Rv3414c (sigD)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: sigma-70 family RNA polymerase sigma factor
- REFSEQ: RNA polymerase sigma factor SigD
- PATRIC: RNA polymerase sigma-70 factor
- TUBERCULIST: Probable alternative RNA polymerase sigma-D factor SigD
- NCBI: Probable alternative RNA polymerase sigma-D factor SigD
- updated information (H37Rv4):
  - gene name: sigD
  - function:
  - reference:
Type: Not Target
Start: 3833038
End: 3833676
Operon:

Trans-membrane region:
Role: II.A.7 - RNA synthesis, RNA modification and DNA transcription
GO terms:
- GO:2000142 - regulation of DNA-templated transcription, initiation (Uniprot)
- GO:0050708 - regulation of protein secretion (Uniprot)
- GO:0019217 - regulation of fatty acid metabolic process (Uniprot)
- GO:0016987 - bacterial sigma factor activity (Uniprot)
- GO:0009408 - response to heat (Uniprot)
- GO:0009405 - pathogenesis (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0006352 - DNA-templated transcription, initiation (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0003700 - DNA binding transcription factor activity (Uniprot)
- GO:0003677 - DNA 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: 3vfz, 3vep
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
3VFZ	100%	Mycobacterium tuberculosis	Crystal structure of -35 promoter binding domain of SigD of Mycobacterium tuberculosis
3VEP	100%	Mycobacterium tuberculosis	Crystal structure of SigD4 in complex with its negative regulator RsdA

Links to additional information on sigD:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.331 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MVDPGVSPGCVRFVTLEISPSMTMQGERLDAVVAEAVAGDRNALREVLETIRPIVVRYCRARVGTVERSGLSADDVAQEVCLATITALPRYRDRGRPFLA
FLYGIAAHKVADAHRAAGRDRAYPAETLPERWSADAGPEQMAIEADSVTRMNELLEILPAKQREILILRVVVGLSAEETAAAVGSTTGAVRVAQHRALQR
LKDEIVAAGDYA

(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; 2 non-insertions in a row out of 9 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 9 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 9 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 9 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 9 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: 0.65
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

Binds To:
Bound By:

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

Binds To:
- Rv2107 (PE22) (Direct binding)
- Rv3414c (sigD) (Direct binding)
Bound By:
- Rv0047c (-) (Direct binding)
- Rv0135c (-) (Direct binding)
- Rv2324 (-) (Direct binding)
- Rv3414c (sigD) (Direct binding)
- Rv3488 (-) (Direct binding)
- Rv0081 (-) (Upstream of operon)
- Rv1033c (trcR) (Upstream of operon)
- Rv1985c (-) (Upstream of operon)

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

Upregulates:
Upregulated by:
- Rv3414c (sigD)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv3414c (sigD)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Regulatory Rv3717	vijayachitra	NAS		EC. Hett, MC. Chao et al. A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog. 2008
Interaction	Regulatory Rv3717	aparna.vchalam	NAS		HI. Boshoff, TG. Myers et al. The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. J. Biol. Chem. 2004
Interaction	Regulatory Rv3717	aparna.vchalam	NAS		EC. Hett, MC. Chao et al. A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog. 2008
Interaction	Regulatory Rv3717	vijayachitra	NAS		HI. Boshoff, TG. Myers et al. The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. J. Biol. Chem. 2004
Interaction	Regulatory Rv3675	jhum4u2006	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv3675	jhum4u2006	IEP		Co-expression (Functional linkage) authors,V. Makarov,G. Manina,K. Mikusova,U. Mllmann,O. Ryabova,B. Saint-Joanis,N. Dhar,MR. Pasca,S. Buroni,AP. Lucarelli,A. Milano,E. De Rossi,M. Belanova,A. Bobovska,P. Dianiskova,J. Kordulakova,C. Sala,E. Fullam,P. Schneider,JD. McKinney,P. Brodin,T. Christophe,S. Waddell,P. Butcher,J. Albrethsen,I. Rosenkrands,R. Brosch,V. Nandi,S. Bharath,S. Gaonkar,RK. Shandil,V. Balasubramanian,T. Balganesh,S. Tyagi,J. Grosset,G. Riccardi,ST. Cole Benzothiazinones kill Mycobacterium tuberculosis by blocking arabinan synthesis. Science 2009
Interaction	Regulatory Rv3647c	poorsekurdhanaraju	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv1884c	swatigandhi19	IMP		Co-expression(Functional Linkage) H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005
Citation	Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. S. Raman, R. Hazra et al. J. Bacteriol. 2004	swatigandhi19	IMP	15375142	Co-expression(Functional Linkage)
Interaction	Regulatory Rv1815	swatigandhi19	IMP		Co-expression(Functional Linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv1884c	swatigandhi19	IMP		Co-expression(Functional Linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv3413c	shefin84	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv3413c	shefin84	IEP		Co-expression (Functional linkage) KG. Thakur,AM. Joshi,B. Gopal Structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function sigma factor sigma(C) from Mycobacterium tuberculosis. J. Biol. Chem. 2007
Citation	The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. H. Calamita, C. Ko et al. Cell. Microbiol. 2005	swatigandhi19	IMP	15659067	Co-expression(Functional Linkage)
Interaction	Regulatory Rv1815	swatigandhi19	IMP		Co-expression(Functional Linkage) H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005
Interaction	Transcription Rv3212	sourish10	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv2889c	shahanup86	IEP		Co-expression (Functional linkage) H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005
Interaction	Translation Rv2441c	priti.priety	IMP		Co expression Analysis H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005
Interaction	Transcription Rv2396	sourish10	IPI		Affinity purification (Physical interaction) SB. Walters, E. Dubnau et al. The Mycobacterium tuberculosis PhoPR two-component system regulates genes essential for virulence and complex lipid biosynthesis. Mol. Microbiol. 2006
Interaction	Transcription Rv2396	sourish10	IPI		Affinity purification (Physical interaction) G. Bai, LA. McCue et al. Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a cyclic AMP receptor protein-like DNA binding protein. J. Bacteriol. 2005
Interaction	Transcription Rv2396	sourish10	IPI		Affinity purification (Physical interaction) H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005
Interaction	Regulatory Rv2348c	akankshajain.21	IEP		Co-expression (Functional linkage) 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
Interaction	Regulatory Rv2348c	akankshajain.21	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv1883c	madhulsbu	IEP		Co-expression (Functional linkage) authors,LM. Iyer,EV. Koonin,L. Aravind Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily. Proteins 2001
Interaction	Regulatory Rv1883c	madhulsbu	IEP		Co-expression (Functional linkage) authors,RP. Carithers,DC. Yoch,DI. Arnon Two forms of nitrogenase from the photosynthetic bacterium Rhodospirillum rubrum. J. Bacteriol. 1979
Interaction	Regulatory Rv1815	madhulsbu	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv1816	madhulsbu	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv1450c	balaganesh727	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv1450c	balaganesh727	IEP		Co-expression (Functional linkage) J. Flores & C. Espitia Differential expression of PE and PE_PGRS genes in Mycobacterium tuberculosis strains. Gene 2003
Interaction	Regulatory Rv1450c	balaganesh727	IEP		Co-expression (Functional linkage) authors,JE. Clark-Curtiss,SE. Haydel Molecular genetics of Mycobacterium tuberculosis pathogenesis. Annu. Rev. Microbiol. 2003
Interaction	Transcription Rv0685	sourish10	IEP		Co-expression (Functional linkage) B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009
Interaction	Transcription Rv0684	sourish10	IEP		Co-expression (Functional linkage) H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005
Interaction	Transcription Rv0684	sourish10	IEP		Co-expression (Functional linkage) B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009
Interaction	Transcription Rv0685	sourish10	IEP		Co-expression (Functional linkage) H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005
Interaction	Regulatory Rv0182c	priti.priety	IEP		Co-expression (Functional linkage) JH. Lee, DE. Geiman et al. Role of stress response sigma factor SigG in Mycobacterium tuberculosis. J. Bacteriol. 2008
Interaction	Regulatory Rv0124	prabhakarsmail	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	RegulatedBy Rv0182c	yamir.moreno	IEP		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. JH. Lee, DE. Geiman et al. Role of stress response sigma factor SigG in Mycobacterium tuberculosis. J. Bacteriol. 2008
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3874	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3875	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3537	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3538	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3417c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009	yamir.moreno	IDA	19228590	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
Interaction	Regulates Rv3418c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008	yamir.moreno	TAS	18985025	Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support.
Interaction	Regulates Rv0341	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
Citation	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008	yamir.moreno	TAS	18985025	Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support.
Interaction	Regulates Rv1815	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
Citation	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008	yamir.moreno	TAS	18985025	Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support.
Interaction	Regulates Rv1884c	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
Citation	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008	yamir.moreno	TAS	18985025	Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support.
Interaction	Regulates Rv3414c	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
Interaction	RegulatedBy Rv3414c	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

Property

Value

Creator

Evidence

PMID

Comment

Interaction

Regulatory Rv3717

vijayachitra

NAS

EC. Hett, MC. Chao et al. A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog. 2008

Interaction

Regulatory Rv3717

aparna.vchalam

NAS

HI. Boshoff, TG. Myers et al. The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. J. Biol. Chem. 2004

Interaction

Regulatory Rv3717

aparna.vchalam

NAS

EC. Hett, MC. Chao et al. A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog. 2008

Interaction

Regulatory Rv3717

vijayachitra

NAS

HI. Boshoff, TG. Myers et al. The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. J. Biol. Chem. 2004

Interaction

Regulatory Rv3675

jhum4u2006

IEP

Co-expression (Functional linkage)
S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004

Interaction

Regulatory Rv3675

jhum4u2006

IEP

Co-expression (Functional linkage)
authors,V. Makarov,G. Manina,K. Mikusova,U. Mllmann,O. Ryabova,B. Saint-Joanis,N. Dhar,MR. Pasca,S. Buroni,AP. Lucarelli,A. Milano,E. De Rossi,M. Belanova,A. Bobovska,P. Dianiskova,J. Kordulakova,C. Sala,E. Fullam,P. Schneider,JD. McKinney,P. Brodin,T. Christophe,S. Waddell,P. Butcher,J. Albrethsen,I. Rosenkrands,R. Brosch,V. Nandi,S. Bharath,S. Gaonkar,RK. Shandil,V. Balasubramanian,T. Balganesh,S. Tyagi,J. Grosset,G. Riccardi,ST. Cole Benzothiazinones kill Mycobacterium tuberculosis by blocking arabinan synthesis. Science 2009

Interaction

Regulatory Rv3647c

poorsekurdhanaraju

IEP

Co-expression (Functional linkage)
S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004

Interaction

Regulatory Rv1884c

swatigandhi19

IMP

Co-expression(Functional Linkage)
H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005

Citation

Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. S. Raman, R. Hazra et al. J. Bacteriol. 2004

swatigandhi19

IMP

15375142

Co-expression(Functional Linkage)

Interaction

Regulatory Rv1815

swatigandhi19

IMP

Co-expression(Functional Linkage)
S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004

Interaction

Regulatory Rv1884c

swatigandhi19

IMP

Co-expression(Functional Linkage)
S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004

Interaction

Regulatory Rv3413c

shefin84

IEP

Co-expression (Functional linkage)
S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004

Interaction

Regulatory Rv3413c

shefin84

IEP

Co-expression (Functional linkage)
KG. Thakur,AM. Joshi,B. Gopal Structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function sigma factor sigma(C) from Mycobacterium tuberculosis. J. Biol. Chem. 2007

Citation

The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. H. Calamita, C. Ko et al. Cell. Microbiol. 2005

swatigandhi19

IMP

15659067

Co-expression(Functional Linkage)

Interaction

Regulatory Rv1815

swatigandhi19

IMP

Interaction

Transcription Rv3212

sourish10

IEP

Co-expression (Functional linkage)
S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004

Interaction

Regulatory Rv2889c

shahanup86

IEP

Co-expression (Functional linkage)
H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005

Interaction

Translation Rv2441c

priti.priety

IMP

Co expression Analysis
H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005

Interaction

Transcription Rv2396

sourish10

IPI

Affinity purification (Physical interaction)
SB. Walters, E. Dubnau et al. The Mycobacterium tuberculosis PhoPR two-component system regulates genes essential for virulence and complex lipid biosynthesis. Mol. Microbiol. 2006

Interaction

Transcription Rv2396

sourish10

IPI

Affinity purification (Physical interaction)
G. Bai, LA. McCue et al. Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a cyclic AMP receptor protein-like DNA binding protein. J. Bacteriol. 2005

Interaction

Transcription Rv2396

sourish10

IPI

Affinity purification (Physical interaction)
H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005

Interaction

Regulatory Rv2348c

akankshajain.21

IEP

Co-expression (Functional linkage)
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

Interaction

Regulatory Rv2348c

akankshajain.21

IEP

Co-expression (Functional linkage)
S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004

Interaction

Regulatory Rv1883c

madhulsbu

IEP

Co-expression (Functional linkage)
authors,LM. Iyer,EV. Koonin,L. Aravind Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily. Proteins 2001

Interaction

Regulatory Rv1883c

madhulsbu

IEP

Co-expression (Functional linkage)
authors,RP. Carithers,DC. Yoch,DI. Arnon Two forms of nitrogenase from the photosynthetic bacterium Rhodospirillum rubrum. J. Bacteriol. 1979

Interaction

Regulatory Rv1815

madhulsbu

IEP

Co-expression (Functional linkage)
S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004

Interaction

Regulatory Rv1816

madhulsbu

IEP

Co-expression (Functional linkage)
S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004

Interaction

Regulatory Rv1450c

balaganesh727

IEP

Co-expression (Functional linkage)
S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004

Interaction

Regulatory Rv1450c

balaganesh727

IEP

Co-expression (Functional linkage)
J. Flores & C. Espitia Differential expression of PE and PE_PGRS genes in Mycobacterium tuberculosis strains. Gene 2003

Interaction

Regulatory Rv1450c

balaganesh727

IEP

Co-expression (Functional linkage)
authors,JE. Clark-Curtiss,SE. Haydel Molecular genetics of Mycobacterium tuberculosis pathogenesis. Annu. Rev. Microbiol. 2003

Interaction

Transcription Rv0685

sourish10

IEP

Co-expression (Functional linkage)
B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009

Interaction

Transcription Rv0684

sourish10

IEP

Interaction

Transcription Rv0684

sourish10

IEP

Co-expression (Functional linkage)
B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009

Interaction

Transcription Rv0685

sourish10

IEP

Interaction

Regulatory Rv0182c

priti.priety

IEP

Co-expression (Functional linkage)
JH. Lee, DE. Geiman et al. Role of stress response sigma factor SigG in Mycobacterium tuberculosis. J. Bacteriol. 2008

Interaction

Regulatory Rv0124

prabhakarsmail

IEP

Co-expression (Functional linkage)
S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004

Interaction

RegulatedBy Rv0182c

yamir.moreno

IEP

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.
JH. Lee, DE. Geiman et al. Role of stress response sigma factor SigG in Mycobacterium tuberculosis. J. Bacteriol. 2008

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv3874

yamir.moreno

IDA

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .
M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv3875

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv3537

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv3538

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv3417c

yamir.moreno

IDA

Citation

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. M. Guo, H. Feng et al. Genome Res. 2009

yamir.moreno

IDA

19228590

One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. .

Interaction

Regulates Rv3418c

yamir.moreno

IDA

Citation

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008

yamir.moreno

TAS

18985025

Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support.

Interaction

Regulates Rv0341

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

Citation

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008

yamir.moreno

TAS

18985025

Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support.

Interaction

Regulates Rv1815

yamir.moreno

TAS

Citation

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008

yamir.moreno

TAS

18985025

Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support.

Interaction

Regulates Rv1884c

yamir.moreno

TAS

Citation

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008

yamir.moreno

TAS

18985025

Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support.

Interaction

Regulates Rv3414c

yamir.moreno

TAS

Interaction

RegulatedBy Rv3414c

yamir.moreno

TAS

Comments