Papers by Keyword: Genomic Island (GI)

Abstract: The genomic islands (GIs) are usually the products of horizontal gene transfer (HGT) that is evolution pattern in prokaryote. Two homologous GIs (WSU1GI^No and KU01GI^No) containing the homologous integrase of Bacteriophage P2 were determined in Enterobacter cloacae through flanking sequence alignment of the homologous integrase. The homologous GIs were integrated into the noncoding sequence. Their common flanking sequence is 5-AAGGCTCCCTCAGGAGC-3, and their integrases share 97% similarity. About two-thirds of the nucleotide sequences between WSU1GI^No and KU01GI^No are highly similar. The different regions between WSU1GI^No and KU01GI^No mainly include hypothetical gene, Phage-related tail gene, capsid gene, and baseplate assembly gene. In conclusion, the tandem arrangement of WSU1GI^No and KU01GI^No will be artificially constructed because of their similar structural characteristics, and phage coat protein assembly will also be analyzed.

Abstract: Pseudomonas putida is a safety gammaproteobacterium that plays an important role in bioremediation. Twenty nine mobile genomic islands were accurately localized in four strains of P. putida, six in P. putida F1, six in P. putida GB-1, nine in P. putida KT2440, and eight in P. putida W619, respectively. The integration sites include the tRNA gene, such as tRNAMet gene, tRNASer gene, tRNALeu gene, tRNAGly gene, tRNAThr gene, tRNACys gene, tRNAPro gene, and some structural genes, such as arsenate reductase gene, DNA mismatch repair protein MutS gene, thymidylate synthase gene, and 6-pyruvoyl tetrahydropterin synthase gene. 6-pyruvoyl tetrahydropterin synthase gene was firstly determined as the integration site of the genomic islands. The action sites of the lambda integrases are the stem-loop sequence, and the action sites of the P4 integrase are the asymmetric sequence. KT2440GI-5 can produce R2-type pyocin particle that is a bacteriocin and can kill sensitive bacterium. KT2440GI-9 can code ectoine-induced proteins that cause the cells to survive in high salt concentration.

Abstract: Eleven genomic islands (GIs) flanked by isocitrate dehydrogenase genes are determined in Escherichia coli and Salmonella enterica. These GIs have at least one mobile gene, such as integrase gene, transposase gene or recombinase gene. Through annotation of internal genes, these GIs are related to lambda prophage. The excisionase gene is associated with the mobile gene in some GIs. An ABC transporter, namely, sitABCD operon, is existed in some GIs and may uptake Fe2+ and Mn2+. Mn2+ is a second cofactor and an essential activator of the isocitrate dehydrogenase. The cleavage site of functional lambda integrase is 5’-TGCTGCGCCA-3’ in direct repeats at 3’-end of icd gene.The truncated lambda integrases (ECP_1132 and ECP_1135) are inactive because the transposon inserted the integrase gene by 5’-CCTGG-3’. This Fe2+/Mn2+ transport operon is predicted that is a recent product of horizontal gene transfer in E. coli because this operon is also existed in S. enterica and is not in a mobile GIs.