Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus

BackgroundNitrogen (N) is a main nutrient required for tree growth and biomass accumulation. In this study, we analyzed the effects of contrasting nitrogen fertilization treatments on the phenotypes of fast growing Eucalyptus hybrids (E. urophylla x E. grandis) with a special focus on xylem secondary cell walls and global gene expression patterns.ResultsHistological observations of the xylem secondary cell walls further confirmed by chemical analyses showed that lignin was reduced by luxuriant fertilization, whereas a consistent lignin deposition was observed in trees grown in N-limiting conditions. Also, the syringyl/guaiacyl (S/G) ratio was significantly lower in luxuriant nitrogen samples. Deep sequencing RNAseq analyses allowed us to identify a high number of differentially expressed genes (1,469) between contrasting N treatments. This number is dramatically higher than those obtained in similar studies performed in poplar but using microarrays. Remarkably, all the genes involved the general phenylpropanoid metabolism and lignin pathway were found to be down-regulated in response to high N availability. These findings further confirmed by RT-qPCR are in agreement with the reduced amount of lignin in xylem secondary cell walls of these plants.ConclusionsThis work enabled us to identify, at the whole genome level, xylem genes differentially regulated by N availability, some of which are involved in the environmental control of xylogenesis. It further illustrates that N fertilization can be used to alter the quantity and quality of lignocellulosic biomass in Eucalyptus, offering exciting prospects for the pulp and paper industry and for the use of short coppices plantations to produce second generation biofuels.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0256-9) contains supplementary material, which is available to authorized users

PhotosynthateRegulation of the Root System Architecture Mediated bythe Heterotrimeric G Protein Complex in Arabidopsis

Assimilate partitioning to the root system is a desirable developmental trait to control but little is known of the signaling pathway underlying partitioning. A null mutation in the gene encoding the Gβ subunit of the heterotrimeric G protein complex, a nexus for a variety of signaling pathways, confers altered sugar partitioning in roots. While fixed carbon rapidly reached the roots of wild type and agb1-2 mutant seedlings, agb1 roots had more of this fixed carbon in the form of glucose, fructose, and sucrose which manifested as a higher lateral root density. Upon glucose treatment, the agb1-2 mutant had abnormal gene expression in the root tip validated by transcriptome analysis. In addition, PIN2 membrane localization and level was altered in the agb1-2 mutant. The heterotrimeric G protein complex integrates photosynthesis-derived sugar signaling incorporating both membrane-and transcriptional-based mechanisms. The time constants for these signaling mechanisms are in the same range as photosynthate delivery to the root, raising the possibility that root cells are able to use changes in carbon fixation in real time to adjust growth behavior

The Fungal Pathogen <em>Moniliophthora perniciosa</em> Has Genes Similar to Plant PR-1 That Are Highly Expressed during Its Interaction with Cacao

<div><p>The widespread SCP/TAPS superfamily (SCP/Tpx-1/Ag5/PR-1/Sc7) has multiple biological functions, including roles in the immune response of plants and animals, development of male reproductive tract in mammals, venom activity in insects and reptiles and host invasion by parasitic worms. Plant Pathogenesis Related 1 (PR-1) proteins belong to this superfamily and have been characterized as markers of induced defense against pathogens. This work presents the characterization of eleven genes homologous to plant <em>PR-1</em> genes, designated as <em>MpPR-1</em>, which were identified in the genome of <em>Moniliophthora perniciosa</em>, a basidiomycete fungus responsible for causing the devastating witches' broom disease in cacao. We describe gene structure, protein alignment and modeling analyses of the MpPR-1 family. Additionally, the expression profiles of <em>MpPR-1</em> genes were assessed by qPCR in different stages throughout the fungal life cycle. A specific expression pattern was verified for each member of the <em>MpPR-1</em> family in the conditions analyzed. Interestingly, some of them were highly and specifically expressed during the interaction of the fungus with cacao, suggesting a role for the MpPR-1 proteins in the infective process of this pathogen. Hypothetical functions assigned to members of the <em>MpPR-1</em> family include neutralization of plant defenses, antimicrobial activity to avoid competitors and fruiting body physiology. This study provides strong evidence on the importance of <em>PR-1-like</em> genes for fungal virulence on plants.</p> </div

Transcriptional profile of <i>MpPR-1</i> family members throughout the <i>M. perniciosa</i> life cycle.

<p>Each <i>MpPR-1</i> gene has a distinct expression profile during fungal development. “Monokaryotic” and “Dikaryotic” hyphae represent the two mycelial stages (biotrophic and necrotrophic) grown under <i>in vitro</i> conditions. “Green broom” and “dry broom” correspond to the biotrophic and necrotrophic stages of <i>M. perniciosa</i>, respectively, during its interaction with cacao. Analyses were performed by qPCR and the <i>M. perniciosa β-actin</i> gene was used as endogenous control to normalize data. Error bars represent standard deviations determined with two biological replicates. Representative drawings of the conditions analyzed are shown on the top.</p

Comparison of MpPR-1 and SCP/TAPS proteins of representative organisms.

<p>(A) Domain arrangement of SCP/TAPS proteins. Hydrophobic signal peptides are shown in black and SCP/TAPS domains are represented in blue. The numbers on the right show the size of each protein. Large N-terminal and C-terminal expansions are observed in MpPR-1b and MpPR-1g, respectively. (B) Alignment of the conserved domain of SCP/TAPS proteins. In general, the SCP/TAPS superfamily members show similarities only over the SCP/TAPS domain. Conserved residues (100% of identity) are shown in blue and semi-conserved residues (at least 60% of identity) in green. Putative active site residues are highlighted in red and cysteines in yellow. Secondary structure elements are shown above the alignment (arrow: β-sheets; helix: α-helixes). P14, tomato PR-1 (GenBank P04284); RBT4, repressed by TUP1 from <i>Candida albicans</i> (GenBank AAG09789); Tex31, SCP/TAPS from the mollusk <i>Conus textile</i> (GenBank CAD36507); Na-ASP-2, <i>Necator americanus</i> secreted protein (GenBank AAP41952); GliPR-1, human glioma PR-1 protein (GenBank P48060); SC7, SCP/TAPS from the basidiomycete <i>Schizophyllum commune</i> (GenBank P35794).</p

Genomic organization and transcriptional profile of the <i>MpPR-1</i> gene cluster found in <i>M. perniciosa</i>.

<p>The <i>MpPR-1c</i>, <i>MpPR-1d</i> and <i>MpPR-1j</i> genes are arranged <i>in tandem</i> over a region of approximately 5 kbp. Analysis of the WBD RNA-seq Atlas shows the expression profile of these <i>MpPR-1</i> genes in different conditions (green broom – <i>in planta</i> development of the biotrophic monokaryotic hyphae; monokaryotic mycelium; dikaryotic mycelium; basidiomata and basidiospores). Data were visualized using the Integrative Genomics Viewer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045929#pone.0045929-Robinson1" target="_blank">[62]</a>. The black coverage plot shows cumulative RNA-seq read coverage along the transcripts in all different conditions. Note that these genes were named according to the order they were identified in the fungal genome, and the nomenclature does not necessarily reflect their relative localization in the genome.</p