Rv1222 (rseA)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: RNA polymerase sigma-70 factor ECF subfamily
- REFSEQ: hypothetical protein
- PATRIC: FIG00820548: hypothetical protein
- TUBERCULIST: Anti-sigma factor RseA
- NCBI: Anti-sigma factor RseA
- updated information (H37Rv4):
  - gene name: rseA
  - function:
  - reference:
Type: Not Target
Start: 1365344
End: 1365808
Operon:

Trans-membrane region:
Role: VI - Unknowns
GO terms:
- GO:0046872 - metal ion binding (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0005737 - cytoplasm (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 rseA:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -3.128 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MADPGSVGHVFRRAFSWLPAQFASQSDAPVGAPRQFRSTEHLSIEAIAAFVDGELRMNAHLRAAHHLSLCAQCAAEVDDQSRARAALRDSHPIRIPSTLL
GLLSEIPRCPPEGPSKGSSGGSSQGPPDGAAAGFGDRFADGDGGNRGRQSRVRR

(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; 1 non-insertions in a row out of 2 sites
Too-Short	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 2 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: 0.79
Uncertain	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:
- Rv0047c (-) (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
Citation	RseA, the SigE specific anti-sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis. S. Barik, K. Sureka et al. Mol. Microbiol. 2010	harsharohiratruefriend	IDA	20025669	mass spectrometry
Interaction	ActivatedBy Rv0018c	harsharohiratruefriend	IDA		mass spectrometry S. Barik, K. Sureka et al. RseA, the SigE specific anti-sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis. Mol. Microbiol. 2010
Citation	Sigma factors and global gene regulation in Mycobacterium tuberculosis. R. Manganelli,R. Provvedi,S. Rodrigue,J. Beaucher,L. Gaudreau,I. Smith,R. Proveddi J. Bacteriol. 2004	harsharohiratruefriend	IDA	14761983	mass spectrometry
Interaction	ActivatedBy Rv0018c	harsharohiratruefriend	IDA		mass spectrometry R. Manganelli,R. Provvedi,S. Rodrigue,J. Beaucher,L. Gaudreau,I. Smith,R. Proveddi Sigma factors and global gene regulation in Mycobacterium tuberculosis. J. Bacteriol. 2004
Interaction	Inhibits Rv1221	deeps8891	IPI		affinity purification V. Don, S. Rodrigue et al. Evidence of complex transcriptional, translational, and posttranslational regulation of the extracytoplasmic function sigma factor sigmaE in Mycobacterium tuberculosis. J. Bacteriol. 2008
Citation	RseA, the SigE specific anti-sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis. S. Barik, K. Sureka et al. Mol. Microbiol. 2010	harsharohiratruefriend	IDA	20025669	affinity purification
Interaction	InhibitedBy Rv0384c	harsharohiratruefriend	IDA		affinity purification S. Barik, K. Sureka et al. RseA, the SigE specific anti-sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis. Mol. Microbiol. 2010
Citation	Sigma factors and global gene regulation in Mycobacterium tuberculosis. R. Manganelli,R. Provvedi,S. Rodrigue,J. Beaucher,L. Gaudreau,I. Smith,R. Proveddi J. Bacteriol. 2004	harsharohiratruefriend	IDA	14761983	affinity purification
Interaction	InhibitedBy Rv0384c	harsharohiratruefriend	IDA		affinity purification R. Manganelli,R. Provvedi,S. Rodrigue,J. Beaucher,L. Gaudreau,I. Smith,R. Proveddi Sigma factors and global gene regulation in Mycobacterium tuberculosis. J. Bacteriol. 2004
Citation	RseA, the SigE specific anti-sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis. S. Barik, K. Sureka et al. Mol. Microbiol. 2010	harsharohiratruefriend	IDA	20025669	mass spectrometry
Interaction	InhibitedBy Rv0014c	harsharohiratruefriend	IDA		mass spectrometry S. Barik, K. Sureka et al. RseA, the SigE specific anti-sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis. Mol. Microbiol. 2010
Citation	Sigma factors and global gene regulation in Mycobacterium tuberculosis. R. Manganelli,R. Provvedi,S. Rodrigue,J. Beaucher,L. Gaudreau,I. Smith,R. Proveddi J. Bacteriol. 2004	harsharohiratruefriend	IDA	14761983	mass spectrometry
Interaction	InhibitedBy Rv0014c	harsharohiratruefriend	IDA		mass spectrometry R. Manganelli,R. Provvedi,S. Rodrigue,J. Beaucher,L. Gaudreau,I. Smith,R. Proveddi Sigma factors and global gene regulation in Mycobacterium tuberculosis. J. Bacteriol. 2004
Citation	RseA, the SigE specific anti-sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis. S. Barik, K. Sureka et al. Mol. Microbiol. 2010	deeps8891	IPI	20025669	affinity purification
Interaction	Inhibits Rv1221	deeps8891	IPI		affinity purification S. Barik, K. Sureka et al. RseA, the SigE specific anti-sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis. Mol. Microbiol. 2010
Citation	Sigma factors and global gene regulation in Mycobacterium tuberculosis. R. Manganelli,R. Provvedi,S. Rodrigue,J. Beaucher,L. Gaudreau,I. Smith,R. Proveddi J. Bacteriol. 2004	deeps8891	IPI	14761983	affinity purification
Interaction	Inhibits Rv1221	deeps8891	IPI		affinity purification R. Manganelli,R. Provvedi,S. Rodrigue,J. Beaucher,L. Gaudreau,I. Smith,R. Proveddi Sigma factors and global gene regulation in Mycobacterium tuberculosis. J. Bacteriol. 2004
Citation	Evidence of complex transcriptional, translational, and posttranslational regulation of the extracytoplasmic function sigma factor sigmaE in Mycobacterium tuberculosis. V. Don, S. Rodrigue et al. J. Bacteriol. 2008	deeps8891	IPI	18606740	affinity purification

TB Genome Annotation Portal