Rv0700 (rpsJ)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: 30S ribosomal protein S10
- REFSEQ: 30S ribosomal protein S10
- PATRIC: SSU ribosomal protein S10p (S20e)
- TUBERCULIST: 30S ribosomal protein S10 RpsJ (transcription antitermination factor NusE)
- NCBI: 30S ribosomal protein S10 RpsJ (transcription antitermination factor NusE)
- updated information (H37Rv4):
  - gene name: rpsJ
  - function:
  - reference:
Type: Not Target
Start: 800487
End: 800792
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:0015935 - small ribosomal subunit (Uniprot)
- GO:0006412 - translation (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005840 - ribosome (Uniprot)
- GO:0005829 - cytosol (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
5V93	100%	Mycobacterium tuberculosis	Cryo-EM structure of the 70S ribosome from Mycobacterium tuberculosis bound with Capreomycin
6DZI	97%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex
6DZK	97%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Cryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosomal subunit with MPY
5ZEU	97%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	M. smegmatis P/P state 30S ribosomal subunit
5ZEP	97%	Mycobacterium smegmatis str. MC2 155	M. smegmatis hibernating state 70S ribosome structure
5ZEB	97%	Mycobacterium smegmatis str. MC2 155	M. Smegmatis P/P state 70S ribosome structure
5XYU	97%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Small subunit of Mycobacterium smegmatis ribosome
5O61	97%	Mycobacterium smegmatis str. MC2 155	The complete structure of the Mycobacterium smegmatis 70S ribosome
5O5J	97%	Mycobacterium smegmatis str. MC2 155	Structure of the 30S small ribosomal subunit from Mycobacterium smegmatis
5TCU	76%	Staphylococcus aureus (strain NCTC 8325)	Methicillin sensitive Staphylococcus aureus 70S ribosome

Links to additional information on rpsJ:
- 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 = -12.87 (from Jeremy Rock's lab)
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VAGQKIRIRLKAYDHEAIDASARKIVETVVRTGASVVGPVPLPTEKNVYCVIRSPHKYKDSREHFEMRTHKRLIDIIDPTPKTVDALMRIDLPASVDVNI
Q

(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
Too-Short	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 6 non-insertions in a row out of 6 sites
Too-Short	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 6 non-insertions in a row out of 6 sites
Too-Short	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 6 non-insertions in a row out of 6 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000450; 6 non-insertions in a row out of 7 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000450; 6 non-insertions in a row out of 7 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.1
Growth-Defect	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:
- Rv1816 (-) (Direct binding)
- Rv3219 (whiB1) (Direct binding)

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 Rv2533c	priyadarshinipriyanka2001	IDA		Structural Analysis B. Gopal, LF. Haire et al. The crystal structure of NusB from Mycobacterium tuberculosis. Nat. Struct. Biol. 2000
Interaction	PhysicalInteraction Rv2533c	priyadarshinipriyanka2001	IDA		Structural Analysis B. Gopal, RA. Cox et al. Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance-B (NusB) from Mycobacterium tuberculosis. Acta Crystallogr. D Biol. Crystallogr. 2000
Interaction	PhysicalInteraction Rv0709	ravirajsoni	IEP		Co-expression (Functional linkage) authors,R. Wang,JT. Prince,EM. Marcotte Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res. 2005
Interaction	PhysicalInteraction Rv0708	ravirajsoni	IEP		Co-expression (Functional linkage) authors,R. Wang,JT. Prince,EM. Marcotte Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res. 2005
Interaction	PhysicalInteraction Rv0707	ravirajsoni	IEP		Co-expression (Functional linkage) authors,R. Wang,JT. Prince,EM. Marcotte Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res. 2005
Interaction	PhysicalInteraction Rv0705	ravirajsoni	IEP		Co-expression (Functional linkage) authors,R. Wang,JT. Prince,EM. Marcotte Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res. 2005
Interaction	PhysicalInteraction Rv0703	ravirajsoni	IEP		Co-expression (Functional linkage) authors,R. Wang,JT. Prince,EM. Marcotte Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res. 2005
Citation	mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. B. Abomoelak, EA. Hoye et al. J. Bacteriol. 2009	ashwinigbhat	IEP	19648248	DNA Microarray Analysis
Interaction	Regulatory Rv0348	ashwinigbhat	IEP		DNA Microarray Analysis B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009
Interaction	Regulatory Rv0703	ravirajsoni	IPI		ChIP (Physical interaction) authors,S. Rodrigue,J. Brodeur,PE. Jacques,AL. Gervais,R. Brzezinski,L. Gaudreau Identification of mycobacterial sigma factor binding sites by chromatin immunoprecipitation assays. J. Bacteriol. 2007
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.. 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. B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009
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.. 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. B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009
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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