Rv1221 RNA polymerase sigma-70 factor, ECF subfamily

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv1221 sigE RNA polymerase sigma-70 factor, ECF subfamily CDS 1364413 1365186 + 774 257 FALSE

Rv1221 (RNA polymerase sigma-70 factor, ECF subfamily) is predicted to be co-regulated in modules bicluster_0129 with residual 0.53 and bicluster_0138 with residual 0.67.

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 0.42 for bicluster_0138 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Product (LegacyBRC) Product (RefSeq)
ALTERNATIVE RNA POLYMERASE SIGMA FACTOR SIGE RNA polymerase sigma factor SigE
Operon # Operon
831
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
15608361 NP_215737.1 Run
GO:0003677

DNA binding

DNA binding

Details: 
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
GO Category: 
molecular_function
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: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:0042542

response to hydrogen peroxide

response to hydrogen peroxide

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 hydrogen peroxide (H2O2) stimulus.
GO Category: 
biological_process
3
Total items in this category:  
GO:0044119

growth of symbiont in host cell

growth of symbiont in host cell

Details: 
The increase in size or mass of symbiont, occurring in its host's cell. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GO Category: 
biological_process
50
Total items in this category:  
GO:0052572

response to host immune response

response to host immune response

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 detecting the immune response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GO Category: 
biological_process
62
Total items in this category:  
No TFOE experiment results were found
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.940000 1.70

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: 0.187821
p-value INH: 0.600311
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.24 U
D3I 3 3 3.83 13.56 I
D3U 3 3 3.83 14.01 U
D5I 9 5 6.00 14.96 I
D5U 17 5 6.00 15.58 U
D7I 18 7 8.14 13.24 I
D7U 19 7 8.14 13.81 U
D14I 4 14 15.63 8.54 I
D14U 4 14 15.63 13.23 U
D17I 3 17 19.15 5.57 I
D17U 3 17 19.15 13.39 U
D21I 4 21 23.23 6.07 I
D21U 4 21 23.23 13.64 U
D24I 3 24 26.60 2.90 I
D24U 3 24 26.60 13.53 U
D28I 4 28 30.61 4.29 I
D28U 4 28 30.61 13.87 U