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

ABSTRACT: 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 Brachypodium distachyon 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.

SUBMITTER: Jensen JK

PROVIDER: S-EPMC5332097 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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

Jensen Jacob Krüger JK Wilkerson Curtis Gene CG

PloS one 20170301 3

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 c ...[more]

PMID: 28248997

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Project description:BACKGROUND AND AIMS: Brachypodium distachyon is a temperate grass with a small stature, rapid life cycle and completely sequenced genome that has great promise as a model system to study grass-specific traits for crop improvement. Under iron (Fe)-deficient conditions, grasses synthesize and secrete Fe(III)-chelating agents called phytosiderophores (PS). In Zea mays, Yellow Stripe1 (ZmYS1) is the transporter responsible for the uptake of Fe(III)-PS complexes from the soil. Some members of the family of related proteins called Yellow Stripe-Like (YSL) have roles in internal Fe translocation of plants, while the function of other members remains uninvestigated. The aim of this study is to establish brachypodium as a model system to study Fe homeostasis in grasses, identify YSL proteins in brachypodium and maize, and analyse their expression profiles in brachypodium in response to Fe deficiency. METHODS: The YSL family of proteins in brachypodium and maize were identified based on sequence similarity to ZmYS1. Expression patterns of the brachypodium YSL genes (BdYSL genes) were determined by quantitative RT-PCR under Fe-deficient and Fe-sufficient conditions. The types of PS secreted, and secretion pattern of PS in brachypodium were analysed by high-performance liquid chromatography. KEY RESULTS: Eighteen YSL family members in maize and 19 members in brachypodium were identified. Phylogenetic analysis revealed that some YSLs group into a grass-specific clade. The Fe status of the plant can regulate expression of brachypodium YSL genes in both shoots and roots. 3-Hydroxy-2'-deoxymugineic acid (HDMA) is the dominant type of PS secreted by brachypodium, and its secretion is diurnally regulated. CONCLUSIONS: PS secretion by brachypodium parallels that of related crop species such as barley and wheat. A single grass species-specific YSL clade is present, and expression of the BdYSL members of this clade could not be detected in shoots or roots, suggesting grass-specific functions in reproductive tissues. Finally, the Fe-responsive expression profiles of several YSLs suggest roles in Fe homeostasis.

Project description:Brachypodium distachyon (Brachypodium) is a model for the temperate grasses which include important cereals such as barley, wheat and oats. Comparison of the Brachypodium genome (accession Bd21) with those of the model dicot Arabidopsis thaliana and the tropical cereal rice (Oryza sativa) provides an opportunity to compare and contrast genetic pathways controlling important traits. We analysed the homologies of genes controlling the induction of flowering using pathways curated in Arabidopsis Reactome as a starting point. Pathways include those detecting and responding to the environmental cues of day length (photoperiod) and extended periods of low temperature (vernalization). Variation in these responses has been selected during cereal domestication, providing an interesting comparison with the wild genome of Brachypodium. Brachypodium Bd21 has well conserved homologues of circadian clock, photoperiod pathway and autonomous pathway genes defined in Arabidopsis and homologues of vernalization pathway genes defined in cereals with the exception of VRN2 which was absent. Bd21 also lacked a member of the CO family (CO3). In both cases flanking genes were conserved showing that these genes are deleted in at least this accession. Segmental duplication explains the presence of two CO-like genes in temperate cereals, of which one (Hd1) is retained in rice, and explains many differences in gene family structure between grasses and Arabidopsis. The conserved fine structure of duplications shows that they largely evolved to their present structure before the divergence of the rice and Brachypodium. Of four flowering-time genes found in rice but absent in Arabidopsis, two were found in Bd21 (Id1, OsMADS51) and two were absent (Ghd7, Ehd1). Overall, results suggest that an ancient core photoperiod pathway promoting flowering via the induction of FT has been modified by the recruitment of additional lineage specific pathways that promote or repress FT expression.

Project description:Computational approaches have promised to organize collections of functional genomics data into testable predictions of gene and protein involvement in biological processes and pathways. However, few such predictions have been experimentally validated on a large scale, leaving many bioinformatic methods unproven and underutilized in the biology community. Further, it remains unclear what biological concerns should be taken into account when using computational methods to drive real-world experimental efforts. To investigate these concerns and to establish the utility of computational predictions of gene function, we experimentally tested hundreds of predictions generated from an ensemble of three complementary methods for the process of mitochondrial organization and biogenesis in Saccharomyces cerevisiae. The biological data with respect to the mitochondria are presented in a companion manuscript published in PLoS Genetics (doi:10.1371/journal.pgen.1000407). Here we analyze and explore the results of this study that are broadly applicable for computationalists applying gene function prediction techniques, including a new experimental comparison with 48 genes representing the genomic background. Our study leads to several conclusions that are important to consider when driving laboratory investigations using computational prediction approaches. While most genes in yeast are already known to participate in at least one biological process, we confirm that genes with known functions can still be strong candidates for annotation of additional gene functions. We find that different analysis techniques and different underlying data can both greatly affect the types of functional predictions produced by computational methods. This diversity allows an ensemble of techniques to substantially broaden the biological scope and breadth of predictions. We also find that performing prediction and validation steps iteratively allows us to more completely characterize a biological area of interest. While this study focused on a specific functional area in yeast, many of these observations may be useful in the contexts of other processes and organisms.

Dataset Information

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

Publications

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

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