Biology subjects

Nishiyama, T.

Publications and source records attributed to Nishiyama, T..

24 records · Page 2Linked to original sources

bioRxiv2021

Discovery of the fastest myosin, its amino acid sequence, and structural features

Cytoplasmic streaming with extremely high velocity (~70 m s-1) occurs in cells of the characean algae (Chara). Because cytoplasmic streaming is caused by organelle-associated myosin XI sliding along actin filaments, it has been suggested that a myosin XI, which has a velocity of 70 m s-1, the fastest myosin measured so far, exists in Chara cells. However, the previously cloned Chara corallina myosin XI (CcXI) moved actin filaments at a velocity of around 20 m s-1, suggesting that an unknown myosin XI with a velocity of 70 m s-1 may be present in Chara. Recently, the genome sequence of Chara braunii has been published, revealing that this alga has four myosin XI genes. In the work reported in this paper, we cloned these four myosin XIs (CbXI-1, 2, 3, and 4) and measured their velocities. While the velocities of CbXI-3 and CbXI-4 were similar to that of CcXI, the velocities of CbXI-1 and CbXI-2 were estimated to be 73 and 66 m s-1, respectively, suggesting that CbXI-1 and CbXI-2 are the main contributors to cytoplasmic streaming in Chara cells and showing that CbXI-1 is the fastest myosin yet found. We also report the first atomic structure (2.8 [A] resolution) of myosin XI using X-ray crystallography. Based on this crystal structure and the recently published cryo-EM structure of acto-myosin XI at low resolution (4.3 [A]), it appears that the actin-binding region contributes to the fast movement of Chara myosin XI. Mutation experiments of actin-binding surface loop 2 support this hypothesis. Significance statementIt has been suggested for more than 50 years that the fastest myosin in the biological world, with a velocity of 70 m s-1, exists in the alga Chara because cytoplasmic streaming with a velocity of 70 m s-1 occurs in Chara cells. However, a myosin with that velocity has not yet been identified. In this work, we succeeded in cloning a myosin XI with a velocity of 73 m s-1, the fastest myosin so far measured. We also successfully crystallized myosin XI for the first time. Structural analyses and mutation experiments suggest that the central regions that define the fast movement of Chara myosin XI are the actin-binding sites.

cell biology↗

bioRxiv2021

A simple Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis

We have developed a simple Agrobacterium-mediated method for the stable transformation of the hornwort Anthoceros agrestis, the fifth bryophyte species for which a genetic manipulation technique becomes available. High transformation efficiency was achieved by using thallus tissue grown under low-light conditions. We generated a total of 216 transgenic A. agrestis lines expressing the {beta}-Glucuronidase (GUS), cyan, green, and yellow fluorescent proteins under the control of the CaMV 35S promoter and several endogenous promoters. Nuclear and plasma membrane localization with multiple color fluorescent proteins was also confirmed. The transformation technique described here should pave the way for detailed molecular and genetic studies of hornwort biology, providing much needed insight into the molecular mechanisms underlying symbiosis, carbon-concentrating mechanism, RNA editing, and land plant evolution in general.

plant biology↗

bioRxiv2020

Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs

Some sea slugs sequester chloroplasts from algal food in their intestinal cells and photosynthesize for months. This phenomenon, kleptoplasty, poses a question of how the chloroplast retains its activity without the algal nucleus. There have been debates on the horizontal transfer of algal genes to the animal nucleus. To settle the arguments, this study reported the genome of a kleptoplastic sea slug Plakobranchus ocellatus and found no evidence of photosynthetic genes encoded on the nucleus. Nevertheless, it was confirmed that light illumination prolongs the life of mollusk under starvation. These data presented a paradigm that a complex adaptive trait, as typified by photosynthesis, can be transferred between eukaryotic kingdoms by a unique organelle transmission without nuclear gene transfer. Our phylogenomic analysis showed that genes for proteolysis and immunity undergo gene expansion and are up-regulated in chloroplast-enriched tissue, suggesting that these molluskan genes are involved in the DNA-independent phenotype acquisition.

evolutionary biology↗

bioRxiv2019

Toward Health Management of Major Labour Force Generation by Using Infection Control Countermeasures for Haematobium Schistosomiasis -assumed to be related to occupational risk- in the Republic of Malawi

BackgroundIn Malawi, haematobium schistosomiasis is highly endemic. According to previous studies, countermeasures have been conducted mainly in school-aged children. In this study, we focused on the age groups, which are assumed to be major labour force generation. Haematobium schistosomiasis is supposed to be related to occupational activities in schistosome endemic countries. MethodsWe chronologically followed the transition of schistosome egg positive prevalence before and after mass drug administration of praziquantel (MDA) by using a urine filtering examination. We also analyzed the effectiveness of urine reagent strips from the cost perspective. FindingsThe egg positive prevalence was 34.3% (95%CI: 28.5-40.5) just before MDA in June 2010 and the highest prevalence was in the age of twenties. The egg positive prevalence reduced to 12.7% (95%CI: 9.2-17.3, p<0.01) eight weeks after the first MDA and the prevalence reduced to 6.9% (95%CI: 4.6-10.0, p<0.01) after the second MDA in August 2011. The egg positive prevalence after MDA in 2013 was reduced from 3.8% (95%CI: 2.1-6.9) to 0.9% (95%CI: 0.3-3.4) and p value was 0.050. Using urine reagent strips after MDA, the positive predictive value decreased, but the negative predictive value remained high. The cost of one urine reagent strip and one tablet of praziquantel were US$0.06 and US$0.125 in 2013 in Malawi. If the egg positive prevalence is 40%, screening subjects for MDA using urine reagent strips, the cost reduction can be estimated to be about 24% -showing an overall cost reduction. ConclusionThe combination of MDA and urine reagent strips could be both a practical and cost-effective countermeasure for haematobium schistosomiasis. It is key to recognize that haematobium schistosomiasis could be considered a disease that is assumed to have some concern with occupational risk in tropical agricultural countries such as Malawi. From this point of view, it is very important to protect the health of workers; the sound labour force generation is vital for economic growth and development in these countries. Author summarySchistosomiasis is widely endemic in the tropical and subtropical countries including Malawi, and it is related that more than 300 million people suffer from associated severe morbidity. The pathway of transmission is mainly contacting infested fresh water and it is inevitable to contact fresh water through their daily activities in Malawi. Then, they are routinely exposed to the risk of schistosome infection. Previously the main targets of schistosome control were school-aged children, but our research showed main population of schistosome infection was twenties that was presumed to be major labour force. Agriculture is the dominant industry in Malawi and it can be related to be at risk of schistosome infection during agricultural work. Schistosomiasis is presumed to have occupation-related risks, we consider that schistosome control will be a valuable step-up to economic development and make a social contribution in Malawi and many low-income tropical countries. FundingThe Ministry of Education, Culture, Sports, Science and Technology of Japans scientific research grant (JSPS KAKENHI Grant Number JP23406025). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

microbiology↗

bioRxiv2018

Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation

BackgroundNext-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression that cannot be studied using populations of cells. The utilization of scRNA-seq is, however, restricted to specific types of cells that can be isolated from their original tissues, and it can be difficult to obtain precise positional information for these cells in situ.\n\nResultsHere, we established single cell-digital gene expression (1cell-DGE), a method of scRNA-seq that uses micromanipulation to extract the contents of individual living cells in intact tissue while recording their positional information. Furthermore, we employed a unique molecular identifier to reduce amplification bias in the cDNA libraries. With 1cell-DGE, we could detect differentially expressed genes (DEGs) during the reprogramming of leaf cells into stem cells in excised tissues of the moss Physcomitrella patens, identifying 6,382 DEGs between cells at 0 h and 24 h after excision. We found substantial variations in both the transcript levels of previously reported reprogramming factors and the overall expression profiles between cells, which appeared to be related to their different reprogramming abilities or the estimated states of the cells according to the pseudotime based on the transcript profiles.\n\nConclusionsWe developed 1cell-DGE with microcapillary manipulation, a technique that can be used to analyze the gene expression of individual cells without detaching them from their tightly associated tissues, enabling us to retain positional information and investigate cell-cell interactions.

plant biology↗

bioRxiv2018

Patterns of polymorphism, selection and linkage disequilibrium in the subgenomes of the allopolyploid Arabidopsis kamchatica

Although genome duplication is widespread in wild and crop plants, little is known about genome-wide selection due to the complexity of polyploid genomes. In allopolyploid species, the patterns of purifying selection and adaptive substitutions would be affected by masking owing to duplicated genes or homeologs as well as by effective population size. We resequenced 25 distribution-wide accessions of the allotetraploid Arabidopsis kamchatica, which has a relatively small genome size (450 Mb) derived from the diploid species A. halleri and A. lyrata. The level of nucleotide polymorphism and linkage disequilibrium decay were comparable to A. thaliana, indicating the feasibility of association studies. A reduction in purifying selection compared with parental species was observed. Interestingly, the proportion of adaptive substitutions () was significantly positive in contrast to the majority of plant species. A recurrent pattern observed in both frequency and divergence-based neutrality tests is that the genome-wide distributions of both subgenomes were similar, but the correlation between homeologous pairs was low. This may increase the opportunity of different evolutionary trajectories such as in the HMA4 gene involved in heavy metal hyperaccumulation.

evolutionary biology↗