Xyloglucan endo-transglycosylase-mediated xyloglucan rearrangements in developing wood of hybrid aspen

Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes

Although salt tolerance is a feature representative of halophytes, most studies on this topic in plants have been conducted on glycophytes. Transcriptome profiles are also available for only a limited number of halophytes. Hence, the present study was conducted to understand the molecular basis of salt tolerance through the transcriptome profiling of the halophyte Suaeda maritima, which is an emerging plant model for research on salt tolerance. Illumina sequencing revealed 72,588 clustered transcripts, including 27,434 that were annotated using BLASTX. Salt application resulted in the 2-fold or greater upregulation of 647 genes and downregulation of 735 genes. Of these, 391 proteins were homologous to proteins in the COGs (cluster of orthologous groups) database, and the majorities were grouped into the poorly characterized category. Approximately 50% of the genes assigned to MapMan pathways showed homology to S. maritima. The majority of such genes represented transcription factors. Several genes also contributed to cell wall and carbohydrate metabolism, ion relation, redox responses and G protein, phosphoinositide and hormone signaling. Real-time PCR was used to validate the results of the deep sequencing for the most of the genes. This study demonstrates the expression of protein kinase C, the target of diacylglycerol in phosphoinositide signaling, for the first time in plants. This study further reveals that the biochemical and molecular responses occurring at several levels are associated with salt tolerance in S. maritima. At the structural level, adaptations to high salinity levels include the remodeling of cell walls and the modification of membrane lipids. At the cellular level, the accumulation of glycinebetaine and the sequestration and exclusion of Na+ appear to be important. Moreover, this study also shows that the processes related to salt tolerance might be highly complex, as reflected by the salt-induced enhancement of transcription factor expression, including hormone-responsive factors, and that this process might be initially triggered by G protein and phosphoinositide signaling.

Plant Fibre: Molecular Structure and Biomechanical Properties, of a Complex Living Material, Influencing Its Deconstruction towards a Biobased Composite

Plant cell walls form an organic complex composite material that fulfils various functions. The hierarchical structure of this material is generated from the integration of its elementary components. This review provides an overview of wood as a composite material followed by its deconstruction into fibres that can then be incorporated into biobased composites. Firstly, the fibres are defined, and their various origins are discussed. Then, the organisation of cell walls and their components are described. The emphasis is on the molecular interactions of the cellulose microfibrils, lignin and hemicelluloses in planta. Hemicelluloses of diverse species and cell walls are described. Details of their organisation in the primary cell wall are provided, as understanding of the role of hemicellulose has recently evolved and is likely to affect our perception and future study of their secondary cell wall homologs. The importance of the presence of water on wood mechanical properties is also discussed. These sections provide the basis for understanding the molecular arrangements and interactions of the components and how they influence changes in fibre properties once isolated. A range of pulping processes can be used to individualise wood fibres, but these can cause damage to the fibres. Therefore, issues relating to fibre production are discussed along with the dispersion of wood fibres during extrusion. The final section explores various ways to improve fibres obtained from wood.

Biosynthesis of the Plant Cell Wall Matrix Polysaccharide Xyloglucan

Xyloglucan (XyG) is a matrix polysaccharide that is present in the cell walls of all land plants. It consists of a β-1,4-linked glucan backbone that is further substituted with xylosyl residues. These xylosyl residues can be further substituted with other glycosyl and nonglycosyl substituents that vary depending on the plant family and specific tissue. Advances in plant mutant isolation and characterization, functional genomics, and DNA sequencing have led to the identification of nearly all transferases and synthases necessary to synthesize XyG. Thus, in terms of the molecular mechanisms of plant cell wall polysaccharide biosynthesis, XyG is the most well understood. However, much remains to be learned about the molecular mechanisms of polysaccharide assembly and the regulation of these processes. Knowledge of the XyG biosynthetic machinery allows the XyG structure to be tailored in planta to ascertain the functions of this polysaccharide and its substituents in plant growth and interactions with the environment.

A subtracted cDNA library identifies genes up-regulated during PHOT1-mediated early step of de-etiolation in tomato (Solanum lycopersicum L.)

Background

De-etiolation is the switch from skoto- to photomorphogenesis, enabling the heterotrophic etiolated seedling to develop into an autotrophic plant. Upon exposure to blue light (BL), reduction of hypocotyl growth rate occurs in two phases: a rapid inhibition mediated by phototropin 1 (PHOT1) within the first 30–40 min of illumination, followed by the cryptochrome 1 (CRY1)-controlled establishment of the steady-state growth rate. Although some information is available for CRY1-mediated de-etiolation, less attention has been given to the PHOT1 phase of de-etiolation.

Results

We generated a subtracted cDNA library using the suppression subtractive hybridization method to investigate the molecular mechanisms of BL-induced de-etiolation in tomato (Solanum lycopersicum L.), an economically important crop. We focused our interest on the first 30 min following the exposure to BL when PHOT1 is required to induce the process. Our library generated 152 expressed sequence tags that were found to be rapidly accumulated upon exposure to BL and consequently potentially regulated by PHOT1. Annotation revealed that biological functions such as modification of chromatin structure, cell wall modification, and transcription/translation comprise an important part of events contributing to the establishment of photomorphogenesis in young tomato seedlings. Our conclusions based on bioinformatics data were supported by qRT-PCR analyses the specific investigation of V-H⁺-ATPase during de-etiolation in tomato.

Conclusions

Our study provides the first report dealing with understanding the PHOT1-mediated phase of de-etiolation. Using subtractive cDNA library, we were able to identify important regulatory mechanisms. The profound induction of transcription/translation, as well as modification of chromatin structure, is relevant in regard to the fact that the entry into photomorphogenesis is based on a deep reprograming of the cell. Also, we postulated that BL restrains the cell expansion by the rapid modification of the cell wall.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2613-6) contains supplementary material, which is available to authorized users.

Global Transcriptome Profiling Analysis of Inhibitory Effects of Paclobutrazol on Leaf Growth in Lily (Lilium Longiflorum-Asiatic Hybrid)

As a popular ornamental flower, potted lily is an important object of lily breeding. Paclobutrazol, a chemical growth retardation compound, is often used to dwarf plant in producing potted lilies. However, in recent years, the plants with inherited dwarf traits by using genetic engineer breeding technology are being developed. The studies on molecular basis of lily dwarfism will offer some target genes which have profound dwarf effect for genetic engineer breeding. Here, we confirmed that paclobutrazol inhibited plant height and leaf size in Lilium Longiflorum-Asiatic hybrid, and then RNA-Seq technique was employed to analyze gene transcripts of Lilium Longiflorum-Asiatic hybrid leaves by paclobutrazol treatment in order to get a deeper insight into dwarfism mechanism of lily. Approximately 38.6 Gb data was obtained and assemble into 53,681 unigenes. Annotation, pathways, functional classification and phylogenetic classification of these data were analyzed based on Nr, Nt, Swiss-Prot, KEGG, COG, and GO databases. 2704 differentially expressed genes were screened by comparing paclobutrazol-treated samples with untreated samples and quantitative real-time PCR was performed to validate expression profiles. By analyzing dynamic changes of differentially expressed genes, nine metabolic pathways and signal transduction pathways were significantly enriched and many potentially interesting genes were identified that encoded putative regulators or key components of cell division, cell expansion, GA metabolism and signaling transduction and these genes were highlighted to reveal their importance in regulation of plant size. These results will provide a better understanding of the molecular mechanism on lily dwarfism and some potential genes related to lily organ size, which will lay the foundation for molecular breeding of potted lilies. These transcriptome data will also serve as valuable public genomic resources for other genetic research in lily.

Identification of differentially expressed transcripts associated with bast fibre development in Corchorus capsularis by suppression subtractive hybridization

The present study documented the predominant role of WRKY transcription factor in controlling genes of different pathways related to fibre formation in jute and could be a candidate gene for the improvement of jute fiber. Understanding of molecular mechanism associated with bast fibre development is of immense significance to achieve desired improvement in jute (Corchorus sp.). Therefore, suppression subtractive hybridization was successfully applied to identify genes involved in fibre developmental process in jute. The subtracted library of normal Corchorus capsularis as tester with respect to its fibre-deficient mutant as driver resulted in 2,685 expressed sequence tags which were assumed to represent the differentially expressed genes between two genotypes. The identified expressed sequence tags were assembled and clustered into 225 contigs and 231 singletons. Among these 456 unigenes, 377 were classified into 15 different functional categories while others were of unknown functional category. Reverse Northern analysis of the unigenes showed distinct variation in hybridization intensity of 11 transcripts between two genotypes tested. The findings were also documented by Northern and real-time PCR analysis. Varied expression level of these transcripts suggested their crucial involvement in fibre development in this species. Among these transcripts, WRKY transcription factor was documented to be a most important transcript which was in agreement with its known role in other plant species in possible regulation related to cell wall biosynthesis, expansion and lignification. This report constitutes first systematic analysis of genes involved in fibre development process in jute. It may be suggested that the information generated in this study would be useful for genetic improvement of fibre traits in this plant species.

Distribution of XTH, expansin, and secondary-wall-related CesA in floral and fruit abscission zones during fruit development in tomato (Solanum lycopersicum)

After fruit development is triggered by pollination, the abscission zone (AZ) in the fruit pedicel strengthens its adhesion to keep the fruit attached. We previously reported that xyloglucan and arabinan accumulation in the AZ accompanies the shedding of unpollinated flowers. After the fruit has developed and is fully ripened, shedding occurs easily in the AZ due to lignin accumulation. Regulation of cell wall metabolism may play an important role in these processes, but it is not well understood. In the present report, we used immunohistochemistry to visualize changes in the distributions of xyloglucan and arabinan metabolism-related enzymes in the AZs of pollinated and unpollinated flowers, and in ripened fruits. During floral abscission, we observed a gradual increase in polyclonal antibody labeling of expansin in the AZ. The intensities of LM6 and LM15 labeling of arabinan and xyloglucan, respectively, also increased. However, during floral abscission, we observed a large 1 day post anthesis (DPA) peak in the polyclonal antibody labeling of XTH in the AZ, which then decreased. These results suggest that expansin and XTH play important, but different roles in the floral abscission process. During fruit abscission, unlike during floral abscission, no AZ-specific expansin and XTH were observed. Although lignification was seen in the AZ of over-ripe fruit pedicels, secondary cell wall-specific cellulose synthase signals were not observed. This suggests that cellulose metabolism-related enzymes do not play important roles in the AZ prior to fruit abscission.

Glycoside Hydrolase Activities in Cell Walls of Sclerenchyma Cells in the Inflorescence Stems of Arabidopsis thaliana Visualized in Situ

Techniques for in situ localization of gene products provide indispensable information for understanding biological function. In the case of enzymes, biological function is directly related to activity, and therefore, knowledge of activity patterns is central to understanding the molecular controls of plant development. We have previously developed a novel type of fluorogenic substrate for revealing glycoside hydrolase activity in planta, based on resorufin β-glycosides Here, we explore a wider range of such substrates to visualize glycoside hydrolase activities in Arabidopsis inflorescence stems in real time, especially highlighting distinct distribution patterns of these activities in the secondary cell walls of sclerenchyma cells. The results demonstrate that β-1,4-glucosidase, β-1,4-glucanase and β-1,4-galactosidase activities accompany secondary wall deposition. In contrast, xyloglucanase activity follows a different pattern, with the highest signal observed in mature cells, concentrated in the middle lamella. These data further the understanding of the process of cell wall deposition and function in sclerenchymatic tissues of plants.

Association of allelic variation in PtoXET16A with growth and wood properties in Populus tomentosa

Xyloglucan endo-transglycosylases (XETs) modify the xyloglucan-cellulose framework of plant cell walls and, thus, affect cell wall expansion and strength. Dissecting the mechanism by which natural variation in XETs affects wood properties can inform breeding efforts to improve wood quality and yield traits. To this end, we isolated a full-length PtoXET16A cDNA clone from Populus tomentosa. Real-time PCR analysis showed that PtoXET16A was maximally expressed in the root, followed by phloem, cambium, and developing xylem, suggesting that PtoXET16A plays important roles in the development of vascular tissues. Nucleotide diversity and linkage disequilibrium analysis revealed that PtoXET16A has high single nucleotide polymorphism (SNP) diversity (π = 0.01266 and θ_w = 0.01392) and low linkage disequilibrium (r² ≥ 0.1, within 900 bp). SNP- and haplotype-based association analyses of 426 individuals from a natural population indicated that nine SNPs (including two non-synonymous markers and one splicing variant) (p ≤ 0.05, false discovery rate Q ≤ 0.01), and nine haplotypes (p ≤ 0.05) were significantly associated with growth and wood properties, each explaining from 3.40%–10.95% of phenotypic variance. This work shows that examination of allelic variation and linkage disequilibrium by a candidate-gene-based approach can help to decipher the genetic basis of wood formation. Moreover, the SNP markers identified in this study can potentially be applied for marker-assisted selection to improve growth and wood-property traits in Populus.

Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis

Development of cambium and its activity is important for our knowledge of the mechanism of secondary growth. Arabidopsis thaliana emerges as a good model plant for such a kind of study. Thus, this paper reports on cellular events taking place in the interfascicular regions of inflorescence stems of A. thaliana, leading to the development of interfascicular cambium from differentiated interfascicular parenchyma cells (IPC). These events are as follows: appearance of auxin accumulation, PIN1 gene expression, polar PIN1 protein localization in the basal plasma membrane and periclinal divisions. Distribution of auxin was observed to be higher in differentiating into cambium parenchyma cells compared to cells within the pith and cortex. Expression of PIN1 in IPC was always preceded by auxin accumulation. Basal localization of PIN1 was already established in the cells prior to their periclinal division. These cellular events initiated within parenchyma cells adjacent to the vascular bundles and successively extended from that point towards the middle region of the interfascicular area, located between neighboring vascular bundles. The final consequence of which was the closure of the cambial ring within the stem. Changes in the chemical composition of IPC walls were also detected and included changes of pectic epitopes, xyloglucans (XG) and extensins rich in hydroxyproline (HRGPs). In summary, results presented in this paper describe interfascicular cambium ontogenesis in terms of successive cellular events in the interfascicular regions of inflorescence stems of Arabidopsis.

The zinc finger protein PtaZFP2 negatively controls stem growth and gene expression responsiveness to external mechanical loads in poplar

Mechanical cues are essential signals regulating plant growth and development. In response to wind, trees develop a thigmomorphogenetic response characterized by a reduction in longitudinal growth, an increase in diameter growth, and changes in mechanical properties. The molecular mechanisms behind these processes are poorly understood. In poplar, PtaZFP2, a C2H2 transcription factor, is rapidly up-regulated after stem bending. To investigate the function of PtaZFP2, we analyzed PtaZFP2-overexpressing poplars (Populus tremula × Populus alba). To unravel the genes downstream PtaZFP2, a transcriptomic analysis was performed. PtaZFP2-overexpressing poplars showed longitudinal and cambial growth reductions together with an increase in the tangent and hardening plastic moduli. The regulation level of mechanoresponsive genes was much weaker after stem bending in PtaZFP2-overexpressing poplars than in wild-type plants, showing that PtaZFP2 negatively modulates plant responsiveness to mechanical stimulation. Microarray analysis revealed a high proportion of down-regulated genes in PtaZFP2-overexpressing poplars. Among these genes, several were also shown to be regulated by mechanical stimulation. Our results confirmed the important role of PtaZFP2 during plant acclimation to mechanical load, in particular through a negative control of plant molecular responsiveness. This desensitization process could modulate the amplitude and duration of the plant response during recurrent stimuli.

Identification and characterization of nuclear genes involved in photosynthesis in Populus

BACKGROUND

The gap between the real and potential photosynthetic rate under field conditions suggests that photosynthesis could potentially be improved. Nuclear genes provide possible targets for improving photosynthetic efficiency. Hence, genome-wide identification and characterization of the nuclear genes affecting photosynthetic traits in woody plants would provide key insights on genetic regulation of photosynthesis and identify candidate processes for improvement of photosynthesis.

RESULTS

Using microarray and bulked segregant analysis strategies, we identified differentially expressed nuclear genes for photosynthesis traits in a segregating population of poplar. We identified 515 differentially expressed genes in this population (FC ≥ 2 or FC ≤ 0.5, P < 0.05), 163 up-regulated and 352 down-regulated. Real-time PCR expression analysis confirmed the microarray data. Singular Enrichment Analysis identified 48 significantly enriched GO terms for molecular functions (28), biological processes (18) and cell components (2). Furthermore, we selected six candidate genes for functional examination by a single-marker association approach, which demonstrated that 20 SNPs in five candidate genes significantly associated with photosynthetic traits, and the phenotypic variance explained by each SNP ranged from 2.3% to 12.6%. This revealed that regulation of photosynthesis by the nuclear genome mainly involves transport, metabolism and response to stimulus functions.

CONCLUSIONS

This study provides new genome-scale strategies for the discovery of potential candidate genes affecting photosynthesis in Populus, and for identification of the functions of genes involved in regulation of photosynthesis. This work also suggests that improving photosynthetic efficiency under field conditions will require the consideration of multiple factors, such as stress responses.

Populus euphratica XTH overexpression enhances salinity tolerance by the development of leaf succulence in transgenic tobacco plants

Populus euphratica is a salt-tolerant tree species that develops leaf succulence after a prolonged period of salinity stress. In the present study, a putative xyloglucan endotransglucosylase/hydrolase gene (PeXTH) from P. euphratica was isolated and transferred to tobacco plants. PeXTH localized exclusively to the endoplasmic reticulum and cell wall. Plants overexpressing PeXTH were more salt tolerant than wild-type tobacco with respect to root and leaf growth, and survival. The increased capacity for salt tolerance was due mainly to the anatomical and physiological alterations caused by PeXTH overexpression. Compared with the wild type, PeXTH-transgenic plants contained 36% higher water content per unit area and 39% higher ratio of fresh weight to dry weight, a hallmark of leaf succulence. However, the increased water storage in the leaves in PeXTH-transgenic plants was not accompanied by greater leaf thickness but was due to highly packed palisade parenchyma cells and fewer intercellular air spaces between mesophyll cells. In addition to the salt dilution effect in response to NaCl, these anatomical changes increased leaf water-retaining capacity, which lowered the increase of salt concentration in the succulent tissues and mesophyll cells. Moreover, the increased number of mesophyll cells reduced the intercellular air space, which improved carbon economy and resulted in a 47-78% greater net photosynthesis under control and salt treatments (100-150 mM NaCl). Taken together, the results indicate that PeXTH overexpression enhanced salt tolerance by the development of succulent leaves in tobacco plants without swelling.

Differential expression of several xyloglucan endotransglucosylase/hydrolase genes regulates flower opening and petal abscission in roses

The movement of petals during flower opening (anthesis) and their separation from the parent plant during abscission requires cell wall modification at the junction (abscission zone) of the petal and thalamus. The present study shows differential ethylene mediated temporal regulation of various members of the rose XTH gene family during flower opening and abscission in the ethylene sensitive, early abscising fragrant rose and the less sensitive late abscising hybrid rose. These studies indicate that large scale changes in xyloglucan crosslinking in cell wall mediated by XTHs may facilitate movement and separation during flower opening and abscission respectively.

Flower opening is a process that requires movement of petals from a closed position to a horizontal open position, while petal abscission requires cell-wall disassembly. Both processes are controlled by ethylene and require cell-wall modification at the junction (abscission zone) of the petal and thalamus to facilitate the movement or separation of petals. In the present study, a family of xyloglucan endotransglucosylase/hydrolase (XTH) genes was studied to understand their role in petal abscission in flowers of Rosa bourboniana (ethylene sensitive, early abscising) and Rosa hybrida (less ethylene sensitive, late abscising). Transcriptome sequencing of petal abscission zone cDNA was performed at different time points (ethylene treated and untreated) and screened for XTH genes. The study identified nine new XTH genes that showed differential changes in gene expression during flower opening and abscission. Of these, RbXTH3, RbXTH5, RbXTH6 and RbXTH12 were rapidly induced by ethylene within 1–4 h of ethylene treatment, corresponding to the period of flower opening. These genes also showed an early up-regulation during flower opening under ethylene-untreated (field abscission) conditions, indicating a possible role in anthesis and petal movement during flower opening. Other genes such as RbXTH4 and RbXTH9 were up-regulated later at 8–12 h after ethylene treatment and at 24–36 h under natural abscission conditions, indicating a possible role in abscission. Treatment with a higher ethylene dose (15 µL L⁻¹ ethylene) accelerated abscission, leading to higher steady-state levels of XTH gene transcripts at an earlier time point compared with 0.5 µL L⁻¹ ethylene. In contrast, transcript accumulation of most of the XTHs was considerably delayed in the late-abscising rose, R. hybrida, in keeping with the slower flower opening and delayed petal abscission. The results suggest coordinated action of different XTHs in cell-wall modification of xyloglucan moieties during flower opening as well as cell separation during abscission.

Xyloglucan endotransglucosylase/hydrolase (XTH) overexpression affects growth and cell wall mechanics in etiolated Arabidopsis hypocotyls

Growth and biomechanics of etiolated hypocotyls from Arabidopsis thaliana lines overexpressing xyloglucan endotransglucosylase/hydrolase AtXTH18, AtXTH19, AtXTH20, and PttXET16-34 were studied. Overexpression of AtXTH18, AtXTH19, and AtXTH20 stimulated growth of hypocotyls, while PttXET16-34 overexpression did not show this effect. In vitro extension of frozen/thawed hypocotyls measured by a constant-load extensiometer started from a high-amplitude initial deformation followed by a slow time-dependent creep. Creep of growing XTH-overexpressing (OE) hypocotyls was more linear in time compared with the wild type at pH 5.0, reflecting their higher potential for long-term extension. XTH-OE plants deposited 65-84% more cell wall material per hypocotyl cross-sectional area than wild-type plants. As a result, their wall stress under each external load was lower than in the wild-type. Growing XTH-OE hypocotyls had higher values of initial deformation·stress(-1) compared with the wild type. Plotting creep rates for each line under different loads against the respective wall stress values gave straight lines. Their slopes and intercepts with the abscissa correspond to ϕ (in vitro cell wall extensibility) and y (in vitro cell wall yield threshold) values characterizing cell wall material properties. The wall material in XTH-OE lines was more pliant than in the wild type due to lower y values. In contrast, the acid-induced wall extension in vitro resulted from increasing ϕ values. Thus, three factors contributed to the XTH-OE-stimulated growth in Arabidopsis hypocotyls: their more linear creep, higher values of initial deformation·stress(-1), and lower y values.

Mixed-linkage glucan:xyloglucan endotransglucosylase (MXE) re-models hemicelluloses in Equisetum shoots but not in barley shoots or Equisetum callus

Among land-plant hemicelluloses, xyloglucan is ubiquitous, whereas mixed-linkage (1→3),(1→4)-β-D-glucan (MLG) is confined to the Poales (e.g. cereals) and Equisetales (horsetails). The enzyme MLG:xyloglucan endotransglucosylase (MXE) grafts MLG to xyloglucan. In Equisetum, MXE often exceeds extractable xyloglucan endotransglucosylase (XET) activity; curiously, cereals lack extractable MXE. We investigated whether barley possesses inextractable MXE. Grafting of endogenous MLG or xyloglucan onto exogenous [(3)H]xyloglucan oligosaccharides in vivo indicated MXE and XET action, respectively. Extractable MXE and XET activities were assayed in vitro. MXE and XET actions were both detectable in living Equisetum fluviatile shoots, the MXE : XET ratio increasing with age. However, only XET action was observed in barley coleoptiles, leaves and roots (which all contained MLG) and in E. fluviatile intercalary meristems and callus (which lacked MLG). In E. fluviatile, extractable MXE activity was high in mature shoots, but extremely low in callus and young shoots; in E. arvense strobili, it was undetectable. Barley possesses neither extractable nor inextractable MXE, despite containing both of its substrates and high XET activity. As the Poales are xyloglucan-poor, the role of their abundant endotransglucosylases remains enigmatic. The distribution of MXE action and activity within Equisetum suggests a strengthening role in ageing tissues.

Group III-A XTH genes of Arabidopsis encode predominant xyloglucan endohydrolases that are dispensable for normal growth

The molecular basis of primary wall extension endures as one of the central enigmas in plant cell morphogenesis. Classical cell wall models suggest that xyloglucan endo-transglycosylase activity is the primary catalyst (together with expansins) of controlled cell wall loosening through the transient cleavage and religation of xyloglucan-cellulose cross links. The genome of Arabidopsis (Arabidopsis thaliana) contains 33 phylogenetically diverse XYLOGLUCAN ENDO-TRANSGLYCOSYLASE/HYDROLASE (XTH) gene products, two of which were predicted to be predominant xyloglucan endohydrolases due to clustering into group III-A. Enzyme kinetic analysis of recombinant AtXTH31 confirmed this prediction and indicated that this enzyme had similar catalytic properties to the nasturtium (Tropaeolum majus) xyloglucanase1 responsible for storage xyloglucan hydrolysis during germination. Global analysis of Genevestigator data indicated that AtXTH31 and the paralogous AtXTH32 were abundantly expressed in expanding tissues. Microscopy analysis, utilizing the resorufin β-glycoside of the xyloglucan oligosaccharide XXXG as an in situ probe, indicated significant xyloglucan endohydrolase activity in specific regions of both roots and hypocotyls, in good correlation with transcriptomic data. Moreover, this hydrolytic activity was essentially completely eliminated in AtXTH31/AtXTH32 double knockout lines. However, single and double knockout lines, as well as individual overexpressing lines, of AtXTH31 and AtXTH32 did not demonstrate significant growth or developmental phenotypes. These results suggest that although xyloglucan polysaccharide hydrolysis occurs in parallel with primary wall expansion, morphological effects are subtle or may be compensated by other mechanisms. We hypothesize that there is likely to be an interplay between these xyloglucan endohydrolases and recently discovered apoplastic exo-glycosidases in the hydrolytic modification of matrix xyloglucans.

Transcriptional analysis of differentially expressed genes in response to stem inclination in young seedlings of pine

The gravitropic response in trees is a widely studied phenomenon, however understanding of the molecular mechanism involved remains unclear. The purpose of this work was to identify differentially expressed genes in response to inclination using a comparative approach for two conifer species. Young seedlings were subjected to inclination and samples were collected at four different times points. First, suppression subtractive hybridisation (SSH) was used to identify differentially regulated genes in radiata pine (Pinus radiata D. Don). cDNA libraries were constructed from the upper and lower part of inclined stems in a time course experiment, ranging from 2.5 h to 1 month. From a total of 3092 sequences obtained, 2203 elements were assembled, displaying homology to a public database. A total of 942 unigene elements were identified using bioinformatic tools after redundancy analysis. Of these, 614 corresponded to known function genes and 328 to unknown function genes, including hypothetical proteins. Comparative analysis between radiata pine and maritime pine (Pinus pinaster Ait.) was performed to validate the differential expression of relevant candidate genes using qPCR. Selected genes were involved in several functional categories: hormone regulation, phenylpropanoid pathway and signal transduction. This comparative approach for the two conifer species helped determine the molecular gene pattern generated by inclination, providing a set of Pinus gene signatures that may be involved in the gravitropic stress response. These genes may also represent relevant candidate genes involved in the gravitropic response and potentially in wood formation.

Modifying crops to increase cell wall digestibility

Improving digestibility of roughage cell walls will improve ruminant animal performance and reduce loss of nutrients to the environment. The main digestibility impediment for dicotyledonous plants is highly lignified secondary cell walls, notably in stem secondary xylem, which become almost non-digestible. Digestibility of grasses is slowed severely by lignification of most tissues, but these cell walls remain largely digestible. Cell wall lignification creates an access barrier to potentially digestible wall material by rumen bacteria if cells have not been physically ruptured. Traditional breeding has focused on increasing total dry matter digestibility rather than cell wall digestibility, which has resulted in minimal reductions in cell wall lignification. Brown midrib mutants in some annual grasses exhibit small reductions in lignin concentration and improved cell wall digestibility. Similarly, transgenic approaches down-regulating genes in monolignol synthesis have produced plants with reduced lignin content and improved cell wall digestibility. While major reductions in lignin concentration have been associated with poor plant fitness, smaller reductions in lignin provided measurable improvements in digestibility without significantly impacting agronomic fitness. Additional targets for genetic modification to enhance digestibility and improve roughages for use as biofuel feedstocks are discussed; including manipulating cell wall polysaccharide composition, novel lignin structures, reduced lignin/polysaccharide cross-linking, smaller lignin polymers, enhanced development of non-lignified tissues, and targeting specific cell types. Greater tissue specificity of transgene expression will be needed to maximize benefits while avoiding negative impacts on plant fitness.cauliflower mosiac virus (CaMV) 35S promoter.

Distinguishing xyloglucanase activity in endo-β(1→4)glucanases

The ability of β-glucanases to cleave xyloglucans, a family of highly decorated β-glucans ubiquitous in plant biomass, has traditionally been overlooked in functional biochemical studies. An emerging body of data indicates, however, that a spectrum of xyloglucan specificity resides in diverse glycoside hydrolases from a range of carbohydrate-active enzyme families-including classic "cellulase" families. This chapter outlines a series of enzyme kinetic and product analysis methods to establish degrees of xyloglucan specificity and modes of action of glycosidases emerging from enzyme discovery projects.

Fluorescent tags to explore cell wall structure and dynamics

Plant cell walls are highly dynamic and heterogeneous structures, which vary between cell types, growth stages but also between microdomains within a single cell wall. In this review, we summarize the imaging techniques using fluorescent tags that are currently being used and which should in the coming years revolutionize our understanding of the dynamics of cell wall architecture and the cellular processes involved in the synthesis of cell wall components.

Petal abscission in rose is associated with the differential expression of two ethylene-responsive xyloglucan endotransglucosylase/hydrolase genes, RbXTH1 and RbXTH2

Abscission is a process that involves shedding of plant organs from the main plant body. In this study it is shown that the process of petal separation in the fragrant rose, Rosa bourboniana, is accompanied by the expression of two xyloglucan endotransglucosylase/hydrolase genes, RbXTH1 and RbXTH2. The sequences of the two genes show 52% amino acid identity but are conserved at the catalytic site. The genes are up-regulated soon after the initiation of the abscission process and their transcription is associated with the progression of abscission, being faster in ethylene-treated flowers but slower during field abscission. Transcription is ethylene responsive, with the ethylene response being tissue-specific for RbXTH1 but largely tissue-independent for RbXTH2. Expression is correlated with an increase in xyloglucan endotransglucosylase (XET) action in petal abscission zones of both ethylene-treated and field abscising flowers. Proximal promoters of both the genes drive β-glucuronidase expression in an ethylene-responsive and abscission-related manner in agrobacteria-infiltrated rose petals, indicating that cis-elements governing ethylene-responsive and abscission-related expression probably lie within the first 700 nucleotides upstream of the translational initiation codon. The results show that cell wall remodelling of the xyloglucan moieties through the XET action of XTHs may be important for cell separation during abscission.

Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles

Background

Cultivated watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an important agriculture crop world-wide. The fruit of watermelon undergoes distinct stages of development with dramatic changes in its size, color, sweetness, texture and aroma. In order to better understand the genetic and molecular basis of these changes and significantly expand the watermelon transcript catalog, we have selected four critical stages of watermelon fruit development and used Roche/454 next-generation sequencing technology to generate a large expressed sequence tag (EST) dataset and a comprehensive transcriptome profile for watermelon fruit flesh tissues.

Results

We performed half Roche/454 GS-FLX run for each of the four watermelon fruit developmental stages (immature white, white-pink flesh, red flesh and over-ripe) and obtained 577,023 high quality ESTs with an average length of 302.8 bp. De novo assembly of these ESTs together with 11,786 watermelon ESTs collected from GenBank produced 75,068 unigenes with a total length of approximately 31.8 Mb. Overall 54.9% of the unigenes showed significant similarities to known sequences in GenBank non-redundant (nr) protein database and around two-thirds of them matched proteins of cucumber, the most closely-related species with a sequenced genome. The unigenes were further assigned with gene ontology (GO) terms and mapped to biochemical pathways. More than 5,000 SSRs were identified from the EST collection. Furthermore we carried out digital gene expression analysis of these ESTs and identified 3,023 genes that were differentially expressed during watermelon fruit development and ripening, which provided novel insights into watermelon fruit biology and a comprehensive resource of candidate genes for future functional analysis. We then generated profiles of several interesting metabolites that are important to fruit quality including pigmentation and sweetness. Integrative analysis of metabolite and digital gene expression profiles helped elucidating molecular mechanisms governing these important quality-related traits during watermelon fruit development.

Conclusion

We have generated a large collection of watermelon ESTs, which represents a significant expansion of the current transcript catalog of watermelon and a valuable resource for future studies on the genomics of watermelon and other closely-related species. Digital expression analysis of this EST collection allowed us to identify a large set of genes that were differentially expressed during watermelon fruit development and ripening, which provide a rich source of candidates for future functional analysis and represent a valuable increase in our knowledge base of watermelon fruit biology.