Transposition of IS2 into the hemB gene of Escherichia coli K-12.

Genetic studies of the hemB gene in Escherichia coli have resulted in the recovery of both stable and unstable mutant strains. The stable strains have been shown to result from large deletions. This study demonstrates that unstable strains result from the insertion of transposable element IS2 primarily into the 5' region of the structural gene; the instability results from precise excision of the element, producing strains with both high and low frequencies of reversion. This first report of IS2 insertion into hemB suggests that this gene may be a preferred target for insertion of this transposable element.     

The structure of the Escherichia coli hemB gene

The Escherichia coli hemB gene, which encodes 5-aminolevulinic acid dehydratase, and was cloned into pTZ18U, a multicopy plasmid, was sequenced. The hemB insert was double-digested with restriction enzymes and recloned back into pTZ18U and pTZ19U to allow for sequencing in two directions. In a second procedure, used to fill in gaps and to confirm the sequence derived from the first procedure, the whole insert was cloned into M13 phages. A nested set of deletions was constructed and recloned into M13. Both the double-digested fragments cloned into plasmids pTZ18U and pTZ19U and the overlapping fragments contained in M13 phages were sequenced using the dideoxy procedure with [35S]dATP. Computer software was used to identify coding regions and the correct reading frame. Two promoter regions, two Shine-Dalgarno sequences and two possible start sites were identified. Extensive homologies with yeast (36%), human liver (40%) and rat liver (40%) amino-acid (aa) sequences were observed, especially in the 16-aa Zn-binding region (75%) and the 4 aa surrounding the essential lysine at the active site (100% for rat and human proteins). Computer analysis of promoter strength and two independent analyses of codon usage indicated that the hemB gene is moderately expressed.     

Rates of transposition in Escherichia coli

The evolutionary role of transposable elements (TEs) is still highly controversial. Two key parameters, the transposition rate (u and w, for replicative and non-replicative transposition) and the excision rate (e) are fundamental to understanding their evolution and maintenance in populations. We have estimated u, w and e for six families of TEs (including eight members: IS1, IS2, IS3, IS4, IS5, IS30, IS150 and IS186) in Escherichia coli, using a mutation accumulation (MA) experiment. In this experiment, mutations accumulate essentially at the rate at which they appear, during a period of 80 500 (1610 generations × 50 lines) generations, and spontaneous transposition events can be detected. This differs from other experiments in which insertions accumulated under strong selective pressure or over a limited genomic target. We therefore provide new estimates for the spontaneous rates of transposition and excision in E. coli. We observed 25 transposition and three excision events in 50 MA lines, leading to overall rate estimates of u ∼ 1.15 × 10^–5, w ∼ 4 × 10⁻⁸ and e ∼ 1.08 × 10⁻⁶ (per element, per generation). Furthermore, extensive variation between elements was found, consistent with previous knowledge of the mechanisms and regulation of transposition for the different elements.     

Insertion of IS1 into the rpsE gene for ribosomal protein S5 causes cold-sensitivity in Escherichia coli

Summary The nucleotide sequence of the rpsE gene for the ribosomal protein S5 of a mutant of E. coli showing cold-sensitive growth revealed the presence of an insertion sequence, IS1, near the 3-end of the gene. This mutant grows very slowly even at the permissive temperature (30°C). At temperatures below 20°C, its growth becomes negligible. It is likely that the presence of IS1 disturbs the continued translation of the polycistronic messenger RNA of the spc-operon from the point of IS1 insertion downwards, especially at the unfavorable temperatures.     

Cloning of the Escherichia coli K-12 hemB gene.

An Escherichia coli heme-requiring, heme-permeable mutant had no detectable 5-aminolevulinate dehydratase or porphobilinogen deaminase activities. The gene which complemented this mutation was cloned to a high-copy-number plasmid, and porphobilinogen deaminase activity was restored to normal levels, but the synthesis of 5-aminolevulinate dehydratase increased 20- to 30-fold. A maxicell procedure confirmed that the gene cloned was hemB.     

Insertion of IS3 Can “Turn-On” a Silent Gene in Escherichia coli

A silent argE gene became reactivated by the integration of IS3 in orientation II. IS3 itself is responsible for this effect, at least in part.     

Imprecise excision of insertion element IS5 from the fliC gene contributes to flagellar diversity in Escherichia coli

Motile strains of Escherichia coli K12 carrying both a chromosomal fliC-H48 gene and a plasmid encoded fliC-H4 gene express both types of flagellins, which are coassembled into functional flagella. By using flagellar-H48-specific antiserum and a plasmid curing procedure, nonmotile mutants were found that carried an IS5 insertion in the chromosomal fliC-H48 gene. Motile revertants were isolated that showed deletions of the IS5 element together with sections of the fliC-H48 gene resulting in an altered flagellar serotype in these strains. As IS5 elements were found associated with 35 of 53 known H-types in wildtype E. coli strains, this insertion element might play a major role in serotype diversity.     

Gene Expression Pattern after Insertion of Dexamethasone-Eluting Electrode into the Guinea Pig Cochlea

A cochlear implant is an indispensable apparatus for a profound hearing loss patient. But insertion of the electrode entails a great deal of stress to the cochlea, and may cause irreversible damage to hair cells and related nerve structure. Although damage prevention effects of dexamethasone have been reported, long-term administration is difficult. In this study, we used a dexamethasone-eluting electrode in the guinea pig cochlea, and compared the gene expression after 7 days insertion with that of a normal electrode and non-surgically treated control by microarray. 40 genes were up-regulated 2-fold or more in the normal electrode group compared to the non-surgically treated group. Most of the up-regulated genes were associated with immune response and inflammation. In the dexamethasone-eluting group, compared to the normal electrode group, 7 of the 40 genes were further up-regulated, while 12 of them were down-regulated and there was a tendency to return to the non-surgical condition. 9 genes were down-regulated 2-fold or less with normal electrode insertion, and 4 of the 9 tended to return to the non-surgical condition in the dexamethasone-eluting group. These genes are certainly involved in the maintenance of the physiological functions of the cochlea. Our results indicate that the dexamethasone-eluting electrode will have an effect on the normalization of homeostasis in the cochlea.     

Insertion of carrier proteins into hydrophilic loops of the Escherichia coli lactose permease

Subcellular distribution of plant endo-beta-N-acetylglucosaminidase (endo-beta-GlcNAc-ase) and high-mannose type free N-glycans produced by the endoglycosidase has been analyzed using cotyledons of pumpkin seedlings as the model plant cells. Each organelle in the cotyledons was fractionated by ultracentrifugation with the sucrose density gradient system and the endo-beta-GlcNAc-ase activity in each fraction was assayed with fluorescence labeled N-glycans as substrates. The endoglycosidase activity was exclusively recovered in the soluble fraction (cytosol fraction) but not in other specific organellar fractions, suggesting that the endoglycosidase would reside predominantly in the cytosol. The quantitative analysis of high-mannose type free N-glycans occurring in each fraction showed that more than 70% of the free N-glycans was recovered from the soluble fraction, suggesting the endoglycosidase would work in the cytosol and the resulting free N-glycans would accumulate in the same fraction. The pumpkin endo-beta-GlcNAc-ase (endo-CM) partially purified from the cotyledons showed optimum activity around pH 6.5, supporting this enzyme would reside in the cytosol. Furthermore, the detailed analysis of substrate specificity of endo-CM using various high-mannose type N-glycans showed that the pumpkin enzyme, as well as other plant endo-beta-N-acetylglucosaminidases, were highly active toward the high-mannose type glycans bearing the Man(alpha1)-2Man(alpha1)-3Man(beta1)-structural unit.     

Insertion of newly synthesized proteins into the outer membrane of Escherichia coli.

The insertion of newly synthesized proteins into the outer membrane of Escherichia coli has been examined. The results show that there is no precurser pool of outer membrane proteins in the cytoplasmic membrane because first, the incorporation of a [35S]methionine pulse into outer membrane proteins completely parallels its incorporation into cytoplasmic membrane proteins, and second, under optimal isolation conditions, no outer membrane proteins are found in the cytoplasmic membrane, even when the membranes are analysed after being labeled for only 15 s. The [35S]methionine present in the outer membrane after a pulse of 15 s was found in protein fragments of varying sizes rather than in specific outer membrane proteins. This label could however be chased into specific proteins within 30--120 s, depending on the size of the protein, indicating that although unfinished protein fragments were present in the outer membrane, they were completed by subsequent chain elongation. Thus, outer membrane proteins are inserted into the outer membrane while still attached to ribosomes. Since ribosomes which are linked to the cell envelope by nascent polypeptide chains are stationary, the mRNA which is being translated by these ribosomes moves along the inner cell surface.     

Increased stability of maintenance of pAT153 in Escherichia coli HB101 due to transposition of IS1 from the chromosome into the tetracycline resistance region of pAT153

Abstract The plasmid vector pAT153 was rapidly lost from carbon-limited continuous cultures of Escherichia coli HB101 (pAT153) at a dilution rate of 0.15 h⁻¹. In one experiment, the plasmid was maintained by 80% of the host bacteria for up to 35 generations. The tetracycline-resistance gene was not expressed from the majority of the plasmid DNA in this population of E. coli HB101 due to transposition of IS1 from the bacterial chromosome into the aminoterminal region of the tet gene of pAT153. This plasmid, pLCX1, when isolated and retransformed into E. coli HB101, was more stably maintained than pAT153. Similar plasmids have been isolated from other glucose, phosphate, ammonium and sulphate-limited chemostats.     

Insertion of the enteropathogenic Escherichia coli Tir virulence protein into membranes in vitro

Insertion of the enteropathogenic Escherichia coli Tir protein into the plasma membrane of intestinal epithelial cells is a crucial event in infection because it provides a receptor for intimate bacterial adherence. This interaction with the bacterial outer membrane protein intimin is also essential in generating a number of signaling activities associated with virulence. Tir can be modified at various sites by phosphorylation and functionally interacts with multiple host proteins. To investigate the mechanism of membrane insertion and to establish a model system in which the multiple interactions/functions of Tir can be uncoupled and independently characterized, we used intrinsic tryptophan fluorescence, surface plasmon resonance, and protease digestion assays to show that Tir can insert directly into phospholipid vesicles in a composition-dependent manner to generate the topology reported in vivo. This is the first time that Tir has been shown to insert into membranes in a simple model system in the absence of chemical modification or other factors. These data are consistent with the protein interacting with lipids through two sites. The major site is localized to the transmembrane/intimin-binding domain region and includes Trp235, which is shown to be an effective reporter of interaction. The minor site is located within the C-terminal domain. Together, these data support a model in which Tir is released into the cytoplasm by the type III translocon and then independently inserts into the plasma membrane from a cytoplasmic location. A thorough understanding of this mechanism will be crucial to understand the subtleties of enteropathogenic E. coli pathogenesis.     

Insertion element IS121 is near proA in the chromosomes of Escherichia coli K-12 strains.

Insertion element IS121 was mapped between proA and a previously mapped IS5A element in two F-prime plasmids. Results of hybridizations of IS121 to chromosomal DNA from four other strains suggest that IS121 is normally present at this position in the chromosomes of Escherichia coli K-12 strains.     

An insertion of Escherichia coli transposable element IS1K into the site immediately before tetracycline-resistance determinant of Bacillus subtilis chromosomal DNA fragment in cloning in E. coli

In cloning in Escherichia coli C600 of a 4.5-kbp HindIII DNA fragment with the tetracycline-resistance determinant (tetBS908) from Bacillus subtilis GSY908 chromosome using a plasmid vector, a 5.2-kbp HindIII DNA fragment was also isolated at a ratio of 2 to 89. The two independently obtained 5.2-kbp fragments were an insertion derivative of the 4.5-kbp fragment and carried E. coli transposable element ISlK, which was inserted at the same site immediately before tetBS908 in the same direction. For the ISlK insertions, the 8-bp sequence CAAATTTT was used as a target, this having no similarity to any published sequences.     

转座因子IS10一个新的插入靶位点的序列分析

转座因子在生物体内广泛存在,它在研究基因的重组机理以及生物染色体的进化方面有着重要意义。IS10是细菌中的一种转座因子,它既能单独作为插入序列,也能作为Tn10的一部分进行转座。利用含sacB基因的质粒pXT3sacB,获得了由转座因子IS10插入而导致sacB基因失活的突变体。通过对插入突变体质粒DNA的序列测定（GenBank登记号为AY580883．1）,结果表明IS10两端分别包括22bp倒置重复区CTGAGAGATCCCCTCATAATTT和AAATCATTAGGGGATTCATCAG,这与前人的报道一致;而IS10两端的插入靶位点序列为TGCTTGGTT,该9bp靶位点序列与前人报道的序列NGCTNAGCN不同。根据文献资料,本研究中的靶位点序列是首次报道。此外,通过Southern blot杂交分析,插入sacB基因中的IS10来源于宿主大肠杆菌DH5α染色体DNA,并且IS10在DH5α染色体中为两个拷贝。此外,本研究利用sacB基因捕获到转座因子IS10,该方法为研究其他插入序列提供了一个有益的体系。     

Insertion sequence (IS) hybridization supports classification of Rhizobium meliloti by phage typing

Sixty-one isolates of Rhizobium meliloti from two field sites which had been previously classified into 15 phage types on the basis of sensitivity to 16 typing phages, were subjected to insertion sequence (IS) hybridization using DNA probes for ISR m 3 and ISR m 5. Isolates from all but one phage type contained ISR m 3 (apparent copy no. 1–11) and all isolates contained ISR m 5 (apparent copy no. 3–11). The isolates were placed into 24 IS classes based on differences in their respective ISR m 3 and ISR m 5 hybridization profiles. At either field site, isolates representing different phage types possessed IS hybridization profiles that differed from each other, while those comprising a specific type had identical or closely related profiles. Isolates from one phage type were unusual since they did not react with any of the typing phages and were shown by IS hybridization to constitute a heterogeneous group. Evidence for spatial effects were provided by isolates from two of six types present at both sites which fell into separate IS classes on the basis of their site of origin. These data have ecological implications and suggest that for a particular site, phage typing may be employed for the rapid assessment of the genetic diversity among field isolates.