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Gene Review

ECs4082  -  sigma(54) modulation protein

Escherichia coli O157:H7 str. Sakai

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Disease relevance of ECs4082

  • A potential promoter with a sequence homologous to that of cAMP-CRP-activated promoters in E. coli was identified upstream of ORF3, the gene preceding mshA [1].
  • The genomic RNA of beet western yellows virus (BWYV) contains a potential translational frameshift signal in the overlap region of open reading frames ORF2 and ORF3 [2].
  • A deletion/insertion mutation lacking the 3' end of ORF1, all of galE, and the 5' end of ORF3 was constructed in the parent Hib strain (RM7004) [3].
  • The ORF3 protein of hepatitis E virus is a phosphoprotein that associates with the cytoskeleton [4].
  • Immediately downstream from the previously isolated Treponema denticola ATCC 35405 prtB gene coding for a chymotrypsinlike protease activity, an open reading frame, ORF3, was identified which shared significant homology with the highly conserved domains (HCDs) of bacterial methyl-accepting chemotaxis proteins (MCPs) [5].

High impact information on ECs4082

  • These results indicate that the impact of EspG/Orf3 on microtubule networks triggers the activation of the RhoA-ROCK signaling pathway via GEF-H1 activity [6].
  • The predicted amino acid sequence of orf3 revealed no close homology to known proteins [7].
  • Here we describe the function of the sixth gene, P450-3, and the cloning and functional analysis of a seventh gene, orf3, located at the left border of the gene cluster [7].
  • Sequence analyses revealed the presence of three open reading frames (ORFs), designated as ORF-1, ORF-2, and ORF-3, and the structural genes of the heptaprenyl diphosphate synthase were proved to consist of ORF-1 (heps-1) and ORF-3 (heps-2) (Koike-Takeshita, A., Koyama, T., Obata, S., and Ogura, K. (1995) J. Biol. Chem. 270, 18396-18400) [8].
  • Computer-assisted analysis of the DNA sequence revealed three putative open reading frames (ORFs), ORF1, ORF2, and ORF3 [9].

Chemical compound and disease context of ECs4082


Biological context of ECs4082

  • To obtain downstream sequence data for ORF3, colony hybridization screening of the HindIII chlamydial DNA library was used to isolate a second recombinant plasmid (pH-11) that contained a 1.7-kilobase chlamydial DNA insert [15].
  • The ORF3 probe also hybridized to a 540 bp transcript consistent with the size of ORF3 alone and supportive of the mutagenesis data of non-linkage [16].
  • A 2.9 kb BclI fragment, previously shown to restore a wild-type phenotype to a glk deletion mutant that lacks the entire segment, contains two complete open reading frames that would encode proteins of 20.1 kDa (ORF2) and 33.1 kDa (ORF3) [17].
  • A second EspG homolog, Orf3, is encoded on the EspC pathogenicity islet [18].
  • The deduced lactoferrin binding protein A (LbpA) sequences from the two strains were found to be 99% identical, the LbpB sequences were 92% identical, and the ORF3 proteins were 98% identical [19].

Anatomical context of ECs4082

  • Here, we show that the type III effectors, EspG and its homolog Orf3, trigger actin stress fiber formation and the destruction of the microtubule networks beneath adherent bacteria [6].
  • Over a limited hydrophilic sequence stretch, bordered by putative transmembrane areas, ORF3 and ORF4 exhibit homology with subunits 4 and 1 of mitochondrial and plastid NADH-ubiquinol oxidoreductases, respectively [20].
  • Analysis of RNA extracted from chlamydia-infected Vero cells detected ORF3-specific transcripts, from 20 h post-infection onwards, mainly as discrete RNA species of 1390 nucleotides comprising the downstream ORF4 sequence [21].

Associations of ECs4082 with chemical compounds

  • One of these, designated wbgU (orf3), has been overexpressed and biochemically characterized to show that it encodes a uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) C4 epimerase, only the second microbial enzyme characterized to have this activity [22].
  • These data suggest that ORF3 encodes a protein involved in the biosynthesis of ornithine, a constituent of phaseolotoxin [23].
  • A lysine residue that is a binding site for pyridoxal phosphate and an arginine residue that is a binding site for the alpha-carboxylate group of the substrate are conserved in ORF3 [23].
  • ORF3 was not essential for complementation; however, both the 23-kDa protein encoded by ORF3 and the predicted amino acid sequence of ORF4 showed homology to glutathione S-transferases [24].
  • The ORF downstream of gcdA (ORF3) is followed by hgdA and hgdB coding for 2-hydroxyglutaryl-CoA dehydratase, the preceding enzyme of the pathway of glutamate fermentation [25].

Analytical, diagnostic and therapeutic context of ECs4082

  • High performance liquid chromatography and gas chromatography-mass spectrometry analyses of the culture fluid of knock-out mutants identified GA1 and GA4, rather than GA3 and GA7, as the major C19-GA products, suggesting that orf3 encodes the GA4 1,2-desaturase [7].
  • By site-specific mutagenesis, we have shown that one of the amino acid residues constituting the active centre of RuvC enzyme (Glu-66) and conserved in ORF3 (Glu-67) is essential for the nucleolytic activity of the M-operon gene product(s) [26].
  • A Bg/II fragment containing ORF2 and ORF3 was cloned into pGK12, and the recombinant plasmid, pTRK135, was transformed into Lactobacillus acidophilus via electroporation [27].
  • Northern blot analysis and promoter extension mapping indicated that ORF3 is expressed as a monocistronic operon from a promoter that resembles the Escherichia coli sigma 70 consensus promoter [28].
  • However, plants inoculated with the aforementioned mutations did not develop symptoms, and Western blot analysis revealed markedly reduced expression of the movement protein (the product of ORF 3) [29].


  1. Cloning and sequencing of Vibrio cholerae mannose-sensitive haemagglutinin pilin gene: localization of mshA within a cluster of type 4 pilin genes. Jonson, G., Lebens, M., Holmgren, J. Mol. Microbiol. (1994) [Pubmed]
  2. Differential response to frameshift signals in eukaryotic and prokaryotic translational systems. Garcia, A., van Duin, J., Pleij, C.W. Nucleic Acids Res. (1993) [Pubmed]
  3. Molecular analysis of a complex locus from Haemophilus influenzae involved in phase-variable lipopolysaccharide biosynthesis. Maskell, D.J., Szabo, M.J., Butler, P.D., Williams, A.E., Moxon, E.R. Mol. Microbiol. (1991) [Pubmed]
  4. The ORF3 protein of hepatitis E virus is a phosphoprotein that associates with the cytoskeleton. Zafrullah, M., Ozdener, M.H., Panda, S.K., Jameel, S. J. Virol. (1997) [Pubmed]
  5. Characterization of a novel methyl-accepting chemotaxis gene, dmcB, from the oral spirochete Treponema denticola. Li, H., Arakawa, S., Deng, Q.D., Kuramitsu, H. Infect. Immun. (1999) [Pubmed]
  6. Enteropathogenic Escherichia coli activates the RhoA signaling pathway via the stimulation of GEF-H1. Matsuzawa, T., Kuwae, A., Yoshida, S., Sasakawa, C., Abe, A. EMBO J. (2004) [Pubmed]
  7. Characterization of the final two genes of the gibberellin biosynthesis gene cluster of Gibberella fujikuroi: des and P450-3 encode GA4 desaturase and the 13-hydroxylase, respectively. Tudzynski, B., Mihlan, M., Rojas, M.C., Linnemannstons, P., Gaskin, P., Hedden, P. J. Biol. Chem. (2003) [Pubmed]
  8. Identification of a novel gene cluster participating in menaquinone (vitamin K2) biosynthesis. Cloning and sequence determination of the 2-heptaprenyl-1,4-naphthoquinone methyltransferase gene of Bacillus stearothermophilus. Koike-Takeshita, A., Koyama, T., Ogura, K. J. Biol. Chem. (1997) [Pubmed]
  9. A relA/spoT homologous gene from Streptomyces coelicolor A3(2) controls antibiotic biosynthetic genes. Martínez-Costa, O.H., Arias, P., Romero, N.M., Parro, V., Mellado, R.P., Malpartida, F. J. Biol. Chem. (1996) [Pubmed]
  10. Cloning and analysis of the poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) biosynthesis genes of Aeromonas caviae. Fukui, T., Doi, Y. J. Bacteriol. (1997) [Pubmed]
  11. Structural organization of a Bacillus subtilis operon encoding menaquinone biosynthetic enzymes. Rowland, B., Hill, K., Miller, P., Driscoll, J., Taber, H. Gene (1995) [Pubmed]
  12. Open reading frame 3, which is adjacent to the mycocerosic acid synthase gene, is expressed as an acyl coenzyme A synthase in Mycobacterium bovis BCG. Fitzmaurice, A.M., Kolattukudy, P.E. J. Bacteriol. (1997) [Pubmed]
  13. Genetic characterization of the beta-glucuronidase enzyme from a human intestinal bacterium, Ruminococcus gnavus. Beaud, D., Tailliez, P., Anba-Mondoloni, J. Microbiology (Reading, Engl.) (2005) [Pubmed]
  14. Identification of Streptomyces violaceoruber Tü22 genes involved in the biosynthesis of granaticin. Bechthold, A., Sohng, J.K., Smith, T.M., Chu, X., Floss, H.G. Mol. Gen. Genet. (1995) [Pubmed]
  15. Cloning and expression of the Chlamydia trachomatis gene for CTP synthetase. Tipples, G., McClarty, G. J. Biol. Chem. (1995) [Pubmed]
  16. The fimA locus of Streptococcus parasanguis encodes an ATP-binding membrane transport system. Fenno, J.C., Shaikh, A., Spatafora, G., Fives-Taylor, P. Mol. Microbiol. (1995) [Pubmed]
  17. The glucose kinase gene of Streptomyces coelicolor A3(2): its nucleotide sequence, transcriptional analysis and role in glucose repression. Angell, S., Schwarz, E., Bibb, M.J. Mol. Microbiol. (1992) [Pubmed]
  18. EspG, a novel type III system-secreted protein from enteropathogenic Escherichia coli with similarities to VirA of Shigella flexneri. Elliott, S.J., Krejany, E.O., Mellies, J.L., Robins-Browne, R.M., Sasakawa, C., Kaper, J.B. Infect. Immun. (2001) [Pubmed]
  19. Cloning and expression of the Moraxella catarrhalis lactoferrin receptor genes. Du, R.P., Wang, Q., Yang, Y.P., Schryvers, A.B., Chong, P., Klein, M.H., Loosmore, S.M. Infect. Immun. (1998) [Pubmed]
  20. Nucleotide sequence and expression of an operon in Escherichia coli coding for formate hydrogenlyase components. Böhm, R., Sauter, M., Böck, A. Mol. Microbiol. (1990) [Pubmed]
  21. Expression of a plasmid gene of Chlamydia trachomatis encoding a novel 28 kDa antigen. Comanducci, M., Cevenini, R., Moroni, A., Giuliani, M.M., Ricci, S., Scarlato, V., Ratti, G. J. Gen. Microbiol. (1993) [Pubmed]
  22. New UDP-GlcNAc C4 epimerase involved in the biosynthesis of 2-acetamino-2-deoxy-L-altruronic acid in the O-antigen repeating units of Plesiomonas shigelloides O17. Kowal, P., Wang, P.G. Biochemistry (2002) [Pubmed]
  23. The phtE locus in the phaseolotoxin gene cluster has ORFs with homologies to genes encoding amino acid transferases, the AraC family of transcriptional factors, and fatty acid desaturases. Zhang, Y.X., Patil, S.S. Mol. Plant Microbe Interact. (1997) [Pubmed]
  24. Sequence analysis of a gene cluster involved in metabolism of 2,4,5-trichlorophenoxyacetic acid by Burkholderia cepacia AC1100. Daubaras, D.L., Hershberger, C.D., Kitano, K., Chakrabarty, A.M. Appl. Environ. Microbiol. (1995) [Pubmed]
  25. Cloning, sequencing and expression of the gene encoding the carboxytransferase subunit of the biotin-dependent Na+ pump glutaconyl-CoA decarboxylase from Acidaminococcus fermentans in Escherichia coli. Bendrat, K., Buckel, W. Eur. J. Biochem. (1993) [Pubmed]
  26. Lactococcus lactis phage operon coding for an endonuclease homologous to RuvC. Bidnenko, E., Ehrlich, S.D., Chopin, M.C. Mol. Microbiol. (1998) [Pubmed]
  27. Cloning, expression, and nucleotide sequence of the Lactobacillus helveticus 481 gene encoding the bacteriocin helveticin J. Joerger, M.C., Klaenhammer, T.R. J. Bacteriol. (1990) [Pubmed]
  28. Characterization of an Azospirillum brasilense Sp7 gene homologous to Alcaligenes eutrophus phbB and to Rhizobium meliloti nodG. Vieille, C., Elmerich, C. Mol. Gen. Genet. (1992) [Pubmed]
  29. ORF 5 of grapevine virus A encodes a nucleic acid-binding protein and affects pathogenesis. Galiakparov, N., Tanne, E., Mawassi, M., Gafny, R., Sela, I. Virus Genes (2003) [Pubmed]
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