Isolation and characterization of two novel root-specific promoters in rice (Oryza sativa L.)

Functional analysis of root-preferential oil palm metallothionein promoter in tobacco

Root-specific or preferential promoters are essential to genetically modify plants with beneficial root traits. We have characterised the promoter from an oil palm metallothionein gene (EgMT) and performed a serial 5' deletion analysis to identify the region(s) essential for transgenes expression in roots. Stable functional characterisation of tobacco transgenic lines using the T1 generation showed that a deletion construct, designated as RSP-2D (1107 bp), directed strong GUS expression at all stages of root development, particularly in mature roots. Other constructs, RSP-2A (2481 bp) and RSP-2C (1639 bp), drove GUS expression in roots with an intensity lower than RSP-2D. The promoter activity was also detectable in seed pods and immature seeds, albeit at lower levels than CaMV35S. The promoter activity may also be induced by wounding as intact GUS staining was observed at the flower- and leaf-cutting sites of T1 samples carrying either RSP-2C or RSP-2D constructs. The promoter sequence contains cis-acting elements that may act as negative regulators and be responsible for root specificity. The results further indicated that the 5' UTR and ATATT sequences are essential for strong promoter activity. This study highlights the potential of RSP-2D promoter as a tool for modifying root traits through genetic engineering.

Evaluation of novel promoters for vascular tissue-specific gene expression in Populus

Due to the extended generation cycle of trees, the breeding process for forest trees tends to be time-consuming. Genetic engineering has emerged as a viable approach to expedite the genetic breeding of forest trees. However, current genetic engineering techniques employed in forest trees often utilize continuous expression promoters such as CaMV 35S, which may result in unintended consequences by introducing genes into non-target tissues. Therefore, it is imperative to develop specific promoters for forest trees to facilitate targeted and precise design and breeding. In this study, we utilized single-cell RNA-Seq data and co-expression network analysis during wood formation to identify three vascular tissue-specific genes in poplar, PP2-A10, PXY, and VNS07, which are expressed in the phloem, cambium/expanding xylem, and mature xylem, respectively. Subsequently, we cloned the promoters of these three genes from '84K' poplar and constructed them into a vector containing the eyGFPuv visual selection marker, along with the 35S mini enhancer to drive GUS gene expression. Transgenic poplars expressing the ProPagPP2-A10::GUS, ProPagPXY::GUS, and ProPagVNS07::GUS constructs were obtained. To further elucidate the tissue specificity of these promoters, we employed qPCR, histochemical staining, and GUS enzyme activity. Our findings not only establish a solid foundation for the future utilization of these promoters to precisely express of specific functional genes in stems but also provide a novel perspective for the modular breeding of forest trees.

Plant Engineering to Enable Platforms for Sustainable Bioproduction of Terpenoids

Terpenoids represent the most diverse class of natural products, with a broad spectrum of industrial relevance including applications in green solvents, flavors and fragrances, nutraceuticals, colorants, and therapeutics. They are typically challenging to extract from their natural sources, where they occur in small amounts and mixtures of related but unwanted byproducts. Formal chemical synthesis, where established, is reliant on petrochemistry. Hence, there is great interest in developing sustainable solutions to assemble biosynthetic pathways in engineered host organisms. Metabolic engineering for chemical production has largely focused on microbial hosts, yet plants offer a sustainable production platform. In addition to containing the precursor pathways that generate the terpenoid building blocks as well as the cell structures and compartments required, or tractable localization for the enzymes involved, plants may provide a low input system to produce these chemicals using carbon dioxide and sunlight only. There have been significant recent advancements in the discovery of pathways to terpenoids of interest as well as strategies to boost yields in host plants. While part of the phytochemical field is focusing on the discovery of biosynthetic pathways, this review will focus on advancements using the pathway toolbox and toward engineering plants for the production of terpenoids. We will highlight strategies currently used to produce target products, optimization of known pathways to improve yields, compartmentalization of pathways within cells, and genetic tools developed to facilitate complex engineering of biosynthetic pathways. These advancements in Synthetic Biology are bringing engineered plant systems closer to commercially relevant hosts for the bioproduction of terpenoids.

Genome-Wide Tissue-Specific Genes Identification for Novel Tissue-Specific Promoters Discovery in Soybean

Promoters play a crucial role in controlling the spatial and temporal expression of genes at transcriptional levels in the process of higher plant growth and development. The spatial, efficient, and correct regulation of exogenous genes expression, as desired, is the key point in plant genetic engineering research. Constitutive promoters widely used in plant genetic transformation are limited because, sometimes, they may cause potential negative effects. This issue can be solved, to a certain extent, by using tissue-specific promoters. Compared with constitutive promoters, a few tissue-specific promoters have been isolated and applied. In this study, based on the transcriptome data, a total of 288 tissue-specific genes were collected, expressed in seven tissues, including the leaves, stems, flowers, pods, seeds, roots, and nodules of soybean (Glycine max). KEGG pathway enrichment analysis was carried out, and 52 metabolites were annotated. A total of 12 tissue-specific genes were selected via the transcription expression level and validated through real-time quantitative PCR, of which 10 genes showed tissue-specific expression. The 3-kb 5' upstream regions of ten genes were obtained as putative promoters. Further analysis showed that all the 10 promoters contained many tissue-specific cis-elements. These results demonstrate that high-throughput transcriptional data can be used as effective tools, providing a guide for high-throughput novel tissue-specific promoter discovery.

Harnessing tissue-specific genome editing in plants through CRISPR/Cas system: current state and future prospects

In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement. CRISPR/Cas is a powerful genome-editing tool with a wide range of applications for the genetic improvement of crops. However, the constitutive genome editing of vital genes is often associated with pleiotropic effects on other genes, needless metabolic burden, or interference in the cellular machinery. Tissue-specific genome editing (TSGE), on the other hand, enables researchers to study those genes in specific cells, tissues, or organs without disturbing neighboring groups of cells. Until recently, there was only limited proof of the TSGE concept, where the CRISPR-TSKO tool was successfully used in Arabidopsis, tomato, and cotton, laying a solid foundation for crop improvement. In this review, we have laid out valuable insights into the concept and application of TSGE on relatively unexplored areas such as grain trait improvement under favorable or unfavorable conditions. We also enlisted some of the prominent tissue-specific promoters and described the procedure of their isolation with several TSGE promoter expression systems in detail. Moreover, we highlighted potential negative regulatory genes that could be targeted through TSGE using tissue-specific promoters. In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement.

Genome-scale mining of root-preferential genes from maize and characterization of their promoter activity

BACKGROUND

Modification of root architecture and improvement of root resistance to stresses can increase crop productivity. Functional analyses of root-specific genes are necessary for root system improvement, and root-specific promoters enable research into the regulation of root development and genetic manipulation of root traits. Maize is an important crop species; however, little systematic mining of root-specific genes and promoters has been performed to date.

RESULTS

Genomic-scale mining based on microarray data sets followed by transcript detection resulted in the identification of 222 root-specific genes. Gene Ontology enrichment analyses revealed that these 222 root-specific genes were mainly involved in responses to chemical, biotic, and abiotic stresses. Of the 222 genes, 33 were verified by quantitative reverse transcription polymerase chain reaction, and 31 showed root-preferential activity. About 2 kb upstream 5 of the 31 identified root-preferential genes were cloned from the maize genome as putative promoters and named p8463, p5023, p1534, p8531 and p6629. GUS staining of transgenic maize-derived promoter-GUS constructs revealed that the five promoters drove GUS expression in a root-preferential manner.

CONCLUSIONS

We mined root-preferential genes and their promoters in maize and verified p8463, p5023, p1534, p8531 and p6629 as root-preferential promoters. Our research enables the identification of other tissue-specific genes and promoters in maize and other species. In addition, the five promoters may enable enhancement of target gene(s) of maize in a root-preferential manner to generate novel maize cultivars with resistance to water, fertilizer constraints, or biotic stresses.

Promoter deletion analysis reveals root-specific expression of the alkenal reductase gene (OsAER1) in Oryza sativa

Root-specific promoters are useful in plant genetic engineering, primarily to improve water and nutrient absorption. The aim of this study was to clone and characterise the promoter of the Oryza sativa L. alkenal reductase (OsAER1) gene encoding 2-alkenal reductase, an NADPH-dependent oxidoreductase. Expression analysis using quantitative real-time PCR confirmed the root-specific expression of the OsAER1 gene. Subsequently, a 3082-bp fragment of the OsAER1 promoter was isolated from a local Indonesian rice cultivar, Awan Kuning. Sequencing and further nucleotide sequence analysis of the 3082-bp promoter fragment (PA-5) revealed the presence of at least 10 root-specific cis-regulatory elements putatively responsible for OsAER1 root-specific expression. Using the 3082-bp promoter fragment to drive the expression of the GUS reporter transgene confirmed that the OsAER1 promoter is root-specific. Further, the analysis indicated that OsAER1 promoter activity was absent in leaves, petioles and shoots during sprouting, vegetative, booting and generative stages of rice development. In contrast, the promoter activity was present in anthers and aleurone layers of immature seeds 7-20 days after anthesis. Moreover, there was no promoter activity observed in the aleurone layers of mature seeds. The OsAER1 promoter activity is induced by Al-toxicity, NaCl and submergence stresses, indicating the OsAER1 promoter activity is induced by those stresses. Exogenous treatments of transgenic plants carrying the PA-5 promoter construct with abscisic acid and indoleacetic acid also induced expression of the GUS reporter transgene, indicating the role of plant growth regulators in controlling OsAER1 promoter activity. Promoter deletion analysis was conducted to identify the cis-acting elements of the promoter responsible for controlling root-specific expression. The GUS reporter gene was fused with various deletion fragments of the OsAER1 promoter and the resulting constructs were transformed in rice plants to generate transgenic plants. The results of this analysis indicated that cis-acting elements controlling root-specific expression are located between -1562 to -1026bp of the OsAER1 CDS. Here we discusses the results of the conducted analyses, the possible role of OsAER1 in rice growth and development, possible contributions and the potential usage of these findings in future plant research.

Over-expression of OsPT2 under a rice root specific promoter Os03g01700

Identification of root-specific promoters is a good method to drive root-specific gene expression for nutrient uptake. Constitutive over-expression of OsPT2 may have negative effects on the growth of rice seedlings under high Pi condition. Thus, characterization and utilization of root-specific promoters are critical for genetic breeding. Here, a root-specific promoter (Os03g01700) with a number of specific regulatory elements has been confirmed. Interestingly, cis-regulatory element S449 is significantly enriched in the -1475∼-2013 bp and -1077∼-1475 bp regions of Os03g01700 promoter. The activities of several deletion derivatives of Os03g01700 promoter were analyzed using both transient expression and genetic transformation system. The results showed that the root-specific cis-acting elements might be present in the -2013 bp～-1475 bp and -1077 bp～-561 bp regions of Os03g01700 promoter. To determine the actual effect of root-specific expression of OsPT2, a construction consisting of Os03g01700 promoter and OsPT2 CDS was used to transform rice. Under Pi-sufficient condition, there were a series of symptoms of phosphorus toxicity in the shoots of OsPT2 over-expressing (Ov-OsPT2) seedlings. Under Pi-deficient condition, more soluble Pi was accumulated in the shoots of Ov-OsPT2 seedlings than that in the wild type. Our data provide a candidate root-specific promoter in the breeding of rice with high phosphorus uptake variety.

Molecular identification of a root apical cell-specific and stress-responsive enhancer from an Arabidopsis enhancer trap line

BACKGROUND

Plant root apex is the major part to direct the root growth and development by responding to various signals/cues from internal and soil environments. To study and understand root system biology particularly at a molecular and cellular level, an Arabidopsis T-DNA insertional enhancer trap line J3411 expressing reporters (GFP) only in the root tip was adopted in this study to isolate a DNA fragment.

RESULTS

Using nested PCR, DNA sequencing and sequence homology search, the T-DNA insertion site(s) and its flanking genes were characterised in J3411 line. Subsequently, a 2000 bp plant DNA-fragment (E_rtip1) upstream of the insert position of the coding T-DNA was in silico analysed, revealing certain putative promoter/enhancer cis-regulatory elements. Cloning and transformation of this DNA fragment and its truncated segments tagged with or without 35S minimal promoter (35Smini), all of which were fused with a GFP or GUS reporter, allowed to detect GFP and GUS expression mediated only by E_rtip1 + 35mini (P_{Ertip1+35Smini}) specifically in the Arabidopsis root tip region. The P_{Ertip1+35Smini} activity was further tested to be strong and stable under many different growth conditions but suppressed by cold, salt, alkaline pH and higher ammonium and phosphorus.

CONCLUSION

This work describes a promising strategy to isolate a tissue-/cell-specific enhancer sequence from the enhancer trap lines, which are publically available. The reported synthetic promoter i.e. P_{Ertip1+35Smini} may provide a valuable and potent molecular-tool for comprehensive investigation of a gene function related to root growth and development as well as molecular engineering of root-architectural formation aiming to improve plant growth.

OsARD4 encoding an acireductone dioxygenase improves root architecture in rice by promoting development of secondary roots

This study was aimed at unravelling the molecular basis of root growth behavior in a drought-tolerant upland rice genotype, Nootripathu. Root tips of Nootripathu were found to possess shorter root caps and a greater number of dividing cells, favoring faster elongation compared to shallow-rooted IR20. Width and length of cortical cells in the roots of rapidly growing Nootripathu were found to be two to three times higher than IR20. Evaluation of shallow-rooted IR20, deep-rooted Nootripathu and their Recombinant Inbred Lines (RILs) for root characteristics revealed the presence of genetic variation for root traits among RILs. 2D-PAGE analysis of proteins in roots of IR20, Nootripathu and bulks of extreme RILs differing in root traits resulted in the identification of proteins co-segregating with root growth behavior and co-localized with QTLs for root traits. A putative candidate gene, OsARD4, encoding an "acireductone dioxygenase" was validated for its role in modulating the root growth pattern through genetic transformation. Transgenic ASD16 rice plants engineered for the overexpression of OsARD4 exhibited root growth characteristics similar to those of Nootripathu, including faster radical emergence, more rapid elongation of primary roots, early initiation of crown/lateral roots, and higher root biomass than the non-transgenic plants.

Complex Regulation of Plant Phosphate Transporters and the Gap between Molecular Mechanisms and Practical Application: What Is Missing?

It has been almost 25 years since the first report of the gene encoding a high-affinity phosphate transporter (PT), PHO84, in yeast. Since then, an increasing number of yeast PHO84 homologs as well as other genes encoding proteins with phosphate (Pi) transport activities have been identified and functionally characterized in diverse plant species. Great progress has been made also in deciphering the molecular mechanism underlying the regulation of the abundance and/or activity of these genes and their products. The regulatory genes affect plant Pi homeostasis commonly through direct or indirect regulation of the abundance of PTs at different levels. However, little has been achieved in the use of PTs for developing genetically modified crops with high phosphorus use efficiency (PUE). This might be a consequence of overemphasizing Pi uptake from the rhizosphere and lack of knowledge about the roles of PTs in Pi transport and recycling within the plant that are required to optimize PUE. Here, we mainly focused on the genes encoding proteins with Pi transport activities and the emerging understanding of their regulation at the transcriptional, post-transcriptional, translational, and post-translational levels. In addition, we propose potential strategies for effective use of PTs in improving plant growth and development.

A strong root-specific expression system for stable transgene expression in bread wheat

A strong, stable and root-specific expression system was developed from a rice root-specific GLYCINE - RICH PROTEIN 7 promoter for use as an enabling technology for genetic manipulation of wheat root traits. Root systems play an important role in wheat productivity. Genetic manipulation of wheat root traits often requires a root-specific or root-predominant expression system as an essential enabling technology. In this study, we investigated promoters from rice root-specific or root-predominant expressed genes for development of a root expression system in bread wheat. Transient expression analysis using a GREEN FLUORESCENT PROTEIN (GFP) reporter gene driven by rice promoters identified six promoters that were strongly expressed in wheat roots. Extensive organ specificity analysis of three rice promoters in transgenic wheat revealed that the promoter of rice GLYCINE-RICH PROTEIN 7 (OsGRP7) gene conferred a root-specific expression pattern in wheat. Strong GFP fluorescence in the seminal and branch roots of wheat expressing GFP reporter driven by the OsGRP7 promoter was detected in epidermal, cortical and endodermal cells in mature parts of the root. The GFP reporter driven by the promoter of rice METALLOTHIONEIN-LIKE PROTEIN 1 (OsMTL1) gene was mainly expressed in the roots with essentially no expression in the leaf, stem or seed. However, it was also expressed in floral organs including glume, lemma, palea and awn. In contrast, strong expression of rice RCg2 promoter-driven GFP was found in many tissues. The GFP expression driven by these three rice promoters was stable in transgenic wheat plants through three generations (T1-T3) examined. These data suggest that the OsGRP7 promoter can provide a strong, stable and root-specific expression system for use as an enabling technology for genetic manipulation of wheat root traits.

Rice tissue-specific promoters and condition-dependent promoters for effective translational application

Rice (Oryza sativa) is one of the most important staple food crops for more than half of the world's population. The demand is increasing for food security because of population growth and environmental challenges triggered by climate changes. This scenario has led to more interest in developing crops with greater productivity and sustainability. The process of genetic transformation, a major tool for crop improvement, utilizes promoters as one of its key elements. Those promoters are generally divided into three types: constitutive, spatiotemporal, and condition-dependent. Transcriptional control of a constitutive promoter often leads to reduced plant growth, due to a negative effect of accumulated molecules during cellular functions or energy consumption. To maximize the effect of a transgene on transgenic plants, it is better to use condition-dependent or tissue-specific promoters. However, until now, those types have not been as widely applied in crop biotechnology. In this review, we introduce and discuss four groups of tissue-specific promoters (50 promoters in total) and six groups of condition-dependent promoters (27 promoters). These promoters can be utilized to fine-tune desirable agronomic traits and develop crops with tolerance to various stresses, enhanced nutritional value, and advanced productivity.

Mitochondrial targeting of catalytic RNAs

Genetic transformation of mitochondria in multicellular eukaryotes has remained inaccessible, hindering fundamental investigations and applications to gene therapy or biotechnology. In this context, we have developed a strategy to target nuclear transgene-encoded RNAs into mitochondria in plants. We describe here mitochondrial targeting of trans-cleaving ribozymes destined to knockdown organelle RNAs for regulation studies and inverse genetics and biotechnological purposes. The design and functional assessment of chimeric RNAs combining the ribozyme and the mitochondrial shuttle are detailed, followed by all procedures to prepare constructs for in vivo expression, generate stable plant transformants, and establish target RNA knockdown in mitochondria.

Identification and molecular characterization of tissue-preferred rice genes and their upstream regularly sequences on a genome-wide level

BACKGROUND

Gene upstream regularly sequences (URSs) can be used as one of the tools to annotate the biological functions of corresponding genes. In addition, tissue-preferred URSs are frequently used to drive the transgene expression exclusively in targeted tissues during plant transgenesis. Although many rice URSs have been molecularly characterized, it is still necessary and valuable to identify URSs that will benefit plant transformation and aid in analyzing gene function.

RESULTS

In this study, we identified and characterized root-, seed-, leaf-, and panicle-preferred genes on a genome-wide level in rice. Subsequently, their expression patterns were confirmed through quantitative real-time RT-PCR (qRT-PCR) by randomly selecting 9candidate tissue-preferred genes. In addition, 5 tissue-preferred URSs were characterized by investigating the URS::GUS transgenic plants. Of these URS::GUS analyses, the transgenic plants harboring LOC_Os03g11350 URS::GUS construct showed the GUS activity only in young pollen. In contrast, when LOC_Os10g22450 URS was used to drive the reporter GUS gene, the GUS activity was detected only in mature pollen. Interestingly, the LOC_Os10g34360 URS was found to be vascular bundle preferred and its activities were restricted only to vascular bundles of leaves, roots and florets. In addition, we have also identified two URSs from genes LOC_Os02G15090 and LOC_Os06g31070 expressed in a seed-preferred manner showing the highest expression levels of GUS activities in mature seeds.

CONCLUSION

By genome-wide analysis, we have identified tissue-preferred URSs, five of which were further characterized using transgenic plants harboring URS::GUS constructs. These data might provide some evidence for possible functions of the genes and be a valuable resource for tissue-preferred candidate URSs for plant transgenesis.

Mining tissue-specific contigs from peanut (Arachis hypogaea L.) for promoter cloning by deep transcriptome sequencing

Peanut (Arachis hypogaea L.), one of the most important oil legumes in the world, is heavily damaged by white grubs. Tissue-specific promoters are needed to incorporate insect resistance genes into peanut by genetic transformation to control the subterranean pests. Transcriptome sequencing is the most effective way to analyze differential gene expression in this non-model species and contribute to promoter cloning. The transcriptomes of the roots, seeds and leaves of peanut were sequenced using Illumina technology. A simple digital expression profile was established based on number of transcripts per million clean tags (TPM) from different tissues. Subsequently, 584 root-specific candidate transcript assembly contigs (TACs) and 316 seed-specific candidate TACs were identified. Among these candidate TACs, 55.3% were root-specific and 64.6% were seed-specific by semi-quantitative RT-PCR analysis. Moreover, the consistency of semi-quantitative RT-PCR with the simple digital expression profile was correlated with the length and TPM value of TACs. The results of gene ontology showed that some root-specific TACs are involved in stress resistance and respond to auxin stimulus, whereas, seed-specific candidate TACs are involved in embryo development, lipid storage and long-chain fatty acid biosynthesis. One root-specific promoter was cloned and characterized. We developed a high-yield screening system in peanut by establishing a simple digital expression profile based on Illumina sequencing. The feasible and rapid method presented by this study can be used for other non-model crops to explore tissue-specific or spatially specific promoters.