Biology subjects

Tsusaka, T.

Publications and source records attributed to Tsusaka, T..

8 recordsLinked to original sources

bioRxiv2025

Progeny-based genomic selection reveals untapped genetic potential in an underutilized medicinal plant, Perilla frutescens

O_LIDespite their substantial therapeutic value, medicinal plants have undergone limited genetic improvement through breeding because of the scarcity of expert breeders. Moreover, quantifying bioactive compounds is expensive. Genomic selection (GS), which leverages genome-wide markers to predict breeding values and assemble favorable alleles, offers a practical way to unlock latent genetic potential. As a model case, we evaluated GS in red perilla (Perilla frutescens). C_LIO_LIBuilding on previous work, we implemented a cross-selection strategy that prioritized segregation variance by selecting crosses based on predicted additive genotypic values of the progeny, and evaluated its effectiveness through actual crossing experiments targeting three key medicinal compounds. C_LIO_LIProgeny from GS-based crosses (Crs1-Crs7) outperformed those from phenotypic selection (Crs8) in the G2 generation, demonstrating a higher mean, greater variance, and superior top individuals. The best G2 individual exhibited nearly twofold higher levels of two target compounds relative to the existing cultivar Sekiho. C_LIO_LIThis study provides the first empirical demonstration that GS can improve multiple medicinal compounds in red perilla and highlights the effectiveness of cross-selection based on predicted progeny performance. In addition, the evidence presented here supports the broader application of GS in underutilized medicinal plants. C_LI

genetics↗

bioRxiv2025

The Integrated Stress Response Pathway Improves Aged Murine Muscle Stem Cell Activation and in vivo Regeneration.

For efficient regeneration, muscle stem cells (MuSCs) transition out of quiescence through a series of progressively more activated states. During MuSC aging, transition through the earliest steps is the slowest and delayed, with the molecular regulators that govern this transition not well characterized. By analyzing the dynamic changes of MuSCs at the molecular (scRNA-Seq and Cell Painting) and phenotypic (heteromotility) level at single cell resolution we found that the Integrated Stress Response (ISR) Pathway is a critical regulator of MuSC transition states. Aged MuSCs have increased baseline ISR activity in quiescence that does not increase during activation to levels observed in adult MuSCs. Rapid and transient pharmacological ISR activation in vitro was sufficient to increase aged MuSC activation rate and migratory behavior as well as alter the transcriptional states toward a younger phenotype. ISR activation also improved aged MuSC potency and aged mouse muscle regeneration in vivo. Therefore, pharmacological activation of the ISR has therapeutic potential to improve MuSC function and skeletal muscle repair during aging.

cell biology↗

bioRxiv2025

Class I histone deacetylases catalyze lysine lactylation

Metabolism and post-translational modifications (PTMs) are intrinsically linked and the number of identified metabolites that can covalently modify proteins continues to increase. This metabolism/PTM crosstalk is especially true for lactate, the product of anaerobic metabolism following glycolysis. Lactate forms an amide bond with the {varepsilon}-amino group of lysine, a modification known as lysine lactylation, or Kla. Multiple independent mechanisms have been proposed in the formation of Kla, including p300/CBP-dependent transfer from lactyl-CoA, via a high-energy intermediate lactoylglutathione species that non-enzymatically lactylates proteins, and several enzymes are reported to have lactyl transferase capability. We recently discovered that class I histone deacetylases (HDACs) 1, 2, and 3 can all reverse their canonical chemical reaction to catalyze lysine {beta}-hydroxybutyrylation. Here we tested the hypothesis that HDACs can also catalyze Kla formation. Using biochemical, pharmacological, and genetic approaches, we found that HDAC-catalyzed lysine lactylation accounts for the majority of Kla formation in cells. Dialysis experiments confirm this is a reversible reaction that depends on lactate concentration. We also directly quantified intracellular lactyl-CoA and found that Kla abundance can be uncoupled from lactyl-CoA levels. Therefore, we propose a model in which the majority of Kla is formed through enzymatic addition of lactate by HDACs 1, 2, and 3.

biochemistry↗

bioRxiv2025

Optimization of crossing strategy based on the usefulness criterion in inter-population crosses considering different genetic effects among populations

In the breeding programs of self-pollinated plants, achieving genetic improvement in multiple traits can be challenging when relying solely on a single biparental population. Interpopulation crosses are employed to integrate favorable alleles from multiple biparental populations to overcome this limitation. In this context, it is crucial to consider the distinct genetic effects in different populations. In this study, we utilized a selection method based on the usefulness criterion (UC) to identify cross pairs suitable for interpopulation crosses. We expanded this approach to enhance breeding programs accounting for varying genetic backgrounds within the genomic selection framework. Using the medicinal plant red perilla as the study material, we conducted simulations to compare the efficacy of selection based on estimated genomic breeding values with that based on UC. Our findings demonstrate that the proposed method is effective in facilitating the simultaneous improvement of multiple traits, particularly by considerably increasing genetic gains among the top-performing individuals in the population. Furthermore, we provide guidelines for implementing interpopulation crosses, including recommendations for the optimal generation for crossing and the appropriate reference generation for calculating the UC. The results obtained in this study offer valuable insights for small-scale breeding programs aimed at simultaneously enhancing multiple traits through inter-population crosses and are applicable to a wide range of crops, including neglected and underutilized species. Key MessageHerein, a method has been proposed for selecting optimal cross pairs based on the genetic potential of progeny in inter-population crosses, considering different genetic effects among populations.

bioinformatics↗

bioRxiv2024

B chromosome and its non-Mendelian inheritance in Atractylodes lancea

Supernumerary B chromosomes contribute to intraspecific karyotypic variation. B chromosomes have been detected in more than 2000 organisms; they possess unique and diverse features, including non-Mendelian inheritance. Here we report one or more B chromosomes in the gynodioecious plant, Atractylodes lancea. Among 54 A. lancea lines, 0-2 B chromosomes were detected in both hermaphroditic and female plants, with the B chromosomes appearing as DAPI-bright regions within the nuclei. Genomic in situ hybridization revealed that the B chromosomes had no conserved A chromosome DNA sequences, which was confirmed by fluorescence in situ hybridization probed with independently dissected B chromosomes. In male meiosis, the B chromosome did not pair with an A chromosome and was therefore eliminated; accordingly, only 20.1% and 18.6% of these univalent B chromosomes remained at the end of meiosis for the 1B lines of KY17-148 and KY17-118, respectively. However, we also found that B chromosomes were transmitted from male parents in 40.8%-44.2% and 47.2% of the next generation; although these transmission rates from male parents were not essentially different from Mendelian inheritance (0.5), the transmission of gametes carrying B chromosomes increased through fertilization or seed development. B chromosomes were transmitted from three of four 1B female parents to 64.3%-92.6% of the next generation, suggesting B chromosome accumulation. We propose that the B chromosome of A. lancea has a specific sequence and persists via non-Mendelian inheritance from female parents. Overall, A. lancea is a useful material for understanding the structure, evolution, and mechanism of non-Mendelian inheritance of B chromosomes.

genetics↗

bioRxiv2023

Reversible histone deacetylase activity catalyzes lysine acylation

Starvation and low carbohydrate diets lead to the accumulation of the ketone body, {beta}-hydroxybutyrate (BHB), whose blood concentrations increase more than 10-fold into the millimolar range. In addition to providing a carbon source, BHB accumulation triggers lysine {beta}-hydroxybutyrylation (Kbhb) of proteins via unknown mechanisms. As with other lysine acylation events, Kbhb marks can be removed by histone deacetylases (HDACs). Here, we report that class I HDACs unexpectedly catalyze protein lysine modification with {beta}-hydroxybutyrate (BHB). Mutational analyses of the HDAC2 active site reveal a shared reliance on key amino acids for classical deacetylation and non-canonical HDAC-catalyzed {beta}-hydroxybutyrylation. Also consistent with reverse HDAC activity, Kbhb formation is driven by mass action and substrate availability. This reverse HDAC activity is not limited to BHB but also extends to multiple short-chain fatty acids. The reversible activity of class I HDACs described here represents a novel mechanism of PTM deposition relevant to metabolically-sensitive proteome modifications.

molecular biology↗

bioRxiv2023

Assessing the potential for genome-assisted breeding in red perilla using quantitative trait locus analysis and genomic prediction

Red perilla is an important medicinal plant used in Kampo medicine, and the development of elite varieties of this species is urgently necessary. Medicinal compounds are generally considered target traits in medicinal plant breeding; however, selection based on the phenotypes of the compounds (i.e., conventional selection) is expensive and time-consuming. Here, we proposed genomic selection (GS) and marker-assisted selection (MAS) as suitable selection methods for medicinal plants, and evaluated the effectiveness of GS and MAS in red perilla breeding. Three breeding populations generated from crosses between one red and three green perilla genotypes were used to elucidate the genetic mechanisms underlying the production of major medicinal compounds using quantitative trait locus analysis and to evaluate the accuracy of genomic prediction (GP). We found that GP had sufficiently high accuracy for all traits, confirming that GS was an effective method for perilla breeding. Moreover, the three populations showed varying degrees of segregation, suggesting that use of these populations in breeding may yield simultaneous enhancements of different target traits. This study can contribute to research on the genetic mechanisms of the major medicinal compounds of red perilla as well as the breeding efficiency of this medicinal plant.

genomics↗

bioRxiv2023

Non-specific recognition of histone modifications by H3K9bhb antibody

Ketone bodies are short chain fatty acids produced in the liver during periods of limited glucose availability that provide an alternative source of energy for the brain, heart, and skeletal muscle. Beyond this classical metabolic role, {beta}-hydroxybutyrate (BHB), is gaining recognition as a pleiotropic signaling molecule. Lysine {beta}-hydroxybutyrylation (Kbhb) is a newly discovered post-translational modification in which BHB is covalently attached to lysine {varepsilon}-amino groups. This novel protein adduct is metabolically sensitive, dependent on BHB concentration, and found on proteins in multiple intracellular compartments, including the mitochondria and nucleus. Therefore, Kbhb is hypothesized to be an important component of ketone body-regulated physiology. Kbhb on histones is proposed to be an epigenetic regulator, which links metabolic alterations to gene expression. However, we found that the widely used antibody against the {beta}-hydroxybutyrylated lysine 9 on histone H3 (H3K9bhb) also recognizes other modification(s), which are increased by deacetylation inhibition and include likely acetylations. Therefore, caution must be used when interpreting gene regulation data acquired with the H3K9bhb antibody.

biochemistry↗