Protein-driven biomineralization: Comparing silica formation in grass silica cells to other biomineralization processes

An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation

Deciphering nature's remarkable way of encoding functions in its biominerals holds the potential to enable the rational development of nature-inspired materials with tailored properties. However, the complex processes that convert solution-state precursors into solid biomaterials remain largely unknown. In this study, an unconventional approach is presented to characterize these precursors for the diatom-derived peptides R5 and synthetic Silaffin-1A1 (synSil-1A1). These molecules can form defined supramolecular assemblies in solution, which act as templates for solid silica structures. Using a tailored structural biology toolbox, the structure-function relationships of these self-assemblies are unveiled. NMR-derived constraints are employed to enable a recently developed fractal-cluster formalism and then reveal the architecture of the peptide assemblies in atomistic detail. Finally, by monitoring the self-assembly activities during silica formation at simultaneous high temporal and residue resolution using real-time spectroscopy, the mechanism is elucidated underlying template-driven silica formation. Thus, it is demonstrated how to exercise morphology control over bioinorganic solids by manipulating the template architectures. It is found that the morphology of the templates is translated into the shape of bioinorganic particles via a mechanism that includes silica nucleation on the solution-state complexes' surfaces followed by complete surface coating and particle precipitation.

Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification

Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.

The draft genome of Nitzschia closterium f. minutissima and transcriptome analysis reveals novel insights into diatom biosilicification

BACKGROUND

Nitzschia closterium f. minutissima is a commonly available diatom that plays important roles in marine aquaculture. It was originally classified as Nitzschia (Bacillariaceae, Bacillariophyta) but is currently regarded as a heterotypic synonym of Phaeodactylum tricornutum. The aim of this study was to obtain the draft genome of the marine microalga N. closterium f. minutissima to understand its phylogenetic placement and evolutionary specialization. Given that the ornate hierarchical silicified cell walls (frustules) of diatoms have immense applications in nanotechnology for biomedical fields, biosensors and optoelectric devices, transcriptomic data were generated by using reference genome-based read mapping to identify significantly differentially expressed genes and elucidate the molecular processes involved in diatom biosilicification.

RESULTS

In this study, we generated 13.81 Gb of pass reads from the PromethION sequencer. The draft genome of N. closterium f. minutissima has a total length of 29.28 Mb, and contains 28 contigs with an N50 value of 1.23 Mb. The GC content was 48.55%, and approximately 18.36% of the genome assembly contained repeat sequences. Gene annotation revealed 9,132 protein-coding genes. The results of comparative genomic analysis showed that N. closterium f. minutissima was clustered as a sister lineage of Phaeodactylum tricornutum and the divergence time between them was estimated to be approximately 17.2 million years ago (Mya). CAFF analysis demonstrated that 220 gene families that significantly changed were unique to N. closterium f. minutissima and that 154 were specific to P. tricornutum, moreover, only 26 gene families overlapped between these two species. A total of 818 DEGs in response to silicon were identified in N. closterium f. minutissima through RNA sequencing, these genes are involved in various molecular processes such as transcription regulator activity. Several genes encoding proteins, including silicon transporters, heat shock factors, methyltransferases, ankyrin repeat domains, cGMP-mediated signaling pathways-related proteins, cytoskeleton-associated proteins, polyamines, glycoproteins and saturated fatty acids may contribute to the formation of frustules in N. closterium f. minutissima.

CONCLUSIONS

Here, we described a draft genome of N. closterium f. minutissima and compared it with those of eight other diatoms, which provided new insight into its evolutionary features. Transcriptome analysis to identify DEGs in response to silicon will help to elucidate the underlying molecular mechanism of diatom biosilicification in N. closterium f. minutissima.

Phytoliths analysis in root, culm, leaf and synflorescence of Rostraria cristata (Poaceae)

Phytoliths (siliceous structures) present in the plants have been employed in the fields of taxonomy and archaeology for many decades. Rostraria cristata is an economically important grass species (Poaceae) which accumulates silica in its different organs in the form of phytoliths. In order to understand the pattern of phytolith production and biochemical architecture of silica in R. cristata, leaf epidermis (blade) using the clearing solution method and different organs using the dry ashing method, X-ray diffraction and Fourier-transform infrared spectroscopy techniques were analyzed. Both abaxial and adaxial leaf epidermis showed the presence of acute bulbosus, rectangular sinuate and stomata phytolith morphotypes. Leaf including sheath and blade had the highest silica content. Characteristic phytolith morphotypes were present in different organs. A total of 34 phytolith morphotypes were present among which nine (9) were articulated and 25 were isolated forms. The most abundant were elongate scrobiculate (48.20%) in root and rectangular sinuate (26.16%) in leaf part. Other common phytolith morphotypes present in different organs of R. cristata were articulated elongate irregular, articulated elongate scrobiculate, acute bulbosus, and polygonal rondel etc. Leaf and synflorescence had the highest similarity based on presence/absence of phytolith morphotypes (Jaccard's similarity index). XRD studies revealed the presence of cristobalite, quartz, tridymite, zeolite etc. forms of silica in different organs. FTIR spectra showed that inplane stretching vibration of Si-C was unique to root, anti-symmetric stretching vibration of C-H was unique to leaf and Al2O3.SiO2 was found in synflorescence only. Our results show the characteristic pattern of phytoliths production in R. cristata.

Thalassiosira pseudonana (Cyclotella nana) (Hustedt) Hasle et Heimdal (Bacillariophyceae): A genetically tractable model organism for studying diatom biology, including biological silica formation

In 2004, Thalassiosira pseudonana was the first eukaryotic marine alga to have its genome sequenced. Since then, this species has quickly emerged as a valuable model species for investigating the molecular underpinnings of essentially all aspects of diatom life, particularly bio-morphogenesis of the cell wall. An important prerequisite for the model status of T. pseudonana is the ongoing development of increasingly precise tools to study the function of gene networks and their encoded proteins in vivo. Here, we briefly review the current toolbox for genetic manipulation, highlight specific examples of its application in studying diatom metabolism, and provide a peek into the role of diatoms in the emerging field of silica biotechnology.

Silica deposition in plants: scaffolding the mineralization

BACKGROUND

Silicon and aluminium oxides make the bulk of agricultural soils. Plants absorb dissolved silicon as silicic acid into their bodies through their roots. The silicic acid moves with transpiration to target tissues in the plant body, where it polymerizes into biogenic silica. Mostly, the mineral forms on a matrix of cell wall polymers to create a composite material. Historically, silica deposition (silicification) was supposed to occur once water evaporated from the plant surface, leaving behind an increased concentration of silicic acid within plant tissues. However, recent publications indicate that certain cell wall polymers and proteins initiate and control the extent of plant silicification.

SCOPE

Here we review recent publications on the polymers that scaffold the formation of biogenic plant silica, and propose a paradigm shift from spontaneous polymerization of silicic acid to dedicated active metabolic processes that control both the location and the extent of the mineralization.

CONCLUSION

Protein activity concentrates silicic acid beyond its saturation level. Polymeric structures at the cell wall stabilize the supersaturated silicic acid and allow its flow with the transpiration stream, or bind it and allow its initial condensation. Silica nucleation and further polymerization are enabled on a polymeric scaffold, which is embedded within the mineral. Deposition is terminated once free silicic acid is consumed or the chemical moieties for its binding are saturated.

Modeling of the Elements Ca2+, Mg2+ and Si in the Sediments and the Body Walls of Sea Cucumbers in the Tropical Seagrass Meadows

The interrelationship of the minerals calcium (Ca2+), magnesium (Mg2+) and silicon (Si) in the sediments and in the body walls of four tropical sea cucumber species was explored by modeling the concentrations of these minerals. The elemental concentrations of Ca2+, Mg2+ and Si were measured in the body walls and in the ambient sediments occupied by the sea cucumbers Holothuria scabra, H. leucospilota, H. atra and Bohadschia marmorata. The results indicate that the concentrations of Ca2+ and Mg2+ in the body walls of the four sea cucumber species are significantly different from each other, indicating a varying degree of biomineralization across sea cucumber taxa. In contrast, only B. marmorata showed a significant difference in the concentration of Si when compared to the rest of the species tested. Further analysis using linear mixed models revealed that the Ca2+, Mg2+ and Si concentrations in the body walls of the tested sea cucumber species are associated with the sediment concentrations of the same elements. The relatively high concentrations of Ca2+ and Mg2+ in the sediments indicate that these minerals are sufficiently high in sea cucumbers to support their biomineralization. The relationship between the Mg/Ca ratio in the body walls of the sea cucumbers and minerals in the sediments revealed that Si was the only mineral that was not correlated with the Mg/Ca ratio. Predicting the relationship of the elements Ca2+, Mg2+ and Si between the sediments and the body walls of sea cucumbers may be complex due to the various factors that influence the metabolism and biomineralization in sea cucumbers.

Phytomanagement of textile wastewater for dual biogas and biochar production: A techno-economic and sustainable approach

Phytoremediation has been widely employed for industrial effluent treatment due to its cost-effectiveness and eco-friendliness. However, this process generates large amounts of exhausted plant biomass, requiring appropriate management strategies to avoid further environmental pollution. To the best of the authors' knowledge, this study is the first to address the recyclability of water hyacinth after textile wastewater (TWW) phytoremediation for dual biogas and biochar production. A hydroponic culture system was occupied by 163 g (plant mass) per L (TWW) and operated under 16:8 h light:dark cycle (sunlight), 70-80% relative humidity, and 22-25 °C temperature. This water hyacinth-based system achieved chemical oxygen demand (COD), ammonia nitrogen (NH₄⁺-N), and dye removal efficiencies of 58.60 ± 2.63%, 35.27 ± 1.65%, and 38.49 ± 2.24%, respectively, at a TWW fraction of 100 %v/v. The plant characterization study revealed that phytoabsorption and phytoextraction could be the main mechanisms involved in TWW pollution reduction. The lignin and hemicellulose of water hyacinth were slightly degraded during phytoremediation, making the cellulose fibers simply accessible to enzymes' attack in the subsequent anaerobic digestion process. This hypothesis was validated by increasing the crystallinity index from 50.13% to 60.21% during TWW phytoremediation. The spent plant was cleaned and then co-digested (37 °C) with cow dung at 1:1 (w/w, dry basis) for bioenergy production. The generated biogas was 162.78 ± 8.34 mL CH₄/g COD (i.e., 225.63 ± 11.36 mL CH₄/g volatile solids), representing about 490% higher than the utilization of raw water hyacinth in a mono-digestion process. The pyrolysis of digestate-containing plant residues yielded biochar with concentrated cationic macroelements (K⁺, Mg²⁺, and Ca²⁺). The economic feasibility of the phytoremediation/co-digestion/pyrolysis combined system showed an initial investment of 2090 USD and a payback period of 9.08 yr. Because the project succeeded in recovering the cost of its initial investment, it could fulfill the targets of several sustainable development goals related to economic profitability, social acceptance, and environmental protection.

Distribution of Biominerals and Mineral-Organic Composites in Plant Trichomes

Biomineralization is a common phenomenon in plants and has been shown to be chemically, functionally and topologically diverse. Silica and calcium carbonate have long been known as structural plant biominerals and calcium phosphate (apatite)–long known from animals–has recently been reported. Strikingly, up to three different biominerals may occur in a single trichome in, e.g., Urticaceae and Loasaceae, and in combination with organic compounds, can form organic/inorganic composite materials. This article presents an extension of previous studies on the distribution of these biominerals in Loasaceae trichomes with a focus on their spatial (three-dimensional) distribution and co-localization with organic substances. Light microscopy and scanning electron microscopy with high-resolution EDX element analyses of sample surfaces and sections illustrate the differential distribution and composition of the different biomineral phases across cell surfaces and cell walls. Raman spectroscopy additionally permits the identification of organic and inorganic compounds side by side. All three biominerals may be found in a nearly pure inorganic phase, e.g., on the plant surfaces and in the barbs of the glochidiate trichomes, or in combination with a larger proportion of organic compounds (cellulose, pectin). The cell lumen may be additionally filled with amorphous mineral deposits. Water-solubility of the mineral fractions differs considerably. Plant trichomes provide an exciting model system for biomineralization and enable the in-vivo study of the formation of complex composite materials with different biomineral and organic compounds involved.

Peptide Gelators to Template Inorganic Nanoparticle Formation

The use of peptides to template inorganic nanoparticle formation has attracted great interest as a green route to advance structures with innovative physicochemical properties for a variety of applications that range from biomedicine and sensing, to catalysis. In particular, short-peptide gelators offer the advantage of providing dynamic supramolecular environments for the templating effect on the formation of inorganic nanoparticles directly in the resulting gels, and ideally without using further reductants or chemical reagents. This mini-review describes the recent progress in the field to outline future research directions towards dynamic functional materials that exploit the synergy between supramolecular chemistry, nanoscience, and the interface between organic and inorganic components for advanced performance.