嗜热链球菌CRISPR序列的检测及原间隔序列预测

CRISPR Detection and Protospacer Prediction in Streptococcus thermophilus

摘要:

CRISPR基因座中的间隔序列能够提供特异性免疫使宿主得以对抗那些携带相同序列的入侵元件，本研究旨在预测实验室3株嗜热链球菌的原间隔序列，为探究其抗噬菌体机制奠定基础。本文检测了3株嗜热链球菌的CRISPR序列，预测嗜热链球菌CRISPR基因座的活性，构建重复序列的系统发育树，并对间隔序列进行同源性分析。结果显示供试菌S0含有3个CRISPR，S4仅含1个CRISPR，79含有4个CRISPR，CRISPR1基因座活性最高，CRISPR2基因座最不活跃。重复序列与标准菌株的相应重复序列高度保守，不同CRISPR的间隔序列在内容及数目上高度可变，它们的原间隔序列绝大部分来源于噬菌体，少数来源于质粒或染色体序列。供试菌79与嗜热链球菌MN-BM-A02及嗜热链球菌ASCC 1275的4个CRISPR序列均高度一致，推测其菌株同源性较高。验证了间隔序列是由宿主遭受噬菌体等外源基因元件侵染而获得的。

Abstract:

The spacers in clustered regularly interspaced short palindromic repeats (CRISPR) loci can provide specific immunity to invasive elements that carry the same or a similar sequence. In the present study, the protospacers of three S. thermophilus strains were predicted to provide a foundation for exploring the phage resistance mechanism. The CRISPR sequences of three S. thermophilus strains were determined, the activity of CRISPR loci in several S. thermophilus strains was predicted, and a phylogenetic tree for repeated sequences was constructed. In addition, repeat or spacer homology was analyzed. The results showed that the tested bacterium S0 contained three CRISPR loci, S4 only had one CRISPR locus, and strain 79 had four CRISPR loci. We hypothesized that the highest and lowest activities would be observed in CRISPR1 and CRISPR2, respectively. The repeated sequences and corresponding repeated sequences in the standard strain were highly conserved, and different CRISPR spacer sequences were highly dynamic in terms of content and number. Most original spacer sequences were derived from bacteriophages, whereas a few were derived from plasmid or chromosomal sequences. The CRISPR sequence of strain 79 was highly consistent with the four CRISPR sequences of S. thermophilus MN-BM-A02 and S. thermophilus ASCC 1275, suggesting that the strains are highly homologous. The results suggest that the spacer sequences were acquired from invasion of the host by the bacteriophage and other exogenous genetic elements.