Biology subjects

Sakuma, S.

Publications and source records attributed to Sakuma, S..

5 recordsLinked to original sources

bioRxiv2026

Homoeo-alleles of wheat GNI2 fuel grain yields across input environments

Grain yield in wheat is frequently driven by pre-anthesis growth and how carbon is directed to reproductive parts, determining the potential size of the grain-producing sink. However, the genetic mechanisms controlling this carbon allocation remain unclear. In this study we discovered a series of loci in tetraploid and hexaploid wheats that, when combined, confer an average grain yield advantage in hexaploid winter wheat of approx. 5-7% under high-input farming while approx. 10-15% under low-input conditions. The responsible gene is GRAIN NUMBER INCREASE 2 (GNI2), ancestral to its duplicate GNI1, and represented by the homoeo-allelic series GNI-A2, GNI-B2, and GNI-D2. GNI1 and all GNI2 copies additively affect floral growth and fertility by modulating reproductive allocation and harvest index. Herewith, we describe a series of grain yield-relevant GNI2 homoeo-alleles with a proven track record for being beneficial in both high- and low-input environments. Their deployment offers a sustainable pathway to raise global grain yields in the future.

plant biology↗

bioRxiv2026

Nup358 Sustains Intestinal Epithelial Homeostasis by Preventing Dvl1 Condensate Formation to Restrain Wnt Signaling

Nucleoporins are increasingly recognized as tissue-specific regulators beyond their structural roles in the nuclear pore complex. Here, we identify nucleoporin Nup358 as a critical repressor of Wnt signaling required for intestinal epithelium integrity. Ablation of Nup358 in adult mice causes a catastrophic loss of crypt-villus architecture and disrupts the intestinal epithelial layer. Notably, while the intestinal stem cell (ISC) pool remains stable, the transit-amplifying (TA) progenitor compartment is depleted. Mechanistically, we show that the interaction of Nup358 with Dvl1 through its N-terminal domain inhibits Dvl1 spontaneous phase separation. In the absence of Nup358, Dvl1 biomolecular condensates promote Tankyrase-mediated degradation of Axin1, leading to the constitutive stabilization of {beta}-catenin and ligand-independent Wnt activation, negatively impacting cell differentiation and TA progenitor survival. Our results demonstrate that Nup358 acts as a molecular safeguard that dampens Wnt signaling levels in intestinal crypts. By preventing Dvl1-mediated Wnt signal amplification, Nup358 allows ISCs to transition into the TA compartment and initiate the differentiation programs essential for intestinal homeostasis.

cell biology↗

bioRxiv2022

Acidophilic nitrification alleviates phosphorus deficiency in hydroponics with biogas digestates

Biogas digestates can be applied to hydroponics via nitrification. However, the low solubility of phosphorus in digestates can cause phosphorus deficiency in plants. Here, we hypothesized that acidophilic nitrification might prevent this deficiency by dissolving phosphorus in the digestate. Acidophilic and neutrophilic nitrification were conducted at a pH of 3.27 and 6.25 using biogas digestates from food wastes. Acidophilic nitrification dissolved about 3.5 times more phosphorus than neutrophilic nitrification, but the increased acidity also reduced the nitrification rate, resulting in residual ammonium. We then grew lettuce hydroponically with filtrates of these digestates. The growth performance suggested that the increased phosphorus improved growth and that the residual ammonium did not inhibit it. Acidophilic nitrification was shown to be effective for use in hydroponics, particularly to alleviate phosphorus deficiency. These findings should provide new insights into resource recycling, which is essential in both urban and space environments. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/522315v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@2d4e2corg.highwire.dtl.DTLVardef@675c08org.highwire.dtl.DTLVardef@1cb3139org.highwire.dtl.DTLVardef@10cd093_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Dosage of duplicated and antifunctionalized homeobox proteins influences spikelet development in barley

Illuminating the mechanisms of inflorescence architecture of grain crops that feed our world may strengthen the goal towards sustainable agriculture. Lateral spikelet development of barley (Hordeum vulgare L.) is such an example of a floral architectural trait regulated by VRS1 (Vulgare Row-type Spike 1 or Six-rowed Spike 1, syn. HvHOX1). Its lateral spikelet-specific expression and the quantitative nature of suppressing spikelet development were previously shown in barley. However, the mechanistic function of this gene and its paralog HvHOX2 on spikelet development is still fragmentary.Here, we show that these duplicated transcription factors (TFs) have contrasting nucleotide diversity in various barley genotypes and several Hordeum species. Despite this difference, both proteins retain their basic properties of the homeodomain leucine zipper class I family of TFs. During spikelet development, these genes exhibit similar spatiotemporal expression patterns yet with anticyclic expression levels. A gene co-expression network analysis suggested that both have an ancestral relationship but their functions appear antagonistic to each other, i.e., HvHOX1 suppresses whereas HvHOX2 rather promotes spikelet development. Our transgenic promoter-swap analysis showed that HvHOX2 can restore suppressed lateral spikelets when expression levels are increased; however, at its low endogenous expression level, HvHOX2 appears dispensable for spikelet development. Collectively, this study proposes that the dosage of the two antagonistic TFs, HvHOX1 and HvHOX2, influence spikelet development in barley.

plant biology↗

bioRxiv2018

Unleashing floret fertility by a mutated homeobox gene improved grain yield during wheat evolution under domestication

Floret fertility is a key trait to determine the number of grains per inflorescence in cereals. During wheat (Triticum sp.) evolution, floret fertility has been increased and current bread wheat (T. aestivum L.) produces three to five grains per spikelet; however, little is known about the genetic basis controlling floret fertility. Here we identify the quantitative trait locus Grain Number Increase 1 (GNI1), encoding a homeodomain leucine zipper class I (HD-Zip I) transcription factor. GNI1 evolved in the Triticeae through gene duplication and functionalization. GNI1 was predominantly expressed in the most apical floret primordia and parts of the rachilla, suggesting that GNI1 inhibits rachilla growth and development. GNI1 expression decreased during wheat evolution, and as a consequence, more fertile florets and grains per spikelet are being produced. Genetic analysis revealed that the reduced-function allele of GNI1-A contributes to increase the number of fertile florets per spikelet. The knockdown of GNI1 in transgenic hexaploid wheat improved fertile floret and grain number. Furthermore, wheat plants carrying the impaired allele increased grain yield under field conditions. Our findings illuminate that gene duplication and functionalization generated evolutionary novelty for floret fertility (i.e. reducing floral numbers) while the mutations towards increased grain production were under selection during wheat evolution under domestication.\n\nSignificance StatementGrain number is a fundamental trait for cereal grain yield; but its underlying genetic basis is mainly unknown in wheat. Here we show for the first time a direct link between increased floret fertility, higher grain number per spike and higher plot-yields of wheat in the field. We have identified GNI1 gene encoding an HD-Zip I transcription factor responsible for increased floret fertility. The wild type allele imposes an inhibitory role specifically during rachilla development, indicating that expression of this protein actively shuts-down grain yield potential; whereas, the reduced-function allele enables more florets and grains to be produced. GNI1 evolved through gene duplication in Triticeae and its mutations were under parallel human selection during wheat and barley evolution under domestication.

plant biology↗