Rv0900 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: POSSIBLE MEMBRANE PROTEIN
- TUBERCULIST: Possible membrane protein
- NCBI: Possible membrane protein
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Type: Not Target
Start: 1003805
End: 1003957
Operon:

Trans-membrane region:
Role: VI - Unknowns
GO terms:
- GO:0044119 - growth of symbiont in host cell (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0005886 - plasma membrane (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): (none with >35% aa id)
Links to additional information on Rv0900:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -0.813 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MDFVIQWSCYLLAFLGGSAVAWVVVTLSIKRASRDEGAAEAPSAAETGAQ

(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; 1 non-insertions in a row out of 2 sites
Too-Short	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 2 sites
Too-Short	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 2 sites
Too-Short	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 2 sites
Too-Short	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 2 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.19
Non-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:
- 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:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Interaction	PhysicalInteraction Rv0901	shahanup86	NAS		Operon (Functional linkage) L. Zhang, Q. Zhong et al. Rv0901 from Mycobacterium tuberculosis, a possible novel virulent gene proved through the recombinant Mycobacterium smegmatis. Jpn. J. Infect. Dis. 2009
Interaction	PhysicalInteraction Rv0901	shahanup86	NAS		Operon (Functional linkage) Q. Zhong, L. Bao et al. [Effect of transfected Rv0901 gene on the activity of mice macrophages] Sichuan Da Xue Xue Bao Yi Xue Ban 2007
Interaction	PhysicalInteraction Rv0901	shahanup86	NAS		Operon (Functional linkage) authors,CM. Sassetti,DH. Boyd,EJ. Rubin Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 2003
Interaction	PhysicalInteraction Rv0901	shahanup86	NAS		Operon (Functional linkage) P. Teriete,Y. Yao,A. Kolodzik,J. Yu,H. Song,M. Niederweis,FM. Marassi Mycobacterium tuberculosis Rv0899 adopts a mixed alpha/beta-structure and does not form a transmembrane beta-barrel. Biochemistry 2010
Interaction	PhysicalInteraction Rv0901	shahanup86	NAS		Operon (Functional linkage) I. Olsen, TB. Johansen et al. A novel IS element, ISMpa1, in Mycobacterium avium subsp. paratuberculosis. Vet. Microbiol. 2004
Interaction	PhysicalInteraction Rv0899	shahanup86	NAS		Operon (Functional linkage) I. Schiller, HM. Vordermeier et al. Assessment of Mycobacterium tuberculosis OmpATb as a novel antigen for the diagnosis of bovine tuberculosis. Clin. Vaccine Immunol. 2009
Citation	Mycobacterium tuberculosis Rv0899 adopts a mixed alpha/beta-structure and does not form a transmembrane beta-barrel. P. Teriete,Y. Yao,A. Kolodzik,J. Yu,H. Song,M. Niederweis,FM. Marassi Biochemistry 2010	shahanup86	NAS	20199110	Operon (Functional linkage)
Interaction	PhysicalInteraction Rv0901	shahanup86	NAS		Operon (Functional linkage) P. Teriete,Y. Yao,A. Kolodzik,J. Yu,H. Song,M. Niederweis,FM. Marassi Mycobacterium tuberculosis Rv0899 adopts a mixed alpha/beta-structure and does not form a transmembrane beta-barrel. Biochemistry 2010
Interaction	PhysicalInteraction Rv0899	shahanup86	NAS		Operon (Functional linkage) P. Teriete,Y. Yao,A. Kolodzik,J. Yu,H. Song,M. Niederweis,FM. Marassi Mycobacterium tuberculosis Rv0899 adopts a mixed alpha/beta-structure and does not form a transmembrane beta-barrel. Biochemistry 2010
Citation	A novel IS element, ISMpa1, in Mycobacterium avium subsp. paratuberculosis. I. Olsen, TB. Johansen et al. Vet. Microbiol. 2004	shahanup86	NAS	15036538	Operon (Functional linkage)
Interaction	PhysicalInteraction Rv0901	shahanup86	NAS		Operon (Functional linkage) I. Olsen, TB. Johansen et al. A novel IS element, ISMpa1, in Mycobacterium avium subsp. paratuberculosis. Vet. Microbiol. 2004
Interaction	PhysicalInteraction Rv0899	shahanup86	NAS		Operon (Functional linkage) I. Olsen, TB. Johansen et al. A novel IS element, ISMpa1, in Mycobacterium avium subsp. paratuberculosis. Vet. Microbiol. 2004
Interaction	PhysicalInteraction Rv0899	shahanup86	NAS		Operon (Functional linkage) authors,Y. Xiong,MJ. Chalmers,FP. Gao,TA. Cross,AG. Marshall Identification of Mycobacterium tuberculosis H37Rv integral membrane proteins by one-dimensional gel electrophoresis and liquid chromatography electrospray ionization tandem mass spectrometry. J. Proteome Res. null
Interaction	PhysicalInteraction Rv0899	shahanup86	NAS		Operon (Functional linkage) H. Song, R. Sandie et al. Identification of outer membrane proteins of Mycobacterium tuberculosis. Tuberculosis (Edinburgh, Scotland) 2008
Interaction	PhysicalInteraction Rv0899	shahanup86	NAS		Operon (Functional linkage) P. Teriete,Y. Yao,A. Kolodzik,J. Yu,H. Song,M. Niederweis,FM. Marassi Mycobacterium tuberculosis Rv0899 adopts a mixed alpha/beta-structure and does not form a transmembrane beta-barrel. Biochemistry 2010

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