Abstract
Intragenic recombination leading to mosaic gene formation is known to alter resistance profiles for particular genes and bacterial species. Few studies have examined to what extent aminoglycoside resistance genes undergo intragenic recombination. We screened the GenBank database for mosaic gene formation in homologs of the aph(3′)-IIa (nptII) gene. APH(3′)-IIa inactivates important aminoglycoside antibiotics. The gene is widely used as a selectable marker in biotechnology and enters the environment via laboratory discharges and the release of transgenic organisms. Such releases may provide opportunities for recombination in competent environmental bacteria. The retrieved GenBank sequences were grouped in three datasets comprising river water samples, duck pathogens and full-length variants from various bacterial genomes and plasmids. Analysis for recombination in these datasets was performed with the Recombination Detection Program (RDP4), and the Genetic Algorithm for Recombination Detection (GARD). From a total of 89 homologous sequences, 83% showed 99–100% sequence identity with aph(3′)-IIa originally described as part of transposon Tn5. Fifty one were unique sequence variants eligible for recombination analysis. Only a single recombination event was identified with high confidence and indicated the involvement of aph(3′)-IIa in the formation of a mosaic gene located on a plasmid of environmental origin in the multi-resistant isolate Pseudomonas aeruginosa PA96. The available data suggest that aph(3′)-IIa is not an archetypical mosaic gene as the divergence between the described sequence variants and the number of detectable recombination events is low. This is in contrast to the numerous mosaic alleles reported for certain penicillin or tetracycline resistance determinants.
Highlights
Mosaic genes are genetic units consisting of DNA segments of different phylogenetic origin leading to sequence patterns which may confer novel phenotypic properties (Smith, 1992; Dowson et al, 1997; Boc and Makarenkov, 2011)
Sequence analysis of antibiotic resistance genes coding for penicillin binding proteins or for tetracycline resistance determinants has revealed horizontal gene transfer events leading to mosaic gene formation (Dowson et al, 1994; Patterson et al, 2007)
The analysis of the recombination potential of aph(3′)-IIa is of biological relevance because this resistance determinant is inactivating important aminoglycoside antibiotics like kanamycin and neomycin which are vital antimicrobial agents for veterinary purposes and in special cases for human therapeutic applications (WHO, 2012)
Summary
Mosaic genes are genetic units consisting of DNA segments of different phylogenetic origin leading to sequence patterns which may confer novel phenotypic properties (Smith, 1992; Dowson et al, 1997; Boc and Makarenkov, 2011). The frequency of homologous recombination decreases in a log-linear relationship with increasing sequence divergence between donor and recipient DNA to the point where it falls below the limit of detection— which is usually the case when pairwise sequence identity drops below 70% (Dowson et al, 1997; Fraser et al, 2007) This stringent similarity requirement may be circumvented by homology-directed illegitimate recombination, a mechanism where the integration of non-homologous DNA fragments is facilitated by the presence of a short homologous anchor sequence in the donor molecule and a region of microhomology on the opposite terminus of the incoming DNA with the target sequence (de Vries and Wackernagel, 2002; Prudhomme et al, 2002); or by double-illegitimate recombination, which is independent of any homology (Hulter and Wackernagel, 2008)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
