Multiple IS insertion sequences near the replication terminus in Escherichia coli K-12

Moszer, Ivan; Glaser, Philippe; Danchin, Antoine

doi:10.1016/0300-9084(91)90166-x

Cited by 11 publications

(11 citation statements)

References 21 publications

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“…The number of amino acids in the coding region would make Lhr the longest protein identified in E. coli. A hypothetical protein, YdbA, encoded by a sequence near the replication terminus and interrupted by an insertion element might be longer, but there is no evidence that such a protein is expressed (15). The amino acid composition associated with the derived sequence of Lhr would correspond to an isoelectric point of 6.73.…”

Section: Resultsmentioning

confidence: 99%

The gene for the longest known Escherichia coli protein is a member of helicase superfamily II

et al. 1995

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The Escherichia coli rnt gene, which encodes the RNA-processing enzyme RNase T, is cotranscribed with a downstream gene. Complete sequencing of this gene indicates that its coding region encompasses 1,538 amino acids, making it the longest known protein in E. coli. The gene (tentatively termed lhr for long helicase related) contains the seven conserved motifs of the DNA and RNA helicase superfamily II. An ϳ170-kDa protein is observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of 35 S-labeled extracts prepared from cells in which lhr is under the control of an induced T7 promoter. This protein is absent when lhr is interrupted or when no plasmid is present. Downstream of lhr is the C-terminal region of a convergent gene with homology to glutaredoxin. Interruptions of chromosomal lhr at two different positions within the gene do not affect the growth of E. coli at various temperatures in rich or minimal medium, indicating that lhr is not essential for usual laboratory growth. lhr interruption also has no effect on anaerobic growth. In addition, cells lacking Lhr recover normally from starvation, plate phage normally, and display normal sensitivities to UV irradiation and H 2 O 2 . Southern analysis showed that no other gene closely related to lhr is present on the E. coli chromosome. These data expand the known size range of E. coli proteins and suggest that very large helicases are present in this organism.The rnt gene encoding RNase T, an enzyme involved in tRNA processing and end turnover (4,5,17,19), is located at approximately 36 min on the Escherichia coli genetic map (4). Sequence analysis of the rnt gene revealed the existence of a downstream open reading frame (ORF) that is cotranscribed with rnt (9). Limited sequence analysis of this ORF (130 amino acids) showed that it contained a high degree of similarity to a common motif found in helicases (8, 23). Because coexpression of an RNA-processing enzyme and a helicase would be unusual and potentially of considerable importance for understanding RNA maturation, we have continued the analysis of this unknown gene.Helicases are an expanding category of enzymes that participate in many aspects of DNA and RNA metabolism (7). They couple the unwinding of double-stranded polynucleotides to the hydrolysis of ATP. While only about 25 proteins have actually been shown to possess helicase activity, close to 10 times that number have been suggested to be helicases on the basis of analyses of their amino acid sequences (7). This has come about because all the known helicases contain conserved sequence motifs that have predictive value as identifiers for this class of enzymes. The large majority of helicases share seven of these motifs, the details of which have been used to group these proteins into families and superfamilies (7). However, as yet, there is no reliable sequence pattern that can be used to conclusively distinguish between the DNA and RNA helicases.In this paper, we present the complete sequence of the gene cotranscribed with rnt. This ge...

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Section: Resultsmentioning

confidence: 99%

The gene for the longest known Escherichia coli protein is a member of helicase superfamily II

et al. 1995

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“…The sequencing strategy used has been extensively described elsewhere (21,41). DNA sequences were compiled by using the program XBAP of Dear and Staden (12).…”

Section: Materuils and Methodsmentioning

confidence: 99%

Bacillus subtilis F0F1 ATPase: DNA sequence of the atp operon and characterization of atp mutants

et al. 1994

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We cloned and sequenced an operon of nine genes coding for the subunits of the Bacillus subtilis FOF, ATP synthase. The arrangement of these genes in the operon is identical to that of the atp operon from Escherichia coli and from three other Bacillus species. The deduced amino acid sequences of the nine subunits are very similar to their counterparts from other organisms. We constructed two B. subtilis strains from which different parts of the atp operon were deleted. These B. subtilis atp mutants were unable to grow with succinate as the sole carbon and energy source. ATP was synthesized in these strains only by substrate-level phosphorylation. The two mutants had a decreased growth yield (43 and 56% of the wild-type level) and a decreased growth rate (61 and 66% of the wild-type level), correlating with a twofold decrease of the intracellular ATP/ADP ratio. In the absence of oxidative phosphorylation, B. subtilis increased ATP synthesis through substrate-level phosphorylation, as shown by the twofold increase of by-product formation (mainly acetate). The increased turnover of glycolysis in the mutant strain presumably led to increased synthesis of NADH, which would account for the observed stimulation of the respiration rate associated with an increase in the expression of genes coding for respiratory enzymes. It therefore appears that B. subtilis and E. coli respond in similar ways to the absence of oxidative phosphorylation.ATP plays a central role in energy transduction in living organisms. Although some ATP is synthesized in aerobiosis by soluble enzyme systems like glycolytic enzymes that perform substrate-level phosphorylation, most is synthesized by membrane-bound enzyme complexes through oxidative phosphorylation. The energy-transducing membranes, where these complexes are found, are the plasma membrane of prokaryotic cells, the inner membrane of mitochondria, and the thylakoid membrane of chloroplasts. ATP synthesis from ADP and Pi is catalyzed by the ATP synthase complex and is driven by the proton gradient. This gradient is generated by respiration in mitochondria and respiring bacteria and by photosynthesis in chloroplasts and photosynthetic bacteria.ATP

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“…DNA sequences were determined using Sander's dideoxy chain termination method as described by Moszer et al (1991).…”

Section: Rna Isolation and Analysismentioning

confidence: 99%

Characterization of polyamine synthesis pathway in Bacillus subtilis 168

Sekowska

Bertin

Danchin

1998

Molecular Microbiology

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SummaryThe ubiquitous polyamines fulfil a variety of functions in all three kingdoms of life. However, little is known about the biosynthesis of these compounds in Grampositive bacteria. We show that, in Bacillus subtilis, there is a single pathway to polyamines, starting from arginine, with agmatine as an intermediate. We first identified the structural gene of arginine decarboxylase, speA (formerly cad ), and then described the speE speB operon, directing synthesis of spermidine synthase and agmatinase. This operon is transcribed into two messenger RNAs, a major one for the speE gene and a minor one for both speE and speB. The promoter of the operon was identified upstream from the speE gene by primer extension analysis. Transcription of this operon indicated that the level of agmatinase synthesis is very low, thus allowing a stringent control on the synthesis of putrescine and, therefore, of all polyamines. This is consistent with the level of polyamines measured in the cell.

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Multiple IS insertion sequences near the replication terminus in Escherichia coli K-12

Cited by 11 publications

References 21 publications

The gene for the longest known Escherichia coli protein is a member of helicase superfamily II

The gene for the longest known Escherichia coli protein is a member of helicase superfamily II

Bacillus subtilis F0F1 ATPase: DNA sequence of the atp operon and characterization of atp mutants

Characterization of polyamine synthesis pathway in Bacillus subtilis 168

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