Mobile Genetic Elements in the Human MGMT Gene and their Regulatory Potential

2021 ◽  
pp. 140-153
Author(s):  
O. V. Pidpala ◽  
L. L. Lukash
Keyword(s):  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Mgmt Gene ◽  
Regulatory Potential

scholarly journals In silico analysis of MGMT gene orthologous in the most ancient mammals Strepsirrhini

2020 ◽  
Vol 26 ◽  
pp. 305-310
Author(s):  
O. V. Pidpala ◽  
L. L. Lukash
Keyword(s):  
Gene Evolution ◽  
In Silico Analysis ◽  
Mobile Genetic Elements ◽  
Endogenous Retrovirus ◽  
Coding Region ◽  
Structural Units ◽  
Genetic Elements ◽  
Mgmt Gene ◽  
Evolutionary Changes ◽  
Silico Analysis

Aim. To analyze the evolution of the MGMT gene with using the example of primitive primates with an emphasis on the participation of mobile genetic elements (MGE) in this process. Methods. The homology between nucleotide sequences was determined by BLAST 2.6.1. The results of the search and identification of MGE were performed using the CENSOR program. Results. It was shown on the the example of variable exons, that non-coding sequences can play a coding role at various stages of gene evolution. In the case of the P.coquereli MGMT gene, it was found that exon sequences could be a source of an additional microintron. Based on a comparison of the sequences of Strepsirrhini primates and H.sapience, it can be assumed that fragmented sequences of the endogenous retrovirus HERV-Fc1 could participate in the formation of the coding region of human exon 5 and 3’UTR. Conclusions. The evolutionary changes in the MGMT gene occur at the level of various structural units (exons and introns), and the MGE can be not only components of introns, but also components of exons in the form of fragmented sequences which could not be identified as mobile genetic elements. Keywords: Strepsirrhini, MGMT gene, MGE, HERV-Fc1.

scholarly journals Species-specific mobile genetic elements in the gene of repair enzyme MGMT in new world monkeys

2021 ◽  
Vol 28 ◽  
pp. 128-134
Author(s):  
O. V. Pidpala ◽  
L. L. Lukash
Keyword(s):  
New World ◽  
Mobile Genetic Elements ◽  
Nucleotide Sequences ◽  
New World Monkeys ◽  
Repair Enzyme ◽  
Genetic Elements ◽  
Mgmt Gene ◽  
Evolutionary Changes ◽  
Species Specific ◽  
Human Specific

Aim.To analyze the distribution of species-specific mobile genetic elements (MGE) in orthologs of the MGMT gene in Platyrrhina. Methods. The homology between nucleotide sequences was determined by BLAST 2.6.1. The results of the search and identification of MGE were performed  using  the  CENSOR program. Results. On the example of orthologs of the MGMT gene in New World monkeys, it has been shown that different species-specific MGE identified in their intron sequences may have different evolutionary chronologies. In the case of the element Alu2_TS, which originated in the Tarsiiformes representative, it was found that in evolutionarily close primates it undergoes deletion degradation, while fragments of the human-specific L1Hs element are found in the genomes of evolutionarily distant primates long before the formation and emergence of this retroelement. Conclusions. The chronology of  evolutionary changes in the gene MGMT and its species-specific MGE can be of different nature and occur in parallele and independently. Keywords: Platyrrhina, MGMT gene, MGE, Alu2_TS, L1Hs.

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.

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