Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue

The exact biochemical steps of xylan backbone synthesis remain elusive. In Arabidopsis, three non-redundant genes from two glycosyltransferase (GT) families, IRX9 and IRX14 from GT43 and IRX10 from GT47, are candidates for forming the xylan backbone. In other plants, evidence exists that different tissues express these three genes at widely different levels, which suggests that diversity in the makeup of the xylan synthase complex exists. Recently we have profiled the transcripts present in the developing mucilaginous tissue of psyllium (Plantago ovata Forsk). This tissue was found to have high expression levels of an IRX10 homolog, but very low levels of the two GT43 family members. This contrasts with recent wheat endosperm tissue profiling that found a relatively high abundance of the GT43 family members. We have performed an in-depth analysis of all GTs genes expressed in four developmental stages of the psyllium mucilagenous layer and in a single stage of the psyllium stem using RNA-Seq. This analysis revealed several IRX10 homologs, an expansion in GT61 (homologs of At3g18170/At3g18180), and several GTs from other GT families that are highly abundant and specifically expressed in the mucilaginous tissue. Our current hypothesis is that the four IRX10 genes present in the mucilagenous tissues have evolved to function without the GT43 genes. These four genes represent some of the most divergent IRX10 genes identified to date. Conversely, those present in the psyllium stem are very similar to those in other eudicots. This suggests these genes are under selective pressure, likely due to the synthesis of the various xylan structures present in mucilage that has a different biochemical role than that present in secondary walls. The numerous GT61 family members also show a wide sequence diversity and may be responsible for the larger number of side chain structures present in the psyllium mucilage

Brachypodium as an experimental system for the study of stem parenchyma biology in grasses

<div><p>Stem parenchyma is a major cell type that serves key metabolic functions for the plant especially in large grasses, such as sugarcane and sweet sorghum, where it serves to store sucrose or other products of photosynthesis. It is therefore desirable to understand the metabolism of this cell type as well as the mechanisms by which it provides its function for the rest of the plant. Ultimately, this information can be used to selectively manipulate this cell type in a controlled manner to achieve crop improvement. In this study, we show that <i>Brachypodium distachyon</i> is a useful model system for stem pith parenchyma biology. Brachypodium can be grown under condition where it resembles the growth patterns of important crops in that it produces large amounts of stem material with the lower leaves senescing and with significant stores of photosynthate located in the stem parenchyma cell types. We further characterize stem plastid morphology as a function of tissue types, as this organelle is central for a number of metabolic pathways, and quantify gene expression for the four main classes of starch biosynthetic genes. Notably, we find several of these genes differentially regulated between stem and leaf. These studies show, consistent with other grasses, that the stem functions as a specialized storage compartment in Brachypodium.</p></div

Expression of starch related genes in stem and leaf.

<p>Expression of starch related genes in stem and leaf.</p

Characterization of Brachypodium growth pattern under two different conditions.

<p>(A) Brachypodium grown under more commonly used growth chamber conditions (20-hour light, 24°C; 4-hour dark, 18°C; 150 μE). (B,C) Brachypodium grown under stem-elongating conditions (16-hour light, 20°C; 8-hour dark, 21°C; 220 μE).</p

Plastid development in the Brachypodium stem.

<p>(A) Decrease of stem chlorophyll in stem from 9- to 12-week-old plants. (B) Chloroplast auto-fluorescence by confocal laser scanning microscopy. Cross-section is equivalent to section in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0173095#pone.0173095.g003" target="_blank">Fig 3F</a> (S-01 internode, above leaf sheath, 12-week-old plant). (C) Merged image of auto-fluorescence in (B) with the bright field channel showing that the strong auto-fluorescence originates from cortex parenchyma cells. (D) TEM analysis of thylakoid membrane stacks in internodes of plants of different age and at different locations within the stem cross-section.</p

Carbon storage in the Brachypodium stem.

<p>(A) Quantification of starch and sucrose levels in leaf, middle part of stem, and bottom part of stem, with and without dark-treatment. (B-G) Iodine staining of Brachypodium stem cross-sections. Progressive stem stages from bottom towards the top of the stem are shown (B, S-04; C, S-03; D, S-02; E and F, S-01). E is from within while F is from above the leaf sheath. More starch is accumulated in the cortex parenchyma in F compared to E (arrow) while the starch levels in the pith parenchyma appear equal in the two samples. G shows iodine staining of starch granules in parenchyma cells in the vascular bundle (arrows).</p

Biomass accumulation in aerial vegetative organs of 12-week-old plants.

<p>Biomass accumulation in aerial vegetative organs of 12-week-old plants.</p

Characterization of Brachypodium growth pattern under stem-elongating conditions.

<p>(A) Number of tillers and length of main stem as a function of plant age. Measurements were performed on three independent batches of plants with similar results whereof one is shown. Standard deviation is shown (n = 16). (B) Diagram showing all stems of a single plant and location of four internodes sampled along the stem, S-01 to S-04. Senescent leaves were removed. The senescent leaves for the main stem are placed at the left.</p

Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis.

Insights into the evolution of plant cell walls have important implications for comprehending these diverse and abundant biological structures. In order to understand the evolving structure-function relationships of the plant cell wall, it is imperative to trace the origin of its different components. The present study is focused on plant 1,4-β-xylan, tracing its evolutionary origin by genome and transcriptome mining followed by phylogenetic analysis, utilizing a large selection of plants and algae. It substantiates the findings by heterologous expression and biochemical characterization of a charophyte alga xylan synthase. Of the 12 known gene classes involved in 1,4-β-xylan formation, XYS1/IRX10 in plants, IRX7, IRX8, IRX9, IRX14 and GUX occurred for the first time in charophyte algae. An XYS1/IRX10 ortholog from Klebsormidium flaccidum, designated K. flaccidumXYLAN SYNTHASE-1 (KfXYS1), possesses 1,4-β-xylan synthase activity, and 1,4-β-xylan occurs in the K. flaccidum cell wall. These data suggest that plant 1,4-β-xylan originated in charophytes and shed light on the origin of one of the key cell wall innovations to occur in charophyte algae, facilitating terrestrialization and emergence of polysaccharide-based plant cell walls