Rv2055c (rpsR2)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: 30S ribosomal protein S18 2
- REFSEQ: 30S ribosomal protein S18
- PATRIC: SSU ribosomal protein S18p @ SSU ribosomal protein S18p zinc-independent
- TUBERCULIST: 30S ribosomal protein S18 RpsR2
- NCBI: 30S ribosomal protein S18 RpsR2
- updated information (H37Rv4):
  - gene name: rpsR2
  - function:
  - reference:
Type: Not Target
Start: 2314087
End: 2314353
Operon:

Trans-membrane region:
Role: II.A.1 - Ribosomal protein synthesis and modification
GO terms:
- GO:0030529 - not-found (Uniprot)
- GO:0022627 - cytosolic small 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)
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
6DZK	63%	Mycobacterium smegmatis	Cryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosomal subunit with MPY
6DZI	63%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex
6S13	57%	Staphylococcus aureus	Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22).
6S0X	57%	Staphylococcus aureus	Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22) in complex with erythromycin.
6FXC	57%	Staphylococcus aureus	The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus
5T7V	57%	Staphylococcus aureus	Methicillin Resistant, Linezolid resistant Staphylococcus aureus 70S ribosome (delta S145 uL3)
5ZEU	57%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	M. smegmatis P/P state 30S ribosomal subunit
5ZEP	57%	Mycobacterium smegmatis str. MC2 155	M. smegmatis hibernating state 70S ribosome structure
5ZEB	57%	Mycobacterium smegmatis str. MC2 155	M. Smegmatis P/P state 70S ribosome structure
5XYU	57%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Small subunit of Mycobacterium smegmatis ribosome

Links to additional information on rpsR2:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.295 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MAAKSARKGPTKAKKNLLDSLGVESVDYKDTATLRVFISDRGKIRSRGVTGLTVQQQRQVAQAIKNAREMALLPYPGQDRQRRAALCP

(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 3 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 3 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 3 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 3 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 3 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: 0.45
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:

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0081 (-) (Direct binding)
- Rv0678 (-) (Direct binding)
- Rv0767c (-) (Direct binding)
- Rv1985c (-) (Upstream of operon)
- Rv2359 (zur) (Upstream of operon)
- Rv3488 (-) (Upstream of operon)
- Rv3597c (lsr2) (Upstream of operon)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv1358 (-)

Property	Value	Creator	Evidence	PMID	Comment
Citation	Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. A. Maciag, E. Dainese et al. J. Bacteriol. 2007	akankshajain.21	IEP	17098899	Co-expression (Functional linkage)
Interaction	RegulatedBy Rv2359	akankshajain.21	IEP		Co-expression (Functional linkage) A. Maciag, E. Dainese et al. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J. Bacteriol. 2007
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

TB Genome Annotation Portal