The pivotal roles of the plant S-adenosylmethionine decarboxylase 5' untranslated leader sequence in regulation of gene expression at the transcriptional and posttranscriptional levels

Polyamines: Their Role in Plant Development and Stress

This review focuses on the intricate relationship between plant polyamines and the genetic circuits and signaling pathways that regulate various developmental programs and the defense responses of plants when faced with biotic and abiotic aggressions. Particular emphasis is placed on genetic evidence supporting the involvement of polyamines in specific processes, such as the pivotal role of thermospermine in regulating xylem cell differentiation and the significant contribution of polyamine metabolism in enhancing plant resilience to drought. Based on the numerous studies describing effects of the manipulation of plant polyamine levels, two conceptually different mechanisms for polyamine activity are discussed: direct participation of polyamines in translational regulation and the indirect production of hydrogen peroxide as a defensive mechanism against pathogens. By describing the multifaceted functions of polyamines, this review underscores the profound significance of these compounds in enabling plants to adapt and thrive in challenging environments.

Plant Promoters and Terminators for High-Precision Bioengineering

High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional levels. Gene transcription is tightly regulated by promoters and terminators. Promoters determine the timing, tissues and cells, and levels of the expression of genes. Terminators mediate transcription termination of genes and affect mRNA levels posttranscriptionally, e.g., the 3'-end processing, stability, translation efficiency, and nuclear to cytoplasmic export of mRNAs. The promoter and terminator combination affects gene expression. In the present article, we review the function and features of plant core promoters, proximal and distal promoters, and terminators, and their effects on and benchmarking strategies for regulating gene expression.

One-Week Scutellar Somatic Embryogenesis in the Monocot Brachypodium distachyon

Plant somatic embryogenesis (SE) is a natural process of vegetative propagation. It can be induced in tissue cultures to investigate developmental transitions, to create transgenic or edited lines, or to multiply valuable crops. We studied the induction of SE in the scutellum of monocots with Brachypodium distachyon as a model system. Towards the in-depth analysis of SE initiation, we determined the earliest stages at which somatic scutellar cells acquired an embryogenic fate, then switched to a morphogenetic mode in a regeneration sequence involving treatments with exogenous hormones: first an auxin (2,4-D) then a cytokinin (kinetin). Our observations indicated that secondary somatic embryos could already develop in the proliferative calli derived from immature zygotic embryo tissues within one week from the start of in vitro culture. Cell states and tissue identity were deduced from detailed histological examination, and in situ hybridization was performed to map the expression of key developmental genes. The fast SE induction method we describe here facilitates the mechanistic study of the processes involved and may significantly shorten the production of transgenic or gene-edited plants.

Targeted mutagenesis of POLYAMINE OXIDASE 5 that negatively regulates mesocotyl elongation enables the generation of direct-seeding rice with improved grain yield

Under conditions of labor or resource scarcity, direct seeding, rather than transplantation, is the preferred mode of rice (Oryza sativa) cultivation. This approach requires varieties that exhibit uniform seedling emergence. Mesocotyl elongation (ME), the main driver of rapid emergence of rice seedlings from soil, is enhanced by darkness and inhibited by light. Plant polyamine oxidases (PAOs) oxidize polyamines (PAs) and release H2O2. Here, we established that OsPAO5 expression in rice seedlings is increased in the presence of light and inhibited by darkness. To determine its role in ME, we created OsPAO5 mutants using CRISPR/Cas9. Compared with the wild type, pao5 mutants had longer mesocotyls, released less H2O2, and synthesized more ethylene. The mutant seedlings emerged at a higher and more uniform rate, indicating their potential for use in direct seeding. Nucleotide polymorphism analysis revealed that an SNP (PAO5-578G/A) located 578 bp upstream of the OsPAO5 start codon alters its expression, and was selected during rice mesocotyl domestication. The PAO5-578G genotype conferring a long mesocotyl mainly exists in wild rice, most Aus accessions, and some Geng (Japonica) accessions. Intriguingly, knocking out OsPAO5 can remarkably increase the grain weight, grain number, and yield potential. In summary, we developed a novel strategy to obtain elite rice with higher emergence vigor and yield potential, which can be conveniently and widely used to breed varieties of direct-seeding rice.

Ribosome profiling reveals the effects of nitrogen application translational regulation of yield recovery after abrupt drought-flood alternation in rice

Abrupt drought-flood alternation is a frequent meteorological disaster during the summer in Southern China. The study of physiological and translation mechanisms of rice yield recovery after abrupt drought-flood alternation has great potential benefits in field production. Our results showed that yield recovery upon nitrogen (N) application after abrupt drought-flood alternation was due to the increase in effective panicle numbers per plant. The N application resulted in the regulation of physiological and biochemical as well as growth development processes, which led to a rapid growth recovery effect after abrupt drought-flood alternation stress in rice. Using ribosome profiling combined with RNA sequencing (RNA-seq) technology, the interactions between transcription and translation for N application after abrupt drought-flood alternation were analyzed. It was found that a small proportion of response genes were shared at the transcriptional and translational levels, that is, 14% of the expressed genes were upregulated and 6.6% downregulated. Further analysis revealed that the translation efficiency (TE) of the genes was influenced by their sequence characteristics, including their GC content, coding sequence length and normalized minimal free energy. Compared with the number of untranslated upstream open reading frames (uORFs), the increased number of translated uORFs promoted the improvement of TE. The TE of the uORFs for N application was lower than the control without N application after abrupt drought-flood alternation. This study characterizes the translational regulatory pattern in response to N application after abrupt drought-flood alternation stress.

Genome-wide identification and characterization of the GDP-L-galactose phosphorylase gene family in bread wheat

BACKGROUND

Ascorbate is a powerful antioxidant in plants and an essential micronutrient for humans. The GDP-L-galactose phosphorylase (GGP) gene encodes the rate-limiting enzyme of the L-galactose pathway-the dominant ascorbate biosynthetic pathway in plants-and is a promising gene candidate for increasing ascorbate in crops. In addition to transcriptional regulation, GGP production is regulated at the translational level through an upstream open reading frame (uORF) in the long 5'-untranslated region (5'UTR). The GGP genes have yet to be identified in bread wheat (Triticum aestivum L.), one of the most important food grain sources for humans.

RESULTS

Bread wheat chromosomal groups 4 and 5 were found to each contain three homoeologous TaGGP genes on the A, B, and D subgenomes (TaGGP2-A/B/D and TaGGP1-A/B/D, respectively) and a highly conserved uORF was present in the long 5'UTR of all six genes. Phylogenetic analyses demonstrated that the TaGGP genes separate into two distinct groups and identified a duplication event of the GGP gene in the ancestor of the Brachypodium/Triticeae lineage. A microsynteny analysis revealed that the TaGGP1 and TaGGP2 subchromosomal regions have no shared synteny suggesting that TaGGP2 may have been duplicated via a transposable element. The two groups of TaGGP genes have distinct expression patterns with the TaGGP1 homoeologs broadly expressed across different tissues and developmental stages and the TaGGP2 homoeologs highly expressed in anthers. Transient transformation of the TaGGP coding sequences in Nicotiana benthamiana leaf tissue increased ascorbate concentrations more than five-fold, confirming their functional role in ascorbate biosynthesis in planta.

CONCLUSIONS

We have identified six TaGGP genes in the bread wheat genome, each with a highly conserved uORF. Phylogenetic and microsynteny analyses highlight that a transposable element may have been responsible for the duplication and specialized expression of GGP2 in anthers in the Brachypodium/Triticeae lineage. Transient transformation of the TaGGP coding sequences in N. benthamiana demonstrated their activity in planta. The six TaGGP genes and uORFs identified in this study provide a valuable genetic resource for increasing ascorbate concentrations in bread wheat.

Increasing Polyamine Contents Enhances the Stress Tolerance via Reinforcement of Antioxidative Properties

The diamine putrescine and the polyamines (PAs), spermidine (Spd) and spermine (Spm), are ubiquitously occurring polycations associated with several important cellular functions, especially antisenescence. Numerous studies have reported increased levels of PA in plant cells under conditions of abiotic and biotic stress such as drought, high salt concentrations, and pathogen attack. However, the physiological mechanism of elevated PA levels in response to abiotic and biotic stresses remains undetermined. Transgenic plants having overexpression of SAMDC complementary DNA and increased levels of putrescine (1.4-fold), Spd (2.3-fold), and Spm (1.8-fold) under unstressed conditions were compared to wild-type (WT) plants in the current study. The most abundant PA in transgenic plants was Spd. Under salt stress conditions, enhancement of endogenous PAs due to overexpression of the SAMDC gene and exogenous treatment with Spd considerably reduces the reactive oxygen species (ROS) accumulation in intra- and extracellular compartments. Conversely, as compared to the WT, PA oxidase transcription rapidly increases in the S16-S-4 transgenic strain subsequent to salt stress. Furthermore, transcription levels of ROS detoxifying enzymes are elevated in transgenic plants as compared to the WT. Our findings with OxyBlot analysis indicate that upregulated amounts of endogenous PAs in transgenic tobacco plants show antioxidative effects for protein homeostasis against stress-induced protein oxidation. These results imply that the increased PAs induce transcription of PA oxidases, which oxidize PAs, which in turn trigger signal antioxidative responses resulting to lower the ROS load. Furthermore, total proteins from leaves with exogenously supplemented Spd and Spm upregulate the chaperone activity. These effects of PAs for antioxidative properties and antiaggregation of proteins contribute towards maintaining the physiological cellular functions against abiotic stresses. It is suggested that these functions of PAs are beneficial for protein homeostasis during abiotic stresses. Taken together, these results indicate that PA molecules function as antisenescence regulators through inducing ROS detoxification, antioxidative properties, and molecular chaperone activity under stress conditions, thereby providing broad-spectrum tolerance against a variety of stresses.

Identification of differentially expressed transcripts at critical developmental stages in sorghum [Sorghum bicolor (L.) Moench] in relation to grain yield heterosis

Evaluation of a set of 10 F₁ hybrids along with their female (27A and 7A) and male parents (C 43, RS 673, RS 627, CB 26, and CB 29) for grain yield and its component traits revealed that grain yield/plant followed by panicle weight, primary branches/panicle, and 100-seed weight exhibited high levels of heterosis. Eight hybrids exhibited 50% or more mid-parent heterosis for grain yield/plant, of which, one hybrid (27A × RS673) recorded heterobeltiosis above 50% (73.61%). Differential display analysis generated about 2995 reproducible transcripts, which were categorized as UPF₁-expressed in any one of the parents and F₁ (10.53-14.76%), BPnF₁-expressed in both parents but not in F₁ (4.56-11.44%), UPnF₁-expressed in either of the parents and not in F₁ (17.95-27.40%), F₁nBP-expressed only in F₁ but not in either of the parents (14.39-20.54%), and UET-expressed in both parents and F₁ (34.52-42.43%). A comparison between high and low heterotic hybrids revealed that the proportions of UPF₁ and F₁nBP transcript patterns were much higher in the former (21.31% and 45.24%) as compared to the latter (16.67% and 32.14%) at the booting and flowering stage, respectively, indicating the role of over-dominance and dominance in the manifestation of grain yield heterosis. Significant positive correlations were observed for differential transcript patterns with mid-parent and better-parent heterosis for the components of grain yield such as primary branches (0.63 and 0.61 at p < 0.01) and 100-seed weight (0.64 and 0.52 at p < 0.01). Cloning and sequence analysis of 16 transcripts that were differentially expressed in hybrids and their parental lines revealed that they code for genes involved in basic cellular processes, cellulose biosynthesis, and assimilate partitioning between various organs and allocation between various pathways, pyrimidine, and polyamine biosynthesis, enhancing ATP production and regulation of plant growth and development.

Polyamines in the life of Arabidopsis: profiling the expression of S-adenosylmethionine decarboxylase (SAMDC) gene family during its life cycle

BACKGROUND

Arabidopsis has 5 paralogs of the S-adenosylmethionine decarboxylase (SAMDC) gene. Neither their specific role in development nor the role of positive/purifying selection in genetic divergence of this gene family is known. While some data are available on organ-specific expression of AtSAMDC1, AtSAMDC2, AtSAMDC3 and AtSAMDC4, not much is known about their promoters including AtSAMDC5, which is believed to be non-functional.

RESULTS

(1) Phylogenetic analysis of the five AtSAMDC genes shows similar divergence pattern for promoters and coding sequences (CDSs), whereas, genetic divergence of 5'UTRs and 3'UTRs was independent of the promoters and CDSs; (2) while AtSAMDC1 and AtSAMDC4 promoters exhibit high activity (constitutive in the former), promoter activities of AtSAMDC2, AtSAMDC3 and AtSAMDC5 are moderate to low in seedlings (depending upon translational or transcriptional fusions), and are localized mainly in the vascular tissues and reproductive organs in mature plants; (3) based on promoter activity, it appears that AtSAMDC5 is both transcriptionally and translationally active, but based on it's coding sequence it seems to produce a non-functional protein; (4) though 5'-UTR based regulation of AtSAMDC expression through upstream open reading frames (uORFs) in the 5'UTR is well known, no such uORFs are present in AtSAMDC4 and AtSAMDC5; (5) the promoter regions of all five AtSAMDC genes contain common stress-responsive elements and hormone-responsive elements; (6) at the organ level, the activity of AtSAMDC enzyme does not correlate with the expression of specific AtSAMDC genes or with the contents of spermidine and spermine.

CONCLUSIONS

Differential roles of positive/purifying selection were observed in genetic divergence of the AtSAMDC gene family. All tissues express one or more AtSAMDC gene with significant redundancy, and concurrently, there is cell/tissue-specificity of gene expression, particularly in mature organs. This study provides valuable information about AtSAMDC promoters, which could be useful in future manipulation of crop plants for nutritive purposes, stress tolerance or bioenergy needs. The AtSAMDC1 core promoter might serve the need of a strong constitutive promoter, and its high expression in the gametophytic cells could be exploited, where strong male/female gametophyte-specific expression is desired; e.g. in transgenic modification of crop varieties.

Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics

BACKGROUND

With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies.

RESULTS

We have adapted a bioinformatics pipeline for discovering bacterial ncRNAs to systematically analyze many fungal genomes. This comparative genomics pipeline integrates information on conserved RNA sequence and structural features with alternative splicing information to reveal fungal RNA motifs that are candidate regulatory domains, or that might have other possible functions. A total of 15 prominent classes of structured ncRNA candidates were identified, including variant HDV self-cleaving ribozyme representatives, atypical snoRNA candidates, and possible structured antisense RNA motifs. Candidate regulatory motifs were also found associated with genes for ribosomal proteins, S-adenosylmethionine decarboxylase (SDC), amidase, and HexA protein involved in Woronin body formation. We experimentally confirm that the variant HDV ribozymes undergo rapid self-cleavage, and we demonstrate that the SDC RNA motif reduces the expression of SAM decarboxylase by translational repression. Furthermore, we provide evidence that several other motifs discovered in this study are likely to be functional ncRNA elements.

CONCLUSIONS

Systematic screening of fungal genomes using a computational discovery pipeline has revealed the existence of a variety of novel structured ncRNAs. Genome contexts and similarities to known ncRNA motifs provide strong evidence for the biological and biochemical functions of some newly found ncRNA motifs. Although initial examinations of several motifs provide evidence for their likely functions, other motifs will require more in-depth analysis to reveal their functions.

Enhancement of cold and salt tolerance of Arabidopsis by transgenic expression of the S-adenosylmethionine decarboxylase gene from Leymus chinensis

Leymus chinensis is an important perennial forage grass natively distributed in the Eurasian Steppe. However, little is known about the molecular mechanism of its adaptation to extreme environmental conditions. Based on L. chinensis cold-treated sequence database, a highly expressed S-adenosylmethionine decarboxylase gene (LcSAMDC1) was isolated from L. chinensis. Gene structure analysis showed that LcSAMDC1 has two introns and three exons as well as three non-overlapping ORFs in its mRNA sequence. One hour of cold exposure caused a significant up-regulation of LcSAMDC1, while abscisic acid (ABA), salt, and osmotic stresses slightly induced its expression. Analysis of gene expression in different tissues showed that LcSAMDC1 was expressed ubiquitously, with higher levels in the young spike and rhizome. Overexpression of the main ORF of LcSAMDC1 in transgenic Arabidopsis promoted increased tolerance to cold and salt stress relative to wild type Arabidopsis. The concentration of polyamines, proline, and chlorophyll was significantly higher in transgenic Arabidopsis, and spermine of polyamines increased more under cold than under salt stress. These results suggest that LcSAMDC1 was induced in response to cold and could influence the production of polyamines involved in stress tolerance of L. chinensis. Moreover, transgenic expression of LcSAMDC1 could be used to improve the abiotic resistance of crops.

Molecular cloning and characterization of S-adenosylmethionine decarboxylase gene in rubber tree (Hevea brasiliensis)

S-Adenosylmethionine decarboxylase (SAMDC) is a key rate-limiting enzyme involved in polyamines biosynthesis, and it plays important roles in plant growth, development and stresses response. However, no SAMDC gene was reported in rubber tree. Here we report characteristics of an SAMDC gene (HbSAMDC1) in rubber tree. HbSAMDC1 contains a 1080 bp open reading frame (ORF) encoding 359 amino acids. Quantitative real-time PCR analyses revealed that HbSAMDC1 exhibited distinct expression patterns in different tissues and was regulated by various stresses, including drought, cold, salt, wounding, and H₂O₂ treatments. HbSAMDC1 5' untranslated region (UTR) contains a highly conserved overlapping tiny and small upstream ORFs (uORFs), encoding 2 and 52 amino acid residues, respectively. No introns were located in the main ORF of HbSAMDC1, whereas two introns were found in the 5' UTR. In transgenic tobaccos, the highly conserved small uORF of HbSAMDC1 is found to be responsible for translational repression of downstream β-glucuronidase reporter. To our knowledge, this is the first report on molecular cloning, expression profiles, and 5' UTR characteristics of HbSAMDC1. These results lay solid foundation for further elucidating HbSAMDC1 function in rubber tree.

Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrients Deficiency

Deficiency of necessary macronutrients, i.e., Potassium (K), Magnesium (Mg), Nitrogen (N), Phosphorus (P), and Sulfate (S) in the soil leads to a reduction in plant growth and yield, which is a result of changes in expression level of various genes. This study was performed to identify the differentially expressed genes and its associated metabolic pathways occurred in soil grown wheat root samples excavated from the control and treated fields. To identify the difference in gene expression levels due to deficiency of the said nutrients, a transcriptomic, meta-analysis was performed on array expression profile data. A set of 435 statistically significant probes encoding 398 Nutrient Deficiency Response Genes (NRGs) responding at-least one nutrients deficiency (ND) were identified. Out of them 55 NRGs were found to response to minimum two ND. Singular Enrichment Analysis (SEA) predicts ontological based classifications and functional analysis of NRGs in different cellular/molecular pathways involved in root development and growth. Functional annotation and reaction mechanism of differentially expressed genes, proteins/enzymes in the different metabolic pathway through MapMan analysis were explored. Further the meta-analysis was performed to revels the active involvement each NRGs in distinct tissues and their comparative potential expression analysis in different stress conditions. The study results in exploring the role of major acting candidate genes such as Non-specific serine/threonine protein kinase, Xyloglucan endotransglucosylase/hydrolase, Peroxides, Glycerophosphoryl diester phosphodiesterase, S-adenosylmethionine decarboxylase proenzyme, Dehydrin family proteins, Transcription factors, Membrane Proteins, Metal binding proteins, Photosystem proteins, Transporter and Transferase associated in different metabolic pathways. Finally, the differences of transcriptional responses in the soil-grown root of T. aestivum cv. and in-vitro grown model plants under nutrients deficiency were summarized.

The Emerging World of Small ORFs

Small open reading frames (sORFs) are an often overlooked feature of plant genomes. Initially found in plant viral RNAs and considered an interesting curiosity, an increasing number of these sORFs have been shown to encode functional peptides or play a regulatory role. The recent discovery that many of these sORFs initiate with start codons other than AUG, together with the identification of functional small peptides encoded in supposedly noncoding primary miRNA transcripts (pri-miRs), has drastically increased the number of potentially functional sORFs within the genome. Here we review how advances in technology, notably ribosome profiling (RP) assays, are complementing bioinformatics and proteogenomic methods to provide powerful ways to identify these elusive features of plant genomes, and highlight the regulatory roles sORFs can play.

Characterization of 5'UTR of rice ClpB-C/Hsp100 gene: evidence of its involvement in post-transcriptional regulation

Rice (Oryza sativa) ClpB-C (OsClpB-C) protein is expressed upon heat stress in vegetative tissues and constitutively in seeds. We produced stably transformed Arabidopsis plants carrying β-glucuronidase (Gus) reporter gene downstream to 1-kb OsClpB-C promoter (1kbPro plants). In the 1kbPro plants, expression of Gus transcript and protein followed the expression pattern of OsClpB-C gene in rice plants, i.e., heat induced in vegetative tissues and constitutive in seeds. Next, we produced transgenic Arabidopsis plants containing Gus downstream to 862-bp fragment of OsClpB-C promoter [lacking 138 nucleotides from 3' end of the 5'untranslated region (5'UTR); ∆UTR plants). In ∆UTR plants, Gus transcript was expressed in heat-inducible manner, but strikingly, Gus protein levels were negligible after heat treatment. However, Gus protein was expressed in ∆UTR seedlings at levels comparable to 1kbPro seedlings when recovery treatment of 22 °C/2 h was given post heat stress (38 °C/15 min). This suggests that 5'UTR of OsClpB-C gene is involved in its post-transcriptional regulation and is an obligate requirement for protein expression during persistent heat stress. Furthermore, the Gus transcript levels were higher in the polysomal RNA fraction in heat-stressed seedlings of 1kbPro plants as compared to ∆UTR plants, indicating that 5'UTR aids in assembly of ribosomes onto the Gus transcript during heat stress. Unlike the case of seedlings, Gus protein was formed constitutively in ∆UTR seeds at levels comparable to 1kbPro seeds. Hence, the function of 5'UTR of OsClpB-C is dispensable for expression in seeds.

Down-Regulating CsHT1, a Cucumber Pollen-Specific Hexose Transporter, Inhibits Pollen Germination, Tube Growth, and Seed Development

Efficient sugar transport is needed to support the high metabolic activity of pollen tubes as they grow through the pistil. Failure of transport results in male sterility. Although sucrose transporters have been shown to play a role in pollen tube development, the role of hexoses and hexose transporters is not as well established. The pollen of some species can grow in vitro on hexose as well as on sucrose, but knockouts of individual hexose transporters have not been shown to impair fertilization, possibly due to transporter redundancy. Here, the functions of CsHT1, a hexose transporter from cucumber (Cucumis sativus), are studied using a combination of heterologous expression in yeast (Saccharomyces cerevisiae), histochemical and immunohistochemical localization, and reverse genetics. The results indicate that CsHT1 is a plasma membrane-localized hexose transporter with high affinity for glucose, exclusively transcribed in pollen development and expressed both at the levels of transcription and translation during pollen grain germination and pollen tube growth. Overexpression of CsHT1 in cucumber pollen results in a higher pollen germination ratio and longer pollen tube growth than wild-type pollen in glucose- or galactose-containing medium. By contrast, antisense suppression of CsHT1 leads to inhibition of pollen germination and pollen tube elongation in the same medium and results in a decrease of seed number per fruit and seed size when antisense transgenic pollen is used to fertilize wild-type or transgenic cucumber plants. The important role of CsHT1 in pollen germination, pollen tube growth, and seed development is discussed.

The transcription factor AREB1 regulates primary metabolic pathways in tomato fruits

Tomato fruit development is regulated both by the action of plant hormones and by tight genetic control. Recent studies suggest that abscisic acid (ABA) signalling may affect different aspects of fruit maturation. Previously, it was shown that SlAREB1, an ABA-regulated transcription factor involved in stress-induced responses, is expressed in seeds and in fruit tissues in tomato. Here, the role of SlAREB1 in regulating the expression of genes relevant for primary metabolic pathways and affecting the metabolic profile of the fruit was investigated using transgenic tomato lines. Metabolite profiling using gas chromatography-time of flight mass spectrometry (GC-TOF-MS) and non-targeted liquid chromatography-mass spectrometry (LC-MS) was performed on pericarp tissue from fruits harvested at three stages of fruit development. Principal component analysis of the data could distinguish the metabolite profiles of non-transgenic fruits from those that overexpress and down-regulate SlAREB1. Overexpression of SlAREB1 resulted in increased content of organic acids, hexoses, hexose-phosphates, and amino acids in immature green, mature green, and red ripe fruits, and these modifications correlated with the up-regulation of enzyme-encoding genes involved in primary carbohydrate and amino acid metabolism. A non-targeted LC-MS analysis indicated that the composition of secondary metabolites is also affected in transgenic lines. In addition, gene expression data revealed that some genes associated with fruit ripening are also up-regulated in SlAREB1-overexpressing lines compared with wild-type and antisense lines. Taken together, the results suggest that SlAREB1 participates in the regulation of the metabolic programming that takes place during fruit ripening and that may explain part of the role of ABA in fruit development in tomato.

Polyamines in response to abiotic stress tolerance through transgenic approaches

The distribution, growth, development and productivity of crop plants are greatly affected by various abiotic stresses. Worldwide, sustainable crop productivity is facing major challenges caused by abiotic stresses by reducing the potential yield in crop plants by as much as 70%. Plants can generally adapt to one or more environmental stresses to some extent. Physiological and molecular studies at transcriptional, translational, and transgenic plant levels have shown the pronounced involvement of naturally occurring plant polyamines (PAs), in controlling, conferring, and modulating abiotic stress tolerance in plants. PAs are small, low molecular weight, non-protein polycations at physiological pH, that are present in all living organisms, and that have strong binding capacity to negatively charged DNA, RNA, and different protein molecules. They play an important role in plant growth and development by controlling the cell cycle, acting as cell signaling molecules in modulating plant tolerance to a variety of abiotic stresses. The commonly known PAs, putrescine, spermidine, and spermine tend to accumulate together accompanied by an increase in the activities of their biosynthetic enzymes under a range of environmental stresses. PAs help plants to combat stresses either directly or by mediating a signal transduction pathway, as shown by molecular cloning and expression studies of PA biosynthesis-related genes, knowledge of the functions of PAs, as demonstrated by developmental studies, and through the analysis of transgenic plants carrying PA genes. This review highlights how PAs in higher plants act during environmental stress and how transgenic strategies have improved our understanding of the molecular mechanisms at play.

Deciphering the role of various cis-acting regulatory elements in controlling SamDC gene expression in rice

Lately we have published on the characterization of the upstream of SamDC gene from rice and investigated the involvement of various cis-elements present in the promoter region in its transcriptional regulation. Analysis of SamDC expression showed that it was inducible by abiotic stresses like salinity, drought, and cold as well as by light and ABA treatment. Furthermore, DNA protein interaction studies have identified transacting actors responsible for its expression after abiotic stresses or light inducibility. Here we have further discussed on the possible role of these cis-elements in modulating the transcriptional network and comment on their function in relation to polyamine biosynthesis during periods of abiotic stress in rice.

Stress and polyamine metabolism in fungi

Fungi, as well as the rest of living organisms must deal with environmental challenges such as stressful stimuli. Fungi are excellent models to study the general mechanisms of the response to stress, because of their simple, but conserved, signal-transduction and metabolic pathways that are often equivalent to those present in other eukaryotic systems. A factor that has been demonstrated to be involved in these responses is polyamine metabolism, essentially of the three most common polyamines: putrescine, spermidine and spermine. The gathered evidences on this subject suggest that polyamines are able to control cellular signal transduction, as well as to modulate protein-protein interactions. In the present review, we will address the recent advances on the study of fungal metabolism of polyamines, ranging from mutant characterization to potential mechanism of action during different kinds of stress in selected fungal models.

Polyamines and abiotic stress in plants: a complex relationship

The physiological relationship between abiotic stress in plants and polyamines was reported more than 40 years ago. Ever since there has been a debate as to whether increased polyamines protect plants against abiotic stress (e.g., due to their ability to deal with oxidative radicals) or cause damage to them (perhaps due to hydrogen peroxide produced by their catabolism). The observation that cellular polyamines are typically elevated in plants under both short-term as well as long-term abiotic stress conditions is consistent with the possibility of their dual effects, i.e., being protectors from as well as perpetrators of stress damage to the cells. The observed increase in tolerance of plants to abiotic stress when their cellular contents are elevated by either exogenous treatment with polyamines or through genetic engineering with genes encoding polyamine biosynthetic enzymes is indicative of a protective role for them. However, through their catabolic production of hydrogen peroxide and acrolein, both strong oxidizers, they can potentially be the cause of cellular harm during stress. In fact, somewhat enigmatic but strong positive relationship between abiotic stress and foliar polyamines has been proposed as a potential biochemical marker of persistent environmental stress in forest trees in which phenotypic symptoms of stress are not yet visible. Such markers may help forewarn forest managers to undertake amelioration strategies before the appearance of visual symptoms of stress and damage at which stage it is often too late for implementing strategies for stress remediation and reversal of damage. This review provides a comprehensive and critical evaluation of the published literature on interactions between abiotic stress and polyamines in plants, and examines the experimental strategies used to understand the functional significance of this relationship with the aim of improving plant productivity, especially under conditions of abiotic stress.

Arabidopsis ribosomal proteins control developmental programs through translational regulation of auxin response factors

Upstream ORFs are elements found in the 5'-leader sequences of specific mRNAs that modulate the translation of downstream ORFs encoding major gene products. In Arabidopsis, the translational control of auxin response factors (ARFs) by upstream ORFs has been proposed as a regulatory mechanism required to respond properly to complex auxin-signaling inputs. In this study, we identify and characterize the aberrant auxin responses in specific ribosomal protein mutants in which multiple ARF transcription factors are simultaneously repressed at the translational level. This characteristic lends itself to the use of these mutants as genetic tools to bypass the genetic redundancy among members of the ARF family in Arabidopsis. Using this approach, we were able to assign unique functions for ARF2, ARF3, and ARF6 in plant development.

Regulation of the fruit-specific PEP carboxylase SlPPC2 promoter at early stages of tomato fruit development

The SlPPC2 phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) gene from tomato (Solanum lycopersicum) is differentially and specifically expressed in expanding tissues of developing tomato fruit. We recently showed that a 1966 bp DNA fragment located upstream of the ATG codon of the SlPPC2 gene (GenBank AJ313434) confers appropriate fruit-specificity in transgenic tomato. In this study, we further investigated the regulation of the SlPPC2 promoter gene by analysing the SlPPC2 cis-regulating region fused to either the firefly luciferase (LUC) or the β-glucuronidase (GUS) reporter gene, using stable genetic transformation and biolistic transient expression assays in the fruit. Biolistic analyses of 5' SlPPC2 promoter deletions fused to LUC in fruits at the 8(th) day after anthesis revealed that positive regulatory regions are mostly located in the distal region of the promoter. In addition, a 5' UTR leader intron present in the 1966 bp fragment contributes to the proper temporal regulation of LUC activity during fruit development. Interestingly, the SlPPC2 promoter responds to hormones (ethylene) and metabolites (sugars) regulating fruit growth and metabolism. When tested by transient expression assays, the chimeric promoter:LUC fusion constructs allowed gene expression in both fruit and leaf, suggesting that integration into the chromatin is required for fruit-specificity. These results clearly demonstrate that SlPPC2 gene is under tight transcriptional regulation in the developing fruit and that its promoter can be employed to drive transgene expression specifically during the cell expansion stage of tomato fruit. Taken together, the SlPPC2 promoter offers great potential as a candidate for driving transgene expression specifically in developing tomato fruit from various tomato cultivars.

Genomic organization of plant aminopropyl transferases

Aminopropyl transferases like spermidine synthase (SPDS; EC 2.5.1.16), spermine synthase and thermospermine synthase (SPMS, tSPMS; EC 2.5.1.22) belong to a class of widely distributed enzymes that use decarboxylated S-adenosylmethionine as an aminopropyl donor and putrescine or spermidine as an amino acceptor to form in that order spermidine, spermine or thermospermine. We describe the analysis of plant genomic sequences encoding SPDS, SPMS, tSPMS and PMT (putrescine N-methyltransferase; EC 2.1.1.53). Genome organization (including exon size, gain and loss, as well as intron number, size, loss, retention, placement and phase, and the presence of transposons) of plant aminopropyl transferase genes were compared between the genomic sequences of SPDS, SPMS and tSPMS from Zea mays, Oryza sativa, Malus x domestica, Populus trichocarpa, Arabidopsis thaliana and Physcomitrella patens. In addition, the genomic organization of plant PMT genes, proposed to be derived from SPDS during the evolution of alkaloid metabolism, is illustrated. Herein, a particular conservation and arrangement of exon and intron sequences between plant SPDS, SPMS and PMT genes that clearly differs with that of ACL5 genes, is shown. The possible acquisition of the plant SPMS exon II and, in particular exon XI in the monocot SPMS genes, is a remarkable feature that allows their differentiation from SPDS genes. In accordance with our in silico analysis, functional complementation experiments of the maize ZmSPMS1 enzyme (previously considered to be SPDS) in yeast demonstrated its spermine synthase activity. Another significant aspect is the conservation of intron sequences among SPDS and PMT paralogs. In addition the existence of microsynteny among some SPDS paralogs, especially in P. trichocarpa and A. thaliana, supports duplication events of plant SPDS genes. Based in our analysis, we hypothesize that SPMS genes appeared with the divergence of vascular plants by a processes of gene duplication and the acquisition of unique exons of as-yet unknown origin.

The upstream open reading frame of the Arabidopsis AtMHX gene has a strong impact on transcript accumulation through the nonsense-mediated mRNA decay pathway

Approximately 20% of plant genes possess upstream open-reading frames (uORFs). The effect of uORFs on gene expression has mainly been studied at the translational level. Very little is known about the impact of plant uORFs on transcript content through the nonsense-mediated mRNA decay (NMD) pathway, which degrades transcripts bearing premature termination codons (PTCs). Here we examine the impact of the uORF of the Arabidopsis AtMHX gene on transcript accumulation. The suggestion that this uORF exposes transcripts containing it to NMD is supported by (i) the increase in transcript levels upon eliminating the uORF from constructs containing it, (ii) experiments with a modified uORF-peptide, which excluded peptide-specific degradation mechanisms, (iii) the increase in levels of the native AtMHX transcript upon treatment with cycloheximide, which inhibits translation and blocks NMD, and (iv) the sensitivity of transcripts containing the uORF of AtMHX to the presence of introns. We also showed that introns can increase NMD efficiency not only in transcripts having relatively short 3' untranslated regions (UTRs), but also in uORF-containing transcripts. AtMHX transcript levels were almost unaltered in mutants of the NMD factors UPF3 and UPF1. Possible reasons, including the existence of a NMD-compensatory mechanism, are discussed. Interestingly, the levels of UPF3 transcript were higher in upf1 mutants, suggesting a compensatory mechanism that links weak function of the NMD machinery to increased expression of UPF3. Our findings highlight that uORFs, which are abundant in plants, can not only inhibit translation but also strongly affect transcript accumulation.

Functional analysis of 5' untranslated region of a TIR-NBS-encoding gene from triploid white poplar

Genome-wide analyses have identified a set of TIR-NBS-encoding genes in plants. However, the molecular mechanism underlying the expression of these genes is still unknown. In this study, we presented a TIR-NBS-encoding gene, PtDrl02, that displayed a low level of tissue-specific expression in a triploid white poplar [(Populus tomentosa x P. bolleana) x P. tomentosa], and analyzed the effects of the 5' untranslated region (UTR) on gene expression. The 5' UTR sequence repressed the reporter activity of beta-glucuronidase (GUS) gene under PtDrl02 promoter by 113.5-fold with a staining ratio of 2.97% in the transgenic tobacco plants. Quantitative RT-PCR assays revealed that the 5' UTR sequence decreased the transcript level of the GUS reporter gene by 13.3-fold, implying a regulatory role of 5' UTR in transcription and/or mRNA destabilization. The comparison of GUS activity with the transcript abundance indicated that the 5' UTR sequence decreased the translation efficiency of target gene by 88.3%. Additionally, the analysis of the transgenic P-985/UTRDelta/GUS plants showed that both the exon1 sequence and the leading intron within the 5' UTR region were responsible for the regulation of gene expression. Our results suggested a negative effect of the 5' UTR of PtDrl02 gene on gene expression.

Post-transcriptional regulation of gene expression in plants during abiotic stress

Land plants are anchored in one place for most of their life cycle and therefore must constantly adapt their growth and metabolism to abiotic stresses such as light intensity, temperature and the availability of water and essential minerals. Thus, plants’ subsistence depends on their ability to regulate rapidly gene expression in order to adapt their physiology to their environment. Recent studies indicate that post-transcriptional regulations of gene expression play an important role in how plants respond to abiotic stresses. We will review the different mechanisms of post-transcriptional regulation of nuclear genes expression including messenger RNA (mRNA) processing, stability, localization and protein translation, and discuss their relative importance for plant adaptation to abiotic stress.

Sucrose control of translation mediated by an upstream open reading frame-encoded peptide

Regulation of gene expression through translational control is common in many organisms. The Arabidopsis (Arabidopsis thaliana) transcription factor bZIP11 is translational repressed in response to sucrose (Suc), resulting in Suc-regulated changes in amino acid metabolism. The 5' leader of the bZIP11 mRNA harbors several upstream open reading frames (uORFs), of which the second uORF is well conserved among bZIP11 homologous genes. The uORF2 element encodes a Suc control peptide (SC-peptide) of 28 residues that is sufficient for imposing Suc-induced repression of translation (SIRT) on a heterologous mRNA. Detailed analysis of the SC-peptide suggests that it functions as an attenuator peptide. Results suggest that the SC-peptide inhibits bZIP11 translation in response to high Suc levels by stalling the ribosome on the mRNA. The conserved noncanonical AUG contexts of bZIP11 uORFs allow inefficient translational initiation of the uORF, resulting in translation initiation of the scanning ribosome at the AUG codon of the bZIP11 main ORF. The results presented show that Suc-dependent signaling mediates differential translation of mRNAs containing SC-peptides encoding uORFs.

Identification and expression of a new delta-12 fatty acid desaturase (FAD2-4) gene in upland cotton and its functional expression in yeast and Arabidopsis thaliana plants

A cotton (Gossypium hirsutum L.) genomic clone encompassing a 17.9-kb DNA fragment was found to contain a delta-12 fatty acid desaturase gene (designated FAD2-4). The FAD2-4 open reading frame has 1,155bp and is uninterrupted, encoding a conceptual FAD2-4 polypeptide of 384 amino acids that has 98% identity with the cotton FAD2-3 polypeptide. The FAD2-4 gene has a single intron of 2,780 bp in its 5'-untranslated region (5'-UTR). The 3'-flanking regions and 5'-UTR introns in the FAD2-4 and FAD2-3 genes are quite different, indicating that the genes might be paralogs in the cotton genome. Reverse transcriptase (RT)-PCR analysis indicated that the FAD2-4 and FAD2-3 genes were expressed in all tissues examined, including seeds, seedling tissues, young and mature leaves, roots, stems, developing flower buds, and ovule fibers. These constitutive patterns of expression were notably different from that of the FAD2-1 gene, which was restricted to seeds and developing flower buds, or to the expression of a newly-identified FAD2-2 gene isoform, which was barely detectable in roots, hypocotyls, stems, and fibers, but was expressed in all other tissues. The FAD2-4 coding region was expressed in yeast and shown to encode a functional delta-12 desaturase, converting oleic acid (C18:1) to linoleic acid (C18:2) in recombinant yeast cells. In addition, both the FAD2-4 and the FAD2-3 genes were transferred into the Arabidopsis thaliana fad2-1 mutant background where they effectively restored wild type fatty acid composition and growth characteristics. Finally, the cotton FAD2-4 green fluorescent protein (GFP) fusion polypeptide appeared to be localized in the endomembrane system of transgenic Arabidopsis plants in the complemented fad2-1 mutant background, supporting a functional ER location for the cotton FAD2-4 polypeptide in this heterologous plant system. Thus, a new functional member of the FAD2 gene family in cotton has been characterized, indicating a complex regulation of membrane lipid desaturation in this important fiber/oilseed crop.

Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics

Drought is the major environmental threat to agricultural production and distribution worldwide. Adaptation by plants to dehydration stress is a complex biological process that involves global changes in gene expression and metabolite composition. Here, using one type of functional genomics analysis, metabolomics, we characterized the metabolic phenotypes of Arabidopsis wild-type and a knockout mutant of the NCED3 gene (nc3-2) under dehydration stress. NCED3 plays a role in the dehydration-inducible biosynthesis of abscisic acid (ABA), a phytohormone that is important in the dehydration-stress response in higher plants. Metabolite profiling performed using two types of mass spectrometry (MS) systems, gas chromatography/time-of-flight MS (GC/TOF-MS) and capillary electrophoresis MS (CE-MS), revealed that accumulation of amino acids depended on ABA production, but the level of the oligosaccharide raffinose was regulated by ABA independently under dehydration stress. Metabolic network analysis showed that global metabolite-metabolite correlations occurred in dehydration-increased amino acids in wild-type, and strong correlations with raffinose were reconstructed in nc3-2. An integrated metabolome and transcriptome analysis revealed ABA-dependent transcriptional regulation of the biosynthesis of the branched-chain amino acids, saccharopine, proline and polyamine. This metabolomics analysis revealed new molecular mechanisms of dynamic metabolic networks in response to dehydration stress.

Putrescine is involved in Arabidopsis freezing tolerance and cold acclimation by regulating abscisic acid levels in response to low temperature

The levels of endogenous polyamines have been shown to increase in plant cells challenged with low temperature; however, the functions of polyamines in the regulation of cold stress responses are unknown. Here, we show that the accumulation of putrescine under cold stress is essential for proper cold acclimation and survival at freezing temperatures because Arabidopsis (Arabidopsis thaliana) mutants defective in putrescine biosynthesis (adc1, adc2) display reduced freezing tolerance compared to wild-type plants. Genes ADC1 and ADC2 show different transcriptional profiles upon cold treatment; however, they show similar and redundant contributions to cold responses in terms of putrescine accumulation kinetics and freezing sensitivity. Our data also demonstrate that detrimental consequences of putrescine depletion during cold stress are due, at least in part, to alterations in the levels of abscisic acid (ABA). Reduced expression of NCED3, a key gene involved in ABA biosynthesis, and down-regulation of ABA-regulated genes are detected in both adc1 and adc2 mutant plants under cold stress. Complementation analysis of adc mutants with ABA and reciprocal complementation tests of the aba2-3 mutant with putrescine support the conclusion that putrescine controls the levels of ABA in response to low temperature by modulating ABA biosynthesis and gene expression.

Conserved upstream open reading frames in higher plants

BACKGROUND

Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants.

RESULTS

We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs.

CONCLUSION

This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

Excretion of polyamines in alfalfa and tobacco suspension-cultured cells and its possible role in maintenance of intracellular polyamine contents

Changes in polyamines (PAs) in cells and cultivation media of alfalfa (Medicago sativa L.) and tobacco bright yellow 2 (BY-2) (Nicotiana tabacum L.) cell suspension cultures were studied over their growth cycles. The total content of PAs (both free and conjugated forms) was nearly 10 times higher in alfalfa, with high level of free putrescine (Put) (in exponential growth phase it represented about 65-73% of the intracellular Put pool). In contrast, the high content of soluble Put conjugates was found in tobacco cells (in exponential phase about 70% of the intracellular Put). Marked differences occurred in the amount of PAs excreted into the cultivation medium: alfalfa cells excreted at the first day after inoculation 2117.0, 230.5, 29.0 and 88.0 nmol g(-1) of cell fresh weight (FW) of Put, spermidine (Spd), spermine (Spm) and cadaverine (Cad), respectively, while at the same time tobacco cells excreted only small amount of Put and Spd (12.7 and 2.4 nmol g(-1) FW, respectively). On day 1 the amounts of Put, Spd, Spm and Cad excreted by alfalfa cells represented 21, 38, 12 and 15% of the total pool (intra- plus extra-cellular contents) of Put, Spd, Spm and Cad, respectively. In the course of lag-phase and the beginning of exponential phase the relative contents of extracellular PAs continually decreased (with the exception of Cad). On day 10, the extracellular Put, Spd, Spm and Cad still represented 11.3, 10.9, 2.1 and 27% of their total pools. The extracellular PAs in tobacco cells represented from day 3 only 0.1% from their total pools. The possible role of PA excretion into the cultivation medium in maintenance of intracellular PA contents in the cells of the two cell culture systems, differing markedly in growth rate and PA metabolism is discussed.

Molecular cloning and characterization of phosphorus starvation responsive genes in common bean (Phaseolus vulgaris L.)

Common bean (Phaseolus vulgaris L.) is one of the most important food legumes in the world and its production is limited by low phosphate (Pi) availability in many arable soils. To gain better insight into the molecular mechanisms by which common bean adapts to low Pi availability, we generated a suppression subtractive cDNA library to identify genes involved in P starvation responses. Over 240 putative Pi starvation-responsive genes were identified. The identified clones were sequenced and BLASTx/BLASTn analysis revealed an array of 82 genes showing a high degree of sequence homology to known and unknown proteins in the database. Transcript abundance of seven genes representing different functional categories was examined by Northern blot analysis. Six genes were strongly induced/enhanced under Pi deficiency confirming the results of SSH. Full length cDNAs for three genes, representing PvIDS4-like, PvPS2, and PvPT1 were cloned and characterized. The open reading frame (ORF) of PvIDS4-like encodes a 281-amino acid protein, containing a SPX domain. The ORF of PvPS2 gene encodes a 271-amino acid protein coding for a putative phosphatase. The PvPT1 encodes a 531-amino acid protein exhibiting high homology with high affinity Pi transporters. Expression patterns of these three genes in relation to Pi availability were evaluated with two contrasting genotypes (P-inefficient Dor364 and P-efficient G19833). Both Northern and RT-PCR results showed enhanced accumulation of phosphate transporters and phosphatases in P-efficient genotype, implying that in addition to modified root morphology and architecture, increased P transport and phosphatases activity might contribute to efficient Pi acquisition and translocation in G19833 common bean genotype under limited Pi conditions.

Cloning, functional identification and structural modelling of Vitis vinifera S-adenosylmethionine decarboxylase

In this paper we report the cloning and full sequencing of S-adenosylmethionine decarboxylase (SAMDC, EC 4.1.1.50) cDNA from Vitis vinifera L. (VV) leaves, an enzyme belonging to the polyamine biosynthetic pathway, which appears to play an important role in the regulation of plant growth and development. The presence of two overlapping ORFs (tiny ORF and small ORF) upstream of the main ORF is reported in the Vitis cDNA. When the Vitis SAMDC cDNA was expressed in yeast without the two upstream ORFs, the resulting activity was about 50 times higher than the activity obtained with the full cDNA. These results demonstrated the strong regulatory activity of the tiny and small ORFs. RT-PCR expression analysis showed evidence of a similar mRNA level in all the tissues tested, with the exception of the petioles. The VV SAMDC was also modelled using its homologues from Solanum tuberosum and Homo sapiens as template. The present work confirmed, for the first time in a woody plant of worldwide economic interest such as grapevine, the presence of a regulatory mechanism of SAMDC, enzyme that has a well-established importance in the modulation of plant growth and development.

Overlapping expression patterns among the genes encodingArabidopsischromosomal high mobility group (HMG) proteins

High mobility group (HMG) proteins are usually considered ubiquitous components of the eukaryotic chromatin. Using HMG gene promoter-GUS reporter gene fusions we have examined the expression of the reporter gene in transgenic Arabidopsis plants. These experiments have revealed that the different HMGA and HMGB promoters display overlapping patterns of activity, but they also show tissue- and developmental stage-specific differences. Moreover, leader introns that are present in some of the HMGB genes can modulate reporter gene expression. The differential HMG gene expression supports the view that the various HMG proteins serve partially different architectural functions in plant chromatin.

Polyamine metabolism and biosynthetic gene expression in Arabidopsis thaliana under salt stress

In the present study we analysed polyamine metabolism in Arabidopsis thaliana (ecotype Columbia) rosette leaves collected at vegetative and reproductive stages from plants germinated and grown under increasing salt stress (0-75 mM NaCl) conditions. The expression level of the different isoforms of polyamine biosynthetic enzymes was analysed by reverse transcriptase-polymerase chain reaction (RT-PCR) and the polyamine biosynthetic enzyme activities were determined both in supernatant and pellet fractions. Free and perchloric acid (PCA)-conjugated (soluble and insoluble) polyamines, were measured. At vegetative stage, plants were able to adapt up to 50 mM NaCl, showing a significant growth inhibition only at 75 mM NaCl. At this growth stage and NaCl concentration there was an up-regulation of spermine biosynthesis. At reproductive stage, plants were able to flower up to 50 mM NaCl, even if with a delay of 7 days. On the contrary, at 75 mM NaCl two different phenotypes were isolated: 75/01 (salt sensitive) and 75/02 (salt tolerant). The sensitive plants (75/01) showed a severely stressed phenotype, compared to the tolerant ones (75/02), and the polyamine metabolism was up-regulated, with the increase of free putrescine and spermine.

Untranslated regions of FbRbcS1 mRNA mediate bundle sheath cell-specific gene expression in leaves of a C4 plant

C4 photosynthesis typically requires two specialized leaf cell types, bundle sheath (bs) and mesophyll (mp), which provide the foundation for this highly efficient carbon assimilation pathway. In leaves of Flaveria bidentis, a dicotyledonous C4 plant, ribulose 1,5-bisphosphate carboxylase (rubisco) accumulates only in bs cells surrounding the vascular centers and not in mp cells. This is in contrast to the more common C3 plants, which accumulate rubisco in all photosynthetic cells. Many previous studies have focused on transcriptional control of C4 cell type-specificity; however, post-transcriptional regulation has also been implicated in the bs-specific expression of genes encoding the rubisco subunits. In this current study, a biolistic leaf transformation assay has provided direct evidence that the 5'- and 3'-untranslated regions (UTRs) of F. bidentis FbRbcS1 mRNA (from a nuclear gene encoding the rubisco small subunit), in themselves, confer strong bs cell-specific expression to gfpA reporter gene transcripts when transcribed from a constitutive CaMV promoter. In transformed leaf regions, strong bs cell-specific GFP expression was accompanied by corresponding bs cell-specific accumulation of the constitutively transcribed FbRbcS1 5'-UTR-gfpA-3'-UTR mRNAs. Control constructs lacking any RbcS mRNA sequences were expressed in all leaf cell types. These findings demonstrate that characteristic cell type-specific FbRbcS1 expression patterns in C4 leaves can be established entirely by sequences contained within the transcribed UTRs of FbRbcS1 mRNAs. We conclude that selective transcript stabilization (in bs cells) or degradation (in mp cells) plays a key role in determining bs cell-specific localization of the rubisco enzyme.

A Dual Upstream Open Reading Frame-based Autoregulatory Circuit Controlling Polyamine-responsive Translation

A novel form of translational regulation is described for the key polyamine biosynthetic enzyme S-adenosylmethionine decarboxylase (AdoMetDC). Plant AdoMetDC mRNA 5' leaders contain two highly conserved overlapping upstream open reading frames (uORFs): the 5' tiny and 3' small uORFs. We demonstrate that the small uORF-encoded peptide is responsible for constitutively repressing downstream translation of the AdoMetDC proenzyme ORF in the absence of increased polyamine levels. This first example of a sequence-dependent uORF to be described in plants is also functional in Saccharomyces cerevisiae. The tiny uORF is required for normal polyamine-responsive AdoMetDC mRNA translation, and we propose that this is achieved by control of ribosomal recognition of the occluded small uORF, either by ribosomal leaky scanning or by programmed -1 frameshifting. In vitro expression demonstrated that both the tiny and the small uORFs are translated. This tiny/small uORF configuration is highly conserved from moss to Arabidopsis thaliana, and a more diverged tiny/small uORF arrangement is found in the AdoMetDC mRNA 5' leader of the single-celled green alga Chlamydomonas reinhardtii, indicating an ancient origin for the uORFs.