Elucidation of salt-tolerance metabolic pathways in contrasting rice genotypes and their segregating progenies

Physiological and Transcriptome Analysis Provide Insights into the Effects of Low and High Selenium on Methionine and Starch Metabolism in Rice Seedlings

Selenium (Se) is an essential micronutrient for the human body and is closely linked to health. Rice (Oryza sativa L.), as a major staple food globally, is the primary source of Se intake for humans. To better achieve Se biofortification in rice, it is crucial to understand the molecular mechanisms behind rice's response to different Se concentrations. This study investigates the morphological and transcriptomic responses of rice seedlings to low (1 µM, LSe) and high (10 µM, HSe) Se concentrations compared to a control (CK). Morphological analyses revealed that LSe promoted growth, enhancing shoot and root length and biomass, whereas HSe treatment inhibited these parameters, indicating Se's dual role in rice growth. Notably, the most significant promotion of rice growth was observed at the Se concentration of 1 µM. The organic Se content and antioxidant enzyme activities (SOD, POD and CAT) in rice seedlings also reached their maximum values simultaneously. Total RNA was extracted for transcriptome sequencing, and differential gene expression analysis was conducted using DESeq2. Transcriptomic sequencing highlighted distinct responses under LSe and HSe conditions. Gene ontology (GO) enrichment analysis revealed significant involvement in processes related to oxidoreductase activity and cellular structures. KEGG pathway analysis emphasized that Se treatments notably enhanced the glutathione metabolism pathway, which is crucial for antioxidant defense. Additionally, significant changes were observed in starch and sucrose metabolism and cysteine (Cys) and methionine (Met) metabolism pathways, showing upregulation under LSe treatment and downregulation under HSe. Six key genes were validated using qRT-PCR, confirming their differential expression under varied Se treatments. The Cys, Met and starch content assays as well as qRT-PCR data demonstrated that LSe promoted the synthesis and accumulation of Cys, Met and starch, supporting enhanced growth and antioxidant capacity. Conversely, HSe inhibited the synthesis and accumulation of Cys, Met and starch in rice seedlings, and these data were also consistent with the physiological phenotype. These findings provide insights into the molecular mechanisms by which rice seedlings adapt to varying Se levels, with implications for Se biofortification and stress management strategies in crops.

Halotolerant Enterobacter asburiae A103 isolated from the halophyte Salix linearistipularis: Genomic analysis and growth-promoting effects on Medicago sativa under alkali stress

Soil salinization negatively affects plant growth and threatens food security. Halotolerant plant growth-promoting bacteria (PGPB) can alleviate salt stress in plants via diverse mechanisms. In the present study, we isolated salt-tolerant bacteria with phosphate-solubilizing abilities from the rhizosphere of Salix linearistipularis, a halophyte distributed in saline-alkali soils. Strain A103 showed high phosphate solubilization activity and was identified as Enterobacter asburiae based on genome analysis. In addition, it can produce indole-3-acetic acid (IAA), siderophores, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Genome mining has also revealed the presence of several functional genes involved in the promotion of plant growth. Inoculation with A103 markedly improved alfalfa growth in the presence of 100 mM NaHCO3. Under alkali stress, the shoot and root dry weights after bacterial inoculation improved by 42.9 % and 21.9 %, respectively. Meanwhile, there was a 35.9-37.1 % increase in the shoot and root lengths after treatment with A103 compared to the NaHCO3-treated group. Soluble sugar content, peroxidase and catalase activities increased in A103-inoculated alfalfa under alkaline stress. A significant decrease in the malondialdehyde content was observed after treatment with strain A103. Metabolomic analysis indicated that strain A103 positively regulated alkali tolerance in alfalfa through the accumulation of metabolites, such as homocarnosine, panthenol, and sorbitol, which could reduce oxidative damage and act as osmolytes. These results suggest that halophytes are valuable resources for bioprospecting halotolerant beneficial bacteria and that the application of halotolerant growth-promoting bacteria is a natural and efficient strategy for developing sustainable agriculture.

FERONIA regulates salt tolerance in Arabidopsis by controlling photorespiratory flux

Photorespiration is an energetically costly metabolic pathway in plants that responds to environmental stresses. The molecular basis of the regulation of the photorespiratory cycle under stress conditions remains unclear. Here, we discovered that FERONIA (FER) regulates photorespiratory flow under salt stress in Arabidopsis (Arabidopsis thaliana). FER mutation results in hypersensitivity to salt stress, but disruption of ferredoxin-dependent glutamate synthase 1 (GLU1), an enzyme that participates in the photorespiratory pathway by producing glutamate, greatly suppresses fer-4 hypersensitivity to salt stress primarily due to reduced glycine yield. In contrast, disrupting mitochondrial serine hydroxymethyltransferase1 (SHM1), which is supposed to increase glycine levels by hampering the conversion of glycine to serine in the photorespiratory cycle, aggravates fer-4 hypersensitivity to salt stress. Biochemical data show that FER interacts with and phosphorylates SHM1, and this phosphorylation modulates SHM1 stability. Additionally, the production of proline and its intermediate △1-pyrroline-5-carboxylate (P5C), which are both synthesized from glutamate, also contributes to fer-4 hypersensitivity to salt stress. In conclusion, this study elucidates the functional mechanism of FER in regulating salt tolerance by modulating photorespiratory flux, which greatly broadens our understanding of how plants adapt to high salinity.

Genome-wide identification of SHMT family genes in cucumber (Cucumis sativus L.) and functional analyses of CsSHMTs in response to hormones and abiotic stresses

Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate-dependent enzyme that plays crucial roles in the photorespiration and one-carbon metabolism of plants. In the present research, we conducted a systematic analysis of the SHMT gene family in cucumber (Cucumis sativus L). Results show that a total of 6 SHMT members were identified from the cucumber genome database. CsSHMT1 and CsSHMT2 participate in a fragment duplication event, indicating that CsSHMTs may complete the expansion of family members through fragment duplication. Gene structure analysis found that the number of exons of CsSHMTs ranges from 4 to 15. Members with the same number of exons are classified into the same class in the phylogenetic analysis. Each class reflects its subcellular distribution. Expression and function analysis reveals that CsSHMTs express in a variety of plant tissues, indicating that SHMT gene expression pattern is not organ-specific. qRT-PCR analysis found that CsSHMT3 and CsSHMT5 positively respond to abscisic acid (ABA), and CsSHMT2-6 are induced by indole-3-acetic acid (IAA) and methyl jasmonate (MeJA). Abiotic stress analysis shows that CsSHMT3 is significantly induced by drought and salt stress. These results may provide useful information for further function and evolution analysis of cucumber SHMT genes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03378-x.

Integrated Multi-Omics Perspective to Strengthen the Understanding of Salt Tolerance in Rice

Salt stress is one of the major constraints to rice cultivation worldwide. Thus, the development of salt-tolerant rice cultivars becomes a hotspot of current rice breeding. Achieving this goal depends in part on understanding how rice responds to salt stress and uncovering the molecular mechanism underlying this trait. Over the past decade, great efforts have been made to understand the mechanism of salt tolerance in rice through genomics, transcriptomics, proteomics, metabolomics, and epigenetics. However, there are few reviews on this aspect. Therefore, we review the research progress of omics related to salt tolerance in rice and discuss how these advances will promote the innovations of salt-tolerant rice breeding. In the future, we expect that the integration of multi-omics salt tolerance data can accelerate the solution of the response mechanism of rice to salt stress, and lay a molecular foundation for precise breeding of salt tolerance.

Genome-wide identification and expression analysis of serine hydroxymethyltransferase (SHMT) gene family in tomato (Solanum lycopersicum)

Serine hydroxymethyltransferase (SHMT) is one of the most important enzyme families in one-carbon metabolic pathway and photorespiration within plant cells. Recently studies reported the active roles of plant SHMTs in defending abiotic stresses. However, genome-scale analysis of SHMT in tomato is currently unknown. In this study, seven SHMT genes were identified in the tomato genome using a genome-wide search approach. In addition, their physicochemical properties, protein secondary structure, subcellular localization, gene structure, conserved motifs, phylogenetic and collinear relationships were analyzed. Our results demonstrated that tomato SHMT members were divided into two group and four subgroups, and they were conserved with the orthologs of other plants. Analysis of cis-acting elements showed that each of the SlSHMT genes contained different kinds of hormones and stress-related cis-acting elements in their promoter regions. Finally, qRT-PCR analysis indicated that SlSHMTs were expressed at different levels in different tissues, and they responded to UV, cold, heat, NaCl, H₂O₂, ABA and PEG treatments. These results provided definite evidence that SlSHMTs might involve in growth, development and stress responses in tomato, which laid a foundation for future functional studies of SlSHMTs.

Modulation in growth, biochemical attributes and proteome profile of rice cultivars under salt stress

One of the major abiotic stresses that affect productivity of rice is salinity. Rice cultivars showed significant genetic variation in response to salt stress. In the present investigation, differential growth pattern and physio-chemical traits-based screening of high yielding rice cultivars of various salt affected areas of India was carried out, and salt-sensitive and salt-tolerant cultivars were identified. Differential responses of antioxidant enzyme activity and tolerance index at maximum level of salt treatment depicted that Jhelum and Vytilla-4 cultivars of rice were sensitive and tolerant to salt stress, respectively. Analysis of growth, morpho-physiological, and biochemical parameters also confirmed the salt-tolerant and salt-sensitive characters of cv. Vytilla-4 and cv. Jhelum, respectively. Nano-LCMS/MS-based proteome profile of these two cultivars was carried out to find out the mechanism lying behind the salt tolerance. A total number of 514 and 770 protein spots were reported in the most salt-tolerant (cv. Vytilla-4) and salt-sensitive (cv. Jhelum) cultivars, respectively. The differentially expressed proteins (DEPs) were found associated with major metabolic pathways including photosynthesis, energy metabolism, amino acid metabolism, nitrogen assimilation and stress and signalling pathways. The changes in the major proteins like Ribulose bisphosphate carboxylase small chain, chlorophyll a-b binding protein, phosphoglycerate kinase, cytochrome c oxidase subunit 5C, glutamine synthetase, glutathione S-transferase, peroxidase, and thioredoxin elucidated the mechanism activated by salt-tolerant cv. Vytilla-4. The transcriptional validation of some of the differentially expressed proteins through real-time quantitative PCR analysis further validated the proteomic results. Outcomes of this work could help in finding out the potential cross-links of different pathways involved in salt-tolerance mechanisms operating in the studied here rice cultivars under salt stress.

PGDH family genes differentially affect Arabidopsis tolerance to salt stress

The first step in the Phosphorylated Pathway of serine (Ser) Biosynthesis (PPSB) is catalyzed by the enzyme Phosphoglycerate Dehydrogenase (PGDH), coded in Arabidopsis thaliana by three genes. Gene expression analysis indicated that PGDH1 and PGDH2 were induced, while PGDH3 was repressed, by salt-stress. Accordingly, PGDH3 overexpressing plants (Oex PGDH3) were more sensitive to salinity than wild type plants (WT), while plants overexpressing PGDH1 (Oex PGDH1) performed better than WT under salinity conditions. Oex PGDH1 lines displayed lower levels of the salt-stress markers proline and raffinose in roots than WT under salt-stress conditions. Besides, the ratio of oxidized glutathione (GSSG) without and with salt-stress was the highest in Oex PGDH1, and the lowest in Oex PGDH3 compared to WT. These results corroborated that PGDH3 activity could be detrimental, while PGDH1 activity could be beneficial for plant salt tolerance. Under salt-stress conditions, PGDH1 overexpression increased Ser content only in roots, while PGDH3 overexpression increased the amino acid level in both aerial parts and roots, compared to the WT. Our results indicate that the response of PGDH family genes to salt-stress depends on the specific gene studied and that increases in Ser content are not always correlated with enhanced plant salt tolerance.

Cysteine and methionine contribute differentially to regulate alternative oxidase in leaves of poplar (Populus deltoides x Populus euramericana 'Nanlin 895') seedlings exposed to different salinity

The effects of different doses of NaCl on the expression profiles of genes involved in the mitochondrial electron transport chain (miETC), H₂O₂ and O₂^- levels, and antioxidant enzymes and amino acid metabolism were investigated in the leaves of poplar (Populus deltoides x Populus euramericana 'Nanlin 895'). In the miETC, complexes II and III and bypasses of the cytochrome c pathway including AOX and UCP displayed higher transcript abundance, whereas COX6b encoding cytochrome c oxidase were suppressed at 200 and 400 mM. H₂O₂ accumulated at 200 mM NaCl but O₂^- was generated at 400 mM. Accordingly, CAT was enhanced at 200 and 400 mM, while G-POD strengthened only at 400 mM. In addition, cysteine was reduced at 400 mM but did not change at 200 mM, although methionine was accumulated at 200 mM but not altered at 400 mM. Exogenous cysteine accumulated H₂S and methionine increased ACC at 200 mM NaCl. At 400 mM NaCl, cysteine elevated the expression of CGS encoding cystathionine gamma-synthase and MS2 encoding methionine synthase as well as ACC and H₂S levels, and methionine increased ACC content with repressed CGS and MS2. Moreover, exogenous KCN decreased cysteine levels, with an augment in H₂S and up-regulation of CYS C1 encoding β-cyanoalanine synthase at all salinity conditions, whereas antimycin A (AA) and salicylhydroxamic acid (SHAM) affected neither the levels of cysteine or H₂S, nor the CYS C1 expression. However, neither KCN, AA nor SHAM affected ACC content. AOX1b was induced both by exogenous cysteine and methionine as well as KCN and AA but suppressed by SHAM at 200 and 400 mM NaCl, in negative correlation with MDA content. These results suggest that poplar leaf evolved diverse strategies in amino acid metabolism of manipulating the AOX pathway to defend against different levels of salt stress.

Photorespiratory serine hydroxymethyltransferase 1 activity impacts abiotic stress tolerance and stomatal closure

The photorespiratory cycle is a crucial pathway in photosynthetic organisms because it removes toxic 2-phosphoglycolate made by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase and retrieves its carbon as 3-phosphoglycerate. Mitochondrial serine hydroxymethyltransferase 1 (SHMT1) is an essential photorespiratory enzyme converting glycine to serine. SHMT1 regulation remains poorly understood although it could involve the phosphorylation of serine 31. Here, we report the complementation of Arabidopsis thaliana shm1-1 by SHMT1 wild-type, phosphorylation-mimetic (S31D) or nonphophorylatable (S31A) forms. All SHMT1 forms could almost fully complement the photorespiratory growth phenotype of shm1-1; however, each transgenic line had only 50% of normal SHMT activity. In response to either a salt or drought stress, Compl-S31D lines showed a more severe growth deficiency compared with the other transgenic lines. This sensitivity to salt appeared to reflect reduced SHMT1-S31D protein amounts and a lower activity that impacted leaf metabolism leading to proline underaccumulation and overaccumulation of polyamines. The S31D mutation in SHMT1 also led to a reduction in salt-induced and ABA-induced stomatal closure. Taken together, our results highlight the importance of maintaining photorespiratory SHMT1 activity in salt and drought stress conditions and indicate that SHMT1 S31 phosphorylation could be involved in modulating SHMT1 protein stability.

Heterologous Expression of Serine Hydroxymethyltransferase-3 From Rice Confers Tolerance to Salinity Stress in E. coli and Arabidopsis

Among abiotic stresses, salt stress adversely affects growth and development in rice. Contrasting salt tolerant (CSR27), and salt sensitive (MI48) rice varieties provided information on an array of genes that may contribute for salt tolerance of rice. Earlier studies on transcriptome and proteome profiling led to the identification of salt stress-induced serine hydroxymethyltransferase-3 (SHMT3) gene. In the present study, the SHMT3 gene was isolated from salt-tolerant (CSR27) rice. OsSHMT3 exhibited salinity-stress induced accentuated and differential expression levels in different tissues of rice. OsSHMT3 was overexpressed in Escherichia coli and assayed for enzymatic activity and modeling protein structure. Further, Arabidopsis transgenic plants overexpressing OsSHMT3 exhibited tolerance toward salt stress. Comparative analyses of OsSHMT3 vis a vis wild type by ionomic, transcriptomic, and metabolic profiling, protein expression and analysis of various traits revealed a pivotal role of OsSHMT3 in conferring tolerance toward salt stress. The gene can further be used in developing gene-based markers for salt stress to be employed in marker assisted breeding programs.

HIGHLIGHTS

- The study provides information on mechanistic details of serine hydroxymethyl transferase gene for its salt tolerance in rice.

Evaluation of proline functions in saline conditions

More than one third of the world's irrigated lands are affected by salinity, which has great impact on plant growth and yield worldwide. Proline accumulation under salt stress has been indicated to correlate with salt tolerance. Exogenous application as well as genetic engineering of metabolic pathways involved in the metabolism of proline has been successful in improving tolerance to salinity. Correlation between proline accumulation as well as its proposed roles and salt adaptation, however, has not been clearly confirmed in several plant species. In addition, the studies relating proline functions and plant salt tolerance are always carried out in growth chambers, and are not successfully verified in field conditions. Further, plant salt tolerance is a complex trait, and studies based solely on proline accumulation do not adequately explain its functions in salinity tolerance, and thus it is difficult to interpret the discrepancies among different data. Moreover, several reports indicate that Pro role in salt tolerance is a matter of debates, as whether Pro accumulation has adaptive significance or is a consequence of alterations in cellular metabolism induced by salinity. As no consensus is obtained on the exact roles of proline production, proline exact roles in the adaptation to saline environments is therefore still lacking and is even a matter of debates. It is obvious that comprehensive future research is needed to establish the proline exact mechanism by which it enhances plant salt tolerance. We propose, however, that proline might be essential for improving salinity tolerance in some species/cultivars, but may not be relevant in others. Evidence supporting both arguments has been presented in order to reassess the feasibility of the proposed roles of Pro in plant salt tolerance mechanism.

Comparative Proteomic and Nutritional Composition Analysis of Independent Transgenic Pigeon Pea Seeds Harboring cry1AcF and cry2Aa Genes and Their Nontransgenic Counterparts

Safety assessment of genetically modified plants is an important aspect prior to deregulation. Demonstration of substantial equivalence of the transgenics compared to their nontransgenic counterparts can be performed using different techniques at various molecular levels. The present study is a first-ever comprehensive evaluation of pigeon pea transgenics harboring two independent cry genes, cry2Aa and cry1AcF. The absence of unintended effects in the transgenic seed components was demonstrated by proteome and nutritional composition profiling. Analysis revealed that no significant differences were found in the various nutritional compositional analyses performed. Additionally, 2-DGE-based proteome analysis of the transgenic and nontransgenic seed protein revealed that there were no major changes in the protein profile, although a minor fold change in the expression of a few proteins was observed. Furthermore, the study also demonstrated that neither the integration of T-DNA nor the expression of the cry genes resulted in the production of unintended effects in the form of new toxins or allergens.