153
et al. 2013 and Wang et al. 2015). Time-series multi-“omics” analyses have identified carbonic anhydrase as the main component of carbon-concentrating mechanisms (CCMs) in C. reinhardtii and elucidated regulatory processes of CCM as well
as interplay between photosynthetic carbon metabolism and other metabolic pathways in response to carbon limitation (Wienkoop et al. 2010; Baba et al. 2011;
Winck et al. 2013; Wang et al. 2015). Additionally, advanced understanding of carbon metabolism and its coordination with other metabolic pathways such as photorespiration and nitrogen metabolism have been established in many model
photosynthetic organisms such as Arabidopsis, rice, tomato, and maize using
multi-“omics” analyses (reviewed in Fukushima and Kusano 2014; Sato and
Yanagisawa 2014). For example, it was shown that responses of plant metabolism
to increasing CO 2 depend largely on the nitrogen conditions. While similar approach
can be adopted to seagrass studies, the availability of full genome sequences for
certain seagrass species makes it possible to develop a genome-scale metabolic
model to investigate fluxes between photosynthesis and other metabolic processes
in these seagrasses. It has been shown that simulation of plant metabolisms using
genome- scale model can successfully predict fluxes between fundamental metabolic pathways such as glycolysis and the TCA cycle in Arabidopsis (Poolman et al.
2009; Williams et al. 2010) and cooperation between mesophyll cells and bundle
sheath cells during C4 photosynthesis (De Oliveira Dal’Molin et al. 2010).
Advanced insights into the function and regulation of the photosynthesis have
come from functional genomic studies in which photosynthetic processes have been
dissected by the molecular tools (Dent et al. 2001, 2005). While omics data provides
an indication of regulatory roles of certain genes or proteins, the future challenge for
seagrass research is the development of mutagenesis experiment which is a powerful
approach to study the function of the genes of interest. Furthermore, proteomics techniques can be applied to investigate protein-protein interaction, posttranslational modifications, and organization of proteins in multi-protein complexes which remain
unexplored in seagrasses. Additionally, chloroplast-targeted transcriptomes and proteomes can provide insights on chloroplast structures and function (Eckardt 2012;
Petersen et al. 2013; Chang et al. 2015). These studies have led to better understanding
of chloroplast protein components and photosynthetic responses to various stressors,
as well as interconnectivity between chloroplast-encoded and nuclear-encoded proteins. Purification of intact chloroplast for quantitative proteomic study has recently
been developed in P. oceanica (Piro et al. 2015a, b), and future organelle-specific
analysis will most likely improve our knowledge on seagrass photosynthetic
mechanisms.
7.5 Conclusion
System biology is an area of research that needs development and represents the key
to a significantly improved understanding of the regulation of photosynthesis and its
interaction with other metabolic pathways. The integration of omics approaches will
7 Photobiology of Seagrasses: A Systems Biology Perspective
et al. 2013 and Wang et al. 2015). Time-series multi-“omics” analyses have identified carbonic anhydrase as the main component of carbon-concentrating mechanisms (CCMs) in C. reinhardtii and elucidated regulatory processes of CCM as well
as interplay between photosynthetic carbon metabolism and other metabolic pathways in response to carbon limitation (Wienkoop et al. 2010; Baba et al. 2011;
Winck et al. 2013; Wang et al. 2015). Additionally, advanced understanding of carbon metabolism and its coordination with other metabolic pathways such as photorespiration and nitrogen metabolism have been established in many model
photosynthetic organisms such as Arabidopsis, rice, tomato, and maize using
multi-“omics” analyses (reviewed in Fukushima and Kusano 2014; Sato and
Yanagisawa 2014). For example, it was shown that responses of plant metabolism
to increasing CO 2 depend largely on the nitrogen conditions. While similar approach
can be adopted to seagrass studies, the availability of full genome sequences for
certain seagrass species makes it possible to develop a genome-scale metabolic
model to investigate fluxes between photosynthesis and other metabolic processes
in these seagrasses. It has been shown that simulation of plant metabolisms using
genome- scale model can successfully predict fluxes between fundamental metabolic pathways such as glycolysis and the TCA cycle in Arabidopsis (Poolman et al.
2009; Williams et al. 2010) and cooperation between mesophyll cells and bundle
sheath cells during C4 photosynthesis (De Oliveira Dal’Molin et al. 2010).
Advanced insights into the function and regulation of the photosynthesis have
come from functional genomic studies in which photosynthetic processes have been
dissected by the molecular tools (Dent et al. 2001, 2005). While omics data provides
an indication of regulatory roles of certain genes or proteins, the future challenge for
seagrass research is the development of mutagenesis experiment which is a powerful
approach to study the function of the genes of interest. Furthermore, proteomics techniques can be applied to investigate protein-protein interaction, posttranslational modifications, and organization of proteins in multi-protein complexes which remain
unexplored in seagrasses. Additionally, chloroplast-targeted transcriptomes and proteomes can provide insights on chloroplast structures and function (Eckardt 2012;
Petersen et al. 2013; Chang et al. 2015). These studies have led to better understanding
of chloroplast protein components and photosynthetic responses to various stressors,
as well as interconnectivity between chloroplast-encoded and nuclear-encoded proteins. Purification of intact chloroplast for quantitative proteomic study has recently
been developed in P. oceanica (Piro et al. 2015a, b), and future organelle-specific
analysis will most likely improve our knowledge on seagrass photosynthetic
mechanisms.
7.5 Conclusion
System biology is an area of research that needs development and represents the key
to a significantly improved understanding of the regulation of photosynthesis and its
interaction with other metabolic pathways. The integration of omics approaches will
7 Photobiology of Seagrasses: A Systems Biology Perspective