Genome-wide Analysis of Phosphoenolpyruvate Carboxylase Gene Family and Their Response to Abiotic Stresses in Soybean

Identification and Analysis of PEPC Gene Family Reveals Functional Diversification in Orchidaceae and the Regulation of Bacterial-Type PEPC

Phosphoenolpyruvate carboxylase (PEPC) gene family plays a crucial role in both plant growth and response to abiotic stress. Approximately half of the Orchidaceae species are estimated to perform CAM pathway, and the availability of sequenced orchid genomes makes them ideal subjects for investigating the PEPC gene family in CAM plants. In this study, a total of 33 PEPC genes were identified across 15 orchids. Specifically, one PEPC gene was found in Cymbidium goeringii and Platanthera guangdongensis; two in Apostasia shenzhenica, Dendrobium chrysotoxum, D. huoshanense, Gastrodia elata, G. menghaiensis, Phalaenopsis aphrodite, Ph. equestris, and Pl. zijinensis; three in C. ensifolium, C. sinense, D. catenatum, D. nobile, and Vanilla planifolia. These PEPC genes were categorized into four subgroups, namely PEPC-i, PEPC-ii, and PEPC-iii (PTPC), and PEPC-iv (BTPC), supported by the comprehensive analyses of their physicochemical properties, motif, and gene structures. Remarkably, PEPC-iv contained a heretofore unreported orchid PEPC gene, identified as VpPEPC4. Differences in the number of PEPC homolog genes among these species were attributed to segmental duplication, whole-genome duplication (WGD), or gene loss events. Cis-elements identified in promoter regions were predominantly associated with light responsiveness, and circadian-related elements were observed in each PEPC-i and PEPC-ii gene. The expression levels of recruited BTPC, VpPEPC4, exhibited a lower expression level than other VpPEPCs in the tested tissues. The expression analyses and RT-qPCR results revealed diverse expression patterns in orchid PEPC genes. Duplicated genes exhibited distinct expression patterns, suggesting functional divergence. This study offered a comprehensive analysis to unveil the evolution and function of PEPC genes in Orchidaceae.

Shoot transcriptome revealed widespread differential expression and potential molecular mechanisms of chickpea (Cicer arietinum L.) against Fusarium wilt

Introduction

The yield of chickpea is severely hampered by infection wilt caused by several races of Fusarium oxysporum f. sp. ciceris (Foc).

Methods

To understand the underlying molecular mechanisms of resistance against Foc4 Fusarium wilt, RNA sequencing-based shoot transcriptome data of two contrasting chickpea genotypes, namely KWR 108 (resistant) and GL 13001 (susceptible), were generated and analyzed.

Results and Discussion

The shoot transcriptome data showed 1,103 and 1,221 significant DEGs in chickpea genotypes KWR 108 and GL 13001, respectively. Among these, 495 and 608 genes were significantly down and up-regulated in genotypes KWR 108, and 427 and 794 genes were significantly down and up-regulated in genotype GL 13001. The gene ontology (GO) analysis of significant DEGs was performed and the GO of the top 50 DEGs in two contrasting chickpea genotypes showed the highest cellular components as membrane and nucleus, and molecular functions including nucleotide binding, metal ion binding, transferase, kinase, and oxidoreductase activity involved in biological processes such as phosphorylation, oxidation-reduction, cell redox homeostasis process, and DNA repair. Compared to the susceptible genotype which showed significant up-regulation of genes involved in processes like DNA repair, the significantly up-regulated DEGs of the resistant genotypes were involved in processes like energy metabolism and environmental adaptation, particularly host-pathogen interaction. This indicates an efficient utilization of environmental adaptation pathways, energy homeostasis, and stable DNA molecules as the strategy to cope with Fusarium wilt infection in chickpea. The findings of the study will be useful in targeting the genes in designing gene-based markers for association mapping with the traits of interest in chickpea under Fusarium wilt which could be efficiently utilized in marker-assisted breeding of chickpea, particularly against Foc4 Fusarium wilt.

Genome-wide identification and expression analysis of the KCS gene family in soybean (Glycine max) reveal their potential roles in response to abiotic stress

Very long chain fatty acids (VLCFAs) are fatty acids with chain lengths of 20 or more carbon atoms, which are the building blocks of various lipids that regulate developmental processes and plant stress responses. 3-ketoacyl-CoA synthase encoded by the KCS gene is the key rate-limiting enzyme in VLCFA biosynthesis, but the KCS gene family in soybean (Glycine max) has not been adequately studied thus far. In this study, 31 KCS genes (namely GmKCS1 - GmKCS31) were identified in the soybean genome, which are unevenly distributed on 14 chromosomes. These GmKCS genes could be phylogenetically classified into seven groups. A total of 27 paralogous GmKCS gene pairs were identified with their Ka/Ks ratios indicating that they had undergone purifying selection during soybean genome expansion. Cis-acting element analysis revealed that GmKCS promoters contained multiple hormone- and stress-responsive elements, indicating that GmKCS gene expression levels may be regulated by various developmental and environmental stimuli. Expression profiles derived from RNA-seq data and qRT-PCR experiments indicated that GmKCS genes were diversely expressed in different organs/tissues, and many GmKCS genes were found to be differentially expressed in the leaves under cold, heat, salt, and drought stresses, suggesting their critical role in soybean resistance to abiotic stress. These results provide fundamental information about the soybean KCS genes and will aid in their further functional elucidation and exploitation.

Transcriptomic and Metabolomic Analyses Reveal the Key Genes Related to Shade Tolerance in Soybean

Soybean (Glycine max) is an important crop, rich in proteins, vegetable oils and several other phytochemicals, which is often affected by light during growth. However, the specific regulatory mechanisms of leaf development under shade conditions have yet to be understood. In this study, the transcriptome and metabolome sequencing of leaves from the shade-tolerant soybean 'Nanxiadou 25' under natural light (ND1) and 50% shade rate (SHND1) were carried out, respectively. A total of 265 differentially expressed genes (DEGs) were identified, including 144 down-regulated and 121 up-regulated genes. Meanwhile, KEGG enrichment analysis of DEGs was performed and 22 DEGs were significantly enriched in the top five pathways, including histidine metabolism, riboflavin metabolism, vitamin B6 metabolism, glycerolipid metabolism and cutin, suberine and wax biosynthesis. Among all the enrichment pathways, the most DEGs were enriched in plant hormone signaling pathways with 19 DEGs being enriched. Transcription factors were screened out and 34 differentially expressed TFs (DETFs) were identified. Weighted gene co-expression network analysis (WGCNA) was performed and identified 10 core hub genes. Combined analysis of transcriptome and metabolome screened out 36 DEGs, and 12 potential candidate genes were screened out and validated by quantitative real-time polymerase chain reaction (qRT-PCR) assay, which may be related to the mechanism of shade tolerance in soybean, such as ATP phosphoribosyl transferase (ATP-PRT2), phosphocholine phosphatase (PEPC), AUXIN-RESPONSIVE PROTEIN (IAA17), PURPLE ACID PHOSPHATASE (PAP), etc. Our results provide new knowledge for the identification and function of candidate genes regulating soybean shade tolerance and provide valuable resources for the genetic dissection of soybean shade tolerance molecular breeding.

An advanced systems biology framework of feature engineering for cold tolerance genes discovery from integrated omics and non-omics data in soybean

Soybean is sensitive to low temperatures during the crop growing season. An urgent demand for breeding cold-tolerant cultivars to alleviate the production loss is apparent to cope with this scenario. Cold-tolerant trait is a complex and quantitative trait controlled by multiple genes, environmental factors, and their interaction. In this study, we proposed an advanced systems biology framework of feature engineering for the discovery of cold tolerance genes (CTgenes) from integrated omics and non-omics (OnO) data in soybean. An integrative pipeline was introduced for feature selection and feature extraction from different layers in the integrated OnO data using data ensemble methods and the non-parameter random forest prioritization to minimize uncertainties and false positives for accuracy improvement of results. In total, 44, 143, and 45 CTgenes were identified in short-, mid-, and long-term cold treatment, respectively, from the corresponding gene-pool. These CTgenes outperformed the remaining genes, the random genes, and the other candidate genes identified by other approaches in an independent RNA-seq database. Furthermore, we applied pathway enrichment and crosstalk network analyses to uncover relevant physiological pathways with the discovery of underlying cold tolerance in hormone- and defense-related modules. Our CTgenes were validated by using 55 SNP genotype data of 56 soybean samples in cold tolerance experiments. This suggests that the CTgenes identified from our proposed systematic framework can effectively distinguish cold-resistant and cold-sensitive lines. It is an important advancement in the soybean cold-stress response. The proposed pipelines provide an alternative solution to biomarker discovery, module discovery, and sample classification underlying a particular trait in plants in a robust and efficient way.

Physiological and Biochemical Regulation Mechanism of Exogenous Hydrogen Peroxide in Alleviating NaCl Stress Toxicity in Tartary Buckwheat (Fagopyrum tataricum (L.) Gaertn)

We aimed to elucidate the physiological and biochemical mechanism by which exogenous hydrogen peroxide (H₂O₂) alleviates salt stress toxicity in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn). Tartary buckwheat “Chuanqiao-2” under 150 mmol·L⁻¹ salt (NaCl) stress was treated with 5 or 10 mmol·L⁻¹ H₂O₂, and seedling growth, physiology and biochemistry, and related gene expression were studied. Treatment with 5 mmol·L⁻¹ H₂O₂ significantly increased plant height (PH), fresh and dry weights of shoots (SFWs/SDWs) and roots (RFWs/RDWs), leaf length (LL) and area (LA), and relative water content (LRWC); increased chlorophyll a (Chl a) and b (Chl b) contents; improved fluorescence parameters; enhanced antioxidant enzyme activity and content; and reduced malondialdehyde (MDA) content. Expressions of all stress-related and enzyme-related genes were up-regulated. The F3′H gene (flavonoid synthesis pathway) exhibited similar up-regulation under 10 mmol·L⁻¹ H₂O₂ treatment. Correlation and principal component analyses showed that 5 mmol·L⁻¹ H₂O₂ could significantly alleviate the toxic effect of salt stress on Tartary buckwheat. Our results show that exogenous 5 mmol·L⁻¹ H₂O₂ can alleviate the inhibitory or toxic effects of 150 mmol·L⁻¹ NaCl stress on Tartary buckwheat by promoting growth, enhancing photosynthesis, improving enzymatic reactions, reducing membrane lipid peroxidation, and inducing the expression of related genes.

The Original Form of C4-Photosynthetic Phosphoenolpyruvate Carboxylase Is Retained in Pooids but Lost in Rice

Poaceae is the most prominent monocot family that contains the primary cereal crops wheat, rice, and maize. These cereal species exhibit physiological diversity, such as different photosynthetic systems and environmental stress tolerance. Phosphoenolpyruvate carboxylase (PEPC) in Poaceae is encoded by a small multigene family and plays a central role in C4-photosynthesis and dicarboxylic acid metabolism. Here, to better understand the molecular basis of the cereal species diversity, we analyzed the PEPC gene family in wheat together with other grass species. We could designate seven plant-type and one bacterial-type grass PEPC groups, ppc1a, ppc1b, ppc2a, ppc2b, ppc3, ppc4, ppcC4, and ppc-b, respectively, among which ppc1b is an uncharacterized type of PEPC. Evolutionary inference revealed that these PEPCs were derived from five types of ancient PEPCs (ppc1, ppc2, ppc3, ppc4, and ppc-b) in three chromosomal blocks of the ancestral Poaceae genome. C4-photosynthetic PEPC (ppcC4 ) had evolved from ppc1b, which seemed to be arisen by a chromosomal duplication event. We observed that ppc1b was lost in many Oryza species but preserved in Pooideae after natural selection. In silico analysis of cereal RNA-Seq data highlighted the preferential expression of ppc1b in upper ground organs, selective up-regulation of ppc1b under osmotic stress conditions, and nitrogen response of ppc1b. Characterization of wheat ppc1b showed high levels of gene expression in young leaves, transcriptional responses under nitrogen and abiotic stress, and the presence of a Dof1 binding site, similar to ppcC4 in maize. Our results indicate the evolving status of Poaceae PEPCs and suggest the functional association of ppc1-derivatives with adaptation to environmental changes.

Exploring the Taxonomic and Functional Diversity of Marine Benthic Micro-Eukaryotes Along the Red Sea Coast of Jeddah City

Backgrounds

Diverse marine habitats along Jeddah's Red Sea coast support rich biodiversity. Few studies have been done on its diverse communities, especially its microbial counterparts. Metagenomic analysis of marine benthic micro-eukaryotic communities was performed for the first time on the Red Sea coast of Jeddah. This research looks into their community structure and metabolic potential.

Methods

Next-generation sequencing was used to examine the micro-eukaryotic communities of seven sedimentary soil samples from four Jeddah coast locations. After isolating DNA from seven benthic sedimentary soil samples, the 18S rDNA V4 regions were amplified and sequenced on the Illumina MiSeq. It was also verified using an Agilent Technologies 2100 Bioanalyzer with a DNA 1000 chip (Agilent Technologies, Fisher Scientific). A standard curve of fluorescence readings generated by qPCR quantification using the Illumina library was achieved using the GS FLX library. Metagenomic data analysis was used to evaluate the microbial communities' biochemical and enzymatic allocations in studied samples.

Results

Blast analysis showed that the top ten phyla were Annelida, Eukaryota, Diatomea, Porifera, Phragmoplastophyta, Arthropoda, Dinoflagellata, Xenacoelomorpha Nematoda, and uncultured. Annelida was also found in the highest percentage (93%), in the sample M followed by Porifera (64%), the most abundant in the control sample then Eukaryotes (61%), Phragmatoplastophyta (55%), Arthropoda, and Diatomea (the least common) (32%). community diversity analysis: using Shannon and inverse Simpson indices showed sediment composition to be effective. Also, PICRUST2 indicated that the most abundant pathways were pyruvate fermentation to isobutanol, pyrimidine deoxyribonucleotide phosphorylation, adenosine ribonucleotide de novo biosynthesis, guanosine ribonucleotide de novo biosynthesis, NAD salvage pathway I, the super pathway of glyoxylate bypass and aerobic respiration I (cytochrome c).

Conclusion

Results showed that high throughput metagenomics could reveal species diversity and estimate gene profiles. Environmental factors appear to be more important than geographic variation in determining the structure of these microbial communities. This study provides the first report of marine benthic micro-eukaryotic communities found on the Red Sea coast of Jeddah and will serve as a good platform for future research.

Conservation and Divergence of Phosphoenolpyruvate Carboxylase Gene Family in Cotton

Phosphoenolpyruvate carboxylase (PEPC) is an important enzyme in plants, which regulates carbon flow through the TCA cycle and controls protein and oil biosynthesis. Although it is important, there is little research on PEPC in cotton, the most important fiber crop in the world. In this study, a total of 125 PEPCs were identified in 15 Gossypium genomes. All PEPC genes in cotton are divided into six groups and each group generally contains one PEPC member in each diploid cotton and two in each tetraploid cotton. This suggests that PEPC genes already existed in cotton before their divergence. There are additional PEPC sub-groups in other plant species, suggesting the different evolution and natural selection during different plant evolution. PEPC genes were independently evolved in each cotton sub-genome. During cotton domestication and evolution, certain PEPC genes were lost and new ones were born to face the new environmental changes and human being needs. The comprehensive analysis of collinearity events and selection pressure shows that genome-wide duplication and fragment duplication are the main methods for the expansion of the PEPC family, and they continue to undergo purification selection during the evolutionary process. PEPC genes were widely expressed with temporal and spatial patterns. The expression patterns of PEPC genes were similar in G. hirsutum and G. barbadense with a slight difference. PEPC2A and 2D were highly expressed in cotton reproductive tissues, including ovule and fiber at all tested developmental stages in both cultivated cottons. However, PEPC1A and 1D were dominantly expressed in vegetative tissues. Abiotic stress also induced the aberrant expression of PEPC genes, in which PEPC1 was induced by both chilling and salinity stresses while PEPC5 was induced by chilling and drought stresses. Each pair (A and D) of PEPC genes showed the similar response to cotton development and different abiotic stress, suggesting the similar function of these PEPCs no matter their origination from A or D sub-genome. However, some divergence was also observed among their origination, such as PEPC5D was induced but PEPC5A was inhibited in G. barbadense during drought treatment, suggesting that a different organized PEPC gene may evolve different functions during cotton evolution. During cotton polyploidization, the homologues genes may refunction and play different roles in different situations.

A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis

Poaceae (the grasses) includes rice, maize, wheat, and other crops, and is the most economically important angiosperm family. Poaceae is also one of the largest plant families, consisting of over 11 000 species with a global distribution that contributes to diverse ecosystems. Poaceae species are classified into 12 subfamilies, with generally strong phylogenetic support for their monophyly. However, many relationships within subfamilies, among tribes and/or subtribes, remain uncertain. To better resolve the Poaceae phylogeny, we generated 342 transcriptomic and seven genomic datasets; these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera, representing 45 tribes and all 12 subfamilies. Over 1200 low-copy nuclear genes were retrieved from these datasets, with several subsets obtained using additional criteria, and used for coalescent analyses to reconstruct a Poaceae phylogeny. Our results strongly support the monophyly of 11 subfamilies; however, the subfamily Puelioideae was separated into two non-sister clades, one for each of the two previously defined tribes, supporting a hypothesis that places each tribe in a separate subfamily. Molecular clock analyses estimated the crown age of Poaceae to be ∼101 million years old. Ancestral character reconstruction of C₃/C₄ photosynthesis supports the hypothesis of multiple independent origins of C₄ photosynthesis. These origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase, which suggests that members of three paralogous subclades (ppc-aL1a, ppc-aL1b, and ppc-B2) were recruited as functional C₄ppc genes. This study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.

Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants

Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C₄and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C₄ and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C₄ species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C₄ photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C₄ and CAM plants and shed light on the adaptation of plants in dry, hot environments.

Novel QTL identification and candidate gene analysis for enhancing salt tolerance in soybean (Glycine max (L.) Merr.)

Soybean, a glycophyte that is sensitive to salt stress, is greatly affected by salinity at all growth stages. A mapping population derived from a cross between a salt-sensitive Korean cultivar, Cheongja 3, and a salt-tolerant landrace, IT162669, was used to identify quantitative trait loci (QTLs) conferring salt tolerance in soybean. Following treatment with 120 mM NaCl for 2 weeks, phenotypic traits representing physiological damage, leaf Na+ content, and K+/Na+ ratio were characterized. Among the QTLs mapped on a high-density genetic map harboring 2,630 single nucleotide polymorphism markers, we found two novel major loci, qST6, on chromosome 6, and qST10, on chromosome 10, which controlled traits related to ion toxicity and physiology in response to salinity, respectively. These loci were distinct from the previously known salt tolerance allele on chromosome 3. Other QTLs associated with abiotic stress overlapped with the genomic regions of qST6 and qST10, or with their paralogous regions. Based on the functional annotation and parental expression differences, we identified eight putative candidate genes, two in qST6 and six in qST10, which included a phosphoenolpyruvate carboxylase and an ethylene response factor. This study provides additional genetic resources to breed soybean cultivars with enhanced salt tolerance.

Differential Expression, Tissue-Specific Distribution, and Posttranslational Controls of Phosphoenolpyruvate Carboxylase

Phosphoenolpyruvate carboxylase (PEPC) is a ubiquitous cytosolic enzyme, which is crucial for plant carbon metabolism. PEPC participates in photosynthesis by catalyzing the initial fixation of atmospheric CO2 and is abundant in both C4 and crassulacean acid metabolism leaves. PEPC is differentially expressed at different stages of plant development, mostly in leaves, but also in developing seeds. PEPC is known to show tissue-specific distribution in leaves and in other plant organs, such as roots, stems, and flowers. Plant PEPC undergoes reversible phosphorylation and monoubiquitination, which are posttranslational modifications playing important roles in regulatory processes and in protein localization. Phosphorylation activates the PEPC enzyme, making it more sensitive to glucose-6-phosphate and less sensitive to malate or aspartate. PEPC phosphorylation is known to be diurnally regulated and delicately changed in response to various environmental stimuli, in addition to light. PEPCs belong to a small gene family encoding several plant-type and distantly related bacterial-type PEPCs. This paper provides a minireview of the general information on PEPCs in both C4 and C3 plants.

Genome-Wide Identification and Analysis of the Phosphoenolpyruvate Carboxylase Gene Family in Suaeda aralocaspica, an Annual Halophyte With Single-Cellular C4 Anatomy

Phosphoenolpyruvate carboxylase (PEPC) plays pivotal roles in the carbon fixation of photosynthesis and a variety of metabolic and stress pathways. Suaeda aralocaspica belongs to a single-cellular C₄ species and carries out a photosynthetic pathway in an unusually elongated chlorenchyma cell, which is expected to have PEPCs with different characteristics. To identify the different isoforms of PEPC genes in S. aralocaspica and comparatively analyze their expression and regulation patterns as well as the biochemical and enzymatic properties in this study, we characterized a bacterial-type PEPC (BTPC; SaPEPC-4) in addition to the two plant-type PEPCs (PTPCs; SaPEPC-1 and SaPEPC-2) using a genome-wide identification. SaPEPC-4 presented a lower expression level in all test combinations with an unknown function; two SaPTPCs showed distinct subcellular localizations and different spatiotemporal expression patterns but positively responded to abiotic stresses. Compared to SaPEPC-2, the expression of SaPEPC-1 specifically in chlorenchyma cell tissues was much more active with the progression of development and under various stresses, particularly sensitive to light, implying the involvement of SaPEPC-1 in a C₄ photosynthetic pathway. In contrast, SaPEPC-2 was more like a non-photosynthetic PEPC. The expression trends of two SaPTPCs in response to light, development, and abiotic stresses were also matched with the changes in PEPC activity in vivo (native) or in vitro (recombinant), and the biochemical properties of the two recombinant SaPTPCs were similar in response to various effectors while the catalytic efficiency, substrate affinity, and enzyme activity of SaPEPC-2 were higher than that of SaPEPC-1 in vitro. All the different properties between these two SaPTPCs might be involved in transcriptional (e.g., specific cis-elements), posttranscriptional [e.g., 5'-untranslated region (5'-UTR) secondary structure], or translational (e.g., PEPC phosphorylation/dephosphorylation) regulatory events. The comparative studies on the different isoforms of the PEPC gene family in S. aralocaspica may help to decipher their exact role in C₄ photosynthesis, plant growth/development, and stress resistance.

Multi-omic dissection of the drought resistance traits of soybean landrace LX

With diverse genetic backgrounds, soybean landraces are valuable resource for breeding programs. Herein, we apply multi-omic approaches to extensively characterize the molecular basis of drought tolerance in the soybean landrace LX. Initial screens established that LX performed better with PEG6000 treatment than control cultivars. LX germinated better than William 82 under drought conditions and accumulated more anthocyanin and flavonoids. Untargeted mass spectrometry in combination with transcriptomic analyses revealed the chemical diversity and genetic basis underlying the overall performance of LX landrace. Under control and drought conditions, significant differences in the expression of a suite of secondary metabolism genes, particularly those involved in the general phenylpropanoid pathway and flavonoid but not lignin biosynthesis, were seen in LX and William 82. The expression of these genes correlated with the corresponding metabolites in LX plants. Further correlation analysis between metabolites and transcripts identified pathway structural genes and transcription factors likely are responsible for the LX agronomic traits. The activities of some key biosynthetic genes or regulators were confirmed through heterologous expression in transgenic Arabidopsis and hairy root transformation in soybean. We propose a regulatory mechanism based on flavonoid secondary metabolism and adaptive traits of this landrace which could be of relevance to cultivated soybean.

Prokaryotic Expression of Phosphoenolpyruvate Carboxylase Fragments from Peanut and Analysis of Osmotic Stress Tolerance of Recombinant Strains

Phosphoenolpyruvate carboxylase (PEPC) is a ubiquitous cytosolic enzyme that catalyzes the irreversible β-carboxylation of phosphoenolpyruvate (PEP) in presence of HCO₃⁻ to produce oxaloacetate (OAA) during carbon fixation and photosynthesis. It is well accepted that PEPC genes are expressed in plants upon stress. PEPC also supports the biosynthesis of biocompatible osmolytes in many plant species under osmotic stress. There are five isoforms of PEPC found in peanut (Arachis hypogaea L.), namely, AhPEPC1, AhPEPC2, AhPEPC3, AhPEPC4, and AhPEPC5. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that the gene expression patterns of these AhPEPC genes were different in mature seeds, stems, roots, flowers, and leaves. The expression of all the plant type PEPC (PTPCs) (AhPEPC1, AhPEPC2, AhPEPC3, and AhPEPC4) was relatively high in roots, while the bacterial type PEPC (BTPC) (AhPEPC5) showed a remarkable expression level in flowers. Principal component analysis (PCA) result showed that AhPEPC3 and AhPEPC4 are correlated with each other, indicating comparatively associations with roots, and AhPEPC5 have a very close relationship with flowers. In order to investigate the function of these AhPEPCs, the fragments of these five AhPEPC cDNA were cloned and expressed in Escherichia coli (E. coli). The recombinant proteins contained a conserved domain with a histidine site, which is important for enzyme catalysis. Results showed that protein fragments of AhPEPC1, AhPEPC2, and AhPEPC5 had remarkable expression levels in E. coli. These three recombinant strains were more sensitive at pH 9.0, and recombinant strains carrying AhPEPC2 and AhPEPC5 fragments exhibited more growth than the control strain with the presence of PEG6000. Our findings showed that the expression of the AhPEPC fragments may enhance the resistance of transformed E. coli to osmotic stress.

H2O2 priming promotes salt tolerance in maize by protecting chloroplasts ultrastructure and primary metabolites modulation

Hydrogen peroxide priming has emerged as a powerful strategy to trigger multiple responses involved in plant acclimation that reinforce tolerance to abiotic stresses, including salt stress. Thus, this study aimed to investigate the impact of foliar H₂O₂ priming on the physiological, biochemical, and ultrastructural traits related to photosynthesis of salt-stressed plants. Besides, we provided comparative leaf metabolomic profiles of Zea mays plants under such conditions. For this, H₂O or H₂O₂ pretreated plants were grown under saline conditions for 12-days. Salinity drastically affected photosynthetic parameters and structural chloroplasts integrity, also increased reactive oxygen species contents promoting disturbance in the plant metabolism when compared to non-saline conditions. Our results suggest that H₂O₂-pretreated plants improved photosynthetic performance avoiding salinity-induced energy excess and ultrastructural damage by preserving stacking thylakoids. It displayed modulation of some metabolites, as arabitol, glucose, asparagine, and tyrosine, which may contribute to the maintenance of osmotic balance and reduced oxidative stress. Hence, our study brings new insights into an understanding of plant acclimation to salinity by H₂O₂ priming based on photosynthesis maintenance and metabolite modulation.

Transcriptional analyses of two soybean cultivars under salt stress

Soybean is an economically important plant, and its production is affected in soils with high salinity levels. It is important to understand the adaptive mechanisms through which plants overcome this kind of stress and to identify potential genes for improving abiotic stress tolerance. RNA-Seq data of two Glycine max cultivars, a drought-sensitive (C08) and a tolerant (Conquista), subjected to different periods of salt stress were analyzed. The transcript expression profile was obtained using a transcriptogram approach, comparing both cultivars and different times of treatment. After 4 h of salt stress, Conquista cultivar had 1400 differentially expressed genes, 647 induced and 753 repressed. Comparative expression revealed that 719 genes share the same pattern of induction or repression between both cultivars. Among them, 393 genes were up- and 326 down-regulated. Salt stress also modified the expression of 54 isoforms of miRNAs in Conquista, by the maturation of 39 different pre-miRNAs. The predicted targets for 12 of those mature miRNAs also have matches with 15 differentially expressed genes from our analyses. We found genes involved in important pathways related to stress adaptation. Genes from both ABA and BR signaling pathways were modulated, with possible crosstalk between them, and with a likely post-transcriptional regulation by miRNAs. Genes related to ethylene biosynthesis, DNA repair, and plastid translation process were those that could be regulated by miRNA.

The plant-type phosphoenolpyruvate carboxylase Gmppc2 is developmentally induced in immature soy seeds at the late maturation stage: a potential protein biomarker for seed chemical composition

Phosphoenolpyruvate carboxylase (PEPC) is a carbon-fixing enzyme with critical roles in seed development. Previously we observed a positive correlation between PEPC activity and protein content in mature seeds among soybean cultivars and varietal differences of PEPC activity in immature seeds, which is concordant with seed protein accumulation. Here, we report a PEPC isoform (Gmppc2) which is preferentially expressed in immature soybean seeds at the late maturation stage. Gmppc2 was co-expressed with enzyme genes involved in starch degradation: α-amylase, hexokinase, and α-glucan phosphorylase. Gmppc2 was developmentally induced in the external seed coats, internal seed coats, hypocotyls, and cotyledons at the late maturation stage. The expression of Gmppc2 protein was negatively regulated by the application of a nitrogen fertilizer, which suppressed nodule formation. These results imply that Gmppc2 is involved in the metabolism of nitrogen originated from nodules into seeds, and Gmppc2 might be applicable as a biomarker of seed protein content.Abbreviations: PEP: phosphoenolpyruvate; PEPC: phosphoenolpyruvate carboxylase; RNA-Seq: RNA sequencing; PCA: principal component analysis; SE: standard error.

C4 photosynthetic enzymes play a key role in wheat spike bracts primary carbon metabolism response under water deficit

C4 photosynthetic enzymes are present in C3 plants and participate in non-photosynthetic metabolism. Wheat spike bracts had a higher drought tolerance, photosynthesis and senesced later compared to the flag leaves under water deficit. This research was conducted to investigate the different response of primary carbon metabolism induced by C4 photosynthetic enzymes in wheat flag leaves and spike bracts including glumes and lemmas under water deficit. The activities of C4 photosynthetic enzymes and Ribulose bisphosphate carboxylase oxygenase (Rubisco), the expression of related genes and primary carbon metabolism contents were demonstrated in wheat flag leaves and spike bracts exposed to water deficit. Results showed that drought stress strongly inhibited wheat photosynthetic metabolism by decreasing Rubisco activity in flag leaves. The activities of phosphoenolpyruvate carboxylase (PEPC), NADP-malic enzyme (NADP-ME), phosphate dikinase (PPDK) and NADP- malic dehydrogenase (NADP-MDH) increased in wheat spike bracts under water deficit. Transcript levels of C4 photosynthetic genes in wheat spike bracts were higher under water deficit than that of control. Furthermore, the results indicated that drought stress induced changes in the contents of primary carbon metabolism including malate, oxaloacetic acid (OAA), citric, fumaric acid were organ-specific. In conclusion, the functions of C4 photosynthetic enzymes appear to be important for wheat spike bracts primary carbon metabolism and defence response under drought stress.

Evolution of PEPC gene family in Gossypium reveals functional diversification and GhPEPC genes responding to abiotic stresses

Phosphoenolpyruvate carboxylase (PEPC) family genes play important roles in regulating plant growth and abiotic stress response. Based on the sequenced Gossypium genomes, we performed comprehensive analysis of PEPC homolog genes in cotton, which six, six, eleven and ten PEPC genes were identified in Gossypium arboreum (A₂), G. raimondii (D₅), G. hirsutum (AD₁) and G. barbadense (AD₂), respectively. These genes were divided into six subgroups: PEPC-i, PEPC-ii, PEPC-iii, PEPC-iv, PEPC-v and PEPC-vi; PEPC genes in each subgroup displayed conserved gene structure and motifs. Segmental duplication and whole genome duplication (WGD) events yielded the expansion of PEPC genes. Expression assays showed that the duplicated PEPC genes displayed diverse expression patterns, indicating that they experienced functional divergence. Of which, genes in PEPC-iv subgroup played crucial role for substrate distribution in cottonseed. Cis-elements, putative miRNAs and expression analyses showed that GhPEPC homologs might respond to abiotic stresses, expression levels of GhPEPC1 and GhPEPC2/GhPEPC2D genes were larger induced than other GhPEPC genes under cold, heat, salt, and drought stresses, indicating the crucial roles in abiotic stresses response. Present study serves new information to decipher the evolution and function of PEPC genes in Gossypium.