RegulonDB RegulonDB 11.1: Gene Form
   

rodZ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rlmN ispG rodZ rodZp2 rodZp2 rodZp1 rodZp1 TSS_2816 TSS_2816 TSS_2815 TSS_2815 TSS_2814 (cluster) TSS_2814 (cluster) TSS_2813 (cluster) TSS_2813 (cluster) ispGp5 ispGp5 ispGp4 ispGp4 TSS_2812 TSS_2812 TSS_2811 (cluster) TSS_2811 (cluster) TSS_2810 TSS_2810 ispGp1 ispGp1 TSS_2809 (cluster) TSS_2809 (cluster)

Gene      
Name: rodZ    Texpresso search in the literature
Synonym(s): ECK2512, EG10015, b2516, yfgA
Genome position(nucleotides): 2641831 <-- 2642844
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.54
External database links:  
ASAP:
 ABE-0008283
ECHOBASE:
 EB0015
ECOLIHUB:
 rodZ
OU-MICROARRAY:
 b2516
STRING:
 511145.b2516
COLOMBOS: rodZ


Product      
Name: cytoskeleton protein RodZ
Synonym(s): RodZ, YfgA, transmembrane component of cytoskeleton
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 36.192
Isoelectric point: 5.461
Motif(s):
 
Type Positions Sequence Comment
1 -> 84 MNTEATHDQNEALTTGARLRNAREQLGLSQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEELLPGLE
18 -> 79 RLRNAREQLGLSQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEEL
19 -> 71 LRNAREQLGLSQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARL UniProt: HTH cro/C1-type.
27 -> 27 G UniProt: In Ref. 7; BAA04685..
30 -> 49 QQAVAERLCLKVSTVRDIEE UniProt: H-T-H motif.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
biological_process GO:0009252 - peptidoglycan biosynthetic process
GO:0043093 - FtsZ-dependent cytokinesis
GO:0008360 - regulation of cell shape
Note(s): Note(s): ...[more].
Evidence: [EXP-IDA] Inferred from direct assay
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Alyahya SA., et al., 2009
[2] Bendezu FO., et al., 2009
[3] Ikebe R., et al., 2018
[4] Jacques PE., et al., 2006
[5] Niba ET., et al., 2010
[6] Porter T., et al., 2016
[7] Shiomi D., et al., 2008
External database links:  
ALPHAFOLD:
 P27434
DIP:
 DIP-12034N
ECOCYC:
 EG10015-MONOMER
ECOLIWIKI:
 b2516
INTERPRO:
 IPR023690
INTERPRO:
 IPR025194
INTERPRO:
 IPR010982
INTERPRO:
 IPR001387
MINT:
 P27434
MODBASE:
 P27434
PFAM:
 PF13464
PFAM:
 PF13413
PRIDE:
 P27434
PRODB:
 PRO_000023803
PROSITE:
 PS50943
REFSEQ:
 NP_417011
SMART:
 SM00530
UNIPROT:
 P27434


Operon      
Name: rodZ         
Operon arrangement:
Transcription unit        Promoter
yfgA


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_2809 (cluster) 2641405 reverse nd [RS-EPT-CBR] [8]
  promoter ispGp1 2641880 reverse nd [COMP-AINF] [9]
  promoter TSS_2810 2641922 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2811 (cluster) 2641929 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2812 2641933 reverse nd [RS-EPT-CBR] [8]
  promoter ispGp4 2641950 reverse nd [COMP-AINF] [9]
  promoter ispGp5 2641954 reverse nd [COMP-AINF] [9]
  promoter TSS_2813 (cluster) 2641985 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2814 (cluster) 2641990 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2815 2641997 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2816 2642045 reverse nd [RS-EPT-CBR] [8]
  promoter rodZp1 2642932 reverse nd [COMP-AINF] [9]
  promoter rodZp2 2642934 reverse nd [COMP-AINF] [9]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Alyahya SA., Alexander R., Costa T., Henriques AO., Emonet T., Jacobs-Wagner C., 2009, RodZ, a component of the bacterial core morphogenic apparatus., Proc Natl Acad Sci U S A 106(4):1239-44

 [2] Bendezu FO., Hale CA., Bernhardt TG., de Boer PA., 2009, RodZ (YfgA) is required for proper assembly of the MreB actin cytoskeleton and cell shape in E. coli., EMBO J 28(3):193-204

 [3] Ikebe R., Kuwabara Y., Chikada T., Niki H., Shiomi D., 2018, The periplasmic disordered domain of RodZ promotes its self-interaction in Escherichia coli., Genes Cells 23(4):307-317

 [4] Jacques PE., Rodrigue S., Gaudreau L., Goulet J., Brzezinski R., 2006, Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs., BMC Bioinformatics 7:423

 [5] Niba ET., Li G., Aoki K., Kitakawa M., 2010, Characterization of rodZ mutants: RodZ is not absolutely required for the cell shape and motility., FEMS Microbiol Lett 309(1):35-42

 [6] Porter T., Frederick D., Johnson E., Jones PG., 2016, A requirement for cell elongation protein RodZ and cell division proteins FtsN and DedD to maintain the small rod morphology of Escherichia coli at growth temperatures near 8°C., J Gen Appl Microbiol 62(4):189-98

 [7] Shiomi D., Sakai M., Niki H., 2008, Determination of bacterial rod shape by a novel cytoskeletal membrane protein., EMBO J 27(23):3081-91

 [8] 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.

 [9] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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