XYLOGENESIS: INITIATION, PROGRESSION, AND CELL DEATH

Combined metabolome and transcriptome analysis reveals a critical role of lignin biosynthesis and lignification in stem-like pneumatophore development of the mangrove Avicennia marina

MAIN CONCLUSION

Transcriptional and metabolic regulation of lignin biosynthesis and lignification plays crucial roles in Avicennia marina pneumatophore development, facilitating its adaptation to coastal habitats. Avicennia marina is a pioneer mangrove species in coastal wetland. To cope with the periodic intertidal flooding and hypoxia environment, this species has developed a complex and extensive root system, with its most unique feature being a pneumatophore with a distinct above- and below-ground morphology and vascular structure. However, the characteristics of pneumatophore lignification remain unknown. Studies comparing the anatomy among above-ground pneumatophore, below-ground pneumatophore, and feeding root have suggested that vascular structure development in the pneumatophore is more like the development of a stem than of a root. Metabolome and transcriptome analysis illustrated that the accumulation of syringyl (S) and guaiacyl (G) units in the pneumatophore plays a critical role in lignification of the stem-like structure. Fourteen differentially accumulated metabolites (DAMs) and 10 differentially expressed genes involved in the lignin biosynthesis pathway were targeted. To identify genes significantly associated with lignification, we analyzed the correlation between 14 genes and 8 metabolites and further built a co-expression network between 10 transcription factors (TFs), including 5 for each of MYB and NAC, and 23 enzyme-coding genes involved in lignin biosynthesis. 4-Coumarate-CoA ligase, shikimate/quinate hydroxycinnamoyl transferase, cinnamyl alcohol dehydrogenase, caffeic acid 3-O-methyltransferase, phenylalanine ammonia-lyase, and peroxidase were identified to be strongly correlated with these TFs. Finally, we examined 9 key candidate genes through quantitative real-time PCR to validate the reliability of transcriptome data. Together, our metabolome and transcriptome findings reveal that lignin biosynthesis and lignification regulate pneumatophore development in the mangrove species A. marina and facilitate its adaptation to coastal habitats.

Biochemical Aspects of the Spiral Grain Formation in Scots Pine (Pinus Sylvestris L.) Wood. Some Differences and Similarities with Biochemical Indicators of Abnormal Xylogenesis in Karelian Birch (Betula Pendula Roth Var. Carelica (Mercl.) Hämet-Ahti)

BACKGROUND

AOS enzymes can be biochemical indicators of abnormal xylogenesis in Scots pine, and this mechanism has similar features with the metabolic base of abnormal xylogenesis in Karelian birch.

OBJECTIVE

AOS enzymes' activity in 150-300-year-old Pinus sylvestris L. wood with straight-- grained wood and right-twisted spiral-grained wood, expressed in varying degrees (5-20 angle), grew in three sample plots in lingonberry and blueberry pine forest stands of different ages (100-300 years) in the middle taiga subzone in the Republic of Karelia.

METHODS

Plant tissues were ground in liquid nitrogen in a uniform mass and homogenized at 4°C in the buffer containing 50 mM HEPES (pH 7.5), 1 mM EDTA, 1 mM EGTA, 3 mM DTT, 5 mM MgCl2 and 0.5 mM PMSF. After 20 min extraction, the homogenate was centrifuged at 10000 g for 20 min (MPW-351R, Poland). The sediment was washed in the buffer thrice. The pooled supernatant and sediment were dialyzed at 4°C for 18-20 h against a tenfold diluted homogenization buffer. The enzymes' activity was determined spectrophotometrically (Spectrophotometer SF-2000, OKB Spectr, Russia). Proteins in the extracts were quantified by the method of Bradford.

RESULTS

The study showed that the activity of SS, ApInv, CAT, POD and PPO in xylem and PPO in phloem were biochemical indicators for abnormal wood of P. sylvestris. We noticed an increase in sucrose metabolism in the apoplast and the activity of POD and PPO under spiral-grain wood formation like under figured wood formation earlier. We assume that the alternative pathway of sucrose metabolism (an indicator of abnormal xylogenesis in B. pendula var. carelica plants) that lead to restructuring of AOS enzymes have the same biochemical regularities in the spiral-grain wood formation in P. sylvestris.

CONCLUSION

The study showed that the differences in the AOS enzyme's activity in P. sylvestris during the formation of straight-grained and spiral-grained wood were revealed for the first time. The increased CAT, POD and PPO activities in xylem with a decrease in SS and an increase in Ap- Inv during spiral-grained wood formation can be biochemical markers of these structural anomalies. Metabolic regularities found in the AOS enzyme complex during spiral-grained wood formation do not contradict those found earlier during figured wood formation in B. pendula var. carelica. The identified patterns can form the base for diagnostics of P. sylvestris wood quality in forest seed plantations and in their natural growth, which is necessary both for fundamental science and in various industry areas while high-quality material harvesting.

Programmed cell death associated with the formation of schizo-lysigenous aerenchyma in Nelumbo nucifera root

Nelumbo nucifera (N. nucifera) is an important aquatic economic crop with high edible, medicinal, ornamental, and ecological restoration values. Aerenchyma formation in N. nucifera root is an adaptive trait to the aquatic environment in long-term evolution. In this study, light microscopy, electron microscopy, and molecular biology techniques were used to study the process of the aerenchyma development and cytological events in N. nucifera root and the dynamic changes of aerenchyma formation under the treatment of exogenous 21% oxygen, ethylene (ET), and ET synthesis i + nhibitor 1-methylcyclopropene (1-MCP). The results showed that programmed cell death (PCD) occurred during the aerenchyma formation in N. nucifera root. Plasmalemma invagination and vacuole membrane rupture appeared in the formation stage, followed by nuclear deformation, chromatin condensation and marginalization, and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) detection was positive at this time. In the expansion stage of the aerenchyma development, cytoplasmic degradation and many vesicles appeared in the cytoplasm, and organelles began to degrade. Then the plasma membrane began to degrade, and the degradation of the cell wall was the last PCD step. After 21% oxygen was continuously filled in the rhizosphere environment of N. nucifera roots, the area of aerenchyma in N. nucifera roots was smaller than that in the control group. Moreover, ET induced the earlier occurrence of aerenchyma in N. nucifera root, but also, the area of aerenchyma became larger than that of the control. On the contrary, 1-MCP inhibited the occurrence of aerenchyma to some extent. Therefore, the formation of aerenchyma in N. nucifera root resulted from PCD, and its formation mode was schizo-lysigenous. A hypoxic environment could induce aerenchyma formation in plants. ET signal was involved in aerenchyma formation in N. nucifera root and had a positive regulatory effect. This study provides relevant data on the formation mechanism of plant aerenchyma and the cytological basis for exploring the regulation mechanism of plant aerenchyma formation.

Brassinosteroid signaling restricts root lignification by antagonizing SHORT-ROOT function in Arabidopsis

Cell wall lignification is a key step in forming functional endodermis and protoxylem (PX) in plant roots. Lignified casparian strips (CS) in endodermis and tracheary elements of PX are essential for selective absorption and transport of water and nutrients. Although multiple key regulators of CS and PX have been identified, the spatial information that drives the developmental shift to root lignification remains unknown. Here, we found that brassinosteroid (BR) signaling plays a key role in inhibiting root lignification in the root elongation zone. The inhibitory activity of BR signaling occurs partially through the direct binding of BRASSINAZOLE-RESISTANT 1 (BZR1) to SHORT-ROOT (SHR), repressing the SHR-mediated activation of downstream genes that are involved in root lignification. Upon entering the mature root zone, BR signaling declines rapidly, which releases SHR activity and initiates root lignification. Our results provide a mechanistic view of the developmental transition to cell wall lignification in Arabidopsis thaliana roots.

Deep conservation and co-option of programmed cell death facilitates evolution of alternative phenotypes at multiple biological levels

Alternative phenotypes, such as polyphenisms and sexual dimorphisms, are widespread in nature and appear at all levels of biological organization, from genes and cells to morphology and behavior. Yet, our understanding of the mechanisms through which alternative phenotypes develop and how they evolve remains understudied. In this review, we explore the association between alternative phenotypes and programmed cell death, a mechanism responsible for the elimination of superfluous cells during development. We discuss the ancient origins and deep conservation of programmed cell death (its function, forms and underlying core regulatory gene networks), and propose that it was co-opted repeatedly to generate alternative phenotypes at the level of cells, tissues, organs, external morphology, and even individuals. We review several examples from across the tree of life to explore the conditions under which programmed cell death is likely to facilitate the evolution of alternative phenotypes.

Auxin concentration and xylem production of Pinus massoniana in a subtropical forest in south China

Auxin is involved in various developmental processes of plants, including cell division in cambium and xylem differentiation. However, most studies linking auxin and xylem cell production are performed in environments with a strong seasonality (i.e., temperate and boreal climates). The temporal dynamics of auxin and cambial activity of subtropical trees remain basically unknown. In this study, we sampled four microcores weekly in three individuals of Chinese red pine (Pinus massoniana Lamb.) from February to December 2015-16 to compare xylem formation with auxin concentration in subtropical China. During the entire period of sampling, the number of cambial cells varied from 2 to 7, while the number of cells in the enlarging zone ranged from 1 to 4 and from 1 to 5 in the wall-thickening zone. In 2015, the average auxin concentration was 3.46 ng g-1, with 33 xylem cells being produced at the end of the year. In 2016, a lower auxin concentration (2.59 ng g-1) corresponded to a reduced annual xylem production (13.7 cells). No significant relationship between auxin concentration and number of xylem cells in differentiation was found at the weekly scale. Unlike in boreal and temperate forests, the lack of wood formation seasonality in subtropical forests makes it more difficult to reveal the relationship between auxin concentration and number of xylem cells in differentiation at the intra-annual scale. The frequent and repeated samplings might have reduced auxin concentration in the developing cambium and xylem, resulting in a lower xylem cell production.

Effects of Excess Manganese on the Xylem Sap Protein Profile of Tomato (Solanum lycopersicum) as Revealed by Shotgun Proteomic Analysis

Metal toxicity is a common problem in crop species worldwide. Some metals are naturally toxic, whereas others such as manganese (Mn) are essential micro-nutrients for plant growth but can become toxic when in excess. Changes in the composition of the xylem sap, which is the main pathway for ion transport within the plant, is therefore vital to understanding the plant's response(s) to metal toxicity. In this study we have assessed the effects of exposure of tomato roots to excess Mn on the protein profile of the xylem sap, using a shotgun proteomics approach. Plants were grown in nutrient solution using 4.6 and 300 µM MnCl2 as control and excess Mn treatments, respectively. This approach yielded 668 proteins reliably identified and quantified. Excess Mn caused statistically significant (at p ≤ 0.05) and biologically relevant changes in relative abundance (≥2-fold increases or ≥50% decreases) in 322 proteins, with 82% of them predicted to be secretory using three different prediction tools, with more decreasing than increasing (181 and 82, respectively), suggesting that this metal stress causes an overall deactivation of metabolic pathways. Processes most affected by excess Mn were in the oxido-reductase, polysaccharide and protein metabolism classes. Excess Mn induced changes in hydrolases and peroxidases involved in cell wall degradation and lignin formation, respectively, consistent with the existence of alterations in the cell wall. Protein turnover was also affected, as indicated by the decrease in proteolytic enzymes and protein synthesis-related proteins. Excess Mn modified the redox environment of the xylem sap, with changes in the abundance of oxido-reductase and defense protein classes indicating a stress scenario. Finally, results indicate that excess Mn decreased the amounts of proteins associated with several signaling pathways, including fasciclin-like arabinogalactan-proteins and lipids, as well as proteases, which may be involved in the release of signaling peptides and protein maturation. The comparison of the proteins changing in abundance in xylem sap and roots indicate the existence of tissue-specific and systemic responses to excess Mn. Data are available via ProteomeXchange with identifier PXD021973.

Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation

Plant xylem cells conduct water and mineral nutrients. Although most plant cells are totipotent, xylem cells are unusual and undergo terminal differentiation. Many genes regulating this process are well characterized, including the Vascular-related NAC Domain 7 (VND7), MYB46, and MYB83 transcription factors, which are proposed to act in interconnected feedforward loops (FFLs). Less is known regarding the molecular mechanisms underlying the terminal transition to xylem cell differentiation. Here, we generate whole-root and single-cell data, which demonstrate that VND7 initiates sharp switching of root cells to xylem cell identity. Based on these data, we identified 4 candidate VND7 downstream target genes capable of generating this switch. Although MYB46 responds to VND7 induction, it is not among these targets. This system provides an important model to study the emergent properties that may give rise to totipotency relative to terminal differentiation and reveals xylem cell subtypes.

CELLULOSE SYNTHASE INTERACTING 1 is required for wood mechanics and leaf morphology in aspen

Cellulose microfibrils synthesized by CELLULOSE SYNTHASE COMPLEXES (CSCs) are the main load-bearing polymers in wood. CELLULOSE SYNTHASE INTERACTING1 (CSI1) connects CSCs with cortical microtubules, which align with cellulose microfibrils. Mechanical properties of wood are dependent on cellulose microfibril alignment and structure in the cell walls, but the molecular mechanism(s) defining these features is unknown. Herein, we investigated the role of CSI1 in hybrid aspen (Populus tremula × Populus tremuloides) by characterizing transgenic lines with significantly reduced CSI1 transcript abundance. Reduction in leaves (50-80%) caused leaf twisting and misshaped pavement cells, while reduction (70-90%) in developing xylem led to impaired mechanical wood properties evident as a decrease in the elastic modulus and rupture. X-ray diffraction measurements indicate that microfibril angle was not impacted by the altered CSI1 abundance in developing wood fibres. Instead, the augmented wood phenotype of the transgenic trees was associated with a reduced cellulose degree of polymerization. These findings establish a function for CSI1 in wood mechanics and in defining leaf cell shape. Furthermore, the results imply that the microfibril angle in wood is defined by CSI1 independent mechanism(s).

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

Single-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but its application to plants has been limited. Here, we used the high-throughput Drop-seq approach to profile >12,000 cells from Arabidopsis roots. This identified numerous distinct cell types, covering all major root tissues and developmental stages, and illuminated specific marker genes for these populations. In addition, we demonstrate the utility of this approach to study the impact of environmental conditions on developmental processes. Analysis of roots grown with or without sucrose supplementation uncovers changes in the relative frequencies of cell types in response to sucrose. Finally, we characterize the transcriptome changes that occur across endodermis development and identify nearly 800 genes with dynamic expression as this tissue differentiates. Collectively, we demonstrate that single-cell RNA-seq can be used to profile developmental processes in plants and show how they can be altered by external stimuli.

The application of single-cell transcriptome profiling to plants has been limited. Shulse et al. performed Drop-seq on Arabidopsis roots, generating a transcriptional resource for >12,000 cells across major populations. This revealed marker genes for distinct cell types, cell frequency changes resulting from sucrose addition, and genes dynamically regulated during development.

Occurrence of autophagy during pioneer root and stem development in Populus trichocarpa

Autophagy is involved in developmentally programmed cell death and is identified during the early development of phloem, as well as xylem with a dual role, as both an inducer and executioner of cell death. The regulation of primary and secondary development of roots and stems is important for the establishment of root systems and for the overall survival of trees. The molecular and cellular basis of the autophagic processes, which are used at distinct moments during the growth of both organs, is crucial to understand the regulation of their development. To address this, we use Populus trichocarpa seedlings grown in a rhizotron system to examine the autophagy processes involved in root and stem development. To monitor the visual aspects of autophagy, transmission electron microscopy (TEM) and immunolocalization of AuTophaGy-related protein (ATG8) enabled observations of the phenomenon at a structural level. To gain further insight into the autophagy process at the protein and molecular level, we evaluated the expression of ATG gene transcripts and ATG protein levels. Alternations in the expression level of specific ATG genes and localization of ATG8 proteins were observed during the course of root or stem primary and secondary development. Specifically, ATG8 was present in the cells exhibiting autophagy, during the differentiation and early development of xylem and phloem tissues, including both xylary and extraxylary fibers. Ultrastructural observations revealed tonoplast invagination with the formation of autophagic-like bodies. Additionally, the accumulation of autophagosomes was identifiable during the differentiation of xylem in both organs, long before the commencement of cell death. Taken together, these results provide evidence in support of the dual role of autophagy in developmental PCD. A specific role of the controller of cell death, which is a committed step with the release of hydrolytic enzymes from the vacuole and final digestion of protoplast, from which there is no return once initiated, is only attributed to mega-autophagy.

Deciphering hydrogen peroxide-induced signalling towards stress tolerance in plants

Plants encounter a variety of adverse environmental conditions, such as high salinity, drought, extreme heat/cold and heavy metals contamination (abiotic stress) or attack of various pathogens (biotic stress). These detrimental environmental factors enhanced the ROS production such as singlet oxygen (¹O₂), superoxide (O₂ ^•-), hydrogen peroxide (H₂O₂) and hydroxyl radicals (OH^•). ROS are highly reactive and directly target several cellular molecules and metabolites, which lead to severe cellular dysfunction. Plants respond to oxidative damages by activating antioxidant machinery to trigger signalling cascades for stress tolerance. H₂O₂ signalling balances the plant metabolism through cross-talk with other signals and plant hormones during growth, development and stress responses. H₂O₂ facilitates the regulation of different stress-responsive transcription factors (TFs) including NAC, Zinc finger, WRKY, ERF, MYB, DREB and bZIP as both upstream and downstream events during stress signalling. The present review focuses on the biological synthesis of the H₂O₂ and its effect on the upregulation of kinase genes and stress related TFs for imparting stress tolerance.

γVPE plays an important role in programmed cell death for xylem fiber cells by activating protease CEP1 maturation in Arabidopsis thaliana

The vacuolar processing enzyme (VPE) plays an important role in PCD and was originally identified as the proteinase responsible for the maturation and activation of vacuolar proteins in plants. We found that γVPE is involved in PCD of xylem fiber cells through the activation of CEP1 proproteases into mature protease in Arabidopsis. The γVPE protein was expressed specifically in cambium cells cambium, the primary phloem and the primary xylem during stem development. The recombinant γVPE appearing as a proenzyme at pH 7.0, and then transforming into a 40-kD mature enzyme at pH 5.5 in vitro by self-cleaving. The mature γVPE protein activated CEP1 maturation in vitro, whereas this activity was inhibited in the γvpe mutant. Transmission electron microscopy showed delayed PCD in fiber cells and thickening of secondary fiber cell walls in the γvpe mutant. Transcriptome analysis showed that the expression of 2001 genes was significantly altered expression in the γvpe mutants, and most of them are important for secondary cell wall formation and PCD. Our results demonstrate that γVPE is a crucial processing enzyme for xylem fiber cells PCD during stem development.

Single cell RNA sequencing and its promise in reconstructing plant vascular cell lineages

In the last decade, recent advances in single-cell RNA sequencing coupled with computational algorithms have opened new avenues to study the cell type composition of tissues and organs as well as to infer cell developmental trajectories. These technologies have been used to resolve and map atlases of tissues and organs in many animal species as well as to further order cell developmental trajectories. Despite these advances in animals, many of the current plant cell type expression profiles confound multiple developmental stages preventing an accurate monitoring of cell lineage. In this review, we propose how the application of single-cell sequencing will improve our molecular understanding of cell type differentiation. Using root vascular cells as a model, we highlight the potential of single cell transcriptomics as well as its limitations to monitor the progression of vascular maturation. By comparing cell morphology, functionality and gene expression, we aim to provide a new perspective of plant cell type differentiation.

Investigation of Morphological Features of Autophagy During Plant Programmed Cell Death

The investigation of autophagy particularly when observed during programmed cell death (PCD) is strongly based on the morphological features recorded with transmission electron microscope (TEM). Here we describe methods to induce and to inhibit autophagy in plants. Also some tips for obtaining better preservation of biological membranes, crucial for the investigation of autophagy, are provided together with information about plant autophagic mutants, use of antibodies and methods for 3D reconstruction of large membrane-bound objects that are commonly formed during autophagic processes leading to PCD in plants.

Xylem Cell Wall Formation in Pioneer Roots and Stems of Populus trichocarpa (Torr. & Gray)

Regulation of gene expression, as determined by the genetics of the tree species, is a major factor in determining wood quality. Therefore, the identification of genes that play a role in xylogenesis is extremely important for understanding the mechanisms shaping the plant phenotype. Efforts to develop new varieties characterized by higher yield and better wood quality will greatly benefit from recognizing and understanding the complex transcriptional network underlying wood development. The present study provides a detailed comparative description of the changes that occur in genes transcription and the biosynthesis of cell-wall-related compounds during xylogenesis in Populus trichocarpa pioneer roots and stems. Even though results of microarray analysis indicated that only approximately 10% of the differentially expressed genes were common to both organs, many fundamental mechanisms were similar; e.g. the pattern of expression of genes involved in the biosynthesis of cell wall proteins, polysaccharides, and lignins. Gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) shows that the composition of monosaccharides was also very similar, with an increasing amount of xylose building secondary cell wall hemicellulose and pectins, especially in the stems. While hemicellulose degradation was typical for stems, possibly due to the intensive level of cell wall lignification. Notably, the main component of lignins in roots were guiacyl units, while syringyl units were dominant in stems, where fibers are especially needed for support. Our study is the first comprehensive analysis, at the structural and molecular level, of xylogenesis in under- and aboveground tree parts, and clearly reveals the great complexity of molecular mechanisms underlying cell wall formation and modification during xylogenesis in different plant organs.

"Programmed Cell Death: A Process of Death for Survival" - How Far Terminology Pertinent for Cell Death in Unicellular Organisms

Programmed cell death (PCD) is genetically regulated phenomenon of selective elimination of target cells that are either under pathological conditions or unwanted for organism’s normal growth and development due to other reasons. The process although being genetically controlled is physiological in nature that renders some hallmarks like blebs in the cell membrane, lobe formation in nuclear membrane, DNA nicks resulting to DNA ladder of 200 bp, and downstream activation of caspases. Moreover, as the process refers to the death of “targeted cell”, the term is exclusively suitable for multicellular organisms. Number of reports advocate similar type of cell death process in unicellular organisms. As cell death in unicellular organisms is also reflected by the signature of PCD obtained in metazoans, such cell death has been grouped under the broad category of PCD. It is pertinent to mention that by definition a unicellular organism is made of a single cell wherein it carries out all of its life processes. Using the term “Programmed Cell Death” with a preset “survival strategy of the organism” for unicellular organisms looks misnomer. Therefore, this correspondence argues and requests recommendation committee on cell death to revisit for the nomenclature of the cell death process in the unicellular organisms.

Global Picture of Protein Regulation in Response to Dibutyl Phthalate (DBP) Stress of Two Brassica parachinensis Cultivars Differing in DBP Accumulation

iTRAQ analysis was used to map the proteomes of two Brassica parachinensis cultivars that differed in dibutyl phthalate (DBP) accumulation. A total of 5699 proteins were identified to obtain 152 differentially regulated proteins, of which 64 and 48 were specific to a high- and a low-DBP-accumulation cultivar, respectively. Genotype-specific biological processes were involved in coping with DBP stress, accounting for the variation in DBP tolerance and accumulation. Formation of high DBP accumulation in B. parachinensis might attribute to the more effective regulation of protein expression in physiology and metabolism, including (a) enhanced cell wall biosynthesis and modification, (b) better maintenance of photosynthesis and energy balance, (c) greatly improved total capacity for antioxidation and detoxification, and (d) enhanced cellular transport and signal transduction. Our novel findings contribute to a global picture of DBP-induced alterations of protein profiles in crops and provide valuable information for the development of molecular-assisted breeds of low-accumulation cultivars.

Plant Vacuoles

Plant vacuoles are multifunctional organelles. On the one hand, most vegetative tissues develop lytic vacuoles that have a role in degradation. On the other hand, seed cells have two types of storage vacuoles: protein storage vacuoles (PSVs) in endosperm and embryonic cells and metabolite storage vacuoles in seed coats. Vacuolar proteins and metabolites are synthesized on the endoplasmic reticulum and then transported to the vacuoles via Golgi-dependent and Golgi-independent pathways. Proprotein precursors delivered to the vacuoles are converted into their respective mature forms by vacuolar processing enzyme, which also regulates various kinds of programmed cell death in plants. We summarize two types of vacuolar membrane dynamics that occur during defense responses: vacuolar membrane collapse to attack viral pathogens and fusion of vacuolar and plasma membranes to attack bacterial pathogens. We also describe the chemical defense against herbivores brought about by the presence of PSVs in the idioblast myrosin cell.

Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylem sap as revealed by shotgun analyses

The aim of this work was to study the effects of Fe and Mn deficiencies on the xylem sap proteome of tomato using a shotgun proteomic approach, with the final goal of elucidating plant response mechanisms to these stresses. This approach yielded 643 proteins reliably identified and quantified with 70% of them predicted as secretory. Iron and Mn deficiencies caused statistically significant and biologically relevant abundance changes in 119 and 118 xylem sap proteins, respectively. In both deficiencies, metabolic pathways most affected were protein metabolism, stress/oxidoreductases and cell wall modifications. First, results suggest that Fe deficiency elicited more stress responses than Mn deficiency, based on the changes in oxidative and proteolytic enzymes. Second, both nutrient deficiencies affect the secondary cell wall metabolism, with changes in Fe deficiency occurring via peroxidase activity, and in Mn deficiency involving peroxidase, Cu-oxidase and fasciclin-like arabinogalactan proteins. Third, the primary cell wall metabolism was affected by both nutrient deficiencies, with changes following opposite directions as judged from the abundances of several glycoside-hydrolases with endo-glycolytic activities and pectin esterases. Fourth, signaling pathways via xylem involving CLE and/or lipids as well as changes in phosphorylation and N-glycosylation also play a role in the responses to these stresses. Biological significance In spite of being essential for the delivery of nutrients to the shoots, our knowledge of xylem responses to nutrient deficiencies is very limited. The present work applies a shotgun proteomic approach to unravel the effects of Fe and Mn deficiencies on the xylem sap proteome. Overall, Fe deficiency seems to elicit more stress in the xylem sap proteome than Mn deficiency, based on the changes measured in proteolytic and oxido-reductase proteins, whereas both nutrients exert modifications in the composition of the primary and secondary cell wall. Cell wall modifications could affect the mechanical and permeability properties of the xylem sap vessels, and therefore ultimately affect solute transport and distribution to the leaves. Results also suggest that signaling cascades involving lipid and peptides might play a role in nutrient stress signaling and pinpoint interesting candidates for future studies. Finally, both nutrient deficiencies seem to affect phosphorylation and glycosylation processes, again following an opposite pattern.

Retrospective Analysis of Wood Anatomical Traits Reveals a Recent Extension in Tree Cambial Activity in Two High-Elevation Conifers

The study of xylogenesis or wood formation is a powerful, yet labor intensive monitoring approach to investigate intra-annual tree growth responses to environmental factors. However, it seldom covers more than a few growing seasons, so is in contrast to the much longer lifespan of woody plants and the time scale of many environmental processes. Here we applied a novel retrospective approach to test the long-term (1926-2012) consistency in the timing of onset and ending of cambial activity, and in the maximum cambial cell division rate in two conifer species, European larch and Norway spruce at high-elevation in the Alps. We correlated daily temperature with time series of cell number and lumen area partitioned into intra-annual sectors. For both species, we found a good correspondence (1-10 days offset) between the periods when anatomical traits had significant correlations with temperature in recent decades (1969-2012) and available xylogenesis data (1996-2005), previously collected at the same site. Yet, results for the 1926-1968 period indicate a later onset and earlier ending of the cambial activity by 6-30 days. Conversely, the peak in the correlation between annual cell number and temperature, which should correspond to the peak in secondary growth rate, was quite stable over time, with just a minor advance of 4-5 days in the recent decades. Our analyses on time series of wood anatomical traits proved useful to infer on past long-term changes in xylogenetic phases. Combined with intensive continuous monitoring, our approach will improve the understanding of tree responses to climate variability in both the short- and long-term context.

Xylogenesis in zinnia (Zinnia elegans) cell cultures: unravelling the regulatory steps in a complex developmental programmed cell death event

MAIN CONCLUSION

Physiological and molecular studies support the view that xylogenesis can largely be determined as a specific form of vacuolar programmed cell death (PCD). The studies in xylogenic zinnia cell culture have led to many breakthroughs in xylogenesis research and provided a background for investigations in other experimental models in vitro and in planta . This review discusses the most essential earlier and recent findings on the regulation of xylem elements differentiation and PCD in zinnia and other xylogenic systems. Xylogenesis (the formation of water conducting vascular tissue) is a paradigm of plant developmental PCD. The xylem vessels are composed of fused tracheary elements (TEs)-dead, hollow cells with patterned lignified secondary cell walls. They result from the differentiation of the procambium and cambium cells and undergo cell death to become functional post-mortem. The TE differentiation proceeds through a well-coordinated sequence of events in which differentiation and the programmed cellular demise are intimately connected. For years a classical experimental model for studies on xylogenesis was the xylogenic zinnia (Zinnia elegans) cell culture derived from leaf mesophyll cells that, upon induction by cytokinin and auxin, transdifferentiate into TEs. This cell system has been proven very efficient for investigations on the regulatory components of xylem differentiation which has led to many discoveries on the mechanisms of xylogenesis. The knowledge gained from this system has potentiated studies in other xylogenic cultures in vitro and in planta. The present review summarises the previous and latest findings on the hormonal and biochemical signalling, metabolic pathways and molecular and gene determinants underlying the regulation of xylem vessels differentiation in zinnia cell culture. Highlighted are breakthroughs achieved through the use of xylogenic systems from other species and newly introduced tools and analytical approaches to study the processes. The mutual dependence between PCD signalling and the differentiation cascade in the program of TE development is discussed.

Establishment and Utilization of Habituated Cell Suspension Cultures for Hormone-Inducible Xylogenesis

The development of inducible cell differentiation in suspension cultures led to multiple breakthroughs. It enabled the understanding of the chronology, duration, regulation and interdependency of the multiple events leading to fully functional specialized cells. The most studied cell differentiation in plants using inducible suspension cultures is the formation of tracheary elements (TEs) - the hydro-mineral sap conducting cells. Several in vitro systems established in different plant species have been developed to trigger TE formation on-demand. Here, we describe the establishment, harvesting and analysis of Arabidopsis thaliana stable habituated cell lines inducible by hormones to differentiate into TEs on-demand. Moreover, we explain the means to monitor and modify the chronology, duration and regulation of the progression of TE formation.

Winter drought impairs xylem phenology, anatomy and growth in Mediterranean Scots pine forests

Continental Mediterranean forests face drought but also cold spells and both climate extremes can impair the resilience capacity of these forests. Climate warming could amplify the negative effects of cold spells by inducing premature dehardening. Here we capitalize on a winter drought-induced dieback triggered by a cold spell which occurred in December 2001 affecting Scots pine forests in eastern Spain. We assessed post-dieback recovery by quantifying and comparing radial growth and xylem anatomy of non-declining (ND, crown cover >50%) and declining (D, crown cover ≤50%) trees in two sites (VP, Villarroya de los Pinares; TO, Torrijas). We also characterized xylogenesis in both sites and aboveground productivity in site VP. Dieback caused legacy effects since needle loss, a 60% reduction in litter fall and radial-growth decline characterized D-trees 3 years after dieback symptoms started appearing in spring 2002. D-trees formed collapsed tracheids in the 2002-ring, particularly in the most affected VP site where xylogenesis differences between ND and D trees were most noticeable. The lower growth rates of D-trees were caused by a shorter duration of their major xylogenesis phases. In site VP the radial-enlargement and wall-thickening of tracheids were significantly reduced in D-trees as compared to ND-trees because these xylogenesis phases tended to start earlier and end later in ND-trees. Gompertz models fitted to tracheid production predicted that maximum growth rates occurred 11-12 days earlier in ND than in D-trees. The formation of radially-enlarging tracheids was enhanced by longer days in both study sites and also by wetter conditions in the driest TO site, but xylogenesis sensitivity to climate was reduced in D-trees. Winter-drought dieback impairs xylem anatomy and phenology, aboveground productivity, xylogenesis and growth in Mediterranean Scots pine populations. Affected stands show a costly post-dieback recovery challenging their resilience ability.

Mass spectrometry data for in vitro protein profiles in early and late stages of Douglas-fir xylogenesis

A Douglas-fir tissue culture system was developed [1] that could be induced to differentiate into tracheary elements (fibers) making it possible to monitor xylogenesis in vitro by a proteomics approach. Two proteomes, one from an early and one from a late stage of fiber differentiation process were analyzed and compared. Obtained mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [2] with the dataset identifiers PXD001484 and DOI:10.6019/ PXD001484 [3].

The mystery of underground death: cell death in roots during ontogeny and in response to environmental factors

Programmed cell death (PCD) is an essential part of the ontogeny of roots and their tolerance/resistance mechanisms, allowing adaptation and growth under adverse conditions. It occurs not only at the cellular and subcellular level, but also at the levels of tissues, organs and even whole plants. This process involves a wide spectrum of mechanisms, from signalling and the expression of specific genes to the degradation of cellular structures. The major goals of this review were to broaden current knowledge about PCD processes in roots, and to identify mechanisms associated with both developmental and stress-associated cell death in roots. Vacuolar cell death, when cell contents are removed by a combination of an autophagy-associated process and the release of hydrolases from a collapsed vacuole, is responsible for programming self-destruction. Regardless of the conditions and factors inducing PCD, its subcellular events usually include the accumulation of autophagosome-like structures, and the formation of massive lytic compartments. In some cases these are followed by the nuclear changes of chromatin condensation and DNA fragmentation. Tonoplast disruption and vacuole implosion occur very rapidly, are irreversible and constitute a definitive step toward cell death in roots. Active cell elimination plays an important role in various biological processes in the life history of plants, leading to controlled cellular death during adaptation to changing environmental conditions, and organ remodelling throughout development and senescence.

Reactive Oxygen Species (ROS): Beneficial Companions of Plants' Developmental Processes

Reactive oxygen species (ROS) are generated inevitably in the redox reactions of plants, including respiration and photosynthesis. In earlier studies, ROS were considered as toxic by-products of aerobic pathways of the metabolism. But in recent years, concept about ROS has changed because they also participate in developmental processes of plants by acting as signaling molecules. In plants, ROS regulate many developmental processes such as cell proliferation and differentiation, programmed cell death, seed germination, gravitropism, root hair growth and pollen tube development, senescence, etc. Despite much progress, a comprehensive update of advances in the understanding of the mechanisms evoked by ROS that mediate in cell proliferation and development are fragmentry and the matter of ROS perception and the signaling cascade remains open. Therefore, keeping in view the above facts, an attempt has been made in this article to summarize the recent findings regarding updates made in the regulatory action of ROS at various plant developmental stages, which are still not well-known.

Phenolic profile within the fine-root branching orders of an evergreen species highlights a disconnect in root tissue quality predicted by elemental- and molecular-level carbon composition

Fine roots constitute a significant source of plant productivity and litter turnover across terrestrial ecosystems, but less is known about the quantitative and qualitative profile of phenolic compounds within the fine-root architecture, which could regulate the potential contribution of plant roots to the soil organic matter pool. To understand the linkage between traditional macro-elemental and morphological traits of roots and their molecular-level carbon chemistry, we analyzed seasonal variations in monomeric yields of the free, bound, and lignin phenols in fine roots (distal five orders) and leaves of Ardisia quinquegona. Fine roots contained two-fold higher concentrations of bound phenols and three-fold higher concentrations of lignin phenols than leaves. Within fine roots, the concentrations of free and bound phenols decreased with increasing root order, and seasonal variation in the phenolic profile was more evident in lower order than in higher order roots. The morphological and macro-elemental root traits were decoupled from the quantity, composition and tissue association of phenolic compounds, revealing the potential inability of these traditional parameters to capture the molecular identity of phenolic carbon within the fine-root architecture and between fine roots and leaves. Our results highlight the molecular-level heterogeneity in phenolic carbon composition within the fine-root architecture, and imply that traits that capture the molecular identity of the root construct might better predict the decomposition dynamics within fine-root orders.

In vitro protein profiles in the early and late stages of Douglas-fir xylogenesis

The process of wood formation is of great interest to control and manipulate wood quality for economically important gymnosperms. A Douglas-fir tissue culture system was developed that could be induced to differentiate into tracheary elements (fibers) making it possible to monitor xylogenesis in vitro by a proteomics approach. Two proteomes were analyzed and compared, one from an early and one from a late stage of the fiber differentiation process. After 18 weeks in a differentiation-inducing medium, 80% of the callus cells were elongated while 20% showed advanced spiral thickening indicating full wood fiber differentiation. Based on 2D electrophoresis, MS, and data analyses (data are available via ProteomeXchange with identifier PXD001484.), it was shown that in nondifferentiated callus (representing an early stage of development), proteins related to protein metabolism, cellular energy, and primary cell wall metabolism were abundant. By comparison, in cells actively differentiating wood fibers (representing a late stage of development), proteins involved in cell wall polysaccharide biosynthesis predominated together with housekeeping and stress-associated proteins.

Dynamics of long-distance signaling via plant vascular tissues

Plant vascular systems are constructed by specific cell wall modifications through which cells are highly specialized to make conduits for water and nutrients. Xylem vessels are formed by thickened cell walls that remain after programmed cell death, and serve as water conduits from the root to the shoot. In contrast, phloem tissues consist of a complex of living cells, including sieve tube elements and their neighboring companion cells, and translocate photosynthetic assimilates from mature leaves to developing young tissues. Intensive studies on the content of vascular flow fluids have unveiled that plant vascular tissues transport various types of gene product, and the transport of some provides the molecular basis for the long-distance communications. Analysis of xylem sap has demonstrated the presence of proteins in the xylem transpiration stream. Recent studies have revealed that CLE and CEP peptides secreted in the roots are transported to above ground via the xylem in response to plant-microbe interaction and soil nitrogen starvation, respectively. Their leucine-rich repeat transmembrane receptors localized in the shoot phloem are required for relaying the signal from the shoot to the root. These findings well-fit to the current scenario of root-to-shoot-to-root feedback signaling, where peptide transport achieves the root-to-shoot signaling, the first half of the signaling process. Meanwhile, it is now well-evidenced that proteins and a range of RNAs are transported via the phloem translocation system, and some of those can exert their physiological functions at their destinations, including roots. Thus, plant vascular systems may serve not only as conduits for the translocation of essential substances but also as long-distance communication pathways that allow plants to adapt to changes in internal and external environments at the whole plant level.

Flavonoid supplementation affects the expression of genes involved in cell wall formation and lignification metabolism and increases sugar content and saccharification in the fast-growing eucalyptus hybrid E. urophylla x E. grandis

BACKGROUND

Eucalyptus species are the most widely planted hardwood species in the world and are renowned for their rapid growth and adaptability. In Brazil, one of the most widely grown Eucalyptus cultivars is the fast-growing Eucalyptus urophylla x Eucalyptus grandis hybrid. In a previous study, we described a chemical characterization of these hybrids when subjected to flavonoid supplementation on 2 distinct timetables, and our results revealed marked differences between the wood composition of the treated and untreated trees.

RESULTS

In this work, we report the transcriptional responses occurring in these trees that may be related to the observed chemical differences. Gene expression was analysed through mRNA-sequencing, and notably, compared to control trees, the treated trees display differential down-regulation of cell wall formation pathways such as phenylpropanoid metabolism as well as differential expression of genes involved in sucrose, starch and minor CHO metabolism and genes that play a role in several stress and environmental responses. We also performed enzymatic hydrolysis of wood samples from the different treatments, and the results indicated higher sugar contents and glucose yields in the flavonoid-treated plants.

CONCLUSIONS

Our results further illustrate the potential use of flavonoids as a nutritional complement for modifying Eucalyptus wood, since, supplementation with flavonoids alters its chemical composition, gene expression and increases saccharification probably as part of a stress response.

New insights into pioneer root xylem development: evidence obtained from Populus trichocarpa plants grown under field conditions

BACKGROUND AND AIMS

Effective programmed xylogenesis is critical to the structural framework of the plant root system and its central role in the acquisition and long-distance transport of water and nutrients. The process of xylem differentiation in pioneer roots under field conditions is poorly understood. In this study it is hypothesized that xylogenesis, an example of developmental programmed cell death (PCD), in the roots of woody plants demonstrates a clearly defined sequence of events resulting in cell death. A comprehensive analysis was therefore undertaken to identify the stages of xylogenesis in pioneer roots from procambial cells to fully functional vessels with lignified cell walls and secondary cell wall thickenings.

METHODS

Xylem differentiation was monitored in the pioneer roots of Populus trichocarpa at the cytological level using rhizotrons under field conditions. Detection and localization of the signalling molecule nitric oxide (NO) and hydrogen peroxide (H2O2) was undertaken and a detailed examination of nuclear changes during xylogenesis was conducted. In addition, analyses of the expression of genes involved in secondary cell wall synthesis were performed in situ.

KEY RESULTS

The primary event in initially differentiating tracheary elements (TEs) was a burst of NO in thin-walled cells, followed by H2O2 synthesis and the appearance of TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling)-positive nuclei. The first changes in nuclear structure were observed in the early stages of xylogenesis of pioneer roots, prior to lignification; however, the nucleus was detectable under transmission electron microscopy in differentiating cells until the stage at which vacuole integrity was maintained, indicating that their degradation was slow and prolonged. The subsequent sequence of events involved secondary cell wall formation and autophagy. Potential gene markers from the cinnamyl alcohol dehydrogenase (CAD) gene family that were related to secondary wall synthesis were associated with primary xylogenesis, showing clear expression in cells that undergo differentiation into TEs and in the thin-walled cells adjacent to the xylem pole.

CONCLUSIONS

The early events of TE formation during pioneer root development are described, together with the timing of xylogenesis from signalling via NO, through secondary cell wall synthesis and autophagy events that are initiated long before lignification. This is the first work describing experiments conducted in planta on roots under field conditions demonstrating that the process of xylogenesis in vivo might be gradual and complex.

Programmes of cell death and autolysis in tracheary elements: when a suicidal cell arranges its own corpse removal

Tracheary element (TE) differentiation represents a unique system to study plant developmental programmed cell death (PCD). TE PCD occurs after deposition of the secondary cell walls when an unknown signal induces tonoplast rupture and the arrest of cytoplasmic streaming. TE PCD is tightly followed by autolysis of the protoplast and partial hydrolysis of the primary cell walls. This review integrates TE differentiation, programmed cell death (PCD), and autolysis in a biological and evolutionary context. The collective evidence from the evolutionary and molecular studies suggests that TE differentiation consists primarily of a programme for cell death and autolysis under the direct control of the transcriptional master switches VASCULAR NAC DOMAIN 6 (VND6) and VND7. In this scenario, secondary cell walls represent a later innovation to improve the water transport capacity of TEs which necessitates transcriptional regulators downstream of VND6 and VND7. One of the most fascinating features of TEs is that they need to prepare their own corpse removal by expression and accumulation of hydrolases that are released from the vacuole after TE cell death. Therefore, TE differentiation involves, in addition to PCD, a programmed autolysis which is initiated before cell death and executed post-mortem. It has recently become clear that TE PCD and autolysis are separate processes with separate molecular regulation. Therefore, the importance of distinguishing between the cell death programme per se and autolysis in all plant PCD research and of careful description of the morphological, biochemical, and molecular sequences in each of these processes, is advocated.

Xylem sap proteomics

Proteomic analysis of xylem sap has recently become a major field of interest to understand several biological questions related to plant development and responses to environmental clues. The xylem sap appears as a dynamic fluid undergoing changes in its proteome upon abiotic and biotic stresses. Unlike cell compartments which are amenable to purification in sufficient amount prior to proteomic analysis, the xylem sap has to be collected in particular conditions to avoid contamination by intracellular proteins and to obtain enough material. A model plant like Arabidopsis thaliana is not suitable for such an analysis because efficient harvesting of xylem sap is difficult. The analysis of the xylem sap proteome also requires specific procedures to concentrate proteins and to focus on proteins predicted to be secreted. Indeed, xylem sap proteins appear to be synthesized and secreted in the root stele or to originate from dying differentiated xylem cells. This chapter describes protocols to collect xylem sap from Brassica species and to prepare total and N-glycoprotein extracts for identification of proteins by mass spectrometry analyses and bioinformatics.

Post mortem function of AtMC9 in xylem vessel elements

Cell death of xylem elements is manifested by rupture of the tonoplast and subsequent autolysis of the cellular contents. Metacaspases have been implicated in various forms of plant cell death but regulation and execution of xylem cell death by metacaspases remains unknown. Analysis of the type II metacaspase gene family in Arabidopsis thaliana supported the function of METACASPASE 9 (AtMC9) in xylem cell death. Progression of xylem cell death was analysed in protoxylem vessel elements of 3-d-old atmc9 mutant roots using reporter gene analysis and electron microscopy. Protoxylem cell death was normally initiated in atmc9 mutant lines, but detailed electron microscopic analyses revealed a role for AtMC9 in clearance of the cell contents post mortem, that is after tonoplast rupture. Subcellular localization of fluorescent AtMC9 reporter fusions supported a post mortem role for AtMC9. Further, probe-based activity profiling suggested a function of AtMC9 on activities of papain-like cysteine proteases. Our data demonstrate that the function of AtMC9 in xylem cell death is to degrade vessel cell contents after vacuolar rupture. We further provide evidence on a proteolytic cascade in post mortem autolysis of xylem vessel elements and suggest that AtMC9 is part of this cascade.

Lignin depletion enhances the digestibility of cellulose in cultured xylem cells

Plant lignocellulose constitutes an abundant and sustainable source of polysaccharides that can be converted into biofuels. However, the enzymatic digestion of native plant cell walls is inefficient, presenting a considerable barrier to cost-effective biofuel production. In addition to the insolubility of cellulose and hemicellulose, the tight association of lignin with these polysaccharides intensifies the problem of cell wall recalcitrance. To determine the extent to which lignin influences the enzymatic digestion of cellulose, specifically in secondary walls that contain the majority of cellulose and lignin in plants, we used a model system consisting of cultured xylem cells from Zinniaelegans. Rather than using purified cell wall substrates or plant tissue, we have applied this system to study cell wall degradation because it predominantly consists of homogeneous populations of single cells exhibiting large deposits of lignocellulose. We depleted lignin in these cells by treating with an oxidative chemical or by inhibiting lignin biosynthesis, and then examined the resulting cellulose digestibility and accessibility using a fluorescent cellulose-binding probe. Following cellulase digestion, we measured a significant decrease in relative cellulose content in lignin-depleted cells, whereas cells with intact lignin remained essentially unaltered. We also observed a significant increase in probe binding after lignin depletion, indicating that decreased lignin levels improve cellulose accessibility. These results indicate that lignin depletion considerably enhances the digestibility of cellulose in the cell wall by increasing the susceptibility of cellulose to enzymatic attack. Although other wall components are likely to contribute, our quantitative study exploits cultured Zinnia xylem cells to demonstrate the dominant influence of lignin on the enzymatic digestion of the cell wall. This system is simple enough for quantitative image analysis, but realistic enough to capture the natural complexity of lignocellulose in the plant cell wall. Consequently, these cells represent a suitable model for analyzing native lignocellulose degradation.

Looking for Arabidopsis thaliana peroxidases involved in lignin biosynthesis

Monolignol polymerization into lignin is catalyzed by peroxidases or laccases. Recently, a Zinnia elegans peroxidase (ZePrx) that is considered responsible for monolignol polymerization in this plant has been molecularly and functionally characterized. Nevertheless, Arabidopsis thaliana has become an alternative model plant for studies of lignification, filling the gaps that may occur with Z. elegans. The arabidopsis genome offers the possibility of performing bioinformatic analyses and data mining that are not yet feasible with other plant species, in order to obtain preliminary evidence on the role of genes and proteins. In our search for arabidopsis homologs to the ZePrx, we performed an exhaustive in silico characterization of everything from the protein to the transcript of Arabidopsis thaliana peroxidases (AtPrxs) homologous to ZePrx, with the aim of identifying one or more peroxidases that may be involved in monolignol polymerization. Nine peroxidases (AtPrx 4, 5, 52, 68, 67, 36, 14, 49 and 72) with an E-value greater than 1e-80 with ZePrx were selected for this study. The results demonstrate that a high level of 1D, 2D and 3D homology between these AtPrxs and ZePrx are not always accompanied by the presence of the same electrostatic and mRNA properties that indicate a peroxidase is involved in lignin biosynthesis. In summary, we can confirm that the peroxidases involved in lignification are among AtPrx 4, 52, 49 and 72. Their structural and mRNA features indicate that exert their action in the cell wall similar to ZePrx.

The Tr-cp 14 cysteine protease in white clover (Trifolium repens) is localized to the endoplasmic reticulum and is associated with programmed cell death during development of tracheary elements

Cysteine proteases are known to be associated with programmed cell death, developmental senescence and some types of pathogen and stress-induced responses. In the present study, we have characterized the cysteine protease Tr-cp 14 in white clover (Trifolium repens). Tr-cp 14 belongs to the C1A family of cysteine proteases with homology to XCP1 and XCP2 from Arabidopsis thaliana and p48h-17 from Zinnia elegans, which previously have been reported to be associated with tracheary element differentiation. The proform as well as the processed form of the protein was detected in petioles, flowers and leaves, but the processed form was more abundant in leaves and petioles than in flowers. The Tr-cp 14 protein was localized to differentiating tracheary elements within the xylem, indicating that the cysteine protease is involved in protein re-mobilization during tracheary element differentiation. Immunogold studies suggest that the protease prior to the burst of the vacuole was associated to the ER cisternae. After disruption of the tonoplast, it was found in the cytoplasm, and, in later stages, associated with disintegrating material dispersed throughout the cell.

Galactoglucomannan oligosaccharides are assumed to affect tracheary element formation via interaction with auxin in Zinnia xylogenic cell culture

Galactoglucomannan oligosaccharides seem to interact with auxin in xylogenic cell culture, thus influencing mainly metaxylem-like tracheary element differentiation depending on timing with hormones and the process kinetics. Complex mapping of Zinnia mesophyll cell transdifferentiation into tracheary elements with or without prior cell division was documented after palisade and spongy parenchyma cell immobilization during the first 4 days of culture. Here, we report a positive effect of galactoglucomannan oligosaccharides on cell viability and density and higher metaxylem-like tracheary element formation in xylogenic cell culture. The maximal positive effect was achieved by the simultaneous addition of the oligosaccharides and growth hormones (auxin, cytokinin) to the cell culture medium. Moreover, a large number of metaxylem-like tracheary elements were observed in a low-auxin medium supplemented with oligosaccharides, but not in a low-cytokinin medium, suggesting a close relationship between auxin and the oligosaccharides during tracheary element formation.

Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species

Background

Eucalyptus is one of the most important sources of industrial cellulose. Three species of this botanical group are intensively used in breeding programs: E. globulus, E. grandis and E. urophylla. E. globulus is adapted to subtropical/temperate areas and is considered a source of high-quality cellulose; E. grandis grows rapidly and is adapted to tropical/subtropical climates; and E. urophylla, though less productive, is considered a source of genes related to robustness. Wood, or secondary xylem, results from cambium vascular differentiation and is mostly composed of cellulose, lignin and hemicelluloses. In this study, the xylem transcriptomes of the three Eucalyptus species were investigated in order to provide insights on the particularities presented by each of these species.

Results

Data analysis showed that (1) most Eucalyptus genes are expressed in xylem; (2) most genes expressed in species-specific way constitutes genes with unknown functions and are interesting targets for future studies; (3) relevant differences were observed in the phenylpropanoid pathway: E. grandis xylem presents higher expression of genes involved in lignin formation whereas E. urophylla seems to deviates the pathway towards flavonoid formation; (4) stress-related genes are considerably more expressed in E. urophylla, suggesting that these genes may contribute to its robustness.

Conclusions

The comparison of these three transcriptomes indicates the molecular signatures underlying some of their distinct wood characteristics. This information may contribute to the understanding of xylogenesis, thus increasing the potential of genetic engineering approaches aiming at the improvement of Eucalyptus forest plantations productivity.

Phytohormones and microRNAs as sensors and regulators of leaf senescence: assigning macro roles to small molecules

Ageing or senescence is an intricate and highly synchronized developmental phase in the life of plant parts including leaf. Senescence not only means death of a plant part, but during this process, different macromolecules undergo degradation and the resulting components are transported to other parts of the plant. During the period from when a leaf is young and green to the stage when it senesces, a multitude of factors such as hormones, environmental factors and senescence associated genes (SAGs) are involved. Plant hormones including salicylic acid, abscisic acid, jasmonic acid and ethylene advance leaf senescence, whereas others like cytokinins, gibberellins, and auxins delay this process. The environmental factors which generally affect plant development and growth, can hasten senescence, the examples being nutrient dearth, water stress, pathogen attack, radiations, high temperature and light intensity, waterlogging, and air, water or soil contamination. Other important influences include carbohydrate accumulation and high carbon/nitrogen level. To date, although several genes involved in this complex process have been identified, still not much information exists in the literature on the signalling mechanism of leaf senescence. Now, the Arabidopsis mutants have paved our way and opened new vistas to elucidate the signalling mechanism of leaf senescence for which various mutants are being utilized. Recent studies demonstrating the role of microRNAs in leaf senescence have reinforced our knowledge of this intricate process. This review provides a comprehensive and critical analysis of the information gained particularly on the roles of several plant growth regulators and microRNAs in regulation of leaf senescence.

Four 13-lipoxygenases contribute to rapid jasmonate synthesis in wounded Arabidopsis thaliana leaves: a role for lipoxygenase 6 in responses to long-distance wound signals

Damage-inducible defenses in plants are controlled in part by jasmonates, fatty acid-derived regulators that start to accumulate within 30 s of wounding a leaf. Using liquid chromatography-tandem mass spectrometry, we sought to identify the 13-lipoxygenases (13-LOXs) that initiate wound-induced jasmonate synthesis within a 190-s timeframe in Arabidopsis thaliana in 19 single, double, triple and quadruple mutant combinations derived from the four 13-LOX genes in this plant. All four 13-LOXs were found to contribute to jasmonate synthesis in wounded leaves: among them LOX6 showed a unique behavior. The relative contribution of LOX6 to jasmonate synthesis increased with distance from a leaf tip wound, and LOX6 was the only 13-LOX necessary for the initiation of early jasmonate synthesis in leaves distal to the wounded leaf. Herbivory assays that compared Spodoptera littoralis feeding on the lox2-1 lox3B lox4A lox6A quadruple mutant and the lox2-1 lox3B lox4A triple mutant revealed a role for LOX6 in defense of the shoot apical meristem. Consistent with this, we found that LOX6 promoter activity was strong in the apical region of rosettes. The LOX6 promoter was active in and near developing xylem cells and in expression domains we term subtrichomal mounds.

The effect of summer shading on flower bud morphogenesis in apricot (Prunus armeniaca L.)

The aim of this investigation was to assess whether imposed summer shading treatments in apricot (Prunus armeniaca L.) can affect the main phenological phases related to the floral morphogenesis (floral differentiation, xylogenesis), flower bud growth and quality in terms of bud capacity to set fruit. Experimental trials were carried out on fully-grown trees of ‘San Castrese’ and ‘Stark Early Orange’ cultivars characterized by different biological and agronomical traits to which shadings were imposed in July and August. Histological analysis was carried out from summer onwards in order to determine the evolution of floral bud differentiation, and the acropetal progression of primary xylem differentiation along the flower bud axis. Periodical recordings to evaluate the bud drop, blooming time, flowering and fruit set rates were performed also. These shade treatments determined a temporary shutdown of floral differentiation, slowed xylem progression up to the resumption of flower bud growth and a reduced entity of flowering and fruit set. These events were particularly marked in ‘San Castrese’ cultivar, which is well known for its adaptability to different climatic conditions. These findings suggest that adequate light penetration within the canopy during the summer season could be the determining factor when defining the qualitative traits of flower buds and their regular growth, and ultimately to obtain good and constant crops.