The treasure trove of algal chloroplast genomes. Surprises in architecture and gene content, and their functional implications
The treasure trove of algal chloroplast genomes. Surprises in architecture and gene content, and their functional implications
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DOI：
10.1104/pp.010908
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发表时间：
2002-07-01
期刊：
影响因子：
7.4
通讯作者：
Stern, DB
中科院分区：
文献类型：
--
作者：
Simpson, CL;Stern, DB
我们实验室完成了莱茵衣藻叶绿体基因组序列的测定（J. Maul，J. Lilly和DB Stern，未发表数据;登录号AF 396929）。因为C. reinhardtii是光合作用和叶绿体基因表达的最遗传和生物化学易处理的真核模型系统（综述见Harris，2001），利用这个机会简要回顾叶绿体基因组学的历史是合适的，更重要的是，采取广泛的和未来的观点，因为在最近难以想象的细节水平上的结构/功能研究的阶段已经确定。叶绿体基因组学的第一阶段在1986年完成烟草（Nicotiana tabacum）和地钱（Marchantia polymorpha）叶绿体基因组序列时达到高潮。本章见证了新的质体编码性状的发现，利用质体表达外源基因，以及对它们的多样性的认识，特别是在维管植物之外。出现了两个主要焦点：功能研究，从光合作用的细节到基因表达和细胞生物学;基因组学，其主要目标是通过序列分析获得进化和比较信息。目前，几乎所有主要藻类的基因组全序列都已获得，C。reinhardtii序列和代表其假定祖先的集胞藻属PCC 6803基因组是完整的。我们现在设想一个新的篇章叶绿体分子遗传学，在那里的进化力量和细胞内机制，形状基因组结构，基因表达和生态适应，被揭示。在这次更新中，我们通过讨论结构和编码多样性，促进藻类质体基因组作为一种未充分利用的资源，特别是完全测序的。因为陆地植物的祖先被认为是在绿色藻类谱系中（Turmel等人，1999 a，2002; Karol等人，2001），藻类质体基因组学也为拟南芥、玉米（Zea mays）和其他模型系统提供了有用的实验指导。重要的是，一些藻类cpDNA保留了陆地植物cpDNA中不存在的新基因或关键基因，这为使用它们来确定基因功能提供了机会，而不是处理复杂的核基因家族和技术地雷。这使得我们不仅提倡C。reinhardtii，但也有其他藻类作为有用的，也许是必要的补充，植物为基础的研究叶绿体生物发生和叶发育。
The completion of the chloroplast genome sequence of the chlorophyte alga Chlamydomonas reinhardtii in our laboratory has been announced recently (J. Maul, J. Lilly, and DB Stern, unpublished data; accession no. AF396929). Because C. reinhardtii is the most genetically and biochemically tractable eukaryotic model system for photosynthesis and chloroplast gene expression (for review, see Harris, 2001), it is appropriate to use this opportunity to reflect briefly upon the history of chloroplast genomics—and more importantly, to take a broad and futuristic view as the stage is set for structure/function studies at a level of detail only recently unimaginable. The first phase of chloroplast genomics culminated with the completion of the tobacco (Nicotiana tabacum) and liverwort (Marchantia polymorpha) chloroplast genome sequences in 1986. The present chapter has witnessed the discovery of new plastid-encoded traits, the use of plastids for foreign gene expression, and an appreciation of their diversity, particularly outside the vascular plants. Two major foci have emerged: functional studies, ranging from details of photosynthesis to gene expression and cell biology; and genomics, whose major goal is to obtain evolutionary and comparative information through sequence analysis. At present, complete genome sequences have been obtained from virtually all the major algal lineages, and the C. reinhardtii sequence and the Synechocystis sp. PCC 6803 genome, representing its presumed ancestor, are complete. We now envision a new chapter of chloroplast molecular genetics, where the evolutionary forces and intracellular mechanisms that shape genome architecture, gene expression, and ecological adaptation, are revealed. In this Update, we promote algal plastid genomes as an underutilized resource, particularly the completely sequenced ones, through a discussion of structural and coding diversity. Because the antecedents of land plants are thought to lie within the green algal lineage (Turmel et al., 1999a, 2002; Karol et al., 2001), algal plastid genomics also offers useful experimental guides for Arabidopsis, maize (Zea mays), and other model systems. Importantly, some algal cpDNAs have retained novel or key genes that are absent in land plant cpDNAs, which provides an opportunity to use them to determine gene function, instead of dealing with complex nuclear gene families and technical land mines. This leads us to advocate not only C. reinhardtii, but also other algae as useful and perhaps essential complements to plantbased studies of chloroplast biogenesis and leaf development.