Rv0668 (rpoC)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: DNA-directed RNA polymerase subunit beta'
- REFSEQ: DNA-directed RNA polymerase subunit beta'
- PATRIC: DNA-directed RNA polymerase beta' subunit (EC 2.7.7.6)
- TUBERCULIST: DNA-directed RNA polymerase (beta' chain) RpoC (transcriptase beta' chain) (RNA polymerase beta' subunit).
- NCBI: DNA-directed RNA polymerase (beta' chain) RpoC (transcriptase beta' chain) (RNA polymerase beta' subunit)
- updated information (H37Rv4):
  - gene name: rpoC
  - function:
  - reference:
Type: Not Target
Start: 763370
End: 767320
Operon:

Trans-membrane region:
Role: II.A.7 - RNA synthesis, RNA modification and DNA transcription
GO terms:
- GO:0040007 - growth (Uniprot)
- GO:0016779 - nucleotidyltransferase activity (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005618 - cell wall (Uniprot)
- GO:0003899 - DNA-directed 5'-3' RNA polymerase activity (Uniprot)
- GO:0003677 - DNA binding (Uniprot)
- GO:0000428 - DNA-directed RNA polymerase complex (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
6KOQ	100%	Mycobacterium tuberculosis H37Rv	Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 10 nt
6KOP	100%	Mycobacterium tuberculosis H37Rv	Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 9 nt
6KOO	100%	Mycobacterium tuberculosis H37Rv	Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 7 nt
6KON	100%	Mycobacterium tuberculosis H37Rv	Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 5 nt
6JCY	100%	Mycobacterium tuberculosis H37Rv	Mycobacterium tuberculosis RNA polymerase transcription initiation open complex with a chimeric ECF sigma factor sigH/E
6JCX	100%	Mycobacterium tuberculosis H37Rv	Mycobacterium tuberculosis transcription initiation complex with ECF sigma factor sigma H and 6nt RNA
5ZX3	100%	Mycobacterium tuberculosis H37Rv	Mycobacterium tuberculosis RNA polymerase holoenzyme with ECF sigma factor sigma H
5ZX2	100%	Mycobacterium tuberculosis H37Rv	Mycobacterium tuberculosis RNA polymerase transcription initiation complex with ECF sigma factor sigma H and 7nt RNA
5UH7	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of beta'MtbSI of Mycobacterium tuberculosis RNA polymerase
6VW0	99%	Mycobacterium tuberculosis	Mycobacterium tuberculosis RNAP S456L mutant open promoter complex

Links to additional information on rpoC:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -9.785 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VLDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAP
VTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDG
GEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRYGEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVA
AFQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLK
SLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNR
APTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQ
PASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDL
AERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDHYEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPII
TIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVE
LAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAA
QSIGEPGTQLTMRTFHQGGVGEDITGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGERFYKITIVPDDGGEEVVYDKISKRQRLRVFKHEDGSERVLS
DGDHVEVGQQLMEGSADPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEP
AAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRNIAVQPTEEARAAAYTIPSYEDQYYSPDFGAA
TGAAVPLDDYGYSDYR

(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
Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 45 non-insertions in a row out of 51 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 42 non-insertions in a row out of 51 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 41 non-insertions in a row out of 51 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 46 non-insertions in a row out of 52 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 46 non-insertions in a row out of 52 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.02
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:
- Rv0023 (-) (Direct binding)
- Rv0081 (-) (Direct binding)
- Rv0135c (-) (Direct binding)
- Rv0324 (-) (Direct binding)
- Rv0576 (-) (Direct binding)
- Rv1816 (-) (Direct binding)
- Rv1985c (-) (Direct binding)
- Rv3133c (devR) (Direct binding)
- Rv3597c (lsr2) (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 Rv1390	ahal4789	ISO		Structural analysis authors,R. Mathew,M. Ramakanth,D. Chatterji Deletion of the gene rpoZ, encoding the omega subunit of RNA polymerase, in Mycobacterium smegmatis results in fragmentation of the beta' subunit in the enzyme assembly. J. Bacteriol. 2005
Interaction	PhysicalInteraction Rv1390	sourish10	ISO		Structural analysis authors,R. Mathew,M. Ramakanth,D. Chatterji Deletion of the gene rpoZ, encoding the omega subunit of RNA polymerase, in Mycobacterium smegmatis results in fragmentation of the beta' subunit in the enzyme assembly. J. Bacteriol. 2005
Interaction	PhysicalInteraction Rv0667	prabhakarsmail	TAS		Kinetic Assays LP. Miller, JT. Crawford et al. The rpoB gene of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 1994
Citation	The rpoB gene of Mycobacterium tuberculosis. LP. Miller, JT. Crawford et al. Antimicrob. Agents Chemother. 1994	prabhakarsmail	TAS	8031050	Kinetic Assays
Interaction	PhysicalInteraction Rv3457c	prabhakarsmail	TAS		Kinetic Assays LP. Miller, JT. Crawford et al. The rpoB gene of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 1994
Interaction	PhysicalInteraction Rv0667	prabhakarsmail	TAS		Kinetic Assays LP. Miller, JT. Crawford et al. The rpoB gene of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 1994
Interaction	PhysicalInteraction Rv2703	prabhakarsmail	TAS		Kinetic Assays LP. Miller, JT. Crawford et al. The rpoB gene of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 1994

TB Genome Annotation Portal