Rv1626 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: response regulator NasT
- REFSEQ: two-component system transcriptional regulator
- PATRIC: response regulator
- TUBERCULIST: Probable two-component system transcriptional regulator
- NCBI: Probable two-component system transcriptional regulator
- updated information (H37Rv4):
  - gene name: PdtaR
  - function: two-component sensor with PdtaS; controls NO and Cu stress response
  - reference: Buglino (2021) PMID: 34003742
Type: Not Target
Start: 1828180
End: 1828797
Operon:

Trans-membrane region:
Role: I.J.2 - Two component systems
GO terms:
- GO:0043168 - anion binding (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0031564 - transcription antitermination (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005622 - intracellular (Uniprot)
- GO:0005618 - cell wall (Uniprot)
- GO:0003723 - RNA binding (Uniprot)
- GO:0000160 - phosphorelay signal transduction system (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
Orthologs among selected mycobacteria
Protein structure: 1sd5, 1s8n
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
1SD5	100%	Mycobacterium tuberculosis	Crystal structure of Rv1626
1S8N	100%	Mycobacterium tuberculosis	Crystal structure of Rv1626 from Mycobacterium tuberculosis
4TMY	44%	Thermotoga maritima	CHEY FROM THERMOTOGA MARITIMA (MG-IV)
4IGA	44%	Thermotoga maritima	The crystal structure of an activated Thermotoga maritima CheY with N-terminal region of FliM
3TMY	44%	Thermotoga maritima	CHEY FROM THERMOTOGA MARITIMA (MN-III)
2TMY	44%	Thermotoga maritima	CHEY FROM THERMOTOGA MARITIMA (APO-II)
1U0S	44%	Thermotoga maritima	Chemotaxis kinase CheA P2 domain in complex with response regulator CheY from the thermophile thermotoga maritima
1TMY	44%	Thermotoga maritima	CHEY FROM THERMOTOGA MARITIMA (APO-I)
6EXR	43%	Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)	CHEMOTAXIS PROTEIN CHEY FROM Pyrococcus horikoshiI
6ER7	43%	Pyrococcus horikoshii	CHEMOTAXIS PROTEIN CHEY FROM Pyrococcus horikoshiI

Links to additional information on Rv1626:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -1.11 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MTGPTTDADAAVPRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKPDLVIMDVKMPRRDGIDAASEIASKRIAPIVVLTAFSQRDLV
ERARDAGAMAYLVKPFSISDLIPAIELAVSRFREITALEGEVATLSERLETRKLVERAKGLLQTKHGMTEPDAFKWIQRAAMDRRTTMKRVAEVVLETLG
TPKDT

(Nucleotide sequence available on KEGG)

Additional Information

PdtaR

PdtaSR: 2-component sensor, controls NO and Cu stress response
  Rv3220c/PdtaS - sensor kinase
  Rv1626/PdtaR - RNA binding response regulator; cytosolic, constitutive

Morth (2005) PMID: 16026786
  interacts with Rip1, and an sRNA (PPE1-5')
  Rip1 controls expression of PPE1-5', which binds PdtaR

Buglino, J. A., Sankhe, G. D., Lazar, N., Bean, J. M. & Glickman, M. S. Integrated sensing
of host stresses by inhibition of a cytoplasmic two-component system controls M. tuberculosis
acute lung infection. Elife 10, e65351 (2021). PMID: 34003742

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across >100 conditions *new*

Classification	Condition	Strain	Method	Reference	Notes
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 5 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 0 non-insertions in a row out of 5 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 0 non-insertions in a row out of 5 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 0 non-insertions in a row out of 5 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 5 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.14
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

Binds To:
Bound By:
- No bindings from other targets were found.

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings to other targets were found.

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Not upregulated by other genes.
Downregulates:
- Rv3853 (rraA)
Downregulated by:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	Comment
Interaction	PhysicalInteraction Rv3320c	shahanup86	IPI	Affinity Purification authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005
Interaction	PhysicalInteraction Rv3320c	shahanup86	IPI	Affinity Purification JP. Morth, S. Gosmann et al. A novel two-component system found in Mycobacterium tuberculosis. FEBS Lett. 2005
Interaction	PhysicalInteraction Rv3320c	vashishtrv	IPI	Affinity Purification authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005
Interaction	PhysicalInteraction Rv3320c	vashishtrv	IPI	Affinity Purification JP. Morth, S. Gosmann et al. A novel two-component system found in Mycobacterium tuberculosis. FEBS Lett. 2005
Interaction	Regulatory Rv3220c	akankshajain.21	IDA	Spectrophotometric JP. Morth, S. Gosmann et al. A novel two-component system found in Mycobacterium tuberculosis. FEBS Lett. 2005
Interaction	Regulatory Rv3220c	akankshajain.21	IDA	Structural Analysis JP. Morth, S. Gosmann et al. A novel two-component system found in Mycobacterium tuberculosis. FEBS Lett. 2005
Interaction	RegulatedBy Rv1221	yamir.moreno	IEP	Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. R. Manganelli, MI. Voskuil et al. The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in global gene expression and survival in macrophages. Mol. Microbiol. 2001

TB Genome Annotation Portal