Analyses of alternatively processed genes in ciliates provide insights into the origins of scrambled genomes and may provide a mechanism for speciation.
Analyses of alternatively processed genes in ciliates provide insights into the origins of scrambled genomes and may provide a mechanism for speciation.
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DOI：
10.1128/mbio.01998-14
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发表时间：
2015-02-03
期刊：
影响因子：
6.4
通讯作者：
Katz LA
中科院分区：
文献类型：
--
作者：
Gao F;Roy SW;Katz LA
染色体重排发生在各种真核生物的生活史中，包括纤毛虫体细胞大核基因组的发育过程中。先前对叶咽类纤毛虫Chilodonella uncinata的研究表明，大核β-微管蛋白和蛋白激酶基因家族共享嵌套在不同区域内的交替加工的生殖线片段。为了进一步研究这种纤毛虫的基因组进化，我们表征了来自纤毛虫形态种C. uncinata的两个隐蔽种的另外两个交替加工基因家族：编码组氨酸酸性磷酸酶蛋白（Hap）和利什曼溶血素家族蛋白（Lei）的基因家族。大核的Hap和雷序列的分析表明，每个基因家族由三个成员的大核是由相同的区域之间的高度发散的区域嵌套标记。调查的微核Hap序列揭示了一个复杂的模式，其中的三个大核序列是来自一个单一的微核区域或从这个共享的区域与额外的重复的Hap的微核拷贝重组的组合。我们提出了一个模型，即基因扰乱进化的基因复制，然后部分和相互降解的重复序列。在这个模型中，交替处理代表了乱序基因进化的中间步骤。最后，我们推测基因组结构在纤毛虫物种形成中可能发挥的作用，通过描述可能发生的变化，如果在细分人群中发生的替代加工位点。基因组重排发生在各种真核细胞中，并且作为产生基因组多样性的重要机制。纤毛虫基因组结构独特，生殖细胞核和体细胞核分离，为进一步研究基因组进化规律提供了理想的体系。以前的分析揭示了复杂形式的染色体重排，包括基因混乱和生殖系染色体的替代加工。在这里，我们描述了更复杂的生殖细胞和体细胞染色体之间的重排比以前看到的替代加工基因家族。利用目前和以前的研究结果，我们提出了一个模型，其中重复的微核区域的替代处理代表了乱序基因进化的中间阶段。在这个模型下，替代加工可能提供洞察纤毛虫物种形成的机制。我们关于基因扰乱和替代处理的数据也增强了对真核生命树中基因组动态性质的看法。
Chromosome rearrangements occur in a variety of eukaryotic life cycles, including during the development of the somatic macronuclear genome in ciliates. Previous work on the phyllopharyngean ciliate Chilodonella uncinata revealed that macronuclear β-tubulin and protein kinase gene families share alternatively processed germ line segments nested within divergent regions. To study genome evolution in this ciliate further, we characterized two additional alternatively processed gene families from two cryptic species of the ciliate morphospecies C. uncinata: those encoding histidine acid phosphatase protein (Hap) and leishmanolysin family protein (Lei). Analyses of the macronuclear Hap and Lei sequences reveal that each gene family consists of three members in the macronucleus that are marked by identical regions nested among highly divergent regions. Investigation of the micronuclear Hap sequences revealed a complex pattern in which the three macronuclear sequences are derived either from a single micronuclear region or from a combination of this shared region recombined with additional duplicate micronuclear copies of Hap. We propose a model whereby gene scrambling evolves by gene duplication followed by partial and reciprocal degradation of the duplicate sequences. In this model, alternative processing represents an intermediate step in the evolution of scrambled genes. Finally, we speculate on the possible role of genome architecture in speciation in ciliates by describing what might happen if changes in alternatively processed loci occur in subdivided populations. Genome rearrangements occur in a variety of eukaryotic cells and serve as an important mechanism for generating genomic diversity. The unusual genome architecture of ciliates with separate germline and somatic nuclei in each cell, provides an ideal system to study further principles of genome evolution. Previous analyses revealed complex forms of chromosome rearrangements, including gene scrambling and alternative processing of germ line chromosomes. Here we describe more complex rearrangements between germ line and somatic chromosomes than previously seen in alternatively processed gene families. Drawing on the present and previous findings, we propose a model in which alternative processing of duplicated micronuclear regions represents an intermediate stage in the evolution of scrambled genes. Under this model, alternative processing may provide insights into a mechanism for speciation in ciliates. Our data on gene scrambling and alternative processing also enhance views on the dynamic nature of genomes across the eukaryotic tree of life.