Bourgougnon Sea Plants

1. Auflage 2014
ISBN: 978-0-12-408107-9
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, Band Volume 71, 580 Seiten

Reihe: Advances in Botanical Research

Advances in Botanical Research publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences. The series features several reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology. This thematic volume, number 71, features reviews on sea plants. Its chapters cover topics such as the role of algae in sustainability; the status of kelp exploitation and marine agronomy; potential applications for enzymatic recovery of metabolites from seaweeds; and many more. - Publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences - Features a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology, and ecology - Volume features reviews on sea plants

Autoren/Hrsg.

Bourgougnon, Nathalie

Leseproben

Chapter Two Seaweed Metabolomics
A New Facet of Functional Genomics
VishalGupta?Rajendra SinghThakur†Ravi SinghBaghel?,‡C.R.K.Reddy?,‡,1BhavanathJha?     ?Discipline of Marine Biotechnology and Ecology, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India     †Analytical Discipline and Centralized Instrument Facility, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India     ‡Academy of Scientific & Innovative Research (AcSIR-CSMCRI), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
1 Corresponding author: e-mail address: [e-mail]. 
Abstract
Metabolomics is one of the emerging areas of functional genomics and provides newer insights in systems biology. The integration of metabolome with transcriptome analysis facilitates our understanding of gene functionality and its regulation in various metabolic pathways. Marine organisms have a variety of unique biological processes and adaptations suitable for their successful propagation. Marine macroalgae, known as ‘seaweeds’, are one of the economically important renewable resources of the oceans and have characteristic morphological and physiological processes quite different from terrestrial plants. Seaweeds being attached forms in intertidal region undergo periodic diverse chronic stresses arising from variations in desiccation, irradiance, ultraviolet radiation, salinity, tidal currents and others from anthropogenic activities. Despite the advancement in transcriptomics for seaweeds in recent times, the genetic regulations controlling various biochemical pathways are still in its inception and largely remain unexplored. The study of metabolomics provides a snapshot of cell’s catalytic and regulatory processes and also deciphers metabolic responses involved in plant and environment interactions. While summarizing the recent advancements made in analytical technology platforms, a comprehensive review of metabolomics was prepared and discussed from the context of functional genomics, systems biology and biotechnology to gain newer insights into various regulatory networks functioning in the seaweeds. Keywords
Functional genomicsMetabolomicsSeaweedSystems biologyTechnology platform Introduction
Marine macroalgae are the large photoautotrophic multicellular benthic plants (occasionally free floating) occurring in marine environments and consist of as many as 25,000 species worldwide with considerable morphological and functional diversity (Holdt & Kraan, 2011). The continuous exploration of seaweeds for various chemicals of immense commercial value has significantly expanded their utility in agrichemicals, cosmetics, biomaterials, bioenergy and their long standing conventional utilisation as food, feed and hydrocolloids (Bixler & Porse, 2011; Holdt & Kraan, 2011). This has resulted spurt in seaweed production from 3.8 million tons in 1990 to whopping 15.8 million tons fresh in 2008 ranking them as one of the major mariculture crops with an annual market value over US$7.4 thousand millions. (FAO, 2010). Seaweeds represent a unique marine environment that is distinct from terrestrial one and experience various chronic stresses arising from fluctuations in various environmental factors such as desiccation, salinity, radiation, temperature and nutrients (Liu & Pang, 2010; Ross & Van Alstyne, 2007). Recently, transcriptome analysis has been employed to gain deeper insight into their evolution and adaptation to hyper-variable environmental conditions (Coelho, Simon, Ahmed, Cock, & Partensky, 2013; Collen, Guisle-Marsollier, Leger, & Boyen, 2007; Dittami et al., 2011; Dittami, Michel, Collen, Boyen, & Tonon, 2010; Dittami et al., 2009; Gravot et al., 2010; Heinrich, Valentin, Frickenhaus, John, & Wiencke, 2012; Pearson et al., 2010). The release of whole genome sequence data of a brown alga Ectocarpus siliculosus (Dillwyn) Lyngbye and a red alga Chondrus crispus (Irish moss) revealed genome features that have been evolved in this group of organisms for their successful propagation and proliferation in coastal environment. For example, the Ectocarpus genome explored the presence of a complex photosynthetic system facilitating its propagation even in highly variable light conditions, flavonoid pathway genes homologous to plants synthesizing high phenolic contents protecting the alga from ultra-violet radiations and also an uncommon halide metabolism has been deciphered based on the presence of 21 putative dehalogenases and 2 haloalkane dehalogenases. Moreover, the genes and gene families associated with the development of multicellularity and evolution of the brown algal lineage have been identified (Cock et al., 2010). Similarly, the genome sequence of red alga has also elucidated metabolic adaptations pertaining to halogen metabolism, synthesis of oxylipins, microRNA and transcription factors for the development of multicellularity (Collen et al., 2013). This study has also revealed unique metabolic features that are otherwise part of bacterial and fungal metabolism (cellulose synthesis and cell-wall remodelling) and are absent in genome of brown alga. A most recent study by Konotchick et al. (2013) conceptualises a depth-dependent physiology of seaweed by transcriptome analysis. Though whole genome sequence studies explored some uncommon genomic features related to primary and secondary metabolism in seaweeds, the large part of the genomic information remained unannotated. Integration of data sets from functional- and comparative genomics with proteomics and metabolomics can generate a more accurate and holistic view of genes of unknown function (Xu, Ismail, & Ronald, 2014). A few studies have recently been carried out to understand the metabolic processes in response to salinity and oxidative stress in a brown alga linking with transcriptome data (Dittami et al., 2011; Gravot et al., 2010; Konotchick et al., 2013). These studies have revealed a few unknown pathways functioning under specific stress condition, and warranted for correlation of metabolites-genomic regulatory networks to disclose the specialised mechanisms, which are quite distinct from terrestrial counterparts. Metabolomics is another addition to ‘omic’ techniques and presents the information of biological relevance as it reflects the immediate biochemical consequences of genomic and transcriptomic activity. In recent times metabolomics is gaining prominence in the area of integrated systems biology, and is emerging as an essential analytical tool in the post-genomic era (Blow, 2008; Hall 2006; Saito & Matsuda, 2010). Since the term ‘metabolome’ was coined in 1998, metabolomics has now become an ancillary high-resolution biochemical phenotyping tool to advance our understanding of primary and secondary metabolism. It has made unprecedented success in assessing responses to environmental stress, biomarker analysis, chemotaxonomy, comparing mutants and different growth stages, drug discovery, studying global effects of genetic manipulation, and natural product discovery (Higashi & Saito, 2013; Kim, Choi, & Verpoorte, 2011; Muranaka & Saito, 2013; Putri et al., 2013). The extensive metabolites information generated from various analytical platforms at different laboratories necessitated to frame international standards for metabolomics studies, most importantly on sample collection, precision in data interpretation and analysis. Sumner et al. (2007) proposed minimum reporting standards for chemical analysis. Subsequently, Nicholson and Lindon (2008) in Nature’s Q&A news reported the facts and factual about metabolomics. Roessner and Bacic (2009) published a technical feature in Australian Biochemist on ‘Dos and Don’ts of Plant Metabolomics’. The discovery of genes by networking metabolite information with functional genomics information has led to the development of softwares enabling to analyse the huge array of data generated from various analytical platforms, attributing their roles in metabolic pathway networks and fluxome (Table 2.1). This has also led to constitute various metabolite libraries (Table 2.2). The most encouraging example of biological component networking or co-expression analysis studies is the model plant Arabidopsis wherein transcriptome and metabolome analysis have successfully discovered the function of genes involved in various metabolic pathways (Quanbeck et al., 2012; Tohge et al., 2005). Such systems biology approaches have recently been gaining importance in medicinal plant research. A specialised metabolic pathway in plants is involved with synchronised action of various genes. Decoding the information of those genes, gene regulatory networks and the association of gene-metabolite are of paramount importance to design metabolic engineering and synthetic...