Rv0651 (rplJ)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: 50S ribosomal protein L10
- REFSEQ: 50S ribosomal protein L10
- PATRIC: LSU ribosomal protein L10p (P0)
- TUBERCULIST: 50S ribosomal protein L10 RplJ
- NCBI: 50S ribosomal protein L10 RplJ
- updated information (H37Rv4):
  - gene name: rplJ
  - function:
  - reference:
Type: Not Target
Start: 748276
End: 748812
Operon:

Trans-membrane region:
Role: II.A.1 - Ribosomal protein synthesis and modification
GO terms:
- GO:0042254 - ribosome biogenesis (Uniprot)
- 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:0005515 - protein binding (Uniprot)
- GO:0003735 - structural constituent of ribosome (Uniprot)
- GO:0003723 - RNA binding (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
6DZP	86%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Cryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit
5ZET	86%	Mycobacterium smegmatis str. MC2 155	M. smegmatis P/P state 50S ribosomal subunit
5ZEP	86%	Mycobacterium smegmatis str. MC2 155	M. smegmatis hibernating state 70S ribosome structure
5ZEB	86%	Mycobacterium smegmatis str. MC2 155	M. Smegmatis P/P state 70S ribosome structure
5O61	86%	Mycobacterium smegmatis str. MC2 155	The complete structure of the Mycobacterium smegmatis 70S ribosome
5O60	86%	Mycobacterium smegmatis str. MC2 155	Structure of the 50S large ribosomal subunit from Mycobacterium smegmatis
6DZI	83%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex
5NJT	42%	Bacillus subtilis subsp. subtilis str. 168	Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.
6TPQ	40%	Bacillus subtilis subsp. subtilis str. 168	RNase M5 bound to 50S ribosome with precursor 5S rRNA
6TNN	40%	Bacillus subtilis subsp. subtilis str. 168	Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA

Links to additional information on rplJ:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -14.022 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- Photo of spot titer

Amino Acid Sequence

MARADKATAVADIAAQFKESTATLITEYRGLTVANLAELRRSLTGSATYAVAKNTLIKRAASEAGIEGLDELFVGPTAIAFVTGEPVDAAKAIKTFAKEH
KALVIKGGYMDGHPLTVAEVERIADLESREVLLAKLAGAMKGNLAKAAGLFNAPASQLARLAAALQEKKACPGPDSAE

(Nucleotide sequence available on KEGG)

Additional Information

Analysis of Positive Selection in Clinical Isolates new

Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
- Moldova: 2,057 clinical isolates
- global set: 5,195 clinical isolates from 15 other countries
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.49 (0.24)	1.61 (0.58)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link

* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"

ESSENTIALITY

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

TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions

Rv0651/rplJ, gene len: 536 bp, num TA sites: 6

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	essential	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	essential	7H9	TRASH	essential if hybridization ratio<0.2
in-vivo (mice)	Sassetti 2003 PNAS	no data	BL6 mice	TRASH	essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol)	Griffin 2011 PPath	essential	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	essential	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=0.0)	cholesterol vs glycerol	resampling-SR	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro	Smith 2022 eLife	essential	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	essential	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=0.0)	in-vivo vs in-vitro	ZINB	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal)	Minato 2019 mSys	essential	minimal medium	HMM
in-vitro (YM rich medium)	Minato 2019 mSys	essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, vitamins)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=0.0)	YM rich vs minimal medium	resampling

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:

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0967 (csoR) (Direct binding)
- Rv1423 (whiA) (Direct binding)
- Rv1990c (-) (Direct binding)
- Rv2324 (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0023 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv3058c (-)
- Rv3223c (sigH)

Property	Value	Creator	Evidence	PMID	Comment
Citation	Measurement of the rates of synthesis of three components of ribosomes of Mycobacterium fortuitum: a theoretical approach to qRT-PCR experimentation. authors,MJ. Garcia,MC. Nuez,RA. Cox PLoS ONE 2010	ahal4789	TAS	20644643	Structural analysis
Interaction	PhysicalInteraction Rv0652	ahal4789	TAS		Structural analysis authors,MJ. Garcia,MC. Nuez,RA. Cox Measurement of the rates of synthesis of three components of ribosomes of Mycobacterium fortuitum: a theoretical approach to qRT-PCR experimentation. PLoS ONE 2010
Citation	Measurement of the rates of synthesis of three components of ribosomes of Mycobacterium fortuitum: a theoretical approach to qRT-PCR experimentation. authors,MJ. Garcia,MC. Nuez,RA. Cox PLoS ONE 2010	sourish10	TAS	20644643	Structural analysis
Interaction	PhysicalInteraction Rv0652	sourish10	TAS		Structural analysis authors,MJ. Garcia,MC. Nuez,RA. Cox Measurement of the rates of synthesis of three components of ribosomes of Mycobacterium fortuitum: a theoretical approach to qRT-PCR experimentation. PLoS ONE 2010
Interaction	RegulatedBy Rv3676	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 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

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