Database-assisted promoter analysis

Plant Cell, 2002

Numerous studies have shown that transcription factors are important in regulating plant responses to environmental stress. However, specific functions for most of the genes encoding transcription factors are unclear. In this study, we used mRNA profiles generated from microarray experiments to deduce the functions of genes encoding known and putative Arabidopsis transcription factors. The mRNA levels of 402 distinct transcription factor genes were examined at different developmental stages and under various stress conditions. Transcription factors potentially controlling downstream gene expression in stress signal transduction pathways were identified by observed activation and repression of the genes after certain stress treatments. The mRNA levels of a number of previously characterized transcription factor genes were changed significantly in connection with other regulatory pathways, suggesting their multifunctional nature. The expression of 74 transcription factor genes responsive to bacterial pathogen infection was reduced or abolished in mutants that have defects in salicylic acid, jasmonic acid, or ethylene signaling. This observation indicates that the regulation of these genes is mediated at least partly by these plant hormones and suggests that the transcription factor genes are involved in the regulation of additional downstream responses mediated by these hormones. Among the 43 transcription factor genes that are induced during senescence, 28 of them also are induced by stress treatment, suggesting extensive overlap responses to these stresses. Statistical analysis of the promoter regions of the genes responsive to cold stress indicated unambiguous enrichment of known conserved transcription factor binding sites for the responses. A highly conserved novel promoter motif was identified in genes responding to a broad set of pathogen infection treatments. This observation strongly suggests that the corresponding transcription factors play general and crucial roles in the coordinated regulation of these specific regulons. Although further validation is needed, these correlative results provide a vast amount of information that can guide hypothesis-driven research to elucidate the molecular mechanisms involved in transcriptional regulation and signaling networks in plants.

The Plant Cell Online, 2002

Numerous studies have shown that transcription factors are important in regulating plant responses to environmental stress. However, specific functions for most of the genes encoding transcription factors are unclear. In this ...

Genome Biology

A comparative study based on four fully sequenced eukaryotic genomes has revealed profound differences in the sets of transcription factors used by plants, fungi and animals. Significance and context The recent completion of the Arabidopsis thaliana genome sequence allowed the first prediction of a full plant proteome. With the completed genome sequences of Saccharomyces cerevisiae (budding yeast), Caenorhabditis elegans and Drosophila melanogaster, complete proteomes from representatives of three eukaryotic kingdoms (plants, fungi and animals) are now available for comprehensive comparative studies. Using a list of protein sequences, domains and motifs from known transcription factors, Riechmann et al. determined the entire complement of these regulators encoded by all four genomes. Both similarities and profound differences were revealed between the sets of transcription factors utilized by representatives of each eukaryotic kingdom. Given that transcription factors act as central regulators of a diversity of developmental and physiological processes, such differences may partly account for the evolutionary distance between these entirely different life forms. Key results Within the Arabidopsis genome, 1,533 genes were found to encode members of known transcription factor families, 45% of which are from families specific for plants. The fraction of transcription factor genes among all genes is slightly higher in Arabidopsis (5.9%) compared with Drosophila, C. elegans and yeast (4.5, 3.5 and 3.5%, respectively). A variety of prominent transcription factor families are present in all four species, including Myb, basic helix-loop-helix, basic leucine zipper, C2H2 zinc finger and homeodomain transcription factors. Except for the conserved DNA-binding domains, however, there are no significant similarities between members of the same transcription factor family from different kingdoms. Three types of evolutionary process appear to be mainly responsible for the observed differences in transcription factor complements: the generation of completely novel families; the specific amplification of families common to all three eukaryotic kingdoms; and domain shuffling, leading to new combinations of common transcription factor domains. As well as several small families, the large families of AP2/EREBP, NAC and WRKY transcription factors, consisting of 144, 109 and 72 members, respectively, are found exclusively in plants. In contrast, nuclear hormone receptors and GAL4-like C6 zinc finger proteins, which are strongly represented in animals and yeast, respectively, appear to be absent from plants. In plants, the Myb superfamily is strongly amplified, comprising 190 members. These regulators, which constitute the largest class of plant transcription factors, are only weakly represented in the other eukaryotic kingdoms. Exon shuffling has led to transcription factors unique to plants that contain both homeodomains and leucine zippers. In addition to these HD-ZIP proteins, leucine zippers can be found in the plant-specific WRKY factors as well as in basic leucine zippers, which are present in all three eukaryotic kingdoms.

Ciencia y Tecnología

Transcription factors (TF) are the elements, which regulate gene expression. Regulatory function of TFs play an important role in plant biological processes and mechanisms. They may interconnect with other transcription factors or functional genes to modulate their expression in response to an internal/external factor like life cycle stage, growth, development and stress. Arabidopsis is the well-known and the most used model organism. Transcription factors of three Arabidopsis species including A. halleri, A. lyrata and A. thaliana, were compared. basic/helix-loop-helix (bHLH) with 220 TFs was the most abundant family among three Arabidopsis species while MYB and MYB related families considering as a whole group were more than bHLH with 308 TFs. No STERILE APETALA (SAP) TF homolog was found for A.halleri. The common transcription factors among three species were 4,172 grouped in 1,212 clusters. The species-specific clustered TFs were 12, 30 and 58 for A. halleri, A. lyrata and A. t...

Plant and Cell Physiology, 2009

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and the Japanese Society of Plant Physiologists are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact [email protected] Transcription factors (TFs) regulate the expression of genes at the transcriptional level. Modifi cation of TF activity dynamically alters the transcriptome, which leads to metabolic and phenotypic changes. Thus, functional analysis of TFs using 'omics-based' methodologies is one of the most important areas of the post-genome era. In this mini-review, we present an overview of Arabidopsis TFs and introduce strategies for the functional analysis of plant TFs, which include both traditional and recently developed technologies. These strategies can be assigned to fi ve categories: bioinformatic analysis; analysis of molecular function; expression analysis; phenotype analysis; and network analysis for the description of entire transcriptional regulatory networks.

Genetic Engineering, 1997

In almost all of the areas of gene expression control except one, plant research has lagged considerably behind studies in yeast, insects and vertebrates. Advances in animal gene expression control have also benefited plant research, as we continue to find that much of the machinery and mechanisms controlling gene expression have been preserved in all eukaryotes. However, there are some interesting differences in gene structure and regulation between plants and animals. First, vertebrate genes can be quite large, often spanning tens of thousands of base pairs and usually separated by numerous large introns, whereas plant genes tend to be much smaller (averaging between 1–2 kb (kilobases) with fewer and smaller introns. Second, as we shall see in the following chapters, plant transcripts retain introns more often than do animal transcripts (30% of all genes in the model plant, Arabidopsis, compared to 10% in humans). Unfortunately, at this time we have only a few plant models for gene regulation, and only Arabidopsis, rice and poplar have been fully sequenced. Since Arabidopsis was the first plant genome to be fully sequenced, most of our information has come from studies of its transcriptome, and it is not known to what extent it truly represents other members of the plant kingdom. In addition, as our knowledge of factors influencing gene expression increases, so too, does our recognition that the current annotations in the gene databases will need to be updated to reflect new information as it appears in the literature. Finally, compared to animals, plants have evolved different signaling mechanisms, partly because plant hormones do not exactly function as do those in animals, and partly because plants must cope with environmental changes differently than animals, since they cannot physically escape their environments except possibly through reproduction. Therefore, plants have evolved very complex, interacting signaling pathways in response to developmental signals and biotic/abiotic stresses. All of these observations ultimately reflect some of the differences plants display in regulating gene expression compared to yeasts, insects and vertebrates. Although we have touched upon some of the differences between animal and plant control of gene expression here, it is equally important to recognize and appreciate the common mechanisms they share. For example, the basic transcriptional machinery via DNA-dependent RNA Polymerase II is virtually the same in plants and animals. Furthermore, some transcription factors, like myb and myc factors are similar in structure and function in both plants and animals. Plants and animals contain introns separating the coding regions of most genes and again, they utilize similar machinery to process the introns and form mature mRNAs. Since translation in all eukaryotes is basically the same, we see more similarities between plants and animals in this process, than differences. These mechanisms relate to mRNA structure, including sequences in the 5′ leader region and those in the 3′ untranslated region which influence the efficiency and selectivity of translation. It is hoped that the following chapters will expose the reader to some of the most recent, novel and fascinating examples of transcriptional and posttranscriptional control of gene expression in plants and, where appropriate, provide comparison to notable examples of animal gene regulation.

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2017

Regulation of gene expression depends on specific cis-regulatory sequences located in the gene promoter regions. These DNA sequences are recognized by transcription factors (TF) in a sequence-specific manner, and their identification could help to elucidate the regulatory networks that underlie plant physiological responses to developmental programs or to environmental adaptation. Here we review recent advances in high throughput methodologies for the identification of plant TF binding sites. Several approaches offer a map of the TF binding locations in vivo and of the dynamics of the gene regulatory networks. As an alternative, high throughput in vitro methods provide comprehensive determination of the DNA sequences recognized by TF. These advances are helping to decipher the regulatory lexicon and to elucidate transcriptional network hierarchies in plants in response to internal or external cues. Highlights  Current status of the determination of transcription factor binding sites in planta is reviewed  SELEX-seq and protein binding microarrays provide comprehensive in vitro determination of bound DNA sequences  Elucidation of transcription networks benefits from in vivo and in vitro

Current Opinion in Plant Biology, 2002

Plos One, 2013

In the present work, the objective has been to analyse the compatibility of plant and human transcriptional machinery. The experiments revealed that nuclear import and export are conserved among plants and mammals. Further it has been shown that transactivation of a human promoter occurs by human transcription factor NF-kB in plant cells, demonstrating that the transcriptional machinery is highly conserved in both kingdoms. Functionality was also seen for regulatory elements of NF-kB such as its inhibitor IkB isoform a that negatively regulated the transactivation activity of the p50/RelA heterodimer by interaction with NF-kB in plant cells. Nuclear export of RelA could be demonstrated by FRAP-measurements so that RelA shows nucleo-cytoplasmic shuttling as reported for RelA in mammalian cells. The data reveals the high level of compatibility of human transcriptional elements with the plant transcriptional machinery. Thus, Arabidopsis thaliana mesophyll protoplasts might provide a new heterologous expression system for the investigation of the human NF-kB signaling pathways. The system successfully enabled the controlled manipulation of NF-kB activity. We suggest the plant protoplast system as a tool for reconstitution and analyses of mammalian pathways and for direct observation of responses to e.g. pharmaceuticals. The major advantage of the system is the absence of interference with endogenous factors that affect and crosstalk with the pathway.