Genome-Wide Identification and Analysis of Stress Response of Trehalose-6-Phosphate Synthase and Trehalose-6-Phosphate Phosphatase Genes in Quinoa

Evolution and amplification of the trehalose-6-phosphate synthase gene family in Theaceae

BACKGROUND

Trehalose-6-phosphate synthase (TPS) is an essential enzyme involved in the production of trehalose, and the genes associated with TPS are crucial for various processes such as growth, development, defense mechanisms, and resistance to stress. However, there has been no documentation regarding the evolution and functional roles of the TPS gene family within Theaceae.

RESULTS

Here, we uncovered the lineage-specific evolution of TPS genes in Theaceae. A total of 102 TPS genes were discovered across ten Theaceae species with sequenced genomes. Consistent with the previous classification, our phylogenetic analysis indicated that the TPS genes in Theaceae can be categorized into two primary subfamilies and six distinct clades (I, II-1, II-2, II-3, II-4, II-5), with clade I containing a greater number of introns compared to those found in clade II. Segmental duplication served as the main catalyst for the evolution of TPS genes within Theaceae, and numerous TPS genes exhibited inter-species synteny among various Theaceae species. Most of the TPS genes were ubiquitously expressed, and expression divergence of TPS paralogous pairs was observed. The cis-acting elements found in TPS genes indicated their involvement in responses to phytohormones and stress.

CONCLUSION

This research enhanced our understanding of the lineage-specific evolution of the TPS gene family in Theaceae and offered important insights for future functional analyses.

The conserved transcriptional regulation mechanism of ADH1 gene in Zanthoxylum armatum to waterlogging stress

Waterlogging stress negatively affects plant growth and survival. However, the ability of Zanthoxylum armatum, a valuable tree species, to tolerate and adapt to waterlogging stress remains poorly understood. Here we report how alcohol dehydrogenase 1 (ZaADH1) confers waterlogging stress tolerance in Z. armatum. ZaADH1 expression was induced after waterlogging treatment. ZaADH1 overexpression increased waterlogging stress by modulating the metabolite levels of the ADH enzyme, soluble sugar, and trehalose, promoting glycolysis and carbohydrate metabolism. The overexpression of ZaADH1 in Arabidopsis thaliana increased the total plant area and chlorophyll content, thereby increasing resistance to waterlogging stress. Physiological and overexpression transcriptome analyses in A. thaliana indicated that ZaADH1 overexpressing lines generated more carbohydrates to meet energy demands, employing a "static" strategy to increase tolerance to waterlogging stress, which confirms the conservation of the ADH1 response to waterlogging stress and represents a potential crucial measure for improving waterlogging tolerance in Z. armatum.

Tandem mass tag (TMT)-based quantitative proteomics analysis reveals the different responses of contrasting alfalfa varieties to drought stress

BACKGROUND

Drought stress restricts the growth, distribution and productivity of alfalfa (Medicago sativa L.). In order to study the response differences of alfalfa cultivars to drought stress, we previously carried out physiological and molecular comparative analysis on two alfalfa varieties with contrasting drought resistance (relatively drought-tolerant Longdong and drought-sensitive Algonquin). However, the differences in proteomic factors of the two varieties in response to drought stress still need to be further studied. Therefore, TMT-based quantitative proteomic analysis was performed using leaf tissues of the two alfalfa cultivars to identify and uncover differentially abundant proteins (DAPs).

RESULTS

In total, 677 DAPs were identified in Algonquin and 277 in Longdong under drought stress. Subsequently, we conducted various bioinformatics analysis on these DAPs, including subcellular location, functional classification and biological pathway enrichment. The first two main COG functional categories of DAPs in both alfalfa varieties after drought stress were 'Translation, ribosomal structure and biogenesis' and 'Posttranslational modification, protein turnover, chaperones'. According to KEGG database, the DAPs of the two alfalfa cultivars after drought treatment were differentially enriched in different biological pathways. The DAPs from Algonquin were enriched in 'photosynthesis' and 'ribosome'. The pathways of 'linoleic acid metabolism', 'protein processing in endoplasmic reticulum' and 'RNA transport' in Longdong were significantly enriched. Finally, we found significant differences in DAP enrichment and expression patterns between Longdong and Algonquin in glycolysis/glycogenesis, TCA cycle, photosynthesis, protein biosynthesis, flavonoid and isoflavonoid biosynthesis, and plant-pathogen interaction pathway after drought treatment.

CONCLUSIONS

The differences of DAPs involved in various metabolic pathways may explain the differences in the resistance of the two varieties to drought stress. These DAPs can be used as candidate proteins for molecular breeding of alfalfa to cultivate new germplasm with more drought tolerance to adapt to unfavorable environments.

Analysis of widely targeted metabolites of quinoa sprouts (Chenopodium quinoa Willd.) under saline-alkali stress provides new insights into nutritional value

Quinoa sprouts are a green vegetable rich in bioactive chemicals, which have multiple health benefits. However, there is limited information on the overall metabolic profiles of quinoa sprouts and the metabolite changes caused by saline-alkali stress. Here, a UHPLC-MS/MS-based widely targeted metabolomics technique was performed to comprehensively evaluate the metabolic profiles of quinoa sprouts and characterize its metabolic response to saline-alkali stress. A total of 930 metabolites were identified of which 232 showed significant response to saline-alkali stress. The contents of lipids and amino acids were significantly increased, while the contents of flavonoids and phenolic acids were significantly reduced under saline-alkali stress. Moreover, the antioxidant activities of quinoa sprouts were significantly affected by saline-alkali stress. The enrichment analysis of the differentially accumulated metabolites revealed that flavonoid, amino acid and carbohydrate biosynthesis/metabolism pathways responded to saline-alkali stress. This study provided an important theoretical basis for evaluating the nutritional value of quinoa sprouts and the changes in metabolites in response to saline-alkali stress.

Bacillus altitudinis AD13-4 Enhances Saline-Alkali Stress Tolerance of Alfalfa and Affects Composition of Rhizosphere Soil Microbial Community

Saline and alkaline stresses limit plant growth and reduce crop yield. Soil salinization and alkalization seriously threaten the sustainable development of agriculture and the virtuous cycle of ecology. Biofertilizers made from plant growth-promoting rhizobacteria (PGPR) not only enhance plant growth and stress tolerance, but also are environmentally friendly and cost-effective. There have been many studies on the mechanisms underlying PGPRs enhancing plant salt resistance. However, there is limited knowledge about the interaction between PGPR and plants under alkaline-sodic stress. To clarify the mechanisms underlying PGPR's improvement of plants' tolerance to alkaline-sodic stress, we screened PGPR from the rhizosphere microorganisms of local plants growing in alkaline-sodic land and selected an efficient strain, Bacillus altitudinis AD13-4, as the research object. Our results indicate that the strain AD13-4 can produce various growth-promoting substances to regulate plant endogenous hormone levels, cell division and differentiation, photosynthesis, antioxidant capacity, etc. Transcriptome analysis revealed that the strain AD13-4 significantly affected metabolism and secondary metabolism, signal transduction, photosynthesis, redox processes, and plant-pathogen interactions. Under alkaline-sodic conditions, inoculation of the strain AD13-4 significantly improved plant biomass and the contents of metabolites (e.g., soluble proteins and sugars) as well as secondary metabolites (e.g., phenols, flavonoids, and terpenoids). The 16S rRNA gene sequencing results indicated that the strain AD13-4 significantly affected the abundance and composition of the rhizospheric microbiota and improved soil activities and physiochemical properties. Our study provides theoretical support for the optimization of saline-alkali-tolerant PGPR and valuable information for elucidating the mechanism of plant alkaline-sodic tolerance.

Genome-Wide Analysis of Trehalose-6-Phosphate Phosphatase Gene Family and Their Expression Profiles in Response to Abiotic Stress in Groundnut

Trehalose-6-phosphate phosphatase (TPP) is a pivotal enzyme in trehalose biosynthesis which plays an essential role in plant development and in the abiotic stress response. However, little is currently known about TPPs in groundnut. In the present study, a total of 16 AhTPP genes were identified, and can be divided into three phylogenetic subgroups. AhTPP members within the same subgroups generally displayed similar exon-intron structures and conserved motifs. Gene collinearity analysis revealed that segmental duplication was the primary factor driving the expansion of the AhTPP family. An analysis of the upstream promoter region of AhTPPs revealed eight hormone- and four stress-related responsive cis-elements. Transcriptomic analysis indicated high expression levels of AhTPP genes in roots or flowers, while RT-qPCR analysis showed upregulation of the six tested genes under different abiotic stresses, suggesting that AhTPPs play roles in growth, development, and response to various abiotic stresses. Subcellular localization analysis showed that AhTPP1A and AhTPP5A were likely located in both the cytoplasm and the nucleus. To further confirm their functions, the genes AhTPP1A and AhTPP5A were individually integrated into yeast expression vectors. Subsequent experiments demonstrated that yeast cells overexpressing these genes displayed increased tolerance to osmotic and salt stress compared to the control group. This study will not only lay the foundation for further study of AhTPP gene functions, but will also provide valuable gene resources for improving abiotic stress tolerance in groundnut and other crops.

Genome- and transcriptome-wide identification of trehalose-6-phosphate phosphatases (TPP) gene family and their expression patterns under abiotic stress and exogenous trehalose in soybean

BACKGROUND

Trehalose-6-phosphate phosphatase (TPP) is an essential enzyme catalyzing trehalose synthesis, an important regulatory factor for plant development and stress response in higher plants. However, the TPP gene family in soybean has not been reported.

RESULTS

A comprehensive analysis of the TPP gene family identified 18 GmTPPs classified into eight groups based on the phylogenetic relationships and the conservation of protein in six monocot and eudicot plants. The closely linked subfamilies had similar motifs and intron/exon numbers. Segmental duplication was the main driving force of soybean GmTPPs expansion. In addition, analysis of the cis-regulatory elements and promoter regions of GmTPPs revealed that GmTPPs regulated the response to several abiotic stresses. Moreover, RNA-seq and qRT-PCR analysis of the tissue-specific GmTPPs under different abiotic stresses revealed that most GmTPPs were associated with response to different stresses, including cold, drought, saline-alkali, and exogenous trehalose. Notably, exogenous trehalose treatment up-regulated the expression of most TPP genes under saline-alkali conditions while increasing the carbohydrate and trehalose levels and reducing reactive oxygen species (ROS) accumulation in soybean sprouts, especially in the saline-alkali tolerant genotype. Furthermore, the interaction network and miRNA target prediction revealed that GmTPPs interacted with abiotic stress response-related transcription factors.

CONCLUSIONS

The findings in this study lay a foundation for further functional studies on TPP-based breeding to improve soybean development and stress tolerance.

The trehalose 6-phosphate phosphatase family in plants

Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, is an essential signalling metabolite linking plant growth and development to carbon metabolism. While recent work has focused predominantly on the enzymes that produce Tre6P, little is known about the proteins that catalyse its degradation, the trehalose 6-phosphate phosphatases (TPPs). Often occurring in large protein families, TPPs exhibit cell-, tissue- and developmental stage-specific expression patterns, suggesting important regulatory functions in controlling local levels of Tre6P and trehalose as well as Tre6P signalling. Furthermore, growing evidence through gene expression studies and transgenic approaches shows that TPPs play an important role in integrating environmental signals with plant metabolism. This review highlights the large diversity of TPP isoforms in model and crop plants and identifies how modulating Tre6P metabolism in certain cell types, tissues, and at different developmental stages may promote stress tolerance, resilience and increased crop yield.

Genome-Wide Analysis and Expression Profiling of Trehalose-6-Phosphate Phosphatase (TPP) in Punica granatum in Response to Abscisic-Acid-Mediated Drought Stress

Trehalose, a nonreducing disaccharide, has been linked to plant growth and development as well as stress response. The enzyme trehalose-6-phosphate phosphatase (TPP) plays a crucial role in the production of trehalose in higher plants. This study identified a total of seven TPP family genes within the pomegranate species (PgTPP1-PgTPP7). Three subgroups of the seven PgTPPs were identified through phylogenetic analysis. The gene length, coding sequence (CD) length, and chromosomal location of the PgTPP genes were studied. In addition, the PgTPP proteins' length, isoelectric point (Ip), grand average of hydropathicity (GRAVY), conserved domains, conserved motifs, synteny, and phylogenetic relationships with Arabidopsis and tomato TPP proteins were examined. The cis-acting elements in the promoter region and the expression of the PgTPP genes under abscisic acid (ABA)-mediated drought stress as well as the differences in expression in the root, flower, and leaf tissues were also assessed. The PgTPP2 and PgTPP5 genes are involved in the response to abscisic-acid-mediated drought stress, as shown by drought-mediated stress transcriptomes. The PgTPP1 and PgTPP2 genes were expressed only in floral tissue and roots, respectively. The remaining PgTPPs did not exhibit any significant alterations in gene expression in roots, flowers, or leaves. The current study has the potential to provide a comprehensive understanding of the biological characteristics of PgTPP proteins in various developmental processes and their role in the pomegranate plant's response to different stressors. However, further research is required to explore their precise biological role. Hence, conducting a comprehensive functional validation study on PgTPPs could contribute to the development of stress-resistant agricultural cultivars.

Genome-Wide Identification and Analysis of R2R3-MYB Genes Response to Saline-Alkali Stress in Quinoa

Soil saline-alkalization inhibits plant growth and development and seriously affects crop yields. Over their long-term evolution, plants have formed complex stress response systems to maintain species continuity. R2R3-MYB transcription factors are one of the largest transcription factor families in plants, widely involved in plant growth and development, metabolism, and stress response. Quinoa (Chenopodium quinoa Willd.), as a crop with high nutritional value, is tolerant to various biotic and abiotic stress. In this study, we identified 65 R2R3-MYB genes in quinoa, which are divided into 26 subfamilies. In addition, we analyzed the evolutionary relationships, protein physicochemical properties, conserved domains and motifs, gene structure, and cis-regulatory elements of CqR2R3-MYB family members. To investigate the roles of CqR2R3-MYB transcription factors in abiotic stress response, we performed transcriptome analysis to figure out the expression file of CqR2R3-MYB genes under saline-alkali stress. The results indicate that the expression of the six CqMYB2R genes was altered significantly in quinoa leaves that had undergone saline-alkali stress. Subcellular localization and transcriptional activation activity analysis revealed that CqMYB2R09, CqMYB2R16, CqMYB2R25, and CqMYB2R62, whose Arabidopsis homologues are involved in salt stress response, are localized in the nucleus and exhibit transcriptional activation activity. Our study provides basic information and effective clues for further functional investigation of CqR2R3-MYB transcription factors in quinoa.