Rv2069 RNA polymerase sigma-54 factor RpoN

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv2069 sigC RNA polymerase sigma-54 factor RpoN CDS 2326944 2327501 + 558 185 TRUE

Rv2069 (RNA polymerase sigma-54 factor RpoN) is predicted to be co-regulated in modules bicluster_0061 with residual 0.63 and bicluster_0556 with residual 0.55.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.00 for bicluster_0061 and 0.02 and 1.40 for bicluster_0556 respectively.

These modules are enriched for following go terms: isomerase activity cobalamin binding.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 10
Gene Target Differential Expression Distance Expression pvalue Type
2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
No 23 -0.08 0.99698 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)
Induced -58 2.2 2.8026e-45 Primary.TSS
No -29 0.15 0.994822 Primary.TSS
No -39 0.16 0.995438 CDS
PE family protein
No -91 -0.47 0.994822 Primary.TSS
FIG055075: Possibly a cell division protein, antigen 84 in Mycobacteria
No 69 0 0.999473 Primary.TSS
No -120 -0.01 0.999473 CDS
transcriptional regulator, AfsR/DnrI/RedD family
No -126 -0.11 0.994822 Internal.TSS
WhiB-like transcription regulator
No 47 0.1 0.995706 Primary.TSS
ATP/GTP binding protein
No -136 0.03 0.999473 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, BlaI family
Repressed -44 -1.44 0.00000011 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
Probable RNA polymerase sigma-C factor RNA polymerase sigma factor SigC
Operon # Operon
1353
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
15609206 NP_216585.1 Run
GO:0001666

response to hypoxia

response to hypoxia

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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
GO Category: 
biological_process
37
Total items in this category:  
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:0009410

response to xenobiotic stimulus

response to xenobiotic stimulus

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 xenobiotic compound stimulus. Xenobiotic compounds are compounds foreign to living organisms.
GO Category: 
biological_process
4
Total items in this category:  
GO:0009415

response to water stimulus

response to water stimulus

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 stimulus reflecting the presence, absence, or concentration of water.
GO Category: 
biological_process
4
Total items in this category:  
GO:0006355

regulation of transcription, DNA-dependent

regulation of transcription, DNA-dependent

Details: 
Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
15
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 GSM1426790 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426791 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426792 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2069_B530 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.790000 1.86

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: 0.203934
p-value INH: 0.0387501
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.50 U
D3I 3 3 3.83 13.07 I
D3U 3 3 3.83 13.14 U
D5I 9 5 6.00 13.15 I
D5U 17 5 6.00 12.99 U
D7I 18 7 8.14 13.73 I
D7U 19 7 8.14 13.68 U
D14I 4 14 15.63 13.87 I
D14U 4 14 15.63 13.63 U
D17I 3 17 19.15 14.62 I
D17U 3 17 19.15 13.84 U
D21I 4 21 23.23 13.79 I
D21U 4 21 23.23 13.78 U
D24I 3 24 26.60 14.35 I
D24U 3 24 26.60 13.80 U
D28I 4 28 30.61 13.31 I
D28U 4 28 30.61 13.26 U