Drought induces variation in the DNA methylation status of the barley HvDME promoter.

Cytosine methylation is an epigenetic modification with essential roles in diverse plant biological processes including vegetative and reproductive development and responsiveness to environmental stimuli. A dynamic process involving DNA methyltransferases and DNA demethylases establishes cytosine DNA methylation levels and distribution along the genome. A DNA demethylase gene from barley (Hordeum vulgare), DEMETER (HvDME), the homologue of the Arabidopsis thaliana DME (AtDME), has been characterized previously and found to respond to drought conditions. Here, the promoter of the HvDME gene was analysed further by in silico and DNA methylation analysis. The effect of drought conditions on the DNA methylation status of HvDME was investigated at single-cytosine resolution using bisulfite sequencing. It was demonstrated that the HvDME promoter can be divided into two discrete regions, in terms of DNA methylation level and density; a relatively unmethylated region proximal to the translational start site that is depleted of non-CG (CHG, CHH) methylation and another distal region, approximately 1500 bp upstream of the translational start site, enriched in CG, as well as non-CG methylation. Drought stress provoked alterations in the methylation status of the HvDME promoter distal region, whereas the DNA methylation of the proximal region remained unaffected. Computational analysis of the HvDME promoter revealed the presence of several putative regulatory elements related to drought responsiveness, as well as transposable elements (TEs) that may affect DNA methylation. Overall, our results expand our investigations of the epigenetic regulation of the HvDME gene in response to drought stress in barley and may contribute to further understanding of the epigenetic mechanisms underlying abiotic stress responses in barley and other cereals.

The study of a barley epigenetic regulator, HvDME, in seed development and under drought.

BACKGROUND: Epigenetic factors such as DNA methylation and histone modifications regulate a wide range of processes in plant development. Cytosine methylation and demethylation exist in a dynamic balance and have been associated with gene silencing or activation, respectively. In Arabidopsis, cytosine demethylation is achieved by specific DNA glycosylases, including AtDME (DEMETER) and AtROS1 (REPRESSOR OF SILENCING1), which have been shown to play important roles in seed development. Nevertheless, studies on monocot DNA glycosylases are limited. Here we present the study of a DME homologue from barley (HvDME), an agronomically important cereal crop, during seed development and in response to conditions of drought. RESULTS: An HvDME gene, identified in GenBank, was found to encode a protein with all the characteristic modules of DME-family DNA glycosylase proteins. Phylogenetic analysis revealed a high degree of homology to other monocot DME glycosylases, and sequence divergence from the ROS1, DML2 and DML3 orthologues. The HvDME gene contains the 5' and 3' Long Terminal Repeats (LTR) of a Copia retrotransposon element within the 3' downstream region. HvDME transcripts were shown to be present both in vegetative and reproductive tissues and accumulated differentially in different seed developmental stages and in two different cultivars with varying seed size. Additionally, remarkable induction of HvDME was evidenced in response to drought treatment in a drought-tolerant barley cultivar. Moreover, variable degrees of DNA methylation in specific regions of the HvDME promoter and gene body were detected in two different cultivars. CONCLUSION: A gene encoding a DNA glycosylase closely related to cereal DME glycosylases was characterized in barley. Expression analysis during seed development and under dehydration conditions suggested a role for HvDME in endosperm development, seed maturation, and in response to drought. Furthermore, differential DNA methylation patterns within the gene in two different cultivars suggested epigenetic regulation of HvDME. The study of a barley DME gene will contribute to our understanding of epigenetic mechanisms operating during seed development and stress response in agronomically important cereal crops.

The study of two barley type I-like MADS-box genes as potential targets of epigenetic regulation during seed development.

BACKGROUND: MADS-box genes constitute a large family of transcription factors functioning as key regulators of many processes during plant vegetative and reproductive development. Type II MADS-box genes have been intensively investigated and are mostly involved in vegetative and flowering development. A growing number of studies of Type I MADS-box genes in Arabidopsis, have assigned crucial roles for these genes in gamete and seed development and have demonstrated that a number of Type I MADS-box genes are epigenetically regulated by DNA methylation and histone modifications. However, reports on agronomically important cereals such as barley and wheat are scarce. RESULTS: Here we report the identification and characterization of two Type I-like MADS-box genes, from barley (Hordeum vulgare), a monocot cereal crop of high agronomic importance. Protein sequence and phylogenetic analysis showed that the putative proteins are related to Type I MADS-box proteins, and classified them in a distinct cereal clade. Significant differences in gene expression among seed developmental stages and between barley cultivars with varying seed size were revealed for both genes. One of these genes was shown to be induced by the seed development- and stress-related hormones ABA and JA whereas in situ hybridizations localized the other gene to specific endosperm sub-compartments. The genomic organization of the latter has high conservation with the cereal Type I-like MADS-box homologues and the chromosomal position of both genes is close to markers associated with seed quality traits. DNA methylation differences are present in the upstream and downstream regulatory regions of the barley Type I-like MADS-box genes in two different developmental stages and in response to ABA treatment which may be associated with gene expression differences. CONCLUSIONS: Two barley MADS-box genes were studied that are related to Type I MADS-box genes. Differential expression in different seed developmental stages as well as in barley cultivars with different seed size was evidenced for both genes. The two barley Type I MADS-box genes were found to be induced by ABA and JA. DNA methylation differences in different seed developmental stages and after exogenous application of ABA is suggestive of epigenetic regulation of gene expression. The study of barley Type I-like MADS-box genes extends our investigations of gene regulation during endosperm and seed development in a monocot crop like barley.

Cloning and characterization of SOC1 homologs in barley (Hordeum vulgare) and their expression during seed development and in response to vernalization.

A number of genes are involved in the vernalization pathway, such as VRN1, VRN2 and VRN3/FT1, whose function has been studied in barley and wheat. However, the function of the flowering and vernalization integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) has not been well studied in Triticeae, and particularly in barley. Herein, we cloned and characterized two barley SOC1-like homologs, HvSOC1-like1 and HvSOC1-like2. Primary sequence analysis of the predicted HvSOC1-like1 and HvSOC1-like2 proteins showed that they are members of the type II MADS-box protein family. Phylogenetic analysis placed the predicted proteins with other SOC1 and SOC1-like proteins from different species neighboring those from other cereal plant species. Primary and secondary structures of the predicted proteins are conserved to each other and more distant to the recently identified barley ODDSOC1 proteins. Genomic organization of HvSOC1-like1 is very similar to the Arabidopsis and Brachypodium SOC1 genes and localized in highly syntenic chromosomal regions. Regulatory cis-acting elements detected in the HvSOC1-like1 promoter include the CArG-box, implicated in the regulation of SOC1 expression in Arabidopsis. Both HvSOC1-like1 and HvSOCI-like2 are expressed in vegetative and reproductive tissues and at different stages of seed development. Both are upregulated in a particular seed developmental stage suggesting their possible implication in seed development. Furthermore, HvSOC1-like1 was induced in two winter barley cultivars after vernalization treatment pointing to its probable involvement in the vernalization process. The study of the SOC1 genes reported here opens the way for a better understanding of both the vernalization process and seed development and germination in this important cereal crop.

The chlamydiales pangenome revisited: structural stability and functional coherence.

The entire publicly available set of 37 genome sequences from the bacterial order Chlamydiales has been subjected to comparative analysis in order to reveal the salient features of this pangenome and its evolutionary history. Over 2,000 protein families are detected across multiple species, with a distribution consistent to other studied pangenomes. Of these, there are 180 protein families with multiple members, 312 families with exactly 37 members corresponding to core genes, 428 families with peripheral genes with varying taxonomic distribution and finally 1,125 smaller families. The fact that, even for smaller genomes of Chlamydiales, core genes represent over a quarter of the average protein complement, signifies a certain degree of structural stability, given the wide range of phylogenetic relationships within the group. In addition, the propagation of a corpus of manually curated annotations within the discovered core families reveals key functional properties, reflecting a coherent repertoire of cellular capabilities for Chlamydiales. We further investigate over 2,000 genes without homologs in the pangenome and discover two new protein sequence domains. Our results, supported by the genome-based phylogeny for this group, are fully consistent with previous analyses and current knowledge, and point to future research directions towards a better understanding of the structural and functional properties of Chlamydiales.

Multiple evidence for the role of an Ovate-like gene in determining fruit shape in pepper.

BACKGROUND: Grafting is a widely used technique contributing to sustainable and ecological production of many vegetables, but important fruit quality characters such as taste, aroma, texture and shape are known for years to be affected by grafting in important vegetables species including pepper. From all the characters affected, fruit shape is the most easily observed and measured. From research in tomato, fruit shape is known to be controlled by many QTLs but only few of them have larger effect on fruit shape variance. In this study we used pepper cultivars with different fruit shape to study the role of a pepper Ovate-like gene, CaOvate, which encodes a negative regulator protein that brings significant changes in tomato fruit shape. RESULTS: We successfully cloned and characterized Ovate-like genes (designated as CaOvate) from two pepper cultivars of different fruit shape, cv. "Mytilini Round" and cv. "Piperaki Long", hereafter referred to as cv. "Round" and cv. "Long" after the shape of their mature fruits. The CaOvate consensus contains a 1008-bp ORF, encodes a 335 amino-acid polypeptide, shares 63% identity with the tomato OVATE protein and exhibits high similarity with OVATE sequences from other Solanaceae species, all placed in the same protein subfamily as outlined by expert sequence analysis. No significant structural differences were detected between the CaOvate genes obtained from the two cultivars. However, relative quantitative expression analysis showed that the expression of CaOvate followed a different developmental profile between the two cultivars, being higher in cv. "Round". Furthermore, down-regulation of CaOvate through VIGS in cv. "Round" changes its fruit to a more oblong form indicating that CaOvate is indeed involved in determining fruit shape in pepper, perhaps by negatively affecting the expression of its target gene, CaGA20ox1, also studied in this work. CONCLUSIONS: Herein, we clone, characterize and study CaOvate and CaGA20ox1 genes, very likely involved in shaping pepper fruit. The oblong phenotype of the fruits in a plant of cv. "Round", where we observed a significant reduction in the expression levels of CaOvate, resembled the change in shape that takes place by grafting the round-fruited cultivar cv. "Round" onto the long-fruited pepper cultivar cv. "Long". Understanding the role of CaOvate and CaGA20ox1, as well as of other genes like Sun also involved in controlling fruit shape in Solanaceae plants like tomato, pave the way to better understand the molecular mechanisms involved in controlling fruit shape in Solanaceae plants in general, and pepper in particular, as well as the changes in fruit quality induced after grafting and perhaps the ways to mitigate them.

famRCA-RACE: a rolling circle amplification race for isolating a family of homologous cDNAs in one reaction and its application to obtain NAC genes transcription factors from crocus (Crocus sativus) flower.

We describe an improvement of the RCA-RACE (rolling circle amplification-rapid amplification of cDNA ends) method, called family RCA-RACE (famRCA-RACE). The method is based on the generation of circular cDNA fragments, followed by rolling circle amplification of the circular cDNA using phi29 DNA polymerase and the application of PCR using degenerate outworking primers, designed for a conserved region of homologous genes, that allows the isolation of homologous cDNA sequences expressed in the mRNA preparation in a single polymerase chain reaction (PCR). As an example we present the isolation of seven NAC-like transcription factors cDNA sequences expressed in Crocus sativus flower, used for saffron production. Sequence alignment revealed that CsatNAC proteins contain the typical domain structure of plant NAC proteins, consisting of the conserved N-terminal NAC domain used to design the primers and the five subdomains. Phylogenetic analysis revealed that CsatNAC proteins fall in subgroup I of the NAC family of proteins.

Epigenetic chromatin modifiers in barley: IV. The study of barley polycomb group (PcG) genes during seed development and in response to external ABA.

BACKGROUND: Epigenetic phenomena have been associated with the regulation of active and silent chromatin states achieved by modifications of chromatin structure through DNA methylation, and histone post-translational modifications. The latter is accomplished, in part, through the action of PcG (Polycomb group) protein complexes which methylate nucleosomal histone tails at specific sites, ultimately leading to chromatin compaction and gene silencing. Different PcG complex variants operating during different developmental stages have been described in plants. In particular, the so-called FIE/MEA/FIS2 complex governs the expression of genes important in embryo and endosperm development in Arabidopsis. In our effort to understand the epigenetic mechanisms regulating seed development in barley (Hordeum vulgare), an agronomically important monocot plant cultivated for its endosperm, we set out to characterize the genes encoding barley PcG proteins. RESULTS: Four barley PcG gene homologues, named HvFIE, HvE(Z), HvSu(z)12a, and HvSu(z)12b were identified and structurally and phylogenetically characterized. The corresponding genes HvFIE, HvE(Z), HvSu(z)12a, and HvSu(z)12b were mapped onto barley chromosomes 7H, 4H, 2H and 5H, respectively. Expression analysis of the PcG genes revealed significant differences in gene expression among tissues and seed developmental stages and between barley cultivars with varying seed size. Furthermore, HvFIE and HvE(Z) gene expression was responsive to the abiotic stress-related hormone abscisic acid (ABA) known to be involved in seed maturation, dormancy and germination. CONCLUSION: This study reports the first characterization of the PcG homologues, HvFIE, HvE(Z), HvSu(z)12a and HvSu(z)12b in barley. All genes co-localized with known chromosomal regions responsible for malting quality related traits, suggesting that they might be used for developing molecular markers to be applied in marker assisted selection. The PcG differential expression pattern in different tissues and seed developmental stages as well as in two barley cultivars with different seed size is suggestive of a role for these genes in barley seed development. HvFIE and HvE(Z) were also found to be induced by the plant hormone ABA implying an association with ABA-mediated processes during seed development, germination and stress response.

Epigenetic chromatin modifiers in barley: I. Cloning, mapping and expression analysis of the plant specific HD2 family of histone deacetylases from barley, during seed development and after hormonal treatment.

Epigenetic phenomena have been associated with modifications of chromatin structure. These are achieved, in part, by histone post-translational modifications including acetylations and deacetylations, the later being catalyzed by histone deacetylaces (HDACs). Eukaryotic HDACs are grouped into three major families, RPD3/HDA1, SIR2 and the plant-specific HD2. HDAC genes have been analyzed from model plants such as Arabidopsis, rice and maize and have been shown to be involved in various cellular processes including seed development, vegetative and reproductive growth and responses to abiotic and biotic stress, but reports on HDACs from other crops are limited. In this work two full-length cDNAs (HvHDAC2-1 and HvHDAC2-2) encoding two members of the plant-specific HD2 family, respectively, were isolated and characterized from barley (Hordeum vulgare), an agronomically important cereal crop. HvHDAC2-1 and HvHDAC2-2 were mapped on barley chromosomes 1H and 3H, respectively, which could prove useful in developing markers for marker-assisted selection in breeding programs. Expression analysis of the barley HD2 genes demonstrated that they are expressed in all tissues and seed developmental stages examined. Significant differences were observed among tissues and seed stages, and between cultivars with varying seed size, suggesting an association of these genes with seed development. Furthermore, the HD2 genes from barley were found to respond to treatments with plant stress-related hormones such as jasmonic acid (JA), abscisic acid (ABA) and salicylic acid (SA) implying an association of these genes with plant resistance to biotic and abiotic stress. The expression pattern of HD2 genes suggests a possible role for these genes in the epigenetic regulation of seed development and stress response.

Characterization and expression analysis of AGAMOUS-like, SEEDSTICK-like, and SEPALLATA-like MADS-box genes in peach (Prunus persica) fruit.

MADS-box genes encode transcriptional regulators that are critical for flowering, flower organogenesis and plant development. Although there are extensive reports on genes involved in flower organogenesis in model and economically important plant species, there are few reports on MADS-box genes in woody plants. In this study, we have cloned and characterized AGAMOUS (AG), SEEDSTICK (STK) and SEPALLATA (SEP) homologs from peach tree (Prunus persica L. Batsch) and studied their expression patterns in different tissues as well as in fruit pericarp during pit hardening. AG- STK- and SEP-like homologs, representative of the C-, D-, E-like MADS-box gene lineages, respectively, play key roles in stamen, carpel, ovule and fruit development in Arabidopsis thaliana. Sequence similarities, phylogenetic analysis and structural characteristics were used to provide classification of the isolated genes in type C (PPERAG), type D (PPERSTK) and type E (PPERSEP1, PPERSEP3, PPERFB9) organ identity genes. Expression patterns were determined and in combination with phylogenetic data provided useful indications on the function of these genes. These data suggest the involvement of MADS-box genes in peach flower and fruit development and provide further evidence for the role of these genes in woody perennial trees that is compatible with their function in model plant species.

Identification of unknown genetically modified material admixed in conventional cotton seed and development of an event-specific detection method

Entering the second decade of commercialization of biotech crops, the global area cultivated with transgenic plants constantly expands and national legislations in many countries, particularly in the European Union, require identification and labeling of genetically modified material in food and feed. We describe here a procedure for characterizing transgenic material of unknown origin present in conventional seed lots using a genome walking strategy for isolation and characterization of the junction between the inserted transgene construct and the host plant genomic DNA. The procedure was applied to transgenic cotton detected as adventitious or technically unavoidable presence in a conventional commercial cultivar. The structure of the isolated region revealed that the transgenic material derived from Monsanto’s event 1445 transgenic cotton. Due to the random incorporation of the transgene into the host plant’s genome, the sequence of the junction region obtained using the genome walking strategy, provided the means to develop an event-specific identification method without prior knowledge for the nature of the transformation event. Thus, we documented a methodology for developing an event-specific detection protocol even without prior knowledge of the genetic modification event.

Characterization and expression analysis of TERMINAL FLOWER1 homologs from cultivated alloteraploid cotton (Gossypium hirsutum) and its diploid progenitors.

The seasonal cycle and persistence of a plant is governed by a combination of the determinate or indeterminate status of shoot and root apical meristems. A perennial plant is one in which the apical meristem of at least one of its shoot axes remains indeterminate beyond the first growth season. TERMINAL FLOWER1 (TFL1) genes play important roles in regulating flowering time, the fate of inflorescence meristem and perenniality. To investigate the role of TFL1-like genes in the determination of the apical meristems in an industrially important crop cultivated for its fibers, we isolated and characterized two TFL1 homologs (TFL1a and TFL1b) from tetraploid cultivated cotton (Gossypium hirsutum) and its diploid progenitors (Gossypium arboreum and Gossypium raimondii). All isolated genes maintain the same exon-intron organization. Their phylogenetic analysis at the amino acid level confirmed that the isolated sequences are TFL1-like genes and collocate in the TFL1 clade of the PEBP protein family. Expression analysis revealed that the genes TFL1a and TFL1b have slightly different expression patterns, suggesting different functional roles in the determination of the meristems. Additionally, promoter analysis by computational methods revealed the presence of common binding motifs in TFL1-like promoters. These are the first reported TFL1-like genes isolated from cotton, the most important crop for the textile industry.

Cloning, structural characterization, and phylogenetic analysis of flower MADS-box genes from crocus (Crocus sativus L.).

Crocus (Crocus sativus L.) is a crop species cultivated for its flowers and, more specifically, for its red stigmas. The flower of crocus is bisexual and sterile, since crocus is a triploid species. Its perianth consists of six petaloid tepals: three tepals in whorl 1 (outer tepals) and three tepals in whorl 2 (inner tepals). The androecium consists of three distinct stamens and the gynoecium consists of a single compound pistil with three carpels, a single three-branched style, and an inferior ovary. The dry form of the stigmas constitutes the commercial saffron used as a food additive, in the coloring industry, and in medicine. In order to uncover and understand the molecular mechanisms controlling flower development in cultivated crocus and its relative wild progenitor species, and characterize a number of crocus flower mutants, we have cloned and characterized different, full-length, cDNA sequences encoding MADS-box transcription factor proteins involved in flower formation. Here we review the different methods followed or developed for obtaining these sequences involving conventional 5 inverted exclamation markä 3 inverted exclamation markä RACE, as well as newly developed methods from our group, named Rolling Circle Amplification C RACE (RCA-RACE) and its modification named familyRCA-RACE (famRCA-RACE). Furthermore, the characteristics of the protein structure and their common and specific domains for each type of MADS-box transcription factors in this lower nongrass monocot belonging to the Iridaceae family are described. Finally, a phylogenetic tree of all the MADS-box sequences available in our lab is presented and discussed in relation to other data from studies of species of the Iridaceae group and closely related families from an evolutionary perspective. The structural and phylogenetic analyses are based on both published and unpublished data.

Heterotopic expression of B-class floral homeotic genes PISTILLATA/GLOBOSA supports a modified model for crocus (Crocus sativus L.) flower formation.

For uncovering and understanding the molecular mechanisms controlling flower development in cultivated Crocus sativus and particularly the transformation of sepals in outer whorl (whorl 1) tepals, we have cloned and characterized the expression of a family of five PISTILLATA/GLOBOSA-like (PI/GLO-like) MADS-box genes expressed in the C. sativus flower. The deduced amino acid sequences of the coded proteins indicated high homology with members of the MADS-box family of transcription factors, and particularly with other members of the PI/GLO family of MADS-box proteins that control floral organ identity. PI/GLO expression studies in cultivated C. sativus uncover the presence of PI/GLO transcripts not only in the second and third whorls of flower organs as expected, but also in the outer whorl tepals that are the sepals in most typical flowers. This heterotopic expression of both B-class genes: PI/GLO and AP3/DEF, known to form heterodimers for stamens and petals (petaloid inner whor l-whorl 2-tepals in C. sativus), explains the homeotic transformation of sepals into outer whorl tepals in this species. Analysis of PI/GLO sequences from C. sativus for putative targets to known micro-RNAs (miRNAs) showed that the target site for ath-miRNA167 found in Arabidopsis thaliana PI is not present in C. sativus, however, the PI/GLO sequences may be regulated by an ath-miRNA163.

Characterization and expression analysis of FRUITFULL- and SHATTERPROOF-like genes from peach (Prunus persica) and their role in split-pit formation.

The fruit canning industry processes large quantities of the clingstone varieties of peach (Prunus persica L. Batch). The occurrence of split-pit formation--the opening of the pit and sometimes splitting of the fruit--causes deterioration of canned fruit quality. The frequency of split-pit formation is influenced by genetic and environmental factors. To increase understanding of the molecular mechanisms underlying split-pit formation in peach, we cloned and characterized the PPERFUL and PPERSHP genes that are homologues to the genes FRUITFULL and SHATTERPROOF, respectively, which are involved in fruit splitting (pod shattering) in Arabidopsis thaliana. The deduced amino acid sequences of the two genes had high homology with members of the MADS-box family of transcription factors, and particularly with other members of the FUL-like family of A-type MADS-box proteins and PLENA-like family of C-type MADS-box proteins, respectively. PPERFUL and PPERSHP were expressed throughout fruit development from full anthesis until fruit harvest. Differences in the mRNA abundance of each gene were compared in a split-pit sensitive and a split-pit resistant variety. Results suggested that temporal regulation of PPERFUL and PPERSHP expression may have an effect on the split-pit process.

The maize alternative oxidase 1a (Aox1a) gene is regulated by signals related to oxidative stress.

We isolated and characterized the expression of Aox1a, a member of the maize alternative oxidase (Aox) small multigene family. Aox1a consists of four exons interrupted by three introns and its promoter harbors diverse stress-specific putative regulatory motifs pointing to complex regulation and response to multiple signals. Responses of Aox1a to such signals were examined and compared with those of maize glutathione S-transferase I (GstI), a typical oxidative stress inducible gene. Potassium cyanide (KCN) and hydrogen peroxide (H2O2) induced a rapid increase of the Aox1a and GstI transcripts, which was persisted in prolonged treatment at high H2O2 concentration only for Aox1a. High concentration of salicylic acid (SA) and salicyl hydroxamic acid (SHAM) induced Aox1a mRNA only after prolonged exposure, while GstI displayed an early strong induction, which declined thereafter. Nitric oxide (NO) induced a high increase of Aox1a after prolonged exposure at high concentration, while GstI displayed a weak response. Our results show that multiple signaling pathways, involved in stress responses, also participate and differentially regulate Aox1a and GstI in maize. A ROS-depended signaling event may be involved, suggesting an essential role of Aox1a under oxidative stress in maize.