Rv0273c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0273c Transcriptional regulator, TetR family CDS 329705 330325 - 621 206 TRUE

Rv0273c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0199 with residual 0.54 and bicluster_0397 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.00 for bicluster_0199 and 0.00 and 0.00 for bicluster_0397 respectively.

These modules are enriched for following go terms: nitrogen compound metabolic process, carbon-oxygen lyase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 30
Gene Target Differential Expression Distance Expression pvalue Type
Vegetative cell wall protein gp1 precursor
Induced -68 0.9 0.00000282 Primary.TSS
Probable cation-transporting ATPase I (EC 3.6.3.-)
No 16 -0.35 0.388847 CDS
Phosphoheptose isomerase (EC 5.3.1.-)
No -46 -0.36 0.574859 CDS
Nicotinamide-nucleotide adenylyltransferase, NadR family (EC 2.7.7.1) / Ribosylnicotinamide kinase (EC 2.7.1.22)
No 68 0.55 0.25479 Primary.TSS
POSSIBLE METHYLTRANSFERASE CLUSTERED WITH NadR
No 68 0.38 0.504153 Internal.TSS
Transcriptional regulator, TetR family
Induced 16 3.26 1.34e-31 Primary.TSS
Glyoxalase family protein
Repressed -8 -2.48 1.01e-23 Primary.TSS
PE-PGRS FAMILY PROTEIN
Repressed 9 -0.81 0.0169661 Primary.TSS
No -14 -0.11 0.811984 Primary.TSS
FIG021574: Possible membrane protein related to de Novo purine biosynthesis
No 14 0.01 0.973731 CDS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
Induced 16 3.26 1.34e-31 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0199
e.value: 
0.000000000000001
Motif Bicluster: 
e.value: 
0.000000085
Motif Bicluster: 
0.54
bicluster_0397
e.value: 
0.000000000016
Motif Bicluster: 
e.value: 
0.000063
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
188 -
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
15607414 NP_214787.1 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 GSM1426443 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426444 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426445 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0273c_B409 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.230000 0.98

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: 0.116766
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 9.80 U
D3I 3 3 3.83 9.42 I
D3U 3 3 3.83 8.85 U
D5I 9 5 6.00 11.57 I
D5U 17 5 6.00 11.31 U
D7I 18 7 8.14 9.89 I
D7U 19 7 8.14 9.22 U
D14I 4 14 15.63 8.06 I
D14U 4 14 15.63 8.12 U
D17I 3 17 19.15 6.92 I
D17U 3 17 19.15 7.38 U
D21I 4 21 23.23 7.40 I
D21U 4 21 23.23 7.62 U
D24I 3 24 26.60 6.24 I
D24U 3 24 26.60 7.21 U
D28I 4 28 30.61 7.00 I
D28U 4 28 30.61 7.62 U