Database Establishment And Structural Analysis Of Genomic Islands In Acinetobacter Baumannii

Genomic islands(GIs)are often the product of horizontal gene transfer,flanked by direct repeats(DRs)and contain mobile genes near the boundary.GIs can be divided into pathogenicity islands,multiple antibiotic resistant islands,heavy metal ion resistant islands,adaptive islands,and secretory islands according to function of them.As they contain mobile genes and the DRs,they can be excised from the strain and transferred to other strains by transduction,conjugation and transformation.Acinetobacter baumannii is a multi-drug resistant strain,which is resistant to?-lactams,quinolones,aminoglycosides,tetracyclines and chloramphenicol.It brings great difficulties to clinical treatment.To date,multiple resistance GIs flanked with5'-ACCGC-3' are mainly integrated in the ATPase(com M)gene.In order to study the various types of GIs in A.baumannii,we firstly need to predict the GIs containing flanking DRs and mobile genes.Most prediction software existing can not provide the DRs of GIs.However,the DRs or the inverted repeat sequence nearby the DRs is the action site of mobile genes in GIs.Our software GIPredictor was developed and used to bulid a database of the GIs in 73 A.baumannii,ensuring that each GI contains at least one mobile gene and are flanked by clearly DRs.19 integrases were selected from the 73 genomes,and GIs that have 16 types of integration sites were predicted by a manual prediction method,which were consistent with the GIs in the database.Structure of these GIs were analyzed.As the frequency of the flanking sequence was the highest,2783 GIs were predicted in the database.Among them,764(27.45%)GIs included integrase or recombinase.The method with the closest distance between the flanking sequence and the mobolie genes predicted totally of 3,406 GIs in the database,in the midst of 916(26.89%)GIs including integrase or recombinase.The GIs were integrated into 6S RNA,tm RNA,t RNA,and structural genes,along with transcribed spacer sequences(two different types of transcribed spacer sequences).The t RNA genes included t RNA-Arg,t RNA-Gly,t RNA-Leu,t RNA-Val and t RNA-Ser,while structural genes encode t RNA dihydrouridine synthase A(dus A),t RNA dihydrouridine synthase B(dus B),aspartate kinase(AK),anthranilate synthase subunit II(AS),pseudouridine synthase(PUS),MFS transporter(MFST),and a hypothetical protein-encoding region(tam B-like).The 6S RNA,AK,AS,PUS,MFST,and tam B-like genes have not previously been recorded as integration sites of the GIs in Acinetobacter baumannii.There were 9 set of tandem GIs in 65 GIs flanked by 6S RNA gene and 10 set of tandem GIs in 55 GIs integrated at the tm RNA gene.One ste of tandem GIs were flanked by t RNA-Val GAC-1-1 gene.Homologous GIstm RNA,GIst RNA-Arg,GIst RNA-Gly,GIst RNA-Leu,GIst RNA-Ser,GIsdus A and GIs AS were found in other exrtaspecies genomes.Genetic distance of integrases in 16 types of the GIs were calculated by software MEGA7.0.DRs of these GIs were analysed by the online website Clustal W,EMBOSS EXPLORER,software RNAstructure 6.0.1 and Seqn Converter.There is matching relationship between the DRs and the integrases in the every type of GIs.Meanwhile,the cutting and bingding sites of every type of integrases were predicted.we identified the negative and positive strains of every type of GIs.Through the establishment of database with GIs in A.baumannii and some GIs structure analysis,we hope to provide data support for clinical research on its drug resistance and offer a molecular foundation for the transfer experiments and functional identification of GIs in the future.