scholarly journals The analisis of human MGMT gene orthologous in protests

2018 ◽  
Vol 22 ◽  
pp. 345-351
Author(s):  
O. V. Pidpala ◽  
L. L. Lukash
Keyword(s):  
Dna Methyltransferase ◽  
Gene Evolution ◽  
Intron Loss ◽  
Group Ii Introns ◽  
Orthologous Genes ◽  
Spliceosomal Introns ◽  
Mgmt Gene ◽  
Group Ii ◽  
Eukaryotic Organisms ◽  
Social Amoebae

Aim. The intron sequences of orthologous О6-methylguanin-DNA methyltransferase (MGMT) genes in Protists on the early stages of their formation in eukaryotic organisms have been analysed. Methods. Homologous regions have been defined by the program BLASTN 2.6.1. Nucleotide sequences of the bacterial and mitochondrial group II introns have been taken from Database for Bacterial Group II Introns. Searching and identifying the MGEs have been realized by using CENSOR. Results. It has been shown that the evolution of the gene does not always coincide with the evolution of the organism. This is shown on the example of intron loss and gain in social amoebae Dictyostelium. Also it has been found the fragmentary nature of homology between various introns and exons of the orthologous genes. Conclusions. The obtained results allow offer a suggestion about the endogenous mosaic character of the evolutional formation of the gene structural units. Keywords: О6-methylguanin-DNA methyltransferase (MGMT) gene orthologous, Protists, gene evolution, spliceosomal introns, intron loss and gain.

Intron Biology, Focusing on Group II Introns, the Ancestors of Spliceosomal Introns

2015 ◽  
pp. 195-219
Author(s):  
María Dolores Molina-Sánchez ◽  
Rafael Nisa-Martínez ◽  
Fernando M. García-Rodríguez ◽  
Francisco Martínez-Abarca ◽  
Nicolás Toro
Keyword(s):  
Group Ii Introns ◽  
Spliceosomal Introns ◽  
Group Ii

scholarly journals Recent mobility of plastid encoded group II introns and twintrons in five strains of the unicellular red alga Porphyridium

2014 ◽  
Author(s):  
Marie-Mathilde Perrineau ◽  
Dana C Price ◽  
Georg Mohr ◽  
Debashish Bhattacharya
Keyword(s):  
Mobile Element ◽  
Red Alga ◽  
Group Ii Introns ◽  
Porphyridium Purpureum ◽  
Spliceosomal Introns ◽  
Plastid Genomes ◽  
Endonuclease Domain ◽  
Eukaryote Evolution ◽  
Group Ii ◽  
First Time

Group II introns are closely linked to eukaryote evolution because nuclear spliceosomal introns and the small RNAs associated with the spliceosome are thought to trace their ancient origins to these mobile elements. Therefore, elucidating how group II introns move, and how they lose mobility can potentially shed light on fundamental aspects of eukaryote biology. To this end, we studied five strains of the unicellular red alga Porphyridium purpureum that surprisingly contain 42 group II introns in their plastid genomes. We focused on a subset of these introns that encode mobility-conferring intron-encoded proteins (IEPs) and found them to be distributed among the strains in a lineage-specific manner. The reverse transcriptase and maturase domains were present in all lineages but the DNA endonuclease domain was deleted in vertically inherited introns, demonstrating a key step in the loss of mobility. P. purpureum plastid intron RNAs had a classic group IIB secondary structure despite variability in the DIII and DVI domains. We report for the first time the presence of twintrons (introns-within-introns, derived from the same mobile element) in Rhodophyta. The P. purpureum IEPs and their mobile introns provide a valuable model for the study of mobile retroelements in eukaryotes and offer promise for biotechnological applications.

scholarly journals Group II Introns Generate Functional Chimeric Relaxase Enzymes with Modified Specificities through Exon Shuffling at Both the RNA and DNA Level

2020 ◽  
Author(s):  
Félix LaRoche-Johnston ◽  
Rafia Bosan ◽  
Benoit Cousineau
Keyword(s):  
Genetic Diversity ◽  
Insertion Site ◽  
Long Terminal Repeat Retrotransposons ◽  
Group Ii Introns ◽  
Gain Of Function ◽  
Intron Insertion ◽  
Spliceosomal Introns ◽  
Biologically Relevant ◽  
Trans Splicing ◽  
Group Ii

Abstract Group II introns are large self-splicing RNA enzymes with a broad but somewhat irregular phylogenetic distribution. These ancient retromobile elements are the proposed ancestors of approximately half the human genome, including the abundant spliceosomal introns and non-long terminal repeat retrotransposons. In contrast to their eukaryotic derivatives, bacterial group II introns have largely been considered as harmful selfish mobile retroelements that parasitize the genome of their host. As a challenge to this view, we recently uncovered a new intergenic trans-splicing pathway that generates an assortment of mRNA chimeras. The ability of group II introns to combine disparate mRNA fragments was proposed to increase the genetic diversity of the bacterial host by shuffling coding sequences. Here, we show that the Ll.LtrB and Ef.PcfG group II introns from Lactococcus lactis and Enterococcus faecalis respectively can both use the intergenic trans-splicing pathway to catalyze the formation of chimeric relaxase mRNAs and functional proteins. We demonstrated that some of these compound relaxase enzymes yield gain-of-function phenotypes, being significantly more efficient than their precursor wild-type enzymes at supporting bacterial conjugation. We also found that relaxase enzymes with shuffled functional domains are produced in biologically relevant settings under natural expression levels. Finally, we uncovered examples of lactococcal chimeric relaxase genes with junctions exactly at the intron insertion site. Overall, our work demonstrates that the genetic diversity generated by group II introns, at the RNA level by intergenic trans-splicing and at the DNA level by recombination, can yield new functional enzymes with shuffled exons, which can lead to gain-of-function phenotypes.

scholarly journals Group II intron inhibits conjugative relaxase expression in bacteria by mRNA targeting

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Guosheng Qu ◽  
Carol Lyn Piazza ◽  
Dorie Smith ◽  
Marlene Belfort
Keyword(s):  
Gene Expression ◽  
Mrna Level ◽  
Mobile Element ◽  
Housekeeping Genes ◽  
Group Ii Intron ◽  
Conjugative Plasmid ◽  
Group Ii Introns ◽  
Potential Force ◽  
Spliceosomal Introns ◽  
Group Ii

Group II introns are mobile ribozymes that are rare in bacterial genomes, often cohabiting with various mobile elements, and seldom interrupting housekeeping genes. What accounts for this distribution has not been well understood. Here, we demonstrate that Ll.LtrB, the group II intron residing in a relaxase gene on a conjugative plasmid from Lactococcus lactis, inhibits its host gene expression and restrains the naturally cohabiting mobile element from conjugative horizontal transfer. We show that reduction in gene expression is mainly at the mRNA level, and results from the interaction between exon-binding sequences (EBSs) in the intron and intron-binding sequences (IBSs) in the mRNA. The spliced intron targets the relaxase mRNA and reopens ligated exons, causing major mRNA loss. Taken together, this study provides an explanation for the distribution and paucity of group II introns in bacteria, and suggests a potential force for those introns to evolve into spliceosomal introns.

scholarly journals Recombinational origin of the nuclear introns

1970 ◽  
pp. 329-334
Author(s):  
O. V. Pidpala ◽  
L. L. Lukash
Keyword(s):  
Dna Methyltransferase ◽  
Mobile Genetic Elements ◽  
Spliceosomal Introns ◽  
Genetic Elements ◽  
C Elegans ◽  
Nuclear Introns ◽  
Early Stages ◽  
Eukaryotic Organisms ◽  
Agt Gene

Aim. It has been analyzed the intron sequences homologs O6-methylguanin-DNA methyltransferase (MGMT, AGT) genes on the early stages of their formation in eukaryotic organisms. Methods. Homologous regions have been defined by the program BLASTN 2.6.1. Searching and identifying of the MGEs have been realized by using CENSOR. Results. It has been found that same homologous fragments without introns genes MGT1 S. cerevisiae and agt D. melanogaster may be take part in the formation of different structure part of the agt-1 C. elegans gene. Also it has been found the fragments of homology between various introns and exons of the agt-1 C. elegans and mgmt D. rerio genes. Conclusions. The obtained results allow suggested about recombinogenic nature of the formation of spliceosomal introns. Keywords: O6-methylguanin-DNA methyltransferase (MGMT or AGT) gene homologs, spliceosomal introns, origin of introns, mobile genetic elements (MGEs), recombinogenesis.

scholarly journals Recent mobility of plastid encoded group II introns and twintrons in five strains of the unicellular red alga Porphyridium

2014 ◽  
Author(s):  
Marie-Mathilde Perrineau ◽  
Dana C Price ◽  
Georg Mohr ◽  
Debashish Bhattacharya
Keyword(s):  
Mobile Element ◽  
Red Alga ◽  
Group Ii Introns ◽  
Porphyridium Purpureum ◽  
Spliceosomal Introns ◽  
Plastid Genomes ◽  
Endonuclease Domain ◽  
Eukaryote Evolution ◽  
Group Ii ◽  
First Time

Group II introns are closely linked to eukaryote evolution because nuclear spliceosomal introns and the small RNAs associated with the spliceosome are thought to trace their ancient origins to these mobile elements. Therefore, elucidating how group II introns move, and how they lose mobility can potentially shed light on fundamental aspects of eukaryote biology. To this end, we studied five strains of the unicellular red alga Porphyridium purpureum that surprisingly contain 42 group II introns in their plastid genomes. We focused on a subset of these introns that encode mobility-conferring intron-encoded proteins (IEPs) and found them to be distributed among the strains in a lineage-specific manner. The reverse transcriptase and maturase domains were present in all lineages but the DNA endonuclease domain was deleted in vertically inherited introns, demonstrating a key step in the loss of mobility. P. purpureum plastid intron RNAs had a classic group IIB secondary structure despite variability in the DIII and DVI domains. We report for the first time the presence of twintrons (introns-within-introns, derived from the same mobile element) in Rhodophyta. The P. purpureum IEPs and their mobile introns provide a valuable model for the study of mobile retroelements in eukaryotes and offer promise for biotechnological applications.

scholarly journals Organellar Introns in Fungi, Algae, and Plants

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 2001
Author(s):  
Jigeesha Mukhopadhyay ◽  
Georg Hausner
Keyword(s):  
Gene Expression ◽  
Ribosomal Proteins ◽  
Heterologous Gene Expression ◽  
Group I Introns ◽  
Group Ii Introns ◽  
Homing Endonucleases ◽  
Organellar Genomes ◽  
Chloroplast Genomes ◽  
Group I ◽  
Group Ii

Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.

scholarly journals Transcriptional Pausing and Activation at Exons-1 and -2, Respectively, Mediate the MGMT Gene Expression in Human Glioblastoma Cells

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 888
Author(s):  
Mohammed A. Ibrahim Al-Obaide ◽  
Kalkunte S. Srivenugopal
Keyword(s):  
Dna Methyltransferase ◽  
Glioblastoma Cells ◽  
Rt Pcr ◽  
Repair Gene ◽  
Exon 2 ◽  
Mgmt Gene ◽  
Dna Repair Gene ◽  
Exon 1 ◽  
Transcriptional Pausing ◽  
Transcription Assays

Background: The therapeutically important DNA repair gene O6-methylguanine DNA methyltransferase (MGMT) is silenced by promoter methylation in human brain cancers. The co-players/regulators associated with this process and the subsequent progression of MGMT gene transcription beyond the non-coding exon 1 are unknown. As a follow-up to our recent finding of a predicted second promoter mapped proximal to the exon 2 [Int. J. Mol. Sci.2021, 22(5), 2492], we addressed its significance in MGMT transcription. Methods: RT-PCR, RT q-PCR, and nuclear run-on transcription assays were performed to compare and contrast the transcription rates of exon 1 and exon 2 of the MGMT gene in glioblastoma cells. Results: Bioinformatic characterization of the predicted MGMT exon 2 promoter showed several consensus TATA box and INR motifs and the absence of CpG islands in contrast to the established TATA-less, CpG-rich, and GAF-bindable exon 1 promoter. RT-PCR showed very weak MGMT-E1 expression in MGMT-proficient SF188 and T98G GBM cells, compared to active transcription of MGMT-E2. In the MGMT-deficient SNB-19 cells, the expression of both exons remained weak. The RT q-PCR revealed that MGMT-E2 and MGMT-E5 expression was about 80- to 175-fold higher than that of E1 in SF188 and T98G cells. Nuclear run-on transcription assays using bromo-uridine immunocapture followed by RT q-PCR confirmed the exceptionally lower and higher transcription rates for MGMT-E1 and MGMT-E2, respectively. Conclusions: The results provide the first evidence for transcriptional pausing at the promoter 1- and non-coding exon 1 junction of the human MGMT gene and its activation/elongation through the protein-coding exons 2 through 5, possibly mediated by a second promoter. The findings offer novel insight into the regulation of MGMT transcription in glioma and other cancer types.

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