Isolation and functional characterization of a novel seed-specific promoter region from peanut

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.

Molecular cloning and functional characterization of the promoter of a novel Aspergillus flavus inducible gene (AhOMT1) from peanut

Peanut is an important oil and food legume crop grown in more than one hundred countries, but the yield and quality are often impaired by different pathogens and diseases, especially aflatoxins jeopardizing human health and causing global concerns. For better management of aflatoxin contamination, we report the cloning and characterization of a novel A. flavus inducible promoter of the O-methyltransferase gene (AhOMT1) from peanut. The AhOMT1 gene was identified as the highest inducible gene by A. flavus infection through genome-wide microarray analysis and verified by qRT-PCR analysis. AhOMT1 gene was studied in detail, and its promoter, fussed with the GUS gene, was introduced into Arabidopsis to generate homozygous transgenic lines. Expression of GUS gene was studied in transgenic plants under the infection of A. flavus. The analysis of AhOMT1 gene characterized by in silico assay, RNAseq, and qRT-PCR revealed minute expression in different organs and tissues with trace or no response to low temperature, drought, hormones, Ca2+, and bacterial stresses, but highly induced by A. flavus infection. It contains four exons encoding 297 aa predicted to transfer the methyl group of S-adenosyl-L-methionine (SAM). The promoter contains different cis-elements responsible for its expression characteristics. Functional characterization of AhOMT1P in transgenic Arabidopsis plants demonstrated highly inducible behavior only under A. flavus infection. The transgenic plants did not show GUS expression in any tissue(s) without inoculation of A. flavus spores. However, GUS activity increased significantly after inoculation of A. flavus and maintained a high level of expression after 48 hours of infection. These results provided a novel way for future management of peanut aflatoxins contamination through driving resistance genes in A. flavus inducible manner.

Identification and Functional Characterization of the RcFAH12 Promoter from Castor Bean in Arabidopsis thaliana

Castor (Ricinus communis L.) seed oil is the commercial source of ricinoleate, a valuable raw material used in many industries. Oleoyl-12-hydroxylase (RcFAH12) is a key enzyme in the biosynthesis of ricinoleate, accumulating nearly 90% of the triacylglycerol in castor seeds. Little is known about the transcriptional regulation of RcFAH12. We used rapid amplification of cDNA 5′ ends (5′RACE) to locate the transcription start site (TSS) of RcFAH12, and the sequence of a 2605 bp region, −2506~+99, surrounding the TSS was cloned. We then investigated these regions to promote β-glucuronidase (GUS) expression in transgenic Arabidopsis by the progressive 5′ and 3′ deletions strategies. The GUS staining showed that the GUS accumulation varied in tissues under the control of different deleted fragments of RcFAH12. In addition, the GUS expression driven by the RcFAH12 promoter markedly accumulated in transgenic seeds, which indicated that RcFAH12 might play an important role in the biosynthesis of ricinoleic acid. This study will lay a potential foundation for developing a tissue-specific promoter in oil-seed crops.

Cloning and Functional Characterization of a Pericarp Abundant Expression Promoter (AhGLP17-1P) From Peanut (Arachis hypogaea L.)

Peanut (Arachis hypogaea L.) is an important oil and food legume crop grown in tropical and subtropical areas of the world. As a geocarpic crop, it is affected by many soil-borne diseases and pathogens. The pericarp, an inedible part of the seed, acts as the first layer of defense against biotic and abiotic stresses. Pericarp promoters could drive the defense-related genes specific expression in pericarp for the defense application. Here, we identified a pericarp-abundant promoter (AhGLP17-1P) through microarray and transcriptome analysis. Besides the core promoter elements, several other important cis-elements were identified using online promoter analysis tools. Semiquantitative and qRT-PCR analyses validated that the AhGLP17-1 gene was specifically expressed only in the pericarp, and no expression was detected in leaves, stem, roots, flowers, gynophore/peg, testa, and embryo in peanut. Transgenic Arabidopsis plants showed strong GUS expression in siliques, while GUS staining was almost absent in remaining tissues, including roots, seedlings, leaf, stem, flowers, cotyledons, embryo, and seed coat confirmed its peanut expressions. Quantitative expression of the GUS gene also supported the GUS staining results. The results strongly suggest that this promoter can drive foreign genes’ expression in a pericarp-abundant manner. This is the first study on the functional characterization of the pericarp-abundant promoters in peanut. The results could provide practical significance to improve the resistance of peanut, and other crops for seed protection uses.

Genetic engineering of parthenocarpic tomato plants using transient SlIAA9 knockdown by novel tissue-specific promoters

Parthenocarpy is the development of an ovary into a seedless fruit without pollination. The ubiquitous downregulation of SlIAA9 induces not only parthenocarpic fruit formation but also an abnormal vegetative phenotype. To make parthenocarpic transgenic tomato plants without unwanted phenotypes, we found two genes, namely, Solyc03g007780 and Solyc02g067760, expressed in ovary tissue but not in vegetative tissues. Solyc03g007780 was expressed in developing ovaries and anthers. Solyc02g067760 mRNA was detected in whole-flower tissues. The promoters of Solyc03g007780 (Psol80) and Solyc02g067760 (Psol60) predominantly induced the expression of genes in the ovule, placenta, endocarp and pollen and in whole-flower tissues, respectively. Psol80/60-SlIAA9i lines, created for SlIAA9-RNA interference controlled by two promoters, successfully formed parthenocarpic fruits without pleiotropic effects in vegetative tissues. Downregulation of SlIAA9, responsible for parthenocarpic fruit formation, was observed in ovules rather than ovaries in the Psol80/60-SlIAA9i lines. Although the weight of parthenocarpic fruits of the Psol80/60-SlIAA9i lines was lower than the weight of pollinated fruits of the wild type (WT), the parthenocarpic fruits presented redder and more saturated colors and higher levels of total soluble solids and titratable acidity than the WT fruits.

Isolation and characterization of a novel seed-specific promoter from peanut (Arachis hypogaea L.)

Peanut, whose seeds are ideal bioreactors for the production of recombinant proteins and/or nutrient metabolites, is one of the most important crop species worldwide. As important molecular tools, seed-specific promoters (SSPs) can direct the expression of foreign proteins specifically in seeds to avoid constitutive expression that can damage plants. However, few SSPs have been identified from this species. In this study, we isolated a novel SSP (we named it AHSSP2) from peanut. Several cis-acting elements commonly found in SSPs, including 3 copies of RYREPEAT elements, were dispersed throughout the 1970-bp sequence of AHSSP2. The sequence was then substituted in place of the 35S promoter sequence in a pBI121 plasmid, which was subsequently transformed into Arabidopsis. Beta-glucuronidase (GUS) staining showed that AHSSP2 can drive GUS gene expression in the mature seeds of transgenic Arabidopsis, excluding within the testa. The cotyledons and hypocotyls of the germinating seeds of transgenic Arabidopsis seedlings also exhibited GUS activity, even after the seedlings became adult plants. No GUS activity was detected in nontransformed Arabidopsis at any stage. These results strongly suggested that AHSSP2 could drive the expression of foreign genes in a seed-specific manner. This study enriched SSP resources, and the results showed that AHSSP2 could be potentially utilized in peanut and other crop species to improve seed quality, such as modifications to seed oil content.

Genome-wide mining seed-specific candidate genes from peanut for promoter cloning

Peanut seeds are ideal bioreactors for the production of foreign recombinant proteins and/or nutrient metabolites. Seed-Specific Promoters (SSPs) are important molecular tools for bioreactor research. However, few SSPs have been characterized in peanut seeds. The mining of Seed-Specific Candidate Genes (SSCGs) is a prerequisite for promoter cloning. Here, we described an approach for the genome-wide mining of SSCGs via comparative gene expression between seed and nonseed tissues. Three hundred thirty-seven SSCGs were ultimately identified, and the top 108 SSCGs were characterized. Gene Ontology (GO) analysis revealed that some SSCGs were involved in seed development, allergens, seed storage and fatty acid metabolism. RY REPEAT and GCN4 motifs, which are commonly found in SSPs, were dispersed throughout most of the promoters of SSCGs. Expression pattern analysis revealed that all 108 SSCGs were expressed specifically or preferentially in the seed. These results indicated that the promoters of the 108 SSCGs may perform functions in a seed-specific and/or seed-preferential manner. Moreover, a novel SSP was cloned and characterized from a paralogous gene of SSCG29 from cultivated peanut. Together with the previously characterized SSP of the SSCG5 paralogous gene in cultivated peanut, these results implied that the method for SSCG identification in this study was feasible and accurate. The SSCGs identified in this work could be widely applied to SSP cloning by other researchers. Additionally, this study identified a low-cost, high-throughput approach for exploring tissue-specific genes in other crop species.

Transgenic approaches for genetic improvement in groundnut (Arachis hypogaea L.) against major biotic and abiotic stress factors

Cultivated groundnut (Arachis hypogaea L.) is considered as one of the primary oilseed crops and a major fodder for cattle industry in most of the developing countries, owing to its rich source of protein. It is due to its geocarpic nature of growth that the overall yield performance of groundnut is hindered by several biotic and abiotic stress factors. Multidimensional attempts were undertaken to combat these factors by developing superior groundnut varieties, modified with integral mechanism of tolerance/resistance; however this approach proved to be futile, owing to inferior pod and kernel quality. As a superior alternative, biotechnological intervention like transformation of foreign genes, either directly (biolistic) or via Agrobacterium, significantly aided in the development of advanced groundnut genotypes equipped with integral resistance against stresses and enhanced yield attributing traits. Several genes triggered by biotic and abiotic stresses, were detected and some of them were cloned and transformed as major parts of transgenic programmes. Application of modern molecular biological techniques, in designing biotic and abiotic stress tolerant/resistant groundnut varieties that exhibited mechanisms of resistance, relied on the expression of specific genes associated to particular stress. The genetically transformed stress tolerant groundnut varieties possess the potential to be employed as donor parents in traditional breeding programmes for developing varieties that are resilient to fungal, bacterial, and viral diseases, as well as to draught and salinity. The present review emphasizes on the retrospect and prospect of genetic transformation tools, implemented for the enhancement of groundnut varieties against key biotic and abiotic stress factors.

A novel mitochondrial orf147 causes cytoplasmic male sterility in pigeonpea by modulating aberrant anther dehiscence

KEY MESSAGE

A novel open reading frame (ORF) identified and cloned from the A4 cytoplasm of Cajanus cajanifolius induced partial to complete male sterility when introduced into Arabidopsis and tobacco. Pigeonpea (Cajanus cajan L. Millsp.) is the only legume known to have commercial hybrid seed technology based on cytoplasmic male sterility (CMS). We identified a novel ORF (orf147) from the A4 cytoplasm of C. cajanifolius that was created via rearrangements in the CMS line and co-transcribes with the known and unknown sequences. The bi/poly-cistronic transcripts cause gain-of-function variants in the mitochondrial genome of CMS pigeonpea lines having distinct processing mechanisms and transcription start sites. In presence of orf147, significant repression of Escherichia coli growth indicated its toxicity to the host cells and induced partial to complete male sterility in transgenic progenies of Arabidopsis thaliana and Nicotiana tabacum where phenotype co-segregated with the transgene. The male sterile plants showed aberrant floral development and reduced lignin content in the anthers. Gene expression studies in male sterile pigeonpea, Arabidopsis and tobacco plants confirmed down-regulation of several anther biogenesis genes and key genes involved in monolignol biosynthesis, indicative of regulation of retrograde signaling. Besides providing evidence for the involvement of orf147 in pigeonpea CMS, this study provides valuable insights into its function. Cytotoxicity and aberrant programmed cell death induced by orf147 could be important for mechanism underlying male sterility that offers opportunities for possible translation for these findings for exploiting hybrid vigor in other recalcitrant crops as well.

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.