High-throughput proteomics and metabolomic studies guide re-engineering of metabolic pathways in eukaryotic microalgae: A review

Key Proteomics Tools for Fundamental and Applied Microalgal Research

Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown to be critical in microalgal research. In the past decade, significant technological advancements have allowed omics technologies to become more affordable and efficient, with huge datasets being generated. In particular, where studies focused on a single or few proteins decades ago, it is now possible to study the whole proteome of a microalgae. The development of mass spectrometry-based methods has provided this leap forward with the high-throughput identification and quantification of proteins. This review specifically provides an overview of the use of proteomics in fundamental (e.g., photosynthesis) and applied (e.g., lipid production for biofuel) microalgal research, and presents future research directions in this field.

Metabolomics-based development of bioproduction processes toward industrial-scale production

Microbial biomanufacturing offers a promising, environment-friendly platform for next-generation chemical production. However, its limited industrial implementation is attributed to the slow production rates of target compounds and the time-intensive engineering of high-yield strains. This review highlights how metabolomics expedites bioproduction development, as demonstrated through case studies of its integration into microbial strain engineering, culture optimization, and model construction. The Design-Build-Test-Learn (DBTL) cycle serves as a standard workflow for strain engineering. Process development, including the optimization of culture conditions and scale-up, is crucial for industrial production. In silico models facilitate the development of strains and processes. Metabolomics is a powerful driver of the DBTL framework, process development, and model construction.

Understanding Macroalgae: A Comprehensive Exploration of Nutraceutical, Pharmaceutical, and Omics Dimensions

Driven by a surge in global interest in natural products, macroalgae or seaweed, has emerged as a prime source for nutraceuticals and pharmaceutical applications. Characterized by remarkable genetic diversity and a crucial role in marine ecosystems, these organisms offer not only substantial nutritional value in proteins, fibers, vitamins, and minerals, but also a diverse array of bioactive molecules with promising pharmaceutical properties. Furthermore, macroalgae produce approximately 80% of the oxygen in the atmosphere, highlighting their ecological significance. The unique combination of nutritional and bioactive attributes positions macroalgae as an ideal resource for food and medicine in various regions worldwide. This comprehensive review consolidates the latest advancements in the field, elucidating the potential applications of macroalgae in developing nutraceuticals and therapeutics. The review emphasizes the pivotal role of omics approaches in deepening our understanding of macroalgae's physiological and molecular characteristics. By highlighting the importance of omics, this review also advocates for continued exploration and utilization of these extraordinary marine organisms in diverse domains, including drug discovery, functional foods, and other industrial applications. The multifaceted potential of macroalgae warrants further research and development to unlock their full benefits and contribute to advancing global health and sustainable industries.

Metabolic sink engineering in cyanobacteria: Perspectives and applications

Recent advances in metabolic engineering have made cyanobacteria emerge as promising and attractive microorganisms for sustainable production, by exploiting their natural capability for producing metabolites. The potential of metabolically engineered cyanobacterium would depend on its source-sink balance in the same way as other phototrophs. In cyanobacteria, the amount of light energy harvested (Source) is incompletely utilized by the cell to fix carbon (sink) resulting in wastage of the absorbed energy causing photoinhibition and cellular damage leading to lowered photosynthetic efficiency. Although regulatory pathways like photo-acclimation and photoprotective processes can be helpful unfortunately they limit the cell's metabolic capacity. This review describes approaches for source-sink balance and engineering heterologous metabolic sinks in cyanobacteria for enhanced photosynthetic efficiency. The advances for engineering additional metabolic pathways in cyanobacteria are also described which will provide a better understanding of the cyanobacterial source-sink balance and approaches for efficient cyanobacterial strains for valuable metabolites.

Dunaliella salina as a Potential Biofactory for Antigens and Vehicle for Mucosal Application

The demand for effective, low-cost vaccines increases research in next-generation biomanufacturing platforms and the study of new vaccine delivery systems (e.g., mucosal vaccines). Applied biotechnology in antigen production guides research toward developing genetic modification techniques in different biological models to achieve the expression of heterologous proteins. These studies are based on various transformation protocols, applied in prokaryotic systems such as Escherichia coli to eukaryotic models such as yeasts, insect cell cultures, animals, and plants, including a particular type of photosynthetic organisms: microalgae, demonstrating the feasibility of recombinant protein expression in these biological models. Microalgae are one of the recombinant protein expression models with the most significant potential and studies in the last decade. Unicellular photosynthetic organisms are widely diverse with biological and growth-specific characteristics. Some examples of the species with commercial interest are Chlamydomonas, Botryococcus, Chlorella, Dunaliella, Haematococcus, and Spirulina. The production of microalgae species at an industrial level through specialized equipment for this purpose allows for proposing microalgae as a basis for producing recombinant proteins at a commercial level. A specie with a particular interest in biotechnology application due to growth characteristics, composition, and protein production capacity is D. salina, which can be cultivated under industrial standards to obtain βcarotene of high interest to humans. D saline currently has advantages over other microalgae species, such as its growth in culture media with a high salt concentration which reduces the risk of contamination, rapid growth, generally considered safe (GRAS), recombinant protein biofactory, and a possible delivery vehicle for mucosal application. This review discusses the status of microalgae D. salina as a platform of expression of recombinant production for its potential mucosal application as a vaccine delivery system, taking an advance on the technology for its production and cultivation at an industrial level.

Metabolic and Proteomic Analysis of Chlorella sorokiniana, Chloroidium saccharofilum, and Chlorella vulgaris Cells Cultured in Autotrophic, Photoheterotrophic, and Mixotrophic Cultivation Modes

Chlorella is one of the most well-known microalgal genera, currently comprising approximately a hundred species of single-celled green algae according to the AlgaeBase. Strains of the genus Chlorella have the ability to metabolize both inorganic and organic carbon sources in various trophic modes and synthesize valuable metabolites that are widely used in many industries. The aim of this work was to investigate the impact of three trophic modes on the growth parameters, productivities of individual cell components, and biochemical composition of Chlorella sorokiniana, Chloroidium saccharofilum, and Chlorella vulgaris cells with special consideration of protein profiles detected by SDS-PAGE gel electrophoresis and two-dimensional gel electrophoresis with MALDI-TOF/TOF MS. Mixotrophic conditions with the use of an agro-industrial by-product stimulated the growth of all Chlorella species, which was confirmed by the highest specific growth rates and the shortest biomass doubling times. The mixotrophic cultivation of all Chlorella species yielded a high amount of protein-rich biomass with reduced contents of chlorophyll a, chlorophyll b, carotenoids, and carbohydrates. Additionally, this work provides the first information about the proteome of Chloroidium saccharofilum, Chlorella sorokiniana, and Chlorella vulgaris cells cultured in molasses supplementation conditions. The proteomic analysis of the three Chlorella species growing photoheterotrophically and mixotrophically showed increased accumulation of proteins involved in the cell energy metabolism and carbon uptake, photosynthesis process, and protein synthesis, as well as proteins involved in intracellular movements and chaperone proteins.

Random Mutagenesis as a Promising Tool for Microalgal Strain Improvement towards Industrial Production

Microalgae have become a promising novel and sustainable feedstock for meeting the rising demand for food and feed. However, microalgae-based products are currently hindered by high production costs. One major reason for this is that commonly cultivated wildtype strains do not possess the robustness and productivity required for successful industrial production. Several strain improvement technologies have been developed towards creating more stress tolerant and productive strains. While classical methods of forward genetics have been extensively used to determine gene function of randomly generated mutants, reverse genetics has been explored to generate specific mutations and target phenotypes. Site-directed mutagenesis can be accomplished by employing different gene editing tools, which enable the generation of tailor-made genotypes. Nevertheless, strategies promoting the selection of randomly generated mutants avoid the introduction of foreign genetic material. In this paper, we review different microalgal strain improvement approaches and their applications, with a primary focus on random mutagenesis. Current challenges hampering strain improvement, selection, and commercialization will be discussed. The combination of these approaches with high-throughput technologies, such as fluorescence-activated cell sorting, as tools to select the most promising mutants, will also be discussed.

Cyanobacterial secondary metabolites towards improved commercial significance through multiomics approaches

Cyanobacteria are ubiquitous photosynthetic prokaryotes responsible for the oxygenation of the earth's reducing atmosphere. Apart from oxygen they are producers of a myriad of bioactive metabolites with diverse complex chemical structures and robust biological activities. These secondary metabolites are known to have a variety of medicinal and therapeutic applications ranging from anti-microbial, anti-viral, anti-inflammatory, anti-cancer, and immunomodulating properties. The present review discusses various aspects of secondary metabolites viz. biosynthesis, types and applications, which highlights the repertoire of bioactive constituents they harbor. Majority of these products have been produced from only a handful of genera. Moreover, with the onset of various OMICS approaches, cyanobacteria have become an attractive chassis for improved secondary metabolites production. Also the intervention of synthetic biology tools such as gene editing technologies and a variety of metabolomics and fluxomics approaches, used for engineering cyanobacteria, have significantly enhanced the production of secondary metabolites.

Chlorella vulgaris cultivation in pilot-scale to treat real swine wastewater and mitigate carbon dioxide for sustainable biodiesel production by direct enzymatic transesterification

This study firstly addressed real swine wastewater (RSW) treatment by an indigenous Chlorella vulgaris MBFJNU-1 in 5-m³ outdoor open raceway ponds and then direct enzymatic transesterification of the resulting lipids from the wet biomass for sustainable biodiesel production. Compared to the control group, C. vulgaris MBFJNU-1 at 3% CO₂ achieved higher microalgal biomass (478.5 mg/L) and total fatty acids content (21.3%), higher CO₂ bio-fixation (63.2 mg/L/d) and lipid (9.1 mg/L/d) productivities, and greater nutrients removals (total nitrogen, 82.1%; total phosphorus, 28.4%; chemical oxygen demand, 37.1%). The highest biodiesel conversion (93.3%) was attained by enzymatic transesterification of wet disrupted Chlorella biomass with 5% lipase TL and 5% phospholipase PLA. Moreover, the enzymatic transesterification gave around 83% biodiesel conversion in a 15-L stirred tank bioreactor. Furthermore, the integrated process was a cost-effective approach to treat RSW and mitigate CO₂ for microalgal biodiesel production, based on the mass and energy balances analysis.

Genetic Engineering of Microalgae for Secondary Metabolite Production: Recent Developments, Challenges, and Future Prospects

Microalgae are highly diverse photosynthetic organisms with higher growth rate and simple nutritional requirements. They are evolved with an efficiency to adapt to a wide range of environmental conditions, resulting in a variety of genetic diversity. Algae accounts for nearly half of global photosynthesis, which makes them a crucial player for CO₂ sequestration. In addition, they have metabolic capacities to produce novel secondary metabolites of pharmaceutical, nutraceutical and industrial applications. Studies have explored the inherent metabolic capacities of microalgae with altered growth conditions for the production of primary and secondary metabolites. However, the production of the targeted metabolites at higher rates is not guaranteed just with the inherent genetic potentials. The strain improvement using genetic engineering is possible hope to overcome the conventional methods of culture condition improvements for metabolite synthesis. Although the advanced gene editing tools are available, the gene manipulation of microalgae remains relatively unexplored. Among the performed gene manipulations studies, most of them focus on primary metabolites with limited focus on secondary metabolite production. The targeted genes can be overexpressed to enhance the production of the desired metabolite or redesigning them using the synthetic biology. A mutant (KOR1) rich in carotenoid and lipid content was developed in a recent study employing mutational breeding in microalgae (Kato, Commun. Biol, 2021, 4, 450). There are lot of challenges in genetic engineering associated with large algal diversity but the numerous applications of secondary metabolites make this field of research very vital for the biotech industries. This review, summarise all the genetic engineering studies and their significance with respect to secondary metabolite production from microalgae. Further, current genetic engineering strategies, their limitations and future strategies are also discussed.

Microalgae Bioactive Carbohydrates as a Novel Sustainable and Eco-Friendly Source of Prebiotics: Emerging Health Functionality and Recent Technologies for Extraction and Detection

There is a global interest in the novel consumption, nutritional trends, and the market of new prebiotic sources and their potential functional impacts. Commercially available nutritional supplements based on microalgae that are approved to be edible by FDA, like Arthrospira platensis (Cyanobacteria) and Chlorella vulgaris (Chlorophyta) become widely attractive. Microalgae are rich in carbohydrates, proteins, and polyunsaturated fatty acids that have high bioactivity. Recently, scientists are studying the microalgae polysaccharides (PS) or their derivatives (as dietary fibers) for their potential action as a novel prebiotic source for functional foods. Besides, the microalgae prebiotic polysaccharides are used for medication due to their antioxidant, anticancer, and antihypertensive bioactivities. This review provides an overview of microalgae prebiotics and other macromolecules’ health benefits. The phytochemistry of various species as alternative future sources of novel polysaccharides were mentioned. The application as well as the production constraints and multidisciplinary approaches for evaluating microalgae phytochemistry were discussed. Additionally, the association between this potential of combining techniques like spectroscopic, chromatographic, and electrochemical analyses for microalgae sensation and analysis novelty compared to the chemical methods was emphasized.

Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review

Metabolomics, an essential tool in modern synthetic biology based on the design-build-test-learn platform, is useful for obtaining a detailed understanding of cellular metabolic mechanisms through comprehensive analyses of the metabolite pool size and its dynamic changes. Metabolomics is critical to the design of a rational metabolic engineering strategy by determining the rate-limiting reaction and assimilated carbon distribution in a biosynthetic pathway of interest. Microalgae and cyanobacteria are promising photosynthetic producers of biofuels and bio-based chemicals, with high potential for developing a bioeconomic society through bio-based carbon neutral manufacturing. Metabolomics technologies optimized for photosynthetic organisms have been developed and utilized in various microalgal and cyanobacterial species. This review provides a concise overview of recent achievements in photosynthetic metabolomics, emphasizing the importance of microalgal and cyanobacterial cell factories that satisfy industrial requirements.

Development of the "Applied Proteomics" Concept for Biotechnology Applications in Microalgae: Example of the Proteome Data in Nannochloropsis gaditana

Most of the marine ecosystems on our planet are still unknown. Among these ecosystems, microalgae act as a baseline due to their role as primary producers. The estimated millions of species of these microorganisms represent an almost infinite source of potentially active biocomponents offering unlimited biotechnology applications. This review considers current research in microalgae using the "omics" approach, which today is probably the most important biotechnology tool. These techniques enable us to obtain a large volume of data from a single experiment. The specific focus of this review is proteomics as a technique capable of generating a large volume of interesting information in a single proteomics assay, and particularly the concept of applied proteomics. As an example, this concept has been applied to the study of Nannochloropsis gaditana, in which proteomics data generated are transformed into information of high commercial value by identifying proteins with direct applications in the biomedical and agri-food fields, such as the protein designated UCA01 which presents antitumor activity, obtained from N. gaditana.

An integrated approach for the efficient separation of specialty compounds from biomass of the marine microalgae Amphidinium carterae

An amphidinol-prioritized fractioning approach was for the first time developed to isolate multiple specialty metabolites such as amphidinols, carotenoids and fatty acids using the biomass of the marine microalgae Amphidinium carterae. The biomass was produced in a raceway photobioreactor and the exhausted culture media were reused, thus fulfilling sustainability criteria employing a circular economy concept. The integrated bioactive compounds-targeted approach presented here consisted of four steps with which recovery percentages of carotenoids, fatty acids and amphidinols of 97%, 82% and 99 %, respectively, were achieved. The proposed process was proved to be a better extraction system for this microalga than another based on a sequential gradient partition with water and four water-immiscible organic solvents (hexane, carbon tetrachloride, dichloromethane and n-butanol). The proposed process could be scaled-up as a commercial solid-phase extraction technology well-established for industrial bioprocesses.

Advances in production of bioplastics by microalgae using food waste hydrolysate and wastewater: A review

Microalgae have emerged as an effective dual strategy for bio-valorisation of food processing wastewater and food waste hydrolysate which favours microalgae cultivation into producing value-added by products mainly lipids, carbohydrates, and proteins to the advantages of bioplastic production. Moreover, various microalgae have successfully removed high amount of organic pollutants from food processing wastewater prior discharging into the environment. Innovation of microalgae cultivating in food processing wastewater greatly reduced the cost of wastewater treatment compared to conventional approach in terms of lower carbon emissions, energy consumption, and chemical usage while producing microalgae biomass which can benefit low-cost fertilizer and bioplastic applications. The study on several microalgae species has all successfully grown on food waste hydrolysates showing high exponential growth rate and biomass production rich in proteins, lipids, carbohydrates, and fatty acids. Multiple techniques have been implemented for the extraction of food wastes to be incorporate into the bioplastic production.

Insights into the genetic and metabolic engineering approaches to enhance the competence of microalgae as biofuel resource: A review

Conventional fuel resources are overburden with speedy global energy demand which ensued the urgent need of alternate energy resources. Biofuel generation efficiency of microalgae is notable due to their comparatively rapid biomass production rate and high oil content. But, the employment of microalgae as biofuel resource is in infancy due to low productivity and high production cost. The issues can be addressed by employing engineered microalgal strains that would be able to efficiently generate enhanced levels of biomass with augmented lipid and/or carbohydrate content for proficient biofuel production. Genetic alterations and metabolic engineering of microalgal species might be helpful in developing high stress-tolerant strains with improved properties for biofuel generation. Various omics approaches appeared significant to upgrade the microalgal lipid production. Intervention of genetic and metabolic engineering approaches would facilitate the development of microalgae as a competent biofuel resource and inflate the economic commercialization of biofuels.

Using green alga Haematococcus pluvialis for astaxanthin and lipid co-production: Advances and outlook

Astaxanthin is one of the secondary carotenoids involved in mediating abiotic stress of microalgae. As an important antioxidant and nutraceutical compound, astaxanthin is widely applied in dietary supplements and cosmetic ingredients. However, most astaxanthin in the market is chemically synthesized, which are structurally heterogeneous and inefficient for biological uptake. Astaxanthin refinery from Haematococcus pluvialis is now a growing industrial sector. H. pluvialis can accumulate astaxanthin to ∼5% of dry weight. As productivity is a key metric to evaluate the production feasibility, understanding the biological mechanisms of astaxanthin accumulation is beneficial for further production optimization. In this review, the biosynthesis mechanism of astaxanthin and production strategies are summarized. The current research on enhancing astaxanthin accumulation and the potential joint-production of astaxanthin with lipids was also discussed. It is conceivable that with further improvement on the productivity of astaxanthin and by-products, the algal-derived astaxanthin would be more accessible to low-profit applications.

Endoplasmic Reticulum Subproteome Analysis Reveals Underlying Defense Mechanisms of Wheat Seedling Leaves under Salt Stress

Salt stress is the second most important abiotic stress factor in the world, which seriously affects crop growth, development and grain production. In this study, we performed the first integrated physiological and endoplasmic reticulum (ER) proteome analysis of wheat seedling leaves under salt stress using a label-free-based quantitative proteomic approach. Salt stress caused significant decrease in seedling height, root length, relative water content and chlorophyll content of wheat seedling leaves, indicating that wheat seedling growth was significantly inhibited under salt stress. The ER proteome analysis identified 233 ER-localized differentially accumulated proteins (DAPs) in response to salt stress, including 202 upregulated and 31 downregulated proteins. The upregulated proteins were mainly involved in the oxidation-reduction process, transmembrane transport, the carboxylic acid metabolic process, stress response, the arbohydrate metabolic process and proteolysis, while the downregulated proteins mainly participated in the metabolic process, biological regulation and the cellular process. In particular, salt stress induced significant upregulation of protein disulfide isomerase-like proteins and heat shock proteins and significant downregulation of ribosomal protein abundance. Further transcript expression analysis revealed that half of the detected DAP genes showed a consistent pattern with their protein levels under salt stress. A putative metabolic pathway of ER subproteome of wheat seedling leaves in response to salt stress was proposed, which reveals the potential roles of wheat ER proteome in salt stress response and defense.

Advantages of Heterotrophic Microalgae as a Host for Phytochemicals Production

Currently, most commercial recombinant technologies rely on host systems. However, each host has their own benefits and drawbacks, depending on the target products. Prokaryote host is lack of post-transcriptional and post-translational mechanisms, making them unsuitable for eukaryotic productions like phytochemicals. Even there are other eukaryote hosts (e.g., transgenic animals, mammalian cell, and transgenic plants), but those hosts have some limitations, such as low yield, high cost, time consuming, virus contamination, and so on. Thus, flexible platforms and efficient methods that can produced phytochemicals are required. The use of heterotrophic microalgae as a host system is interesting because it possibly overcome those obstacles. This paper presents a comprehensive review of heterotrophic microalgal expression host including advantages of heterotrophic microalgae as a host, genetic engineering of microalgae, genetic transformation of microalgae, microalgal engineering for phytochemicals production, challenges of microalgal hosts, key market trends, and future view. Finally, this review might be a directions of the alternative microalgae host for high-value phytochemicals production in the next few years.