Conserved nucleotide sequences in highly expressed genes in plants

Comparative LC-MS/MS-based molecular networking, DNA fingerprinting, and in vitro anti-Helicobacter pylori activity of three Egyptian Ficus cultivars

Ficus species (Moraceae) have been used for nutrition and traditional medicine, and plants from this family are phytochemically abundant and serve as a potential source of natural products. As a result of the inherent complexity of the plant metabolomes and the fact that these Ficus species chemical space has not yet been fully decoded, it is still difficult to characterize their phytochemistry. Therefore, this study, we suggest the use of the molecular networking to elucidate the chemical classes existing in leaves of three Ficus species (F. deltoidei Jack, F. drupacea Thunb and F. sycomorus L.) and highlight the importance of molecular networking in examining their chemotaxonomy . By using computational tools, 90 metabolites were annotated , including phenolic acids, flavonoids, furanocoumarins, fatty acids and terpenoids. Phenolic acids were detected as the main class present in the three studied species. Flavonoids-C-glycosides, flavonoids-O-glycosides and isoflavonoids were mainly present in F. drupacea and F. sycomorus, while furanocoumarins were proposed in F. sycomorus. Vomifoliol-based sesquiterpenes were proposed in F. deltoidei. The chemotaxonomic differentiation agreed with the DNA fingerprinting using SCOT and ISSR markers. F. deltoidei, in particular, had a divergent chemical fingerprint as well as a different genotype. Chemotype differentiation using chemical fingerprints, in conjunction with the proposed genetic markers, creates an effective identification tool for the quality control of the raw materials and products derived from those three Ficus species. As well, F. drupacea exploited the most potent inhibition of H. pylori with MIC of 7.81 µg/ mL compared with clarithromycin. Overall, molecular networking provides a promising approach for the exploration of the chemical space of plant metabolomes and the elucidation of chemotaxonomy.

Investigating the geographical, phenotypic and genetic diversity of Sickleweed populations by bioclimatic parameters, morphological traits and SCoT molecular markers

Sickleweed (Falcaria vulgaris) is important due to its nutritional value and medicinal effects on the human body. The 15 different Sickleweed populations were collected based on an unbalanced nest design with 10 replications and nine morphological traits were measured on them. The diversity was investigated with 15 primers of SCoT marker. The genetic diversity was investigated by ANOVA, cluster analysis and Bayesian statistical model based on morphological traits, bioclimatic and SCoT. Grouping the study areas based on bioclimatic parameters by UPGMA method showed that these areas were divided into two groups and were similar in terms of climatic similarities and bioclimatic information. The results of analysis of variance showed that there was a significant difference between populations at the level of one percent for the studied traits. The cluster analysis based traits by the UPGMA method divided these populations into two groups. The phenotypic diversity of these populations was largely consistent with the geographical diversity. The primers used for SCoT marker produced 137 polymorphic bands on the populations, The UPGMA cluster analysis with molecular data placed the studied populations into three groups and four subgroups. Grouping based on the Bayesian method placed the populations into nine groups, although the populations were not differentiated and were a mixture of all nine groups. High genetic diversity for the studied Sickleweed populations have showed valuable insights into the evolution of this plant and provides basic data for designing appropriate management practices for breeding Sickleweed populations.

Heteroblastic Inflorescence of Lamium amplexicaule L. in Egyptian Flora

Lamium amplexicaule L. (Family: Lamiaceae) is a cosmopolitan weed whose eradication is challenging. The phenoplasticity of this species is related to its heteroblastic inflorescence, which has not received adequate research worldwide in its morphological and genetic aspects. This inflorescence hosts two flower types, a cleistogamous (CL: closed flower) and a chasmogamous (CH: opened flower). This species subjected to detailed investigation is a model species to clarify: (1) the existence of the CL and CH flowers in relation to the time and individual plants. (2) the predominant flower morphs in Egypt. (3) the morphological and genetic variability between these morphs. Among the novel data retrieved from this work is the Presence of this species in three distinct morphs coexisting during winter. These morphs showed remarkable phenoplasticity, particularly in flower organs. Significant differences were observed between the three morphs in pollen fertility, nutlets productivity and sculpture, flowering time, and seed viability. These differences were extended to the genetic profile of these three morphs assessed by the inter simple sequence repeats (ISSRs) and start codon targeted (SCoT). This work highlights the urgent need to study the heteroblastic inflorescence of crop weeds to facilitate its eradication.

Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects

The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.

Natural Biostimulant Attenuates Salinity Stress Effects in Chili Pepper by Remodeling Antioxidant, Ion, and Phytohormone Balances, and Augments Gene Expression

A biostimulant is any microorganism or substance used to enhance the efficiency of nutrition, tolerance to abiotic stress and/or quality traits of crops, depending on its contents from nutrients. Plant biostimulants like honey bee (HB) and silymarin (Sm) are a strategic trend for managing stressed crops by promoting nutritional and hormonal balance, regulating osmotic protectors, antioxidants, and genetic potential, reflecting plant growth and productivity. We applied diluted honey bee (HB) and silymarin-enriched honey bee (HB- Sm) as foliar nourishment to investigate their improving influences on growth, yield, nutritional and hormonal balance, various osmoprotectant levels, different components of antioxidant system, and genetic potential of chili pepper plants grown under NaCl-salinity stress (10 dS m‒1). HB significantly promoted the examined attributes and HB-Sm conferred optimal values, including growth, productivity, K+/Na+ ratio, capsaicin, and Sm contents. The antioxidative defense components were significantly better than those obtained with HB alone. Conversely, levels of oxidative stress markers (superoxide ions and hydrogen peroxide) and parameters related to membrane damage (malondialdehyde level, stability index, ionic leakage, Na+, and Cl- contents) were significantly reduced. HB-Sm significantly affects inactive gene expression, as a natural biostimulator silencing active gene expression. SCoT primers were used as proof in salt-treated or untreated chili pepper plants. There were 41 cDNA amplicons selected by SCoT-primers. Twenty of them were EcDNA amplicons (cDNA-amplicons that enhanced their genes by one or more treatments) representing 49% of all cDNA amplicons, whereas 7 amplicons for ScDNA (whose genes were silenced in one or more treatments) represented 17%, and 14 McDNA (monomorphic cDNA-amplicons with control) amplicons were represented by 34% from all cDNA amplicons. This indicates the high effect of BH-Sm treatments in expression enhancement of some inactive genes and their silenced effect for expression of some active genes, also confirming that cDNA-SCoT markers succeeded in detection of variable gene expression patterns between the untreated and treated plants. In conclusion, HB-Sm as a natural multi-biostimulator can attenuate salt stress effects in chili pepper plants by remodeling the antioxidant defense system and ameliorating plant productivity.

Genetic Similarity of Avena sativa L. Varieties as an Example of a Narrow Genetic Pool of Contemporary Cereal Species

The assessment of the genetic diversity of cultivated varieties is a very important element of breeding programs. This allows the determination of the level of genetic differentiation of cultivated varieties, their genetic distinctiveness, and is also of great importance in the selection of parental components for crossbreeding. The aim of the present study was to determine the level of genetic diversity of oat varieties currently grown in Central Europe based on two marker systems: ISSR and SCoT. The research conducted showed that both these types of markers were suitable for conducting analyses relating to the assessment of genetic diversity. The calculated coefficients showed that the analyzed cultivars were characterized by a high genetic similarity. However, the UPGMA and PCoA analyses clearly indicated the distinctiveness of the breeding programs conducted in Central European countries. The high genetic similarity of the analyzed forms allow us to conclude that it is necessary to expand the genetic pool of oat varieties. Numerous studies show that landraces may be the donor of genetic variation.

Genetic diversity and structure of Capsicum annuum as revealed by start codon targeted and directed amplified minisatellite DNA markers

BACKGROUND

Identification of high resolving DNA-based markers is of paramount importance to unlock the potential of genetic diversity and selection of unique accessions of Capsicum annuum L., within Cross River and Ebonyi States of Nigeria, for breeding and conservation. Therefore, we comparatively explored the effectiveness of start codon targeted (SCoT) and directed amplified minisatellite DNA (DAMD) markers for diversity analysis of the accessions. Fifteen accessions were collected for DNA extraction and amplifications with the markers.

RESULTS

Dendrograms from SCoT and DAMD categorized the accessions into five and three genetic groups, respectively, while the principal component analysis identified five genetic clusters, each from the markers. The average values of allele, gene diversity and polymorphic information content detected with SCoT and DAMD demonstrate that the two markers were effective and efficient, especially, SCoT in genetic diversity study of the accessions of pepper. Number of polymorphic loci (NPL) and percentage polymorphic loci (PPL) from SCoT (NPL = 64, PPL = 80.00-95.73%) and DAMD (NPL = 56, PPL = 53.33-86.67%) were high, but higher in SCoT markers. Other effective genetic parameters (effective number of alleles, Nei's genetic diversity and Shannon's information indices) identified with the two marker systems elucidated the allelic richness, rich genetic diversity within the populations and informative nature of the markers, especially SCoT. The intraspecific genetic diversity, interspecific genetic diversity, and coefficient of differentiation obtained with SCoT and DAMD further exposed the genetic structure with more genetic divergence within than among the populations of the accessions. Estimate of gene flow from the SCoT markers was 3.8375 and 0.6.2042 for the DAMD markers. The estimate of gene flow values from the markers indicated extensiveness with SCoT (Nm = 3.8375) and extremely extensive with DAMD (Nm = 6.2042) among the populations.

CONCLUSION

This study shows that SCoT markers may be more useful and informative than DAMD in measuring genetic diversity and differentiation of the accessions of the genus Capsicum. Genetic parameters obtained with SCoT showed that the accessions from Cross River were more genetically diverse than the ones from Ebonyi State. Therefore, SCoT may be a preferred marker in evaluating genetic diversity for improvement and conservation of this spicy crop, C. capsicum.

Study of polymorphism of maize using dna and protein markers

In the present investigation 40 genotypes of maize from Czechoslovakia, Hungary, Poland, Union of Soviet Socialist Republics, Slovakia and Yugoslavia were analysed using 20 start codon targeted (SCoT) markers, 10 simple sequence repeat (SSR) markers, 13 random amplified polymorphic (RAPD) markers and using SDS-PAGE markers. Twenty SCoT primers produced 114 DNA fragments with an average of 5.7 bands per primer. Out of the total of 114 amplified fragments, 86 (76.43 %) were polymorphic, with an average of 4.30 polymorphic bands per primer. Ten SSR primers revealed a total of 65 alleles ranging from 4 (UMC1060) to 8 (UMC2002 and UMC1155) alleles per locus with a mean value of 6.50 alleles per locus. 20 SCoT primers produced total 114 fragments across 40 maize genotypes, of which 86 (76.43 %) were polymorphic with an average of 4.30 polymorphic fragments per primer and number of amplified fragments ranged from 2 (SCoT 45) to 8 (SCoT 28 and SCoT 63). The number of total scorable protein bands was twentythree as a result of SDS-PAGE technique but those that were not cosistent in reproducibility and showed occasional variation in sharpness and density were not considered. Based on these bands forty accessions of maize were screened. Out of twentythree polypeptide bands, 6 (31%) were commonly present in all accessions and considered as monomorphic, while 17 (65%) showed variations and considered as polymorphic. The dendrogram of 40 old maize genotypes based on SSR, SCoT, RAPD and SDS-PAGE markers using UGMA algorithm was constructed.

Detection genetic variability of secale cereale L. by scot markers

Rye (Secale cereale L.) is our traditional cereal used for baking. The genetic variability of grown rye has been reduced by modern agronomic practices, which subsequently prompted the importance of search for species that could be useful as a gene pool for the improving of flour quality for human consumption or for other industrial uses. Therefore, the aim of this study was to detect genetic variability among the set of 45 rye genotypes using 8 SCoT markers. Amplification of genomic DNA of 45 genotypes, using SCoT analysis, yielded 114 fragments, with an average of 14.25 polymorphic fragments per primer. The most polymorphic primer was SCoT 36, where 21 polymorphic amplification products were detected. In contract the lowest polymorphic primer was SCoT 45 with 5 polymorphic products. Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The hierarchical cluster analysis showed that the rye genotypes were divided into 2 main clusters. One rye genotype Motto, origin from Poland formed a separate subcluster (1b). Subscluster 2a included only genotype Valtické (CSK). In this experiment, SCoT proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars.

Structural and functional characterisation of a class I endochitinase of the carnivorous sundew (Drosera rotundifolia L.)

Chitinase gene from the carnivorous plant, Drosera rotundifolia , was cloned and functionally characterised. Plant chitinases are believed to play an important role in the developmental and physiological processes and in responses to biotic and abiotic stress. In addition, there is growing evidence that carnivorous plants can use them to digest insect prey. In this study, a full-length genomic clone consisting of the 1665-bp chitinase gene (gDrChit) and adjacent promoter region of the 698 bp in length were isolated from Drosera rotundifolia L. using degenerate PCR and a genome-walking approach. The corresponding coding sequence of chitinase gene (DrChit) was obtained following RNA isolation from the leaves of aseptically grown in vitro plants, cDNA synthesis with a gene-specific primer and PCR amplification. The open reading frame of cDNA clone consisted of 978 nucleotides and encoded 325 amino acid residues. Sequence analysis indicated that DrChit belongs to the class I group of plant chitinases. Phylogenetic analysis within the Caryophyllales class I chitinases demonstrated a significant evolutionary relatedness of DrChit with clade Ib, which contains the extracellular orthologues that play a role in carnivory. Comparative expression analysis revealed that the DrChit is expressed predominantly in tentacles and is up-regulated by treatment with inducers that mimick insect prey. Enzymatic activity of rDrChit protein expressed in Escherichia coli was confirmed and purified protein exhibited a long oligomer-specific endochitinase activity on glycol-chitin and FITC-chitin. The isolation and expression profile of a chitinase gene from D. rotundifolia has not been reported so far. The obtained results support the role of specific chitinases in digestive processes in carnivorous plant species.

Start codon targeted (scot) polymorphism reveals genetic diversity in european old maize (Zea mays L.) Genotypes

Maize (Zea mays L.) is one of the world's most important crop plants following wheat and rice, which provides staple food to large number of human population in the world. It is cultivated in a wider range of environments than wheat and rice because of its greater adaptability. Molecular characterization is frequently used by maize breeders as an alternative method for selecting more promising genotypes and reducing the cost and time needed to develop hybrid combinations. In the present investigation 40 genotypes of maize from Czechoslovakia, Hungary, Poland, Union of Soviet Socialist Republics, Slovakia and Yugoslavia were analysed using 20 Start codon targeted (SCoT) markers. These primers produced total 114 fragments across 40 maize genotypes, of which 86 (76.43%) were polymorphic with an average of 4.30 polymorphic fragments per primer and number of amplified fragments ranged from 2 (SCoT 45) to 8 (SCoT 28 and SCoT 63). The polymorphic information content (PIC) value ranged from 0.374 (ScoT 45) to 0.846 (SCoT 28) with an average of 0.739. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared. The hierarchical cluster analysis showed that the maize genotypes were divided into two main clusters. Unique maize genotype (cluster 1), Zuta Brzica, originating from Yugoslavia separated from others. Cluster 2 was divided into two main clusters (2a and 2b). Subcluster 2a contained one Yugoslavian genotype Juhoslavanska and subcluster 2b was divided in two subclusters 2ba and 2bb. The present study shows effectiveness of employing SCoT markers in analysis of maize, and would be useful for further studies in population genetics, conservation genetics and genotypes improvement.

Comparative analysis of contextual bias around the translation initiation sites in plant genomes

Nucleotide distribution around translation initiation site (TIS) is thought to play an important role in determining translation efficiency. Kozak in vertebrates and later Joshi et al. in plants identified context sequence having a key role in translation efficiency, but a great variation regarding this context sequence has been observed among different taxa. The present study aims to refine the context sequence around initiation codon in plants and addresses the sampling error problem by using complete genomes of 7 monocots and 7 dicots separately. Besides positions -3 and +4, significant conservation at -2 and +5 positions was also found and nucleotide bias at the latter two positions was shown to directly influence translation efficiency in the taxon studied. About 1.8% (monocots) and 2.4% (dicots) of the total sequences fit the context sequence from positions -3 to +5, which might be indicative of lower number of housekeeping genes in the transcriptome. A three base periodicity was observed in 5' UTR and CDS of monocots and only in CDS of dicots as confirmed against random occurrence and annotation errors. Deterministic enrichment of GCNAUGGC in monocots, AANAUGGC in dicots and GCNAUGGC in plants around TIS was also established (where AUG denotes the start codon), which can serve as an arbiter of putative TIS with efficient translation in plants.

Novel strong promoter of antimicrobial peptides gene pro-SmAMP2 from chickweed (Stellaria media)

BACKGROUND

In a previous study we found that in chickweed the expression level of the pro-SmAMP2 gene was comparable or even higher to that of the β-actin gene. This high level of the gene expression has attracted our attention as an opportunity for the identification of novel strong promoters of plant origin, which could find its application in plant biotechnology. Therefore, in the present study we focused on the nucleotide sequence identification and the functional characteristics of the pro-SmAMP2 promoter in transgenic plants.

RESULTS

In chickweed (Stellaria media), a 2120 bp promoter region of the pro-SmAMP2 gene encoding antifungal peptides was sequenced. Six 5'-deletion variants -2120, -1504, -1149, -822, -455, and -290 bp of pro-SmAMP2 gene promoter were fused with the coding region of the reporter gene gusA in the plant expression vector pCambia1381Z. Independent transgenic plants of tobacco Nicotiana tabacum were obtained with each genetic structure. GUS protein activity assay in extracts from transgenic plants showed that all deletion variants of the promoter, except -290 bp, expressed the gusA gene. In most transgenic plants, the GUS activity level was comparable or higher than in plants with the viral promoter CaMV 35S. GUS activity remains high in progenies and its level correlates positively with the amount of gusA gene mRNA in T3 homozygous plants. The activity of the рro-SmAMP2 promoter was detected in all organs of the transgenic plants studied, during meiosis and in pollen as well.

CONCLUSION

Our results show that the рro-SmAMP2 promoter can be used for target genes expression control in transgenic plants.

Potential Start Codon Targeted (SCoT) and Inter-retrotransposon Amplified Polymorphism (IRAP) Markers for Evaluation of Genetic Diversity and Conservation of Wild Pistacia Species Population

Wild pistachio species is important species in forests regions Iran and provide protection wind and soil erosion. Even though cultivation and utilization of Pistacia are fully exploited, the evolutionary history of the Pistacia genus and the relationships among the species and accessions is still not well understood. Two molecular marker strategies, SCoT and IRAP markers were analyzed for assessment of 50 accessions of this species accumulated from diverse geographical areas of Iran. A thorough of 115 bands were amplified using eight IRAP primers, of which 104 (90.4 %) have been polymorphic, and 246 polymorphic bands (68.7 %) had been located in 358 bands amplified by way of forty-four SCoT primers. Average PIC for IRAP and SCoT markers became 0.32 and 0.48, respectively. This is exposed that SCoT markers have been extra informative than IRAP for the assessment of variety among pistachio accessions. Primarily based on the two extraordinary molecular markers, cluster evaluation revealed that the 50 accessions taken for the evaluation may be divided into three distinct clusters. Those results recommend that the performance of SCoT and IRAP markers was highly the equal in fingerprinting of accessions. The results affirmed a low genetic differentiation among populations, indicating the opportunity of gene drift most of the studied populations. These findings might render striking information in breeding management strategies for genetic conservation and cultivar improvement.

Oral Rabies Vaccine Design for Expression in Plants

Vaccination is the sensitization process of the immune system against any pathogen. Generally, recombinant subunit vaccines are considered safer than attenuated vaccines. As whole pathogenic organisms are used in the immunization process, the attenuated vaccines are considered more risky than subunit vaccines. Rabies is the oldest known zoonosis which spreads through a neurotropic Lyssavirus primarily mediated through infected canine bites. Rabies causes worldwide loss of more than 60,000 human lives every year. Animal vaccination is equally important to check the transmission of rabies into humans. Rabies oral vaccination can be a good alternative where multiple booster and priming regimens are required while the painful vaccination process can continue for long durations. Introduction of oral vaccines was made to ease the discomfort associated with the mode of introduction of conventional vaccines into the body. Although the rabies oral vaccine can substantially reduce the cost of vaccination in the developing countries, mass immunization programs need larger quantities of vaccines which should be delivered at nominal cost. Expression of recombinant antigen proteins in E. coli is often not viable because of lack of post-translational modifications and folding requirements. Though yeast and insect cell line expression systems have post-translational processing and modifications, significantly different immunological response against their post-translational modification pattern limits their deployment as an expression system. As an alternative, plants are emerging as a promising system to express and deliver wide range of functionally active biopharmaceutical product at lower cost for mass immunization programs. As generation of vaccine antigenic proteins in plant systems are cheaper, the strategy will benefit developing countries where this disease causes thousands of deaths every year. In this chapter, we will discuss about our efforts toward development of oral rabies vaccine and the methodological steps involved during this procedure in detail.

Genetic relationship and diversity among coconut (Cocos nucifera L.) accessions revealed through SCoT analysis

Coconut (Cocos nucifera L.) is one of the important palms grown both as a homestead and plantation crop in countries and most island territories of tropical regions. Different DNA-based marker systems have been utilized to assess the extent of genetic diversity in coconut. Advances in genomics research have resulted in the development of novel gene-targeted markers. In the present study, we have used a simple and novel marker system, start codon targeted polymorphism (SCoT), for its evaluation as a potential marker system in coconut. SCoT markers were utilized for assessment of genetic diversity in 23 coconut accessions (10 talls and 13 dwarfs), representing different geographical regions. Out of 25 SCoT primers screened, 15 primers were selected for this study based on their consistent amplification patterns. A total of 102 scorable bands were produced by the 15 primers, 88 % of which were polymorphic. The scored data were used to construct a similarity matrix. The similarity coefficient values ranged between 0.37 and 0.91. These coefficients were utilized to construct a dendrogram using the unweighted pair group of arithmetic means (UPGMA). The extent of genetic diversity observed based on SCoT analysis of coconut accessions was comparable to earlier findings using other marker systems. Tall and dwarf coconut accessions were clearly demarcated, and in general, coconut accessions from the same geographical region clustered together. The results indicate the potential of SCoT markers to be utilized as molecular markers to detect DNA polymorphism in coconut accessions.

Anti-infective immunoadhesins from plants

Immunoadhesins are recombinant proteins that combine the ligand-binding region of a receptor or adhesion molecule with immunoglobulin constant domains. All FDA-approved immunoadhesins are designed to modulate the interaction of a human receptor with its normal ligand, such as Etanercept (Enbrel(®) ), which interferes with the binding of tumour necrosis factor (TNF) to the TNF-alpha receptor and is used to treat inflammatory diseases such as rheumatoid arthritis. Like antibodies, immunoadhesins have long circulating half-lives, are readily purified by affinity-based methods and have the avidity advantages conferred by bivalency. Immunoadhesins that incorporate normal cellular receptors for viruses or bacterial toxins hold great, but as yet unrealized, potential for treating infectious disease. As decoy receptors, immunoadhesins have potential advantages over pathogen-targeted monoclonal antibodies. Planet Biotechnology has specialized in developing anti-infective immunoadhesins using plant expression systems. An immunoadhesin incorporating the cellular receptor for anthrax toxin, CMG2, potently blocks toxin activity in vitro and protects animals against inhalational anthrax. An immunoadhesin based on the receptor for human rhinovirus, ICAM-1, potently blocks infection of human cells by one of the major causes of the common cold. An immunoadhesin targeting the MERS coronavirus is in an early stage of development. We describe here the unique challenges involved in designing and developing immunoadhesins targeting infectious diseases in the hope of inspiring further research into this promising class of drugs.

Abscisic acid and abiotic stress tolerance - different tiers of regulation

Abiotic stresses affect plant growth, metabolism and sustainability in a significant way and hinder plant productivity. Plants combat these stresses in myriad ways. The analysis of the mechanisms underlying abiotic stress tolerance has led to the identification of a highly complex, yet tightly regulated signal transduction pathway consisting of phosphatases, kinases, transcription factors and other regulatory elements. It is becoming increasingly clear that also epigenetic processes cooperate in a concerted manner with ABA-mediated gene expression in combating stress conditions. Dynamic stress-induced mechanisms, involving changes in the apoplastic pool of ABA, are transmitted by a chain of phosphatases and kinases, resulting in the expression of stress inducible genes. Processes involving DNA methylation and chromatin modification as well as post transcriptional, post translational and epigenetic control mechanisms, forming multiple tiers of regulation, regulate this gene expression. With recent advances in transgenic technology, it has now become possible to engineer plants expressing stress-inducible genes under the control of an inducible promoter, enhancing their ability to withstand adverse conditions. This review briefly discusses the synthesis of ABA, components of the ABA signal transduction pathway and the plants' responses at the genetic and epigenetic levels. It further focuses on the role of RNAs in regulating stress responses and various approaches to develop stress-tolerant transgenic plants.

A study on the influence of different promoter and 5'UTR (URM) cassettes from Arabidopsis thaliana on the expression level of the reporter gene β glucuronidase in tobacco and cotton

Several reports of promoters from plants, viral and artificial origin that confer high constitutive expression are known. Among these the CaMV 35S promoter is used extensively for transgene expression in plants. We identified candidate promoters from Arabidopsis based on their transcript levels (meta-analysis of available microarray control datasets) to test their activity in comparison to the CaMV 35S promoter. A set of 11 candidate genes were identified which showed high transcript levels in the aerial tissue (i.e. leaf, shoot, flower and stem). In the initial part of the study binary vectors were developed wherein the promoter and 5'UTR region of these candidate genes (Upstream Regulatory Module, URM) were cloned upstream to the reporter gene β glucuronidase (gus). The promoter strengths were tested in transformed callus of Nicotiana tabacum and Gossypium hirsutum. On the basis of the results obtained from the callus, the influence of the URM cassettes on transgene expression was tested in transgenic tobacco. The URM regions of the genes encoding a subunit of photosystem I (PHOTO) and geranyl geranyl reductase (GGR) in A. thaliana genome showed significantly high levels of GUS activity in comparison to the CaMV 35S promoter. Further, when the 5'UTRs of both the genes were placed downstream to the CaMV 35S promoter it led to a substantial increase in GUS activity in transgenic tobacco lines and cotton callus. The enhancement observed was even higher to that observed with the viral leader sequences like Ω and AMV, known translational enhancers. Our results indicate that the two URM cassettes or the 5'UTR regions of PHOTO and GGR when placed downstream to the CaMV 35S promoter can be used to drive high levels of transgene expression in dicotyledons.

Start codon targeted (SCoT) polymorphism in toxic and non-toxic accessions of Jatropha curcas L. and development of a codominant SCAR marker

Thirty six start codon targeted (SCoT) primers were used for characterization of 48 accessions of Jatropha curcas from different countries and include material with genetic variation for levels of phorbol esters, yield, seed oil content, test weight and plant type. SCoT analysis revealed high polymorphism and 74% of the primers generated polymorphic profiles. The SCoT6 primer discriminated edible and toxic accessions in a single reaction while the SCoT26 and 27 primers produced amplicons specific to toxic and non-toxic accessions, respectively. The polymorphic SCoT markers obtained with these three primers were converted to sequence characterized amplicon regions (SCARs) which resulted in codominant SCARs with SCoT6 primer and dominant SCARs with SCoT 26 and 27 primers. The codominant nature of SCoT6 primer and the resultant SCAR6 primer were validated on intraspecific hybrids derived from a cross between non-toxic and toxic accessions. The accession JP38 from Madagascar was found to be distinct and showed accession specific bands with 9 different SCoT primers. Sequence analysis of polymorphic amplicons obtained with SCoT6 primer showed a 65 bp deletion in accessions with low/zero phorbol esters. Diversity analysis separated the toxic and non-toxic accessions into two groups and the accessions JP29 and JP48 from Mexico formed a third cluster.

A synthetic tuber-specific and cold-induced promoter is applicable in controlling potato cold-induced sweetening

Cold-induced sweetening (CIS) in potato seriously hinders the potato processing industry. It could be of great value for genetic improvement of potato CIS to have a target gene specifically expressed in cold stored tubers. In this study, we used a synthetic promoter, pCL, in potato transformation to drive an antisense expression of StvacINV1, the acid vacuolar invertase gene from Solanum tuberosum. The measurements of expression and enzyme activity of target gene showed that pCL promoter could efficiently govern target gene to express specifically and remarkably regulate the activity of acid vacuolar invertase in potato tubers at low temperature, furthermore, it had almost no effect in other tissues or the tubers under room temperature. The transgenic tubers showed decrease in reducing sugar content during storage at low temperature and acceptable chip color without significant changes observed in plant morphology and tuberization between the nontransgenic and transgenic lines. This tuber-specific and cold-induced feature could maximally reduce the background expression of the target gene which might bring about potential negative or detrimental effects to plant development. The synthetic promoter confirmed here would be optimal for gene function research in potato tubers in response to low temperature.

Trichome-specific expression of the amorpha-4,11-diene 12-hydroxylase (cyp71av1) gene, encoding a key enzyme of artemisinin biosynthesis in Artemisia annua, as reported by a promoter-GUS fusion

Artemisinin derivatives are effective anti-malarial drugs. In order to design transgenic plants of Artemisia annua with enhanced biosynthesis of artemisinin, we are studying the promoters of genes encoding enzymes involved in artemisinin biosynthesis. A 1,151 bp promoter region of the cyp71av1 gene, encoding amorpha-4,11-diene 12-hydroxylase, was cloned. Alignment of the cloned promoter and other cyp71av1 promoter sequences indicated that the cyp71av1 promoter may be different in different A. annua varieties. Comparison to the promoter of amorpha-4,11-diene synthase gene showed a number of putative cis-acting regulatory elements in common, suggesting a co-regulation of the two genes. The cyp71av1 promoter sequence was fused to the β-glucuronidase (GUS) reporter gene and two varieties of A. annua and Nicotiana tabacum were transformed. In A. annua, GUS expression was exclusively localized to glandular secretory trichomes (GSTs) of leaf primordia and top expanded leaves. In older leaves, there is a shift of expression to T-shaped trichomes (TSTs). Only TSTs showed GUS staining in lower leaves and there is no GUS staining in old leaves. GUS expression in flower buds was specifically localized to GSTs. The recombinant promoter carries the cis-acting regulatory elements required for GST-specific expression. The cyp71av1 promoter shows activity in young tissues. The recombinant promoter was up to 200 times more active than the wild type promoter. GUS expression in transgenic N. tabacum was localized to glandular heads. Transcript levels were up-regulated by MeJA. Wound responsiveness experiment showed that the cyp71av1 promoter does not appear to play any role in the response of A. annua to mechanical stress.

Cis-acting motifs in artificially synthesized expression cassette leads to enhanced transgene expression in tomato (Solanum lycopersicum L.)

Efficacy of artificial synthetic expression modules was compared with native CaMV35S and DECaMV35S promoter in transgenic tomato developed by Agrobacterium-mediated transformation. The promoters under trial were CaMV35S-mec (PcamI), CaMV35S (PcamII), DECaMV35S (PcamIII), synthetic minimal expression cassette (Pmec), complete expression cassette (Pcec), double enhancer expression cassette (Pdec) and triple enhancer expression cassette (Ptec) for driving the uidA gene for β-glucuronidase (GUS) activity. The promoter efficiency based on average of GUS expression in T(0) and T(1) transgenic tomato was in the order Pcec > Pdec > PcamIII > PcamII > PcamI > Ptec > Pmec. The two promoters Pcec and PcamIII were deployed for development of insect-resistant transgenic tomato with optimal expression of modified cry1Ac insecticidal toxin gene from Bacillus thuringiensis (Bt). The transgenic status and copy number of the cry1Ac in T(0) transgenic tomato was confirmed through PCR, Southern hybridization, RT-PCR and Western immunoassay, while toxin expression was monitored by DAS-ELISA. The expression level of Cry1Ac toxin driven by Pcec in T(0) population ranged from 0.08 to 0.8% of total soluble protein (TSP) that was significantly higher to PcamIII which ranged from 0.02 to 0.13% of TSP. The outcome of insect mortality bioassay with Helicoverpa armigera correlated well with the results of DAS-ELISA. The higher expression of cry1Ac gene driven by Pcec promoter in transgenic tomato did not show any yield penalty and reflected complete protection, while low recovery of promising transgenics expressing Cry1Ac toxin driven by PcamIII was a major limitation for complete protection against the fruit borer insect.

Genetic diversity and effect of temperature and pH on the growth of Macrophomina phaseolina isolates from sunflower fields in Hungary

The effects of temperature and pH on the growth of 45 Hungarian Macrophomina phaseolina isolates from different locations and hosts were compared on the basis of their genetic diversity. One Spanish and two Serbian isolates were also included in the experiment. The most favourable temperature regimes for the development of the isolates ranged between 25 and 35 °C. The optimal pH for the pathogen varied between 4.0 and 6.0, but growth was observed on potato dextrose agar even at pH values of 3.0, 7.0 and 8.0. RAPD analysis with 13 different primer pairs generated 148 unambiguous bands. RFLP analysis involving 8 different restriction endonucleases was performed on a 1550 bp fragment of the rDNA region containing internal transcribed spacers (ITS1, ITS2), the 5.8S rDNA and part of the 25S rDNA. The greatest genetic distance values were obtained for three isolates, two from Hungary and one from Spain, which had similar values, but were quite distinct from all the others. A strong positive correlation was observed between the genetic distances and the growth parameters measured at various temperatures, and between the geographical data and the growth data sets at different pH values, but the correlation was less strong in the latter case. While Hungarian M. phaseolina populations are thought to reproduce clonally, the present results indicate the coexistence of different haplotypes in this area, and besides the geographical dominance of a given haplotype it was found that a closer genetic relationship might exist between spatially distinct haplotypes.

Designer promoter: an artwork of cis engineering

Advances in systematic computational biology and rapid elucidation of synergistic interplay between cis and trans factors governing transcriptional control have facilitated functional annotation of gene networks. The generation of data through deconstructive, reconstructive and database assisted promoter studies, and its integration to principles of synthetic engineering has started an era of designer promoters. Exploration of natural promoter architecture and the concept of cis engineering have not only enabled fine tuning of single or multiple transgene expression in response to perturbations in the chemical, physiological and environmental stimuli but also provided researchers with a unique answer to various problems in crop improvement in the form of bidirectional promoters.

Effect of point mutations in translation initiation context on the expression of recombinant human alpha(1)-proteinase inhibitor in transgenic tomato plants

The functional and biological significance of translation initiation context sequence in determining high-level expression of modified synthetic human alpha(1)-proteinase inhibitor (alpha(1)-PI) gene was documented in stable transgenic tomato plants. Context sequence of initiator ATG codon derived from statistical analysis of databases was identified as taaA(A/C)aATGGCt in highly expressed dicot plant genes. Removal of initiator ATG context sequence reduced the expression of recombinant alpha(1)-PI protein to fourfolds. The mutation of consensus base at +4 position to a pyrimidine either alone or with substitution at -3 position eliminated most of the alpha(1)-PI expression, while mutation at -3 alone resulted in about sevenfold reduction. The presence of steady-state levels of alpha(1)-PI transcript in transgenic plants indicated that the variation in expression is entirely due to the point mutations incorporated in translation initiation context. These results indicated the significance of conserved nucleotide sequence around initiator ATG codon in augmenting post-transcriptional events and high-level expression of heterologous genes in transgenic plants.

A T9G mutation in the prototype TATA-box TCACTATATATAG determines nucleosome formation and synergy with upstream activator sequences in plant promoters

We had earlier reported that mutations to G and C at the seventh and eighth positions in the prototype TATA-box TCACTATATATAG inhibited light-dependent activation of transcription from the promoter. In this study, we characterized mutations at the ninth position of the prototype TATA-box. Substitution of T at the ninth position with G or C enhanced transcription from the promoter in transgenic tobacco (Nicotiana tabacum) plants. The effect of T9G/C mutations was not light dependent, although the 9G/C TATA-box showed synergy with the light-responsive element (lre). However, the 9G/C mutants in the presence of lre failed to respond to phytochromes, sugar, and calcium signaling, in contrast to the prototype TATA-box with lre. The 9G/C mutation shifted the point of initiation of transcription, and transcription activation was dependent upon the type of activating element present upstream. The synergy in activation was noticed with lre and legumin activators but not with rbcS, Pcec, and PR-1a activators. The 9G mutation resulted in a micrococcal nuclease-sensitive region over the TATA-box, suggesting a nucleosome-free region, in contrast to the prototype promoter, which had a distinct nucleosome on the TATA-box. Thus, the transcriptional augmentation with mutation at the ninth position might be because of the loss of a repressive nucleosomal structure on the TATA-box. In agreement with our findings, the promoters containing TATAGATA as identified by genome-wide analysis of Arabidopsis (Arabidopsis thaliana) are not tightly repressed.

Expression and purification of an anti-Foot-and-mouth disease virus single chain variable antibody fragment in tobacco plants

Low-cost recombinant antibodies could provide a new strategy to control Foot-and-mouth disease virus (FMDV) outbreaks by passive immunization of susceptible animals. In this study, a single chain variable antibody fragment (scFv) recognizing FMDV coat protein VP1 was expressed in transgenic tobacco plants. To enhance the accumulation of scFv protein, the codon-usage of a murine hybridoma-derived scFv gene was adjusted to mimic highly expressed tobacco genes and fused to an elastin-like polypeptide (ELP) tag. This scFv-ELP fusion accumulated up to 0.8% of total soluble leaf protein in transgenic tobacco. To recover scFv-ELP protein from the leaf extract, a simple and scalable purification strategy was established. Purified scFv-ELP fusion was cleaved to separate the scFv portion. Finally, it was shown that the purified scFv proteins retained their capacity to bind the FMDV in the absence or presence of ELP fusion.

The TATA-box sequence in the basal promoter contributes to determining light-dependent gene expression in plants

A prototype 13-bp TATA-box sequence, TCACTATATATAG, was mutated at each nucleotide position and examined for its function in the core promoter. Specific nucleotides in the first TATA, the second TATA, as well as the flanking sequences influenced promoter function in transient transformation of tobacco (Nicotiana tabacum var Petit Havana) leaves. The effect of a given mutation on reporter gene expression in light versus dark was variable and sometimes contrasting. Some mutations, like T(7) or A(8)-->C or G, completely inactivated the expression of the minimal promoter in light but not in dark. In general, the sequence requirement for dark expression was less stringent than that for light expression. The selective effect of TATA-box mutations on light versus dark expression was exerted on core promoter function in the chromatin-integrated state also. Even in the presence of an upstream light response activator element, TATA-box mutations influenced modulation of the promoter by light. An A at the eighth position was specifically involved in the red light response of the promoter. Selectivity in gene expression was associated with a high level of transcript initiation from a site that was not active in the dark. Nuclear proteins from dark- and light-grown seedlings showed that the sequence variation within the TATA-box governs the formation of alternative transcriptional complexes. The experiments give direct evidence for the role of a core TATA-box sequence in determining the level as well as selectivity of gene expression in plants.

Analysis of polarity in the expression from a multifactorial bidirectional promoter designed for high-level expression of transgenes in plants

A synthetic bidirectional expression module was constructed by placing a computationally designed minimal promoter sequence on the 5' and 3' sides of a transcription activation module. The activation of transcription from the unidirectional and bidirectional promoters constructed from the same sequence elements was evaluated by using the reporter genes gusA and gfp. The analysis based on transient and stable transformation of tobacco showed that the artificially designed multifactorial activation module activated transcription simultaneously to comparable levels in both the directions. The transcription activation module responded to elicitors like salicylic acid, NaCl and IAA in the forward as well as reverse directions. The concentration of the elicitor required for highest gene activation was similar for the two directions in case of the three activators. The kinetics of time of induction was similar in the two directions for salicylic acid and NaCl. In the case of IAA, the transcription activation was faster in the reverse direction. The results show that constitutive and chemically inducible bidirectional promoters can be deployed for predictable simultaneous regulation of two genes for genetic engineering in plants.

A variety of synergistic and antagonistic interactions mediated by cis-acting DNA motifs regulate gene expression in plant cells and modulate stability of the transcription complex formed on a basal promoter

Several synthetic promoters containing a variety of commonly found cis-acting DNA sequence motifs were constructed to study the motif-motif and motif-protein interactions involved in gene expression in plants. Transient expression of the reporter gene gusA in tobacco leaves was used to demonstrate that several sequence elements can be arranged upstream of a basal promoter to function synergistically in enhancing gene expression. A cis-acting DNA motif could function as an activator by itself as well as a synergizing activator in the presence of other homologous as well as heterologous motifs in the neighbourhood. The function of a complex promoter comprising several activation motifs was arrested nearly completely in vivo, following titration with any one of the motifs. The results suggested a hierarchical assembly of several motif-binding factors, leading to the stabilization of the transcriptional complex formed on the TATA-box.

Development of a hybrid delta-endotoxin and its expression in tobacco and cotton for control of a polyphagous pest Spodoptera litura

A hybrid delta-endotoxin protein was designed against a polyphagous lepidopteran insect pest Spodoptera litura, which is tolerant to most of the known delta-endotoxins. The hybrid delta-endotoxin was created by replacing amino acid residues 530-587 in a poorly active natural Cry1Ea protein, with a highly homologous 70 amino acid region of Cry1Ca in domain III. The truncated delta-endotoxins Cry1Ea, Cry1Ca and the hybrid protein Cry1EC accumulated in Escherichia coli to form inclusion bodies. The solubilised Cry1EC made from E. coli was 4- fold more toxic to the larvae of S. litura than Cry1Ca, the best known delta-endotoxin against Spodoptera sp. None of the two truncated toxins, solubilised from E. coli caused larval mortality. However, trypsinised Cry1Ca protoxin obtained from E. coli and solubilised from inclusion bodies caused mortality of S. litura with LC50 513 ng/ml semi synthetic diet. A synthetic gene coding for the hybrid delta-endotoxin Cry1EC was designed for high level expression in plants, taking into consideration several features found in the highly expressed plant genes. Transgenic, single copy plants of tobacco as well as cotton were developed. The selected lines expressed Cry1EC at 0.1-0.7% of soluble leaf protein. Such plants were completely resistant to S. litura and caused 100% mortality in all stages of larval development. Hence, unlike in E. coli, the hybrid delta-endotoxin folded into a functionally active conformation in both tobacco and cotton leaves. The truncated Cry1EC expressed in tobacco leaves was about 8-fold more toxic (LC50 58 ng/ml diet) compared to expression in E. coli.

Complex nested promoters control tissue-specific expression of acetyl-CoA carboxylase genes in wheat

Cis-acting regulatory elements of the wheat acetyl-CoA carboxylase (ACC) gene family were identified by comparing the promoter activity of 5' end gene fragments fused to a reporter gene in two transient expression systems: wheat protoplasts and epidermal cells of mature embryos. Expression of the plastid and the cytosolic ACC genes is each driven by two nested promoters responsible for the synthesis of two transcript types. The internal promoter is located in an intron removed from transcripts originating at the first promoter. These complex promoters, which are different for the cytosolic and plastid ACC genes, control tissue-specific expression of the enzymatic activity supplying cytosolic, plastid, and mitochondrial pools of malonyl-CoA. The activity of one such complex promoter, driving expression of one of the cytosolic ACC genes, was studied throughout development of transgenic wheat plants carrying a full-length promoter-reporter gene fusion. High activity of the promoter was detected in the coleoptile, in the upper sheath section of the leaf, on the top surface of the ovary, in some sections of the main veins in the lemma and glume, and in abaxial epidermis hair cells of the lemma, glume, and rachis. The findings are consistent with the developmental and environmental requirements for very-long-chain fatty acids and flavonoids, whose synthesis begins with the ACC reaction in the cytosol of these specific cell types.

Strategies for development of functionally equivalent promoters with minimum sequence homology for transgene expression in plants: cis-elements in a novel DNA context versus domain swapping

The cauliflower mosaic virus 35S (35S) promoter has been extensively used for the constitutive expression of transgenes in dicotyledonous plants. The repetitive use of the same promoter is known to induce transgene inactivation due to promoter homology. As a way to circumvent this problem, we tested two different strategies for the development of synthetic promoters that are functionally equivalent but have a minimum sequence homology. Such promoters can be generated by (a) introducing known cis-elements in a novel or synthetic stretch of DNA or (b) "domain swapping," wherein domains of one promoter can be replaced with functionally equivalent domains from other heterologous promoters. We evaluated the two strategies for promoter modifications using domain A (consisting of minimal promoter and subdomain A1) of the 35S promoter as a model. A set of modified 35S promoters were developed whose strength was compared with the 35S promoter per se using beta-glucuronidase as the reporter gene. Analysis of the expression of the reporter gene in transient assay system showed that domain swapping led to a significant fall in promoter activity. In contrast, promoters developed by placing cis-elements in a novel DNA context showed levels of expression comparable with that of the 35S. Two promoter constructs Mod2A1T and Mod3A1T were then designed by placing the core sequences of minimal promoter and subdomain A1 in divergent DNA sequences. Transgenics developed in tobacco (Nicotiana tabacum) with the two constructs and with 35S as control were used to assess the promoter activity in different tissues of primary transformants. Mod2A1T and Mod3A1T were found to be active in all of the tissues tested, at levels comparable with that of 35S. Further, the expression of the Mod2A1T promoter in the seedlings of the T1 generation was also similar to that of the 35S promoter. The present strategy opens up the possibility of creating a set of synthetic promoters with minimum sequence homology and with expression levels comparable with the wild-type prototype by modifying sequences present between cis-elements for transgene expression in plants.

Sequence architecture downstream of the initiator codon enhances gene expression and protein stability in plants

Nucleotide positions conserved on the 3' side of the initiator codon ATG and the corresponding N-terminal amino acid residues in a number of highly abundant plant proteins were identified by computational analysis of a dataset of highly expressed plant genes. The reporter genes uidA and gfp were modified to introduce these features. Insertion of GCT TCC TCC after the initiator codon ATG augmented expression for both the reporter genes. The insertion of each successive codon improved the expression of beta-glucuronidase (GUS) in an incremental fashion in transient transformation of tobacco (Nicotiana tabacum) leaves. The insertion of alanine-serine (Ser)-Ser resulted in about a 2-fold increase in the stability of GUS. However, this did not account for the 30- to 40-fold increase in GUS activity between the constructs coding for methionine-alanine-Ser-Ser-GUS and the native enzyme. Substitution of the codon for Ser at the third amino acid residue with synonymous codons reduced GUS expression. The results suggest a role for the conserved nucleotides in the +4 to +11 region in augmenting posttranscriptional events in the expression of genes in plants.