a Faculty of Biology, Genetics and Experimental Bioinformatics , University of Freiburg , Freiburg , Germany.
b Instituto de Bioquímica Vegetal y Fotosíntesis , Consejo Superior de Investigaciones Científicas and Universidad de Sevilla , Seville , Spain.
RNA Biol. 2019 Apr;16(4):518-529. doi: 10.1080/15476286.2018.1493330. Epub 2018 Aug 15.
Novel CRISPR-Cas systems possess substantial potential for genome editing and manipulation of gene expression. The types and numbers of CRISPR-Cas systems vary substantially between different organisms. Some filamentous cyanobacteria harbor > 40 different putative CRISPR repeat-spacer cassettes, while the number of cas gene instances is much lower. Here we addressed the types and diversity of CRISPR-Cas systems and of CRISPR-like repeat-spacer arrays in 171 publicly available genomes of multicellular cyanobacteria. The number of 1328 repeat-spacer arrays exceeded the total of 391 encoded Cas1 proteins suggesting a tendency for fragmentation or the involvement of alternative adaptation factors. The model cyanobacterium Anabaena sp. PCC 7120 contains only three cas1 genes but hosts three Class 1, possibly one Class 2 and five orphan repeat-spacer arrays, all of which exhibit crRNA-typical expression patterns suggesting active transcription, maturation and incorporation into CRISPR complexes. The CRISPR-Cas system within the element interrupting the Anabaena sp. PCC 7120 fdxN gene, as well as analogous arrangements in other strains, occupy the genetic elements that become excised during the differentiation-related programmed site-specific recombination. This fact indicates the propensity of these elements for the integration of CRISPR-cas systems and points to a previously not recognized connection. The gene all3613 resembling a possible Class 2 effector protein is linked to a short repeat-spacer array and a single tRNA gene, similar to its homologs in other cyanobacteria. The diversity and presence of numerous CRISPR-Cas systems in DNA elements that are programmed for homologous recombination make filamentous cyanobacteria a prolific resource for their study. Abbreviations: Cas: CRISPR associated sequences; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; C2c: Class 2 candidate; SDR: small dispersed repeat; TSS: transcriptional start site; UTR: untranslated region.
新型 CRISPR-Cas 系统在基因组编辑和基因表达操纵方面具有巨大潜力。不同生物体之间的 CRISPR-Cas 系统的类型和数量差异很大。一些丝状蓝藻含有> 40 种不同的假定 CRISPR 重复-间隔体盒，而 cas 基因实例的数量要低得多。在这里，我们研究了 171 个多细胞蓝藻的公共基因组中的 CRISPR-Cas 系统和 CRISPR 样重复-间隔体阵列的类型和多样性。1328 个重复-间隔体阵列的数量超过了 391 个编码 Cas1 蛋白的总数，这表明存在碎片化的趋势或涉及替代的适应因子。模式蓝藻集胞藻 PCC 7120 仅包含三个 cas1 基因，但宿主三个 1 类，可能一个 2 类和五个孤儿重复-间隔体阵列，所有这些都表现出 crRNA 典型的表达模式，表明转录、成熟和掺入 CRISPR 复合物是活跃的。中断集胞藻 PCC 7120 fdxN 基因的元件内的 CRISPR-Cas 系统，以及其他菌株中的类似排列，占据了在与分化相关的程序性特定位点重组过程中被切除的遗传元件。这一事实表明这些元件具有整合 CRISPR-cas 系统的倾向，并指出了以前未被认识到的联系。与其他蓝藻的同源物相似，类似于可能的 2 类效应蛋白的基因 all3613 与一个短重复-间隔体阵列和一个单个 tRNA 基因相连。在被编程用于同源重组的 DNA 元件中，CRISPR-Cas 系统的多样性和存在使丝状蓝藻成为研究它们的丰富资源。缩写：Cas：CRISPR 相关序列；CRISPR：成簇规律间隔短回文重复序列；C2c：候选 2 类；SDR：小分散重复；TSS：转录起始位点；UTR：非翻译区。
