![]() ![]() ![]() ![]() |
Name: | artJ | ||||||||||
Gene(s): | artJ Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | Based on DNA microarray analysis, the mechanism of bacterial inactivation by carvacrol and citral was studied Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017. Treatment by both compounds caused membrane damage and activated metabolism through the production of nucleotides required for DNA and RNA synthesis and metabolic processes Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017. A total of 76 and 156 genes demonstrated significant transcriptional differences by carvacrol and citral, respectively. Genes upregulated by carvacrol treatment included the multidrug efflux pump genes acrA and mdtM, genes related to the phage shock response, pspA, pspB, pspC, pspD, pspF, and pspG, and genes whose products are important for biosynthesis of arginine (argC, argG, artJ) and purine nucleotides (purC, purM). Genes upregulated by citral treatment included purH, pyrB, and pyrI. On the other hand, mutations in several differentially expressed genes confirmed the roles of ygaV, yjbO, pspC, sdhA, yejG, and ygaV in mechanisms of inactivation by carvacrol and citral Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017. | ||||||||||
Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified | ||||||||||
Reference(s): |
[1] Wissenbach U., et al., 1993 [2] Wissenbach U., et al., 1995 |
||||||||||
Promoter | |||||||||||
Name: | artJp | ||||||||||
+1: | 900626 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 51 | ||||||||||
Sequence: |
catttaaattatttaatcatgtttattgcatataaattcacttgatggcattgttatcccAtgccgcagacacggccaaaa -35 -10 +1 |
||||||||||
Note(s): | Inhibition of artJp by ArgR is mediated by steric exclusion of the RNA polymerase Caldara M,2007 | ||||||||||
Evidence: |
[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
||||||||||
Reference(s): |
[3] Caldara M., et al., 2007 [4] Huerta AM., et al., 2003 [5] Maciag A., et al., 2011 [6] Salgado H, et al., 2012 [2] Wissenbach U., et al., 1995 |
||||||||||
Terminator(s) | |||||||||||
Type: | rho-dependent | ||||||||||
Sequence: | agcaataaaaAAGCCGCATGTGCGGCTTcagattgctg | ||||||||||
Reference(s): | [2] Wissenbach U., et al., 1995 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | ArgR-L-arginine | repressor | artJp | 900645 | 900663 | -27.5 | taatcatgttTATTGCATATAAATTCACTtgatggcatt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [3], [7] |
proximal | ArgR-L-arginine | repressor | artJp | 900666 | 900684 | -48.5 | ttttatttcaTTTAAATTATTTAATCATGtttattgcat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [3], [7] |
RNA cis-regulatory element | ![]() |
---|
Regulation, transcriptional elongation | |
Attenuator type: | Transcriptional |
Strand: | reverse |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
---|---|---|---|---|---|
terminator | -19.0 | 900687 | 900726 | ttcttataatGAAGACGGACAACCCACTAAGTTGTCCGTCTTTTTTATTtcatttaaat | |
anti-terminator | -5.6 | 900718 | 900758 | ggacgccttaTCCGGCCTACATAGTGCATAAATTCTTATAATGAAGACGGacaacccact | |
anti-anti-terminator | -31.5 | 900742 | 900795 | tcagacatcaGCACGGTGCCTGTGCCGGATGCGGCGGGGACGCCTTATCCGGCCTACATAGTGcataaattct |
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos" |
Reference(s) |
![]() |
---|---|