Rv3219 WhiB-like transcription regulator

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3219 whiB1 WhiB-like transcription regulator CDS 3595713 3595967 + 255 84 TRUE

Rv3219 (WhiB-like transcription regulator) is predicted to be co-regulated in modules bicluster_0402 with residual 0.39 and bicluster_0475 with residual 0.40.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 650.00 for bicluster_0402 and 0.00 and 9.10 for bicluster_0475 respectively.

These modules are enriched for following go terms: fatty acid synthase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 23
Gene Target Differential Expression Distance Expression pvalue Type
Porphobilinogen deaminase (EC 2.5.1.61)
No -43 -0.06 0.999923 Internal.TSS
Porphobilinogen deaminase (EC 2.5.1.61)
No -137 -0.06 0.999923 Internal.TSS
Uroporphyrinogen-III methyltransferase (EC 2.1.1.107) / Uroporphyrinogen-III synthase (EC 4.2.1.75)
No -137 0.04 0.999923 Primary.TSS
PE-PGRS FAMILY PROTEIN
No 12 -0.14 0.999923 Primary.TSS
No -11 -0.05 0.999923 Primary.TSS
DNA-directed RNA polymerase beta subunit (EC 2.7.7.6)
No 8 0.14 0.999923 Primary.TSS
SSU ribosomal protein S12p (S23e)
No 11 0.07 0.999923 Primary.TSS
SSU ribosomal protein S10p (S20e)
No -2 0.03 0.999923 Primary.TSS
LSU ribosomal protein L14p (L23e)
No -12 0.04 0.999923 Primary.TSS
No -27 -0.1 0.999923 Primary.TSS
Displaying 1 - 10 of 18
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No -13 -0.28 0.625386 Primary.TSS
No -16 0.2 0.676599 Primary.TSS
Transcriptional regulator, TetR family
No 57 0.22 0.81111 Primary.TSS
Transcriptional regulator, ArsR family
No -24 -0.37 0.282733 Primary.TSS
DNA-binding response regulator
No -81 -0.32 0.402626 Primary.TSS
Transcriptional regulator, AsnC family
No 10 0.18 0.924139 Primary.TSS
DNA-binding response regulator TrcR
No -17 -0.19 0.876649 Primary.TSS
Transcriptional regulator, TetR family
No 24 -0.59 0.231133 Primary.TSS
HTH-type transcriptional regulator
No -28 0.21 0.655431 Primary.TSS
RNA polymerase sigma-54 factor RpoN
No 47 0.1 0.995706 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB1 transcriptional regulatory protein WHIB-like WHIB1
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
15610355 NP_217735.1 Run
GO:0005515

protein binding

protein binding

Details: 
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GO Category: 
molecular_function
135
Total items in this category:  
GO:0015035

protein disulfide oxidoreductase activity

protein disulfide oxidoreductase activity

Details: 
Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
GO Category: 
molecular_function
7
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:0047134

protein-disulfide reductase activity

protein-disulfide reductase activity

Details: 
Catalysis of the reaction: protein-dithiol + NAD(P)+ = protein-disulfide + NAD(P)H + H+.
GO Category: 
molecular_function
2
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 GSM1426951 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426952 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426953 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3219_B188 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
NA NA

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: 0.00204395
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D17I 3 17 19.15 17.45 I
D17U 3 17 19.15 14.25 U
D24I 3 24 26.60 18.34 I
D24U 3 24 26.60 14.10 U
D3I 3 3 3.83 13.53 I
D3U 3 3 3.83 13.44 U
D14I 4 14 15.63 16.46 I
D14U 4 14 15.63 14.16 U
D21I 4 21 23.23 17.15 I
D21U 4 21 23.23 14.07 U
D28I 4 28 30.61 17.69 I
D28U 4 28 30.61 13.78 U
D5I 9 5 6.00 13.53 I
D5U 17 5 6.00 13.29 U
D7I 18 7 8.14 14.17 I
D7U 19 7 8.14 13.47 U
D0U 27 0 0.00 12.89 U