Origins of genome-editing excisases as illuminated by the somatic genome of the ciliate Blepharisma.
Origins of genome-editing excisases as illuminated by the somatic genome of the ciliate Blepharisma.
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纤毛虫 Blepharisma 的体细胞基因组阐明了基因组编辑切除的起源。
DOI：
10.1073/pnas.2213887120
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发表时间：
2023-01-24
影响因子：
11.1
通讯作者：
Swart, Estienne C.
中科院分区：
文献类型：
--
作者：
Singh, Minakshi;Seah, Brandon K. B.;Emmerich, Christiane;Singh, Aditi;Woehle, Christian;Huettel, Bruno;Byerly, Adam;Stover, Naomi A.;Sugiura, Mayumi;Harumoto, Terue;Swart, Estienne C.
纤毛虫的基因组编辑是一个广泛的、自然的过程，可以产生彻底重组的体细胞基因组。所研究的纤毛虫之间的这一过程显着不同，所提出的 DNA 切除具有不同的起源。 PiggyBac 转座酶同源物与纤毛虫草履虫和四膜虫模型中的 DNA 缺失有关。在这里，我们描述了一个远亲 Blepharisma stoltei 的体细胞基因组。该基因组包含多个 PiggyBac 转座酶同源物，其删除的 DNA 类似于草履虫。系统发育分析表明纤毛虫 PiggyBac 衍生的切除源于广泛 DNA 切除之前的单一驯化事件。这项工作通过比较 Blepharisma 体细胞基因组发育的替代途径，为区分与减数分裂和受精相关的表达与与基因组编辑直接相关的表达奠定了基础。纤毛虫是普遍存在的微生物真核生物，在同一细胞中具有体细胞核和种系细胞核，大量 DNA 切除经常发生。在精简体细胞基因组的发育过程中，散布在纤毛虫种系基因组中的数以万计的内部消除序列（IES）被删除。 Blepharisma 属代表两个高级纤毛虫进化枝（Postciliodesmatophora 亚门）之一，并且不同寻常地具有体细胞核和基因组发育的双重途径。这使得它成为研究这些过程的功能和演变的理想选择。在这里，我们报告了 Blepharisma stoltei 菌株 ATCC 30299 (41 Mbp) 的体细胞基因组组装，排列为许多端粒加帽的微型染色体亚型。该基因组编码八个 PiggyBac 转座酶同源物，不再由转座子携带。所有这些似乎都受到纯化选择的影响，但只有一种，即假定的 IES 切除酶，具有完整的催化三联体。我们假设 PiggyBac 同源物是祖先的切除，使得广泛的自然基因组编辑得以进化。
Genome editing in ciliates is an extensive, natural process that produces radically restructured somatic genomes. This process is strikingly different between the ciliates investigated, with distinct origins for the proposed DNA excisases. PiggyBac transposase homologs are implicated in DNA deletion in the model ciliates Paramecium and Tetrahymena. Here we describe the somatic genome of a distant relative, Blepharisma stoltei. This genome contains multiple PiggyBac transposase homologs, and its deleted DNA resembles that of Paramecium. Phylogenetic analysis suggests ciliate PiggyBac-derived excisases descended from a single domestication event that preceded widespread DNA excision. This work sets the stage for distinguishing expression associated with meiosis and fertilization from that directly associated with genome editing, by comparing Blepharisma’s alternative pathways of somatic genome development. Massive DNA excision occurs regularly in ciliates, ubiquitous microbial eukaryotes with somatic and germline nuclei in the same cell. Tens of thousands of internally eliminated sequences (IESs) scattered throughout the ciliate germline genome are deleted during the development of the streamlined somatic genome. The genus Blepharisma represents one of the two high-level ciliate clades (subphylum Postciliodesmatophora) and, unusually, has dual pathways of somatic nuclear and genome development. This makes it ideal for investigating the functioning and evolution of these processes. Here we report the somatic genome assembly of Blepharisma stoltei strain ATCC 30299 (41 Mbp), arranged as numerous telomere-capped minichromosomal isoforms. This genome encodes eight PiggyBac transposase homologs no longer harbored by transposons. All appear subject to purifying selection, but just one, the putative IES excisase, has a complete catalytic triad. We hypothesize that PiggyBac homologs were ancestral excisases that enabled the evolution of extensive natural genome editing.
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影响因子：
64.8
作者：
Aury, Jean-Marc;Jaillon, Olivier;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
48
作者：
Chin, Chen-Shan;Peluso, Paul;Schatz, Michael C.
通讯作者：
Schatz, Michael C.
影响因子：
10.7
作者：
Katoh K;Standley DM
通讯作者：
Standley DM
DOI：
10.1093/bioinformatics/bts199
发表时间：
2012-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Kearse M;Moir R;Wilson A;Stones-Havas S;Cheung M;Sturrock S;Buxton S;Cooper A;Markowitz S;Duran C;Thierer T;Ashton B;Meintjes P;Drummond A
通讯作者：
Drummond A
影响因子：
64.5
作者：
Chen X;Bracht JR;Goldman AD;Dolzhenko E;Clay DM;Swart EC;Perlman DH;Doak TG;Stuart A;Amemiya CT;Sebra RP;Landweber LF
通讯作者：
Landweber LF