Gene expression programs during Brassica oleracea seed maturation, osmopriming, and germination are indicators of progression of the germination process and the stress tolerance level

Dehydrin metabolism is altered during seed osmopriming and subsequent germination under chilling and desiccation in Spinacia oleracea L. cv. Bloomsdale: possible role in stress tolerance

Osmopriming improves seed germination performance as well as stress tolerance. To understand the biochemistry of osmopriming-induced seed stress tolerance, we investigated dehydrin (DHN) accumulation patterns at protein and transcript level (determined by immunoblotting and qPCR) during priming, and subsequent germination under optimal and stress conditions (i.e. chilling and desiccation) in spinach (Spinacia oleracea L. cv. Bloomsdale) seeds. Our data indicate enhanced germination performance of primed seeds is accompanied by increased accumulation of three dehydrin-like proteins (DLPs): 30, 26, and 19-kD. Moreover, 30, 26 and 19-kD DLPs that first only transiently accumulated during priming re-accumulated in response to stresses, suggesting an evidence for 'cross-tolerance', which is initially induced by priming and later recruited during post-priming germination under stresses. Study with CAP85, a spinach DHN, corroborates above observations at the gene-expression and protein accumulation level. Additionally, our results suggest that during seed germination and seedling establishment, CAP85 expression may be regulated by the interplay of two factors: seedling development and stress responses. In conclusion, our data suggest that 30, 26, and 19-kD dehydrin-like proteins and CAP85 may be used as potential biochemical/molecular markers for priming-induced stress tolerance in 'Bloomsdale' spinach.

Seed germination and vigor

Germination vigor is driven by the ability of the plant embryo, embedded within the seed, to resume its metabolic activity in a coordinated and sequential manner. Studies using "-omics" approaches support the finding that a main contributor of seed germination success is the quality of the messenger RNAs stored during embryo maturation on the mother plant. In addition, proteostasis and DNA integrity play a major role in the germination phenotype. Because of its pivotal role in cell metabolism and its close relationships with hormone signaling pathways regulating seed germination, the sulfur amino acid metabolism pathway represents a key biochemical determinant of the commitment of the seed to initiate its development toward germination. This review highlights that germination vigor depends on multiple biochemical and molecular variables. Their characterization is expected to deliver new markers of seed quality that can be used in breeding programs and/or in biotechnological approaches to improve crop yields.

Catalase is a key enzyme in seed recovery from ageing during priming

Ageing induces seed deterioration expressed as the loss of seed vigour and/or viability. Priming treatment, which consists in soaking of seeds in a solution of low water potential, has been shown to reinvigorate aged seeds. We investigate the importance of catalase in oxidation protection during accelerated ageing and repair during subsequent priming treatment of sunflower (Helianthus annuus L.) seeds. Seeds equilibrated to 0.29g H2Og(-1) dry matter (DM) were aged at 35°C for different durations and then primed by incubation for 7 days at 15°C in a solution of polyethylene glycol 8000 at -2MPa. Accelerated ageing affected seed germination and priming treatment reversed partially the ageing effect. The inhibition of catalase by the addition of aminotriazol during priming treatment reduced seed repair indicating that catalase plays a key role in protection and repair systems during ageing. Ageing was associated with H2O2 accumulation as showed by biochemical quantification and CeCl3 staining. Catalase was reduced at the level of gene expression, protein content and affinity. Interestingly, priming induced catalase synthesis by activating expression and translation of the enzyme. Immunocytolocalization of catalase showed that the enzyme co-localized with H2O2 in the cytosol. These results clearly indicate that priming induce the synthesis of catalase which is involved in seed recovery during priming.

Seed imbibition in Medicago truncatula Gaertn.: Expression profiles of DNA repair genes in relation to PEG-mediated stress

The expression profiles of genes involved in DNA repair, namely MtTdp1 (tyrosyl-DNA phosphodiesterase), top1 (DNA topoisomerase I), MtTFIIS (transcription elongation factor II-S) and MtTFIIS-like, were evaluated in Medicago truncatula Gaertn. during seed imbibition carried out with the osmotic agent polyethylene glycol (PEG6000, 100g/L). The use of PEG6000 resulted in delayed water up-take by seeds, and reduced levels of oxidative DNA damage, measured in terms of 7,8-dihydro-8-oxoguanine (8-oxo-dG) were observed compared to seeds imbibed with water. The prolonged exposure to PEG6000 caused an increase in DNA oxidative damage; after 24h of treatment with the osmotic agent, the estimated amount of 8-oxo-dG was 1.25-fold higher compared to the value detected in seeds imbibed with water. Three days after imbibition, consistent cell damage and reactive oxygen species (ROS) production were also detected in radicles emerging from the PEG-treated seeds. All of the tested genes were known to be up-regulated during seed imbibition, with the highest transcript levels accumulating at approximately 8-12h of rehydration. Exposure to PEG6000 caused a delayed up-regulation of MtTdp1α and MtTdp1β genes, with transcript peaks occurring at 12-24h, when the highest levels of DNA damage were also recorded. For the top1, MtTFIIS and MtTFIIS-like genes, different expression profiles were observed in response to PEG6000. The possible roles of these genes in the repair response activated during seed imbibition are discussed.

Proteomics reveals potential biomarkers of seed vigor in sugarbeet

To unravel biomarkers of seed vigor, an important trait conditioning crop yield, a comparative proteomic study was conducted with sugarbeet seed samples of varying vigor as generated by an invigoration treatment called hydropriming and an aging treatment called controlled deterioration. Comparative proteomics revealed proteins exhibiting contrasting behavior between seed samples. Thus, 18 proteins were up-regulated during priming and down-regulated during aging and further displayed an up-regulation upon priming of the aged seeds, meaning that down-regulation of these spot volumes during aging was reversible upon subsequent priming. Also, 11 proteins exhibited the converse behavior characterized by a decrease and an increase of the spot volumes during priming and aging of the control seeds, respectively, and a decrease in the spot volumes upon priming of the aged seeds. The results underpinned the role in seed vigor of several metabolic pathways involved in lipid and starch mobilization, protein synthesis or the methyl cycle. They also corroborate previous studies suggesting that the glyoxylate enzyme isocitrate lyase, the capacity of protein synthesis and components of abscisic acid signaling pathways are likely contributors of seed vigor.

Ascorbate-glutathione cycle of mitochondria in osmoprimed soybean cotyledons in response to imbibitional chilling injury

Osmopriming treatment of chilling-sensitive soybean (Glycine max L. cv. Zhonghuang-22) seeds for 72h at 25°C with polyethylene glycol (PEG8000) solution at -1.5MPa strongly improves chilling resistance. The aim of the present work was to investigate whether the beneficial effect of osmopriming is associated with restoration of the ascorbate-glutathione (ASC-GSH) cycle of mitochondria in soybean seeds. Compared with the control, both H(2)O(2) and malondialdehyde (MDA) contents in mitochondria of osmoprimed seeds decreased after chilling treatment, and these changes were associated with increased activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione reductase (GR), monodehydroascorbate reductase (MDHAR) and L-galactono-γ-lactone dehydrogenase (GLDH). However, the activity of dehydroascorbate reductase (DHAR) showed no obvious change during osmopriming treatment. Increased ASC and GSH contents accompanied prolonged osmopriming, and the reduced/oxidized ratios of ASC and GSH increased differently during osmopriming. These results indicate that osmopriming treatment enhances activity of the ASC-GSH cycle of mitochondria, which raises the chilling tolerance in soybean seeds and protects against H(2)O(2) that is generated in mitochondria during imbibition at low temperature.

Dynamics of the antioxidant system during seed osmopriming, post-priming germination, and seedling establishment in Spinach (Spinacia oleracea)

Osmopriming is a pre-sowing treatment that improves seed germination performance and stress tolerance. To understand osmopriming physiology, and its association with post-priming stress tolerance, we investigated the antioxidant system dynamics during three stages: during osmopriming, post-priming germination, and seedling establishment. Spinach seeds (Spinacia oleracea L. cv. Bloomsdale) were primed with -0.6 MPa PEG at 15°C for 8 d, and dried at room temperature for 2 d. Unprimed and primed germinating seeds/seedlings were subjected to a chilling and desiccation stresses. Seed/seedling samples were collected for antioxidant assays and germination performance and stress tolerance were evaluated. Our data indicate that: (1) during osmopriming the transition of seeds from dry to germinating state represses the antioxidant pathways (residing in dry seeds) that involve CAT and SOD enzymes but stimulates another pathway (only detectable in imbibed seeds) involving APX; (2) a renewal of antioxidant system, possibly required by seedling establishment, occurs after roughly 5 d of germination; (3) osmopriming strengthens the antioxidant system and increases seed germination potential, resulting in an increased stress tolerance in germinating seeds. Osmopriming-mediated promotive effect on stress tolerance, however, may diminish in relatively older (e.g. ~5-week) seedlings.

Standardizing seed dormancy research

Seeds are very attractive and convenient for molecular genetic studies that challenge principal biological phenomena related to the initiation and suppression of growth (e.g., germination and dormancy, respectively). The number of reports in this field is rapidly expanding. Seed dormancy is a widely misinterpreted biological attribute. One of the main reasons is the general neglect of reliable dormancy assays; often, the sole criterion of current dormancy assays is the total germination of a seed population after a defined period of time. This is a very insensitive and inaccurate method, particularly when comparing dormancy levels of seeds from different genotypes, seeds subjected to different treatments, or seeds originating from different environments. Other seed parameters are far more useful. Furthermore, before undertaking comprehensive molecular and biochemical studies to elucidate the underlying mechanisms of dormancy of a given species, it is pivotal to determine the general types or categories of dormancy that are imposed and whether these are influenced by the external environment. Research strategies should be adjusted to this. In order to distinguish dead from dormant seeds, a viability test should be developed. This chapter addresses in a very general way these pitfalls in dormancy research with a focus on current plant model systems in molecular genetics, such as Arabidopsis thaliana and Medicago truncatula.

Monitoring the expression of maize genes in developing kernels under drought stress using oligo-microarray

Preharvest aflatoxin contamination of grain grown on the US southeastern Coast Plain is provoked and aggravated by abiotic stress. The primary abiotic stress is drought along with high temperatures. The objectives of the present study were to monitor gene expression in developing kernels in response to drought stress and to identify drought-responsive genes for possible use in germplasm assessment. The maize breeding line Tex6 was used, and gene expression profiles were analyzed in developing kernels under drought stress verses well-watered conditions at the stages of 25, 30, 35, 40, 45 d after pollination (DAP) using the 70 mer maize oligo-arrays. A total of 9 573 positive array spots were detected with unique gene IDs, and 7 988 were common in both stressed and well-watered samples. Expression patterns of some genes in several stress response-associated pathways, including abscisic acid, jasmonic acid and phenylalanine ammonia-lyase, were examined, and these specific genes were responsive to drought stress positively. Real-time quantitative polymerase chain reaction validated microarray expression data. The comparison between Tex6 and B73 revealed that there were significant differences in specific gene expression, patterns and levels. Several defense-related genes had been downregulated, even though some defense-related or drought responsive genes were upregulated at the later stages.

A genetic locus and gene expression patterns associated with the priming effect on lettuce seed germination at elevated temperatures

Seeds of most cultivated varieties of lettuce (Lactuca sativa L.) fail to germinate at warm temperatures (i.e., above 25-30 degrees C). Seed priming (controlled hydration followed by drying) alleviates this thermoinhibition by increasing the maximum germination temperature. We conducted a quantitative trait locus (QTL) analysis of seed germination responses to priming using a recombinant inbred line (RIL) population derived from a cross between L. sativa cv. Salinas and L. serriola accession UC96US23. Priming significantly increased the maximum germination temperature of the RIL population, and a single major QTL was responsible for 47% of the phenotypic variation due to priming. This QTL collocated with Htg6.1, a major QTL from UC96US23 associated with high temperature germination capacity. Seeds of three near-isogenic lines (NILs) carrying an Htg6.1 introgression from UC96US23 in a Salinas genetic background exhibited synergistic increases in maximum germination temperature in response to priming. LsNCED4, a gene encoding a key enzyme (9-cis-epoxycarotinoid dioxygenase) in the abscisic acid biosynthetic pathway, maps precisely with Htg6.1. Expression of LsNCED4 after imbibition for 24 h at high temperature was greater in non-primed seeds of Salinas, of a second cultivar (Titan) and of NILs containing Htg6.1 compared to primed seeds of the same genotypes. In contrast, expression of genes encoding regulated enzymes in the gibberellin and ethylene biosynthetic pathways (LsGA3ox1 and LsACS1, respectively) was enhanced by priming and suppressed by imbibition at elevated temperatures. Developmental and temperature regulation of hormonal biosynthetic pathways is associated with seed priming effects on germination temperature sensitivity.

Priming and re-drying improve the survival of mature seeds of Digitalis purpurea during storage

BACKGROUND AND AIMS

Most priming studies have been conducted on commercial seed lots of unspecified uniformity and maturity, and subsequent seed longevity has been reported to both increase and decrease. Here a seed lot of Digitalis purpurea L. with relatively uniform maturity and known history was used to analyse the effects of priming on seed longevity in air-dry storage.

METHODS

Seeds collected close to natural dispersal and dried at 15% relative humidity (RH), 15 degrees C, were placed into experimental storage (60% RH, 45 degrees C) for 14 or 28 d, primed for 48 h at 0, -1, -2, -5, -10 or -15 MPa, re-equilibrated (47% RH, 20 degrees C) and then returned to storage. Further seed samples were primed for 2 or 48 h at -1 MPa and either dried at 15% RH, 15 degrees C or immediately re-equilibrated for experimental storage. Finally, some seeds were given up to three cycles of experimental storage and priming (48 h at -1 MPa).

KEY RESULTS

Priming at -1 MPa had a variable effect on subsequent survival during experimental storage. The shortest lived seeds in the control population showed slightly increased life spans; the longer lived seeds showed reduced life spans. In contrast, seeds first stored for 14 or 28 d before priming had substantially increased life spans. The increase tended to be greatest in the shortest lived fraction of the seed population. Both the period of rehydration and the subsequent drying conditions had significant effects on longevity. Interrupting air-dry storage with additional cycles of priming also increased longevity.

CONCLUSIONS

The extent of prior deterioration and the post-priming desiccation environment affect the benefits of priming to the subsequent survival of mature seeds. Rehydration-dehydration treatments may have potential as an adjunct or alternative to the regeneration of seed accessions maintained in gene banks for plant biodiversity conservation or plant breeding.

Stress-related genes define essential steps in the response of maize seedlings to smoke-water

Smoke from burning vegetation is widely recognised as a germination cue for seed germination and recent reports suggest that smoke treatments can improve seedling vigour also. We investigated the effect of smoke-water on seedling vigour and changes of the global transcriptome in the early post-germination phase in maize. Application of smoke-water improved the germination characteristics and seedling vigour. The transcriptional response of embryos and emerging radicles 24 and 48 h after the onset of smoke treatment was investigated. The microarray study revealed a number of smoke-responsive genes amongst which stress- and abscisic acid (ABA)-related genes were over-represented. The global promoter analysis of the smoke-responsive genes revealed a tight correlation with the results obtained from Gene Ontology annotations. This concerted over-expression shows that smoke treatment induces stress and ABA-related responses in the early post-germination phase which leads to better adaptation to environmental stress factors occurring during germination, eventually resulting in greater seedling vigour.

Transcript profiles uncover temporal and stress-induced changes of metabolic pathways in germinating sugar beet seeds

BACKGROUND

With a cultivation area of 1.75 Mio ha and sugar yield of 16.7 Mio tons in 2006, sugar beet is a crop of great economic importance in Europe. The productivity of sugar beet is determined significantly by seed vigour and field emergence potential; however, little is known about the molecular mechanisms underlying these traits. Both traits exhibit large variations within sugar beet germplasm that have been difficult to ascribe to either environmental or genetic causes. Among potential targets for trait improvement, an enhancement of stress tolerance is considered because of the high negative influence of environmental stresses on trait parameters. Extending our knowledge of genetic and molecular determinants of sugar beet germination, stress response and adaptation mechanisms would facilitate the detection of new targets for breeding crop with an enhanced field emergence potential.

RESULTS

To gain insight into the sugar beet germination we initiated an analysis of gene expression in a well emerging sugar beet hybrid showing high germination potential under various environmental conditions. A total of 2,784 ESTs representing 2,251 'unigenes' was generated from dry mature and germinating seeds. Analysis of the temporal expression of these genes during germination under non-stress conditions uncovered drastic transcriptional changes accompanying a shift from quiescent to metabolically active stages of the plant life cycle. Assay of germination under stressful conditions revealed 157 genes showing significantly different expression patterns in response to stress. As deduced from transcriptome data, stress adaptation mechanisms included an alteration in reserve mobilization pathways, an accumulation of the osmoprotectant glycine betaine, late embryogenesis abundant proteins and detoxification enzymes. The observed transcriptional changes are supposed to be regulated by ABA-dependent signal transduction pathway.

CONCLUSION

This study provides an important step toward the understanding of main events and metabolic pathways during germination in sugar beet. The reported alterations of gene expression in response to stress shed light on sugar beet stress adaptation mechanisms. Some of the identified stress-responsive genes provide a new potential source for improvement of sugar beet stress tolerance during germination and field emergence.

Cadmium stress alters gene expression of DNA mismatch repair related genes in Arabidopsis seedlings

Cadmium (Cd) is a non essential element, and is a widespread environmental pollutant. Exposure to Cd can result in a variety of adverse health effects in plant and humans. In the current study, Arabidopsis seedlings were used as a bio-indicator of Cd pollution. Seedlings were grown on MS media containing 0-6.0 mg L(-1) Cd for 18 days, and the gene expression patterns were used to link increased Cd exposure with progressive biological effects. Reduction of total soluble protein content in shoots of the Arabidopsis seedlings occurred with increase in Cd concentrations. For the gene expression patterns, seven genes known to be involved in cell division and DNA mismatch repair (MMR) system were investigated by semi-quantitative RT-PCR, and normalized using 18S rRNA gene expression. Expression of the proliferating cell nuclear antigen 2 (atPCNA 2), MutS 3 homolog (atMSH 3) and MutL1 homolog (atMLH1) genes in shoots of Arabidopsis was strongly induced by exposure to 0.75 mg L(-1) Cd, but were repressed by other Cd concentrations whereas exposure to 0.75-6 mg L(-1) of Cd resulted in a decreased expression of atPCNA1, atMSH 2, 6 and 7 genes independently of any observable biological effects, including survival, fresh weight and chlorophyll level of shoots. This work demonstrated that specific gene expression changes could serve as useful molecular biomarkers indicative of Cd exposure and related biological effects.

Proteome-wide characterization of seed aging in Arabidopsis: a comparison between artificial and natural aging protocols

A variety of mechanisms have been proposed to account for the extension of life span in seeds (seed longevity). In this work, we used Arabidopsis (Arabidopsis thaliana) seeds as a model and carried out differential proteomics to investigate this trait, which is of both ecological and agricultural importance. In our system based on a controlled deterioration treatment (CDT), we compared seed samples treated for different periods of time up to 7 d. Germination tests showed a progressive decrease of germination vigor depending on the duration of CDT. Proteomic analyses revealed that this loss in seed vigor can be accounted for by protein changes in the dry seeds and by an inability of the low-vigor seeds to display a normal proteome during germination. Furthermore, CDT strongly increased the extent of protein oxidation (carbonylation), which might induce a loss of functional properties of seed proteins and enzymes and/or enhance their susceptibility toward proteolysis. These results revealed essential mechanisms for seed vigor, such as translational capacity, mobilization of seed storage reserves, and detoxification efficiency. Finally, this work shows that similar molecular events accompany artificial and natural seed aging.

Deciphering transcriptional networks that govern Coffea arabica seed development using combined cDNA array and real-time RT-PCR approaches

Due to its economic importance, Coffea arabica is becoming the subject of increasing genomic research and, in particular, the genes involved in the final chemical composition of the bean and the sensorial quality of the coffee beverage. The aim of the present study was to decipher the transcriptional networks that govern the development of the C. arabica seed, a model for non-orthodox albuminous seeds of tropical origin. For this purpose, we developed a transcriptomic approach combining two techniques: targeted cDNA arrays, containing 266 selected candidate gene sequences, and real-time RT-PCR on a large subset of 111 genes. The combination of the two techniques allowed us to limit detection of false positives and to reveal the advantages of using large real-time RT-PCR screening. Multivariate analysis was conducted on both datasets and results were broadly convergent. First, principle component analysis (PCA) revealed a dramatic re-programming of the transcriptional machinery between early cell division and elongation, storage and maturation phases. Second, hierarchical clustering analysis (HCA) led to the identification of 11 distinct patterns of gene expression during seed development as well as to the detection of genes expressed at specific developmental stages that can be used as functional markers of phenological changes. In addition, this study led to the description of gene expression profiles for quality-related genes, most of them formerly uncharacterised in Coffea. Their involvement in storage compound synthesis and accumulation during endosperm development and final metabolic re-adjustments during maturation is discussed.

Specific elements of the glyoxylate pathway play a significant role in the functional transition of the soybean cotyledon during seedling development

BACKGROUND

The soybean (Glycine max) cotyledon is a specialized tissue whose main function is to serve as a nutrient reserve that supplies the needs of the young plant throughout seedling development. During this process the cotyledons experience a functional transition to a mainly photosynthetic tissue. To identify at the genetic level the specific active elements that participate in the natural transition of the cotyledon from storage to photosynthetic activity, we studied the transcript abundance profile at different time points using a new soybean oligonucleotide chip containing 19,200 probes (70-mer long).

RESULTS

After normalization and statistical analysis we determined that 3,594 genes presented a statistically significant altered expression in relation to the imbibed seed in at least one of the time points defined for the study. Detailed analysis of this data identified individual, specific elements of the glyoxylate pathway that play a fundamental role during the functional transition of the cotyledon from nutrient storage to photosynthesis. The dynamics between glyoxysomes and peroxisomes is evident during these series of events. We also identified several other genes whose products could participate co-ordinately throughout the functional transition and the associated mechanisms of control and regulation and we described multiple unknown genetic elements that by association have the potential to make a major contribution to this biological process.

CONCLUSION

We demonstrate that the global transcript profile of the soybean cotyledon during seedling development is extremely active, highly regulated and dynamic. We defined the expression profiles of individual gene family members, enzymatic isoforms and protein subunits and classified them accordingly to their involvement in different functional activities relevant to seedling development and the cotyledonary functional transition in soybean, especially the ones associated with the glyoxylate cycle. Our data suggests that in the soybean cotyledon a very complex and synchronized system of control and regulation of several metabolic pathways is essential to carry out the necessary functions during this developmental process.

Enhancing the carotenoid content of Brassica napus seeds by downregulating lycopene epsilon cyclase

The accumulation of carotenoids in higher plants is regulated by the environment, tissue type and developmental stage. In Brassica napus leaves, beta-carotene and lutein were the main carotenoids present while petals primarily accumulated lutein and violaxanthin. Carotenoid accumulation in seeds was developmentally regulated with the highest levels detected at 35-40 days post anthesis. The carotenoid biosynthesis pathway branches after the formation of lycopene. One branch forms carotenoids with two beta rings such as beta-carotene, zeaxanthin and violaxanthin, while the other introduces both beta- and epsilon-rings in lycopene to form alpha-carotene and lutein. By reducing the expression of lycopene epsilon-cyclase (epsilon-CYC) using RNAi, we investigated altering carotenoid accumulation in seeds of B. napus. Transgenic seeds expressing this construct had increased levels of beta-carotene, zeaxanthin, violaxanthin and, unexpectedly, lutein. The higher total carotenoid content resulting from reduction of epsilon-CYC expression in seeds suggests that this gene is a rate-limiting step in the carotenoid biosynthesis pathway. epsilon-CYC activity and carotenoid production may also be related to fatty acid biosynthesis in seeds as transgenic seeds showed an overall decrease in total fatty acid content and minor changes in the proportions of various fatty acids.

Proteomics of European beech (Fagus sylvatica L.) seed dormancy breaking: Influence of abscisic and gibberellic acids

A proteomic approach was used to analyze mechanisms of dormancy breaking in beech (Fagus sylvatica L.) seeds and the participation of abscisic and gibberellic acids (ABA and GA) in this process. After imbibition in water, ABA, or GA3 solutions, beechnuts were subjected to cold stratification, which breaks their dormancy. ABA delayed, whereas GA3 promoted seed dormancy breaking. Proteome maps for water, ABA, and GA3 were established, which displayed 1544 silver-stained spots. A total of 74 spots, showing significant changes in volume, were identified by MS. Of these, 18, 45, and 16 spots were identified as water-, ABA-, and GA3-responsive, respectively (five were regulated by both hormones). The classification of proteins showed that most of the proteins associated with dormancy breaking in water are involved in energy metabolism and protein destination. Most of the ABA-responsive proteins are involved in protein destination, energy metabolism, and development. Most of the GA3-responsive proteins are involved in energy metabolism (many more than for ABA and water) and plant defense. We conclude that the mechanism of seed dormancy breaking involves the proteins of many processes, beginning with hormone signal initiation, through signal transduction, transcription, protein synthesis, energy metabolism, storage materials, and ending with the cell cycle.

Combined transcriptome and proteome analysis identifies pathways and markers associated with the establishment of rapeseed microspore-derived embryo development

Microspore-derived embryo (MDE) cultures are used as a model system to study plant cell totipotency and as an in vitro system to study embryo development. We characterized and compared the transcriptome and proteome of rapeseed (Brassica napus) MDEs from the few-celled stage to the globular/heart stage using two MDE culture systems: conventional cultures in which MDEs initially develop as unorganized clusters that usually lack a suspensor, and a novel suspensor-bearing embryo culture system in which the embryo proper originates from the distal cell of a suspensor-like structure and undergoes the same ordered cell divisions as the zygotic embryo. Improved histodifferentiation of suspensor-bearing MDEs suggests a new role for the suspensor in driving embryo cell identity and patterning. An MDE culture cDNA array and two-dimensional gel electrophoresis and protein sequencing were used to compile global and specific expression profiles for the two types of MDE cultures. Analysis of the identities of 220 candidate embryo markers, as well as the identities of 32 sequenced embryo up-regulated protein spots, indicate general roles for protein synthesis, glycolysis, and ascorbate metabolism in the establishment of MDE development. A collection of 135 robust markers for the transition to MDE development was identified, a number of which may be coregulated at the gene and protein expression level. Comparison of the expression profiles of preglobular-stage conventional MDEs and suspensor-bearing MDEs identified genes whose differential expression may reflect improved histodifferentiation of suspensor-bearing embryos. This collection of early embryo-expressed genes and proteins serves as a starting point for future marker development and gene function studies aimed at understanding the molecular regulation of cell totipotency and early embryo development in plants.

Transcriptome profiling uncovers metabolic and regulatory processes occurring during the transition from desiccation-sensitive to desiccation-tolerant stages in Medicago truncatula seeds

To investigate regulatory processes and protective mechanisms leading to desiccation tolerance (DT) in seeds, 16086-element microarrays were used to monitor changes in the transcriptome of desiccation-sensitive 3-mm-long radicles of Medicago truncatula seeds at different time points during incubation in a polyethylene glycol (PEG) solution at -1.7 MPa, resulting in a gradual re-establishment of DT. Gene profiling was also performed on embryos before and after the acquisition of DT during maturation. More than 1300 genes were differentially expressed during the PEG incubation. A large number of genes involved in C metabolism are expressed during the re-establishment of DT. Quantification of C reserves confirms that lipids, starch and oligosaccharides were mobilised, coinciding with the production of sucrose during the early osmotic adjustment. Several clusters of gene profiles were identified with different time-scales. Genes expressed early during the PEG incubation belonged to classes involved in early stress and adaptation responses. Interestingly, several regulatory genes typically expressed during abiotic/drought stresses were also upregulated during maturation, arguing for the partial overlap of ABA-dependent and -independent regulatory pathways involved in both drought and DT. At later time points, in parallel to the re-establishment of DT, upregulated genes are comparable with those involved in late seed maturation. Concomitantly, a massive repression of genes belonging to numerous classes occurred, including cell cycle, biogenesis, primary and energy metabolism. The re-establishment of DT in the germinated radicles appears to concur with a partial return to the quiescent state prior to germination.

Comparative analysis of the heat stable proteome of radicles of Medicago truncatula seeds during germination identifies late embryogenesis abundant proteins associated with desiccation tolerance

A proteomic analysis was performed on the heat stable protein fraction of imbibed radicles of Medicago truncatula seeds to investigate whether proteins can be identified that are specifically linked to desiccation tolerance (DT). Radicles were compared before and after emergence (2.8 mm long) in association with the loss of DT, and after reinduction of DT by an osmotic treatment. To separate proteins induced by the osmotic treatment from those linked with DT, the comparison was extended to 5 mm long emerged radicles for which DT could no longer be reinduced, albeit that drought tolerance was increased. The abundance of 15 polypeptides was linked with DT, out of which 11 were identified as late embryogenesis abundant proteins from different groups: MtEm6 (group 1), one isoform of DHN3 (dehydrins), MtPM25 (group 5), and three members of group 3 (MP2, an isoform of PM18, and all the isoforms of SBP65). In silico analysis revealed that their expression is likely seed specific, except for DHN3. Other isoforms of DNH3 and PM18 as well as three isoforms of the dehydrin Budcar5 were associated with drought tolerance. Changes in the abundance of MtEm6 and MtPM25 in imbibed cotyledons during the loss of DT and in developing embryos during the acquisition of DT confirmed the link of these two proteins with DT. Fourier transform infrared spectroscopy revealed that the recombinant MtPM25 and MtEm6 exhibited a certain degree of order in the hydrated state, but that they became more structured by adopting alpha helices and beta sheets during drying. A model is presented in which DT-linked late embryogenesis abundant proteins might exert different protective functions at high and low hydration levels.

Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives

DNA microarrays have been used to characterize plant transcriptomes to answer various biological questions. While many studies have provided significant insights, there has been great debate about the general reliability of the technology and data analysis. When compared to well-established transcript analysis technologies, such as RNA blot analysis or quantitative reverse transcription-PCR, discrepancies have frequently been observed. The reasons for these discrepancies often relate to the technical and experimental systems. This review-tutorial addresses common problems in microarray analysis and describes: (i) methods to maximize extraction of valuable biological information from the vast amount of microarray data and (ii) approaches to balance resource availability with high scientific standards and technological innovation with peer acceptability.

Dynamic histone acetylation of late embryonic genes during seed germination

Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated. Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at 1 day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes.

Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination

To test the inferences of spotted microarray technology against a biochemically well-studied process, we performed transcriptional profiling of conidial germination in the filamentous fungus, Neurospora crassa. We first constructed a 70 base oligomer microarray that assays 3366 predicted genes. To estimate the relative gene expression levels and changes in gene expression during conidial germination, we analyzed a circuit design of competitive hybridizations throughout a time course using a Bayesian analysis of gene expression level. Remarkable consistency of mRNA profiles with previously published northern data was observed. Genes were hierarchically clustered into groups with respect to their expression profiles over the time course of conidial germination. A functional classification database was employed to characterize the global picture of gene expression. Consensus motif searches identified a putative regulatory component associated with genes involved in ribosomal biogenesis. Our transcriptional profiling data correlate well with biochemical and physiological processes associated with conidial germination and will facilitate functional predictions of novel genes in N.crassa and other filamentous ascomycete species. Furthermore, our dataset on conidial germination allowed comparisons to transcriptional mechanisms associated with germination processes of diverse propagules, such as teliospores of the phytopathogenic fungus Ustilago maydis and spores of the social amoeba Dictyostelium discoideum.

Transcriptional profiling of imbibed Brassica napus seed

Using an Arabidopsis microarray, we compared gene expression between germinating Brassica napus seeds and seeds in which germination was inhibited either by polyethylene glycol (PEG) or by the abscisic acid (ABA) analog PBI429, which produces stronger and longer lasting ABA-like effects. A total of 40 genes were induced relative to the germinating control by both treatments. Conspicuous among these were genes associated with late seed development. We identified 36 genes that were downregulated by both PEG and PBI429. Functions of these genes included carbohydrate metabolism, cell wall-related processes, detoxification of reactive oxygen, and triacylglycerol breakdown. The PBI429 treatment produced an increase in endogenous ABA and increased ABA catabolism. However, PEG treatment did not result in similar effects. The transcription factor ABI5 was consistently upregulated by both treatments and PKL was downregulated. These results suggest a greater importance of ABA signaling and reduced importance of GA signaling in nongerminating seeds.