Entfellner Elisabeth, Li Ruibao, Jiang Yiming, Ru Jinlong, Blom Jochen, Deng Li, Kurmayer Rainer
Research Department for Limnology, University of Innsbruck, Mondsee, Austria.
Institute of Virology, Helmholtz Zentrum München, Munich, Germany.
Front Microbiol. 2022 Jul 28;13:901762. doi: 10.3389/fmicb.2022.901762. eCollection 2022.
It has been generally hypothesized that mobile elements can induce genomic rearrangements and influence the distribution and functionality of toxic/bioactive peptide synthesis pathways in microbes. In this study, we performed in depth genomic analysis by completing the genomes of 13 phylogenetically diverse strains of the bloom-forming freshwater cyanobacteria spp. to investigate the role of insertion sequence (IS) elements in seven pathways. Chromosome size varied from 4.7-4.8 Mbp (phylogenetic Lineage 1 of / thriving in shallow waterbodies) to 5.4-5.6 Mbp (Lineage 2 of / thriving in deeper physically stratified lakes and reservoirs) and 6.3-6.6 Mbp (Lineage 3, / including planktic and benthic ecotypes). Although the variation in chromosome size was positively related to the proportion of IS elements (1.1-3.7% on chromosome), quantitatively, IS elements and other paralogs only had a minor share in chromosome size variation. Thus, the major part of genomic variation must have resulted from gene loss processes (ancestor of Lineages 1 and 2) and horizontal gene transfer (HGT). Six of seven peptide synthesis gene clusters were found located on the chromosome and occurred already in the ancestor of /, and became partly lost during evolution of Lineage 1. In general, no increased IS element frequency in the vicinity of peptide synthesis gene clusters was observed. We found a higher proportion of IS elements in ten breaking regions related to chromosomal rearrangements and a tendency for colocalization of toxic/bioactive peptide synthesis gene clusters on the chromosome.
一般认为，移动元件可诱导基因组重排，并影响微生物中毒性/生物活性肽合成途径的分布和功能。在本研究中，我们通过完成13种系统发育不同的淡水蓝藻水华形成菌株的基因组测序，进行了深入的基因组分析，以研究插入序列（IS）元件在七条途径中的作用。染色体大小从4.7-4.8 Mbp（浅水水体中生长的系统发育谱系1）到5.4-5.6 Mbp（深水物理分层湖泊和水库中生长的谱系2）以及6.3-6.6 Mbp（谱系3，包括浮游和底栖生态型）不等。虽然染色体大小的变化与IS元件的比例呈正相关（染色体上为1.1-3.7%），但从数量上看，IS元件和其他旁系同源物在染色体大小变化中只占较小比例。因此，基因组变异的主要部分一定是由基因丢失过程（谱系1和2的祖先）和水平基因转移（HGT）导致的。七个肽合成基因簇中有六个位于染色体上，在/的祖先中就已存在，并在谱系1的进化过程中部分丢失。总体而言，在肽合成基因簇附近未观察到IS元件频率增加。我们在与染色体重排相关的十个断裂区域中发现了较高比例的IS元件，并且有毒/生物活性肽合成基因簇在染色体上有共定位的趋势。
