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

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.

2019 ◽  
Vol 24 ◽  
pp. 338-344
Author(s):  
O. V. Pidpala ◽  
L. L. Lukash

Aim. Analyze the formation of a human-specific L1Hs element in the intron 3 of the MGMT gene on an example of a hominid.  Methods. The results of the search and identification of mobile genetic elements were performed using the CENSOR program. The homology between nucleotide sequences was determined by BLAST 2.6.1. Results. The components of the cluster, where the L1Hs element in the human being was formed, are fragments of the L1PA6 element, which are common in the monkeys of the Old and New World. In the gibbon, among the L1 element groups, there are representatives of older subfamilies (L1PB, L1MC, L1MD and L1ME), and the partial homology to the L1Hs of the element is predominantly of elements of groups that have arisen in the mammalian genomes. Conclusions. Formation of a human-specific L1Hs element occurred during the evolution of Hominoidea in parallel with the formation of the cluster structure of MGE in humans from different subfamilies of LINE1-elements whose component components, obviously, also involved in the formation of the L1Hs element. Keywords: Hominoidea, MGMT gene, intron 3, human-specific L1Hs element.


2020 ◽  
Vol 26 ◽  
pp. 305-310
Author(s):  
O. V. Pidpala ◽  
L. L. Lukash

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.


2021 ◽  
Author(s):  
Preeti P ◽  
Tapan Kumar Baral ◽  
Kamal Rawal

Mobile genetic elements (MGEs) represent a large portion of the human genome. Its ability tochange their position within the genome has contributed to evolution, however, the same has alsoresulted in several mutations. Many of such mutations are known to cause exon skipping orpremature truncation that result in non-functional or dysfunctional protein, leading to cancer. Here,in this study we aim to determine the distribution of MGEs in cancer-associated genes as comparedto non-cancer associated genes. We curated a list of genes for both the categories and downloadedthe nucleotide sequences of these genes and ran on RepeatMasker to identify the MGEs in eachgene. All the data generated with respect to each gene was parsed and compared. The resultsshowed that the number and the sequence length covered by the identified MGEs in cancer-associated genes were comparatively high. The abundance of MGEs may be correlated with thehigh risk of deletion/insertion of large DNA segments in these genes, that results in higher risk ofcancer. Further studies need to be performed for better clarity on these associations.


2022 ◽  
Author(s):  
João Botelho ◽  
Adrian Cazares ◽  
Hinrich Schulenburg

Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to the spread of virulence and antibiotic resistance genes in human pathogens, including the particularly problematic group of ESKAPE pathogens, such as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp. Here, we performed the first systematic analysis of MGEs, including plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs), in the ESKAPE pathogens. We characterized over 1700 complete ESKAPE genomes and found that different MGE types are asymmetrically distributed across these pathogens. While some MGEs are capable of exchanging DNA beyond the genus (and phylum) barrier, horizontal gene transfer (HGT) is mainly restricted by phylum or genus. We further observed that most genes on MGEs have unknown functions and show intricate distribution patterns. Moreover, AMR genes and anti-CRISPRs are overrepresented in the ESKAPE mobilome. Our results also underscored species-specific trends shaping the number of MGEs, AMR, and virulence genes across pairs of conspecific ESKAPE genomes with and without CRISPR-Cas systems. Finally, we found that CRISPR targets vary according to MGE type: while plasmid CRISPRs almost exclusively target other plasmids, ICEs/IME CRISPRs preferentially target ICEs/IMEs and prophages. Overall, our study highlights the general importance of the ESKAPE mobilome in contributing to the spread of AMR and mediating conflict among MGEs.


PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241487
Author(s):  
Délia Cristina Figueira Aguiar ◽  
Washington Luiz Assunção Pereira ◽  
Gyselly de Cássia Bastos de Matos ◽  
Klena Sarges Marruaz da Silva ◽  
Rosane do Socorro Pompeu de Loiola ◽  
...  

ABH antigens are histo-antigens, but were first described on the surface of human erythrocytes. They are found in those cells only in great apes and humans, while in more primitive animals they are found in tissues and body fluids. ABH antigens are mainly distributed in tissues that are in contact with the external environment and may serve as ligands for pathogens in tissues or block their connection. Description of the distribution of these molecules in non-human primate tissues is restricted to a few tissues and species. This paper describes the expression of human A, B and H type antigens in different organs from four species of New World Primates, obtained from the Centro Nacional de Primatas, as well as comparing that expression with what has been described for humans. In this study, although the tissue description of the antigens is similar to the genetic model for humans, some differences in expression between some organs from those species and those of humans were found. The differences occurred mainly in endodermal organs that have secretory functions and are probably under the control of the human-type FUT-2 enzyme. In the mesodermal-origin organs there was a reduction or absence of A and B antigen marking, particularly in the H precursor substance, indicating that those organs are under the control of the human-type FUT-1 enzyme. These findings have demonstrated that there is similar ABH antigen reactivity in tissue distribution between the species, although there are some species-specific cases.


2021 ◽  
Author(s):  
Anna Cusco ◽  
Daniel Perez ◽  
Joaquim Vines ◽  
Norma Fabregas ◽  
Olga Francino

Long-read metagenomics facilitates the assembly of high-quality metagenome-assembled genomes (HQ MAGs) out of complex microbiomes. It provides highly contiguous assemblies by spanning repetitive regions, complete ribosomal genes, and mobile genetic elements. Hi-C proximity ligation data bins the long contigs and their associated extra-chromosomal elements to their bacterial host. Here, we characterized a canine fecal sample combining a long-read metagenomics assembly with Hi-C data, and further correcting frameshift errors. We retrieved 27 HQ MAGs and seven medium-quality (MQ) MAGs considering MIMAG criteria. All the long-read canine MAGs improved previous short-read MAGs from public datasets regarding contiguity of the assembly, presence, and completeness of the ribosomal operons, and presence of canonical tRNAs. This trend was also observed when comparing to representative genomes from a pure culture (short-read assemblies). Moreover, Hi-C data linked six potential plasmids to their bacterial hosts. Finally, we identified 51 bacteriophages integrated into their bacterial host, providing novel host information for eight viral clusters that included Gut Phage Database viral genomes. Even though three viral clusters were species-specific, most of them presented a broader host range. In conclusion, long-read metagenomics retrieved long contigs harboring complete assembled ribosomal operons, prophages, and other mobile genetic elements. Hi-C binned together the long contigs into HQ and MQ MAGs, some of them representing closely related species. Long-read metagenomics and Hi-C proximity ligation are likely to become a comprehensive approach to HQ MAGs discovery and assignment of extra-chromosomal elements to their bacterial host.


Mobile DNA ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Birgit Henrich ◽  
Stephanie Hammerlage ◽  
Sebastian Scharf ◽  
Diana Haberhausen ◽  
Ursula Fürnkranz ◽  
...  

Abstract Background Mobile genetic elements are found in genomes throughout the microbial world, mediating genome plasticity and important prokaryotic phenotypes. Even the cell wall-less mycoplasmas, which are known to harbour a minimal set of genes, seem to accumulate mobile genetic elements. In Mycoplasma hominis, a facultative pathogen of the human urogenital tract and an inherently very heterogeneous species, four different MGE-classes had been detected until now: insertion sequence ISMhom-1, prophage MHoV-1, a tetracycline resistance mediating transposon, and ICEHo, a species-specific variant of a mycoplasma integrative and conjugative element encoding a T4SS secretion system (termed MICE). Results To characterize the prevalence of these MGEs, genomes of 23 M. hominis isolates were assembled using whole genome sequencing and bioinformatically analysed for the presence of mobile genetic elements. In addition to the previously described MGEs, a new ICEHo variant was found, which we designate ICEHo-II. Of 15 ICEHo-II genes, five are common MICE genes; eight are unique to ICEHo-II; and two represent a duplication of a gene also present in ICEHo-I. In 150 M. hominis isolates and based on a screening PCR, prevalence of ICEHo-I was 40.7%; of ICEHo-II, 28.7%; and of both elements, 15.3%. Activity of ICEHo-I and -II was demonstrated by detection of circularized extrachromosomal forms of the elements through PCR and subsequent Sanger sequencing. Conclusions Nanopore sequencing enabled the identification of mobile genetic elements and of ICEHo-II, a novel MICE element of M. hominis, whose phenotypic impact and potential impact on pathogenicity can now be elucidated.


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