cDNA-AFLP analysis of seed germination in Arabidopsis thaliana identifies transposons and new genomic sequences

DNA damage and genetic methylation changes caused by Cd in Arabidopsis thaliana seedlings

Amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MASP) techniques are sensitive to deoxyribonucleic acid (DNA) damage and genetic methylation, respectively. Using these 2 techniques, Arabidopsis thaliana cultured with 0 mg/L (control), 0.5 mg/L, 1.5 mg/L, and 5.0 mg/L Cd(2+) for 16 d was used to analyze the DNA damage and methylation changes as a result of cadmium (Cd). The DNA was amplified by 14 AFLP primer pairs and 13 MSAP primer combinations. In the AFLP experiment, 62 polymorphic sites were found in the patterns of 11 primer combinations and a total of 1116 fragments were obtained in these patterns. There were no polymorphic bands in the remaining 3 pairs. The proportions of polymorphic sites in the 0.5-mg/L Cd(2+) and 5.0-mg/L Cd(2+) treatments were significantly different. Seven polymorphic fragments were then separated and successfully sequenced, yielding 6 nucleobase substitutions and 1 nucleobase deletion. Similarly, in the MSAP experiment, the MSAP% and number of demethylated-type bands were unchanged after Cd treatment, but the number of methylated-type bands was increased significantly in the 5.0-mg/L Cd(2+) treatment group, a finding that may be associated with the AFLP results. The polymorphic bands were also sequenced and the functions of their homologous genes were determined. The DNA damage and methylation changes may be the primary cause of certain pathology changes as a result of Cd uptake in plants.

Novel durum wheat genes up-regulated in response to a combination of heat and drought stress

We report the effect of heat, drought and combined stress on the expression of a group of genes that are up-regulated under these conditions in durum wheat (Triticum turgidum subsp. durum) plants. Modulation of gene expression was studied by cDNA-AFLP performed on RNAs extracted from flag leaves. By this approach, we identified several novel durum wheat genes whose expression is modulated under different stress conditions. We focused on a group of hitherto undescribed up-regulated genes in durum wheat, among these, 7 are up-regulated by heat, 8 by drought stress, 15 by combined heat and drought stress, 4 are up-regulated by both heat and combined stress, and 3 by both drought and combined stress. The functional characterization of these genes will provide new data that could help the developing of strategies aimed at improving durum wheat tolerance to field stress.

Identification of candidate genes associated with senescence in durum wheat (Triticum turgidum subsp. durum) using cDNA-AFLP

Senescence is an integrated response of plants to various internal (developmental) and external (environmental) signals. It is a highly regulated process leading eventually to the death of cells, single organs such as leaves, or even whole plants. In cereals, which are monocarpic plants, senescence represents the final stage of development. In order to study senescence in durum wheat (Triticum turgidum subsp. durum), a cDNA-AFLP analysis was performed. The transcription profiles of plants at different developmental stages (flowering and senescent) were compared. About 2000 cDNA fragments, ranging in size from 160 to 1900 bp, were reproducibly detected. This allowed the identification of 57 differentially expressed cDNAs corresponding to genes belonging to different functional categories related to cellular metabolism, transcription, maintenance of DNA structure, transport and signal transduction. This paper reports the identification of novel durum wheat candidate genes involved in the senescence process, and provides new information about the senescence programme of this important crop species.

Histological and molecular analysis of pollen-pistil interaction in clementine

In contrast to model species, the self-incompatibility reaction in citrus has been poorly studied. It is assumed to be gametophytically determined and genetically controlled by the S-locus, which in other species encodes for glycoproteins (S-RNases) showing ribonuclease activity. To investigate pollen-pistil interaction, the pollen tube growth of two clementine varieties, 'Comune' (self-incompatible) and 'Monreal' (a 'Comune' self-compatible mutation) was analysed by histological assays in self- and cross-pollination conditions. Cross-pollination assays demonstrated that the mutation leading to self-compatibility in 'Monreal' occurred in the stylar tissues. Similar rates of pollen germination were observed in both genotypes. However, 'Comune' pollen tubes showed altered morphology and arrested growth in the upper style while in 'Monreal' they grew straight toward the ovary. Moreover, to identify genes putatively involved in pollen-pistil interaction and self-incompatibility, research based on the complementary DNA-amplified fragment length polymorphism technique was carried out to compare the transcript profiles of unpollinated and self-pollinated styles and stigmas of the two cultivars. This analysis identified 96 unigenes such as receptor-like kinases, stress-induced genes, transcripts involved in the phenylpropanoid pathway, transcription factors and genes related to calcium and hormone signalling. Surprisingly, a high percentage of active long terminal repeat (LTR) and non-LTR retrotransposons were identified among the unigenes, indicating their activation in response to pollination and their possible role in the regulation of self-incompatibility genes. The quantitative reverse trascription-polymerase chain reaction analysis of selected gene tags showed transcriptional differences between the two genotypes during pollen germination and pollen tube elongation.

The DING family of proteins: ubiquitous in eukaryotes, but where are the genes?

PstS and DING proteins are members of a superfamily of secreted, high-affinity phosphate-binding proteins. Whereas microbial PstS have a well-defined role in phosphate ABC transporters, the physiological function of DING proteins, named after their DINGGG N termini, still needs to be determined. PstS and DING proteins co-exist in some Pseudomonas strains, to which they confer a highly adhesive and virulent phenotype. More than 30 DING proteins have now been purified, mostly from eukaryotes. They are often associated with infections or with dysregulation of cell proliferation. Consequently, eukaryotic DING proteins could also be involved in cell-cell communication or adherence. The ubiquitous presence in eukaryotes of proteins structurally and functionally related to bacterial virulence factors is intriguing, as is the absence of eukaryotic genes encoding DING proteins in databases. DING proteins in eukaryotes could originate from unidentified commensal or symbiotic bacteria and could contribute to essential functions. Alternatively, DING proteins could be encoded by eukaryotic genes sharing special features that prevent their cloning. Both hypotheses are discussed.

Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology

Background

After 10-year-use of AFLP (Amplified Fragment Length Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO), consisting in three structured vocabularies (i.e. ontologies) describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology.

Results

Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species.

Conclusion

Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization of the experimental steps and the statistical parameters adopted. The Blast2GO software was shown to represent a comprehensive bioinformatics solution for an annotation-based functional analysis. According to the whole set of GO annotations, the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families. The utility of this technology for structural and functional genomics in plants can be implemented by serial annotation analyses of genome-anchored fragments and organ/tissue-specific repertories of transcriptome-derived fragments.

Identification of genes expressed during early somatic embryogenesis in Pinus radiata

Analysis of cDNA-AFLPs was used to study gene expression underlying the early embryogenic process in the gymnosperm Pinus radiata. Somatic embryogenesis in this species was used as a model as it resulted in the generation of a large number of embryos at defined stages of development. The gene expression patterns of three embryogenic stages were compared with non-embryogenic cells. Fifty transcript-derived fragments (TDFs) that are upregulated and 32 TDFs that are down-regulated in the embryogenic stages were selected, sequenced and their homologies sought in the databases. Expression of a selected subset of differentially expressed genes was confirmed by RT-PCR and their levels of expression were quantified. Of the 50 up-regulated TDFs, 16 are homologous to genes encoding either known or putative proteins in higher plants, 19 are homologous to conifer ESTs and 15 did not show significant matches. Of the down-regulated TDFs, 8 are homologous to genes encoding either known or putative proteins, 20 are homologous to conifer ESTs and 4 of them did not show significant matches in DNA or protein sequence database. The known up-regulated genes were similar to genes involved in cellular metabolism and in the stress response and the known down-regulated genes were similar to genes involved in proteolysis, cell wall modification and signaling pathways. Their putative individual function is briefly reviewed based on published information, and the potential roles of these genes in embryo development are discussed.

Oxidative signaling in seed germination and dormancy

Reactive Oxygen Species (ROS) play a key role in various events of seed life. In orthodox seeds, ROS are produced from embryogenesis to germination, i.e., in metabolically active cells, but also in quiescent dry tissues during after ripening and storage, owing various mechanisms depending on the seed moisture content. Although ROS have been up to now widely considered as detrimental to seeds, recent advances in plant physiology signaling pathways has lead to reconsider their role. ROS accumulation can therefore be also beneficial for seed germination and seedling growth by regulating cellular growth, ensuring a protection against pathogens or controlling the cell redox status. ROS probably also act as a positive signal in seed dormancy release. They interact with abscisic acid and gibberellins transduction pathway and are likely to control numerous transcription factors and properties of specific protein through their carbonylation.

A review of the functionality of probiotics in the larviculture food chain

During the past two decades, the use of probiotics as an alternative to the use of antibiotics has shown to be promising in aquaculture, particularly in fish and shellfish larviculture. This article reviews the studies on probiotics in larviculture, focusing on the current knowledge of their in vivo mechanisms of action. The article highlights that the in vivo mechanisms of action largely remain to be unravelled. Several methodologies are suggested for further in vivo research, including studies on gut microbiota composition, the use of gnotobiotic animals as test models, and the application of molecular techniques to study host-microbe and microbe-microbe interactions.

The prohibitin genes in Arabidopsis thaliana: expression in seeds, hormonal regulation and possible role in cell cycle control during seed germination

A fragment encoding a partial sequence of a prohibitin (Phb) gene was isolated. The expression of Phb mRNA and protein in seeds of wild type and mutant Arabidopsis thaliana is presented. Phb mRNA is abundant in wild-type seeds; thus, it may have sequence or structural characteristics responsible for this stability. The 3' untranslated region sequence of a Phb gene has interesting features. We found that Arabidopsis Phb does not interact with a retinoblastoma-related protein or E2F in a yeast two-hybrid system, thus suggesting that the plant protein may have not conserved such interaction, described for mammalian Phb. The possible role of Phb in cell cycle regulation during germination is discussed.