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Gene Review

hemF  -  coproporphyrinogen III oxidase

Escherichia coli str. K-12 substr. MG1655

Synonyms: ECK2431, JW2429, popB, sec
 
 
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Disease relevance of hemF

  • The hemF gene was mapped to 52.6 min of the E. coli chromosome [1].
  • Sequence comparisons revealed 43% amino acid sequence identity with the product of the S. cerevisiae HEM13 gene and 90% identity with the product of the recently cloned Salmonella typhimurium hemF gene, while a structural relationship to the proposed anaerobic enzyme from Rhodobacter sphaeroides was not obvious [1].
  • In Gram-negative bacteria ATP, a membrane potential, the products of the sec genes and leader peptidases (enzymes which cleave the N-terminal signal peptides of the precursor proteins) are required [2].
  • The lag times measured for several bacteriophage and bacterial promoters differed widely (10 sec to several minutes) and in most cases corresponded to the rate-limiting step in the initiation process [3].
  • Identification of a new plasmid-encoded sec-dependent bacteriocin produced by Listeria innocua 743 [4].
 

High impact information on hemF

  • Autoregulation is achieved by modulating the longevity of this 3.6-kb mRNA, whose half-life ranges from < 40 sec to > 8 min depending on the level of RNase E activity in the cell [5].
  • One of the strategies used by Gram-negative bacteria to secrete proteins across the two membranes which delimit the cells, is sec independent and dedicated to proteins lacking an N-terminal signal peptide [6].
  • The NMR data show that approximately 20% of the total intensity for each of the unfolded tryptophan resonances is present at 1.5 sec, indicating that these two phases may represent the complete unfolding of the two different populations of the native protein [7].
  • Stopped-flow measurements of the fluorescence and circular dichroism changes associated with the urea-induced unfolding show a fast phase (half-time of about 1 sec) representing 20% of the total amplitude in addition to the slow phase mentioned above [7].
  • When annealed with a primer where thymine or cytosine is paired opposite template m6G, about half the molecules were replicated in the first 15 sec, and no significant further replication was seen over a 1-hr period [8].
 

Chemical compound and disease context of hemF

 

Biological context of hemF

  • Isolation of the hemF operon containing the gene for the Escherichia coli aerobic coproporphyrinogen III oxidase by in vivo complementation of a yeast HEM13 mutant [1].
  • An open reading frame (orf3) transcribed in a direction opposite that of the hemF gene was found downstream of the hemF gene [1].
  • Coproporphyrinogen III oxidase, an enzyme involved in heme biosynthesis, catalyzes the oxidative decarboxylation of coproporphyrinogen III to form protoporphyrinogen IX [1].
  • During a brief pulse (5 sec at 30 degrees), the radioactivity incorporated into the complementary strand was found in chains much shorter than one genome length [12].
  • The kinetics of digestion at 37 degrees C indicates that the rate of translocation of DNA from each side of a bound enzyme is about 200 base pairs per second, and the cuts are completed within 15-25 sec of the time neighboring enzymes meet [13].
 

Anatomical context of hemF

  • The hemF gene is in an operon with an upstream open reading frame (orf1) encoding a 31.7-kDa protein with homology to an amidase involved in cell wall metabolism [1].
  • Baseplate-defective phage mutant T412- and isolated adsorption organelles of smaller viruses fail to cause an effect. di-O-C5[3]-labeled cells respond to T4 at a multiplicity of infection greater than or equal to 40 within 1 sec [10].
  • Effects of two sec genes on protein assembly into the plasma membrane of Escherichia coli [14].
  • In addition, these constructs provide proof in principle for the development of novel chimeric CT-like or LT-like vaccine candidates containing CTA(2) fusion proteins that cannot be delivered to the periplasm of E. coli by use of the sec secretion pathway [15].
  • The rate of both female and male sec spy gamete transmission was higher in plants heterozygous for both mutations than in plants heterozygous for sec and homozygous for spy [16].
 

Associations of hemF with chemical compounds

  • Only the addition of manganese fully restored coproporphyrinogen III oxidase activity [9].
  • Phosphatidylglycerol and cardiolipin are transfocated very rapidly, with half-lives shorter than 30 sec [17].
  • Consideration of dipolar relaxation and chemical shift anisotrophy led to a calculated rotational correlation time of 1.6 +/- 0.4 x 10(-8) sec for the adenines and 1.3 +/- 0.3 x 10(-8) sec for the ribose carbons [18].
  • However, after 6 sec the lactose flux is within 0.1% of steady state, and so an ever changing environment must be invoked to continually expose beta-galactosidase to selection [19].
  • Thirty of 54 patients given M/T and 13 of 54 patients given T/T developed prothrombin times that were greater than or equal to 2 sec beyond control values (P less than .001) after a mean of 6.5 days of antimicrobial therapy [20].
 

Analytical, diagnostic and therapeutic context of hemF

  • This review summarizes genetic analyses of SecY, SecE and some other protein translocation factors, utilizing 'prl' mutations, 'sec' mutations, 'suppressor-directed inactivation', 'Sec titration', dominant negative mutations and their suppressors [21].
  • Two predicted sites separated by 11 bp found within the nrd promoter region, and one in the tgt/sec promoter, were also confirmed by gel shift analysis [22].
  • By use of secB'-lacZ gene fusions and immunoprecipitation experiments, SecB production was studied in E. coli strains containing conditional lethal mutations in chaperone or sec genes [23].
  • Filtration at 63.7 cm/sec gave 99.98% and 99.996% removal (3.7 and 4.4 log10-unit reduction in concentration) of Escherichia coli and Pseudomonas aeruginosa, respectively [24].
  • From sedimentation equilibrium ultracentrifugation, a molecular weight of 70,100 was obtained, which is in good agreement with the value obtained by the Sephadex G-150 gel filtration method (69,000); the diffusion constant was calculated to be 5.88X10(-7) cm2/sec [25].

References

  1. Isolation of the hemF operon containing the gene for the Escherichia coli aerobic coproporphyrinogen III oxidase by in vivo complementation of a yeast HEM13 mutant. Troup, B., Jahn, M., Hungerer, C., Jahn, D. J. Bacteriol. (1994) [Pubmed]
  2. Phosphatidylglycerol is involved in protein translocation across Escherichia coli inner membranes. de Vrije, T., de Swart, R.L., Dowhan, W., Tommassen, J., de Kruijff, B. Nature (1988) [Pubmed]
  3. Rate-limiting steps in RNA chain initiation. McClure, W.R. Proc. Natl. Acad. Sci. U.S.A. (1980) [Pubmed]
  4. Identification of a new plasmid-encoded sec-dependent bacteriocin produced by Listeria innocua 743. Kalmokoff, M.L., Banerjee, S.K., Cyr, T., Hefford, M.A., Gleeson, T. Appl. Environ. Microbiol. (2001) [Pubmed]
  5. RNase E autoregulates its synthesis by controlling the degradation rate of its own mRNA in Escherichia coli: unusual sensitivity of the rne transcript to RNase E activity. Jain, C., Belasco, J.G. Genes Dev. (1995) [Pubmed]
  6. Protein secretion in gram-negative bacteria: assembly of the three components of ABC protein-mediated exporters is ordered and promoted by substrate binding. Létoffé, S., Delepelaire, P., Wandersman, C. EMBO J. (1996) [Pubmed]
  7. Stopped-flow NMR spectroscopy: real-time unfolding studies of 6-19F-tryptophan-labeled Escherichia coli dihydrofolate reductase. Hoeltzli, S.D., Frieden, C. Proc. Natl. Acad. Sci. U.S.A. (1995) [Pubmed]
  8. Evidence from in vitro replication that O6-methylguanine can adopt multiple conformations. Dosanjh, M.K., Loechler, E.L., Singer, B. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  9. Oxygen-dependent coproporphyrinogen III oxidase (HemF) from Escherichia coli is stimulated by manganese. Breckau, D., Mahlitz, E., Sauerwald, A., Layer, G., Jahn, D. J. Biol. Chem. (2003) [Pubmed]
  10. Fast responses of bacterial membranes to virus adsorption: a fluorescence study. Bayer, M.E., Bayer, M.H. Proc. Natl. Acad. Sci. U.S.A. (1981) [Pubmed]
  11. Investigation of Escherichia coli dimethyl sulfoxide reductase assembly and processing in strains defective for the sec-independent protein translocation system membrane targeting and translocation. Sambasivarao, D., Dawson, H.A., Zhang, G., Shaw, G., Hu, J., Weiner, J.H. J. Biol. Chem. (2001) [Pubmed]
  12. Discontinuous replication of replicative form DNA from bacteriophage phiX174. Machida, Y., Okazaki, T., Okazaki, R. Proc. Natl. Acad. Sci. U.S.A. (1977) [Pubmed]
  13. Model for how type I restriction enzymes select cleavage sites in DNA. Studier, F.W., Bandyopadhyay, P.K. Proc. Natl. Acad. Sci. U.S.A. (1988) [Pubmed]
  14. Effects of two sec genes on protein assembly into the plasma membrane of Escherichia coli. Wolfe, P.B., Rice, M., Wickner, W. J. Biol. Chem. (1985) [Pubmed]
  15. Characterization of fluorescent chimeras of cholera toxin and Escherichia coli heat-labile enterotoxins produced by use of the twin arginine translocation system. Tinker, J.K., Erbe, J.L., Holmes, R.K. Infect. Immun. (2005) [Pubmed]
  16. Two O-linked N-acetylglucosamine transferase genes of Arabidopsis thaliana L. Heynh. have overlapping functions necessary for gamete and seed development. Hartweck, L.M., Scott, C.L., Olszewski, N.E. Genetics (2002) [Pubmed]
  17. Translocation of phospholipids from the inner to the outer membrane of Escherichia coli. Donohue-Rolfe, A.M., Schaechter, M. Proc. Natl. Acad. Sci. U.S.A. (1980) [Pubmed]
  18. Transfer RNA structure by carbon NMR: C2 of adenine, uracil and cytosine. Schmidt, P.G., Tompson, J.G., Agris, P.F. Nucleic Acids Res. (1980) [Pubmed]
  19. Fitness, flux and phantoms in temporally variable environments. Dean, A.M. Genetics (1994) [Pubmed]
  20. Hypoprothrombinemia in febrile, neutropenic patients with cancer: association with antimicrobial suppression of intestinal microflora. Conly, J.M., Ramotar, K., Chubb, H., Bow, E.J., Louie, T.J. J. Infect. Dis. (1984) [Pubmed]
  21. SecY and integral membrane components of the Escherichia coli protein translocation system. Ito, K. Mol. Microbiol. (1992) [Pubmed]
  22. Information analysis of Fis binding sites. Hengen, P.N., Bartram, S.L., Stewart, L.E., Schneider, T.D. Nucleic Acids Res. (1997) [Pubmed]
  23. Influence of impaired chaperone or secretion function on SecB production in Escherichia coli. Müller, J.P. J. Bacteriol. (1996) [Pubmed]
  24. Removal of airborne bacteria by filtration using a composite microporous membrane made of a pyridinium-type polymer showing strong affinity with microbial cells. Kawabata, N., Kawato, S. Epidemiol. Infect. (1998) [Pubmed]
  25. Pantothenate synthetase of Escherichia coli B. I. Physicochemical properties. Miyatake, K., Nakano, Y., Kitaoka, S. J. Biochem. (1976) [Pubmed]
 
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