Biology subjects

Akimoto, S.

Publications and source records attributed to Akimoto, S..

7 recordsLinked to original sources

bioRxiv2022

Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120

Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits are identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 is inserted at the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide novel insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs.

plant biology↗

bioRxiv2022

Phosphorylation of light-harvesting complex II controls excitation energy spillover between photosystems

Land plants and microalgae convert solar energy into electrochemical energy by using cooperative two photosystems (PSI and PSII). To maintain optimal photosynthetic rates under variable light conditions in nature, phosphorylation of light-harvesting complex for PSII (LHCII) balances the excitation energy distribution between the two photosystems. Here, we investigated the mechanism of this balancing in a green alga. We show that phospho-LHCIIs physically bind to both photosystems. The energy transfer from the LHCIIs to the PSII core complexes becomes less efficient, whereas the excitation level of PSI increases. The time-resolved fluorescence spectra showed an increase in delayed PSI fluorescence, which represents energetical spillover from PSII to PSI. In addition, the spillover is likely mediated by phospho-LHCIIs and PSI antennas. We hypothesize that the spillover explains the larger extent of phospho-LHCIIs dependent energy balancing in the green alga than land plants, which is important for the short-term photoadaptaion in the algal habitat.

plant biology↗

bioRxiv2022

Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes

Photosystem I (PSI) contributes to light-conversion reactions; however, its oligomerization state is variable among photosynthetic organisms. Herein we present a 3.8-[A] resolution cryo-electron microscopic structure of tetrameric PSI isolated from a glaucophyte alga Cyanophora paradoxa. The PSI tetramer is organized in a dimer of dimers form with a C2 symmetry. Different from cyanobacterial PSI tetramer, two of the four monomers are rotated around 90{degrees}, resulting in a totally different pattern of monomer-monomer interactions. Excitation-energy transfer among chlorophylls differs significantly between Cyanophora and cyanobacterial PSI tetramers. These structural and spectroscopic features reveal characteristic interactions and energy transfer in the Cyanophora PSI tetramer, thus offering an attractive idea for the changes of PSI from prokaryotes to eukaryotes.

plant biology↗

bioRxiv2021

Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI

Photosystem I (PSI) of photosynthetic organisms is a multi-subunit pigment-protein complex and functions in light harvesting and photochemical charge-separation reactions, followed by reduction of NADP to NADPH required for CO2 fixation. PSI from different photosynthetic organisms has a variety of chlorophylls (Chls), some of which are at lower-energy levels than its reaction center P700, a special pair of Chls, and are called low-energy Chls. However, the site of low-energy Chls is still under debate. Here, we solved a 2.04-[A] resolution structure of a PSI trimer by cryo-electron microscopy from a primitive cyanobacterium Gloeobacter violaceus PCC 7421, which has no low-energy Chls. The structure showed absence of some subunits commonly found in other cyanobacteria, confirming the primitive nature of this cyanobacterium. Comparison with the known structures of PSI from other cyanobacteria and eukaryotic organisms reveals that one dimeric and one trimeric Chls are lacking in the Gloeobacter PSI. The dimeric and trimeric Chls are named Low1 and Low2, respectively. Low2 does not exist in some cyanobacterial and eukaryotic PSIs, whereas Low1 is absent only in Gloeobacter. Since Gloeobacter is susceptible to light, this indicates that Low1 serves as a main photoprotection site in most oxyphototrophs, whereas Low2 is involved in either energy transfer or energy quenching in some of the oxyphototrophs. Thus, these findings provide insights into not only the functional significance of low-energy Chls in PSI, but also the evolutionary changes of low-energy Chls responsible for the photoprotection machinery from photosynthetic prokaryotes to eukaryotes.

plant biology↗

bioRxiv2021

Strategy for detecting off-target sites in genome-edited rice

Genome-editing using the CRISPR-Cas9 system can substantially accelerate crop breeding. Because off-target editing is the main problem with this system, a reliable method for comprehensively detecting off-target sites is required for the editing of food crop genomes. However, a method that accurately predicts off-target sites has not been established. In this study, we performed a SITE-Seq analysis to predict potential off-target sites. SITE-Seq is an unbiased method applicable for the in vitro detection of double-strand breaks (DSBs). To analyze SITE-Seq data, we developed a novel Galaxy system, which can perform simple and reproducible analyses without a command line operation. We conducted a SITE-Seq analysis of a rice genome modified by OsFH15 gRNA-Cas9, and identified 41 DSB sites in the annotated regions. Amplicon-sequencing revealed mutations at one off-target site in the genome-edited rice. The presence of an uncommon protospacer adjacent motif (NTG PAM) likely makes this off-target site difficult to identify using in silico methods. Of the six tested programs, only CRISPRdirect predicted this off-target site, but it also predicted 6,080 off-target sites in total. These results suggest the SITE-Seq method presented herein can efficiently predict off-target sites and is useful for assessing the safety of genome-edited food.

bioinformatics↗

bioRxiv2021

Seasonal variation in the relative importance of assembly processes in marine fish communities as determined by environmental DNA analyses

Compositional variation among local communities reflects the differences in abiotic environments, though the extent of the influence varies in natural systems. Generally, the environmental filtering is expected to be strong if the environmental gradient encompasses severe habitats where species sorting is highly likely to work. However, this hypothesis has rarely been tested in dynamic systems, where the higher dispersal ability of species allows them to easily respond to stressful environments. Here, with the dynamics of fish communities in a Japanese bay revealed by environmental DNA analyses as a model case, we examined how harmful seasonal hypoxia (low concentration of oxygen in bottom waters in summer) affected the strength of environmental filtering. We found that, in summer, dissolved oxygen (DO) concentration was significantly low and fish species richness decreased in the bottom water compared to the surface, suggesting that the organisms were adversely affected by the hypoxia. At the same time, the between-depths heterogeneity in DO concentration was larger, but species composition was less divergent and the influence of DO on species composition appeared weaker during summer. These results imply that environmental filtering is weakened when the bottom water was characterized by extremely severe environments. Furthermore, there was a shift in the species occurrence from bottom to surface waters in summer that was consistent across species, suggesting that the extremely severe hypoxia adversely affected fish species irrespective of their identity. These results collectively suggest that environmental filtering is weaker during summer despite more severity and heterogeneity in environments, most likely because individual movements to avoid unpreferable environments in the bottom waters occurred quasi-neutrally. By providing evidence against the prevailing understanding that environmental filtering strongly works in severe environments, these findings invoke further investigation on how the filtering acts in various conditions.

ecology↗

bioRxiv2020

Development of a humanized mouse model to analyze antibodies specific for human leukocyte antigen (HLA)

In organ transplantation, human leukocyte antigen (HLA)-mismatch grafts not only induce the activation of cellular mediated immune response but also the development of chronic antibody-mediated rejection due to the donor-specific anti-HLA antibody (DSA) produced by B cells and plasma cells interacting with the graft endothelium. Significant improvement in long-term survival after transplantation can be expected if antibody-mediated rejection due to the DSA can be overcome. However, the mechanism of producing or controlling the DSA remains to be elucidated. In recent decades, "humanized mouse model" have been widely used for the basic research of human immune systems, but a humanized mouse model to analyze the mechanism of DSA production has not been established yet. Thus, we aimed to create a humanized mouse using a severe immunodeficiency mouse (NSG mouse) administered with human peripheral blood mononuclear cells (PBMCs). Initially, we detected very low level of human total-IgG and no anti-HLA antibodies (Abs) in these mice. The responder PBMCs with antibody-producing B cell activating factors added or regulatory T cells depleted were subsequently co-cultured with the irradiated stimulator PBMCs in vitro, and these whole cells were administered into naive NSG mice. The humanized model with sufficient human total-IgG and anti-HLA antibody production was consequently established. Interestingly, in all these mouse models, allo-specific anti-HLA Abs production was prominently suppressed, whereas non-allo-specific anti-HLA Abs were sufficiently detectable. Therefore, this novel humanized mouse model might be useful for analyzing the mechanism of anti-allogeneic human B cell tolerance induction.

immunology↗