Quantitative analysis of the grain amyloplast proteome reveals differences in metabolism between two wheat cultivars at two stages of grain development

Preferentially expressed endosperm genes reveal unique activities in wheat endosperm during grain filling

BACKGROUND

Bread wheat (Triticum aestivum L.) endosperm contains starch and proteins, which determine the final yield, quality, and nutritional value of wheat grain. The preferentially expressed endosperm genes can precisely provide targets in the endosperm for improving wheat grain quality and nutrition using modern bioengineering technologies. However, the genes specifically expressed in developing endosperms remain largely unknown.

RESULTS

In this study, 315 preferentially expressed endosperm genes (PEEGs) in the spring wheat landrace, Chinese Spring, were screened using data obtained from an open bioinformatics database, which reveals a unique grain reserve deposition process and special signal transduction in a developing wheat endosperm. Furthermore, transcription and accumulation of storage proteins in the wheat cultivar, XC26 were evaluated. The results revealed that 315 PEEG plays a critical role in storage protein fragment deposition and is a potential candidate for modifying grain quality and nutrition.

CONCLUSION

These results provide new insights into endosperm development and candidate genes and promoters for improving wheat grain quality through genetic engineering and plant breeding techniques.

Changes in carbon allocation and subplastidal amyloplast structures of specialised Ipomoea batatas (sweet potato) storage root phenotypes

Vitamin A deficiency (VAD) in Low and Medium Income countries remains a major health concern. Ipomoea batatas, orange sweet potato (OSP), is one of the biofortification solutions being implemented by the World Health Organisation (WHO) to combat VAD. However, high provitamin A (β-carotene) content has been associated with a reduction in dry matter, reducing calorific value and having adverse effects on consumer traits. Both starch and carotenoid formation are located in amyloplasts and could potentially compete for the same precursors. Hence, five different sweet potato storage root phenotypes were characterized through spatial metabolomics and proteomics at the sub-plastidal level. The metabolite data suggested an indirect correlation of starch and carotenoids through the TCA cycle and pentose phosphate pathway. Furthermore, a change in lipid composition was observed to accommodate the storage of carotenoids in the hydrophilic environment of the amyloplast. The data suggests an alteration of cellular ultra-structures and perturbation of metabolism in high β-carotene producing sweet potato roots. This corroborates with previous gene expression analysis through biochemical analysis of sweet potato root tissue.

"Omics" insights into plastid behavior toward improved carotenoid accumulation

Plastids are a group of diverse organelles with conserved carotenoids synthesizing and sequestering functions in plants. They optimize the carotenoid composition and content in response to developmental transitions and environmental stimuli. In this review, we describe the turbulence and reforming of transcripts, proteins, and metabolic pathways for carotenoid metabolism and storage in various plastid types upon organogenesis and external influences, which have been studied using approaches including genomics, transcriptomics, proteomics, and metabonomics. Meanwhile, the coordination of plastid signaling and carotenoid metabolism including the effects of disturbed carotenoid biosynthesis on plastid morphology and function are also discussed. The "omics" insight extends our understanding of the interaction between plastids and carotenoids and provides significant implications for designing strategies for carotenoid-biofortified crops.

The N uptake-associated physiological processes at late growth stage in wheat (Triticum aestivum) under N deprivation combined with deficit irrigation condition

Elucidating physiological mechanisms underlying the plant N uptake benefits breeding of high N use efficiency (NUE) crop cultivars. In this study, we investigated the growth and N uptake-associated processes in wheat under N deprivation and deficit irrigation, using two contrasting NUE cultivars. Compared with sufficient-N (SN), deficient-N (DN) treatment reduced plant biomass, N accumulation, and yields in two cultivars (high NUE Shinong 086 and N deprivation-sensitive Jimai 585), suggesting that N deprivation negatively regulates plant growth and N uptake. Shinong 086 was better on growth and N uptake-associated traits than Jimai 585 due to the improved root biomass across soil profile, which was consistent with the decrease of available N contents in soil layers. These results suggested that the improved root system architecture (RAS) enhances plant acquirement for soil N under N- and water-deprivation condition, contributing to the plant N uptake and yield formation capacities. Transcriptome investigation revealed that numerous genes were differentially expressed (DE) in the N-deprived Shinong 086 plants, which involve the regulation of complicate biochemical pathways. These results suggested that the modified RAS and N uptake in high NUE plants are accomplished underlying the regulation of numerous DE genes. TaWRKY20, a gene in ZFP transcription factor family, was functionally characterized for the role in mediating plant N uptake. Overexpression of it conferred plants improved growth and N uptake under DN due to its regulation on TaNRT2.1 and TaNRT2.2, two nitrate transporter genes. Our investigation provides insights in high NUE mechanisms in wheat under N deprivation.

Chromoplast differentiation in bell pepper (Capsicum annuum) fruits

We report here a detailed analysis of the proteome adjustments that accompany chromoplast differentiation from chloroplasts during bell pepper (Capsicum annuum) fruit ripening. While the two photosystems are disassembled and their constituents degraded, the cytochrome b₆ f complex, the ATPase complex, and Calvin cycle enzymes are maintained at high levels up to fully mature chromoplasts. This is also true for ferredoxin (Fd) and Fd-dependent NADP reductase, suggesting that ferredoxin retains a central role in the chromoplasts' redox metabolism. There is a significant increase in the amount of enzymes of the typical metabolism of heterotrophic plastids, such as the oxidative pentose phosphate pathway (OPPP) and amino acid and fatty acid biosynthesis. Enzymes of chlorophyll catabolism and carotenoid biosynthesis increase in abundance, supporting the pigment reorganization that goes together with chromoplast differentiation. The majority of plastid encoded proteins decline but constituents of the plastid ribosome and AccD increase in abundance. Furthermore, the amount of plastid terminal oxidase (PTOX) remains unchanged despite a significant increase in phytoene desaturase (PDS) levels, suggesting that the electrons from phytoene desaturation are consumed by another oxidase. This may be a particularity of non-climacteric fruits such as bell pepper that lack a respiratory burst at the onset of fruit ripening.

Genome Wide Identification and Comparative Analysis of the Serpin Gene Family in Brachypodium and Barley

Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in the model plant for temperate grasses Brachypodium distachyon and barley Hordeum vulgare using bioinformatic tools at the genome level for the first time. We identified a total of 27 BdSRPs and 25 HvSRP genes in Brachypodium and barley, respectively, showing an unexpectedly high gene number in these model plants. Gene structure, conserved motifs and phylogenetic comparisons of serpin genes supported the role of duplication events in the expansion and evolution of serpin gene family. Further, purifying selection pressure was found to be a main driving force in the evolution of serpin genes. Genome synteny analysis indicated that BdSRP genes were present in syntenic regions of barley, rice, sorghum and maize, suggesting that they evolved before the divergence of these species from common ancestor. The distinct expression pattern in specific tissues further suggested a specialization of functions during development and in plant defense. These results suggest that the LR serpins (serpins with Leu-Arg residues at P2-P1') identified here can be utilized as candidates for exploitation in disease resistance, pest control and preventing stress-induced cell death. Additionally, serpins were identified that could lead to further research aimed at validating and functionally characterizing the role of potential serpin genes from other plants.

Molecular cloning and functional characterisation of the galactolipid biosynthetic gene TaMGD in wheat grain

Monogalactosyl diacylglycerol (MGDG), the main component of the plastid membrane, is essential for chloroplast photosynthesis; however, little information is available about the function of MGDG synthases gene (TaMGD) in wheat grain. In this manuscript, three homologous genes were identified in wheat grain, and their functions were investigated by gene silencing and overexpression techniques. Three TaMGD homologous genes, TaMGD-6A, -6B, and -6D, located on chromosome 6A, 6B, and 6D, respectively, were isolated from common wheat. The transcription of TaMGD was detected in stems, roots, leaves and grains, and high levels of gene transcripts were detected in stems and leaves. Silencing of TaMGD in common wheat spikes resulted in a decrease in grain weight and starch content, and proteomic analysis showed that the differentially expressed proteins mainly included carbohydrate metabolism- and nucleic acid-related proteins. In comparison with wild-type, transgenic rice plants overexpressing TaMGD-6A and -6D showed an increase in thousand kernel weight, as well as an increase in the expression level of genes related to starch biosynthesis, whereas transgenic rice plants overexpressing TaMGD-6B showed increased grain yield and grain number per spike. The results of gene silencing and overexpression indicated that TaMGD plays an important role in wheat grain weight, which might be associated with carbohydrate metabolism. Hence, this study provides new insights regarding the role of TaMGD in wheat grain characteristics.

Transcriptomic and proteomic analysis reveals mechanisms of low pollen-pistil compatibility during water lily cross breeding

BACKGROUND

In water lily (Nymphaea) hybrid breeding, breeders often encounter non-viable seeds, which make it difficult to transfer desired or targeted genes of different Nymphaea germplasm. We found that pre-fertilization barriers were the main factor in the failure of the hybridization of Nymphaea. The mechanism of low compatibility between the pollen and stigma remains unclear; therefore, we studied the differences of stigma transcripts and proteomes at 0, 2, and 6 h after pollination (HAP). Moreover, some regulatory genes and functional proteins that may cause low pollen-pistil compatibility in Nymphaea were identified.

RESULTS

RNA-seq was performed for three comparisons (2 vs 0 HAP, 6 vs 2 HAP, 6 vs 0 HAP), and the number of differentially expressed genes (DEGs) was 8789 (4680 were up-regulated), 6401 (3020 were up-regulated), and 11,284 (6148 were up-regulated), respectively. Using label-free analysis, 75 (2 vs 0 HAP) proteins (43 increased and 32 decreased), nine (6 vs 2 HAP) proteins (three increased and six decreased), and 90 (6 vs 0 HAP) proteins (52 increased and 38 decreased) were defined as differentially expressed proteins (DEPs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs and DEPs were mainly involved in cell wall organization or biogenesis, S-adenosylmethionine (SAM) metabolism, hydrogen peroxide decomposition and metabolism, reactive oxygen species (ROS) metabolism, secondary metabolism, secondary metabolite biosynthesis, and phenylpropanoid biosynthesis.

CONCLUSIONS

Our transcriptomic and proteomic analysis highlighted specific genes, incuding those in ROS metabolism, biosynthesis of flavonoids, SAM metabolism, cell wall organization or biogenesis and phenylpropanoid biosynthesis that warrant further study in investigations of the pollen-stigma interaction of water lily. This study strengthens our understanding of the mechanism of low pollen-pistil compatibility in Nymphaea at the molecular level, and provides a theoretical basis for overcoming the pre-fertilization barriers in Nymphaea in the future.