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PubMed2001

Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12.

Escherichia coli O157:H7 is a major food-borne infectious pathogen that causes diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. Here we report the complete chromosome sequence of an O157:H7 strain isolated from the Sakai outbreak, and the results of genomic comparison with a benign laboratory strain, K-12 MG1655. The chromosome is 5.5 Mb in size, 859 Kb larger than that of K-12. We identified a 4.1-Mb sequence highly conserved between the two strains, which may represent the fundamental backbone of the E. coli chromosome. The remaining 1.4-Mb sequence comprises of O157:H7-specific sequences, most of which are horizontally transferred foreign DNAs. The predominant roles of bacteriophages in the emergence of O157:H7 is evident by the presence of 24 prophages and prophage-like elements that occupy more than half of the O157:H7-specific sequences. The O157:H7 chromosome encodes 1632 proteins and 20 tRNAs that are not present in K-12. Among these, at least 131 proteins are assumed to have virulence-related functions. Genome-wide codon usage analysis suggested that the O157:H7-specific tRNAs are involved in the efficient expression of the strain-specific genes. A complete set of the genes specific to O157:H7 presented here sheds new insight into the pathogenicity and the physiology of O157:H7, and will open a way to fully understand the molecular mechanisms underlying the O157:H7 infection.

Bacterial Proteins↗
PubMed2003

Divergence of mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity.

Bacteria adapt rapidly to environmental stimuli, such as exposure to xenobiotics. Mobile genetic elements (MGEs) play a major role in such bacterial adaptation, via the dispersal of catabolic capacity; and, in fact, genes that encode the degradation enzymes for xenobiotics are often located on MGEs. The list of reported catabolic MGEs keeps growing as researchers continue to isolate and characterize xenobiotic degraders and the corresponding catabolic genes. Major catabolic MGEs include (conjugative) plasmids, transposons, and conjugative transposons. Catabolic transposons can be divided into class I elements (composite transposons) and class II elements (Tn 3 family transposons). This review includes a comprehensive list of naturally occurring discrete catabolic MGEs, together with a brief description for each. While MGEs are often rather large, genome-wide or large-scale sequence analyses have provided useful information on the whole genetic structure of MGEs, with clues to their function (transfer, maintenance, catabolism, etc.) and behavior in a complex natural environment. This review also gives an insight into MGE functions, based on the complete sequencing of several catabolic plasmids and two Pseudomonas genomes.

Adaptation, Biological↗
PubMed2003

Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.

The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.

Adhesins, Bacterial↗
PubMed2001

Genomic and genetic definition of a functional human centromere.

The definition of centromeres of human chromosomes requires a complete genomic understanding of these regions. Toward this end, we report integration of physical mapping, genetic, and functional approaches, together with sequencing of selected regions, to define the centromere of the human X chromosome and to explore the evolution of sequences responsible for chromosome segregation. The transitional region between expressed sequences on the short arm of the X and the chromosome-specific alpha satellite array DXZ1 spans about 450 kilobases and is satellite-rich. At the junction between this satellite region and canonical DXZ1 repeats, diverged repeat units provide direct evidence of unequal crossover as the homogenizing force of these arrays. Results from deletion analysis of mitotically stable chromosome rearrangements and from a human artificial chromosome assay demonstrate that DXZ1 DNA is sufficient for centromere function. Evolutionary studies indicate that, while alpha satellite DNA present throughout the pericentromeric region of the X chromosome appears to be a descendant of an ancestral primate centromere, the current functional centromere based on DXZ1 sequences is the product of the much more recent concerted evolution of this satellite DNA.

Animals↗
PubMed1998

Interspersed centromeric element with a CENP-B box-like motif in Chironomus pallidivittatus.

Short mobile elements are present in different recombined forms as interspersed GC-rich islands between AT rich centromeric 155 bp tandem repeats in the dipteran Chironomus pallidivittatus . The basic element is 80 bp long, has a pronounced invert repeat structure and contains a 17 bp segment similar to the CENP-B box in mammals. The element inserts into a specific site of the 155 bp repeat in a defined orientation surrounded by 2 bp direct repeats. The total number per genome of the main variant is <20. Elements can be present in all centromeres from C.pallidivittatus and the sibling species Chironomus tentans with pronounced differences in distribution within and between species.

Animals↗
PubMed1993

Comparison of the human and mouse erythropoietin genes shows extensive homology in the flanking regions.

Considerable insights into important cis regulatory elements in a gene can be gleaned from the identification of sequence homologies among different species. To extend and optimize the sequence comparison between human and mouse erythropoietin (Epo) genes, we have obtained new human sequence from 5,547 to 385 bp upstream of the cap site and extended the 3' flank by 489 bp. In addition, we have obtained new sequence information on the mouse Epo gene extending from within the 3' untranslated region (UTR) to 1,001 bp downstream of the polyadenylation site. Analysis of these additional sequences shows considerable homology between human and mouse Epo genes as far as 4 kb (human) or 3 kb (mouse) upstream of the cap sites, as well as far more homology at the 3' end than was previously realized. In addition, both species were found to have a high frequency of short interspersed (SINE) repetitive sequences that interrupt homologies in both the 5' flank and within the transcription unit.

Amino Acid Sequence↗
PubMed2002

Human genome dispersal and evolution of 4q35 duplications and interspersed LSau repeats.

We have investigated the evolutionary history of the 4q35 paralogous region, and of a sub-family of interspersed LSau repeats. In HSA, 4q35 duplications were localized at 1q12, 3p12.3, 4q35, 10q26, 20cen, whereas duplicons and interspersed LSau repeats simultaneously labeled the p arm of acrocentric chromosomes. A multi-site localization of 4q35-like sequences was also observed in PTR, GGO, PPY, HLA (Hominoidea) and PAN (Old World monkey), thus indicating that duplications of this region have occurred extensively in the two clades, which diverged at least 25 million years ago. In HSA, PTR and PAN, 4q35-derived duplicons co-localized with rDNA, whereas in GGO and PPY this association was partially lacking. In PAN, the single- and multi-site distribution of rDNA and paralogous sequences, respectively, indicates a different timing of sequence dispersal. The sub-family of interspersed LSau repeats showed a lesser dispersal than 4q35 duplications both in man and great apes. This finding suggests that duplications and repeated sequences have undergone different expansion/contraction events during evolution. The mechanisms underlying the dispersal of paralogous regions may be further derived through studies comparing the detailed structural organization of these genomic regions in man and primates.

Animals↗
PubMed2000

[The role of P-element sequences in the transcription activation].

A study was made of mutations resulting from insertion of the P element in the regulatory region of the yellow gene. Excision of the P element enhanced expression of yellow. Molecular analysis implicated P-element terminal sequences, which remained in the locus after the element was excised, in transcription activation of the yellow gene.

Animals↗
PubMed2006

Recoding in bacteriophages and bacterial IS elements.

Dynamic shifts between open reading frames and the redefinition of codon meaning at specific sites, programmed by signals in mRNA, permits versatility of gene expression. Such alterations are characteristic of organisms in all domains of life and serve a variety of functional purposes. In this article, we concentrate on programmed ribosomal frameshifting, stop codon read-through and transcriptional slippage in the decoding of phage genes and bacterial mobile elements. Together with their eukaryotic counterparts, the genes encoding these elements are the richest known source of nonstandard decoding. Recent analyses revealed several novel sequences encoding programmed alterations in gene decoding and provide a glimpse of the emerging picture.

Bacteriophages↗
PubMed2003

Informatics for unveiling hidden genome signatures.

With the increasing amount of available genome sequences, novel tools are needed for comprehensive analysis of species-specific sequence characteristics for a wide variety of genomes. We used an unsupervised neural network algorithm, a self-organizing map (SOM), to analyze di-, tri-, and tetranucleotide frequencies in a wide variety of prokaryotic and eukaryotic genomes. The SOM, which can cluster complex data efficiently, was shown to be an excellent tool for analyzing global characteristics of genome sequences and for revealing key combinations of oligonucleotides representing individual genomes. From analysis of 1- and 10-kb genomic sequences derived from 65 bacteria (a total of 170 Mb) and from 6 eukaryotes (460 Mb), clear species-specific separations of major portions of the sequences were obtained with the di-, tri-, and tetranucleotide SOMs. The unsupervised algorithm could recognize, in most 10-kb sequences, the species-specific characteristics (key combinations of oligonucleotide frequencies) that are signature features of each genome. We were able to classify DNA sequences within one and between many species into subgroups that corresponded generally to biological categories. Because the classification power is very high, the SOM is an efficient and fundamental bioinformatic strategy for extracting a wide range of genomic information from a vast amount of sequences.

Animals↗
PubMed1993

Mus spretus-specific LINE-1 DNA probes applied to the cloning of the murine pearl locus.

LINE-1 is the major family of long, interspersed, repetitive DNA sequences found in mammalian genomes. The mouse species Mus spretus contains large LINE-1 subfamilies that are distinguishable from the LINE-1 elements of laboratory Mus domesticus strains by their content of particular nucleotide differences. Oligonucleotides containing these differences act as M. spretus-specific LINE-1 hybridization probes. We have used these probes as a novel genetic tool in conjunction with an interspecific hybrid congenic mouse, in which the M. spretus allele of the pearl gene has been transferred onto a M. domesticus background. From a lambda library prepared from this congenic mouse, four clones were isolated by hybridization to the M. spretus-specific probes. After derivation of genetic markers from these clones, two of them were found to be linked to the pearl gene. These markers are the first two of up to 75 that could be isolated to support cloning the pearl gene. Considering the interspersed nature of LINE-1, we propose that species-specific LINE-1 probes could also be used to isolate markers for many other target genes.

Animals↗
PubMed2004

Eukaryotic gene regulation by targeted chromatin re-modeling at dispersed, middle-repetitive sequence elements.

RNA interference might have evolved to minimize the deleterious impact of transposable elements and viruses on eukaryotic genomes, because mutations in genes within the RNAi pathway cause mobilization of transposons in nematodes and flies. Although the first examples of RNAi involved post-transcriptional gene silencing, recently the pathway has been shown to act at the transcriptional level. It does so by establishing a chromatin configuration on the target DNA that has many of the hallmarks of heterochromatin, thus preventing its transcription. Members of dispersed, repeated sequence families appear to have been utilized by the RNAi machinery to regulate nearby genes in yeast. The unusual genomic distribution of three repeated element families in the chicken, fruit-fly and nematode genomes prompts speculation that some of these repeats have been co-opted to control gene expression, either locally or over extended chromosomal domains.

Animals↗
PubMed2003

Origins of bidirectional promoters: computational analyses of intergenic distance in the human genome.

We have analyzed intergenic distances and searched for the presence of bidirectional genes using the complete sequences and mapping information of human chromosomes 20, 21, and 22, which contain 2,122 known and predicted genes. Intergenic distances between genes with divergent transcripts were distributed in a biphasic manner with a strong peak of 25 kb and a weak peak of 0.3 kb between the divergent transcripts, suggesting that the genes might share a common promoter. The weak peak was not observed at the transcriptional ends of genes. Seventy-three percent (55/75 pairs of genes, from a total of 150 genes) of these divergent transcripts located within 1 kb of one another were CpG islands. Expression of the divergent transcript genes was not concordant in various human tissues, suggesting that they were independently regulated. Analyses of the frequency of occurrence of interspersed repeats in the intergenic sequences suggested that these repeats are strongly excluded from the regions of transcriptional starts. This exclusion might be responsible for the existence of these divergent transcripts.

Computational Biology↗
PubMed2003

A novel reiterated family of transcribed oligo(A)-terminated, interspersed DNA elements in the genome of Trypanosoma cruzi.

We report the molecular characterization of a novel reiterated family of transcribed oligo(A)-terminated, interspersed DNA elements in the genome of Trypanosoma cruzi. Steady-state level of transcripts of this sequence family appeared to be developmentally regulated, since only in the replicative forms the parasite showed expression of related sequences with a major band around 3 kb. The presence of frame shifts or premature stop codons predicts that transcripts are not translated. The sequence family also contains truncated forms of retrotransposons elements that may become potential hot spots for retroelement insertion. Sequences homologous to this family are interspersed at many chromosomes including the subtelomeric regions.

Animals↗
PubMed2004

Monosomy 1p36 breakpoints indicate repetitive DNA sequence elements may be involved in generating and/or stabilizing some terminal deletions.

Monosomy 1p36 is the most commonly observed terminal deletion syndrome in humans. Our previous molecular studies on a large cohort of subjects suggest that monosomy 1p36 can result from a variety of chromosomal rearrangements including terminal truncations, interstitial deletions, derivative chromosomes, inverted duplications, and complex rearrangements. However, the mechanism(s) by which rearrangements of 1p36 are generated and/or stabilized is not understood. Sequence analysis of breakpoint junctions may provide valuable clues to the underlying mechanisms of many chromosomal aberrations. In this report, we analyze the breakpoints at the DNA-sequence level in four subjects with variable-sized deletions of 1p36. All four breakpoints fall within repetitive DNA-sequence elements (LINEs, SINEs, etc). This suggests that repetitive DNA-sequence elements may play an important role in generating and/or stabilizing terminal deletions of 1p36. Mechanisms by which repetitive elements may be involved in the process of terminal deletion formation and stabilization are discussed.

Chromosome Breakage↗
PubMed2002

[Mycobacterial bovis BCG cutaneous infections following mesotherapy: 2 cases].

INTRODUCTION: Infectious complications following mesotherapy are usually due to ordinary bacteria or atypical mycobacteria. We report two new cases of mycobacterial bovis BCG infections following mesotherapy. To our knowledge only one case has already been reported. CASES REPORTS: A 52 year-old woman developed vaccinal MERIEUX BCG cutaneous abscesses following mesotherapy. Identification was made by a novel class of repeated sequences: Mycobacterial interspersed repetitive units. Despite prolonged anti-tuberculous therapy, complete remission was not obtained and surgical excision was performed. The second case was a 49 year-old man who developed a mycobacterial bovis BCG cutaneous abscess (Connaught) after mesotherapy, the regression of which was obtained with anti-tuberculous therapy. DISCUSSION: The severity of these two mycobacterial infections following mesotherapy illustrate the potential risks of mesotherapy. Identification is possible by molecular biology techniques (PCR and sequencing). The origin of this infection is unclear and therapeutic decision is difficult. Some authors recommend anti-tuberculous therapy but surgical excision may be necessary as in our cases.

Abscess↗