Composition and Diversity of CRISPR-Cas13a Systems in the Genus Leptotrichia
Composition and Diversity of CRISPR-Cas13a Systems in the Genus Leptotrichia
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DOI：
10.3389/fmicb.2019.02838
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发表时间：
2019-12-10
影响因子：
5.2
通讯作者：
Cui, Longzhu
中科院分区：
文献类型：
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作者：
Watanabe, Shinya;Cui, Bintao;Cui, Longzhu
规则间隔短回文重复序列（CRISPR）-Cas 13 a，以前称为CRISPR-C2 c2，是最近发现的RNA引导的RNA靶向CRISPR-Cas系统，具有靶向和附带单链RNA（ssRNA）切割活性的独特特征。该系统首先在Leptotrichia shahii中鉴定。在此，确定了11种Leptotrichia属菌株的完整全基因组序列，并与18种公开可用的Leptotrichia属基因组在CRISPR-Cas 13 a和其他CRISPR-Cas系统的组成、发生和多样性方面进行了比较。发现各种类型的CRISPR-Cas系统在Leptotrichia基因组中分布不均匀，包括I-B型（10/29，34.4%），II-C（1/29，2.6%），III-A（6/29，15.4%）、III-D（6/29，15.4%）、III样（3/29，7.7%）和VI-A（11/29，37.9%），而8株（20.5%）根本没有CRISPR-Cas系统。Cas 13 a效应子与L. shahii，但其导致细菌生长受阻的附带ssRNA切割活性是保守的。CRISPR-Cas间隔区代表了以前入侵者遭遇的连续成就，保留的间隔区反映了菌株的进化同源性或相关性。两个菌株间的间隔区含量和数目差异较大，只有4.4%（40/889）的间隔区为两个菌株所共有。由所有登记的Leptotrichia物种编码的CRISPR-Cas系统（I-VI型）的组织和分布揭示了CRISPR-Cas系统的效应子或间隔区序列非常不同，并且I型、III型和VI型的流行率几乎相等。只有一个菌株携带II型，而没有携带IV型或V型。这些结果提供了新的见解，在Leptotrichia物种之间的CRISPR-Cas系统的特征和分歧。
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13a, previously known as CRISPR-C2c2, is the most recently identified RNA-guided RNA-targeting CRISPR-Cas system that has the unique characteristics of both targeted and collateral single-stranded RNA (ssRNA) cleavage activities. This system was first identified in Leptotrichia shahii. Here, the complete whole genome sequences of 11 Leptotrichia strains were determined and compared with 18 publicly available Leptotrichia genomes in regard to the composition, occurrence and diversity of the CRISPR-Cas13a, and other CRISPR-Cas systems. Various types of CRISPR-Cas systems were found to be unevenly distributed among the Leptotrichia genomes, including types I-B (10/29, 34.4%), II-C (1/29, 2.6%), III-A (6/29, 15.4%), III-D (6/29, 15.4%), III-like (3/29, 7.7%), and VI-A (11/29, 37.9%), while 8 strains (20.5%) had no CRISPR-Cas system at all. The Cas13a effectors were found to be highly divergent with amino acid sequence similarities ranging from 61% to 90% to that of L. shahii, but their collateral ssRNA cleavage activities leading to impediment of bacterial growth were conserved. CRISPR-Cas spacers represent a sequential achievement of former intruder encounters, and the retained spacers reflect the evolutionary phylogeny or relatedness of strains. Analysis of spacer contents and numbers among Leptotrichia species showed considerable diversity with only 4.4% of spacers (40/889) were shared by two strains. The organization and distribution of CRISPR-Cas systems (type I-VI) encoded by all registered Leptotrichia species revealed that effector or spacer sequences of the CRISPR-Cas systems were very divergent, and the prevalence of types I, III, and VI was almost equal. There was only one strain carrying type II, while none carried type IV or V. These results provide new insights into the characteristics and divergences of CRISPR-Cas systems among Leptotrichia species.