Journal articles: 'Integrative and mobilizable element'

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Doublet, Benoît, David Boyd, Michael R. Mulvey, and Axel Cloeckaert. "TheSalmonellagenomic island 1 is an integrative mobilizable element." Molecular Microbiology 55, no. 6 (February 4, 2005): 1911–24. http://dx.doi.org/10.1111/j.1365-2958.2005.04520.x.

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Durand, Romain, Florence Deschênes, and Vincent Burrus. "Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids." PLOS Genetics 17, no. 8 (August 20, 2021): e1009669. http://dx.doi.org/10.1371/journal.pgen.1009669.

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Salmonella Genomic Island 1 (SGI1) and its variants are significant contributors to the spread of antibiotic resistance among Gammaproteobacteria. All known SGI1 variants integrate at the 3’ end of trmE, a gene coding for a tRNA modification enzyme. SGI1 variants are mobilized specifically by conjugative plasmids of the incompatibility groups A and C (IncA and IncC). Using a comparative genomics approach based on genes conserved among members of the SGI1 group, we identified diverse integrative elements distantly related to SGI1 in several species of Vibrio, Aeromonas, Salmonella, Pokkaliibacter, and Escherichia. Unlike SGI1, these elements target two alternative chromosomal loci, the 5’ end of dusA and the 3’ end of yicC. Although they share many features with SGI1, they lack antibiotic resistance genes and carry alternative integration/excision modules. Functional characterization of IMEVchUSA3, a dusA-specific integrative element, revealed promoters that respond to AcaCD, the master activator of IncC plasmid transfer genes. Quantitative PCR and mating assays confirmed that IMEVchUSA3 excises from the chromosome and is mobilized by an IncC helper plasmid from Vibrio cholerae to Escherichia coli. IMEVchUSA3 encodes the AcaC homolog SgaC that associates with AcaD to form a hybrid activator complex AcaD/SgaC essential for its excision and mobilization. We identified the dusA-specific recombination directionality factor RdfN required for the integrase-mediated excision of dusA-specific elements from the chromosome. Like xis in SGI1, rdfN is under the control of an AcaCD-responsive promoter. Although the integration of IMEVchUSA3 disrupts dusA, it provides a new promoter sequence and restores the reading frame of dusA for proper expression of the tRNA-dihydrouridine synthase A. Phylogenetic analysis of the conserved proteins encoded by SGI1-like elements targeting dusA, yicC, and trmE gives a fresh perspective on the possible origin of SGI1 and its variants.

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Lorenzo-Diaz, Fabian, Cris Fernández-Lopez, Pierre-Emmanuel Douarre, Adrian Baez-Ortega, Carlos Flores, Philippe Glaser, and Manuel Espinosa. "Streptococcal group B integrative and mobilizable element IMESag- rpsI encodes a functional relaxase involved in its transfer." Open Biology 6, no. 10 (October 2016): 160084. http://dx.doi.org/10.1098/rsob.160084.

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Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance. Although IMEs seem to be the most prevalent class of elements transferable by conjugation, they are poorly known. Here, we have studied a GBS-IME, termed IMESag- rpsI , which is widely distributed in GBS despite not carrying any apparent virulence trait. Analyses of 240 whole genomes showed that IMESag- rpsI is present in approximately 47% of the genomes, has a roughly constant size (approx. 9 kb) and is always integrated at a single location, the 3′-end of the gene encoding the ribosomal protein S9 ( rpsI ). Based on their genetic variation, several IMESag- rpsI types were defined (A–J) and classified in clonal complexes (CCs). CC1 was the most populated by IMESag- rpsI (more than 95%), mostly of type-A (71%). One CC1 strain ( S. agalactiae HRC) was deep-sequenced to understand the rationale underlying type-A IMESag- rpsI enrichment in GBS. Thirteen open reading frames were identified, one of them encoding a protein (MobSag) belonging to the broadly distributed family of relaxases MOB V1 . Protein MobSag was purified and, by a newly developed method, shown to cleave DNA at a specific dinucleotide. The S. agalactiae HRC-IMESag- rpsI is able to excise from the chromosome, as shown by the presence of circular intermediates, and it harbours a fully functional mobilization module. Further, the mobSag gene encoded by this mobile element is able to promote plasmid transfer among pneumococcal strains, suggesting that MobSag facilitates the spread of IMESag- rpsI and that this spread would explain the presence of the same IMESag- rpsI type in GBS strains belonging to different CCs.

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Lao, Julie, Gérard Guédon, Thomas Lacroix, Florence Charron-Bourgoin, Virginie Libante, Valentin Loux, Hélène Chiapello, Sophie Payot, and Nathalie Leblond-Bourget. "Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment." Genes 11, no. 9 (August 26, 2020): 999. http://dx.doi.org/10.3390/genes11090999.

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Streptococcus salivarius is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in S. salivarius genome diversity. For this purpose, we performed an in-depth analysis of 75 genomes of S. salivarius and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in S. salivarius genomes. The identification of almost all ICE and IME boundaries allowed the identification of the genes in which these elements are inserted. Furthermore, the exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions such as resistance to stress, to antibiotics or to toxic compounds, and numerous enzymes involved in diverse cellular metabolic pathways. These data support the idea that not only ICEs but also IMEs and decayed elements play an important role in S. salivarius adaptation to the environment.

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Woudstra, Cedric, and Sophie A. Granier. "A Glimpse at the Anti-Phage Defenses Landscape in the Foodborne Pathogen Salmonella enterica subsp. enterica Serovar Typhimurium." Viruses 15, no. 2 (January 24, 2023): 333. http://dx.doi.org/10.3390/v15020333.

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Bacteriophages, which specifically infect and kill bacteria, are currently used as additives to control pathogens such as Salmonella in human food (PhageGuard S®) or animal feed (SalmoFREE®, Bafasal®). Indeed, salmonellosis is among the most important zoonotic foodborne illnesses. The presence of anti-phage defenses protecting bacteria against phage infection could impair phage applications aiming at reducing the burden of foodborne pathogens such as Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) to the food industry. In this study, the landscape of S. Typhimurium anti-phage defenses was bioinformatically investigated in publicly available genomes using the webserver PADLOC. The primary anti-phage systems identified in S. Typhimurium use nucleic acid degradation and abortive infection mechanisms. Reference systems were identified on an integrative and conjugative element, a transposon, a putative integrative and mobilizable element, and prophages. Additionally, the mobile genetic elements (MGEs) containing a subset of anti-phage systems were found in the Salmonella enterica species. Lastly, the MGEs alone were also identified in the Enterobacteriaceae family. The presented diversity assessment of the anti-phage defenses and investigation of their dissemination through MGEs in S. Typhimurium constitute a first step towards the design of preventive measures against the spread of phage resistance that may hinder phage applications.

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Wang, Jun, Nadja B. Shoemaker, Gui-Rong Wang, and Abigail A. Salyers. "Characterization of a Bacteroides Mobilizable Transposon, NBU2, Which Carries a Functional Lincomycin Resistance Gene." Journal of Bacteriology 182, no. 12 (June 15, 2000): 3559–71. http://dx.doi.org/10.1128/jb.182.12.3559-3571.2000.

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ABSTRACT The mobilizable Bacteroides element NBU2 (11 kbp) was found originally in two Bacteroides clinical isolates,Bacteroides fragilis ERL and B. thetaiotaomicron DOT. At first, NBU2 appeared to be very similar to another mobilizable Bacteroides element, NBU1, in a 2.5-kbp internal region, but further examination of the full DNA sequence of NBU2 now reveals that the region of near identity between NBU1 and NBU2 is limited to this small region and that, outside this region, there is little sequence similarity between the two elements. The integrase gene of NBU2, intN2, was located at one end of the element. This gene was necessary and sufficient for the integration of NBU2. The integrase of NBU2 has the conserved amino acids (R-H-R-Y) in the C-terminal end that are found in members of the lambda family of site-specific integrases. This was also the only region in which the NBU1 and NBU2 integrases shared any similarity (28% amino acid sequence identity and 49% sequence similarity). Integration of NBU2 was site specific in Bacteroidesspecies. Integration occurred in two primary sites in B. thetaiotaomicron. Both of these sites were located in the 3′ end of a serine-tRNA gene NBU2 also integrated in Escherichia coli, but integration was much less site specific than inB. thetaiotaomicron. Analysis of the sequence of NBU2 revealed two potential antibiotic resistance genes. The amino acid sequences of the putative proteins encoded by these genes had similarity to resistances found in gram-positive bacteria. Only one of these genes was expressed in B. thetaiotaomicron, the homolog of linA, a lincomycin resistance gene fromStaphylococcus aureus. To determine how widespread elements related to NBU1 and NBU2 are in Bacteroides species, we screened 291 Bacteroides strains. Elements with some sequence similarity to NBU2 and NBU1 were widespread inBacteroides strains, and the presence oflinAN in Bacteroides strains was highly correlated with the presence of NBU2, suggesting that NBU2 has been responsible for the spread of this gene amongBacteroides strains. Our results suggest that the NBU-related elements form a large and heterogeneous family, whose members have similar integration mechanisms but have different target sites and differ in whether they carry resistance genes.

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Libante, Virginie, Nazim Sarica, Abbas Mohamad Ali, Chloé Gapp, Anissa Oussalah, Gérard Guédon, Nathalie Leblond-Bourget, and Sophie Payot. "Mobilization of IMEs Integrated in the oriT of ICEs Involves Their Own Relaxase Belonging to the Rep-Trans Family of Proteins." Genes 11, no. 9 (August 26, 2020): 1004. http://dx.doi.org/10.3390/genes11091004.

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Integrative mobilizable elements (IMEs) are widespread but very poorly studied integrated elements that can excise and hijack the transfer apparatus of co-resident conjugative elements to promote their own spreading. Sixty-four putative IMEs, harboring closely related mobilization and recombination modules, were found in 14 Streptococcus species and in Staphylococcus aureus. Fifty-three are integrated into the origin of transfer (oriT) of a host integrative conjugative element (ICE), encoding a MobT relaxase and belonging to three distant families: ICESt3, Tn916, and ICE6013. The others are integrated into an unrelated IME or in chromosomal sites. After labeling by an antibiotic resistance gene, the conjugative transfer of one of these IMEs (named IME_oriTs) and its host ICE was measured. Although the IME is integrated in an ICE, it does not transfer as a part of the host ICE (no cis-mobilization). The IME excises and transfers separately from the ICE (without impacting its transfer rate) using its own relaxase, distantly related to all known MobT relaxases, and integrates in the oriT of the ICE after transfer. Overall, IME_oriTs use MobT-encoding ICEs both as hosts and as helpers for conjugative transfer. As half of them carry lsa(C), they actively participate in the dissemination of lincosamide–streptogramin A–pleuromutilin resistance among Firmicutes.

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Shoemaker, N. B., G. R. Wang, A. M. Stevens, and A. A. Salyers. "Excision, transfer, and integration of NBU1, a mobilizable site-selective insertion element." Journal of Bacteriology 175, no. 20 (1993): 6578–87. http://dx.doi.org/10.1128/jb.175.20.6578-6587.1993.

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Veschetti, Laura, Angela Sandri, Helle Krogh Johansen, Maria M. Lleò, and Giovanni Malerba. "Hypermutation as an Evolutionary Mechanism for Achromobacter xylosoxidans in Cystic Fibrosis Lung Infection." Pathogens 9, no. 2 (January 21, 2020): 72. http://dx.doi.org/10.3390/pathogens9020072.

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Achromobacter xylosoxidans can cause chronic infections in the lungs of patients with cystic fibrosis (CF) by adapting to the specific environment. The study of longitudinal isolates allows to investigate its within-host evolution to unravel the adaptive mechanisms contributing to successful colonization. In this study, four clinical isolates longitudinally collected from two chronically infected patients underwent whole genome sequencing, de novo assembly and sequence analysis. Phenotypic assays were also performed. The isolates coming from one of the patients (patient A) presented a greater number of genetic variants, diverse integrative and conjugative elements, and different protease secretion. In the first of these isolates (strain A1), we also found a large deletion in the mutS gene, involved in DNA mismatch repair (MMR). In contrast, isolates from patient B showed a lower number of variants, only one integrative and mobilizable element, no phenotypic changes, and no mutations in the MMR system. These results suggest that in the two patients the establishment of a chronic infection was mediated by different adaptive mechanisms. While the strains isolated from patient B showed a longitudinal microevolution, strain A1 can be clearly classified as a hypermutator, confirming the occurrence and importance of this adaptive mechanism in A. xylosoxidans infection.

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Libante, Virginie, Yves Nombre, Charles Coluzzi, Johan Staub, Gérard Guédon, Marcelo Gottschalk, Sarah Teatero, Nahuel Fittipaldi, Nathalie Leblond-Bourget, and Sophie Payot. "Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes." Pathogens 9, no. 1 (December 25, 2019): 22. http://dx.doi.org/10.3390/pathogens9010022.

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Streptococcus suis is a zoonotic pathogen suspected to be a reservoir of antimicrobial resistance (AMR) genes. The genomes of 214 strains of 27 serotypes were screened for AMR genes and chromosomal Mobile Genetic Elements (MGEs), in particular Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs). The functionality of two ICEs that host IMEs carrying AMR genes was investigated by excision tests and conjugation experiments. In silico search revealed 416 ICE-related and 457 IME-related elements. These MGEs exhibit an impressive diversity and plasticity with tandem accretions, integration of ICEs or IMEs inside ICEs and recombination between the elements. All of the detected 393 AMR genes are carried by MGEs. As previously described, ICEs are major vehicles of AMR genes in S. suis. Tn5252-related ICEs also appear to carry bacteriocin clusters. Furthermore, whereas the association of IME-AMR genes has never been described in S. suis, we found that most AMR genes are actually carried by IMEs. The autonomous transfer of an ICE to another bacterial species (Streptococcus thermophilus)—leading to the cis-mobilization of an IME carrying tet(O)—was obtained. These results show that besides ICEs, IMEs likely play a major role in the dissemination of AMR genes in S. suis.

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Berbel, Dàmaris, Jordi Càmara, Aida González-Díaz, Meritxell Cubero, Guillem López de Egea, Sara Martí, Fe Tubau, M. Angeles Domínguez, and Carmen Ardanuy. "Deciphering mobile genetic elements disseminating macrolide resistance in Streptococcus pyogenes over a 21 year period in Barcelona, Spain." Journal of Antimicrobial Chemotherapy 76, no. 8 (May 20, 2021): 1991–2003. http://dx.doi.org/10.1093/jac/dkab130.

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Abstract Objectives To phenotypically and genetically characterize the antibiotic resistance determinants and associated mobile genetic elements (MGEs) among macrolide-resistant (MR) Streptococcus pyogenes [Group A streptococci (GAS)] clinical isolates collected in Barcelona, Spain. Methods Antibiotic susceptibility testing was performed by microdilution. Isolates were emm and MLST typed and 55 were whole-genome sequenced to determine the nature of the macrolide resistance (MR) determinants and their larger MGE and chromosomal context. Results Between 1998 and 2018, 142 of 1028 GAS (13.8%) were MR. Among 108 isolates available for molecular characterization, 41.7% had cMLSB, 30.5% iMLSB and 27.8% M phenotype. Eight erm(B)-containing strains were notable in having an MDR phenotype conferred by an MGE encoding several antibiotic resistance genes. MR isolates were comprised of several distinct genetic lineages as defined by the combination of emm and ST. Although most lineages were only transiently present, the emm11/ST403 clone persisted throughout the period. Two lineages, emm9/ST75 with erm(B) and emm77/ST63 with erm(TR), emerged in 2016–18. The erm(B) was predominantly encoded on the Tn916 family of transposons (21/31) with different genetic contexts, and in other MGEs (Tn6263, ICESpHKU372 and one harbouring an MDR cluster called ICESp1070HUB). The erm(TR) was found in ICESp2905 (8/17), ICESp1108-like (4/17), ICESpHKU165 (3/17) and two structures described in this study (IMESp316HUB and ICESp3729HUB). The M phenotype [mef(A)-msr(D)] was linked to phage φ1207.3. Eight integrative conjugative element/integrative mobilizable element (ICE/IME) cluster groups were classified on the basis of gene content within conjugation modules. These groups were found among MGEs, which corresponded with the MR-containing element or the site of integration. Conclusions We detected several different MGEs harbouring erm(B) or erm(TR). This is the first known description of Tn6263 in GAS and three MGEs [IMESp316HUB, ICESp3729HUB and ICESp1070HUB] associated with MR. Periods of high MR rates in our area were mainly associated with the expansion of certain predominant lineages, while in low MR periods different sporadic and low prevalence lineages were more frequent.

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Pavlovic, Guillaume, Vincent Burrus, Brigitte Gintz, Bernard Decaris, and Gérard Guédon. "Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus." Microbiology 150, no. 4 (April 1, 2004): 759–74. http://dx.doi.org/10.1099/mic.0.26883-0.

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The 34 734-bp integrative and potentially conjugative element (putative ICE) ICESt1 has been previously found to be site-specifically integrated in the 3′ end of the fda locus of Streptococcus thermophilus CNRZ368. Four types of genomic islands related to ICESt1 are integrated in the same position in seven other strains of S. thermophilus. One of these elements, ICESt3, harbours conjugation and recombination modules closely related to those of ICESt1 and excises by site-specific recombination. Two other types of elements, CIME19258 and CIME302, are flanked by site-specific attachment sites closely related to attL and attR of ICESt1 and ICESt3, whereas ΔCIME308 only possesses a putative attR site; none of these three elements carry complete conjugation and recombination modules. ICESt1 contains a functional internal recombination site, attL′, that is almost identical to attL of CIME19258. The recombination between attL′ and attR of ICESt1 leads to the excision of the expected circular molecule (putative ICE); a cis-mobilizable element (CIME) flanked by an attL site and an attB′ site remains integrated into the 3′ end of fda. Furthermore, sequences that could be truncated att sites were found within ICESt1, ICESt3 and CIME302. All together, these data suggest that these genomic islands evolved by deletion and tandem accretion of ICEs and CIMEs resulting from site-specific recombination. A model for this evolution is proposed and its application to other genomic islands is discussed.

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Belhocine, Kamila, Karen K. Yam, and Benoit Cousineau. "Conjugative Transfer of the Lactococcus lactis Chromosomal Sex Factor Promotes Dissemination of the Ll.LtrB Group II Intron." Journal of Bacteriology 187, no. 3 (February 1, 2005): 930–39. http://dx.doi.org/10.1128/jb.187.3.930-939.2005.

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ABSTRACT The Ll.LtrB group II intron from the low-G+C gram-positive bacterium Lactococcus lactis was the first bacterial group II intron shown to splice and mobilize in vivo. This retroelement interrupts the relaxase gene (ltrB) of three L. lactis conjugative elements: plasmids pRS01 and pAH90 and the chromosomal sex factor. Conjugative transfer of a plasmid harboring a segment of the pRS01 conjugative plasmid including the Ll.LtrB intron allows dissemination of Ll.LtrB among L. lactis strains and lateral transfer of this retroelement from L. lactis to Enterococcus faecalis. Here we report the dissemination of the Ll.LtrB group II intron among L. lactis strains following conjugative transfer of the native chromosomally embedded L. lactis sex factor. We demonstrated that Ll.LtrB dissemination is highly variable and often more efficient from this integrative and conjugative element than from an engineered conjugative plasmid. Cotransfer among L. lactis strains of both Ll.LtrB-containing elements, the conjugative plasmid and the sex factor, was detected and shown to be synergistic. Moreover, following their concurrent transfer, both mobilizable elements supported the spread of their respective copies of the Ll.LtrB intron. Our findings explain the unusually high efficiency of Ll.LtrB mobility observed following conjugation of intron-containing plasmids.

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Zhang, Yucheng, and Rosemary Loria. "Emergence of Novel Pathogenic Streptomyces Species by Site-Specific Accretion and cis-Mobilization of Pathogenicity Islands." Molecular Plant-Microbe Interactions® 30, no. 1 (January 2017): 72–82. http://dx.doi.org/10.1094/mpmi-09-16-0190-r.

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The main pathogenicity factor of Streptomyces species associated with the potato common scab disease is a nitrated diketopiperazine called thaxtomin A (ThxA). In Streptomyces scabiei (syn. S. scabies), which is thought to be the most ancient pathogenic Streptomyces species, the ThxA biosynthetic cluster is located within a mobile genomic island called the toxicogenic region (TR). Three attachment (att) sites further separate TR into two subregions (TR1 and TR2). TR1 contains the ThxA biosynthetic cluster and is conserved among several pathogenic Streptomyces species. However, TR2, an integrative and conjugative element, is missing in most pathogenic species. In our previous study, we demonstrated the mobilization of the whole TR element or TR2 alone between S. scabiei and nonpathogenic Streptomyces species. TR1 alone did not mobilize in these experiments. These data suggest that TR2 is required for the mobilization of TR1. Here, we show that TR2 can self mobilize to pathogenic Streptomyces species harboring only TR1 and integrate into the att site of TR1, leading to the tandem accretion of resident TR1 and incoming TR2. The incoming TR2 can further mobilize resident TR1 in cis and transfer to a new recipient cell. Our study demonstrated that TR1 is a nonautonomous cis-mobilizable element and that it can hijack TR2 recombination and conjugation machinery to excise, transfer, and integrate, leading to the dissemination of pathogenicity genes and emergence of novel pathogenic species. Additionally, comparative genomic analysis of 23 pathogenic Streptomyces isolates from ten species revealed that the composite pathogenicity island (PAI) formed by TR1 and TR2 is dynamic and various compositions of the island exist within the population of newly emerged pathogenic species, indicating the structural instability of this composite PAI.

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Shoemaker, N. B., G. R. Wang, and A. A. Salyers. "NBU1, a mobilizable site-specific integrated element from Bacteroides spp., can integrate nonspecifically in Escherichia coli." Journal of bacteriology 178, no. 12 (1996): 3601–7. http://dx.doi.org/10.1128/jb.178.12.3601-3607.1996.

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LeGault, Kristen N., Stephanie G. Hays, Angus Angermeyer, Amelia C. McKitterick, Fatema-tuz Johura, Marzia Sultana, Tahmeed Ahmed, Munirul Alam, and Kimberley D. Seed. "Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts." Science 373, no. 6554 (July 29, 2021): eabg2166. http://dx.doi.org/10.1126/science.abg2166.

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Bacteriophage predation selects for diverse antiphage systems that frequently cluster on mobilizable defense islands in bacterial genomes. However, molecular insight into the reciprocal dynamics of phage-bacterial adaptations in nature is lacking, particularly in clinical contexts where there is need to inform phage therapy efforts and to understand how phages drive pathogen evolution. Using time-shift experiments, we uncovered fluctuations in Vibrio cholerae’s resistance to phages in clinical samples. We mapped phage resistance determinants to SXT integrative and conjugative elements (ICEs), which notoriously also confer antibiotic resistance. We found that SXT ICEs, which are widespread in γ-proteobacteria, invariably encode phage defense systems localized to a single hotspot of genetic exchange. We identified mechanisms that allow phage to counter SXT-mediated defense in clinical samples, and document the selection of a novel phage-encoded defense inhibitor. Phage infection stimulates high-frequency SXT ICE conjugation, leading to the concurrent dissemination of phage and antibiotic resistances.

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Schultz, Eliette, Marisa Haenni, Laurent Mereghetti, Eliane Siebor, Catherine Neuwirth, Jean-Yves Madec, Axel Cloeckaert, and Benoît Doublet. "Survey of multidrug resistance integrative mobilizable elements SGI1 and PGI1 inProteus mirabilisin humans and dogs in France, 2010–13." Journal of Antimicrobial Chemotherapy 70, no. 9 (June 11, 2015): 2543–46. http://dx.doi.org/10.1093/jac/dkv154.

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Tarrah, Armin, Shadi Pakroo, Viviana Corich, and Alessio Giacomini. "Identification and Transferability of Tetracycline Resistance in Streptococcus thermophilus during Milk Fermentation, Storage, and Gastrointestinal Transit." Fermentation 7, no. 2 (April 28, 2021): 65. http://dx.doi.org/10.3390/fermentation7020065.

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The existence of antibiotic-resistant bacteria in food products, particularly those carrying acquired resistance genes, has increased concerns about the transmission of these genes from beneficial microbes to human pathogens. In this study, we evaluated the antibiotic resistance-susceptibility patterns of 16 antibiotics in eight S. thermophilus strains, whose genome sequence is available, using phenotypic and genomic approaches. The minimal inhibitory concentration values collected revealed intermediate resistance to aminoglycosides, whereas susceptibility was detected for different classes of β-lactams, quinolones, glycopeptide, macrolides, and sulfonamides in all strains. A high tetracycline resistance level has been detected in strain M17PTZA496, whose genome analysis indicated the presence of the tet(S) gene and the multidrug and toxic compound extrusion (MATE) family efflux pump. Moreover, an in-depth genomic analysis revealed genomic islands and an integrative and mobilizable element (IME) in the proximity of the gene tet(S). However, despite the presence of a prophage, genomic islands, and IME, no horizontal gene transfer was detected to Lactobacillus delbrueckii subsp. lactis DSM 20355 and Lactobacillusrhamnosus GG during 24 h of skim milk fermentation, 2 weeks of refrigerated storage, and 4 h of simulated gastrointestinal transit.

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López, María, Beatriz Rojo-Bezares, Gabriela Chichón, and Yolanda Sáenz. "Resistance to Fluoroquinolones in Pseudomonas aeruginosa from Human, Animal, Food and Environmental Origin: The Role of CrpP and Mobilizable ICEs." Antibiotics 11, no. 9 (September 19, 2022): 1271. http://dx.doi.org/10.3390/antibiotics11091271.

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Fluoroquinolone resistance and the associated genetic mechanisms were assessed by antimicrobial susceptibility and whole genome sequencing in 56 Pseudomonas aeruginosa strains from human, animal, food and environmental origins. P. aeruginosa PAO1, PA7 and PA14 reference strains were also included in the study. Twenty-two strains (37%) were resistant to, at least, one fluoroquinolone agent. Correlation between the number of changes in GyrA and ParC proteins and the level of fluoroquinolone resistance was observed. Mutations or absence of genes, such as mexZ, mvaT and nalD encoding efflux pumps regulators, were also found in resistant strains. The crpP gene was detected in 43 strains (72.9%; 17 of them non-clinical strains), and coded seven different CrpP variants, including a novel one (CrpP-7). The crpP gene was located in 23 different chromosomal mobile integrative and conjugative elements (ICEs), inserted in two tRNAs integration sites. A great variety of structures was detected in the crpP-ICEs elements, e.g., the fimbriae related cup clusters, the mercury resistance mer operon, the pyocin S5 or S8 bacteriocin encoding genes, and mobilization genes. The location of crpP-like genes in mobilizable ICEs and linked to heavy metal resistance and virulence factors is of significant concern in P. aeruginosa. This work provides a genetic explanation of the fluoroquinolone resistance and crpP-associated pathogenesis of P. aeruginosa from a One-Health approach.

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Doublet, Benoît, Karine Praud, Sophie Bertrand, Jean-Marc Collard, François-Xavier Weill, and Axel Cloeckaert. "Novel Insertion Sequence- and Transposon-Mediated Genetic Rearrangements in Genomic Island SGI1 of Salmonella enterica Serovar Kentucky." Antimicrobial Agents and Chemotherapy 52, no. 10 (August 1, 2008): 3745–54. http://dx.doi.org/10.1128/aac.00525-08.

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ABSTRACT Salmonella genomic island 1 (SGI1) is an integrative mobilizable element that harbors a multidrug resistance (MDR) gene cluster. Since its identification in epidemic Salmonella enterica serovar Typhimurium DT104 strains, variant SGI1 MDR gene clusters conferring different MDR phenotypes have been identified in several S. enterica serovars and classified as SGI1-A to -O. A study was undertaken to characterize SGI1 from serovar Kentucky strains isolated from travelers returning from Africa. Several strains tested were found to contain the partially characterized variant SGI1-K, recently described in a serovar Kentucky strain isolated in Australia. This variant contained only one cassette array, aac(3)-Id-aadA7, and an adjacent mercury resistance module. Here, the uncharacterized part of SGI1-K was sequenced. Downstream of the mer module similar to that found in Tn21, a mosaic genetic structure was found, comprising (i) part of Tn1721 containing the tetracycline resistance genes tetR and tet(A); (ii) part of Tn5393 containing the streptomycin resistance genes strAB, IS1133, and a truncated tnpR gene; and (iii) a Tn3-like region containing the tnpR gene and the β-lactamase bla TEM-1 gene flanked by two IS26 elements in opposite orientations. The rightmost IS26 element was shown to be inserted into the S044 open reading frame of the SGI1 backbone. This variant MDR region was named SGI1-K1 according to the previously described variant SGI1-K. Other SGI1-K MDR regions due to different IS26 locations, inversion, and partial deletions were characterized and named SGI1-K2 to -K5. Two new SGI1 variants named SGI1-P1 and -P2 contained only the Tn3-like region comprising the β-lactamase bla TEM-1 gene flanked by the two IS26 elements inserted into the SGI1 backbone. Three other new variants harbored only one IS26 element inserted in place of the MDR region of SGI1 and were named SGI1-Q1 to -Q3. Thus, in serovar Kentucky, the SGI1 MDR region undergoes recombinational and insertional events of transposon and insertion sequences, resulting in a higher diversity of MDR gene clusters than previously reported and consequently a higher diversity of MDR phenotypes.

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Michaelis, Claudia, and Elisabeth Grohmann. "Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms." Antibiotics 12, no. 2 (February 4, 2023): 328. http://dx.doi.org/10.3390/antibiotics12020328.

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Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.

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Lyras, Dena, Vicki Adams, Isabelle Lucet, and Julian I. Rood. "The large resolvase TnpX is the only transposon-encoded protein required for transposition of the Tn4451/3 family of integrative mobilizable elements." Molecular Microbiology 51, no. 6 (March 4, 2004): 1787–800. http://dx.doi.org/10.1111/j.1365-2958.2003.03950.x.

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Puymège, Aurore, Stéphane Bertin, Gérard Guédon, and Sophie Payot. "Analysis of Streptococcus agalactiae pan-genome for prevalence, diversity and functionality of integrative and conjugative or mobilizable elements integrated in the tRNALys CTT gene." Molecular Genetics and Genomics 290, no. 5 (April 2, 2015): 1727–40. http://dx.doi.org/10.1007/s00438-015-1031-9.

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Wang, Hongmei, Adam P. Roberts, Dena Lyras, Julian I. Rood, Mark Wilks, and Peter Mullany. "Characterization of the Ends and Target Sites of the Novel Conjugative Transposon Tn5397 from Clostridium difficile: Excision and Circularization Is Mediated by the Large Resolvase, TndX." Journal of Bacteriology 182, no. 13 (July 1, 2000): 3775–83. http://dx.doi.org/10.1128/jb.182.13.3775-3783.2000.

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ABSTRACT Tn5397 is a conjugative transposon that was originally isolated from Clostridium difficile. Previous analysis had shown that the central region of Tn5397 was closely related to the conjugative transposon Tn916. However, in this work we obtained the DNA sequence of the ends of Tn5397 and showed that they are completely different to those of Tn916. Tn5397 did not contain theint and xis genes, which are required for the excision and integration of Tn916. Instead, the right end of Tn5397 contained a gene, tndX, that appears to encode a member of the large resolvase family of site-specific recombinases. TndX is closely related to the TnpX resolvase from the mobilizable but nonconjugative chloramphenicol resistance transposons, Tn4451 from Clostridium perfringens and Tn4453 from C. difficile. Like the latter elements, inserted copies of Tn5397 were flanked by a direct repeat of a GA dinucleotide. The Tn5397target sites were also shown to contain a central GA dinucleotide. Excision of the element in C. difficile completely regenerated the original target sequence. A circular form of the transposon, in which the left and right ends of the element were separated by a GA dinucleotide, was detected by PCR in bothBacillus subtilis and C. difficile. A Tn5397 mutant in which part of tndX was deleted was constructed in B. subtilis. This mutant was nonconjugative and did not produce the circular form of Tn5397, indicating that the TndX resolvase has an essential role in the excision and transposition of Tn5397 and is thus the first example of a member of the large resolvase family of recombinases being involved in conjugative transposon mobility. Finally, we showed that introduction of Tn916 into a strain containing Tn5397 induced the loss of the latter element in 95.6% of recipients.

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Shoemaker, Nadja B., Gui-Rong Wang, and Abigail A. Salyers. "Multiple Gene Products and Sequences Required for Excision of the Mobilizable Integrated BacteroidesElement NBU1." Journal of Bacteriology 182, no. 4 (February 15, 2000): 928–36. http://dx.doi.org/10.1128/jb.182.4.928-936.2000.

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ABSTRACT NBU1 is an integrated 10.3-kbp Bacteroides element, which can excise and transfer to Bacteroides orEscherichia coli recipients, where it integrates into the recipient genome. NBU1 relies on large, >60-kbp, conjugative transposons for factors that trigger excision and for mobilization of the circular form to recipients. Previously, we showed that a single integrase gene, intN1, was necessary and sufficient for integration of NBU1 into its target site on the Bacteroidesor E. coli genome. We now show that an unexpectedly large region of NBU1 is required for excision. This region includes, in addition to intN1, four open reading frames plus a large region downstream of the fourth gene, prmN1. This downstream sequence was designated XRS, for “excision-required sequence.” XRS contains the oriT of the circular form of NBU1 and about two-thirds of the adjacent mobilization gene,mobN1. This is the first time an oriT, which is involved in conjugal transfer of the circular form, has been implicated in excision. Disruption of the gene immediately downstream ofintN1, orf2, completely abolished excision. The next open reading frame, orf2x, was too small to be disrupted, so we still do not know whether it plays a role in the excision reaction. Deletions were made in each of two open reading frames downstream of orf2x, orf3 andprmN1. Both of these deletions abolished excision, indicating that these genes are also essential for excision. Attempts to complement various mutations in the excision region led us to realize that a portion of the excision region carryingprmN1 and part of the XRS (XRSHIII) inhibited excision when provided in trans on a multicopy plasmid (8 to 10 copies per cell). However, a fragment carrying prmN1, XRS, and the entire mobilization gene, mobN1, did not have this effect. The smaller fragment may be interfering with excision by attracting proteins made by the intact NBU1 and thus removing them from the excision complex. Our results show clearly that excision is a complex process that involves several proteins and acis-acting region (XRS) which includes theoriT. We suggest that this complex excision machinery may be necessary to allow NBU1 to coordinate nicking at the ends during excision and nicking at the oriT during conjugal transfer, to prevent premature nicking at the oriT before NBU1 has excised and circularized.

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Le Hello, Simon, François-Xavier Weill, Véronique Guibert, Karine Praud, Axel Cloeckaert, and Benoît Doublet. "Early Strains of Multidrug-Resistant Salmonella enterica Serovar Kentucky Sequence Type 198 from Southeast Asia Harbor Salmonella Genomic Island 1-J Variants with a Novel Insertion Sequence." Antimicrobial Agents and Chemotherapy 56, no. 10 (July 16, 2012): 5096–102. http://dx.doi.org/10.1128/aac.00732-12.

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ABSTRACTSalmonellagenomic island 1 (SGI1) is a 43-kb integrative mobilizable element that harbors a great diversity of multidrug resistance gene clusters described in numerousSalmonella entericaserovars and also inProteus mirabilis. The majority of SGI1 variants contain an In104-derivative complex class 1 integron inserted between resolvase generesand open reading frame (ORF) S044 in SGI1. Recently, the international spread of ciprofloxacin-resistantS. entericaserovar Kentucky sequence type 198 (ST198) containing SGI1-K variants has been reported. A retrospective study was undertaken to characterize ST198S. Kentucky strains isolated before the spread of the epidemic ST198-SGI1-K population in Africa and the Middle East. Here, we characterized 12 ST198S. Kentucky strains isolated between 1969 and 1999, mainly from humans returning from Southeast Asia (n= 10 strains) or Israel (n= 1 strain) or from meat in Egypt (n= 1 strain). All these ST198S. Kentucky strains did not belong to the XbaI pulsotype X1 associated with the African epidemic clone but to pulsotype X2. SGI1-J subgroup variants containing different complex integrons with a partial transposition module and inserted within ORF S023 of SGI1 were detected in six strains. The SGI1-J4 variant containing a partially deleted class 1 integron and thus showing a narrow resistance phenotype to sulfonamides was identified in two epidemiologically unrelated strains from Indonesia. The four remaining strains harbored a novel SGI1-J variant, named SGI1-J6, which containedaadA2,floR2,tetR(G)-tetA(G), andsul1resistance genes within its complex integron. Moreover, in all theseS. Kentucky isolates, a novel insertion sequence related to the IS630family and named ISSen5was found inserted upstream of the SGI1 complex integron in ORF S023. Thus, two subpopulations ofS. Kentucky ST198 independently and exclusively acquired the SGI1 during the 1980s and 1990s. Unlike the ST198-X1 African epidemic subpopulation, the ST198-X2 subpopulation mainly from Asia harbors variants of the SGI1-J subgroup that are encountered mainly in the Far East, as previously described forS. entericaserovars Emek and Virchow.

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DE FREITAS ORTIZ, MAURO, and ELGION LUCIO SILVA LORETO. "Thehobo-related elements in themelanogasterspecies group." Genetics Research 90, no. 3 (June 2008): 243–52. http://dx.doi.org/10.1017/s0016672308009312.

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SummaryThehobo-related sequences (hRSs) were considered as degenerate and inactive elements until recently, when one mobilizable copy was described. Using this sequence as the initial seed to search for homologous sequences in 12 availableDrosophilagenomes, in addition to searching for these sequences by PCR and Southern blot in nine other species, we found homologous sequences in every species of theDrosophila melanogasterspecies subgroup. Some evidence suggests that these non-autonomous sequences were kept mobilizable for at least 0·4 million years. Also, some very short sequences with miniature inverted-repeat transposable element (MITE) characteristics were found among thesehRSs. ThesehRSs and their ‘MITE-like’ counterparts could provide a good example of the steps proposed in models that describe the MITEs origin.

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Bonafede, M. E., L. L. Carias, and L. B. Rice. "Enterococcal transposon Tn5384: evolution of a composite transposon through cointegration of enterococcal and staphylococcal plasmids." Antimicrobial Agents and Chemotherapy 41, no. 9 (September 1997): 1854–58. http://dx.doi.org/10.1128/aac.41.9.1854.

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Mechanisms for the possible transfer of antimicrobial resistance genes between staphylococci and enterococci remain poorly defined. We have previously reported the transfer between Enterococcus faecalis strains of a multiresistance chromosomal element (beta-lactamase positive and resistance to erythromycin, gentamicin, mercuric chloride, streptomycin, and tetracycline) which we have tentatively designated Tn5385. Tn5385 is a composite of several smaller transposable elements, including Tn5384, a 26-kb composite transposon conferring resistance to erythromycin, gentamicin, and mercuric chloride. Analyses of 7 kb within Tn5384 and flanking sequences within the larger element revealed sequences characteristic of staphylococcal beta-lactamase and small, mobilizable plasmids flanking a region with a sequence identical to those of the replication genes previously described for enterococcal and streptococcal broad-host-range plasmids. These diverse regions are linked by insertion sequences IS256 and IS257 in a manner which suggests a series of cointegration events as the genesis of the current relationship. Taken together, these data suggest that Tn5384 and the larger element within which it is incorporated (Tn5385) evolved at least in part as a result of cointegration between an enterococcal broad-host-range plasmid and staphylococcal beta-lactamase and small mobilizable plasmids. These results implicate broad-host-range plasmids in the transfer of resistance determinants from staphylococci to enterococci.

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Rékási, Márk, and T. Filep. "Effect of Microelement Loads on the Element Fractions of Soil and Plant Uptake." Agrokémia és Talajtan 55, no. 1 (March 1, 2006): 213–22. http://dx.doi.org/10.1556/agrokem.55.2006.1.23.

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The effect of microelement loads was investigated on the mobile (1 M NH 4 NO 3 soluble), mobilizable (NH 4 -acetate + EDTA soluble) and pseudo total (cc. HNO 3 + H 2 O 2 ) element concentrations of a calcareous chernozem soil in a long-term field experiment. Salts of 13 microelements were applied on four levels: 0, 90, 270 and 810 kg/ha in the spring of 1991 prior to sowing maize. The relations between the mobile, mobilizable and pseudo total fractions of a heavy metal contaminated soil were defined and quantified. According to this, Ba, Mo, Sr and Se have the greatest mobility, while Cu, Ni and Zn showed strong fixation on the examined soil. The maximum quantities of elements incorporated in the whole above-ground yield of maize were as follows (in g/ha): Al 1548, Zn 543, Mo 352, Ba 269, Cd 201, Se 153, Sr 116, Cu 64, Pb 22, Ni 15, Hg 8, Cr 4 and As <1. Transfer coefficients calculated as a quotient of different soil element fractions and maize grain and stem element contents were compared. In the case of grain the greatest accumulation was found in relation to the Ni, Cu and Se contents of the mobile fraction. The coefficient values were 3, 5 and 7, respectively. Coefficients for stem may exceed those obtained for grain. The accumulation decreases as a function of loads. The coefficients for NH 4 NO 3 extractions show the greatest standard deviation, thus this quotient indicates the heavy metal and toxic element accumulation in plants with the greatest sensitiveness.

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30

Osman, Ashraf S., and Malcolm D. Bolton. "A new design method for retaining walls in clay." Canadian Geotechnical Journal 41, no. 3 (June 1, 2004): 451–66. http://dx.doi.org/10.1139/t04-003.

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Geotechnical design engineers used to rely on arbitrary rules and definitions of "factor of safety" on peak soil strength in limit analysis calculations. They used elastic stiffness for deformation calculations, but the selection of equivalent linear elastic models was always arbitrary. Therefore, there is a need for a simple unified design method that addresses the real nature of serviceability and collapse limits in soils, which always show a nonlinear and sometimes brittle response. An approach to this method can be based on a new application of the theory of plasticity accompanied by the introduction of the concept of "mobilizable soil strength." This approach can satisfy both safety and serviceability and lead to simple design calculations within which all geotechnical design objectives can be achieved in a single step of calculation. The proposed method treats a stress path in an element, representative of some soil zone, as a curve of plastic soil strength mobilized as strains develop. Designers enter these strains into a plastic deformation mechanism to predict boundary displacements. The particular case of a cantilevered retaining wall supporting an excavation in clay is selected for a spectrum of soil conditions and wall flexibilities. The possible use of the mobilizable strength design (MSD) method in decision-making and design is explored and illustrated.Key words: retaining wall, plasticity theory, design, finite element.

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Wasels, François, Patrizia Spigaglia, Fabrizio Barbanti, and Paola Mastrantonio. "Clostridium difficile erm(B)-containing elements and the burden on the in vitro fitness." Journal of Medical Microbiology 62, no. 9 (September 1, 2013): 1461–67. http://dx.doi.org/10.1099/jmm.0.057117-0.

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In Clostridium difficile, resistance to the macrolide-lincosamide-streptogramin B group of antibiotics generally relies on erm(B) genes. In this study, we investigated elements with a genetic organization different from Tn5398, the mobilizable non-conjugative element identified in C. difficile strain 630. Our results suggested that the elements most frequently found in strains isolated during the European surveillance study in 2005 were related to Tn6194, the conjugative transposon recently detected in different C. difficile types, including PCR-ribotype 027. We characterized a Tn6194-like and a novel element rarely found in clinical isolates. A burden on the in vitro fitness of C. difficile was observed after the acquisition of these elements as well as of Tn5398.

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McCarron, M., A. Duttaroy, G. Doughty, and A. Chovnick. "Drosophila P element transposase induces male recombination additively and without a requirement for P element excision or insertion." Genetics 136, no. 3 (March 1, 1994): 1013–23. http://dx.doi.org/10.1093/genetics/136.3.1013.

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Abstract P element dysgenesis-associated male recombination in Drosophila was examined with a selective system focused upon a section of the third chromosome divided into eight recombination segments. Tests compared crossing over in the presence of none, one and two doses of P(delta 2-3)(99B), a non-mobile transposase source, in the absence of a mobilizable P element target in the genome. In the presence of the P transposase source, and without a P element target, significant male recombination occurred in genomic regions physically separated from the P(delta 2-3) site. Using two doses of P(delta 2-3) without a P element target, the male recombination rate doubled, and 90% of the crossovers occurred in the pericentric region. The distribution of recombination events, in the absence of P element targets approximates that seen in studies of radiation induced mitotic crossing over and the metaphase chromosome map. Another experiment examined the effects of one dose of P(delta 2-3) on a genome with a single P element target, P(lArB)(87C9), in the third recombination segment. Crossovers increased 58-fold in the immediate region of the P element target.

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Schirova, I. A. "Text as an Element of Integrative Scientific Space." RUSSIAN JOURNAL OF LINGUISTICS 21, no. 1 (2017): 362–78. http://dx.doi.org/10.22363/2312-9182-2017-21-2-362-378.

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34

Chanchaithong, Pattrarat, Vincent Perreten, and Sybille Schwendener. "Macrococcus canis contains recombinogenic methicillin resistance elements and the mecB plasmid found in Staphylococcus aureus." Journal of Antimicrobial Chemotherapy 74, no. 9 (June 26, 2019): 2531–36. http://dx.doi.org/10.1093/jac/dkz260.

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Abstract Objectives To analyse the genetic context of mecB in two Macrococcus canis strains from dogs, compare the mecB-containing elements with those found in other Macrococcus and Staphylococcus species, and identify possible mobilizable mecB subunits. Methods Whole genomes of the M. canis strains Epi0076A and KM0218 were sequenced using next-generation sequencing technologies. Multiple PCRs and restriction analysis confirmed structures of mecB-containing elements, circularization and recombination of mecB subunits. Results Both M. canis strains contained novel composite pseudo (Ψ) staphylococcal cassette chromosome mec (SCCmec) elements. Integration site sequences for SCC flanked and subdivided composite ΨSCCmecEpi0076A (69569 bp) into ΨSCC1Epi0076A-ΨSCCmecEpi0076A-ΨSCC2Epi0076A and composite ΨSCCmecKM0218 (24554 bp) into ΨSCCKM0218-ΨSCCmecKM0218. Putative γ-haemolysin genes (hlgB and hlgC) were found at the 3′ end of both composite elements. ΨSCCmecKM0218 contained a complete mecB gene complex (mecIm-mecR1m-mecB-blaZm) downstream of a new IS21-family member (ISMaca1). ΨSCCmecEpi0076A carried a blaZm-deleted mecB gene complex similar to that reported in ‘Macrococcus goetzii’ CCM4927T. A second mecB gene was found on the 81325 bp MDR plasmid pKM0218 in KM0218. This plasmid contained a complete Tn6045-associated mecB gene complex distinct from that of ΨSCCmecKM0218. pKM0218 was almost identical to the mecB-containing plasmid recently reported in Staphylococcus aureus (overall 99.96% nucleotide identity). Mobilization of mecB within an unconventional circularizable structure was observed in Epi0076A as well as chromosomal plasmid insertion via recombination of mecB operons in KM0218. Conclusions Our findings provide evidence of both the continuing evolution of mecB-containing elements in macrococci and M. canis as a potential source of the mecB-containing plasmid found in staphylococci.

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Ceccarelli, Daniela, Aurélie Daccord, Mélissa René, and Vincent Burrus. "Identification of the Origin of Transfer (oriT) and a New Gene Required for Mobilization of the SXT/R391 Family of Integrating Conjugative Elements." Journal of Bacteriology 190, no. 15 (June 6, 2008): 5328–38. http://dx.doi.org/10.1128/jb.00150-08.

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ABSTRACT Integrating conjugative elements (ICEs) are self-transmissible, mobile elements that are widespread among bacteria. Following their excision from the chromosome, ICEs transfer by conjugation, a process initiated by a single-stranded DNA break at a specific locus called the origin of transfer (oriT). The SXT/R391 family of ICEs includes SXTMO10, R391, and more than 25 related ICEs found in gammaproteobacteria. A previous study mapped the oriT locus of SXTMO10 to a 550-bp intergenic region between traD and s043. We suspected that this was not the correct oriT locus, because the identical traD-s043 region in R391 and other SXT/R391 family ICEs was annotated as a gene of an unknown function. Here, we investigated the location and structure of the oriT locus in the ICEs of the SXT/R391 family and demonstrated that oriT SXT corresponds to a 299-bp sequence that contains multiple imperfect direct and inverted repeats and is located in the intergenic region between s003 and rumB′. The oriT SXT locus is well conserved among SXT/R391 ICEs, like R391, R997, and pMERPH, and cross-recognition of oriT SXT and oriT R391 by R391 and SXTMO10 was demonstrated. Furthermore, we identified a previously unannotated gene, mobI, located immediately downstream from oriT SXT, which proved to be essential for SXTMO10 transfer and SXTMO10-mediated chromosomal DNA mobilization. Deletion of mobI did not impair the SXTMO10-dependent transfer of the mobilizable plasmid CloDF13, suggesting that mobI has no role in the assembly of the SXTMO10 mating pair apparatus. Instead, mobI appears to be involved in the recognition of oriT SXT.

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Timmery, Sophie, Pauline Modrie, Olivier Minet, and Jacques Mahillon. "Plasmid Capture by the Bacillus thuringiensis Conjugative Plasmid pXO16." Journal of Bacteriology 191, no. 7 (January 30, 2009): 2197–205. http://dx.doi.org/10.1128/jb.01700-08.

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ABSTRACTConjugation, mobilization, and retromobilization are three related mechanisms of horizontal gene transfer in bacteria. They have been extensively studied in gram-negative species, where retromobilization, the capture of DNA from a recipient by a donor cell, was shown to result from two successive steps: the transfer of the conjugative plasmid from the donor to the recipient followed by the retrotransfer of the mobilizable plasmid to the donor. This successive model was established for gram-negative bacteria but was lacking experimental data from the gram-positive counterparts. In the present work, the mobilization and retromobilization abilities of the conjugative plasmid pXO16 fromBacillus thuringiensissubsp.israelensiswere studied using the mobilizable plasmids pUB110 and pE194 and the “nonmobilizable” element pC194 lacking themobandoriTfeatures (all fromStaphylococcus aureus). Experimental data suggested a successive model, since different retromobilization frequencies were observed between the small plasmids. More importantly, retromobilization was shown to be delayed by 50 and 150 min for pUB110 and pE194, respectively, compared to pXO16 conjugation. Natural liquid foods (cow milk, soy milk, and rice milk) were used to evaluate the putative ecological impact of these transfers. In cow and soy milk, conjugation, mobilization, and retromobilization were shown to occur at frequencies of 8.0 × 10−1, 1.0 × 10−2, and 1.2 × 10−4transconjugants per recipient, respectively. These data are comparable to those obtained with LB medium and about 10-fold lower than in the case of rice milk. Taken together, these results emphasize the potential role of plasmid capture played byB. thuringiensisin natural environments.

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Cappuyns, Valérie. "A Critical Evaluation of Single Extractions from the SMT Program to Determine Trace Element Mobility in Sediments." Applied and Environmental Soil Science 2012 (2012): 1–15. http://dx.doi.org/10.1155/2012/672914.

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Two commonly applied single extractions procedures, namely extractions with ammonium-EDTA and acetic acid, were evaluated based on the analysis of 72 samples from alluvial sediments. For most trace elements (Cu, Zn, Cd, Ni, As, and Pb), a significant linear relationship could be established between their ammonium-EDTA or acetic acid extractable concentrations and their total concentrations, the organic carbon content, pH, and Fe , Al, and/or Ca content in the sediments. The scientific understanding of trace element partitioning in the complex soil-water system with these simple models is rather limited, but they offer the opportunity to use data from single extractions in a more comprehensive way. Despite the fact that these extractions cannot directly be related to the bioavailability of elements, they can provide input data for use in risk assessment models. Additionally, they also offer possibilities to perform a fast screening of the mobilizable pool of elements in soils and/or sediments.

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Vedantam, Gayatri, and David W. Hecht. "Isolation and Characterization of BTF-37: Chromosomal DNA Captured from Bacteroides fragilis That Confers Self-Transferability and Expresses a Pilus-Like Structure in Bacteroides spp. and Escherichia coli." Journal of Bacteriology 184, no. 3 (February 1, 2002): 728–38. http://dx.doi.org/10.1128/jb.184.3.728-738.2002.

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ABSTRACT We report the isolation and preliminary characterization of BTF-37, a new 52-kb transfer factor isolated from Bacteroides fragilis clinical isolate LV23. BTF-37 was obtained by the capture of new DNA in the nonmobilizable Bacteroides-Escherichia coli shuttle vector pGAT400ΔBglII using a functional assay. BTF-37 is self-transferable within and from Bacteroides and also self-transfers in E. coli. Partial DNA sequencing, colony hybridization, and PCR revealed the presence of Tet element-specific sequences in BTF-37. In addition, Tn5520, a small mobilizable transposon that we described previously (G. Vedantam, T. J. Novicki, and D. W. Hecht, J. Bacteriol. 181:2564–2571, 1999), was also coisolated within BTF-37. Scanning and transmission electron microscopy of Tet element-containing Bacteroides spp. and BTF-37-harboring Bacteroides and E. coli strains revealed the presence of pilus-like cell surface structures. These structures were visualized in Bacteroides spp. only when BTF-37 and Tet element strains were induced with subinhibitory concentrations of tetracycline and resembled those encoded by E. coli broad-host-range plasmids. We conclude that we have captured a new, self-transferable transfer factor from B. fragilis LV23 and that this new factor encodes a tetracycline-inducible Bacteroides sp. conjugation apparatus.

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Zhang, Qing Wen, Ying Jie Xu, Wei Hong Zhang, and Jun Wang. "Integrative Analysis of the Injection Molding Process and Mechanical Behavior of Plastic Part." Advanced Materials Research 705 (June 2013): 181–86. http://dx.doi.org/10.4028/www.scientific.net/amr.705.181.

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For parts made of plastics, injection molding is a common manufacturing process. Warpage and residual stress induced during the injection molding process have very important influences on the mechanical performance of injection products. In this paper, an integrative analysis of the injection molding process and mechanical performance of plastic parts is proposed. This integrative approach incorporates the effects of the manufacturing process in the mechanical simulation: (a) firstly, the finite element package MoldFlow is used to simulate the injection molding process and obtain the warpage and residual stress results. (b) Then the finite element model of plastic part including the process induced warpage and residual stress is established. Explicit dynamic finite element program LS-DYNA is used to simulate the mechanical behaviors of the molded part. Based on the integrative analysis, the influences of injection molding process parameters on mechanical behavior of a PC windshield against impact loading are studied.

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Heather, Zoe, Matthew T. G. Holden, Karen F. Steward, Julian Parkhill, Lijiang Song, Gregory L. Challis, Carl Robinson, Nicholas Davis-Poynter, and Andrew S. Waller. "A novel streptococcal integrative conjugative element involved in iron acquisition." Molecular Microbiology 70, no. 5 (December 2008): 1274–92. http://dx.doi.org/10.1111/j.1365-2958.2008.06481.x.

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41

Zhao, Sihui, and Kelly P. Williams. "Integrative Genetic Element That Reverses the Usual Target Gene Orientation." Journal of Bacteriology 184, no. 3 (February 1, 2002): 859–60. http://dx.doi.org/10.1128/jb.184.3.859-860.2002.

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ABSTRACT A genetic element integrating site specifically into a prokaryotic gene usually carries a copy of the 3′ portion of that gene that restores the active gene even as the original is disrupted. A cryptic element in Mesorhizobium loti instead carries a copy of the 5′ end of the tRNA gene into which it integrated. This has implications for the evolution of new integrase-site combinations.

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Iannelli, Francesco, Francesco Santoro, Marco R. Oggioni, and Gianni Pozzi. "Nucleotide Sequence Analysis of Integrative Conjugative Element Tn5253of Streptococcus pneumoniae." Antimicrobial Agents and Chemotherapy 58, no. 2 (December 2, 2013): 1235–39. http://dx.doi.org/10.1128/aac.01764-13.

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ABSTRACTConjugative transposon Tn5253, an integrative conjugative element (ICE) ofStreptococcus pneumoniaecarrying thecatandtet(M) genes, was shown to be 64,528 bp in size and to contain 79 open reading frames, of which only 38 could be annotated. Two distinct genetic elements were found integrated into Tn5253: Tn5251(18,033 bp), of the Tn916-Tn1545family of ICEs, and Ωcat(pC194) (7,627 bp), which could not conjugate but was capable of intracellular mobility by excision, circularization, and integration by homologous recombination. The highest conjugation frequency of Tn5253was observed whenStreptococcus pyogeneswas the donor (6.7 × 10−3transconjugants/donor).

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Taviani, Elisa, Christopher J. Grim, Jongsik Chun, Anwar Huq, and R. R. Colwell. "Genomic analysis of a novel integrative conjugative element inVibrio cholerae." FEBS Letters 583, no. 22 (October 20, 2009): 3630–36. http://dx.doi.org/10.1016/j.febslet.2009.10.041.

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Száková, J., J. Sysalová, and P. Tlustoš. "Particular aspects of environmental impact of potentially risk elements from airborne particulate matter." Plant, Soil and Environment 51, No. 8 (November 19, 2011): 376–83. http://dx.doi.org/10.17221/3613-pse.

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Two simple experiments were carried out to demonstrate two possible ways of environmental impact of element contents in airborne particulate matter. In the first part of the experiment, the response of three rural dust samples applied into the soil were assessed in pot experiment to observe uptake of As, Cd, Pb, and Zn by aboveground biomass of oat (Avena sativa L.). Although the element contents in dust samples exceeded significantly total element contents in soil, the element content in plants was not affected by single-rate soil amendment with rural dust sample. Soil sorption capacity and neutral pH of the experimental soil (7.0) was sufficient for immobilization of the elements. However, potentially mobilizable portions (0.005 mol/l DTPA extractable) of elements significantly increased (Cd by 116%, Pb by 39%, Zn by 50%) in the treated soil, which suggests a possible release of these elements in long-term horizon. On the contrary, high percentages of potentially toxic elements (Cd, Zn, Ni) in the most mobile (exchangeable) fractions were determined in the second part of investigation in two urban dust samples collected in Prague Letná automobile tunnel, and Prague subway station Museum. These results suggest possible direct impact of mobile, and thus potentially bio-available, element fractions on human environment. The results of both particular experiments cannot give complete information concerning behavior of harmful pollutants in airborne particulate matter and their influence on human health. They can however indicate two of possible ways of environmental pollution with this material. Yet, it would require a more detailed investigation in future.

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Takács, Anita, Katalin Kovács, Gábor Halász, Zoltán Győri, Ilona Fekete, György Heltai, and Márk Horváth. "Improvement of the sequential extraction procedure based on supercritical CO2 and subcritical H2O solvents for the estimation of the environmentally mobile potentially toxic element fractions of sediments and soils." Agrokémia és Talajtan 67, no. 1 (June 2018): 35–48. http://dx.doi.org/10.1556/0088.2018.67.1.3.

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The estimation of environmental risk caused by pollution with potentially toxic elements (PTE) is usually carried out using the (3+1) step sequential extraction procedure suggested in 1993 by the Community Bureau of Reference (BCR). In the 1st step the water-soluble, exchangeable and carbonate-bound element content is extracted with acetic acid. In 2002 a fractionation procedure based on the application of supercritical CO2, subcritical H2O and of a mixture of subcritical H2O/CO2 was proposed, which allowed the water-soluble and carbonatebound element contents to be extracted separately from sediment or soil samples weighed into the preparative column of a supercritical fluid extractor and diluted with quartz sand in a mass ratio of 1:20. The aim of the present study was to develop a new reduced-size column construction with which this dilution rate could be decreased to 1:2. A kinetic study was performed to determine the extraction time necessary for samples with different carbonate contents and the extracted element contents were compared to the results of the BCR sequential procedure on the same samples. It was established that fractionation using the reduced-size column may be a rapid way to obtain more reliable information on the easily mobilizable (watersoluble and carbonate-bound) PTE content of soils and sediments than was previously available to supplement BCR fractionation.

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Creuzburg, Kristina, Bernd Köhler, Helena Hempel, Peter Schreier, Enno Jacobs, and Herbert Schmidt. "Genetic structure and chromosomal integration site of the cryptic prophage CP-1639 encoding Shiga toxin 1." Microbiology 151, no. 3 (March 1, 2005): 941–50. http://dx.doi.org/10.1099/mic.0.27632-0.

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The sequence of 50 625 bp of chromosomal DNA derived from Shiga-toxin (Stx)-producing Escherichia coli (STEC) O111 : H− strain 1639/77 was determined. This DNA fragment contains the cryptic Stx1-encoding prophage CP-1639 and its flanking chromosomal regions. The genome of CP-1639 basically resembles that of lambdoid phages in structure, but contains three IS629 elements, one of which disrupts the gene of a tail fibre component. The prophage genome lacks parts of the recombination region including integrase and excisionase genes. Moreover, a capsid protein gene is absent. CP-1639 is closely associated with an integrase gene of an ancient integrative element. This element consists of three ORFs of unknown origin and a truncated integrase gene homologous to intA of CP4-57. By PCR analysis and sequencing, it was shown that this integrative element is present in a number of non-O157 STEC serotypes and in non-STEC strains, where it is located at the 3′-end of the chromosomal ssrA gene. Whereas in most E. coli O111 : H− strains, prophages are inserted in this site, E. coli O26 strains contain the integrative element not connected to a prophage. In E. coli O103 strains, the genetic structure of this region is variable. Comparison of DNA sequences of this particular site in E. coli O157 : H7 strain EDL933, E. coli O111 : H− strain 1639/77 and E. coli K-12 strain MG1655 showed that the ssrA gene is associated in all cases with the presence of foreign DNA. The results of this study have shown that the cryptic prophage CP-1639 is associated with an integrative element at a particular site in the E. coli chromosome that possesses high genetic variability.

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Lyras, Dena, Vicki Adams, Susan A. Ballard, Wee L. Teng, Pauline M. Howarth, Paul K. Crellin, Trudi L. Bannam, J. Glenn Songer, and Julian I. Rood. "tISCpe8, an IS1595-Family Lincomycin Resistance Element Located on a Conjugative Plasmid in Clostridium perfringens." Journal of Bacteriology 191, no. 20 (August 14, 2009): 6345–51. http://dx.doi.org/10.1128/jb.00668-09.

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ABSTRACT Clostridium perfringens is a normal gastrointestinal organism that is a reservoir for antibiotic resistance genes and can potentially act as a source from which mobile elements and their associated resistance determinants can be transferred to other bacterial pathogens. Lincomycin resistance in C. perfringens is common and is usually encoded by erm genes that confer macrolide-lincosamide-streptogramin B resistance. In this study we identified strains that are lincomycin resistant but erythromycin sensitive and showed that the lincomycin resistance determinant was plasmid borne and could be transferred to other C. perfringens isolates by conjugation. The plasmid, pJIR2774, is the first conjugative C. perfringens R-plasmid to be identified that does not confer tetracycline resistance. Further analysis showed that resistance was encoded by the lnuP gene, which encoded a putative lincosamide nucleotidyltransferase and was located on tISCpe8, a functional transposable genetic element that was a member of the IS1595 family of transposon-like insertion sequences. This element had significant similarity to the mobilizable lincomycin resistance element tISSag10 from Streptococcus agalactiae. Like tISSag10, tISCpe8 carries a functional origin of transfer within the resistance gene, allowing the element to be mobilized by the conjugative transposon Tn916. The similarity of these elements and the finding that they both contain an oriT-like region support the hypothesis that conjugation may result in the movement of DNA modules that are not obviously mobile since they are not linked to conjugation or mobilization functions. This process likely plays a significant role in bacterial adaptation and evolution.

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Collart, M. A., N. Tourkine, D. Belin, P. Vassalli, P. Jeanteur, and J. M. Blanchard. "c-fos gene transcription in murine macrophages is modulated by a calcium-dependent block to elongation in intron 1." Molecular and Cellular Biology 11, no. 5 (May 1991): 2826–31. http://dx.doi.org/10.1128/mcb.11.5.2826-2831.1991.

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Cultured mouse thioglycolate-elicited peritoneal macrophages exhibit a strong block to transcriptional elongation beyond the end of the c-fos gene first exon. This block is absent in freshly isolated peritoneal cells, appears slowly during culture, and does not require adherence of the cells. The extent of this block is largely responsible for the levels of c-fos mRNA in cultured macrophages, even after modulation by agents such as the tumor promoter phorbol myristate acetate and increased intracellular cyclic AMP, which also increase the activity of the c-fos promoter. When macrophages are cultured in the absence of mobilizable calcium, the block can no longer be relieved by any inducing agent. Conversely, upon calcium influxes, there is little alteration in the level of transcriptional initiation, but transcription proceeds efficiently through the entire c-fos locus. These results suggest the presence of an intragenic calcium-responsive element in the c-fos gene and illustrate its key role in the control of c-fos gene transcription.

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49

Collart, M. A., N. Tourkine, D. Belin, P. Vassalli, P. Jeanteur, and J. M. Blanchard. "c-fos gene transcription in murine macrophages is modulated by a calcium-dependent block to elongation in intron 1." Molecular and Cellular Biology 11, no. 5 (May 1991): 2826–31. http://dx.doi.org/10.1128/mcb.11.5.2826.

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Cultured mouse thioglycolate-elicited peritoneal macrophages exhibit a strong block to transcriptional elongation beyond the end of the c-fos gene first exon. This block is absent in freshly isolated peritoneal cells, appears slowly during culture, and does not require adherence of the cells. The extent of this block is largely responsible for the levels of c-fos mRNA in cultured macrophages, even after modulation by agents such as the tumor promoter phorbol myristate acetate and increased intracellular cyclic AMP, which also increase the activity of the c-fos promoter. When macrophages are cultured in the absence of mobilizable calcium, the block can no longer be relieved by any inducing agent. Conversely, upon calcium influxes, there is little alteration in the level of transcriptional initiation, but transcription proceeds efficiently through the entire c-fos locus. These results suggest the presence of an intragenic calcium-responsive element in the c-fos gene and illustrate its key role in the control of c-fos gene transcription.

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50

Carraro, Nicolas, Virginie Libante, Catherine Morel, Florence Charron-Bourgoin, Pierre Leblond, and Gérard Guédon. "Plasmid-like replication of a minimal streptococcal integrative and conjugative element." Microbiology 162, no. 4 (April 1, 2016): 622–32. http://dx.doi.org/10.1099/mic.0.000219.

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Journal articles on the topic 'Integrative and mobilizable element'

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