Rv0719 (rplF)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: 50S ribosomal protein L6
- REFSEQ: 50S ribosomal protein L6
- PATRIC: LSU ribosomal protein L6p (L9e)
- TUBERCULIST: 50S ribosomal protein L6 RplF
- NCBI: 50S ribosomal protein L6 RplF
- updated information (H37Rv4):
  - gene name: rplF
  - function:
  - reference:
Type: Not Target
Start: 813398
End: 813937
Operon:

Trans-membrane region:
Role: II.A.1 - Ribosomal protein synthesis and modification
GO terms:
- GO:0040007 - growth (Uniprot)
- GO:0030529 - not-found (Uniprot)
- GO:0022625 - cytosolic large ribosomal subunit (Uniprot)
- GO:0019843 - rRNA binding (Uniprot)
- GO:0006412 - translation (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005840 - ribosome (Uniprot)
- GO:0005622 - intracellular (Uniprot)
- GO:0005618 - cell wall (Uniprot)
- GO:0003735 - structural constituent of ribosome (Uniprot)
- GO:0003723 - RNA binding (Uniprot)
- GO:0002181 - cytoplasmic translation (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
5V93	100%	Mycobacterium tuberculosis	Cryo-EM structure of the 70S ribosome from Mycobacterium tuberculosis bound with Capreomycin
5V7Q	100%	Mycobacterium tuberculosis	Cryo-EM structure of the large ribosomal subunit from Mycobacterium tuberculosis bound with a potent linezolid analog
6DZP	87%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Cryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit
5ZET	87%	Mycobacterium smegmatis str. MC2 155	M. smegmatis P/P state 50S ribosomal subunit
5ZEP	87%	Mycobacterium smegmatis str. MC2 155	M. smegmatis hibernating state 70S ribosome structure
5ZEB	87%	Mycobacterium smegmatis str. MC2 155	M. Smegmatis P/P state 70S ribosome structure
5XYM	87%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Large subunit of Mycobacterium smegmatis
5O61	87%	Mycobacterium smegmatis str. MC2 155	The complete structure of the Mycobacterium smegmatis 70S ribosome
5O60	87%	Mycobacterium smegmatis str. MC2 155	Structure of the 50S large ribosomal subunit from Mycobacterium smegmatis
6DZI	86%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex

Links to additional information on rplF:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -17.254 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MSRIGKQPIPVPAGVDVTIEGQSISVKGPKGTLGLTVAEPIKVARNDDGAIVVTRPDDERRNRSLHGLSRTLVSNLVTGVTQGYTTKMEIFGVGYRVQLK
GSNLEFALGYSHPVVIEAPEGITFAVQAPTKFTVSGIDKQKVGQIAANIRRLRRPDPYKGKGVRYEGEQIRRKVGKTGK

(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
Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.999500; 15 non-insertions in a row out of 15 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 15 non-insertions in a row out of 15 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 15 non-insertions in a row out of 15 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 16 non-insertions in a row out of 16 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 16 non-insertions in a row out of 16 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.03
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:
- 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:
- Rv1033c (trcR) (Direct binding)
- Rv2034 (-) (Direct binding)
- Rv1994c (cmtR) (Upstream of operon)

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:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Interaction	PhysicalInteraction Rv0704	anshula.arora1990	IEP		co-expression authors,L. Tailleux,SJ. Waddell,M. Pelizzola,A. Mortellaro,M. Withers,A. Tanne,PR. Castagnoli,B. Gicquel,NG. Stoker,PD. Butcher,M. Foti,O. Neyrolles Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS ONE 2008
Interaction	PhysicalInteraction Rv0714	anshula.arora1990	IEP		co-expression authors,L. Tailleux,SJ. Waddell,M. Pelizzola,A. Mortellaro,M. Withers,A. Tanne,PR. Castagnoli,B. Gicquel,NG. Stoker,PD. Butcher,M. Foti,O. Neyrolles Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS ONE 2008
Interaction	PhysicalInteraction Rv0719	anshula.arora1990	IEP		co-expression authors,L. Tailleux,SJ. Waddell,M. Pelizzola,A. Mortellaro,M. Withers,A. Tanne,PR. Castagnoli,B. Gicquel,NG. Stoker,PD. Butcher,M. Foti,O. Neyrolles Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS ONE 2008
Interaction	PhysicalInteraction Rv0719	anshula.arora1990	IEP		co-expression authors,L. Tailleux,SJ. Waddell,M. Pelizzola,A. Mortellaro,M. Withers,A. Tanne,PR. Castagnoli,B. Gicquel,NG. Stoker,PD. Butcher,M. Foti,O. Neyrolles Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS ONE 2008
Citation	Comparison of ribosomes and ribosomal proteins of sensitive and resistant mycobacteria. authors,I. Medow,S. Rsch-Gerdes,KH. Schrder Zentralbl Bakteriol Mikrobiol Hyg A 1987	anshula.arora1990	IEP	3125705	co-expression
Interaction	PhysicalInteraction Rv0704	anshula.arora1990	IEP		co-expression authors,I. Medow,S. Rsch-Gerdes,KH. Schrder Comparison of ribosomes and ribosomal proteins of sensitive and resistant mycobacteria. Zentralbl Bakteriol Mikrobiol Hyg A 1987
Interaction	PhysicalInteraction Rv0714	anshula.arora1990	IEP		co-expression authors,I. Medow,S. Rsch-Gerdes,KH. Schrder Comparison of ribosomes and ribosomal proteins of sensitive and resistant mycobacteria. Zentralbl Bakteriol Mikrobiol Hyg A 1987
Interaction	PhysicalInteraction Rv0719	anshula.arora1990	IEP		co-expression authors,I. Medow,S. Rsch-Gerdes,KH. Schrder Comparison of ribosomes and ribosomal proteins of sensitive and resistant mycobacteria. Zentralbl Bakteriol Mikrobiol Hyg A 1987
Interaction	PhysicalInteraction Rv0719	anshula.arora1990	IEP		co-expression authors,I. Medow,S. Rsch-Gerdes,KH. Schrder Comparison of ribosomes and ribosomal proteins of sensitive and resistant mycobacteria. Zentralbl Bakteriol Mikrobiol Hyg A 1987
Citation	Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. authors,L. Tailleux,SJ. Waddell,M. Pelizzola,A. Mortellaro,M. Withers,A. Tanne,PR. Castagnoli,B. Gicquel,NG. Stoker,PD. Butcher,M. Foti,O. Neyrolles PLoS ONE 2008	anshula.arora1990	IEP	18167562	co-expression
Interaction	RegulatedBy Rv0348	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.. B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009

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