The expansin superfamily

The dilemma of bacterial expansins evolution. The unusual case of Streptomyces acidiscabies and Kutzneria sp. 744

Expansins are a superfamily of proteins mainly present in plants that are also found in bacteria, fungi and amoebozoa. Expansin proteins bind the plant cells wall and relax the cellulose microfibrils without any enzymatic action. The evolution of this kind of proteins exposes a complex pattern of horizontal gene transferences that makes difficult to determine the precise origin of non-plant expansins. We performed a genome-wide search of inter-domain horizontal gene transfer events using Streptomyces species and found a plant-like expansin in the Streptomyces acidiscabies proteome. This finding leads us to study in deep the origin and the characteristics of this peculiar protein, also present in the species Kutzneria sp.744. Using phylogenetic analyses, we determine that indeed S. acidiscabies and Kutzneria sp.744 expansins are located inside the plants expansins A clade. Using secondary and tertiary structural information, we observed that the electrostatic potentials and the folding of expansins are similar, independently of the proteins' origin. Using all this information, we conclude that S. acidiscabies and Kutzneria sp.744 expansins have a plant origin but differ from plant and bacterial canonical expansins. This finding suggests that the experimental research around this kind of expansins can be promissory in the future.

α-Expansin EXPA4 Positively Regulates Abiotic Stress Tolerance but Negatively Regulates Pathogen Resistance in Nicotiana tabacum

Since they function as cell wall-loosening proteins, expansins can affect plant growth, developmental processes and environmental stress responses. Our previous study demonstrated that changes in Nicotiana tabacum α-expansin 4 (EXPA4) expression affect the sensitivity of tobacco to Tobacco mosaic virus [recombinant TMV encoding green fluorescent protein (TMV-GFP)] infection by Agrobacterium-mediated transient expression. In this study, to characterize the function of tobacco EXPA4 further, EXPA4 RNA interfernce (RNAi) mutants and overexpression lines were generated and assayed for their tolerance to abiotic stress and resistance to pathogens. First, the differential phenotypes and histomorphology of transgenic plants with altered EXPA4 expression indicated that EXPA4 is essential for normal tobacco growth and development. By utilizing tobacco EXPA4 mutants with abiotic stress, it was demonstrated that RNAi mutants have increased hypersensitivity to salt and drought stress. In contrast, the overexpression of EXPA4 in tobacco conferred greater tolerance to salt and drought stress, as indicated by less cell damage, higher fresh weight, higher soluble sugar and proline accumulation, and higher expression levels of several stress-responsive genes. In addition, the overexpression lines were more susceptible to the viral pathogen TMV-GFP when compared with the wild type or RNAi mutants. The induction of the antioxidant system, several defense-associated phytohormones and gene expression was down-regulated in overexpression lines but up-regulated in RNAi mutants when compared with the wild type following TMV-GFP infection. In addition, EXPA4 overexpression also accelerated the disease development of Pseudomonas syringae DC3000 on tobacco. Taken together, these results suggested that EXPA4 appears to be important in tobacco growth and responses to abiotic and biotic stress.

Comparative transcriptome analysis of Zea mays in response to petroleum hydrocarbon stress

The use of plants for the improvement of soils contaminated with hydrocarbons has been a primary research focus in phytoremediation studies. Obtaining insights regarding genes that are differentially induced by petroleum hydrocarbon stress and understanding plant response mechanisms against petroleum hydrocarbons at molecular level is essential for developing better phytoremediation strategies to remove these hazardous contaminants. The purpose of this study was to analyze the transcriptomal profile changes under hydrocarbon stress in maize plants and identify the genes associated with the phytoremediative capacity. Zea mays GeneChips were used to analyze the global transcriptome profiles of maize treated with different concentrations of petroleum hydrocarbons. In total, 883, 1281, and 2162 genes were differentially induced or suppressed in the comparisons of 0 (control) vs. 1% crude petroleum, 1 vs. 5% crude petroleum, and 0 vs. 5% crude petroleum, respectively. The differentially expressed genes were functionally associated with the osmotic stress response mechanism, likely preventing the uptake of water from the roots, and the phytoremediative capacity of plants, e.g., secretory pathway genes. The results presented here show the regulatory mechanisms in the response to petroleum hydrocarbon pollution in soil. Our study provides global gene expression data of Z. mays in response to petroleum hydrocarbon stress that could be useful for further studies investigating the biodegradation mechanism in maize and other plants.

Massive up-regulation of LBD transcription factors and EXPANSINs highlights the regulatory programs of rhizomania disease

Rhizomania of sugar beet, caused by Beet necrotic yellow vein virus (BNYVV), is characterized by excessive lateral root (LR) formation leading to dramatic reduction of taproot weight and massive yield losses. LR formation represents a developmental process tightly controlled by auxin signaling through AUX/IAA-ARF responsive module and LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcriptional network. Several LBD transcription factors play central roles in auxin-regulated LR development and act upstream of EXPANSINS (EXPs), cell wall (CW)-loosening proteins involved in plant development via disruption of the extracellular matrix for CW relaxation and expansion. Here, we present evidence that BNYVV hijacks these auxin-regulated pathways resulting in formation LR and root hairs (RH). We identified an AUX/IAA protein (BvAUX28) as interacting with P25, a viral virulence factor. Mutational analysis indicated that P25 interacts with domains I and II of BvAUX28. Subcellular localization of co-expressed P25 and BvAUX28 showed that P25 inhibits BvAUX28 nuclear localization. Moreover, root-specific LBDs and EXPs were greatly upregulated during rhizomania development. Based on these data, we present a model in which BNYVV P25 protein mimics action of auxin by removing BvAUX28 transcriptional repressor, leading to activation of LBDs and EXPs. Thus, the evidence highlights two pathways operating in parallel and leading to uncontrolled formation of LRs and RHs, the main manifestation of the rhizomania syndrome.

Effects of heat treatment on enzyme activity and expression of key genes controlling cell wall remodeling in strawberry fruit

Modification of cell wall polymers composition and structure is one of the main factors contributing to textural changes during strawberry (Fragaria x ananassa, Duch.) fruit ripening and storage. The present study aimed to provide new data to understand the molecular basis underlying the postharvest preservation of strawberry cell wall structure by heat treatment. Ripe fruit (cv. Aroma) were heat-treated in air oven (3 h at 45 °C) and then stored 8 days at 4 °C + 2 days at 20 °C, while maintaining a set of non-treated fruit as controls. The effect of heat stress on the expression pattern of key genes controlling strawberry cell wall metabolism, as well as some enzymatic activities was investigated. The expression of genes proved to be relevant for pectin disassembly and fruit softening process (FaPG1, FaPLB, FaPLC, FaAra1, FaβGal4) were down-regulated by heat treatment, while the expression of genes being involved in the reinforcement of cell wall as pectin-methylesterase (FaPME1) and xyloglucan endo-transglycosilase (FaXTH1) was up-regulated. Total cell wall amount as well as cellulose, hemicellulose, neutral sugars and ionically and covalently bounded pectins were higher in heat-stressed fruit compared to controls, which might be related to higher firmness values. Interestingly, heat stress was able to arrest the in vitro cell wall swelling process during postharvest fruit ripening, suggesting a preservation of cell wall structure, which was in agreement with a lower growth rate of Botrytis cinerea on plates containing cell walls from heat-stressed fruit when compared to controls.

In silico insights on diverse interacting partners and phosphorylation sites of respiratory burst oxidase homolog (Rbohs) gene families from Arabidopsis and rice

BACKGROUND

NADPH oxidase (Nox) is a critical enzyme involved in the generation of apoplastic superoxide (O₂^-), a type of reactive oxygen species (ROS) and hence regulate a wide range of biological functions in many organisms. Plant Noxes are the homologs of the catalytic subunit from mammalian NADPH oxidases and are known as respiratory burst oxidase homologs (Rbohs). Previous studies have highlighted their versatile roles in tackling different kind of stresses and in plant growth and development. In the current study, potential interacting partners and phosphorylation sites were predicted for Rboh proteins from two model species (10 Rbohs from Arabidopsis thaliana and 9 from Oryza sativa japonica). The present work is the first step towards in silico prediction of interacting partners and phosphorylation sites for Rboh proteins from two plant species.

RESULTS

In this work, an extensive range of potential partners (unique and common), leading to diverse functions were revealed from interaction networks and gene ontology classifications, where majority of AtRbohs and OsRbohs play role in stress-related activities, followed by cellular development. Further, 68 and 38 potential phosphorylation sites were identified in AtRbohs and OsRbohs, respectively. Their distribution, location and kinase specificities were also predicted and correlated with experimental data as well as verified with the other EF-hand containing proteins within both genomes.

CONCLUSIONS

Analysis of regulatory mechanisms including interaction with diverse partners and post-translational modifications like phosphorylation have provided insights regarding functional multiplicity of Rbohs. The bioinformatics-based workflow in the current study can be used to get insights for interacting partners and phosphorylation sites from Rbohs of other plant species.

Acidic cell elongation drives cell differentiation in the Arabidopsis root

In multicellular systems, the control of cell size is fundamental in regulating the development and growth of the different organs and of the whole organism. In most systems, major changes in cell size can be observed during differentiation processes where cells change their volume to adapt their shape to their final function. How relevant changes in cell volume are in driving the differentiation program is a long-standing fundamental question in developmental biology. In the Arabidopsis root meristem, characteristic changes in the size of the distal meristematic cells identify cells that initiated the differentiation program. Here, we show that changes in cell size are essential for the initial steps of cell differentiation and that these changes depend on the concomitant activation by the plant hormone cytokinin of the EXPAs proteins and the AHA1 and AHA2 proton pumps. These findings identify a growth module that builds on a synergy between cytokinin-dependent pH modification and wall remodeling to drive differentiation through the mechanical control of cell walls.

Molecular Mechanisms Preventing Senescence in Response to Prolonged Darkness in a Desiccation-Tolerant Plant

The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress- and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast- and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senescence, also was down-regulated. In response to darkness, most of the photosynthesis- and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degradation. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglycerol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chlorophyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness.

GW2 Functions as an E3 Ubiquitin Ligase for Rice Expansin-Like 1

Seed size is one of the most important traits determining the yield of cereal crops. Many studies have been performed to uncover the mechanism of seed development. However, much remains to be understood, especially at the molecular level, although several genes involved in seed size have been identified. Here, we show that rice Grain Width 2 (GW2), a RING-type E3 ubiquitin ligase, can control seed development by catalyzing the ubiquitination of expansin-like 1 (EXPLA1), a cell wall-loosening protein that increases cell growth. Microscopic examination revealed that a GW2 mutant had a chalky endosperm due to the presence of loosely packed, spherical starch granules, although the grain shape was normal. Yeast two-hybrid and in vitro pull-down assays showed a strong interaction between GW2 and EXPLA1. In vitro ubiquitination analysis demonstrated that EXPLA1 was ubiquitinated by GW2 at lysine 279 (K279). GW2 and EXPLA1 colocalized to the nucleus when expressed simultaneously. These results suggest that GW2 negatively regulates seed size by targeting EXPLA1 for degradation through its E3 ubiquitin ligase activity.

Plant-like bacterial expansins play contrasting roles in two tomato vascular pathogens

Expansin proteins, which loosen plant cell walls, play critical roles in normal plant growth and development. The horizontal acquisition of functional plant-like expansin genes in numerous xylem-colonizing phytopathogenic bacteria suggests that bacterial expansins may also contribute to virulence. To investigate the role of bacterial expansins in plant diseases, we mutated the non-chimeric expansin genes (CmEXLX2 and RsEXLX) of two xylem-inhabiting bacterial pathogens, the Actinobacterium Clavibacter michiganensis ssp. michiganensis (Cmm) and the β-proteobacterium Ralstonia solanacearum (Rs), respectively. The Cmm ΔCmEXLX2 mutant caused increased symptom development on tomato, which was characterized by more rapid wilting, greater vascular necrosis and abundant atypical lesions on distant petioles. This increased disease severity correlated with larger in planta populations of the ΔCmEXLX2 mutant, even though the strains grew as well as the wild-type in vitro. Similarly, when inoculated onto tomato fruit, ΔCmEXLX2 caused significantly larger lesions with larger necrotic centres. In contrast, the Rs ΔRsEXLX mutant showed reduced virulence on tomato following root inoculation, but not following direct petiole inoculation, suggesting that the RsEXLX expansin contributes to early virulence at the root infection stage. Consistent with this finding, ΔRsEXLX attached to tomato seedling roots better than the wild-type Rs, which may prevent mutants from invading the plant's vasculature. These contrasting results demonstrate the diverse roles of non-chimeric bacterial expansins and highlight their importance in plant-bacterial interactions.

Differential reinforcement of enzymatic hydrolysis by adding chemicals and accessory proteins to high solid loading substrates with different pretreatments

High dosage of enzyme is required to achieve effective lignocellulose hydrolysis, especially at high-solid loadings, which is a significant barrier to large-scale bioconversion of lignocellulose. Here, we screened four chemical additives and three accessory proteins for their effects on the enzymatic hydrolysis of various lignocellulosic materials. The effects were found to be highly dependent on the composition and solid loadings of substrates. For xylan-extracted lignin-rich corncob residue, the enhancing effect of PEG 6000 was most pronounced and negligibly affected by solid content, which reduced more than half of enzyme demand at 20% dry matter (DM). Lytic polysaccharide monooxygenase enhanced the hydrolysis of ammonium sulfite wheat straw pulp, and its addition reduced about half of protein demand at the solid loading of 20% DM. Supplementation of the additives in the hydrolysis of pure cellulose and complex lignocellulosic materials revealed that their effects are tightly linked to pretreatment strategies.

Waterlogging affects plant morphology and the expression of key genes in tef (Eragrostis tef)

Tef [Eragrostis tef (Zucc.) Trotter], an allotetraploid cereal that is a staple food to over 60 million people in the Horn of Africa, has a high nutritional content and is resistant to many biotic and abiotic stresses such as waterlogging and drought. Three tef genotypes, Alba, Tsedey, and Quncho, were subjected to waterlogging conditions and their growth, physiology, and change in transcript expression were measured with the goal of identifying targets for breeding cultivars with improved waterlogging tolerance. Root and shoot growth and dry weight were observed over 22 days. Stomatal conductance and chlorophyll and carotenoid contents were quantified. Microscopy was used to monitor changes in the stem cross sections. Illumina RNA sequencing was used to obtain the expression profiles of tef under flooding and control conditions and was verified using qPCR. Results indicated differences in growth between the three genotypes. Waterlogged Tsedey plants grew higher and had more root biomass than normally watered Tsedey plants. Quncho and Alba genotypes were more susceptible to the excess moisture stress. The effects of these changes were observed on the plant physiology. Among the three tested tef genotypes, Tsedey formed more aerenchyma than Alba and had accelerated growth under waterlogging. Tsedey and Quncho had constitutive aerenchyma. Genes affecting carbohydrate metabolism, cell growth, response to reactive oxygen species, transport, signaling, and stress responses were found to change under excess moisture stress. In general, these results show the presence of substantial anatomical and physiological differences among tef genotypes when waterlogged during the early growth stage.

Genome-wide identification of wheat (Triticum aestivum) expansins and expansin expression analysis in cold-tolerant and cold-sensitive wheat cultivars

Plant expansins are proteins involved in cell wall loosening, plant growth, and development, as well as in response to plant diseases and other stresses. In this study, we identified 128 expansin coding sequences from the wheat (Triticum aestivum) genome. These sequences belong to 45 homoeologous copies of TaEXPs, including 26 TaEXPAs, 15 TaEXPBs and four TaEXLAs. No TaEXLB was identified. Gene expression and sub-expression profiles revealed that most of the TaEXPs were expressed either only in root tissues or in multiple organs. Real-time qPCR analysis showed that many TaEXPs were differentially expressed in four different tissues of the two wheat cultivars—the cold-sensitive ‘Chinese Spring (CS)’ and the cold-tolerant ‘Dongnongdongmai 1 (D1)’ cultivars. Our results suggest that the differential expression of TaEXPs could be related to low-temperature tolerance or sensitivity of different wheat cultivars. Our study expands our knowledge on wheat expansins and sheds new light on the functions of expansins in plant development and stress response.

Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms

Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication (WGD) doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, and thus are considered as a major driving force in species diversification. We performed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene duplication events by surveying tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approximately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes.

Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members

The glycoside hydrolase family 45 (GH45) of carbohydrate modifying enzymes is mostly comprised of β-1,4-endoglucanases. Significant diversity between the GH45 members has prompted the division of this family into three subfamilies: A, B and C, which may differ in terms of the mechanism, general architecture, substrate binding and cleavage. Here, we use a combination of X-ray crystallography, bioinformatics, enzymatic assays, molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure, substrate binding and enzymatic specificity of the GH45 subfamily C endoglucanase from Phanerochaete chrysosporium (PcCel45A). We investigated the role played by different residues in the binding of the enzyme to cellulose oligomers of different lengths and examined the structural characteristics and dynamics of PcCel45A that make subfamily C so dissimilar to other members of the GH45 family. Due to the structural similarity shared between PcCel45A and domain I of expansins, comparative analysis of their substrate binding was also carried out. Our bioinformatics sequence analyses revealed that the hydrolysis mechanisms in GH45 subfamily C is not restricted to use of the imidic asparagine as a general base in the "Newton's cradle" catalytic mechanism recently proposed for this subfamily.

Integration of Bacterial Expansin on Agarolytic Complexes to Enhance the Degrading Activity of Red Algae by Control of Gelling Properties

Expansin act by loosening hydrogen bonds in densely packed polysaccharides. This work characterizes the biological functions of expansin in the gelling and degradation of algal polysaccharides. In this study, the bacterial expansin BpEX from Bacillus pumilus was fused with the dockerin module of a cellulosome system for assembly with agarolytic complexes. The assembly of chimeric expansin caused an indicative enhancement in agarase activity. The enzymatic activities on agar substrate and natural biomass were 3.7-fold and 3.3-fold higher respectively than that of agarase as a single enzyme. To validate the effect on the agar degradation, the regulation potential of parameters related to gel rheology by bacterial expansin was experimentally investigated to indicate that the bacterial expansin lowered the gelling temperature and viscosity of agar. Thus, these results demonstrated the possibility of advancing more efficient strategies for utilizing agar as oligo sugar source in the biorefinery field that uses marine biomass as feedstocks.

Tobacco alpha-expansin EXPA4 plays a role in Nicotiana benthamiana defence against Tobacco mosaic virus

MAIN CONCLUSION

Tobacco EXPA4 plays a role in Nicotiana benthamiana defence against virus attack and affects antioxidative metabolism and phytohormone-mediated immunity responses in tobacco. Expansins are cell wall-loosening proteins known for their endogenous functions in cell wall extensibility during plant growth. The effects of expansins on plant growth, developmental processes and environment stress responses have been well studied. However, the exploration of expansins in plant virus resistance is rarely reported. In the present study, virus-induced gene silencing (VIGS) and Agrobacterium-mediated transient overexpression were conducted to investigate the role of Nicotiana tabacum alpha-expansin 4 (EXPA4) in modulating Tobacco mosaic virus (TMV-GFP) resistance in Nicotiana benthamiana. The results indicated that silencing of EXPA4 reduced the sensitivity of N. benthamiana to TMV-GFP, and EXPA4 overexpression accelerated virus reproduction on tobacco. In addition, our data suggested that the changes of virus accumulation in response to EXPA4 expression levels could further affect the antioxidative metabolism and phytohormone-related pathways in tobacco induced by virus inoculation. EXPA4-silenced plants with TMV-GFP have enhanced antioxidant enzymes activities, which were down-regulated in virus-inoculated 35S:EXPA4 plants. Salicylic acid accumulation and SA-mediated defence genes induced by TMV-GFP were up-regulated in EXPA4-silenced plants, but depressed in 35S:EXPA4 plants. Furthermore, a VIGS approach was used in combination with exogenous phytohormone treatments, suggesting that EXPA4 has different responses to different phytohormones. Taken together, these results suggested that EXPA4 plays a role in tobacco defence against viral pathogens.

Real-time adsorption and action of expansin on cellulose

BACKGROUND

Biological pretreatment is an environmentally safe method for disrupting recalcitrant structures of lignocellulose and thereby improving their hydrolysis efficiency. Expansin and expansin-like proteins act synergistically with cellulases during hydrolysis. A systematic analysis of the adsorption behavior and mechanism of action of expansin family proteins can provide a basis for the development of highly efficient pretreatment methods for cellulosic substrates using expansins.

RESULTS

Adsorption of Bacillus subtilis expansin (BsEXLX1) onto cellulose film under different conditions was monitored in real time using a quartz crystal microbalance with dissipation. A model was established to describe the adsorption of BsEXLX1 onto the film. High temperatures increased the initial adsorption rate while reducing the maximum amount of BsEXLX1 adsorbed onto the cellulose. Non-ionic surfactants (polyethylene glycol 4000 and Tween 80) at low concentrations enhanced BsEXLX1 adsorption; whereas, high concentrations had the opposite effect. However, sodium dodecyl sulfate inhibited adsorption at both low and high concentrations. We also investigated the structural changes of cellulose upon BsEXLX1 adsorption and found that BsEXLX1 adsorption decreased the crystallinity index, disrupted hydrogen bonding, and increased the surface area of cellulose, indicating greater accessibility of the substrate to the protein.

CONCLUSIONS

These results increase our understanding of the interaction between expansin and cellulose, and provide evidence for expansin treatment as a promising strategy to enhance enzymatic hydrolysis of lignocellulose.

Transcriptome dynamic of Arabidopsis roots infected with Phytophthora parasitica identifies VQ29, a gene induced during the penetration and involved in the restriction of infection

Little is known about the responses of plant roots to filamentous pathogens, particularly to oomycetes. To assess the molecular dialog established between the host and the pathogen during early stages of infection, we investigated the overall changes in gene expression in A. thaliana roots challenged with P. parasitica. We analyzed various infection stages, from penetration and establishment of the interaction to the switch from biotrophy to necrotrophy.

We identified 3390 genes for which expression was modulated during the infection. The A. thaliana transcriptome displays a dynamic response to P. parasitica infection, from penetration onwards. Some genes were specifically coregulated during penetration and biotrophic growth of the pathogen. Many of these genes have functions relating to primary metabolism, plant growth, and defense responses. In addition, many genes encoding VQ motif-containing proteins were found to be upregulated in plant roots, early in infection. Inactivation of VQ29 gene significantly increased susceptibility to P. parasitica during the late stages of infection. This finding suggests that the gene contributes to restricting oomycete development within plant tissues. Furthermore, the vq29 mutant phenotype was not associated with an impairment of plant defenses involving SA-, JA-, and ET-dependent signaling pathways, camalexin biosynthesis, or PTI signaling. Collectively, the data presented here thus show that infection triggers a specific genetic program in roots, beginning as soon as the pathogen penetrates the first cells.

Metabolome and transcriptome profiling reveal new insights into somatic embryo germination in Norway spruce (Picea abies)

Transcriptome, metabolome and histological profiling were performed on normal and aberrant somatic embryo germinants of Norway spruce (Picea abies L. Karst) providing a simplistic systems biology description of conifer germination. Aberrant germinants (AGs) formed periderm-like tissue at the apical pole and lacked shoot growth above the cotyledons. Transcriptome profiling (RNA-Sequencing) revealed a total of 370 differentially expressed genes at ≥1 or ≤-1 log2-fold change, where 92% were down-regulated in AGs compared with normal germinants (NGs). Genes associated with shoot apical meristem formation were down-regulated in AGs, or not differentially expressed between AGs and NGs. Genes involved in hormone signaling and transport were also down-regulated. Metabolite profiling by gas chromatography-mass spectrometry (MS) and liquid chromatography-MS revealed biochemical difference between AGs and NGs, notably increased levels of sugars including glucose in AGs. Genes involved in glucose signaling were down-regulated and genes involved in starch biosynthesis were up-regulated, suggesting involvement of sugar signaling during late embryo development and germination. The overall results provide new data enabling further studies to confirm potential markers for a normal germination process in conifers.

NbEXPA1, an α-expansin, is plasmodesmata-specific and a novel host factor for potyviral infection

Plasmodesmata (PD), unique to the plant kingdom, are structurally complex microchannels that cross the cell wall to establish symplastic communication between neighbouring cells. Viral intercellular movement occurs through PD. To better understand the involvement of PD in viral infection, we conducted a quantitative proteomic study on the PD-enriched fraction from Nicotiana benthamiana leaves in response to infection by Turnip mosaic virus (TuMV). We report the identification of a total of 1070 PD protein candidates, of which 100 (≥2-fold increase) and 48 (≥2-fold reduction) are significantly differentially accumulated in the PD-enriched fraction, when compared with protein levels in the corresponding healthy control. Among the differentially accumulated PD protein candidates, we show that an α-expansin designated NbEXPA1, a cell wall loosening protein, is PD-specific. TuMV infection downregulates NbEXPA1 mRNA expression and protein accumulation. We further demonstrate that NbEXPA1 is recruited to the viral replication complex via the interaction with NIb, the only RNA-dependent RNA polymerase of TuMV. Silencing of NbEXPA1 inhibits plant growth and TuMV infection, whereas overexpression of NbEXPA1 promotes viral replication and intercellular movement. These data suggest that NbEXPA1 is a host factor for potyviral infection. This study not only generates a PD-proteome dataset that is useful in future studies to expound PD biology and PD-mediated virus-host interactions but also characterizes NbEXPA1 as the first PD-specific cell wall loosening protein and its essential role in potyviral infection.

Nanobubble Water's Promotion Effect of Barley (Hordeum vulgare L.) Sprouts Supported by RNA-Seq Analysis

The physiological promotion effect of nanobubble (NB) water on living organisms is still a poorly understood phenomenon which was discovered 1 decade ago. Here, we analyzed the barley (Hordeum vulgare L.) embryo transcriptome following the exposure to NB water and low-concentration hydrogen peroxide (H₂O₂) using RNA-Seq. We found that 349 genes were differentially expressed after 24 h exposure to NB water and 97 genes were differentially expressed after exposure to H₂O₂ solution. Gene ontology enrichment and cluster analyses revealed that NB water induced expression of genes related to cell division and cell wall loosening. RNA-Seq, quantitative real-time polymerase chain reaction, and enzyme activity measurements all pointed to gene-encoding peroxidases as a major factor responsible for the effects of physiological enhancement due to NB water. The exogenous hydroxyl radical (•OH) produced by NB water significantly increased the expression of genes related to peroxidase and NADPH, thus leading to an increased endogenous superoxide anion (O₂^•-) inside the barley seed. Appropriately, low concentrations of exogenously added reactive oxygen species (ROS) and endogenous ROS played important roles in plant growth and development. When ROS levels were low, the endogenous ROS was eliminated by ascorbate peroxidase and other peroxidases instead of activating the catalase and superoxidase dismutase. This data set will serve as the foundation for a system biology approach to understand physiological promotion effects of NB water on living organisms.

Integrated analysis of mRNA and miRNA expression profiling in rice backcrossed progenies (BC2F12) with different plant height

Inter-specific hybridization and backcrossing commonly occur in plants. The use of progeny generated from inter-specific hybridization and backcrossing has been developed as a novel model system to explore gene expression divergence. The present study investigated the analysis of gene expression and miRNA regulation in backcrossed introgression lines constructed from cultivated and wild rice. High-throughput sequencing was used to compare gene and miRNA expression profiles in three progeny lines (L1710, L1817 and L1730), with different plant heights resulting from the backcrossing of introgression lines (BC₂F₁₂) and their parents (O. sativa and O. longistaminata). A total of 25,387 to 26,139 mRNAs and 379 to 419 miRNAs were obtained in these rice lines. More differentially expressed genes and miRNAs were detected in progeny/O. longistaminata comparison groups than in progeny/O. sativa comparison groups. Approximately 80% of the genes and miRNAs showed expression level dominance to O. sativa, indicating that three progeny lines were closer to the recurrent parent, which might be influenced by their parental genome dosage. Approximately 16% to 64% of the differentially expressed miRNAs possessing coherent target genes were predicted, and many of these miRNAs regulated multiple target genes. Most genes were up-regulated in progeny lines compared with their parents, but down-regulated in the higher plant height line in the comparison groups among the three progeny lines. Moreover, certain genes related to cell walls and plant hormones might play crucial roles in the plant height variations of the three progeny lines. Taken together, these results provided valuable information on the molecular mechanisms of hybrid backcrossing and plant height variations based on the gene and miRNA expression levels in the three progeny lines.

Comparative RNA-Seq Analysis Uncovers a Complex Regulatory Network for Soybean Cyst Nematode Resistance in Wild Soybean (Glycine soja)

Soybean cyst nematode (SCN) is the most damaging pest of soybean worldwide. The molecular mechanism of SCN resistance remains largely unknown. We conducted a global RNA-seq comparison between a resistant genotype (S54) and a susceptible genotype (S67) of Glycine soja, the wild progenitor of soybean, to understand its regulatory network in SCN defense. The number of differentially expressed genes (DEGs) in S54 (2,290) was much larger than that in S67 (555). A number of defense-related genes/pathways were significantly induced only in S54, while photosynthesis and several metabolic pathways were affected in both genotypes with SCN infection. These defense-associated DEGs were involved in pathogen recognition, calcium/calmodulin-mediated defense signaling, jasmonic acid (JA)/ethylene (ET) and sialic acid (SA)-involved signaling, the MAPK signaling cascade, and WRKY-involved transcriptional regulation. Our results revealed a comprehensive regulatory network involved in SCN resistance and provided insights into the complex molecular mechanisms of SCN resistance in wild soybean.

Dynamic transcriptomic analysis of the early response of female flowers of Populus alba × P. glandulosa to pollination

Pollination is an important event in plant sexual reproduction, and post-pollination response is an essential process for reproduction. Populus alba × P. glandulosa is used widely in scientific research, especially in cross breeding as parents. Adult female P. alba × P. glandulosa flowers are highly compatible with pollen from male P. tomentosa, but the early post-pollination response of flowers at the molecular levels is unclear. In this study, RNA-seq was employed to comprehensively understand the response of female P. alba × P. glandulosa flowers to pollination. Enrichment analysis reveals that the 'plant hormone signal transduction' pathway is enhanced during pollen-pistil interaction. Moreover, genes related to auxin, gibberellin and ethylene biosynthesis were significantly up-regulated. Ca2+ and H+-related genes and cell wall-related genes are interrelated, and all of them are essential for pollen tube elongation in pistil, especially, free Ca2+ providing a concentration gradient for pollen tube guidance and involved in signal transduction. Furthermore, RNA-seq results indicate that genes involved in the adhesion and guidance for pollen germination and pollen tube growth are abundantly present in the extracellular matrix. Our study provides an overview and detailed information for understanding the molecular mechanism of early post-pollination response in this hybrid poplar reproduction.

Transcriptional mechanisms associated with seed dormancy and dormancy loss in the gibberellin-insensitive sly1-2 mutant of Arabidopsis thaliana

While widespread transcriptome changes were previously observed with seed dormancy loss, this study specifically characterized transcriptional changes associated with the increased seed dormancy and dormancy loss of the gibberellin (GA) hormone-insensitive sleepy1-2 (sly1-2) mutant. The SLY1 gene encodes the F-box subunit of an SCF E3 ubiquitin ligase needed for GA-triggered proteolysis of DELLA repressors of seed germination. DELLA overaccumulation in sly1-2 seeds leads to increased dormancy that can be rescued without DELLA protein destruction either by overexpression of the GA receptor, GA-INSENSITIVE DWARF1b (GID1b-OE) (74% germination) or by extended dry after-ripening (11 months, 51% germination). After-ripening of sly1 resulted in different transcriptional changes in early versus late Phase II of germination that were consistent with the processes known to occur. Approximately half of the transcriptome changes with after-ripening appear to depend on SLY1-triggered DELLA proteolysis. Given that many of these SLY1/GA-dependent changes are genes involved in protein translation, it appears that GA signaling increases germination capacity in part by activating translation. While sly1-2 after-ripening was associated with transcript-level changes in 4594 genes over two imbibition timepoints, rescue of sly1-2 germination by GID1b-OE was associated with changes in only 23 genes. Thus, a big change in sly1-2 germination phenotype can occur with relatively little change in the global pattern of gene expression during the process of germination. Most GID1b-OE-responsive transcripts showed similar changes with after-ripening in early Phase II of imbibition, but opposite changes with after-ripening by late Phase II. This suggests that GID1b-OE stimulates germination early in imbibition, but may later trigger negative feedback regulation.

Activity-independent screening of secreted proteins using split GFP

The large-scale industrial production of proteins requires efficient secretion, as provided, for instance, by the Sec system of Gram-positive bacteria. Protein engineering approaches to optimize secretion often involve the screening of large libraries, e.g. comprising a target protein fused to many different signal peptides. Respective high-throughput screening methods are usually based on photometric or fluorimetric assays enabling fast and simple determination of enzymatic activities. Here, we report on an alternative method for quantification of secreted proteins based on the split GFP assay. We analyzed the secretion by Bacillus subtilis of a homologous lipase and a heterologous cutinase by determination of GFP fluorescence and enzyme activity assays. Furthermore, we identified from a signal peptide library a variant of the biotechnologically relevant B. subtilis protein swollenin EXLX1 with up to 5-fold increased secretion. Our results demonstrate that the split GFP assay can be used to monitor secretion of enzymatic and non-enzymatic proteins in B. subtilis in a high-throughput manner.

Transcriptional and computational study of expansins differentially expressed in response to inclination in radiata pine

Plants have the ability to reorient their vertical growth when exposed to inclination. This response can be as quick as 2 h in inclined young pine (Pinus radiata D. Don) seedlings, with over accumulation of lignin observed after 9 days s. Several studies have identified expansins involved in cell expansion among other developmental processes in plants. Six putative expansin genes were identified in cDNA libraries isolated from inclined pine stems. A differential transcript abundance was observed by qPCR analysis over a time course of inclination. Five genes changed their transcript accumulation in both stem sides in a spatial and temporal manner compared with non-inclined stem. To compare these expansin genes, and to suggest a possible mechanism of action at molecular level, the structures of the predicted proteins were built by comparative modeling methodology. An open groove on the surface of the proteins composed of conserved zresidues was observed. Using a cellulose polymer as ligand the protein-ligand interaction was evaluated, with the results showing differences in the protein-ligand interaction mode. Differences in the binding energy interaction can be explained by changes in some residues that generate differences in electrostatic surface in the open groove region, supporting the participation of six members of multifamily proteins in this specific process. The data suggests participation of different expansin proteins in the dissembling and remodeling of the complex cell wall matrix during the reorientation response to inclination.

Proteomics analysis reveals the molecular mechanism underlying the transition from primary to secondary growth of poplar

Wood is the most important natural source of energy and also provides fuel and fiber. Considering the significant role of wood, it is critical to understand how wood is formed. Integration of knowledge about wood development at the cellular and molecular levels will allow more comprehensive understanding of this complex process. In the present study, we used a comparative proteomic approach to investigate the differences in protein profiles between primary and secondary growth in young poplar stems using tandem mass tag (TMT)-labeling. More than 10,816 proteins were identified, and, among these, 3106 proteins were differentially expressed during primary to secondary growth. Proteomic data were validated using a combination of histochemical staining, enzyme activity assays, and quantitative real-time PCR. Bioinformatics analysis revealed that these differentially expressed proteins are related to various metabolic pathways, mainly including signaling, phytohormones, cell cycle, cell wall, secondary metabolism, carbohydrate and energy metabolism, and protein metabolism as well as redox and stress pathways. This large proteomics dataset will be valuable for uncovering the molecular changes occurring during the transition from primary to secondary growth. Further, it provides new and accurate information for tree breeding to modify wood properties.

Molecular features of grass allergens and development of biotechnological approaches for allergy prevention

Allergic diseases are characterized by elevated allergen-specific IgE and excessive inflammatory cell responses. Among the reported plant allergens, grass pollen and grain allergens, derived from agriculturally important members of the Poaceae family such as rice, wheat and barley, are the most dominant and difficult to prevent. Although many allergen homologs have been predicted from species such as wheat and timothy grass, fundamental aspects such as the evolution and function of plant pollen allergens remain largely unclear. With the development of genetic engineering and genomics, more primary sequences, functions and structures of plant allergens have been uncovered, and molecular component-based allergen-specific immunotherapies are being developed. In this review, we aim to provide an update on (i) the distribution and importance of pollen and grain allergens of the Poaceae family, (ii) the origin and evolution, and functional aspects of plant pollen allergens, (iii) developments of allergen-specific immunotherapy for pollen allergy using biotechnology and (iv) development of less allergenic plants using gene engineering techniques. We also discuss future trends in revealing fundamental aspects of grass pollen allergens and possible biotechnological approaches to reduce the amount of pollen allergens in grasses.

Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene

Expansins are plant cell wall-loosening proteins involved in adaptive responses to environmental stimuli and various developmental processes. The first genome-wide analysis of the expansin superfamily in the Arachis genus identified 40 members in A. duranensis and 44 in A. ipaënsis, the wild progenitors of cultivated peanut (A. hypogaea). These expansins were further characterized regarding their subfamily classification, distribution along the genomes, duplication events, molecular structure, and phylogeny. A RNA-seq expression analysis in different Arachis species showed that the majority of these expansins are modulated in response to diverse stresses such as water deficit, root-knot nematode (RKN) infection, and UV exposure, with an expansin-like B gene (AraEXLB8) displaying a highly distinct stress-responsive expression profile. Further analysis of the AraEXLB8 coding sequences showed high conservation across the Arachis genotypes, with eight haplotypes identified. The modulation of AraEXLB8 expression in response to the aforementioned stresses was confirmed by qRT-PCR analysis in distinct Arachis genotypes, whilst in situ hybridization revealed transcripts in different root tissues according to the stress imposed. The overexpression of AraEXLB8 in soybean (Glycine max) composite plants remarkably decreased the number of galls in transformed hairy roots inoculated with RKN. This study improves the current understanding of the molecular evolution, divergence, and gene expression of expansins in Arachis, and provides molecular and functional insights into the role of expansin-like B, the less-studied plant expansin subfamily.

Genome-wide computational analysis of the secretome of brown algae (Phaeophyceae)

Brown algae have evolved complex multicellularity in the heterokont lineage. They are phylogenetically distant to land plants, fungi and animals. Especially, the members of Laminariales (so-called kelps) have developed highly differentiated tissues. Extracellular matrix (ECM) plays pivotal roles in a number of essential processes in multicellular organisms, such as cell adhesion, cell and tissue differentiations, cell-to-cell communication, and responses to environmental stimuli. In these processes, a set of extracellular secreted proteins called the secretome operates remodeling of the physicochemical nature of ECM and signal transduction by interacting with cell surface proteins and signaling molecules. Characterization of the secretome is a critical step to clarify the contributions of ECM to the multicellularity of brown algae. However, the identity of the brown algal secretome has been poorly understood. In order to reveal the repertory of the brown algal secretome and its involvement in the evolution of Laminariales, we conducted a genome-wide analysis of the brown algal secretome utilizing the published complete genome data of Ectocarpus siliculosus and Saccharina japonica as well as newly obtained RNA-seq data of seven laminarialean species (Agarum clathratum, Alaria crassifolia, Aureophycus aleuticus, Costaria costata, Pseudochorda nagaii, Saccharina angustata and Undaria pinnatifida) largely covering the laminarialean families. We established the in silico pipeline to systematically and accurately detect the secretome by combining multiple prediction algorithms for the N-terminal signal peptide and transmembrane domain within the protein sequence. From 16,189 proteins of E. siliculosus and 18,733 proteins of S. japonica, 552 and 964 proteins respectively were predicted to be classified as the secretome. Conserved domain analysis showed that the domain repertory were very similar to each other, and that of the brown algal secretome was partially common with that of the secretome of other multicellular organisms (land plants, fungi and animals). In the laminarialean species, it was estimated that the gene abundance and the domain architecture of putative ECM remodeling-related proteins were altered compared with those of E. siliculosus, and that the alteration started from the basal group of Laminariales. These results suggested that brown algae have developed their own secretome, and its functions became more elaborated in the more derived members in Laminariales.

Overexpression of the carbohydrate binding module from Solanum lycopersicum expansin 1 (Sl-EXP1) modifies tomato fruit firmness and Botrytis cinerea susceptibility

Firmness, one of the major determinants of postharvest quality and shelf life of fruits is determined by the mechanical resistance imposed by the plant cell wall. Expansins (EXP) are involved in the non-hydrolytic metabolic disassembly of plant cell walls, particularly in processes where relaxation of the wall is necessary, such as fruit development and ripening. As many carbohydrate-associated proteins, expansins have a putative catalytic domain and a carbohydrate-binding module (CBM). Several strategies have been pursued to control the loss of fruit firmness during storage. Most of the approaches have been to suppress the expression of key enzymes involved in the cell wall metabolism, but this is the first time that a CBM was overexpressed in a fruit aimed to control cell wall degradation and fruit softening. We report the constitutive overexpression of the CBM of Solanum lycopersicum expansin 1 (CBM-SlExp1) in the cell wall of tomato plants, and its effects on plant and fruit phenotype. Overexpression of CBM-SlExp1 increased the mechanical resistance of leaves, whereas it did not modify plant growth and general phenotype. However, transgenic plants showed delayed softening and firmer fruits. In addition, fruits were less susceptible to Botrytis cinerea infection, and the "in vitro" growth of the fungus on media containing AIR from the pericarp of transgenic fruits was lower than controls. The possibility of overexpressing a CBM of a fruit-specific expansin to control cell wall degradation and fruit softening is discussed.

Ectopic expression of wheat expansin gene TaEXPA2 improved the salt tolerance of transgenic tobacco by regulating Na+ /K+ and antioxidant competence

High salinity is one of the most serious environmental stresses that limit crop growth. Expansins are cell wall proteins that regulate plant development and abiotic stress tolerance by mediating cell wall expansion. We studied the function of a wheat expansin gene, TaEXPA2, in salt stress tolerance by overexpressing it in tobacco. Overexpression of TaEXPA2 enhanced the salt stress tolerance of transgenic tobacco plants as indicated by the presence of higher germination rates, longer root length, more lateral roots, higher survival rates and more green leaves under salt stress than in the wild type (WT). Further, when leaf disks of WT plants were incubated in cell wall protein extracts from the transgenic tobacco plants, their chlorophyll content was higher under salt stress, and this improvement from TaEXPA2 overexpression in transgenic tobacco was inhibited by TaEXPA2 protein antibody. The water status of transgenic tobacco plants was improved, perhaps by the accumulation of osmolytes such as proline and soluble sugar. TaEXPA2-overexpressing tobacco lines exhibited lower Na+ but higher K+ accumulation than WT plants. Antioxidant competence increased in the transgenic plants because of the increased activity of antioxidant enzymes. TaEXPA2 protein abundance in wheat was induced by NaCl, and ABA signaling was involved. Gene expression regulation was involved in the enhanced salt stress tolerance of the TaEXPA2 transgenic plants. Our results suggest that TaEXPA2 overexpression confers salt stress tolerance on the transgenic plants, and this is associated with improved water status, Na+ /K+ homeostasis, and antioxidant competence. ABA signaling participates in TaEXPA2-regulated salt stress tolerance.

Smart Parasitic Nematodes Use Multifaceted Strategies to Parasitize Plants

Nematodes are omnipresent in nature including many species which are parasitic to plants and cause enormous economic losses in various crops. During the process of parasitism, sedentary phytonematodes use their stylet to secrete effector proteins into the plant cells to induce the development of specialized feeding structures. These effectors are used by the nematodes to develop compatible interactions with plants, partly by mimicking the expression of host genes. Intensive research is going on to investigate the molecular function of these effector proteins in the plants. In this review, we have summarized which physiological and molecular changes occur when endoparasitic nematodes invade the plant roots and how they develop a successful interaction with plants using the effector proteins. We have also mentioned the host genes which are induced by the nematodes for a compatible interaction. Additionally, we discuss how nematodes modulate the reactive oxygen species (ROS) and RNA silencing pathways in addition to post-translational modifications in their own favor for successful parasitism in plants.

Transcriptome Analysis of Maize Immature Embryos Reveals the Roles of Cysteine in Improving Agrobacterium Infection Efficiency

Maize Agrobacterium-mediated transformation efficiency has been greatly improved in recent years. Antioxidants, such as, cysteine, can significantly improve maize transformation frequency through improving the Agrobacterium infection efficiency. However, the mechanism underlying the transformation improvement after cysteine exposure has not been elucidated. In this study, we showed that the addition of cysteine to the co-cultivation medium significantly increased the Agrobacterium infection efficiency of hybrid HiII and inbred line Z31 maize embryos. Reactive oxygen species contents were higher in embryos treated with cysteine than that without cysteine. We further investigated the mechanism behind cysteine-related infection efficiency increase using transcriptome analysis. The results showed that the cysteine treatment up-regulated 939 genes and down-regulated 549 genes in both Z31 and HiII. Additionally, more differentially expressed genes were found in HiII embryos than those in Z31 embryos, suggesting that HiII was more sensitive to the cysteine treatment than Z31. GO analysis showed that the up-regulated genes were mainly involved in the oxidation reduction process. The up-regulation of these genes could help maize embryos to cope with the oxidative stress stimulated by Agrobacterium infection. The down-regulated genes were mainly involved in the cell wall and membrane metabolism, such as, aquaporin and expansin genes. Decreased expression of these cell wall integrity genes could loosen the cell wall, thereby improving the entry of Agrobacterium into plant cells. This study offers insight into the role of cysteine in improving Agrobacterium-mediated transformation of maize immature embryos.

Involvement of the Fusarium graminearum cerato-platanin proteins in fungal growth and plant infection

The genome of Fusarium graminearum, a necrotrophic fungal pathogen causing Fusarium head blight (FHB) disease of wheat, barley and other cereal grains, contains five genes putatively encoding for proteins with a cerato-platanin domain. Cerato-platanins are small secreted cysteine-rich proteins possibly localized in the fungal cell walls and also contributing to the virulence. Two of these F. graminearum proteins (FgCPP1 and FgCPP2) belong to the class of SnodProt proteins which exhibit phytotoxic activity in the fungal pathogens Botrytis cinerea and Magnaporthe grisea. In order to verify their contribution during plant infection and fungal growth, single and double gene knock-out mutants were produced and no reduction in symptoms severity was observed compared to the wild type strain on both soybean and wheat spikes. Histological analysis performed by fluorescence microscopy on wheat spikelets infected with mutants constitutively expressing the dsRed confirmed that FgCPPs do not contribute to fungal virulence. In particular, the formation of compound appressoria on wheat paleas was unchanged. Looking for other functions of these proteins, the double mutant was characterized by in vitro experiments. The mutant was inhibited by salt and H2O2 stress similarly to wild type. Though no growth difference was observed on glucose, the mutant grew better than wild type on carboxymethyl cellulose. Additionally, the mutant's mycelium was more affected by treatments with chitinase and β-1,3-glucanase, thus indicating that FgCPPs could protect fungal cell wall polysaccharides from enzymatic degradation.

The Target of β-Expansin EXPB1 in Maize Cell Walls from Binding and Solid-State NMR Studies

The wall-loosening actions of β-expansins are known primarily from studies of EXPB1 extracted from maize (Zea mays) pollen. EXPB1 selectively loosens cell walls (CWs) of grasses, but its specific binding target is unknown. We characterized EXPB1 binding to sequentially extracted maize CWs, finding that the protein primarily binds glucuronoarabinoxylan (GAX), the major matrix polysaccharide in grass CWs. This binding is strongly reduced by salts, indicating that it is predominantly electrostatic in nature. For direct molecular evidence of EXPB1 binding, we conducted solid-state nuclear magnetic resonance experiments using paramagnetic relaxation enhancement (PRE), which is sensitive to distances between unpaired electrons and nuclei. By mixing ¹³C-enriched maize CWs with EXPB1 functionalized with a Mn²⁺ tag, we measured Mn²⁺-induced PRE Strong ¹H and ¹³C PREs were observed for the carboxyls of GAX, followed by more moderate PREs for carboxyl groups in homogalacturonan and rhamnogalacturonan-I, indicating that EXPB1 preferentially binds GAX In contrast, no PRE was observed for cellulose, indicating very weak interaction of EXPB1 with cellulose. Dynamics experiments show that EXPB1 changes GAX mobility in a complex manner: the rigid fraction of GAX became more rigid upon EXPB1 binding while the dynamic fraction became more mobile. Combining these data with previous results, we propose that EXPB1 loosens grass CWs by disrupting noncovalent junctions between highly substituted GAX and GAX of low substitution, which binds cellulose. This study provides molecular evidence of β-expansin's target in grass CWs and demonstrates a new strategy for investigating ligand binding for proteins that are difficult to express heterologously.

Expression profiles and hormonal regulation of tobacco expansin genes and their involvement in abiotic stress response

Changes in the expression levels of tobacco expansin genes NtEXPA1, NtEXPA4, NtEXPA5, and NtEXPA6 were studied in different organs of tobacco (Nicotiana tabacum L.) as well as in response to phytohormone and stress treatments. It was shown that NtEXPA1, NtEXPA4 and NtEXPA5 transcripts were predominantly expressed in the shoot apices and young leaves, but almost absent in mature leaves and roots. The NtEXPA6 mRNA was found at high levels in calluses containing a large number of undifferentiated cells, but hardly detectable in the leaves of different ages and roots. In young leaves, expression levels of NtEXPA1, NtEXPA4 and NtEXPA5 genes were induced by cytokinins, auxins and gibberellins. Cytokinins and auxins were also found to increase NtEXPA6 transcripts in young leaves but to the much lower levels than the other expansin mRNAs. Expression analysis demonstrated that brassinosteroid phytohormones were able either to up-regulate or to down-regulate expression of different expansins in leaves of different ages. Furthermore, transcript levels of NtEXPA1, NtEXPA4, and NtEXPA5 genes were increased in response to NaCl, drought, cold, heat, and 10μM abscisic acid (ABA) treatments but reduced in response to more severe stresses, i.e. cadmium, freezing, and 100μM ABA. In contrast, no substantial changes were found in NtEXPA6 transcript level after all stress treatments. In addition, we examined the involvement of tobacco expansins in the regulation of abiotic stress tolerance by transgenic approaches. Transgenic tobacco plants with constitutive expression of NtEXPA1 and NtEXPA5 exhibited improved tolerance to salt stress: these plants showed higher growth indices after NaCl treatment and minimized water loss by reducing stomatal density. In contrast, NtEXPA4-silenced plants were characterized by a considerable growth reduction under salinity and enhanced water loss. Our findings indicate that expression levels of all studied tobacco expansins genes are modulated by plant hormones whereas NtEXPA1, NtEXPA4, and NtEXPA5 expansins may be involved in the regulation of stress tolerance in tobacco plants.

Proteomic analysis of soybean root exposed to varying sizes of silver nanoparticles under flooding stress

Silver nanoparticles (Ag-NPs) are excessively used as antibacterial agents; however, environmental interaction specifically with the plants remain uncertain. To study the size-dependent effects of Ag-NPs on soybean under flooding, a proteomic technique was used. Morphological analysis revealed that treatment with Ag-NPs of 15nm promoted soybean growth under flooding compared to 2 and 50-80nm. A total of 228 common proteins that significantly changed in abundance under flooding without and with Ag-NPs of 2, 15, and 50-80nm. Under varying sizes of Ag-NPs, number of protein synthesis related proteins decreased compared to flooding while number of amino acid synthesis related proteins were increased under Ag-NPs of 15nm. Hierarchical clustering identified the ribosomal proteins that increased under Ag-NPs of 15nm while decreased under other sizes. In silico protein-protein interaction indicated the beta ketoacyl reducatse 1 as the most interacted protein under Ag-NPs of 15nm while least interacted under other sizes. The beta ketoacyl reductase 1 was up-regulated under Ag-NPs of 15nm while its enzyme activity was decreased. These results suggest that the different sizes of Ag-NPs might affect the soybean growth under flooding by regulating the proteins related to amino acid synthesis and wax formation.

BIOLOGICAL SIGNIFICANCE

This study highlighted the response of soybean proteins towards varying sizes of Ag NPs under flooding stress using gel-free proteomic technique. The Ag NPs of 15nm improved the length of root including hypocotyl of soybean. The proteins related to protein metabolism, cell division/organization, and amino acid metabolism were differentially changed under the varying sizes of Ag NPs. The protein synthesis-related proteins were decreased while amino acid metabolism-related proteins were increased under varying sizes of Ag NPs. The ribosomal proteins were increased under Ag NPs of 15nm. The beta ketoacyl reductase 1 was identified as the most interacted protein under varying sizes of Ag NPs. The mRNA expression level of beta ketoacyl reductase was up-regulated under Ag NPs of 15nm while its activity was decreased. These results suggest that the Ag NPs of 15nm improved the soybean growth under flooding stress by increasing the proteins related to amino acid synthesis and waxes formation.

Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum)

Expansins are pH-dependent cell wall loosening proteins which form a large family in plants. They have been shown to be involved in various developmental processes and been implicated in enabling plants' ability to absorb nutrients from the soil as well as conferring biotic and abiotic stress resistances. It is therefore clear that they can be potential targets in genetic engineering for crop improvement. Tobacco (Nicotiana tabacum) is a major crop species as well as a model organism. Considering that only a few tobacco expansins have been studied, a genome-wide analysis of the tobacco expansin gene family is necessary. In this study, we identified 52 expansins in tobacco, which were classified into four subfamilies: 36 NtEXPAs, 6 NtEXPBs, 3 NtEXLAs and 7 NtEXLBs. Compared to other species, the NtEXLB subfamily size was relatively larger. Phylogenetic analysis showed that the 52 tobacco expansins were divided into 13 subgroups. Gene structure analysis revealed that genes within subfamilies/subgroups exhibited similar characteristics such as gene structure and protein motif arrangement. Whole-genome duplication and tandem duplication events may have played important roles in the expanding of tobacco expansins. Cis-Acting element analysis revealed that each expansin gene was regulated or several expansin genes were co-regulated by both internal and environmental factors. 35 of these genes were identified as being expressed according to a microarray analysis. In contrast to most NtEXPAs which had higher expression levels in young organs, NtEXLAs and NtEXLBs were preferentially expressed in mature or senescent tissues, suggesting that they might play different roles in different organs or at different developmental stages. As the first step towards genome-wide analysis of the tobacco expansin gene family, our work provides solid background information related to structure, evolution and expression as well as regulatory cis-acting elements of the tobacco expansins. This information will provide a strong foundation for cloning and functional exploration of expansin genes in tobacco.

Cell wall dynamics during apple development and storage involves hemicellulose modifications and related expressed genes

BACKGROUND

Fruit quality depends on a series of biochemical events that modify appearance, flavour and texture throughout fruit development and ripening. Cell wall polysaccharide remodelling largely contributes to the elaboration of fleshy fruit texture. Although several genes and enzymes involved in cell wall polysaccharide biosynthesis and modifications are known, their coordinated activity in these processes is yet to be discovered.

RESULTS

Combined transcriptomic and biochemical analyses allowed the identification of putative enzymes and related annotated members of gene families involved in cell wall polysaccharide composition and structural changes during apple fruit growth and ripening. The early development genes were mainly related to cell wall biosynthesis and degradation with a particular target on hemicelluloses. Fine structural evolutions of galactoglucomannan were strongly correlated with mannan synthase, glucanase (GH9) and β-galactosidase gene expression. In contrast, fewer genes related to pectin metabolism and cell expansion (expansin genes) were observed in ripening fruit combined with expected changes in cell wall polysaccharide composition.

CONCLUSIONS

Hemicelluloses undergo major structural changes particularly during early fruit development. The high number of early expressed β-galactosidase genes questions their function on galactosylated structures during fruit development and storage. Their activity and cell wall substrate remains to be identified. Moreover, new insights into the potential role of peroxidases and transporters, along with cell wall metabolism open the way to further studies on concomitant mechanisms involved in cell wall assembly/disassembly during fruit development and storage.

Functional characterization of the native swollenin from Trichoderma reesei: study of its possible role as C1 factor of enzymatic lignocellulose conversion

BACKGROUND

Through binding to cellulose, expansin-like proteins are thought to loosen the structural order of crystalline surface material, thus making it more accessible for degradation by hydrolytic enzymes. Swollenin SWO1 is the major expansin-like protein from the fungus Trichoderma reesei. Here, we have performed a detailed characterization of a recombinant native form of SWO1 with respect to its possible auxiliary role in the enzymatic saccharification of lignocellulosic substrates.

RESULTS

The swo1 gene was overexpressed in T. reesei QM9414 Δxyr1 mutant, featuring downregulated cellulase production, and the protein was purified from culture supernatant. SWO1 was N-glycosylated and its circular dichroism spectrum suggested a folded protein. Adsorption isotherms (25 °C, pH 5.0, 1.0 mg substrate/mL) revealed SWO1 to be 120- and 20-fold more specific for binding to birchwood xylan and kraft lignin, respectively, than for binding to Avicel PH-101. The SWO1 binding capacity on lignin (25 µmol/g) exceeded 12-fold that on Avicel PH-101 (2.1 µmol/g). On xylan, not only the binding capacity (22 µmol/g) but also the affinity of SWO1 (K d = 0.08 µM) was enhanced compared to Avicel PH-101 (K d = 0.89 µM). SWO1 caused rapid release of a tiny amount of reducing sugars (<1 % of total) from different substrates (Avicel PH-101, nanocrystalline cellulose, steam-pretreated wheat straw, barley β-glucan, cellotetraose) but did not promote continued saccharification. Atomic force microscopy revealed that amorphous cellulose films were not affected by SWO1. Also with AFM, binding of SWO1 to cellulose nanocrystallites was demonstrated at the single-molecule level, but adsorption did not affect this cellulose. SWO1 exhibited no synergy with T. reesei cellulases in the hydrolysis of the different celluloses. However, SWO1 boosted slightly (1.5-fold) the reducing sugar release from a native grass substrate.

CONCLUSIONS

SWO1 is a strongly glycosylated protein, which has implications for producing it in heterologous hosts. Although SWO1 binds to crystalline cellulose, its adsorption to xylan is much stronger. SWO1 is not an auxiliary factor of the enzymatic degradation of a variety of cellulosic substrates. Effect of SWO1 on sugar release from intact plant cell walls might be exploitable with certain (e.g., mildly pretreated) lignocellulosic feedstocks.

Gibberellin-Regulation and Genetic Variations in Leaf Elongation for Tall Fescue in Association with Differential Gene Expression Controlling Cell Expansion

Leaf elongation rate (LER) is an important factor controlling plant growth and productivity. The objective of this study was to determine whether genetic variation in LER for a fast-growing ('K-31'), and a dwarf cultivar ('Bonsai') of tall fescue (Festuca arundinacea) and gibberellic acid (GA) regulation of LER were associated with differential expression of cell-expansion genes. Plants were treated with GA3, trinexapac-ethyl (TE) (GA inhibitor), or water (untreated control) in a hydroponic system. LER of 'K-31' was 63% greater than that of 'Bonsai', which corresponded with 32% higher endogenous GA4 content in leaf and greater cell elongation and production rates under the untreated control condition. Exogenous application of GA3 significantly enhanced LER while TE treatment inhibited leaf elongation due to GA3-stimulation or TE-inhibition of cell elongation and production rate in leaves for both cultivars. Real-time quantitative polymerase chain reaction analysis revealed that three α-expansins, one β-expansin, and three xyloglucan endotransglycosylase (XET) genes were associated with GA-stimulation of leaf elongation, of which, the differential expression of EXPA4 and EXPA7 was related to the genotypic variation in LER of two cultivars. Those differentially-expressed expansin and XET genes could play major roles in genetic variation and GA-regulated leaf elongation in tall fescue.