A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene

Abstract

Genomic islands play a key role in prokaryotic genome plasticity. Genomic islands integrate into chromosomal loci such as transfer RNA genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. A gene encoding a putative integrase was identified at a single site within the 5′ end of the dusA gene in the genomes of over 200 bacteria. This integrase was discovered to be a component of numerous genomic islands, which appear to share a target site within the dusA gene. dusA encodes the tRNA-dihydrouridine synthase A enzyme, which catalyses the post-transcriptional reduction of uridine to dihydrouridine in tRNA. Genomic islands encoding homologous dusA-associated integrases were found at a much lower frequency within the related dusB and dusC genes, and non-dus genes. Excision of these dusA-associated islands from the chromosome as circularized intermediates was confirmed by polymerase chain reaction. Analysis of the dusA-associated islands indicated that they were highly diverse, with the integrase gene representing the only universal common feature.

Essential Gene Clusters Involved in Copper Tolerance Identified in Acinetobacter baumannii Clinical and Environmental Isolates

“…This finding is consistent with other that have reported A. baumannii strain AYE and ATCC17978-harbored copper tolerance genes on G08 and G62, respectively [13,15]. Similar to other prophages and genomic islands that have been reported in A. baumannii [35], G08 detected in AB003 was integrated within the tRNA-dihydrouridine synthase A (dusA) gene. Here, our bioinformatics analysis also found that G08 and untypeable GEIs carried cluster C were detected on conjugative plasmids of various Acinetobacter spp.…”

Zinc stress induces copper depletion in Acinetobacter baumannii

“…3h), which has been previously reported in A. baumannii strain LAC-4 [63]. In addition to strain ATCC 17978, strains AB0057 and AB6870155 also encode part of this island, which has inserted into the dusA locus [64]. Furthermore, genes orthologous to the CDF family system encoded by A1S_2929 in the ATCC 17978 Cu-resistance island are also found in AB0057, AB6870155, ATCC 19606T and ACICU, but at different loci (Fig.…”

Prophage induction, but not production of phage particles, is required for lethal disease in a microbiome-replete murine model of enterohemorrhagicE. coliinfection

“…100 bp into the coding sequence of dusA , which encodes tRNA-dihydroxyuridine synthase A. A recent study [67] revealed that known integrase genes, at least half of which belong to prophages, were found adjacent to the host dusA gene in over 200 bacterial species. Furthermore, a 21 base pair motif found at the prophage-host DNA junctions in many bacteria was present at the prophage junctions, attL and attR , of C. rodentium (Φ stx 2dact ) and C. rodentium (ΦΔ stx 2dact ::kan R ), as well as at the presumed attB phage insertion site in the parental C. rodentium dusA gene (Fig.…”

“…Bent arrows indicate direction of transcription of Q, stx , and phage late genes. Depicted are attL and attR sequence motifs, characteristic of other prophages inserted within the host dusA gene ([67]). Within this sequence, a bolded seven-base “core” sequence, perfectly conserved in attL and attR , as well as in the Φ stx 2dact attP sequence and the parental attB sequence in C. rodentium dusA (not shown), is the cross-over site for phage integration and excision.…”

“…To investigate phage functions required for C. rodentium (Φ stx 2dact ) to produce Stx and cause disease in conventional mice, we first characterized prophage genetic structure. Φ stx 2dac t prophage was integrated into the C. rodentium dusA gene, an integration site utilized by prophages in over 200 bacterial species [67]. Although the orientation of the regulatory and late genes within the Φ stx 2dact prophage is noncanonical with respect to attL and attR (with int adjacent to attL ; Fig.…”