Biology subjects

Yazaki, E.

Publications and source records attributed to Yazaki, E..

6 recordsLinked to original sources

bioRxiv2026

Evolution of form I-related RuBisCOs updated: Uncertainties and diversity encompassing Bacteria and Archaea.

Forms I&prime, I&Prime, and I RuBisCOs were recently identified in bacterial metagenome-assembled genomes (MAGs) and are significant for evolutionarily bridging form I, which is responsible for the major part of carbon fixation on Earth, and other forms. Pioneering studies focused mainly on the biochemical and structural characteristics of "form I-related" RuBisCOs and deduced the evolution of this protein family over phylogenetic relationships among form I and form I-related sequences. We here surveyed form I-related sequences in public databases and conducted phylogenetic analyses incorporating the updated diversity of form I-related RuBisCOs. This study yielded two major outcomes regarding RuBisCO evolution. First, the analyses presented here suggest uncertainties overlooked in the previously published studies. It appeared to be difficult to conclude (i) the phylogenetic relationship among forms I, I&prime, and I&Prime, (ii) the monophyly of form I&prime, or (iii) the monophyly of form I. Second, we identified a gene encoding form I RuBisCO in an archaeal MAG, and this protein is likely involved in the pentose bisphosphate pathway. The results presented here suggest that the evolutionary route leading to form I in RuBisCO evolution remains unsettled.

evolutionary biology↗

bioRxiv2025

Glissandra oviformis n. sp.: a novel predatory flagellate illuminates the character evolution within the eukaryotic clade CRuMs

Culturing protists offers a powerful approach to exploring eukaryotic diversity, especially for deep-branching lineages. In this study, we cultured and described a novel protist species, named Glissan-dra oviformis n sp., within the poorly studied and unclassified genus Glissandra. While an SSU rDNA gene phylogeny failed to resolve its phylogenetic placement in the eukaryotic tree, a phylogenomic analysis of 340 proteins indicated G. oviformis as a deep-branching member of the CRuMs clade. Prior to this study, this clade consisted of diverse het-erotrophic amoeba and flagellates and lacks clear synapomorphies. Ultrastructural observations re-vealed that G. oviformis shares the characteristics with some CRuMs members, including the pellicle underlying the plasma membrane and an internal sleeve surrounding the central pair of the axoneme at the flagellar transitional region. Our findings suggest potential shared characteristics and synapomorphies for CRuMs and contribute to a deeper understanding of the character evolution within CRuMs.

evolutionary biology↗

bioRxiv2023

Encyclopaedia of DNA polymerases localized in organelles: Contribution of genes from diverse bacteria including the proto-mitochondrion.

DNA polymerases (DNAPs) synthesize DNA from deoxyribonucleotides in a semi-conservative manner and serve as the core of DNA replication and repair machineries. In eukaryotic cells, there are two genome-containing organelles, mitochondria and plastids, that were derived from an -proteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNAPs that localize and work in them to maintain their genomes. The evolution of organellar DNAPs has yet to be fully understood because of two unsettled issues. First, the diversity of organellar DNAPs has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNAPs that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNAPs known to date show no phylogenetic affinity to those of the extant -proteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNAP sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNAPs were further examined experimentally. The results presented here suggest that the diversity of organellar DNAPs has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed two mitochondrial DNAPs, POP and a candidate of the direct descendant of the proto-mitochondrial DNAP, rdxPolA, identified in this study.

evolutionary biology↗

bioRxiv2023

Massive RNA editing in ascetosporean mitochondria

Ascetosporeans are parasitic protists of invertebrates. As only two species of Mikrocytida, an ascetosporean subgroup, have ever been sequenced deeply and analyzed using cells isolated from infected organisms, it was shown that their mitochondria are functionally reduced and the organellar genome is lacking. However, molecular studies on other ascetosporeans have not been conducted, and whether reduced mitochondria is common in ascetosporeans remains unclear. In the present study, we established two cultures of Paradinida, another ascetosporean subgroup, and reconstructed their mitochondrial genomes. As they were compared with their RNA-seq data, massive A-to-I and C-to-U types of RNA editing were detected. Many editing sites are shared between two paradinids, but strain-unique sites also exist. As the mitochondrial genes are involved in the electron transfer system, their mitochondria are not functionally reduced, unlike that in Mikrocytida. Furthermore, we detected adenosine deaminase acting on RNA (ADAR), which is a key enzyme of A-to-I substitution, in paradinids as well as several other protists. Immunostaining showed that this ADAR is specifically localized in the mitochondria of paradinids, suggesting that A-to-I substitution in paradinid mitochondria is mediated by ADAR. These findings elucidated the functional diversity and evolutionary process of ascetosporean mitochondria as well as ADAR.

evolutionary biology↗

bioRxiv2021

Phylogenomics invokes the clade housing Cryptista, Archaeplastida, and Microheliella maris.

As-yet-undescribed branches in the tree of eukaryotes are potentially represented by some of "orphan" protists (unicellular micro-eukaryotes), of which phylogenetic affiliations have not been clarified in previous studies. By clarifying the phylogenetic positions of orphan protists, we may fill the previous gaps in the diversity of eukaryotes and further uncover the novel affiliation between two (or more) major lineages in eukaryotes. Microheliella maris was originally described as a member of the phylum Heliozoa, but a pioneering large-scale phylogenetic analysis failed to place this organism within the previously described species/lineages with confidence. In this study, we analyzed a 319-gene alignment and demonstrated that M. maris represents a basal lineage of one of the major eukaryotic lineages, Cryptista. We here propose a new clade name "Pancryptista" for Cryptista plus M. maris. The 319-gene analyses also indicated that M. maris is a key taxon to recover the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista, which is collectively called as "CAM clade" here. Significantly, Cryptophyceae tend to be attracted to Rhodophyta depending on the taxon sampling (ex., in the absence of M. maris and Rhodelphidia) and the particular phylogenetic "signal" most likely hindered the stable recovery of the monophyly of Archaeplastida in previous studies. We hypothesize that many cryptophycean genes (including those in the 319-gene alignment) recombined partially with the homologous genes transferred from the red algal endosymbiont during secondary endosymbiosis and bear a faint phylogenetic affinity to the rhodophytan genes.

evolutionary biology↗

bioRxiv2019

Barthelonids represent a deep-branching Metamonad clade with mitochondrion-related organelles generating no ATP.

We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. Barthelona spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one Barthelona strain (PAP020) was used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. Strain PAP020 is most likely incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected the putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.

evolutionary biology↗