Connecting color with assembly in the fluorescent B‐phycoerythrin protein complex

Sustainable microalgal biomass as a potential functional food and its applications in food industry: a comprehensive review

Microalgae (MA) are the most abundant seaweeds with high nutritional properties. They are accepted as potential biocatalysts for the bioremediation of wastewater. They are widely used in food, feed, and biofuel industries and can potentially be food for future generations. MA-based purification of wastewater technology could be a universal alternative solution for the recovery of resources from wastewater for low-cost biomass feedstock for industry. They provide a wide range of functional components, viz. omega-3 fatty acids, along with a plenteous number of pigments such as ß-carotene, astaxanthin, lutein, phycocyanin, and chlorophyll, which are used extensively as food additives and nutraceuticals. Further, proteins, lipids, vitamins, and carbohydrates are described as nutritional characteristics in MA. They are investigated as single-cell protein, thickening/stabilizing agents, and pigment sources in the food industry. The review emphasizes the production and extraction of nutritional and functional components of algal biomass and the role of microalgal polysaccharides in digestion and nutritional absorption in the gastrointestinal tract. Further, the use of MA in the food industry was also investigated along with their potential therapeutic applications.

Purified Pyropia yezoensis Pigment Extract-Based Tandem Dye Synthesis

Red phycoerythrin (R-PE) is a highly valuable protein found in an edible seaweed, Pyropia yezoensis. It is used extensively in biotechnological applications due to its strong fluorescence and stability in diverse environments. However, the current methods for extracting and purifying R-PE are costly and unsustainable. The aim of the present study was to enhance the financial viability of the process by improving the extraction and purification of R-PE from dried P. yezoensis and to further enhance R-PE value by incorporating it into a tandem dye for molecular biology applications. A combination of ultrafiltration, ion exchange chromatography, and gel filtration yielded concentrated (1 mg·mL-1) R-PE at 99% purity. Using purified PE and Cyanine5 (Cy5), an organic tandem dye, phycoerythrin-Cy5 (PE-Cy5), was subsequently established. In comparison to a commercially available tandem dye, PE-Cy5 exhibited 202.3% stronger fluorescence, rendering it suitable for imaging and analyzes that require high sensitivity, enhanced signal-to-noise ratio, broad dynamic range, or shorter exposure times to minimize potential damage to samples. The techno-economic analysis confirmed the financial feasibility of the innovative technique for the extraction and purification of R-PE and PE-Cy5 production.

Recent Progress of Natural and Recombinant Phycobiliproteins as Fluorescent Probes

Phycobiliproteins (PBPs) are natural water-soluble pigment proteins, which constitute light-collecting antennae, and function in algae photosynthesis, existing in cyanobacteria, red algae, and cryptomonads. They are special pigment-protein complexes in algae with a unique structure and function. According to their spectral properties, PBPs can be mainly divided into three types: allophycocyanin, phycocyanin, and PE. At present, there are two main sources of PBPs: one is natural PBPs extracted from algae and the other way is recombinant PBPs which are produced in engineered microorganisms. The covalent connection between PBP and streptavidin was realized by gene fusion. The bridge cascade reaction not only improved the sensitivity of PBP as a fluorescent probe but also saved the preparation time of the probe, which expands the application range of PBPs as fluorescent probes. In addition to its function as a light-collecting antenna in photosynthesis, PBPs also have the functions of biological detection, ion detection, and fluorescence imaging. Notably, increasing studies have designed novel PBP-based far-red fluorescent proteins, which enable the tracking of gene expression and cell fate.

Extraction and purification of phycobiliproteins from algae and their applications

Microalgae, macroalgae and cyanobacteria are photosynthetic microorganisms, prokaryotic or eukaryotic, living in saline or freshwater environments. These have been recognized as valuable carbon sources, able to be used for food, feed, chemicals, and biopharmaceuticals. From the range of valuable compounds produced by these cells, some of the most interesting are the pigments, including chlorophylls, carotenoids, and phycobiliproteins. Phycobiliproteins are photosynthetic light-harvesting and water-soluble proteins. In this work, the downstream processes being applied to recover fluorescent proteins from marine and freshwater biomass are reviewed. The various types of biomasses, namely macroalgae, microalgae, and cyanobacteria, are highlighted and the solvents and techniques applied in the extraction and purification of the fluorescent proteins, as well as their main applications while being fluorescent/luminescent are discussed. In the end, a critical perspective on how the phycobiliproteins business may benefit from the development of cost-effective downstream processes and their integration with the final application demands, namely regarding their stability, will be provided.

Phycobiliproteins, the pigment-protein complex form of natural food colorants and bioactive ingredients

Currently, the use of synthetic pigments in foods is restricted since synthetic pigments are proven and suspected to be harmful to human health. Phycobiliproteins (PBPs), existed in phycobilisomes (PBSs) of algae, are a kind of pigment-proteins with intense color. The specific color of PBPs (red and blue) is given by the water-soluble open-chained tetrapyrrole chromophore (phycobilin) that covalently attaches to the apo-protein via thioether linkages to cysteine residues. According to the spectral characteristics of PBPs, they can be categorized as phycoerythrins (PEs), phycocyanins (PCs), allophycocyanins (APCs), and phycoerythrocyanins (PECs). PBPs can be used as natural food colorants, fluorescent substances, and bioactive ingredients in food applications owing to their color characteristics and physiological activities. This paper mainly summarizes the extraction and purification methods of the PBPs and reviews their characteristics and applications. Moreover, the use of several strategies such as additives, microencapsulation, electrospray, and cross-linking to improve the stability and bioavailability of PBPs as well as the future outlooks of PBPs as natural colorants in food commercialization are elucidated.

Comparison of Production and Fluorescence Characteristics of Phycoerythrin from Three Strains of Porphyridium

Phycoerythrin, a special photosynthetic pigment, is widely used as fluorescent dye and has lots of underlying beneficial effects on health. A marine red microalga Porphyridium is considered as the potential feedstock for phycoerythrin production. However, the phycoerythrin-related properties of Porphyridium have not been systematically evaluated, especially between the species of P. cruentum and P. purpureum. The present study aimed to evaluate the production and fluorescence characteristics of phycoerythrin of three strains of Porphyridium. The results showed that P. purpureum SCS-02 presented the highest biomass, phycoerythrin content and yield were 6.43 g L⁻¹, 9.18% DW and 0.288 g L⁻¹, respectively. There was no significant difference between P. purpureum and P. cruentum in α and β subunits amino acid sequences of phycoerythrin and in fluorescence characteristics. The high gene expression level of the key enzymes in phycoerythrobilin synthesis (porphobilinogen synthase and oxygen-dependent coproporphyrinogen-III oxidase) could be related to the high phycoerythrin content of Porphyridium. Based on systematic evaluation, P. purpureum SCS-02 was selected due to its high biomass and phycoerythrin yield. P. purpureum and P. cruentum were highly similar in the phylogenetic tree, as well as in fluorescence characteristics; therefore, it was speculated that they might be the same Porphyridium species.

Probing heavy metal binding to phycobiliproteins

Blue-green algae, also known as cyanobacteria, contain some of the most efficient light-harvesting complexes known. These large, colourful complexes consist of phycobiliproteins which are extremely valuable in the cosmetics, food, nutraceutical and pharmaceutical industries. Additionally, the colourful and fluorescent properties of phycobiliproteins can be modulated by metal ions, making them highly attractive as heavy metal sensors and heavy metal scavengers. Although the overall quenching ability metal ions have on phycobiliproteins is known, the mechanism of heavy metal binding to phycobiliproteins is not fully understood, limiting their widespread quantitative applications. Here, we show using high-resolution native mass spectrometry that phycobiliprotein complexes bind metal ions in different manners. Through monitoring the binding equilibria and metal-binding stoichiometry, we show in particular copper and silver to have drastic, yet different effects on phycobiliprotein structure, both copper and silver modulate the overall complex properties. Together, the data reveals the mechanisms by which metal ions can modulate phycobiliprotein properties which can be used as a basis for the future design of metal-related phycobiliprotein applications.

Semi-continuous immobilized cultivation of Porphyridium cruentum for sulfated polysaccharides production

In this study, semi-continuous immobilized cultivation of Porphyridium cruentum through calcium alginate beads was performed for sulfated polysaccharides (SPs) production. The cell biomass and daily SPs productivity in the calcium alginate bead immobilized culture were increased by up to 79 ± 3.4% and 45.6 ± 3.2%, compared to those in the control, respectively. Furthermore, simultaneous application of immobilization and blue wavelength illumination further increased the phycobiliproteins content by 260 ± 9%, compared to those in the control. Similarly, nutrient deficiencies in combination with immobilization increased daily SPs productivity by about twice that of the control. The chemical composition and biological activity of the extracellular polymeric substances produced through immobilization were similar to those of the control. This study suggests the potential application of calcium alginate beads-based immobilization for continuous and high-efficiency SPs production using P. cruentum.

Rapid Cyanobacteria Species Identification with High Sensitivity Using Native Mass Spectrometry

Cyanobacteria have evolved over billions of years to adapt and survive in diverse climates. Environmentally, this presents a huge challenge because cyanobacteria can now rapidly form algae blooms that are detrimental to aquatic life. In addition, many cyanobacteria produce toxins, making them hazardous to animals and humans that they encounter. Rapid identification of cyanobacteria is essential to monitor and prevent toxic algae blooms. Here, we show for the first time how native mass spectrometry can quickly and precisely identify cyanobacteria from diverse aquatic environments. By monitoring phycobiliproteins, abundant protein complexes within cyanobacteria, simple, easy-to-understand mass spectral "fingerprints" were created that were unique to each species. Moreover, our method is 10-fold more sensitive than the current MALDI-TOF mass spectrometric methods, meaning that cyanobacteria can be monitored using this technology prior to bloom formation. Together, the data show great promise for the simultaneous detection and identification of co-existing cyanobacteria in situ.

High-Resolution Native Mass Spectrometry

Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of—among others—biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein–ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.

Searching for Appropriate Storage Conditions for Short-Term Wet Preservation of Porphyridium purpureum

It is often impossible in practice to process micro-algae immediately after their cultivation and harvest. This study, therefore, aimed to identify appropriate storage conditions for the wet preservation of Porphyridium purpureum. Algae were stored either as a concentrate or as a dilute culture at 4 °C, 8 °C, or 20 °C for 14 days and their quality was monitored. Concentrate storage tended to result in higher microbial numbers than dilute culture storage and clearly led to higher concentrations of malodorous organic acids. Butyric and isovaleric acid concentrations were about two orders of magnitude larger than their odor threshold values after 14 days of concentrate storage at 20 °C. Average B-phycoeryhrin (B-PE) levels were slightly higher after concentrate storage (2.5 ± 0.2 g B-PE/100 g organic matter) than after dilute culture storage (2.2 ± 0.5 g B-PE/100 g organic matter), probably due to respiration losses of other organic compounds in the first case. Significant amounts of organic matter got lost during concentrate storage (4–35%) as a result of carbohydrate degradation. The main restriction of concentrate storage was the rapid viscosity increase and formation of a weak gel structure complicating the later processing of the concentrates. These findings are highly relevant for P. purpureum cultivators and processors who have to store Porphyridium suspensions, even on a term of one day or less.

Expansion of phycobilisome linker gene families in mesophilic red algae

The common ancestor of red algae (Rhodophyta) has undergone massive genome reduction, whereby 25% of the gene inventory has been lost, followed by its split into the species-poor extremophilic Cyanidiophytina and the broadly distributed mesophilic red algae. Success of the mesophile radiation is surprising given their highly reduced gene inventory. To address this latter issue, we combine an improved genome assembly from the unicellular red alga Porphyridium purpureum with a diverse collection of other algal genomes to reconstruct ancient endosymbiotic gene transfers (EGTs) and gene duplications. We find EGTs associated with the core photosynthetic machinery that may have played important roles in plastid establishment. More significant are the extensive duplications and diversification of nuclear gene families encoding phycobilisome linker proteins that stabilize light-harvesting functions. We speculate that the origin of these complex families in mesophilic red algae may have contributed to their adaptation to a diversity of light environments.

Widely distributed red algae have experienced massive genome reduction during evolution. Here, using an improved genome assembly of Porphyridium purpureum, Lee et al. show the role of endosymbiotic gene transfer in plastid evolution and the correlation between phycobilisome linker diversification and the red algal radiation.

Subunit pI Can Influence Protein Complex Dissociation Characteristics

Mass spectrometry is frequently used to determine protein complex topology. By combining in-solution and gas-phase dissociation measurements, information can be indirectly inferred about the original composition of the protein complex. Although the mechanisms behind gas-phase complex dissociation are becoming more established, protein complex dissociation is not always predictable. Here, we looked into the effect of the protein subunits pI on complex dissociation. We chose two structurally similar, hexameric protein complexes that consist of a ring of alternating alpha and beta subunits. For one complex, allophycocyanin, the alpha and beta subunits are structurally similar, almost identical in mass, but have distinct pIs. In contrast, the other complex, phycoerythrin, is structural similar to allophycocyanin, yet the subunits have identical pIs. As predicted based on the structural arrangement, dissociation of phycoerythrin resulted in the observation of both the alpha and beta monomeric subunits in the mass spectrometer. However, for allophycocyanin, the results differed dramatically, with only the alpha monomeric subunit being detected upon gas-phase dissociation. Together, the results highlighted the importance of considering the isoelectric points of individual subunits within a protein complex when using tandem mass spectrometry data to elucidate protein complex topology.

A strategy for the identification of protein architectures directly from ion mobility mass spectrometry data reveals stabilizing subunit interactions in light harvesting complexes

Biotechnological applications of protein complexes require detailed information about their structure and composition, which can be challenging to obtain for proteins from natural sources. Prominent examples are the ring-shaped phycoerythrin (PE) and phycocyanin (PC) complexes isolated from the light-harvesting antennae of red algae and cyanobacteria. Despite their widespread use as fluorescent probes in biotechnology and medicine, the structures and interactions of their noncrystallizable central subunits are largely unknown. Here, we employ ion mobility mass spectrometry to reveal varying stabilities of the PC and PE complexes and identify their closest architectural homologues among all protein assemblies in the Protein Data Bank (PDB). Our results suggest that the central subunits of PC and PE complexes, although absent from the crystal structures, may be crucial for their stability, and thus of unexpected importance for their biotechnological applications.

Cyanobacterial pigments: Perspectives and biotechnological approaches

Cyanobacteria are the oxygenic photosynthesis performing prokaryotes and show a connecting link between plastids of eukaryotic autotrophs and prokaryotes. A variety of pigments, like chlorophyll, carotenoids and phycobiliproteins which exhibit different colors are present in cyanobacteria. Increasing consciousness about the harmful effects of synthetic or chemical dyes encouraged people to give more preference towards the usage of natural products, such as plant or microbial-derived colors in food and cosmetics. That is why cyanobacteria are exploited as a source of natural colors and have high commercial value in many industries. This review mainly focuses on different cyanobacterial pigments, their applications and modern biotechnological approaches such as genetic engineering, systems biology to enhance the production of biopigments for their potential use in pharmaceuticals, food, research, and cosmetics industries.