孤児作物のゲノム遺伝学およびその展望
多くの栽培植物でゲノム研究が進められている現在, イネ・コムギ・トウモロコシなどの主要作物だけでなく限定された地域で栽培される孤児作物の研究も進んでいる. 我々はその一つであるソバの全ゲノムを解読し進化遺伝学的な解析を実施した. その結果, （１）フツウソバFagopyrum esculemtum（および近縁種F. homotropicum）とダッタンソバF. tataricumの遺伝的分化（ゲノムサイズやセントロメア）への転移因子の関与, （２）ソバ属進化系統における２回の全ゲノム重複, （３）異型花型自家不和合性におけるS-ELF3遺伝子の花の形態と自家不和合性の制御, （４）栽培型フツウソバ（ssp. esculemtum）のチベット南東部の野生型ソバ（ssp. ancestral）由来などを示した. これらのデータに基づいたソバ育種への展望なども簡単に紹介する.
Evolution and switching of mitochondrion-localized DNA polymerases in Euglenozoa
The replication of mitochondrial (mt) genomes requires DNA polymerases, together with other proteins, encoded by the nuclear genomes. So far, evolutionarily distinct types of DNA polymerase have been reported to be localized in mitochondria. DNA polymerase gamma (Polγ) has been well studied as the mt-localized DNA polymerase in human and yeast. Trypanosomatids are known to possess multiple DNA polymerases (PolIA, B, C, and D) for their mitochondrial DNA replication. Another type of mt-localized DNA polymerase (plant and protist organellar DNA polymerase or POP) has been found in phylogenetically diverse protists. All of these DNA polymerases bear a sequence similarity to bacterial DNA polymerase I (PolI). In this study, we surveyed PolI-like DNA polymerases in diverse eukaryotes to depict the diversity and evolution of mt-localized DNA polymerases. We found that Discoba species except Euglenozoa have a novel type of mt-localized DNA polymerase that showed an evident phylogenetic affinity to alpha-proteobacterial PolI. Thus, we propose that this mt-localized DNA polymerase is the direct descendent of the PolI of the alpha-proteobacterial endosymbiont taken up by the last common ancestor of eukaryotes (LECA). Considering the finding of the novel mt-localized DNA polymerase, we will overview and discuss the evolution of mt-localized DNA polymerases during the divergence of euglenozoans.
Has the DNA polymerase of the proto-mitochondrion been retained in Discoba, Malawimonadidae, and Ancyromonadida?
The replication of mitochondrial (mt) genomes requires DNA polymerases that cooperate with other proteins encoded by the nuclear genomes. So far, evolutionarily distinct types of DNA polymerase have been reported to be localized in mitochondria. DNA polymerase gamma (Polγ) has been well studied as the mt-localized DNA polymerase in human and yeast. Trypanosomatids are known to possess multiple DNA polymerases (PolIA, B, C, and D) for their mitochondrial DNA replication. Another type of mt-localized DNA polymerase (plant and protist organellar DNA polymerase or POP) has been found in phylogenetically diverse protists. All of these DNA polymerases bear a sequence similarity to bacterial DNA polymerase I (PolI). In this study, we surveyed PolI-like DNA polymerases in diverse eukaryotes to depict the diversity and evolution of mt-localized DNA polymerases. We detected none of the above-mentioned mt-localized DNA polymerases in the species belonging to Malawimonadidae, Ancyromonadida, and Discoba (except for Euglenozoa). Instead, these species appeared to share a unique type of PolI-like polymerase. The novel PolI-like polymerases likely bear typical mitochondrial-targeting signals (MTS) at the N-termini, and the N-terminal amino acid sequences functioned as the MTS in yeast cells. Thus, we conclude that the novel PolI-like polymerases are localized in the mitochondria of Malawimonadidae, Ancyromonadida, and Discoba, all of which are the candidates for early branches of the tree of eukaryotes. Furthermore, the novel PolI-like polymerases showed a strong phylogenetic affinity to the PolI sequences of alpha-proteobacteria. Combined, we propose the mt-localized PolI-like polymerase occurred very early in eukaryotic evolution or is the direct descendant of the PolI of the alpha-proteobacterium that gave rise to the mitochondrion (i.e., proto-mitochondrion).
Mitochondrial RNA editing in ascetosporean amoebae
Ascetosporea is a subgroup of Endomyxa and all species are parasites of marine invertebrates. Any cultures have not been established and their complete life cycles were not understood. In the previous studies, the cells of Mikrocytida, which is an ascetosporean subgroup, were isolated from the infected oysters/crabs and analyzed. They showed that their mitochondria were reduced to mitochondrion related organelles and their organellar genome was lacking. In the present study, we established two axenic cultures of Paradinida, which is another subgroup of Ascetosporea. DNA-seq on them reveled that they possessed ca. 20 kbp of circular organellar genomes, respectively. However, their genes were fragmented by the insertions of stop codon, suggesting that they were either pseudogenes or involved in RNA editing. As reconstructed genome sequences were compared with their RNA-seq data, massive RNA editing, i.e., substitutions from adenosine and cytidine to inosine and uridine, respectively, was confirmed. Many of the editing sites were shared between two paradinid cultures, but strain-unique editing sites were also detected. The gene sequences after the editing seemed operative and they were involved in electron transfer system. Hence, the mitochondria of Paradinida are not functionary reduced, unlike Mikrocytida. Further, we also detected adenosine deaminase acting on RNA (ADAR), which is a key enzyme of A- to-I substitution, from paradinids as well as other several protists. As we analyzed its localization in paradinids’ cell using the commercially available anti-human-ADAR antibody, they were clearly and specifically localized in their mitochondria. Since ADAR was thought to be unique in metazoans and function in nucleus for a long period, it was surprising and speculated that ADAR may have originated in the last eukaryotic common ancestor. ADAR of paradinids may have a function to mask some lethal substitution in their mitochondrial genomes, which may help their diversification.