Enzymic characterization of two recombinant xyloglucan endotransglucosylase/hydrolase (XTH) proteins of Arabidopsis and their effect on root growth and cell wall extension

Nanoparticles and root traits: mineral nutrition, stress tolerance and interaction with rhizosphere microbiota

MAIN CONCLUSION

This review article highlights a broader perspective of NPs and plant-root interaction by focusing on their beneficial and deleterious impacts on root system architecture (RSA). The root performs a vital function by securing itself in the soil, absorbing and transporting water and nutrients to facilitate plant growth and productivity. In dicots, the architecture of the root system (RSA) is markedly shaped by the development of the primary root and its branches, showcasing considerable adaptability in response to changes in the environment. For promoting agriculture and combating global food hunger, the use of nanoparticles (NPs) may be an exciting option, for which it is essential to understand the behaviour of plants under NPs exposure. The nature of NPs and their physicochemical characteristics play a significant role in the positive/negative response of roots and shoots. Root morphological features, such as root length, root mass and root development features, may regulated positively/negatively by different types of NPs. In addition, application of NPs may also enhance nutrient transport and soil fertility by the promotion of soil microorganisms including plant growth-promoting rhizobacteria (PGPRs) and also soil enzymes. Interestingly the interaction of nanomaterials (NMs) with rhizospheric bacteria can enhance plant development and soil health. However, some studies also suggested that the increased use of several types of engineered nanoparticles (ENPs) may disrupt the equilibrium of the soil-root interface and unsafe morphogenesis by causing the browning of roots and suppressing the growth of root and soil microbes. Thus, this review article has sought to compile a broader perspective of NPs and plant-root interaction by focusing on their beneficial or deleterious impacts on RSA.

PdRabG3f interfered with gibberellin-mediated internode elongation and xylem developing in poplar

As a member of the small GTPases family, Rab GTPases play a key role in specifying transport pathways in the intracellular membrane trafficking system and are involved in plant growth and development. By quantitative trait locus (QTL) mapping, PdRabG3f was identified as a candidate gene associated with shoot height in a hybrid offspring of Populus deltoides 'Danhong' × Populus simonii 'Tongliao1'. PdRabG3f localized to the nucleus, endoplasmic reticulum and tonoplast and was primarily expressed in the xylem and cambium. Overexpression of PdRabG3f in Populus alba × Populus glandulosa (84 K poplar) had inhibitory effects on vertical and radical growth. In the transgenic lines, there were evident changes in the levels of 15 gibberellin (GA) derivatives, and the application of exogenous GA3 partially restored the phenotypes mediated by GAs deficiency. The interaction between PdRabG3f and RIC4, which was the GA-responsive factor, provided additional explanation for PdRabG3f's inhibitory effect on poplar growth. RNA-seq analysis revealed differentially expressed genes (DEGs) associated with cell wall, xylem, and gibberellin response. PdRabG3f interfering endogenous GAs levels in poplar might involve the participation of MYBs and ultimately affected internode elongation and xylem development. This study provides a potential mechanism for gibberellin-mediated regulation of plant growth through Rab GTPases.

Transcription factor CsMYB36 regulates fruit neck length via mediating cell expansion in cucumber

The fruit neck is an important agronomic trait of cucumber (Cucumis sativus). However, the underlying genes and regulatory mechanisms involved in fruit neck development are poorly understood. We previously identified a cucumber yellow-green peel (ygp) mutant, whose causal gene is MYB DOMAIN PROTEIN 36 (CsMYB36). This study showed that the ygp mutant exhibited a shortened fruit neck and repressed cell expansion in the fruit neck. Further functional analysis showed that CsMYB36 was also a target gene, and its expression was enriched in the fruit neck. Overexpression of CsMYB36 in the ygp mutant rescued shortened fruit necks. Furthermore, transcriptome analysis and reverse transcription quantitative PCR (RT-qPCR) assays revealed that CsMYB36 positively regulates the expression of an expansin-like A3 (CsEXLA3) in the fruit neck, which is essential for cell expansion. Yeast 1-hybrid and dual-luciferase assays revealed that CsMYB36 regulates fruit neck elongation by directly binding to the promoter of CsEXLA3. Collectively, these findings demonstrate that CsMYB36 is an important gene in the regulation of fruit neck length in cucumber plants.

BnXTH1 regulates cadmium tolerance by modulating vacuolar compartmentalization and the cadmium binding capacity of cell walls in ramie (Boehmeria nivea)

Xyloglucan endotransglucosylase/hydrolases (XTH) are cell wall-modifying enzymes important in plant response to abiotic stress. However, the role of XTH in cadmium (Cd) tolerance in ramie remains largely unknown. Here, we identified and cloned BnXTH1, a member of the XTH family, in response to Cd stress in ramie. The BnXTH1 promoter (BnXTH1p) demonstrated that MeJA induces the response of BnXTH1p to Cd stress. Moreover, overexpressing BnXTH1 in Boehmeria nivea increased Cd tolerance by significantly increasing the Cd content in the cell wall and decreasing Cd inside ramie cells. Cadmium stress induced BnXTH1-expression and consequently increased xyloglucan endotransglucosylase (XET) activity, leading to high xyloglucan contents and increased hemicellulose contents in ramie. The elevated hemicellulose content increased Cd chelation onto the cell walls and reduced the level of intracellular Cd. Interestingly, overexpressing BnXTH1 significantly increased the content of Cd in vacuoles of ramie and vacuolar compartmentalization genes. Altogether, these results evidence that Cd stress induced MeJA accumulation in ramie, thus, activating BnXTH1 expression and increasing the content of xyloglucan to enhance the hemicellulose binding capacity and increase Cd chelation onto cell walls. BnXTH1 also enhances the vacuolar Cd compartmentalization and reduces the level of Cd entering the organelles and soluble solution.

Structure and growth of plant cell walls

Plant cells build nanofibrillar walls that are central to plant growth, morphogenesis and mechanics. Starting from simple sugars, three groups of polysaccharides, namely, cellulose, hemicelluloses and pectins, with very different physical properties are assembled by the cell to make a strong yet extensible wall. This Review describes the physics of wall growth and its regulation by cellular processes such as cellulose production by cellulose synthase, modulation of wall pH by plasma membrane H+-ATPase, wall loosening by expansin and signalling by plant hormones such as auxin and brassinosteroid. In addition, this Review discusses the nuanced roles, properties and interactions of cellulose, matrix polysaccharides and cell wall proteins and describes how wall stress and wall loosening cooperatively result in cell wall growth.

Transcriptomic analysis of the defense response in "Cabernet Sauvignon" grape leaf induced by Apolygus lucorum feeding

To investigate the molecular mechanism of the defense response of "Cabernet Sauvignon" grapes to feeding by Apolygus lucorum, high-throughput sequencing technology was used to analyze the transcriptome of grape leaves under three different treatments: feeding by A. lucorum, puncture injury, and an untreated control. The research findings indicated that the differentially expressed genes were primarily enriched in three aspects: cellular composition, molecular function, and biological process. These genes were found to be involved in 42 metabolic pathways, particularly in plant hormone signaling metabolism, plant-pathogen interaction, MAPK signaling pathway, and other metabolic pathways associated with plant-induced insect resistance. Feeding by A. lucorum stimulated and upregulated a significant number of genes related to jasmonic acid and calcium ion pathways, suggesting their crucial role in the defense molecular mechanism of "Cabernet Sauvignon" grapes. The consistency between the gene expression and transcriptome sequencing results further supports these findings. This study provides a reference for the further exploration of the defense response in "Cabernet Sauvignon" grapes by elucidating the expression of relevant genes during feeding by A. lucorum.

WOX2 functions redundantly with WOX1 and WOX4 to positively regulate seed germination in Arabidopsis

MAIN CONCLUSION

WOX family gene WOX2 is highly expressed during seed development, which functions redundantly with WOX1 and WOX4 to positively regulate seed germination. WOX (WUSCHEL-related homeobox) is a family of transcription factors in plants. They play essential roles in the regulation of plant growth and development, but their function in seed germination is not well understood. In this report, we show that WOX1, WOX2, and WOX4 are close homologues in Arabidopsis. WOX2 has a redundant function with WOX1 and WOX4, respectively, in seed germination. WOX2 is highly expressed during seed development, from the globular embryonic stage to mature dry seeds, and its expression is decreased after germination. Loss of function single mutant wox2, and double mutants wox1 wox2 and wox2 wox4-1 show decreased germination speed. WOX2 and WOX4 are essential for hypocotyl-radicle zone elongation during germination, potentially by promoting the expression of cell wall-related genes. We also found that WOX2 and WOX4 regulate germination through the gibberellin (GA) pathway. These results suggest that WOX2 and WOX4 integrate the GA pathway and downstream cell wall-related genes during germination.

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.

Biological control of potato common scab and growth promotion of potato by Bacillus velezensis Y6

Potato common scab, caused mainly by Streptomyces scabies, causes surface necrosis and reduces the economic value of potato tubers, but effective chemical control is still lacking. In this study, an attempt was made to control potato common scab by inoculating potatoes with Bacillus velezensis (B. velezensis) and to further investigate the mechanism of biological control. The results showed that B. velezensis Y6 could reduce the disease severity of potato common scab from 49.92 ± 25.74% [inoculated with Streptomyces scabies (S. scabies) only] to 5.56 ± 1.89% (inoculated with S. scabies and Y6 on the same day) and increase the potato yield by 37.32% compared with the control under pot experiment in this study. Moreover, in the field trial, it was found that Y6 could also significantly reduce disease severity from 13.20 ± 1.00% to 4.00 ± 0.70% and increase the potato yield from 2.07 ± 0.10 ton/mu to 2.87 ± 0.28 ton/mu (p < 0.01; Tukey's test). Furthermore, RNA-seq analysis indicated that 256 potato genes were upregulated and 183 potato genes were downregulated in response to B. velezensis Y6 inoculation. In addition, strain Y6 was found to induce the expression of plant growth-related genes in potato, including cell wall organization, biogenesis, brassinosteroid biosynthesis, and plant hormone transduction genes, by 1.01-4.29 times. As well as up-regulate hydroquinone metabolism-related genes and several transcription factors (bHLH, MYB, and NAC) by 1.13-4.21 times. In summary, our study will help to understand the molecular mechanism of biological control of potato common scab and improve potato yield.

Genetic architecture of the response of Arabidopsis thaliana to a native plant-growth-promoting bacterial strain

By improving plant nutrition and alleviating abiotic and biotic stresses, plant growth-promoting bacteria (PGPB) can help to develop eco-friendly and sustainable agricultural practices. Besides climatic conditions, soil conditions, and microbe-microbe interactions, the host genotype influences the effectiveness of PGPB. Yet, most GWAS conducted to characterize the genetic architecture of response to PGPB are based on non-native interactions between a host plant and PGPB strains isolated from the belowground compartment of other plants. In this study, a GWAS was set up under in vitro conditions to describe the genetic architecture of the response of Arabidopsis thaliana to the PGPB Pseudomonas siliginis, by inoculating seeds of 162 natural accessions from the southwest of France with one strain isolated from the leaf compartment in the same geographical region. Strong genetic variation of plant growth response to this native PGPB was observed at a regional scale, with the strain having a positive effect on the vegetative growth of small plants and a negative effect on the vegetative growth of large plants. The polygenic genetic architecture underlying this negative trade-off showed suggestive signatures of local adaptation. The main eco-evolutionary relevant candidate genes are involved in seed and root development.

Tissue-Specific Transcriptomes in the Secondary Cell Wall Provide an Understanding of Stem Growth Enhancement in Solidago canadensis during Invasion

Invasive plants generally present a significant enhancement in aboveground vegetative growth, which is mainly caused by variation in secondary cell wall (SCW) deposition and vascular tissue development. However, the coordination of the transcriptional regulators of SCW biosynthesis is complex, and a comprehensive regulation map has not yet been clarified at a transcriptional level to explain the invasive mechanism of S. canadensis. Here, RNA sequencing was performed in the phloem and xylem of two typical native (US01) and invasive (CN25) S. canadensis populations with different stem morphologies. A total of 296.14 million high-quality clean reads were generated; 438,605 transcripts and 156,968 unigenes were assembled; and 66,648 and 19,510 differential expression genes (DEGs) were identified in the phloem and xylem, respectively. Bioinformatics analysis indicated that the SCW transcriptional network was dramatically altered during the successful invasion of S.canadensis. Based on a comprehensive analysis of SCW deposition gene expression profiles, we revealed that the invasive population is dedicated to synthesizing cellulose and reducing lignification, leading to an SCW with high cellulose content and low lignin content. A hypothesis thus has been proposed to explain the enhanced stem growth of S. canadensis through the modification of the SCW composition.

Study on the Interactions of Cyclins with CDKs Involved in Auxin Signal during Leaf Development by WGCNA in Populus alba

Cell division plays an indispensable role in leaf morphogenesis, which is regulated via the complexes formed by cyclin and cyclin-dependent kinase (CDK). In this study, gene family analysis, exogenous auxin stimulation, RNA-seq and WGCNA analysis were all used to investigate the molecular mechanisms by which cell-cycle-related factors participated in the auxin signaling pathway on leaf morphogenesis. Sixty-three cyclin members and seventeen CDK members in Populus alba were identified and systematically analyzed. During the evolution, WGD was the main reason that resulted in the expansion of cyclin and CDK genes. Firstly, after a short time treating with auxin to matured leaves of seedlings, genes related to cell division including GRF and ARGOS were both upregulated to restart the transition of cells from G1-to-S phase. Secondly, with three days of continuous auxin stimulation to leaves at different developmental stages, leaves area variation, transcriptomes and hormones were analyzed. By PCA, PCoA and WGCNA analyses, the turquoise module was both positively related to leaf development and auxin. Based on the co-expression analysis and Y2H experiment, PoalbCYCD1;4, PoalbCYCD3;3 and PoalbCYCD3;5 were supposed to interact with PoalbCDKA;1, which could be the trigger to promote the G1-to-S phase transition. The ARF transcription factor might play the key role of connecting the auxin signaling pathway and cell division in leaf morphogenesis by affecting CYC-CDK complexes.

An analysis of differentially expressed and differentially m6A-modified transcripts in soybean roots treated with lead

Lead is one of the most common toxic heavy metal pollutants in nature, and exposure to lead can cause serious toxicity to many organisms. In this study, we collected root growth data from soybean plants exposed to lead for seven days and confirmed that lead significantly inhibited root growth. We performed a transcriptome-wide m6A methylation analysis to study the response of soybean RNA methylation groups to lead. The m6A modified regions were enriched near the 3'UTR region and stop codon, and m6A methylation was positively correlated with transcript abundance. In the presence of lead, the transcriptome range of m6A RNA methylation peaks increased, and we identified 1144 m6A modification peaks and 1094 differentially expressed genes. The integration of m6A methylation and transcriptomic results enabled us to identify 16 candidate genes whose transcripts were differentially methylated and differentially expressed under lead stress. Annotation results suggest that these genes may promote abiotic stress tolerance by impacting lead uptake, transport, and accumulation through ROS pathways, enzymes, transporters, and hormones. These results provide candidate genes for future studies of lead stress tolerance mechanisms in soybean roots and provide genetic resources for studying plant heavy metal stress in soybean breeding.

Transcriptome analysis provides insights into the cell wall and aluminum toxicity related to rusty root syndrome of Panax ginseng

Rusty root syndrome is a common and serious disease in the process of Panax ginseng cultivation. This disease greatly decreases the production and quality of P. ginseng and causes a severe threat to the healthy development of the ginseng industry. However, its pathogenic mechanism remains unclear. In this study, Illumina high-throughput sequencing (RNA-seq) technology was used for comparative transcriptome analysis of healthy and rusty root-affected ginseng. The roots of rusty ginseng showed 672 upregulated genes and 526 downregulated genes compared with the healthy ginseng roots. There were significant differences in the expression of genes involved in the biosynthesis of secondary metabolites, plant hormone signal transduction, and plant-pathogen interaction. Further analysis showed that the cell wall synthesis and modification of ginseng has a strong response to rusty root syndrome. Furthermore, the rusty ginseng increased aluminum tolerance by inhibiting Al entering cells through external chelating Al and cell wall-binding Al. The present study establishes a molecular model of the ginseng response to rusty roots. Our findings provide new insights into the occurrence of rusty root syndrome, which will reveal the underlying molecular mechanisms of ginseng response to this disease.

A genome-wide association study identifies novel players in Na and Fe homeostasis in Arabidopsis thaliana under alkaline-salinity stress

In nature, multiple stress factors occur simultaneously. The screening of natural diversity panels and subsequent Genome-Wide Association Studies (GWAS) is a powerful approach to identify genetic components of various stress responses. Here, the nutritional status variation of a set of 270 natural accessions of Arabidopsis thaliana grown on a natural saline-carbonated soil is evaluated. We report significant natural variation on leaf Na (LNa) and Fe (LFe) concentrations in the studied accessions. Allelic variation in the NINJA and YUC8 genes is associated with LNa diversity, and variation in the ALA3 is associated with LFe diversity. The allelic variation detected in these three genes leads to changes in their mRNA expression and correlates with plant differential growth performance when plants are exposed to alkaline salinity treatment under hydroponic conditions. We propose that YUC8 and NINJA expression patters regulate auxin and jasmonic signaling pathways affecting plant tolerance to alkaline salinity. Finally, we describe an impairment in growth and leaf Fe acquisition associated with differences in root expression of ALA3, encoding a phospholipid translocase active in plasma membrane and the trans Golgi network which directly interacts with proteins essential for the trafficking of PIN auxin transporters, reinforcing the role of phytohormonal processes in regulating ion homeostasis under alkaline salinity.

Genome-Wide Identification and Expression Analysis of the Xyloglucan Endotransglucosylase/Hydrolase Gene Family in Sweet Potato [Ipomoea batatas (L.) Lam]

The xyloglucan endotransglucosylase/hydrolase (XET/XEH, also named XTH) family is a multigene family, the function of which plays a significant role in cell-wall rebuilding and stress tolerance in plants. However, the specific traits of the XTH gene family members and their expression pattern in different tissues and under stress have not been carried out in sweet potato. Thirty-six XTH genes were identified in I. batatas, all of which had conserved structures (Glyco_hydro_16). Based on Neighbor-Joining phylogenetic analysis the IbXTHs can be divided into three subfamilies-the I/II, IIIA, and IIIB subfamilies, which were unevenly distributed on 13 chromosomes, with the exception of Chr9 and Chr15. Multiple cis-acting regions related to growth and development, as well as stress responses, may be found in the IbXTH gene promoters. The segmental duplication occurrences greatly aided the evolution of IbXTHs. The results of a collinearity analysis showed that the XTH genes of sweet potato shared evolutionary history with three additional species, including A. thaliana, G. max, and O. sativa. Additionally, based on the transcriptome sequencing data, the results revealed that the IbXTHs have different expression patterns in leaves, stems, the root body (RB), the distal end (DE), the root stock (RS), the proximal end (PE), the initiative storage root (ISR), and the fibrous root (FR), and many of them are well expressed in the roots. Differentially expressed gene (DEG) analysis of FRs after hormone treatment of the roots indicated that IbXTH28 and IbXTH30 are up-regulated under salicylic acid (SA) treatment but down-regulated under methyl jasmonate (MeJA) treatment. Attentionally, there were only two genes showing down-regulation under the cold and drought treatment. Collectively, all of the findings suggested that genes from the XTH family are crucial for root specificity. This study could provide a theoretical basis for further research on the molecular function of sweet potato XTH genes.

Genome-Wide Analysis of the AAAP Gene Family in Populus and Functional Analysis of PsAAAP21 in Root Growth and Amino Acid Transport

The adventitious root (AR) is the basis for successful propagation by plant cuttings and tissue culture and is essential for maintaining the positive traits of a variety. Members of the amino acid/auxin permease (AAAP) gene family play indispensable roles in various plant metabolisms and have few studies on root growth and amino acid transport. In this study, with a systematic bioinformatics analysis of the Populus AAAP family, 83 PtrAAAPs were identified from Populus trichocarpa and grouped into 8 subfamilies. Subsequently, chromosomal distribution, genetic structure, cis-elements analysis, and expression pattern analysis of the AAAP family were performed and the potential gene AAAP21 regulating root development was screened by combining the results of RNA-Seq and QTL mapping. PsAAAP21 was proven as promoting root development by enhancing AR formation. Differentially expressed genes (DEGs) from RNA-seq results of overexpressing lines were enriched to multiple amino acid-related pathways, and the amino acid treatment to transgenic lines indicated that PsAAAP21 regulated amino acid transport, including tyrosine, methionine, and arginine. Analysis of the AAAP gene family provided a theoretical basis for uncovering the functions of AAAP genes. The identification of PsAAAP21 on root promotion and amino acid transport in Populus will help with breeding new woody plant species with strong rooting ability.

Genome-wide analysis of the XTH gene family and functional analysis of DlXTH23.5/25 during early longan somatic embryogenesis

INTRODUCTION

Xyloglucan endotransglucosylase (XET)/hydrolase (XTH) is a cell wall-modifying protein that affects cell expansion and loosening of the cell wall.

RESULTS

This study focused on the regulatory mechanism of DlXTH genes during early somatic embryogenesis (SE) and the heat stress response in longan. Mining of the available D. longan genome sequence yielded 25 putative XTH genes. Transcript profiles based on RNA sequencing (RNA-seq) data showed that most of the 17 detected DlXTH genes were highly expressed in the embryogenic callus (EC) (8) and globular embryo (GE) (8), and 13 of them responded significantly to heat stress. The assay for transposase-accessible chromatin sequencing (ATAC-seq) data analysis showed that in terms of chromatin accessibility, 22 of the 25 DlXTH genes were open during early SE, and most of the peak DlXTH genes with transcription differences during early SE were associated with high levels of H3K4me1. The most differentially expressed genes, DlXTH23.5 and DlXTH25, were selected for analysis. According to subcellular localization and quantitative real-time PCR (qRT-PCR) analysis, DlXTH23.5/25, which encode cell membrane-localized proteins, were expressed at the highest level in the GE and significantly responded to heat stress. Dual-luciferase assays and transient transformation showed that the transcription factors (TFs) DlWRKY31, DlERF1, and DlERF5 might bind to the DlXTH23.5/25 promoters to activate gene transcription. Transient overexpression of TFs and DlXTH23.5/25 induced XET activity in Nicotiana benthamiana leaves. Under heat stress in the longan EC, the XET activities and expression levels of TFs and DlXTH23.5/25 were significantly increased, and a high concentration of XET might inhibit longan SE.

DISCUSSIONS

Thus, the regulatory network composed of DlXTH23.5/25 and its related TFs may regulate early longan SE and participate in the regulatory pathway of longan under heat stress via cell wall repair through the action of XET.

Shank-localized cell wall growth contributes to Arabidopsis root hair elongation

Root hairs are highly elongated tubular extensions of root epidermal cells with a plethora of physiological functions, particularly in establishing the root-rhizosphere interface. Anisotropic expansion of root hairs is generally thought to be exclusively mediated by tip growth-a highly controlled apically localized secretion of cell wall material-enriched vesicles that drives the extension of the apical dome. Here we show that tip growth is not the only mode of root hair elongation. We identified events of substantial shank-localized cell wall expansion along the polar growth axis of Arabidopsis root hairs using morphometric analysis with quantum dots. These regions expanded after in vivo immunolocalization using cell wall-directed antibodies and appeared as distinct bands that were devoid of cell wall labelling. Application of a novel click chemistry-enabled galactose analogue for pulse chase and real-time imaging allowed us to label xyloglucan, a major root hair glycan, and demonstrate its de novo deposition and enzymatic remodelling in these shank regions. Our data reveal a previously unknown aspect of root hair growth in which both tip- and shank-localized dynamic cell wall deposition and remodelling contribute to root hair elongation.

Identification of Key Genes during Ethylene-Induced Adventitious Root Development in Cucumber (Cucumis sativus L.)

Ethylene (ETH), as a key plant hormone, plays critical roles in various processes of plant growth and development. ETH has been reported to induce adventitious rooting. Moreover, our previous studies have shown that exogenous ETH may induce plant adventitious root development in cucumber (Cucumis sativus L.). However, the key genes involved in this process are still unclear. To explore the key genes in ETH-induced adventitious root development, we employed a transcriptome technique and revealed 1415 differentially expressed genes (DEGs), with 687 DEGs up-regulated and 728 DEGs down-regulated. Using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, we further identified critical pathways that were involved in ETH-induced adventitious root development, including carbon metabolism (starch and sucrose metabolism, glycolysis/gluconeogenesis, citrate cycle (TCA cycle), oxidative phosphorylation, fatty acid biosynthesis, and fatty acid degradation), secondary metabolism (phenylalanine metabolism and flavonoid biosynthesis) and plant hormone signal transduction. In carbon metabolism, ETH reduced the content of sucrose, glucose, starch, the activity of sucrose synthase (SS), sucrose–phosphate synthase (SPS) and hexokinase (HK), and the expressions of CsHK2, pyruvate kinase2 (CsPK2), and CsCYP86A1, whereas it enhanced the expressions of β-amylase 1 (CsBAM1) and β-amylase 3 (CsBAM3). In secondary metabolism, the transcript levels of phenylalanine ammonia-lyase (CsPAL) and flavonoid 3′-monooxygenase (CsF3′M) were negatively regulated, and that of primary-amine oxidase (CsPAO) was positively regulated by ETH. Additionally, the indole-3-acetic acid (IAA) content and the expressions of auxin and ETH signaling transduction-related genes (auxin transporter-like protein 5 (CsLAX5), CsGH3.17, CsSUAR50, and CsERS) were suppressed, whereas the abscisic acid (ABA) content and the expressions of ABA and BR signaling transduction-related genes (CsPYL1, CsPYL5, CsPYL8, BRI1-associated kinase 1 (CsBAK1), and CsXTH3) were promoted by ETH. Furthermore, the mRNA levels of these genes were confirmed by real-time PCR (RT-qPCR). These results indicate that genes related to carbon metabolism, secondary metabolite biosynthesis, and plant hormone signaling transduction are involved in ETH-induced adventitious root development. This work identified the key pathways and genes in ETH-induced adventitious rooting in cucumber, which may provide new insights into ETH-induced adventitious root development and will be useful for investigating the molecular roles of key genes in this process in further studies.

The peptide SCOOP12 acts on reactive oxygen species homeostasis to modulate cell division and elongation in Arabidopsis primary root

Small secreted peptides have been described as key contributors to complex signalling networks that control plant development and stress responses. The Brassicaceae-specific PROSCOOP family encodes precursors of Serine riCh endOgenOus Peptides (SCOOPs). In Arabidopsis SCOOP12 has been shown to promote the defence response against pathogens and to be involved in root development. Here, we explore its role as a moderator of Arabidopsis primary root development. We show that the PROSCOOP12 null mutation leads to longer primary roots through the development of longer differentiated cells while PROSCOOP12 overexpression induces dramatic plant growth impairments. In comparison, the exogenous application of synthetic SCOOP12 peptide shortens roots through meristem size and cell length reductions. Moreover, superoxide anion (O2·-) and hydrogen peroxide (H2O2) production in root tips vary according to SCOOP12 abundance. By using reactive oxygen species scavengers that suppress the proscoop12 phenotype, we showed that root growth regulation by SCOOP12 is associated with reactive oxygen species metabolism. Furthermore, our results suggest that peroxidases act as potential SCOOP12 downstream targets to regulate H2O2 production, which in turn triggers cell wall modifications in root. Finally, a massive transcriptional reprogramming, including the induction of genes from numerous other pathways, including ethylene, salicylic acid, and glucosinolates biosynthesis, was observed, emphasizing its dual role in defence and development.

Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia

Hypoxia is an abiotic stress in plants. Flooding resulting from climate change is a major crop threat that increases the risk of hypoxic stress. The molecular mechanisms underlying hypoxia in plants were elucidated in recent years, but new genes related to this stress remain to be discovered. Thus, we aimed to perform a meta-analysis of the RNA sequencing (RNA-Seq) data of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) under hypoxia. We collected 29 (Arabidopsis) and 26 (rice) pairs of RNA-Seq data involving hypoxic (including submergence) and normoxic (control) treatments and extracted the genes that were commonly upregulated or downregulated in the majority of the experiments. The meta-analysis revealed 40 and 19 commonly upregulated and downregulated genes, respectively, in the two species. Several WRKY transcription factors and cinnamate-4-hydroxylase were commonly upregulated, but their involvement in hypoxia remains unclear. Our meta-analysis identified candidate genes for novel molecular mechanisms in plants under hypoxia.

Elongating Effect of the Peptide AEDL on the Root of Nicotiana tabacum under Salinity

The overall survival of a plant depends on the development, growth, and functioning of the roots. Root development and growth are not only genetically programmed but are constantly influenced by environmental factors, with the roots adapting to such changes. The peptide AEDL (alanine–glutamine acid–asparagine acid–leucine) at a concentration of 10⁻⁷ M had an elongating effect on the root cells of Nicotiana tabacum seedlings. The action of this peptide at such a low concentration is similar to that of peptide phytohormones. In the presence of 150 mM NaCl, a strong distortion in the development and architecture of the tobacco roots was observed. However, the combined presence of AEDL and NaCl resulted in normal root development. In the presence of AEDL, reactive oxygen species (ROS) were detected in the elongation and root hair zones of the roots. The ROS marker fluorescence intensity in plant cells grown with AEDL was much lower than that of plant cells grown without the peptide. Thus, AEDL protected the root tissue from damage by oxidative stress caused by the toxic effects of NaCl. Localization and accumulation of AEDL at the root were tissue-specific. Fluorescence microscopy showed that FITC-AEDL predominantly localized in the zones of elongation and root hairs, with insignificant localization in the meristem zone. AEDL induced a change in the structural organization of chromatin. Structural changes in chromatin caused significant changes in the expression of numerous genes associated with the development and differentiation of the root system. In the roots of tobacco seedlings grown in the presence of AEDL, the expression of WOX family genes decreased, and differentiation of stem cells increased, which led to root elongation. However, in the presence of NaCl, elongation of the tobacco root occurred via a different mechanism involving genes of the expansin family that weaken the cell wall in the elongation zone. Root elongation of plants is of fundamental importance in biology and is especially relevant to crop production as it can affect crop yields.

Narrow lpa1 Metaxylems Enhance Drought Tolerance and Optimize Water Use for Grain Filling in Dwarf Rice

Rice cultivation needs extensive amounts of water. Moreover, increased frequency of droughts and water scarcity has become a global concern for rice cultivation. Hence, optimization of water use is crucial for sustainable agriculture. Here, we characterized Loose Plant Architecture 1 (LPA1) in vasculature development, water transport, drought resistance, and grain yield. We performed genetic combination of lpa1 with semi-dwarf mutant to offer the optimum rice architecture for more efficient water use. LPA1 expressed in pre-vascular cells of leaf primordia regulates genes associated with carbohydrate metabolism and cell enlargement. Thus, it plays a role in metaxylem enlargement of the aerial organs. Narrow metaxylem of lpa1 exhibit leaves curling on sunny day and convey drought tolerance but reduce grain yield in mature plants. However, the genetic combination of lpa1 with semi-dwarf mutant (dep1-ko or d2) offer optimal water supply and drought resistance without impacting grain-filling rates. Our results show that water use, and transports can be genetically controlled by optimizing metaxylem vessel size and plant height, which may be utilized for enhancing drought tolerance and offers the potential solution to face the more frequent harsh climate condition in the future.

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.

Forgotten Actors: Glycoside Hydrolases During Elongation Growth of Maize Primary Root

Plant cell enlargement is coupled to dynamic changes in cell wall composition and properties. Such rearrangements are provided, besides the differential synthesis of individual cell wall components, by enzymes that modify polysaccharides in muro. To reveal enzymes that may contribute to these modifications and relate them to stages of elongation growth in grasses, we carried out a transcriptomic study of five zones of the primary maize root. In the initiation of elongation, significant changes occur with xyloglucan: once synthesized in the meristem, it can be linked to other polysaccharides through the action of hetero-specific xyloglucan endotransglycosidases, whose expression boosts at this stage. Later, genes for xyloglucan hydrolases are upregulated. Two different sets of enzymes capable of modifying glucuronoarabinoxylans, mainly bifunctional α-arabinofuranosidases/β-xylosidases and β-xylanases, are expressed in the maize root to treat the xylans of primary and secondary cell walls, respectively. The first set is highly pronounced in the stage of active elongation, while the second is at elongation termination. Genes encoding several glycoside hydrolases that are able to degrade mixed-linkage glucan are downregulated specifically at the active elongation. It indicates the significance of mixed-linkage glucans for the cell elongation process. The possibility that many glycoside hydrolases act as transglycosylases in muro is discussed.

The Xyloglucan Endotransglucosylase/Hydrolase Gene XTH22/TCH4 Regulates Plant Growth by Disrupting the Cell Wall Homeostasis in Arabidopsis under Boron Deficiency

TCH4 is a xyloglucan endotransglucosylase/hydrolase (XTH) family member. Extensive studies have shown that XTHs are very important in cell wall homeostasis for plant growth and development. Boron (B), as an essential micronutrient for plants, plays an essential role in the cross-linking of cell wall pectin. However, the effect of B on cell wall organization is unclear. This study aimed to explore the mechanism of plant adaption to B stress by investigating the role of TCH4 in cell wall homeostasis. We conducted both plate and hydroponic cultures of wild-type Col-0 and overexpression and gene knockout lines of XTH22/TCH4 to analyze the phenotype, components, and characteristics of the cell wall using immunofluorescence, atomic force microscopy (AFM), and transmission electron microscopy (TEM). B deficiency induces the expression of TCH4. The overexpression lines of TCH4 presented more sensitivity to B deficiency than the wild-type Col-0, while the knockout lines of TCH4 were more resistant to low B stress. Up-regulation of TCH4 influenced the ratio of chelator-soluble pectin to alkali-soluble pectin and decreased the degree of methylesterification of pectin under B-deficient conditions. Moreover, we found that B deficiency disturbed the arrangement of cellulose, enlarged the gap between cellulose microfibrils, and decreased the mechanical strength of the cell wall, leading to the formation of a thickened and deformed triangular region of the cell wall. These symptoms were more profound in the TCH4 overexpression lines. Consistently, compared with Col-0, the O₂^- and MDA contents in the TCH4 overexpression lines increased under B-deficient conditions. This study identified the B-deficiency-induced TCH4 gene, which regulates cell wall homeostasis to influence plant growth under B-deficient conditions.

The XTH Gene Family in Schima superba: Genome-Wide Identification, Expression Profiles, and Functional Interaction Network Analysis

Xyloglucan endotransglucosylase/hydrolase (XTH), belonging to glycoside hydrolase family 16, is one of the key enzymes in plant cell wall remodeling. Schima superba is an important timber and fireproof tree species in southern China. However, little is known about XTHs in S. superba. In the present study, a total of 34 SsuXTHs were obtained, which were classified into three subfamilies based on the phylogenetic relationship and unevenly distributed on 18 chromosomes. Furthermore, the intron-exon structure and conserved motif composition of them supported the classification and the members belonging to the same subfamily shared similar gene structures. Segmental and tandem duplication events did not lead to SsuXTH gene family expansion, and strong purifying selection pressures during evolution led to similar structure and function of SsuXTH gene family. The interaction network and cis-acting regulatory elements analysis revealed the SsuXTH expression might be regulated by multiple hormones, abiotic stresses and transcription factors. Finally, expression profiles and GO enrichment analysis showed most of the tandem repeat genes were mainly expressed in the phloem and xylem and they mainly participated in glycoside metabolic processes through the transfer and hydrolysis of xyloglucan in the cell wall and then regulated fiber elongation.

Proteomic and physiological analysis provides an elucidation of Fusarium proliferatum infection causing crown rot on banana fruit

Fusarium proliferatum causes the crown rot of harvested banana fruit but the underling infection mechanism remains unclear. Here, proteomic changes of the banana peel with and without inoculation of F. proliferatum were evaluated. In addition, we investigated the effects of F. proliferatum infection on cell structure, hormone content, primary metabolites and defense-related enzyme activities in the banana peel. Our results showed that F. proliferatum infection mainly affects cell wall components and inhibits the activities of polyphenoloxidase, peroxidase, and chitinase. Gel free quantitative proteomic analysis showed 92 down-regulated and 29 up-regulated proteins of banana peel after F. proliferatum infection. These proteins were mainly related to defense response to biotic stress, chloroplast structure and function, JA signaling pathway, and primary metabolism. Although jasmonic acid (JA) content and JA signaling component coronatine-insensitive (COI) protein were induced by F. proliferatum infection, JA-responsible defense genes/proteins were downregulated. In contrast, expression of senescence-related genes was induced by F. proliferatum, indicating that F. proliferatum modulated the JA signaling to accelerate the senescence of banana fruit. Additionally, salicylic acid (SA) content and SA signaling for resistance acquisition were inhibited by F. proliferatum. Taken together, these results suggest that F. proliferatum depolymerizes the cell wall barrier, impairs the defense system in banana fruit, and activates non-defensive JA-signaling pathway accelerated the senescence of banana fruit. This study provided the elucidation of the prominent pathways disturbed by F. proliferatum in banana fruit, which will facilitate the development of a new strategy to control crown rot of banana fruit and improvement of banana cultivars.

PERK13 modulates phosphate deficiency-induced root hair elongation in Arabidopsis

Phosphate starvation (-Pi)-induced root hair is crucial for enhancing plants' Pi absorption. Proline-rich extensin-like receptor kinase 13 (PERK13) is transcriptionally induced by -Pi and co-expressed with genes associated with root hair growth. However, how PERK13 participates in -Pi-induced root hair growth remains unclear. Here, we found that PERK13 was transcriptionally responsive to Pi, nitrogen, and iron deficiencies. Loss of PERK13 function (perk13) enhanced root hair growth under Pi/nitrogen limitation. Similar phenotype was also observed in transgenic lines overexpressing PERK13 (PERK13ox). Under -Pi, both perk13 and PERK13ox showed prolonged root hair elongation and increased reactive oxygen species (ROS). Deletion analysis showed, in PERK13ox, the extracellular domain was indispensable for PERK13 in -Pi-induced root hair growth. Different transcription profiles were observed under -Pi between perk13 and PERK13ox with the jasmonate zim-domain genes being repressed in perk13 and genes involved in cell wall remodeling being increased in PERK13ox. Taken together, we demonstrated that PERK13 participates in -Pi-induced root hair growth probably via regulating root hair elongation and the generation of ROS. Our study also suggested PERK13 probably being a vital hub coupling the environmental cues and root hair growth, and might play dual roles in -Pi-induced root hair growth via different processes.

Elongation of wood fibers combines features of diffuse and tip growth

Xylem fibers are highly elongated cells that are key constituents of wood, play major physiological roles in plants, comprise an important terrestrial carbon reservoir, and thus have enormous ecological and economic importance. As they develop, from fusiform initials, their bodies remain the same length while their tips elongate and intrude into intercellular spaces. To elucidate mechanisms of tip elongation, we studied the cell wall along the length of isolated, elongating aspen xylem fibers and used computer simulations to predict the forces driving the intercellular space formation required for their growth. We found pectin matrix epitopes (JIM5, LM7) concentrated at the tips where cellulose microfibrils have transverse orientation, and xyloglucan epitopes (CCRC-M89, CCRC-M58) in fiber bodies where microfibrils are disordered. These features are accompanied by changes in cell wall thickness, indicating that while the cell wall elongates strictly at the tips, it is deposited all over fibers. Computer modeling revealed that the intercellular space formation needed for intrusive growth may only require targeted release of cell adhesion, which allows turgor pressure in neighboring fiber cells to 'round' the cells creating spaces. These characteristics show that xylem fibers' elongation involves a distinct mechanism that combines features of both diffuse and tip growth.

Comparative transcriptome analysis reveals differential gene expression in sterile and fertile rubber tree varieties during flower bud differentiation

Plant male sterility (MS) is an important agronomic trait that provides an efficient tool for hybridization and heterosis utilization of crops. Based on phenotypic and cytological observations, our study performed a multi-comparison transcriptome analysis strategy on multiple sterile and fertile rubber tree varieties using RNA-seq. Compared with the male-fertile varieties, a total of 1590 differentially expressed genes (DEGs) were detected in male-sterile varieties, including 970 up-regulated and 620 down-regulated transcripts in sterile varieties. Key DEGs were further assessed focusing on anther development, microsporogenesis and plant hormone metabolism. Twenty DEGs were selected randomly to validate transcriptome data using quantitative real-time PCR (qRT-PCR). Eleven key genes were subjected to expression pattern analysis using qRT-PCR and fluorescence in situ hybridization. Among them, nine genes, i.e., A6, GAI1, ACA7, TKPR1, CYP704B1, XTH26, MS1, MS35 and MYB33, that regulate callose metabolism, pollen wall formation, tapetum and microspores development were identified as candidate male-sterile genes. These findings provide insights into the molecular mechanism of male sterility in rubber tree.

Phytohormone signalling and cross-talk to alleviate aluminium toxicity in plants

Aluminium (Al) is one of the most abundant metals in earth crust, which becomes toxic to the plants growing in acidic soil. Phytohormones like ethylene, auxin, cytokinin, abscisic acid, jasmonic acid and gibberellic acid are known to play important role in regulating Al toxicity tolerance in plants. Exogenous applications of auxin, cytokinin and abscisic acid have shown significant effect on Al-induced root growth inhibition. Moreover, ethylene and cytokinin act synergistically with auxin in responding against Al toxicity. A number of studies showed that phytohormones play vital roles in controlling root responses to Al toxicity by modulating reactive oxygen species (ROS) signalling, cell wall modifications, organic acid exudation from roots and expression of Al responsive genes and transcription factors. This review provides a summary of recent studies related to involvement of phytohormone signalling and cross-talk with other pathways in regulating response against Al toxicity in plants.

Identification of tomato root growth regulatory genes and transcription factors through comparative transcriptomic profiling of different tissues

Tomato is an economically important vegetable crop and a model for development and stress response studies. Although studied extensively for understanding fruit ripening and pathogen responses, its role as a model for root development remains less explored. In this study, an Illumina-based comparative differential transcriptomic analysis of tomato root with different aerial tissues was carried out to identify genes that are predominantly expressed during root growth. Sequential comparisons revealed ~ 15,000 commonly expressed genes and ~ 3000 genes of several classes that were mainly expressed or regulated in roots. These included 1069 transcription factors (TFs) of which 100 were differentially regulated. Prominent amongst these were members of families encoding Zn finger, MYB, ARM, bHLH, AP2/ERF, WRKY and NAC proteins. A large number of kinases, phosphatases and F-box proteins were also expressed in the root transcriptome. The major hormones regulating root growth were represented by the auxin, ethylene, JA, ABA and GA pathways with root-specific expression of certain components. Genes encoding carbon metabolism and photosynthetic components showed reduced expression while several protease inhibitors were amongst the most highly expressed. Overall, the study sheds light on genes governing root growth in tomato and provides a resource for manipulation of root growth for plant improvement.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01015-0.

HOMEODOMAIN PROTEIN8 mediates jasmonate-triggered trichome elongation in tomato

Plant hormones can adjust the physiology and development of plants to enhance their adaptation to biotic and abiotic challenges. Jasmonic acid (JA), one of the immunity hormones in plants, triggers genome-wide transcriptional changes in response to insect attack and wounding. Although JA is known to affect the development of trichomes, epidermal appendages that form a protective barrier against various stresses, it remains unclear how JA interacts with developmental programs that regulate trichome development. In this study, we show that JA affects trichome length in tomato by releasing the transcriptional repression mediated by Jasmonate ZIM (JAZ) proteins. We identified SlJAZ4, a negative regulator preferentially expressed in trichomes, as the critical component in JA signaling in tomato trichomes. We also identified a homeodomain-leucine zipper gene, SlHD8, as the downstream regulator of JA signaling that promotes trichome elongation. SlHD8 is also highly expressed in trichomes and physically interacts with SlJAZ4. Loss-of-function mutations in SlHD8 caused shorter trichomes, a phenotype that was only partially rescued by methyl jasmonate treatment. Our dual-luciferase and chromatin immunoprecipitation-quantitative PCR assays revealed that SlHD8 regulates trichome elongation by directly binding to the promoters of a set of cell-wall-loosening protein genes and activating their transcription. Together, our findings define SlHD8-SlJAZ4 as a key module mediating JA-induced trichome elongation in tomato.

Proteomic analysis of early-stage incompatible and compatible interactions between grapevine and P. viticola

Wild grapevines can show strong resistance to the downy mildew pathogen P. viticola, but the associated mechanisms are poorly described, especially at early stages of infection. Here, we performed comparative proteomic analyses of grapevine leaves from the resistant genotype V. davidii "LiuBa-8" (LB) and susceptible V. vinifera "Pinot Noir" (PN) 12 h after inoculation with P. viticola. By employing the iTRAQ technique, a total of 444 and 349 differentially expressed proteins (DEPs) were identified in LB and PN, respectively. The majority of these DEPs were related to photosynthesis, respiration, cell wall modification, protein metabolism, stress, and redox homeostasis. Compared with PN, LB showed fewer downregulated proteins associated with photosynthesis and more upregulated proteins associated with metabolism. At least a subset of PR proteins (PR10.2 and PR10.3) was upregulated upon inoculation in both genotypes, whereas HSP (HSP70.2 and HSP90.6) and cell wall-related XTH and BXL1 proteins were specifically upregulated in LB and PN, respectively. In the incompatible interaction, ROS signaling was evident by the accumulation of H₂O₂, and multiple APX and GST proteins were upregulated. These DEPs may play crucial roles in the grapevine response to downy mildew. Our results provide new insights into molecular events associated with downy mildew resistance in grapevine, which may be exploited to develop novel protection strategies against this disease.

Microscopic and Transcriptomic Analysis of Pollination Processes in Self-Incompatible Taraxacum koksaghyz

The transition of the Russian dandelion Taraxacum koksaghyz (Asteraceae) to a profitable, alternative crop producing natural rubber and inulin requires the optimization of several agronomic traits, cultivation conditions and harvesting procedures to improve the yield. However, efficient breeding is hindered by the obligatory sexual outcrossing of this species. Several other asters have been investigated to determine the mechanism of self-incompatibility, but the underlying molecular basis remains unclear. We therefore investigated the self-pollination and cross-pollination of two compatible T. koksaghyz varieties (TkMS2 and TkMS3) by microscopy and transcriptomic analysis to shed light on the pollination process. Self-pollination showed typical sporophytic self-incompatibility characteristics, with the rare pollen swelling at the pollen tube apex. In contrast, cross-pollination was characterized by pollen germination and penetration of the stigma by the growing pollen tubes. RNA-Seq was used to profile gene expression in the floret tissue during self-pollination and cross-pollination, and the differentially expressed genes were identified. This revealed three candidates for the early regulation of pollination in T. koksaghyz, which can be used to examine self-incompatibility mechanisms in more detail and to facilitate breeding programs.

Coleorhiza-enforced seed dormancy: a novel mechanism to control germination in grasses

How the biophysical properties of overlaying tissues control growth, such as the embryonic root (radicle) during seed germination, is a fundamental question. In eudicot seeds the endosperm surrounding the radicle confers coat dormancy and controls germination responses through modulation of its cell wall mechanical properties. Far less is known for grass caryopses that differ in tissue morphology. Here we report that the coleorhiza, a sheath-like organ that surrounds the radicle in grass embryos, performs the same role in the grass weed Avena fatua (common wild oat). We combined innovative biomechanical techniques, tissue ablation, microscopy, tissue-specific gene and enzyme activity expression with the analysis of hormones and oligosaccharides. The combined experimental work demonstrates that in grass caryopses the coleorhiza indeed controls germination for which we provide direct biomechanical evidence. We show that the coleorhiza becomes reinforced during dormancy maintenance and weakened during germination. Xyloglucan endotransglycosylases/hydrolases may have a role in coleorhiza reinforcement through cell wall remodelling to confer coat dormancy. The control of germination by coleorhiza-enforced dormancy in grasses is an example of the convergent evolution of mechanical restraint by overlaying tissues.

Xyloglucan endotransglycosylase/hydrolase increases tightly-bound xyloglucan and chain number but decreases chain length contributing to the defense response that Glycine max has to Heterodera glycines

The Glycine max xyloglucan endotransglycosylase/hydrolase (EC 2.4.1.207), GmXTH43, has been identified through RNA sequencing of RNA isolated through laser microdissection of Heterodera glycines-parasitized root cells (syncytia) undergoing the process of defense. Experiments reveal that genetically increasing XTH43 transcript abundance in the H. glycines-susceptible genotype G. max[Williams 82/PI 518671] decreases parasitism. Experiments presented here show decreasing XTH43 transcript abundance through RNA interference (RNAi) in the H. glycines-resistant G. max[Peking/PI 548402] increases susceptibility, but it is unclear what role XTH43 performs. The experiments presented here show XTH43 overexpression decreases the relative length of xyloglucan (XyG) chains, however, there is an increase in the amount of those shorter chains. In contrast, XTH43 RNAi increases XyG chain length. The experiments show that XTH43 has the capability to function, when increased in its expression, to limit XyG chain extension. This outcome would likely impair the ability of the cell wall to expand. Consequently, XTH43 could provide an enzymatically-driven capability to the cell that would allow it to limit the ability of parasitic nematodes like H. glycines to develop a feeding structure that, otherwise, would facilitate parasitism. The experiments presented here provide experimentally-based proof that XTHs can function in ways that could be viewed as being able to limit the expansion of the cell wall.

Plant Xyloglucan Xyloglucosyl Transferases and the Cell Wall Structure: Subtle but Significant

Plant xyloglucan xyloglucosyl transferases or xyloglucan endo-transglycosylases (XET; EC 2.4.1.207) catalogued in the glycoside hydrolase family 16 constitute cell wall-modifying enzymes that play a fundamental role in the cell wall expansion and re-modelling. Over the past thirty years, it has been established that XET enzymes catalyse homo-transglycosylation reactions with xyloglucan (XG)-derived substrates and hetero-transglycosylation reactions with neutral and charged donor and acceptor substrates other than XG-derived. This broad specificity in XET isoforms is credited to a high degree of structural and catalytic plasticity that has evolved ubiquitously in algal, moss, fern, basic Angiosperm, monocot, and eudicot enzymes. These XET isoforms constitute gene families that are differentially expressed in tissues in time- and space-dependent manners during plant growth and development, and in response to biotic and abiotic stresses. Here, we discuss the current state of knowledge of broad specific plant XET enzymes and how their inherently carbohydrate-based transglycosylation reactions tightly link with structural diversity that underlies the complexity of plant cell walls and their mechanics. Based on this knowledge, we conclude that multi- or poly-specific XET enzymes are widespread in plants to allow for modifications of the cell wall structure in muro, a feature that implements the multifaceted roles in plant cells.

Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum

BACKGROUND

Sulfur is a major component of biological molecules and thus an essential element for plants. Deficiency of sulfate, the main source of sulfur in soils, negatively influences plant growth and crop yield. The effect of sulfate deficiency on plants has been well characterized at the physiological, transcriptomic and metabolomic levels in Arabidopsis thaliana and a limited number of crop plants. However, we still lack a thorough understanding of the molecular mechanisms and regulatory networks underlying sulfate deficiency in most plants. In this work we analyzed the impact of sulfate starvation on the transcriptome of tomato plants to identify regulatory networks and key transcriptional regulators at a temporal and organ scale.

RESULTS

Sulfate starvation reduces the growth of roots and leaves which is accompanied by major changes in the organ transcriptome, with the response being temporally earlier in roots than leaves. Comparative analysis showed that a major part of the Arabidopsis and tomato transcriptomic response to sulfate starvation is conserved between these plants and allowed for the identification of processes specifically regulated in tomato at the transcript level, including the control of internal phosphate levels. Integrative gene network analysis uncovered key transcription factors controlling the temporal expression of genes involved in sulfate assimilation, as well as cell cycle, cell division and photosynthesis during sulfate starvation in tomato roots and leaves. Interestingly, one of these transcription factors presents a high identity with SULFUR LIMITATION1, a central component of the sulfate starvation response in Arabidopsis.

CONCLUSIONS

Together, our results provide the first comprehensive catalog of sulfate-responsive genes in tomato, as well as novel regulatory targets for future functional analyses in tomato and other crops.

Three highly acidic Equisetum XTHs differ from hetero-trans-β-glucanase in donor substrate specificity and are predominantly xyloglucan homo-transglucosylases

Transglycanases are enzymes that remodel the primary cell wall in plants, potentially loosening and/or strengthening it. Xyloglucan endotransglucosylase (XET; EC 2.4.1.207), ubiquitous in land plants, is a homo-transglucanase activity (donor, xyloglucan; acceptor, xyloglucan) exhibited by XTH (xyloglucan endotransglucosylase/hydrolase) proteins. By contrast, hetero-trans-β-glucanase (HTG) is the only known enzyme that is preferentially a hetero-transglucanase. Its two main hetero-transglucanase activities are MLG : xyloglucan endotransglucosylase (MXE) and cellulose : xyloglucan endotransglucosylase (CXE). HTG is highly acidic and found only in the evolutionarily isolated genus of fern-allies, Equisetum. We now report genes for three new highly acidic HTG-related XTHs in E. fluviatile (EfXTH-A, EfXTH-H and EfXTH-I). We expressed them heterologously in Pichia and tested the encoded proteins' enzymic activities to determine whether their acidity and/or their Equisetum-specific sequences might confer high hetero-transglucanase activity. Untransformed Pichia was found to secrete MLG-degrading enzyme(s), which had to be removed for reliable MXE assays. All three acidic EfXTHs exhibited very predominantly XET activity, although low but measurable hetero-transglucanase activities (MXE and CXE) were also detected in EfXTH-H and EfXTH-I. We conclude that the extremely high hetero-transglucanase activities of Equisetum HTG are not emulated by similarly acidic Equisetum XTHs that share up to 55.5% sequence identity with HTG.

AtSK11 and AtSK12 Mediate the Mild Osmotic Stress-Induced Root Growth Response in Arabidopsis

Although most osmotic stresses are harmful to plant growth and development, certain drought- or polyethylene glycol (PEG)-induced mild osmotic stresses promote plant root growth. The underlying regulatory mechanisms of this response remain elusive. Here, we report that the GLYCOGEN SYNTHASE KINASE 3 (GSK3) genes ARABIDOPSIS THALIANA SHAGGY-RELATED KINASE 11 (AtSK11) (AT5G26751) and AtSK12 (AT3G05840) are involved in the mild osmotic stress (−0.4 MPa) response in Arabidopsis thaliana. When grown on plant medium infused with different concentrations of PEG to mimic osmotic stress, both wild-type (WT) and atsk11atsk12 plants showed stimulated root growth under mild osmotic stress (−0.4 MPa) but repressed root growth under relatively strong osmotic stress (−0.5, −0.6, −0.7 MPa) as compared to the mock condition (−0.25 MPa). The root growth stimulation of atsk11atsk12 was more sensitive to −0.4 MPa treatment than was that of WT, indicating that AtSK11 and AtSK12 inhibit the mild stress-induced root growth response. RNA-seq analysis of WT and atsk11atsk12 plants under three water potentials (−0.25 MPa, −0.4 MPa, −0.6 MPa) revealed 10 differentially expressed candidate genes mainly involved in cell wall homeostasis, which were regulated by AtSK11 and AtSK12 to regulate root growth in response to the mild stress condition (−0.4 MPa). Promoter motif and transcription factor binding analyses suggested that the basic helix-loop-helix (bHLH) transcription factor bHLH69/LJRHL1-LIKE 2 (LRL2) may directly regulate the expression of most −0.4 MPa-responsive genes. These findings indicate that mild osmotic stress (−0.4 MPa) promotes plant growth and that the GSK3 family kinase genes AtSK11 and AtSK12 play a negative role in the induction of root growth in response to mild osmotic stress.

A Group of O-Acetyltransferases Catalyze Xyloglucan Backbone Acetylation and Can Alter Xyloglucan Xylosylation Pattern and Plant Growth When Expressed in Arabidopsis

Xyloglucan is a major hemicellulose in plant cell walls and exists in two distinct types, XXXG and XXGG. While the XXXG-type xyloglucan from dicot species only contains O-acetyl groups on side-chain galactose (Gal) residues, the XXGG-type xyloglucan from Poaceae (grasses) and Solanaceae bears O-acetyl groups on backbone glucosyl (Glc) residues. Although O-acetyltransferases responsible for xyloglucan Gal acetylation have been characterized, the biochemical mechanism underlying xyloglucan backbone acetylation remains to be elucidated. In this study, we showed that recombinant proteins of a group of DUF231 members from rice and tomato were capable of transferring acetyl groups onto O-6 of Glc residues in cello-oligomer acceptors, indicating that they are xyloglucan backbone 6-O-acetyltransferases (XyBATs). We further demonstrated that XyBAT-acetylated cellohexaose oligomers could be readily xylosylated by AtXXT1 (Arabidopsis xyloglucan xylosyltransferase 1) to generate acetylated, xylosylated cello-oligomers, whereas AtXXT1-xylosylated cellohexaose oligomers were much less effectively acetylated by XyBATs. Heterologous expression of a rice XyBAT in Arabidopsis led to a severe reduction in cell expansion and plant growth and a drastic alteration in xyloglucan xylosylation pattern with the formation of acetylated XXGG-type units, including XGG, XGGG, XXGG, XXGG,XXGGG and XXGGG (G denotes acetylated Glc). In addition, recombinant proteins of two Arabidopsis XyBAT homologs also exhibited O-acetyltransferase activity toward cellohexaose, suggesting their possible role in mediating xyloglucan backbone acetylation in vivo. Our findings provide new insights into the biochemical mechanism underlying xyloglucan backbone acetylation and indicate the importance of maintaining the regular xyloglucan xylosylation pattern in cell wall function.

Characterization of FcXTH2, a Novel Xyloglucan Endotransglycosylase/Hydrolase Enzyme of Chilean Strawberry with Hydrolase Activity

Xyloglucan endotransglycosylase/hydrolases (XTHs) are cell wall enzymes with hydrolase (XEH) and/or endotransglycosylase (XET) activities. As they are involved in the modification of the xyloglucans, a type of hemicellulose present in the cell wall, they are believed to be very important in different processes, including growth, development, and fruit ripening. Previous studies suggest that XTHs might play a key role in development and ripening of Fragaria chiloensis fruit, and its characterization is pending. Therefore, in order to provide a biochemical characterization of the FcXTH2 enzyme to explain its possible role in strawberry development, the molecular cloning and the heterologous expression of FcXTH2 were performed. The recombinant FcXTH2 was active and displayed mainly XEH activity. The optimal pH and temperature are 5.5 and 37 °C, respectively. A KM value of 0.029 mg mL-1 was determined. Additionally, its protein structural model was built through comparative modeling methodology. The model showed a typically β-jelly-roll type folding in which the catalytic motif was oriented towards the FcXTH2 central cavity. Using molecular docking, protein-ligand interactions were explored, finding better interaction with xyloglucan than with cellulose. The data provided groundwork for understanding, at a molecular level, the enzymatic mechanism of FcXTH2, an important enzyme acting during the development of the Chilean strawberry.

Novel Aspects on The Interaction Between Grapevine and Plasmopara viticola: Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection

Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a V. vinifera susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen, were used to identify P. viticola effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in P. viticola transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in V. vinifera. Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in V. vinifera of a putative P. viticola susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to P. viticola.

Comparative Transcriptome Analysis Reveals Stem Secondary Growth of Grafted Rosa rugosa 'Rosea' Scion and R. multiflora 'Innermis' Rootstock

Grafted plant is a chimeric organism formed by the connection of scion and rootstock through stems, so stem growth and development become one of the important factors to affect grafted plant state. However, information regarding the molecular responses of stems secondary growth after grafting is limited. A grafted Rosa plant, with R. rugosa 'Rosea' as the scion (Rr_scion) grafted onto R. multiflora 'Innermis' as the stock (Rm_stock), has been shown to significantly improve stem thickness. To elucidate the molecular mechanisms of stem secondary growth in grafted plant, a genome-wide transcription analysis was performed using an RNA sequence (RNA-seq) method between the scion and rootstock. Comparing ungrafted R. rugosa 'Rosea' (Rr) and R. multiflora 'Innermis' (Rm) plants, there were much more differentially expressed genes (DEGs) identified in Rr_scion (6887) than Rm_stock (229). Functional annotations revealed that DEGs in Rr_scion are involved in two Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways: the phenylpropanoid biosynthesis metabolism and plant hormone signal transduction, whereas DEGs in Rm_stock were associated with starch and sucrose metabolism pathway. Moreover, different kinds of signal transduction-related DEGs, e.g., receptor-like serine/threonine protein kinases (RLKs), transcription factor (TF), and transporters, were identified and could affect the stem secondary growth of both the scion and rootstock. This work provided new information regarding the underlying molecular mechanism between scion and rootstock after grafting.

Transcriptomic and metabolomic analyses reveal that melatonin promotes melon root development under copper stress by inhibiting jasmonic acid biosynthesis

Melatonin has been shown to alleviate the effects of abiotic stress and to regulate plant development. Copper, a common heavy metal and soil pollutant, can suppress plant growth and development. In this work, we explored the protective effects of exogenous melatonin on lateral root formation in response to copper stress using melon seeds subjected to three germination treatments: CK1 (control), CK2 (300 μmol/L CuSO₄), and MT3 (300 μmol/L melatonin + 300 μmol/L CuSO₄). Melatonin pretreatment increased the antioxidant enzyme activities and root vigor, and decreased the proline and malondialdehyde (MDA) contents in the roots of copper-stressed melon seedlings. We then used transcriptomic and metabolomic analyses to explore the mechanisms by which exogenous melatonin protects against copper stress. There were 70 significant differentially expressed genes (DEGs) (28 upregulated, 42 downregulated) and 318 significantly differentially expressed metabolites (DEMs) (168 upregulated, 150 downregulated) between the MT3 and CK2 treatments. Melatonin pretreatment altered the expression of genes related to redox and cell wall formation processes. In addition, we found that members of the AP2/ERF, BBR/BPC, GRAS, and HD-ZIP transcription factor families may have vital roles in lateral root development. Melatonin also increased the level of Glutathione (GSH), which chelates excess Cu²⁺. The combined transcriptomic and metabolomic analysis revealed DEGs and DEMs involved in jasmonic acid (JA) biosynthesis, including four lipoxygenase-related genes and two metabolites (linoleic acid and lecithin) related to melatonin's alleviation effect on copper toxicity. This research elucidated the molecular mechanisms of melatonin's protective effects in copper-stressed melon.

Higher expression of the strawberry xyloglucan endotransglucosylase/hydrolase genes FvXTH9 and FvXTH6 accelerates fruit ripening

Fruit softening in Fragaria (strawberry) is proposed to be associated with the modification of cell wall components such as xyloglucan by the action of cell wall-modifying enzymes. This study focuses on the in vitro and in vivo characterization of two recombinant xyloglucan endotransglucosylase/hydrolases (XTHs) from Fragaria vesca, FvXTH9 and FvXTH6. Mining of the publicly available F. vesca genome sequence yielded 28 putative XTH genes. FvXTH9 showed the highest expression level of all FvXTHs in a fruit transcriptome data set and was selected with the closely related FvXTH6 for further analysis. To investigate their role in fruit ripening in more detail, the coding sequences of FvXTH9 and FvXTH6 were cloned into the vector pYES2 and expressed in Saccharomyces cerevisiae. FvXTH9 and FvXTH6 displayed xyloglucan endotransglucosylase (XET) activity towards various acceptor substrates using xyloglucan as the donor substrate. Interestingly, FvXTH9 showed activity of mixed-linkage glucan:xyloglucan endotransglucosylase (MXE) and cellulose:xyloglucan endotransglucosylase (CXE). The optimum pH of both FvXTH9 and FvXTH6 was 6.5. The prediction of subcellular localization suggested localization to the secretory pathway, which was confirmed by localization studies in Nicotiana tabacum. Overexpression showed that Fragaria × ananassa fruits infiltrated with FvXTH9 and FvXTH6 ripened faster and showed decreased firmness compared with the empty vector control pBI121. Thus FvXTH9 and also FvXTH6 might promote strawberry fruit ripening by the modification of cell wall components.