Basel Khraiwesh, Kenan Jijakli, Joseph Swift,

Amphun Chaiboonchoe, Rasha Abdrabu, Pei-Wen Chao, Laising Yen and Kourosh Salehi-Ashtiani

Abstract Synthetic Biology is an interdisciplinary approach combining biotech­nology, evolutionary biology, molecular biology, systems biology and biophysics. While the exact definition of Synthetic Biology might still be debatable, its focus on design and construction of biological devices that perform useful functions is clear and of great utility to engineering algae. This relies on the re-engineering of bio­logical circuits and optimization of certain metabolic pathways to reprogram algae and introduce new functions in them via the use of genetic modules. Genetic editing tools are primary enabling techniques in Synthetic Biology and this chapter dis­cusses common techniques that show promise for algal gene editing. The genetic editing tools discussed in this chapter include RNA interference (RNAi) and arti­ficial microRNAs, RNA scaffolds, transcription activator-like effector nucleases (TALENs), RNA guided Cas9 endonucleases (CRISPR), and multiplex automated genome engineering (MAGE). DNA and whole genome synthesis is another enabling technology in Synthetic Biology and might present an alternative approach to drastically and readily modify algae. Clear and powerful examples of the potential of whole genome synthesis for algal engineering are presented. Also, the development of relevant computational tools, and genetic part registries has stim­ulated further advancements in the field and their utility in algal research and engineering is described. For now, the majority of synthetic biology efforts are

B. Khraiwesh • A. Chaiboonchoe • R. Abdrabu • K. Salehi-Ashtiani (H)

Division of Science and Math, and Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, 129188, Abu Dhabi, United Arab Emirates e-mail: ksa3@nyu. edu

K. Jijakli

Division of Engineering, New York University Abu Dhabi, 129188, Abu Dhabi United Arab Emirates

J. Swift

Department of Biology, New York University, 12 Waverly Place, New York 10003, USA P.-W. Chao • L. Yen

Department of Pathology and Immunology, Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA

© Springer International Publishing Switzerland 2015

N. R. Moheimani et al. (eds.), Biomass and Biofuels from Microalgae,

Biofuel and Biorefinery Technologies 2, DOI 10.1007/978-3-319-16640-7_8 focused on microbes as many pressing problems, such as sustainability in food and energy production rely on modification of microorganisms. Synthetic modifications of algal strains to enhance desired physiological properties could lead to improvements in their utility.

8.1 Introduction

More basic research is needed before algal biotechnology can reach a capacity to compete with other systems (Stephen and Joshi 2010). Because many physiologi­cal, morphological, biochemical, or molecular characteristics of algae are quite different from higher plants or animals, algae can meet several requirements that other systems cannot (Hallmann 2007). The demand for improved systems of production of nutraceuticals and cost-effective protein expression systems (both industrial and pharmaceutical applications) lend themselves to explore the potential useful capacities of algae (Hallmann 2007).

Synthetic biology is the design and construction of biological devices and systems for a specific purpose (Ferry et al. 2012). This is an area of biological research and technology that combines biology and engineering, thus often over­lapping with bioengineering and biomedical engineering (Serrano 2007). It encompasses a variety of different approaches, methodologies, and disciplines with a focus on bioengineering and biotechnology. Through the innovative re-engineering of biological circuits and optimization of certain metabolic path­ways, biological modules can be designed to reprogram organisms to produce products, or exhibit desired metabolic behaviors (Khalil and Collins 2010). Synthetic biology can enable model transferability to address a multitude of industrial needs and projects (Anderson et al. 2012). Researchers in this field are realistically optimistic that synthetic biology can provide solutions to a multitude of worldwide problems from health to energy (Purnick and Weiss 2009). The success of synthetic biology as a promising approach is demonstrated by a number of successful attempts in constructing microbial strains to lower production cost of pharmaceutical products (Khalil and Collins 2010). Similarly, there are ongoing works to introduce desirable traits into algae, and to re-engineer algal cells (Ferry et al. 2012; Gimpel et al. 2013; Rabinovitch-Deere et al. 2013).

Although sometimes referred to as genetic engineering, synthetic biology differs in terms of scale, scope, techniques of manipulation, and application (Serrano

2007) . Genetic engineering focuses on the alteration of a single characteristic of an organism through transgenic hybrids or genetic chimeras that carry altered genes, or genes from other organisms. In contrast, synthetic biology seeks to reconfigure, design, and construct new pathways, whole processes, or novel systems for the purpose of achieving some desired biosynthetic activity or phenotype (Alper and Stephanopoulos 2009; Khalil and Collins 2010).

Microalgae exhibit enormous biodiversity, and have the potential for producing large quantities of biomass containing high concentrations of lipids (Gimpel et al.

2013) . Synthetic, systems, and post-genomics biology are terms that are increas­ingly encountered in the biofuels and biotechnology research space with all such approaches likely to be deployed to enable algal biofuels to become economically competitive with fossil fuels. In order to create a viable technology, the field of synthetic biology has been moving towards modular genetic systems. Modularity encompasses the reliance on standardized genetic parts and circuitry models—just like the field of electronics and electric circuits relies on standard collections of resistors, transistors, and capacitors (Fig. 8.1).

RNA-mediated silencing and targeted genome editing tools, including artificial microRNA (Khraiwesh et al. 2011), RNA scaffolds (Delebecque et al. 2012), TALENs, and RNA guided Cas9 endonucleases (Gaj et al. 2013), have allowed synthetic biology to develop gene circuits designed to perform specific functions, often by combining components from multiple organisms to generate novel func­tionality. These new research endeavors will undoubtedly increase our knowledge and usage of these important primary-producing organisms.