Integrated metabolomic and transcriptomic analyses provide insights into regulation mechanisms during bulbous stem development in the Chinese medicinal herb plant, Stephania kwangsiensis.

BACKGROUND: Stephania kwangsiensis Lo (Menispermaceae) is a well-known Chinese herbal medicine, and its bulbous stems are used medicinally. The storage stem of S. kwangsiensis originated from the hypocotyls. To date, there are no reports on the growth and development of S. kwangsiensis storage stems. RESULTS: The bulbous stem of S. kwangsiensis, the starch diameter was larger at the stable expanding stage (S3T) than at the unexpanded stage (S1T) or the rapidly expanding stage (S2T) at the three different time points. We used ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and Illumina sequencing to identify key genes involved in bulbous stem development. A large number of differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) were identified. Based on the differential expression profiles of the metabolites, alkaloids, lipids, and phenolic acids were the top three differentially expressed classes. Compared with S2T, significant changes in plant signal transduction and isoquinoline alkaloid biosynthesis pathways occurred at both the transcriptional and metabolic levels in S1T. In S2T compared with S3T, several metabolites involved in tyrosine metabolism were decreased. Temporal analysis of S1T to S3T indicated the downregulation of phenylpropanoid biosynthesis, including lignin biosynthesis. The annotation of key pathways showed an up-down trend for genes and metabolites involved in isoquinoline alkaloid biosynthesis, whereas phenylpropanoid biosynthesis was not completely consistent. CONCLUSIONS: Downregulation of the phenylpropanoid biosynthesis pathway may be the result of carbon flow into alkaloid synthesis and storage of lipids and starch during the development of S. kwangsiensis bulbous stems. A decrease in the number of metabolites involved in tyrosine metabolism may also lead to a decrease in the upstream substrates of phenylpropane biosynthesis. Downregulation of lignin synthesis during phenylpropanoid biosynthesis may loosen restrictions on bulbous stem expansion. This study provides the first comprehensive analysis of the metabolome and transcriptome profiles of S. kwangsiensis bulbous stems. These data provide guidance for the cultivation, breeding, and harvesting of S. kwangsiensis.

Transcriptional dynamics in source-sink tissues identifies molecular factors regulating the corm development process in saffron (Crocus sativus L.).

AIMS: Geophytic plants have evolved to develop underground storage organs (USO) in the active growing season to withstand harsh environments as well as to coordinate growth and reproduction when conditions are favourable. Saffron is an autumn flowering geophyte and an expensive spice crop restricted to certain geographical locations in the world. Saffron, being sterile, does not produce seeds and thus propagates only through corms, the quality of which determines its yield. Corm development in saffron is unexplored and the underlying molecular mechanism is still elusive. In this study, we performed an extensive characterisation of the transcriptional dynamics in the source (leaf) and sink (corm) tissues during corm development in saffron. KEY RESULTS: Via morphological and transcriptome studies, we identified molecular factors regulating corm development process in saffron, which defined corm development into three stages: the initiation stage demonstrates enhanced vegetative growth aboveground and swelling of shoot base belowground due to active cell division & carbohydrate storage; the bulking stage comprises of increased source and sink strength, active photosynthesis, circadian gating and starch accumulation; the maturation stage represents reduced source and sink strength, lowered photosynthesis, sugar transport, starch synthesis and cell cycle arrest. UTILITY: The global view of transcriptional changes in source and sink identifies similar and new molecular factors involved in the saffron corm development process compared to USO formation in other geophytes and provides a valuable resource for dissecting the molecular network underlying the corm development. We propose a hypothetical model based on data analysis, of how molecular factors via environmental cues can regulate the corm development process in saffron.

Effects of dietary forage neutral detergent fiber and rumen degradable starch ratios on chewing activity, ruminal fermentation, ruminal microbes and nutrient digestibility of Hu sheep fed a pelleted total mixed ration.

Pelleted total mixed ration (P-TMR) feeding, which has become a common practice in providing nutrition for fattening sheep, requires careful consideration of the balance between forage neutral detergent fiber (FNDF) and rumen degradable starch (RDS) to maintain proper rumen functions. The present study aimed to investigate the effects of the dietary FNDF/RDS ratio (FRR) on chewing activity, ruminal fermentation, ruminal microbes, and nutrient digestibility in Hu sheep fed a P-TMR diet. This study utilized eight ruminally cannulated male Hu sheep, following a 4 × 4 Latin square design with 31 d each period. Diets consisted of four FRR levels: 1.0 (high FNDF/RDS ratio, HFRR), 0.8 (middle high FNDF/RDS ratio, MHFRR), 0.6 (middle low FNDF/RDS ratio, MLFRR), and 0.4 (low FNDF/RDS ratio, LFRR). Reducing the dietary FRR levels resulted in a linear decrease in ruminal minimum pH and mean pH, while linearly increasing the duration and area of pH below 5.8 and 5.6, as well as the acidosis index. Sheep in the HFRR and MHFRR groups did not experience subacute ruminal acidosis (SARA), whereas sheep in another two groups did. The concentration of total volatile fatty acid and the molar ratios of propionate and valerate, as well as the concentrate of lactate in the rumen linearly increased with reducing dietary FRR, while the molar ratio of acetate and acetate to propionate ratio linearly decreased. The degradability of NDF and ADF for alfalfa hay has a quadratic response with reducing the dietary FRR. The apparent digestibility of dry matter, organic matter, neutral detergent fiber, and acid detergent fiber linearly decreased when the dietary FRR was reduced. In addition, reducing the dietary FRR caused a linear decrease in OTUs, Chao1, and Ace index of ruminal microflora. Reducing FRR in the diet increased the percentage of reads assigned as Firmicutes, but it decreased the percentage of reads assigned as Bacteroidetes in the rumen. At genus level, the percentage of reads assigned as Prevotella, Ruminococcus, Succinivibrio, and Butyrivibrio linearly decreased when the dietary FRR was reduced. The results of this study demonstrate that the dietary FRR of 0.8 is crucial in preventing the onset of SARA and promotes an enhanced richness of ruminal microbes and also improves fiber digestibility, which is a recommended dietary FRR reference when formulating P-TMR diets for sheep.

Forage neutral detergent fiber (FNDF) and rumen degradable starch (RDS) are key components of carbohydrates in the diet for ruminants, which would reflect saliva secretion and the acid production potential of feed. However, appropriate FNDF to RDS ratios (FRR) applicable to ruminants under the condition of pelleted total mixed ration (P-TMR) feeding have not been reported. In this study, we investigated the effects of the dietary FRR on chewing activity, ruminal fermentation, ruminal microbial communities, and nutrient digestibility of Hu sheep under P-TMR feeding. The results indicate that reducing dietary FRR levels would induce acidosis in sheep, which negatively affected fiber utilization and ruminal bacterial communities. The FRR of 0.8 was a recommended dietary FRR when formulating a P-TMR diet for fattening sheep, as indicated by decreased ruminal acidosis risk and increased richness of ruminal microbes in the rumen as well as nutrient digestibility.

The roles of non-structural carbohydrates in fruiting: a review focusing on mango (Mangifera indica).

Reproductive development of fruiting trees, including mango (Mangifera indica L.), is limited by non-structural carbohydrates. Competition for sugars increases with cropping, and consequently, vegetative growth and replenishment of starch reserves may reduce with high yields, resulting in interannual production variability. While the effect of crop load on photosynthesis and the distribution of starch within the mango tree has been studied, the contribution of starch and sugars to different phases of reproductive development requires attention. This review focuses on mango and examines the roles of non-structural carbohydrates in fruiting trees to clarify the repercussions of crop load on reproductive development. Starch buffers the plant's carbon availability to regulate supply with demand, while sugars provide a direct resource for carbon translocation. Sugar signalling and interactions with phytohormones play a crucial role in flowering, fruit set, growth, ripening and retention, as well as regulating starch, sugar and secondary metabolites in fruit. The balance between the leaf and fruit biomass affects the availability and contributions of starch and sugars to fruiting. Crop load impacts photosynthesis and interactions between sources and sinks. As a result, the onset and rate of reproductive processes are affected, with repercussions for fruit size, composition, and the inter-annual bearing pattern.

Comparative physiology and transcriptome response patterns in cold-tolerant and cold-sensitive varieties of Solanum melongena.

BACKGROUND: Climate change has led to severe cold events, adversely impacting global crop production. Eggplant (Solanum melongena L.), a significant economic crop, is highly susceptible to cold damage, affecting both yield and quality. Unraveling the molecular mechanisms governing cold resistance, including the identification of key genes and comprehensive transcriptional regulatory pathways, is crucial for developing new varieties with enhanced tolerance. RESULTS: In this study, we conducted a comparative analysis of leaf physiological indices and transcriptome sequencing results. The orthogonal partial least squares discriminant analysis (OPLS-DA) highlighted peroxidase (POD) activity and soluble protein as crucial physiological indicators for both varieties. RNA-seq data analysis revealed that a total of 7024 and 6209 differentially expressed genes (DEGs) were identified from variety "A" and variety "B", respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of DEGs demonstrated that the significant roles of starch and sucrose metabolism, glutathione metabolism, terpenoid synthesis, and energy metabolism (sucrose and starch metabolism) were the key pathways in eggplant. Weighted gene co-expression network analysis (WGCNA) shown that the enrichment of numerous cold-responsive genes, pathways, and soluble proteins in the MEgrep60 modules. Core hub genes identified in the co-expression network included POD, membrane transporter-related gene MDR1, abscisic acid-related genes, growth factor enrichment gene DELLA, core components of the biological clock PRR7, and five transcription factors. Among these, the core transcription factor MYB demonstrated co-expression with signal transduction, plant hormone, biosynthesis, and metabolism-related genes, suggesting a pivotal role in the cold response network. CONCLUSION: This study integrates physiological indicators and transcriptomics to unveil the molecular mechanisms responsible for the differences in cold tolerance between the eggplant cold-tolerant variety "A" and the cold-sensitive variety "B". These mechanisms include modulation of reactive oxygen species (ROS), elevation in osmotic carbohydrate and free proline content, and the expression of terpenoid synthesis genes. This comprehensive understanding contributes valuable insights into the molecular underpinnings of cold stress tolerance, ultimately aiding in the improvement of crop cold tolerance.

ATP-free in vitro biotransformation of starch-derived maltodextrin into poly-3-hydroxybutyrate via acetyl-CoA.

In vitro biotransformation (ivBT) facilitated by in vitro synthetic enzymatic biosystems (ivSEBs) has emerged as a highly promising biosynthetic platform. Several ivSEBs have been constructed to produce poly-3-hydroxybutyrate (PHB) via acetyl-coenzyme A (acetyl-CoA). However, some systems are hindered by their reliance on costly ATP, limiting their practicality. This study presents the design of an ATP-free ivSEB for one-pot PHB biosynthesis via acetyl-CoA utilizing starch-derived maltodextrin as the sole substrate. Stoichiometric analysis indicates this ivSEB can self-maintain NADP+/NADPH balance and achieve a theoretical molar yield of 133.3%. Leveraging simple one-pot reactions, our ivSEBs achieved a near-theoretical molar yield of 125.5%, the highest PHB titer (208.3 mM, approximately 17.9 g/L) and the fastest PHB production rate (9.4 mM/h, approximately 0.8 g/L/h) among all the reported ivSEBs to date, and demonstrated easy scalability. This study unveils the promising potential of ivBT for the industrial-scale production of PHB and other acetyl-CoA-derived chemicals from starch.

Metabolome and transcriptome analyses reveal changes of rapeseed in response to ABA signal during early seedling development.

Seed germination is an important development process in plant growth. The phytohormone abscisic acid (ABA) plays a critical role during seed germination. However, the mechanism of rapeseed in response to ABA is still elusive. In order to understand changes of rapeseed under exogenous ABA treatment, we explored differentially expressed metabolites (DEMs) and the differentially expressed genes (DEGs) between mock- and ABA-treated seedlings. A widely targeted LC-MS/MS based metabolomics were used to identify and quantify metabolic changes in response to ABA during seed germination, and a total of 186 significantly DEMs were identified. There are many compounds which are involved in ABA stimuli, especially some specific ABA transportation-related metabolites such as starches and lipids were screened out. Meanwhile, a total of 4440 significantly DEGs were identified by transcriptomic analyses. There was a significant enrichment of DEGs related to phenylpropanoid and cell wall organization. It suggests that exogenous ABA mainly affects seed germination by regulating cell wall loosening. Finally, the correlation analysis of the key DEMs and DEGs indicates that many DEGs play a direct or indirect regulatory role in DEMs metabolism. The integrative analysis between DEGs and DEMs suggests that the starch and sucrose pathways were the key pathway in ABA responses. The two metabolites from starch and sucrose pathways, levan and cellobiose, both were found significantly down-regulated in ABA-treated seedlings. These comprehensive metabolic and transcript analyses provide useful information for the subsequent post-transcriptional modification and post germination growth of rapeseed in response to ABA signals and stresses.

Transcriptomic analysis of potato (Solanum tuberosum L.) tuber development reveals new insights into starch biosynthesis.

Potato tubers are rich sources of various nutrients and unique sources of starch. Many genes play major roles in different pathways, including carbohydrate metabolism during the potato tuber's life cycle. Despite substantial scientific evidence about the physiological and morphological development of potato tubers, the molecular genetic aspects of mechanisms underlying tuber formation have not yet been fully understood. In this study, for the first time, RNA-seq analysis was performed to shed light on the expression of genes involved in starch biosynthesis during potato tuber development. To this end, samples were collected at the hook-like stolon (Stage I), swollen tips stolon (Stage II), and tuber initiation (Stage III) stages of tuber formation. Overall, 23 GB of raw data were generated and assembled. There were more than 20000 differentially expressed genes (DEGs); the expression of 73 genes involved in starch metabolism was further studied. Moreover, qRT-PCR analysis revealed that the expression profile of the starch biosynthesis DEGs was consistent with that of the RNA-seq data, which further supported the role of the DEGs in starch biosynthesis. This study provides substantial resources on potato tuber development and several starch synthesis isoforms associated with starch biosynthesis.

Exploring the structural assembly of rice ADP-glucose pyrophosphorylase subunits using MD simulation.

ADP-glucose pyrophosphorylase plays a pivotal role as an allosteric enzyme, essential for starch biosynthesis in plants. The higher plant AGPase comparises of a pair of large and a pair of small subunits to form a heterotetrameric complex. Growing evidence indicates that each subunit plays a distinct role in regulating the underlying mechanism of starch biosynthesis. In the rice genome, there are four large subunit genes (OsL1-L4) and three small subunit genes (OsS1, OsS2a, and OsS2b). While the structural assembly of cytosolic rice AGPase subunits (OsL2:OsS2b) has been elucidated, there is currently no such documented research available for plastidial rice AGPases (OsL1:OsS1). In this study, we employed protein modeling and MD simulation approaches to gain insights into the structural association of plastidial rice AGPase subunits. Our results demonstrate that the heterotetrameric association of OsL1:OsS1 is very similar to that of cytosolic OsL2:OsS2b and potato AGPase heterotetramer (StLS:StSS). Moreover, the yeast-two-hybrid results on OsL1:OsS1, which resemble StLS:StSS, suggest a differential protein assembly for OsL2:OsS2b. Thus, the regulatory and catalytic mechanisms for plastidial AGPases (OsL1:OsS1) could be different in rice culm and developing endosperm compared to those of OsL2:OsS2b, which are predominantly found in rice endosperm.

[Influence of chronic immobilization stress on vitamin status in rats fed different diets].

The influence of a stress factor, widespread in modern conditions, on the vitamin status has not been studied enough. At the same time, the negative stress impact can be aggravated against the background of unhealthy nutrition, which in turn affects the vitamin status of the organism. In this regard, the goal of the research was to evaluate the effect of chronic restrict stress on the vitamin supply in rats fed a diet with adequate and increased content of fat, sugar and cholesterol. Material and methods. The experiment was carried out on 37 growing male Wistar rats (initial body weight of 45±5 g) divided into 4 groups. Animals of the 1st (control) and the 2nd groups received a complete semi-synthetic diet (CSSD) (20% protein, 10% fat, 58% carbohydrates in the form of starch, 384 kcal/100 g) for 92 days. The levels of all vitamins and mineral elements in the rats' diets were adequate for growing rats. Rats of the 3rd and the 4th groups were fed a high-calorie, high-fat high-carbohydrate diet (HFHCD) (20% protein, 28% fat, 2% cholesterol, 18% carbohydrates in the form of starch, 20% sucrose, 511 kcal/100 g). Animals of groups 2 and 4 were subjected to daily 90-minute immobilization. The concentration of vitamins A (retinol and retinol palmitate) and E (α-tocopherol) in the blood serum and liver were determined by high-performance liquid chromatography, vitamins B1 and B2 in the liver and urine, as well as riboflavin in the blood serum and 4-pyridoxic acid (4-PA) in urine were determined by fluorimetric methods. Biochemical parameters of blood serum were determined on a biochemical analyzer; the total content of fat, triglycerides (TG) and cholesterol (CH) was determined in the liver. Results. Replacing CSSD with HFHCD, both under restraint stress and without, was accompanied by an increase in liver weight by 1.8-2.0 fold, in its fat content by 2.6-3.3 fold, cholesterol by 32.6-35.3 fold and TG - by 33.0-57.6 fold (p=<0.001). An increase in alanine aminotransferase (ALT) activity by 1.7-2.0 fold (p=<0.01), in low-density lipoprotein (LDL) cholesterol level by 5.4 fold (p=<0.05) and the atherogenic coefficient by 2.5 fold (p<0.01) as well as a decrease in creatinine and urea level (p=<0.05) in blood serum were revealed. Immobilization was accompanied by a decrease in body weight, liver and liver fat in rats fed both CSSD and HFHCD (p<0.05), but didn't affect the blood serum biochemical parameters, with the exception of an increase in ALT activity. If the activity of alkaline phosphatase (ALP) did not change during immobilization of rats fed the CSSD, then in animals fed the high-calorie diet it decreased by 37.5% (p=<0.05 from the control) under its increase against the background of restrict stress by 78.7% (p=<0.01) compared to the indicator of rats of the 3rd group. Immobilization of rats treated with CSSD was accompanied by an increase in both absolute serum α-tocopherol level and concentration correlated with the level of cholesterol and triglycerides by 26.0-57.5% (p<0.05), with a simultaneous decrease in its content in the liver per 1 g of wet tissue by 22.1% (p=0.041) relative to the indicators of intact animals. Immobilization reduced the level of retinol palmitate in the liver by 2.3 times (p<0.01), but did not affect retinol level in the blood serum. At the same time, indicators of B vitamin status (the content of vitamins B1 and B2 in the liver per 1 g of wet tissue and per organ, blood serum riboflavin level, urinary excretion of riboflavin and 4-PA) did not change, with the exception of thiamine urinary excretion, which reduced compared to the control by 38.8%. In rats fed HFHCD, immobilization had no additional effect on the supply with vitamins A and E. The content of vitamins B1 and B2 in the liver in terms of the whole organ was reduced by 14.0-26.7% relative to the indicator in animals of the 3rd group, not subjected to chronic stress, only due to differences in liver weight in animals of these groups. Conclusion. The data obtained indicate that chronic stress has a negative effect on the vitamin status of the body, worsening the supply with vitamins A, E and B1, and substantiate the feasibility of studying the mechanisms of this effect in order to develop effective vitamin complexes for the treatment and prevention of diseases caused by long-term stress.

Genome-Wide Identification, Characterization, and Expression Analysis of Four Subgroup Members of the GH13 Family in Wheat (Triticum aestivum L.).

The glycoside hydrolase 13 (GH13) family is crucial for catalyzing α-glucoside linkages, and plays a key role in plant growth, development, and stress responses. Despite its significance, its role in plants remains understudied. This study targeted four GH13 subgroups in wheat, identifying 66 GH13 members from the latest wheat database (IWGSC RefSeq v2.1), including 36 α-amylase (AMY) members, 18 1,4-α-glucan-branching enzyme (SBE) members, 9 isoamylase (ISA) members, and 3 pullulanase (PU) members. Chromosomal distribution reveals a concentration of wheat group 7 chromosomes. Phylogenetic analysis underscores significant evolutionary distance variations among the subgroups, with distinct molecular structures. Replication events shaped subgroup evolution, particularly in regard to AMY members. Subcellular localization indicates AMY member predominance in extracellular and chloroplast regions, while others localize solely in chloroplasts, confirmed by the heterologous expression of TaSEB16 and TaAMY1 in tobacco. Moreover, 3D structural analysis shows the consistency of GH13 across species. Promoter cis-acting elements are suggested to be involved in growth, stress tolerance, and starch metabolism signaling. The RNA-seq data revealed TaGH13 expression changes under drought and submergence stress, and significant expression variation was observed between strong and weak gluten varieties during seed germination using quantitative real-time PCR (qRT-PCR), correlating with seed starch content. These findings demonstrate the pivotal role of GH13 family gene expression in wheat germination, concerning variety preference and environmental stress. Overall, this study advances the understanding of wheat GH13 subgroups, laying the groundwork for further functional studies.

Allelic variation in the autotetraploid potato: genes involved in starch and steroidal glycoalkaloid metabolism as a case study.

BACKGROUND: Tuber starch and steroidal glycoalkaloid (SGA)-related traits have been consistently prioritized in potato breeding, while allelic variation pattern of genes that underlie these traits is less explored. RESULTS: Here, we focused on the genes involved in two important metabolic pathways in the potato: starch metabolism and SGA biosynthesis. We identified 119 genes consisting of 81 involved in starch metabolism and 38 in the biosynthesis of steroidal glycoalkaloids, and discovered 96,166 allelic variants among 2,169 gene haplotypes in six autotetraploid potato genomes. Comparative analyses revealed an uneven distribution of allelic variants among gene haplotypes and that the vast majority of deleterious mutations in these genes are retained in heterozygous state in the autotetraploid potato genomes. Leveraging full-length cDNA sequencing data, we find that approximately 70% of haplotypes of the 119 genes are transcribable. Population genetic analyses identify starch and SGA biosynthetic genes that are potentially conserved or diverged between potato varieties with varying starch or SGA content. CONCLUSIONS: These results deepen the understanding of haplotypic diversity within functionally important genes in autotetraploid genomes and may facilitate functional characterization of genes or haplotypes contributing to traits related to starch and SGA in potato.

Insights into the Structure-Function Relationship of GH70 GtfB α-Glucanotransferases from the Crystal Structure and Molecular Dynamic Simulation of a Newly Characterized Limosilactobacillus reuteri N1 GtfB Enzyme.

α-Glucanotransferases of the CAZy family GH70 convert starch-derived donors to industrially important α-glucans. Here, we describe characteristics of a novel GtfB-type 4,6-α-glucanotransferase of high enzyme activity (60.8 U mg-1) from Limosilactobacillus reuteri N1 (LrN1 GtfB), which produces surprisingly large quantities of soluble protein in heterologous expression (173 mg pure protein per L of culture) and synthesizes the reuteran-like α-glucan with (α1 → 6) linkages in linear chains and branch points. Protein structural analysis of LrN1 GtfB revealed the potential crucial residues at subsites -2∼+2, particularly H265, Y214, and R302, in the active center as well as previously unidentified surface binding sites. Furthermore, molecular dynamic simulations have provided unprecedented insights into linkage specificity hallmarks of the enzyme. Therefore, LrN1 GtfB represents a potent enzymatic tool for starch conversion, and this study promotes our knowledge on the structure-function relationship of GH70 GtfB α-glucanotransferases, which might facilitate the production of tailored α-glucans by enzyme engineering in future.

DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages.

Malus sieversii is considered the ancestor of the modern cultivated apple, with a high value for apple tolerance breeding. Despite studies on the temperature adaptability of M. sieversii carried out at a physiological response and the genome level, information on the proteome changes of M. sieversii during dormancy is limited, especially about the M. sieversii subtypes. In this study, a DIA-based approach was employed to screen and identify differential proteins involved in three overwintering periods of flower buds in two M. sieversii subtypes (Malus sieversii f. luteolus, GL; Malus sieversii f. aromaticus, HC) with different overwintering adaptabilities. The proteomic analysis revealed that the number of the down-regulated differential expression proteins (DEPs) was obviously higher than that of the up-regulated DEPs in the HC vs. GL groups, especially at the dormancy stage and dormancy-release stage. Through functional classification of those DEPs, the majority of the DEPs in the HC vs. GL groups were associated with protein processing in the endoplasmic reticulum, oxidative phosphorylation, starch and sucrose metabolism and ribosomes. Through WGCNA analysis, tricarboxylic acid cycle and pyruvate metabolism were highly correlated with the overwintering stages; oxidative phosphorylation and starch and sucrose metabolism were highly correlated with the Malus sieversii subtypes. This result suggests that the down-regulation of DEPs, which are predominantly enriched in these pathways, could potentially contribute to the lower cold tolerance observed in HC during overwintering stage.

Chalkiness and premature controlled by energy homeostasis in OsNAC02 Ko-mutant during vegetative endosperm development.

BACKGROUND: Chalkiness is a common phenotype induced by various reasons, such as abiotic stress or the imbalance of starch synthesis and metabolism during the development period. However, the reason mainly for one gene losing its function such as NAC (TFs has a large family in rice) which may cause premature is rarely known to us. RESULTS: The Ko-Osnac02 mutant demonstrated an obviously early maturation stage compared to the wild type (WT) with 15 days earlier. The result showed that the mature endosperm of Ko-Osnac02 mutant exhibited chalkiness, characterized by white-core and white-belly in mature endosperm. As grain filling rate is a crucial factor in determining the yield and quality of rice (Oryza sativa, ssp. japonica), it's significant that mutant has a lower amylose content (AC) and higher soluble sugar content in the mature endosperm. Interestingly among the top DEGs in the RNA sequencing of N2 (3DAP) and WT seeds revealed that the OsBAM2 (LOC_Os10g32810) expressed significantly high in N2 mutant, which involved in Maltose up-regulated by the starch degradation. As Prediction of Protein interaction showed in the chalky endosperm formation in N2 seeds (3 DAP), seven genes were expressed at a lower-level which should be verified by a heatmap diagrams based on DEGs of N2 versus WT. The Tubulin genes controlling cell cycle are downregulated together with the MCM family genes MCM4 ( ↓), MCM7 ( ↑), which may cause white-core in the early endosperm development. In conclusion, the developing period drastically decreased in the Ko-Osnac02 mutants, which might cause the chalkiness in seeds during the early endosperm development. CONCLUSIONS: The gene OsNAC02 which controls a great genetic co-network for cell cycle regulation in early development, and KO-Osnac02 mutant shows prematurity and white-core in endosperm.

Dynamics of starch formation and gene expression during grain filling and its possible influence on grain quality.

In rice, grain filling is a crucial stage where asynchronous filling of the pollinated spikelet's of the panicle occurs. It can influence both grain quality and yield. In rice grain, starch is the dominant component and contains amylose and amylopectin. Amylose content is the chief cooking quality parameter, however, rice varieties having similar amylose content varied in other parameters. Hence, in this study, a set of varieties varying in yield (04) and another set (12) of varieties that are similar in amylose content with variation in gel consistency and alkali spreading value were used. Panicles were collected at various intervals and analysed for individual grain weight and quantities of amylose and amylopectin. Gas exchange parameters were measured in varieties varying in yield. Upper branches of the panicles were collected from rice varieties having similar amylose content and were subjected to gene expression analysis with fourteen gene specific primers of starch synthesis. Results indicate that grain filling was initiated simultaneously in multiple branches. Amylose and amylopectin quantities increased with the increase in individual grain weight. However, the pattern of regression lines of amylose and amylopectin percentages with increase in individual grain weight varied among the varieties. Gas exchange parameters like photosynthetic rate, stomatal conductance, intercellular CO2 and transpiration rate decreased with the increase in grain filling period in both good and poor yielding varieties. However, they decreased more in poor yielders. Expression of fourteen genes varied among the varieties and absence of SBE2b can be responsible for medium or soft gel consistency.

N1019D Mutant of Limosilactobacillus reuteri 121 4,6-α-Glucanotransferase GtfB Significantly Improved Catalytic Activity.

Limosilactobacillus reuteri 121 4,6-α-glucanotransferase GtfB (Lr 121 GtfB), belonging to glycoside hydrolase family 70 (GH70), synthesizes linear isomalto/malto polysaccharides having (α1→6) linkages attached to the nonreducing ends of (α1→4) linked maltose oligosaccharide segments using starch or maltodextrin as a substrate. Since Lr 121 GtfB has low catalytic activity and efficiency, it leads to substrate regeneration and reduced substrate utilization. In this study, we superimposed the crystal structure of Lr 121 GtfB-ΔNΔV with that of L. reuteri NCC 2613 GtfB-ΔNΔV (Lr 2613 GtfB-ΔNΔV) to identify the acceptor binding subsites +1 to +3 and constructed five single-residue mutants and a random mutagenesis of N1019. Compared with the wild-type, N1019D Lr 121 GtfB-ΔN did not alter the product specificity, increased the catalytic activity and efficiency by 420 and 590%, respectively, and maintained >80% relative activity in the pH 3.5-6.5 interval. The findings will contribute to the industrial application of Lr 121 GtfB and provide new solutions for starch synthesis of higher value derivatives.

Comparative transcriptome and coexpression network analysis reveals key pathways and hub candidate genes associated with sunflower (Helianthus annuus L.) drought tolerance.

BACKGROUND: Drought severely limits sunflower production especially at the seedling stage. To investigate the response mechanism of sunflowers to drought stress, we utilized two genotypes of sunflower materials with different drought resistances as test materials. The physiological responses were investigated under well-watered (0 h) and drought-stressed conditions (24 h, 48 h, and 72 h). RESULTS: ANOVA revealed the greatest differences in physiological indices between 72 h of drought stress and 0 h of drought stress. Transcriptome analysis was performed after 72 h of drought stress. At 0 h, there were 7482 and 5627 differentially expressed genes (DEGs) in the leaves of K55 and K58, respectively, and 2150 and 2527 DEGs in the roots of K55 and K58, respectively. A total of 870 transcription factors (TFs) were identified among theDEGs, among which the high-abundance TF families included AP2/ERF, MYB, bHLH,and WRKY. Five modules were screened using weighted gene coexpressionnetwork analysis (WGCNA), three and two of which were positively and negatively, respectively, related to physiological traits. KEGG analysis revealedthat under drought stress, "photosynthesis", "carotenoid biosynthesis", "starch and sucrose metabolism", "ribosome", "carotenoid biosynthesis", "starch and sucrose metabolism", "protein phosphorylation" and "phytohormone signaling" are six important metabolic pathways involved in the response of sunflower to drought stress. Cytoscape software was used to visualize the three key modules, and the hub genes were screened. Finally, a total of 99 important candidate genes that may be associated with the drought response in sunflower plants were obtained, and the homology of these genes was compared with that in Arabidopsis thaliana. CONCLUSIONS: Taken together, our findings could lead to a better understanding of drought tolerance in sunflowers and facilitate the selection of drought-tolerant sunflower varieties.

Tempeh fermentation improves the nutritional and functional characteristics of Jack beans (Canavalia ensiformis (L.) DC).

The effect of two processing methods of Jack beans (i.e. cooked bean (CB) and cooked tempeh (CT)) on the in vitro digestibility of protein and starch, as well as the production of short chain fatty acids (SCFAs), γ-aminobutyric acid (GABA), and tryptophan (Trp) metabolites after in vitro colonic fermentation, was investigated. CT was obtained by fungal fermentation after cooking under acidic conditions. CT had significantly higher protein, lower digestible starch, lower total fiber, higher free phenolic compounds, and higher ash content compared to CB. CT exhibited better in vitro protein digestibility than CB and less glucose release during in vitro digestion than CB. A comparable concentration of total SCFAs and GABA was produced after in vitro fermentation of CB and CT, but CB produced more indole than CT, resulting in higher amounts of total Trp metabolites. In summary, our findings show that tempeh fermentation improves the nutritional quality of Jack beans and describe the impact of fermentation on the digestibility of nutrients and the formation of metabolites during colonic fermentation.

Impact of polyphenol-loaded edible starch nanomaterials on antioxidant capacity and gut microbiota.

Starch nanoparticles (SNPs) have the capability to adsorb polyphenol components from apple pomace efficiently, forming bound polyphenols (P-SNPs). These bound polyphenols may have potential bioactivities to affect human health positively. Therefore, in-depth in vivo observation of the antioxidant activity and evaluation of its gut microbiota regulatory function are essential. The results revealed that P-SNPs indicated significant scavenging abilities against DPPH, ABTS, and hydroxyl radicals. Furthermore, the nanomaterials exhibited non-toxic properties, devoid of hepatorenal and intestinal damage, while concurrently stimulating the production of short-chain fatty acids (SCFAs) within the gastrointestinal tract. Notably, P-SNPs significantly enhanced antioxidant capacity in serum, liver, and kidney tissues, fostering the proliferation of beneficial bacteria (Lactobacillus, Bacillus, norank_f__Muribaculaceae) while suppressing pathogenic bacterial growth (Helicobacter, Odoribacter). This study proposes a novel research concept for the scientific use of polyphenols in promoting gut health.