Rv1816 Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1816 Transcriptional regulator, TetR family CDS 2058256 2058960 + 705 234 TRUE

Rv1816 (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0173 with residual 0.41 and bicluster_0443 with residual 0.45.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 11.00 and 12,000.00 for bicluster_0173 and 0.00 and 0.40 for bicluster_0443 respectively.

These modules are enriched for following go terms: cellular biosynthetic process, organic substance biosynthetic process, cytoplasm, RNA binding.

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score Distance to Tuberculist Start Codon Internal TSS Re-Annotated Start Tuberculist Annotated Start
-1.121 18 2058274 2058274 2058256
Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-13619 MT1864 518
Displaying 1 - 10 of 143
Gene Target Differential Expression Distance Expression pvalue Type
SSU ribosomal protein S6p
No -25 -0.57 0.325103 Primary.TSS
No 29 0 0.999356 CDS
Hydrogen peroxide-inducible genes activator
No 43 0.16 0.882886 Primary.TSS
Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]
No -122 -0.08 0.877338 CDS
No -71 -0.18 0.833612 Primary.TSS
Transcriptional regulator, TetR family
No -81 -0.17 0.697447 Internal.TSS
MCE-family lipoprotein LprK (MCE-family lipoprotein Mce1e)
No 61 -0.48 0.292867 CDS
Possible lipoprotein LprO
No -86 0.12 0.86117 Primary.TSS
ATP binding cassette (ABC) transporter homolog
No -38 0.08 0.920771 CDS
PROBABLE CONSERVED MEMBRANE PROTEIN
No 50 0.07 0.930752 CDS
Displaying 1 - 9 of 9
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, IclR family
No 60 0.79 0.0625588 Antisense.TSS
Transcriptional regulator, TetR family
Induced -19 1.84 0.000000000000392 Internal.TSS
ESX-1 secreted protein regulator EspR
Repressed -4 -1.04 0.0000144 Internal.TSS
Transcriptional regulator, IclR family
No 42 0.79 0.0625588 Internal.TSS
Transcriptional regulator, ArsR family
Induced 26 0.86 0.00000724 Internal.TSS
ESX-1 secreted protein regulator EspR
Repressed 14 -1.04 0.0000144 CDS
Beta-carotene ketolase (EC 1.14.-.-)
No 11 -0.02 0.999473 Internal.TSS
Beta-carotene ketolase (EC 1.14.-.-)
No 29 -0.02 0.999473 CDS
Transcriptional regulator, TetR family
Induced -1 1.84 0.000000000000392 CDS
Motif 1 Motif 2 Residual
bicluster_0173
e.value: 
11
Motif Bicluster: 
e.value: 
12000
Motif Bicluster: 
0.41
bicluster_0443
e.value: 
0.00000000019
Motif Bicluster: 
e.value: 
0.4
Motif Bicluster: 
0.45
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv1816_MT1864 transcriptional regulatory protein
Operon # Operon
1193
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
15608953 NP_216332.1 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 GSM1426726 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426727 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426728 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1816_B460 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.970000 2.60

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: 0.000803583
p-value INH: 0.362066
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.07 U
D3I 3 3 3.83 12.26 I
D3U 3 3 3.83 11.96 U
D5I 9 5 6.00 12.69 I
D5U 17 5 6.00 12.43 U
D7I 18 7 8.14 12.30 I
D7U 19 7 8.14 11.73 U
D14I 4 14 15.63 13.41 I
D14U 4 14 15.63 12.52 U
D17I 3 17 19.15 13.71 I
D17U 3 17 19.15 12.66 U
D21I 4 21 23.23 13.23 I
D21U 4 21 23.23 12.39 U
D24I 3 24 26.60 13.29 I
D24U 3 24 26.60 12.22 U
D28I 4 28 30.61 12.79 I
D28U 4 28 30.61 12.00 U