Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions

Perrone, Rosalba; Lavezzo, Enrico; Riello, Erika; Manganelli, Riccardo; Palù, Giorgio; Toppo, Stefano; Provvedi, Roberta; Richter, Sara N.

doi:10.1038/s41598-017-05867-z

Cited by 80 publications

(68 citation statements)

References 66 publications

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“…The TP‐G4 and OX‐1T‐G4 structures that were used for investigating the G4 resolution activity of MtUvrD1 have been derived from the murine immunoglobulin switch region and Oxytricha telomeric sequences, respectively . Mycobacterium tuberculosis genome is GC rich and possesses > 10 000 potential G4 DNA forming motifs . To test whether MtUvrD1 can unwind G4 structures that are derived from the potential G4 forming sequences from the M. tuberculosis genome, we identified recA , trpD , and MFS potential G4 forming sequences using G4 analysis tool QGRS Mapper (Table ).…”

Section: Resultsmentioning

confidence: 99%

“…It is likely that Mycobacterial UvrD binds to the 3′‐overhangs, translocates in a 3′ → 5′ direction and unwinds G4 structures. Mycobacterium tuberculosis genome possesses > 10 000 potential G4 DNA forming sequences and many of these sequences are located in promoters of various genes . Previously, we have shown that PE_PGRS2, mce1R, and moeb1 gene promoter G‐rich sequences form G4 structures .…”

Section: Discussionmentioning

confidence: 99%

“…Escherichia coli genome possesses > 3000 potential G4 motifs . Mycobacterium tuberculosis that infects one‐third of the world population and cause tuberculosis is a GC rich (65%) pathogen and contains > 10 000 potential G4 forming motifs . Although G4 structures have been implicated in various biological processes, formation of G4 structures during replication, transcription, or transient changes in the superhelicity of the chromosomal DNA impede genome duplication.…”

Section: Introductionmentioning

confidence: 99%

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Mycobacterium tuberculosis UvrD1 and UvrD2 helicases unwind G‐quadruplex DNA

et al. 2019

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Unresolved G‐quadruplex (G4) DNA secondary structures impede DNA replication and can lead to DNA breaks and to genome instability. Helicases are known to unwind G4 structures and thereby facilitate genome duplication. Escherichia coli UvrD is a multifunctional helicase that participates in DNA repair, recombination and replication. Previously, we had demonstrated a novel role of E. coli UvrD helicase in resolving G4 structures. Mycobacterium tuberculosis genome encodes two orthologs of E. coli UvrD helicase, UvrD1 and UvrD2. It is unclear whether UvrD1 or UvrD2 or both helicases unwind G4 DNA structures. Here, we demonstrate that M. tuberculosis UvrD1 and UvrD2 unwind G4 tetraplexes. Both helicases were proficient in resolving previously characterized tetramolecular G4 structures in an ATP hydrolysis and single‐stranded 3′‐tail‐dependent manner. Notably, M. tuberculosis UvrD1 and UvrD2 were efficient in unwinding G4 structures derived from the potential G4 forming sequences present in the M. tuberculosis genome. These data suggest an extended role for M. tuberculosis UvrD1 and UvrD2 helicases in resolving G4 DNA structures and provide insights into the maintenance of genome integrity via G4 DNA resolution.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mycobacterium tuberculosis UvrD1 and UvrD2 helicases unwind G‐quadruplex DNA

et al. 2019

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“…One genome per each group of aligned sequences was chosen to serve as reference sequence, possibly belonging to the manually curated RefSeq database [https://www.ncbi.nlm.nih.gov/ refseq/]. The complete list of selected reference sequences is reported in S1 Table. PQSs were searched in all multiple-aligned nucleotide sequences with an in-house developed tool, as previously described [36,52]. Briefly, a PQS was reported when at least four consecutive guanine islands (G-islands) were detected.…”

Section: Pqs Detection and Evaluation Of Conservationmentioning

confidence: 99%

G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide

et al. 2018

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G-quadruplexes are non-canonical nucleic-acid structures that control transcription, replication, and recombination in organisms. G-quadruplexes are present in eukaryotes, prokaryotes, and viruses. In the latter, mounting evidence indicates their key biological activity. Since data on viruses are scattered, we here present a comprehensive analysis of potential quadruplex-forming sequences (PQS) in the genome of all known viruses that can infect humans. We show that occurrence and location of PQSs are features characteristic of each virus class and family. Our statistical analysis proves that their presence within the viral genome is orderly arranged, as indicated by the possibility to correctly assign up to two-thirds of viruses to their exact class based on the PQS classification. For each virus we provide: i) the list of all PQS present in the genome (positive and negative strands), ii) their position in the viral genome, iii) the degree of conservation among strains of each PQS in its genome context, iv) the statistical significance of PQS abundance. This information is accessible from a database to allow the easy navigation of the results: http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=g4virus. The availability of these data will greatly expedite research on G-quadruplex in viruses, with the possibility to accelerate finding therapeutic opportunities to numerous and some fearsome human diseases.

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“…G4 patterns were searched in all nucleotide sequences with an in-house developed tool, as previously described (Perrone et al 2017a;Perrone et al 2017b). Briefly, a G4 was reported when at least four consecutive guanine islands (G-islands) were detected.…”

Section: Methodsmentioning

confidence: 99%

G-quadruplex forming sequences in the genome of all known human viruses: a comprehensive guide

Lavezzo

Berselli

Frasson

et al. 2018

Preprint

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G-quadruplexes are non-canonical nucleic acid structures that control transcription, replication, and recombination in organisms. G-quadruplexes are present in eukaryotes, prokaryotes, and viruses. In the latter, mounting evidence indicates their key biological activity. Since data on viruses are scattered, we here present a comprehensive analysis of putative G-quadruplexes in the genome of all known viruses that can infect humans. We show that the presence, distribution, and location of G-quadruplexes are features characteristic of each virus class and family. Our statistical analysis proves that their presence within the viral genome is orderly arranged, as indicated by the possibility to correctly assign up to two-thirds of viruses to their exact class based on the G-quadruplex classification. For each virus we provide: i) the list of all G-quadruplexes formed by GG-, GGG-and GGGG-islands present in the genome (positive and negative strands), ii) their position in the viral genome along with the known function of that region, iii) the degree of conservation among strains of each G-quadruplex in its genome context, iv) the statistical significance of G-quadruplex formation. This information is accessible from a database

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Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions

Cited by 80 publications

References 66 publications

Mycobacterium tuberculosis UvrD1 and UvrD2 helicases unwind G‐quadruplex DNA

Mycobacterium tuberculosis UvrD1 and UvrD2 helicases unwind G‐quadruplex DNA

G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide

G-quadruplex forming sequences in the genome of all known human viruses: a comprehensive guide

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