Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development

During its sexual reproduction, the stichotrichous ciliate Oxytricha trifallax orchestrates a remarkable transformation of one of the newly formed germline micronuclear genomes. Hundreds of thousands of gene pieces are stitched together, excised from chromosomes, and replicated dozens of times to yield a functional somatic macronuclear genome composed of ~16,000 distinct DNA molecules that typically encode a single gene. Little is known about the proteins that carry out this process. We profiled mRNA expression as a function of macronuclear development and identified hundreds of mRNAs preferentially expressed at specific times during the program. We find that a disproportionate number of these mRNAs encode proteins that are involved in DNA and RNA functions. Many mRNAs preferentially expressed during macronuclear development have paralogs that are either expressed constitutively or are expressed at different times during macronuclear development, including many components of the RNA polymerase II machinery and homologous recombination complexes. Hundreds of macronuclear development-specific genes encode proteins that are well-conserved among multicellular eukaryotes, including many with links to germline functions or development. Our work implicates dozens of DNA and RNA-binding proteins with diverse evolutionary trajectories in macronuclear development in O. trifallax. It suggests functional connections between the process of macronuclear development in unicellular ciliates and germline specialization and differentiation in multicellular organisms, and argues that gene duplication is a key source of evolutionary innovation in this process.在有性生殖过程中，列纤毛类纤毛虫（stichotrichous ciliate）尖毛虫（Oxytricha trifallax）会对其中一个新形成的生殖系小核基因组实施一场极具特色的重塑过程。数十万段基因片段会被拼接整合、从染色体上切除，并历经数十次复制，最终形成由约16000种独立DNA分子组成的功能性体细胞大核基因组（somatic macronuclear genome），这类DNA分子通常仅编码单个基因。目前对于执行该基因组重塑过程的相关蛋白，学界仍知之甚少。我们以大核发育进程为时间标尺分析了mRNA表达谱，鉴定出数百种在该过程的特定时段优先表达的mRNA。我们发现，此类在特定时段优先表达的mRNA中，编码参与DNA与RNA相关功能的蛋白的基因占比显著偏高。诸多在大核发育过程中优先表达的mRNA拥有旁系同源基因（paralogs）：这些旁系同源基因要么呈组成型表达，要么在大核发育的不同时段表达，其中涵盖RNA聚合酶II（RNA polymerase II）复合物的诸多组分以及同源重组（homologous recombination）复合体的组成蛋白。数百种大核发育特异性基因所编码的蛋白在多细胞真核生物中高度保守，其中诸多蛋白与生殖系功能或发育过程存在关联。本研究将数十种具有不同进化轨迹的DNA结合蛋白与RNA结合蛋白，与尖毛虫的大核发育过程建立了功能关联。该研究揭示了单细胞纤毛虫的大核发育过程，与多细胞生物的生殖系特化及分化过程之间存在功能关联，并提出基因复制是该过程中进化创新的关键来源。