RegulonDB RegulonDB 10.7: Operon Form
   

clpPX-lon operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: clpPX
Gene(s): clpP, clpX   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is a possible factor-dependent transcription terminator downstream of clpP. clpX can be expressed independently from clpP by using its own promoter, but this promoter has not been clearly identified.
The expression of the clpP gene, and probably the expression of the complete clpPX operon that codes for a protease, is affected by antibiotic pressure. As the antibiotic (tetracycline) concentration increases, the gene expression also increases. The role of the induced protease could be the degradation of porins to protect the cell against the antibiotic |CITS: [17426813]|.
Evidence: [LTED] Length of transcript experimentally determined
[LTED] Length of transcript experimentally determined
Reference(s): [1] Gottesman S., et al., 1993
[2] Li C., et al., 2000
Promoter
Name: clpPp1
+1: 456577
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 100
Sequence: accgtgcgaaaagcctctttcggtgttagcgtaacaacaaaagattgttatgcttgaaatAtggtgatgccgtacccataa
                          -35                    -10        +1                   
Evidence: [HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Maurizi MR., et al., 1990
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: agttaaccaaAAAGGGGGGATTTTATCTCCCCTTTaatttttcct
Reference(s): [1] Gottesman S., et al., 1993


Transcription unit       
Name: clpPX
Gene(s): clpP, clpX   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is a possible factor-dependent transcription terminator downstream of clpP. clpX can be expressed independently from clpP by using its own promoter, but this promoter has not been clearly identified.
The expression of the clpP gene, and probably the expression of the complete clpPX operon that codes for a protease, is affected by antibiotic pressure. As the antibiotic (tetracycline) concentration increases, the gene expression also increases. The role of the induced protease could be the degradation of porins to protect the cell against the antibiotic |CITS: [17426813]|.
Evidence: [LTED] Length of transcript experimentally determined
[LTED] Length of transcript experimentally determined
Reference(s): [1] Gottesman S., et al., 1993
[2] Li C., et al., 2000
Promoter
Name: clpPp3
+1: 456605
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 72
Sequence: gcgtaacaacaaaagattgttatgcttgaaatatggtgatgccgtacccataacacagggActagctgataatccgtccat
                          -35                 -10           +1                   
Evidence: [IDA]
[IEP]
[RS-EPT-CBR]
[TIM] ; Method: Primer Extension
[TIM]
Reference(s): [2] Li C., et al., 2000
[5] Nonaka G., et al., 2006
[4] Salgado H, et al., 2012
[6] Wade JT., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: agttaaccaaAAAGGGGGGATTTTATCTCCCCTTTaatttttcct
Reference(s): [1] Gottesman S., et al., 1993


Transcription unit       
Name: clpPX
Gene(s): clpP, clpX   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is a possible factor-dependent transcription terminator downstream of clpP. clpX can be expressed independently from clpP by using its own promoter, but this promoter has not been clearly identified.
The expression of the clpP gene, and probably the expression of the complete clpPX operon that codes for a protease, is affected by antibiotic pressure. As the antibiotic (tetracycline) concentration increases, the gene expression also increases. The role of the induced protease could be the degradation of porins to protect the cell against the antibiotic |CITS: [17426813]|.
Evidence: [LTED] Length of transcript experimentally determined
[LTED] Length of transcript experimentally determined
Reference(s): [1] Gottesman S., et al., 1993
[2] Li C., et al., 2000
Promoter
Name: clpPp2
+1: 456646
Distance from start of the gene: 31
Sequence: ccgtacccataacacagggactagctgataatccgtccataaggttacaatcggtacagcAggttttttcaattttatcca
Note(s): The σ32 factor likely regulates the activity of the clpPp2 promoter, since transcription of this operon in cells grown at 42°C is about 2-fold higher than that found in cells grown at 32°C.
Evidence: [HIPP]
[TIM]
Reference(s): [3] Maurizi MR., et al., 1990
Terminator(s)
Type: rho-independent
Sequence: agttaaccaaAAAGGGGGGATTTTATCTCCCCTTTaatttttcct
Reference(s): [1] Gottesman S., et al., 1993


Transcription unit       
Name: clpX-lon
Gene(s): clpX, lon   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITC] Inferred through co-regulation
Reference(s): [7] Rhodius VA., et al., 2005
Promoter
Name: clpXp
+1: 457202
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 224
Sequence: attctgaaagttaaagggcgcatgaatgaacttatggcgcttcatacgggtcaatcattaGaacagattgaacgtgatacc
                            -35                  -10        +1                   
Evidence: [AIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [7] Rhodius VA., et al., 2005
[4] Salgado H, et al., 2012


Transcription unit          
Name: lon
Gene(s): lon   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
[IEP] Inferred from expression pattern
Reference(s): [5] Nonaka G., et al., 2006
Promoter
Name: lonp
+1: 458815
Sigma Factor: Sigma32, Sigma70
Distance from start of the gene: 73
Sequence: taatttttcctctattctcggcgttgaatgtgggggaaacatccccatatactgacgtacAtgttaatagatggcgtgaag
                        -35                -10              +1                   
Evidence: [HIPP]
[IDA]
[IEP]
[RS-EPT-CBR]
Reference(s): [8] Chin DT., et al., 1988
[5] Nonaka G., et al., 2006
[4] Salgado H, et al., 2012
[6] Wade JT., et al., 2006
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadX activator lonp nd nd nd nd nd [GEA] [9]


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  gcvB unknown unknown repressor       [IMP] [8]
[5]
[10]
[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: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [11] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -20.6 456462 456499 aattcgcacaAAGGCCCGTCACCGCCAGGTGGTGGGCTTTTTTTTGTcatgaatttt
  terminator -14.2 458731 458763 gttaaccaaaAAGGGGGGATTTTATCTCCCCTTTAATTTTTCctctattctc
  anti-terminator -18.0 456410 456477 tttcaacgagCTGATGAACCAGCAGGCGTAATTTACGCAGCATAACGCGCTAAATTCGCACAAAGGCCCGTCACCGCcaggtggtgg
  anti-terminator -4.0 458707 458741 taattaaccaTTCCCATACAATTAGTTAACCAAAAAGGGGGGATtttatctccc
  anti-anti-terminator -11.21 458662 458715 ttgctgatttATGGCAAGCCGGAAGCGCAACAGGCATCTGGTGAATAATTAACCATTCCCATAcaattagtta
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)    

 [1] Gottesman S., Clark WP., de Crecy-Lagard V., Maurizi MR., 1993, ClpX, an alternative subunit for the ATP-dependent Clp protease of Escherichia coli. Sequence and in vivo activities., J Biol Chem 268(30):22618-26

 [2] Li C., Tao YP., Simon LD., 2000, Expression of different-size transcripts from the clpP-clpX operon of Escherichia coli during carbon deprivation., J Bacteriol 182(23):6630-7

 [3] Maurizi MR., Clark WP., Katayama Y., Rudikoff S., Pumphrey J., Bowers B., Gottesman S., 1990, Sequence and structure of Clp P, the proteolytic component of the ATP-dependent Clp protease of Escherichia coli., J Biol Chem 265(21):12536-45

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [5] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [6] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [7] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

 [8] Chin DT., Goff SA., Webster T., Smith T., Goldberg AL., 1988, Sequence of the lon gene in Escherichia coli. A heat-shock gene which encodes the ATP-dependent protease La., J Biol Chem 263(24):11718-28

 [9] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [10] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, Role of the sRNA GcvB in regulation of cycA in Escherichia coli., Microbiology 155(Pt 1):106-14

 [11] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.


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