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In nature, plants can recognize potential pathogens, thus activating intricate networks of defense signals and reactions. Inducible defense is often mediated by the detection of microbe or pathogen associated molecular pattern elicitors, such as flagellin and chitin. Chitosan, the deacetylated form of chitin, plays a role in inducing protection against pathogens in many plant species. We evaluated the ability of chitosan to confer resistance to Botrytis cinerea in Arabidopsis leaves. We subsequently treated Arabidopsis seedlings with chitosan and carried out a transcript profiling analysis using both ATH1 GeneChip microarrays and quantitative RT-PCR. The results showed that defense response genes, including camalexin biosynthesis genes, were up-regulated by chitosan, both in wild-type and in the chitin-insensitive cerk1 mutant, indicating that chitosan is perceived through a CERK1-independent pathway.

The unicellular green alga Chlamydomonas reinhardtii contains two iron (Fe)-hydrogenases which are responsible for hydrogen production under anoxia. In the present work the patterns of expression of alcohol dehydrogenase, a typical anaerobic gene in plants, of the hydrogenases genes (HYD1, HYD2) and of the genes responsible for their maturation (HYDEF, HYDG), were analysed. The expression patterns were analysed by real-time reverse-transcription polymerase chain reaction in Chlamydomonas cultures during the day–night cycle, as well as in response to oxygen availability. The results indicated that ADH1, HYD1, HYD2, HYDEF and HYDG were expressed following precise day–night fluctuations. ADH1 and HYD2 were modulated by the day–night cycle. Low oxygen plays an important role for the induction of HYD1, HYDEF and HYDG, while ADH1 and HYD2 expression was relatively insensitive to oxygen availability. The regulation of the anaerobic gene expression in Chlamydomonas is only partly explained by responses to anoxia. The cell cycle and light–dark cycles are equally important elements in the regulatory network modulating the anaerobic response in Chlamydomonas.

Soil flooding, which results in a decline in the availability of oxygen to submerged organs, negatively affects the growth and productivity of most crops. Although tomato (Solanum lycopersicum) is known for its sensitivity to waterlogging, its ability to produce adventitious roots (ARs) increases plant survival when the level of oxygen is decreased in the root zone. Ethylene entrapment by water may represent the first warning signal to the plant indicating waterlogging. We found that treatment with the ethylene biosynthesis inhibitor aminoethoxyvinylglycine (AVG) and the auxin transport inhibitor 1-naphthylphthalamic acid (NPA) resulted in a reduction of AR formation in waterlogged plants. We observed that ethylene, perceived by the Never Ripe receptor, stimulated auxin transport. In a process requiring the Diageotropica gene, auxin accumulation in the stem triggered additional ethylene synthesis, which further stimulated a flux of auxin towards to the flooded parts of the plant. Auxin accumulation in the base of the plant induces growth of pre-formed root initials. This response of tomato plants results in a new root system that is capable of replacing the original one when it has been damaged by submergence.

Tomato (Solanum lycopersicum L.) cv. Micro-Tom plants were transformed with the Arabidopsis thaliana (L.) Heyhn MYB75/PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT 1) gene. This gene codifies a transcription factor which is involved in anthocyanin production and is modulated by light and sucrose. The transgenic tomato plants expressing AtMYB75 were characterized by a significantly higher anthocyanin production under normal growth conditions in leaves, stems, roots, flowers and interestingly, in fruits. In the vegetative organs of the transgenic plants, where AtMYB75 overexpression was determined, a clear up-regulation of all the main genes involved in flavonoid pathway was also detected. On the contrary, no effect was produced on the expression of the tomato MYB-gene ANT1 (ANTHOCYANIN1) that had previously been identified as a transcriptional regulator of anthocyanin biosynthesis. Additionally, induction of many but not all the structural genes of the biosynthetic pathway was observed in the fruits. The higher basal content of anthocyanins in the leaves of the transgenic plants could be further increased in the presence of high light conditions and contributed to mitigate photobleaching damages under high irradiance. Transformation of Anthocyanin fruit (Aft) and Ailsa Craig (AC) tomato genotypes were also performed obtaining similar results. Molecular characterizations of these transgenic plants are in progress.

Sugar status regulates mechanisms controlling growth and development of plants. We studied the effects of sucrose at a genome-wide level in dark-grown 4-day-old Arabidopsis thaliana seedlings, identifying 797 genes strongly responsive to sucrose. Starting from the microarray analysis data, four up-regulated (At5g41670, At1g20950, At1g61800, and At2g28900) and four down-regulated (DIN6, At4g37220, At1g28330, and At1g74670) genes were chosen for further characterisation and as sugar sensing markers for in vivo analysis. The sugar modulation pattern of all eight genes was confirmed by real time RT-PCR analysis, revealing different concentration thresholds for sugar modulation. Finally, sugar-regulation of gene expression was demonstrated in vivo by using the starchless pgm mutant, which is unable to produce transitory starch. Sucrose-inducible genes are upregulated in pgm leaves at the end of a light treatment, when soluble sugars levels are higher than in the wild type. Conversely, sucrose-repressible genes show a higher expression at the end of the dark period in the mutant, when the levels of sugars in the leaf are lower. The results obtained indicate that the transcriptional response to exogenous sucrose allows the identification of genes displaying a pattern of expression in leaves compatible with their sugar-modulation in vivo.

Planarian regeneration, based upon totipotent stem cells, the neoblasts, provides a unique opportunity to study in vivo the molecular program that defines a stem cell. In this study, we report the identification of DjPiwi-1, a planarian homologue of Drosophila Piwi. Expression analysis showed that DjPiwi-1 transcripts are preferentially accumulated in small cells distributed along the midline of the dorsal parenchyma. DjPiwi-1 transcripts were not detectable after X-ray irradiation by whole mount in situ hybridization. Real time reverse transcriptase polymerase chain reaction analysis confirmed the significant reduction of DjPiwi-1 expression after X-ray treatment. However, the presence of residual DjPiwi-1 transcription suggests that, although the majority of DjPiwi-1-positive cells can be neoblasts, this gene is also expressed in differentiating/differentiated cells. During regeneration DjPiwi-1-positive cells reorganize along the midline of the stump and no accumulation of hybridization signal was observed either in the blastema area or in the parenchymal region beneath the blastema. DjPiwi-1-positive cells, as well as the DjMCM2-expressing neoblasts located along the midline and those spread all over the parenchyma, showed a lower tolerance to X-ray with respect to the DjMCM2-expressing neoblasts distributed along the lateral lines of the parenchyma. Taken together, these findings suggest the presence of different neoblast subpopulations in planarians.

Sugars acting as signalling molecules regulate many developmental processes in plants, including lateral and adventitious root production. Turanose, a non-metabolizable sucrose analogue, profoundly affects the growth pattern of Arabidopsis seedlings. Turanose-treated seedlings are characterized by a very short primary root and a short hypocotyl showing the production of adventitious roots. A turanose-insensitive (tin) mutant was identified and characterized. Because of a T-DNA insertion and a chromosomal translocation, tin expresses a chimeric form of WOX5, a gene known to be expressed in the root quiescent centre. The tin mutation can be complemented by overexpression of WOX5, suggesting it is a loss-of-function mutant. We found that WOX5 is both turanose- and auxin-inducible. Moreover, turanose insensitivity is associated with altered auxin homeostasis, as demonstrated by the constitutive activation of indole acetic acid (IAA) conjugation and SUPERROOT2 expression in tin. On the basis of turanose effects on wild-type seedlings and the tin molecular and hormonal phenotype, we propose a role for WOX5 in the root apical meristem as a negative trigger of IAA homeostatic mechanisms allowing the maintenance of a restricted area of auxin maximum, which is required for a correct root-formation pattern.

BACKGROUND AND AIMS: The use of microarrays to characterize the transcript profile of Arabidopsis under various experimental conditions is rapidly expanding. This technique provides a huge amount of expression data, requiring bioinformatics tools to allow the proposal of working hypotheses. The aim of this study was to test the usefulness of this approach to examine the anaerobic response of Arabidopsis by evaluating the reliability of microarray data sets and by interrogation of microarray databases for the expression data of a set of anoxia-inducible genes. METHODS: User-driven software tools that display large gene expression datasets onto diagrams of metabolic pathways were used. The Genevestigator software was used to explore the expression of anoxia-inducible genes throughout the life cycle of Arabidopsis as well as relative to plant organs. T-DNA tagged mutants for selected genes identified from our microarray analysis were searched in the Arabidopsis thaliana Insertion Database, looking for insertional mutants from the Salk collection. KEY RESULTS: The results indicate that microarray data can provide the basis for new hypotheses in the field of plant responses to anaerobiosis and also provide knowledge for a targeted screening of Arabidopsis mutants. CONCLUSIONS: Research on plant responses to anaerobiosis can enormously benefit from the microarray technology.

Tolerance to low oxygen availability is likely due to the interaction of several factors. Sugar availability is one of the elements required to support anaerobic metabolism. In cereal grains the availability of soluble sugars is limited, while starch is stored in large amount. Degradation of starch under anoxia is therefore needed to avoid sugar starvation leading to rapid cell death. The striking difference in the ability to produce a-amylase when comparing the anoxia-tolerant rice (Oryza sativa L.) grains with grains of other cereals is not easily explained. Rice is able to respond to gibberellins under anoxia, but the response is too slow to explain the rapid production of a-amylase enzyme. In the present work we demonstrated that a-amylase production during the first 2 days after imbibition is mostly due to the activity of the Ramy3D gene, encoding for the G and H isoforms of a-amylase. The induction of Ramy3D transcription is likely resulting from a low sugar content in the grains incubated under anoxia. The ability of rice embryos to sense sugars under anoxia is reported.

Rice grains can germinate under anoxia, while most other cereals fail to behave similarly. The ability of rice grains to degrade starch, thanks to the successful production of a-amylase even in the absence of oxygen is likely one of the factors allowing rice to germinate anaerobically. In this paper we review the most recent results obtained about the physiology and molecular biology related to the expression of a-amylase genes under anoxia. The current view is that expression of sugar-starvation induced isoforms of a-amylase play a major role during germination under anoxia, while gibberellin induced a-amylase predominates under aerobic conditions.

We studied the effects of anoxia on a-amylase induction, comparing rice (Oryza sativa L.) and barley (Hordeum vulgare L.) grains. While gibberellic acid (GA3) induces a-amylase in rice half-grains under either aerobic or anaerobic conditions, barley half-grains are insensitive to this hormone when applied under anoxia. The possible repressive role of ethanol and abscisic acid (ABA) were investigated. Exogenously added ethanol at concentrations mirroring those found in anaerobically treated tissues was unable to repress a-amylase. The level of ABA in anoxic tissues was found to be much lower than the threshold for a-amylase repression. Overall, the results indicated that these two compounds cannot be held responsible for the failure of barley grains to respond to gibberellic acid. Furthermore, anoxia repressed the induction of a-amylase downstream of the slender mutation, indicating that the repression is independent of effects related to gibberellin perception. Overall, the results suggested that the ability of rice to respond to gibberellins under anoxia is an adaptative trait independent of known negative regulators of a-amylase induction.