Rv3597c Histone protein Lsr2

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3597c lsr2 Histone protein Lsr2 CDS 4040981 4041319 - 339 112 TRUE

Rv3597c (Histone protein Lsr2) is predicted to be co-regulated in modules bicluster_0140 with residual 0.62 and bicluster_0436 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_0140 and 140.00 and 9,000.00 for bicluster_0436 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 184
Gene Target Differential Expression Distance Expression pvalue Type
Oxidoreductase
No -51 0.05 0.972157 Internal.TSS
Putative metal chaperone, involved in Zn homeostasis, GTPase of COG0523 family
No -25 -0.15 0.860852 CDS
No -36 -0.36 0.541038 Primary.TSS
Aldehyde dehydrogenase (EC 1.2.1.3)
No -26 -0.12 0.616318 Primary.TSS
No -78 -0.04 0.952118 Primary.TSS
PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
No 2 0.3 0.414341 CDS
ATP binding cassette (ABC) transporter homolog
No -129 0.33 0.209234 CDS
tRNA (guanine46-N7-)-methyltransferase (EC 2.1.1.33)
No 17 0 0.998523 Internal.TSS
PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
No 1 0.09 0.880441 CDS
Cell division protein DivIC (FtsB), stabilizes FtsL against RasP cleavage
No -65 -0.41 0.0536656 CDS
Displaying 1 - 10 of 11
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No 43 0.22 0.999974 Primary.TSS
Transcriptional regulator, ArsR family
No -42 0.16 0.511849 Primary.TSS
\Transcriptional regulator, XRE family\\\""
No 33 -0.02 0.978361 Primary.TSS
HTH-type transcriptional regulator
No 54 0.19 0.531865 Primary.TSS
putative two-component system response regulator
No 46 0.13 0.758895 Primary.TSS
Iron-sulfur cluster regulator SufR
No 55 -0.19 0.85991 Primary.TSS
Transcriptional regulator kstR (Rv3574), TetR family
No 36 0.1 0.718429 Primary.TSS
Transcriptional regulatory protein
No 35 0.35 0.114939 Primary.TSS
Transcriptional regulator, IclR family
No 45 -0.13 0.841071 Primary.TSS
DNA-binding response regulator TrcR
No 43 -0.28 0.548488 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0140
e.value: 
0.0000061
Motif Bicluster: 
e.value: 
0.000019
Motif Bicluster: 
0.62
bicluster_0436
e.value: 
140
Motif Bicluster: 
e.value: 
9000
Motif Bicluster: 
0.55
Product (LegacyBRC) Product (RefSeq)
Protein lsr2 iron-regulated LSR2 protein precursor
Operon # Operon
2345
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
15610733 NP_218114.1 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: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:0010039

response to iron ion

response to iron ion

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 an iron ion stimulus.
GO Category: 
biological_process
8
Total items in this category:  
GO:0040007

growth

growth

Details: 
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO Category: 
biological_process
621
Total items in this category:  
GO:0051260

protein homooligomerization

protein homooligomerization

Details: 
The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
GO Category: 
biological_process
31
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 GSM1427016 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427017 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427018 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427019 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427016 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427017 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427018 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427019 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427016 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427017 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3597c_B241 UCSC Browser Tracks
Rv3597c_B289 UCSC Browser Tracks
Rv3597c_B550 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
NA NA

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: 0.0905292
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.23 U
D3I 3 3 3.83 12.54 I
D3U 3 3 3.83 11.81 U
D5I 9 5 6.00 14.38 I
D5U 17 5 6.00 14.34 U
D7I 18 7 8.14 12.54 I
D7U 19 7 8.14 13.00 U
D14I 4 14 15.63 13.04 I
D14U 4 14 15.63 13.70 U
D17I 3 17 19.15 12.58 I
D17U 3 17 19.15 13.67 U
D21I 4 21 23.23 12.68 I
D21U 4 21 23.23 13.83 U
D24I 3 24 26.60 12.35 I
D24U 3 24 26.60 13.82 U
D28I 4 28 30.61 12.08 I
D28U 4 28 30.61 14.28 U