Rv3855 Transcriptional repressor EthR, TetR family

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3855 ethR Transcriptional repressor EthR, TetR family CDS 4327549 4328199 + 651 216 TRUE

Rv3855 (Transcriptional repressor EthR, TetR family) is predicted to be co-regulated in modules bicluster_0129 with residual 0.53 and bicluster_0478 with residual 0.49.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 2.40 for bicluster_0129 and 0.00 and 0.09 for bicluster_0478 respectively.

These modules are enriched for following go terms: single-organism process, transport, establishment of localization, localization, arsenite transmembrane transporter activ..., anion transmembrane transporter activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 24
Gene Target Differential Expression Distance Expression pvalue Type
Programmed cell death toxin YdcE
No 55 0.02 0.99061 Primary.TSS
No results were found NA 55 Internal.TSS
No -85 0.07 0.963275 CDS
Cytochrome P450 130
No 7 0.06 0.962884 CDS
No -25 0.53 0.803699 CDS
Probable phiRV1 phage protein
No -41 -0.04 0.987568 CDS
Chalcone synthase (EC 2.3.1.74)
No -40 -0.06 0.958811 Primary.TSS
Transcriptional repressor Mce3R, TetR family
No 40 0.32 0.828075 Primary.TSS
Transporter, LysE family
No -10 0.07 0.971123 Primary.TSS
PE family protein
No -24 0.33 0.902839 Primary.TSS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No 1 -0.45 0.316577 Primary.TSS
Transcriptional regulator, TetR family
No -15 -0.51 0.28834 Primary.TSS
Transcriptional repressor EthR, TetR family
Induced -1 3.28 3.01e-23 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN [TETR-FAMILY] ETHR transcriptional regulatory repressor protein (TETR-family) ETHR
Operon # Operon
2523
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
15610991 NP_218372.1 Run
GO:0005829

cytosol

cytosol

Details: 
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO Category: 
cellular_component
371
Total items in this category:  
GO:0042803

protein homodimerization activity

protein homodimerization activity

Details: 
Interacting selectively and non-covalently with an identical protein to form a homodimer.
GO Category: 
molecular_function
83
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:0046677

response to antibiotic

response to antibiotic

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
GO Category: 
biological_process
15
Total items in this category:  
GO:0051260

protein homooligomerization

protein homooligomerization

Details: 
The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
GO Category: 
biological_process
31
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 GSM1427053 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427054 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427055 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427053 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427054 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427055 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3855_B179 UCSC Browser Tracks
Rv3855_B563 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.090000 1.23

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: 0.510348
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.82 U
D3I 3 3 3.83 13.36 I
D3U 3 3 3.83 13.28 U
D5I 9 5 6.00 13.62 I
D5U 17 5 6.00 13.44 U
D7I 18 7 8.14 13.50 I
D7U 19 7 8.14 13.24 U
D14I 4 14 15.63 13.21 I
D14U 4 14 15.63 13.43 U
D17I 3 17 19.15 12.86 I
D17U 3 17 19.15 13.33 U
D21I 4 21 23.23 12.79 I
D21U 4 21 23.23 13.49 U
D24I 3 24 26.60 11.76 I
D24U 3 24 26.60 13.13 U
D28I 4 28 30.61 12.02 I
D28U 4 28 30.61 13.15 U