################################################################
  E.coli news vol. 3  2003.10.11
################################################################

This is a digest of daily PubMed searching of E.coli new finding.

***this year finding***

  >>>New amidase<<<

(JW1319/ycjI)

J Bacteriol. 2003 Jan;185(2):679-82.
   
Identification of MpaA, an amidase in Escherichia coli that hydrolyzes the gamma-D-glutamyl-meso-diaminopimelate bond in murein peptides.
Uehara T, Park JT.
Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.

MpaA amidase was identified in Escherichia coli by its amino acid sequence homology with the ENP1 endopeptidase from Bacillus sphaericus. The enzymatic activity of MpaA, i.e., hydrolysis of the gamma-D-glutamyl-diaminopimelic acid bond in the murein tripeptide L-alanyl-gamma-D-glutamyl-meso-diaminopimelic acid, was demonstrated in the cell extract of a strain expressing mpaA from a multicopy plasmid. An mpaA mpl (murein peptide ligase) double mutant accumulated large amounts of murein tripeptide in its cytoplasm, consistent with the premise that MpaA degrades the tripeptide if its recycling via the peptidoglycan biosynthetic pathway is blocked.

PMID: 12511517

  >>>flavorubredoxin nitric oxide reductase<<<

(JW2680?/flrD)

FEMS Microbiol Lett. 2003 Jan 28;218(2):385-93.

Regulation of the flavorubredoxin nitric oxide reductase gene in Escherichia coli: nitrate repression, nitrite induction, and possible post-transcription control.
da Costa PN, Teixeira M, Saraiva LM.
Instituto de Tecnologia Qui;mica e Biologica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.

Escherichia coli flavorubredoxin is a new type of cytoplasmic nitric oxide (NO) reductase, which shows NO reductase activity within the range of the canonical membrane-bound heme b(3)-iron NO reductases. Using reverse-transcription polymerase chain reaction we show that although the flavorubredoxin gene (flrd) is transcribed in both aerobic and anaerobic conditions, anaerobiosis induced transcription up to 12-fold, under fermentative conditions; a 28-fold stimulation was observed in an E. coli fnr mutant strain, showing that the flavorubredoxin gene is negatively regulated by FNR. The level of anaerobic transcription was repressed three-fold by nitrate, but induced 47-fold by nitrite. The transcription factors NarL and NarP are not essential for flrd expression. Furthermore, the addition of NO within the physiological range of concentrations does not induce anaerobic transcription of flrd. Since two other E. coli proteins are known to exhibit NO reductase activity,

  flavohemoglobin and the pentaheme cytochrome c nitrite reductase, we have also compared the concentrations of their mRNAs with those of flavorubredoxin, under the same growth conditions. Transcription of the putative transcriptional activator of flavorubredoxin, ygaA, is also regulated by the absence of oxygen and the presence of nitrite. Levels of FlRd protein did not correlate with mRNA levels. The results reveal that a complex regulation of flavorubredoxin expression is operative, possibly by both transcriptional and post-transcriptional mechanisms.

PMID: 12586421

  >>>2-phosphoglycolate phosphatase<<<

(JW3348/gph)

J Bacteriol. 2003 Oct;185(19):5815-21. 
   
Role of 2-phosphoglycolate phosphatase of Escherichia coli in metabolism of the 2-phosphoglycolate formed in DNA repair.
Teresa Pellicer M, Felisa Nunez M, Aguilar J, Badia J, Baldoma L.
Department of Biochemistry, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain.

The enzyme 2-phosphoglycolate phosphatase from Escherichia coli, encoded by the gph gene, was purified and characterized. The enzyme was highly specific for 2-phosphoglycolate and showed good catalytic efficiency (k(cat)/K(m)), which enabled the conversion of this substrate even at low intracellular concentrations. A comparison of the structural and functional features of this enzyme with those of 2-phosphoglycolate phosphatases of different origins showed a high similarity of the sequences, implying the use of the same catalytic mechanism. Western blot analysis revealed constitutive expression of the gph gene, regardless of the carbon source used, growth stage, or oxidative stress conditions. We showed that this housekeeping enzyme is involved in the dissimilation of the intracellular 2-phosphoglycolate formed in the DNA repair of 3'-phosphoglycolate ends. DNA strand breaks of this kind are caused by agents such as the radiomimetic compound bleomycin. The differen

tial response between a 2-phosphoglycolate phosphatase-deficient mutant and its parental strain after treatment with bleomycin allowed us to connect the intracellular formation of 2-phosphoglycolate with the production of glycolate, which is subsequently incorporated into general metabolism. We thus provide evidence for a salvage function of 2-phosphoglycolate phosphatase in the metabolism of a two-carbon compound generated by the cellular DNA repair machinery.

PMID: 13129953

  >>>novel sRNA component<<<

Mol Microbiol. 2003 May;48(3):657-70. 

A novel sRNA component of the carbon storage regulatory system of Escherichia coli.
Weilbacher T, Suzuki K, Dubey AK, Wang X, Gudapaty S, Morozov I, Baker CS, Georgellis D, Babitzke P, Romeo T.
Department of Molecular Biology and Immunology, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX 76107-2699, USA.

Small untranslated RNAs (sRNAs) perform a variety of important functions in bacteria. The 245 nucleotide sRNA of Escherichia coli, CsrC, was discovered using a genetic screen for factors that regulate glycogen biosynthesis. CsrC RNA binds multiple copies of CsrA, a protein that post-transcriptionally regulates central carbon flux, biofilm formation and motility in E. coli. CsrC antagonizes the regulatory effects of CsrA, presumably by sequestering this protein. The discovery of CsrC is intriguing, in that a similar sRNA, CsrB, performs essentially the same function. Both sRNAs possess similar imperfect repeat sequences (18 in CsrB, nine in CsrC), primarily localized in the loops of predicted hairpins, which may serve as CsrA binding elements. Transcription of csrC increases as the culture approaches the stationary phase of growth and is indirectly activated by CsrA via the response regulator UvrY. Because CsrB and CsrC antagonize CsrA activity and depend on CsrA fo

r their synthesis, a csrB null mutation causes a modest compensatory increase in CsrC levels and vice versa. Homologues of csrC are apparent in several Enterobacteriaceae. The regulatory and evolutionary implications of these findings are discussed.

PMID: 12694612

***additional finding***

(E. coli have cellulose synthase genes.)

Mol Microbiol. 2002 Feb;43(3):793-808. 
   
Genetic analysis of Salmonella enteritidis biofilm formation: critical role of cellulose.
Solano C, Garcia B, Valle J, Berasain C, Ghigo JM, Gamazo C, Lasa I.
Instituto de Agrobiotecnologia y Recursos Naturales and Departamento de Produccion Agraria, Universidad Publica de Navarra-Consejo Superior de Investigaciones Cientificas, 31006 Pamplona, Spain.

We report here a new screening method based on the fluorescence of colonies on calcofluor agar plates to identify transposon insertion mutants of Salmonella enteritidis that are defective in biofilm development. The results not only confirmed the requirement of genes already described for the modulation of multicellular behaviour in Salmonella typhimurium and other species, but also revealed new aspects of the biofilm formation process, such as two new genetic elements, named as bcsABZC and bcsEFG operons, required for the synthesis of an exopolysaccharide, digestible with cellulase. Non-polar mutations of bcsC and bcsE genes and complementation experiments demonstrated that both operons are responsible for cellulose biosynthesis in both S. enteritidis and S. typhimurium. Using two different growth media, ATM and LB, we showed that the biofilm produced by S. enteritidis is made of different constituents, suggesting that biofilm composition and regulation depends on

  environmental conditions. Bacterial adherence and invasion assays of eukaryotic cells and in vivo virulence studies of cellulose-deficient mutants indicated that, at least under our experimental conditions, the production of cellulose is not involved in the virulence of S. enteritidis. However, cellulose-deficient mutants were more sensitive to chlorine treatments, suggesting that cellulose production and biofilm formation may be an important factor for the survival of S. enteritidis on surface environments.

PMID: 11929533