Rv1129c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: transcriptional regulator
- REFSEQ: transcriptional regulator protein
- PATRIC: Transcriptional regulator XRE family
- TUBERCULIST: Probable transcriptional regulator protein
- NCBI: Probable transcriptional regulator protein
- updated information (H37Rv4):
  - gene name: prpR
  - function: regulates methylcitrate cycle
  - reference: Masiewicz (2012) PMID: 22916289
Type: Conditional
Start: 1253074
End: 1254534
Operon:

Trans-membrane region:
Role: I.J.1 - Repressors/activators
GO terms:
- GO:0052572 - response to host immune response (Uniprot)
- GO:0043565 - sequence-specific DNA binding (Uniprot)
- GO:0019679 - propionate metabolic process, methylcitrate cycle (Uniprot)
- GO:0008203 - cholesterol metabolic process (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0003677 - DNA binding (Uniprot)
- GO:0001666 - response to hypoxia (Uniprot)
- GO:0009405 - pathogenesis (FLUTE) (FLUTE Assigned!)
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:
Search for Homologs in PDB

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

PDB	aa ident	species	PDB title
6D2S	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterium tuberculosis transcriptional regulator
6CYY	99%	Mycobacterium tuberculosis	Mycobacterium tuberculosis transcriptional regulator
6CZ6	99%	Mycobacterium tuberculosis	Mycobacterium tuberculosis transcriptional regulator
6CYJ	99%	Mycobacterium tuberculosis	Mycobacterium tuberculosis transcriptional regulator

Links to additional information on Rv1129c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.437 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MTRSNVLPVARTYSRTFSGARLRRLRQERGLTQVALAKALDLSTSYVNQLENDQRPITVPVLLLLTERFDLSAQYFSSDSDARLVADLSDVFTDIGVEHA
VSGAQIEEFVARMPEVGHSLVAVHRRLRAATEELEGYRSRATAETELPPARPMPFEEVRDFFYDRNNYIHDLDMAAERMFTESGMRTGGLDIQLAELMRD
RFGISVVIDDNLPDTAKRRYHPDTKVLRVAHWLMPGQRAFQIATQLALVGQSDLISSIVATDDQLSTEARGVARIGLANYFAGAFLLPYREFHRAAEQLR
YDIDLLGRRFGVGFETVCHRLSTLQRPRQRGIPFIFVRTDKAGNISKRQSATAFHFSRVGGSCPLWVVHDAFAQPERIVRQVAQMPDGRSYFWVAKTTAA
DGLGYLGPHKNFAVGLGCDLAHAHKLVYSTGVVLDDPSTEVPIGAGCKICNRTSCAQRAFPYLGGRVAVDENAGSSLPYSSTEQSV

(Nucleotide sequence available on KEGG)

Additional Information

PrpR - regulator of methylcitrate cycles; Masiewicz (2012) PMID: 22916289

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
Uncertain	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.055550; 4 non-insertions in a row out of 27 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 27 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 27 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 5 non-insertions in a row out of 27 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.993950; 11 non-insertions in a row out of 27 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
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

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0023 (-) (Direct binding)
- Rv0081 (-) (Direct binding)
- Rv0465c (-) (Direct binding)
- Rv0678 (-) (Direct binding)
- Rv1985c (-) (Direct binding)
- Rv2887 (-) (Direct binding)
- Rv3133c (devR) (Direct binding)
- Rv3249c (-) (Direct binding)
- Rv3597c (lsr2) (Direct binding)

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

Upregulates:
Upregulated by:
Downregulates:
Downregulated by:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Regulatory Rv1131	anshula.arora1990	NAS		co-expression X. Pang, P. Vu et al. Evidence for complex interactions of stress-associated regulons in an mprAB deletion mutant of Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 2007
Citation	Evidence for complex interactions of stress-associated regulons in an mprAB deletion mutant of Mycobacterium tuberculosis. X. Pang, P. Vu et al. Microbiology (Reading, Engl.) 2007	ashwinigbhat	IMP	17379732	Mutant studies
Interaction	Regulatory Rv1221	ashwinigbhat	IMP		Mutant studies X. Pang, P. Vu et al. Evidence for complex interactions of stress-associated regulons in an mprAB deletion mutant of Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 2007
Citation	Evidence for complex interactions of stress-associated regulons in an mprAB deletion mutant of Mycobacterium tuberculosis. X. Pang, P. Vu et al. Microbiology (Reading, Engl.) 2007	anshula.arora1990	NAS	17379732	co-expression
Interaction	Regulatory Rv1130	anshula.arora1990	NAS		co-expression X. Pang, P. Vu et al. Evidence for complex interactions of stress-associated regulons in an mprAB deletion mutant of Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 2007
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

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