Rv2744c (35kd_ag)
Current annotations:
TBCAP: (community-based annotations - see table at bottom of page )
TBDB: phage shock protein A
REFSEQ: hypothetical protein
PATRIC: Phage shock protein A (IM30) suppresses sigma54-dependent transcription
TUBERCULIST: Conserved 35 kDa alanine rich protein
NCBI: Conserved 35 kDa alanine rich protein
updated information (H37Rv4):
gene name: 35kd_ag
function: pspA ortholog; implicated in cell-wall stress response, lipid droplet formation, and NRP
reference: Armstrong (2016) PMID: 27002134
Type: Not Target
Start: 3057251
End: 3058063
Operon:
Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
Reaction(s) (based on iSM810 metabolic model):
Gene Expression Profile Gene Modules 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 35kd_ag:
Amino Acid Sequence
MANPFVKAWKYLMALFSSKIDEHADPKVQIQQAIEEAQRTHQALTQQAAQVIGNQRQLEMRLNRQLADIEKLQVNVRQALTLADQATAAGDAAKATEYNN
AAEAFAAQLVTAEQSVEDLKTLHDQALSAAAQAKKAVERNAMVLQQKIAERTKLLSQLEQAKMQEQVSASLRSMSELAAPGNTPSLDEVRDKIERRYANA
IGSAELAESSVQGRMLEVEQAGIQMAGHSRLEQIRASMRGEALPAGGTTATPRPATETSGGAIAEQPYGQ
(
Nucleotide sequence available on
KEGG )
Additional Information
Analysis of Positive Selection in Clinical Isolates
*new*
Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods )
Moldova: 2,057 clinical isolates
global set: 5,195 clinical isolates from 15 other countries
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.
Moldova (2,057) global set (5,195)
under significant positive selection? NO YES
omega peak height (95%CI lower bound) 1.52 (0.16) 2.48 (1.27)
codons under selection 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248
omega plots
genetic variants* link link
statistics at each codon link link
* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"
MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb
TnSeqCorr
Rv2744c/35kd_ag,
gene len: 812 bp, num TA sites: 10
condition dataset call medium method notes
in-vitro DeJesus 2017 mBio non-essential 7H9 HMM fully saturated, 14 TnSeq libraries combined
in-vitro Sassetti 2003 Mol Micro non-essential 7H9 TRASH essential if hybridization ratio<0.2
in-vivo (mice) Sassetti 2003 PNAS non-essential BL6 mice TRASH essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol) Griffin 2011 PPath non-essential M9 minimal+glycerol Gumbel 2 replicates; Padj<0.05
in-vitro (cholesterol) Griffin 2011 PPath non-essential M9 minimal+cholesterol Gumbel 3 replicates; Padj<0.05
differentially essential in cholesterol Griffin 2011 PPath NO (LFC=-1.05) cholesterol vs glycerol resampling-SR YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro Smith 2022 eLife non-essential 7H9 HMM 6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice) Smith 2022 eLife non-essential BL6 mice HMM 6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice Smith 2022 eLife NO (LFC=-0.457) in-vivo vs in-vitro ZINB YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal) Minato 2019 mSys non-essential minimal medium HMM
in-vitro (YM rich medium) Minato 2019 mSys non-essential YM rich medium HMM 7H9 supplemented with ~20 metabolites (amino acids, vitamins)
differentially essential in YM rich medium Minato 2019 mSys NO (LFC=-1.72) YM rich vs minimal medium resampling
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
Translation, ribosomal structure and biogenesis
Cell wall/membrane/envelope biogenesis
Replication, recombination and repair
Posttranslational modification, protein turnover, chaperones
Secondary metabolites biosynthesis, transport and catabolism
Inorganic ion transport and metabolism
General function prediction only
Intracellular trafficking, secretion, and vesicular transport
Signal transduction mechanisms
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).
Binds To:
No bindings to other targets were found.
Bound By:
No bindings from other targets were found.
Binds To:
No bindings to other targets were found.
Bound By:
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 Regulatory Rv2743c balaganesh727 IEP Co-expression (Functional linkage)R. Provvedi, F. Boldrin et al. Global transcriptional response to vancomycin in Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 2009
Interaction Regulatory Rv2745c balaganesh727 IEP Co-expression (Functional linkage)R. Provvedi, F. Boldrin et al. Global transcriptional response to vancomycin in Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 2009
Citation Mycobacterium tuberculosis Sigma Factor E Regulon Modulates the Host Inflammatory Response. PA. Fontn, V. Aris et al. J. Infect. Dis. 2008 balaganesh727 IEP 18657035 Co-expression (Functional linkage)
Interaction Regulatory Rv1221 balaganesh727 IEP Co-expression (Functional linkage)PA. Fontn, V. Aris et al. Mycobacterium tuberculosis Sigma Factor E Regulon Modulates the Host Inflammatory Response. J. Infect. Dis. 2008
Citation The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in global gene expression and survival in macrophages. R. Manganelli, MI. Voskuil et al. Mol. Microbiol. 2001 balaganesh727 IEP 11489128 Co-expression (Functional linkage)
Interaction Regulatory Rv1221 balaganesh727 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
Citation The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in global gene expression and survival in macrophages. R. Manganelli, MI. Voskuil et al. Mol. Microbiol. 2001 balaganesh727 IEP 11489128 Co-expression (Functional linkage)
Interaction Regulatory Rv2743c balaganesh727 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 Rv2745c balaganesh727 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
Citation Global transcriptional response to vancomycin in Mycobacterium tuberculosis. R. Provvedi, F. Boldrin et al. Microbiology (Reading, Engl.) 2009 balaganesh727 IEP 19332811 Co-expression (Functional linkage)
Interaction Regulatory Rv2743c balaganesh727 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 Rv2743c balaganesh727 IEP Co-expression (Functional linkage)R. Provvedi, F. Boldrin et al. Global transcriptional response to vancomycin in Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 2009
Interaction Regulatory Rv0757 singhpankaj2116 IEP Co-expression (Functional linkage)ML. Chesne-Seck, N. Barilone et al. A point mutation in the two-component regulator PhoP-PhoR accounts for the absence of polyketide-derived acyltrehaloses but not that of phthiocerol dimycocerosates in Mycobacterium tuberculosis H37Ra. J. Bacteriol. 2008
Interaction Regulatory Rv0757 singhpankaj2116 IEP Co-expression (Functional linkage)authors,A. Sola-Landa,RS. Moura,JF. Martn The two-component PhoR-PhoP system controls both primary metabolism and secondary metabolite biosynthesis in Streptomyces lividans. Proc. Natl. Acad. Sci. U.S.A. 2003
Interaction Regulatory Rv0757 singhpankaj2116 IEP Co-expression (Functional linkage)J. Gonzalo Asensio, C. Maia et al. The virulence-associated two-component PhoP-PhoR system controls the biosynthesis of polyketide-derived lipids in Mycobacterium tuberculosis. J. Biol. Chem. 2006
Interaction Regulatory Rv0757 singhpankaj2116 IEP Co-expression (Functional linkage)J. Gonzalo-Asensio, CY. Soto et al. The Mycobacterium tuberculosis phoPR operon is positively autoregulated in the virulent strain H37Rv. J. Bacteriol. 2008
Interaction Regulatory Rv0757 singhpankaj2116 IEP Co-expression (Functional linkage)A. Sinha, S. Gupta et al. PhoP-PhoP interaction at adjacent PhoP binding sites is influenced by protein phosphorylation. J. Bacteriol. 2008
Interaction Regulatory Rv0757 singhpankaj2116 IEP Co-expression (Functional linkage)J. Gonzalo Asensio, C. Maia et al. The virulence-associated two-component PhoP-PhoR system controls the biosynthesis of polyketide-derived lipids in Mycobacterium tuberculosis. J. Biol. Chem. 2006
Interaction Regulatory Rv0757 singhpankaj2116 IEP Co-expression (Functional linkage)M. Ryndak, S. Wang et al. PhoP, a key player in Mycobacterium tuberculosis virulence. Trends Microbiol. 2008
Interaction Regulatory Rv0757 singhpankaj2116 IEP Co-expression (Functional linkage)JA. Asensio, A. Arbus et al. Live tuberculosis vaccines based on phoP mutants: a step towards clinical trials. Expert opinion on biological therapy 2008
Interaction Regulatory Rv0757 singhpankaj2116 IEP Co-expression (Functional linkage)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 Regulatory Rv0757 singhpankaj2116 IEP Co-expression (Functional linkage)J. Gonzalo-Asensio, S. Mostowy et al. PhoP: a missing piece in the intricate puzzle of Mycobacterium tuberculosis virulence. PLoS ONE 2008
Interaction RegulatedBy Rv0757 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..J. Gonzalo Asensio, C. Maia et al. The virulence-associated two-component PhoP-PhoR system controls the biosynthesis of polyketide-derived lipids in Mycobacterium tuberculosis. J. Biol. Chem. 2006
Interaction RegulatedBy Rv1221 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..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
