Transcriptional regulation of the cinnamyl alcohol dehydrogenase gene from sweet potato in response to plant developmental stage and environmental stress

Characterization of the Moroccan Barley Germplasm Preserved in the Polish Genebank as a First Step towards Selecting Forms with Increased Drought Tolerance

In marginal, arid, and semi-arid areas of Morocco, crops are often exposed to multiple abiotic and biotic stresses that have a major impact on yield. Farmer-maintained Moroccan landraces have been shaped by the impact of very strong selection pressures, gradually adapting to the local ecosystem and obsolete low-input agricultural practices without improvement towards high yield and quality. Considering the increasing threat of drought in Poland, it is necessary to introduce germplasm with tolerance to water deficit into barley breeding programs. The aim of this research was a DArTseq-based genetic characterization of a collection of germplasm of Moroccan origin, conserved in the Polish genebank. The results showed that all conserved landraces have a high level of heterogeneity and their gene pool is different from the material developed by Polish breeders. Based on the analysis of eco-geographical data, locations with extremely different intensities of drought stress were selected. A total of 129 SNPs unique to accessions from these locations were identified. In the neighborhood of the clusters of unique SNPs on chromosomes 5H and 6H, genes that may be associated with plant response to drought stress were identified. The results obtained may provide a roadmap for further research to support Polish barley breeding for increased drought tolerance.

Comparative transcriptomic and proteomic analysis reveals common molecular factors responsive to heat and drought stresses in sweetpotaoto (Ipomoea batatas)

Introduction

Crops are affected by various abiotic stresses, among which heat (HT) and drought (DR) stresses are the most common in summer. Many studies have been conducted on HT and DR, but relatively little is known about how drought and heat combination (DH) affects plants at molecular level.

Methods

Here, we investigated the responses of sweetpotato to HT, DR, and DH stresses by RNA-seq and data-independent acquisition (DIA) technologies, using controlled experiments and the quantification of both gene and protein levels in paired samples.

Results

Twelve cDNA libraries were created under HT, DR, and DH conditions and controls. We identified 536, 389, and 907 DEGs in response to HT, DR, and DH stresses, respectively. Of these, 147 genes were common and 447 were specifically associated with DH stress. Proteomic analysis identified 1609, 1168, and 1535 DEPs under HT, DR, and DH treatments, respectively, compared with the control, of which 656 were common and 358 were exclusive to DH stress. Further analysis revealed the DEGs/DEPs were associated with heat shock proteins, carbon metabolism, phenylalanine metabolism, starch and cellulose metabolism, and plant defense, amongst others. Correlation analysis identified 6465, 6607, and 6435 co-expressed genes and proteins under HT, DR, and DH stresses respectively. In addition, a combined analysis of the transcriptomic and proteomic data identified 59, 35, and 86 significantly co-expressed DEGs and DEPs under HT, DR, and DH stresses, respectively. Especially, top 5 up-regulated co-expressed DEGs and DEPs (At5g58770, C24B11.05, Os04g0679100, BACOVA_02659 and HSP70-5) and down-regulated co-expressed DEGs and DEPs (AN3, PMT2, TUBB5, FL and CYP98A3) were identified under DH stress.

Discussion

This is the first study of differential genes and proteins in sweetpotato under DH stress, and it is hoped that the findings will assist in clarifying the molecular mechanisms involved in sweetpotato resistance to heat and drought stress.

Identification and Functional Analysis of CAD Gene Family in Pomegranate (Punica granatum)

[Objective] Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis. The aim of this study was to identify CAD gene family members in pomegranate and its expression correlation with seed hardness. [Methods] Based on the reported CAD sequence of Arabidopsis, the CAD gene family of pomegranate was identified by homologous comparison, and then phylogenetic, molecular characterization, and expression profile analysis were performed. [Results] Pomegranate CAD gene family has 25 members, distributed on seven chromosomes of pomegranate. All pomegranate CAD proteins have similar physical and chemical properties. We divide the family into four groups based on evolutionary relationships. The member of group I, called bona fide CAD, was involved in lignin synthesis. Most of the members of group II were involved in stress resistance. The functions of groups III and IV need to be explored. We found four duplicated modes (whole genome duplication or segmental (WGD), tandem duplication (TD), dispersed duplication (DSD), proximal duplication (PD) in this family; TD (36%) had the largest number of them. We predicted that 20 cis-acting elements were involved in lignin synthesis, stress resistance, and response to various hormones. Gene expression profiles further demonstrated that the PgCAD gene family had multiple functions. [Conclusions] Pomegranate CAD gene family is involved in lignin synthesis of hard-seeded cultivar Hongyushizi and Baiyushizi, but its role in seed hardness of soft-seeded cultivar Tunisia needs to be further studied.

Global proteome analyses of phosphorylation and succinylation of barley root proteins in response to phosphate starvation and recovery

Phosphate (Pi) stress is an important environmental factor that limits plant growth and development. Of various posttranslational modifications (PTMs), protein phosphorylation and succinylation are the two most important PTMs that regulate multiple biological processes in response to Pi stress. However, these PTMs have been investigated individually but their interactions with proteins in response to Pi stress remain poorly understood. In this study, to elucidate the underlying mechanisms of protein phosphorylation and succinylation in response to Pi stress, we performed a global analysis of the barley root phosphorylome and succinylome in Pi starvation and recovery stages, respectively. A total of 3,634 and 884 unique phosphorylated and succinylated proteins, respectively, corresponding to 11,538 and 2,840 phospho- and succinyl-sites, were identified; of these, 275 proteins were found to be simultaneously phosphorylated and succinylated. Gene Set Enrichment Analysis was performed with a Kyoto Encyclopedia of Genes and Genomes pathway database revealing pathways that significantly enriched in the phosphorylome and succinylome. Such pathways, were dynamically regulated by Pi starvation and recovery treatments, and could be partitioned into distinct metabolic processes. In particular, phosphorylated proteins related to purine, the mitogen-activated protein kinase (MAPK) signaling pathway, pyrimidine, and ATP-binding cassette (ABC) transporters were upregulated in both Pi deprivation and recovery stages. Succinylated proteins, significantly upregulated by both Pi starvation and recovery, were enriched in nitrogen metabolism and phenylpropanoid biosynthesis. Meanwhile, succinylated proteins that were significantly downregulated by both Pi starvation and recovery were enriched in lysine degradation and tryptophan metabolism. This highlighted the importance of these metabolic pathways in regulating Pi homeostasis. Furthermore, protein-protein interaction network analyses showed that the response of central metabolic pathways to Pi starvation and recovery was significantly modulated by phosphorylation or succinylation, both individually and together. In addition, we discovered relevant proteins involved in MAPK signaling and phenylpropanoid biosynthetic pathways existing in interactions between phosphorylated and succinylated proteins in response to Pi recovery. The current study not only provides a comprehensive analysis of phosphorylated and succinylated proteins in plant responses to Pi starvation and recovery, but also reveals detailed interactions between phosphorylated and succinylated proteins in barley roots.

Endophytic bacterium Bacillus aryabhattai induces novel transcriptomic changes to stimulate plant growth

In nature, plants interact with a wide range of microorganisms, and most of these microorganisms could induce growth through the activation of important molecular pathways. The current study evaluated whether the endophytic bacterium Bacillus aryabhattai encourages plant growth and the transcriptional changes that might be implicated in this effect. The endophytic bacterium promotes the growth of Arabidopsis and tobacco plants. The transcriptional changes in Arabidopsis plants treated with the bacterium were also identified, and the results showed that various genes, such as cinnamyl alcohol dehydrogenase, apyrase, thioredoxin H8, benzaldehyde dehydrogenase, indoleacetaldoxime dehydratase, berberine bridge enzyme-like and gibberellin-regulated protein, were highly expressed. Also, endophytic bacterial genes, such as arginine decarboxylase, D-hydantoinase, ATP synthase gamma chain and 2-hydroxyhexa-2,4-dienoate hydratase, were activated during the interaction. These findings demonstrate that the expression of novel plant growth-related genes is induced by interaction with the endophytic bacterium B. aryabhattai and that these changes may promote plant growth in sustainable agriculture.

Meta-analysis of transcriptomic responses to cold stress in plants

Transcriptomic analyses are needful tools to gain insight into the molecular mechanisms underlying plant responses to abiotic stresses. The aim of this study was to identify key genes differentially regulated in response to chilling stress in various plant species with different levels of tolerance to low temperatures. A meta-analysis was performed using the RNA-Seq data of published studies whose experimental conditions were comparable. The results confirmed the importance of ethylene in the hormonal cross-talk modulating the defensive responses against chilling stress, especially in sensitive species. The transcriptomic activity of five Ethylene Response Factors genes and a REDOX Responsive Transcription Factor 1 involved in hormone-related pathways belonging to ethylene metabolism and signal transduction were induced. Transcription activity of two genes encoding for heat shock factors was enhanced, together with various genes associated with developmental processes. Several transcription factor families showed to be commonly induced between different plant species. Protein-protein interaction networks highlighted the role of the photosystems I and II, as well as genes encoding for HSF and WRKY transcription factors. A model of gene regulatory network underlying plant responses to chilling stress was developed, allowing the delivery of new candidate genes for genetic improvement of crops towards low temperatures tolerance.

Genome-wide analysis of the CAD gene family reveals two bona fide CAD genes in oil palm

Cinnamyl alcohol dehydrogenase (CAD) is the key enzyme for lignin biosynthesis in plants. In this study, genome-wide analysis was performed to identify CAD genes in oil palm (Elaeis guineensis). Phylogenetic analysis was then conducted to select the bona fide EgCADs. The bona fide EgCAD genes and their respective 5' flanking regions were cloned and analysed. Their expression profiles were evaluated in various organs using RT-PCR. Seven EgCAD genes (EgCAD1-7) were identified and divided into four phylogenetic groups. EgCAD1 and EgCAD2 display high sequence similarities with other bona fide CADs and possess all the signature motifs of the bona fide CAD. They also display similar 3D protein structures. Gene expression analysis showed that EgCAD1 was expressed most abundantly in the root tissues, while EgCAD2 was expressed constitutively in all the tissues studied. EgCAD1 possesses only one transcription start site, while EgCAD2 has five. Interestingly, a TC microsatellite was found in the 5' flanking region of EgCAD2. The 5' flanking regions of EgCAD1 and EgCAD2 contain lignin-associated regulatory elements i.e. AC-elements, and other defence-related motifs, including W-box, GT-1 motif and CGTCA-motif. Altogether, these results imply that EgCAD1 and EgCAD2 are bona fide CAD involved in lignin biosynthesis during the normal development of oil palm and in response to stresses. Our findings shed some light on the roles of the bona fide CAD genes in oil palm and pave the way for manipulating lignin content in oil palm through a genetic approach.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03208-0.

Proteomic analysis reveals the molecular mechanism underlying the cold acclimation and freezing tolerance of wheat (Triticum aestivum L.)

Cold acclimation (CA) is an important evolutionary adaptive mechanism for wheat freezing resistence. To clarify the molecular basis of wheat CA and freezing tolerance, the effects of CA (4 °C) and non-CA (20 °C) treatments and freezing stress (-5 °C) on the proteins in the wheat crown were characterized via an iTRAQ-based proteomic analysis. A total of 669 differentially accumulated proteins (DAPs) were identified after the CA, of which seven were also DAPs in the CA plants exposed to freezing stress. Additionally, the 15 DAPs in the CA group and the 23 DAPs in the non-CA group after the freezing treatment differed substantially. Functional analyses indicated that CA enhanced freezing tolerance by regulating proteins involved in signal transduction, carbohydrate metabolism, stress and defense responses, and phenylpropanoid biosynthesis. An integrated transcriptomic, proteomic, and metabolomic analysis revealed significant changes in various components of the glutathione metabolic pathway. The overexpression and silencing of Wdhn13 in Arabidopsis and wheat resulted in increased tolerance and sensitivity to freezing stress, respectively, suggesting Wdhn13 promotes freezing tolerance. Overall, our study offers insights into the regulatory network underlying the CA and freezing tolerance of wheat, which may be useful for elucidating wheat freezing resistance.

Transcriptome expression profiles reveal response mechanisms to drought and drought-stress mitigation mechanisms by exogenous glycine betaine in maize

Drought stress is one of the major abiotic stresses that limit growth, development and yield of maize crops. To better understand the responses of maize inbred lines with different levels of drought resistance and the molecular mechanism of exogenous glycine betaine (GB) in alleviating drought stress, the responses of two maize inbred lines to drought stress and to the stress-mitigating effects of exogenous GB were investigated. Seedling morphology, physiological and biochemical indexes, root cell morphology and root transcriptome expression profiles were compared between a drought-tolerant inbred line Chang 7-2 and drought-sensitive inbred line TS141. Plants of both lines were subjected to treatments of drought stress alone and drought stress with application of exogenous GB. The results showed that with the increase of drought treatment time, the growth and development of TS141 were inhibited, while those of Chang 7-2 were not significantly different from those of the control (no drought stress and GB). Compared with the corresponding data of the drought-stress group, every index measured from the two inbred lines indicated mitigating effects from exogenous GB, and TS141 produced stronger mitigating responses due to the GB. Transcriptome analysis showed that 562 differentially expressed genes (DEGs) were up-regulated and 824 DEGs were down-regulated in both inbred lines under drought stress. Due to the exogenous GB, 1061 DEGs were up-regulated and 424 DEGs were down-regulated in both lines. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify 10 DEGs screened from the different treatments. These results showed that the expression of 9 DEGs were basically consistent with their respective transcriptome expression profiles. The results of this study provide models of potential mechanisms of drought tolerance in maize as well as potential mechanisms of how exogenous GB may regulate drought tolerance.

Integrative transcriptomic and metabolomic data provide insights into gene networks associated with lignification in postharvest Lei bamboo shoots under low temperature

Lei bamboo (Phyllostachys violascens) shoots are delicious food in Asia. Here, the molecular basis of lignification in postharvest Lei bamboo shoots under low temperature (LT) is revealed by transcriptomic and metabolomics analyses for the first time. We identified substantial accumulations of jasmonates (JAs) and major lignin biosynthesis precursors (coumarin, trans-4-coumaric acid, trans-ferulic acid and L-phenylalanine). Transcriptome analysis indicated that some regulatory genes were significantly differentially expressed, and the expression patterns of them were highly consistent with the changes in the key lignin precursors or JA profiles. Co-expression analysis showed that the LT responsive genes PvCRPK-4/-5, PvICE2-1/2, PvDREB2B might form a network module with the lignin (PvC3H-2/3, PvC4H-2/4, PvCAD-1/2/3/4, etc.) or JA biosynthesis genes (PvOPR2, PvJAZ-4 and PvPEX5, etc.), indicating a LT-lignification or LT-JA-lignification regulatory pathway in Lei bamboo shoots. Above all, our findings provide new an insight into the LT-associated lignification in postharvest bamboo shoots.

Homo- and Hetero-Dimers of CAD Enzymes Regulate Lignification and Abiotic Stress Response in Moso Bamboo

Lignin biosynthesis enzymes form complexes for metabolic channelling during lignification and these enzymes also play an essential role in biotic and abiotic stress response. Cinnamyl alcohol dehydrogenase (CAD) is a vital enzyme that catalyses the reduction of aldehydes to alcohols, which is the final step in the lignin biosynthesis pathway. In the present study, we identified 49 CAD enzymes in five Bambusoideae species and analysed their phylogenetic relationships and conserved domains. Expression analysis of Moso bamboo PheCAD genes in several developmental tissues and stages revealed that among the PheCAD genes, PheCAD2 has the highest expression level and is expressed in many tissues and PheCAD1, PheCAD6, PheCAD8 and PheCAD12 were also expressed in most of the tissues studied. Co-expression analysis identified that the PheCAD2 positively correlates with most lignin biosynthesis enzymes, indicating that PheCAD2 might be the key enzyme involved in lignin biosynthesis. Further, more than 35% of the co-expressed genes with PheCADs were involved in biotic or abiotic stress responses. Abiotic stress transcriptomic data (SA, ABA, drought, and salt) analysis identified that PheCAD2, PheCAD3 and PheCAD5 genes were highly upregulated, confirming their involvement in abiotic stress response. Through yeast two-hybrid analysis, we found that PheCAD1, PheCAD2 and PheCAD8 form homo-dimers. Interestingly, BiFC and pull-down experiments identified that these enzymes form both homo- and hetero- dimers. These data suggest that PheCAD genes are involved in abiotic stress response and PheCAD2 might be a key lignin biosynthesis pathway enzyme. Moreover, this is the first report to show that three PheCAD enzymes form complexes and that the formation of PheCAD homo- and hetero- dimers might be tissue specific.

Tuberous roots of transgenic sweetpotato overexpressing IbCAD1 have enhanced low-temperature storage phenotypes

Lignin is associated with cell wall rigidity, water and solute transport, and resistance to diverse stresses in plants. Lignin consists of polymerized monolignols (p-coumaryl, coniferyl, and sinapyl alcohols), which are synthesized by cinnamyl alcohol dehydrogenase (CAD) in the phenylpropanoid pathway. We previously investigated cold-induced IbCAD1 expression by transcriptome profiling of cold-stored tuberous roots of sweetpotato (Ipomoea batatas [L.] Lam). In this study, we confirmed that IbCAD1 expression levels depended on the sweetpotato root type and were strongly induced by several abiotic stresses. We generated transgenic sweetpotato plants overexpressing IbCAD1 (TC plants) to investigate CAD1 physiological functions in sweetpotato. TC plants displayed lower root weights and lower ratios of tuberous roots to pencil roots than non-transgenic (NT) plants. The lignin contents in tuberous roots of NT and TC plants differed slightly, but these differences were not significant. By contrast, monolignol levels and syringyl (S)/guaiacyl (G) ratios were higher in TC plants than NT plants, primarily owing to syringyl unit accumulation. Tuberous roots of TC plants displayed enhanced low-temperature (4 °C) storage with lower malondialdehyde and H₂O₂ contents than NT plants. We propose that high monolignol levels in TC tuberous roots served as substrates for increased peroxidase activity, thereby enhancing antioxidation capacity against cold stress-induced reactive oxygen species. Increased monolignol contents and/or increased S/G ratios might contribute to pathogen-induced stress tolerance as a secondary chilling-damage response in sweetpotato. These results provide novel information about CAD1 function in cold stress tolerance and root formation mechanisms in sweetpotato.

Drought-induced ABA, H2O2 and JA positively regulate CmCAD genes and lignin synthesis in melon stems

BACKGROUND

Cinnamyl alcohol dehydrogenase (CAD) is an important enzyme functions at the last step in lignin monomer synthesis pathway. Our previous work found that drought induced the expressions of CmCAD genes and promoted lignin biosynthesis in melon stems.

RESULTS

Here we studied the effects of abscisic acid (ABA), hydrogen peroxide (H2O2) and jasmonic acid (JA) to CmCADs under drought stress. Results discovered that drought-induced ABA, H2O2 and MeJA were prevented efficiently from increasing in melon stems pretreated with fluridone (Flu, ABA inhibitor), imidazole (Imi, H2O2 scavenger) and ibuprofen (Ibu, JA inhibitor). ABA and H2O2 are involved in the positive regulations to CmCAD1, 2, 3, and 5, and JA is involved in the positive regulations to CmCAD2, 3, and 5. According to the expression profiles of lignin biosynthesis genes, ABA, H2O2 and MeJA all showed positive regulations to CmPAL2-like, CmPOD1-like, CmPOD2-like and CmLAC4-like. In addition, positive regulations were also observed with ABA to CmPAL1-like, CmC4H and CmCOMT, with H2O2 to CmPAL1-like, CmC4H, CmCCR and CmLAC17-like, and with JA to CmCCR, CmCOMT, CmLAC11-like and CmLAC17-like. As expected, the signal molecules positively regulated CAD activity and lignin biosynthesis under drought stress. Promoter::GUS assays not only further confirmed the regulations of the signal molecules to CmCAD1~3, but also revealed the important role of CmCAD3 in lignin synthesis due to the strongest staining of CmCAD3 promoter::GUS.

CONCLUSIONS

CmCADs but CmCAD4 are positively regulated by ABA, H2O2 and JA under drought stress and participate in lignin synthesis.

Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes

The final stage of leaf ontogenesis is represented by senescence, a highly regulated process driven by a sequential cellular breakdown involving, as the first step, chloroplast dismantling with consequent reduction of photosynthetic efficiency. Different processes, such as pigment accumulation, could protect the vulnerable photosynthetic apparatus of senescent leaves. Although several studies have produced transcriptomic data on foliar senescence, just few works have attempted to explain differences in red and green leaves throughout ontogenesis. In this work, a transcriptomic approach was used on green and red leaves of Prunus cerasifera to unveil molecular differences from leaf maturity to senescence. Our analysis revealed a higher gene regulation in red leaves compared to green ones, during leaf transition. Most of the observed DEGs were shared and involved in transcription factor activities, senescing processes and cell wall remodelling. Significant differences were detected in cellular functions: genes related to photosystem I and II were highly down-regulated in the green genotype, whereas transcripts involved in flavonoid biosynthesis, such as UDP glucose-flavonoid-3-O-glucosyltransferase (UFGT) were exclusively up-regulated in red leaves. In addition, cellular functions involved in stress response (glutathione-S-transferase, Pathogen-Related) and sugar metabolism, such as three threalose-6-phosphate synthases, were activated in senescent red leaves. In conclusion, data suggests that P. cerasifera red genotypes can regulate a set of genes and molecular mechanisms that cope with senescence, promoting more advantages during leaf ontogenesis than compared to the green ones.

Changes in Proteome and Protein Phosphorylation Reveal the Protective Roles of Exogenous Nitrogen in Alleviating Cadmium Toxicity in Poplar Plants

Phytoremediation soil polluted by cadmium has drawn worldwide attention. However, how to improve the efficiency of plant remediation of cadmium contaminated soil remains unknown. Previous studies showed that nitrogen (N) significantly enhances cadmium uptake and accumulation in poplar plants. In order to explore the important role of nitrogen in plants’ responses to cadmium stress, this study investigates the poplar proteome and phosphoproteome difference between Cd stress and Cd + N treatment. In total, 6573 proteins were identified, and 5838 of them were quantified. With a fold-change threshold of > 1.3, and a p-value < 0.05, 375 and 108 proteins were up- and down-regulated by Cd stress when compared to the control, respectively. Compared to the Cd stress group, 42 and 89 proteins were up- and down-regulated by Cd + N treatment, respectively. Moreover, 522 and 127 proteins were up- and down-regulated by Cd + N treatment compared to the CK group. In addition, 1471 phosphosites in 721 proteins were identified. Based on a fold-change threshold of > 1.2, and a p-value < 0.05, the Cd stress up-regulated eight proteins containing eight phosphosites, and down-regulated 58 proteins containing 69 phosphosites, whereas N + Cd treatment up-regulated 86 proteins containing 95 phosphosites, and down-regulated 17 proteins containing 17 phosphosites, when compared to Cd stress alone. N + Cd treatment up-regulated 60 proteins containing 74 phosphosites and down-regulated 37 proteins containing 42 phosphosites, when compared to the control. Several putative responses to stress proteins, as well as transcriptional and translational regulation factors, were up-regulated by the addition of exogenous nitrogen following Cd stress. Especially, heat shock protein 70 (HSP70), 14-3-3 protein, peroxidase (POD), zinc finger protein (ZFP), ABC transporter protein, eukaryotic translation initiation factor (elF) and splicing factor 3 B subunit 1-like (SF3BI) were up-regulated by Cd + N treatment at both the proteome and the phosphoproteome levels. Combing the proteomic data and phosphoproteomics data, the mechanism by which exogenous nitrogen can alleviate cadmium toxicity in poplar plants was explained at the molecular level. The results of this study will establish the solid molecular foundation of the phytoremediation method to improve cadmium-contaminated soil.

Comparative Proteomics Analysis of the Seedling Root Response of Drought-sensitive and Drought-tolerant Maize Varieties to Drought Stress

The growth and development of maize roots are closely related to drought tolerance. In order to clarify the molecular mechanisms of drought tolerance between different maize (Zea mays L.) varieties at the protein level, the isobaric tags for relative and absolute quantitation (iTRAQ) quantitative proteomics were used for the comparative analysis of protein expression in the seedling roots of the drought-tolerant Chang 7-2 and drought-sensitive TS141 maize varieties under 20% polyethylene glycol 6000 (PEG 6000)-simulated drought stress. We identified a total of 7723 differentially expressed proteins (DEPs), 1243 were significantly differentially expressed in Chang 7-2 following drought stress, 572 of which were up-regulated and 671 were down-regulated; 419 DEPs were identified in TS141, 172 of which were up-regulated and 247 were down-regulated. In Chang 7-2, the DEPs were associated with ribosome pathway, glycolysis/gluconeogenesis pathway, and amino sugar and nucleotide sugar metabolism. In TS141, the DEPs were associated with metabolic pathway, phenylpropanoid biosynthesis pathway, and starch and sucrose metabolism. Compared with TS141, the higher drought tolerance of Chang 7-2 root system was attributed to a stronger water retention capacity; the synergistic effect of antioxidant enzymes; the strengthen cell wall; the osmotic stabilization of plasma membrane proteins; the effectiveness of recycling amino acid; and an improvement in the degree of lignification. The common mechanisms of the drought stress response between the two varieties included: The promotion of enzymes in the glycolysis/gluconeogenesis pathway; cross-protection against the toxicity of aldehydes and ammonia; maintenance of the cell membrane stability. Based on the proteome sequencing information, the coding region sequences of eight DEP-related genes were analyzed at the mRNA level by quantitative real-time PCR (qRT-PCR). The findings of this study can inform the future breeding of drought-tolerant maize varieties.

Spatial identification of transcripts and biological processes in laser micro-dissected sub-regions of waterlogged corn roots with altered expression of phytoglobin

Over-expression of the corn phytoglobin ZmPgb1.2 increases tolerance to waterlogging, while suppression of ZmPgb1.2 compromises plant growth. To unravel compartment-specific transcriptional changes evoked by ZmPgb1.2 during hypoxia, laser micro-dissected sub-regions from waterlogged roots of WT and ZmPgb1.2 overexpressing [ZmPgb1.2(S)] plants were probed for global transcriptional analysis using next generation RNA sequencing. These sub-regions included compartments within the meristematic, elongation, and maturation zone. Of the 149 genes differentially expressed by the up-regulation of ZmPgb1.2, 78 occurred within the meristematic region and included genes involved in jasmonic acid synthesis and response, ascorbic acid metabolism, and ethylene signalling. The ZmPgb1.2 regulation of these genes, discussed in the context of known functions of Pgbs, was further validated by monitoring their expression in meristematic cells of waterlogged roots suppressing ZmPgb1.2. Of the 27 genes differentially expressed by the over-expression of ZmPgb1.2 in the elongation zone, pyruvate kinase and alcohol dehydrogenase showed an expression pattern correlated to the level of ZmPgb1.2 in the tissue. The transcriptional induction of these two enzymes in hypoxic domains of the elongation zone over-expressing ZmPgb1.2 suggests the activation of the fermentation pathway which might be required to sustain metabolic flux and production of ATP in support of cell elongation.

Physiological and quantitative proteomic analyses unraveling potassium deficiency stress response in alligator weed (Alternanthera philoxeroides L.) root

Physiological and iTRAQ based proteomic analysis provided new insights into potassium deficiency stress response in alligator weed root. Alligator weed (Alternanthera philoxeroides) has a strong ability to adapt to potassium deficiency (LK) stress. Proteomic changes in response to this stress are largely unknown in alligator weed. In this study, we investigated physiological and molecular mechanisms under LK using isobaric tags for relative and absolute quantitation to characterize proteome-level changes in this plant. First, root physiology, 2, 3, 5-Triphenyl-trazolium chloride (TTC) assay and peroxidase activity were significantly altered after 10 and 15 days of LK treatment. The comparative proteomic analysis suggested a total of 375 proteins were differential abundance proteins. The proteomic results were verified by western blot assays and quantitative real-time PCR. Correlation analysis of transcription and proteomics suggested protein processing in the endoplasmic reticulum, endocytosis, and spliceosome pathways were significantly enriched. The protein responsible for energy metabolism, signal sensing and transduction and protein degradation played crucial roles in this stress. Twelve ubiquitin pathway related proteins were identified in our study, among them 11 proteins were up-regulated. All protein ubiquitination of lysine using pan antibodies were also increased after LK treatment. Our study provide a valuable insights of molecular mechanism underlying LK stress response in alligator weed roots and afford a vital basis to further study potassium nutrition molecular breeding of other plant species.

Fine mapping of QTL qCTB10-2 that confers cold tolerance at the booting stage in rice

The QTL qCTB10 - 2 controlling cold tolerance at the booting stage in rice was delimited to a 132.5 kb region containing 17 candidate genes and 4 genes were cold-inducible. Low temperature at the booting stage is a major abiotic stress-limiting rice production. Although some QTL for cold tolerance in rice have been reported, fine mapping of those QTL effective at the booting stage is few. Here, the near-isogenic line ZL31-2, selected from a BC₇F₂ population derived from a cross between cold-tolerant variety Kunmingxiaobaigu (KMXBG) and the cold-sensitive variety Towada, was used to map a QTL on chromosome 10 for cold tolerance at the booting stage. Using BC₇F₃ and BC₇F₄ populations, we firstly confirmed qCTB10-2 and gained confidence that it could be fine mapped. QTL qCTB10-2 explained 13.9 and 15.9% of the phenotypic variances in those two generations, respectively. Using homozygous recombinants screened from larger BC₇F₄ and BC₇F₅ populations, qCTB10-2 was delimited to a 132.5 kb region between markers RM25121 and MM0568. 17 putative predicted genes were located in the region and only 5 were predicted to encode expressed proteins. Expression patterns of these five genes demonstrated that, except for constant expression of LOC_Os10g11820, LOC_Os10g11730, LOC_Os10g11770, and LOC_Os10g11810 were highly induced by cold stress in ZL31-2 compared to Towada, while LOC_Os10g11750 showed little difference. Our results provide a basis for identifying the genes underlying qCTB10-2 and indicate that markers linked to the qCTB10-2 locus can be used to improve the cold tolerance of rice at the booting stage by marker-assisted selection.

Integrated analysis of transcriptomic and metabolomic data reveals critical metabolic pathways involved in polyphenol biosynthesis in Nicotiana tabacum under chilling stress

Chilling stress increases the amount of polyphenols, especially lignin, which protects tobacco (Nicotiana tabacum L. cv. k326) from chilling stress. To clarify the molecular biosynthesis mechanism of the key representative compounds, specifically lignin, RNA sequencing and ultra-high pressure liquid chromatography coupled to quadrupole-time of flight mass spectrometry technologies were used to construct transcriptomic and metabolomic libraries from the leaves of tobacco plants subjected to normal (25°C) and chilling (4°C) temperature treatments. Transcriptomic libraries from the different samples were sequenced, generating more than 40million raw reads. Among nine samples, metabolomic analysis identified a total of 97 encoding enzymes that function in the key steps of pathways related to polyphenol biosynthesis, where 42 metabolites were also located. An integrated analysis of metabolic and transcriptomic data revealed that most of the intermediate metabolites and enzymes related to lignin biosynthesis were synthesised in the leaves under chilling stress, which suggests that the biosynthesis of lignin plays an important role in the response of tobacco leaves to cold temperatures. In addition, the cold insensitivity of chalcone synthase genes might be considered to be an important rate-limiting factor in the process of precursor substance flow to flavonoid biosynthesis under chilling stress. Furthermore, the upregulated expression of phenylalanine ammonia lyase (PAL), hydroxycinnamoyl transferase (HCT) and cinnamyl-alcohol dehydrogenase (CAD) under chilling stress is the key to an increase in lignin synthesis. This study provides a hypothetical basis for the screening of new active metabolites and the metabolic engineering of polyphenols in tobacco.

Reciprocal Interactions between Cadmium-Induced Cell Wall Responses and Oxidative Stress in Plants

Cadmium (Cd) pollution renders many soils across the world unsuited or unsafe for food- or feed-orientated agriculture. The main mechanism of Cd phytotoxicity is the induction of oxidative stress, amongst others through the depletion of glutathione. Oxidative stress can damage lipids, proteins, and nucleic acids, leading to growth inhibition or even cell death. The plant cell has a variety of tools to defend itself against Cd stress. First and foremost, cell walls might prevent Cd from entering and damaging the protoplast. Both the primary and secondary cell wall have an array of defensive mechanisms that can be adapted to cope with Cd. Pectin, which contains most of the negative charges within the primary cell wall, can sequester Cd very effectively. In the secondary cell wall, lignification can serve to immobilize Cd and create a tougher barrier for entry. Changes in cell wall composition are, however, dependent on nutrients and conversely might affect their uptake. Additionally, the role of ascorbate (AsA) as most important apoplastic antioxidant is of considerable interest, due to the fact that oxidative stress is a major mechanism underlying Cd toxicity, and that AsA biosynthesis shares several links with cell wall construction. In this review, modifications of the plant cell wall in response to Cd exposure are discussed. Focus lies on pectin in the primary cell wall, lignification in the secondary cell wall and the importance of AsA in the apoplast. Regarding lignification, we attempt to answer the question whether increased lignification is merely a consequence of Cd toxicity, or rather an elicited defense response. We propose a model for lignification as defense response, with a central role for hydrogen peroxide as substrate and signaling molecule.

Differential Proteomic Analysis Reveals the Effect of Calcium on Malus baccata Borkh. Leaves under Temperature Stress

In the cool apple-producing areas of northern China, air temperature during early spring changes in a rapid and dramatic manner, which affects the growth and development of apple trees at the early stage of the growing season. Previous studies have shown that the treatment of calcium can increase the cold tolerance of Malus baccata Borkh., a widely-used rootstock apple tree in northern China. To better understand the physiological function of calcium in the response of M. baccata to temperature stress, we analyzed the effect of calcium treatment (2% CaCl₂) on M. baccata leaves under temperature stress. Physiological analysis showed that temperature stress aggravated membrane lipid peroxidation, reduced chlorophyll content and induced photo-inhibition in leaves, whereas these indicators of stress injuries were alleviated by the application of calcium. An isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics approach was used in this study. Among the 2114 proteins that were detected in M. baccata leaves, 41, 25, and 34 proteins were differentially regulated by the increasing, decreasing, and changing temperature treatments, respectively. Calcium treatment induced 9 and 15 proteins after increasing and decreasing temperature, respectively, in comparison with non-treated plants. These calcium-responsive proteins were mainly related to catalytic activity, binding, and structural molecule activity. Hierarchical cluster analysis indicated that the changes in abundance of the proteins under increasing temperature and changing temperature treatments were similar, and the changes in protein abundance under decreasing temperature and increasing temperature with calcium treatment were similar. The findings of this study will allow a better understanding of the mechanisms underlying the role of calcium in M. baccata leaves under temperature stress.

Spatial regulation of monolignol biosynthesis and laccase genes control developmental and stress-related lignin in flax

BACKGROUND

Bast fibres are characterized by very thick secondary cell walls containing high amounts of cellulose and low lignin contents in contrast to the heavily lignified cell walls typically found in the xylem tissues. To improve the quality of the fiber-based products in the future, a thorough understanding of the main cell wall polymer biosynthetic pathways is required. In this study we have carried out a characterization of the genes involved in lignin biosynthesis in flax along with some of their regulation mechanisms.

RESULTS

We have first identified the members of the phenylpropanoid gene families through a combination of in silico approaches. The more specific lignin genes were further characterized by high throughput transcriptomic approaches in different organs and physiological conditions and their cell/tissue expression was localized in the stems, roots and leaves. Laccases play an important role in the polymerization of monolignols. This multigenic family was determined and a miRNA was identified to play a role in the posttranscriptional regulation by cleaving the transcripts of some specific genes shown to be expressed in lignified tissues. In situ hybridization also showed that the miRNA precursor was expressed in the young xylem cells located near the vascular cambium. The results obtained in this work also allowed us to determine that most of the genes involved in lignin biosynthesis are included in a unique co-expression cluster and that MYB transcription factors are potentially good candidates for regulating these genes.

CONCLUSIONS

Target engineering of cell walls to improve plant product quality requires good knowledge of the genes responsible for the production of the main polymers. For bast fiber plants such as flax, it is important to target the correct genes from the beginning since the difficulty to produce transgenic material does not make possible to test a large number of genes. Our work determined which of these genes could be potentially modified and showed that it was possible to target different regulatory pathways to modify lignification.

Ethephon induced oxidative stress in the olive leaf abscission zone enables development of a selective abscission compound

BACKGROUND

Table olives (Olea europaea L.), despite their widespread production, are still harvested manually. The low efficiency of manual harvesting and the rising costs of labor have reduced the profitability of this crop. A selective abscission treatment, inducing abscission of fruits but not leaves, is crucial for the adoption of mechanical harvesting of table olives. In the present work we studied the anatomical and molecular differences between the three abscission zones (AZs) of olive fruits and leaves.

RESULTS

The fruit abscission zone 3 (FAZ3), located between the fruit and the pedicel, was found to be the active AZ in mature fruits and is sensitive to ethephon, whereas FAZ2, between the pedicel and the rachis, is the flower active AZ as well as functioning as the most ethephon induced fruit AZ. We found anatomical differences between the leaf AZ (LAZ) and the two FAZs. Unlike the FAZs, the LAZ is characterized by small cells with less pectin compared to neighboring cells. In an attempt to differentiate between the fruit and leaf AZs, we examined the effect of treating olive-bearing trees with ethephon, an ethylene-releasing compound, with or without antioxidants, on the detachment force (DF) of fruits and leaves 5 days after the treatment. Ethephon treatment enhanced pectinase activity and reduced DF in all the three olive AZs. A transcriptomic analysis of the three olive AZs after ethephon treatment revealed induction of several genes encoding for hormones (ethylene, auxin and ABA), as well as for several cell wall degrading enzymes. However, up-regulation of cellulase genes was found only in the LAZ. Many genes involved in oxidative stress were induced by the ethephon treatment in the LAZ alone. In addition, we found that reactive oxygen species (ROS) mediated abscission in response to ethephon only in leaves. Thus, adding antioxidants such as ascorbic acid or butyric acid to the ethephon inhibited leaf abscission but enhanced fruit abscission.

CONCLUSION

Our findings suggest that treating olive-bearing trees with a combination of ethephon and antioxidants reduces the detachment force (DF) of fruit without weakening that of the leaves. Hence, this selective abscission treatment may be used in turn to promote mechanized harvest of olives.

The enhancement of tolerance to salt and cold stresses by modifying the redox state and salicylic acid content via the cytosolic malate dehydrogenase gene in transgenic apple plants

In this study, we characterized the role of an apple cytosolic malate dehydrogenase gene (MdcyMDH) in the tolerance to salt and cold stresses and investigated its regulation mechanism in stress tolerance. The MdcyMDH transcript was induced by mild cold and salt treatments, and MdcyMDH-overexpressing apple plants possessed improved cold and salt tolerance compared to wild-type (WT) plants. A digital gene expression tag profiling analysis revealed that MdcyMDH overexpression largely altered some biological processes, including hormone signal transduction, photosynthesis, citrate cycle and oxidation-reduction. Further experiments verified that MdcyMDH overexpression modified the mitochondrial and chloroplast metabolisms and elevated the level of reducing power, primarily caused by increased ascorbate and glutathione, as well as the increased ratios of ascorbate/dehydroascorbate and glutathione/glutathione disulphide, under normal and especially stress conditions. Concurrently, the transgenic plants produced a high H2 O2 content, but a low O2·- production rate was observed compared to the WT plants. On the other hand, the transgenic plants accumulated more free and total salicylic acid (SA) than the WT plants under normal and stress conditions. Taken together, MdcyMDH conferred the transgenic apple plants a higher stress tolerance by producing more reductive redox states and increasing the SA level; MdcyMDH could serve as a target gene to genetically engineer salt- and cold-tolerant trees.

Comparative proteomic analysis of the response to silver ions and yeast extract in Salvia miltiorrhiza hairy root cultures

Biotic and abiotic stresses can inhibit plant growth, resulting in losses of crop productivity. However, moderate adverse stress can promote the accumulation of valuable natural products in medicinal plants. Elucidating the underlying molecular mechanisms thus might help optimize the variety of available plant medicinal materials and improve their quality. In this study, Salvia miltiorrhiza hairy root cultures were employed as an in vitro model of the Chinese herb Danshen. A comparative proteomic analysis using 2-dimensional gel electrophoresis and MALDI-TOF-MS was performed. By comparing the gel images of groups exposed to the stress of yeast extract (YE) combined with Ag(+) and controls, 64 proteins were identified that showed significant changes in protein abundance for at least one time point after treatment. According to analysis based on the KEGG and related physiological experimental verification, it was found that YE and Ag(+) stress induced a burst of reactive oxygen species and activated the Ca(2+)/calmodulin signaling pathway. Expression of immune-suppressive proteins increased. Epidermal cells underwent programmed cell death. Energy metabolism was enhanced and carbon metabolism shifted to favor the production of secondary metabolites such as lignin, tanshinone and salvianolic acids. The tanshinone and salvianolic acids were deposited on the collapsed epidermal cells forming a physicochemical barrier. The defense proteins and these natural products together enhanced the stress resistance of the plants. Since higher levels of natural products represent good quality in medicinal materials, this study sheds new light on quality formation mechanisms of medicinal plants and will hopefully encourage further research on how the planting environment affects the efficacy of herbal medicines.

Quantitative Proteomic Analysis Provides Novel Insights into Cold Stress Responses in Petunia Seedlings

Low temperature is a major adverse environmental factor that impairs petunia growth and development. To better understand the molecular mechanisms of cold stress adaptation of petunia plants, a quantitative proteomic analysis using iTRAQ technology was performed to detect the effects of cold stress on protein expression profiles in petunia seedlings which had been subjected to 2°C for 5 days. Of the 2430 proteins whose levels were quantitated, a total of 117 proteins were discovered to be differentially expressed under low temperature stress in comparison to unstressed controls. As an initial study, 44 proteins including well known and novel cold-responsive proteins were successfully annotated. By integrating the results of two independent Gene Ontology (GO) enrichment analyses, seven common GO terms were found of which "oxidation-reduction process" was the most notable for the cold-responsive proteins. By using the subcellular localization tool Plant-mPLoc predictor, as much as 40.2% of the cold-responsive protein group was found to be located within chloroplasts, suggesting that the chloroplast proteome is particularly affected by cold stress. Gene expression analyses of 11 cold-responsive proteins by real time PCR demonstrated that the mRNA levels were not strongly correlated with the respective protein levels. Further activity assay of anti-oxidative enzymes showed different alterations in cold treated petunia seedlings. Our investigation has highlighted the role of antioxidation mechanisms and also epigenetic factors in the regulation of cold stress responses. Our work has provided novel insights into the plant response to cold stress and should facilitate further studies regarding the molecular mechanisms which determine how plant cells cope with environmental perturbation. The data have been deposited to the ProteomeXchange with identifier PXD002189.

The Alcohol Dehydrogenase Gene Family in Melon (Cucumis melo L.): Bioinformatic Analysis and Expression Patterns

Alcohol dehydrogenases (ADH), encoded by multigene family in plants, play a critical role in plant growth, development, adaptation, fruit ripening and aroma production. Thirteen ADH genes were identified in melon genome, including 12 ADHs and one formaldehyde dehydrogenease (FDH), designated CmADH1-12 and CmFDH1, in which CmADH1 and CmADH2 have been isolated in Cantaloupe. ADH genes shared a lower identity with each other at the protein level and had different intron-exon structure at nucleotide level. No typical signal peptides were found in all CmADHs, and CmADH proteins might locate in the cytoplasm. The phylogenetic tree revealed that 13 ADH genes were divided into three groups respectively, namely long-, medium-, and short-chain ADH subfamily, and CmADH1,3-11, which belongs to the medium-chain ADH subfamily, fell into six medium-chain ADH subgroups. CmADH12 may belong to the long-chain ADH subfamily, while CmFDH1 may be a Class III ADH and serve as an ancestral ADH in melon. Expression profiling revealed that CmADH1, CmADH2, CmADH10 and CmFDH1 were moderately or strongly expressed in different vegetative tissues and fruit at medium and late developmental stages, while CmADH8 and CmADH12 were highly expressed in fruit after 20 days. CmADH3 showed preferential expression in young tissues. CmADH4 only had slight expression in root. Promoter analysis revealed several motifs of CmADH genes involved in the gene expression modulated by various hormones, and the response pattern of CmADH genes to ABA, IAA and ethylene were different. These CmADHs were divided into ethylene-sensitive and -insensitive groups, and the functions of CmADHs were discussed.

Mechanism of regulation of tomato TRN1 gene expression in late infection with tomato leaf curl New Delhi virus (ToLCNDV)

Tomato leaf curl disease caused by geminiviruses is manifested by curling and puckering of leaves and thickening of veins, resembling developmental defects. This is probably due to the long-term altered regulation of expression of development related gene(s). Our results show that in the infected leaves the transcript level of TORNADO1 (SlTRN1), a gene important for cell expansion and vein formation, increased significantly. SlTRN1 is transcribed from two start sites. The preferential usage of one start site governs its expression in viral-stressed plants. To investigate the role of specific promoter elements in mediating differential expression of SlTRN1, we performed SlTRN1 promoter analysis. The promoter-regulatory sequences harbor multiple W-boxes. The SlWRKY16 transcription factor actively interacts with one of the W-boxes. WRKY proteins are commonly induced by salicylic acid (SA), and consequently SA treatment increased transcript level of SlWRKY16 and SlTRN1. Further mutational analyses confirmed the role of W-boxes in mediating SlTRN1 induction during ToLCNDV infection or SA treatment. We postulate that the activation of SA pathway during stress-response in tomato induces WRKY16, which in turn modulates transcription of SlTRN1 gene. This study unravels the mechanism of regulation of a developmental gene during stress-response, which may affect the severity of symptoms.

Lignin and lignans in plant defence: insight from expression profiling of cinnamyl alcohol dehydrogenase genes during development and following fungal infection in Populus

Cinnamyl alcohol dehydrogenase (CAD) catalyses the final step in the biosynthesis of monolignol, the main component of lignin. Lignins, deposited in the secondary cell wall, play a role in plant defence against pathogens. We re-analysed the phylogeny of CAD/CAD-like genes using sequences from recently sequenced genomes, and analysed the temporal and spatial expression profiles of CAD/CAD-like genes in Populus trichocarpa healthy and infected plants. Three fungal pathogens (Rhizoctonia solani, Fusarium oxysporum, and Cytospora sp.), varying in lifestyle and pathogenicity, were used for plant infection. Phylogenetic analyses showed that CAD/CAD-like genes were distributed in classes represented by all members from angiosperm lineages including basal angiosperms and Selaginella. The analysed genes showed different expression profiles during development and demonstrated that three genes were involved in primary xylem maturation while five may function in secondary xylem formation. Expression analysis following inoculation with fungal pathogens, showed that five genes were induced in either stem or leaves. These results add further evidence that CAD/CAD-like genes have evolved specialised functions in plant development and defence against various pest and pathogens. Two genes (PoptrCAD11 and PoptrCAD15), which were induced under various stresses, could be treated as universal markers of plant defence using lignification or lignan biosynthesis.

Molecular cloning and functional analysis of nine cinnamyl alcohol dehydrogenase family members in Populus tomentosa

Nine CAD/CAD-like genes in P. tomentosa were classified into four classes based on expression patterns, phylogenetic analysis and biochemical properties with modification for the previous claim of SAD. Cinnamyl alcohol dehydrogenase (CAD) functions in monolignol biosynthesis and plays a critical role in wood development and defense. In this study, we isolated and cloned nine CAD/CAD-like genes in the Populus tomentosa genome. We investigated differential expression using microarray chips and found that PtoCAD1 was highly expressed in bud, root and vascular tissues (xylem and phloem) with the greatest expression in the root. Differential expression in tissues was demonstrated for PtoCAD3, PtoCAD6 and PtoCAD9. Biochemical analysis of purified PtoCADs in vitro indicated PtoCAD1, PtoCAD2 and PtoCAD8 had detectable activity against both coniferaldehyde and sinapaldehyde. PtoCAD1 used both substrates with high efficiency. PtoCAD2 showed no specific requirement for sinapaldehyde in spite of its high identity with so-called PtrSAD (sinapyl alcohol dehydrogenase). In addition, the enzymatic activity of PtoCAD1 and PtoCAD2 was affected by temperature. We classified these nine CAD/CAD-like genes into four classes: class I included PtoCAD1, which was a bone fide CAD with the highest activity; class II included PtoCAD2, -5, -7, -8, which might function in monolignol biosynthesis and defense; class III genes included PtoCAD3, -6, -9, which have a distinct expression pattern; class IV included PtoCAD12, which has a distinct structure. These data suggest divergence of the PtoCADs and its homologs, related to their functions. We propose genes in class II are a subset of CAD genes that evolved before angiosperms appeared. These results suggest CAD/CAD-like genes in classes I and II play a role in monolignol biosynthesis and contribute to our knowledge of lignin biosynthesis in P. tomentosa.

The cinnamyl alcohol dehydrogenase gene family in melon (Cucumis melo L.): bioinformatic analysis and expression patterns

Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis. However, little was known about CADs in melon. Five CAD-like genes were identified in the genome of melons, namely CmCAD1 to CmCAD5. The signal peptides analysis and CAD proteins prediction showed no typical signal peptides were found in all CmCADs and CmCAD proteins may locate in the cytoplasm. Multiple alignments implied that some motifs may be responsible for the high specificity of these CAD proteins, and may be one of the key residues in the catalytic mechanism. The phylogenetic tree revealed seven groups of CAD and melon CAD genes fell into four main groups. CmCAD1 and CmCAD2 belonged to the bona fide CAD group, in which these CAD genes, as representative from angiosperms, were involved in lignin synthesis. Other CmCADs were distributed in group II, V and VII, respectively. Semi-quantitative PCR and real time qPCR revealed differential expression of CmCADs, and CmCAD5 was expressed in different vegetative tissues except mature leaves, with the highest expression in flower, while CmCAD2 and CmCAD5 were strongly expressed in flesh during development. Promoter analysis revealed several motifs of CAD genes involved in the gene expression modulated by various hormones. Treatment of abscisic acid (ABA) elevated the expression of CmCADs in flesh, whereas the transcript levels of CmCAD1 and CmCAD5 were induced by auxin (IAA); Ethylene induced the expression of CmCADs, while 1-MCP repressed the effect, apart from CmCAD4. Taken together, these data suggested that CmCAD4 may be a pseudogene and that all other CmCADs may be involved in the lignin biosynthesis induced by both abiotic and biotic stresses and in tissue-specific developmental lignification through a CAD genes family network, and CmCAD2 may be the main CAD enzymes for lignification of melon flesh and CmCAD5 may also function in flower development.

Identification and characterization of cis-acting elements involved in the regulation of ABA- and/or GA-mediated LuPLR1 gene expression and lignan biosynthesis in flax (Linum usitatissimum L.) cell cultures

Pinoresinol lariciresinol reductase 1, encoded by the LuPLR1 gene in flax (Linum usitatissimum L.), is responsible for the biosynthesis of (+)-secoisolariciresinol, a cancer chemopreventive phytoestrogenic lignan accumulated in high amount in the hull of flaxseed. Our recent studies have demonstrated a key role of abscisic acid (ABA) in the regulation of LuPLR1 gene expression and thus of the (+)-secoisolariciresinol synthesis during the flax seedcoat development. It is well accepted that gibberellins (GA) and ABA play antagonistic roles in the regulation of numerous developmental processes; therefore it is of interest to clarify their respective effects on lignan biosynthesis. Herein, using flax cell suspension cultures, we demonstrate that LuPLR1 gene expression and (+)-secoisolariciresinol synthesis are up-regulated by ABA and down-regulated by GA. The LuPLR1 gene promoter analysis and mutation experiments allow us to identify and characterize two important cis-acting sequences (ABRE and MYB2) required for these regulations. These results imply that a cross-talk between ABA and GA signaling orchestrated by transcription factors is involved in the regulation of lignan biosynthesis. This is particularly evidenced in the case of the ABRE cis-regulatory sequence of LuPLR1 gene promoter that appears to be a common target sequence of GA and ABA signals.

Molecular cloning, functional analysis of three cinnamyl alcohol dehydrogenase (CAD) genes in the leaves of tea plant, Camellia sinensis

Cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.195) is considered to be a key enzyme in lignin biosynthesis, but little was known about CADs in tea plants (Camellia sinensis). A full-length cDNA sequence (CsCAD2) was isolated by suppressive subtractive hybridization (SSH) in Ectropis oblique feeding-induced tea plants, and another two full-length cDNA sequences (CsCAD1 and CsCAD3) were obtained from a transcriptome obtained by deep sequencing. However, they showed only 20-54% identities. Phylogenetic analysis revealed that they belonged to three different families. DNA gel blotting analysis revealed that two copies of CsCAD1 and CsCAD2 genes existed in tea genome, but CsCAD3 likely had only one copy. Recombinant proteins of these CsCADs were produced in Escherichia coli. The activity of purified recombinant CsCAD2 protein was up to 0.43 μmol min(-1) mg(-1). However, the other two recombinant proteins had lower activities, probably due to incomplete refolding. qRT-PCR analysis indicated that while CsCAD3 was strongly up-regulated in tea plants after E. oblique attack and mechanical damage, CsCAD1 and CsCAD2 showed only moderate or no changes in transcript levels. Treatment of defence-related hormones methyl jasmonate (MeJA) and salicylic acid (SA) elevated the expression of CsCAD1 and CsCAD2, but decreased the transcript abundance of CsCAD3. The transcript levels of CsCAD2 did not change after applying abscisic acid (ABA), whereas CsCAD1 and CsCAD3 were induced. These results suggested that these three CsCAD genes in tea plants may play a role in defense against insects and pathogens and adaptation to abiotic stresses and these genes likely have divergant functions.

Cell wall compositional modifications of Miscanthus ecotypes in response to cold acclimation

Miscanthus, a potential energy crop grass, can be damaged by late frost when shoots emerge too early in the spring and during the first winter after planting. The effects of cold acclimation on cell wall composition were investigated in a frost-sensitive clone of Miscanthus x giganteus compared to frost-tolerant clone, Miscanthus sinensis August Feder, and an intermediate frost-tolerant clone, M. sinensis Goliath. Cellulose and lignin contents were higher in M. x giganteus than in the M. sinensis genotypes. In ambient temperature controls, each clone displayed different glucuronoarabinoxylan (GAX) contents and degree of arabinose substitution on the xylan backbone. During cold acclimation, an increase in (1→3),(1→4)-β-D-glucan content was observed in all genotypes. Uronic acid level increased in the frost sensitive genotype but decreased in the frost tolerant genotypes in response to cold. In all clones, major changes in cell wall composition were observed with modifications in phenylalanine ammonia-lyase (PAL) and cinnamyl alcohol dehydrogenase (CAD) activities in both non- and cold-acclimated experiments. A large increase in CAD activity under cold stress was displayed in each clone, but it was largest in the frost-tolerant clone, M. sinensis August Feder. The marked increase in PAL activity observed in the frost-tolerant clones under cold acclimation, suggests a reorientation of the products towards the phenylpropanoid pathway or aromatic synthesis. How changes in cell wall physical properties can impact frost tolerance is discussed.

Expression patterns of a cinnamyl alcohol dehydrogenase gene involved in lignin biosynthesis and environmental stress in Ginkgo biloba

The cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis as it catalyzes the final step in the synthesis of monolignols. A cDNA sequence encoding the CAD gene was isolated from the leaves of Ginkgo biloba L, designated as GbCAD1. The full-length cDNA of GbCAD1 was 1,494 bp containing a 1,074 bp open reading frame encoding a polypeptide of 357 amino acids with a calculated molecular mass of 38.7 kDa and an isoelectric point of 5.74. Comparative and bioinformatic analyses revealed that GbCAD1 showed extensive homology with CADs from other gymnosperm species. Southern blot analysis indicated that GbCAD1 belonged to a multi-gene family. Phylogenetic tree analysis revealed that GbCAD1 shared the same ancestor in evolution with other CADs and had a further relationship with other gymnosperm species. GbCAD1 was an enzyme being pH-dependent and temperature-sensitive, and showing a selected catalyzing. Tissue expression pattern analysis showed that GbCAD1 was constitutively expressed in stems and roots, especially in the parts of the pest and disease infection, with the lower expression being found in two- to four-year-old stem. Further analysis showed the change in lignin content had some linear correlation with the expression level of GbCAD1 mRNA in different tissues. The increased expression of GbCAD1 was detected when the seedling were treated with exogenous abscisic acid, salicylic acid, ethephon, ultraviolet and wounding. These results indicate that the GbCAD1 gene may play a role in the resistance mechanism to biotic and abiotic stresses as well as in tissue-specific developmental lignification.

Phylogeny and structure of the cinnamyl alcohol dehydrogenase gene family in Brachypodium distachyon

Cinnamyl alcohol dehydrogenase (CAD) catalyses the final step of the monolignol biosynthesis, the conversion of cinnamyl aldehydes to alcohols, using NADPH as a cofactor. Seven members of the CAD gene family were identified in the genome of Brachypodium distachyon and five of these were isolated and cloned from genomic DNA. Semi-quantitative reverse-transcription PCR revealed differential expression of the cloned genes, with BdCAD5 being expressed in all tissues and highest in root and stem while BdCAD3 was only expressed in stem and spikes. A phylogenetic analysis of CAD-like proteins placed BdCAD5 on the same branch as bona fide CAD proteins from maize (ZmCAD2), rice (OsCAD2), sorghum (SbCAD2) and Arabidopsis (AtCAD4, 5). The predicted three-dimensional structures of both BdCAD3 and BdCAD5 resemble that of AtCAD5. However, the amino-acid residues in the substrate-binding domains of BdCAD3 and BdCAD5 are distributed symmetrically and BdCAD3 is similar to that of poplar sinapyl alcohol dehydrogenase (PotSAD). BdCAD3 and BdCAD5 expressed and purified from Escherichia coli both showed a temperature optimum of about 50 °C and molar weight of 49 kDa. The optimal pH for the reduction of coniferyl aldehyde were pH 5.2 and 6.2 and the pH for the oxidation of coniferyl alcohol were pH 8 and 9.5, for BdCAD3 and BdCAD5 respectively. Kinetic parameters for conversion of coniferyl aldehyde and coniferyl alcohol showed that BdCAD5 was clearly the most efficient enzyme of the two. These data suggest that BdCAD5 is the main CAD enzyme for lignin biosynthesis and that BdCAD3 has a different role in Brachypodium. All CAD enzymes are cytosolic except for BdCAD4, which has a putative chloroplast signal peptide adding to the diversity of CAD functions.

Environmental stresses of field growth allow cinnamyl alcohol dehydrogenase-deficient Nicotiana attenuata plants to compensate for their structural deficiencies

The organized lignocellulosic assemblies of cell walls provide the structural integrity required for the large statures of terrestrial plants. Silencing two CINNAMYL ALCOHOL DEHYDROGENASE (CAD) genes in Nicotiana attenuata produced plants (ir-CAD) with thin, red-pigmented stems, low CAD and sinapyl alcohol dehydrogenase activity, low lignin contents, and rubbery, structurally unstable stems when grown in the glasshouse (GH). However, when planted into their native desert habitat, ir-CAD plants produced robust stems that survived wind storms as well as the wild-type plants. Despite efficient silencing of NaCAD transcripts and enzymatic activity, field-grown ir-CAD plants had delayed and restricted spread of red stem pigmentation, a color change reflecting blocked lignification by CAD silencing, and attained wild-type-comparable total lignin contents. The rubbery GH phenotype was largely restored when field-grown ir-CAD plants were protected from wind, herbivore attack, and ultraviolet B exposure and grown in restricted rooting volumes; conversely, it was lost when ir-CAD plants were experimentally exposed to wind, ultraviolet B, and grown in large pots in growth chambers. Transcript and liquid chromatography-electrospray ionization-time-of-flight analysis revealed that these environmental stresses enhanced the accumulation of various phenylpropanoids in stems of field-grown plants; gas chromatography-mass spectrometry and nuclear magnetic resonance analysis revealed that the lignin of field-grown ir-CAD plants had GH-grown comparable levels of sinapaldehyde and syringaldehyde cross-linked into their lignins. Additionally, field-grown ir-CAD plants had short, thick stems with normal xylem element traits, which collectively enabled field-grown ir-CAD plants to compensate for the structural deficiencies associated with CAD silencing. Environmental stresses play an essential role in regulating lignin biosynthesis in lignin-deficient plants.

Abscisic acid regulates pinoresinol-lariciresinol reductase gene expression and secoisolariciresinol accumulation in developing flax (Linum usitatissimum L.) seeds

Secoisolariciresinol diglucoside (SDG), the main phytoestrogenic lignan of Linum usitatissimum, is accumulated in the seed coat of flax during its development and pinoresinol-lariciresinol reductase (PLR) is a key enzyme in flax for its synthesis. The promoter of LuPLR1, a flax gene encoding a pinoresinol lariciresinol reductase, contains putative regulatory boxes related to transcription activation by abscisic acid (ABA). Gel mobility shift experiments evidenced an interaction of nuclear proteins extracted from immature flax seed coat with a putative cis-acting element involved in ABA response. As ABA regulates a number of physiological events during seed development and maturation we have investigated its involvement in the regulation of this lignan synthesis by different means. ABA and SDG accumulation time courses in the seed as well as LuPLR1 expression were first determined in natural conditions. These results showed that ABA timing and localization of accumulation in the flax seed coat could be correlated with the LuPLR1 gene expression and SDG biosynthesis. Experimental modulations of ABA levels were performed by exogenous application of ABA or fluridone, an inhibitor of ABA synthesis. When submitted to exogenous ABA, immature seeds synthesized 3-times more SDG, whereas synthesis of SDG was reduced in immature seeds treated with fluridone. Similarly, the expression of LuPLR1 gene in the seed coat was up-regulated by exogenous ABA and down-regulated when fluridone was applied. These results demonstrate that SDG biosynthesis in the flax seed coat is positively controlled by ABA through the transcriptional regulation of LuPLR1 gene.

Designer promoter: an artwork of cis engineering

Advances in systematic computational biology and rapid elucidation of synergistic interplay between cis and trans factors governing transcriptional control have facilitated functional annotation of gene networks. The generation of data through deconstructive, reconstructive and database assisted promoter studies, and its integration to principles of synthetic engineering has started an era of designer promoters. Exploration of natural promoter architecture and the concept of cis engineering have not only enabled fine tuning of single or multiple transgene expression in response to perturbations in the chemical, physiological and environmental stimuli but also provided researchers with a unique answer to various problems in crop improvement in the form of bidirectional promoters.