Shaping the genome – restriction–modification systems as mobile genetic elements

1999 ◽  
Vol 9 (6) ◽  
pp. 649-656 ◽  
Author(s):  
Ichizo Kobayashi ◽  
Ayaka Nobusato ◽  
Noriko Kobayashi-Takahashi ◽  
Ikuo Uchiyama
Keyword(s):  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Restriction Modification ◽  
Restriction Modification Systems

scholarly journals Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer

2017 ◽  
Vol 83 (13) ◽  
Author(s):  
Narimane Dahmane ◽  
Virginie Libante ◽  
Florence Charron-Bourgoin ◽  
Eric Guédon ◽  
Gérard Guédon ◽  
...  
Keyword(s):  
Sequence Divergence ◽  
Mobile Genetic Elements ◽  
Selective Advantage ◽  
Streptococcus Salivarius ◽  
Cadmium Resistance ◽  
Content Type ◽  
Genetic Elements ◽  
Integrative And Conjugative Elements ◽  
Restriction Modification ◽  
Restriction Modification Systems

ABSTRACT Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole-genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3′ end of the fda, rpsI, or rpmG gene) with the conjugation module of the ICESt3 subfamily. Sequence analyses also pointed out a recombination occurring at oriT (likely mediated by the relaxase) as a mechanism of ICE evolution. Despite a similar organization in two operons including three conserved genes, the regulation modules show a high diversity (about 50% amino acid sequence divergence for the encoded regulators and presence of unrelated additional genes) with a probable impact on the regulation of ICE activity. Concerning the accessory genes, ICEs of the ICESt3 subfamily appear particularly rich in restriction-modification systems and orphan methyltransferase genes. Other cargo genes that could confer a selective advantage to the cell hosting the ICE were identified, in particular, genes for bacteriocin synthesis and cadmium resistance. The functionality of 2 ICEs of S. salivarius was investigated. Autonomous conjugative transfer to other S. salivarius strains, to S. thermophilus, and to Enterococcus faecalis was observed. The analysis of the ICE-fda border sequence in these transconjugants allowed the localization of the DNA cutting site of the ICE integrase. IMPORTANCE The ICESt3 subfamily of ICEs appears to be widespread in streptococci and targets diverse chromosomal integration sites. These ICEs carry diverse cargo genes that can confer a selective advantage to the host strain. The maintenance of these mobile genetic elements likely relies in part on self-encoded restriction-modification systems. In this study, intra- and interspecies transfer was demonstrated for 2 ICEs of S. salivarius. Closely related ICEs were also detected in silico in other Streptococcus species (S. pneumoniae and S. parasanguinis), thus indicating that diffusion of ICESt3-related elements probably plays a significant role in horizontal gene transfer (HGT) occurring in the oral cavity but also in the digestive tract, where S. salivarius is present.

scholarly journals Giant Viruses and their mobile genetic elements: the molecular symbiotic hypothesis

2018 ◽  
Author(s):  
Jonathan Filée
Keyword(s):  
Mobile Genetic Elements ◽  
List Type ◽  
Symbiotic Association ◽  
Protective Effects ◽  
Ratchet Effect ◽  
Genetic Elements ◽  
Mutualistic Symbiosis ◽  
Virus World ◽  
Giant Viruses ◽  
Restriction Modification

SummaryAmong the virus world, Giant viruses (GVs) compose one of the most successful eukaryovirus families. In contrast with other eukaryoviruses, GV genomes encode a wide array of mobile genetic elements (MGEs) that encompass diverse, mostly prokaryotic-like, transposable element families, introns, inteins, restriction-modification systems and enigmatic classes of mobile elements having little similarities with known families. Interestingly, several of these MGEs may be beneficial to the GVs, fulfilling two kinds of functions: 1) degrading host or competing virus/ virophages DNA and 2) promoting viral genome integration, dissemination and excision into the host genomes.By providing fitness advantages to the virus in which they reside, these MGES compose a kind of molecular symbiotic association in which both partners should be regarded as grantees. Thus, protective effects provided by some of these MGEs may have generated an arms race between competing GVs in order to encode the most diverse arsenal of anti-viral weapons, explaining the unusual abundance of MGEs in GV genomes by a kind of ratchet effect.Highlight-Giant Virus (GV) genomes are loaded with diverse classes of mobile genetic elements (MGEs)-MGEs cooperate with GV genes in order to fulfill viral functions.-Site-specific endonucleases encoded by MGEs are used as anti-host or anti-competing viral compounds-Integrase/transposase genes derived from MGEs have been recruited to generate integrative proviral forms.-MGEs and GVs may thus compose a mutualistic symbiosis

ISSR-PCR markers and mobile genetic elements in horse (Equus caballus) genome

2014 ◽  
pp. 42-57 ◽  
Author(s):  
N.V. Bardukov ◽  
◽  
A.V. Feofilov ◽  
T.T. Glazko ◽  
V.I. Glazko ◽  
...  
Keyword(s):  
Equus Caballus ◽  
Mobile Genetic Elements ◽  
Pcr Markers ◽  
Genetic Elements ◽  
Issr Pcr

scholarly journals Genomic evolution of antimicrobial resistance in Escherichia coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pimlapas Leekitcharoenphon ◽  
Markus Hans Kristofer Johansson ◽  
Patrick Munk ◽  
Burkhard Malorny ◽  
Magdalena Skarżyńska ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Mobile Genetic Elements ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Fecal Samples ◽  
E Coli ◽  
Genetic Elements

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

scholarly journals Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete genome sequencing

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuan Wu ◽  
Lin Yang ◽  
Wen-Ge Li ◽  
Wen Zhu Zhang ◽  
Zheng Jie Liu ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Resistance Genes ◽  
Point Mutations ◽  
Evolutionary Process ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Clostridioides Difficile ◽  
Hospitalized Elderly ◽  
Great Heterogeneity ◽  
High Level

Abstract Background Clade 5 Clostridioides difficile diverges significantly from the other clades and is therefore, attracting increasing attention due its great heterogeneity. In this study, we used third-generation sequencing techniques to sequence the complete whole genomes of three ST11 C. difficile isolates, RT078 and another two new ribotypes (RTs), obtained from three independent hospitalized elderly patients undergoing antibiotics treatment. Mobile genetic elements (MGEs), antibiotic-resistance, drug resistance genes, and virulent-related genes were analyzed and compared within these three isolates. Results Isolates 10,010 and 12,038 carried a distinct deletion in tcdA compared with isolate 21,062. Furthermore, all three isolates had identical deletions and point-mutations in tcdC, which was once thought to be a unique characteristic of RT078. Isolate 21,062 (RT078) had a unique plasmid, different numbers of transposons and genetic organization, and harboring special CRISPR spacers. All three isolates retained high-level sensitivity to 11 drugs and isolate 21,062 (RT078) carried distinct drug-resistance genes and loss of numerous flagellum-related genes. Conclusions We concluded that capillary electrophoresis based PCR-ribotyping is important for confirming RT078. Furthermore, RT078 isolates displayed specific MGEs, indicating an independent evolutionary process. In the further study, we could testify these findings with more RT078 isolates of divergent origins.

Sign in / Sign up

Export Citation Format

Share Document