Rv1787 (PPE25)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: PPE family protein
- REFSEQ: PPE family protein
- PATRIC: PPE family protein
- TUBERCULIST: PPE family protein PPE25
- NCBI: PPE family protein PPE25
- updated information (H37Rv4):
  - gene name: PPE25
  - function:
  - reference:
Type: Not Target
Start: 2025301
End: 2026398
Operon:

Trans-membrane region:
Role: IV.C.2 - PPE family
GO terms:
- No terms 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
5XFS	61%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of PE8-PPE15 in complex with EspG5 from M. tuberculosis
6VHR	42%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group I422
6UUJ	42%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group P212121

Links to additional information on PPE25:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.523 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

LDFGALPPEINSGRMYCGPGSGPMLAAAAAWDGVAVELGLAATGYASVIAELTGAPWVGAASLSMVAAATPYVAWLSQAAARAEQAGMQAAAAAAAYEAA
FVMTVPPPVITANRVLVMTLIATNFFGQNSAAIAVAEAQYAEMWAQDAVAMYGYAAASASASRLIPFAAPPKTTNSAGVVAQVAAVAAMPGLLQRLSSAA
SVSWSNPNDWWLVRLLGSITPTERTTIVRLLGQSYFATGMAQFFASIAQQLTFGPGGTTAGSGGAWYPTPQFAGLGASRAVSASLARANKIGALSVPPSW
VKTTALTESPVAHAVSANPTVGSSHGPHGLLRGLPLGSRITRRSGAFAHRYGFRHSVVARPPSAG

(Nucleotide sequence available on KEGG)

Additional Information

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; 2 non-insertions in a row out of 19 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 19 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 19 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 10 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 10 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 2.91
Growth-Advantage	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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0818 (-)
- Rv3416 (whiB3)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0324 (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0818 (-)
- Rv3416 (whiB3)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Interaction	PhysicalInteraction Rv1788	akankshajain.21	IGC		S. Tundup, Y. Akhter et al. Clusters of PE and PPE genes of Mycobacterium tuberculosis are organized in operons: evidence that PE Rv2431c is co-transcribed with PPE Rv2430c and their gene products interact with each other. FEBS Lett. 2006
Citation	Clusters of PE and PPE genes of Mycobacterium tuberculosis are organized in operons: evidence that PE Rv2431c is co-transcribed with PPE Rv2430c and their gene products interact with each other. S. Tundup, Y. Akhter et al. FEBS Lett. 2006	akankshajain.21	IGC	16458305	None
Interaction	PhysicalInteraction Rv1788	akankshajain.21	IGC		S. Tundup, Y. Akhter et al. Clusters of PE and PPE genes of Mycobacterium tuberculosis are organized in operons: evidence that PE Rv2431c is co-transcribed with PPE Rv2430c and their gene products interact with each other. FEBS Lett. 2006
Citation	Virulence-related Mycobacterium avium subsp hominissuis MAV_2928 gene is associated with vacuole remodeling in macrophages. authors,SS. Jha,L. Danelishvili,D. Wagner,J. Maser,YJ. Li,I. Moric,S. Vogt,Y. Yamazaki,B. Lai,LE. Bermudez BMC Microbiol. 2010	akankshajain.21	IGC	20359357	None
Interaction	PhysicalInteraction Rv1788	akankshajain.21	IGC		authors,SS. Jha,L. Danelishvili,D. Wagner,J. Maser,YJ. Li,I. Moric,S. Vogt,Y. Yamazaki,B. Lai,LE. Bermudez Virulence-related Mycobacterium avium subsp hominissuis MAV_2928 gene is associated with vacuole remodeling in macrophages. BMC Microbiol. 2010
Symbol	PPE25-PE19	jlew			Mutant is defective in ESXN and PPE41 secretion. Mutant is attenuated in macrophages and SCID mice. authors,D. Bottai,M. Di Luca,L. Majlessi,W. Frigui,R. Simeone,F. Sayes,W. Bitter,MJ. Brennan,C. Leclerc,G. Batoni,M. Campa,R. Brosch,S. Esin Disruption of the ESX-5 system of Mycobacterium tuberculosis causes loss of PPE protein secretion, reduction of cell wall integrity and strong attenuation. Molecular microbiology 2012
Citation	Disruption of the ESX-5 system of Mycobacterium tuberculosis causes loss of PPE protein secretion, reduction of cell wall integrity and strong attenuation. authors,D. Bottai,M. Di Luca,L. Majlessi,W. Frigui,R. Simeone,F. Sayes,W. Bitter,MJ. Brennan,C. Leclerc,G. Batoni,M. Campa,R. Brosch,S. Esin Molecular microbiology 2012	jlew		22340629	Mutant is defective in ESXN and PPE41 secretion. Mutant is attenuated in macrophages and SCID mice.

TB Genome Annotation Portal