10.7 Cytosine/purines/uracil/thiamine/allantoin permease
    MSMEG1178R 3.5 Transcriptional regulator
10 1385631-1385671 6.48 MSMEG1292L* 2.4 Dehydrogenase protein
    MSMEG1293R* 4.2 Xanthine/uracil permeases family protein
11 1684231-1684271 64.6 MSMEG1597 2.8 Transcription factor WhiB
12 1832291-1832331 46.5 MSMEG1738 -13.2 Probable conserved transmembrane protein
13 1965171-1965211 19.3 MSMEG1886 No DE Fatty acid desaturase
14 2000471-2000511 10.9 MSMEG1919 No DE Transcription factor WhiB
15 2070111-2070151 9.9 MSMEG1987* 120.7 Putative uncharacterised protein
16 2081471-2081511 19.5 MSMEG1999 -2.1 Putative uncharacterised protein
17 2260871-2260911 39.9 MSMEG2183L 2.3 Conserved hypothetical protein
    MSMEG2184R* 38.8 Amino acid permease
18 2414891-2414931 67.9 MSMEG2332 10.1g Amino acid carrier protein
19 2508191-2508231 101.5 MSMEG2425* 98.8 amtB Ammonium transporter
20 2592931-2592971 18.6 MSMEG2506* -4.1 Carboxyvinyl-carboxyphosphonate phosphorylmutase
21 2608351-2608391 171.1 MSMEG2522* 165.9 Efflux ABC transporter, permease protein
22 2612531-2612571 331.2 MSMEG2526 782.4 Copper amine oxidase
23 2655531-2655571 56.3 MSMEG2570* 50.8 Xanthine/uracil permease
24 3048291-3048331 105.9 MSMEG2982* 583.8 Putative periplasmic binding protein
25 3206851-3206891 8.7 MSMEG3131L -1.44 Polypeptide: AMP-binding protein
    MSMEG3132R No DE Polypeptide: DNA-binding protein
26 3237471-3237511 6.5 MSMEG3166 No DE Enzyme: beta-lactamase
27 3471571-3471611 8.2 MSMEG3400* 228.0 Glutamyl-tRNA(Gln) amidotransferase subunit A
28 4043191-4043231 22.8 MSMEG3975 2.1 Putative regulatory protein, PucR family
29 4069251-4069291 58.9 MSMEG3995 9.7 N-carbomoyl-L-amino acid amidohydrolase
30 4070051-4070091 13.2 MSMEG3996L 8.3 hydA Dihydropyrimidinase
    MSMEG3997R 6.5 Regulatory protein, PucR family
31 4082411-4082451 77.2 MSMEG4008* 49.2 Oxidoreductase, 2OG-Fe(II) oxygenase family protein
32 4136531-4136571 7.4 MSMEG4063 No DE Polypeptide: amidohydrolase
33 4290471-4290511 8.0 MSMEG4206 115.7 Molybdopterin oxidoreductase
34 4374791-4374831 184.7 MSMEG4290 20.0 glnA Glutamine synthetase
35 4381891-4381931 49.8 MSMEG4294 12.6 glnA Glutamine synthetase, type I
36 4580191-4580231 384.4 MSMEG4501 103.3 Sodium:dicarboxylate symporter
37 4722511-4722551 17.1 MSMEG4635* 102.0 amtA Ammonium transporter
38 4726751-4726791 63.6 MSMEG4639* 57.3 Putative uncharacterised protein
39 4729431-4729471 11.1 MSMEG4643 No DE Resuscitation-promoting factor
40 4729931-4729971 34.4 MSMEG4643 No DE Resuscitation-promoting factor
41 5183411-5183451 57.5 MSMEG5084* 27.1 Glycosyl transferase, group 2 family protein
42 5440611-5440651 233.9 MSMEG5358 14.9 Acetamidase/Formamidase family protein
43 5442051-5442091 27.2 MSMEG5360* 29.1 Formate/nitrate transporter
44 5651011-5651051 18.6 MSMEG5561 1.40 HPP family protein
45 5840591-5840631 11.6 MSMEG5765 4.1 glbN Globin
46 6177591-6177631 31.6 MSMEG6116 24.8 Putative allantoicase
47 6323551-6323591 23.7 MSMEG6259 255.9 amt1 Ammonium transporter
48 6714291-6714331 16.3 MSMEG6660 8.1 Cytosine/purine/uracil/thiamine/allantoin permease
49 6747051-6747091 9.9 MSMEG6695L No DE Cytochrome P450
    MSMEG6697R No DE IS1096, tnpA protein
50 6782771-6782811 17.7 MSMEG6735* 128.3 Amino acid permease, putative
51 6865371-6865411 199.7 MSMEG6816 385.3 Molybdopterin oxidoreductase
52 6867931-6867971 12.7 N/A N/A N/A
53 6930751-6930791 10.8 MSMEG6881 5.8 Transcriptional regulator, GntR family
  1. aassigned peak number, bpeak coordinates on the M. smegmatis genome, cfold enrichment of each peak compared to the input control calculated using SISSRs, dadjacent gene(s) to peak, efold change in gene expression (WT vs ΔglnR) and gfold change in gene expression normalized to sigA from qRT-PCR (WT vs ΔglnR). L = left and R = right indicates the direction of the gene in relation to GlnR binding where GlnR is proposed to control divergent genes. Genes in operons are denoted by *. Peaks that represent binding sites with no corresponding differential expression of adjacent genes are labelled no DE.