Nozaki Hisayoshi, Onishi Keisuke, Morita Eiko
Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
J Mol Evol. 2002 Oct;55(4):414-30. doi: 10.1007/s00239-002-2338-9.
Chloromonas is distinguished from Chlamydomonas primarily by the absence of pyrenoids, which are structures that are present in the chloroplasts of most algae and are composed primarily of the CO2-fixing enzyme Rubisco. In this study we compared sequences of the rbcL (Rubisco large subunit-encoding) 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. This kind of elevated substitution rate was not observed, however, in the deduced proteins encoded by two other chloroplast genes that we analyzed: atpB and psaB. The rates of synonymous and nonsynonymous nucleotide substitutions in the rbcL genes indicate that the rapid evolution of these genes in members of the Chloromonas lineage is not due to relaxed selection (as it presumably is in parasitic land plants). A phylogenetic tree based on rbcL nucleotide sequences nested two Chlamydomonas species as a "pyrenoid-regained" clade within a monophyletic Chloromonas "pyrenoid-lost" clade. Character-state optimization with this tree suggested that the loss and the regain of pyrenoids were accompanied by eight synapomorphic amino acid replacements in the Rubisco large subunit, four of which are positioned in the region involved in its dimerization. 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.
绿梭藻与衣藻的主要区别在于缺乏蛋白核，蛋白核是大多数藻类叶绿体中存在的结构，主要由固定二氧化碳的酶核酮糖-1,5-二磷酸羧化酶/加氧酶（Rubisco）组成。在本研究中，我们比较了“绿梭藻谱系”中无蛋白核的绿梭藻物种与亲缘关系密切的含蛋白核衣藻物种以及其他45种绿藻的rbcL（编码Rubisco大亚基）基因序列。我们发现，rbcL基因编码的蛋白质在绿梭藻谱系成员中的氨基酸替换水平比在其他藻类中高得多。然而，在我们分析的另外两个叶绿体基因atpB和psaB编码的推导蛋白质中未观察到这种升高的替换率。rbcL基因中同义核苷酸替换和非同义核苷酸替换的速率表明，这些基因在绿梭藻谱系成员中的快速进化并非由于选择放松（推测寄生陆生植物是这种情况）。基于rbcL核苷酸序列构建的系统发育树将两个衣藻物种嵌套为一个单系绿梭藻“失去蛋白核”分支内的“重新获得蛋白核”分支。用此树进行的特征状态优化表明，蛋白核的丢失和重新获得伴随着Rubisco大亚基中的八个共衍征氨基酸替换，其中四个位于其二聚化相关区域。然而，atpB和psaB序列数据都有力支持了一组截然不同的系统发育关系，其中“失去蛋白核”分支和“重新获得蛋白核”分支均未得到解析。基于rbcL的树中此类分支的出现可能是大亚基区域发生趋同进化变化的产物，该区域决定了Rubisco分子是否会聚集形成可见的蛋白核。
