The XTH gene family: an update on enzyme structure, function, and phylogeny in xyloglucan remodeling

Plant BCL-Domain Homologues play a conserved role in SWI/SNF complex stability

The SWItch/Sucrose Non-Fermenting (SWI/SNF) complexes are evolutionarily conserved, ATP-dependent chromatin remodelers crucial for multiple nuclear functions in eukaryotes. Recently, plant BCL-Domain Homolog (BDH) proteins were identified as shared subunits of all plant SWI/SNF complexes, significantly impacting chromatin accessibility and various developmental processes in Arabidopsis. In this study, we performed a comprehensive characterization of bdh mutants, revealing a previously overlooked impact on hypocotyl cell elongation. Through detailed analysis of BDH domains, we identified a plant-specific N-terminal domain that facilitates the interaction between BDH and the rest of the complex. Additionally, we uncovered the critical role of the BDH β-hairpin domain, which is phylogenetically related to metazoan BCL7 SWI/SNF subunits. While phylogenetic analyses did not identify BDH/BCL7 orthologs in fungi, structure prediction modeling demonstrated strong similarities between the SWI/SNF catalytic modules of plants, animals, and fungi, and revealed the yeast Rtt102 protein as a structural homolog of BDH and BCL7. This finding is supported by the ability of Rtt102 to interact with the Arabidopsis catalytic module subunit ARP7 and partially rescue the bdh mutant phenotypes. Further experiments revealed that BDH promotes the stability of the ARP4-ARP7 heterodimer, leading to the partial destabilization of ARP4 in the SWI/SNF complexes. In summary, our study unveils the molecular function of BDH proteins in plant SWI/SNF complexes and suggests that β-hairpin-containing proteins are evolutionarily conserved subunits crucial for ARP heterodimer stability and SWI/SNF activity across eukaryotes.

MdWRKY31-MdNAC7 regulatory network: orchestrating fruit softening by modulating cell wall-modifying enzyme MdXTH2 in response to ethylene signalling

Softening in fruit adversely impacts their edible quality and commercial value, leading to substantial economic losses during fruit ripening, long-term storage, long-distance transportation, and marketing. As the apple fruit demonstrates climacteric respiration, its firmness decreases with increasing ethylene release rate during fruit ripening and postharvest storage. However, the molecular mechanisms underlying ethylene-mediated regulation of fruit softening in apple remain poorly understood. In this study, we identified a WRKY transcription factor (TF) MdWRKY31, which is repressed by ethylene treatment. Using transgenic approaches, we found that overexpression of MdWRKY31 delays softening by negatively regulating xyloglucan endotransglucosylase/hydrolases 2 (MdXTH2) expression. Yeast one-hybrid (Y1H), electrophoretic mobility shift (EMSA), and dual-luciferase assays further suggested that MdWRKY31 directly binds to the MdXTH2 promoter via a W-box element and represses its transcription. Transient overexpression of ethylene-induced MdNAC7, a NAC TF, in apple fruit promoted softening by decreasing cellulose content and increasing water-soluble pectin content in fruit. MdNAC7 interacted with MdWRKY31 to form a protein complex, and their interaction decreased the transcriptional repression of MdWRKY31 on MdXTH2. Furthermore, MdNAC7 does not directly regulate MdXTH2 expression, but the protein complex formed with MdWRKY31 hinders MdWRKY31 from binding to the promoter of MdXTH2. Our findings underscore the significance of the regulatory complex NAC7-WRKY31 in ethylene-responsive signalling, connecting the ethylene signal to XTH2 expression to promote fruit softening. This sheds light on the intricate mechanisms governing apple fruit firmness and opens avenues for enhancing fruit quality and reducing economic losses associated with softening.

Genome sequencing of Elaeocarpus spp. stem blight pathogen Pseudocryphonectria elaeocarpicola reveals potential adaptations to colonize woody bark

BACKGROUND

Elaeocarpus spp. stem blight, caused by Pseudocryphonectria elaeocarpicola, is a destructive disease, which will significantly reduce the productivity and longevity of Elaeocarpus spp. plants, especially in the Guangdong Province of China. However, few information is available for P. elaeocarpicola. To unravel the potential adaptation mechanism of stem adaptation, the whole genome of P. elaeocarpicola was sequenced by using the DNBSEQ and PacBio platforms.

RESULTS

P. elaeocarpicola harbors 44.49 Mb genome with 10,894 predicted coding genes. Genome analysis revealed that the P. elaeocarpicola genome encodes a plethora of pathogenicity-related genes. Analysis of carbohydrate-active enzymes (CAZymes) revealed a rich variety of enzymes participated in plant cell wall degradation, which could effectively degrade cellulose, hemicellulose and xyloglucans in the plant cell wall and promote the invasion of the host plant. There are 213 CAZyme families found in P. elaeocarpicola, among which glycoside hydrolase (GH) family has the largest number, far exceeding other tested fungi by 53%. Besides, P. elaeocarpicola has twice as many genes encoding chitin and cellulose degradation as Cryphonectria parasitica, which belong to the same family. The predicted typical secreted proteins of P. elaeocarpicola are numerous and functional, including many known virulence effector factors, indicating that P. elaeocarpicola has great potential to secrete virulence effectors to promote pathogenicity on host plants. AntiSMASH revealed that the genome encoded 61 secondary metabolic gene clusters including 86 secondary metabolic core genes which was much higher than C. parasitica (49). Among them, two gene cluster of P. elaeocarpicola, cluster12 and cluster52 showed 100% similarity with the mycotoxins synthesis clusters from Aspergillus steynii and Alternaria alternata, respectively. In addition, we annotated cytochrome P450 related enzymes, transporters, and transcription factors in P. elaeocarpicola, which are important virulence determinants of pathogenic fungi.

CONCLUSIONS

Taken together, our study represents the first genome assembly for P. elaeocarpicola and reveals the key virulence factors in the pathogenic process of P. elaeocarpicola, which will promote our understanding of its pathogenic mechanism. The acquired knowledge lays a foundation for further exploration of molecular interactions with the host and provide target for management strategies in future research.

Cell size and xylem differentiation regulating genes from Salicornia europaea contribute to plant salt tolerance

Cell wall is involved in plant growth and plays pivotal roles in plant adaptation to environmental stresses. Cell wall remodelling may be crucial to salt adaptation in the euhalophyte Salicornia europaea. However, the mechanism underlying this process is still unclear. Here, full-length transcriptome indicated cell wall-related genes were comprehensively regulated under salinity. The morphology and cell wall components in S. europaea shoot were largely modified under salinity. Through the weighted gene co-expression network analysis, SeXTH2 encoding xyloglucan endotransglucosylase/hydrolases, and two SeLACs encoding laccases were focused. Meanwhile, SeEXPB was focused according to expansin activity and the expression profiling. Function analysis in Arabidopsis validated the functions of these genes in enhancing salt tolerance. SeXTH2 and SeEXPB overexpression led to larger cells and leaves with hemicellulose and pectin content alteration. SeLAC1 and SeLAC2 overexpression led to more xylem vessels, increased secondary cell wall thickness and lignin content. Notably, SeXTH2 transgenic rice exhibited enhanced salt tolerance and higher grain yield. Altogether, these genes may function in the succulence and lignification process in S. europaea. This work throws light on the regulatory mechanism of cell wall remodelling in S. europaea under salinity and provides potential strategies for improving crop salt tolerance and yields.

Genome-Wide Analysis of the Xyloglucan Endotransglucosylase/Hydrolase (XTH) Gene Family: Expression Pattern during Magnesium Stress Treatment in the Mulberry Plant (Morus alba L.) Leaves

Mulberry (Morus alba L.), a significant fruit tree crop, requires magnesium (Mg) for its optimal growth and productivity. Nonetheless, our understanding of the molecular basis underlying magnesium stress tolerance in mulberry plants remains unexplored. In our previous study, we identified several differential candidate genes associated with Mg homeostasis via transcriptome analysis, including the xyloglucan endotransglucosylase/hydrolase (XTH) gene family. The XTH gene family is crucial for plant cell wall reconstruction and stress responses. These genes have been identified and thoroughly investigated in various plant species. However, there is no research pertaining to XTH genes within the M. alba plant. This research systematically examined the M. alba XTH (MaXTH) gene family at the genomic level using a bioinformatic approach. In total, 22 MaXTH genes were discovered and contained the Glyco_hydro_16 and XET_C conserved domains. The MaXTHs were categorized into five distinct groups by their phylogenetic relationships. The gene structure possesses four exons and three introns. Furthermore, the MaXTH gene promoter analysis reveals a plethora of cis-regulatory elements, mainly stress responsiveness, phytohormone responsiveness, and growth and development. GO analysis indicated that MaXTHs encode proteins that exhibit xyloglucan xyloglucosyl transferase and hydrolase activities in addition to cell wall biogenesis as well as xyloglucan and carbohydrate metabolic processes. Moreover, a synteny analysis unveiled an evolutionary relationship between the XTH genes in M. alba and those in three other species: A. thaliana, P. trichocarpa, and Zea mays. Expression profiles from RNA-Seq data displayed distinct expression patterns of XTH genes in M. alba leaf tissue during Mg treatments. Real-time quantitative PCR analysis confirmed the expression of the MaXTH genes in Mg stress response. Overall, this research enhances our understanding of the characteristics of MaXTH gene family members and lays the foundation for future functional genomic study in M. alba.

Effect of terminal heat stress on osmolyte accumulation and gene expression during grain filling in bread wheat (Triticum aestivum L.)

The grain-filling stage in Triticum aestivum (wheat) is highly vulnerable to increasing temperature as terminal heat stress diminishes grain quality and yield. To examine the mechanism of terminal heat tolerance, we performed the biochemical and gene expression analyses using two heat-tolerant (WH730 and WH1218) and two heat-sensitive (WH711 and WH157) wheat genotypes. We observed a significant increase in total soluble sugar (25%-47%), proline (7%-15%), and glycine betaine (GB) (22%-34%) contents in flag leaf, whereas a decrease in grain-filling duration, 1000-kernel weight (8%-25%), and grain yield per plant (11%-23%) was observed under the late-sown compared to the timely sown. The maximum content of osmolytes, including total soluble sugar, proline, and GB, was observed in heat-tolerant genotypes compared to heat-sensitive genotypes. The expression of 10 heat-responsive genes associated with heat shock proteins (sHsp-1, Hsp17, and HsfA4), flavonoid biosynthesis (F3'-1 and PAL), β-glucan synthesis (CslF6 and CslH), and xyloglucan metabolism (XTH1, XTH2, and XTH5) was studied in flag leaf exposed to different heat treatments (34, 36, 38, and 40°C) at 15 days after anthesis by quantitative real-time polymerase chain reaction. A significant increase in the relative fold expression of these genes with increasing temperature indicated their involvement in providing heat-stress tolerance. The high differential expression of most of the genes in heat-tolerant genotype "WH730" followed by "WH1218" indicates the high adaptability of these genotypes to heat stress compared to heat-sensitive wheat genotypes. Based on the previous results, "WH730" performed better in terms of maximum osmolyte accumulation, grain yield, and gene expression under heat stress.

Genome and GWAS analysis identified genes significantly related to phenotypic state of Rhododendron bark

As an important horticultural plant, Rhododendron is often used in urban greening and landscape design. However, factors such as the high rate of genetic recombination, frequent outcrossing in the wild, weak linkage disequilibrium, and the susceptibility of gene expression to environmental factors limit further exploration of functional genes related to important horticultural traits, and make the breeding of new varieties require a longer time. Therefore, we choose bark as the target trait which is not easily affected by environmental factors, but also has ornamental properties. Genome-wide association study (GWAS) of Rhododendron delavayi (30 samples), R. irroratum (30 samples) and their F1 generation R. agastum (200 samples) was conducted on the roughness of bark phenotypes. Finally, we obtained 2416.31 Gbp of clean data and identified 5 328 800 high-quality SNPs. According to the P-value and the degree of linkage disequilibrium of SNPs, we further identified 4 out of 11 candidate genes that affect bark roughness. The results of gene differential expression analysis further indicated that the expression levels of Rhdel02G0243600 and Rhdel08G0220700 in different bark phenotypes were significantly different. Our study identified functional genes that influence important horticultural traits of Rhododendron, and illustrated the powerful utility and great potential of GWAS in understanding and exploiting wild germplasm genetic resources of Rhododendron.

Leaf rust (Puccinia recondita f. sp. secalis) triggers substantial changes in rye (Secale cereale L.) at the transcriptome and metabolome levels

BACKGROUND

Rye (Secale cereale L.) is a cereal crop highly tolerant to environmental stresses, including abiotic and biotic stresses (e.g., fungal diseases). Among these fungal diseases, leaf rust (LR) is a major threat to rye production. Despite extensive research, the genetic basis of the rye immune response to LR remains unclear.

RESULTS

An RNA-seq analysis was conducted to examine the immune response of three unrelated rye inbred lines (D33, D39, and L318) infected with compatible and incompatible Puccinia recondita f. sp. secalis (Prs) isolates. In total, 877 unique differentially expressed genes (DEGs) were identified at 20 and 36 h post-treatment (hpt). Most of the DEGs were up-regulated. Two lines (D39 and L318) had more up-regulated genes than down-regulated genes, whereas the opposite trend was observed for line D33. The functional classification of the DEGs helped identify the largest gene groups regulated by LR. Notably, these groups included several DEGs encoding cytochrome P450, receptor-like kinases, methylesterases, pathogenesis-related protein-1, xyloglucan endotransglucosylases/hydrolases, and peroxidases. The metabolomic response was highly conserved among the genotypes, with line D33 displaying the most genotype-specific changes in secondary metabolites. The effect of pathogen compatibility on metabolomic changes was less than the effects of the time-points and genotypes. Accordingly, the secondary metabolome of rye is altered by the recognition of the pathogen rather than by a successful infection. The results of the enrichment analysis of the DEGs and differentially accumulated metabolites (DAMs) reflected the involvement of phenylpropanoid and diterpenoid biosynthesis as well as thiamine metabolism in the rye immune response.

CONCLUSION

Our work provides novel insights into the genetic and metabolic responses of rye to LR. Numerous immune response-related DEGs and DAMs were identified, thereby clarifying the mechanisms underlying the rye response to compatible and incompatible Prs isolates during the early stages of LR development. The integration of transcriptomic and metabolomic analyses elucidated the contributions of phenylpropanoid biosynthesis and flavonoid pathways to the rye immune response to Prs. This combined analysis of omics data provides valuable insights relevant for future research conducted to enhance rye resistance to LR.

Exploring the mechanism of Lycium barbarum fruit cell wall polysaccharide remodeling reveals potential pectin accumulation contributors

The level of polysaccharides in the mature Lycium barbarum fruit (LBF) cell wall depends on their metabolism, trafficking, and reassembly within the cell. In this study, we examined the composition, content, and ultrastructure of the cell wall polysaccharides of LBF during maturation, and further analyzed cell wall polysaccharide remodeling using isotope tagging with relative and absolute quantification (iTRAQ)-based proteomics. The results showed that the contents of cellulose and hemicellulose tended to increase in the pre-maturation stage and decrease in the later stage, while pectin level increased before fruit maturing. The differential expression of the 54 proteins involved in the metabolic pathways for glucose, fructose, galactose, galacturonic acid and arabinose was found to be responsible for these alterations. The work provides a biological framework for the reorganization of polysaccharides in the LBF cell wall, and supports the hypothesis that pectic polysaccharide glycosyl donors come from starch, cellulose, hemicellulose and isomorphic pectin.

Single-cell transcriptomic analysis of pea shoot development and cell-type-specific responses to boron deficiency

Understanding how nutrient stress impacts plant growth is fundamentally important to the development of approaches to improve crop production under nutrient limitation. Here we applied single-cell RNA sequencing to shoot apices of Pisum sativum grown under boron (B) deficiency. We identified up to 15 cell clusters based on the clustering of gene expression profiles and verified cell identity with cell-type-specific marker gene expression. Different cell types responded differently to B deficiency. Specifically, the expression of photosynthetic genes in mesophyll cells (MCs) was down-regulated by B deficiency, consistent with impaired photosynthetic rate. Furthermore, the down-regulation of stomatal development genes in guard cells, including homologs of MUTE and TOO MANY MOUTHS, correlated with a decrease in stomatal density under B deficiency. We also constructed the developmental trajectory of the shoot apical meristem (SAM) cells and a transcription factor interaction network. The developmental progression of SAM to MC was characterized by up-regulation of genes encoding histones and chromatin assembly and remodeling proteins including homologs of FASCIATA1 (FAS1) and SWITCH DEFECTIVE/SUCROSE NON-FERMENTABLE (SWI/SNF) complex. However, B deficiency suppressed their expression, which helps to explain impaired SAM development under B deficiency. These results represent a major advance over bulk-tissue RNA-seq analysis in which cell-type-specific responses are lost and hence important physiological responses to B deficiency are missed. The reported findings reveal strategies by which plants adapt to B deficiency thus offering breeders a set of specific targets for genetic improvement. The reported approach and resources have potential applications well beyond P. sativum species and could be applied to various legumes to improve their adaptability to multiple nutrient or abiotic stresses.

Growth-inhibiting effects of the unconventional plant APYRASE 7 of Arabidopsis thaliana influences the LRX/RALF/FER growth regulatory module

Plant cell growth involves coordination of numerous processes and signaling cascades among the different cellular compartments to concomitantly enlarge the protoplast and the surrounding cell wall. The cell wall integrity-sensing process involves the extracellular LRX (LRR-Extensin) proteins that bind RALF (Rapid ALkalinization Factor) peptide hormones and, in vegetative tissues, interact with the transmembrane receptor kinase FERONIA (FER). This LRX/RALF/FER signaling module influences cell wall composition and regulates cell growth. The numerous proteins involved in or influenced by this module are beginning to be characterized. In a genetic screen, mutations in Apyrase 7 (APY7) were identified to suppress growth defects observed in lrx1 and fer mutants. APY7 encodes a Golgi-localized NTP-diphosphohydrolase, but opposed to other apyrases of Arabidopsis, APY7 revealed to be a negative regulator of cell growth. APY7 modulates the growth-inhibiting effect of RALF1, influences the cell wall architecture and -composition, and alters the pH of the extracellular matrix, all of which affect cell growth. Together, this study reveals a function of APY7 in cell wall formation and cell growth that is connected to growth processes influenced by the LRX/RALF/FER signaling module.

Genome-wide characterization of the xyloglucan endotransglucosylase/hydrolase family genes and their response to plant hormone in sugar beet

Xyloglucan endotransglucosylase/hydrolases (XTHs) play a crucial role in plant growth and development. However, their functional response to phytohormone in sugar beet still remains obscure. In this study, we identified 30 putative BvXTH genes in the sugar beet genome. Phylogenetic and evolutionary relationship analysis revealed that they were clustered into three groups and have gone through eight tandem duplication events under purifying selection. Gene structure and motif composition analysis demonstrated that they were highly conserved and all contained one conserved glycoside hydrolase family 16 domain (Glyco_hydro_16) and one xyloglucan endotransglycosylase C-terminus (XET_C) domain. Transcriptional expression analysis exhibited that all BvXTHs were ubiquitously expressed in leaves, root hairs and tuberous roots, and most of them were up-regulated by brassinolide (BR), jasmonic acid (JA), abscisic acid (ABA) and gibberellic acid (GA3). Further mutant complementary experiment demonstrated that expression of BvXTH17 rescued the retarded growth phenotype of xth22, an Arabidopsis knock out mutant of AtXTH22. The findings in our work provide fundamental information on the structure and evolutionary relationship of the XTH family genes in sugar beet, and reveal the potential function of BvXTH17 in plant growth and hormone response.

Enzymes in 3D: Synthesis, remodelling, and hydrolysis of cell wall (1,3;1,4)-β-glucans

Recent breakthroughs in structural biology have provided valuable new insights into enzymes involved in plant cell wall metabolism. More specifically, the molecular mechanism of synthesis of (1,3;1,4)-β-glucans, which are widespread in cell walls of commercially important cereals and grasses, has been the topic of debate and intense research activity for decades. However, an inability to purify these integral membrane enzymes or apply transgenic approaches without interpretative problems associated with pleiotropic effects has presented barriers to attempts to define their synthetic mechanisms. Following the demonstration that some members of the CslF sub-family of GT2 family enzymes mediate (1,3;1,4)-β-glucan synthesis, the expression of the corresponding genes in a heterologous system that is free of background complications has now been achieved. Biochemical analyses of the (1,3;1,4)-β-glucan synthesized in vitro, combined with 3-dimensional (3D) cryogenic-electron microscopy and AlphaFold protein structure predictions, have demonstrated how a single CslF6 enzyme, without exogenous primers, can incorporate both (1,3)- and (1,4)-β-linkages into the nascent polysaccharide chain. Similarly, 3D structures of xyloglucan endo-transglycosylases and (1,3;1,4)-β-glucan endo- and exohydrolases have allowed the mechanisms of (1,3;1,4)-β-glucan modification and degradation to be defined. X-ray crystallography and multi-scale modeling of a broad specificity GH3 β-glucan exohydrolase recently revealed a previously unknown and remarkable molecular mechanism with reactant trajectories through which a polysaccharide exohydrolase can act with a processive action pattern. The availability of high-quality protein 3D structural predictions should prove invaluable for defining structures, dynamics, and functions of other enzymes involved in plant cell wall metabolism in the immediate future.

Engineering of substrate specificity in a plant cell-wall modifying enzyme through alterations of carboxyl-terminal amino acid residues

Structural determinants of substrate recognition remain inadequately defined in broad specific cell-wall modifying enzymes, termed xyloglucan xyloglucosyl transferases (XETs). Here, we investigate the Tropaeolum majus seed TmXET6.3 isoform, a member of the GH16_20 subfamily of the GH16 network. This enzyme recognises xyloglucan (XG)-derived donors and acceptors, and a wide spectrum of other chiefly saccharide substrates, although it lacks the activity with homogalacturonan (pectin) fragments. We focus on defining the functionality of carboxyl-terminal residues in TmXET6.3, which extend acceptor binding regions in the GH16_20 subfamily but are absent in the related GH16_21 subfamily. Site-directed mutagenesis using double to quintuple mutants in the carboxyl-terminal region - substitutions emulated on barley XETs recognising the XG/penta-galacturonide acceptor substrate pair - demonstrated that this activity could be gained in TmXET6.3. We demonstrate the roles of semi-conserved Arg238 and Lys237 residues, introducing a net positive charge in the carboxyl-terminal region (which complements a negative charge of the acidic penta-galacturonide) for the transfer of xyloglucan fragments. Experimental data, supported by molecular modelling of TmXET6.3 with the XG oligosaccharide donor and penta-galacturonide acceptor substrates, indicated that they could be accommodated in the active site. Our findings support the conclusion on the significance of positively charged residues at the carboxyl terminus of TmXET6.3 and suggest that a broad specificity could be engineered via modifications of an acceptor binding site. The definition of substrate specificity in XETs should prove invaluable for defining the structure, dynamics, and function of plant cell walls, and their metabolism; these data could be applicable in various biotechnologies.

Genome-wide identification and expression analysis of xyloglucan endotransglucosylase/hydrolase genes family in Salicaceae during grafting

BACKGROUND

Poplar (Populus cathayana)and willow (Salix rehderiana) are important fast-growing trees in China. Grafting plays an important role in improving plant stress resistance and construction of ornamental plants. It is found that willow scions grafted onto poplar rootstocks can form ornamental plants. However, this grafted combination has a low survival rate. Many studies have reported that the xyloglucan endotransglucosylase/hydrolase (XTH) family plays an important role in the healing process of grafts.

RESULTS

A total of 38 PtrXTHs and 32 SpuXTHs were identified in poplar and willow respectively, and were classified into three subfamilies. Tandem duplication was the main reason for the expansion of the PtrXTHs. Grafting treatment and Quantitative real time PCR (RT-qPCR) analysis revealed that five XTH genes differentially expressed between self-grafted and reciprocal grafted combinations. Specifically, the high expression levels of SrXTH16, SrXTH17, SrXTH25, PcXTH22 and PcXTH17 may contribute to the high survival rate of the grafted combination with willow scion and poplar rootstock. Subcellular localization identified that the SrXTH16, SrXTH17, SrXTH25, PcXTH17 and PcXTH22 proteins were located on the cell walls. Transcription factors (NAC, MYB and DOF) may regulate the five XTH genes.

CONCLUSIONS

This study provides a new understanding of the roles of PcXTH and SrXTH genes and their roles in grafting. Our results will give some hints to explore the molecular mechanisms of PcXTH and SrXTH genes involved in grafting in the future.

Analysis of the apoplast fluid proteome during the induction of systemic acquired resistance in Arabidopsis thaliana

Background

Plant-pathogen interactions occur in the apoplast comprising the cell wall matrix and the fluid in the extracellular space outside the plasma membrane. However, little is known regarding the contribution of the apoplastic proteome to systemic acquired resistance (SAR).

Methods

Specifically, SAR was induced by inoculating plants with Pst DC3000 avrRps4. The apoplast washing fluid (AWF) was collected from the systemic leaves of the SAR-induced or mock-treated plants. A label free quantitative proteomic analysis was performed to identified the proteins related to SAR in AWF.

Results

A total of 117 proteins were designated as differentially accumulated proteins (DAPs), including numerous pathogenesis-related proteins, kinases, glycosyl hydrolases, and redox-related proteins. Functional enrichment analyses shown that these DAPs were mainly enriched in carbohydrate metabolic process, cell wall organization, hydrogen peroxide catabolic process, and positive regulation of catalytic activity. Comparative analysis of proteome data indicated that these DAPs were selectively enriched in the apoplast during the induction of SAR.

Conclusions

The findings of this study indicate the apoplastic proteome is involved in SAR. The data presented herein may be useful for future investigations on the molecular mechanism mediating the establishment of SAR.

Identification and characterization of long noncoding RNAs in two contrasting olive (Olea europaea L.) genotypes subjected to aluminum toxicity

Aluminum (Al) toxcity is considered to be the primary factor limiting crop productivity in acidic soil. Many studies indicate that long non-coding RNAs (lncRNAs) fulfil a crucial role in plant growth and responses to different abiotic stress. However, identification and characterization of lncRNAs responsive to Al stress at a genome-wide level in olive tree is still lacking. Here, we performed comparative analysis on lncRNA transcriptome between Zhonglan (an Al-tolerant genotype) and Frantoio selezione (Al-sensitive) responding to Al exposure. A total of 19,498 novel lncRNAs were identified from both genotypes, and 6900 lncRNA-target pairs were identified as cis-acting and 2311 supposed to be trans-acting. Among them, 2076 lncRNAs were appraised as Al tolerance-associated lncRNAs due to their distinctly genotype-specific expression profiles under Al exposure. Target prediction and functional analyses revealed several key lncRNAs are related to genes encoding pectinesterases, xyloglucan endotransglucosylase/hydrolase, WRKY and MYB transcription factors, which mainly participate in the modification of cell wall for Al tolerance. Furthermore, gene co-expression network analysis showed 8 lncRNA-mRNA-miRNA modules participate in transcriptional regulation of downstream Al resistant genes. Our findings increased our understanding about the function of lncRNAs in responding to Al stress in olive and identified potential promising lncRNAs for further investigation.

Azospirillum brasilense activates peroxidase-mediated cell wall modification to inhibit root cell elongation

The molecular mechanism of beneficial bacterium Azospirillum brasilense-mediated root developmental remain elusive. A. brasilense elicited extensively transcriptional changes but inhibited primary root elongation in Arabidopsis. By analyzing root cell type-specific developmental markers, we demonstrated that A. brasilense affected neither overall organization nor cell division of primary root meristem. The cessation of primary root resulted from reduction of cell elongation, which is probably because of bacterially activated peroxidase that will lead to cell wall cross-linking at consuming of H2O2. The activated peroxidase combined with downregulated cell wall loosening enzymes consequently led to cell wall thickness, whereas inhibiting peroxidase restored root growth under A. brasilense inoculation. We further showed that peroxidase activity was probably promoted by cadaverine secreted by A. brasilense. These results suggest that A. brasilense inhibits root elongation by activating peroxidase and inducing cell wall modification in Arabidopsis, in which cadaverine released by A. brasilense is a potential signal compound.

A Surprising Diversity of Xyloglucan Endotransglucosylase/Hydrolase in Wheat: New in Sight to the Roles in Drought Tolerance

Drought has become a major limiting factor for wheat productivity, and its negative impact on crop growth is anticipated to increase with climate deterioration in arid areas. Xyloglucan endoglycosylases/hydrolases (XTHs) are involved in constructing and remodeling cell wall structures and play an essential role in regulating cell wall extensibility and stress responses. However, there are no systematic studies on the wheat XTH gene family. In this study, 71 wheat XTH genes (TaXTHs) were characterized and classified into three subgroups through phylogenetic analysis. Genomic replication promoted the expansion of TaXTHs. We found a catalytically active motif and a potential N-linked glycosylation domain in all TaXTHs. Further expression analysis revealed that many TaXTHs in the roots and shoots were significantly associated with drought stress. The wheat TaXTH12.5a gene was transferred into Arabidopsis to verify a possible role of TaXTHs in stress response. The transgenic plants possessed higher seed germination rates and longer roots and exhibited improved tolerance to drought. In conclusion, bioinformatics and gene expression pattern analysis indicated that the TaXTH genes played a role in regulating drought response in wheat. The expression of TaXTH12.5a enhanced drought tolerance in Arabidopsis and supported the XTH genes' role in regulating drought stress response in plants.

A high-confidence Physcomitrium patens plasmodesmata proteome by iterative scoring and validation reveals diversification of cell wall proteins during evolution

Plasmodesmata (PD) facilitate movement of molecules between plant cells. Regulation of this movement is still not understood. Plasmodesmata are hard to study, being deeply embedded within cell walls and incorporating several membrane types. Thus, structure and protein composition of PD remain enigmatic. Previous studies of PD protein composition identified protein lists with few validations, making functional conclusions difficult. We developed a PD scoring approach in iteration with large-scale systematic localization, defining a high-confidence PD proteome of Physcomitrium patens (HC300). HC300, together with bona fide PD proteins from literature, were placed in Pddb. About 65% of proteins in HC300 were not previously PD-localized. Callose-degrading glycolyl hydrolase family 17 (GHL17) is an abundant protein family with representatives across evolutionary scale. Among GHL17s, we exclusively found members of one phylogenetic clade with PD localization and orthologs occur only in species with developed PD. Phylogenetic comparison was expanded to xyloglucan endotransglucosylases/hydrolases and Exordium-like proteins, which also diversified into PD-localized and non-PD-localized members on distinct phylogenetic clades. Our high-confidence PD proteome HC300 provides insights into diversification of large protein families. Iterative and systematic large-scale localization across plant species strengthens the reliability of HC300 as basis for exploring structure, function, and evolution of this important organelle.

CiXTH29 and CiLEA4 Role in Water Stress Tolerance in Cichorium intybus Varieties

Drought causes massive crop quality and yield losses. Limiting the adverse effects of water deficits on crop yield is an urgent goal for a more sustainable agriculture. With this aim, six chicory varieties were subjected to drought conditions during seed germination and at the six week-old plant growth stage, in order to identify some morphological and/or molecular markers of drought resistance. Selvatica, Zuccherina di Trieste and Galatina varieties, with a high vegetative development, showed a major germination index, greater seedling development (6 days of growth) and a greater dehydration resistance (6 weeks of growth plus 10 days without water) than the other ones (Brindisina, Esportazione and Rossa Italiana). Due to the reported involvement, in the abiotic stress response, of xyloglucan endotransglucosylase/hydrolases (XTHs) and late embryogenesis abundant (LEA) multigene families, XTH29 and LEA4 expression profiles were investigated under stress conditions for all analyzed chicory varieties. We showed evidence that chicory varieties with high CiXTH29 and CiLEA4 basal expression and vegetative development levels better tolerate drought stress conditions than varieties that show overexpression of the two genes only in response to drought. Other specific morphological traits characterized almost all chicory varieties during dehydration, i.e., the appearance of lysigen cavities and a general increase of the amount of xyloglucans in the cell walls of bundle xylem vessels. Our results highlighted that high CiXTH29 and CiLEA4 basal expression, associated with a high level of vegetative growth, is a potential marker for drought stress tolerance.

Exogenous 6-BA inhibited hypocotyl elongation under darkness in Picea crassifolia Kom revealed by transcriptome profiling

Hypocotyl elongation is an important process in plant growth and development, and is under hormonal regulatory signaling pathways. In our study, exogenous 6-BA significantly inhibited Picea crassifolia hypocotyl elongation more than ethylene in the dark, indicating the existence of different regulatory strategies in conifers, therefore, the P. crassifolia transcriptome was studied to explore the responsive genes and their regulatory pathways for exogenous N⁶-benzyladenine (6-BA) inhibition of hypocotyl elongation using RNA-Sequencing approach. We present the first transcriptome assembly of P. crassifolia obtained from 24.38 Gb clean data. With lowly-expressed and short contigs excluded, the assembly contains roughly 130,612 unigenes with an N50 length of 1,278 bp. Differential expression analysis found 3,629 differentially expressed genes (DEGs) and found that the differential expression fold of genes was mainly concentrated between 2 and 8 (1 ≤ log2FoldChange ≤ 3). Functional annotation showed that the GO term with the highest number of enriched genes (83 unigenes) was the shoot system development (GO: 0048367) and the KEGG category, plant hormone signal transduction (ko04075), was enriched 30 unigenes. Further analysis revealed that several cytokinin dehydrogenase genes (PcCTD1, PcCTD3 and PcCTD6) catabolized cytokinins, while xyloglucan endotransglucosylase hydrolase gene (PcXTH31), WALLS ARE THIN 1-like gene (PcWAT1-1) and Small auxin-induced gene (PcSAUR15) were strongly repressed thus synergistically completing the inhibition of hypocotyl elongation in P. crassifolia. Besides, PcbHLH149, PcMYB44 and PcERF14 were predicted to be potential core TFs that may form a multi-layered regulatory network with the above proteins for the regulation of hypocotyl growth.

Populus endo-glucanase 16 localizes to the cell walls of developing tissues

The hemicelluloses comprise a group of matrix glycans that interact with cellulose microfibrils in plant cell walls and play important roles in establishing wall architecture. The structures of hemicelluloses are determined by carbohydrate-active enzymes (CAZymes) that synthesize, integrate, and break down these polymers. Specifically, endo-glucanase 16 (EG16) enzymes, which are related to the well-known xyloglucan endotransglycosylase/hydrolase (XTH) gene products in Glycoside Hydrolase Family 16 (GH16), have been implicated in the degradation of the β(1,4)-linked backbone of mixed-linkage β(1,3);β(1,4)-glucans (MLG) and xyloglucans. EG16 members are single-copy genes found in most plant clades but are absent from many eudicots, including the model plant Arabidopsis thaliana. Until recently, EG16 members had only been characterized in vitro, establishing their substrate specificity, protein structure, and phylogenetic history, but their biological function was unknown. Here we used a hybrid polar, Populus alba × Populus grandidentata (P39), as a model to examine EG16 expression, subcellular localization, and pheno- and chemotypes of EG16-downregulated P39 plants. Populus EG16 expression is strong in young tissues, but RNAi-mediated downregulation did not impact plant growth nor the fine structure of the hemicellulose xyloglucan, suggesting a restricted or currently unknown role in angiosperm physiology.

A wide foodomics approach coupled with metagenomics elucidates the environmental signature of potatoes

The term "terroir" has been widely employed to link differential geographic phenotypes with sensorial signatures of agricultural food products, influenced by agricultural practices, soil type, and climate. Nowadays, the geographical indications labeling has been developed to safeguard the quality of plant-derived food that is linked to a certain terroir and is generally considered as an indication of superior organoleptic properties. As the dynamics of agroecosystems are highly intricate, consisting of tangled networks of interactions between plants, microorganisms, and the surrounding environment, the recognition of the key molecular components of terroir fingerprinting remains a great challenge to protect both the origin and the safety of food commodities. Furthermore, the contribution of microbiome as a potential driver of the terroir signature has been underestimated. Herein, we present a first comprehensive view of the multi-omic landscape related to transcriptome, proteome, epigenome, and metagenome of the popular Protected Geographical Indication potatoes of Naxos.

Leaf physiology variations are modulated by natural variations that underlie stomatal morphology in Populus

Stomata are essential for photosynthesis and abiotic stress tolerance. Here, we used multiomics approaches to dissect the genetic architecture and adaptive mechanisms that underlie stomatal morphology in Populus tomentosa juvenile natural population (303 accessions). We detected 46 candidate genes and 15 epistatic gene-pairs, associated with 5 stomatal morphologies and 18 leaf development and photosynthesis traits, through genome-wide association studies. Expression quantitative trait locus mapping revealed that stomata-associated gene loci were significantly associated with the expression of leaf-related genes; selective sweep analysis uncovered significant differentiation in the allele frequencies of genes that underlie stomatal variations. An allelic regulatory network operating under drought stress and adequate precipitation conditions, with three key regulators (DUF538, TRA2 and AbFH2) and eight interacting genes, was identified that might regulate leaf physiology via modulation of stomatal shape and density. Validation of candidate gene variations in drought-tolerant and F₁ hybrid populations of P. tomentosa showed that the DUF538, TRA2 and AbFH2 loci cause functional stabilisation of spatiotemporal regulatory, whose favourable alleles can be faithfully transmitted to offspring. This study provides insights concerning leaf physiology and stress tolerance via the regulation of stomatal determination in perennial plants.

Identification of expansin genes as promoting or repressing factors for leaf elongation in tall fescue

Expansins are cell-wall loosening proteins involved in plant cell expansion and elongation. Objectives of this study were to identify expansins related to leaf elongation in a perennial grass species and determine the relationship between the expression of expansin genes and leaf elongation. A total of 20 expansin genes were identified in tall fescue (Festuca arundinacea), out of which nine genes belonged to the EXPA- and 11 to the EXPB subfamily. Two genotypes ("TF007" and "TF116") with different growth rates were used to determine the correlation between expansins and leaf growth. Among the 20 expansins, 16 were differentially expressed in the leaf growth zone in "TF007" and "TF116." The further analysis of gene expression in different leaf segments of "TF007" and "TF116" revealed that the expression level of FaEXPB16 was positively correlated with leaf elongation rate, and "TF007" had a higher leaf elongation rate than "TF116" due to the greater expression level of FaEXPB16. FaEXPA7 exhibited significantly higher expression level in leaves of the rapid-growing genotypes than the slow-growing genotypes, suggesting that FaEXPA7 acts as a positive regulator for leaf elongation. FaEXPA7 also exhibited its highest expression level in the cell division zone located in the leaf base. FaEXPB3, FaEXPB4-2, and FaEXPB11-2 showed a negative correlation with the leaf elongation rate in "TF007" and "TF116" and were highly expressed in leaves of the slow-growing genotypes. As promoting or repressing factors for leaf growth, these five expansins could be used as candidate genes in developing the rapid or slow-growing perennial grass species.

ROS and calcium oscillations are required for polarized root hair growth

Root hairs are filamentous extensions from epidermis of plant roots with growth limited to the apical dome. Cell expansion undergoes tightly regulated processes, including the coordination between cell wall loosening and cell wall crosslinking, to form the final shape and size. Tip-focused gradients and oscillations of reactive oxygen species (ROS) together with calcium ions (Ca²⁺) as indispensable regulated mechanisms control rapid and polarized elongation of root hair cells. ROS homeostasis mediated by plasma membrane-localized NADPH oxidases, known as respiratory burst oxidase homologues (RBOHs), and class III cell wall peroxidases (PRXs), modulates cell wall properties during cell expansion. The expression levels of RBOHC, an NADPH oxidase that produces ROS, and class III PRXs are directly upregulated by ROOT HAIR DEFECTIVE SIX-LIKE 4 (RSL4), encoding a basic-helix-loop-helix (bHLH) transcription factor, to modulate root hair elongation. Cyclic nucleotide-gated channels (CNGCs), as central regulators of Ca²⁺ oscillations, also regulate root hair extension. Here, we review how the gradients and oscillations of Ca²⁺ and ROS interact to promote the expansion of root hair cells.

Transcriptome profiling of celery petiole tissues reveals peculiarities of the collenchyma cell wall formation

Transcriptome and biochemical analyses are applied to individual plant cell types to reveal potential players involved in the molecular machinery of cell wall formation in specialized cells such as collenchyma. Plant collenchyma is a mechanical tissue characterized by an irregular, thickened cell wall and the ability to support cell elongation. The composition of the collenchyma cell wall resembles that of the primary cell wall and includes cellulose, xyloglucan, and pectin; lignin is absent. Thus, the processes associated with the formation of the primary cell wall in the collenchyma can be more pronounced compared to other tissues due to its thickening. Primary cell walls intrinsic to different tissues may differ in structure and composition, which should be reflected at the transcriptomic level. For the first time, we conducted transcriptome profiling of collenchyma strands isolated from young celery petioles and compared them with other tissues, such as parenchyma and vascular bundles. Genes encoding proteins involved in the primary cell wall formation during cell elongation, such as xyloglucan endotransglucosylase/hydrolases, expansins, and leucine-rich repeat proteins, were significantly activated in the collenchyma. As the key players in the transcriptome orchestra of collenchyma, xyloglucan endotransglucosylase/hydrolase transcripts were characterized in more detail, including phylogeny and expression patterns. The comprehensive approach that included transcriptome and biochemical analyses allowed us to reveal peculiarities of collenchyma cell wall formation and modification, matching the abundance of upregulated transcripts and their potential substrates for revealed gene products. As a result, specific isoforms of multigene families were determined for further functional investigation.

Identification of the Xyloglucan Endotransglycosylase/Hydrolase (XTH) Gene Family Members Expressed in Boehmeria nivea in Response to Cadmium Stress

Xyloglucan endotransglycosylase/hydrolase (XTH) genes play an important role in plant resistance to abiotic stress. However, systematic studies of the response of Boehmeria nivea (ramie) XTH genes (BnXTHs) to cadmium (Cd) stress are lacking. We sought to identify the BnXTH-family genes in ramie through bioinformatics analyses and to investigate their responses to Cd stress. We identified 19 members of the BnXTH gene family from the ramie genome, referred to as BnXTH1-19, among which BnXTH18 and BnXTH19 were located on no chromosomes and the remaining genes were unevenly distributed across 11 chromosomes. The 19 members were divided into four groups, Groups I/II/IIIA/IIIB, according to their phylogenetic relationships, and these groups were supported by analyses of intron-exon structure and conserved motif composition. A highly conserved catalytic site (HDEIDFEFLG) was observed in all BnXTH proteins. Additionally, three gene pairs (BnXTH6-BnXTH16, BnXTH8-BnXTH9, and BnXTH17-BnXTH18) were obtained with a fragment and tandem-repeat event analysis of the ramie genome. An analysis of cisregulatory elements revealed that BnXTH expression might be regulated by multiple hormones and abiotic and biotic stress responses. In particular, 17 cisregulatory elements related to abiotic and biotic stress responses and 11 cisregulatory elements related to hormone responses were identified. We also found that most BnXTH genes responded to Cd stress, and BnXTH1, BnXTH3, BnXTH6, and BnXTH15 were most likely to contribute to the Cd tolerance of ramie, as evidenced by the substantial increases in expression under Cd treatment. Heterologous expression of BnXTH1, BnXTH6, and BnXTH15 significantly enhanced the Cd tolerance of transgenic yeast cells. These results suggest that the BnXTH gene family is involved in Cd stress responses, laying a theoretical foundation for functional studies of BnXTH genes and the innovative breeding of Cd-tolerant ramie.

Synthetic fragments of plant polysaccharides as tools for cell wall biology

A sustainable bioeconomy that includes increased agricultural productivity and new technologies to convert renewable biomass to value-added products may help meet the demands of a growing world population for food, energy and materials. The potential use of plant biomass is determined by the properties of the cell walls, consisting of polysaccharides, proteins, and the polyphenolic polymer lignin. Comprehensive knowledge of cell wall glycan structure and biosynthesis is therefore essential for optimal utilization. However, several areas of plant cell wall research are hampered by a lack of available pure oligosaccharide samples that represent structural features of cell wall glycans. Here, we provide an update on recent chemical syntheses of plant cell wall oligosaccharides and their application in characterizing plant cell wall-directed antibodies and carbohydrate-active enzymes including glycosyltransferases and glycosyl hydrolases, with a particular focus on glycan array technology.

Genome-wide identification of XTH genes in Liriodendron chinense and functional characterization of LcXTH21

Liriodendron chinense is a relic tree species of the family Magnoliaceae with multiple uses in timber production, landscape decoration, and afforestation. L. chinense often experiences drought stress in arid areas. However, the molecular basis underlying the drought response of L. chinense remains unclear. Many studies have reported that the xyloglucan endotransglucosylase/hydrolase (XTH) family plays an important role in drought stress resistance. Hereby, to explore the drought resistance mechanism of L. chinense, we identify XTH genes on a genome-wide scale in L. chinense. A total of 27 XTH genes were identified in L. chinense, and these genes were classified into three subfamilies. Drought treatment and RT-qPCR analysis revealed that six LcXTH genes significantly responded to drought stress, especially LcXTH21. Hence, we cloned the LcXTH21 gene and overexpressed it in tobacco via gene transfer to analyze its function. The roots of transgenic plants were more developed than those of wild-type plants under different polyethylene glycol (PEG) concentration, and further RT-qPCR analysis showed that LcXTH21 highly expressed in root compared to aboveground organs, indicating that LcXTH21 may play a role in drought resistance through promoting root development. The results of this study provide new insights into the roles of LcXTH genes in the drought stress response. Our findings will also aid future studies of the molecular mechanisms by which LcXTH genes contribute to the drought response.

Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry

Xyloglucan endotransglycosylases (XETs) play key roles in the remodelling and reconstruction of plant cell walls. These enzymes catalyse homo-transglycosylation reactions with xyloglucan-derived donor and acceptor substrates and hetero-transglycosylation reactions with a variety of structurally diverse polysaccharides. In this work, we describe the basis of acceptor substrate binding specificity in non-specific Tropaeolum majus (TmXET6.3) and specific Populus tremula x tremuloides (PttXET16A) XETs, using molecular docking and molecular dynamics (MD) simulations combined with binding free energy calculations. The data indicate that the enzyme-donor (xyloglucan heptaoligosaccharide or XG-OS7)/acceptor complexes with the linear acceptors, where a backbone consisted of glucose (Glc) moieties linked via (1,4)- or (1,3)-β-glycosidic linkages, were bound stably in the active sites of TmXET6.3 and PttXET16A. Conversely, the acceptors with the (1,6)-β-linked Glc moieties were bound stably in TmXET6.3 but not in PttXET16A. When in the (1,4)-β-linked Glc containing acceptors, the saccharide moieties were replaced with mannose or xylose, they bound stably in TmXET6.3 but lacked stability in PttXET16A. MD simulations of the XET-donor/acceptor complexes with acceptors derived from (1,4;1,3)-β-glucans highlighted the importance of (1,3)-β-glycosidic linkages and side chain positions in the acceptor substrates. Our findings explain the differences in acceptor binding specificity between non-specific and specific XETs and associate theoretical to experimental data.

PagDET2 promotes cambium cell division and xylem differentiation in poplar stem

Secondary growth of the woody tree stem is governed by meristematic cell division and differentiation in the vascular cambium. Multiple hormonal signals and endogenous developmental programs regulate vascular cambium activity. Brassinosteroids (BRs) significantly promote secondary stem growth and wood formation in poplar trees. However, the underlying regulatory mechanisms of BRs within the vascular tissue remain unclear. Genetic and anatomical approaches were used here to elucidate the role of PagDET2, the rate-limiting enzyme for BRs biosynthesis, in regulating secondary vascular cambium activity in Populus. This study showed that the elevated endogenous castasterone (CS) levels in tree stems through overexpressing PagDET2 could enhance cambium meristem cell activity and xylem (XY) differentiation to promote secondary stem growth. RNA-seq analysis revealed that genes involved in BRs response, vascular cambium cell division, XY differentiation, and secondary cell wall synthesis were up-regulated.

Identifying plant genes shaping microbiota composition in the barley rhizosphere

A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant's capacity of shaping rhizosphere microbes.

Identification and expression analysis of xyloglucan endotransglucosylase/hydrolase (XTH) family in grapevine (Vitis vinifera L.)

Xyloglucan endotransglucosylases/hydrolases (XTH) are key enzymes in cell wall reformulation. They have the dual functions of catalyzing xyloglucan endotransglucosylase (XET) and xyloglucan endonuclease (XEH) activity and play a crucial role in the responses against abiotic stresses, such as drought, salinity, and freezing. However, a comprehensive analysis of the XTH family and its functions in grapevine (Vitis vinifera L.) has not yet been completed. In this study, 34 XTHs were identified in the whole grapevine genome and then named according to their distribution on chromosomes. Based on a phylogenetic analysis including Arabidopsis XTHs, the VvXTHs were classified into three groups. Cis-element analysis indicated that these family members are related to most abiotic stresses. We further selected 14 VvXTHs from different groups and then examined their transcription levels under drought and salt stress. The results indicated that the transcription levels of selected VvXTHs in the leaves and roots presented the largest changes, suggesting that VvXTHs are likely to take part in the responses to drought and salt stress in grapevines. These results provide useful evidence for the further investigation of VvXTHs function in response to abiotic stresses in grapevine.

Genome-wide identification of xyloglucan endotransglucosylase/hydrolase gene family members in peanut and their expression profiles during seed germination

Seed germination marks the beginning of a new plant life cycle. Improving the germination rate of seeds and the consistency of seedling emergence in the field could improve crop yields. Many genes are involved in the regulation of seed germination. Our previous study found that some peanut XTHs (xyloglucan endotransglucosylases/hydrolases) were expressed at higher levels at the newly germinated stage. However, studies of the XTH gene family in peanut have not been reported. In this study, a total of 58 AhXTH genes were identified in the peanut genome. Phylogenetic analysis showed that these AhXTHs, along with 33 AtXTHs from Arabidopsis and 61 GmXTHs from soybean, were classified into three subgroups: the I/II, IIIA and IIIB subclades. All AhXTH genes were unevenly distributed on the 18 peanut chromosomes, with the exception of chr. 07 and 17, and they had relatively conserved exon-intron patterns, most with three to four introns. Through chromosomal distribution pattern and synteny analysis, it was found that the AhXTH family experienced many replication events, including 42 pairs of segmental duplications and 23 pairs of tandem duplications, during genome evolution. Conserved motif analysis indicated that their encoded proteins contained the conserved ExDxE domain and N-linked glycosylation sites and displayed the conserved secondary structural loops 1-3 in members of the same group. Expression profile analysis of freshly harvested seeds, dried seeds, and newly germinated seeds using transcriptome data revealed that 26 AhXTH genes, which account for 45% of the gene family, had relatively higher expression levels at the seed germination stage, implying the important roles of AhXTHs in regulating seed germination. The results of quantitative real-time PCR also confirmed that some AhXTHs were upregulated during seed germination. The results of GUS histochemical staining showed that AhXTH4 was mainly expressed in germinated seeds and etiolated seedlings and had higher expression levels in elongated hypocotyls. AhXTH4 was also verified to play a crucial role in the cell elongation of hypocotyls during seed germination.

Selenate regulates the activity of cell wall enzymes to influence cell wall component concentration and thereby affects the uptake and translocation of Cd in the roots of Brassica rapa L

Selenium (Se) can be used to counteract cadmium (Cd) toxicity in plants. However, mechanisms underlying the alleviation of Cd toxicity by Se have not been completely elucidated, especially those by which Se reduces Cd translocation. A hydroponic experiment was performed to illustrate the regulatory mechanisms of Cd transport by selenate (Se (VI)) in pakchoi (Brassica rapa L., LvYou 102). The results showed that this plant had a high accumulation capacity for Cd, and Se(VI) addition restricted Cd translocation from roots to shoots. Se(VI) exposure stimulated the concentrations of pectins and hemicellulose II but reduced the concentration of hemicellulose I in the roots. In many cases, the enzymes pectin methylesterase, polygalacturonase, and β-galactosidase were dose-dependently triggered by Se(VI) under Cd exposure, but root calcium concentration was significantly lowered (p < 0.05). Xyloglucan endoglycosidase (hydrolase) was triggered by Se(VI) under 2 mg L^-1 Cd exposure and cellulase was generally activated by Se(VI) under Cd stress. The above results suggest that Se(VI) up-regulates pectin methylesterase activity, stimulates synthesis of pectins, and down-regulates root Ca concentration to release free carboxyl groups to combine Cd. In this study, the relationships between enzyme activity (e.g., peroxidase, superoxidase and β-galactosidase), hydrogen peroxide, cell wall structure strengthening/loosening, and Cd toxicity affected by Se(VI) were also discussed.

Transcriptome profiling of cashew apples (Anacardium occidentale) genotypes reveals specific genes linked to firmness and color during pseudofruit development

We found 34 and 71 key genes potentially involved in flavonoid biosynthesis and cell wall disassembly, respectively, which could be associated with specific peel coloration and softening of each genotype. Cashew apple (Anacardium occidentale) has a great economic importance worldwide due to its high nutritional value, peculiar flavor and aroma. During ripening, the peduncle develops different peel color and becomes quickly fragile due to its oversoftening, impacting its consumers' acceptance. In view of this, the understanding about its transcriptional dynamics throughout ripening is imperative. In this study, we performed a transcriptome sequencing of two cashew apple genotypes (CCP 76 and BRS 265), presenting different firmness and color peel, in the immature and ripe stages. Comparative transcriptome analysis between immature and ripe cashew apple revealed 4374 and 3266 differentially expressed genes (DEGs) to CCP 76 and BRS 265 genotypes, respectively. These genes included 71 and 34 GDEs involved in the cell wall disassembly and flavonoid biosynthesis, respectively, which could be associated with firmness loss and anthocyanin accumulation during cashew apple development. Then, softer peduncle of CCP 76 could be justified by down-regulated EXP and up-regulation of genes involved in pectin degradation (PG, PL and PAE) and in cell wall biosynthesis. Moreover, genes related to flavonoid biosynthesis (PAL, C4H and CHS) could be associated with early high accumulation of anthocyanin in red-peel peduncle of BRS 265. Finally, expression patterns of the selected genes were tested by real-time quantitative PCR (qRT-PCR), and the qRT-PCR results were consistent with transcriptome data. The information generated in this work will provide insights into transcriptome responses to cashew apple ripening and hence, it will be helpful for cashew breeding programs aimed at developing genotypes with improved quality traits.

SHORT-ROOT Controls Cell Elongation in the Etiolated Arabidopsis Hypocotyl

Transcriptional regulation, a core component of gene regulatory networks, plays a key role in controlling individual organism's growth and development. To understand how plants modulate cellular processes for growth and development, the identification and characterization of gene regulatory networks are of importance. The SHORT-ROOT (SHR) transcription factor is known for its role in cell divisions in Arabidopsis (Arabidopsis thaliana). However, whether SHR is involved in hypocotyl cell elongation remains unknown. Here, we reveal that SHR controls hypocotyl cell elongation via the transcriptional regulation of XTH18, XTH22, and XTH24, which encode cell wall remodeling enzymes called xyloglucan endotransglucosylase/hydrolases (XTHs). Interestingly, SHR activates transcription of the XTH genes, independently of its partner SCARECROW (SCR), which is different from the known mode of action. In addition, overexpression of the XTH genes can promote cell elongation in the etiolated hypocotyl. Moreover, confinement of SHR protein in the stele still induces cell elongation, despite the aberrant organization in the hypocotyl ground tissue. Therefore, it is likely that SHR-mediated growth is uncoupled from SHR-mediated radial patterning in the etiolated hypocotyl. Our findings also suggest that intertissue communication between stele and endodermis plays a role in coordinating hypocotyl cell elongation of the Arabidopsis seedling. Taken together, our study identifies SHR as a new crucial regulator that is necessary for cell elongation in the etiolated hypocotyl.

Emerging Roles of β-Glucanases in Plant Development and Adaptative Responses

Plant β-glucanases are enzymes involved in the synthesis, remodelling and turnover of cell wall components during multiple physiological processes. Based on the type of the glycoside bond they cleave, plant β-glucanases have been grouped into three categories: (i) β-1,4-glucanases degrade cellulose and other polysaccharides containing 1,4-glycosidic bonds to remodel and disassemble the wall during cell growth. (ii) β-1,3-glucanases are responsible for the mobilization of callose, governing the symplastic trafficking through plasmodesmata. (iii) β-1,3-1,4-glucanases degrade mixed linkage glucan, a transient wall polysaccharide found in cereals, which is broken down to obtain energy during rapid seedling growth. In addition to their roles in the turnover of self-glucan structures, plant β-glucanases are crucial in regulating the outcome in symbiotic and hostile plant-microbe interactions by degrading non-self glucan structures. Plants use these enzymes to hydrolyse β-glucans found in the walls of microbes, not only by contributing to a local antimicrobial defence barrier, but also by generating signalling glucans triggering the activation of global responses. As a counterpart, microbes developed strategies to hijack plant β-glucanases to their advantage to successfully colonize plant tissues. This review outlines our current understanding on plant β-glucanases, with a particular focus on the latest advances on their roles in adaptative responses.

Elastic and collapsible: current understanding of cell walls in succulent plants

Succulent plants represent a large functional group of drought-resistant plants that store water in specialized tissues. Several co-adaptive traits accompany this water-storage capacity to constitute the succulent syndrome. A widely reported anatomical adaptation of cell walls in succulent tissues allows them to fold in a regular fashion during extended drought, thus preventing irreversible damage and permitting reversible volume changes. Although ongoing research on crop and model species continuously reports the importance of cell walls and their dynamics in drought resistance, the cell walls of succulent plants have received relatively little attention to date, despite the potential of succulents as natural capital to mitigate the effects of climate change. In this review, we summarize current knowledge of cell walls in drought-avoiding succulents and their effects on tissue biomechanics, water relations, and photosynthesis. We also highlight the existing knowledge gaps and propose a hypothetical model for regulated cell wall folding in succulent tissues upon dehydration. Future perspectives of methodological development in succulent cell wall characterization, including the latest technological advances in molecular and imaging techniques, are also presented.

Genome-Wide Identification and Expression Analysis of XTH Gene Family during Flower-Opening Stages in Osmanthus fragrans

Osmanthus fragrans is an aromatic plant which is widely used in landscaping and garden greening in China. However, the process of flower opening is significantly affected by ambient temperature changes. Cell expansion in petals is the primary factor responsible for flower opening. Xyloglucan endoglycolase/hydrolase (XTH) is a cell-wall-loosening protein involved in cell expansion or cell-wall weakening. Through whole-genome analysis, 38 OfXTH genes were identified in O. fragrans which belong to the four main phylogenetic groups. The gene structure, chromosomal location, synteny relationship, and cis-acting elements prediction and expression patterns were analyzed on a genome-wide scale. The expression patterns showed that most OfXTHs were closely associated with the flower-opening period of O. fragrans. At the early flower-opening stage (S1 and S2), transcriptome and qRT-PCR analysis revealed the expression of OfXTH24, 27, 32, 35, and 36 significantly increased under low ambient temperature (19 °C). It is speculated that the five genes might be involved in the regulation of flower opening by responding to ambient temperature changes. Our results provide solid foundation for the functional analysis of OfXTH genes and help to explore the mechanism of flower opening responding to ambient temperature in O. fragrans.

Comparative efficacy of bio-selenium nanoparticles and sodium selenite on morpho-physiochemical attributes under normal and salt stress conditions, besides selenium detoxification pathways in Brassica napus L

Selenium nanoparticles (SeNPs) have attracted considerable attention globally due to their significant potential for alleviating abiotic stresses in plants. Accordingly, further research has been conducted to develop nanoparticles using chemical ways. However, our knowledge about the potential benefit or phytotoxicity of bioSeNPs in rapeseed is still unclear. Herein, we investigated the effect of bioSeNPs on growth and physiochemical attributes, and selenium detoxification pathways compared to sodium selenite (Se (IV)) during the early seedling stage under normal and salt stress conditions. Our findings showed that the range between optimal and toxic levels of bioSeNPs was wider than Se (IV), which increased the plant’s ability to reduce salinity-induced oxidative stress. BioSeNPs improved the phenotypic characteristics of rapeseed seedlings without the sign of toxicity, markedly elevated germination, growth, photosynthetic efficiency and osmolyte accumulation versus Se (IV) under normal and salt stress conditions. In addition to modulation of Na⁺ and K⁺ uptake, bioSeNPs minimized the ROS level and MDA content by activating the antioxidant enzymes engaged in ROS detoxification by regulating these enzyme-related genes expression patterns. Importantly, the main effect of bioSeNPs and Se (IV) on plant growth appeared to be correlated with the change in the expression levels of Se-related genes. Our qRT-PCR results revealed that the genes involved in Se detoxification in root tissue were upregulated upon Se (IV) treated seedlings compared to NPs, indicating that bioSeNPs have a slightly toxic effect under higher concentrations. Furthermore, bioSeNPs might improve lateral root production by increasing the expression level of LBD16. Taken together, transamination and selenation were more functional methods of Se detoxification and proposed different degradation pathways that synthesized malformed or deformed selenoproteins, which provided essential mechanisms to increase Se tolerance at higher concentrations in rapeseed seedlings. Current findings could add more knowledge regarding the mechanisms underlying bioSeNPs induced plant growth.

Reconsidering the function of the xyloglucan endotransglucosylase/hydrolase family

Plants possess an outer cell layer called the cell wall. This matrix comprises various molecules, such as polysaccharides and proteins, and serves a wide array of physiologically important functions. This structure is not static but rather flexible in response to the environment. One of the factors responsible for this plasticity is the xyloglucan endotransglucosylase/hydrolase (XTH) family, which cleaves and reconnects xyloglucan molecules. Since xyloglucan molecules have been hypothesised to tether cellulose microfibrils forming the main load-bearing network in the primary cell wall, XTHs have been thought to play a central role in cell wall loosening for plant cell expansion. However, multiple lines of recent evidence have questioned this classic model. Nevertheless, reverse genetic analyses have proven the biological importance of XTHs; therefore, a major challenge at present is to reconsider the role of XTHs in planta. Recent advances in analytical techniques have allowed for gathering rich information on the structure of the primary cell wall. Thus, the integration of accumulated knowledge in current XTH studies may offer a turning point for unveiling the precise functions of XTHs. In the present review, we redefine the biological function of the XTH family based on the recent architectural model of the cell wall. We highlight three key findings regarding this enzyme family: (1) XTHs are not strictly required for cell wall loosening during plant cell expansion but play vital roles in response to specific biotic or abiotic stresses; (2) in addition to their transglycosylase activity, the hydrolase activity of XTHs is involved in physiological benefits; and (3) XTHs can recognise a wide range of polysaccharides other than xyloglucans.

Highlighting the factors governing transglycosylation in the GH5_5 endo-1,4-β-glucanase RBcel1

Transglycosylating glycoside hydrolases (GHs) offer great potential for the enzymatic synthesis of oligosaccharides. Although knowledge is progressing, there is no unique strategy to improve the transglycosylation yield. Obtaining efficient enzymatic tools for glycan synthesis with GHs remains dependent on an improved understanding of the molecular factors governing the balance between hydrolysis and transglycosylation. This enzymatic and structural study of RBcel1, a transglycosylase from the GH5_5 subfamily isolated from an uncultured bacterium, aims to unravel such factors. The size of the acceptor and donor sugars was found to be critical since transglycosylation is efficient with oligosaccharides at least the size of cellotetraose as the donor and cellotriose as the acceptor. The reaction pH is important in driving the balance between hydrolysis and transglycosylation: hydrolysis is favored at pH values below 8, while transglycosylation becomes the major reaction at basic pH. Solving the structures of two RBcel1 variants, RBcel1_E135Q and RBcel1_Y201F, in complex with ligands has brought to light some of the molecular factors behind transglycosylation. The structure of RBcel1_E135Q in complex with cellotriose allowed a +3 subsite to be defined, in accordance with the requirement for cellotriose as a transglycosylation acceptor. The structure of RBcel1_Y201F has been obtained with several transglycosylation intermediates, providing crystallographic evidence of transglycosylation. The catalytic cleft is filled with (i) donors ranging from cellotriose to cellohexaose in the negative subsites and (ii) cellobiose and cellotriose in the positive subsites. Such a structure is particularly relevant since it is the first structure of a GH5 enzyme in complex with transglycosylation products that has been obtained with neither of the catalytic glutamate residues modified.

Physcomitrium (Physcomitrella) patens endo-glucanase 16 is involved in the cell wall development of young tissue

Plants maintain large repertoires of carbohydrate-active enzymes (CAZymes)-comprising between 3% and 10% of their genomes-to synthesize, modify, and degrade the polysaccharide components of the cell wall. We recently identified a unique group of plant endo-glucanases from Glycoside Hydrolase Family 16, viz. EG16 orthologs, which constitute a sister clade to the well-known XYLOGLUCAN ENDO-TRANSGLYCOSYLASE/HYDROLASE (XTH) gene products. Biochemical analysis of EG16 orthologs from poplar (Populus trichocarpa), grapevine (Vitis vinifera), and spreading earthmoss (Physcomitrium patens) has demonstrated that these endo-glucanases are distinctly active on cell wall matrix glycans, mixed-linkage β(1,3);β(1,4)-glucan and xyloglucan (XyG), and that enzyme structure and specificity is highly conserved across diverse plant lineages. However, the physiological role of EG16 orthologs in any species is presently unknown. To shed light on EG16 function in vivo, here we performed reverse genetics and protein localization analyses of the single EG16 ortholog in the model moss P. patens, where this gene is highly expressed in young, expanding tissues, particularly in protonema. Surprisingly, deletion of the PpEG16 gene by homologous recombination led to an increase in growth, as well as accelerated senescence. Notably, the PpEG16 protein was shown to co-localize with XyG in the cell wall of protonema tissue, specifically at cell tips, despite lacking a secretion signal peptide. Although the precise biological role of EG16 orthologs remains elusive, our results implicate these highly conserved glycoside hydrolases in cell wall polysaccharide remodeling and recycling. We anticipate that these foundational results will inform future studies on EG16 function across plant lineages.

Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera

In land plants, heteroblasty broadly refers to a drastic change in morphology during growth through ontogeny. Juniperus flaccida and Pinus cembroides are conifers of independent lineages known to exhibit leaf heteroblasty between the juvenile and adult life stage of development. Juvenile leaves of P. cembroides develop spirally on the main stem and appear decurrent, flattened, and needle-like; whereas adult photosynthetic leaves are triangular or semi-circular needle-like, and grow in whorls on secondary or tertiary compact dwarf shoots. By comparison, J. flaccida juvenile leaves are decurrent and needle-like, and adult leaves are compact, short, and scale-like. Comparative analyses were performed to evaluate differences in anatomy and gene expression patterns between developmental phases in both species. RNA from 12 samples was sequenced and analyzed with available software. They were assembled de novo from the RNA-Seq reads. Following assembly, 63,741 high-quality transcripts were functionally annotated in P. cembroides and 69,448 in J. flaccida. Evaluation of the orthologous groups yielded 4140 shared gene families among the four references (adult and juvenile from each species). Activities related to cell division and development were more abundant in juveniles than adults in P. cembroides, and more abundant in adults than juveniles in J. flaccida. Overall, there were 509 up-regulated and 81 down-regulated genes in the juvenile condition of P. cembroides and 14 up-regulated and 22 down-regulated genes in J. flaccida. Gene interaction network analysis showed evidence of co-expression and co-localization of up-regulated genes involved in cell wall and cuticle formation, development, and phenylpropanoid pathway, in juvenile P. cembroides leaves. Whereas in J. flaccida, differential expression and gene interaction patterns were detected in genes involved in photosynthesis and chloroplast biogenesis. Although J. flaccida and P. cembroides both exhibit leaf heteroblastic development, little overlap was detected, and unique genes and pathways were highlighted in this study.

Broad Specific Xyloglucan:Xyloglucosyl Transferases Are Formidable Players in the Re-Modelling of Plant Cell Wall Structures

Plant xyloglucan:xyloglucosyl transferases, known as xyloglucan endo-transglycosylases (XETs) are the key players that underlie plant cell wall dynamics and mechanics. These fundamental roles are central for the assembly and modifications of cell walls during embryogenesis, vegetative and reproductive growth, and adaptations to living environments under biotic and abiotic (environmental) stresses. XET enzymes (EC 2.4.1.207) have the β-sandwich architecture and the β-jelly-roll topology, and are classified in the glycoside hydrolase family 16 based on their evolutionary history. XET enzymes catalyse transglycosylation reactions with xyloglucan (XG)-derived and other than XG-derived donors and acceptors, and this poly-specificity originates from the structural plasticity and evolutionary diversification that has evolved through expansion and duplication. In phyletic groups, XETs form the gene families that are differentially expressed in organs and tissues in time- and space-dependent manners, and in response to environmental conditions. Here, we examine higher plant XET enzymes and dissect how their exclusively carbohydrate-linked transglycosylation catalytic function inter-connects complex plant cell wall components. Further, we discuss progress in technologies that advance the knowledge of plant cell walls and how this knowledge defines the roles of XETs. We construe that the broad specificity of the plant XETs underscores their roles in continuous cell wall restructuring and re-modelling.

Cryogenian Origin and Subsequent Diversification of the Plant Cell-Wall Enzyme XTH Family

All land plants encode large multigene families of xyloglucan endotransglucosylase/hydrolases (XTHs), plant-specific enzymes that cleave and reconnect plant cell-wall polysaccharides. Despite the ubiquity of these enzymes, considerable uncertainty remains regarding the evolutionary history of the XTH family. Phylogenomic and comparative analyses in this study traced the non-plant origins of the XTH family to Alphaproteobacteria ExoKs, bacterial enzymes involved in loosening biofilms, rather than Firmicutes licheninases, plant biomass digesting enzymes, as previously supposed. The relevant horizontal gene transfer (HGT) event was mapped to the divergence of non-swimming charophycean algae in the Cryogenian geological period. This HGT event was the likely origin of charophycean EG16-2s, which are putative intermediates between ExoKs and XTHs. Another HGT event in the Cryogenian may have led from EG16-2s or ExoKs to fungal Congo Red Hypersensitive proteins (CRHs) to fungal CRHs, enzymes that cleave and reconnect chitin and glucans in fungal cell walls. This successive transfer of enzyme-encoding genes may have supported the adaptation of plants and fungi to the ancient icy environment by facilitating their sessile lifestyles. Furthermore, several protein evolutionary steps, including coevolution of substrate-interacting residues and putative intra-family gene fusion, occurred in the land plant lineage and drove diversification of the XTH family. At least some of those events correlated with the evolutionary gain of broader substrate specificities, which may have underpinned the expansion of the XTH family by enhancing duplicated gene survival. Together, this study highlights the Precambrian evolution of life and the mode of multigene family expansion in the evolutionary history of the XTH family.

Gene Expression Profiles Suggest a Better Cold Acclimation of Polyploids in the Alpine Species Ranunculus kuepferi (Ranunculaceae)

Alpine habitats are shaped by harsh abiotic conditions and cold climates. Temperature stress can affect phenotypic plasticity, reproduction, and epigenetic profiles, which may affect acclimation and adaptation. Distribution patterns suggest that polyploidy seems to be advantageous under cold conditions. Nevertheless, whether temperature stress can induce gene expression changes in different cytotypes, and how the response is initialized through gene set pathways and epigenetic control remain vague for non-model plants. The perennial alpine plant Ranunculus kuepferi was used to investigate the effect of cold stress on gene expression profiles. Diploid and autotetraploid individuals were exposed to cold and warm conditions in climate growth chambers and analyzed via transcriptome sequencing and qRT-PCR. Overall, cold stress changed gene expression profiles of both cytotypes and induced cold acclimation. Diploids changed more gene set pathways than tetraploids, and suppressed pathways involved in ion/cation homeostasis. Tetraploids mostly activated gene set pathways related to cell wall and plasma membrane. An epigenetic background for gene regulation in response to temperature conditions is indicated. Results suggest that perennial alpine plants can respond to temperature extremes via altered gene expression. Tetraploids are better acclimated to cold conditions, enabling them to colonize colder climatic areas in the Alps.