Bickhart Derek M, Gogarten Johann P, Lapierre Pascal, Tisa Louis S, Normand Philippe, Benson David R
Department of Molecular and Cell Biology, U-3125, University of Connecticut, Storrs, CT, USA.
BMC Genomics. 2009 Oct 12;10:468. doi: 10.1186/1471-2164-10-468.
Genome analysis of three Frankia sp. strains has revealed a high number of transposable elements in two of the strains. Twelve out of the 20 major families of bacterial Insertion Sequence (IS) elements are represented in the 148 annotated transposases of Frankia strain HFPCcI3 (CcI3) comprising 3% of its total coding sequences (CDS). EAN1pec (EAN) has 183 transposase ORFs from 13 IS families comprising 2.2% of its CDS. Strain ACN14a (ACN) differs significantly from the other strains with only 33 transposase ORFs (0.5% of the total CDS) from 9 IS families.
Insertion sequences in the Frankia genomes were analyzed using BLAST searches, PHYML phylogenies and the IRF (Inverted Repeat Finder) algorithms. To identify putative or decaying IS elements, a PSI-TBLASTN search was performed on all three genomes, identifying 36%, 39% and 12% additional putative transposase ORFs than originally annotated in strains CcI3, EAN and ACN, respectively. The distribution of transposase ORFs in each strain was then analysed using a sliding window, revealing significant clustering of elements in regions of the EAN and CcI3 genomes. Lastly the three genomes were aligned with the MAUVE multiple genome alignment tool, revealing several Large Chromosome Rearrangement (LCR) events; many of which correlate to transposase clusters.
Analysis of transposase ORFs in Frankia sp. revealed low inter-strain diversity of transposases, suggesting that the majority of transposase proliferation occurred without recent horizontal transfer of novel mobile elements from outside the genus. Exceptions to this include representatives from the IS3 family in strain EAN and seven IS4 transposases in all three strains that have a lower G+C content, suggesting recent horizontal transfer. The clustering of transposase ORFs near LCRs revealed a tendency for IS elements to be associated with regions of chromosome instability in the three strains. The results of this study suggest that IS elements may help drive chromosome differences in different Frankia sp. strains as they have adapted to a variety of hosts and environments.
对三株弗兰克氏菌属（Frankia sp.）菌株的基因组分析显示，其中两株含有大量转座元件。在弗兰克氏菌HFPCcI3（CcI3）菌株的148个注释转座酶中，代表了细菌插入序列（IS）元件20个主要家族中的12个，占其总编码序列（CDS）的3%。EAN1pec（EAN）有来自13个IS家族的183个转座酶开放阅读框（ORF），占其CDS的2.2%。菌株ACN14a（ACN）与其他菌株有显著差异，只有来自9个IS家族的33个转座酶ORF（占总CDS的0.5%）。
利用BLAST搜索、PHYML系统发育分析和IRF（反向重复查找器）算法对弗兰克氏菌基因组中的插入序列进行了分析。为了鉴定推定的或衰退的IS元件，对所有三个基因组进行了PSI-TBLASTN搜索，分别鉴定出比菌株CcI3、EAN和ACN中最初注释的推定转座酶ORF多36%、39%和12%。然后使用滑动窗口分析每个菌株中转座酶ORF的分布，揭示了EAN和CcI3基因组区域中元件的显著聚类。最后，使用MAUVE多基因组比对工具对这三个基因组进行比对，揭示了几个大染色体重排（LCR）事件；其中许多与转座酶簇相关。
对弗兰克氏菌属中转座酶ORF的分析表明，转座酶的菌株间多样性较低，这表明大多数转座酶增殖发生时，没有近期来自该属以外新移动元件的水平转移。例外情况包括EAN菌株中IS3家族的代表以及所有三个菌株中的七个IS4转座酶，它们的G+C含量较低，表明有近期水平转移。转座酶ORF在LCR附近的聚类揭示了IS元件在这三个菌株中与染色体不稳定区域相关的趋势。本研究结果表明，IS元件在不同弗兰克氏菌属菌株适应各种宿主和环境时，可能有助于推动染色体差异。
