RegulonDB RegulonDB 10.8: Gene Form
   

rssB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rssB galU rssA TSS_1568 TSS_1568 TSS_1567 TSS_1567 TSS_1566 TSS_1566 TSS_1565 (cluster) TSS_1565 (cluster) galUp galUp TSS_1563 (cluster) TSS_1563 (cluster) TSS_1562 TSS_1562 rssBp rssBp

Gene      
Name: rssB    Texpresso search in the literature
Synonym(s): ECK1230, EG12121, b1235, hnr, sprE, ychL
Genome position(nucleotides): 1290242 --> 1291255 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.62
External database links:  
ASAP:
ABE-0004147
CGSC:
37471
ECHOBASE:
EB2042
OU-MICROARRAY:
b1235
PortEco:
rssB
STRING:
511145.b1235
COLOMBOS: rssB


Product      
Name: regulator of RpoS
Synonym(s): Hnr, RssB, SprE, YchL
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 37.302
Isoelectric point: 5.639
Motif(s):
 
Type Positions Sequence
58 -> 58 D
109 -> 109 P
9 -> 123 QILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLGGFTPDLMICDIAMPRMNGLKLLEHIRNRGDQTPVLVISATENMADIAKALRLGVEDVLLKPVKDLNRLREMVFAC
10 -> 120 ILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLGGFTPDLMICDIAMPRMNGLKLLEHIRNRGDQTPVLVISATENMADIAKALRLGVEDVLLKPVKDLNRLREMV
143 -> 143 W

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.6 - turnover, degradation
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.4 - proteases, cleavage of compounds
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0032993 - protein-DNA complex
molecular_function GO:0005515 - protein binding
GO:0016989 - sigma factor antagonist activity
GO:0003700 - DNA-binding transcription factor activity
GO:0000156 - phosphorelay response regulator activity
GO:0000976 - transcription regulatory region sequence-specific DNA binding
GO:0001216 - DNA-binding transcription activator activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0000160 - phosphorelay signal transduction system
GO:0010468 - regulation of gene expression
GO:0031648 - protein destabilization
GO:0045862 - positive regulation of proteolysis
GO:1903507 - negative regulation of nucleic acid-templated transcription
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
Reference(s): [1] Alper H., et al., 2008
[2] Battesti A., et al., 2015
[3] Bosl M., et al., 1994
[4] Carabetta VJ., et al., 2010
[5] Dorich V., et al., 2019
[6] Fredriksson A., et al., 2007
[7] Hansen S., et al., 2008
[8] Hirakawa H., et al., 2003
[9] Lacour S., et al., 2003
[10] Mandel MJ., et al., 2005
[11] Sarkar N., et al., 2002
[12] Spira B., et al., 2011
[13] Studemann A., et al., 2003
[14] Zhou Y., et al., 2006
External database links:  
ECOCYC:
EG12121-MONOMER
ECOLIWIKI:
b1235
INTERPRO:
IPR001789
INTERPRO:
IPR039420
INTERPRO:
IPR036457
INTERPRO:
IPR028616
INTERPRO:
IPR011006
MODBASE:
P0AEV1
PANTHER:
PTHR26402
PDB:
3EOD
PFAM:
PF00072
PRIDE:
P0AEV1
PRODB:
PRO_000022908
PROSITE:
PS50110
REFSEQ:
NP_415751
SMART:
SM00448
SMR:
P0AEV1
UNIPROT:
P0AEV1


Operon      
Name: rssAB         
Operon arrangement:
Transcription unit        Promoter
rssAB
rssB


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_1562 1291321 forward nd [RS-EPT-CBR] [15]
  promoter TSS_1563 (cluster) 1291343 forward For this promoter, there
Read more >
[RS-EPT-CBR] [15]
  promoter TSS_1565 (cluster) 1291414 forward For this promoter, there
Read more >
[RS-EPT-CBR] [15]
  promoter TSS_1566 1291421 forward nd [RS-EPT-CBR] [15]
  promoter TSS_1567 1291580 forward nd [RS-EPT-CBR] [15]
  promoter TSS_1568 1291585 forward nd [RS-EPT-CBR] [15]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Alper H., Stephanopoulos G., 2008, Uncovering the gene knockout landscape for improved lycopene production in E. coli., Appl Microbiol Biotechnol 78(5):801-10

 [2] Battesti A., Majdalani N., Gottesman S., 2015, Stress sigma factor RpoS degradation and translation are sensitive to the state of central metabolism., Proc Natl Acad Sci U S A 112(16):5159-64

 [3] Bosl M., Kersten H., 1994, Organization and functions of genes in the upstream region of tyrT of Escherichia coli: phenotypes of mutants with partial deletion of a new gene (tgs)., J Bacteriol 176(1):221-31

 [4] Carabetta VJ., Li T., Shakya A., Greco TM., Cristea IM., 2010, Integrating Lys-N proteolysis and N-terminal guanidination for improved fragmentation and relative quantification of singly-charged ions., J Am Soc Mass Spectrom 21(6):1050-60

 [5] Dorich V., Brugger C., Tripathi A., Hoskins JR., Tong S., Suhanovsky MM., Sastry A., Wickner S., Gottesman S., Deaconescu AM., 2019, Structural basis for inhibition of a response regulator of σS stability by a ClpXP antiadaptor., Genes Dev 33(11-12):718-732

 [6] Fredriksson A., Ballesteros M., Peterson CN., Persson O., Silhavy TJ., Nystrom T., 2007, Decline in ribosomal fidelity contributes to the accumulation and stabilization of the master stress response regulator sigmaS upon carbon starvation., Genes Dev 21(7):862-74

 [7] Hansen S., Lewis K., Vulic M., 2008, Role of global regulators and nucleotide metabolism in antibiotic tolerance in Escherichia coli., Antimicrob Agents Chemother 52(8):2718-26

 [8] Hirakawa H., Nishino K., Hirata T., Yamaguchi A., 2003, Comprehensive studies of drug resistance mediated by overexpression of response regulators of two-component signal transduction systems in Escherichia coli., J Bacteriol 185(6):1851-6

 [9] Lacour S., Kolb A., Landini P., 2003, Nucleotides from -16 to -12 determine specific promoter recognition by bacterial sigmaS-RNA polymerase., J Biol Chem 278(39):37160-8

 [10] Mandel MJ., Silhavy TJ., 2005, Starvation for different nutrients in Escherichia coli results in differential modulation of RpoS levels and stability., J Bacteriol 187(2):434-42

 [11] Sarkar N., Cao GJ., Jain C., 2002, Identification of multicopy suppressors of the pcnB plasmid copy number defect in Escherichia coli., Mol Genet Genomics 268(1):62-9

 [12] Spira B., de Almeida Toledo R., Maharjan RP., Ferenci T., 2011, The uncertain consequences of transferring bacterial strains between laboratories - rpoS instability as an example., BMC Microbiol 11:248

 [13] Studemann A., Noirclerc-Savoye M., Klauck E., Becker G., Schneider D., Hengge R., 2003, Sequential recognition of two distinct sites in sigma(S) by the proteolytic targeting factor RssB and ClpX., EMBO J 22(16):4111-20

 [14] Zhou Y., Gottesman S., 2006, Modes of regulation of RpoS by H-NS., J Bacteriol 188(19):7022-5

 [15] 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.


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