Evaluation of metabolite extraction protocols and determination ofphysiological response to drought stress via reporter metabolites in model plant Brachypodium distachyon

Abstract

IntroductionMetabolomics links to physiology with the integration of DNA, RNA, protein, and metabolite analyses through metabolic pathways that are driven by enzymes and DNA encodes these enzymes. Thus, this integrative information generates an overall picture of the functional status of an organism (Dixon et al., 2006;Nikerel et al., 2012). The metabolome of an organism, in return, refers to the complete set of small-molecule chemicals and is a reflection of its metabolic state, hence giving information about the activated biological processes under particular conditions (Faijes et al., 2007). Metabolomics studies consist of 2 main stages: the extraction of metabolites from the cellular matrix and the quantification of the extracted metabolites. For successful metabolome studies, metabolite extraction is a key step in providing useful and reliable data. Significant efforts have been made for the selection of optimal metabolite extraction procedures for different platforms and organisms (Tambellini et al., 2013).The world population is expected to exceed 9 billion by 2050 and global agricultural production needs to grow approximately by 70% in order to maintain the need for food supply (FAO, 2009). Environmental disasters, climate change, and other stress factors including cold, drought, and heavy metals or salinity, with limited land resources available for agricultural expansion, significantly worsen the current situation (Velthuizen et al., 2007). Improving plant adaptation to stress conditions is an urgent need to minimize yield loss of crops. Inducers creating stress in plants are divided into two major groups including abiotic stress factors (e.g., drought, salinity) and biotic stress factors such as pathogens. Drought, which can be described basically as water deficiency or incapability to access to water, is one of the greatest abiotic stress factors Abstract: Metabolomics aims to systematically gather (quantitative) information on metabolites in the cell and is commonly viewed as the "missing link" between genomics, transcriptomics, and physiology. Typical metabolomics platforms consist of two main steps, the quenching and extraction of metabolites from plant material and the (un)targeted quantification of the extracted metabolites. Brachypodium distachyon, a native grass species of the Mediterranean region, is an attractive model plant to study temperate crops. In recent years, despite an increasing interest in genomic and transcriptomic studies, metabolomics studies for B. distachyon are still in their infancy. Drought, an abiotic stress factor, causes severe loss in plant productivity and it is therefore crucial to understand its effect on plant metabolism, in particular its metabolome. The objective of this study is to set up a quantitative plant metabolomics platform for B. distachyon to evaluate and optimize alternative metabolite extraction protocols (methanol and methanol-chloroform extraction). Focusing on three reporter metabolites (ATP, glucose, and starch) for metabolite quantification and tw...

Genome size variation among natural populations of Brachypodium distachyon and B. hybridum collected from different regions of Turkey

“…Our collection is also a part of this collection. Some of the genotypes from our collection have been used as biological materials in various research related to genetic diversity (Filiz et al, 2009;Vogel et al, 2009), cytogenetic analyses (Wolny and Hasterok, 2009), genome structure (Dinh Thi et al, 2014), diversity (Gordon et al, 2014), molecular phylogeny analyses (López-Alvarez et al, 2012), ecological niches (López-Alvarez et al, 2015), drought tolerance (Tatlı et al, 2015;Luo et al, 2016), and pan-genome correlations (Gordon et al, 2017). Meanwhile, new materials have been added to our collection.…”

İçme Suyu Katkısı Olarak Kullanılan Myrtus communis L. Bitki Özütünün Yaşlı Yumurtacı Tavuklarda Performans, Bazı Kan Parametreleri, Yumurta Kalitesi ve Bağışıklık Tepkisi Üzerine Etkileri

“…Many dietary herbal products (powder, extracts, and essential oils) showed good effects on the performance parameters (eggs production, internal and external egg quality) of laying hens [2] . The chemical components of many plant extracts have antioxidant properties which help to eliminate free radicals in the body to cover stressrelated problems and therefore improve the health status of hens [3] .…”

Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress

“…The biological knowledge obtained from these genomic scale approaches is translated into many potential applications, such as engineering agronomic traits and designing stress response gene circuits in crops. Understanding plant response mechanisms requires comprehensive integration of all the outputs of multi-omics approaches (Tatli et al, 2015 ). In recent years, there have been many profiling studies of the transcriptome, proteome, and metabolome focused on how plants interact with the environment when subjected to stress (Rensink et al, 2005 ; Budak et al, 2013 ; Kim et al, 2015 ; Koç et al, 2015c ).…”