Rv1033c DNA-binding response regulator TrcR

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv1033c trcR DNA-binding response regulator TrcR CDS 1157963 1158736 - 774 257 TRUE

Rv1033c (DNA-binding response regulator TrcR) is predicted to be co-regulated in modules bicluster_0028 with residual 0.52 and bicluster_0299 with residual 0.50.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 1.50 for bicluster_0028 and 0.00 and 48.00 for bicluster_0299 respectively.

These modules are enriched for following go terms: signal transduction, signaling, single organism signaling, cell communication, response to stimulus, signal transducer activity, molecular transducer activity, phosphorelay sensor kinase activity, receptor activity, signaling receptor activity .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:11
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-18310 MT1062 1988
Displaying 1 - 10 of 246
Gene Target Differential Expression Distance Expression pvalue Type
Zn-ribbon-containing, possibly RNA-binding protein and truncated derivatives
No 28 -0.08 0.877564 CDS
No -45 -0.4 0.000800963 Primary.TSS
WhiB family transcriptional regulator
No 56 -0.09 0.885287 CDS
Transcriptional regulatory protein
No -97 0.47 0.350351 CDS
2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
Induced -64 2.81 3.78e-18 Primary.TSS
No 59 0.21 0.700016 Internal.TSS
No -91 0.21 0.700016 Internal.TSS
Replicative DNA helicase (EC 3.6.1.-) @ intein-containing
No -91 0.29 0.314894 Primary.TSS
Lead, cadmium, zinc and mercury transporting ATPase (EC 3.6.3.3) (EC 3.6.3.5); Copper-translocating P-type ATPase (EC 3.6.3.4)
No -94 0.2 0.566183 Primary.TSS
Phosphoheptose isomerase (EC 5.3.1.-)
No -69 0.64 0.1038 CDS
Displaying 1 - 8 of 8
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, ArsR family
Repressed 22 -3.03 3.94045e-42 Primary.TSS
DNA-binding response regulator TrcR
Induced 8 4.05 4.81e-37 Primary.TSS
transcriptional regulator, ArsR family
Repressed 43 -1.77 1.88e-16 Primary.TSS
HTH-type transcriptional regulator
Repressed 57 -0.91 0.00153306 Primary.TSS
Transcriptional regulator, ArsR family
Repressed 60 -1.12 0.000028 Primary.TSS
Repressed 63 -2.18 0.00000000000000219 Primary.TSS
Histone protein Lsr2
No 65 -0.66 0.119946 Primary.TSS
Two component DNA binding Transcriptional regulatory protein TcrA
No 43 0.18 0.826938 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0028
e.value: 
0.00029
Motif Bicluster: 
e.value: 
1.5
Motif Bicluster: 
0.52
bicluster_0299
e.value: 
0.0000035
Motif Bicluster: 
e.value: 
48
Motif Bicluster: 
0.50
Product (LegacyBRC) Product (RefSeq)
TWO COMPONENT TRANSCRIPTIONAL REGULATOR TRCR two component transcriptional regulator TRCR
Operon # Operon
691 -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Two-component system

53
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15608173 NP_215549.1 Run
GO:0008150

biological_process

biological_process

Details: 
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
GO Category: 
biological_process
66
Total items in this category:  
GO:0008150

biological_process

biological_process

Details: 
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
GO Category: 
biological_process
66
Total items in this category:  
GO:0003677

DNA binding

DNA binding

Details: 
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
GO Category: 
molecular_function
37
Total items in this category:  
GO:0045892

negative regulation of transcription, DNA-dependent

negative regulation of transcription, DNA-dependent

Details: 
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
10
Total items in this category:  
GO:0045893

positive regulation of transcription, DNA-dependent

positive regulation of transcription, DNA-dependent

Details: 
Any process that activates or increases the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
14
Total items in this category:  
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 GSM1426608 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426609 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426610 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1033c_B432 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.650000 1.47

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: 0.000456169
p-value INH: 0.938436
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.55 U
D3I 3 3 3.83 11.61 I
D3U 3 3 3.83 11.08 U
D5I 9 5 6.00 10.97 I
D5U 17 5 6.00 11.46 U
D7I 18 7 8.14 10.63 I
D7U 19 7 8.14 11.98 U
D14I 4 14 15.63 6.31 I
D14U 4 14 15.63 10.65 U
D17I 3 17 19.15 2.70 I
D17U 3 17 19.15 9.95 U
D21I 4 21 23.23 7.95 I
D21U 4 21 23.23 9.70 U
D24I 3 24 26.60 I
D24U 3 24 26.60 9.04 U
D28I 4 28 30.61 4.20 I
D28U 4 28 30.61 9.07 U