Identification of the minimal bacterial 2′‐deoxy‐7‐amido‐7‐deazaguanine synthesis machinery

Yuan, Yifeng; Hutinet, Geoffrey; Valera, Jacqueline Gamboa; Hu, Jennifer; Hillebrand, Roman; Gustafson, Andrew; Iwata‐Reuyl, Dirk; Dedon, Peter C.; Crécy‐Lagard, Valérie de

doi:10.1111/mmi.14113

Cited by 16 publications

(29 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We also wanted to understand how dADG is synthesized by CP220 and CPt10 phages. dADG has already been detected in bacterial DNA as part of a novel restriction-modification system and is synthesized from the precursor base 7-cyano-deazaguanine (PreQ 0 ) (19). The Firehammervirus genomes harbor homologs of folE, queD, queE, and queC, encoding proteins that metabolize PreQ 0 from GTP.…”

Section: Resultsmentioning

confidence: 99%

Deoxyinosine and 7-Deaza-2-Deoxyguanosine as Carriers of Genetic Information in the DNA of Campylobacter Viruses

Crippen

Lee

Hutinet

et al. 2019

J Virol

Self Cite

View full text Add to dashboard Cite

Several reports have demonstrated that Campylobacter bacteriophage DNA is refractory to manipulation, suggesting that these phages encode modified DNA. The characterized Campylobacter jejuni phages fall into two phylogenetic groups within the Myoviridae: the genera Firehammervirus and Fletchervirus. Analysis of genomic nucleosides from several of these phages by high-pressure liquid chromatography-mass spectrometry confirmed that 100% of the 2′-deoxyguanosine (dG) residues are replaced by modified bases. Fletcherviruses replace dG with 2′-deoxyinosine, while the firehammerviruses replace dG with 2′-deoxy-7-amido-7-deazaguanosine (dADG), noncanonical nucleotides previously described, but a 100% base substitution has never been observed to have been made in a virus. We analyzed the genome sequences of all available phages representing both groups to elucidate the biosynthetic pathway of these noncanonical bases. Putative ADG biosynthetic genes are encoded by the Firehammervirus phages and functionally complement mutants in the Escherichia coli queuosine pathway, of which ADG is an intermediate. To investigate the mechanism of DNA modification, we isolated nucleotide pools and identified dITP after phage infection, suggesting that this modification is made before nucleotides are incorporated into the phage genome. However, we were unable to observe any form of dADG phosphate, implying a novel mechanism of ADG incorporation into an existing DNA strand. Our results imply that Fletchervirus and Firehammervirus phages have evolved distinct mechanisms to express dG-free DNA. IMPORTANCE Bacteriophages are in a constant evolutionary struggle to overcome their microbial hosts’ defenses and must adapt in unconventional ways to remain viable as infectious agents. One mode of adaptation is modifying the viral genome to contain noncanonical nucleotides. Genome modification in phages is becoming more commonly reported as analytical techniques improve, but guanosine modifications have been underreported. To date, two genomic guanosine modifications have been observed in phage genomes, and both are low in genomic abundance. The significance of our research is in the identification of two novel DNA modification systems in Campylobacter-infecting phages, which replace all guanosine bases in the genome in a genus-specific manner.

show abstract

Section: Resultsmentioning

confidence: 99%

Deoxyinosine and 7-Deaza-2-Deoxyguanosine as Carriers of Genetic Information in the DNA of Campylobacter Viruses

Crippen

Lee

Hutinet

et al. 2019

J Virol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Detection of Queuosine in Bulk tRNA. Detection of the presence of Q in tRNA is based on a method originally developed by Igloi and Kössel (42) and later improved (73), as detailed in SI Appendix.…”

Section: Methodsmentioning

confidence: 99%

Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens

Yuan

Zallot

Grove

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

Queuosine (Q) is a complex tRNA modification widespread in eukaryotes and bacteria that contributes to the efficiency and accuracy of protein synthesis. Eukaryotes are not capable of Q synthesis and rely on salvage of the queuine base (q) as a Q precursor. While many bacteria are capable of Q de novo synthesis, salvage of the prokaryotic Q precursors preQ0 and preQ1 also occurs. With the exception of Escherichia coli YhhQ, shown to transport preQ0 and preQ1, the enzymes and transporters involved in Q salvage and recycling have not been well described. We discovered and characterized 2 Q salvage pathways present in many pathogenic and commensal bacteria. The first, found in the intracellular pathogen Chlamydia trachomatis, uses YhhQ and tRNA guanine transglycosylase (TGT) homologs that have changed substrate specificities to directly salvage q, mimicking the eukaryotic pathway. The second, found in bacteria from the gut flora such as Clostridioides difficile, salvages preQ1 from q through an unprecedented reaction catalyzed by a newly defined subgroup of the radical-SAM enzyme family. The source of q can be external through transport by members of the energy-coupling factor (ECF) family or internal through hydrolysis of Q by a dedicated nucleosidase. This work reinforces the concept that hosts and members of their associated microbiota compete for the salvage of Q precursors micronutrients.

show abstract

“…DUF328 domains are present in DpdC proteins that are predicted dPreQ0 nitrile hydratases (10) and DUF328 genes physically cluster with queF genes encoding PreQ0 reductase (Fig. 1B).…”

Section: Yaaaec Role Is Preq0-independentmentioning

confidence: 99%

“…Bioinformatic analyses of the DUF328 family have indicated a link between these proteins and nucleic acid metabolism, particularly to the metabolism of the 7-deazaguanosine modified nucleosides (9). A DUF328 domain is found in DpdC proteins involved in the formation of 2′deoxy-7-amido-7-deazaguanosine (dADG) from 2′-deoxy-7-cyano-7-deazaguanosine (dPreQ0) in vivo (10). The 7-deazaguanosine derivatives dADG and dPreQ0 are recently discovered DNA modifications encoded by the dpd cluster found in a diverse set of bacteria.…”

Section: Introductionmentioning

confidence: 99%

“…The 7-deazaguanosine derivatives dADG and dPreQ0 are recently discovered DNA modifications encoded by the dpd cluster found in a diverse set of bacteria. Of the 11 genes found in the Salmonella serovar Montevideo dpd cluster (dpdA-dpdK), dpdC probably encodes an enzyme that hydrolyzes dPreQ0 to dADG (10). E. coli K12 MG1655 has the queuosine-tRNA (Q-tRNA) pathway but no dpd genes, suggesting that YaaAEc is likely to have a distinct function.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The DUF328 family member YaaA is a DNA-binding protein with a novel fold

Prahlad

Yuan

Lin

et al. 2020

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

DUF328 family proteins are present in many prokaryotes, however their molecular activities are unknown. The Escherichia coli DUF328 protein YaaA is a member of the OxyR regulon and is protective against oxidative stress. Because uncharacterized proteins involved in prokaryotic oxidative stress response are rare, we sought to learn more about the DUF328 family. Using comparative genomics, we found a robust association between the DUF328 family and genes involved in DNA recombination and the oxidative stress response. In some proteins, DUF328 domains are fused to other domains involved in DNA binding, recombination, and repair. Co-fitness analysis indicates that DUF328 family genes associate with recombination-mediated DNA repair pathways, particularly the RecFOR pathway. Purified recombinant YaaA binds to double-stranded DNA, duplex DNA containing bubbles of unpaired nucleotides, and Holliday junction constructs in vitro with dissociation equilibrium constants of 200-300 nM. YaaA binds DNA with positive cooperativity, forming multiple shifted species in electrophoretic mobility shift assays. The 1.65 Å resolution X-ray crystal structure of YaaA reveals that the protein possesses a new fold that we name the cantaloupe fold. YaaA has a positively charged cleft and a helix-hairpin-helix (HhH) DNA binding motif found in other DNA repair enzymes. Our results demonstrate that YaaA is a new type of DNA-binding protein associated with the oxidative stress response and that this molecular function is likely conserved in other DUF328 family members.

show abstract

Identification of the minimal bacterial 2′‐deoxy‐7‐amido‐7‐deazaguanine synthesis machinery

Cited by 16 publications

References 55 publications

Deoxyinosine and 7-Deaza-2-Deoxyguanosine as Carriers of Genetic Information in the DNA of Campylobacter Viruses

Deoxyinosine and 7-Deaza-2-Deoxyguanosine as Carriers of Genetic Information in the DNA of Campylobacter Viruses

Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens

The DUF328 family member YaaA is a DNA-binding protein with a novel fold

Contact Info

Product

Resources

About