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At least 1,405 records · Page 78Linked to original sources
PubMed2005

Complement C2 receptor inhibitor trispanning: from man to schistosome.

Horizontal gene transfer (HGT), in relation to genetic transfer between hosts and parasites, is a little described mechanism. Since the complement inhibitor CRIT was first discovered in the human Schistosoma parasite (the causative agent of Bilharzia) and in Trypanosoma cruzi (a parasite causing Chagas' disease), it has been found to be distributed amongst various species, ranging from the early teleost cod to rats and humans. In terms of evolutionary distance, as measured in a phylogenetic analysis of these CRIT genes at nucleotide level, the parasitic species are as removed from their human host as is the rat sequence, suggesting HGT. The hypotheses that CRIT in humans and schistosomes is orthologous and that the presence of CRIT in schistosomes occurs as a result of host-to-parasite HGT are presented in the light of empirical data and the growing body of data on mobile genetic elements in human and schistosome genomes. In summary, these data indicate phylogenetic proximity between Schistosoma and human CRIT, identity of function, high nucleotide/amino acid identity and secondary protein structure, as well as identical genomic organization.

Amino Acid Sequence↗
PubMed2026

Genomic Insights into Mammaliicoccus sciuri from Subclinical Bovine Mastitis to Unveil Key Resistance, Virulence, Biofilm and Adaptation Traits.

The Mammaliicoccus sciuri (M. sciuri), is recognized as a reservoir of antimicrobial resistance (AMR) genes, poses challenges in the Indian dairy sector where antibiotic use is poorly regulated. This study aimed to genomically characterize M. sciuri (formerly Staphylococcus sciuri) isolates recovered from subclinical mastitis (SCM) cattle milk. A total of 128 composite (quarter-wise pooled) milk samples were collected from 199 households (HH) across 16 epiunits /villages in four blocks of Chikkaballapur district, Karnataka, India. Of these, 36 milk samples (28.13%, 36/128; 95% CI: 21.06–36.46%) were diagnosed with SCM using the California Mastitis Test (CMT) and bacteriological culture yielded 113 isolates (88.28%; 113/128; 95% CI: 81.56–92.77%) were phenotypically identified as Staph spp. Through molecular technique PCR targeting the gap gene, two isolates (1.77%; 2/113; 95% CI: 0.49–6.22%) from Hosuru and Gattamaranahalli epiunits were confirmed as M. sciuri and both isolates were mecA-positives indicating methicillin resistance. Whole genome sequencing (WGS) identified 36–37 resistance genes (mecA and blaZ), conferring resistance to β-lactams, macrolides, fluoroquinolones and aminoglycosides. Horizontal gene transfer (HGT) was evidenced by diverse mobile genetic elements (MGEs) such as SCCmec variants, insertion sequences, transposons (IS3, IS6, IS256, and IS1182) and plasmids (Rep1, Rep13, RepUS5 and RepUS43). Virulence profiling uncovered biofilm-associated genes (ica, bap) and heavy metal resistance operons (ars, cop, znu) suggesting mechanisms for environmental persistence and co-selection of resistance traits. Phylogenetic analysis of 99 global isolates revealed host-and geography-specific clustering with Indian isolates occupying distinct evolutionary niches. These findings highlights its possible role as an AMR reservoir and also in bovine mastitis.

Animals↗
PubMed2026

Genomic Characterisation of Carbapenem-Resistant Klebsiella pneumoniae and Enterobacter hormaechei Clinical Isolates from Nigeria: Evidence of Resistance, Virulence, and Putative Plasmid-Mediated Gene Sharing.

The global proliferation of carbapenem-resistant Enterobacterales (CRE) constitutes one of the most urgent public health threats, yet high-resolution genomic data from sub-Saharan Africa remain critically scarce. We applied whole-genome sequencing (WGS) and comparative phylogenomics to characterise antimicrobial resistance determinants, virulence genes, and mobile genetic elements (MGEs) in three carbapenem-resistant clinical isolates originating from three tertiary hospitals (selected from a broader surveillance collection spanning four facilities) in Osun State, southwestern Nigeria. We purposively selected three isolates, two Klebsiella pneumoniae subsp. pneumoniae (K22, ST411; K31, ST17) and one Enterobacter hormaechei subsp. steigerwaltii (K32, ST45) from a broader surveillance collection of 27 carbapenem-non-susceptible Enterobacterales, to represent phenotypically and genotypically divergent lineages. Resistome analysis revealed extensive plasmid-associated β-lactam and aminoglycoside resistance in K31 (including blaCTX-M-15, blaOXA-1, and blaTEM-1). K32 harboured an intrinsic chromosomal blaACT-17 AmpC gene, while IS26 and ISEcp1 insertion sequences, consistent with transposon-mediated mobilisation, flanked its acquired aminoglycoside and sulfonamide resistance cassettes. K22 lacked detected acquired carbapenemase, ESBL, or plasmid-mediated AmpC genes, indicating that its carbapenem-resistant phenotype may involve non-carbapenemase mechanisms such as porin alteration or efflux-mediated reduced susceptibility; however, this mechanism requires confirmation by direct ompK35/ompK36 sequence analysis and/or phenotypic outer membrane protein profiling. Virulome profiling identified a broader repertoire of siderophore, adhesion, and biofilm genes in both K. pneumoniae isolates than in E. hormaechei. Phylogenomic analysis demonstrated that K22 and K31 cluster within the broader K. pneumoniae population framework but represent distinct high-risk lineages (ST411 and ST17) rather than a single clonal outbreak. Analysis also identified a shared plasmid backbone between K31 and K32, supporting interspecies horizontal gene transfer. These descriptive genomic findings identify clinically relevant resistance and virulence determinants in three purposively selected carbapenem-resistant Enterobacterales from Nigerian tertiary-care hospitals. The detection of shared resistance elements between K. pneumoniae and E. hormaechei suggests possible plasmid-mediated gene sharing. Still, larger WGS studies with long-read sequencing and patient-level epidemiological data are required to define transmission and dissemination patterns.

Nigeria↗
PubMed2001

The hAT family: a versatile transposon group common to plants, fungi, animals, and man.

Transposons are ubiquitous mobile genetic elements found in all eu- and prokaryotic cells. The first transposon identified, the maize Activator element, belongs to the hAT family. hAT transposons have been identified in most eukaryotic lineages, including plants, fungi, animals and even man. The basic structural and functional features of this transposon family and its phylogenetic roots are discussed in detail, including a phylogenetic tree deduced from the amino acid sequence of the most conserved part of the transposon-encoded transposase. Emphasis is given to the use of hAT transposons as tools for gene tagging and insect transformation as well as to their biological function, i.e. are they selfish DNA, beneficial companions, or even both?

Amino Acid Sequence↗
PubMed2002

Cloning and sequencing of an envelope-like gene in Gossypium.

Eukaryotic genomes harbor mobile genetic elements known as long terminal repeat (LTR) retrotransposons. LTR retrotransposons are closely related to the infectious and endogenous retroviruses. The viral envelope (env) gene of the retroviruses, which is responsible for their infective properties, distinguishes them from the LTR retrotransposons. Here, we report the cloning and sequencing of an envelope-like gene in Gossypium, implying that enveloped retroviruses are not limited to animals.

Base Sequence↗
PubMed2006

Both sense and antisense strands of the LTR of the Schistosoma mansoni Pao-like retrotransposon Sinbad drive luciferase expression.

Long terminal repeat (LTR) retrotransposons, mobile genetic elements comprising substantial proportions of many eukaryotic genomes, are so named for the presence of LTRs, direct repeats about 250-600 bp in length flanking the open reading frames that encode the retrotransposon enzymes and structural proteins. LTRs include promotor functions as well as other roles in retrotransposition. LTR retrotransposons, including the Gypsy-like Boudicca and the Pao/BEL-like Sinbad elements, comprise a substantial proportion of the genome of the human blood fluke, Schistosoma mansoni. In order to deduce the capability of specific copies of Boudicca and Sinbad LTRs to function as promotors, these LTRs were investigated analytically and experimentally. Sequence analysis revealed the presence of TATA boxes, canonical polyadenylation signals, and direct inverted repeats within the LTRs of both the Boudicca and Sinbad retrotransposons. Inserted in the reporter plasmid pGL3, the LTR of Sinbad drove firefly luciferase activity in HeLa cells in its forward and inverted orientation. In contrast, the LTR of Boudicca did not drive luciferase activity in HeLa cells. The ability of the Sinbad LTR to transcribe in both its forward and inverted orientation represents one of few documented examples of bidirectional promotor function.

Animals↗
PubMed1997

Flipper, a mobile Fot1-like transposable element in Botrytis cinerea.

A transposable element, Flipper, was isolated from the phytopathogenic fungus Botrytis cinerea. The element was identified as an insertion sequence within the coding region of the nitrate reductase gene. The Flipper sequence is 1842 bp long with perfect inverted terminal repeats (ITRs) of 48 bp and an open reading frame (ORF) of 533 amino acids, potentially encoding for a transposase; the element is flanked by the dinucleotide TA. The encoded protein is very similar to the putative transposases of three elements from other phytopathogenic fungi, Fot1 from Fusarium oxysporum, and Pot2 and MGR586 from Magnaporthe grisea. The number of Flipper elements in strains of B. cinerea varied from 0 to 20 copies per genome. Analysis of the descendants of one cross showed that the segregation ratio of Flipper elements was 2:2 and that the copies were not linked.

Amino Acid Sequence↗
PubMed1998

Tdd-3, a tRNA gene-associated poly(A) retrotransposon from Dictyostelium discoideum.

The full-length 5218-bp sequence of the mobile genetic element Tdd-3 from Dictyostelium discoideum is described. Tdd-3 encodes two overlapping open reading frames (ORFs) flanked by non-redundant, untranslated regions. The deduced amino acid sequence of ORF2 is homologous to reverse transcriptases (RTs) encoded by the class of poly(A) retrotransposons. ORF2 also encodes a putative protein domain related to the family of apurinic/apyrimidinic (AP) endonucleases, whose retroelement-encoded homologs have recently been proposed to represent the integrase function of poly(A) retrotransposons. Comparison of several genomic Tdd-3 copies revealed that element insertion is orientation specific and occurs about 100 bp downstream of tRNA genes in the D. discoideum genome. These properties of Tdd-3 suggest that the element is a tRNA gene-associated poly(A) retroelement present in the D. discoideum genome. Analysis of several cloned cDNAs derived from Tdd-3-specific plus strand RNAs indicate that the element is transcribed and polyadenylated during the growth of D. discoideum cells.

Animals↗
PubMed2005

Agrobacterium T-DNA integration in Arabidopsis is correlated with DNA sequence compositions that occur frequently in gene promoter regions.

Mobile insertion elements such as transposons and T-DNA generate useful genetic variation and are important tools for functional genomics studies in plants and animals. The spectrum of mutations obtained in different systems can be highly influenced by target site preferences inherent in the mechanism of DNA integration. We investigated the target site preferences of Agrobacterium T-DNA insertions in the chromosomes of the model plant Arabidopsis thaliana. The relative frequencies of insertions in genic and intergenic regions of the genome were calculated and DNA composition features associated with the insertion site flanking sequences were identified. Insertion frequencies across the genome indicate that T-strand integration is suppressed near centromeres and rDNA loci, progressively increases towards telomeres, and is highly correlated with gene density. At the gene level, T-DNA integration events show a statistically significant preference for insertion in the 5' and 3' flanking regions of protein coding sequences as well as the promoter region of RNA polymerase I transcribed rRNA gene repeats. The increased insertion frequencies in 5' upstream regions compared to coding sequences are positively correlated with gene expression activity and DNA sequence composition. Analysis of the relationship between DNA sequence composition and gene activity further demonstrates that DNA sequences with high CG-skew ratios are consistently correlated with T-DNA insertion site preference and high gene expression. The results demonstrate genomic and gene-specific preferences for T-strand integration and suggest that DNA sequences with a pronounced transition in CG- and AT-skew ratios are preferred targets for T-DNA integration.

Arabidopsis↗
PubMed2026

Characteristics of an NDM-1-producing Klebsiella pneumoniae strain belonging to ST105.

Uncommon multilocus sequence types (MLSTs) of NDM-producing Klebsiella pneumoniae may pose a significant threat to patients, although they are often overlooked in surveillance studies. Characterizing these isolates is therefore important for infection control. In this study, the antimicrobial susceptibility and pathogenicity of K. pneumoniae strain KP_WXD, pertaining to the atypical sequence type ST105, were evaluated, including capsular polysaccharide (CPS) production, biofilm formation, and resistance to serum killing. Whole-genome sequencing (WGS) was performed to analyze its genomic features. K. pneumoniae KP_WXD strain was resistant to all tested β-lactam agents. Its virulence was lower than that of K. pneumoniae strains ST11-KL64 and NTUH-k2044 used as references, while its biofilm formation ability was stronger than that of both strains. WGS analysis revealed carriage of IncF and IncN plasmids carrying multiple antibiotic resistance genes, alongside blaNDM-1 and blaCTX-M, integrated into well-characterized mobile genetic elements. Moreover, both blaNDM-1 and blaCTX-M-harboring plasmids were transferable to E. coli J53 by conjugation without significant fitness cost on the recipient strain.

Klebsiella pneumoniae↗
PubMed2005

Analysis of the genome of Azotobacter vinelandii revealed the presence of two genetically distinct group II introns on the chromosome.

Azotobacter vinelandii belongs to the y subdivision of eubacteria and has one of the highest respiratory rates. It is considered to be among the probable progenitors of mitochondria. Group II introns were originally identified on organelle genomes. Analysis of the A. vinelandii genome for the presence of group II introns using a deduced group II intron consensus sequence identified two putative introns. The first intron (AVI) which was found to be inserted in the groEL, an essential gene, was already characterized. Our study identified another group II intron (AV2) in A. vinelandii genome. This intron is inserted in a mobile genetic element, similar to most of the group II introns in bacteria, which in this case is a transposase like gene, tnpAl. This putative TnpAl protein is 52% identical to TnpA, the transposase of bacteriophage Lambda, and 85% identical to TnpAl of Pseudomonas stutzeri. Sequence analysis showed that this intron encodes a reverse transcriptase (RT) like motif in domain IV, similar to other group II introns. The RT of this intron open reading frame (ORF) is 53% homologous with that of AVI intron and 66% homologous with that of Pseudomonas putida (Tn5041c) intron. Secondary structure analysis showed that this intron has the typical sub-group IIB1 structure, but the EBS2-IBS2 interaction appears to be missing. Using the RNA generated by in vitro transcription of the intron sequence with its flanking exons, in vitro splicing experiments were performed. It was found that the AV2 intron is functional, despite of lacking the EBS2-IBS2 interaction that plays a role in exon recognition.

Amino Acid Sequence↗
PubMed2026

Genomic diversity and resistance determinants of staphylococci from cow and buffalo milk.

BACKGROUND: Staphylococci are important mastitis pathogens in dairy animals and serve as reservoirs of antimicrobial resistance genes (ARGs) having zoonotic potential. Genomic characterization of resistant isolates is essential to understand their diversity, resistance mechanisms, and One Health implications. METHODS AND RESULTS: A total of 363 cow and buffalo milk samples-including 108 from animals with mastitis-were screened, yielding 98 staphylococcal isolates, comprising 20 Staphylococcus aureus and 78 coagulase-negative staphylococci (CoNS). Antimicrobial susceptibility testing revealed resistance to cefoxitin (CoNS: 21.7%; S. aureus: 10%), tetracycline (CoNS: 19.2%; S. aureus: 10%), erythromycin (CoNS:16.7%; S. aureus: 10%), gentamicin (CoNS: 10.2%; S. aureus: 10%) and fluoroquinolone (CoNS: 10.2%), while the majority were sensitive to chloramphenicol, cotrimoxazole (~ 95%, each), linezolid (~ 97%), and vancomycin (100%). Nineteen isolates, including two S. aureus, were cefoxitin-resistant, and eight carried the mecA gene. Whole genome sequencing of these eight isolates revealed genome sizes ranging from 2.27 to 2.78 MB, with the methicillin resistant S. aureus (MRSA, ERSST98) isolate possessing the largest genome and the highest rRNA copy number. Comparative genomic analysis revealed various SCCmec types along with an extensive array of resistance determinants, encompassing aminoglycosides, macrolides, tetracyclines, efflux systems, and heavy metals, underscoring the multifaceted resistance repertoire of these strains. Virulence profiling of ERSST98 demonstrated a broad arsenal of adhesins, toxins, and biofilm‑associated genes, highlighting its pathogenic capacity. Mobile genetic elements with diverse plasmid replicons and insertion sequence families further contributed to genomic plasticity. CONCLUSIONS: Collectively, this study underscores the genomic diversity of methicillin-resistant staphylococci from dairy animals with extensive resistance determinants and highlights their zoonotic relevance within One Health framework.

Animals↗
PubMed2005

Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes.

Virus DNA was isolated from horse faeces and cloned in a sequence-independent fashion. 268 clones were sequenced and 178140 nucleotides of sequence obtained. Statistical analysis suggests the library contains 17560 distinct clones derived from up to 233 different virus genomes. TBLASTX analysis showed that 32% of the clones had significant identity to GenBank entries. Of these 63% were viral; 20% bacterial; 7% archaeal; 6% eukarya; and 5% were related to mobile genetic elements. Fifty-two percent of the virus identities were with Siphoviridae; 26% unclassified phages; 17% Myoviridae; 4% Podoviridae; and one clone (2%) was a vertebrate Orthopoxvirus. Genes coding for predicted virus structural proteins, proteases, glycosidases and nucleic acid-binding proteins were common.

Animals↗
PubMed1994

HNF1 alpha activates the aminopeptidase N promoter in intestinal (Caco-2) cells.

The importance of HNF1 binding proteins for intestinal aminopeptidase N expression was investigated using the Caco-2 cell-line. Aminopeptidase N promoter activity in Caco-2 cells depends on the HNF1 element (positions -85 to -58) and co-transfection with an HNF1 alpha expression vector demonstrates a direct activation of the promoter by HNF1 alpha through this element. Electrophoretic mobility shift assays using nuclear extracts from Caco-2 cells show the presence of high amounts of HNF1 binding proteins irrespective of their state of differentiation.

Aminopeptidases↗
PubMed1995

The Gag polypeptides of the Drosophila 1731 retrotransposon are associated to virus-like particles and to nuclei.

1731 is a Drosophila melanogaster retrotransposon whose nucleotide sequence shows a proviral architecture with two long terminal repeats (LTRs) framing two internal Open Reading Frames (ORFs). The pol ORF2 of this mobile genetic element was demonstrated to code for an active Reverse Transcriptase (RT) and the ORF1 is expected to code for the structural Gag proteins of the virus-like particles (VLP). Using specific anti-Gag antibodies, we have characterized the 1731 Gag polypeptides expressed either in vitro or in Kc Drosophila melanogaster cultured cells. Together with the 1731 RT, the largest, likely post-translationaly-modified Gag polypeptides are gathered into cytoplasmic virus-like particles. Moreover and consistent with the nuclear localization signal present in the Gag sequence, we observed that a short 1731 Gag polypeptide is associated to the cell nuclei.

Amino Acid Sequence↗
PubMed1989

The nature of spontaneous mutations.

The induction of mutations is often expressed in relation to spontaneous mutations and designated for instance by the doubling-dose concept. A problem in that context is the fact that the mutational spectrum for spontaneous and induced mutations is not the same and it can furthermore vary considerably between loci. This is illustrated by molecular characterization of spontaneous and ionizing-radiation-induced mutations in mammalian cells. Furthermore changes of the genetic machinery are not limited to those endpoints usually measured in mutational assays, that is, base substitutions, frameshifts, classical chromosomal aberrations and numerical alterations of chromosomes. Additional alterations, of which far less is known, include insertion mutations, recombinogenic events and disproportionate replication of DNA giving rise to gene amplifications, and changes of gene expression through methylation of cytosine. There are reasons to believe that these endpoints are of importance in the development of tumors. Amplification of oncogenes is a well-known phenomenon in tumorigenicity and lately mutations by the insertion of mobile DNA elements have been demonstrated in cancer cells. Often these alterations are induced by stress and they constitute a manifestation of the dynamics and instability of DNA and the genetic system revealed in recent years. It is of interest in that context that the flow of genetic information does not only occur in one direction that is, DNA-RNA-protein, but also from RNA to DNA through reverse transcription and possibly even from the protein end of the sequence.

Animals↗
PubMed1995

Botulinal neurotoxin C1 complex genes, clostridial neurotoxin homology and genetic transfer in Clostridium botulinum.

The botulinal neurotoxins (BoNT) associate with non-toxic proteins (ANTP) by non-covalent bonds to form large complexes. In C. botulinum C, the BoNT/C1 locus consists of six genes which are organized in three clusters. Cluster 1 encompasses the genes of BoNT/C1 and ANTP/139 which could be involved in the resistance of the BoNT/C1 to the acidic pH and protease degradation. The second cluster consists of three genes which encode hemagglutinin components. The last gene encodes a DNA binding protein (Orf22) which might regulate the BoNT/C1 complex gene expression. BoNT and tetanus toxin (TeTx) display similar structure and mechanism of action at the molecular level. Their identity at the amino acid level range from 34 to 96.8%, indicating that the clostridial neurotoxin genes probably derive from a common ancestor. The fact that Clostridium other than C. botulinum such as C. butyricum and C. baratii can produce a BoNT suggests that the BoNT genes can be transferred between Clostridium strains. The toxigenic C. butyricum strains seem to derive from originally non-toxic strains by neurotoxin gene transfer from C. botulinum E, probably including a mobile DNA element. In C. botulinum C and D the gene encoding the exoenzyme C3 has been localized in a transposon-like element of 21.5 kbp. Transposons could be involved in BoNT gene transfer in C. botulinum.

Amino Acid Sequence↗
PubMed1981

Direct repeats flank three small nuclear RNA pseudogenes in the human genome.

We previously demonstrated that pseudogenes complementary to the small nuclear RNAs U1, U2 and U3 are dispersed and abundant in the human genome. Here we report that three pseudogenes (U1.101, U2.13 and U3.5) are flanked by perfect short direct repeats of 16 to 19 base pairs. In all three pseudogenes. the upstream direct repeat abuts a DNA sequence corresponding to the 5' end of the mature snRNA; in U2.13 and U3.5, the downstream direct repeat immediately follows the truncated 3' end of the snRNA sequence, whereas in U1.101, the downstream direct repeat is separated from the 3, end of the full-length snRNA sequence by a short A-rich region. We consider the direct repeats to be an indication that these three pseudogenes were created by insertion of snRNA information into a new chromosomal locus. To explain why the upstream repeat abuts a DNA sequence complementary to the 5' end of the mature snRNA, we propose a model for insertion that uses a reverse transcript of the snRNA as an intermediate. Furthermore, we note similarities between the structure of all three pseudogene loci and the Alu family of middle repetitive DNA sequences. These similarities suggest that some Alu family sequences are mobile genetic elements that can transpose to new chromosomal loci using as an intermediate a cDNA copy of an RNA transcribed from the Alu family element by RNA polymerase III.

Animals↗