The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

Abstract

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the~120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

Inactivation of genes coding for mitochondrial Nd7 and Nd9 complex I subunits in Chlamydomonas reinhardtii. Impact of complex I loss on respiration and energetic metabolism

“…To be efficiently expressed, mitochondrial genes that have been transferred to the nucleus have to acquire several distinct traits typical of nuclear genes and absent in mitochondrial genes genes is typical of nuclear genes (Table S1). Moreover, the GC content of both genes is about 63% and fits well with that of the nuclear genome (64%) (Merchant et al, 2007). In contrast, the GC content is only 45 % for mtDNA (GenBank U03843 accession number).…”

“…In photosynthetic organisms, reducing equivalents generated by photosynthetic electron transfer chain can in part be consumed by the mitochondrial respiratory chain, owing to metabolic exchanges between the two organelles (reviewed in Cardol et al, 2011;Noctor et al, 2007). This process can be mediated by the activity of the malate-aspartate shuttle (Noguchi and Yoshida, 2008), whose genes are present in Chlamydomonas (Merchant et al, 2007).…”

“…Several exceptions to this distribution between mitochondrion-encoded membrane constituents and nucleus-encoded matricial subunits however exist in the green lineage: (i) the mt-DNA of most land plants code for 49 kD (NAD7) and 30 kD (NAD9) hydrophilic subunits; (ii) in the liverwort Marchantia polymorpha, a nad7 pseudogene is located in the mtDNA whereas a functional nad7 gene copy is found in the nuclear genome (Kobayashi et al, 1997); and (iii) the mitochondrial genomes of several chlorophycean unicellular green algae (including Chlamydomonas reinhardtii and Scenedesmus obliquus) code only for five complex I subunits (ND1, 2, 4, 5 and 6) (Bullerwell and Gray, 2004). Thanks to the sequencing of the nuclear genome of C. reinhardtii (Merchant et al, 2007), the NUO3, NUO7, NUO9, and NUO11 algal nuclear genes have been identified as homologs of the ND3, ND7, ND9 and ND4L mitochondrial coding sequences from higher plants (Cardol et al, 2005).…”

Cellulose degradation and assimilation by the unicellular phototrophic eukaryote Chlamydomonas reinhardtii

“…This organism is arguably one of the best model systems available for biotechnology-driven light to biomass 9,10 and light to biofuel 11 production research. As a wellestablished genetic model system C. reinhardtii has the benefits of a fully sequenced genome 12 , existing transformation protocols, well-known biochemical pathways and culturing requirements. Importantly, this alga has yielded the highest rates of biomethane 13 and hydrogen production in eukaryotes to date 14,15 .…”

“…Importantly, this alga has yielded the highest rates of biomethane 13 and hydrogen production in eukaryotes to date 14,15 . Furthermore, C. reinhardtii combines plant, as well as animal features, and has retained many genes of the last common plant-animal ancestor, which were lost from the genomes of angiosperms (flowering plants) 12 . Another important difference between flowering plants and C. reinhardtii is its use of fermentative pathways characteristic for anaerobic chemotrophs, but not for oxygenic phototrophs, which can be explained by extended periods of anoxia experienced by this soildwelling photosynthetic microbe 16 .…”