Rv3223c RNA polymerase sigma-54 factor RpoN

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3223c sigH RNA polymerase sigma-54 factor RpoN CDS 3598901 3599551 - 651 216 TRUE

Rv3223c (RNA polymerase sigma-54 factor RpoN) is predicted to be co-regulated in modules bicluster_0224 with residual 0.55 and bicluster_0470 with residual 0.49.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 480.00 and 27.00 for bicluster_0224 and 150.00 and 8,000.00 for bicluster_0470 respectively.

These modules are enriched for following go terms: regulation of cellular process, regulation of biological process, biological regulation .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.097 56 3599679 3599623 3599551
Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15742 MT3320 2628
Displaying 1 - 10 of 21
Gene Target Differential Expression Distance Expression pvalue Type
SSU ribosomal protein S6p
Repressed -33 -1.4 0.00000403 Primary.TSS
DNA-directed RNA polymerase beta subunit (EC 2.7.7.6)
No 24 -0.15 0.503979 Primary.TSS
No -81 -0.26 0.408089 CDS
LSU ribosomal protein L31p
No -23 0.09 0.859926 Primary.TSS
Peptide chain release factor 1
No -107 0.12 0.740412 Primary.TSS
Thioredoxin TrxB1
Induced 9 2.94 3.57e-16 CDS
PROBABLE CONSERVED POLYKETIDE SYNTHASE ASSOCIATED PROTEIN PAPA4
Induced 59 5.07 0 Antisense.TSS
Pyridoxine 5'-phosphate oxidase
Induced -150 2.67 3.86e-27 CDS
probable iron binding protein from the HesB_IscA_SufA family
No -25 0.46 0.0101722 Primary.TSS
Glycerate kinase (EC 2.7.1.31)
No -47 0.2 0.273013 Antisense.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
RNA polymerase sigma-54 factor RpoN
Induced 29 1.41 5.27e-17 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0224
e.value: 
480
Motif Bicluster: 
e.value: 
27
Motif Bicluster: 
0.55
bicluster_0470
e.value: 
150
Motif Bicluster: 
e.value: 
8000
Motif Bicluster: 
0.49
Product (LegacyBRC) Product (RefSeq)
RNA polymerase sigma-E factor RNA polymerase sigma factor RpoE
Operon # Operon
2109 -
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
15610359 NP_217739.1 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:0006950

response to stress

response to stress

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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
GO Category: 
biological_process
9
Total items in this category:  
GO:0006979

response to oxidative stress

response to oxidative stress

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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
GO Category: 
biological_process
13
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:0034605

cellular response to heat

cellular response to heat

Details: 
Any process that results in a change in state or activity of a cell (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
2
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:  
GO:0051409

response to nitrosative stress

response to nitrosative stress

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 nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions.
GO Category: 
biological_process
14
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:  
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 GSM1426954 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426955 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426956 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426954 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426955 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426956 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426954 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426955 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426956 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426954 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3223c_B126 UCSC Browser Tracks
Rv3223c_B527 UCSC Browser Tracks
Rv3223c_B540 UCSC Browser Tracks
Rv3223c_B566 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.020000 4.20

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: 0.00000000260875
p-value INH: 0.00680433
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.11 U
D3I 3 3 3.83 12.34 I
D3U 3 3 3.83 12.50 U
D5I 9 5 6.00 11.70 I
D5U 17 5 6.00 12.90 U
D7I 18 7 8.14 10.93 I
D7U 19 7 8.14 12.56 U
D14I 4 14 15.63 6.07 I
D14U 4 14 15.63 12.09 U
D17I 3 17 19.15 4.47 I
D17U 3 17 19.15 12.25 U
D21I 4 21 23.23 8.86 I
D21U 4 21 23.23 12.37 U
D24I 3 24 26.60 I
D24U 3 24 26.60 12.55 U
D28I 4 28 30.61 4.40 I
D28U 4 28 30.61 12.53 U