Rv3414c RNA polymerase sigma-70 factor

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3414c sigD RNA polymerase sigma-70 factor CDS 3833038 3833676 - 639 212 TRUE

Rv3414c (RNA polymerase sigma-70 factor) is predicted to be co-regulated in modules bicluster_0316 with residual 0.52 and bicluster_0393 with residual 0.48.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.49 and 70.00 for bicluster_0316 and 0.00 and 14.00 for bicluster_0393 respectively.

These modules are enriched for following go terms: nucleotide biosynthetic process, nucleoside phosphate biosynthetic proces..., nucleotide metabolic process, hydroxymethyl-, formyl- and related tran... .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score Distance to Tuberculist Start Codon Internal TSS New Internal UTR Re-Annotated Start Tuberculist Annotated Start
-1.201 73 3833603 -10 3833613 3833676
Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-13621 MT3523 998
Displaying 1 - 3 of 3
Gene Target Differential Expression Distance Expression pvalue Type
PE family protein
No -31 -0.06 0.999898 Primary.TSS
RNA polymerase sigma-70 factor
Induced -43 1.31 0.0000000016 Internal.TSS
RNA polymerase sigma-70 factor
Induced -116 1.31 0.0000000016 CDS
Displaying 1 - 8 of 8
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, AsnC family
No 60 0.41 0.303113 CDS
RNA polymerase sigma-70 factor
Induced -43 1.31 0.0000000016 Internal.TSS
Transcriptional regulator, PadR family
No -49 -0.09 0.840848 CDS
RNA polymerase sigma-70 factor
Induced -116 1.31 0.0000000016 CDS
Transcriptional regulator, PadR family
No 24 -0.09 0.840848 Internal.TSS
Transcriptional regulator, TetR family
No 34 -0.01 0.99058 CDS
Transcriptional regulator, PadR family
No -52 0.22 0.962221 CDS
Transcriptional regulator, PadR family
No 21 0.22 0.962221 Internal.TSS
Motif 1 Motif 2 Residual
bicluster_0316
e.value: 
0.49
Motif Bicluster: 
e.value: 
70
Motif Bicluster: 
0.52
bicluster_0393
e.value: 
0.00043
Motif Bicluster: 
e.value: 
14
Motif Bicluster: 
0.48
Product (LegacyBRC) Product (RefSeq)
Probable RNA polymerase sigma-D factor RNA polymerase sigma factor SigD
Operon # Operon
2233 - -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

RNA polymerase

17
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15610550 NP_217931.1 Run
GO:0009405

pathogenesis

pathogenesis

Details: 
The set of specific processes that generate the ability of an organism to cause disease in another.
GO Category: 
biological_process
65
Total items in this category:  
GO:0009408

response to heat

response to heat

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 a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
GO Category: 
biological_process
11
Total items in this category:  
GO:0016987

sigma factor activity

sigma factor activity

Details: 
A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes.
GO Category: 
molecular_function
6
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 GSM1426993 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426994 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426995 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426993 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426994 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426995 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3414c_B532 UCSC Browser Tracks
Rv3414c_B638 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.120000 1.49

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: 0.663843
p-value INH: 0.832328
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.15 U
D3I 3 3 3.83 13.20 I
D3U 3 3 3.83 12.67 U
D5I 9 5 6.00 13.16 I
D5U 17 5 6.00 13.09 U
D7I 18 7 8.14 12.90 I
D7U 19 7 8.14 13.02 U
D14I 4 14 15.63 12.98 I
D14U 4 14 15.63 13.35 U
D17I 3 17 19.15 12.98 I
D17U 3 17 19.15 13.47 U
D21I 4 21 23.23 12.46 I
D21U 4 21 23.23 13.38 U
D24I 3 24 26.60 12.11 I
D24U 3 24 26.60 13.33 U
D28I 4 28 30.61 11.55 I
D28U 4 28 30.61 12.99 U