Comparative Studies for Deducing Functions of Chloroplast Structures in Green Plants

本文对绿单胞菌属及相关种衣原体的蛋白核形态和CO2浓缩机制（CCM）进行了研究。基于所获得的结果，据推测，具有高浓度的Rubisco分子的典型类蛋白核的存在与CCM中的大Ci池的形成有关。根据Rubisco大亚基基因rbcL的序列推断了这些衣原体/氯单胞菌菌株和以前研究的蛋白核较少的氯单胞菌菌株之间的详细系统发育关系。两个单系群解决了高自助值。基于解析的树形拓扑结构，可以推断，在两组中可能独立地发生了伴随细胞内Ci池减少的典型类蛋白核的损失。这是第一次展示的具体功能的叶绿体结构pyrenoid.We的rbcL基因序列的pyrenoid-less Chloromonas物种与那些密切相关的pyrenoid-containing衣原体物种的“Chloromonas谱系”和那些其他45个绿色藻类进行了进一步比较。我们发现，由rbcL基因编码的蛋白质在氯单胞菌谱系的成员中具有比在其他藻类中高得多的水平的氨基酸取代。基于rbcL核苷酸序列的系统发育树嵌套两个衣原体物种作为一个“蛋白核恢复”的分支内的单系绿单胞菌“蛋白核丢失”的分支。然而，atpB和psaB的序列数据提供了强大的支持，而不同的一组系统发育关系，其中既没有“蛋白核丢失”，也没有“蛋白核恢复”的分支被解决。在基于rbcL的树中出现这样的分支可能是在大亚基的一个区域中发生的收敛进化变化的产物，该区域决定Rubisco分子是否聚集形成可见的蛋白核。

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.