Genomics and proteomics of nucleomorph-containing algae

阿奇博尔德实验室使用分子生物学和计算方法来研究真核生物（含核）的基因和基因组。我们的研究重点是隐生植物和绿蛛纲植物，这是两种极不寻常的藻类，它们通过“次生内共生”的过程获得光合作用。当一个吞噬性（噬细胞）真核生物吞噬一个光合真核生物并保留其光收集装置（质体）时，就会发生这种情况，并产生了地球上一些最具生态意义的光养生物。在大多数含次生质体的藻类（如硅藻和海带）中，次生内共生体的细胞核已经完全消失，将所有必需的基因转移到宿主细胞的核基因组中。然而，在隐生植物和绿蛛形植物中，内共生体的细胞核以一种被称为“核形态”的微缩形式存在，而内共生体衍生的细胞质（“质周空间”）被保留为DNA复制、转录和翻译等基本细胞过程的场所。由于核形态基因组的编码能力是极其有限的，大多数在质周空间中起作用的蛋白质必须是宿主核编码的，但是在这个不寻常的细胞空间中发生的细胞过程的多样性目前尚不清楚。利用一系列分子、生化和比较基因组学技术，我们将分析隐生和绿蛛形藻类的质体、周质体和核形态蛋白质组，以便：(1)阐明它们真正的生化复杂性；(2)了解宿主和内生共生体衍生的蛋白质在多大程度上促进了宿主和内生共生体细胞质区室中分子机器的运作。这项研究将提供对维持核心真核细胞过程所需的最小分子机制的见解，更广泛地说，揭示了一个内共生过程，这个过程已经在地球上产生了无数种含有次级质体的藻类。

The Archibald Laboratory uses molecular biological and computational methods to study the genes and genomes of eukaryotic (nucleus-containing) organisms. Our work focuses on the cryptophytes and chlorarachniophytes, two highly unusual groups of algae that acquired photosynthesis through a process called 'secondary endosymbiosis'. This occurs when a phagotrophic (cell-eating) eukaryote engulfs a photosynthetic eukaryote and retains its light-harvesting apparatus (plastid), and has given rise to some of the most ecologically significant phototrophs on the planet. In most secondary plastid-containing algae, (e.g., diatoms and kelp), the nucleus of the secondary endosymbiont has completely disappeared, having transferred all essential genes to the nuclear genome of the host cell. However, in cryptophytes and chlorarachniophytes, the endosymbiont nucleus persists in a miniaturized form called a 'nucleomorph', and the endosymbiont-derived cytoplasm (the 'periplasmic space') is retained as the site of essential cellular processes such as DNA replication, transcription and translation. As the coding capacity of nucleomorph genomes is extremely limited, most of the proteins functioning in the periplastid space must be host nucleus-encoded, but the diversity of cellular processes taking place in this unusual cellular compartment are currently unknown. Using a battery of molecular, biochemical and comparative genomic techniques, we will analyze the plastid, periplastid and nucleomorph proteomes of cryptophyte and chlorarachniophyte algae in order to (1) elucidate their true biochemical complexity and (2) understand the extent to which host- and endosymbiont-derived proteins have contributed to the molecular machines now functioning in both the host and endosymbiont cytoplasmic compartments. This research will provide insight into the minimal molecular machinery required to sustain core eukaryotic cellular processes and, more generally, shed light on an endosymbiotic process that has given rise to countless species of secondary plastid-containing algae on Earth.