RegulonDB RegulonDB 10.8: Operon Form

hscBA-fdx-iscX operon and associated TUs in Escherichia coli K-12 genome

Name: hscBA-fdx-iscX
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit       
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
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: [BTEI] Boundaries of transcription experimentally identified
[ITC] Inferred through co-regulation
[PAGTSBP] 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
Name: hscBp
+1: 2659524
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 57
Sequence: cggcgaaagcttccacgtttgatgcgcataccgataaccccaccgtggtcgcctgcgcgtGgggtttgttttacctgattc
                            -35                  -10        +1                   
Evidence: [TIM]
Reference(s): [1] Lelivelt MJ., et al., 1995
Type: rho-independent
Sequence: cgcagccaacGCATCTGCGGCGTGAAGCATGACGCggaaattatt
Reference(s): [3] Ta DT., et al., 1992

Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  ryhB antisense post-transcriptional regulation repressor       [IMP] [7]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"

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"