Rv1195 (PE13)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: PE family protein
- PATRIC: FIG018298: PE family protein
- TUBERCULIST: PE family protein PE13
- NCBI: PE family protein PE13
- updated information (H37Rv4):
  - gene name: PE13
  - function:
  - reference:
Type: Not Target
Start: 1339003
End: 1339302
Operon:

Trans-membrane region:
Role: IV.C.1.a - PE subfamily
GO terms:
- GO:0009405 - pathogenesis (Uniprot)
- GO:0005618 - cell wall (Uniprot)
- GO:0005576 - extracellular region (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:
Search for Homologs in PDB
Top 10 Homologs in PDB (as of Nov 2020):

PDB aa ident species PDB title

5XFS 56% Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) Crystal structure of PE8-PPE15 in complex with EspG5 from M. tuberculosis
Links to additional information on PE13:
- KEGG - nucleotide and amino acid sequences of gene
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.436 (from Jeremy Rock's lab)
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

PDB	aa ident	species	PDB title
5XFS	56%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of PE8-PPE15 in complex with EspG5 from M. tuberculosis

Amino Acid Sequence

VSFVMAYPEMLAAAADTLQSIGATTVASNAAAAAPTTGVVPPAADEVSALTAAHFAAHAAMYQSVSARAAAIHDQFVATLASSASSYAATEVANAAAAS

(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; 1 non-insertions in a row out of 5 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 5 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 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 6 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 0 non-insertions in a row out of 6 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
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

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:
- No bindings to other targets were found.
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:
- Does not downregulate other genes.
Downregulated by:
- Rv0022c (whiB5)

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv1195 (PE13)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Transcription Rv2359	ahal4789	IDA		Band shift A. Maciag, E. Dainese et al. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J. Bacteriol. 2007
Citation	Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. S. Denkin, S. Byrne et al. Arch. Microbiol. 2005	ahal4789	IDA	16175359	Band shift
Interaction	Transcription Rv2359	ahal4789	IDA		Band shift S. Denkin, S. Byrne et al. Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. Arch. Microbiol. 2005
Citation	The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. RM. Goldstone, SD. Goonesekera et al. Infect. Immun. 2009	ahal4789	IEP	19651861	Co-expression (Functional linkage)
Interaction	Regulatory Rv0485	ahal4789	IEP		Co-expression (Functional linkage) RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009
Citation	The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. RM. Goldstone, SD. Goonesekera et al. Infect. Immun. 2009	ahal4789	TAS	19651861	None
Interaction	PhysicalInteraction Rv1196	ahal4789	TAS		RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009
Citation	Differential expression of PE and PE_PGRS genes in Mycobacterium tuberculosis strains. J. Flores & C. Espitia Gene 2003	ahal4789	NAS	14585500	None
Interaction	Regulatory Rv0279c	ahal4789	NAS		J. Flores & C. Espitia Differential expression of PE and PE_PGRS genes in Mycobacterium tuberculosis strains. Gene 2003
Citation	Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. S. Denkin, S. Byrne et al. Arch. Microbiol. 2005	ahal4789	NAS	16175359	None
Interaction	Regulatory Rv0279c	ahal4789	NAS		S. Denkin, S. Byrne et al. Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. Arch. Microbiol. 2005
Citation	Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. A. Maciag, E. Dainese et al. J. Bacteriol. 2007	ahal4789	IDA	17098899	Band shift
Interaction	Regulatory Rv0485	yashabhasin	IMP		Affinity purification (Physical interaction) RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009
Interaction	RegulatedBy Rv0485	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.. qRT-PCR. mRNA expression levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using qRT-PCR technique. RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009
Interaction	RegulatedBy Rv0485	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.. qRT-PCR. mRNA expression levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using qRT-PCR technique. RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009
Interaction	RegulatedBy Rv0981	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.. H. He, R. Hovey et al. MprAB is a stress-responsive two-component system that directly regulates expression of sigma factors SigB and SigE in Mycobacterium tuberculosis. J. Bacteriol. 2006
Interaction	RegulatedBy Rv2359	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.. A. Maciag, E. Dainese et al. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J. Bacteriol. 2007
Interaction	RegulatedBy Rv2359	yamir.moreno	TAS		Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	RegulatedBy Rv3286c	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.. qRT-PCR. mRNA expression levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using qRT-PCR technique. EP. Williams, JH. Lee et al. Mycobacterium tuberculosis SigF regulates genes encoding cell wall-associated proteins and directly regulates the transcriptional regulatory gene phoY1. J. Bacteriol. 2007
Interaction	RegulatedBy Rv3286c	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.. qRT-PCR. mRNA expression levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using qRT-PCR technique. EP. Williams, JH. Lee et al. Mycobacterium tuberculosis SigF regulates genes encoding cell wall-associated proteins and directly regulates the transcriptional regulatory gene phoY1. J. Bacteriol. 2007
Interaction	RegulatedBy Rv0491	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.. T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Citation	The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. RM. Goldstone, SD. Goonesekera et al. Infect. Immun. 2009	jlew		19651861	reduced expression in Rv0485 mutant. Defined the Rv0485 regulon
Citation	Mycobacterium tuberculosis SigF regulates genes encoding cell wall-associated proteins and directly regulates the transcriptional regulatory gene phoY1. EP. Williams, JH. Lee et al. J. Bacteriol. 2007	jlew		17384187	We found that overexpression of sigF resulted in the differential regulation of many cell wall-associated proteins, including members of the MmpL, PE, and PPE families.

Property

Value

Creator

Evidence

PMID

Comment

Interaction

Transcription Rv2359

ahal4789

IDA

Band shift
A. Maciag, E. Dainese et al. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J. Bacteriol. 2007

Citation

Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. S. Denkin, S. Byrne et al. Arch. Microbiol. 2005

ahal4789

IDA

16175359

Band shift

Interaction

Transcription Rv2359

ahal4789

IDA

Band shift
S. Denkin, S. Byrne et al. Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. Arch. Microbiol. 2005

Citation

The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. RM. Goldstone, SD. Goonesekera et al. Infect. Immun. 2009

ahal4789

IEP

19651861

Co-expression (Functional linkage)

Interaction

Regulatory Rv0485

ahal4789

IEP

Co-expression (Functional linkage)
RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009

Citation

ahal4789

TAS

19651861

None

Interaction

PhysicalInteraction Rv1196

ahal4789

TAS

RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009

Citation

Differential expression of PE and PE_PGRS genes in Mycobacterium tuberculosis strains. J. Flores & C. Espitia Gene 2003

ahal4789

NAS

14585500

None

Interaction

Regulatory Rv0279c

ahal4789

NAS

J. Flores & C. Espitia Differential expression of PE and PE_PGRS genes in Mycobacterium tuberculosis strains. Gene 2003

Citation

Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. S. Denkin, S. Byrne et al. Arch. Microbiol. 2005

ahal4789

NAS

16175359

None

Interaction

Regulatory Rv0279c

ahal4789

NAS

S. Denkin, S. Byrne et al. Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. Arch. Microbiol. 2005

Citation

Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. A. Maciag, E. Dainese et al. J. Bacteriol. 2007

ahal4789

IDA

17098899

Band shift

Interaction

Regulatory Rv0485

yashabhasin

IMP

Affinity purification (Physical interaction)
RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009

Interaction

RegulatedBy Rv0485

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.. qRT-PCR. mRNA expression levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using qRT-PCR technique.
RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009

Interaction

RegulatedBy Rv0485

yamir.moreno

IEP

Interaction

RegulatedBy Rv0981

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..
H. He, R. Hovey et al. MprAB is a stress-responsive two-component system that directly regulates expression of sigma factors SigB and SigE in Mycobacterium tuberculosis. J. Bacteriol. 2006

Interaction

RegulatedBy Rv2359

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..
A. Maciag, E. Dainese et al. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J. Bacteriol. 2007

Interaction

RegulatedBy Rv2359

yamir.moreno

TAS

Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support.
G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008

Interaction

RegulatedBy Rv3286c

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.. qRT-PCR. mRNA expression levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using qRT-PCR technique.
EP. Williams, JH. Lee et al. Mycobacterium tuberculosis SigF regulates genes encoding cell wall-associated proteins and directly regulates the transcriptional regulatory gene phoY1. J. Bacteriol. 2007

Interaction

RegulatedBy Rv3286c

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.. qRT-PCR. mRNA expression levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using qRT-PCR technique.
EP. Williams, JH. Lee et al. Mycobacterium tuberculosis SigF regulates genes encoding cell wall-associated proteins and directly regulates the transcriptional regulatory gene phoY1. J. Bacteriol. 2007

Interaction

RegulatedBy Rv0491

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..
T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003

Citation

jlew

19651861

reduced expression in Rv0485 mutant. Defined the Rv0485 regulon

Citation

Mycobacterium tuberculosis SigF regulates genes encoding cell wall-associated proteins and directly regulates the transcriptional regulatory gene phoY1. EP. Williams, JH. Lee et al. J. Bacteriol. 2007

jlew

17384187

We found that overexpression of sigF resulted in the differential regulation of many cell wall-associated proteins, including members of the MmpL, PE, and PPE families.

Comments