Genome-Wide Survey of Invertase Encoding Genes and Functional Characterization of an Extracellular Fungal Pathogen-Responsive Invertase in Glycine max

Editing Metabolism, Sex, and Microbiome: How Can We Help Poplar Resist Pathogens?

Poplar (Populus) is a genus of woody plants of great economic value. Due to the growing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens. Genetic engineering can create organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly effective tool for creating valuable genotypes. In this review, we summarize the latest research data on poplar diseases, the biology of their pathogens and how these plants resist pathogens. In the final section, we propose to plant male or mixed poplar populations; consider the genes of the MLO group, transcription factors of the WRKY and MYB families and defensive proteins BbChit1, LJAMP2, MsrA2 and PtDef as the most promising targets for genetic engineering; and also pay attention to the possibility of microbiome engineering.

Identification, characterisation and expression analysis of peanut sugar invertase genes reveal their vital roles in response to abiotic stress

KEY MESSAGE

Sucrose invertase activity is positively related to osmotic and salt stress resistance in peanut. Sucrose invertases (INVs) have important functions in plant growth and response to environmental stresses. However, their biological roles in peanut are still not fully revealed. In this research, we identified 42 AhINV genes in the peanut genome. They were highly conserved and clustered into three groups with 24 segmental duplication events occurred under purifying selection. Transcriptional expression analysis exhibited that they were all ubiquitously expressed, and most of them were up-regulated by osmotic and salt stresses, with AhINV09, AhINV23 and AhINV19 showed the most significant up-regulation. Further physiochemical analysis showed that the resistance of peanut to osmotic and salt stress was positively related to the high sugar content and sucrose invertase activity. Our results provided fundamental information on the structure and evolutionary relationship of INV gene family in peanut and gave theoretical guideline for further functional study of AhINV genes in response to abiotic stress.

Structure and Expression Analysis of PtrSUS, PtrINV, PtrHXK, PtrPGM, and PtrUGP Gene Families in Populus trichocarpa Torr. and Gray

Exogenous nitrogen and carbon can affect plant cell walls, which are composed of structural carbon. Sucrose synthase (SUS), invertase (INV), hexokinase (HXK), phosphoglucomutase (PGM), and UDP-glucose pyrophosphorylase (UGP) are the key enzymes of sucrose metabolism involved in cell wall synthesis. To understand whether these genes are regulated by carbon and nitrogen to participate in structural carbon biosynthesis, we performed genome-wide identification, analyzed their expression patterns under different carbon and nitrogen treatments, and conducted preliminary functional verification. Different concentrations of nitrogen and carbon were applied to poplar (Populus trichocarpa Torr. and Gray), which caused changes in cellulose, lignin, and hemicellulose contents. In poplar, 6 SUSs, 20 INVs, 6 HXKs, 4 PGMs, and 2 UGPs were identified. Moreover, the physicochemical properties, collinearity, and tissue specificity were analyzed. The correlation analysis showed that the expression levels of PtrSUS3/5, PtrNINV1/2/3/5/12, PtrCWINV3, PtrVINV2, PtrHXK5/6, PtrPGM1/2, and PtrUGP1 were positively correlated with the cellulose content. Meanwhile, the knockout of PtrNINV12 significantly reduced the cellulose content. This study could lay the foundation for revealing the functions of SUSs, INVs, HXKs, PGMs, and UGPs, which affected structural carbon synthesis regulated by nitrogen and carbon, proving that PtrNINV12 is involved in cell wall synthesis.

Characteristics and Expression Analysis of Invertase Gene Family in Common Wheat (Triticum aestivum L.)

Invertase (INV) irreversibly catalyzes the conversion of sucrose into glucose and fructose, playing important role in plant development and stress tolerance. However, the functions of INV genes in wheat have been less studied. In this study, a total of 126 TaINV genes were identified using a genome-wide search method, which could be classified into five classes (TaCWI-α, TaCWI-β, TaCI-α, TaCI-β, and TaVI) based on phylogenetic relationship. A total of 101 TaINVs were collinear with their ancestors in the synteny analysis, and we speculated that polyploidy events were the main force in the expansion of the TaINV gene family. Compared with TaCI, TaCWI and TaVI are more similar in gene structure and protein properties. Transcriptome sequencing analysis showed that TaINVs expressed in multiple tissues with different expression levels. Among 19 tissue-specific expressed TaINVs, 12 TaINVs showed grain-specific expression pattern and might play an important role in wheat grain development. In addition, qRT-PCR results further confirmed that TaCWI50 and TaVI27 show different expression in grain weight NILs. Our results demonstrated that the high expression of TaCWI50 and TaVI27 may be associated with a larger TGW phenotype. This work provides the foundations for understanding the grain development mechanism.

Genome-wide identification of invertases in Fabaceae, focusing on transcriptional regulation of Pisum sativum invertases in seed subjected to drought

Invertases are key enzymes for carbon metabolism, cleaving sucrose into energy-rich and signaling metabolites, glucose and fructose. Invertases play pivotal roles in development and stress response, determining yield and quality of seed production. In this context, the repertoire of invertase gene families is critically scarce in legumes. Here, we performed a systematic search for invertase families in 16 Fabaceae genomes. For instance, we identified 19 invertase genes in the model plant Medicago and 17 accessions in the agronomic crop Pisum sativum. Our comprehensive phylogenetic analysis sets a milestone for the scientific community as we propose a new nomenclature to correctly name plant invertases. Thus, neutral invertases were classified into four clades of cytosolic invertase (CINV). Acid invertases were classified into two cell wall invertase clades (CWINV) and two vacuolar invertase clades (VINV). Then, we explored transcriptional regulation of the pea invertase family, focusing on seed development and water stress. Invertase expression decreased sharply from embryogenesis to seed-filling stages, consistent with higher sucrose and lower monosaccharide contents. The vacuolar invertase PsVINV1.1 clearly marked the transition between both developmental stages. We hypothesize that the predominantly expressed cell wall invertase, PsCWINV1.2, may drive sucrose unloading towards developing seeds. The same candidates, PsVINV1.1 and PsCWINV1.2, were also regulated by water deficit during embryonic stage. We suggest that PsVINV1.1 along with vacuolar sugar transporters maintain cellular osmotic pressure and PsCWINV1.2 control hexose provision, thereby ensuring embryo survival in drought conditions. Altogether, our findings provide novel insights into the regulation of plant carbon metabolism in a challenging environment.

Functional Characterization of a Cucumber (Cucumis sativus L.) Vacuolar Invertase, CsVI1, Involved in Hexose Accumulation and Response to Low Temperature Stress

Cucumber (Cucumis sativus L.), an important vegetable plant species, is susceptible to low temperature stress especially during the seedling stage. Vacuolar invertase (VI) plays important roles in plant responses to abiotic stress. However, the molecular and biochemical mechanisms of VI function in cucumber, have not yet been completely understood and VI responses to low temperature stress and it functions in cold tolerance in cucumber seedlings are also in need of exploration. The present study found that hexose accumulation in the roots of cucumber seedlings under low temperature stress is closely related to the observed enhancement of invertase activity. Our genome-wide search for the vacuolar invertase (VI) genes in cucumber identified the candidate VI-encoding gene CsVI1. Expression profiling of CsVI1 showed that it was mainly expressed in the young roots of cucumber seedlings. In addition, transcriptional analysis indicated that CsVI1 expression could respond to low temperature stress. Recombinant CsVI1 proteins purified from Pichia pastoris and Nicotiana benthamiana leaves could hydrolyze sucrose into hexoses. Further, overexpression of CsVI1 in cucumber plants could increase their hexose contents and improve their low temperature tolerance. Lastly, a putative cucumber invertase inhibitor was found could form a complex with CsVI1. In summary, these results confirmed that CsVI1 functions as an acid invertase involved in hexose accumulation and responds to low temperature stress in cucumber seedlings.

Importance of inositols and their derivatives in cowpea under root dehydration: An omics perspective

This work presents a robust analysis of the inositols (INSs) and raffinose family oligosaccharides (RFOs) pathways, using genomic and transcriptomic tools in cowpea under root dehydration. Nineteen (~70%) of the 26 scrutinized enzymes presented transcriptional up-regulation in at least one treatment time. The transcriptional orchestration allowed categorization of the analyzed enzymes as time-independent (those showing the same regulation throughout the assay) and time-dependent (those showing different transcriptional regulation over time). It is suggested that up-regulated time-independent enzymes (INSs: myo-inositol oxygenase, inositol-tetrakisphosphate 1-kinase 3, phosphatidylinositol 4-phosphate 5-kinase 4-like, 1-phosphatidylinositol-3-phosphate 5-kinase, phosphoinositide phospholipase C, and non-specific phospholipase C; RFOs: α-galactosidase, invertase, and raffinose synthase) actively participate in the reorganization of cowpea molecular physiology under the applied stress. In turn, time-dependent enzymes, especially those up-regulated in some of the treatment times (INSs: inositol-pentakisphosphate 2-kinase, phosphatidylinositol 4-kinase, phosphatidylinositol synthase, multiple inositol polyphosphate phosphatase 1, methylmalonate-semialdehyde dehydrogenase, triosephosphate isomerase, myo-inositol-3-phosphate synthase, phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and protein-tyrosine-phosphatase, and phosphatidylinositol 3-kinase; RFOs: galactinol synthase) seem to participate in fine-tuning of the molecular physiology, helping the cowpea plants to acclimatize under dehydration stress. Not all loci encoding the studied enzymes were expressed during the assay; most of the expressed ones exhibited a variable transcriptional profile in the different treatment times. Genes of the INSs and RFOs pathways showed high orthology with analyzed Phaseoleae members, suggesting a relevant role within this legume group. Regarding the promoter regions of INSs and RFOs genes, some bona fide cis-regulatory elements were identified in association with seven transcription factor families (AP2-EFR, Dof-type, MADS-box, bZIP, CPP, ZF-HD, and GATA-type). Members of INSs and RFOs pathways potentially participate in other processes regulated by these proteins in cowpea.

Structure and Expression Analysis of Sucrose Phosphate Synthase, Sucrose Synthase and Invertase Gene Families in Solanum lycopersicum

Sucrose phosphate synthase (SPS), sucrose synthase (SUS) and invertase (INV) are all encoded by multigene families. In tomato (Solanum lycopersicum), a comprehensive analysis of structure characteristics of these family genes is still lacking, and the functions of individual isoforms of these families are mostly unclear under stress. Here, the structure characteristics of the three families in tomato were analyzed; moreover, as a first step toward understanding the functions of isoforms of these proteins under stress, the tissue expression pattern and stress response of these genes were also investigated. The results showed that four SPS genes, six SUS genes and nineteen INV genes were identified in tomato. The subfamily differentiation of SlSPS and SlSUS might have completed before the split of monocotyledons and dicotyledons. The conserved motifs were mostly consistent within each protein family/subfamily. These genes demonstrated differential expressions among family members and tissues, and in response to polyethylene glycerol, NaCl, H₂O₂, abscisic acid or salicylic acid treatment. Our results suggest that each isoform of these families may have different functions in different tissues and under environmental stimuli. SlSPS1, SlSPS3, SlSUS1, SlSUS3, SlSUS4, SlINVAN5 and SlINVAN7 demonstrated consistent expression responses and may be the major genes responding to exogenous stimuli.

Systematic Analysis of Alkaline/Neutral Invertase Genes Reveals the Involvement of Smi-miR399 in Regulation of SmNINV3 and SmNINV4 in Salvia miltiorrhiza

Alkaline/neutral invertases (NINVs), which irreversibly catalyze the hydrolysis of sucrose into fructose and glucose, play crucial roles in carbohydrate metabolism and plant development. Comprehensive insights into NINV genes are lacking in Salvia miltiorrhiza, a well-known traditional Chinese medicinal (TCM) plant with significant medicinal and economic value. Through genome-wide prediction, nine putative SmNINV genes, termed SmNINV1-SmNINV9, were identified. Integrated analysis of gene structures, sequence features, conserved domains, conserved motifs and phylogenetic trees revealed the conservation and divergence of SmNINVs. The identified SmNINVs were differentially expressed in roots, stems, leaves, flowers, and different root tissues. They also responded to drought, salicylic acid, yeast extract, and methyl jasmonate treatments. More importantly, computational prediction and experimental validation showed that SmNINV3 and SmNINV4 were targets of Smi-miR399, a conserved miRNA previously shown to affect Pi uptake and translocation through the cleavage of PHOSPHATE2 (PHO2). Consistently, analysis of 43 NINV genes and 26 miR399 sequences from Arabidopsis thaliana, Populus trichocarpa, Manihot esculenta, and Solanum lycopersicum showed that various AtNINV, PtNINV, MeNINV, and SlNINV genes were regulated by miR399. It indicates that the miR399-NINV module exists widely in plants. Furthermore, Smi-miR399 also cleaved SmPHO2 transcripts in S. miltiorrhiza, suggesting the complexity of NINVs, PHO2, and miR399 networks.

Noninvasive Phenotyping of Plant-Pathogen Interaction: Consecutive In Situ Imaging of Fluorescing Pseudomonas syringae, Plant Phenolic Fluorescence, and Chlorophyll Fluorescence in Arabidopsis Leaves

Plant-pathogen interactions have been widely studied, but mostly from the site of the plant secondary defense. Less is known about the effects of pathogen infection on plant primary metabolism. The possibility to transform a fluorescing protein into prokaryotes is a promising phenotyping tool to follow a bacterial infection in plants in a noninvasive manner. In the present study, virulent and avirulent Pseudomonas syringae strains were transformed with green fluorescent protein (GFP) to follow the spread of bacteria in vivo by imaging Pulse-Amplitude-Modulation (PAM) fluorescence and conventional binocular microscopy. The combination of various wavelengths and filters allowed simultaneous detection of GFP-transformed bacteria, PAM chlorophyll fluorescence, and phenolic fluorescence from pathogen-infected plant leaves. The results show that fluorescence imaging allows spatiotemporal monitoring of pathogen spread as well as phenolic and chlorophyll fluorescence in situ, thus providing a novel means to study complex plant-pathogen interactions and relate the responses of primary and secondary metabolism to pathogen spread and multiplication. The study establishes a deeper understanding of imaging data and their implementation into disease screening.

Functional Characterization of a Drought-Responsive Invertase Inhibitor from Maize (Zea mays L.)

Invertases (INVs) play essential roles in plant growth in response to environmental cues. Previous work showed that plant invertases can be post-translationally regulated by small protein inhibitors (INVINHs). Here, this study characterizes a proteinaceous inhibitor of INVs in maize (Zm-INVINH4). A functional analysis of the recombinant Zm-INVINH4 protein revealed that it inhibited both cell wall and vacuolar invertase activities from maize leaves. A Zm-INVINH4::green fluorescent protein fusion experiment indicated that this protein localized in the apoplast. Transcript analysis showed that Zm-INVINH4 is specifically expressed in maize sink tissues, such as the base part of the leaves and young kernels. Moreover, drought stress perturbation significantly induced Zm-INVINH4 expression, which was accompanied with a decrease of cell wall invertase (CWI) activities and an increase of sucrose accumulation in both base parts of the leaves 2 to 7 days after pollinated kernels. In summary, the results support the hypothesis that INV-related sink growth in response to drought treatment is (partially) caused by a silencing of INV activity via drought-induced induction of Zm-INVINH4 protein.

Genome-Wide Characterization of AspATs in Populus: Gene Expression Variation and Enzyme Activities in Response to Nitrogen Perturbations

Aspartate aminotransferase (AspAT) catalyzes a reversible transamination reaction between glutamate and oxaloacetate to yield aspartate and 2-oxoglutarate, exerting a primary role in amino acid biosynthesis and homeostasis of nitrogen (N) and carbon metabolism within all cellular organisms. While progress in biochemical characterization of AspAT has been made for decades, the molecular and physiological characteristics of different members of the AspAT gene family remain poorly known particularly in forest trees. Here, extensive genome-wide survey of AspAT encoding genes was implemented in black cottonwood (Populus trichocarpa Torr. & A. Gray), a model species of woody plants. Thorough inspection of the phylogenies, gene structures, chromosomal distribution, cis-elements, conserved motifs, and subcellular targeting resulted in the identification of 10 AspAT isogenes (PtAspAT1-10) in the Populus genome. RNA-seq along with quantitative real-time polymerase chain reaction (qRT-PCR) validation revealed that PtAspATs displayed diverse patterns of tissue-specific expression. Spatiotemporal expressions of homologous AspATs in the poplar hybrid clone ‘Nanlin895’ were further evaluated, showing that gene expressions varied depending on source-sink dynamics. The impact on AspAT transcripts upon N starvation and seasonal senescence showed the upregulation of five AspAT in leaves concurrent with drastic downregulation of six or more AspATs in roots. Additionally, marked reductions of many more AspATs transcripts were observed in roots upon N excess. Accordingly, AspAT activities were significantly suppressed upon N starvation by an in-gel assay, prompting the argument that enzyme activity was a more direct indicator of the growth morphology under a N stress regime. Taken together, the expression profiling and enzyme activities upon stress cues provide a theoretical basis for unraveling the physiological significance of specific gene(s) in regulation of N acquisition and remobilization in woody plants.

Functional Characterization of Invertase Inhibitors PtC/VIF1 and 2 Revealed Their Involvements in the Defense Response to Fungal Pathogen in Populus trichocarpa

In higher plants, cell wall invertase (CWI) and vacuolar invertase (VI) were considered to be essential coordinators in carbohydrate partitioning, sink strength determination, and stress responses. An increasing body of evidence revealed that the tight regulation of CWI and VI substantially depends on the post-translational mechanisms, which were mediated by small proteinaceous inhibitors (C/VIFs, Inhibitor of β-Fructosidases). As yet, the extensive survey of the molecular basis and biochemical property of C/VIFs remains largely unknown in black cottonwood (Populus trichocarpa Torr. & A. Gray), a model species of woody plants. In the present work, we have initiated a systematic review of the genomic structures, phylogenies, cis-regulatory elements, and conserved motifs as well as the tissue-specific expression, resulting in the identification of 39 genes encoding C/VIF in poplar genome. We characterized two putative invertase inhibitors PtC/VIF1 and 2, showing predominant transcript levels in the roots and highly divergent responses to the selected stress cues including fusarium wilt, drought, ABA, wound, and senescence. In silico prediction of the signal peptide hinted us that they both likely had the apoplastic targets. Based on the experimental visualization via the transient and stable transformation assays, we confirmed that PtC/VIF1 and 2 indeed secreted to the extracellular compartments. Further validation of their recombinant enzymes revealed that they displayed the potent inhibitory affinities on the extracted CWI, supporting the patterns that act as the typical apoplastic invertase inhibitors. To our knowledge, it is the first report on molecular characterization of the functional C/VIF proteins in poplar. Our results indicate that PtC/VIF1 and 2 may exert essential roles in defense- and stress-related responses. Moreover, novel findings of the up- and downregulated C/VIF genes and functional enzyme activities enable us to further unravel the molecular mechanisms in the promotion of woody plant performance and adapted-biotic stress, underlying the homeostatic control of sugar in the apoplast.