Monterey Bay Aquarium Research Institute, Moss Landing, California, USA.
Mol Biol Evol. 2010 Oct;27(10):2268-83. doi: 10.1093/molbev/msq113. Epub 2010 May 9.
The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (≤ 2 μm diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer-probes targeting a subset of these, as well as housekeeping genes, in RCC299. All those investigated showed expression either under standard growth conditions or under nitrogen depletion. Like other recent publications, our findings show a higher degree of "mixed lineage gene affiliations" among eukaryotes than anticipated, and even the most phylogenetically anomalous versions appear to be functional. Nitrogen is often considered a regulating factor for phytoplankton populations. This study provides a springboard for exploring the use and functional diversification of inorganic nitrogen transporters and related genes in eukaryotic phytoplankton.
甲藻目包含几个广泛分布的海洋微微型浮游植物（≤ 2 μm 直径）类群，包括微拟球藻和海链藻。有两个微拟球藻分离株 CCMP1545 和 RCC299 的完整基因组序列可用。我们对 CCMP1545 和 RCC299 中的氮转运体和相关同化基因进行了计算机分析，并将这些基因与其他绿线生物以及 Chromalveolata、真菌、细菌和古菌进行了比较。铵转运体（AMT）基因的系统发育重建显示，每个甲藻目基因组中都包含不同类型的基因。有些与植物和绿藻 AMT1 基因有关，有些与细菌 AMT2 基因有关。陆地植物 AMT2 基因与古菌转运体的亲缘关系比与甲藻目 AMT2 基因的亲缘关系更近。甲藻目是第一个含有 AMT2 基因的绿藻基因组，而 AMT2 基因在 Chlorella 和 Chlamydomonas 或分析的 Chromalveolata 藻类中都不存在，但在卵菌中存在。在甲藻目中鉴定出的硝酸盐转运体（NRT）比 AMT 基因少。除 CCMP1545 外，所有 NRT1 均被发现，与甲藻目和变形菌 NRT 具有最高相似性。NRT2 基因形成一个支持 Bootstrap 的分支，位于其他绿线生物之前。几个与氮有关的基因位于一起，形成一个氮基因簇。总体而言，RCC299 在各种甲藻目中的氮转运体中表现出最具差异的一套，我们针对这些氮转运体中的一部分以及 RCC299 中的管家基因设计了 TaqMan 定量聚合酶链反应引物-探针。所有这些调查对象在标准生长条件或氮缺乏条件下均表现出表达。与其他最近的出版物一样，我们的发现表明，真核生物之间的“混合谱系基因关联”程度高于预期，即使是最具系统发育异常的版本似乎也具有功能。氮通常被认为是浮游植物种群的调节因子。本研究为探索真核浮游植物无机氮转运体和相关基因的利用和功能多样化提供了一个起点。
