Polynucleotide Sequence Divergence Among Strains of Escherichia coli and Closely Related Organisms

Polynucleotide sequence similarity tests were carried out to determine the extent of divergence present in a number of Escherichia coli strains, obtained from diverse human, animal, and laboratory sources, and closely related strains of Shigella, Salmonella, and the Alkalescens-Dispar group. At 60 C, relative reassociation of deoxyribonucleic acid (DNA) from the various strains with E. coli K-12 DNA ranged from 100 to 36%, with the highest level of reassociation found for three strains derived from K-12, and the lowest levels for two “atypical” E. coli strains and S. typhimurium. The change in thermal elution midpoint, which indicates the stability of DNA duplexes, ranged from 0.1 to 14.5 C, with thermal stability closely following the reassociation data. Reassociation experiments performed at 75 C, at which temperature only the more closely related DNA species form stable duplexes, gave similar indications of relatedness. At both temperatures, Alkalescens-Dispar strains showed close relatedness to E. coli, supporting the idea that they should be included in the genus Escherichia. Reciprocal binding experiments with E. coli BB, 02A, and K-12 yielded different reassociation values, suggesting that the genomes of these strains are of different size. The BB genome was calculated to be 9% larger than that of K-12, and that of 02A 9% larger than that of BB. Calculation of genome size for a series of E. coli strains yielded values ranging from 2.29 × 10⁹ to 2.97 × 10⁹ daltons. E. coli strains and closely related organisms were compared by Adansonian analysis for their relatedness to a hypothetical median strain. E. coli 0128a was the most closely related to this median organism. In general, these data compared well with the data from reassociation experiments among E. coli strains. However, anomalous results were obtained in the cases of Shigella flexneri, S. typhimurium, and “atypical” E. coli strains.     

Variation within and between Closely Related Species Uncovers High Intra-Specific Variability in Dispersal

Mounting evidence shows that contrasting selection pressures generate variability in dispersal patterns among individuals or populations of the same species, with potential impacts on both species dynamics and evolution. However, this variability is hardly considered in empirical works, where a single dispersal function is considered to adequately reflect the species-specific dispersal ability, suggesting thereby that within-species variation is negligible as regard to inter-specific differences in dispersal abilities. We propose here an original method to make the comparison of intra- and inter-specific variability in dispersal, by decomposing the diversity of that trait along a phylogeny of closely related species. We used as test group European butterflies that are classic study organisms in spatial ecology. We apply the analysis separately to eight metrics that reflect the dispersal propensity, the dispersal ability or the dispersal efficiency of populations and species. At the inter-specific level, only the dispersal ability showed the signature of a phylogenetic signal while neither the dispersal propensity nor the dispersal efficiency did. At the within-species level, the partitioning of dispersal diversity showed that dispersal was variable or highly variable among populations: intra-specific variability represented from 11% to 133% of inter-specific variability in dispersal metrics. This finding shows that dispersal variation is far from negligible in the wild. Understanding the processes behind this high within-species variation should allow us to properly account for dispersal in demographic models. Accordingly, to encompass the within species variability in life histories the use of more than one value per trait per species should be encouraged in the construction of databases aiming at being sources for modelling purposes.     

Closely Related NDM-1-Encoding Plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan

Objective

Two plasmids carrying bla _NDM-1 isolated from carbapenem-resistant Klebsiella pneumoniae (CR-KP) and carbapenem-resistant Escherichia coli (CR-EC) were sequenced. CR-KP and CR-EC were isolated from two Taiwanese patients without travel histories.

Methods

Complete sequencing of the plasmids (pLK75 and pLK78) was conducted using a shotgun approach. Annotation of the contigs was performed using the RAST Server, followed by manual inspection and correction.

Results

These similar plasmids were obtained from two patients with overlapping stays at the same hospital. The pLK75 and pLK78 plasmids were 56,489-bp and 56,072-bp in length, respectively. Plasmid annotation revealed a common backbone similar to the IncN plasmid pR46. The regions flanking the bla _NDM-1 genes in these plasmids were very similar to plasmid pNDM-HU01 in Japan, which contains a complex class 1 integron located next to an ISCR1 element. The ISCR1 element has been suggested to provide a powerful mechanism for mobilising antibiotic resistance genes.

Conclusion

Two indigenous NDM-1-producing Enterobacteriaceae cases were identified for the first time in Taiwan, highlighting the alarming introduction of NDM-1-producing Enterobacteriaceae in this region.     

O-Specific Polysaccharides (O-Antigens) of a New Species of Enteric Bacteria Escherichia albertii Closely Related to Escherichia coli

Russian Journal of Bioorganic Chemistry - The data on the structure of O-specific polysaccharides (O-antigens) of all nine known molecular types (potential O-serotypes) of a new type of...     

High Frequency of Mutator Strains among Human Uropathogenic Escherichia coli Isolates

By using a panel of 603 commensal and pathogenic Escherichia coli and Shigella isolates, we showed that mutation rates of strains vary considerably among different ecotypes. Uropathogenic strains had the highest frequency of mutators, while strains from patients with bacteremia had the lowest mutation rates. No correlation between the mutation rates and antibiotic resistance was observed among the studied strains.     

Divergent MicroRNA Targetomes of Closely Related Circulating Strains of a Polyomavirus

Hundreds of virus-encoded microRNAs (miRNAs) have been uncovered, but an in-depth functional understanding is lacking for most. A major challenge for the field is separating those miRNA targets that are biologically relevant from those that are not advantageous to the virus. Here, we show that miRNAs from related variants of the polyomavirus simian vacuolating virus 40 (SV40) have differing host target repertoires (targetomes) while their direct autoregulatory activity on virus-encoded early gene products is completely preserved. These results underscore the importance of miRNA-mediated viral gene autoregulation in some polyomavirus life cycles. More broadly, these findings imply that some host targets of virus-encoded miRNAs are likely to be of little selective advantage to the virus, and our approach provides a strategy for prioritizing relevant targets.     

Maturation of [NiFe]-hydrogenases in Escherichia coli

Hydrogenases catalyze the reversible oxidation of dihydrogen. Catalysis occurs at bimetallic active sites that contain either nickel and iron or only iron and the nature of these active sites forms the basis of categorizing the enzymes into three classes, the [NiFe]-hydrogenases, the [FeFe]-hydrogenases and the iron sulfur cluster-free [Fe]-hydrogenases. The [NiFe]-hydrogenases and the [FeFe]-hydrogenases are unrelated at the amino acid sequence level but the active sites share the unusual feature of having diatomic ligands associated with the Fe atoms in the these enzymes. Combined structural and spectroscopic studies of [NiFe]-hydrogenases identified these diatomic ligands as CN- and CO groups. Major advances in our understanding of the biosynthesis of these ligands have been achieved primarily through the study of the membrane-associated [NiFe]-hydrogenases of Escherichia coli. A complex biosynthetic machinery is involved in synthesis and attachment of these ligands to the iron atom, insertion of the Fe(CN)2CO group into the apo-hydrogenase, introduction of the nickel atom into the pre-formed active site and ensuring that the holoenzyme is correctly folded prior to delivery to the membrane. Although much remains to be uncovered regarding each of the individual biochemical steps on the pathway to synthesis of a fully functional enzyme, our understanding of the initial steps in CN- synthesis have revealed that it is generated from carbamoyl phosphate. What is becoming increasingly clear is that the metabolic origins of the carbonyl group may be different.     

Amino Acid Differences in a 30S Ribosomal Protein from Two Strains of Escherichia coli

The 30S ribosomal proteins of the K-12 and B strains of Escherichia coli differ in at least one protein component. This component, which is allelic in the two strains, has been isolated from both organisms. Amino acid analyses show that the protein from strain B contains between 20 and 28 more amino acids than does the analogue protein from strain K-12.     

Detection of Clostridium proteoclasticum and Closely Related Strains in the Rumen by Competitive PCR

A competitive PCR technique was used to enumerate the proteolytic bacterium Clostridium proteoclasticum from the rumen. A PCR primer, which circumscribes this organism and several closely related strains, was designed for a variable region within their 16S rRNA genes and was used in conjunction with a universal forward primer. This primer pair was tested for specificity against 85 ruminal bacterial strains. An internal control DNA was constructed for use in competitive PCRs and was shown to amplify under the same reaction conditions and with the same amplification efficiency as the target DNA. DNA from a known number of C. proteoclasticum cells was coamplified with the internal control to construct a standard curve. Rumen samples were collected from eight dairy cows fed four diets in rotation: high nitrogen, high nitrogen supplemented with carbohydrate, low nitrogen, and low nitrogen supplemented with carbohydrate. DNA extracted from these and spiked with internal control DNA was amplified with the C. proteoclasticum primer pair. The relative intensities of the PCR products were used to quantitate the numbers of C. proteoclasticum cell equivalents from the rumen samples. The numbers ranged from 2.01 × 10⁶ ml⁻¹ to 3.12 × 10⁷ ml⁻¹. There was no significant effect on the numbers of C. proteoclasticum detected in rumen samples among cows fed the four diets. The utility of the competitive PCR approach for quantifying ruminal bacterial populations in vivo and the occurrence of C. proteoclasticum in forage-fed dairy cows are discussed.     

Maturation of the Escherichia coli divisome occurs in two steps

Cell division proteins FtsZ (FtsA, ZipA, ZapA), FtsE/X, FtsK, FtsQ, FtsL/B, FtsW, PBP3, FtsN and AmiC localize at mid cell in Escherichia coli in an interdependent order as listed. To investigate whether this reflects a time dependent maturation of the divisome, the average cell age at which FtsZ, FtsQ, FtsW, PBP3 and FtsN arrive at their destination was determined by immuno- and GFP-fluorescence microscopy of steady state grown cells at a variety of growth rates. Consistently, a time delay of 14-21 min, depending on the growth rate, between Z-ring formation and the mid cell recruitment of proteins down stream of FtsK was found. We suggest a two-step model for bacterial division in which the Z-ring is involved in the switch from cylindrical to polar peptidoglycan synthesis, whereas the much later localizing cell division proteins are responsible for the modification of the envelope shape into that of two new poles.     

Thiamine-Binding Protein of Escherichia coli

The ability to transport thiamine in Escherichia coli was reduced by osmotic shock treatment with a concomitant release of a thiamine-binding protein; its formation was repressed by thiamine added to the growth medium.     

New Flagellin-Specifying Genes in Some Escherichia coli Strains

Data for further development of the flagellar antigen genetics of the species Escherichia coli are reported. Two new flagellin genes named fllA and flmA were found in E. coli 781-55, E2987-73, and E223-69, the test strains for E. coli flagellar antigens H44, H55, and H54, respectively (collection of the International Escherichia and Klebsiella Centre of the World Health Organization, Copenhagen, Denmark). Two alleles of fllA were identified that encode flagellar antigens H44 (fllA₄₄) and H55 (fllA₅₅), and the only flmA allele found (flmA₅₄) encodes antigen H54. The sites of their integration in the E. coli K-12 chromosome after P1-mediated transduction were approximately determined and found to be separate from each other and from the known regions of flagellar genes of E. coli and salmonellae. The region of flm₅₄ was found to repress the expression of some alleles of the flagellin gene fliC. In addition, cryptic genes encoding antigens H4 and H38 were found in phenotypically monophasic test strains 781-55 and E2987-73, respectively.     

Protein export in Escherichia coli.

The export of protein from Escherichia coli has been studied by genetic, biochemical and biophysical techniques. These studies have defined a number of steps in the export pathway and have identified the cellular components required for the translocation process. New information is presented on the function of some of these components.     

甲状旁腺素相关蛋白cDNA的克隆及其在大肠杆菌中的表达

采用ＲＴＰＣＲ方法从中国人肾癌细胞株中克隆到甲状旁腺素相关蛋白（Ｐａｒａｔｈｙｒｏｉｄｈｏｒｍｎｏｅｒｅｌａｔｅｄｐｒｏｔｅｉｎ,ＰＴＨｒＰ）ｃＤＮＡ,其核苷酸序列与国外发表资料相比,有６个核苷酸不同,其中仅９２位密码子的不同导致氨基酸变异,即由脯氨酸变为丝氨酸。将克隆的ＰＴＨｒＰｃＤＮＡ插到原核表达载体ｐＥＴ３ａ的Ｔ７噬菌体启动子下游,转化大肠杆菌后得到高效表达,并经Ｗｅｓｔｅｒｎｂｌｏｔ和生物学活性检测对表达产物作了鉴定。     

Penicillin-Binding Protein 2 Is Essential for the Integrity of Growing Cells of Escherichia coli ponB Strains

Analysis of Escherichia coli pbpA(Ts) or rodA(Ts) strains defective for penicillin-binding protein (PBP) 1A or PBP 1B indicated that the activity of PBP 2 is essential to prevent cell lysis in PBP 1B(-) strains and suggested that PBP 2 is active or activatable in rodA(Ts) mutants under restrictive conditions.     

Genetic Analysis of Cold-Sensitive Ribosome Maturation Mutants of Escherichia coli

Four cold-sensitive mutants of Escherichia coli, which have defects in the maturation of the 50S ribosomal subunit, were isolated. Each of the mutations was shown to map at a different locus. The loci were assigned the name rim (ribosome maturation) and were shown to map as follows: rimA is co-transduced with ilvD and with pyrE; rimB is co-transduced with aroD; conjugation experiments limited rimD to a region between ilv and malB, and conjugation experiments limited rimC to the 22 to 30 min region of the chromosome. In merodiploids heterozygous for rimA, rimB, or rimD, the wild-type allele was shown to be dominant to the mutant allele. The observation that the rim loci lie outside the strA region and separate from each other, as well as the recessive character of the rim loci, suggests that the mutants may be defective in ribosome maturation factors rather than being defective in ribosomal structural proteins.