A High Resolution Genome-Wide Scan of HNF4α Recognition Sites Infers a Regulatory Gene Network in Colon Cancer

The hepatic nuclear factor HNF4α is a versatile transcription factor and controls expression of many genes in development, metabolism and disease. To delineate its regulatory gene network in colon cancer and to define novel gene targets a comprehensive genome-wide scan was carried out at a resolution of 35 bp with chromatin IP DNA obtained from the human colon carcinoma cell line Caco-2 that is a particularly rich source of HNF4α. More than 90% of HNF4α binding sites were mapped as promoter distal sequences while enhancer elements could be defined to foster chromatin loops for interaction with other promoter-bound transcription factors. Sequence motif analysis by various genetic algorithms evidenced a unique enhanceosome that consisted of the nuclear proteins ERα, AP1, GATA and HNF1α as cooperating transcription factors. Overall >17,500 DNA binding sites were identified with a gene/binding site ratio that differed >6-fold between chromosomes and clustered in distinct chromosomal regions amongst >6600 genes targeted by HNF4α. Evidence is presented for nuclear receptor cross-talk of HNF4α and estrogen receptor α that is recapitulated at the sequence level. Remarkably, the Y-chromosome is devoid of HNF4α binding sites. The functional importance of enrichment sites was confirmed in genome-wide gene expression studies at varying HNF4α protein levels. Taken collectively, a genome-wide scan of HNF4α binding sites is reported to better understand basic mechanisms of transcriptional control of HNF4α targeted genes. Novel promoter distal binding sites are identified which form an enhanceosome thereby facilitating RNA processing events

Expression patterns within the Arabidopsis C/S1 bZIP transcription factor network: availability of heterodimerization partners controls gene expression during stress response and development

Members of the Arabidopsis group C/S1 basic leucine zipper (bZIP) transcription factor (TF) network are proposed to implement transcriptional reprogramming of plant growth in response to energy deprivation and environmental stresses. The four group C and five group S1 members form specific heterodimers and are, therefore, considered to cooperate functionally. For example, the interplay of C/S1 bZIP TFs in regulating seed maturation genes was analyzed by expression studies and target gene regulation in both protoplasts and transgenic plants. The abundance of the heterodimerization partners significantly affects target gene transcription. Therefore, a detailed analysis of the developmental and stress related expression patterns was performed by comparing promoter: GUS and transcription data. The idea that the C/S1 network plays a role in the allocation of nutrients is supported by the defined and partially overlapping expression patterns in sink leaves, seeds and anthers. Accordingly, metabolic signals strongly affect bZIP expression on the transcriptional and/or post-transcriptional level. Sucrose induced repression of translation (SIRT) was demonstrated for all group S1 bZIPs. In particular, transcription of group S1 genes strongly responds to various abiotic stresses, such as salt (AtbZIP1) or cold (AtbZIP44). In summary, heterodimerization and expression data provide a basic framework to further determine the functional impact of the C/S1 network in regulating the plant energy balance and nutrient allocation

Foliar application of microdoses of sucrose to reduce codling moth Cydia pomonella L. (Lepidoptera: Tortricidae) damage to apple trees

Abstract BACKGROUND The effects of foliar applications of microdoses of sucrose to reduce the damage by the codling moth have been reported from nine trials carried in France and Algeria from 2009 to 2014. The activity of sucrose alone was assessed by comparison with an untreated control and some treatments with the Cydia pomonella granulovirus or a chemical insecticide. The addition of sucrose to these different treatments was also investigated. RESULTS The application of sucrose at 0.01% reduced the means of infested fruits with a value of Abbott's efficacy of 41.0 ± 10.0%. This involved the induction of resistance by antixenosis to insect egg laying. Indeed, it seems that acceptance of egg laying on leaves treated with sucrose was reduced. The addition of sucrose to thiacloprid improved its efficacy (59.5% ± 12.8) by 18.4%. However, the sucrose had no added value when associated with C. pomonella granulovirus treatments. CONCLUSION Foliar applications of microdoses of sucrose every 20 days in commercial orchards can partially protect against the codling moth. Its addition to thiacloprid increases the efficacy in integrated control strategies, contrary to C. pomonella granulovirus treatments. This work opens a route for the development of new biocontrol strategies

A TSC22-like motif defines a novel antiapoptotic protein family

The apoptotic programme is evolutionarily conserved between yeast and metazoan organisms. We have previously identified a number of mammalian cDNAs capable of suppressing the deleterious effects of Bax expression in yeast. We herein report that one such suppressor, named Tsc22(86), represents the C-terminal 86 amino acids of the previously characterized leucine zipper (LZ) motif-containing transcriptional regulator Tsc22. Employing a genome-wide two-hybrid screen, functional genomics, and deletion mutagenesis approaches, we conclude that Tsc22(86)-mediated antiapoptosis is independent of the LZ motif and is likely independent of effects on gene transcription. Rather, a 16-residue sequence within the conserved 56-residue TSC22 domain is necessary for antiapoptosis. The presence of a similar sequence was used to predict an antiapoptotic role for two yeast proteins, Sno1p and Fyv10p. Overexpression and knock-out experiments were used to validate this prediction. These findings demonstrate the potential of studying heterologous proteins in yeast to uncover novel biological insights into the regulation of apoptosis

Characterization of tomato Cycling Dof Factors reveals conserved and new functions in the control of flowering time and abiotic stress responses

[EN] DNA binding with One Finger (DOF) transcription factors are involved in multiple aspects of plant growth and development but their precise roles in abiotic stress tolerance are largely unknown. Here we report a group of five tomato DOF genes, homologous to Arabidopsis Cycling DOF Factors (CDFs), that function as transcriptional regulators involved in responses to drought and salt stress and flowering-time control in a gene-specific manner. SlCDF15 are nuclear proteins that display specific binding with different affinities to canonical DNA target sequences and present diverse transcriptional activation capacities in vivo. SlCDF15 genes exhibited distinct diurnal expression patterns and were differentially induced in response to osmotic, salt, heat, and low-temperature stresses. Arabidopsis plants overexpressing SlCDF1 or SlCDF3 showed increased drought and salt tolerance. In addition, the expression of various stress-responsive genes, such as COR15, RD29A, and RD10, were differentially activated in the overexpressing lines. Interestingly, overexpression in Arabidopsis of SlCDF3 but not SlCDF1 promotes late flowering through modulation of the expression of flowering control genes such as CO and FT. Overall, our data connect SlCDFs to undescribed functions related to abiotic stress tolerance and flowering time through the regulation of specific target genes and an increase in particular metabolites.This work was supported by grants from Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA; project numbers: 2009-0004-C01, 2012-0008-C01), the Spanish Ministry of Science and Innovation (project number: BIO2010-14871), and the MERIT Project (FP7 ITN2010-264474). ARC was supported by a pre-doctoral fellowship from the INIA. 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The Role of bZIP Transcription Factors in Green Plant Evolution: Adaptive Features Emerging from Four Founder Genes

BACKGROUND: Transcription factors of the basic leucine zipper (bZIP) family control important processes in all eukaryotes. In plants, bZIPs are regulators of many central developmental and physiological processes including photomorphogenesis, leaf and seed formation, energy homeostasis, and abiotic and biotic stress responses. Here we performed a comprehensive phylogenetic analysis of bZIP genes from algae, mosses, ferns, gymnosperms and angiosperms. METHODOLOGY/PRINCIPAL FINDINGS: We identified 13 groups of bZIP homologues in angiosperms, three more than known before, that represent 34 Possible Groups of Orthologues (PoGOs). The 34 PoGOs may correspond to the complete set of ancestral angiosperm bZIP genes that participated in the diversification of flowering plants. Homologous genes dedicated to seed-related processes and ABA-mediated stress responses originated in the common ancestor of seed plants, and three groups of homologues emerged in the angiosperm lineage, of which one group plays a role in optimizing the use of energy. CONCLUSIONS/SIGNIFICANCE: Our data suggest that the ancestor of green plants possessed four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments

Construction of a network describing asparagine metabolism in plants and its application to the identification of genes affecting asparagine metabolism in wheat under drought and nutritional stress

© 2018 The Authors. A detailed network describing asparagine metabolism in plants was constructed using published data from Arabidopsis (Arabidopsis thaliana) maize (Zea mays), wheat (Triticum aestivum), pea (Pisum sativum), soybean (Glycine max), lupin (Lupus albus), and other species, including animals. Asparagine synthesis and degradation is a major part of amino acid and nitrogen metabolism in plants. The complexity of its metabolism, including limiting and regulatory factors, was represented in a logical sequence in a pathway diagram built using yED graph editor software. The network was used with a Unique Network Identification Pipeline in the analysis of data from 18 publicly available transcriptomic data studies. This identified links between genes involved in asparagine metabolism in wheat roots under drought stress, wheat leaves under drought stress, and wheat leaves under conditions of sulfur and nitrogen deficiency. The network represents a powerful aid for interpreting the interactions not only between the genes in the pathway but also among enzymes, metabolites and smaller molecules. It provides a concise, clear understanding of the complexity of asparagine metabolism that could aid the interpretation of data relating to wider amino acid metabolism and other metabolic processes.Biotechnology and Biological Sciences Research Council. Grant Number: BB/I020918/1; Designing Future Whea

A network of heterodimerising C/S1 AtbZIP transcription factors and its function in senescence, stress response and seed development

Transkriptionsfaktoren der bZIP (basic region leucine zipper) Familie kommen in allen bisher analysierten eukaryotischen Organismen vor. Eine besondere Eigenschaft von Transkriptionsfaktoren dieser Gruppe ist, dass sie als Dimere an DNA binden, wobei einige bZIP-Transkriptionsfaktoren spezifische Heterodimere mit anderen bZIP-Transkriptionsfaktoren bilden können. Im Rahmen dieser Dissertation konnte gezeigt werden, dass in dem Modellorganismus Arabidopsis thaliana die bZIP-Transkriptionsfaktoren der Gruppe C (AtbZIP9, 10, 25 und 63) mit den bZIP-Faktoren der Gruppe S1 (AtbZIP1, 2, 11, 44 und 53) spezifische Heterodimere formen. Um die Funktion dieses Heterodimerisierungsnetzwerkes zu verstehen, wurden die Expressionsmuster der AtbZIP-Transkriptionsfaktoren mit Hilfe von Promotor-GUS Fusion, Northern Analysen und Daten aus Mikroarray-Datenbanken analysiert. Dabei zeigte sich, dass die Expression der AtbZIP-Gene vor allem durch die Zucker Glukose und Saccharose und durch Seneszenz, aber auch durch Stresse wie Osmolarität oder Salzstress reguliert wird. Zusätzlich fanden sich Gewebe-spezifische Expressionsmuster, z.B. in den Pollen oder Samen. Für die funktionelle Charakterisierung der bZIP-Transkriptionsfaktoren wurden Überexpressions-Pflanzen und T-DNA Insertionsmutanten erzeugt. Durch Transkriptomanalysen dieser Pflanzen mit Hilfe von Mikroarrays wurden mögliche Zielgene von AtbZIP1 und AtbZIP53 identifiziert. Ektopische Überexpression von AtbZIP1 oder AtbZIP53 (35S:AtbZIP1 und 35S:AtbZIP53) führte zur Aktivierung von Samenspeicherprotein-Genen, Pollenspezifischen Genen sowie Seneszenz-assoziierten Genen. Unter diesen Genen waren vermehrt Gene des Aminosäure-Metabolismus, und für zwei von ihnen, ein Prolin- Dehydrogenase Gen (ProDH) und ein Asparagin Synthetase Gen (ASN1), wurde mittels Chromatin-Immunopräzipitation (ChIP) gezeigt, dass es sich um direkte Zielgene von AtbZIP53 handelt. Für die ProDH konnte in transienten Protoplasten-Assays gezeigt werden, dass AtbZIP53 alleine in der Lage ist den Promotor zu aktivieren, dass jedoch eine Koexpression mit Gruppe C Faktoren zu einer weiter verstärkten Aktivierung führt, was die Bedeutung der Heterodimerisierung in Pflanzen belegt. In einer phänotypischen Charakterisierung zeigten 35S:AtbZIP53 Pflanzen eine erhöhte Salzresistenz. Zudem konnte gezeigt werden, dass AtbZIP53 die Expression von Genen der Samenreifung vermittelt. Während dieser Phase bilden die Samen ihre Austrocknungstoleranz aus, ein Prozess der Parallelen zur Ausbildung von Salzresistenz zeigt. Für 35S:AtbZIP1 Pflanzen konnte ein früheres Eintreten in eine Dunkel-induzierte Seneszenz gezeigt werden, das sich wahrscheinlich auf die in diesen Pflanzen verstärkt exprimierten Seneszenz-assoziierten Gene zurückführen lässt. Die in dieser Arbeit gezeigte deutliche Repression von AtbZIP1 durch Zucker hat wahrscheinlich die Funktion, das Einsetzen der Dunkel-induzierten Seneszenz zu verhindern, solange die Zellen noch über ausreichende Energie-Reserven verfügen.Da AtbZIP-Transkriptionsfaktoren der Gruppen C und S1 stark durch Zucker, aber auch durch Stresse und entwicklungsbiologische Signale reguliert werden, und die Mehrheit der identifizierten putativen Zielgene Enzyme des Metabolismus kodieren, wird die Hypothese aufgestellt, dass C/S1 Heterodimere eine komplexe, auf der einen Seite von der Verfügbarkeit von Zuckern, auf der anderen Seite von Stressen und entwicklungsbiologischen Signalen abhängige Regulation des Metabolismus vermitteln