Comparative Studies for Deducing Functions of Chloroplast Structures in Green Plants

研究了衣藻属(Chlamydomonas)及其近缘种中类蛋白核的形态和二氧化碳浓缩机制(CCM)的生理机制。根据所得结果，推测具有较高Rubisco分子浓度的典型类蛋白核的存在与CCM中较大的Ci池的形成有关。根据Rubisco大亚基基因rbcL的序列，推测了衣藻/绿单胞菌与先前研究的不含蛋白核的绿单胞菌之间详细的系统发育关系。用较高的自举值解析了两个单系类群。根据分解的树状拓扑结构，推测典型的蛋白核丢失伴随着细胞内Ci池的减少可能在两组中独立发生。这是对叶绿体结构蛋白核的具体功能的首次证明。我们进一步比较了不含蛋白核的绿单胞菌的rbcL基因序列，以及与其他45种绿藻的rbcL基因序列。我们发现，rbcL基因编码的蛋白质在氯单胞菌谱系中的氨基酸取代水平比在其他藻类中要高得多。一个基于rbcL核苷酸序列的系统发育树将两个衣藻作为一个“类蛋白核恢复”支系嵌套在一个单系统分类的“类蛋白核缺失”支系中。然而，atpB和psaB序列数据都有力地支持了一组截然不同的系统发育关系，在这种关系中，既没有解决“类蛋白核丢失”的分支，也没有解决“类蛋白核恢复”的分支。这种分支在基于rbcL的树中的出现可能是在决定Rubisco分子是否聚集形成可见的蛋白核的大亚基区域中发生的收敛进化变化的产物。

The morphology of the pyrenoid and the physiology of the CO2-concentrating mechanism (CCM) were investigated in Chloromonas and related species of Chlamydomonas. Based on the results obtained, it was speculated that the presence of typical pyrenoids with a high concentration of Rubisco molecules is related to the formation of large Ci pools in the CCM. Detailed phylogenetic relationships among these Chlamydomonas/Chloromonas strains and the pyrenoid-less Chloromonas strains previously investigated were inferred based on the sequence of rbcL, the gene for the large subunit of Rubisco. Two monophyletic groups were resolved with high bootstrap values. Based on the tree topology resolved, it was inferred that loss of the typical pyrenoids accompanied by a decrease in intracellular Ci pools might have taken place independently in the two groups. This is the first demonstration of concrete function of the chloroplast structure pyrenoid.We further compared sequences of the rbcL genes of pyrenoid-less Chloromonas species with those of closely related pyrenoid-containing Chlamydomonas species in the "Chloromonas lineage" and with those of 45 other green algae. We found that the proteins encoded by the rbcL genes had a much higher level of amino acid substitution in members of the Chloromonas lineage than they did in other algae. A phylogenetic tree based on rbcL nucleotide sequences nested two Chlamydomonas species as a "pyrenoid-regained" clade within a monophyletic Chloromonas "pyrenoid-lost" clade. However, both the atpB and the psaB sequence data gave robust support for a rather different set of phylogenetic relationships in which neither the "pyrenoid-lost" nor the "pyrenoid-regained" clade was resolved. The appearance of such clades in the rbcL-based tree may be an artifact of convergent evolutionary changes that have occurred in a region of the large subunit that determines whether Rubisco molecules will aggregate to form a visible pyrenoid.