Isolation and expression analysis of novel silicon absorption gene from roots of mangrove (Rhizophora apiculata) via suppression subtractive hybridization

Comprehensive Study of Si-Based Compounds in Selected Plants (Pisum sativum L., Medicago sativa L., Triticum aestivum L.)

This review describes the role of silicon (Si) in plants. Methods of silicon determination and speciation are also reported. The mechanisms of Si uptake by plants, silicon fractions in the soil, and the participation of flora and fauna in the Si cycle in terrestrial ecosystems have been overviewed. Plants of Fabaceae (especially Pisum sativum L. and Medicago sativa L.) and Poaceae (particularly Triticum aestivum L.) families with different Si accumulation capabilities were taken into consideration to describe the role of Si in the alleviation of the negative effects of biotic and abiotic stresses. The article focuses on sample preparation, which includes extraction methods and analytical techniques. The methods of isolation and the characterization of the Si-based biologically active compounds from plants have been overviewed. The antimicrobial properties and cytotoxic effects of known bioactive compounds obtained from pea, alfalfa, and wheat were also described.

Physio-anatomical modifications and elemental allocation pattern in Acanthus ilicifolius L. subjected to zinc stress

Physio-anatomical modifications and elemental distribution pattern in Acanthus ilicifolius subjected to Zn stress were analysed in this study. Survival of A. ilicifolius plants under a high concentration of ZnSO4 was compensated by the reduction in the photosynthetic efficacy. Micro and macro-elemental distribution pattern in the root tissues was significantly influenced by heavy metal exposure. Tolerance towards the excess toxic metal ions in the tissue of A. ilicifolius was aided by the modified anatomical features. Moreover, the increased deposition of Zn around the central vasculature of the root confirms the complexation of Zn2+ in the xylem vessels. Metal induced molecular level changes of root and leaf samples indicate the presence of OH, NH2, and CH3 deformation as well as C-O-H and C-O-C stretch. A prominent band corresponding to CH3 deformation, pointing hemicellulose fortification, occurs in the cell walls of the xylem, aiding in Zn localization. The phytostabilisation potential of A. ilicifolius is dependent on the coordinated responses which endow with phenotypic plasticity necessary to cope with Zn toxicity.

Silicon in the Soil-Plant Continuum: Intricate Feedback Mechanisms within Ecosystems

Plants' ability to take up silicon from the soil, accumulate it within their tissues and then reincorporate it into the soil through litter creates an intricate network of feedback mechanisms in ecosystems. Here, we provide a concise review of silicon's roles in soil chemistry and physics and in plant physiology and ecology, focusing on the processes that form these feedback mechanisms. Through this review and analysis, we demonstrate how this feedback network drives ecosystem processes and affects ecosystem functioning. Consequently, we show that Si uptake and accumulation by plants is involved in several ecosystem services like soil appropriation, biomass supply, and carbon sequestration. Considering the demand for food of an increasing global population and the challenges of climate change, a detailed understanding of the underlying processes of these ecosystem services is of prime importance. Silicon and its role in ecosystem functioning and services thus should be the main focus of future research.

Phytolith Formation in Plants: From Soil to Cell

Silica is deposited extra- and intracellularly in plants in solid form, as phytoliths. Phytoliths have emerged as accepted taxonomic tools and proxies for reconstructing ancient flora, agricultural economies, environment, and climate. The discovery of silicon transporter genes has aided in the understanding of the mechanism of silicon transport and deposition within the plant body and reconstructing plant phylogeny that is based on the ability of plants to accumulate silica. However, a precise understanding of the process of silica deposition and the formation of phytoliths is still an enigma and the information regarding the proteins that are involved in plant biosilicification is still scarce. With the observation of various shapes and morphologies of phytoliths, it is essential to understand which factors control this mechanism. During the last two decades, significant research has been done in this regard and silicon research has expanded as an Earth-life science superdiscipline. We review and integrate the recent knowledge and concepts on the uptake and transport of silica and its deposition as phytoliths in plants. We also discuss how different factors define the shape, size, and chemistry of the phytoliths and how biosilicification evolved in plants. The role of channel-type and efflux silicon transporters, proline-rich proteins, and siliplant1 protein in transport and deposition of silica is presented. The role of phytoliths against biotic and abiotic stress, as mechanical barriers, and their use as taxonomic tools and proxies, is highlighted.

Further confirmation of second- and third-generation Eimeria necatrix merozoite DEGs using suppression subtractive hybridization

In our previous study, we obtained a large number of differentially expressed genes (DEGs) between second-generation merozoites (MZ-2) and third-generation merozoites (MZ-3) of Eimeria necatrix using RNA sequencing (RNA-seq). Here, we report two subtractive cDNA libraries for MZ₂ (forward library) and MZ₃ (reverse library) that were constructed using suppression subtractive hybridization (SSH). PCR amplification revealed that the MZ₂ and MZ₃ libraries contained approximately 96.7% and 95% recombinant clones, respectively, and the length of the inserted fragments ranged from 0.5 to 1.5 kb. A total of 106 and 111 unique sequences were obtained from the MZ₂ and MZ₃ libraries, respectively, and were assembled into 13 specific consensus sequences (contigs or genes) (5 from MZ₂ and 8 from MZ₃). The qRT-PCR results revealed that 11 out of 13 genes were differentially expressed between MZ-2 and MZ-3. Of 13 genes, 11 genes were found in both SSH and our RNA-seq data and displayed a similar expression trend between SSH and RNA-seq data, and the remaining 2 genes have not been reported in both E. necatrix genome and our RNA-seq data. Among the 11 genes, the expression trends of 8 genes were highly consistent between SSH and our RNA-seq data. These DEGs may provide specialized functions related to the life-cycle transitions of Eimeria species.

Screening and Expression of a Silicon Transporter Gene (Lsi1) in Wild-Type Indica Rice Cultivars

Silicon (Si) is one of the most prevalent elements in the soil. It is beneficial for plant growth and development, and it contributes to plant defense against different stresses. The Lsi1 gene encodes a Si transporter that was identified in a mutant Japonica rice variety. This gene was not identified in fourteen Malaysian rice varieties during screening. Then, a mutant version of Lsi1 was substituted for the native version in the three most common Malaysian rice varieties, MR219, MR220, and MR276, to evaluate the function of the transgene. Real-time PCR was used to explore the differential expression of Lsi1 in the three transgenic rice varieties. Silicon concentrations in the roots and leaves of transgenic plants were significantly higher than in wild-type plants. Transgenic varieties showed significant increases in the activities of the enzymes SOD, POD, APX, and CAT; photosynthesis; and chlorophyll content; however, the highest chlorophyll A and B levels were observed in transgenic MR276. Transgenic varieties have shown a stronger root and leaf structure, as well as hairier roots, compared to the wild-type plants. This suggests that Lsi1 plays a key role in rice, increasing the absorption and accumulation of Si, then alters antioxidant activities, and improves morphological properties.

Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives

Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.

Silicon and the Plant Extracellular Matrix

Silicon (Si) is one of the most abundant elements on earth. Although not considered essential for the growth and development of higher plants, it is nonetheless known to increase vigor and to play protective roles. Its protective effects include for instance alleviation of (a)biotic stress damages and heavy metal toxicity. Si was shown to interact with several components of the plant cell walls in the form of silica (SiO2). In plants SiO2 promotes strengthening of the cell walls and provides increased mechanical support to the aerial parts. The relationship SiO2-plant cell wall has been well documented in monocots and pteridophytes, which are known Si accumulators, while much less is known on the interaction of Si with the cell walls of dicots. We here provide a concise up-to-date survey on the interaction between Si and plant cell wall components by focussing on cellulose, hemicelluloses, callose, pectins, lignin, and proteins. We also describe the effects of Si on cell wall-related processes by discussing the published results in both monocots and dicots. We conclude our survey with a description of the possible mechanisms by which Si exerts priming in plants.

Selection of genes associated with variations in the Circle of Willis in gerbils using suppression subtractive hybridization

Deformities in the Circle of Willis (CoW) can significantly increase the risk of cerebrovascular disease in humans. However, the molecular mechanisms underlying these deformities have not been understood. Based on our previous studies, variations in the CoW of gerbils are hereditary. A normal CoW is observed in approximately 60% of gerbils, a percentage that also applies to humans. Thus, gerbil is an ideal experimental model for studying variations in the CoW. To study the mechanisms underlying these variations, we selected genes associated with different types of the CoW using suppression subtractive hybridization (SSH). After evaluating the efficiency of SSH using quantitative real-time polymerase chain reaction (qPCR) on subtracted and unsubtracted cDNA and Southern blotting on SSH PCR products, 12 SSH libraries were established. We identified 4 genes (CST3, GNAS, GPx4 and PFN2) associated with variations in the CoW. These genes were identified with qPCR and Western blotting using 70 expressed sequence tags from the SSH libraries. Cloning and sequencing allowed us to demonstrate that the 4 genes were closely related to mouse genes. We may assume that these 4 genes play an important role in the development of variations in the CoW. This study provides a foundation for further research of genes related to development of variations in the CoW and the mechanisms of dysmorphosis of cerebral vessels.

Importance of silicon and mechanisms of biosilica formation in plants

Silicon (Si) is one of the most prevalent macroelements, performing an essential function in healing plants in response to environmental stresses. The purpose of using Si is to induce resistance to distinct stresses, diseases, and pathogens. Additionally, Si can improve the condition of soils, which contain toxic levels of heavy metals along with other chemical elements. Silicon minimizes toxicity of Fe, Al, and Mn, increases the availability of P, and enhances drought along with salt tolerance in plants through the formation of silicified tissues in plants. However, the concentration of Si depends on the plants genotype and organisms. Hence, the physiological mechanisms and metabolic activities of plants may be affected by Si application. Peptides as well as amino acids can effectively create polysilicic species through interactions with different species of silicate inside solution. The carboxylic acid and the alcohol groups of serine and asparagine tend not to engage in any significant role in polysilicates formation, but the hydroxyl group side chain can be involved in the formation of hydrogen bond with Si(OH)4. The mechanisms and trend of Si absorption are different between plant species. Furthermore, the transportation of Si requires an energy mechanism; thus, low temperatures and metabolic repressors inhibit Si transportation.