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At least 739 records · Page 41Linked to original sources
PubMed1994

Diversity and relative strength of tandem promoters for the antibiotic-resistance genes of several integrons.

The integron is a new type of mobile element containing one or more antibiotic-resistance-encoding genes site-specifically integrated as cassettes. The integrated genes are expressed from a common promoter region located in an adjacent conserved segment. Sequence analysis has revealed the existence of four versions of the integron promoters. In this study, we have determined the relative strength of the different integron promoters and compared their activity with that of the tac promoter. Each version of the promoter was cloned upstream from a promoter-less chloramphenicol acetyltransferase-encoding gene (cat) in plasmid pKK232-8. CAT activity was used to measure transcriptional expression from the promoters of the antibiotic-resistance operon. The strongest promoter is the version (TTGACAN17TAAACT) found in plasmid R388 and in transposon Tn1696. This promoter is six times more efficient than the derepressed tac promoter.

Acetylation↗
PubMed2004

Organization and regulation of the neurotoxin genes in Clostridium botulinum and Clostridium tetani.

Botulinum and tetanus neurotoxins are structurally and functionally related 150 kDa proteins that are potent inhibitors of neuroexocytosis. Botulinum neurotoxin associates with non-toxic proteins to form complexes of various sizes. The botulinum neurotoxin and non-toxic protein genes are clustered in a DNA segment called the botulinum locus. This locus is probably located on a mobile or degenerate mobile element, which accounts for the various genomic localizations (chromosome, plasmid, phage) in different Clostridium botulinum types. The botulinum neurotoxin and non-toxic protein genes are organized in two polycistronic operons (ntnh-bont and ha operons) transcribed in opposite orientations. The gene that separates the two operons of the botulinum locus in C. botulinum A encodes a 21 kDa protein BotR/A, which is a positive regulator of the expression of the botulinum locus genes. Similarly, in Clostridium tetani, the gene located immediately upstream of the tetanus toxin gene, encodes a positive regulatory protein, TetR. BotR and TetR are possibly alternative sigma factors related to TxeR and UviA, which regulate C. difficile toxin and C. perfringens bacteriocin production, respectively. TxeR and UviA define a new sub-group of the sigma(70) family of RNA polymerase initiation factors. In addition, the C. botulinum genome contains predicted two-component system genes, some of which are possibly involved in regulation of toxinogenesis.

Journal Article↗
PubMed2006

An alternative intron-exon pairing scheme implied by unexpected in vitro activities of group II intron RmInt1 from Sinorhizobium meliloti.

RmInt1 is a mobile group II intron which interrupts ISRm2011-2, another mobile element from the bacterium Sinorhizobium meliloti. Ribozyme constructs derived from intron RmInt1 self-splice in vitro when incubated under permissive conditions, but the excised intron and ligated exons are largely replaced by unconventional products. These include a slightly shorter, 5'-end truncated 3' exon, truncated variants of the linear and lariat forms of the intron-3' exon reaction intermediate, as well as presumably circular molecules derived from the latter. Two factors explain the abundance of these products: (i) nucleotides 5-11 of the 3' exon (IBS1*) provide a better match to the EBS1 5'-exon-binding site than the authentic IBS1 sequence in the 5' exon; (ii) exon ligation is unusually inefficient, and especially so when the 5' exon is truncated close to the second (IBS2) intron-binding site. We propose that reactions at the IBS1* site play a part in the regulation of the intron ISRm2011-2 host in vivo.

Alternative Splicing↗
PubMed2004

Protein localization in proteomics.

A global analysis of the localization of 4156 yeast proteins has just been accomplished. Smaller scale analyses have been performed in a variety of organisms. These studies typically use green fluorescent protein as a tag for proteins in living cells. Improvements in the yellow and sapphire color variants will increase their utility. Reengineering of the red fluorescent protein has produced faster maturing tetrameric and monomeric variants not prone to aggregation. Techniques for high-throughput tagging of proteins include integration by homologous recombination, integration using mobile elements or recombinational cloning to produce plasmids expressing fusion proteins. Alternatives to localizing tagged proteins are to use antibodies or aptamers to detect the untagged protein.

Animals↗
PubMed2006

Geochemical variations in aeolian mineral particles from the Sahara-Sahel Dust Corridor.

The Sahara-Sahel Dust Corridor runs from Chad to Mauritania and expels huge amounts of mineral aerosols into the Atlantic Ocean. Data on samples collected from Algeria, Chad, Niger, and Western Sahara illustrate how corridor dust mineralogy and chemistry relate to geological source and weathering/transport history. Dusts sourced directly from igneous and metamorphic massifs are geochemically immature, retaining soluble cations (e.g., K, Na, Rb, Sr) and accessory minerals containing HFSE (e.g., Zr, Hf, U, Th) and REE. In contrast, silicate dust chemistry in desert basins (e.g., Bodélé Depression) is influenced by a longer history of transport, physical winnowing (e.g., loss of Zr, Hf, Th), chemical leaching (e.g., loss of Na, K, Rb), and mixing with intrabasinal materials such as diatoms and evaporitic salts. Mineral aerosols blown along the corridor by the winter Harmattan winds mix these basinal and basement materials. Dusts blown into the corridor from sub-Saharan Africa during the summer monsoon source from deeply chemically weathered terrains and are therefore likely to be more kaolinitic and stripped of mobile elements (e.g., Na, K, Mg, Ca, LILE), but retain immobile and resistant elements (e.g., Zr, Hf, REE). Finally, dusts blown southwestwards into the corridor from along the Atlantic Coastal Basin will be enriched in carbonate from Mesozoic-Cenozoic marine limestones, depleted in Th, Nb, and Ta, and locally contaminated by uranium-bearing phosphate deposits.

Aerosols↗
PubMed2004

Gram-positive merA gene in gram-negative oral and urine bacteria.

Clinical mercury resistant (Hg(r)) Gram-negative bacteria carrying Gram-positive mercury reductase (merA)-like genes were characterized using DNA-DNA hybridization, PCR and sequencing. A PCR assay was developed which discriminated between the merA genes related to Staphylococcus and those related to the Bacillus/Streptococcus merA genes by the difference in size of the PCR product. DNA sequence analysis correlated with the PCR assay. The merA genes from Acinetobacter junii, Enterobacter cloacae and Escherichia coli were sequenced and shared 98-99% identical nucleotide (nt) and 99.6-100% amino acid identity with the Staphylococcus aureus MerA protein. A fourth merA gene, from Pantoeae agglomerans, was partially sequenced (60%) and had 99% identical nt and 100% amino acid identity with the Streptococcus oralis MerA protein. All the Hg(r) Gram-negative bacteria transferred their Gram-positive merA genes to a Gram-positive Enterococcus faecalis recipient with the resulting transconjugants expressing mercury resistance. These Gram-positive merA genes join Gram-positive tetracycline resistance and Gram-positive macrolide resistance genes in their association with mobile elements which are able to transfer and express in Gram-negative bacteria.

Amino Acid Sequence↗
PubMed2004

Those interfering little RNAs! Silencing and eliminating chromatin.

RNA interference (RNAi) is widely used for knocking down expression of genes of interest and in systematic screens for desired phenotypes. In post-transcriptional gene silencing, double-stranded RNA triggers are processed to small interfering RNAs, which act to seek out and destroy homologous transcripts. A variety of organisms utilise the RNAi pathway to silence expression of potentially harmful endogenous mobile elements and to eliminate unnecessary sequences. In plants and fission yeast, RNAi can also mediate chromatin-based silencing resulting in transcriptional shutdown of homologous transcription units (transcriptional gene silencing) and the formation of centromeric heterochromatin. In metazoans, the expression of non-coding RNAs is often associated with the formation of silent chromatin domains but it remains to be determined if RNAi is involved.

Animals↗
PubMed2004

Genomic changes following host restriction in bacteria.

Many genomic sequences have been recently published for bacteria that can replicate only within eukaryotic hosts. Comparisons of genomic features with those of closely related bacteria retaining free-living stages indicate that rapid evolutionary change often occurs immediately after host restriction. Typical changes include a large increase in the frequency of mobile elements in the genome, chromosomal rearrangements mediated by recombination among these elements, pseudogene formation, and deletions of varying size. In anciently host-restricted lineages, the frequency of insertion sequence elements decreases as genomes become extremely small and strictly clonal. These changes represent a general syndrome of genome evolution, which is observed repeatedly in host-restricted lineages from numerous phylogenetic groups. Considerable variation also exists, however, in part reflecting unstudied aspects of the population structure and ecology of host-restricted bacterial lineages.

Bacteria↗
PubMed2006

Focusing on comparative ape population genetics in the post-genomic age.

The initial human and chimpanzee genome sequences have been published, and additional primate genomes, including those of gorilla and orang-utan, are in progress. With these new resources, we can now address what makes our species unique, by focusing on the underlying genetic differences associated with phenotypes. Comparative primate population genomics, including studies of structural changes, mobile elements, gene expression and functional analyses, will shed light on how natural selection and population demography are involved in the processes that lead to differences among great apes. Historically, this research has focused on the human perspective; however, we will learn much about ourselves with a focus on genomic diversity in hominoids as a group.

Animals↗
PubMed2004

The molecular phylogeny of oysters based on a satellite DNA related to transposons.

We have analysed a centromeric satellite DNA family that is conserved in several commercial and non-commercial oyster species (Ostrea edulis, O. stentina, Crassostrea angulata, C. gigas, C. gasar, C. ariakensis, C. virginica and C. sikamea). This satellite DNA family is composed of AT-rich repeat sequences of 166+/-2 bp and presents a 9-bp motif similar to the mammalian CENP-B box. The homology of oyster HindIII satellite DNA with satellite DNAs from other bivalves and its relation to a part of a mobile element suggest the existence of an ancient transposable element as a generating unit of satellite DNA in bivalve molluscs. Taking advantage of its degree of conservation in oyster species, we have used this element as a taxonomic marker. This marker clearly supports a high degree of differentiation between O. edulis and O. stentina, and, conversely, upholds the contention that C. gigas and C. angulata are the same species. Finally, we have used HindIII satellite DNA as a phylogenetic marker between these species, revealing two clades, one formed by Asiatic species (C. angulata, C. gigas and C. ariakensis) and another by the European, American and African species (O. edulis, C. virginica and C. gasar, respectively).

Animals↗
PubMed2005

Parasite histories and novel phylogenetic tools: alternative approaches to inferring parasite evolution from molecular markers.

Parasitological research is often contingent on the knowledge of the phylogeny/genealogy of the studied group. Although molecular phylogenetics has proved to be a powerful tool in such investigations, its application in the traditional fashion, based on a tree inference from the primary nucleotide sequences may, in many cases, be insufficient or even improper. These limitations are due to a number of factors, such as a scarcity/ambiguity of phylogenetic information in the sequences, an intricacy of gene relationships at low phylogenetic levels, or a lack of criteria when deciding among several competing coevolutionary scenarios. With respect to the importance of a precise and reliable phylogenetic background in many biological studies, attempts are being made to extend molecular phylogenetics with a variety of new data sources and methodologies. In this review, selected approaches potentially applicable to parasitological research are presented and their advantages as well as drawbacks are discussed. These issues include the usage of idiosyncratic markers (unique features with presumably low probability of homoplasy), such as insertion of mobile elements, gene rearrangements and secondary structure features; the problem of ancestral polymorphism and reticulate relationships at low phylogenetic levels; and the utility of a molecular clock to facilitate discrimination among alternative scenarios in host-parasite coevolution.

Animals↗
PubMed2004

A member of a repeat family is the source of an insertion-deletion polymorphism inside a developmentally eliminated sequence of Tetrahymena thermophila.

In Tetrahymena thermophila, the development of a transcriptionally active macronucleus from a transcriptionally inert micronucleus is accompanied by the elimination of numerous DNA segments, called internally eliminated sequences (IESs), many of which belong to dispersed repetitive sequence families. To examine the relationship between the insertion and deletion events expected to occur during evolution of the repeats and the developmental elimination process, IESs were compared among different Tetrahymena strains. A 600 base-pair DNA segment, the R Indel, was discovered inside the R IES, one of the ten sequenced IESs out of an estimated 6000 total in the Tetrahymena genome. The R Indel was found in strains B3 and C2 but not in several other strains examined, indicating that the Indel was probably present in a progenitor of strains B3 and C2. The R Indel was found to belong to a moderately large sequence family of about 200 members; however, BLAST searches did not reveal meaningful similarities with other mobile elements. Sequence comparisons revealed that a 300 base-pair stretch, very closely related to the first half of the R Indel, was present inside the previously described B IES, another of the ten sequenced IESs. This is the first example of shared sequences between two of the known IESs.

Animals↗
PubMed2006

Is there an emerging endosymbiotic relationship between mycobacteria and the human host based on horizontal transfer of genetic sequences?

While not negating the seriousness of tuberculosis and the need to prevent and combat the disease effectively, the large percentage of infected, apparently healthy individuals who harbour latent infections warrants consideration whether an endosymbiotic relationship is being established between mycobacteria and man. By means of a gene decay process eliminating their most metabolically important pathogenic genes associated with an increasing need for host gene products during prolonged intracellular survival, mycobacteria appears to be undergoing a process of establishing a less dangerous relationship with its host. To have tolerated this relationship over time, humans must have benefited. This is suggested to have occurred via changes in DNA higher order structure altering combinatorially regulated gene expression allowing increased cerebrodiversity. It can be expected that, beyond a certain threshold, negative effects ensued, leading to neuropathology and increased susceptibility for certain psychiatric disorders. These processes have probably been happening since the earliest contact with mycobacteria, but recently may have become modified by the emergence of epidemic tuberculosis and waves of increased oxidative stress following the circumstances associated with the Industrial Revolution and the more recent AIDS pandemic. The organism seems to have uniquely exploited the normal stress reaction of the host. Genomic stresses include changes associated with glucocorticoid effects as well as upregulated reactive oxygen species and stress/(heat shock) protein production, the latter two of which result in host cell cycle delay. Subsequently replication dependent chromosomal fragile sites appear in the host genome and together with upregulated chaperonins and mobile element activation, the scene is set for sequence exchange between the organism and host. If proven, these events raise the possibility of modifying chromatin epigenetically to retain the proposed advantages while silencing pathogenicity factors.

Gene Transfer, Horizontal↗
PubMed2006

A biased detection of the flexible genome content: missing large restriction fragments in comparative genomics.

Gene content variation between closely related bacteria is largely due to mobile elements and gene erosion. Various techniques are available to assess this variation, yet biased pools of restriction fragments have been used in several comparative genomics studies. Excluding important large restriction fragments from the actual hybridisation or from post-hybridisation amplification reactions compromise the comprehensiveness of these studies.

Bacteria↗
PubMed2026

A single-cell meta-analysis evidences transposable element dysregulation in sex-based differences in Parkinson's disease.

Transposable elements (TEs) (mobile genetic elements comprising ∼45% of the human genome) have recently emerged as potential contributors to Parkinson's disease (PD); however their role and sex-specific impact remain poorly understood. Here, we present the first integrative meta-analysis of TE expression across 4 substantia nigra single-nucleus RNA-seq datasets, comprising a total of 66 donors, generating a cell-type-resolved atlas of TE dysregulation in PD. We identified widespread TE activation across major brain cell types (i.e. neurons, astrocytes, oligodendrocytes and microglia), with marked upregulation of L1s in neurons and HERVs in oligodendrocytes. Sex-stratified analyses revealed distinct male- and female-biased TE signatures, indicating regulatory programs uniquely affected in each sex, including MIR elements in microglia and Alu subfamilies in neurons. Correlation and genomic proximity analyses also uncovered TE-gene associations linked to important PD pathways such as neuroinflammation or myelination. Collectively, our study positions TEs as potential sex-modulated contributors to PD pathology and also provides a public web resource (PATOSS) to explore PD-associated TE transcriptional deregulation.

Parkinson's disease↗
PubMed2006

Identification of staphylococcal cassette chromosome mec encoding methicillin resistance in Staphylococcus aureus isolates at Charles Nicolle Hospital of Tunis.

Staphylococcal cassette chromosome is a mobile element that carries the gene mecA mediating the methicillin resistance in staphylococci. In Staphylococcus aureus five types of SCCmec have been described, which differs in size and genetic composition among strains. SCCmec typing of 34 non redundant methicillin-resistant S. aureus (MRSA) recovered in 2004 at Charles Nicolle Hospital of Tunis was carried out. The isolates were identified by conventional methods. Methicillin resistance was detected by oxacillin and cefoxitin disks and confirmed by mecA PCR. The SCCmec complex types were determined by using PCR which amplify a sequence overlapping the right SCCmec chromosome junction. Strains were recovered mainly from cutaneous pus (61.7%) and blood cultures (17.64%). They were isolated from different wards: medicine (53.1%) especially from dermatology (41.2%); surgery (40.6%) and pediatrics (3.1%). Only two strains were community-acquired MRSA. Two strains (5.9%) were harboring SCCmec type I; five (14.7%) SCCmec type II and 27 (79.4%) SCCmec type III. The two community-acquired MRSA were harboring type II and III SCCmec, usually found in hospital acquired MRSA. Our findings indicate that there are only three SCCmec types at Charles Nicolle Hospital. However, the existence of SCCmec types II and III in community incite us to investigate more community-acquired MRSA.

Bacterial Proteins↗
PubMed2004

The SHV-5 extended-spectrum beta-lactamase gene of pACM1 is located on the remnant of a compound transposon.

The SHV-5 extended-spectrum beta-lactamase gene of pACM1 was previously shown to reside on a segment of DNA ( approximately 7.9 kb) homologous to part of the Klebsiella pneumoniae chromosome. Regions of pACM1 overlapping the ends of the homology were sequenced. A defective copy of IS26 was found on each side of, and immediately adjacent to, the homology. The copies were oriented as direct repeats reminiscent of the compound transposon Tn2680. Other mobile elements and a putative mutagenesis gene, several of which were also defective, were also located in the vicinity of the homology. An intact precursor to the transposon remnant might have contributed to the dissemination of the SHV-5 gene.

DNA Transposable Elements↗
PubMed2004

Genome-wide comparison reveals great inter- and intraspecies variability in B. pseudomallei and B. mallei pathogens.

Burkholderia mallei and B. pseudomallei, closely related Gram-negative bacteria, are causative agents of serious infectious diseases of humans and animals: glanders and melioidosis, respectively. Despite numerous studies of these pathogens, the detailed mechanism of their pathogenesis is still unknown. The problem is even more complicated due to natural variability of B. pseudomallei and B. mallei strains, the understanding of which is a prerequisite for rational design of tools for diagnostics, prophylaxis and therapy of the diseases. Using a subtractive hybridization technique, we compared the genomes of B. pseudomallei C-141 and B. mallei C-5 strains. A subtracted library of DNA fragments specific for B. pseudomallei C-141 and absent from B. mallei C-5 was obtained and analyzed. A variety of differences have been detected and mapped on the recently sequenced genome of B. pseudomallei K96243. A comparative sequence analysis also revealed considerable genomic differences between B. pseudomallei C-141 and B. mallei ATCC 23344 strains sequenced at The Institute for Genomic Research (TIGR). We also observed significant genomic differences between B. pseudomallei C-141 and B. pseudomallei K96243. Some of the differential DNA fragments displayed similarity to different mobile elements which have not yet been described for B. pseudomallei, whereas the others matched various prophage components, components of active transport systems, different enzymes and transcription regulators. A substantial proportion of the differential clones had no database matches either at the nucleotide or protein level. The results provide evidence for great genome-wide variability of B. pseudomallei, further confirmed by Southern blot analysis of various B. pseudomallei strains. The data obtained can be useful for future development of efficient diagnostic tools allowing rapid identification of species, strains and isolates of B. mallei and B. pseudomallei.

Bacterial Typing Techniques↗