Dynamics of Chloroplast Translation during Chloroplast Differentiation in Maize.
Dynamics of Chloroplast Translation during Chloroplast Differentiation in Maize.
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DOI：
10.1371/journal.pgen.1006106
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发表时间：
2016-07
期刊：
影响因子：
4.5
通讯作者：
Barkan A
中科院分区：
文献类型：
--
作者：
Chotewutmontri P;Barkan A
陆地植物的叶绿体基因组包含大约100个基因，其中大部分位于来自蓝藻操纵子的多顺反子转录单位中。叶绿体基因的表达被整合到发育程序中，这些程序是光合细胞从非光合祖细胞分化的基础。在C4植物中，光合作用在两种细胞类型（维管束鞘和叶肉）之间的分配增加了额外的复杂性。我们使用核糖体分析和RNA-seq生成一个全面的描述叶绿体基因表达在叶绿体分化的四个阶段，显示沿着玉米幼苗叶片。大多数基因的蛋白质输出速率在发育早期增加，一旦光合机构成熟则下降。蛋白质输出的发育动力学分为几种模式。mRNA丰度的程序性变化对蛋白质输出的发育转变有很大贡献，但输出还受翻译效率变化的影响。在发育早期优先翻译的RNA主要参与叶绿体基因表达，而在光合组织中优先翻译的RNA通常参与光合作用。在维管束鞘和叶肉叶绿体的差异基因表达的结果主要从mRNA丰度的差异，但在某些情况下，翻译效率的差异放大mRNA水平的影响。在大多数情况下，蛋白质输出率接近稳态蛋白质化学计量，这意味着在非应激条件下蛋白质水解在消除未组装或受损蛋白质方面的作用有限。调谐的蛋白质输出是由翻译效率和mRNA丰度之间的基因特异性权衡引起的，两者都跨越很大的动态范围。在RNA编辑位点的核糖体足迹分析表明，叶绿体翻译机制通常不会区分编辑和未编辑的RNA。然而，在rpl 2起始密码子处将ACG编辑为AUG对于翻译起始是必不可少的，表明ACG在玉米叶绿体中不充当起始密码子。叶绿体是植物和藻类中的亚细胞器，进行光合作用的核心反应。叶绿体起源于蓝藻内共生体。随后与真核宿主的共同进化导致基因大量转移到核基因组中，获得新的基因表达机制，并将叶绿体功能整合到宿主程序中。多细胞植物中的叶绿体由非光合作用的原质体发育而来，这一过程涉及编码光合机构组分的叶绿体基因表达的巨大增加。我们使用RNA测序和核糖体分析，以产生一个全面的描述过程中的叶绿体基因表达的动力学的前质体转化成不同的叶绿体类型中发现的维管束鞘和叶肉细胞在玉米。编码构成叶绿体基因表达机制的蛋白质的基因在发育中比编码在光合作用中起作用的蛋白质的基因更早地达到蛋白质输出的峰值。翻译效率的程序性变化影响着mRNA丰度的变化，从而随着叶绿体发育的进行而改变蛋白质输出的平衡。我们还挖掘了这些数据，以深入了解叶绿体基因表达的一般特征，例如相对翻译效率，RNA编辑对翻译的影响，以及基因表达中限速步骤的识别。这些发现澄清了决定叶绿体基因产物丰度的参数，并揭示了未来研究中需要解决的意外现象。
Chloroplast genomes in land plants contain approximately 100 genes, the majority of which reside in polycistronic transcription units derived from cyanobacterial operons. The expression of chloroplast genes is integrated into developmental programs underlying the differentiation of photosynthetic cells from non-photosynthetic progenitors. In C4 plants, the partitioning of photosynthesis between two cell types, bundle sheath and mesophyll, adds an additional layer of complexity. We used ribosome profiling and RNA-seq to generate a comprehensive description of chloroplast gene expression at four stages of chloroplast differentiation, as displayed along the maize seedling leaf blade. The rate of protein output of most genes increases early in development and declines once the photosynthetic apparatus is mature. The developmental dynamics of protein output fall into several patterns. Programmed changes in mRNA abundance make a strong contribution to the developmental shifts in protein output, but output is further adjusted by changes in translational efficiency. RNAs with prioritized translation early in development are largely involved in chloroplast gene expression, whereas those with prioritized translation in photosynthetic tissues are generally involved in photosynthesis. Differential gene expression in bundle sheath and mesophyll chloroplasts results primarily from differences in mRNA abundance, but differences in translational efficiency amplify mRNA-level effects in some instances. In most cases, rates of protein output approximate steady-state protein stoichiometries, implying a limited role for proteolysis in eliminating unassembled or damaged proteins under non-stress conditions. Tuned protein output results from gene-specific trade-offs between translational efficiency and mRNA abundance, both of which span a large dynamic range. Analysis of ribosome footprints at sites of RNA editing showed that the chloroplast translation machinery does not generally discriminate between edited and unedited RNAs. However, editing of ACG to AUG at the rpl2 start codon is essential for translation initiation, demonstrating that ACG does not serve as a start codon in maize chloroplasts. Chloroplasts are subcellular organelles in plants and algae that carry out the core reactions of photosynthesis. Chloroplasts originated as cyanobacterial endosymbionts. Subsequent coevolution with their eukaryotic host resulted in a massive transfer of genes to the nuclear genome, the acquisition of new gene expression mechanisms, and the integration of chloroplast functions into host programs. Chloroplasts in multicellular plants develop from non-photosynthetic proplastids, a process that involves a prodigious increase in the expression of chloroplast genes encoding components of the photosynthetic apparatus. We used RNA sequencing and ribosome profiling to generate a comprehensive description of the dynamics of chloroplast gene expression during the transformation of proplastids into the distinct chloroplast types found in bundle sheath and mesophyll cells in maize. Genes encoding proteins that make up the chloroplast gene expression machinery peak in protein output earlier in development than do those encoding proteins that function in photosynthesis. Programmed changes in translational efficiencies superimpose on changes in mRNA abundance to shift the balance of protein output as chloroplast development proceeds. We also mined the data to gain insight into general features of chloroplast gene expression, such as relative translational efficiencies, the impact of RNA editing on translation, and the identification of rate limiting steps in gene expression. The findings clarify the parameters that dictate the abundance of chloroplast gene products and revealed unanticipated phenomena to be addressed in future studies.