Rv1353c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1353c Transcriptional regulator, TetR family CDS 1519200 1519985 - 786 261 TRUE

Rv1353c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0418 with residual 0.49 and bicluster_0511 with residual 0.52.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 7.60 for bicluster_0418 and 670.00 and 6,900.00 for bicluster_0511 respectively.

These modules are enriched for following go terms: phosphopantetheine binding, modified amino acid binding, amide binding, amino acid binding.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 238
Gene Target Differential Expression Distance Expression pvalue Type
Serine/threonine phosphatase PPP (EC 3.1.3.16)
No -46 0.2 0.200616 Primary.TSS
No -18 -0.52 0.0576808 CDS
No 55 -0.22 0.651797 CDS
Oxidoreductase
No -66 0.07 0.955751 CDS
Probable cation-transporting ATPase I (EC 3.6.3.-)
Repressed 18 -0.64 0.0018937 CDS
Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
No -90 -0.4 0.456934 CDS
Serine protease PepA
No 65 -0.08 0.868955 Primary.TSS
No 69 -0.01 0.988838 Primary.TSS
MCE-family protein Mce1A
No -33 -0.21 0.714166 Antisense.TSS
FIG033285: Conserved MCE associated transmembrane protein
No -97 0.23 0.279056 Internal.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0418
e.value: 
0.00032
Motif Bicluster: 
e.value: 
7.6
Motif Bicluster: 
0.49
bicluster_0511
e.value: 
670
Motif Bicluster: 
e.value: 
6900
Motif Bicluster: 
0.52
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv1353c_MT1396 transcriptional regulatory protein
Operon # Operon
910 - - -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

not assigned to any KEGG Pathway.
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15608493 NP_215869.1 Run
Description:Expression data from transcription factor over expression experiments. TFOE are matched to the ChIP-seq experiment done simultaneously. This dataset is described in Rustad et al. 2014, Genome Biology.
BioProject Accession GEO Series References Repository Sample Method Sample Type
PRJNA254351 GSM1426658 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426659 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426660 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1353c_B612 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.370000 3.33

How essentiality calculations were done?

The relative representation of each mutant was determined by calculating the fold change (sequence reads/insertion in cholesterol divided by sequence reads/insertion in glycerol) for each gene. Statistical significance was determined by t-test. Each insertion site in each replicate sample was treated as a separate data point. The hyperbola used for defining genes specifically required for growth in cholesterol was defined by the formula, y = 3.8/x+0.7. Genes above this line are annotated as required for growth on cholesterol.

TRIP log2 fold abundance change

reports the log2 abundance fold change of each TFI strain, relative to no induction, in absence or presence of drug, averaged across experimental replicates. Also reported are the accompanying z-scores and two-sided t-test p-values for each TFI strain under each condition. Please refer to Ma et al., 2020, Nature Microbiology for more information.

p-value Untreated: 0.0000000300551
p-value INH: 0.501382
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.53 U
D3I 3 3 3.83 11.57 I
D3U 3 3 3.83 12.19 U
D5I 9 5 6.00 8.02 I
D5U 17 5 6.00 10.51 U
D7I 18 7 8.14 7.58 I
D7U 19 7 8.14 10.54 U
D14I 4 14 15.63 2.57 I
D14U 4 14 15.63 9.74 U
D17I 3 17 19.15 2.30 I
D17U 3 17 19.15 9.50 U
D21I 4 21 23.23 I
D21U 4 21 23.23 8.60 U
D24I 3 24 26.60 I
D24U 3 24 26.60 8.86 U
D28I 4 28 30.61 1.11 I
D28U 4 28 30.61 7.94 U