Rv3849 ESX-1 secreted protein regulator EspR

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3849 espR ESX-1 secreted protein regulator EspR CDS 4323499 4323897 + 399 132 TRUE

Rv3849 (ESX-1 secreted protein regulator EspR) is predicted to be co-regulated in modules bicluster_0033 with residual 0.56 and bicluster_0349 with residual 0.51.

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_0033 and 2.40 and 4,600.00 for bicluster_0349 respectively.

These modules are enriched for following go terms: lipopolysaccharide metabolic process, lipopolysaccharide biosynthetic process, carbon-carbon lyase activity, oxo-acid-lyase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 46
Gene Target Differential Expression Distance Expression pvalue Type
Possible membrane protein
No -68 0.48 0.0771699 CDS
Acyl carrier protein
Repressed -37 -1.95 0.0000509 CDS
Dihydroflavonol-4-reductase (EC 1.1.1.219)
No -3 0.27 0.069127 Antisense.TSS
MCE-family protein Mce1D
Repressed 20 -0.71 0.00490873 Internal.TSS
13E12 repeat family protein
Induced 5 0.81 0.00415535 CDS
Malonyl CoA-acyl carrier protein transacylase (EC 2.3.1.39)
No -57 -0.58 0.0176348 CDS
No -60 -0.53 0.0119302 Primary.TSS
Translation elongation factor G
No -120 -0.33 0.0139247 CDS
SSU ribosomal protein S14p (S29e) @ SSU ribosomal protein S14p (S29e), zinc-dependent
No 70 0.01 0.966756 CDS
Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2)
Repressed 66 -0.63 0.0000726 Primary.TSS
Displaying 1 - 4 of 4
ChipSeq TF Differential Expression Distance Expression pvalue Type
WhiB-type transcription regulator
No -17 0.42 0.999973 Internal.TSS
Organic hydroperoxide resistance transcriptional regulator
No -76 0.43 0.114598 CDS
transcriptional regulator, ArsR family
No -67 0.47 0.000320385 CDS
DNA-binding response regulator TrcR
No -144 0.1 0.880067 CDS
Motif 1 Motif 2 Residual
bicluster_0033
e.value: 
0.00027
Motif Bicluster: 
e.value: 
0.00094
Motif Bicluster: 
0.56
bicluster_0349
e.value: 
2.4
Motif Bicluster: 
e.value: 
4600
Motif Bicluster: 
0.51
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein
Operon # Operon
2519
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
15610985 NP_218366.1 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:0005576

extracellular region

extracellular region

Details: 
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
GO Category: 
cellular_component
272
Total items in this category:  
GO:0005618

cell wall

cell wall

Details: 
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan.
GO Category: 
cellular_component
320
Total items in this category:  
GO:0005829

cytosol

cytosol

Details: 
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO Category: 
cellular_component
371
Total items in this category:  
GO:0005886

plasma membrane

plasma membrane

Details: 
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO Category: 
cellular_component
1284
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:0050708

regulation of protein secretion

regulation of protein secretion

Details: 
Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell or group of cells.
GO Category: 
biological_process
1
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 GSM1427047 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427048 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427049 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427047 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427048 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427049 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3849_B507 UCSC Browser Tracks
Rv3849_B562 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.720000 2.44

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: 5.88923e-16
p-value INH: 0.00369919
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.23 U
D3I 3 3 3.83 13.51 I
D3U 3 3 3.83 13.04 U
D5I 9 5 6.00 11.14 I
D5U 17 5 6.00 13.45 U
D7I 18 7 8.14 9.66 I
D7U 19 7 8.14 13.18 U
D14I 4 14 15.63 5.61 I
D14U 4 14 15.63 11.74 U
D17I 3 17 19.15 I
D17U 3 17 19.15 11.46 U
D21I 4 21 23.23 6.02 I
D21U 4 21 23.23 11.59 U
D24I 3 24 26.60 I
D24U 3 24 26.60 11.34 U
D28I 4 28 30.61 3.90 I
D28U 4 28 30.61 11.36 U