Transcription factor encoding gene OsC1 regulates leaf sheath color through anthocyanidin metabolism in Oryza rufipogon and Oryza sativa.

Carbohydrates, proteins, lipids, minerals and vitamins are nutrient substances commonly seen in rice grains, but anthocyanidin, with benefit for plant growth and animal health, exists mainly in the common wild rice but hardly in the cultivated rice. To screen the rice germplasm with high intensity of anthocyanidins and identify the variations, we used metabolomics technique and detected significant different accumulation of anthocyanidins in common wild rice (Oryza rufipogon, with purple leaf sheath) and cultivated rice (Oryza sativa, with green leaf sheath). In this study, we identified and characterized a well-known MYB transcription factor, OsC1, through phenotypic (leaf sheath color) and metabolic (metabolite profiling) genome-wide association studies (pGWAS and mGWAS) in 160 common wild rice (O. rufipogon) and 151 cultivated (O. sativa) rice varieties. Transgenic experiments demonstrated that biosynthesis and accumulation of cyanidin-3-Galc, cyanidin 3-O-rutinoside and cyanidin O-syringic acid, as well as purple pigmentation in leaf sheath were regulated by OsC1. A total of 25 sequence variations of OsC1 constructed 16 functional haplotypes (higher accumulation of the three anthocyanidin types within purple leaf sheath) and 9 non-functional haplotypes (less accumulation of anthocyanidins within green leaf sheath). Three haplotypes of OsC1 were newly identified in our germplasm, which have potential values in functional genomics and molecular breeding of rice. Gene-to-metabolite analysis by mGWAS and pGWAS provides a useful and efficient tool for functional gene identification and omics-based crop genetic improvement.

Creation and gene expression analysis of a giant embryo rice mutant with high GABA content.

Gamma-amino butyric acid (GABA) is a natural non-protein amino acid involved in stress, signal transmission, carbon and nitrogen balance, and other physiological processes in plants. In the human body, GABA has the effects of lowering blood pressure, anti-aging, and activating the liver and kidneys. However, there are few studies on the molecular regulation mechanism of genes in the metabolic pathways of GABA during grain development of giant embryo rice with high GABA content. In this study, three glant embryo (ge) mutants of different embryo sizes were obtained by CRISPR/Cas9 knockout, and it was found that GABA, protein, crude fat, and various mineral contents of the ge mutants were significantly increased. RNA-seq and qRT-PCR analysis showed that in the GABA shunt and polyamine degradation pathways, the expression levels of most of the genes encoding enzymes promoting GABA accumulation were significantly upregulated in the ge-1 mutant, whereas, the expression levels of most of the genes encoding enzymes involved GABA degradation were significantly downregulated in the ge-1 mutant. This is most likely responsible for the significant increase in GABA content of the ge mutant. These results help reveal the molecular regulatory network of GABA metabolism in giant embryo rice and provide a theoretical basis for the study of its development mechanisms, which is conducive to the rapid cultivation of GABA-rich rice varieties, promoting human nutrition, and ensuring health. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01353-1.

The genetic basis of grain protein content in rice by genome-wide association analysis.

The grain protein content (GPC) of rice is an important factor that determines its nutritional, cooking, and eating qualities. To date, although a number of genes affecting GPC have been identified in rice, most of them have been cloned using mutants, and only a few genes have been cloned in the natural population. In this study, 135 significant loci were detected in a genome-wide association study (GWAS), many of which could be repeatedly detected across different years and populations. Four minor quantitative trait loci affecting rice GPC at four significant association loci, qPC2.1, qPC7.1, qPC7.2, and qPC1.1, were further identified and validated in near-isogenic line F2 populations (NIL-F2), explaining 9.82, 43.4, 29.2, and 13.6% of the phenotypic variation, respectively. The role of the associated flo5 was evaluated with knockdown mutants, which exhibited both increased grain chalkiness rate and GPC. Three candidate genes in a significant association locus region were analyzed using haplotype and expression profiles. The findings of this study will help elucidate the genetic regulatory network of protein synthesis and accumulation in rice through cloning of GPC genes and provide new insights on dominant alleles for marker-assisted selection in the genetic improvement of rice grain quality. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01347-z.

Improvement of Rice Blast Resistance in TGMS Line HD9802S through Optimized Anther Culture and Molecular Marker-Assisted Selection.

Rice blast caused by Magnaporthe oryzae is one of the most serious rice diseases worldwide. The early indica rice thermosensitive genic male sterile (TGMS) line HD9802S has the characteristics of stable fertility, reproducibility, a high outcrossing rate, excellent rice quality, and strong combining ability. However, this line exhibits poor blast resistance and is highly susceptible to leaf and neck blasts. In this study, backcross introduction, molecular marker-assisted selection, gene chipping, anther culture, and resistance identification in the field were used to introduce the broad-spectrum blast-resistance gene R6 into HD9802S to improve its rice blast resistance. Six induction media were prepared by varying the content of each component in the culture medium. Murashige and Skoog's medium with 3 mg/L 2,4-dichlorophenoxyacetic acid, 2 mg/L 1-naphthaleneacetic acid, and 1 mg/L kinetin and N6 medium with 800 mg/L casein hydrolysate, 600 mg/L proline, and 500 mg/L glutamine could improve the callus induction rate and have a higher green seedling rate and a lower white seedling rate. Compared to HD9802S, two doubled haploid lines containing R6 with stable fertility showed significantly enhanced resistance to rice blast and no significant difference in spikelet number per panicle, 1000-grain weight, or grain shape. Our findings highlight a rapid and effective method for improving rice blast resistance in TGMS lines.

The Mitogen-Activated Protein Kinase PlMAPK2 Is Involved in Zoosporogenesis and Pathogenicity of Peronophythoralitchii.

As an evolutionarily conserved pathway, mitogen-activated protein kinase (MAPK) cascades function as the key signal transducers that convey information by protein phosphorylation. Here we identified PlMAPK2 as one of 14 predicted MAPKs encoding genes in the plant pathogenic oomycete Peronophythora litchii. PlMAPK2 is conserved in P.litchii and Phytophthora species. We found that PlMAPK2 was up-regulated in sporangium, zoospore, cyst, cyst germination and early stage of infection. We generated PlMAPK2 knockout mutants using the CRISPR/Cas9 method. Compared with wild-type strain, the PlMAPK2 mutants showed no significant difference in vegetative growth, oospore production and sensitivity to various abiotic stresses. However, the sporangium release was severely impaired. We further found that the cleavage of the cytoplasm into uninucleate zoospores was disrupted in the PlMAPK2 mutants, and this developmental phenotype was accompanied by reduction in the transcription levels of PlMAD1 and PlMYB1 genes. Meanwhile, the PlMAPK2 mutants exhibited lower laccase activity and reduced virulence to lychee leaves. Overall, this study identified a MAPK that is critical for zoosporogenesis by regulating the sporangial cleavage and pathogenicity of P.litchii, likely by regulating laccase activity.

Evidence for a mutualistic relationship between the cyanobacteria Nostoc and fungi Aspergilli in different environments.

Symbiotic partnerships are widespread in nature and in industrial applications yet there are limited examples of laboratory communities. Therefore, using common photobionts and mycobionts similar to those in natural lichens, we create an artificial lichen-like symbiosis. While Aspergillus nidulans and Aspergillus niger could not obtain nutrients from the green algae, Chlorella, and Scenedesmus, the cyanobacteria Nostoc sp. PCC 6720 was able to support fungal growth and also elevated the accumulation of total biomass. The Nostoc-Aspergillus co-cultures grew on light and CO2 in an inorganic BG11 liquid medium without any external organic carbon and fungal mycelia were observed to peripherally contact with the Nostoc cells in liquid and on solid media at lower cell densities. Overall biomass levels were reduced after implementing physical barriers to indicate that physical contact between cyanobacteria and heterotrophic microbes may promote symbiotic growth. The synthetic Nostoc-Aspergillus nidulans co-cultures also exhibited robust growth and stability when cultivated in wastewater over days to weeks in a semi-continuous manner when compared with axenic cultivation of either species. These Nostoc-Aspergillus consortia reveal species-dependent and mutually beneficial design principles that can yield stable lichen-like co-cultures and provide insights into microbial communities that can facilitate sustainability studies and broader applications in the future. KEY POINTS: • Artificial lichen-like symbiosis was built with wild-type cyanobacteria and fungi. • Physical barriers decreased biomass production from artificial lichen co-cultures. • Artificial lichen adapted to grow and survive in wastewater for 5 weeks.

LncRNA ST3Gal6-AS1/ST3Gal6 axis mediates colorectal cancer progression by regulating α-2,3 sialylation via PI3K/Akt signaling.

Sialylation is associated with cancer progression. Long noncoding RNAs (lncRNAs) have important roles in diverse diseases including cancer. The lncRNA ST3Gal6 antisense 1 (ST3Gal6-AS1) derives from the promoter region of sialyltransferase ST3Gal6. However, the mechanisms by which ST3Gal6-AS1 modulates colorectal cancer (CRC) development through sialylation remain largely unknown. Here, we found that ST3Gal6-AS1 and ST3Gal6 levels were lower in tumor tissues than adjacent normal tissues of CRC patients. The correlation between ST3Gal6-AS1 and ST3Gal6 was further validated in several types of CRC cell lines. In addition, ST3Gal6 was dysregulated and positively correlated to ST3Gal6-AS1. ST3Gal6-AS1 recruited histone methyltransferase MLL1 to the promoter region of ST3Gal6, induced H3K4me3 modification and activated ST3Gal6 transcription. Furthermore, ST3Gal6-AS1/ST3Gal6 axis mediated α-2, 3 sialylation and inhibited the activation of PI3K/Akt signaling, thereby resulting in Foxo1 nuclear translocation in CRC cells. ST3Gal6-AS1 was a target of transcription factor Foxo1 and regulated by Foxo1. ST3Gal6-AS1 also inhibited CRC cell proliferation, metastasis, and promoted cell apoptosis in vitro. Overexpression of ST3Gal6-AS1 significantly decreased the tumorigenesis, lung and liver metastasis of SW620 cells in vivo. ST3Gal6-AS1 expression was negatively correlated with tumor size, lymphatic metastasis, distant metastasis and tumor stage in CRC patients. Collectively, these data indicated that ST3Gal6-AS1, ST3Gal6, PI3K/Akt, and Foxo1 formed a positive feedback loop, which might play a key role in CRC progression.

Exosomes in Pathogenesis, Diagnosis, and Treatment of Alzheimer's Disease.

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the accumulation of ß-amyloid peptide 1-42 and phosphorylation of tau protein in the brain. Thus far, the transfer mechanism of these cytotoxic proteins between nerve cells remains unclear. Recent studies have shown that nanoscale extracellular vesicles (exosomes) originating from cells may play important roles in this transfer process. In addition, several genetic materials and proteins are also involved in intercellular communication by the secretion of the exosomes. That proposes novel avenues for early diagnosis and biological treatment in AD, based on exosome detection and intervention. In this review, exosome-related pathways of cytotoxic protein intercellular transfer in AD, and the effect of membrane proteins on exosomes targeting cells are first introduced. The advances in exosome-related biomarker detection in AD are summarized. Finally, the advantages and challenges of reducing cytotoxic protein accumulation via exosomal intervention for AD treatment are discussed. It is envisaged that future research in exosomes may well provide new insights into the pathogenesis, diagnosis, and treatment of AD.

The influence of ABCB1 and P2Y12 genetic variants on clinical outcomes in Chinese intracranial artery stenosis patients.

For intracranial artery stenosis patients, high inter-individual variability in response to antiplatelet drug therapy results in recurrent ischemic events. We aimed to evaluate the association of drug-related genetic polymorphisms with adverse clinical outcomes. We consecutively enrolled 157 patients receiving dual-antiplatelet therapy (aspirin plus clopidogrel), and adverse clinical events occurred in 10 patients during the one year follow-up. The P2Y12 polymorphisms (rs9859538 and rs10935842) were associated with increased likelihood of relapse events (OR=2.934, 95%CI=1.022-8.425, P-value=0.045), and the two variants are in complete linkage disequilibrium. The mutation of ABCB1 rs1128503 may decrease the recurrence of clinical events (OR=0.211, 95%CI=0.046-0.957, P-value=0.044). Genetic testing (ABCB1 and P2Y12) may provide useful information to prevent ischemic events prior to the initiation of antiplatelet therapy. This article is protected by copyright. All rights reserved.

A Puf RNA-binding protein encoding gene PlM90 regulates the sexual and asexual life stages of the litchi downy blight pathogen Peronophythora litchii.

Sexual and asexual reproduction are two key processes in the pathogenic cycle of many filamentous pathogens. However in Peronophythora litchii, the causal pathogen for the litchi downy blight disease, critical regulator(s) of sexual or asexual differentiation has not been elucidated. In this study, we cloned a gene named PlM90 from P. litchii, which encodes a putative Puf RNA-binding protein. We found that PlM90 was highly expressed during asexual development, and much higher than that during sexual development, while relatively lower during cyst germination and plant infection. By polyethylene glycol (PEG)-mediated protoplast transformation, we generated three PlM90-silenced transformants and found a severely impaired ability in sexual spore production and a delay in stages of zoospore release and encystment. However, the pathogenicity of P. litchii was not affected by PlM90-silencing. Therefore we conclude that PlM90 specifically regulates the sexual and asexual differentiation of P. litchii.

WDFY1 mediates TLR3/4 signaling by recruiting TRIF.

Toll-like receptors (TLRs) are pattern recognition receptors that sense a variety of pathogens, initiate innate immune responses, and direct adaptive immunity. All TLRs except TLR3 recruit the adaptor MyD88 to ultimately elicit inflammatory gene expression, whereas TLR3 and internalized TLR4 use TIR-domain-containing adaptor TRIF for the induction of type I interferon and inflammatory cytokines. Here, we identify the WD repeat and FYVE-domain-containing protein WDFY1 as a crucial adaptor protein in the TLR3/4 signaling pathway. Overexpression of WDFY1 potentiates TLR3- and TLR4-mediated activation of NF-κB, interferon regulatory factor 3 (IRF3), and production of type I interferons and inflammatory cytokines. WDFY1 depletion has the opposite effect. WDFY1 interacts with TLR3 and TLR4 and mediates the recruitment of TRIF to these receptors. Our findings suggest a crucial role for WDFY1 in bridging the TLR-TRIF interaction, which is necessary for TLR signaling.

Production of D-lactate from glucose using Klebsiella pneumoniae mutants.

BACKGROUND: D-Lactate is a valued chemical which can be produced by some bacteria including Klebsiella pneumoniae. However, only a few studies have focused on K. pneumoniae for D-lactate production with a significant amount of by-products, which complicated the purification process and decreased the yield of D-lactate. RESULTS: Based on the redirection of carbon towards by-product formation, the effects of single-gene and multiple-gene deletions in K. pneumoniae on D-lactate production from glucose via acetolactate synthase (budB), acetate kinase (ackA), and alcohol dehydrogenase (adhE) were tested. Klebsiella pneumoniae mutants had different production behaviours. The accumulation of the main by-products was decreased in the mutants. The triple mutant strain had the most powerful ability to produce optically pure D-lactate from glucose, and was tested with xylose and arabinose as carbon sources. Fed-batch fermentation was also carried out under various aeration rates, and the strain accumulated 125.1 g/L D-lactate with a yield of 0.91 g/g glucose at 2.5 vvm. CONCLUSIONS: Knocking out by-product synthesis genes had a remarkable influence on the production and yield of D-lactate. This study demonstrated, for the first time, that K. pneumoniae has great potential to convert monosaccharides into D-lactate. The results provide new insights for industrial production of D-lactate by K. pneumoniae.

A dabigatran etexilate phospholipid complex nanoemulsion system for further oral bioavailability by reducing drug-leakage in the gastrointestinal tract.

Dabigatran etexilate (DE) is insoluble at neutral pH values but soluble at low pH values due to protonation, which is the major cause for the poor bioavailability of commercial DE products. Here, we first developed a DE nanoemulsion system and improved dissolution in simulated intestinal fluids by encapsulating DE into an oil phase, but 35.8% of the drug still leaked out. Further, we prepared a DE-phospholipid complex (DE-PC) to enhance lipophilicity and solubility of DE. The resulting DE-PC nanoemulsions significantly (P<0.05) reduced drug leakage and subsequent precipitation. As a result, the relative bioavailability of DE-PC nanoemulsions increased to 147.3% and 606.6% compared to DE nanoemulsions and commercial DE products, respectively. Thus, the presently developed drug-phospholipid complex nanoemulsion system is a promising drug delivery system for improving the oral bioavailability of pH-dependent soluble drugs.

Quercetin-containing self-assemble proliposome preparation and evaluation.

The purpose of this study was to develop a liquid self-assemble proliposome for quercetin oral delivery. This liquid proliposome was prepared by dissolving phospholipids, surfactants and drug in ethanol. There was only one step in the preparation process of this liquid self-assemble proliposome and no special devices were required. The mechanism about proliposome transformation was discussed. Quercetin proliposomes with different cremorphor RH40 concentrations (0%, 20%, 23%, 26%, 30%) were prepared. The particle size and polydispersity index decreased as cremorphor RH40 concentration increased. Meantime, the drug entrapped efficiency decreased slightly with an increase in cremorphor RH40 concentration. The in vitro drug release showed prolonged drug release in case of proliposome and the release of quercetin was slower when cremorphor RH40 concentration was higher. The absorption of quercetin and its in vivo bioavailability were significantly improved by proliposome, which was evidenced by the in situ intestinal absorption and pharmacokinetic study. Besides, the obtained quercetin proliposome was with good stability when stored at room temperature. In conclusion, quercetin liquid self-assemble proliposome was successfully prepared. It could transform into liposomal vesicle with satisfied particle size and polydispersity index instantly when cremorphor RH40 was added. Cremorphor RH40 concentration in the formulation should below 26% to get higher drug entrapped efficiency (>90%) and less irritation. The drug release was affected by the cremorphor RH40 concentration and the required drug release could be obtained by adjusting cremorphor RH40 content. The enhanced bioavailability showed liquid self-assemble proliposome could be a promising vehicle for the oral delivery of quercetin.

Jasmonate regulates the inducer of cbf expression-C-repeat binding factor/DRE binding factor1 cascade and freezing tolerance in Arabidopsis.

The inducer of cbf expression (ICE)-C-repeat binding factor/DRE binding factor1 (CBF/DREB1) transcriptional pathway plays a critical role in modulating cold stress responses in Arabidopsis thaliana. Dissecting crucial upstream regulatory signals or components of the ICE-CBF/DREB1 cascade will enhance our understanding of plant cold-tolerance mechanisms. Here, we show that jasmonate positively regulates plant responses to freezing stress in Arabidopsis. Exogenous application of jasmonate significantly enhanced plant freezing tolerance with or without cold acclimation. By contrast, blocking endogenous jasmonate biosynthesis and signaling rendered plants hypersensitive to freezing stress. Consistent with the positive role of jasmonate in freezing stress, production of endogenous jasmonate was triggered by cold treatment. In addition, cold induction of genes acting in the CBF/DREB1 signaling pathway was upregulated by jasmonate. Further investigation revealed that several jasmonate ZIM-domain (JAZ) proteins, the repressors of jasmonate signaling, physically interact with ICE1 and ICE2 transcription factors. JAZ1 and JAZ4 repress the transcriptional function of ICE1, thereby attenuating the expression of its regulon. Consistent with this, overexpression of JAZ1 or JAZ4 represses freezing stress responses of Arabidopsis. Taken together, our study provides evidence that jasmonate functions as a critical upstream signal of the ICE-CBF/DREB1 pathway to positively regulate Arabidopsis freezing tolerance.

Study of KOH/Al2O3 as heterogeneous catalyst for biodiesel production via in situ transesterification from microalgae.

Heterogeneous KOH/Al2O3 catalysts, synthesized by the wet impregnation method with different KOH loadings (20-40 wt%) and calcination temperatures from 400°C to 800°C, were used to produce biodiesel from Chlorella vulgaris biomass by in situ transesterification. The highest yield of biodiesel of 89.53±1.58% was achieved at calcination temperature of 700°C for 2 h and 35 wt% loading of KOH, and at the optimal reaction condition of 10 wt% of catalyst content, 8 mL/g of methanol to biomass ratio and at 60°C for 5 h. The characteristics of the catalysts were analysed by X-ray diffraction, scanning electron microscopy and Brunauer-Emmett-Teller.

FoxO1 negatively regulates cellular antiviral response by promoting degradation of IRF3.

Viral infection causes activation of the transcription factor IRF3, which is critical for production of type I interferons (IFNs) and innate antiviral immune response. How virus-induced type I IFN signaling is controlled is not fully understood. Here we identified the transcription factor FoxO1 as a negative regulator for virus-triggered IFN-ß induction. Overexpression of FoxO1 inhibited virus-triggered ISRE activation, IFN-ß induction as well as cellular antiviral response, whereas knockdown of FoxO1 had opposite effects. FoxO1 interacted with IRF3 in a viral infection-dependent manner and promoted K48-linked polyubiquitination and degradation of IRF3 in the cytosol. Furthermore, FoxO1-mediated degradation of IRF3 was independent of the known E3 ubiquitin ligases for IRF3, including RBCK1 and RAUL. Our findings thus suggest that FoxO1 negatively regulates cellular antiviral response by promoting IRF3 ubiquitination and degradation, providing a previously unknown mechanism for control of type I IFN induction and cellular antiviral response.

Multi-faceted effects of NaCl on salt-tolerant microalgae Golenkinia sp. SDEC-16.

The salt-tolerant microalgae are extremely few and salt-tolerance mechanism is unclear, requiring urgent exploration of salt-tolerance mechanism of known microalgae. This study was first to reveal the salt-tolerance mechanism of Golenkinia sp. SDEC-16 by investigating the growth and metabolism under different salinities and high salinity long-term cultivation. SDEC-16 can survive under high salinity and resume normal growth after NaCl removal. Under long-term stress, SDEC-16 had higher lipid content and productivity than BG11. However, the suppressed Fv/Fm (58.4%) and Fv/F0 (84.0%) along with the increased reactive oxygen species (×6.6), and superoxide dismutase (×1.7) during the treatment revealed NaCl-induced photosynthetic inhibition and oxidative stress. RNA sequencing results showed inhibition of the photosynthetic system, and the enhancement of pathways such as nitrogen metabolism, energy metabolism, and lipid synthesis contributed to the good function of chloroplast, energy supply, and metabolic activity of SDEC-16. This study provides theoretical support for large-scale microalgal cultivation in seawater.

Unveiling the Roles of LncRNA MOIRAs in Rice Blast Disease Resistance.

Rice blast disease, caused by the fungal pathogen Magnaporthe oryzae, is a major threat to rice production worldwide. This study investigates the role of long non-coding RNAs (lncRNAs) in rice's response to this destructive disease, with a focus on their impacts on disease resistance and yield traits. Three specific lncRNAs coded by M. oryzae infection-responsive lncRNAs (MOIRAs), MOIRA1, MOIRA2, and MOIRA3, were identified as key regulators of rice's response to M. oryzae infection. Strikingly, when MOIRA1 and MOIRA2 were overexpressed, they exhibited a dual function: they increased rice's susceptibility to blast fungus, indicating a negative role in disease resistance, while simultaneously enhancing tiller numbers and single-plant yield, with no adverse effects on other yield-related traits. This unexpected improvement in productivity suggests the possibility of overcoming the traditional trade-off between disease resistance and crop yield. These findings provide a novel perspective on crop enhancement, offering a promising solution to global food security challenges by developing rice varieties that effectively balance disease resistance and increased productivity.