Towards a synthetic nuclear transcription system in green algae: Characterization of Chlamydomonas reinhardtii nuclear transcription factors and identification of targeted promoters

Microbial meat: A sustainable vegan protein source produced from agri-waste to feed the world

In the modern world, animal and plant protein may not meet the sustainability criteria due to their high need for arable land and potable water consumption, among other practices. Considering the growing population and food shortage, finding alternative protein sources for human consumption is an urgent issue that needs to be solved, especially in developing countries. In this context, microbial bioconversion of valuable materials in nutritious microbial cells represent a sustainable alternative to the food chain. Microbial protein, also known as single-cell protein (SCP), consist of algae biomass, fungi or bacteria that are currently used as food source for both humans and animals. Besides contributing as a sustainable source of protein to feed the world, producing SCP, is important to reduce waste disposal problems and production costs meeting the sustainable development goals. However, for microbial protein as feed or food to become an important and sustainable alternative, addressing the challenges of raising awareness and achieving wider public regulatory acceptance is real and must be addressed with care and convenience. In this work, we critically reviewed the potential technologies for microbial protein production, its benefits, safety, and limitations associated with its uses, and perspectives for broader large-scale implementation. We argue that the information documented in this manuscript will assist in developing microbial meat as a major protein source for the vegan world.

Promoting cell growth and characterizing partial symbiotic relationships in the co-cultivation of green alga Chlamydomonas reinhardtii and Escherichia coli

BACKGROUND

By co-culturing selected microalgae and heterotrophic microorganisms, the growth rate of microalgae can be improved even under atmospheric conditions with a low CO₂ concentration. However, the detailed mechanism of improvement of proliferative capacity by co-culture has not been elucidated. In this study, we investigated changes in the proliferative capacity of the green alga Chlamydomonas reinhardtii by co-culturing with Escherichia coli.

MAIN METHODS AND MAJOR RESULTS

In the co-culture, the number of C. reinhardtii cells reached 2.22 × 10¹⁰  cell/L on day 14 of culture. This was about 1.9 times the number of cells (1.16 × 10¹⁰  cell/L) on day 14 compared to C. reinhardtii cells in monoculture. The starch content per cell in the co-culture of C. reinhardtii and E. coli on the 14th day (2.09 × 10^-11  g/cell) was 1.3 times higher than that in the C. reinhardtii monoculture (1.59 × 10^-11  g/cell), and the starch content per culture medium improved 2.5 times with co-cultivation. By analyzing the gene transcription profiles and key media components, we clarified that E. coli produced CO₂ from the organic carbon in the medium and the organic carbon produced by photosynthesis of C. reinhardtii, and this CO₂ likely enhanced the growth of C. reinhardtii.

CONCLUSIONS

Consequently, E. coli plays a key role in promoting the growth of C. reinhardtii as well as the accumulation of starch which is a valuable intermediate for the production of a range of useful chemicals from CO₂ .

Chlamydomonas reinhardtii: A Factory of Nutraceutical and Food Supplements for Human Health

Chlamydomonas reinhardtii (C. reinhardtii) is one of the most well-studied microalgae organisms that revealed important information for the photosynthetic and metabolic processes of plants and eukaryotes. Numerous extensive studies have also underpinned its great potential as a biochemical factory, capable of producing various highly desired molecules with a direct impact on human health and longevity. Polysaccharides, lipids, functional proteins, pigments, hormones, vaccines, and antibodies are among the valuable biomolecules that are produced spontaneously or under well-defined conditions by C. reinhardtii and can be directly linked to human nutrition and diet. The aim of this review is to highlight the recent advances in the field focusing on the most relevant applications related to the production of important biomolecules for human health that are also linked with human nutrition and diet. The limitations and challenges are critically discussed along with the potential future applications of C. reinhardtii biomass and processed products in the field of nutraceuticals and food supplements. The increasing need for high-value and low-cost biomolecules produced in an environmentally and economy sustainable manner also underline the important role of C. reinhardtii.

Production, Processing, and Protection of Microalgal n-3 PUFA-Rich Oil

Microalgae have been increasingly considered as a sustainable “biofactory” with huge potentials to fill up the current and future shortages of food and nutrition. They have become an economically and technologically viable solution to produce a great diversity of high-value bioactive compounds, including n-3 polyunsaturated fatty acids (PUFA). The n-3 PUFA, especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), possess an array of biological activities and positively affect a number of diseases, including cardiovascular and neurodegenerative disorders. As such, the global market of n-3 PUFA has been increasing at a fast pace in the past two decades. Nowadays, the supply of n-3 PUFA is facing serious challenges as a result of global warming and maximal/over marine fisheries catches. Although increasing rapidly in recent years, aquaculture as an alternative source of n-3 PUFA appears insufficient to meet the fast increase in consumption and market demand. Therefore, the cultivation of microalgae stands out as a potential solution to meet the shortages of the n-3 PUFA market and provides unique fatty acids for the special groups of the population. This review focuses on the biosynthesis pathways and recombinant engineering approaches that can be used to enhance the production of n-3 PUFA, the impact of environmental conditions in heterotrophic cultivation on n-3 PUFA production, and the technologies that have been applied in the food industry to extract and purify oil in microalgae and protect n-3 PUFA from oxidation.

The Spermidine Synthase Gene SPD1: A Novel Auxotrophic Marker for Chlamydomonas reinhardtii Designed by Enhanced CRISPR/Cas9 Gene Editing

Biotechnological application of the green microalga Chlamydomonas reinhardtii hinges on the availability of selectable markers for effective expression of multiple transgenes. However, biological safety concerns limit the establishment of new antibiotic resistance genes and until today, only a few auxotrophic markers exist for C. reinhardtii. The recent improvements in gene editing via CRISPR/Cas allow directed exploration of new endogenous selectable markers. Since editing frequencies remain comparably low, a Cas9-sgRNA ribonucleoprotein (RNP) delivery protocol was strategically optimized by applying nitrogen starvation to the pre-culture, which improved successful gene edits from 10% to 66% after pre-selection. Probing the essential polyamine biosynthesis pathway, the spermidine synthase gene (SPD1) is shown to be a potent selectable marker with versatile biotechnological applicability. Very low levels of spermidine (0.75 mg/L) were required to maintain normal mixotrophic and phototrophic growth in newly designed spermidine auxotrophic strains. Complementation of these strains with a synthetic SPD1 gene was achieved when the mature protein was expressed in the cytosol or targeted to the chloroplast. This work highlights the potential of new selectable markers for biotechnology as well as basic research and proposes an effective pipeline for the identification of new auxotrophies in C. reinhardtii.

Engineering microalgae: transition from empirical design to programmable cells

Domesticated microalgae hold great promise for the sustainable provision of various bioresources for human domestic and industrial consumption. Efforts to exploit their potential are far from being fully realized due to limitations in the know-how of microalgal engineering. The associated technologies are not as well developed as those for heterotrophic microbes, cyanobacteria, and plants. However, recent studies on microalgal metabolic engineering, genome editing, and synthetic biology have immensely helped to enhance transformation efficiencies and are bringing new insights into this field. Therefore, this article, summarizes recent developments in microalgal biotechnology and examines the prospects for generating specialty and commodity products through the processes of metabolic engineering and synthetic biology. After a brief examination of empirical engineering methods and vector design, this article focuses on quantitative transformation cassette design, elaborates on target editing methods and emerging digital design of algal cellular metabolism to arrive at high yields of valuable products. These advances have enabled a transition of manners in microalgal engineering from single-gene and enzyme-based metabolic engineering to systems-level precision engineering, from cells created with genetically modified (GM) tags to that without GM tags, and ultimately from proof of concept to tangible industrial applications. Finally, future trends are proposed in microalgal engineering, aiming to establish individualized transformation systems in newly identified species for strain-specific specialty and commodity products, while developing sophisticated universal toolkits in model algal species.

Primary metabolites from overproducing microbial system using sustainable substrates

Primary (or secondary) metabolites are produced by animals, plants, or microbial cell systems either intracellularly or extracellularly. Production capabilities of microbial cell systems for many types of primary metabolites have been exploited at a commercial scale. But the high production cost of metabolites is a big challenge for most of the bioprocess industries and commercial production needs to be achieved. This issue can be solved to some extent by screening and developing the engineered microbial systems via reconstruction of the genome-scale metabolic model. The predicted genetic modification is applied for an increased flux in biosynthesis pathways toward the desired product. Wherein the resulting microbial strain is capable of converting a large amount of carbon substrate to the expected product with minimum by-product formation in the optimal operating conditions. Metabolic engineering efforts have also resulted in significant improvement of metabolite yields, depending on the nature of the products, microbial cell factory modification, and the types of substrate used. The objective of this review is to comprehend the state of art for the production of various primary metabolites by microbial strains system, focusing on the selection of efficient strain and genetic or pathway modifications, applied during strain engineering.

Microalgae as a future food source

One of the key challenges that we face in the 21st century is the need to feed an ever-increasing human population with increasingly limited natural resources. Even today it is estimated that roughly 1 out of 9 people in the world are undernourished, of which the most important factor is protein-energy malnutrition. By establishing microalgae as a new food and feed platform, we have the opportunity to increase the supply of these essential products to address global demands in a more efficient and environmentally sustainable way. Many types of algae are nutritionally complete foods, their yields outperform most plant crops, and there is a growing set of tools to develop improved strains of algae. Similar improvements were achieved in traditional crops through thousands of years of breeding and strain selection, whereas with the newest genetic engineering tools and advanced strain selection techniques, similar changes can be implemented in microalgae in just a few years. Here we describe different strategies that could be used to enhance the nutritional content, productivity, and organoleptic traits of algae to help drive development of this new crop. Clearly developing more efficient, sustainable, and nutritious foods and feed would be an enormous benefit for the planet, and algae represents an opportunity to develop a new crop that would complement traditional agriculture, and one that could potential result in a more efficient means to meet the world's food and feed supply.

Increased biomass and lipid production by continuous cultivation of Nannochloropsis salina transformant overexpressing a bHLH transcription factor

Microalgae are promising feedstocks for sustainable and eco-friendly production of biomaterials, which can be improved by genetic engineering. It is also necessary to optimize the processes to produce biomaterials from engineered microalgae. We previously reported that genetic improvements of an industrial microalga Nannochloropsis salina by overexpressing a basic helix-loop-helix transcription factor (NsbHLH2). These transformants showed an improved growth and lipid production particularly during the early phase of culture under batch culture. However, they had faster uptake of nutrients, resulting in earlier starvation and reduced growth during the later stages. We attempted to optimize the growth and lipid production by growing one of the transformants in continuous culture with variable dilution rate and feed nitrogen concentration. Relative to wild-type, NsbHLH2 transformant consumed more nitrate at a high dilution rate (0.5 day ^-1 ), and had greater biomass production. Subsequently, nitrogen limitation at continuous cultivation led to an increased fatty acid methyl ester production by 83.6 mg l ^-1 day ^-1 . To elucidate genetic mechanisms, we identified the genes containing E-boxes, known as binding sites for bHLH transcription factors. Among these, we selected 18 genes involved in the growth and lipid metabolism, and revealed their positive contribution to the phenotypes via quantitative real-time polymerase chain reaction. These results provide proof-of-concept that NsbHLH2 can be used to produce biomass and lipids.

Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production

In the wake of the uprising global energy crisis, microalgae have emerged as an alternate feedstock for biofuel production. In addition, microalgae bear immense potential as bio-cell factories in terms of producing key chemicals, recombinant proteins, enzymes, lipid, hydrogen and alcohol. Abstraction of such high-value products (algal biorefinery approach) facilitates to make microalgae-based renewable energy an economically viable option. Synthetic biology is an emerging field that harmoniously blends science and engineering to help design and construct novel biological systems, with an aim to achieve rationally formulated objectives. However, resources and tools used for such nuclear manipulation, construction of synthetic gene network and genome-scale reconstruction of microalgae are limited. Herein, we present recent developments in the upcoming field of microalgae employed as a model system for synthetic biology applications and highlight the importance of genome-scale reconstruction models and kinetic models, to maximize the metabolic output by understanding the intricacies of algal growth. This review also examines the role played by microalgae as biorefineries, microalgal culture conditions and various operating parameters that need to be optimized to yield biofuel that can be economically competitive with fossil fuels.