Conservation and over-representation of G-quadruplex sequences in regulatory regions of mitochondrial DNA across distinct taxonomic sub-groups

Bohálová, Natália; Dobrovolná, Michaela; Brázda, Václav; Bidula, Stefan

doi:10.1016/j.biochi.2021.12.006

Cited by 10 publications

(10 citation statements)

References 31 publications

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“…Conversely, MPXV genomes were replete with IRs. This observation agrees with our previous analysis of mitochondrial genomes, whereby the number of IRs in the genome were inversely proportional to the number of G4‐forming sequences 17 . However, we believe the large number of long IR sequences occurring in the two genomes from Slovenia (ON609725 and ON631241) occurred as an artifact of the sequencing process.…”

Section: Discussionsupporting

confidence: 92%

“…This observation agrees with our previous analysis of mitochondrial genomes, whereby the number of IRs in the genome were inversely proportional to the number of G4‐forming sequences. 17 However, we believe the large number of long IR sequences occurring in the two genomes from Slovenia (ON609725 and ON631241) occurred as an artifact of the sequencing process. Both these genomes were sequenced simultaneously, came from two different lineages, and this observation was not made in other genomes from these lineages.…”

Section: Discussionmentioning

confidence: 95%

“…This observation agrees with our previous analysis of mitochondrial genomes, whereby the number of IRs in the genome were inversely proportional to the number of G4-forming sequences. 17 describing the activity of these other APOBEC3 members is currently lacking and further investigation is necessary. However, one could hypothesize that unlike APOBEC3G, F, and H, there will be other APOBEC family members with activity against MPXV.…”

Section: Discussionmentioning

confidence: 99%

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Inverted repeats in the monkeypox virus genome are hot spots for mutation

Dobrovolná

Brázda

Warner

et al. 2022

Journal of Medical Virology

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The current monkeypox virus (MPXV) strain differs from the strain arising in 2018 by 50+ single nucleotide polymorphisms (SNPs) and is mutating much faster than expected. The cytidine deaminase apolipoprotein B messenger RNA editing enzyme, catalytic subunit B (APOBEC3) was hypothesized to be driving this increased mutation. APOBEC has recently been identified to preferentially mutate cruciform DNA secondary structures formed by inverted repeats (IRs). IRs were recently identified as hot spots for mutation in severe acute respiratory syndrome coronavirus 2, and we aimed to identify whether IRs were also hot spots for mutation within MPXV genomes. We found that MPXV genomes were replete with IR sequences. Of the 50+ SNPs identified in the 2022 outbreak strain, 63.9% of these were found to have arisen within IR regions in the 2018 reference strain (MT903344.1). Notably, IR sequences found in the 2018 reference strain were significantly lost over time, with an average of 32.5% of these sequences being conserved in the 2022 MPXV genomes. This evidence was highly indicative that mutations were arising within IRs. This data provides further support to the hypothesis that APOBEC may be driving MPXV mutation and highlights the necessity for greater surveillance of IRs of MPXV genomes to detect new mutations.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

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Inverted repeats in the monkeypox virus genome are hot spots for mutation

Dobrovolná

Brázda

Warner

et al. 2022

Journal of Medical Virology

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“…This result indicates the importance of PQS in circular and especially mitochondrial genomes. While in algae and fungi the frequency of PQS in mtDNA is lower than in plants, including Arabidopsis thaliana , in vertebrates the frequency of PQS in mtDNA is even significantly higher [ 26 ]. Although such large-scale predictions are computationally extensive, it would be beneficial to also inspect other higher plants in the future to see if this trend (frequency of PQS in nuclear DNA < frequency of PQS in plastid DNA < frequency of PQS in mitochondrial DNA) is always the same.…”

Section: Discussionmentioning

confidence: 99%

Analysis of G-Quadruplex-Forming Sequences in Drought Stress-Responsive Genes, and Synthesis Genes of Phenolic Compounds in Arabidopsis thaliana

Pečínka

Bohálová

Volná

et al. 2023

Life

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Sequences of nucleic acids with the potential to form four-stranded G-quadruplex structures are intensively studied mainly in the context of human diseases, pathogens, or extremophile organisms; nonetheless, the knowledge about their occurrence and putative role in plants is still limited. This work is focused on G-quadruplex-forming sites in two gene sets of interest: drought stress-responsive genes, and genes related to the production/biosynthesis of phenolic compounds in the model plant organism Arabidopsis thaliana. In addition, 20 housekeeping genes were analyzed as well, where the constitutive gene expression was expected (with no need for precise regulation depending on internal or external factors). The results have shown that none of the tested gene sets differed significantly in the content of G-quadruplex-forming sites, however, the highest frequency of G-quadruplex-forming sites was found in the 5′-UTR regions of phenolic compounds’ biosynthesis genes, which indicates the possibility of their regulation at the mRNA level. In addition, mainly within the introns and 1000 bp flanks downstream gene regions, G-quadruplex-forming sites were highly underrepresented. Finally, cluster analysis allowed us to observe similarities between particular genes in terms of their PQS characteristics. We believe that the original approach used in this study may become useful for further and more comprehensive bioinformatic studies in the field of G-quadruplex genomics.

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“…PQSs also had different localizations in mtDNA compared to PQS localization in nuclear DNA; therefore, we suggest that G4-formation and regulatory pathways differ in circular and linear DNAs. Interestingly the comparison of mtDNA PQS frequencies among various species showed an increased PQS frequency for vertebrates as well as for land plants, contrary to a lower PQS frequency in the mtDNA of protists and fungi [ 38 ]. In animals, it has been shown that G4s play a direct role in mitochondrial genome replication, transcription processivity, and respiratory function [ 39 ].…”

Section: Discussionmentioning

confidence: 99%

The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences—Implications for Evolution and Biological Regulation

Dobrovolná

Bohálová

Peška

et al. 2022

IJMS

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G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional relevance in bacteria and animals, including humans, their importance has been recently demonstrated in evolutionarily distinct plant species. In this study, we analyzed the genome of Pisum sativum (garden pea, or the so-called green pea), a unique member of the Fabaceae family. Our results showed that this genome contained putative G4 sequences (PQSs). Interestingly, these PQSs were located nonrandomly in the nuclear genome. We also found PQSs in mitochondrial (mt) and chloroplast (cp) DNA, and we experimentally confirmed G4 formation for sequences found in these two organelles. The frequency of PQSs for nuclear DNA was 0.42 PQSs per thousand base pairs (kbp), in the same range as for cpDNA (0.53/kbp), but significantly lower than what was found for mitochondrial DNA (1.58/kbp). In the nuclear genome, PQSs were mainly associated with regulatory regions, including 5′UTRs, and upstream of the rRNA region. In contrast to genomic DNA, PQSs were located around RNA genes in cpDNA and mtDNA. Interestingly, PQSs were also associated with specific transposable elements such as TIR and LTR and around them, pointing to their role in their spreading in nuclear DNA. The nonrandom localization of PQSs uncovered their evolutionary and functional significance in the Pisum sativum genome.

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Conservation and over-representation of G-quadruplex sequences in regulatory regions of mitochondrial DNA across distinct taxonomic sub-groups

Cited by 10 publications

References 31 publications

Inverted repeats in the monkeypox virus genome are hot spots for mutation

Inverted repeats in the monkeypox virus genome are hot spots for mutation

Analysis of G-Quadruplex-Forming Sequences in Drought Stress-Responsive Genes, and Synthesis Genes of Phenolic Compounds in Arabidopsis thaliana

The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences—Implications for Evolution and Biological Regulation

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