Metabolomics: an emerging frontier of systems biology in marine macrophytes

Manoj Kumar, Unnikrishnan Kuzhiumparambil, Mathieu Pernice, Zhijian Jiang, Peter J. Ralph
2016 Algal Research  
7 a r t i c l e i n f o 8 Available online xxxx 13 14 15 16 17 18 Metabolomics is a rapidly emerging discipline within functional genomics which is increasingly being applied to 19 understand biochemical phenotypes across a range of biological systems. Metabolomics measures all (or a 20 subset) metabolites in a cell at a specific time point, reflecting a snapshot of all the regulatory events responding 21 to the external environmental conditions. Although metabolomics and system biology
more » ... es have been ap-22 plied to the study of terrestrial plants, few marine macrophytes have been examined using these novel technol-23 ogies. Marine macrophytes (including seaweeds and seagrasses) are marine ecosystem engineers delivering a 24 range of ecologically and economically valuable biological services; however they are under threat from a wide 25 range of anthropogenic stressors, climate variation, invasive species and pathogens. Investigating metabolomic 26 regulation in these organisms is crucial to understand their acclimation, adaptation and defence responses to 27 environmental challenges. This review describes the current analytical tools available to study metabolomics 28 in marine macrophytes, along with their limitations for both targeted and non-targeted workflows. To illustrate 29 recent advances in system biology studies in marine macrophytes, we describe how metabolites are used in 30 chemical defence to deter a broad range of invasive species and pathogens, as well as metabolomic 31 reprogramming leading to acclimation or adaptive strategies to environmental and anthropogenic stresses. 32 Where possible, the mechanistic processes associated with primary and secondary plant metabolism governing 33 cellular homeostasis under extreme environments are discussed. Functional integration of metabolomics with 34 the allied "omics" disciplines of transcriptomics and proteomics, as well as the emerging discipline of "fluxomics" 35 are discussed in the context of developing biological system networks, the identification of unknown gene/pro-36 tein functions and the analysis of metabolic pathways in marine plants exposed to stress. Finally, we provide a 37 comprehensive overview of an in silico plant metabolome database that can be utilized to advance our knowl-38 edge from a system biology approach to marine macrophytes. 39 128 for future molecular studies [9-11]. However, the decreased cost and in-129 creased sequencing efficiency of Next Generation Sequencing make pos-130 sible to examine different species of marine macrophytes besides these 131 model organisms, providing new opportunities for comparative geno-132 mics within the same group of seaweeds or seagrasses. In this respect, 133 transcriptome-based analysis of marine macrophytes has provided 134 novel insights into their successful propagation and adaptation to the 135 highly dynamic marine environment [12-23]. Overall, these studies 136 have inferred a complex regulation pattern for diverse gene networks; 137 however, coherent explanation that connects these transcriptional re-138 157 ganic compounds (VOCs) are other classes of targeted metabolites 158 that are gaining interest in studies of the stress response in macrophytes 159 [32-38]. Metabolomic database information generated for marine mac-160 rophytes is in its infancy [6,7] when compared to terrestrial plants 161 where a range of metabolomic databases are available (Tables 1 and 162 2). The terrestrial plant KNApSAck database [39] for example, contains 163 50,000 plant metabolite entries. In comparison, the seaweed metabo-164 lite database (SWMD; http://www.swmd.co.in), the only macrophyte 165 metabolomics database available, contains only 500 metabolites entries 166 and mostly from the red seaweed Laurencia [40]; and there is currently 167 no metabolic library available for seagrasses. This review provides a 168 comprehensive overview of the use and capabilities of diverse 169 metabolomic analytical tools in a targeted and non-targeted metabolo-170 mics workflow in marine macrophytes. Recent advances in understand-171 ing the chemical defence mechanisms of marine macrophytes used to 172 deter a broad range of invasive species and pathogens are discussed. 173 Further, we summarize the metabolite re-programming of marine mac-174 rophytes in response to extreme environments that provide new in-175 sights on their adaptation and/or acclimation mechanism to different 176 stressors. The stress metabolites that are described include: amino 177 acids, sugars, sugar alcohols, oxylipins, polyunsaturated fatty acids, 178 polyamines, organic acids and phenolic compounds. The integration 179 of metabolomics with the allied 'omics disciplines of transcriptomic, 180 proteomic and fluxomics approaches are discussed in the context of 181 developing biological systems networks, identification of unknown 182 gene/protein functions, and metabolic pathways in marine plants 183 exposed to stress conditions. Finally, we provide a comprehensive 184 overview of in silico plant metabolome database information that 185 can be utilized for the interpretation of marine plant metabolomic 186 data sets. 2 M. Kumar et al. / Algal Research xxx (2015) xxx-xxx Please cite this article as: M. Kumar, et al., Metabolomics: an emerging frontier of system biology in marine macrophytes, Algal Res. (2015), http:// dx.VocBinBase http://fiehnlab.ucdavis.edu/projects/VocBinBase GC-TOF-MS An automated peak annotation database system from 18 plant species. t1:45 XCMS and XCMS2 https://xcmsonline.scripps.edu/ LC,GC-MS, and MS2 A data analysis programme allows nonlinear retention time alignment, peak detection and matching without using internal standards.
doi:10.1016/j.algal.2016.02.033 fatcat:fgic4jcw35drjn3qwlioefkdti