Silicon Is the Next Frontier in Plant Synthetic Biology

Abstract

Silicon has a striking similarity to carbon and is found in plant cells. However, there is no specific role that has been assigned to silicon in the life cycle of plants. The amount of silicon in plant cells is species specific and can reach levels comparable to macronutrients. Silicon is used extensively in artificial intelligence, nanotechnology, and the digital revolution, and thus can serve as an informational molecule such as nucleic acids. The diverse potential of silicon to bond with different chemical species is analogous to carbon; thus, it can serve as a structural candidate similar to proteins. The discovery of large amounts of silicon on Mars and the moon, along with the recent development of enzyme that can incorporate silicon into organic molecules, has propelled the theory of creating silicon-based life. The bacterial cytochrome has been modified through directed evolution such that it could cleave silicon–carbon bonds in organo-silicon compounds. This consolidates the idea of utilizing silicon in biomolecules. In this article, the potential of silicon-based life forms has been hypothesized, along with the reasoning that autotrophic virus-like particles could be used to investigate such potential. Such investigations in the field of synthetic biology and astrobiology will have corollary benefits for Earth in the areas of medicine, sustainable agriculture, and environmental sustainability.

1. Introduction to Silicon

This article hypothesizes that synthetic biology has the potential to integrate silicon into organic molecules to such an extent that silicon-based life would be possible in the future. Based on established knowledge from molecular biology, evolution, and virology, along with the power of synthetic biology, we hypothesize a potential path to create such lifeforms. Life as we know so far is mainly made of four elements, namely carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), with some other light elements required in small amounts [1]. It is interesting to note that silicon (Si), despite being the second most abundant element on Earth’s crust and having a striking chemical similarity to carbon, does not find itself in the list of elements that are required for life. Silicon is tetravalent and can bond with various chemical species; thus, it is chemically the closest analog of carbon. This has attracted the imagination of scientists interested in silicon-based life. The idea received significant attention with respect to space colonization after the discovery of Si as being second most abundant element on the moon and Mars, where carbon is found in extremely low amounts [2]. The excitement is not unfounded, because though Si is not deemed to be required by lifeforms, it is found in various living organisms, including diatoms and plants [3,4].

2. Silicon and Plant Physiology

Plant physiologists do not consider silicon to be an essential element for the growth and development of plants. The amount of Si in several plant species is comparable to many macronutrients. Plants sequester Si in the form of Si(OH)₄ (silicic acid) and polymerize it to silica, which contributes to the rigidity of aboveground plant parts [5,6]. The deposition of Si in apoplastic barriers was previously thought to be a passive process resulting from the byproduct of active physiological processes. However, recent reports indicate the intricate role of proteins and cell signaling in such deposits [7]. The symplastic transport of Si(OH)₄ involves aquaporins such as Nod 26-like intrinsic proteins or NIPs [5,8,9]. Between 0.1% to 10% of the total dry weight of plants can be constituted by Si [10]. Several studies have indicated the phytoprotective role of Si in plants with respect to countering abiotic and biotic stress [11,12,13]. Besides its role in abiotic and biotic stress management, the element also has a structural role in cell walls and is hypothesized to have a signaling role that impacts cellular metabolism, it alters metabolism in plants through modulating endogenous phytohormones [14,15]. Silicon imparts mechanical strength to the cell wall of plants and is found in the form of silica (SiO₂). Many pteridophytes and monocots have noticeable deposits of silicon [16]. Silicon can bind with hydroxyl groups of sugars to form silicate esters and has been classified according to its biochemical and physiological role in plants [17]. Due to the beneficial roles of Si in plants, the International Plant Nutrition Institute (IPNI) recently classified it as a beneficial element [6].

3. Silicon: From Abiogenic to Biogenic

Si is biocompatible due to its non-reactive nature; thus, it is widely used in medical devices, pharmaceuticals, and in the agricultural industry. The foundation of the digital revolution, computation, electronics, and artificial intelligence is attributed to Si. The element is a prime candidate for the chemical and green synthesis of nanoparticles (NPs). Silicon-based NPs have wide biological applications. For the abovementioned reasons, it can be stated empirically that Si can serve in structural, functional, and informational roles similar to protein, RNA, and DNA, respectively. The element itself, in a solitary capacity, might not be able to play a role as complex as the biological macromolecules; however, it can bind with other organic and inorganic molecules to achieve such activity. The current literature supports such evidence where Si is attributed to structural (cell wall), functional (cell signaling), and informational (semiconductor) roles [16,18,19]. Thus, it is not an exaggeration to hypothesize that Si can serve as the element that can serve as a key matrix for synthetic life, besides being a useful element for sustaining life on Mars and the moon. Silicon bonds being weaker than carbon bonds might add a lot of flexibility to the repertoire of chemical groups that it can bind when the right conditions are provided [20]. Thus, it can be utilized to design synthetic particles that have virus-like properties and would be an intermediate lifeform. Such synthetic particles must have the capability to capture energy, multiply vigorously, and convert inorganic carbon to biogenic carbon compounds. Thus, analogous to the oxygenation of the Earth, silicon-based life forms can be utilized for terraforming Mars and the moon to create conditions that are conducive for the propagation of autotrophs. Viruses can infect autotrophs and can utilize the cellular machinery of the autotrophs to produce viral particles. Thus, synthetic genomes derived from autotrophs can be designed and utilized to create virus-like synthetic particles. Similar to cyanobacteria, such particles would be autotrophic in nature. These virus-like synthetic particles would be able to terraform planets such as Mars into Earth-like planets through the synthesis of biogenic carbon. Viruses are obligate intracellular parasites; thus, virus-like particles, as hypothesized above, would require a host for their survival and multiplication. This challenge can be circumvented if such particles can multiply in a chemical environment such as the “primordial soup”, which has enough chemical diversity to result in thermodynamically stable reactions, thus leading to the formation of complex molecules. The existence of LTR (long terminal repeat) transposons and their significant implication in plant genome evolution [21] indicates that virus–autotroph interactions result in the natural modification of life forms. Synthetic particles containing polymerases with higher fidelity and proofreading activities could be designed, while the proteins used to construct capsids could be designed to be more resistant to ultraviolet rays. This would increase their chances of survival in an environment that is bombarded with high ultraviolet radiation. Since the moon and Mars experience high amounts of ultraviolet radiation, such synthetic particles would have an advantage over cellular-life forms, which are less resistant to radiation. The cellular and molecular mechanism by which organisms such as tardigrades, extremophiles, and bacteria such as Deinococcus radiodurans survive harsh environmental conditions will be of great interest when designing synthetic genomes and lifeforms that can withstand the harsh environment outside of the Earth’s atmosphere.

The progress in artificial intelligence, metabolic engineering, computation, synthetic biology, and genome editing techniques such as CRISPR has enhanced the likelihood of artificial life. Such technologies can be integrated and their potential can be harnessed to modulate life forms and initiate the terraforming of extraterrestrial planets. The biology of transposons, prions, viroid, virus, archaea, and extremophiles makes it obvious that besides the conventional understanding of life, there are powerful anomalies that reflect the 4 billion years of the evolutionary history of life on Earth. The scientific community has accepted the theory of the abiogenic origin of life. Thus, it is plausible that synthetic life could be made for terraforming by utilizing the powerful scientific tools at our disposal and utilizing the longstanding scientific knowledge of the past 300 years.

The chemical signatures of water molecules on the moon and Mars, along with the current developments in spaceflight technologies, suggest that a primordial soup similar to early earth could be created. Such biochemical precursors may be utilized as a matrix for the directed evolution of synthetic life forms. The idea proposed here is different from the conventional hypothesis of silicon-based life because, instead of directly creating silicon-based plants and animals, here, the role of an intermediate lifeform where silicon will play a key role is proposed. Such virus-like particles could sequester and enrich carbon on the surface of the planets. The sequestration of carbon would establish and accelerate the conditions that will be necessary for carbon-based autotrophic life on uninhabited planets. The strength of this hypothesis is that a more gradual route of directed evolution is proposed. This seems more able to procreate lifeforms than those with challenges inherent to directly creating silicon-based plants and animals. In addition, virus-like particles would be more amenable to the harsh environment than cellular lifeforms, and their vigorous multiplication would accelerate the process of converting inorganic carbon to biogenic forms. The methodological feasibility of the construction of such virus-like particles by utilizing metabolic engineering, gene editing and synthetic biology can be ascertained from several recent publications [22,23,24,25,26,27,28,29].

4. Genetic Engineering and Synthetic Life

Synthetic genomes have been utilized to reconstruct virus, bacteria and eukaryotic cells, thus leading to breakthrough discoveries in medicine, agriculture and the fundamental understanding of cells [25]. Nonstandard amino acids have been incorporated into proteins, thus enhancing the chemical functionalities of enzymes and expanding the genetic code [30]. Synthetic biology has made significant advances such that the theoretical concepts of the resurrection of extinct plants and animals are being actively tested [31,32]. Barring rare exceptions, the biomolecules found in living organisms maintain a chirality that is represented by D-sugar and L-amino acids. However, mirror-image macromolecules such as nucleic acids and functional proteins have been synthesized with altered chirality [33]. This supersedes the incremental stages of molecular evolution and is a significant step towards the creation of mirror cells; however, it has subsequently raised concerns regarding their potential impact on health and the environment [34]. Though scientists are skeptical, without further research it will be preemptive to conclude the potential and dangers of mirror cells. It is increasingly evident, from the early genetic engineering technology such as terminator technology [35] to the most recent CRISPR gene-editing technology [36], that biological organisms can be manipulated and their propagation can be controlled. Our understanding and modification of the genome, epigenome, proteome, metabolome, interactome, signaling pathways, viruses, bacteria, and eukaryotes reinforces that genetic engineering can be utilized to modify cells. Cellular modification through synthetic biology has resulted in innovative products such as Impossible Burger, Sitgaliptin (type 1 diabetes drug), ProveN fertilizer, Kymriah (leukemia drug), hyaline (transparent biofilm for optics and electronics), and the edible oil Calyno [37]. Scientists can now modulate cells with more precision to synthesize products of commercial interest and promote sustainability. Thus, the concept of silicon-based acellular or synthetic microbial life forms may become a reality. These can accelerate terraforming, besides having applications in agriculture, medicine, the environment, fuel, textiles, and beyond. Such microbial life can be bioengineered towards self-destruction after a certain time period. This will act as a safeguard to prevent pandemic or environmental catastrophe.

Genetic engineering is utilized efficiently to manipulate life [38]; however, if we think of creating novel lifeforms, then an interdisciplinary approach such as synthetic biology seems more plausible. The DBTL cycle, involving designing, building, testing, and learning, makes synthetic biology a more powerful technology compared to genetic engineering. The fundamental basis of life is inorganic elements; thus, the macromolecular building blocks of life depend upon inorganic elements. It is important to use a multipronged approach involving biology, chemistry, physics, and artificial intelligence to generate synthetic lifeforms, where Si can replace or complement carbon as the predominant element. Since Si is abundantly available on Mars and the moon, it can be utilized to create molecules for structural, enzymatic and informational roles, or can be assimilated with carbon to form organosilicon compounds with such properties. The corollary benefits of such intelligent and synthetic lifeforms might be reflected on the Earth, where they could be utilized for a multitude of purposes including environmental reclamation, medical breakthroughs, and agricultural improvements. Researchers in the California Institute of Technology were able to synthesize organo-silicon compounds by mutating cytochrome c from bacteria. The mutation resulted in the incorporation of Si into hydrocarbons and the results were replicable in vivo under physiological conditions [39]. Conversely, a recent report demonstrated the engineering of an enzyme (bacterial cytochrome P450BM3) through directed evolution that can cleave the silicon–carbon bonds in linear and cyclic volatile methylsiloxanes. This has led to major progress in organosilicon chemistry [40]. The abovementioned discoveries [39,40] illustrate the potential of two enzymes for Si metabolism in prokaryotes, thus stimulating the investigation and manipulation of several enzymes in prokaryotes and eukaryotes concerning the utilization of Si in biomolecules. Such work of directed evolution can pave the way for silicon-based synthetic life. Highly selective and efficient reactions mediated by biocatalysts have been developed with high synthetic value. Such methods can be utilized for the synthesis and degradation of organosilicon molecules [41].

5. Current Developments and Future Directions

Several metabolites, bioactive compounds, and natural products are derived from plants and used as drugs, biofuel, and components of the human diet. Through the metabolic engineering of microbes, several of these products have been commercially synthesized. Plant cells have been recently utilized to synthesize such products, leading to the advent of plant synthetic biology. Plant physiology, genetics, molecular biology, and engineering principles are utilized to create genetic circuits and biosynthetic pathways that yield synthetic products of commercial value. Plant natural products such as isoprenoids, monoterpenoids, sesquiterpenoids, diterpenoids, triterpenoids, tetraterpenoids, phenylpropanoids, alkaloids, and vitamins have been produced by modifying biosynthetic pathways. Next-generation sequencing, nuclear gene editing, plastid genome engineering, and transformation have advanced the field of plant synthetic biology [42]. Synthetic biology has employed bio-inspired approaches to produce biofuels, bioplastics, and sequester carbon by utilizing cyanobacteria. The high photosynthetic rate, rapid growth, and minimal growth requirements of cyanobacteria make them an ideal candidate for modification by synthetic biologists to tackle global challenges [43].

Due to the limited efficacy of silicate fertilizers, silicon nanoparticles (SiNPs) are increasingly being explored as a substitute for silicate fertilizers. Most reports indicate their beneficial effect in plant growth and development, though reports of toxicity are also recorded. The synthesis, application, uptake and role of SiNPs in plant health and crop productivity have been widely investigated; however, their safe use is still an area of investigation [44]. SiNPs have shown promising results in sustainable agriculture and are emerging as an efficient and cost-effective strategy for managing plant stress (abiotic and biotic). The green synthesis of SiNPs using agricultural wastes is reported to be a viable option for large-scale production. SiNPs are increasingly being used as nanocarriers for the delivery of phytohormones and pesticides [45]. The use of nanoparticles as pesticides, herbicides, and carriers for delivering biomolecules in plants is gaining momentum; however, the physical and chemical methods of their production are cost-prohibitive and environmentally unsustainable. Thus, the biological synthesis or green synthesis of nanoparticles using bacteria, yeast, fungi and plants is a viable option. Recent reports indicate that SiNPs synthesized from the fungus Fusarium oxysporum are very effective in controlling the root knot nematode Meloidogyne incognita [46].

Synthetic biology has advanced due to the availability of the cell-free gene expression system, where genetic circuits can be tested. However, due to the prohibitive cost, such systems are limited to developed countries. Researchers are using silica beads, modified reactions, and additives to create such systems that are cost-efficient and may become accessible to a wider scientific community [47]. Giant unilamellar vesicles or GUVs mimic biological membranes as they allow the controlled exchange of reactants, thus providing a responsive compartment. The encapsulation of functional biomolecules in GUVs is a major experimental hurdle in the research related to synthetic cells. Recently, continuous droplet interface crossing encapsulation or the cDICE method has been utilized to generate GUVs with high reproducibility and a high encapsulation efficiency for a wide range of biomolecules, including actin cytoskeleton and DNA nanostructures [48]. Microcavity biosensors are extremely sensitive to environmental change and can detect a wide range of biomolecules and nanoparticles. Recent advances have created a paradigm shift in the detection methods that allow single-molecule sensing. The detection of a single molecule of protein, conformational changes and ions could have far-reaching effects in the study of enzyme kinetics and synthetic biology [49]. Biomaterials derived from silicon nitride are emerging as a novel material for various medical applications such as prosthetics, reconstructive surgeries, tissue engineering, and vehicles for drug delivery. Silicon nitride is inexpensive, strong, inert, biocompatible, conducive to electronics, and resistant to corrosion; thus, it is increasingly used in medical applications [50]. Due to the similarity of Si to carbon, it is widely investigated in the field of medicinal chemistry. “Silicon switch” or silicon–carbon substitution has resulted in silicon containing novel analogs of bioactive molecules and are explored in drug design and pharmacokinetics. These compounds tend to be more hydrophobic and lipophilic, and thus have higher membrane penetrability. Significant progress has been made in the synthesis and cleavage of carbon–silicon bonds, thus paving the way for the incorporation of Si and the separation of Si from organic molecules [51].

Synthetic biology is an emerging field that promises to solve many of the pressing problems that humanity faces. It is an interdisciplinary field that amalgamates principles of engineering, artificial intelligence, computation, cell biology, molecular biology, and genetics. Several commercial products that have been produced using synthetic biology approaches are available, and in the near future, this area of science will influence our lives in many ways, such as medicine, textiles, communication, food, and transport. The design, build, test and learn approach (DBTL) allows synthetic biologists to develop systems and products that are not found naturally. Due to the enormous potential of this powerful technology, there is excitement in the scientific community. SynBio uses bottom-up approaches to build systems that could ultimately result in the creation of synthetic organelles and cells that could sequester energy from the sun and synthesize enzymes for metabolism.

6. Silicon and Plant SynBio

Silicon alleviates abiotic and biotic stress in plants, thus providing evidence of its unsuspected role in plant physiology [4]. However, the protective role of Si in plants was initially attributed to its deposition in the cell wall. Their role in hormonal cross-talk and metabolism has been confirmed, and the use of silicon nanoparticles (SiNPs) to improve the commercially valuable traits of crops has been explored [15]. Besides plants, biosilicification has been reported in several invertebrates and marine organisms; thus, investigating the molecular mechanism of such processes could offer biotechnological candidates for the manufacturing of silicon-based commercial products [52]. Plant synthetic biology is an emerging field with a history of nearly 20 years and holds significant promise in several areas, including global food security and clean energy [53]. It employs the engineering of metabolic pathways to elicit user-tailored plant traits. It is considered the next frontier in plant biology, where the physiological and developmental pathways of plants are reprogrammed for the production of adequate food, feed, fuel and pharmaceuticals with minimum inputs, thus propelling sustainable environment and agriculture [54,55]. The current trends in Si research and the progress in synthetic biology make it obvious that the amalgamation of both towards a product or process of human value is imminent. It is clear that Si has a much larger role in plants than previously expected. Due to several regulatory laws that are essential for animal research, plants can be used as an excellent model to estimate the effect of silicon-based biomolecules in eukaryotic cells. Conversely, the Si-enriched product synthesized within plant cells can be harvested and used to analyze their effect with regard to human consumption and use.

7. Conclusions and Assessment

The detection of signatures for life in the form of microorganisms or organic compounds has been explored through several technological developments. The investigation of topographies in Earth and extraterrestrial entities is underway [56,57,58]. Lava tube speleothems are considered to have analogous environments compared to Mars and the moon; thus, the molecular, chemical, biochemical and mineralogical investigation of such environments may gather insights into potential extraterrestrial biosignatures [59]. The potential of Si to complement carbon or serve as a major element for the development of lifeforms that can terraform Mars and other extraterrestrial entities into habitable environments will reinforce such astrobiological efforts regarding the pursuit of life beyond Earth. The role of Si in ameliorating biotic and abiotic stress in plants, along with the discovery of Si transporters in plant cells, indicates that the element might have an unsuspected physiological role in plant life [60,61]. Recent reports classify Si as an essential micronutrient for some plants [19,62]. The demands for microgreen are increasing, and with the development of modern agriculture technologies such as precision agriculture, climate-smart agriculture, hydroponics, and artificial-intelligence-augmented agriculture, it will be possible to investigate the role of Si in the mass production of microgreens. Estimating the effects of Si in the mass production of such edible plant products in a controlled environment will help scientists better understand the role of the element in securing food sustainability in contained spaces, such as the space station and habitats on Mars and the moon. The role of Si in improving the nutritive value of edible plant products needs to be assessed more carefully. The recent discovery of enzymes that can incorporate or cleave Si in organosilicon compounds holds immense promise regarding the use of this element in biogenic heterogenous molecules. Plant synthetic biology is an emerging field, and the use of silicon in producing mirror cells or the reprogramming of plant cells for the synthesis of silicon-enriched products of commercial value is imminent. The element should receive more attention from plant scientists to investigate the physiological and molecular role of the element in plant life. Such investigations may lead to the development of Si-rich resilient crops on Earth and autotrophic life forms in space.

Viruses utilize the cellular machinery to redirect cell functions to benefit the propagation of viruses and ultimately contribute to their evolutionary fitness. The vast array of biological entities, such as regulatory RNAs, transposons, viroids, viruses, phages, prions, prokaryotic and eukaryotic cells, along with their dynamic interactions, indicates their relatedness and coevolutionary history. The exponential growth of “omics” has led to the development and incorporation of non-standard amino acids and nucleic acid bases into cells. Synthetic genomes and chromosomes have been developed for viruses, bacteria, and yeast, while the development of mirror cells that radically depart from known lifeforms is being undertaken [25,34,63]. Artificial photosynthesis directed towards the synthesis of organic molecules has been reported [64]. The advent of synthetic biology has enabled the development of programmable cells based on engineering principles. Thus, the abovementioned knowledge and technological advancements indicate that the development of autotrophic silicon-based virus-like particles that can be utilized for human benefit on earth and in space colonization is feasible.