RegulonDB RegulonDB 10.9: Operon Form
   

infA-serW operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: infA-serW
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: serW
Gene(s): serW   Genome Browser M3D Gene expression COLOMBOS
Note(s): A substantial amount of serW transcription originates upstream of serWp1; this suggests that infA and serW may be partially cotranscribed. Such transcripts are likely degraded back to the terminator of infA following excision and processing of the tRNA Cummings HS,1994.
Both the serWp1 and serWp2 promoters make comparable contributions to the expression of serW under the conditions of rapid exponential cell growth Cummings HS,1994. These two promoters resemble the structures of many operons for the synthesis of rRNA and tRNAs, where one of the two operons is regulated by growth rate (metabolic control) and one is subjected to stringent control Cummings HS,1994.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Cummings HS., et al., 1994
Promoter
Name: serWp2
+1: 926006
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 35
Sequence: aataattatcattaaaattcttcttgaccgttttactccaactccctatagtagcgccccGttgccacccatgaggtttgg
                        -35                    -10          +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [1] Cummings HS., et al., 1994
[2] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: ataaaatgcgAAAAAAAAGCTCGCACTTTCGTACGAGCTcttctttaaa
Reference(s): [1] Cummings HS., et al., 1994
[3] Peters JM., et al., 2009
[4] Zuker M. 2003
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition serWp2 nd serWp2 appears to be under stringent control, since the -10 region is followed by a GCGCCCC (G/C-rich) sequence characteristic of promoters regulated by ppGpp Cummings HS,1994. 6154042 This would negatively affect serW transcription as well as other tRNAs 6154042 [IHBCE] [1]
Evidence: [IHBCE] Inferred by a human based on computational evidence
Reference(s): [1] Cummings HS., et al., 1994


Transcription unit       
Name: serW
Gene(s): serW   Genome Browser M3D Gene expression COLOMBOS
Note(s): A substantial amount of serW transcription originates upstream of serWpI; this suggests that infA and serW may be partially cotranscribed. Such transcripts are likely degraded back to the terminator of infA following excision and processing of the tRNA Cummings HS,1994.
Both the serWp1 and serWp2 promoters make comparable contributions to the expression of serW under the conditions of rapid exponential cell growth Cummings HS,1994. These two promoters resemble the structures of many operons for the synthesis of rRNA and tRNAs, where one of the two operons is regulated by growth rate (metabolic control) and one is subjected to stringent control Cummings HS,1994.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Cummings HS., et al., 1994
Promoter
Name: serWp1
+1: 926043
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 72
Sequence: agatatactgcacaacttgtttacagtatgagcaaacaataattatcattaaaattcttcTtgaccgttttactccaactc
                            -35                   -10       +1                   
Evidence: [IHBCE]
[TIM]
Reference(s): [1] Cummings HS., et al., 1994
Terminator(s)
Type: rho-independent
Sequence: ataaaatgcgAAAAAAAAGCTCGCACTTTCGTACGAGCTcttctttaaa
Reference(s): [1] Cummings HS., et al., 1994
[3] Peters JM., et al., 2009
[4] Zuker M. 2003


Transcription unit       
Name: infA
Gene(s): infA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [5] Cummings HS., et al., 1991
Promoter
Name: infAp2
+1: 926479
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 36
Sequence: tttgttgcgatttagcgcgcaaatctttacttatttacagaacttcggcattatcttgccGgttcaaattacggtagtgat
                          -35                       -10     +1                   
Note(s): The activity of the infAp2 promoter increases as the growth rate of the cell increases Cummings HS,1991
Evidence: [AIPP]
[ICWHO]
[TIM]
Reference(s): [5] Cummings HS., et al., 1991
[2] Huerta AM., et al., 2003
[6] Ko JH., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: tcacaaaataAAAAGGCCGGTTAAACCGACCTTTTactcgttctt
Reference(s): [5] Cummings HS., et al., 1991


Transcription unit       
Name: infA
Gene(s): infA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [5] Cummings HS., et al., 1991
Promoter
Name: infAp1
+1: 926685
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 242
Sequence: ttttcaccacaagaatgaatgttttcggcacatttctccccagagtgttataattgcggtCgcagagttggttacgctcat
                      -35                        -10        +1                   
Note(s): infAp1 promoter activity is induced by cold shock Ko JH,2006.
Evidence: [AIPP]
[ICWHO]
[TIM]
Reference(s): [5] Cummings HS., et al., 1991
[2] Huerta AM., et al., 2003
[6] Ko JH., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: tcacaaaataAAAAGGCCGGTTAAACCGACCTTTTactcgttctt
Reference(s): [5] Cummings HS., et al., 1991


Transcription unit       
Name: infA-serW
Gene(s): serW, infA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Cummings HS., et al., 1994


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.6 926154 926186 aagaacgagtAAAAGGTCGGTTTAACCGGCCTTTTTATTTTGtgatatgtat
  terminator -8.3 926458 926488 acttcggcatTATCTTGCCGGTTCAAATTACGGTAGTGATaccccagagg
  anti-terminator -8.6 926176 926217 tgattgttttACCGCCTGATGGGCGAAGAGAAAGAACGAGTAAAAGGTCGGtttaaccggc
  anti-anti-terminator -5.3 926203 926215 attgttttacCGCCTGATGGGCgaagagaaag
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"





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