|
|
| Operon |  |
|---|---|
| Name: | hscBA-fdx-iscX |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | hscBA-fdx-iscX |
| Gene(s): | iscX, fdx, hscA, hscB Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | Lelivelt and Kamula (1995) Lelivelt MJ,1995mentioned that the primer extension used by Seaton and Vickery (1994) Seaton BL,1994was extracted from cells containing a cloned copy of hscA provided in trans which did not contain the upstream hscB gene and in addition did not contain an authentic chromosomal promoter Lelivelt MJ,1995 Lelivelt and Kamula (1995) Lelivelt MJ,1995determined the transcriptional start site by using total RNA prepared from a plasmidless strain, and therefore they proposed that the only source of hscBA mRNA was chromosomal Lelivelt MJ,1995 The hscA gene is upregulated by short-term (30 min) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020. Based on the improved computational program DTI (Direct Information criterion), which is an extension of the concept of MI that allows investigators to measure the direction of information flow between two random variables, and DTInfer, a new R-package for the inference of gene regulatory networks from microarrays based on directed information, the fdx, hcsA, hcsB, and iscX genes were identified as new targets of IscR with high Z-scores Kaleta C,2010 In addition, there are other clues that suggest that IscR regulates the hcsAB-fdx-iscX operon, including the following findings: all of these genes are involved in the formation of an iron-sulfur cluster Kaleta C,2010and references therein|; IscR regulates the iscRSCUA operon, which is situated directly upstream of the hcsAB-fdx-iscX operon Kaleta C,2010 both operons can be cotranscribed Takahashi Y,1999. Tokumoto U,2001. Giel JL,2006 the high Z-scores for all genes suggest that both operons, hcsAB-fdx-iscX and iscRSCUA, belong to the same operon or are at least tightly coregulated Kaleta C,2010 |
| Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IEP-COREGULATION] Inferred through co-regulation [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process |
| Reference(s): |
[1] Lelivelt MJ., et al., 1995 [2] Seaton BL., et al., 1994 [3] Ta DT., et al., 1992 [4] Takahashi Y., et al., 1999 [5] Tokumoto U., et al., 2002 [6] Tokumoto U., et al., 2001 |
| Promoter | |
| Name: | hscBp |
| +1: | 2659524 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 57 |
| Sequence: |
cggcgaaagcttccacgtttgatgcgcataccgataaccccaccgtggtcgcctgcgcgtGgggtttgttttacctgattc -35 -10 +1 |
| Evidence: |
[COMP-AINF] [COMP-HINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
| Reference(s): |
[7] Huerta AM., et al., 2003 [1] Lelivelt MJ., et al., 1995 |
| Terminator(s) | |
| Type: | rho-independent |
| Sequence: | cgcagccaacGCATCTGCGGCGTGAAGCATGACGCggaaattatt |
| Reference(s): | [3] Ta DT., et al., 1992 |
| RNA cis-regulatory element | |
|---|
| Regulation, transcriptional elongation | |
| Attenuator type: | Transcriptional |
| Strand: | reverse |
| Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
|---|---|---|---|---|---|
| terminator | -18.4 | 2659513 | 2659549 | gcataccgatAACCCCACCGTGGTCGCCTGCGCGTGGGGTTTGTTTtacctgattc | |
| anti-terminator | -7.33 | 2659533 | 2659582 | tgtggttgcgGCGAAAGCTTCCACGTTTGATGCGCATACCGATAACCCCACCGTGGTCGcctgcgcgtg | |
| anti-anti-terminator | -14.5 | 2659561 | 2659605 | ccaacccgaaCGTCAAAGATGAGTGTGGTTGCGGCGAAAGCTTCCACGTTTGATgcgcataccg |
| 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) |
|
|---|---|
[COMP-AINF] Inferred computationally without human oversight