Roles of Alkaline Phosphatase PhoA in Algal Metabolic Regulation under Phosphorus-replete Conditions

Synthetic Biology Strategies and Tools to Modulate Photosynthesis in Microbes

The utilization of photosynthetic microbes, such as cyanobacteria and microalgae, offers sustainable solutions to addressing global resource shortages and pollution. While these microorganisms have demonstrated significant potential in biomanufacturing, their industrial application is limited by suboptimal photosynthetic efficiency. Synthetic biology integrates molecular biology, systems biology, and engineering principles to provide a powerful tool for elucidating photosynthetic mechanisms and rationally optimizing photosynthetic platforms. This review summarizes recent advancements in regulating photosynthesis in cyanobacteria and microalgae via synthetic biology, focusing on strategies to enhance light energy absorption, optimize electron transport chains, and improve carbon assimilation. Furthermore, we discuss key challenges in translating these genetic modifications to large-scale bioproduction, highlighting specific bottlenecks in strain stability, metabolic burden, and process scalability. Finally, we propose potential solutions, such as AI-assisted metabolic engineering, synthetic microbial consortia, and next-generation photobioreactor designs, to overcome these limitations. Overall, while synthetic biology holds great promise for enhancing photosynthetic efficiency in cyanobacteria and microalgae, further research is needed to refine genetic strategies and develop scalable production systems.

Microplastics impair extracellular enzymatic activities and organic matter cycling in oligotrophic sandy marine sediments

Microplastics (MPs) are ubiquitous and constantly accumulating in the marine environment, especially sediments. Yet, it is not well clarified if and how their carbon backbone could interact with surrounding sediments, eventually impairing key benthic processes. We assessed the effects of a 'pulse' contamination event of MPs on sedimentary organic matter (OM) quantity, quality and extracellular enzymatic activities (EEAs), which are well established descriptors of benthic ecosystem functioning. Marine sediments were exposed for 30 days to environmentally relevant concentrations (∼0.2 % in weight) of naturally weathered particles (size range 70-210 μm) of polyurethane, polyethylene, and a mixture of the most common polymers that are documented to accumulate in marine sediments. Despite the low concentration, contaminated sediments showed significantly different composition of OM, showing a decrease in lipid content and increase in protein. Moreover, we document a significant decrease (over 25 %) in quantity of biopolymeric C already after 15 days of exposure, compared to controls. Contaminated sediments showed lower C degradation rates (up to -40 %) and altered EEAs, with alkaline phosphatase being ∼50 % enhanced and aminopeptidase being reduced over 35 % compared to control treatments. Overall, the effects generated by the mixture of polymers were smaller than those exerted by the same amount of a single polymer. Our results provide insights on how that MPs can significantly alter marine sedimentary biogeochemistry through altered benthic processes, that could cumulatively impair whole benthic trophic webs by enhancing the accumulation and possible longer-term storage of recalcitrant organic C in the seabed.

In Silico Prediction of Alkaline Phosphatase Interaction with the Natural Inhibitory 5-Azaindoles Guitarrin C and D

The natural 5-azaindoles, marine sponge guitarrin C and D, were observed to exert inhibitory activity against a highly active alkaline phosphatase (ALP) CmAP of the PhoA family from the marine bacterium Cobetia amphilecti, with IC50 values of 8.5 and 110 µM, respectively. The superimposition of CmAP complexes with p-nitrophenyl phosphate (pNPP), a commonly used chromogenic aryl substrate for ALP, and the inhibitory guitarrins C, D, and the non-inhibitory guitarrins A, B, and E revealed that the presence of a carboxyl group at C6 together with a hydroxyl group at C8 is a prerequisite for the inhibitory effect of 5-azaindoles on ALP activity. The 10-fold more active guitarrin C could compete with pNPP for binding sites in the ALP active site due to similarities in size, three-dimensional structure, and the orientation of the COOH group along the phosphate group. However, the inhibition of CmAP and calf intestinal ALP (CIAP) by guitarrin C was observed to occur via a non-competitive mode of action, as evidenced by a twofold decrease in Vmax and an unchanged Km. In contrast, the kinetic model with guitarrin D, with an additional OH group at C7, reflected a mixed type of inhibition, with a decrease in both values. The sensitivity of CIAP to guitarrins C and D was shown to be slightly lower than that of CmAP, with IC50 values of 195 and 230 µM, respectively. Nevertheless, these findings prompted the prediction of complexes of human ALP isoenzymes with guitarrins C and D.

Physiological and Transcriptional Responses to Phosphorus Deficiency and Glucose-6-Phosphate Supplementation in Neopyropia yezoensis

Neopyropia yezoensis, a marine red algae species, has significant economic and ecological value. However, phosphorus (P) deficiency has emerged as a growing concern in many cultivation regions, negatively impacting its growth. To adapt to P deficiency, algae have evolved various strategies, including using dissolved organic phosphorus (DOP) sources to sustain growth. Despite its prevalence as a form of DOP, the utilization mechanism of glucose-6-phosphate (G6P) by N. yezoensis remains unclear. In this study, the physiological and transcriptional responses of N. yezoensis to P deficiency and G6P supplementation were examined. The results demonstrated that prolonged P deficiency significantly inhibited the growth of N. yezoensis and had a negative impact on physiological indicators such as photosynthetic pigments and antioxidant enzyme activity. However, G6P treatment gradually alleviated these adverse effects over time. Both P deficiency and G6P treatment were associated with increased expression of genes involved in signal transduction and P starvation responses while concurrently downregulating genes related to photosynthesis and antioxidant defenses. In contrast, the suppression of gene expression was less significant under G6P treatment. This study elucidates the adaptive strategies of N. yezoensis in response to P deficiency and clarifies the regulatory pathways involved in G6P utilization, providing novel insights into its P nutrient acquisition and metabolic regulation.

Phosphorous Utilization in Microalgae: Physiological Aspects and Applied Implications

Phosphorus (P) is a fundamental element for life, playing an integral role in cellular metabolism including energy transfer, nucleic acid synthesis, and membrane structure. This nutrient is critical to the physiological ecology in all photosynthetic organisms including eukaryotic microalgae and cyanobacteria. The review, here presented, delves into the intricate mechanisms governing phosphorus acquisition from the environment, its utilization in plant metabolism, and regulation in these photosynthetic microorganisms. Furthermore, it comprehensively explores the strategies employed by microalgae to cope with phosphorus limitation, such as the activation of high-affinity phosphate transporters and the synthesis of phosphorus storage compounds. On the other hand, the ability to consume abundant phosphate makes microalgae exploitable organisms for environmental remediation processes. The knowledge synthesized in this review contributes to the broader understanding of microalgal physiology, offering insights into the ecological and biotechnological implications of phosphorus assimilation in these microorganisms.

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.

Alkaline Phosphatase PhoD Mutation Induces Fatty Acid and Long-Chain Polyunsaturated Fatty Acid (LC-PUFA)-Bound Phospholipid Production in the Model Diatom Phaeodactylum tricornutum

With rapid growth and high lipid contents, microalgae have become promising environmentally friendly candidates for renewable biodiesel and health supplements in our era of global warming and energy depletion. Various pathways have been explored to enhance algal lipid production, especially gene editing. Previously, we found that the functional loss of PhoD-type alkaline phosphatase (AP), a phosphorus-stress indicator in phytoplankton, could lead to increased lipid contents in the model diatom Phaeodactylum tricornutum, but how the AP mutation may change lipid composition remains unexplored. This study addresses the gap in the research and investigates the effects of PhoD-type AP mutation on the lipid composition and metabolic regulation in P. tricornutum using transcriptomic and lipidomic analyses. We observed significantly modified lipid composition and elevated production of fatty acids, lysophosphatidylcholine, lysophosphatidylethanolamine, ceramide, phosphatidylinositol bisphosphate, and monogalactosylmonoacylglycerol after PhoD_45757 mutation. Meanwhile, genes involved in fatty acid biosynthesis were upregulated in mutant cells. Moreover, the mutant exhibited increased contents of ω-3 long-chain polyunsaturated fatty acid (LC-PUFA)-bound phospholipids, indicating that PhoD_45757 mutation could improve the potential bioavailability of PUFAs. Our findings indicate that AP mutation could influence cellular lipid synthesis and probably redirect carbon toward lipid production and further demonstrate that AP mutation is a promising approach for the development of high-value microalgal strains for biomedical and other applications.

Design, synthesis, biochemical and in silico characterization of novel naphthalene-thiourea conjugates as potential and selective inhibitors of alkaline phosphatase

Naphthalene ring is present in a number of FDA-approved, commercially available medications, including naphyrone, terbinafine, propranolol, naproxen, duloxetine, lasofoxetine, and bedaquiline. By reacting newly obtained 1-naphthoyl isothiocyanate with properly modified anilines, a library of ten novel naphthalene-thiourea conjugates (5a-5j) were produced with good to exceptional yields and high purity. The newly synthesized compounds were observed for their potential to inhibit alkaline phosphatase (ALP) and scavenge free radicals. All of the investigated compounds displayed a more powerful inhibitory profile than the reference agent, KH2PO4 particularly compound 5h and 5a exhibited strong inhibitory potential against ALP with IC50 value of 0.365 ± 0.011 and 0.436 ± 0.057 µM respectively. In addition, Lineweaver-Burk plots revealed the non-competitive inhibition mode of the most powerful derivative i.e., 5h (ki value 0.5 µM). To investigate the putative binding mode of selective inhibitor interactions, molecular docking was performed. It is recommended that future research will focus on developing selective alkaline phosphatase inhibitors by modifying the structure of the 5h derivative.

Transcriptome Sequencing of the Diatom Asterionellopsis thurstonii and In Silico Identification of Enzymes Potentially Involved in the Synthesis of Bioactive Molecules

Microalgae produce a plethora of primary and secondary metabolites with possible applications in several market sectors, including cosmetics, human nutrition, aquaculture, biodiesel production and treatment/prevention of human diseases. Diatoms, in particular, are the most diversified microalgal group, many species of which are known to have anti-cancer, anti-oxidant, anti-diabetes, anti-inflammatory and immunomodulatory properties. Compounds responsible for these activities are often still unknown. The aim of this study was to de novo sequence the full transcriptome of two strains of the diatom Asterionellopsis thurstonii, sampled from two different locations and cultured in both control and phosphate starvation conditions. We used an RNA-sequencing approach to in silico identify transcripts potentially involved in the synthesis/degradation of compounds with anti-cancer and immunomodulatory properties. We identified transcript coding for L-asparaginase I, polyketide cyclase/dehydrase, bifunctional polyketide phosphatase/kinase, 1-deoxy-D-xylulose-5-phosphate synthase (fragment), inositol polyphosphate 5-phosphatase INPP5B/F, catechol O-Methyltransferase, digalactosyldiacylglycerol synthase (DGD1), 1,2-diacylglycerol-3-beta-galactosyltransferase and glycerolphosphodiester phosphodiesterase. Differential expression analysis also allowed to identify in which culturing condition these enzymes are more expressed. Overall, these data give new insights on the annotation of diatom genes, enzymatic pathways involved in the generation of bioactive molecules and possible exploitation of Asterionellopsis thurstonii.

Combined analysis of chromatin accessibility and gene expression profiles provide insight into Fucoxanthin biosynthesis in Isochrysis galbana under green light

Isochrysis galbana, as a potential accumulator of fucoxanthin, has become a valuable material to develop functional foods for humans. Our previous research revealed that green light effectively promotes the accumulation of fucoxanthin in I. galbana, but there is little research on chromatin accessibility in the process of transcriptional regulation. This study was conducted to reveal the mechanism of fucoxanthin biosynthesis in I. galbana under green light by analyzing promoter accessibility and gene expression profiles. Differentially accessible chromatin regions (DARs)-associated genes were enriched in carotenoid biosynthesis and photosynthesis-antenna protein formation, including IgLHCA1, IgLHCA4, IgPDS, IgZ-ISO, IglcyB, IgZEP, and IgVDE. The motifs for the MYB family were also identified as candidates controlling metabolic regulation responses to green light culture of I. galbana, including IgMYB1, IgMYB2, IgMYB33, IgMYB42, IgMYB98, IgMYB118, and IgMYB119. The results of differential expression analysis and WGCNA showed that several genes or transcription factors (TFs) related to carotenoid metabolism and photosynthesis exhibited a higher expression level and were significantly upregulated in A-G5d compared with A-0d and A-W5d, including IgMYB98, IgLHCA1, IgLHCX2, IgLHCB4, and IgLHCB5. This suggests that upregulation of these genes by green light may be the key factor leading to fucoxanthin accumulation by regulating the photosynthesis-antenna protein pathway. An integrated analysis of ATAC-seq and RNA-seq showed that 3 (IgphoA, IgPKN1, IgOTC) of 34 DARs-associated genes displayed obvious changes in their chromatin regions in ATAC-seq data, suggesting that these genes specific for green light may play a key role in fucoxanthin biosynthesis in I. galbana through a complex regulatory network of multiple metabolic pathways interacting with each other. These findings will facilitate in-depth understanding the molecular regulation mechanisms of fucoxanthin in I. galbana and its role in response to green light regulation, providing technical support for the construction of high fucoxanthin content strains.

Unraveling the metabolic effects of benzophenone-3 on the endosymbiotic dinoflagellate Cladocopium goreaui

As a well-known pseudo-persistent environmental pollutant, oxybenzone (BP-3) and its related organic ultraviolet (UV) filters have been verified to directly contribute to the increasing mortality rate of coral reefs. Previous studies have revealed the potential role of symbiotic Symbiodiniaceae in protecting corals from the toxic effects of UV filters. However, the detailed protection mechanism(s) have not been explained. Here, the impacts of BP-3 on the symbiotic Symbiodiniaceae Cladocopium goreaui were explored. C. goreaui cells exhibited distinct cell growth at different BP-3 doses, with increasing growth at the lower concentration (2 mg L^-1) and rapid death at a higher concentration (20 mg L^-1). Furthermore, C. goreaui cells showed a significant BP-3 uptake at the lower BP-3 concentration. BP-3 absorbing cells exhibited elevated photosynthetic efficiency, and decreased cellular carbon and nitrogen contents. Besides, the derivatives of BP-3 and aromatic amino acid metabolism highly responded to BP-3 absorption and biodegradation. Our physiological and metabolic results reveal that the symbiotic Symbiodiniaceae could resist the toxicity of a range of BP-3 through promoting cell division, photosynthesis, and reprogramming amino acid metabolism. This study provides novel insights into the influences of organic UV filters to coral reef ecosystems, which urgently needs increasing attention and management.

SPX-related genes regulate phosphorus homeostasis in the marine phytoplankton, Phaeodactylum tricornutum

Phosphorus (P) is an essential nutrient for marine phytoplankton. Maintaining intracellular P homeostasis against environmental P variability is critical for phytoplankton, but how they achieve this is poorly understood. Here we identify a SPX gene and investigate its role in Phaeodactylum tricornutum. SPX knockout led to significant increases in the expression of phosphate transporters, alkaline phosphatases (the P acquisition machinery) and phospholipid hydrolases (a mechanism to reduce P demand). These demonstrate that SPX is a negative regulator of both P uptake and P-stress responses. Furthermore, we show that SPX regulation of P uptake and metabolism involves a phosphate starvation response regulator (PHR) as an intermediate. Additionally, we find the SPX related genes exist and operate across the phytoplankton phylogenetic spectrum and in the global oceans, indicating its universal importance in marine phytoplankton. This study lays a foundation for better understanding phytoplankton adaptation to P variability in the future changing oceans.