DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants

DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21 061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically

Expression analysis of four flower-specific promoters of Brassica spp. in the heterogeneous host tobacco

The 5’-flanking region of ca. 1200 bp upstream of the translation start site (TSS) of a putative cell wall protein gene was cloned from Brassica campestris, B. chinensis, B. napus and B. oleracea, and transferred to tobacco via Agrobacterium-mediation after fused to promoter-less beta-glucuronidase(GUS) reporter gene. Histochemical GUS staining and fluorometric quantification of the transgenic tobacco showed that all four promoters conferred GUS expression in petal, anther, pollen and stigma ofthe flower, not in any vegetative organs or tissues of the plants. A series of 5’-end deletion of the promoter from B. napus disclosed that the region -104 to -17 relative to TSS was sufficient to confer flower-specific expression, and the region -181 to -161 played a key role in maintaining strong drivingpower of the promoter. Besides, several enhancer and suppressor regions were also identified in the promoter

AthaMap web tools for the analysis and identification of co-regulated genes

The AthaMap database generates a map of cis-regulatory elements for the whole Arabidopsis thaliana genome. This database has been extended by new tools to identify common cis-regulatory elements in specific regions of user-provided gene sets. A resulting table displays all cis-regulatory elements annotated in AthaMap including positional information relative to the respective gene. Further tables show overviews with the number of individual transcription factor binding sites (TFBS) present and TFBS common to the whole set of genes. Over represented cis-elements are easily identified. These features were used to detect specific enrichment of drought-responsive elements in cold-induced genes. For identification of co-regulated genes, the output table of the colocalization function was extended to show the closest genes and their relative distances to the colocalizing TFBS. Gene sets determined by this function can be used for a co-regulation analysis in microarray gene expression databases such as Genevestigator or PathoPlant. Additional improvements of AthaMap include display of the gene structure in the sequence window and a significant data increase. AthaMap is freely available at

Identification of a β-galactosidase fruit pulp-specific promoter and its use in silencing constructs to reduce fruit softening in papaya

β-Galactosidases have been proposed as key hydrolytic enzymes involved in cell wall degradation and rapid softening during postharvest processing and storage of papaya. To genetically improve the shelf life of papaya, we identified a softening-related β-Gal gene in fruit pulp at the 50% pericarp yellowing stage and isolated a novel β-Gal promoter region. An online database search predicted that the core promoter motifs and cis-acting elements in the isolated sequence were related to phytohormones, particularly to ethylene and stress responsiveness. GUS staining revealed different patterns of transient GUS expression in papaya organs driven by the putative promoter, with the highest level in the fruit pulp followed by the embryo and the root. Further, such expression was wound inducible in vascular tissues. Co-transformation of the two T-DNAs was performed, mediated by Agrobacterium tumefaciens  harboring a plant expression vector with the fruit pulp-specific promoter and an inverted repeat β-Gal cassette in one T-DNA and marker genes in the other T-DNA. A total of 24 regenerated plantlets were obtained, one of which was identified to be co-transformed using GUS staining, PCR assay and Southern blotting.Keywords: β-Gal, Carica papaya, fruit softening, gene silencing, marker-free transgenic plants, two-T-DNA transformationAfrican Journal of Biotechnology Vol. 12(18), pp. 2427-243

Sl-ERF2, a Tomato Ethylene Response Factor Involved in Ethylene Response and Seed Germination

Ethylene response factors (ERFs) are plant transcriptional regulators mediating ethylene-dependent gene expression via binding to the GCC motif found in the promoter region of ethylene-regulated genes. We report here on the structural and functional characterization of the tomato Sl-ERF2 gene that belongs to a distinct class of the large ERF gene family. Both spliced and unspliced versions of Sl-ERF2 transcripts were amplified from RNA samples and the search in the public tomato expressed sequence tag (EST) database confirmed the existence of the two transcript species in a number of cDNA libraries. The unspliced transcript contains two open reading frames yielding two hypothetical proteins, a small highly truncated version lacking the APETALA2 domain and a bigger protein lacking the N-terminal MCGGAAII/L consensus peptide specific to ERF members from subfamily IV. Nevertheless, functional Sl-ERF2 protein may only derive from spliced transcripts since, depending on the tissue, the level of the spliced transcript is much higher than that of the unspliced transcript. Sl-ERF2 is expressed in all plant tissues tested, though its transcript accumulates preferentially in germinating seeds and ripening fruit. Overexpression of the Sl-ERF2 gene in transgenic tomato lines results in premature seed germination and enhanced hook formation of darkgrown seedlings, which is indicative of increased ethylene sensitivity. The expression of the mannanase2 gene is upregulated in Sl-ERF2-overexpressing seeds, suggesting that Sl-ERF2 stimulates seed germination through the induction of the mannanase2 gene. It is noteworthy that the exaggerated hook phenotype is abolished when ethylene perception is blocked, strongly suggesting that Sl-ERF2 requires other ethylene-dependent components to impact the hook formation process

Búsqueda y caracterización de promotores de begomovirus endémicos de Colombia con potencial biotecnológico.

Los begomovirus tienen genoma de DNA circular cadena sencilla, son transmitidos por mosca blanca Bemisia tabaci y afectan plantas dicotiledóneas de importancia económica. Las regiones promotoras de éstos virus fusionados a genes reporteros han mostrado una fuerte expresión tejido-específica en mesófilo y tejido vascular vegetal, lo que los convierte en excelente fuente de promotores que permitan la expresión biotecnológica diferencial de proteínas en plantas. El objetivo del presente trabajo fue buscar y caracterizar a nivel molecular, in silico y biológico la región promotora del gen de la proteína de la cápside (AR1) de begomovirus endémicos de Colombia con potencial biotecnológico. Se colectaron arvenses y se detectó por PCR la presencia de begomovirus. Se clonaron, secuenciaron y analizaron con herramientas bioinformáticas fragmentos virales que portan la región promotora del gen AR1. Finalmente, mediante ensayos de expresión transitoria sobre hojas de tabaco, se evaluó la expresión del promotor del gen AR1 del virus del mosaico amarillo de la papa (PYMV) en presencia y ausencia de un transactivador (TrAp). Se detectó la presencia de begomovirus en 19 arvenses, de las cuales, Sida acuta y Acalypha sp, constituyen un reporte nuevo a nivel de Colombia y Latinoamérica como hospedero begomoviral. Se identificaron dos nuevos begomovirus aislados de las arvenses Rivina humilis y Malvastrum sp. El análisis de las regiones promotoras de AR1 de los begomovirus aislados de arvenses y PYMV permitió identificar 12 elementos cis regulatorios: Cajas I, Cajas P, cajas G, cajas W, elemento C-Repeat-DRE, elemento ABRE, elemento ERE, elemento TGACG, elemento AS-1, motivo TCT, motivo TGA y CLEs. La organización de éstos elementos cis regulatorios podría explicar la regulación en el tropismo de tejido observado en el gen AR1 de PYMV, la cual es especifica de mesofilo y en presencia de su propia fuente de TrAP este es capaz de invadir células vasculares.//Abstract: Begomoviruses have a single-stranded circular DNA genome, are transmitted by whitefly Bemisia tabaci and affect dicotyledonous plants of economic importance. The promoter regions of these viruses fused to reporter genes have shown strong tissue-specific expression in mesophyll and vascular plant tissue, which makes them an excellent source of promoters that allow the differential biotechnological expression of proteins in plants. The objective of the present work was to search and characterize at the molecular, in silico and biological level the promoter region of the capsid protein gene (AR1) of Colombian endemic begomoviruses with biotechnological potential. Weeds were collected and the presence of begomovirus was detected by PCR. Viral fragments carrying the promoter region of the AR1 gene were cloned, sequenced and analyzed with bioinformatics tools. Finally, through transient expression assays on tobacco leaves, the expression of the promoter of the AR1 gene of potato yellow mosaic virus (PYMV) was evaluated in the presence and absence of a transactivator (TrAp). The presence of begomovirus was detected in 19 weeds, of which, Sida acuta and Acalypha sp, a new level of Colombia and Latin America was reported as a begomoviral host. Two new begomoviruses was isolated from the weeds Rivina humilis and Malvastrum sp. The analysis of the AR1 promoter regions of the begomoviruses isolated from weeds and PYMV allowed the identification of 12 cis regulatory elements: Boxes I, Boxes P, Boxes G, Boxes W, element C-Repeat-DRE, element ABRE, Element ERE, element TGACG, element AS-1, motif TCT, motif TGA and CLEs. The organization of these cis regulatory elements could explain the regulation in tissue tropism observed in the AR1 gene of PYMV, which is mesophilic specific and in the presence of its own source of TrAP it is capable of invading vascular cells.Maestrí

Comparative Expression Profiles of SUVH7 in Sexual and Apomict Boechera spp. Display Differential Expression

Genomic imprinting is parent-of-origin specific gene expression in embryo nourishing tissues endosperm and placenta in flowering plants and mammals, respectively. Seeds are formed with double fertilization in flowering plants and the endosperm has a 3n chromosome set with the contribution of 2 maternal and 1 paternal genome. Any deviation from this ratio (2m%2B1p) results in seed abortion in many species, however, apomict species modify their gametogenesis or fertilization to survive. Boechera divaricarpa is a diploid apomict plant species that can produce seeds with a 4m%253A1p parental genome ratio in endosperm and produce viable seeds. SUVH7, on the other hand, is a histone methyltransferase that has a catalytic SET domain responsible for epigenetic control of gene expression. In this study, we characterized the structures of the SUVH7 gene and compared the mRNA levels of SUVH7 in diploid apomict and sexual Boechera spp. in unopened immature buds and manually pollinated siliques representing the -pre and -post pollination stages, respectively. The expression level of SUVH7 in apomict B. divaricarpa has reached the max level 48 hours later following pollination, while in sexual B. stricta its expression level has dramatically decreased. Therefore, our study suggests the importance of epigenetic reprogramming in apomicts during seed development since chromatin marks via SUVH7 are commonly associated with the activation of transcription in plants

AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>Construction of transcriptional regulatory networks (TRNs) is of priority concern in systems biology. Numerous high-throughput approaches, including microarray and next-generation sequencing, are extensively adopted to examine transcriptional expression patterns on the whole-genome scale; those data are helpful in reconstructing TRNs. Identifying transcription factor binding sites (TFBSs) in a gene promoter is the initial step in elucidating the transcriptional regulation mechanism. Since transcription factors usually co-regulate a common group of genes by forming regulatory modules with similar TFBSs. Therefore, the combinatorial interactions of transcription factors must be modeled to reconstruct the gene regulatory networks.</p> <p>Description For systems biology applications, this work develops a novel database called <it>Arabidopsis thaliana </it>Promoter Analysis Net (AtPAN), capable of detecting TFBSs and their corresponding transcription factors (TFs) in a promoter or a set of promoters in <it>Arabidopsis</it>. For further analysis, according to the microarray expression data and literature, the co-expressed TFs and their target genes can be retrieved from AtPAN. Additionally, proteins interacting with the co-expressed TFs are also incorporated to reconstruct co-expressed TRNs. Moreover, combinatorial TFs can be detected by the frequency of TFBSs co-occurrence in a group of gene promoters. In addition, TFBSs in the conserved regions between the two input sequences or homologous genes in <it>Arabidopsis </it>and rice are also provided in AtPAN. The output results also suggest conducting wet experiments in the future.</p> <p>Conclusions</p> <p>The AtPAN, which has a user-friendly input/output interface and provide graphical view of the TRNs. This novel and creative resource is freely available online at <url>http://AtPAN.itps.ncku.edu.tw/</url>.</p

Comparative Analyses of Plant Transcription Factor Databases

Transcription factors (TFs) are proteinaceous complex, which bind to the promoter regions in the DNA and affect transcription initiation. Plant TFs control gene expressions and genes control many physiological processes, which in turn trigger cascades of biochemical reactions in plant cells. The databases available for plant TFs are somewhat abundant but all convey different information and in different formats. Some of the publicly available plant TF databases may be narrow, while others are broad in scopes. For example, some of the best TF databases are ones that are very specific with just one plant species, but there are also other databases that contain a total of up to 20 different plant species. In this review plant TF databases ranging from a single species to many will be assessed and described. The comparative analyses of all the databases and their advantages and disadvantages are also discussed