Lei Song

Publications (3)4.01 Total impact

• Article: Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens

  Lei Song, XueHong Zhang
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  ABSTRACT: Mobile genomic islands (GIs) can be excised from the chromosome, then form a circular intermediate and be reintegrated into the chromosome by the GI internal integrase. Some mobile GIs can also be transferred into a new receptor cell by transformation, conjugation, or transduction. The action sites of the integrase are usually flanked direct repeats (DRs) of the GIs. Accurate localization of the flanking sequences is a precondition for determining the mobility of the GI. Mobile GIs are generally associated with transfer RNAs (tRNAs). Based on the correlation between flanking sequences and tRNA sequences, the flanking sequences of 11 putative mobile GIs in Pseudomonas aeruginosa PAO1, P. aeruginosa PA14, P. fluorescens Pf-5 and P. fluorescens Pf0-1 were identified. Among the 11 GIs, Pf0-1GI-1 is responsible for benzoate degradation. PAO1GI-1, Pf5GI-2, Pf5GI-3, and Pf5GI-4 were confirmed experimentally to be excised from a chromosome to form a circular intermediate. The action sites of the integrases are these GIs direct repeats. Due to distinct DRs, cutting sites for the internal integrase of PAO1GI-1, Pf5GI-2, Pf5GI-3 and Pf5GI-4 were determined outside the T-loop of the tRNAGly gene, outside the anticodon loop of the tRNASer gene and tRNALys gene, and at the asymmetric 3′-end of the tRNALeu gene, respectively. PAO1GI-1 and other mobile GIs may be transferred into many different strains that belong to different phyla because of the clear flanking sequences. This study describes basic information about the action sites of the integrases, assesses the mobility of GIs, and can help design and transfer mobile GIs to candidate strains. Keywords Pseudomonas –genomic islands–accurate localization–excision–integrase
  Chinese Science Bulletin 04/2012; 56(10):987-995. · 1.32 Impact Factor
• Article: Innovation for ascertaining genomic islands in PAO1 and PA14 of Pseudomonas aeruginosa

  Lei Song, XueHong Zhang
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  ABSTRACT: Based on three distinct traits of genomic islands, a novel approach was developed to search for and determine genomic islands in special strains. Two genomic islands in Pseudomonas aeruginosa PAO1 and 7 genomic islands in Pseudomonas aeruginosa PA14 were defined with this method. Among the 9 genomic islands, 4 islands had been characterized before, while the other 5 islands were initially determined. The insert sites of 6 genomic islands are tRNA sequences, direct repeats of PA14GI-3 are relative to tRNALeu, and direct repeats of PA14GI-2 are at the 3′ end of bifunctional GMP synthase/glutamine amidotransferase. Only direct repeats of PA14GI-4 are not clear. Among the 5 newly-found genomic islands, it was supposed that PA14GI-2 is a genomic island related to Hg2+ uptake, PA14GI-3 is a secretory activity genomic island, PA14GI-6 is a pathogenicity island, and functions of PA14GI-1 and PA14GI-5 are not clear. Finally, the tyrosine type integrases in PAO1GI-1, PA14GI-5 and PA14GI-7 were analyzed, and their binding and restriction sites were predicted.
  Chinese Science Bulletin 04/2012; 54(21):3991-3999. · 1.32 Impact Factor
• Article: Structural characteristics of genomic islands associated with GMP synthases as integration hotspot among sequenced microbial genomes.

  Lei Song, Yuting Pan, Sihong Chen, Xuehong Zhang
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  ABSTRACT: tRNA, tmRNA and some small RNA genes are recognized as general integration hotspots of genomic islands (GIs). The GMP synthase gene (guaA) has been firstly identified as one insertion hotspot of foreign DNA fragments. Thirty four islands integrated into the guaA genes were identified in the 987 completely sequenced archaeal and bacterial genomes. These alien islands were widely distributed within the host strains belonging to Proteobacteria, Firmicutes and Actinobacteria. The analysis of structural characteristics of these GIs is important for further determination of the island mobility and transference into suitable hosts. The putative functional integrases encoded by guaA-associated islands were mainly composed of phage P4 integrases, and followed by phage PhiLC3 integrases. Interestingly, island-encoding AlpA is close to P4 integrase and is deduced to be the positive transcriptional regulatory factor of P4 integrase while the XRE protein is close to PhiLC3 integrase and may be the negative transcriptional regulatory factor of PhiLC3 integrase. An 8-bp consensus sequence (5'-GAGTGGGA-3') within the direct repeats of these GIs is the cutting site of the P4 integrases encoding by guaA-associated islands, in which the third nucleotide (G) is the key site. The large-scale investigation of the content of GMP synthase gene hotspots may be useful to find important functional islands within members of many key bacterial species and to transfer useful islands into more suitable hosts.
  Computational biology and chemistry 02/2012; 36:62-70. · 1.37 Impact Factor